Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 647 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 998 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 43 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 644 infection 139 virus 100 patient 87 respiratory 69 cell 62 SARS 51 disease 44 RSV 39 HIV 38 COVID-19 36 IFN 33 RNA 32 PCR 29 child 28 human 25 Fig 25 CMV 20 treatment 19 clinical 19 cause 19 United 18 figure 17 viral 16 risk 15 study 15 dna 15 covid-19 15 MRSA 14 States 14 CoV-2 14 China 14 CD4 13 pneumonia 13 influenza 12 HRV 11 response 11 animal 11 HCV 11 H1N1 11 CNS 10 lung 10 care 10 Health 10 EBV 10 CD8 9 vaccine 9 transplant 9 sign 9 result 9 neonatal Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 63712 infection 37684 virus 27411 patient 27116 cell 23870 % 21402 disease 16708 study 11203 case 10031 response 9956 influenza 9937 child 9763 treatment 9069 mouse 8758 risk 7945 day 7154 protein 7004 vaccine 6799 year 6729 type 6689 host 6668 result 6641 antibody 6455 factor 6364 pneumonia 6355 animal 6208 gene 6176 time 6120 transmission 6046 strain 6045 effect 6031 pathogen 5965 therapy 5963 lung 5900 rate 5817 level 5791 group 5789 use 5699 control 5542 diagnosis 5425 blood 5347 age 5238 number 5128 care 5094 system 5061 analysis 4992 symptom 4978 model 4904 tract 4840 fever 4824 role Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 12139 al 10341 et 8910 . 5073 SARS 3757 RSV 3309 PCR 3096 HIV 2886 IFN 2882 RNA 2873 T 2458 COVID-19 2362 ⁄ 2271 C. 2264 S. 2250 CoV-2 1991 C 1951 B 1911 • 1886 Fig 1747 mg 1739 A 1738 United 1522 H1N1 1511 CMV 1500 States 1472 Health 1396 MRSA 1322 der 1314 CD4 1297 NK 1270 China 1262 HRV 1240 CoV 1173 Table 1143 Staphylococcus 1052 M. 1038 Influenza 1037 E. 1010 II 980 Disease 976 HCV 951 CD8 914 USA 877 RT 870 H5N1 851 AIDS 844 Salmonella 836 B. 819 Control 800 Human Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 12283 it 7835 we 4884 they 2857 i 1314 them 1260 he 784 she 534 one 349 itself 276 us 197 themselves 132 you 37 him 29 her 15 mg 14 himself 11 me 9 ourselves 8 herself 7 yourself 7 ifih1 6 ours 6 's 5 pdcs 5 oneself 5 ifitm3 4 ybt 4 s 4 em 3 nr-818 3 mrnas 3 isgf3 3 interleukin-10 3 ifnar1 3 https://doi.org/10.1101/2020.04.20.20072942 3 fusb 2 λr1 2 mtorc1 2 imagej 2 il-12 2 igg4 2 he16 2 deÀ 2 covid-19 2 clustalx 2 ccr5Δ32 1 ™ 1 ‫ﺍ‬ 1 ω-3 1 α=0.08 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 201189 be 39503 have 13441 use 11329 include 10808 associate 9453 cause 8477 show 7859 increase 7721 infect 7062 occur 6047 develop 6008 report 5993 do 5606 find 5550 induce 5241 follow 4936 reduce 4687 identify 4574 base 4186 result 4094 suggest 4014 detect 3991 require 3815 lead 3656 compare 3578 see 3504 relate 3481 consider 3454 provide 3377 prevent 3236 describe 3182 observe 3136 treat 3136 produce 3078 involve 2948 demonstrate 2857 present 2839 affect 2814 know 2804 perform 2790 give 2734 determine 2636 make 2635 isolate 2633 indicate 2546 remain 2445 acquire 2435 become 2368 decrease 2349 control Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 17701 not 16193 respiratory 14587 viral 12736 also 11948 clinical 11270 other 10364 - 10169 human 10089 high 9454 more 8788 most 8509 such 7938 immune 7689 severe 7224 acute 7052 low 6643 however 6108 common 5673 well 5523 only 5165 specific 5153 bacterial 4803 infectious 4609 important 4602 first 4583 early 4465 different 4257 positive 4167 as 3942 new 3917 chronic 3822 many 3811 infected 3549 often 3495 several 3403 pulmonary 3358 non 3288 primary 3284 resistant 3283 large 3267 inflammatory 3266 significant 3147 long 3070 less 3013 antiviral 2997 negative 2977 small 2932 usually 2925 old 2837 normal Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 2305 most 972 Most 882 least 657 high 548 good 269 great 189 large 168 low 81 common 80 early 71 late 39 strong 39 bad 35 big 32 close 29 young 28 small 25 short 25 long 19 simple 18 old 17 poor 16 safe 15 ⁄ 15 near 11 fast 10 easy 9 new 8 wide 7 preS1 6 mild 5 narrow 5 fit 4 strict 4 slight 4 few 3 deadly 3 busy 2 warm 2 steep 2 sick 2 risky 2 rich 2 rare 2 likeli 2 grave 2 cold 2 clear 2 broad 2 -β Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 6483 most 732 least 238 well 5 long 3 lowest 3 hard 2 α2-ar 2 smallest 2 oldest 2 highest 2 fast 2 early 2 -sialyllactose 1 youngest 1 worst 1 near 1 furthest 1 aunps 1 -wheeze 1 -just 1 -detect Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 100 doi.org 22 www.who.int 22 www.cdc.gov 15 www.biomedcentral.com 13 www.ncbi.nlm.nih.gov 11 www 7 www.dovepress.com 7 dx.doi.org 5 orcid.org 4 www.youtube.com 4 www.mdpi.com 3 www.informatics.jax.org 3 www.geneontology.org 3 www.fda.gov 3 www.blast2go.com 2 www.worldometers.info 2 www.r-project.org 2 www.oie.int 2 www.gisaid.org 2 www.frontiersin.org 2 www.eurosurveillance.org 2 www.eucomm.org 2 www.ebi.ac.uk 2 sysbio.cvm.msstate.edu 2 creativecommons.org 2 creativecommons 2 clinicaltrials.gov 2 bizfil.com 1 www2.aap.org 1 www.wsj.com 1 www.wma.net 1 www.vi-vi.org 1 www.vetcancerregistry.com 1 www.turkeyfed.com.au 1 www.tbfacts.org 1 www.stat.gov.tw 1 www.sign.ac.uk 1 www.sensetime.com 1 www.sciencemag.org 1 www.sanquin.nl 1 www.sanger.ac.uk 1 www.rzpd.de 1 www.rki.de 1 www.reuters.com 1 www.python.org 1 www.plosone.org 1 www.picornastudygroup.com 1 www.pfizer.com 1 www.paho.org 1 www.nrzhygiene.de Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 13 http://www.biomedcentral.com/1471-2105/15/333 13 http://doi.org/10.1101/2020.10.09.20210245 13 http://doi.org/10.1101/2020.09.18.20197467 12 http://doi.org/10.1101/2020.10.28.20221259 11 http://www 11 http://doi.org/10.1101/2020.05.20.20107169 7 http://doi.org/10.1101/2020.09.15.20195297 6 http://doi.org/10.1101/2020.05.20.20107516 6 http://doi.org/10.1101/2020.04.27.20081505 5 http://doi.org/10 4 http://doi.org/10.1101/2020.10.16.20212753 4 http://doi.org/10.1101/2020.04.08.20057414 4 http://doi.org/10.1101/2020.04 3 http://www.ncbi.nlm.nih.gov/geo/ 3 http://www.cdc.gov/ncidod/sars 3 http://www.blast2go.com/ 3 http://doi.org/10.1101/2020.04.20.20072942 3 http://doi.org/10.1101/2020 2 http://www.worldometers.info/coronavirus 2 http://www.who.int/csr/ 2 http://www.who.int/ 2 http://www.r-project.org/ 2 http://www.oie.int/ 2 http://www.ncbi.nlm.nih.gov/geo/query/ 2 http://www.informatics.jax.org/ 2 http://www.geneontology.org 2 http://www.eurosurveillance.org 2 http://www.ebi.ac.uk/arrayexpress/ 2 http://www.dovepress.com/testimonials.php 2 http://www.dovepress.com/ 2 http://www.cdc.gov/ncidod/ 2 http://www.cdc.gov/ 2 http://sysbio.cvm.msstate.edu/IPMiner 2 http://doi.org/10.1101/2020.09 2 http://doi.org/10.1101/2020.07.01.20105379 2 http://creativecommons.org/licenses/by/4.0/ 2 http://creativecommons 1 http://www2.aap.org/immunization/families/ 1 http://www.youtube.com/watch?v=lp8fpDVDOCE 1 http://www.youtube.com/watch?v=aF06jlbcF8E 1 http://www.youtube.com/watch?v=G-1StrWaHKA 1 http://www.youtube.com/ 1 http://www.wsj.com/arti 1 http://www.wma.net 1 http://www.who.int/hiv/data/en/ 1 http://www.who.int/emergencies/mers-cov/en/ 1 http://www.who.int/emergencies/ 1 http://www.who.int/emergen 1 http://www.who.int/emerge 1 http://www.who.int/docs/defaultsource/coronaviruse/who-china-joint-mission-on-covid-19-final-report.pdf Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 yuhj@chinacdc.cn 1 thosaka@pd6.so-net.ne.jp 1 skkabra@hotmail.com 1 shohei@mbk.nifty.com 1 research@f1000.com 1 rahme@molbio.mgh.harvard.edu 1 pp.pastoret@oie.int 1 morikawa@iph.pref.osaka.jp 1 mengelle.c@chu-toulouse.fr 1 kohdera@nakano-kodomo.or.jp 1 kasetetsuo@iph.pref.osaka.jp 1 jamilah.jantan@nkfs.org 1 hiroi@iph.pref.osaka.jp 1 gming@pennmedicine.upenn.edu 1 g.reina@ibmc-cnrs.unistra.fr 1 fmalergue@beckman.com 1 easloffice@easloffice.eu 1 c89040507@yahoo.com.tw 1 amy.patick@pfizer.com 1 alice3030301@yahoo.com.tw 1 a.bianco@ibmc-cnrs.unistra.fr 1 cheryl_bletchly@health.qld.gov.au 1 .ishii@gmail.com Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 76 infection is not 57 infection is usually 47 disease is not 44 vaccines are available 41 infections are more 38 infections are common 37 infection has not 37 virus is not 36 infection does not 36 infections are often 34 infection is often 33 studies have also 33 virus does not 32 vaccine is available 30 viruses do not 30 years was confi 29 infections are asymptomatic 29 infections are not 28 infection is also 26 disease is usually 26 infection has also 26 infection is more 26 infections are also 26 infections were more 26 treatment is not 25 infection is common 24 vaccine is not 23 infection was not 22 infection is likely 22 studies have not 22 treatment is supportive 21 infections are usually 21 virus was not 20 patients did not 20 virus is present 19 cells are not 19 disease is often 19 infection is most 19 infection is rare 19 infections do not 19 patients do not 19 pneumonia requiring hospitalization 18 disease is more 18 infection did not 18 infections were not 18 study did not 18 virus has also 18 virus was first 17 cells are also 17 disease are not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 5 infection has not yet 5 infection is not always 4 infection is not well 4 vaccine is not available 3 infections are not uncommon 3 infections is not clear 3 mice are not susceptible 3 patients had no underlying 3 treatment is not necessary 3 vaccine is no longer 3 vaccine is not yet 3 vaccines are not available 3 virus is not easily 2 % had no virus 2 animals are not able 2 antibodies are not effective 2 cases are not due 2 cells is not as 2 cells is not only 2 disease are not synonymous 2 disease is not always 2 disease is not as 2 disease is not generally 2 disease is not perfectly 2 disease is not well 2 disease is not yet 2 diseases are not well 2 infection do not clearly 2 infection does not necessarily 2 infection has no specific 2 infection is not as 2 infection is not common 2 infection is not fully 2 infection is not optimal 2 infection is not present 2 infection was not present 2 infections are not detectable 2 infections are not only 2 infections are not well 2 infections is not straightforward 2 infections were not available 2 mice are not permissible 2 mice are not permissive 2 mice are not vulnerable 2 mice have no clinical 2 mice were no longer 2 patient had no evidence 2 patient has no complaints 2 patients are not only 2 patients are not possible A rudimentary bibliography -------------------------- id = cord-018061-jy3km0fr author = AL KASSAA, Imad title = Antiviral Probiotics: A New Concept in Medical Sciences date = 2016-12-02 keywords = LGG; gram; infection; lactobacillus; probiotic; strain summary = rhamnosus GG (LGG), a famous probiotic strain, was evaluated and showed an anti-infl uenza virus activity on intranasal and oral administration [ 26 , 27 ] . Moreover, the antiviral effect of probiotics by immunomodulatory mechanisms depends on the immune system status, which can be explained in the study conducted by Lehtoranta et al., who showed that the combination of four probiotic strains worked very well in children but not in the elderly [ 61 ] . The role of commensal bacteria in the persistence of enteric viral infections has previously been shown in a series of recent studies published in 2011, using poliovirus, reovirus and mouse mammary tumor virus (MMTV) as EnV models [ 99 -101 ] . Differential effects of Escherichia coli Nissle and Lactobacillus rhamnosus Strain GG on human rotavirus binding, infection, and B cell immunity doi = 10.1007/978-3-319-49688-7_1 id = cord-022084-hap7flng author = ARRUDA, EURICO title = Respiratory Tract Viral Infections date = 2009-05-15 keywords = HMPV; HRV; PCR; RNA; RSV; SARS; child; infection; respiratory; virus summary = The Centers for Disease Control and Prevention (CDC) recommends the immunization of persons aged 50 years and older; residents of nursing homes; children and adults with chronic cardiovascular or pulmonary disease, including asthma; persons chronically ill with diabetes mellitus, renal dysfunction, or hemoglobinopathies; immunosuppressed patients including those with HIV infection; children and adolescents on chronic aspirin therapy who may develop postinfluenza Reye'' s syndrome; women who will be pregnant during the influenza season; children aged 6 to 23 months; those who can transmit influenza to persons at high risk, such as health-care workers and household contacts of those at high risk including children 0 to 23 months of age; crew members of cruise ships; providers of essential services; and unimmunized travelers to areas where influenza may be circulating, including the tropics, the southern hemisphere between April and September, and those traveling in large organized tourist groups. doi = 10.1016/b978-0-443-06668-9.50064-8 id = cord-034436-yhb8m1si author = Abdulah, Deldar Morad title = Relation of Dietary Factors with Infection and Mortality Rates of COVID-19 across the World date = 2020-07-04 keywords = COVID-19; infection; rate summary = We aimed to explore the relation of dietary factors with global infection and mortality rates of COVID-19 in this study. DESIGN: In the current ecological study, the countries that had national dietary data from the Global Dietary Databases of the United Nations and Coronavirus disease statistics from the World Health Organization (WHO) were included. CONCLUSION: The present study showed the higher intake of fruits and sugar-sweetened beverages had a positive effect on infection and mortally rates by COVID-19, respectively. The present study showed that the crude infection rate by COVID-19 has been increased by raising consuming fruits, calcium and decreased with increasing consuming beans and legumes. Therefore, we can make the further hypothesis that the aged population of the countries with high infection rates has been the main factor in the low immune system. The present study showed the higher intake of fruits and sugar-sweetened beverages had a positive effect on infection and mortally rates by COVID-19, respectively. doi = 10.1007/s12603-020-1512-3 id = cord-258145-usr7b6dk author = Abdulah, Deldar Morad title = Relation of Dietary Factors with Infection and Mortality Rates of COVID-19 Across the World date = 2020-07-04 keywords = COVID-19; infection; rate summary = We aimed to explore the relation of dietary factors with global infection and mortality rates of COVID-19 in this study. DESIGN: In the current ecological study, the countries that had national dietary data from the Global Dietary Databases of the United Nations and Coronavirus disease statistics from the World Health Organization (WHO) were included. CONCLUSION: The present study showed the higher intake of fruits and sugar-sweetened beverages had a positive effect on infection and mortally rates by COVID-19, respectively. The present study showed that the crude infection rate by COVID-19 has been increased by raising consuming fruits, calcium and decreased with increasing consuming beans and legumes. Therefore, we can make the further hypothesis that the aged population of the countries with high infection rates has been the main factor in the low immune system. The present study showed the higher intake of fruits and sugar-sweetened beverages had a positive effect on infection and mortally rates by COVID-19, respectively. doi = 10.1007/s12603-020-1434-0 id = cord-315726-ltjurdrq author = Acheson, D.W.K. title = Food and Waterborne Illnesses date = 2009-02-17 keywords = Campylobacter; Salmonella; States; United; food; infection summary = A wide variety of the common foodborne pathogens is discussed, with a brief description of what they are, the types of illness they cause, and the kinds of food most frequently associated with them along with some commentary with regard to treatment. Examples include the hemolytic uremic syndrome (HUS) secondary to Shiga toxin-producing Escherichia coli (STEC), the development of Guillain-Barré syndrome (GBS) after Campylobacter infection, and the association of a number of enteric bacterial pathogens with reactive arthritis and postinfectious irritable bowel syndrome. ETEC are transmitted through contaminated water and food and have caused a number of large outbreaks in the United States; however, their importance in sporadic disease is not known. doi = 10.1016/b978-012373944-5.00183-8 id = cord-346253-0mnsm6s4 author = Ahanchian, Hamid title = Respiratory viral infections in children with asthma: do they matter and can we prevent them? date = 2012-09-13 keywords = HRV; RSV; asthma; infection; respiratory summary = HRV are the most common viral agents [33] ; Other respiratory tract viruses detected in children with an asthma exacerbation include RSV, influenza, coronavirus, hMPV, parainfluenza virus, adenovirus, and bocavirus [34] [35] [36] . Beside importance for bone health, vitamin D plays an important role in adequate function of both the innate and adaptive immune systems including development of dendritic cells and regulatory T lymphocytes [151, 152] production of antimicrobial proteins by airway epithelium [153] , modifying the effect of intestinal flora on inflammatory disorders [107] , and modulation of the inflammatory response to viral infections [154] . In a recent study of 48 children from five to 18 years of age, with newly diagnosed asthma, vitamin D supplementation during the northern hemisphere winter months (September to July) prevented declining serum concentrations of 25(OH) D and reduced the risk of asthma exacerbation triggered by acute respiratory tract infections [161] . doi = 10.1186/1471-2431-12-147 id = cord-324788-echu0zmf author = Aich, Palok title = Modern approaches to understanding stress and disease susceptibility: A review with special emphasis on respiratory disease date = 2009-07-30 keywords = HPA; IL-6; disease; infection; response; stress summary = The current review focuses on (a) the effects of psychological stressors in humans and animals, (b) various methodologies employed to understand stress responses and their outcomes, and (c) the current status of the attempts to correlate stress and disease with respiratory disease as model system. While many genes and environmental factors contribute to susceptibility and resistance to autoimmune/infl ammatory diseases, a full understanding of the molecular mechanisms by which a combination of neuropeptides, neurohormones and neurotransmitters can modulate immune responses is essential for effective design of future interventions. We conducted bovine microarray analyses of RNA isolated from blood mononuclear cells to determine if changes in gene expression correlated with either stress or the severity of BRD infection; results support the conclusion that differential regulation of pro-infl ammatory responses is a major mechanism contributing to increased disease susceptibility. doi = nan id = cord-278839-uu2wlpmp author = Alberca, Ricardo Wesley title = Pregnancy, Viral Infection, and COVID-19 date = 2020-07-07 keywords = COVID-19; MERS; SARS; infection; maternal; pregnancy summary = doi = 10.3389/fimmu.2020.01672 id = cord-310205-j57x9ke6 author = Alcaide, Maria L. title = Pharyngitis and Epiglottitis date = 2007-06-08 keywords = acute; clinical; gas; infection; patient; pharyngitis summary = A major task of the primary care physician is to identify those patients with acute pharyngitis who require specific antimicrobial therapy and to avoid unnecessary and potentially deleterious treatment in the great majority who suffer from a benign, self-limited, usually viral infection. In the minority of patients who are severely ill or toxic at presentation and in whom clinical and epidemiologic evidence leads to a high index of suspicion, oral antimicrobial therapy may be initiated while awaiting the results of the throat culture. Treatment of GAS pharyngitis is recommended to prevent acute rheumatic fever, prevent suppurative complications [28] , shorten the clinical course (although only modestly) [28] , and reduce transmission of the infection in family and school units. Within days to weeks after initial infection with HIV type 1, 50% to 90% of patients develop a constellation of symptoms known as the ''''acute retroviral syndrome.'''' Fever, sore throat, lymphadenopathy, maculopapular rash, myalgia, arthralgias, and mucocutaneous ulcerations are the landmarks of the syndrome [58] [59] [60] [61] . doi = 10.1016/j.idc.2007.03.001 id = cord-325436-pp3q022y author = Alkhatib, Ahmad title = Antiviral Functional Foods and Exercise Lifestyle Prevention of Coronavirus date = 2020-08-28 keywords = COVID-19; exercise; immune; infection; vitamin summary = This review presents key evidence on how functional foods and lifestyle approaches, including physical activity, effective for cardiometabolic disease prevention outcomes [9] , can also optimize the immune system response to viral infection, especially respiratory tract infections and COVID-19. Enhancing the antiviral immune defence can benefit from the functional food intake of a considerable variety of plant, animal, and fungi species, consumed across different diets and cultural practices including traditional herbal medicine such as teas, roots, mushrooms, and fermented plants and leaves; MD components such as olive-based products, oily fish, seeds, fruits, and vegetables; popular beverages such as coffee; and protein-rich foods such as chicken extract and soybean peptides. Below is a review of popular foods within various dietary patterns, including olive oil nutraceuticals, popular vitamins such as vitamin D, traditional medicinal herbs and roots, and protein peptides for preventing viral infections including COVID-19, especially when they are adopted as part of an active lifestyle. doi = 10.3390/nu12092633 id = cord-307016-4hdsb5oq author = Allen, Upton title = Prevention and Treatment of Infectious Complications After Solid Organ Transplantation in Children date = 2010-04-30 keywords = CMV; EBV; infection; recipient; transplant summary = This review summarizes the major infections that occur after pediatric organ transplantation, highlighting the current treatment and prevention strategies, based on the available data and/or consensus. In the first month, there are 3 major causes of infection: (1) infection that was present in the recipient before transplant, with its effects now increased as a result of surgery, anesthesia, and immunosuppressive therapy; (2) infection conveyed with a contaminated allograft; and (3) the same bacterial and candidal infections of the wound, lungs, drainage catheters, and vascular access devices that are seen in nonimmunosuppressed patients undergoing comparable surgery. Despite this limitation, experience supports dividing individuals with infections during this last time period into 2 main categories: (1) most patients with a good result from transplantation (maintenance immunosuppression, good allograft function) are at greatest risk from typical community-acquired infections (such as influenza, parainfluenza, and respiratory syncytial virus); (2) a smaller group of patients with poorer outcomes from transplantation (excessive acute and chronic immunosuppression, poor allograft function, and, often, chronic viral infection). doi = 10.1016/j.pcl.2010.01.005 id = cord-326961-ti6mrzxf author = Aly, Mariam Mohsen title = Impact of novel coronavirus disease (COVID-19) on Egyptian dentists’ fear and dental practice (a cross-sectional survey) date = 2020-10-12 keywords = COVID-19; dental; infection summary = OBJECTIVES: This study aimed to evaluate the fear of infection among Egyptian dentists practicing during the current coronavirus disease 2019 (COVID-19) pandemic and to explore the dentist''s knowledge about guidelines to fight the virus and to assess various modifications in dental practice. 7 Different practical guidelines were recommended for dental professionals by the Centers for Disease Control and Prevention (CDC), the American Dental Association (ADA), and the WHO to control the spread of COVID-19 and like other contagious infections, these recommendations include personal protective equipment, hand washing, detailed patient evaluation, rubber dam isolation, anti-retraction handpiece, mouth rinsing before dental procedures, and disinfection of the clinic. This cross-sectional study assessed the fear of infection between Egyptian dentists practicing during the present COVID-19 pandemic and to explore their knowledge about guidelines to fight the virus and various modifications in dental practice through an online survey. doi = 10.1038/s41405-020-00047-0 id = cord-016208-u12ngkpc author = Andersen, Bjørg Marit title = Intensive Patient Treatment date = 2018-09-25 keywords = ICU; infection; intensive; patient summary = Intensive care units (ICUs) are treating hospital''s poorest patients that need medical assistance during the most extreme period of their life. Intensive patients are treated with extensive invasive procedures, which may cause a risk of hospital infections in 10–30% of the cases. The hospital''s management should provide resources and written guidelines regarding infection control work, proper patient/care ratio, sufficient patient areas, isolation capacity and documented competence. Intensive care unit (ICU) should have a large enough area and furnished for a good, safe and effective infection protection [1] . Recent studies indicate that patients in separate ICU rooms will have fewer hospital infections and thus a lower risk of fatal outcome [72, 73] . An outbreak of multidrug-resistant Pseudomonas aeruginosa associated with increased risk of patient death in an intensive care unit Single rooms may help to prevent nosocomial blood stream infection and cross-transmission of methicillin-resistant Staphylococcus aureus in intensive care units doi = 10.1007/978-3-319-99921-0_45 id = cord-016223-nk8xwa0t author = Andersen, Bjørg Marit title = Strict Isolation date = 2018-09-25 keywords = PPE; infection; isolation summary = The unit should be located in a separate ward, preferably in a separate building with direct access via an external sluice and internal access through a negative air pressure sluice with sufficient areal for donning and doffing and for a safe treatment of infectious equipment and waste. Technical staff, handling medical equipment, including collection tanks and autoclaves, shall be specially trained in infection control and must be able to use a sluice function with the use of PPE, when entering these disinfection areas. • Out sluicing needs plenty of space for washbasin and suitable hand disinfectant, for doffing (undressing) and for the use of at least three waste bags (disposal, textiles and reusable equipment). Option if not autoclave/decontaminator in the isolation unit: Infectious waste bag is treated exterior with 5% chloramine and double packed in new yellow thick plastic bag in the sluice. doi = 10.1007/978-3-319-99921-0_19 id = cord-017140-k4lzwfge author = Andersen, Bjørg Marit title = Protection of Upper Respiratory Tract, Mouth and Eyes date = 2018-09-25 keywords = infection; mask; protection; respiratory summary = doi = 10.1007/978-3-319-99921-0_13 id = cord-017531-fm8gl5b3 author = Andersen, Bjørg Marit title = Scenarios: Serious, Infectious Diseases date = 2018-09-25 keywords = contact; infection; patient summary = All transport of infectious patients from the place of arrival to the hospital should take place in ambulances using the same infection control regime as for the individual infectious disease (contact infection, airborne infection, strict isolation); see isolation regimes; Chaps. • Ambulance staff and other personnel use the contact and airborne infection regime when picking up and transporting a patient. Short-time airborne isolation of exposed cases until the infection state is clarified/effect of antibacterial therapy 82.5.6 Anthrax After Staying in Turkey, Sick on the Plane Home 82.5.6.1 Patient: Strict Isolation-Air Pressure Isolate with Pressure [21, 22] Example: Two out of six people who have been on family visits in Turkey for a week, on farms with goats and skin production, are acutely ill on the plane home with cough, shortness of breath and fever. Less severe disease: isolation of index case and close contacts • Registering: All exposed persons are registered (name, address, telephone number) and followed up. doi = 10.1007/978-3-319-99921-0_82 id = cord-017534-0ai8chbu author = Andersen, Bjørg Marit title = Background Information: Isolation Routines date = 2018-09-25 keywords = Norway; hospital; infection; isolation; patient summary = There is an increased need of isolates for patients with infections, especially due to pulmonary tuberculosis, MRSA, VRE, Clostridium difficile (CD), multiresistant gram-negative bacteria and other "multidrug-resistant organisms" (MDRO) [23, 24, 36, 37, [48] [49] [50] [51] . In 2009, a European investigation was done as regards the number of "high-level isolation rooms" (HIRs), i.e. airborne infection isolation units with negative pressure (not defined) with at least 6 air changes per hour and sluice (anteroom) [61] . CDC defines contact isolation, using gown and gloves when in contact with patients infected with resistant bacteria like MRSA and other MDROs (multidrug-resistant organisms), and single rooms are recommended [19] . Spread of pathogenic infectious agents through the air and droplets requires a defined negative pressure ventilation isolate and a system which reduces airborne infection in the patient''s room. doi = 10.1007/978-3-319-99921-0_21 id = cord-017575-msc99cit author = Andersen, Bjørg Marit title = Dangerous Microbes date = 2018-09-25 keywords = handbook; infection summary = The most dangerous microbes for humans are those that are easily transmitted, virulent and invasive to the central organs like the blood and lung, robust survivors in the environment, have a low infection dose and are without any specific treatment or vaccine [2] [3] [4] [5] . The most dangerous microbes for humans are those that are easily transmitted, virulent and invasive to the central organs like the blood and lung, robust survivors in the environment, have a low infection dose and are without any specific treatment or vaccine [2] [3] [4] [5] . They easily spread via contact and air from animals and food, survive in the environment for months especially during colder seasons, are very easily transmitted and may cause nosocomial infections, chronic febris undulans, septicaemia and lung diseases. doi = 10.1007/978-3-319-99921-0_80 id = cord-017815-0t7jvvz5 author = Andersen, Bjørg Marit title = General Information date = 2018-09-25 keywords = infection; patient; room summary = A modern isolate for patients with infections comprises (1) a sluice with a good space for dressing and undressing of personal protective equipment (PPE) and for hand hygiene, (2) a large patient room and (3) a bathroom/disinfection room with own decontaminator or autoclave and with separate entrance from the patient''s room. A modern isolate for patients with impaired immune defence is similar to the infection isolates, with following exceptions: usually no need for decontaminator, hepafiltered clean air into the room and with a defined positive air pressure. Airborne infection isolation units: at least 10% of the bed capacity for adults and 10-15% of children in hospitals should be isolates well equipped with negative pressure, separate ventilation and private bath/disinfection room with decontaminator. Protective isolation: good hand hygiene, clean gown, surgical mask, surgical cap, room-bound shoes. doi = 10.1007/978-3-319-99921-0_15 id = cord-321949-s1qu3odd author = Anderson, Evan J title = Rotavirus infection in adults date = 2004-01-28 keywords = adult; child; gastroenteritis; infection; rotavirus summary = Spread by faecal-oral transmission, rotavirus infection in adults typically manifests with nausea, malaise, headache, abdominal cramping, diarrhoea, and fever. In this review we intend to familiarise clinicians who primarily provide care for adult patients with the salient features of rotavirus pathophysiology, clinical presentation, epidemiology, treatment, and prevention. In a separate study, 14 parents of children with rotavirus gastroenteritis developed serological evidence of infection, but only three had diarrhoea. Rotavirus infections in adult patients infected with HIV-1 frequently present as a chronic diarrhoea with sustained viral shedding in stools. In a small prospective study in the UK, rotavirus caused 4·1% of acute diarrhoea in adults admitted to hospital. 79 In a study of Mexican adults, 63% of patients presenting with acute gastroenteritis during winter months were positive for rotavirus. Rotavirus infections in adults in association with acute gastroenteritis doi = 10.1016/s1473-3099(04)00928-4 id = cord-299786-wuve0tjz author = Anderson, Robert title = Manipulation of cell surface macromolecules by flaviviruses date = 2004-02-27 keywords = Halstead; MHC; cell; dengue; infection; virus summary = Dengue virus infection of immature myeloid dendritic cells has been shown to induce their maturation accompanied by the expression of major histocompatibility complex (MHC) class I and II antigens; the costimulatory molecules CD40, CD80, and CD86; and the dendritic cell marker CD83 (Libraty et al., 2001) . Flaviviruses, including dengue and West Nile (Shen et al., 1997) viruses, activate endothelial cell adhesion molecule expression by either direct (virus-mediated) or indirect (cytokine-mediated) mechanisms (see Section V,C). A major candidate event in such a route is the activation of endothelial cell adhesion molecules by a factor(s) (particularly TNF-) produced by dengue virus-infected blood monocytes . Thus the roles of prior immunity, antibody-enhanced virus infection, and immune-mediated pathologic effects on the vascular system are key points in understanding the pathogenesis of dengue hemorrhagic disease. Activation of endothelial cells via antibody-enhanced dengue virus infection of peripheral blood monocytes doi = 10.1016/s0065-3527(03)59007-8 id = cord-284195-qarz4o2z author = Ansumali, Santosh title = A Very Flat Peak: Exponential growth phase of COVID-19 is mostly followed by a prolonged linear growth phase, not an immediate saturation date = 2020-04-11 keywords = daily; infection; number summary = As such, a few weeks after these strict measures, and noting the reported success of China, governments of various provinces and countries are waiting for the new daily infections to cross over the peak. To date, other than China which continues to report nearly zero new infected cases every day for the past few weeks, all other countries are either in an exponential phase or a linear growth phase. In this work, we note by studying the COVID-19 infection data from several countries which implemented quarantine that the exponential growth phase ends, but it is followed by a linear growth phase. As much as the linear regime suggests the end of the exponential growth phase, a correlation of the daily cases with the average number of infections at the time of transition seems to suggest that the growth is only maintained in a "pause", frozen at the state where the quarantines are implemented. doi = 10.1101/2020.04.07.20055772 id = cord-310239-mmvuij3k author = Arentz, Susan title = Clinical significance summary: Preliminary results of a rapid review of zinc for the prevention and treatment of SARS-CoV-2 and other acute viral respiratory infections date = 2020-08-01 keywords = CoV-2; SARS; infection; zinc summary = Indirect evidence from systematic reviews have found zinc supplementation is effective for the prevention of acute respiratory infections in young children and zinc lozenges may reduce the duration of the common cold in adults. As of the 9 June 2020, the preliminary findings of a rapid review of zinc for the prevention or treatment Pending any definitive evidence, clinicians might consider assessing the zinc status of people with chronic disease co-morbidities and older adults as part of a SARS-CoV-2 clinical work-up, as both groups have a higher risk of zinc deficiency/insufficiency and poorer outcomes from SARS-CoV-2. The primary objective of this rapid review was to assess the effects of zinc on the incidence, duration and severity of acute upper or lower respiratory tract infections caused by SARS-CoV-2 infection in people of any age and of any zinc status when used as a preventive supplement or as a therapy. doi = 10.1016/j.aimed.2020.07.009 id = cord-350928-vj5qlzpj author = Arnott, Alicia title = Human bocavirus amongst an all‐ages population hospitalised with acute lower respiratory infections in Cambodia date = 2012-04-25 keywords = HBoV; infection; respiratory summary = Objectives To investigate the prevalence and genetic diversity of HBoV amongst hospitalized patients with acute lower respiratory infection (ALRI) in Cambodia. In patients where HBoV is the only virus detected, the clinical symptoms reported are similar to those occurring as a result of infection with respiratory syncytial virus (RSV) and human metapneumovirus (HMPV), including bronchiolitis, bronchitis, pneumonia and exacerbation of asthma. 20 Here, we report the findings of the first study investigating the prevalence, seasonality, clinical characteristics and the molecular epidemiology of HBoV in amongst an all-ages population of patients hospitalized for acute lower respiratory illness (ALRI) in Cambodia over 3 consecutive years. 5 In this study, ALRI patient samples were screened for HBoV infection using a highly sensitive multiplex PCR assay previously shown to have a lower limit of detection of 4 copies of HBoV DNA ⁄ ll of viral transport medium. doi = 10.1111/j.1750-2659.2012.00369.x id = cord-275166-qduf08kp author = Assane, Dieng title = Viral and Bacterial Etiologies of Acute Respiratory Infections Among Children Under 5 Years in Senegal date = 2018-02-13 keywords = infection; respiratory summary = doi = 10.1177/1178636118758651 id = cord-256508-ce59ovan author = Asselah, Tarik title = COVID-19: discovery, diagnostics and drug development date = 2020-10-08 keywords = COVID-19; China; CoV-2; RNA; SARS; infection; patient summary = To date, with the exception of intravenous Remdesivir and dexamethasone, which have modest effects in moderate to severe COVID-19, no strong clinical evidence supports the efficacy and safety of any other drugs against SARS-CoV-2. The current diagnostic strategy to identify patients with COVID-19 is to test samples taken from the respiratory tract to assess for the presence of SARS-CoV-2 specific nucleic acid targets [47] . The neutralization assay is a laboratory-based test that uses live virus and cell culture methods to determine if patient antibodies can prevent viral infection in vitro [72] . A randomized, controlled, openlabel trial involving hospitalized adult patients with confirmed SARS-CoV-2 infection and severe respiratory illness COVID-19 was performed [126] . Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals doi = 10.1016/j.jhep.2020.09.031 id = cord-311908-sgdq6j6x author = Atkins, G. J. title = Transient virus infection and multiple sclerosis date = 2000-09-28 keywords = CNS; infection; virus summary = Multiple sclerosis (MS) is a chronic, demyelinating disease of the CNS in which autoimmunity to myelin plays a role in pathogenesis. These include subacute sclerosing panencephalitis (SSPE), caused by a persistent measles virus infection, and human T cell lymphotropic virus-I (HTLV-I)associated myelopathy, which is a slowly progressive neurological disease characterised by in¯ammatory in®ltrates and demyelination in the CNS, and is caused by an exogenous retrovirus. Another study that does not involve virus infection, but may nonetheless provide information concerning the possible viral aetiology of MS, concerns the exacerbation of brain damage following EAE induction. With regard to the activity of known human viruses in the induction of myelin damage, there is evidence that virus infections associated with CNS demyelination can cause damage to oligodendrocytes. It is possible that virus infection could induce secretion of pro-in¯ammatory cytokines that could penetrate the CNS parenchyma from the blood and lead to the recrudescence of anti-myelin autoimmunity by reactivation of previously primed T-cells. doi = 10.1002/1099-1654(200009/10)10:5<291::aid-rmv278>3.0.co;2-u id = cord-299918-0ahvoak4 author = Aykac, Kubra title = Respiratory viral infections in infants with possible sepsis date = 2018-09-24 keywords = infection summary = doi = 10.1002/jmv.25309 id = cord-310042-9z8rkzq8 author = Aysha, Al‐Ani title = Practical management of inflammatory bowel disease patients during the COVID‐19 pandemic: expert commentary from the Gastroenterological Society of Australia Inflammatory Bowel Disease faculty date = 2020-07-12 keywords = COVID-19; IBD; SARS; infection summary = This review aims to summarise the current literature and provide guidance on the management of inflammatory bowel disease (IBD) patients in the context of the COVID‐19 pandemic in the Australasian setting. A significant proportion of IBD patients are treated with long-term immunomodulator/immunosuppressive therapy which potentially places them at increased risk of infections and associated complications. Practitioners and patients alike are therefore concerned about the risk and implications of COVID-19 infection in the IBD patient, despite a paucity of evidence supporting an altered predisposition to disease or more severe disease course. Despite concerns regarding immunosuppression and consequent predisposition to infection, there is no evidence to suggest increased infection rates of COVID-19 in IBD patients to date. 8, 9 Hence, expert consensus currently is that patients with IBD do not appear to be at increased risk of SARS-CoV-2 infection compared with the general population. 2 • Reducing disease activitythere is evidence that moderate to severe disease activity increases the risk of infection in IBD patients. doi = 10.1111/imj.14889 id = cord-022453-xe5v7947 author = BABIUK, L.A. title = Viral Gastroenteritis in Ruminants date = 2013-11-17 keywords = infection; virus summary = Rotavirus infection is generally limited to the small intestine in calves, pigs and humans (Middleton et al., 1974; Mebus and Newman, 1977; McAdaragh et al., 1980) , but antigen can be found in the colon of lambs (Snodgrass et al., 1977) , pigs (Theil et al., 1978) and mice (Little and Shadduck, 1982) . Bovine Coronavirus diarrhea, like rotavirus diarrhea, occurs within 15-24 h p.i. Early in infection the villous epithelial cells appear morphological normal but they contain large amounts of antigen. Since diarrhea occurs before denudation and loss of enterocytes it is postulated that it is a direct result of infection of the cell and the ensuing redirection of cellular functions from absorption to virus replication. Because of the replication in lymphoid tissue this disease can be more severe, especially in small animals, than other viral infections, because of interference with immune responses and damage to the crypts. doi = 10.1016/b978-0-444-87312-5.50076-x id = cord-307899-427a7i3h author = BITTLE, JAMES L. title = Vaccines Produced by Conventional Means to Control Major Infectious Diseases of Man and Animals date = 1989-12-31 keywords = States; United; cause; disease; infection; vaccine; virus summary = Adenoviruses cause significant disease in dogs, foxes, and man, but have also been isolated from cattle, swine, goats, sheep, horses, turkeys, and chickens, where they produce mild infections, mainly associated with the respiratory and intestinal tracts. The latter modified the virus by serial passage in porcine and canine tissue cultures; the resulting vaccine immunized dogs and did not produce clinical signs of infection except for occasional corneal opacity similar to that caused by natural infection. The immunity produced by the attenuated live-virus CAV-1 vaccines is long lasting and has drastically reduced the incidence of the canine disease. The exception is human hepatitis A virus, which causes a serious disease and has one serotype; the development of both inactivated virus and attenuated live-virus vaccines is in progress (Hilleman et al., 1982; Provost et al., 1983) . An attenuated live-virus yellow fever vaccine was developed by passage of the virulent Asibi strain in mouse brain and cell culture until it had lost its pathogenicity for monkeys and man (Theiler, 1951) . doi = 10.1016/b978-0-12-039233-9.50005-6 id = cord-257114-pxmflm2c author = BURGUETE, SERGIO R. title = Lung transplant infection date = 2012-12-26 keywords = BOS; CMV; LTR; infection; lung; transplant summary = This article will review the common infections that develop in the lung transplant recipient, including the general risk factors for infection in this population, and the most frequent bacterial, viral, fungal and other less frequent opportunistic infections. Resistant Gramnegative organisms pose perhaps the greatest risk, and some studies suggest an association between pretransplant colonizing organisms from patients with suppurative lung disease and pneumonias following LT. A Cochrane Review comparing prophylaxis in different groups of solid organ transplant patients with antivirals versus placebo or no treatment showed a significant reduction in disease (relative risk 0.42), infection (relative risk 0.61), mortality from CMV disease (relative risk 0.26) and allcause mortality (relative risk 0.63). 114 In general, the choice for antifungal prophylaxis depends, in part, on the presence of specific risk factors such as colonization with Aspergillus, presence of airway stents or ischaemia, single lung transplantation, CMV infection, hypogammaglobulinaemia or treatment of acute rejection. doi = 10.1111/j.1440-1843.2012.02196.x id = cord-321835-qn33sx8x author = Bailey, Emily S. title = A Mini Review of the Zoonotic Threat Potential of Influenza Viruses, Coronaviruses, Adenoviruses, and Enteroviruses date = 2018-04-09 keywords = human; infection; virus summary = In particular, respiratory infections are problematic; in early 2003, World Health Organization issued a worldwide alert for a previously unrecognized illness that was subsequently found to be caused by a novel coronavirus [severe acute respiratory syndrome (SARS) virus]. Influenza A virus H3N2 subtypes are frequently reported in swine, avian, and canine hosts that are responsible for highly infectious respiratory diseases in pigs and have been examined as a potential cause of influenza in humans. In a recent review of the risks of potential outbreaks associated with zoonotic Ad (48) , it was noted that intense human-animal interaction is likely to increase the probability of emergent cross-species Ad infection. This suggests that strategies for novel virus detection should incorporate global surveillance at the human-animal interface to detect potentially emerging zoonotic viruses. Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome doi = 10.3389/fpubh.2018.00104 id = cord-314359-fw14b5cv author = Bajaj, Satish Kumar title = Respiratory infections in immunocompromised patients: Lung findings using chest computed tomography date = 2016-11-23 keywords = Fig; infection; pneumonia summary = Patient who present with classical symptoms like fever, rigors, chills, cough with expectoration, chest pain, dyspnea and whose chest radiographic findings are suggestive of common bacterial infections is considered to have typical pneumonia. Clinical features such as patient age, immune status, time of year, illness in other family members, community outbreaks, different stages of the underlying disease at onset, severity and duration of symptoms, and presence of a rash remain important in diagnosing viral causes of atypical pneumonia in immune-competent as well as ICPs. CXR is an essential tool for rapid diagnosis of lung changes and may also be help in follow up of the treatment response. However, in hospitalized patients with similar radiological features without any relevant clinical and laboratory findings consistent with lung infection, a possible diagnosis of atelectasis, old changes and organizing pneumonias following a course of antibiotics should be considered. doi = 10.1016/j.jrid.2016.11.001 id = cord-253256-909chgl0 author = Bajwa, Sukhminder Jit Singh title = Peri-operative and critical care concerns in coronavirus pandemic date = 2020-03-28 keywords = care; case; covid-19; infection; patient summary = In this article, all outbreak response measures including triaging, preparation of isolation rooms, decontamination and disinfection protocols as well as fundamental principles of critical care and anaesthetic management in Covid-19 cases is being discussed. The need of the hour therefore is to update ourselves with clinicopathological spectrum of the deadly disease and provide evidence based medical services to all hospitalized cases with suspected Covid-19 infection. All the recommendations below have been influenced by the past experiences of corona virus outbreaks and desire improved measures for personal protection of health care workers and consequent prevention of nosocomial transmission of infection. Planning for anaesthesiaand surgery in covid-suspect cases Anaesthesiologists and intensivists are the soldiers at the final frontier of corona disaster as all patients landing up in the hospital with severe respiratory distress will be primarily seen under their domain. Air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a symptomatic patient doi = 10.4103/ija.ija_272_20 id = cord-302277-c66xm2n4 author = Bakaletz, Lauren O. title = Developing animal models for polymicrobial diseases date = 2004 keywords = Candida; disease; infection; model; virus summary = doi = 10.1038/nrmicro928 id = cord-283138-18q23z8l author = Balasubramanian, S. title = Coronavirus Disease 2019 (COVID-19) in Children - What We Know So Far and What We Do Not date = 2020-04-09 keywords = COVID-19; SARS; child; infection summary = doi = 10.1007/s13312-020-1819-5 id = cord-262524-ununcin0 author = Bankhead, Armand title = A Simulation Framework to Investigate in vitro Viral Infection Dynamics date = 2011-12-31 keywords = cell; infection; model summary = In this paper we present a tool to address these issues: a cellular automata model describing critical aspects of in vitro viral infections taking into account spatial characteristics of virus spreading within a culture well. We interrogate the model using a Latin Hypercube sensitivity analysis to identify which mechanisms are critical to the observed infection of host cells and the release of measured virus particles. We also show that the model can explain the experimentally observed virus titer data and allows a deeper understanding of the infection dynamics in the in vitro experiments. Infectious: Assembled virion is being released from the host cell according to the release function (Section 2.4) By examining the experimental viral titer data shown in Figure 1 we derived temporal delay of the state transition between Containing and Infectious. p BP represents the probability of a virus-receptor binding event leading to a cell''s infection by a single viral particle during a given model time step. doi = 10.1016/j.procs.2011.04.195 id = cord-257255-n5o368ih author = Barker, J. title = Spread and prevention of some common viral infections in community facilities and domestic homes date = 2001-12-21 keywords = infection; surface; virus summary = Amongst health care professionals there is growing awareness that improved standards of hand, surface and air hygiene in community settings could do much to prevent the spread of viral infections within these environments. In a preschool daycare centre, respiratory and gastrointestinal infections decreased following implementation of measures which included reinforcing existing handwashing procedures and education of staff and families on issues of infection control including environmental surface cleaning and disinfection and disinfection of toys (Krilov et al. Nevertheless, overall, there is convincing circumstantial evidence to suggest that improved standards of hygiene can have a signi®cant impact in reducing the rates of respiratory, intestinal and other viral infections in childcare facilities, domestic homes, hospitals and adult care centres and the circulation of infections between these communities. Potential role of hands in the spread of respiratory viral infections Ð studies with human parain¯uenza virus 3 and rhinovirus 14 doi = 10.1046/j.1365-2672.2001.01364.x id = cord-337284-joq1aqn6 author = Barrera‐López, Pedro title = Co‐infection of other respiratory pathogens and HIV in COVID‐19 patients: is there a pattern? date = 2020-07-24 keywords = infection summary = The pandemic caused by SARS-CoV-2 has led to the elaboration of multiple studies to increase its knowledge and understanding, hence, having the ability to accomplish an adequate and timely diagnosis and give an optimal treatment according to the patient''s condition. The clinical manifestations of COVID-19 pose a series of challenges both in understanding and delimiting the disease secondary to the SARS-CoV-2 infection. The general analysis, that includes a total of 300 patients, revealed that the most frequent pathogen associated with co-infection was Influenza A 6-8 (mentioned in 8 of the 19 articles focused on co-infection with respiratory pathogens), possibly following a seasonal pattern; these studies showed a slight predominance of the male sex, without preference for any age group. The foregoing, to optimize the analysis of these cases and establish if there are characteristics that allow establishing the possibility of carrying an additional infection to that of SARS-CoV-2 and the implications for the management and prognosis of the patient. doi = 10.1002/jmv.26331 id = cord-257729-s0vo7dlk author = Bauer, Melissa title = Obstetric Anesthesia During the Coronavirus Disease 2019 Pandemic date = 2020-04-20 keywords = SARS; covid-19; infection; patient summary = T he management of obstetric patients infected with Coronavirus Disease 2019 (COVID19) due to human-to-human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires quite unique considerations-from caring for critically ill pregnant and postpartum women to protecting health care workers from exposure during the delivery hospitalization (health care providers, personnel, family members, and beyond). 4 An additional manifestation noted among patients with COVID-19 infection is the sudden loss (or reduction) of the sense of smell and taste, which is currently recommended by the American Academy of Otolaryngology-Head With increasing numbers of Coronavirus Disease 2019 (COVID 19) cases due to efficient human-to-human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the United States, preparation for the unpredictable setting of labor and delivery is paramount. doi = 10.1213/ane.0000000000004856 id = cord-006464-s8rjoyse author = Bauer, Michael title = Infectious and Immunologic Phenotype of MECP2 Duplication Syndrome date = 2015-02-27 keywords = Fig; duplication; infection; mecp2; patient summary = Our data for the first time show systematically that increased susceptibility to infections in MECP2 duplication syndrome is associated with IgA/IgG(2)-deficiency, low antibody titers against pneumococci and elevated acute-phase responses. The single patient who has to date not developed severe infections despite We further investigated whether patients with MECP2 duplication syndrome showed stronger acute phase responses, which we could confirm in 7/10 patients in terms of elevated CRP values above 200 mg/l during non-invasive infections, mainly pneumoniae. In summary we here show for the first time systematically that patients with MECP2 duplication syndrome are at increased risk for in particular non-invasive but also for invasive infections with potentially encapsulated bacteria, that this increased susceptibility to infections may be associated with IgG 2 -subclass deficiency/ low titers against pneumococci and elevated acute-phase responses, while the precise role of T-cell immunity and in particular the extent of impaired IFNγsecretion and its role for the observed infectious phenotype is still to be defined. doi = 10.1007/s10875-015-0129-5 id = cord-352230-8mazd3eu author = Beeraka, Narasimha M. title = Strategies for Targeting SARS CoV-2: Small Molecule Inhibitors—The Current Status date = 2020-09-18 keywords = ACE-2; CoV-2; Nrf-2; SARS; TMPRSS2; coronavirus; infection summary = Severe Acute Respiratory Syndrome-Corona Virus-2 (SARS-CoV-2) induced Coronavirus Disease 19 (COVID-19) cases have been increasing at an alarming rate (7.4 million positive cases as on June 11 2020), causing high mortality (4,17,956 deaths as on June 11 2020) and economic loss (a 3.2% shrink in global economy in 2020) across 212 countries globally. SARS-CoV-2 infection is mediated by the binding of viral Spike proteins (S-protein) to human cells through a 2-step process, which involves Angiotensin Converting Enzyme-2 (ACE2) and Transmembrane Serine Protease (TMPRSS)-2. Therefore, in this review, we have reviewed structural features of SARS-CoV-2 with special emphasis on key molecular targets and their known modulators that can be considered for the development of NSMIs. COVID-19 is a devastating disease caused by a coronavirus related to the one that caused outbreaks of Severe Acute Respiratory Syndrome (SARS) in the year 2002 (1, 2) . doi = 10.3389/fimmu.2020.552925 id = cord-272955-kkkrkgg1 author = Belsy, Acosta title = Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes date = 2009-03-12 keywords = PCR; adenovirus; human; infection summary = doi = 10.1007/s00705-009-0338-4 id = cord-302056-wvf6cpib author = Benatia, D. title = Estimating COVID-19 Prevalence in the United States: A Sample Selection Model Approach date = 2020-04-30 keywords = April; infection; population summary = doi = 10.1101/2020.04.20.20072942 id = cord-255781-55zrmgxq author = Bergman, Scott J. title = Interferons as Therapeutic Agents for Infectious Diseases date = 2011-12-31 keywords = HCV; IFN; infection; interferon; treatment summary = These agents consist of naturally occurring small proteins with molecular weights of 15,000 to 27,600 Da. 3 Each is considered a first-line option for the treatment of chronic hepatitis C virus (HCV) infection in combination with ribavirin. Along with the list of additional indications approved by the Food and Drug Administration shown in Table 1 , IFN-a was shown to be an effective treatment for the symptoms of an aggressive case of chronic active Epstein-Barr virus, but did not eliminate infection entirely. IFNs have been tested repeatedly against infectious diseases, but injections are used mostly for the treatment of viral hepatitis C and prevention of infections in patients with chronic granulomatous disease clinically. Phase 1b study of pegylated interferon lambda 1 with or without ribavirin in patients with chronic genotype 1 hepatitis C virus infection doi = 10.1016/j.idc.2011.07.008 id = cord-022122-6ssdamhp author = Berry, Winter S. title = Otitis, Sinusitis, and Mastoiditis: Ear or Facial Pain Following a Common Cold date = 2018-10-15 keywords = AOM; EAC; infection summary = The presence of gastroesophageal reflux disease, allergic rhinitis, and viral upper respiratory infections can all lead to inflammation of the eustachian tube and surrounding tissues resulting in the presence of increased secretions in the middle ear that accumulates because the eustachian tube is not fully patent [2] [3] [4] . The most common bacterial causes of AOM include Streptococcus pneumoniae, non-typeable Haemophilus influenzae, and Moraxella catarrhalis. S. aureus should be included on the list of possible infecting agents in patients who have tympanostomy tubes, as these medical devices serve as a conduit between the bacteria normally present in the EAC and the middle ear. Acute bacterial rhinosinusitis is a more precise name for the condition caused by bacterial pathogens, and like AOM, it typically occurs when drainage is impaired secondary to the inflammation associated with a recent viral infection. doi = 10.1007/978-3-319-91080-2_4 id = cord-314600-x8mmuf3y author = Biagi, Carlotta title = Rhinovirus Infection in Children with Acute Bronchiolitis and Its Impact on Recurrent Wheezing and Asthma Development date = 2020-10-21 keywords = RSV; bronchiolitis; infection summary = Bronchiolitis is defined by the American Academy of Pediatrics (AAP) as a constellation of signs and symptoms, including a viral upper respiratory tract prodrome, followed by increased respiratory effort and wheezing in children under the age of two [9] .In Europe, by contrast, the term bronchiolitis is generally referred to as a first episode of acute lower airway infection in infants younger than one year [7] . Many studies have investigated whether the severity of acute bronchiolitis-mainly measured by clinical score indexes (CSIs), oxygen requirement, ventilatory support, Pediatric Intensive Care Unit (PICU) admission, and length of hospital stay (LOS)-is associated with specific viral infections or co-infections, with controversial results. Finally, also in a prospective multicenter study focusing on 363 hospitalized infants with moderate-severe bronchiolitis, no significant differences appeared between RV infection-even when they considered viral types-and other single virus-infections regarding either oxygen requirement, ventilation need, or nasogastric feeding [31] . doi = 10.3390/microorganisms8101620 id = cord-007362-pjpkz6wv author = Bielefeldt-Ohmann, Helle title = The Pathologies of Bovine Viral Diarrhea Virus Infection: A Window on the Pathogenesis date = 2016-01-06 keywords = BVDV; Fig; bovine; cell; infection; virus summary = Pathologic lesions caused by bovine viral diarrhea virus (BVDV) infections comprise a wide spectrum of type, degree, and, by implication, pathogenesis, including congenital defects, necrotic-erosive lesions in mucosal epithelia and skin, and reactive as well as degenerative changes in lymphoid tissues. 3, 22, 29 In PI calves, BVDV can be isolated from lung tissue, and virus antigen is widespread in bronchiolar and alveolar epithelial cells, however, without accompanying histopathologic changes (see section on persistent infection without overt clinical disease and Fig. 5 ).17 Conversely, a proportion (the size varying with study) of cattle succumbing to BRD are positive for BVDV, by virus isolation from or antigen detection in lung tissue, but the ensuing pathologic changes cannot be distinguished from those of other viral pathogens in the BRD complex (perhaps with the exception of BHV-P5), and usually are dominated by the pathology caused by the secondary bacterial agent. doi = 10.1016/s0749-0720(15)30461-8 id = cord-300314-fbppvt75 author = Bikov, Andras title = 13th ERS Lung Science Conference. The most important take home messages: News from the Underground date = 2015-06-17 keywords = ERS; LSC; infection summary = doi = 10.1183/20734735.04015 id = cord-018907-c84t1bo5 author = Bin-Hussain, Ibrahim title = Infections in the Immunocompromised Host date = 2012 keywords = gram; infection; patient; risk summary = In providing empirical antibiotic therapy in patient with pulmonary infiltrate and defect in cell-mediated immunity one need to consider Pneumocystis jiroveci, nocardia, legionella, mycoplasma, in addition to aerobic Gram-positive cocci and Gram-negative bacilli therefore it is advised to use trimethoprim-sulfamethoxazole, macrolides including erythromycin or clarithromycin and agent active against Gram-positive and Gram-negative; for example, thirdgeneration cephalosporin with or without aminoglycoside with anti-Gram-positive either nafcillin or vancomycin based on the incidence of methicillin-resistant Staphylococcus aureus (MRSA) and penicillin resistant Streptococcus pneumoniae. The factors influencing antimicrobial selection include the types of bacterial isolates found in the institution, antibiotic susceptibility patterns, drug allergies, presence of organ dysfunction, chemotherapeutic regimen whether the patient was receiving prophylactic antibiotics, and condition of the patient at diagnosis, for example, presence of signs and symptoms at initial evaluation and presence of documented sites requiring additional therapy. doi = 10.1007/978-3-642-02202-9_68 id = cord-310371-pylrg91h author = Bishop, R.F. title = Enteric Viruses date = 2008-07-30 keywords = RNA; human; infection; virus summary = The onset of acute enteritis is associated with infection by viruses that replicate at or near the site of entry into the intestinal mucosa, including caliciviruses, rotaviruses, adenoviruses, astroviruses, and coronaviruses. . viruses causing localized inflammation at any level of the intestinal tract, predominantly in small intestinal mucosa, resulting in acute gastroenteritis, for example, rotaviruses, caliciviruses, adenoviruses, astroviruses; . The family Caliciviridae contain small RNA viruses that cause enteric disease in a wide variety of hosts including cattle, pigs, rabbits, and humans. Caliciviruses causing enteric infections (in humans and other animals) are classified as belonging to the family Caliciviridae, which is divided into four genera. The recent demonstration that human noroviruses can infect and replicate in a three-dimensional cell culture model of human intestinal epithelium, should improve our understanding of the pathogenesis, and antigenic diversity of this important group of enteric viruses. doi = 10.1016/b978-012374410-4.00386-1 id = cord-318944-13zk6cco author = Bizzoca, Maria Eleonora title = Covid-19 Pandemic: What Changes for Dentists and Oral Medicine Experts? A Narrative Review and Novel Approaches to Infection Containment date = 2020-05-27 keywords = COVID-19; PPE; SARS; dental; infection; patient; procedure summary = The authors performed a narrative review on Severe Acute Respiratory SyndromeCoronaVirus-2 ( SARS-CoV-2) and all infectious agents with the primary endpoints to illustrate the most accepted models of safety protocols in dentistry and oral medicine, and to propose an easy view of the problem and a comparison (prevs post-COVID19) for the most common dental procedures. After a brief excursus on all infectious agents transmittable at the dental chair, the authors described all the personal protective equipment (PPE) actually on the market and their indications, and on the basis of the literature, they compared (before and after COVID-19 onset) the correct safety procedures for each dental practice studied, underlining the danger of underestimating, in general, dental cross-infections. The precautions for infection control require wearing gloves, aprons, as well as eye and mouth protection (goggles and mask, such as medical masks and Filtering Face Piece or FPP) for each procedure involving direct contact with the patient body fluids. doi = 10.3390/ijerph17113793 id = cord-318172-bdotp9ko author = Blanco, Jorge C. G. title = PROPHYLACTIC ANTIBODY TREATMENT AND INTRAMUSCULAR IMMUNIZATION REDUCE INFECTIOUS HUMAN RHINOVIRUS 16 LOAD IN THE LOWER RESPIRATORY TRACT OF CHALLENGED COTTON RATS date = 2014-01-01 keywords = HRV16; cotton; infection; rat; virus summary = In this work we show that, without requiring any genetic modification of either the host or the virus, intranasal infection of cotton rats with HRV16 resulted in measurable lower respiratory tract pathology, mucus production, and expression of interferon-activated genes. Over the years, the cotton rat (Sigmodon hispidus) has been shown to support replication of a broad spectrum of human viruses including respiratory syncytial virus (RSV) [25] , nonadapted strains of human influenza [26, 27] , and measles [28, 29] , among others [30] , providing modeling capabilities for the corresponding infections. The results of the described experimental work show that HRV16 infection in the cotton rat reproduces aspects of HRVassociated human disease in the respiratory tract, causing detectable inflammation in the lower airways and lung parenchyma and mucus production, and inducing a transient expression of interferon-stimulated genes that merits further investigation. In addition we demonstrated that passive transfer of antibodies generated in vaccinated cotton rats can protect naïve animals from Infectious virus titers in the lung were determined by plaque assay at the indicated times p.i. doi = 10.1016/j.trivac.2014.02.003 id = cord-326887-lyewg2c9 author = Bloomfield, Sally F. title = The effectiveness of hand hygiene procedures in reducing the risks of infections in home and community settings including handwashing and alcohol-based hand sanitizers date = 2007-12-10 keywords = ABHS; MRSA; United; hand; hygiene; infection summary = The effectiveness of hand hygiene procedures in reducing the risks of infections in home and community settings including handwashing and alcohol-based hand sanitizers There can be no doubt that advances in hygiene during the 19th and 20th centuries, along with other aspects of modern medicine, have combined to improve both the length and quality of our lives. The data suggest the following: d For reservoir sites such as the sink waste pipes or toilets, although the probability of contamination (potentially pathogenic bacteria or viruses) is high, the risk of transfer is limited unless there is a particular risk situation (eg, a family member with enteric infection and fluid diarrhea, when toilet flushing can produce splashing or aerosol formation that can settle on contact surfaces around the toilet). Although handwashing intervention studies provide data supporting the causal link between hand contamination and ID transmission, defining the importance of hand hygiene relative to other hygiene practices, such as surface and cleaning cloth hygiene, or the risks associated with airborne transmission is difficult because of the close interdependence of these factors. doi = 10.1016/j.ajic.2007.07.001 id = cord-310942-191m0e65 author = Boga, Jose Antonio title = Beneficial actions of melatonin in the management of viral infections: a new use for this “molecular handyman”? date = 2012-04-18 keywords = IFN; TNF; cell; infection; melatonin; virus summary = The potential protective mechanisms include melatonin acting as a free radical scavenger, an antioxidant enzyme inducer, a positive regulator of immune functions and an inhibitor of inflammation, as well as a regulator of programmed cell death (PCD) [ Table 2 ]. Melatonin treatment also caused a rise in protein expression of the nuclear factor erythroid 2 (Nrf2), a transcription factor that plays a critical role by binding to the antioxidant response element in the promoter region of a number of genes encoding for antioxidant and detoxifying enzymes in several types of cells and tissues [109] . Respiratory syncytial virus infection of human respiratory epithelial cells enhances inducible nitric oxide synthase gene expression Melatonin decreases nitric oxide production and lipid peroxidation and increases interleukin-1 beta in the brain of mice infected by the Venezuelan equine encephalomyelitis virus doi = 10.1002/rmv.1714 id = cord-017537-ztdz4a2s author = Bologna, Mauro title = Biological Agents and Bioterrorism date = 2014-09-18 keywords = human; infection; specie; virus summary = For this very stimulating course, I want to share with you some of my studies and even some of my scientific and phylosophical considerations on biological agents living in the environment and their relations with humans, in the very wide concepts of ecological relationships, parasitism, immunolgical defenses and infectious disease mechanisms. All these concepts must be studied and considered in the event of criminal use of biological agents (bioterrorism) aimed at harming human populations in time and in geographical space. In the light of recent concern and interest about the potential for biological terrorism (biofarware) there are several diseases and bacterial toxins that must be considered in particular, like anthrax [ 1 , 2 ] , smallpox [ 3 , 4 ] , plague [ 5 ] , botulinum toxin [ 6 ] , and tularemia [ 7 ] . doi = 10.1007/978-94-017-9238-7_1 id = cord-016601-gp259urb author = Bonadonna, Lucia title = Analysis of Microorganisms in Hospital Environments and Potential Risks date = 2017-03-24 keywords = hospital; infection; patient summary = doi = 10.1007/978-3-319-49160-8_5 id = cord-025628-9611eglg author = Bonagura, Vincent Robert title = Infections that cause secondary immune deficiency date = 2020-05-29 keywords = CD4; HIV; IL-10; cell; infection summary = Herein we discuss some of the secondary immune defects caused by select viruses (measles, influenza, HIV1, HTLV), parasites, (leishmania, malaria), and bacteria (Bordetella pertussis). In this chapter, we discuss how some microbes manipulate or, in the case of the human immune deficiency virus (HIV), exhaust protective innate and/or adaptive immunity, ultimately leading to severe microbial superinfections by other infectious organisms that cause significant morbidity and, on occasion, mortality from secondary infections. 74 While influenza-related mortality can in part be attributed to direct effects on the respiratory system, many of the deaths associated with IV infection are caused by increases in susceptibility to secondary bacterial pneumonia. Impaired function of HIV-infected macrophages and dendritic cells contributes to the failure of effective innate and adaptive immune responses to secondary infection. Taken together, HTLV induces cytotoxic T cells to kill virus-infected cells, alters CD4 þ T cell function and cytokine production and it decreases NK cell activation leading to susceptibility to subsequent disseminated parasitic infections. doi = 10.1016/b978-0-12-816768-7.00049-1 id = cord-339039-6gyo9rya author = Bonvehí, Pablo E. title = Transmission and Control of Respiratory Viral Infections in the Healthcare Setting date = 2018-04-30 keywords = RSV; infection; respiratory; table summary = The purpose of this review is to describe the most frequent and relevant nosocomial viral respiratory infections, their mechanisms of transmission and the infection control measures to prevent their spread in the healthcare setting. RECENT FINDINGS: Although most mechanisms of transmission and control measures of nosocomial viral infections are already known, improved diagnostic tools allow better characterization of these infections and also lead to the discovery of new viruses such as the coronavirus, which is the cause of the Middle East Respiratory Syndrome, or the human bocavirus. Influenza virus can be transmitted through infectious droplets eliminated by patients when coughing or sneezing, or through direct contact with surfaces contaminated by respiratory secretions from symptomatic infected subjects (Table 1 ) [32] . Preventive measures to avoid adenovirus nosocomial infections include patient cohorting, reduction of visitors and contact and droplet precautions, along with the exclusion of infected healthcare workers from clinical duties (Table 2 ) [13, 36] . doi = 10.1007/s40506-018-0163-y id = cord-284322-synuzaxm author = Borel, Nicole title = Mixed infections with Chlamydia and porcine epidemic diarrhea virus - a new in vitro model of chlamydial persistence date = 2010-07-27 keywords = Chlamydia; PEDV; Vero; infection summary = doi = 10.1186/1471-2180-10-201 id = cord-103436-y1br5hy8 author = Bourgoin, P. title = CD64 and CD169 could help differentiate bacterial from viral infections in Emergency Department date = 2020-11-03 keywords = November; infection; preprint summary = Objectives: The aim of this study was to assess discriminative performances of two biomarkers, CD64 on neutrophils (nCD64) and CD169 on monocytes (mCD169), using a new flow cytometry procedure, in patients presenting with fever to the ED. We developed a rapid flow cytometry assay, able to measure leucocytes biomarkers expressions within 10 minutes (12) , and demonstrated promising results for the triage of patients with fever at the Emergency Department (13, 14) , with CD64 on neutrophils (nCD64), increased in case of bacterial infections (15) , and CD169 on monocytes (mCD169), increased in case of viral infections (16) . -clinical data: time from onset, symptoms, X-ray examination results (performed and atypical chest X-ray or ultrasound or CT scan), final diagnosis established by the ED practitioner, outcome of the ED visit (released home, conventional or critical care hospitalization), and eventually duration of the hospitalization; -and biological data: white blood cell (WBC) and polymorphonuclear neutrophil (PMN) counts, CRP and PCT levels, biochemical measurements (urea, sodium, glucose, hematocrit, hemoglobin), and name of the identified pathogens if isolated. doi = 10.1101/2020.10.28.20221259 id = cord-324635-27q3nxte author = Bouza, Emilio title = The situation of infection in the elderly in Spain: a multidisciplinary opinion document date = 2020-09-08 keywords = Spain; age; care; elderly; health; home; infection; old; patient; study; year summary = Thus, for long-term care facility (LTCF) residents and in hospitalised elderly people, UTI is the number one cause of infection and is the second most common in older women living in the community [19] . The first data on infection in nursing homes in Spain come from the EPINGER study, conducted in community health centres in Catalonia, which reported a prevalence of 6.5%, although it should be pointed out that in Catalonia the concept of the community health centre would include medium-long term patients, while in the rest of the Spanish autonomous communities this concept would be limited to nursing homes [40] . This is a multi-centre system for monitoring nosocomial infections, based on the production of an annual prevalence study, which has been conducted since 1990 in a large group of hospitals in Spain and was promoted by the Spanish Society of Preventive Medicine, Public Health and Hygiene. The studies reviewed allow us to estimate a prevalence of infection of between 4 and 10% in nursing homes in Spain, depending on their complexity, and between 6 and 9% in hospitalised elderly people. doi = 10.37201/req/057.2020 id = cord-318282-ocgfgx9r author = Boyce, John M title = Meticillin-resistant Staphylococcus aureus date = 2005-10-31 keywords = MRSA; Staphylococcus; USA; hospital; infection; patient summary = Measures recommended by the Society for Healthcare Epidemiology of America for controlling health-care-associated MRSA include the use of screening cultures to detect colonised patients, placing patients in private rooms or cohorting patients, wearing gloves for room entry, gowns for substantial contact with patients or their environment, and hand hygiene before and after patient contact. Further studies are necessary to establish the relative efficacy of control measures such as screening cultures, cohort nursing, increased staffing levels, and improved hand hygiene adherence rates in controlling transmission of MRSA in health-care facilities. Revised guidelines for the control of methicillin resistant Staphylococcus aureus infections in hospitals Comparison of community-and health care-associated methicillin-resistant Staphylococcus aureus infection Epidemiology of emerging methicillin-resistant Staphylococcus aureus (MRSA) in Denmark: a nationwide study in a country with low prevalence of MRSA infection Effectiveness of a hospitalwide selective screening programme for methicillin-resistant Staphylococcus aureus (MRSA) carriers at hospital admission to prevent hospital-acquired MRSA infections doi = 10.1016/s1473-3099(05)70243-7 id = cord-283545-vu8lt3w6 author = Brabb, Thea title = Infectious Diseases date = 2011-12-16 keywords = Baker; Barthold; ETIOLOGY; Fox; Percy; Post; Songer; Wagner; clinical; guinea; infection; pig summary = Although guinea pigs are sensitive and susceptible to the development of lesions from a wide range of viruses, bacteria, protozoa, and parasites, only a small number of organisms cause natural infection and only a portion of that group cause clinical disease. Although guinea pigs are sensitive and susceptible to the development of lesions from a wide range of viruses, bacteria, protozoa, and parasites, only a small number of organisms cause natural infection and only a portion of that group cause clinical disease. The efficacy of canine, porcine, human, and autogenous Bordetella vaccines and bacterins has been evaluated by several individuals; reports suggest that these vaccines do not completely protect guinea pigs from infection, but a decrease in the incidence and severity of clinical disease has been noted in experimentally challenged animals (Matherne et al., 1987; Stephenson et al., 1989) . doi = 10.1016/b978-0-12-380920-9.00023-7 id = cord-021499-up5vftj4 author = Brayton, Cory title = Viral Infections date = 2007-09-02 keywords = Barthold; Council; MHV; MPV; National; Research; infection; mouse; virus summary = Depending on inoculation route, dose, strain, and age of mice, experimental infections may result in inflammation or cytomegaly with inclusion bodies in a variety of tissues, pneumonitis, myocarditis, meningoencephalitis, or splenic necrosis in susceptible strains (National Research Council, 1991; Osborn, 1982; Percy and Barthold, 2001) . Both strains are apathogenic for adult mice, but the immunosuppressive variant is more pathogenic for neonatal mice than is MMVp. Serological surveys show that the mouse is the primary natural host (Parker et al., 1970; Smith et al., 1993b; Singleton et al., 2000) , but the virus is also infective for rats, hamsters (Garant et al., 1980; Ward and Tattersall, 1982) , and Mastomys (Haag et al., 2000) during foetal development or after parenteral inoculation. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS, and intestine. doi = 10.1016/b978-012336425-8/50076-5 id = cord-335871-zieuc7vk author = Brazee, Patricia L. title = Targeting the Linear Ubiquitin Assembly Complex to Modulate the Host Response and Improve Influenza A Virus Induced Lung Injury date = 2020-05-13 keywords = IAV; LUBAC; infection; response summary = title: Targeting the Linear Ubiquitin Assembly Complex to Modulate the Host Response and Improve Influenza A Virus Induced Lung Injury Data from retrospective human studies as well as experimental animal models of influenza virus infection highlight the fine line between an excessive and an inadequate immune response, where the host response must balance viral clearance with exuberant inflammation. We have reported that the amplitude of the inflammatory response is regulated by Linear Ubiquitin Assembly Complex (LUBAC) activity and that dampening of LUBAC activity is protective during severe influenza virus infection. Here we review the evidence for modulating inflammation to ameliorate influenza virus infection-induced lung injury, data on current anti-inflammatory strategies, and potential new avenues to target viral inflammation and improve outcomes. Recent reports show that destabilization of respiratory epithelial LUBAC, via loss of the non-catalytic component HOIL-1L, dampens the host response during severe influenza and promotes survival with reduced lung injury as well as reduced viral titers. doi = 10.1016/j.arbres.2020.04.019 id = cord-296635-8r3tm966 author = Breed, Andrew C. title = Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management date = 2011-12-14 keywords = Hendra; Pteropus; infection; virus summary = title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management This study investigated the seroepidemiology of Hendra virus in a spectacled flying-fox (Pteropus conspicillatus) population in northern Australia, near the location of an equine and associated human Hendra virus infection in late 2004. Hendra virus (HeV) and Nipah virus (NiV) are paramyxoviruses of the genus Henipavirus with pteropid bats (i.e. flying-foxes; Pteropus sp., Family Pteropodidae) being the primary wildlife reservoir [1] . Henipaviruses have the potential to infect a wide range of mammalian species, and Hendra virus has spread from flying-foxes to horses in Australia on at least 20 reported separate occasions (five involving horse-human transmission), most recently in 2011 [5, 6, 7] . [14] on the infection dynamics of HeV in the little red flying-fox, Pteropus scapulatus, in the Northern Territory of Australia suggested that viral transmission may be predominantly horizontal, with pregnancy and lactation suggested as risk factors for infection. doi = 10.1371/journal.pone.0028816 id = cord-022163-7klzsrpu author = Broder, Christopher C. title = Henipaviruses date = 2016-09-09 keywords = CNS; Hendra; Nipah; infection; virus summary = Central pathological features of both HeV and NiV infection in humans and several susceptible animal species is a severe systemic and often fatal neurologic and/or respiratory disease (Abdullah and Tan 2014 ; Wong and Ong 2011 ; Playford et al. A new paramyxovirus was isolated and identifi ed in 1994 in an outbreak of fatal cases of respiratory disease in horses and humans in the Brisbane suburb of Hendra, Australia, and was shown to be distantly related to measles virus and other morbilliviruses (Murray et al. HeV in nature appears less transmissible and naturally acquired infections have been observed only in bats, horses, dogs and humans; however, experimentally, HeV can infect and cause disease in guinea pigs, cats, hamsters, ferrets, mice and African green monkeys (reviewed in Geisbert et al. More recently, several viral vector-based henipavirus vaccines have also been examined in animal challenge studies; these have included immunizations using the vesicular stomatitis virus based platform (VSV) expressing either the NiV G or F glycoprotein in the hamster model (DeBuysscher et al. doi = 10.1007/978-3-319-33133-1_3 id = cord-272752-cobroc5h author = Brook, Itzhak title = The challenges of treating tracheobronchitis in a laryngectomee due to nontypeable Haemophilus influenzae: a case report date = 2018-08-20 keywords = HME; infection summary = BACKGROUND: Laryngectomees run the risk of developing severe respiratory tract infections especially during the winter and when they do not wear a stoma cover. CASE PRESENTATION: A 76-year-old Caucasian man, a laryngectomee, presented with bacterial tracheobronchitis and conjunctivitis due to beta-lactamase-producing nontypeable Haemophilus influenzae. CONCLUSIONS: Maintaining the patency of the airway in laryngectomees who suffer from lower respiratory tract infection is of utmost importance as the mucus can be very dry and viscous and can stick to the walls of the trachea and the stoma. Tracheobronchitis in laryngectomees was described as a "suffocating" respiratory infection because of the difficulties in maintaining a patent airway in these patients [6, 7] . Laryngectomees especially those who do not wear an HME or have uncovered stoma are therefore at a higher risk for lower respiratory infections. Laryngectomees are at a higher risk of developing lower respiratory tract infections especially in the winter and when not wearing an HME. doi = 10.1186/s13256-018-1764-2 id = cord-302918-0nk7zyod author = Broor, S. title = Human metapneumovirus: a new respiratory pathogen date = 2008-11-01 keywords = Human; RSV; infection summary = Human metapneumovirus is a recently recognized pathogen of acute respiratory tract infection (ARI) in children as well as elderly and immunocompromised adults. Recent experimental work using primates (chimpanzees, cynomolgus and rhesus macaques, African green monkeys) and small animals (hamsters, cotton rats, mice and ferrets) has been performed to characterize the pathogenesis associated with this viral infection; hMPV replicates to a various extent in the upper and lower respiratory tracts of these experimental animals, although clinical symptoms after intranasal challenge have only been observed in chimpanzees, Cynomolgus macaques and BALB/c mice so far (van den Hoogen et al 2001; Alvarez et al 2004; Kuiken et al 2004; Skiadopoulos et al 2004; . Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups First Detection of Human Metapneumovirus in Children with Acute Respiratory Infection in India: a Preliminary Report doi = 10.1007/s12038-008-0067-y id = cord-278816-l92lkj69 author = Brouard, J. title = Prise en charge des pathologies respiratoires à adénovirus chez l’enfant immunocompétent À propos d’une étude rétrospective de 116 enfants hospitalisés date = 2004-05-31 keywords = des; infection; les summary = authors: Brouard, J.; Vabret, A.; Bach, N.; Toutain, F.; Duhamel, J. Freymuth Les adénovirus sont une cause commune d''atteinte respiratoire ; bien que dépendant du sérotype, ils peuvent également être la cause d''atteintes extrarespiratoires. Elle est par contre plus restreinte pour les enfants a priori sains : or chez eux des altérations bronchiolaires et bronchiques peuvent être à l''origine de lésions définitives parfois d''expression retardée. Les pneumopathies virales se définissent par l''existence d''une atteinte parenchymateuse : elles ne représentent qu''une faible part des infections respiratoires basses, environ 5 %. En dehors de ce contexte ces infections respiratoires sont le plus souvent bénignes, mais par-fois cette symptomatologie peut être marquée même chez l''enfant sain [18] . Les infections subaiguës des voies respiratoires par les AdV pourraient être impliquées dans la genèse de certaines formes de bronchopathies chroniques obstructives chez l''enfant et chez l''adulte. Les critères d''hospitalisation lors d''une pneumopathie supposée virale sont communs avec ceux des infections bactériennes. doi = 10.1016/s1294-5501(04)94248-3 id = cord-300965-ivczo1a7 author = Brown, M. M. title = Don’t be the “Fifth Guy”: Risk, Responsibility, and the Rhetoric of Handwashing Campaigns date = 2017-08-29 keywords = Ben; Handwashing; Health; hand; infection; risk summary = Some scholars—for example, Peterson and Lupton (1996)—term this model the "new public health." In this essay, I describe how the focus on personal responsibility for infection risk shapes the promotion of hand hygiene and other forms of illness etiquette. Personal responsibility may be a cornerstone of public health, but hand hygiene promotion is an especially persuasive vehicle for popularizing an individualistic conception of infection risk. Even in developed countries, where the assumption of personal responsibility is less likely to be impeded by structural issues, hand hygiene promotion may nevertheless skew perceptions of contextual or social determinants of infection risk. Created by the Florida Department of Health in response to H1N1, the BFifth Guy^campaign illustrates the use of a constitutive, stigmatizing rhetoric to endorse the assumption of personal responsibility for infection risk. doi = 10.1007/s10912-017-9470-4 id = cord-262104-oig3qrr7 author = Brüssow, Harald title = COVID‐19: Test, Trace and Isolate‐New Epidemiological Data date = 2020-06-08 keywords = China; SARS; Wuhan; case; covid-19; infection summary = Very similar information was reported in data describing household transmission in Wuhan, where children showed a 4% infection rate compared with 17% in adults. 1.6 million tests were used to identify 1''400 SARS-CoV-2-positive cases; 1000 patients had had exposure to infected people from Hubei. In Wuhan, 105 index cases of patients suffering from moderate COVID-19 symptoms (fever, cough, fatigue) were investigated for secondary transmission to 392 household contacts. The control measures that stopped the epidemic locally have included: intense infection surveillance of incoming travelers; isolation of COVID-19 cases in hospitals; contact tracing and quarantine in holiday camps; and school closure but no lock-down, thus preventing the crisis from having a negative economic impact. Model calculations showed that the containment measures (the quarantine of exposed, and the isolation of infected persons) which depleted the number of susceptible individuals for the virus, reproduced the actually observed case development. doi = 10.1111/1462-2920.15118 id = cord-242132-fhepdgz9 author = Burlak, Gennadiy title = Is it possible to suspend the spread of an epidemic infection? The dynamic Monte Carlo approach date = 2020-05-28 keywords = DMC; infection summary = We study a dynamics of the epidemiological infection spreading at different values of the risk factor $beta$ (a control parameter) with the using of dynamic Monte Carlo approach (DMC). We study a dynamics of the epidemiological infection spreading at different values of the risk factor β (a control parameter) with the using of dynamic Monte Carlo approach (DMC). We study the spread of epidemiological infection at different values of the risk factors beta with the use of the dynamic Monte Carlo (DMC) method. Such observation leads to an interesting assumption that the studied dynamics of the infection spread can (asymptotically) be associated with a critical transition in the two-dimensional (2D) percolation system, that occurs when the occupation probability of defects is p c = 0.594 12 , 11 , 13 , 14 , 15 see Fig.3 . Fig.7 shows the dynamics of infections (order parameter A) for different values of the risk factor β = 0.99, 0.94, 0.9, 0.8 at situation without the quarantine when only the personal immunity M > 0 presents (see Eq. doi = nan id = cord-257662-viy65y72 author = Burrack, Kristina S. title = The Role of Myeloid Cell Activation and Arginine Metabolism in the Pathogenesis of Virus-Induced Diseases date = 2014-09-08 keywords = Arg1; IFN; cell; infection summary = doi = 10.3389/fimmu.2014.00428 id = cord-341548-gazsszs6 author = Buscho, R. O. title = Infections with Viruses and Mycoplasma pneumoniae during Exacerbations of Chronic Bronchitis date = 1978-04-17 keywords = exacerbation; infection summary = The association of viral and Mycoplasma pneumoniae infections with acute exacerbations of chronic bronchitis was studied by serologic or isolation techniques in 46 adult men during the five years from 1964 through 1968. Because of the high prevalence and morbidity of chronic bronchitis among patients of Veterans Administration Hospitals, we have conducted surveillance of one of these groups to assess the impact of respiratory tract infections on the natural course of this disease and to investigate further the occurrence and relative importance of viruses and mycoplasmas in exacerbations [3] . Evidence of viral and Mycoplasma pneumoniae infections (obtained mainly by serologic testing and to a lesser extent by isolation of organisms) was correlated with the pattern of clinical disease in patients with chronic bronchitis. pneumoniae were detected in 50 (30.1%) of 166 exacerbations of chronic bronchitis in the 46 adult patients studied (table 2) . doi = 10.1093/infdis/137.4.377 id = cord-022337-f3a349cb author = Busse, William W. title = Infections date = 2007-05-09 keywords = RSV; infection; respiratory summary = There is also evidence that the viruses which cause wheezing with respiratory tract infections may be age dependent; for example, infants wheeze with RSV while older children have exacerbations of asthma with rhinovirus.^^ To extend these observations. However, as already discussed, the increased frequency of LARs to antigen was still noted 4 weeks after the viral infection, suggesting that a viral respiratory infection has a greater, and possibly more lasting, effect on factors that participate in the development of LARs. Virus-associated airway hyperresponsiveness is a multifactorial process involving a complex interplay of IgE-dependent reactions, epithelial activation or damage, autonomic nervous system dysfunction and, of particular interest and relevance to our discussion, enhanced allergic inflammation."^^ In IgE-mediated reactions, the tissue response, be it the skin, nose or airway, is influenced by I g E sensitization of mast cells and basophils, release of bronchospastic and inflammatory mediators from sensitized cells, and the response of the target organ, which in asthma is bronchial smooth muscle. doi = 10.1016/b978-012079027-2/50112-x id = cord-305890-mdwjrfzp author = Bönsch, Claudia title = Chloroquine and Its Derivatives Exacerbate B19V-Associated Anemia by Promoting Viral Replication date = 2010-04-27 keywords = Epo; b19v; infection summary = The aims of this study were to assess the effect of CQ and other common antimalarial drugs on B19V infection in vitro and the possible epidemiological consequences for children from Papua New Guinea (PNG). METHODOLOGY/PRINCIPAL FINDINGS: Viral RNA, DNA and proteins were analyzed in different cell types following infection with B19V in the presence of a range of antimalarial drugs. Relationships between B19V infection status, prior 4-aminoquinoline use and anemia were assessed in 200 PNG children <10 years of age participating in a case-control study of severe infections. In addition, we examined the relationship between B19V infection and use of 4-aminoquinoline drugs in a sample of children from PNG who were hospitalized with severe anemia. The expression of structural viral proteins in extracts of infected UT7/Epo cells was also increased in the presence of 25 mM CQ ( Figure 1C ). Human parvovirus infection in children and severe anemia seen in an area endemic for malaria doi = 10.1371/journal.pntd.0000669 id = cord-303517-8971aq02 author = Cajamarca-Baron, Jairo title = SARS-CoV-2 (COVID-19) in Patients with some Degree of Immunosuppression date = 2020-10-16 keywords = COVID-19; China; CoV-2; Coronavirus; SARS; infection; patient summary = doi = 10.1016/j.reumae.2020.08.001 id = cord-020700-iko8gy1e author = Calvo, Cristina title = Respiratory viral infections in a cohort of children during the first year of life and their role in the development of wheezing() date = 2017-07-06 keywords = infection; respiratory summary = INTRODUCTION: It is known that infants with viral respiratory infections severe enough to require hospital admission have a high risk of developing recurrent wheezing. The main aim of this study was to analyse symptomatic and asymptomatic respiratory viral infections during the first year of life in a cohort of infants, recruited at birth, and the development of recurrent wheezing. The objective of our prospective study was to analyse asymptomatic and symptomatic infections of varying severity in a cohort of newborns during the first year of life and assess their role in the development of recurrent wheezing. We defined ''''first detected viral infection'''' as PCR detecting a respiratory virus in a sample for the first time in the life of a child, whether the infection was asymptomatic, symptomatic and managed at the outpatient level, or symptomatic and requiring hospital admission. doi = 10.1016/j.anpede.2016.08.008 id = cord-300747-fnli688g author = Calvo, Cristina title = Infections and coinfections by respiratory human bocavirus during eight seasons in hospitalized children date = 2016-05-06 keywords = HBoV; RSV; infection summary = The main objectives of the study were: to determine the incidence of HBoV in hospitalized children; to describe the main clinical features of the positive children; and to compare the data with those from other viral infections in the same population. Clinical characteristics of patients with respiratory episodes associated to single HBoV detections were analyzed (Table I ).These childrenś group mean age was 21 months (standard deviation; 24 months). The clinical characteristics of the 80 patients with single HBoV detection were compared with the single infections associated with RSV, RV, and hMPV in the same period. Although some authors [Martin et al., 2010] do not find differential clinical data in outpatients positive for HBoV, our series describes a set of characteristic clinical data in hospitalized children, different from single infections caused by other viruses as RSV or hMPV. Clinical characteristics of human bocavirus infections compared with other respiratory viruses in Spanish children doi = 10.1002/jmv.24562 id = cord-023724-5at0rhqk author = Cann, Alan J. title = Infection date = 2015-07-24 keywords = IFN; MHC; RNA; cell; dna; infection; virus summary = The problems plant viruses face in initiating infections of host cells have already been described (Chapter 4), as has the fact that no known plant virus employs a specific cellular receptor of the types that animal and bacterial viruses use to attach to cells. There are probably many different mechanisms involved in systemic resistance, but in general terms there is a tendency of these processes to increase local necrosis when substances such as proteases and peroxidases are produced by the plant to destroy the virus and to prevent its spread and subsequent systemic infection. Virus-resistant plants have been created by the production of transgenic plants expressing recombinant virus proteins or nucleic acids which interfere with virus replication without producing the pathogenic consequences of infection, for example: I Virus coat proteins, which have a variety of complex effects, including inhibition of virus uncoating and interference of expression of the virus at the level of RNA ("gene silencing" by "untranslatable" RNAs), I Intact or partial virus replicases which interfere with genome replication, I Antisense RNAs, I Defective virus genomes, I Satellite sequences (see Chapter 8), I Catalytic RNA sequences (ribozymes), I Modified movement proteins. doi = 10.1016/b978-0-12-801946-7.00006-7 id = cord-347761-wgodcsav author = Cant, Andrew title = Infections in the Immunocompromised date = 2009-10-24 keywords = CMV; CVC; HSCT; PCP; infection summary = Pneumocystis jiroveci pneumonia (PCP), CMV and Aspergillus are particularly important and well recognized sources of infection in the immunocompromised host; however, other significant pathogens have more recently been identified. Lung biopsy may be particularly important in the diagnosis of fungal infection, especially when there is a negative BAL in patients with persistent signs, symptoms or chest x-ray changes. PCP has historically been associated with HIV but is also a significant cause of morbidity in other groups of immunocompromised patients, particularly those with haematological malignancies, brain tumours requiring prolonged courses of steroids, prolonged neutropaenia or lymphopaenia, and those undergoing HSCT. Prophylaxis to prevent CMV and HSV reactivation is used for children undergoing HSCT and many SOTs. Surveillance in high-risk patients enables pre-emptive treatment to be given before damaging disease occurs. Adenovirus is usually responsible for relatively minor upper respiratory tract or gastrointestinal infection but can result in life-threatening pneumonia, meningitis, encephalitis and disseminated disease in the immunocompromised. doi = 10.1007/978-1-4419-0981-7_1 id = cord-316500-vik30moa author = Cardillo, Lorena title = Lifestyle as Risk Factor for Infectious Causes of Death in Young Dogs: A Retrospective Study in Southern Italy (2015–2017) date = 2020-06-05 keywords = CPV; PCR; canine; dog; infection summary = Here, we aimed to determine the infectious causes of death in young dogs aged up to 1 year, examining how it relates to age (under and over 6 months), lifestyle (owned versus ownerless), breed (purebred and crossbreed), and gender. In the first days of life, bacterial infections are described to be the prevalent cause of neonatal disease and death [2] ; in contrast, at other ages, many factors have been attributed for outbreaks of viral diseases, including age, vaccination status, breed [3, 4] , habitat [5] , and seasons [6] . After examining bacterial and viral prevalence, infection risk was examined for the most frequently detected pathogens related to the four variables considered in the study (Table 4) . To assess infectious causes of death in dogs aged under 1 year of age, the circulation of agents in Southern Italy and whether age, lifestyle, gender, or breed can influence infections and relative lesion generalisation, a survey was conducted on 138 deceased pups. doi = 10.1155/2020/6207297 id = cord-320145-582kmoyo author = Cardinal, R. N. title = Simulating a community mental health service during the COVID-19 pandemic: effects of clinician-clinician encounters, clinician-patient-family encounters, symptom-triggered protective behaviour, and household clustering date = 2020-05-03 keywords = COVID-19; clinician; infection summary = title: Simulating a community mental health service during the COVID-19 pandemic: effects of clinician-clinician encounters, clinician-patient-family encounters, symptom-triggered protective behaviour, and household clustering We also varied clinician-clinician contact; baseline and ongoing "external" infection rates; whether overt symptoms reduced transmission risk behaviourally (e.g. via personal protective equipment, PPE); and household clustering. Appointment type and inter-clinician contact had greater effects at low external infection rates and without a behavioural symptom response. In Experiment 1, whole-population infection was dominated by baseline and external infection rates (with infection spreading primarily via intra-household contacts), plus the behavioural response to symptoms (all p⋘α), with only very small contributions from the appointment type and clinician-clinician meetings (Figure 2A) . The beneficial effects of symptom-triggered behaviour were proportionally greater with lower external infection rates, for higher-risk appointment types, and without clinician meetings. doi = 10.1101/2020.04.27.20081505 id = cord-010570-ytv7dwr0 author = Casadevall, Arturo title = Return to the Past: The Case for Antibody-Based Therapies in Infectious Diseases date = 1995-07-17 keywords = antibody; human; infection; serum; therapy; treatment summary = doi = 10.1093/clinids/21.1.150 id = cord-323463-osf6t7cw author = Cercenado, Emilia title = Update on bacterial pathogens: virulence and resistance date = 2008-04-30 keywords = MRSA; PVL; Staphylococcus; infection; isolate; patient; strain; study summary = This paper focus on a variety of diseases that pose major clinical and public health challenges today; and include infections produced by community-acquired methicillin-resistant Staphylococcus aureus and S. Although predictions during the 20th century indicated that the incidence of infectious diseases would diminish as a result of improvements in sanitation and by the introduction of many vaccines and antibiotics, at the beginning of the 21st century the rates of infections produced by new pathogens or by reemerging microorganisms possessing new virulence or resistance phenotypes is increasing, threatening the overall human health [1] [2] [3] [4] [5] . It is in this scenario where community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as the most common pathogen isolated from patients with skin and soft-tissue infections attending to the emergency departments in many United States and Australian cities 8, 9 , and at present, its incidence is increasing in other parts of the world 10, 11 . doi = 10.1016/s0213-005x(08)76378-x id = cord-013837-x95r6bz8 author = Chai, Qiyao title = New insights into the evasion of host innate immunity by Mycobacterium tuberculosis date = 2020-07-29 keywords = Mtb; Mycobacterium; dna; host; immune; infection summary = In this review, we describe the emerging role of cytosolic nucleic acid-sensing pathways at the host–Mtb interface and summarize recently revealed mechanisms by which Mtb circumvents host cellular innate immune strategies such as membrane trafficking and integrity, cell death and autophagy. [19] [20] [21] The involvement of the cGAS-mediated DNA-sensing pathway in host anti-Mtb immunity is indicated by the findings that cGAS expression is upregulated and that cGAS is colocalized with mycobacteria in human TB lesions, and its deficiency impairs the induction of type I IFN responses and autophagy in Mtb-infected macrophages. 23 Therefore, specifically targeting mycobacterial ESX-1 products or host regulatory factors might enable the selective regulation of inflammasome and cGAS/STING pathway activation and, hence, contribute to the recovery of the equilibrium between Th1-type cytokine and type I IFN responses in TB patients to improve their anti-Mtb immunity. doi = 10.1038/s41423-020-0502-z id = cord-290385-0smnl70i author = Chan, Jasper F.W. title = Zika fever and congenital Zika syndrome: An unexpected emerging arboviral disease date = 2016-03-03 keywords = Aedes; Brazil; DENV; ZIKV; Zika; infection; virus summary = Unlike its mosquito-borne relatives, such as dengue, West Nile, and Japanese encephalitis viruses, which can cause severe human diseases, Zika virus (ZIKV) has emerged from obscurity by its association with a suspected "congenital Zika syndrome", while causing asymptomatic or mild exanthematous febrile infections which are dengueor rubella-like in infected individuals. ZIKV RNA could be detected in breast milk and saliva of infected women, although replicative virus particles have not been demonstrated 78, 79 Perinatal transmission of other arboviruses, including DENV, CHIKV, WNV, and YFV, has also been reported. 115,120 74/ 8750 (0.8%) patients with suspected ZIKV infection in the French Polynesia outbreak developed neurological syndromes after presenting with a Zika fever-like illness. Zika fever-related death appears to be extremely rare but a number of probable cases have been reported, especially among immunocompromised patients and neonates with suspected congenital ZIKV infection. doi = 10.1016/j.jinf.2016.02.011 id = cord-007013-tlvgyzft author = Chan, Kok Fei title = Investigating Viral Interference Between Influenza A Virus and Human Respiratory Syncytial Virus in a Ferret Model of Infection date = 2018-08-01 keywords = IFN; figure; infection summary = Previously, we used the ferret model to demonstrate that viral interference can occur following infection with human influenza A and B viruses and will prevent, delay, or limit subsequent infection with an influenza virus of a different type, subtype, or lineage [10, 11] . The peak of hRSV shedding was delayed in ferrets infected with A(H1N1)pdm09 followed by hRSV as compared to control animals infected with hRSV alone (median, 8 vs 6 days; P = .0091 by the Mann-Whitney test; Figure 2Ci ). The median duration of A(H1N1)pdm09 shedding was increased in ferrets infected with hRSV followed by A(H1N1)pdm09 as compared to control animals infected with A(H1N1)pdm09 alone (8 vs 7 days; P = .0196 by the Mann-Whitney test; Figure 2Civ ). Notably, increased expression of inflammatory mediators following infection with influenza virus as compared to hRSV has been observed in studies assessing human clinical samples and in vitro airway epithelial cell cultures [36] [37] [38] [39] . doi = 10.1093/infdis/jiy184 id = cord-299255-wnf8fozk author = Chan, M.Y. title = Infections in Pregnancy date = 2017-11-27 keywords = CDC; Zika; birth; infection; pregnancy summary = doi = 10.1016/b978-0-12-801238-3.64293-9 id = cord-278682-s4gfbsqy author = Chan, W-M title = Precautions in ophthalmic practice in a hospital with a major acute SARS outbreak: an experience from Hong Kong date = 2005-04-29 keywords = SARS; infection; patient summary = doi = 10.1038/sj.eye.6701885 id = cord-347460-9vechh4x author = Chang, Feng-Yee title = Immunologic aspects of characteristics, diagnosis, and treatment of coronavirus disease 2019 (COVID-19) date = 2020-06-04 keywords = COVID-19; CoV; IFN; MERS; SARS; infection summary = Three components are crucial for SARS-CoV induced diseases: 1) the role of CD8+ T cells in defense against the virus, which causes apoptosis in the infected cells, 2) interactions of the virus with macrophages and dendritic cells, which initiate the early innate and subsequent adaptive immune responses, and 3) type I interferon (IFN) system, an innate response against viral infections, which can inhibit virus replication in the early phase. Existing information suggests that the SARS-CoV-infected airways and alveolar epithelial cells secrete abundant chemokines to attract immune cell infiltrations to the lungs, including macrophages and neutrophils, thereby causing damage due to high levels of proinflammatory cytokines and other mediators secreted by these cell types. After a decade of research on coronavirus, unfortunately, still there are no licensed vaccines, effective specific antivirals, nor drug combinations supported by high-level evidence to treat the infection, especially for newly emerging strains such as SARS-COV-2 [59] . doi = 10.1186/s12929-020-00663-w id = cord-284386-emh9feb3 author = Chatterjee, Saptarshi title = Studying the progress of COVID-19 outbreak in India using SIRD model date = 2020-06-23 keywords = Fig; India; infection summary = doi = 10.1007/s12648-020-01766-8 id = cord-024134-ym7ce5ux author = Chawla, Sonam title = Preparing for the Perpetual Challenges of Pandemics of Coronavirus Infections with Special Focus on SARS-CoV-2 date = 2020-04-30 keywords = COVID-19; China; disease; infection; pandemic summary = From a bird''s eye view, the COVID-19 pandemic management relies on revolutionizing the disease surveillance by incorporating artificial intelligence and data analytics, boosting the response strategies—extensive testing, case isolation, contact tracing, and social distancing—and promoting awareness and access to pharmaceutical and non-pharmaceutical interventions, which are discussed in the present chapter. MeSH database defines pandemics as-"Epidemics of infectious disease that have spread to many countries, often more than one continent, and usually affecting a large number of people." Such emergencies compromise human health, society, economics, and politics-a case in point: the COVID-19 pandemic is forecasted to cost the global economy one trillion US dollars (https://www.ncbi.nlm.nih.gov/mesh/? • Healthcare workers and essential service providers • Groups at high risk of death and severe complications requiring hospitalization • Individuals (adults and children aged more than 6 months) in the community who have chronic cardiovascular, pulmonary, metabolic or renal disease, or are immunocompromised • Persons without risk factors for complications (https://www.who.int/csr/ resources/publications/influenza/11_29_01_A.pdf) doi = 10.1007/978-981-15-4814-7_14 id = cord-018319-tylkbh4h author = Chemaly, Roy F. title = Respiratory Viruses date = 2011-01-04 keywords = HSCT; RSV; infection; respiratory; virus summary = Historically, the most common causes of respiratory infections in cancer patients were thought to be opportunistic bacteria and fungi, but newer diagnostic methods have revealed that respiratory viruses can cause serious morbidity and mortality in such patients, including leukemia patients and hematopoietic stem cell transplant (HSCT) recipients. Many viruses are known to cause respiratory tract infections, but the most common in hospitalized cancer patients are influenza viruses, respiratory syncytial virus (RSV), and parainfluenza viruses (PIV) [1, 2] . Although the combination of ribavirin and intravenous immunoglobulin (IVIG) or palivizumab has not been evaluated in a randomized trial, it is sometimes used in severely ill patients with RSV pneumonia, especially HSCT recipients, given that they have high mortality rates from this infection [3, 11, 14] . However, because other viruses can produce the same syndrome and influenza infection can produce other respiratory syndromes, a confirmatory test detecting the virus or viral antigens in nasal washes, throat swabs, respiratory tract secretions, or bronchoalveolar lavage specimens is needed in sporadic cases and in immunocompromised patients. doi = 10.1007/978-1-60761-644-3_32 id = cord-285785-29ohzeug author = Chen, Xiaolan title = Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System date = 2020-08-12 keywords = ALV; IBDV; MDV; Marek; RNA; infection summary = doi = 10.3390/life10080148 id = cord-318984-8m9ygzn5 author = Chen, Yin-Yin title = Surveillance on secular trends of incidence and mortality for device–associated infection in the intensive care unit setting at a tertiary medical center in Taiwan, 2000–2008: A retrospective observational study date = 2012-09-10 keywords = DAI; ICU; infection summary = We examined the rates of DAI by antimicrobial-resistant pathogens, and 30–day and in–hospital mortality in the intensive care unit (ICU). Decreased susceptibility of both gram-positive and gram-negative microbes to antibiotics has been well described in several surveillance studies over the past decade, and increases in the rate of bloodstream infection caused by multi-drug resistant (MDR) gramnegative bacteria have been reported to be 16-fold [5, [8] [9] [10] [11] . In this study, prospective surveillance was conducted to determine the DAI rate and prevalence of antibiotic-resistant isolates at an adult medical-surgical ICU (MS ICU). Our aim was to analyze the secular trend of incidence for different types of DAIs, determine the common pathogens involved, and determine the rates of antimicrobial resistance and overall 30-day and in-hospital mortality during the period 2000-2008. The involved patient demographic information, the dates and sites of infection, device-utilization (DU) ratio, pathogens, antimicrobial susceptibilities, invasive procedures, and overall 30-day mortality and in-hospital crude mortality were recorded. doi = 10.1186/1471-2334-12-209 id = cord-278935-3lgud7l8 author = Chen, Zheng‐Rong title = Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China date = 2014-04-30 keywords = HBoV; infection; respiratory summary = title: Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China Furthermore, epidemiological data shows that HBoV is present year-round with different incidence rates from 2.2% to 19% in children with lower respiratory tract infection [Manning et al., 2006; Weissbrich et al., 2006; Allander et al., 2007; Canducci et al., 2008] . The purpose of this study was to ascertain the frequency, seasonal, and clinical characteristics in hospitalized children with lower respiratory tract infection and evaluate the effects of meteorological factors on the incidence of HBoV in a subtropical region of China. Based on the data from this study, HBoV was the third most common pathogen after RSV and Mycoplasma pneumoniae with an incidence of 6.6% in all hospitalized children with lower respiratory tract infection in Suzhou area. doi = 10.1002/jmv.23952 id = cord-353786-284qn075 author = Chen, Zhi-Min title = Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus date = 2020-02-05 keywords = case; infection; patient; respiratory summary = title: Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus At the onset of the disease, infected children mainly present with fever, fatigue and cough, which may be accompanied by nasal congestion, runny nose, expectoration, diarrhea, headache, etc. 2. Children with a history of contacting patients with fever or respiratory symptoms who have a travel or residence history in Wuhan City and neighboring areas, or in other areas with persistent local transmission within 14 days prior to disease onset. 3. Children with a history of contacting confirmed or suspected cases infected with 2019-nCoV within 14 days prior to disease onset. 4. Children who are related with a cluster outbreak: in addition to this patient, there are other patients with fever or respiratory symptoms, including suspected or confirmed cases infected with 2019-nCoV. Most of the cases have normal or decreased white blood cell counts, while severely infected children show reduced level of lymphocyte count. doi = 10.1007/s12519-020-00345-5 id = cord-323643-lu3ngt6r author = Chow, C.B. title = Post-SARS infection control in the hospital and clinic date = 2004-11-05 keywords = Hong; Kong; SARS; infection summary = The recent severe acute respiratory syndrome (SARS) outbreak has almost mandated a re-evaluation of infection control practices in hospitals, clinics, schools and domestic environments, especially for patients with respiratory tract symptoms. PAEDIATRIC Summary The recent severe acute respiratory syndrome (SARS) outbreak has almost mandated a re-evaluation of infection control practices in hospitals, clinics, schools and domestic environments, especially for patients with respiratory tract symptoms. 17 Despite great concerns, compliance to infection control precautions by community general practitioners in Hong Kong lagged behind their hospital counterparts -97.7% had not worn masks at all times, a third did not wash their hands after seeing/examining a patient and half did not wear gowns. In a study looking into factors affecting nosocomial infection in Hong Kong, it was found that all HCWs consistently used N95s or surgical masks and perceived that the inadequacy of personal protective equipment (PPE) supply, infection control training <2 h and inconsistent use of goggles, gowns, gloves and caps were significant independent risk factors for SARS infection. doi = 10.1016/j.prrv.2004.07.006 id = cord-010255-gvkc2hjd author = Chrystie, I.L. title = ASYMPTOMATIC ENDEMIC ROTAVIRUS INFECTIONS IN THE NEWBORN date = 1978-06-03 keywords = infection; rotavirus summary = RoTAViRUSES are the commonest cause of acute nonbacterial gastroenteritis in infancy and childhood,'','' and a common cause of severe diarrhoeal disease in newborn calves3 and piglets.4 Rotavirus infection is world-wide and iri children admitted to hospital is most common between 6 months and 2 years of age;5 virus is seldom detected in the stools of symptomless age-matched controls. '' 7 Although the babies were infected as early as the third day of life, virus excretion was most frequent among 5-9 day-old babies, who showed few if any of the symptoms of infection found in older children.'' This paper describes a 12-month study of the incidence of infection, the amount of virus excreted by breast-fed and bottle-fed babies, and the pattern of virus spread during the transfer of maternity wards to quarters in a newly built hospital wing. doi = 10.1016/s0140-6736(78)90967-4 id = cord-267791-v10eh408 author = Chughtai, Abrar Ahmad title = Use of personal protective equipment to protect against respiratory infections in Pakistan: A systematic review date = 2019-02-07 keywords = PPE; Pakistan; infection summary = doi = 10.1016/j.jiph.2019.01.064 id = cord-305146-iprzeigk author = Chughtai, Abrar Ahmad title = Use of personal protective equipment to protect against respiratory infections in Pakistan: A systematic review date = 2020-03-04 keywords = PPE; Pakistan; infection summary = We conducted a systematic review of studies on PPE use for respiratory infections in healthcare settings in Pakistan. Face masks (or medical masks) and respirators are the most commonly used PPE to protect from influenza and other respiratory infection in healthcare settings. The aim of this study was to examine the use of PPE for respiratory infections in healthcare settings in Pakistan. Studies where PPE was examined for general infection control were also included, given respiratory protective equipment (face masks and/or respirators) was mentioned. Two studies examined the guidelines and current practices on the use of face masks/respirators for influenza, tuberculosis and SARS in Pakistan [21, 22] . Medical masks were generally used to protect from influenza, tuberculosis and other respiratory infections, while the use of respirators was limited to high-risk situations [21, 22] . doi = 10.1016/j.jiph.2020.02.032 id = cord-345222-otfnrarh author = Ciccarelli, Simona title = Management strategies in the treatment of neonatal and pediatric gastroenteritis date = 2013-10-29 keywords = Escherichia; Shigella; acute; cause; child; diarrhea; gastroenteritis; infection summary = 4 In spite of the intense promotion of oral rehydration solution (ORS) at the community level and the training of health care workers, diarrhea mortality remains unacceptably high: more than 2 million children aged less than 5 years die each year from gastroenteritis, almost all living in resource-constrained nations, where acute diarrhea represents a leading cause of child mortality, second only to pneumonia. Probiotics, also defined as food supplements, improve the intestinal microbial balance of the host, have beneficial effects on health, prevent outbreaks of community-acquired diarrhea, reduce colonization of infants with pathogenic microorganisms, and reduce the duration and severity of diarrheal infections, balancing the intestinal ecosystem. 143 The European Society of Gastroenterology, Hepatology, and Nutrition and the National Institute for Health and Clinical Excellence have suggested the use of probiotic strains with proven efficacy and in appropriate doses for the management of children with acute gastroenteritis as an adjunct to rehydration therapy. doi = 10.2147/idr.s12718 id = cord-299261-ew99nraq author = Cipriano, L. E. title = IMPACT OF UNIVERSITY RE-OPENING ON TOTAL COMMUNITY COVID-19 BURDEN date = 2020-09-18 keywords = covid-19; infection; population; student summary = In a scenario in which students immediately engage in a 24% contact reduction compared to pre-COVID levels, the total number of infections in the community increases by 87% (from 3,900 without the students to 7,299 infections with the students), with 71% of the incremental infections occurring in the general population, causing social and economic restrictions to be re-engaged 3 weeks earlier and an incremental 17 COVID-19 deaths. The timing and magnitude of the city''s COVID-19 outbreak, excluding any impacts from students, is determined by the initial number of COVID-19 infections in the community, the level of participation in physical distancing, the responsiveness of the community to increasing critical care cases and COVID-19 deaths, and the proportion of contacts that are protected with mask wearing (Appendix Figures 5-7) . 16 In the base case, we also assume that students are equally responsive as the general population to COVID-19 outcomes in the community reducing their contacts in response to high numbers of critical care hospitalizations and deaths. doi = 10.1101/2020.09.18.20197467 id = cord-270091-sqrh8ylt author = Cohen, Pascal title = Vascularites associées aux infections virales date = 2004-11-30 keywords = B19; infection; vasculitis; virus summary = Résumé Des virus, causes de vascularites Si la plupart des vascularites systémiques sont de cause inconnue, la responsabilité d''une infection virale a été démontrée de façon formelle pour certaines d''entre elles, un traitement spécifique pouvant les guérir définitivement. Cryoglobulinemia related to the hepatitis C virus (HCV) The clinical manifestations are those of systemic vasculitis with particular tropism for the skin (involvement generally inaugural and almost constant), peripheral nerves and the glomerula. Des virus, causes de vascularites Si la plupart des vascularites systémiques sont de cause inconnue, la responsabilité d''une infection virale a été démontrée de façon formelle pour certaines d''entre elles, un traitement spécifique pouvant les guérir définitivement. L''infection à HTLV1 est rarement compliquée de vascularite ;cette dernière a un tropisme neurologique central 181 192, 193 qui fut le premier à décrire la responsabilité liée à l''hépatite B au cours de la périartérite noueuse 194 , nous décidâmes d''inclure dans un protocole prospectif tous les patients atteints de PAN HBV+ et de traiter les patients par une combinaison d''antiviraux et d''échanges plasmatiques 195 . doi = 10.1016/s0755-4982(04)98936-1 id = cord-021596-5s8lksxp author = Colegrove, Kathleen M. title = Pinnipediae date = 2018-10-26 keywords = California; Fig; PCR; Phoca; Zalophus; infection; lion; seal summary = Hepatic hemosiderosois is seen frequently in several pinniped species including young northern elephant and harbor seals, Hawaiian monk seals, northern fur seals, and CSLs. Mild chronic cholecystitis and portal hepatitis are common findings in wild pinnipeds secondary to trematode infection and trematode-associated pigment accumulation can occur. is most commonly reported in free-ranging pinnipeds including CSLs, harbor, and northern elephant seals along the Pacific coast of North America (Colegrove et al., 2005b; Gulland et al., 1996b) . pinnipedii has not been reported for any phocid species; however, the potential host range is broad and transmission from infected fur seals and sea lions has been described for zoo species, domestic cattle, and humans (Cousins et al., 2003; Kiers et al., 2008; Loeffler et al., 2014; Moser et al., 2008; Thompson et al., 1993; Thorel et al., 1998) . Harbor seals are the most commonly reported species to develop severe fatal disease with infection, and in California subadults and adults are primarily affected (Barbosa et al., 2015; Miller, 2008) . doi = 10.1016/b978-0-12-805306-5.00023-7 id = cord-017867-8cn4c6cu author = Collántes-Fernández, Esther title = Trichomonas date = 2017-11-08 keywords = Amin; Gookin; PCR; Skirrow; Trichomonas; Tritrichomonas; dna; foetus; infection summary = In addition, the OIE Terrestrial Manual also provides recommendations for PCR analyses, which can be applied in combination either with or after culture as an ancillary test or-more often-direct as the primary test to examine bovine samples-i.e., preputial material, uterine or vaginal secretions, or abomasal content of aborted fetuses. In bovine tritrichomonosis cultivation became an important diagnostic tool, because parasite numbers in bovine samples-e.g., preputial smegma or cervico-vaginal mucus-are usually too low to be detected by direct microscopy and a multiplication of parasites after a few days of cultivation increases the chance to find infected bulls. Sensitivity and specificity of culture and PCR of smegma samples of bulls experimentally infected with Tritrichomonas foetus Evaluation of a PCR test for the diagnosis of Tritrichomonas foetus infection in bulls: effects of sample collection method, storage and transport medium on the test Comparison of sampling and culture methods for the diagnosis of Tritrichomonas foetus infection in bulls doi = 10.1007/978-3-319-70132-5_14 id = cord-355872-z6vsjmxn author = Colón-López, Daisy D. title = Emerging viral infections date = 2019-08-15 keywords = Ebola; infection; viral; virus summary = Characterization of bacterial and viral relationships in mosquito arthropods demonstrated a symbiotic relationship between the bacterium and host, limiting dengue virus infection and potentially revealing new antiviral strategies [39, 40] . The Ebola virus outbreak in West Africa resulted in 26,648 cases and 11,017 documented deaths, and genomic sequencing was applied in near real-time to provide information to aid in containing the outbreak [44, 45] . During the Ebola virus outbreak, sequence analysis of the viral genome over time demonstrated changes which could make the pathogen resistant to therapeutics such as siRNAs, phosphorodiamidate morpholino oligomers (PMOs), and antibodies [56] . This agnostic method is appropriate for identifying changes in the human transcriptome as a result of an emerging viral infection to show specific mechanisms of immune response evasion and other effects in the host''s biology at the transcriptomic level. doi = 10.1016/b978-0-12-801496-7.00010-1 id = cord-354656-9ao33rq8 author = Cossart, Yvonne E title = The rise and fall of infectious diseases: Australian perspectives, 1914‐2014 date = 2014-07-07 keywords = Australia; country; disease; infection summary = 2 The success of rat extermination in controlling plague in Sydney 3 provided a triumphant validation of new microbiological theories; Joseph Lister''s carbolic spray was adopted by local surgeons; 4 Emil von Behring''s antitoxin treatment reduced mortality from diphtheria; 5 and Paul Ehrlich''s vision of a magic bullet to cure all infections was given credibility by the effi cacy of Salvarsan (arsphenamine, an arsenic-containing compound) against syphilis. 9,10 9,10 During World War II (WWII), intensive screening of Australian troops by miniature x-ray was followed up with bacteriological testing to identify patients with active infection, for whom treatment was compulsory. Tests were developed to screen donated blood and it soon became apparent that injecting drug use had silently amplifi ed prevalence of hepatitis C infection in young people in Western countries. doi = 10.5694/mja14.00112 id = cord-277327-il8uaavn author = Couch, MD, Robert B. title = Respiratory Viral Infections in Immunocompetent and Immunocompromised Persons date = 1997-03-17 keywords = infection; respiratory; virus summary = doi = 10.1016/s0002-9343(97)00003-x id = cord-266963-belin2jq author = Cowling, Benjamin J title = Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak date = 2020-02-13 keywords = China; Wuhan; infection summary = doi = 10.2807/1560-7917.es.2020.25.6.2000110 id = cord-256282-vqus7vlg author = Cox, Michael J title = Co-infections: potentially lethal and unexplored in COVID-19 date = 2020-04-24 keywords = infection summary = doi = 10.1016/s2666-5247(20)30009-4 id = cord-021588-ec7udsmw author = Craighead, John E. title = Enteric Viral Disease date = 2007-05-09 keywords = infection; virus summary = This virus and its soon-to-be-discovered close relatives (the so-called Norwalk-like viruses [NLVs]) proved to be important causes of explosive outbreaks of diarrhea in both children and adults. But, this painstaking approach has now yielded evidence to indicate that viruses of at least six families may contribute to enteric illness in children and in adult citizens whose immunity has waned (Figure 32.1, Table 32 .1). The etiological role of these viruses as a cause of intestinal disease was established by demonstrating a temporal association of naturally occurring infections (as demonstrated by stool examination using electron microscopy) with illness and by experimental induction of disease in both human volunteers and experimental animals (Hall et al, 1984) . Volunteer studies have yielded important histological and ultrastructural documentation of the profound but relatively transient changes that occur in the mucosa of the small intestine during the course of infections with NLVs (Agus ei al, 1973; Schreiber ei al, 1973 Schreiber ei al, , 1974 Dolin ei al, 1975) . doi = 10.1016/b978-012195160-3/50033-9 id = cord-290783-ipoelk4h author = Crouch, C. F. title = Vaccination against enteric rota and coronaviruses in cattle and pigs: Enhancement of lactogenic immunity date = 1985-09-30 keywords = antibody; calf; infection; rotavirus summary = This article examines methods currently used to enhance the titre and duration of specific antibody in the mammary secretions of cows and pigs with particular reference to rotavirus and coronavirus infections. The situation in neonatal piglets is less clear, rotavirus infections are apparently common 6.t4-tt, w.hilst transmissible gastroenteritis virus (TGEV), the prototype enteric coronavirus in swine, is an example of a seasonal cold-weather disease, probably related to both the thermal sensitivity of the virus ~ and the effect of cold-stress on converting subclinical to clinical infections ~8. It is apparent that the enhancement of lactogenic immunity through the vaccination of the dam provides a suitable mechanism by which neonatal pigs and calves can be protected against rotavirus and coronavirus infections. Passive immunity in calf rotavirus infections: Maternal vaccination increases and prolongs immunoglobulin G 1 antibody secretion in milk Antibody responses in serum, colostrum and milk of swine after infection or vaccination with transmissible gastroenteritis virus doi = 10.1016/s0264-410x(85)90056-8 id = cord-324775-3x5os79m author = Crowe, J.E. title = Human Respiratory Viruses date = 2008-07-30 keywords = RSV; disease; infection; respiratory; virus summary = Respiratory syncytial virus (RSV) is the most common pathogen, with hMPV, PIV-3, influenza viruses, and rhinoviruses accounting for the majority of the remainder of acute viral respiratory infections. Respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), adenoviruses, and influenza viruses were identified initially as the most common causes of serious lower respiratory tract disease in infants and children. These patients also suffer more frequent and more severe disease including mortality with common respiratory viruses, including RSV, hMPV, PIV, influenza viruses, rhinoviruses, and adenoviruses. Enterovirus infections occur most commonly in the summer months in temperate areas, which differs from the season of many of the other most common respiratory viruses such as paramyxoviruses and influenza virus. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory tract disease. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory tract disease. doi = 10.1016/b978-012374410-4.00488-x id = cord-017364-d9zmdm23 author = Crowe, James E. title = Paramyxoviruses: Respiratory Syncytial Virus and Human Metapneumovirus date = 2014-02-27 keywords = MPV; RSV; human; infection; metapneumovirus; respiratory; syncytial; virus summary = A virus causing a similar cytopathic effect in cultured cells was recovered from infants with respiratory illness shortly after, and studies of human antibodies in the serum of infants and children indicated that infection was common early in life [ 1 , 2 ] . Higher titers of virus in respiratory secretions usually are associated with increased severity of disease, in prospective studies of natural infection [ 114 ] or of clinical vaccine trials [ 115 ] . Most epidemiologic studies of MPV in children show that the virus is the second leading cause of lower respiratory infection after RSV. Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: a 2-year study The impact of infection with human metapneumovirus and other respiratory viruses in young infants and children at high risk for severe pulmonary disease Comparison of risk factors for human metapneumovirus and respiratory syncytial virus disease severity in young children doi = 10.1007/978-1-4899-7448-8_26 id = cord-259194-9zllvfqb author = Cupples, Sandra A. title = Transplant Infectious Disease: Implications for Critical Care Nurses date = 2011-11-02 keywords = CMV; EBV; infection; transplant summary = 4 Patient-related risk factors for infection include older age, poor nutritional status, indwelling catheters, prolonged intubation, postoperative bleeding, blood transfusions, multiorgan dysfunction, comorbidities such as diabetes mellitus and obesity, prolonged hospitalization before VAD implantation, and surgical reexploration. Factors that promote infection in potential organ donors include the use of medical devices and the treatment of patients in certain units that have high rates of bacterial contamination. Risk factors for PTLD include pretransplant EBV-negative serostatus, primary EBV infection, high EBV viral load, CMV serostatus mismatch (recipient is CMV negative and donor is CMV positive), CMV disease, potent rejection treatment, and type of allograft. 27 Risk factors for fungal infections include the use of high-dose corticosteroids and broad-spectrum antibiotics, rejection that requires increased immunosuppression, allograft dysfunction, and a simultaneous infection with an immunomodulating virus such as CMV. The risk of posttransplant mediastinitis is higher if the patient had a mechanical circulatory assist device or a total artificial heart as a bridge to transplantation. doi = 10.1016/j.ccell.2011.08.001 id = cord-314449-ukqux772 author = Curtis, L.T. title = Prevention of hospital-acquired infections: review of non-pharmacological interventions date = 2008-06-02 keywords = MRSA; hospital; infection; patient; study summary = Interventions such as proper hand and surface cleaning, better nutrition, sufficient numbers of nurses, better ventilator management, use of coated urinary and central venous catheters and use of high-efficiency particulate air (HEPA) filters have all been associated with significantly lower nosocomial infection rates. This review is not exhaustive and will not attempt mathematical data analysis but will examine recent research that examines non-pharmacological interventions for reducing HAIs. It will also include a brief description of the morbidity, mortality and medical costs associated with nosocomial infections, along with a brief discussion of the routes by which HAIs spread. Many terms were used in the literature searches including nosocomial, hospital acquired, MRSA (meticillin-resistant Staphylococcus aureus), staphyloccoccus, streptococcus, VRE (vancomycinresistant enterococcus), Clostridium difficile, legionella, klebsiella, tuberculosis, airborne infection, waterborne infection, hand washing, hospital cleaning, urinary catheters, central catheters, haemodialysis, ultraviolet light, HEPA (high-efficiency particulate air) filtration and many others. doi = 10.1016/j.jhin.2008.03.018 id = cord-031252-ji0ef0by author = D''Angelo, Lawrence title = Infectious Disease Problems in Adolescents date = 2020-09-01 keywords = Barr; EBV; Epstein; adolescent; hepatitis; infection summary = When prevention is impossible or unsuccessful, treatment with amantadine can shorten the duration of fever and systemic and respiratory symptoms by about 50% if the illness is caused by type A virus and the drug therapy is initiated within the first 48 hours of infection. Mononucleosis is an acute infection most commonly caused by the Epstein-Barr virus, a member of the herpesvirus group. In general, the incidence of mononucleosis is greatest in individuals who have not encountered the virus prior to adolescence, although EBV can cause illness in younger children (3) . In adolescents and young adults, other infectious agents can cause illnesses that mimic EBV-induced mononucleosis. Most genital lesions encountered in adolescents and young adults are due to STDs. The most common lesions are vaginal warts and herpes simplex infection, usually with type II virus. Evidence for active Epstein-Barr virus infection in patients with persistent unexplained illnesses: Elevated anti-early antigen antibodies doi = 10.1016/s0197-0070(20)30007-3 id = cord-279849-zzkliu76 author = DaPalma, T. title = A systematic approach to virus–virus interactions date = 2010-01-20 keywords = HIV; VVI; infection; virus summary = Therefore, in this review we identify known and potential types of virus-virus interactions (VVIs) and organize them into three categories: (1) direct interactions of viral genes or gene products, (2) indirect interactions that result from alterations in the host environment, and (3) a subset of indirect interactions called immunological interactions, unique to organisms equipped with an adaptive immune system. One of the first helper-dependent viruses described was bacteriophage P4, a bacteria-infecting virus that is able to replicate its own genome, but requires the presence of a coinfecting bacteriophage, such as P2, to provide capsid components and cell lysis (Shore et al., 1978; Six and Klug, 1973) . While direct binding and activation of viral transactivating proteins to heterologous viral promoters has been documented, more common are reports of viral infections inducing increased expression or activation of cellular transcription factors, which then act on promoters of coinfecting viruses. Human cytomegalovirus TRS1 and IRS1 gene products block the double-stranded-RNA-activated host protein shutoff response induced by herpes simplex virus type 1 infection doi = 10.1016/j.virusres.2010.01.002 id = cord-021399-gs3i7wbe author = Dada, M.A. title = SUDDEN NATURAL DEATH | Infectious Diseases date = 2005-11-18 keywords = cause; death; infection; sudden summary = Despite the advances in the diagnosis and treatment of infectious diseases, a substantial number of sudden and unexpected deaths are caused by infections. Forensic pathologists should be aware of the importance of infectious causes of sudden death in the present era of bioterrorism and emergent and reemergent diseases. Sudden death due to infectious disease may be classified by organ system involvement (e.g., cardiac -myocarditis; nervous system -meningitis and encephalitis) or according to the etiological agent (e.g., viral, chlamydial, bacterial, fungal, protozoal, or helminthic) . The common infectious causes of sudden death by organ system are listed in Table 1 . Viral infections causing sudden death usually involve the cardiac, respiratory, or the central nervous system. Bacterial infections of the respiratory system Sudden death from acute epiglottitis occurs from respiratory obstruction caused by swelling of the epiglottic folds, uvula, and vocal cords. doi = 10.1016/b0-12-369399-3/00357-8 id = cord-016109-vbzy11hc author = Damjanovic, V. title = Outbreaks of Infection in the ICU: What’s up at the Beginning of the Twenty-First Century? date = 2011-08-10 keywords = ICU; MRSA; infection; outbreak summary = We used the same framework as in the second edition of this book; however, outbreaks were not presented separately per ICU type but according to causative organisms, in the following order: methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), aerobic Gramnegative bacilli (AGNB), Pseudomonas spp., Acinetobacter spp. A paper from Italy published in 2002 reported a unique experience of controlling a MRSA outbreak of 8 months'' duration in a medical/surgical AICU in 1998 using enterally administered vancomycin in mechanically ventilated patients [5] . In 2005, a report from Italy described an outbreak of VRE colonisation and infection in an ICU that lasted 16 months (2001-2002) [12] . A report from The Netherlands published in 2001 described an outbreak of infections with a multi-drug-resistant Klebsiella strain [19] associated with contaminated roll boards in operating rooms. doi = 10.1007/978-88-470-1601-9_12 id = cord-006819-sxz1s6kz author = Daniel Givens, M. title = Infectious causes of embryonic and fetal mortality date = 2008-05-27 keywords = abortion; cause; disease; infection; virus summary = The clinical presentations of disease due to reproductive pathogens are emphasized, with a focus on assisting development of complete lists of causes that result in abortion and infertility in these species. Fetal maceration results when abortion or parturition fails to occur following fetal death and CL regression (occasionally in bovine www.theriojournal.com Available online at www.sciencedirect.com Theriogenology 70 (2008) 270-285 Table 1 Infectious causes of infertility and abortion in domestic animals Infected animals can experience signs of infertility due to early embryonic death and abortion between 4 and 7 months of gestation. Transmission occurs via contact with materials contaminated by infected respiratory or vaginal discharges; the bacteria then spread hematogenously to the fetus. Affected animals might have no clinical signs of disease, but serve as a source of infection, or they can abort late in gestation and have stillbirths. doi = 10.1016/j.theriogenology.2008.04.018 id = cord-268758-2o2dwulc author = Daniel, Krupa title = Repeat cesarean section in a COVID-19 positive mother in the United States date = 2020-10-22 keywords = covid-19; infection summary = doi = 10.1177/2050313x20945536 id = cord-018659-rxzy6k3b author = Danziger-Isakov, Lara title = Posttransplant Complications and Comorbidities date = 2018-01-08 keywords = CMV; infection; lung summary = cenocepacia has been associated with increased posttransplant mortality (relative risk 8.4) with one study reporting 1-year survival of 29% compared to 92% in those uninfected and is considered by many centers as a contraindication to transplant (Shoham and Shah 2013) . Risk factors for invasive disease include ischemia at the anastomosis site, single lung transplant, hypogammaglobulinemia, placement of bronchial stent, CMV infection, and colonization (Robertson et al. Treatment of invasive fungal infection in pediatric lung transplant recipients should include input from an infectious diseases specialist particularly regarding drug choice and dosage. Epidemiology and Risk Pediatric solid organ transplant recipients and particularly lung transplant recipients are at increased risk of medical complications and mortality when acquiring common respiratory viral infections (Manuel et al. There are no other vaccines available for the prevention of respiratory infection in most pediatric lung transplant recipients. Posttransplant, infections remain a significant factor causing both morbidity and mortality in pediatric lung transplant recipients. doi = 10.1007/978-3-319-07284-5_71 id = cord-328720-o9h1vquo author = Davis, Cristina E. title = Breath analysis for respiratory infections date = 2020-09-18 keywords = breath; infection; study summary = Indeed, recruiting those with the same symptoms in the control groups, including noninfectious disease subjects, such as sarcoidosis patients in the case of breath sampling for tuberculosis, is an increasingly essential parameter in a study design. Breath studies to diagnose bacterial infections caused by Mycobacterium tuberculosis (Mtb) are more likely to succeed than any other approach due to the extensive groundwork done by the Belgian-Tanzanian group APOPO (Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling) who have evaluated the volatiles from tens of thousands of sputum samples using trained giant Gambian rats. Beccaria and colleagues conducted two studies evaluating the use of human breath collected and stored on thermal desorption tubes and analyzed by comprehensive gas chromatographyetime-of-flight mass spectrometry (GCÂGC-TOFMS) to diagnose active TB in subjects with confirmed Mtb infection. In this particular case, however, cells inoculated with just RSV did not yield a sufficient change to the volatile profile for accurate diagnoses, providing evidence that each respiratory viral infection may have to be independently evaluated for its ability to be detected directly in breath samples. doi = 10.1016/b978-0-12-819967-1.00021-9 id = cord-103630-nt3ogyzl author = Deal, C. L. title = Recurrent respiratory viral diseases and chronic sequelae due to dominant negative IFIH1 date = 2020-07-06 keywords = IFIH1; infection; variant summary = Genomic sequencing identified compound heterozygous variants in the IFIH1 gene, encoding the protein Melanoma Differentiation Association Protein 5 (MDA5), a RIG-I-like cytoplasmic sensor of RNA intracellular infections. Furthermore, biallelic loss of function variants in IFIH1 result in severe infections due to common viral illnesses (2, 3) , and one study suggested a possible dominant negative role for heterozygous loss-of-function variants (1) . Patients with loss-of-function variants in IFIH1 are susceptible to common viral pathogens, particularly human rhinovirus. In summary, we present the oldest case of an individual suffering from compound heterozygous IFIH1 variants resulting in a phenotype of recurrent viral infections, nasal polyposis and chronic pansinusitis due to bacterial and fungal organisms, marked chronic eosinophilia, severe asthma with ground glass opacities and bronchiectasis, as well as neuropathy. Severe viral respiratory infections in children with IFIH1 loss-of-function mutations Loss-of-function mutations E627X and I923V of IFIH1 are associated with lower poly(I:C)-induced interferon-β production in peripheral blood mononuclear cells of type 1 diabetes patients doi = 10.1101/2020.07.01.20105379 id = cord-263811-w0983x19 author = Decaro, Nicola title = Canine Adenoviruses and Herpesvirus date = 2008-05-22 keywords = CAV-2; CHV; canine; dog; infection summary = doi = 10.1016/j.cvsm.2008.02.006 id = cord-021555-rrverrsj author = Delano, Margaret L. title = Biology and Diseases of Ruminants: Sheep, Goats, and Cattle date = 2007-09-02 keywords = Smith; States; United; animal; bovine; cattle; cause; clinical; day; diagnosis; differential; disease; etiology; goat; infection; lesion; necropsy; organism; ruminant; sheep; sign; treatment; virus summary = These references also provide information regarding vaccination products licensed for use in ruminants and typical herd and flock vaccination parasite control schedules ("Current Veterinary Therapy," 1986 , 1999 "Council report," 1994; "Large Animal Internal Medicine," 1996; Smith and Sherman, 1994) When designing a vaccination program during qualification of a source or at the research facility, it is important to evaluate the local disease incidence and the potential for exposure. Clinical signs in chronic cases in older animals, such as adult goats, include soft stools, weight loss, anorexia, depression, and severe diarrhea, sometimes with mucus and blood. This pathogen does present a complication due to the carrier status of some animals, the likelihood of herd outbreaks, the severity of disease in younger animals, and the morbidity, possible progression to uveitis, and time and treatment costs associated with infections. doi = 10.1016/b978-012263951-7/50017-x id = cord-257539-01s21vh0 author = Delvecchio, Rodrigo title = Chloroquine, an Endocytosis Blocking Agent, Inhibits Zika Virus Infection in Different Cell Models date = 2016-11-29 keywords = ZIKV; Zika; cell; figure; infection summary = Immunofluorescence staining corroborated these results ( Figure 1B ) and additionally, chloroquine decreased the production of infectious ( Figure 1C ) and total ( Figure 1D ) virus particles, including defective viral particles, by ZIKV-infected cells. Incubation of Vero cells with chloroquine at 0 h postinfection had a greater impact on the production of ZIKV particles, decreasing viral RNA 64-fold over the controls ( Figure 3A ). To evaluate which step of the viral cycle was susceptible to inhibition, chloroquine was added to Vero cells at different time points post-infection with ZIKV MR766. To evaluate which step of the viral cycle was susceptible to inhibition, chloroquine was added to Vero cells at different time points post-infection with ZIKV MR766. Incubation of Vero cells with chloroquine at 0 h post-infection had a greater impact on the production of ZIKV particles, decreasing viral RNA 64-fold over the controls ( Figure 3A ). doi = 10.3390/v8120322 id = cord-308201-lavcsqov author = Desforges, Marc title = Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System? date = 2019-12-20 keywords = CNS; OC43; acute; human; infection; respiratory; virus summary = Viruses infecting human CNS cells could then cause different types of encephalopathy, including encephalitis, and long-term neurological diseases. Even though no clear cause and effect link has ever been made with the onset of human neurological diseases, their neuropathogenicity is being increasingly recognized in humans, as several recent reports associated cases of encephalitis [244] , acute flaccid paralysis [271] and other neurological symptoms, including possible complications of HCoV infection such as Guillain-Barré syndrome or ADEM [249, [272] [273] [274] [275] [276] [277] [278] [279] . Like for several other respiratory viruses, accumulating evidence now indicate that HCoV are neuroinvasive in humans and we hypothesize that these recognized respiratory pathogens are potentially neurovirulent as well, as they could participate in short-and long-term neurological disorders either as a result of inadequate host immune responses and/or viral propagation in the CNS, which directly induces damage to resident cells. doi = 10.3390/v12010014 id = cord-017583-72mbsib7 author = Devarajan, Padma V. title = Infectious Diseases: Need for Targeted Drug Delivery date = 2014-09-01 keywords = Mycobacterium; Salmonella; cell; delivery; drug; infection; macrophage; receptor; target summary = The adaptive mechanisms of Mycobacterium tuberculosis to survive inside the macrophages are prevention of fusion of the phagosome with lysosomes by producing tryptophan-aspartate-containing coat protein (TACO). In case of Mycobacterium tuberculosis infection, alveolar macrophages (dust cells), along with dendritic cells engulf bacteria and exhibit innate as well as an adaptive immune response. Infection of macrophages leads to changes in the expression pattern of the concerned receptors, which can be exploited for targeted drug delivery employing nanocarriers. Table 3 .6 is a summary of the important receptors on macrophages and illustrative examples of ligands for the same that could play a role in designing targeted nanocarriers for infectious disease therapy. Targeted drug delivery to enhance effi cacy and shorten treatment duration in disseminated Mycobacterium avium infection in mi host factors infl uencing the preferential localization of sterically stabilized liposomes in klebsiella pneumoniae-infected rat lung tissue Targeted intracellular delivery of antituberculosis drugs to mycobacterium tuberculosis-infected macrophages via functionalized mesoporous silica nanoparticles doi = 10.1007/978-3-319-11355-5_3 id = cord-279255-v861kk0i author = Dhama, Kuldeep title = Coronavirus Disease 2019–COVID-19 date = 2020-06-24 keywords = COVID-19; China; CoV-2; MERS; SARS; Wuhan; clinical; coronavirus; human; infection; novel; outbreak summary = Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Recently, a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID19) , emerged in late 2019, and it has posed a global health threat, causing an ongoing pandemic in many countries and territories (1) . Health workers worldwide are currently making efforts to control further disease outbreaks caused by the novel CoV (originally named 2019-nCoV), which was first identified in Wuhan City, Hubei Province, China, on 12 December 2019. doi = 10.1128/cmr.00028-20 id = cord-300230-a3jk6w90 author = Ding, Ji-Guang title = Retrospective analysis of nosocomial infections in the intensive care unit of a tertiary hospital in China during 2003 and 2007 date = 2009-07-25 keywords = ICU; infection; nosocomial summary = doi = 10.1186/1471-2334-9-115 id = cord-017518-u2gsa4lg author = Divatia, J. V. title = Nosocomial Infections and Ventilator-Associated Pneumonia in Cancer Patients date = 2019-07-09 keywords = CAUTI; HAP; ICU; VAP; infection; patient summary = These infection rates can be significantly reduced by the implementing and improving compliance with the "care bundles." This chapter will address the common nosocomial infections such as ventilator-associated pneumonia (VAP), catheter-associated urinary tract infections (CAUTI), and surgical site infections (SSI), including preventive strategies and care bundles for the same. (a) Patient factors such as extremes of age, immunosuppression due to malignancy, acquired immunodeficiency syndrome (AIDS), patients requiring emergency admission to the intensive care unit (ICU), duration of stay more than 7 days, chronic illness like renal failure, diabetes mellitus, chronic liver disease, presence of indwelling catheters, ventilation, total parenteral nutrition, trauma, abdominal surgeries, and impaired functional status [44, 45] (b) Organizational factors such as the poor environmental hygiene inside the hospital or ICU, lack of efficient infection control measures, inadequate manpower such as an inadequate nurse to patient ratio or inadequate waste management staff, and inadequate equipment for patient use (c) Iatrogenic factors such as ignorance regarding infection control practices, lack of training in infection control, etc. doi = 10.1007/978-3-319-74588-6_125 id = cord-267973-uvz7kavu author = Do, Lien Anh Ha title = Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity date = 2016-08-08 keywords = RSV; infection; respiratory summary = title: Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity This study aims to describe the viral etiologies, the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a lower respiratory tract infections (LRTI), focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity. However, information on detailed clinical, epidemiological features and virological characteristics of RSV infections (e.g. disease burden, demographics, seasonal variations of RSV and other viral infections, circulating genotypes and subgroups, viral load) or on the frequency / impact of other respiratory viruses among Vietnamese children under two years old are limited [6] . Here, we aimed to describe the viral etiologies and the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a LRTI, focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity. doi = 10.1371/journal.pone.0160606 id = cord-309488-8guapzke author = Dodd, R. title = Other emerging viral pathogens date = 2006-08-15 keywords = USA; infection; virus summary = Attention was refocused on viral infections as a result of the outbreak of West Nile virus (WNV) disease in the USA along with the recognition that it was transmissible by transfusion [1] . In 1997, Blackbourn and colleagues [17] reported on the detection of HHV-8 DNA in the blood of a seropositive blood donor; based on evidence of in vitro passage of the virus to allogeneic cells, the authors expressed concern about the potential for transmission by transfusion. This concern is based upon the historical fact that there have been periodic pandemics associated with the circulation of new strains of the virus in humans and the current outbreak of the H5N1 strain of avian influenza, which causes high mortality when it does infect humans [27] . Seroprevalence of human herpes virus 8 antibody in populations at high or low risk of transfusion, graft, or sexual transmission of viruses Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent doi = 10.1111/j.1751-2824.2006.00043.x id = cord-306111-wn1gxhk9 author = Dommett, R. M. title = Mannose‐binding lectin in innate immunity: past, present and future date = 2006-09-01 keywords = HIV; MBL; infection; lectin; mannose; protein summary = Third MBL mutation in codon 52 (variant D) described (52) 1995 Polymorphisms found in promoter region of MBL gene (55) 1997 Second MASP found to activate complement (20) MBL mutations are an important risk factor for infections in children (132) 1998 Reconstitution of opsonizing activity by infusion of purified MBL into MBL-deficient humans (112) 1999 Truncated form of MASP-2 -MAp19 (21) 2000 Complement-activating complex of ficolins and MASP (133) MBL shown to bind to clinically relevant organisms (15) Structural aspects of MBL doi = 10.1111/j.1399-0039.2006.00649.x id = cord-018545-fk17n2bx author = Dorofaeff, Tavey title = Infections in the PICU date = 2012 keywords = CMV; HIV; HSV; PICU; care; cause; child; infection; patient summary = Herpes Simplex Virus (HSV, types 1 and 2) (a) Systemic infection in the neonate with shock and coagulopathy and severe liver failure (b) Encephalitis, hepatitis (c) Local (mouth, esophagus, larynx, lungs, heart, liver, kidneys, CNS) or systemic disease in organ and stem cell transplant and immunocompromised patients 2. Pneumonia means inflammation of the lung parenchyma caused by infection and the diagnosis is made clinically in a febrile child with respiratory signs and symptoms who has evidence of consolidation on CXR. • Development of an empyema or less commonly a lung abscess • Underlying lung disease such as: bronchopulmonary dysplasia (BPD, in ex-premies), cystic fibrosis, inhaled foreign body, tracheobronchomalacia or post tracheal surgery, or infected congenital lung cyst • Diagnosed or undiagnosed immunodeficiency states (primary, HIV, leukemia) • Children with neuromuscular diseases, weakness, or spasticity such as muscular dystrophies, myasthenia, spinal muscular atrophy, or cerebral palsy • Inappropriate antibiotics, inappropriately low dose or resistant bacteria • Non bacterial pneumonia (viral pneumonia or alternative pathogen such as Tuberculosis) doi = 10.1007/978-3-642-02202-9_268 id = cord-022203-t2f0vr1w author = Dowers, Kristy L title = The pyrexic cat date = 2009-05-15 keywords = FIP; cat; clinical; disease; fever; infection; sign summary = Clinical signs are often non-specific and include fever, anorexia and weight loss. Gastrointestinal signs are uncommon in cats compared to dogs, and include chronic diarrhea, mesenteric lymphadenopathy and anorexia. • Dysfunction of any organ system may result from granuloma formation within the tissue of that organ, e.g., liver, kidney, spleen, intestines, lungs, etc., however, organ failure producing clinical signs only rarely occurs, and most dysfunction is only detected on biochemical tests. Clinical signs in the acute, fatal form of extraintestinal disease are caused primarily by tissue damage from the rapidly dividing tachyzoites. • Young kittens are more likely to have gastrointestinal signs, although mild clinical disease has been reported in adult cats as well. Systemic signs, which are not present in all cats, include fever, anorexia, lethargy, vomiting, diarrhea and lymphadenopathy. Systemic signs such as fever, anorexia and depression are commonly reported (44% of cats) and can be seen with skin lesions. doi = 10.1016/b978-0-7020-2488-7.50024-7 id = cord-272117-erzpz3c0 author = Downey, Jeffrey title = Dissecting host cell death programs in the pathogenesis of influenza date = 2018-04-18 keywords = IAV; IFN; cell; infection summary = Experimentally, apoptosis of IAV-infected epithelial cells was shown to be dependent upon viral replication, as an inactivated virus failed to induce apoptosis in mice [46] and human cells [47] . PKR can directly sense dsRNA generated during viral replication to induce Fas expression and FADD-dependent apoptosis [52] , as well as inhibit host and viral protein translation through the phosphorylation of eIF2a [53] in IAV-infected cells [54] . Additionally, pandemic and highly virulent strains of the virus, including HPAI and the 1918 H1N1 strain, are known to completely exhaust the replicative niche of epithelial cells of the lung over the course of infection as a by-product of overly exuberant replication and failure of immune response to control viral propagation. Collectively, these findings suggest that in contrast to the biphasic role of epithelial cell apoptosis in preventing or promoting pathogenesis, highly virulent IAV rapidly infects and induces early death in pulmonary M4 to suppress antiviral responses. doi = 10.1016/j.micinf.2018.03.005 id = cord-312964-vsrqmmv7 author = Doyle, William J. title = Prevention of otitis media caused by viral upper respiratory tract infection: Vaccines, antivirals, and other approaches date = 2003 keywords = AOM; infection; virus; vuri summary = Past studies show that new episodes of OM are usually a complication of viral upper respiratory infection (vURI), and therefore, a rational approach to achieving that goal is to develop intervention strategies that target vURIassociated OM. Past studies show that new episodes of OM are usually a complication of viral upper respiratory infection (vURI), and therefore, a rational approach to achieving that goal is to develop intervention strategies that target vURIassociated OM. Active synergy between certain upper respiratory viruses and nasopharyngeal pathogens was demonstrated for OM pathogenesis in chinchillas and humans [27] [28] [29] , and pre-existing or concurrent vURI in infants and children with acute, bacterial OM is frequently observed [24, 25] . In one double-blind clinical study, intranasal steroid (fluticasone propionate) was administered for 7 days immediately after onset of vURI symptoms in an attempt to decrease nasopharyngeal inflammation (and possible eustachian-tube obstruction), but was not efficacious in preventing AOM and might have increased OM incidence during rhinovirus infection [69] . doi = 10.1007/s11882-003-0093-7 id = cord-261756-4lybl57r author = Dubert, Marie title = Late viral or bacterial respiratory infections in lung transplanted patients: impact on respiratory function date = 2020-02-24 keywords = BOS; infection; respiratory summary = doi = 10.1186/s12879-020-4877-3 id = cord-314500-89ovdnxl author = Dunachie, Susanna title = The double burden of diabetes and global infection in low and middle-income countries date = 2018-12-04 keywords = diabetes; increase; infection; risk summary = Diabetes increases susceptibility to infection and worsens outcomes for some of the world''s major infectious diseases such as tuberculosis, melioidosis and dengue, but the relationship between diabetes and many neglected tropical diseases is yet to be accurately characterised. A greater understanding of the impact of diabetes on risks and outcomes for infections causing significant diseases in LMIC is essential in order to develop vaccines and therapies for the growing number of people with diabetes at risk of infection, and to prioritise research agendas, public health interventions and policy. In a metaanalysis of five case-control studies of acute dengue, diabetes was associated with an increased risk of a severe clinical presentation of dengue compared with either asymptomatic infection or non-severe acute dengue, 43 although given the limited data, the authors emphasised this was only suggestive of a link. doi = 10.1093/trstmh/try124 id = cord-018220-8m11ig06 author = Duncan, Coley B. title = Viral Infections date = 2009-02-02 keywords = HCV; RSV; United; infection summary = The recommendations of the Advisory Committee on Immunization Practices (ACIP) 2007 relating to the elderly, include vaccination of all persons ³ 50 years, vaccination of residents of nursing homes and chronic-care facilities, vaccination of healthcare personnel, and vaccination of healthy household contacts (including children) and caregivers of adults ³ 50 years (3) . In a prospective study from Rochester, NY, using a combination of viral culture, RT-PCR and serology for diagnosis, RSV infection was documented in 3-7% of 608 healthy elderly and 4-10% of adults with chronic cardiopulmonary conditions over four winter seasons (16) . In healthy elderly patients and in adults with chronic pulmonary disease, low serum neutralizing antibody titers are associated with increased risk of hospitalization with RSV infection suggesting a vaccine may be beneficial. Although PIV infections are not commonly documented in older adults, several studies of community-acquired pneumonia and chronic obstructive pulmonary disease (COPD) exacerbations implicate PIV as a cause in 2-17% of cases (25, 26) . doi = 10.1007/978-1-60327-534-7_23 id = cord-269975-1ebmq7t8 author = Duplantier, Allen J. title = Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges date = 2020-05-27 keywords = Burkholderia; Ebola; FDA; RNA; host; infection; treatment; virus summary = None of the filoviruses or henipaviruses has any FDA-approved therapeutics or vaccines available for prevention or treatment of human disease, and while ribavirin is sometimes used to treat Lassa fever, it is not a terribly effective drug against this viral infection [28] . Many of the therapeutics that are in different stages of either preclinical or clinical development for select biothreat pathogens include small molecule antivirals (Tables 7.3 and 7.4), antibody (or antibody cocktails) against viruses or bacteria/virulence factors (Table 7 .5), and combination drug therapy (Table 7 .6). Although no FDA-approved HDT therapies are yet available for treating infectious diseases, we have summarized in this section the antimicrobial Primary screening of small molecule chemical libraries in the phenotypic HCI assay will identify compounds that inhibit pathogen infection as well as those that may contribute to cellular toxicity. doi = 10.1016/b978-0-12-818480-6.00007-2 id = cord-021453-vf8xbaug author = Dysko, Robert C. title = Biology and Diseases of Dogs date = 2007-09-02 keywords = Animal; Ferguson; Peterson; Swaim; Veterinary; canine; cause; cell; clinical; day; diagnosis; disease; dog; infection; research; sign; treatment; tumor; wound summary = The use of dogs continued as biomedical research advanced, and they were featured in many noteworthy studies, including those by Pavlov to observe and document the conditioned reflex response and by Banting and Best to identify the role of insulin in diabetes mellitus. Especially noted in this chapter are infectious diseases associated with the use of random-source dogs that have unknown vaccination history and have had intensive contact with other similar animals at pounds and/or shelters, or conditions seen frequently in the beagle, the most common breed used in biomedical research. Culture requires selective isolation media, and growth is favored by reduced oxygen tension and a temperature of 42~ Any disorder that can cause diarrhea in dogs should be considered as a differential diagnosis, including canine parvovirus, coronavirus, distemper virus, Giardia, and Salmonella infections; helminth infestations; and hemorrhagic gastroenteritis. doi = 10.1016/b978-012263951-7/50014-4 id = cord-303299-p15irs4e author = Dzien, Alexander title = Will the COVID-19 pandemic slow down in the Northern hemisphere by the onset of summer? An epidemiological hypothesis date = 2020-06-23 keywords = infection; respiratory summary = The infection caused by the human corona virus COVID-19 (SARS-CoV2) resulted in a worldwide pandemic affecting several million people and causing severe disease and fatality mostly based on virus mediated lung failure [1, 2] . However, epidemics with respiratory virus such as not only influenza but also human corona viruses are prevalent in the Northern hemisphere over several months during the cold season and then disappear whereas influenza remains prevalent in tropical regions throughout the whole year [5] [6] [7] . The grey lines indicate seasons where no specific pandemic respiratory infections are recorded. If COVID-19 would behave similar to other respiratory viruses causing respiratory infections including human corona viruses which peak during winter time and early spring, there is hope that the COVID-19 pandemic can be slowed down by this seasonal trend [7, 9] . However, pandemics with new viruses such as the influenza H1N1v can circulate independent of typical respiratory viral seasons throughout the whole year [10] . doi = 10.1007/s15010-020-01460-1 id = cord-022393-s26d54ew author = E. Newcomer, Christian title = Zoonoses and Other Human Health Hazards date = 2007-09-02 keywords = LCMV; Mus; animal; disease; human; infection; laboratory; mouse; virus summary = Wild caught mice that are maintained in naturalistic housing environments in the laboratory, laboratory mice that have contact with wild or feral mice, and mice kept as pets in the home environment are examples of animal management conditions that would be conducive to the expression and transmission of zoonotic diseases and other mouse-associated implications in the New World serocomplex group are present among the wild rodents endemic to the United States such as Neotoma spp. Many published reports of human LCM infection are associated with laboratory animal and pet contact, particularly mice and hamsters, and these studies now span many decades (Armstrong and Lillie 1934; Bowen et al. The apparent ease with which LCMV is transmitted to humans also occurs in a variety of other laboratory animal species; hamsters, guinea pigs, swine, dogs, and nonhuman primates, especially callitrichids, which readily sustain natural infections. akari infections depend on the prevention of wild mice and the mite vector from entering laboratory animal facilities and human dwellings. doi = 10.1016/b978-012369454-6/50054-6 id = cord-003855-so8xl199 author = Ebert, Gregor title = Virology Downunder, a meeting commentary from the 2019 Lorne Infection and Immunity Conference, Australia date = 2019-09-02 keywords = IFN; Infection summary = The bat innate immune response appears to be ''pre-activated'' with higher basal levels of type I interferon expression, in contrast to humans, who are very quick responders to viral infections, but require a lot more dampening of their immune signals afterwards to get back to basal levels. demonstrated that bats'' response to stress in form of viral infections is more targeted and thus potentially more effective by numerous adaptions and modifications of the innate immune system. In the ''Pathogenesis and Prevention of Infection'' session, Rosa Coldbeck-Shackley working with Michael Beard at the University of Adelaide, Australia, and also colleagues at the Hudson Institute, presented findings on the importance of interferon-epsilon (IFN-ɛ) in the innate immune response to ZIKV infection. Also in the ''Pathogenesis and Prevention of Infection'' session, Allison Abendroth (University of Sydney) presented ''Disarming the killer: targeting of natural killer cells by varicella zoster virus''. doi = 10.1186/s12985-019-1217-6 id = cord-312197-d5d8amk7 author = Edmond, Karen title = New Approaches to Preventing, Diagnosing, and Treating Neonatal Sepsis date = 2010-03-09 keywords = PCR; country; infection; neonatal; sepsis summary = Health facility infections are also a major problem in lowincome countries, but the more pressing issues are the high proportion of home deliveries in unclean environments predisposing to sepsis and ensuring that all neonates have access to effective interventions from health care providers in the first days of life 2 . Randomised controlled trials (RCTs) of maternal protein-calorie and multiple micronutrient and supplementation have demonstrated significant improvements in rates of prematurity and birth weight and variable impact on mortality; but no studies have examined their impact on rates of neonatal sepsis [20, 21] . New studies from Malawi and Nepal indicate that maternal antisepsis interventions such as vaginal chlorhexidine during labour may have a significant impact on rates of neonatal mortality and sepsis in developing countries [33] . Intrapartum antibiotic prophylaxis has been highly effective in reducing both early-onset neonatal bacterial and maternal sepsis in developed countries [35] . doi = 10.1371/journal.pmed.1000213 id = cord-342464-6vk2oxo5 author = Edwards, Michael R. title = The microbiology of asthma date = 2012-06-06 keywords = RSV; asthma; cell; infection summary = The hygiene hypothesis posits that repeated exposure to diverse common infections (in particular, with bacteria, food-borne and oro faecal parasites 4 , and hookworms 5 ) and exposure to environmental microbiota during childhood 6, 7 are strongly associated with a healthy maturation of the immune system and with protection from the development of asthma and allergies later in life 8, 9 . Case control studies show a clear link between respiratory virus infection together with allergen exposure in sensitized children 108 and adults 109 in increasing the risk of hospital admissions due to asthma exacerbations. 5. Excessive T H 2 type responses are implicated in the pathogenesis of RSV-mediated bronchiolitis 110 , and increased production of IL-5 by T cells at birth is associated with a greater risk of severe respiratory infection 111 . doi = 10.1038/nrmicro2801 id = cord-289406-54vyzxjf author = Edwards, Suzanne title = An Experimental Model for Myocarditis and Congestive Heart Failure after Rabbit Coronavirus Infection date = 1992-01-17 keywords = heart; infection; virus summary = In a model for virus-induced myocarditis and congestive heart failure, rabbit coronavirus infection was divided into acute (days 2–5) and subacute (days 6–12) phases on the basis of day of death and pathologic findings. Both Coxsackie Band encephalomyocarditis virus infections in mice may progress to myocarditis and congestive heart failure, and some survi-vors may progress to a dilated cardiomyopathy later in life [5, [14] [15] [16] . Rabbits that died on days 10-12 had pleural effusion, pulmonary edema, ascites, enlarged hearts, dilated right and left ventricular cavities, and congestion in the lungs and liver. It seems likely that pleural effusion disease virus infection also results in a significant percentage of animals dying from heart failure, since degeneration and necrosis of myocytes, pulmonary edema, pleural effusion, dilated ventricles, and congestion of the lungs, liver, and spleen are common [18, 26] . doi = 10.1093/infdis/165.1.134 id = cord-006841-3u56erru author = Einsele, Hermann title = Infectious complications after allogeneic stem cell transplantation: epidemiology and interventional therapy strategies: Guidelines of the Infectious Diseases Working Party (AGIHO) of the German Society of Hematology and Oncology (DGHO) date = 2003-09-10 keywords = CMV; cell; infection; patient summary = doi = 10.1007/s00277-003-0772-4 id = cord-292367-ocbsmmt6 author = El-Masri, Maher M. title = Exploring the influence of enforcing infection control directives on the risk of developing healthcare associated infections in the intensive care unit: A retrospective study date = 2012-02-29 keywords = SARS; infection summary = Such comparison is intended to provide a surrogate measure of the influence that strict enforcement of infection control strategies during the SARS outbreak may have had on the risk of HAIs. Methods A retrospective chart review was conducted on the medical records of 400 intensive care patients who were admitted to the ICU three months before and during the 2003 SARS outbreak. The intent of such comparison is to provide a surrogate measure of the influence that strict enforcement of infection control guidelines might have had on the risk of developing HAIs. A retrospective chart review was conducted on the medical records of 400 patients who were admitted to the intensive care unit of a community-based hospital in Southwestern Ontario. doi = 10.1016/j.iccn.2011.10.003 id = cord-003598-m2fsrwvw author = Elbahesh, Husni title = Response Modifiers: Tweaking the Immune Response Against Influenza A Virus date = 2019-04-12 keywords = IAV; infection; influenza; virus summary = Like many viruses, IAV is reliant on host factors and signaling-pathways for its replication, which could potentially offer alternative options to treat infections. Clinical treatment options for severe influenza virus infections remain limited and relying heavily on the administration of antiviral neuraminidase inhibitors (NAIs) and supportive critical care (9). While virus-targeted therapies remain the standard approach, IV''s mutability and adaptation to current antivirals has highlighted the need for new therapeutic options that target host factors that regulate IV infections and resulting immune responses. Host kinases regulate not only IAV entry and replication but also initiate antiviral signaling cascades that regulate expression of pro-inflammatory chemokines and cytokines during infections and present viable targets for intervention (24, (49) (50) (51) (52) (53) (54) (55) (56) (57) (58) . Inhibition of p38 mitogen-activated protein kinase impairs influenza virus-induced primary and secondary host gene responses and protects mice from lethal H5N1 infection doi = 10.3389/fimmu.2019.00809 id = cord-018461-lq1m9h41 author = Elgazzar, Abdelhamid H. title = Inflammation date = 2014-06-27 keywords = FDG; ammation; infection; infl summary = Exudate should be differentiated from "transudate," which is a fl uid with low protein Facilitates phagocytosis of bacteria by macrophages (opsonization of bacteria) Kinin system Bradykinin included in the system is the most important vascular permeability factor, also a mediator for pain which is a major feature of acute infl ammation Coagulation factors It may be followed in some organisms by necrosis and liquefaction and walling off of the pus, which results in abscess formation that can be present with both acute and chronic infl ammation. F-18 fl uorodeoxyglucose (FDG-PET) has emerged as an important diagnostic agent for infectious and noninfectious soft tissue and skeletal infl ammations including infl ammatory bowel disease, fevers of unknown origin, rheumatologic disorders, tuberculosis infection, fungal infection, pneumonia, abscess, postarthroplasy infections, chronic and vertebral osteomyelitis, sarcoidosis, and chemotherapy-induced pneumonitis [ 72 -74 ] . doi = 10.1007/978-3-319-06112-2_4 id = cord-336510-qzm9wgde author = Ellermann-Eriksen, Svend title = Macrophages and cytokines in the early defence against herpes simplex virus date = 2005-08-03 keywords = HSV; IFN; IL-12; IL-4; TNF; cell; infection; virus summary = In a first wave of responses, cytokines, primarily type I interferons (IFN) and tumour necrosis factor are produced and exert a direct antiviral effect and activate the macrophages themselves. Generally the type I IFNs exhibit a huge range of biological effects, such as antiviral and antiproliferative effects, stimulation of immune cells such as T cells, natural killer (NK) cells, monocytes, macrophages, and dendritic cells, increased expression of MHC-I, activation of pro-apoptotic genes and inhibition of anti-apoptotic mechanisms, modulation of cellular differentiation, and inhibition of angiogenesis [171] . Effect of IL-4 and IL-13 on IFN-gamma-induced production of nitric oxide in mouse macrophages infected with herpes simplex virus type 2 Herpes Simplex virus type 1-induced interferon production and activation of natural killer cells in mice NF-kappaB activation is responsible for the synergistic effect of herpes simplex virus type 2 infection on interferon-gamma-induced nitric oxide production in macrophages doi = 10.1186/1743-422x-2-59 id = cord-267041-i94lyfsh author = Ellner, Jerrold J. title = Management of acute and chronic respiratory tract infections date = 1988-09-16 keywords = infection; patient summary = ELLNER, M.D. Cleveland, CM Pharyngitis, bronchitis, and pneumonia represent the most common respiratory tract infections. Potentially pathogenic bacteria can be isolated in most sputum specimens from persons with chronic bronchitis, even in the absence of symptoms of acute infectious exacerbation, Although it is true that Streptococcus pneumoniae is isolated in increased quantities when patients experience exacerbation [Sl, it is not clear in the SYMPOSIUM ON CEFIXIME / ELLNER Determination of the Cause of Pneumonia * Is the current condition accurately termed "acute," or is it really chronic? Although the Gram''s stain may suggest that the cause of a pneumonia is not bacterial by the finding of inflammatory cells and no organisms, the clinical presentation can be even more useful for distinguishing a bacterial from a nonbacterial infection. The search for elastin fibers appears to be a generally useful adjunct for diagnosis not only in hospitalized patients but in all persons with pneumonia, particularly when symptoms do not fit the classic patterns of either bacterial or nonbacterial syndromes. doi = 10.1016/0002-9343(88)90456-1 id = cord-344084-z4t2wkgk author = Ellwanger, Joel Henrique title = Beyond HIV infection: neglected and varied impacts of CCR5 and CCR5Δ32 on viral diseases date = 2020-05-30 keywords = CCR5; CCR5Δ32; HBV; HCV; HIV; WNV; infection summary = The genetic variant CCR5Δ32 (32 base-pair deletion in CCR5 gene) impairs CCR5 expression on the cell surface and is associated with protection against HIV infection in homozygous individuals. In this context, this review discusses the involvement of CCR5 and the effects of the CCR5Δ32 in human infections caused by the following pathogens: West Nile virus, Influenza virus, Human papillomavirus, Hepatitis B virus, Hepatitis C virus, Poliovirus, Dengue virus, Human cytomegalovirus, Crimean-Congo hemorrhagic fever virus, Enterovirus, Japanese encephalitis virus, and Hantavirus. In agreement with studies showing that CCR5Δ32 homozygous genotype is a risk factor for symptomatic WNV infection in humans, Ccr5-/-WNV-infected mice showed a reduced capacity of viral control, increased disease severity, impaired leukocyte trafficking towards the brain, and high mortality rates than Ccr5 wild-type mice. In conclusion, although tissue analysis and evidence obtained in vitro suggest that the CCR5 is potentially involved in the pathogenesis of HPV, most studies point to a lack of involvement of CCR5Δ32 in susceptibility to HPV infection or HPV-associated diseases. doi = 10.1016/j.virusres.2020.198040 id = cord-034133-tx0hciiv author = Engda, Tigist title = The contribution of medical educational system of the College of Medicine, and Health Sciences of the University of Gondar in Ethiopia on the knowledge, attitudes, and practices of graduate students of Health Sciences in relation to the prevention and control of nosocomial infections during the academic year of 2018 date = 2020-10-22 keywords = Health; infection; knowledge summary = title: The contribution of medical educational system of the College of Medicine, and Health Sciences of the University of Gondar in Ethiopia on the knowledge, attitudes, and practices of graduate students of Health Sciences in relation to the prevention and control of nosocomial infections during the academic year of 2018 This study aimed to assess the contribution of the medical education system on the knowledge, attitudes, and practices of the graduate students of health sciences about the prevention and control of nosocomial infection in the College of Medicine and Health Sciences at the University of Gondar in the Academic Year of 2018. Therefore, the current study intended to determine the impact of the medical education system on the knowledge, attitude, and practice of graduate health sciences students about the prevention and control of nosocomial infections at the University of Gondar. doi = 10.1186/s12909-020-02271-6 id = cord-288113-ex4yi28u author = Epalza, Cristina title = Role of Viral Molecular Panels in Diagnosing the Etiology of Fever in Infants Younger Than 3 Months date = 2019-11-09 keywords = SBI; infant; infection summary = As infants with proven viral infection present lower risk of bacterial infection, we evaluated how molecular methods detecting viruses on respiratory secretions could contribute to etiological diagnostic of these febrile episodes. The management of febrile infants younger than 3 months in the emergency room (ER) is challenging as they have a higher risk of serious bacterial infection (SBI) than older children and because clinical evaluation has a low sensitivity and specificity in identifying those infants with SBI. The aims of this prospective study were to evaluate the analytical performances of a multiplex diagnostic tool detecting the most frequent respiratory viruses as compared with our set of homemade real-time PCRs and the potential contribution of these molecular methods to the etiologic diagnosis of febrile episodes in infants younger than 3 months of life. The present evaluation demonstrates that molecular techniques greatly improve the detection rate of viral infections, especially in the challenging group of febrile infants without clinical source, among which the increase in microbiological documentation was nearly 20%. doi = 10.1177/0009922819884582 id = cord-310840-h49dx92d author = Eslamy, Hedieh K. title = Pneumonia in Normal and Immunocompromised Children: An Overview and Update date = 2011-09-30 keywords = Fig; child; infection; lung; pneumonia summary = The role of imaging is to detect the presence of pneumonia, and determine its location and extent, exclude other thoracic causes of respiratory symptoms, and show complications such as effusion/empyema and suppurative lung changes. The role of imaging, including chest radiographs, ultrasound (US) and computed tomography (CT), is to detect the presence of pneumonia, determine its location and extent, exclude other thoracic causes of respiratory symptoms, and show complications such as parapneumonic effusion/ empyema and suppurative lung complications. CT is often used to further evaluate: (1) suppurative lung complications and to differentiate these from parapneumonic effusion/empyema; (2) patients with recurrent or chronic pneumonia and concern for an underlying lesion; and (3) immunocompromised children with noncontributory or confusing chest radiographs and clinical findings that could be secondary to lung infection. The chest radiograph of acute focal pneumonia usually shows a dense, typically more peripheral airspace opacity, which may appear segmental, lobar, or spherical ( Figs. doi = 10.1016/j.rcl.2011.06.007 id = cord-306278-c4q4la5c author = Esposito, Susanna title = Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date = 2016-04-05 keywords = PCR; infection; respiratory summary = To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. To evaluate the circulation of the different HAdV types and the possible relationship between viral load, viral genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children consecutively attending the Emergency Room of the Fondazione IRCCS Ca'' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection. However, further studies are needed to identify the potential pathogenetic role of the different species and types of HAdV and the importance of viral load in the severity of infection. doi = 10.1371/journal.pone.0152375 id = cord-296256-ipe92w4y author = Evelyn, Obando title = Prevalence, clinical outcomes and rainfall association of acute respiratory infection by human metapneumovirus in children in Bogotá, Colombia date = 2019-10-10 keywords = HMPV; infection summary = title: Prevalence, clinical outcomes and rainfall association of acute respiratory infection by human metapneumovirus in children in Bogotá, Colombia Human metapneumovirus (HMPV) has recently been described as a cause of severe acute respiratory infection and its prevalence and clinical behavior in children at moderate altitudes is unknown. RESULTS: Out of a total of 14,760 discharged patients, multiplex RT-PCR was performed on 502 and a virus was detected in 420 children with acute respiratory infection (ARI). CONCLUSIONS: Human metapneumovirus was the fifth most frequently isolated virus in children with ARI, had similar clinical behavior and severity to other viruses but a higher rate of viral coinfection. The data was taken from the institutional electronic charts of children who were hospitalized for acute respiratory infections and who received multiplex RT-PCR (FilmArray® BioMériux), the analyte used in this technique for HMPV detection was Type 16, A1 IA10-2003 Zeptometrix 0810161CF. doi = 10.1186/s12887-019-1734-x id = cord-001120-fxd533b4 author = Everitt, Aaron R. title = Defining the Range of Pathogens Susceptible to Ifitm3 Restriction Using a Knockout Mouse Model date = 2013-11-21 keywords = Ifitm3; RSV; figure; infection; virus summary = We showed that Ifitm3 does not impact on the restriction or pathogenesis of bacterial (Salmonella typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis) or protozoan (Plasmodium berghei) pathogens, despite in vitro evidence. Here we sought therefore to expand and define the role of Ifitm3 in pathogen restriction by assessing the susceptibility of Ifitm3-deficient (Ifitm3 -/-) mice to bacteria (Salmonella Typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis), a parasite (Plasmodium berghei) and a virus (respiratory syncytial virus, RSV) to determine the specificity of this crucial antimicrobial protein. Similarly, bacterial counts revealed no significant differences between wild type and Ifitm3 -/-mice; together showing that Ifitm3 does not play a role in resistance or susceptibility to Salmonella infection. The experimental challenge revealed there to be no significant difference in phenotype seen in Ifitm3 -/-mice compared with wild type littermate controls, with both showing susceptibility to ECM ( Figure 5A ). doi = 10.1371/journal.pone.0080723 id = cord-347246-0vofftmj author = Everitt, J I title = Infectious diseases of the upper respiratory tract: implications for toxicology studies. date = 1990-04-17 keywords = Sendai; infection; respiratory summary = This paper reviews several important infectious diseases of the upper airway of rats and mice and discusses the potential influence of these conditions on the results of toxicology studies. All three agents cause significant rodent respiratory disease, with lesions in the upper airways, including the nasal passages. Although there are many excellent descriptive studies ofthe histogenesis of Sendai virus-induced lesions within the lower respiratory tract, few pathology reports include a description of lesions in the nasal cavity and upper airway. Although numerous bacteria can infect the upper airway of the rat and mouse, they are not generally prevalent in well-conducted toxicology studies begun with animals free of adventitious murine pathogens and maintained with modern methods of laboratory animal husbandry. A variety of important microbial pathogens including viruses, mycoplasmas, bacteria, and fungi infect the upper respiratory tract of the mouse and rat and result in significant pathologic alterations. doi = nan id = cord-009380-5uptbat3 author = Evermann, James F. title = Diagnostic Medicine: The Challenge of Differentiating Infection from Disease and Making Sense for the Veterinary Clinician date = 2007-09-28 keywords = detection; disease; infection summary = Diagnostic medicine has taken on a new, broader meaning in the 1990s and reflects an expansion of clinical investigation from the diagnosis of disease to include detection of infection (Evermann, 1998) . Disease diagnosis has customarily used diagnostic assays for early recognition of disease and rapid implementation of therapy in an individual animal basis, and when appropriate use of corrective management (segregation, culling, vaccination, etc.) on a population basis. With a combination of more sensitive diagnostic assays, the veterinarian''s concern to know the state of the preclinical infection, economic incentives to minimize disease by effectively controlling the infection, and concern over potential zoonotic diseases, laboratory diagnosis has taken on a different strategy. However, with early testing the problems of detecting cross-reacting viruses (feline enteric coronaviruses) increases, as does the question of whether the preclinical result accurately identifies an animal that is just infected or will progress onto disease (Evermann et al., 1995; Foley et al., 1997) . doi = 10.1016/s0065-3519(99)80006-8 id = cord-261867-6n0g3bz5 author = Evermann, James F. title = Canine Reproductive, Respiratory, and Ocular Diseases due to Canine Herpesvirus date = 2011-10-28 keywords = CHV; PCR; canine; dog; infection; ocular summary = doi = 10.1016/j.cvsm.2011.08.007 id = cord-351319-ylg93l9q author = Evers, Dorothea title = Red cell alloimmunisation in patients with different types of infections date = 2016-08-18 keywords = alloimmunisation; cell; infection; red summary = Patients developing a first transfusion‐induced red cell alloantibody (N = 505) were each compared with two similarly exposed, but non‐alloimmunised controls (N = 1010) during a 5‐week ''alloimmunisation risk period'' using multivariate logistic regression analysis. In this nested case-control study, we quantified relative alloimmunisation risks for patients receiving red cell units during an infectious episode, according to the type of infection, its intensity, and the patient''s inflammatory response to it. Using this design, we compared patients who developed red cell alloantibodies following transfusion with non-alloimmunised controls on the basis of supposed causal attributes, including various types of infections. In conclusion, our data suggest a potential risk modifying influence of infection-associated inflammation on red cell alloimmunisation in transfused patients. doi = 10.1111/bjh.14307 id = cord-334027-xhfmio7k author = Fagre, Anna C. title = Can Bats Serve as Reservoirs for Arboviruses? date = 2019-03-03 keywords = Artibeus; Uganda; bat; egyptian; infection; japanese; virus summary = No demonstrable pathologic effects noted during infection of three bat species [big brown bats (Eptesicus fuscus), little brown bats (Myotis lucifigus) and Mexican free-tailed bats (Tadarida brasiliensie mexicana) with various strains of JBEV or St. Louis encephalitis virus (SLEV) [69] . While experimental data demonstrated that some bat species can sustain JBEV infections and support mosquito-borne transmission of this virus, the epidemiological significance of these observations in the field remains unclear. To truly elucidate the role of bats as reservoirs for arboviruses, field surveillance studies documenting natural infection and transmission dynamics among vector and vertebrate species must be supplemented with experimental infections to characterize viremia profiles and infectiousness to vectors, virus-induced pathology, and immune kinetics following infection. The isolation of Marburg virus from Egyptian rousette bats in Uganda in addition to experimental infections demonstrating viremia and shedding in the absence of overt pathology support the role of this bat species as the reservoir for Marburg virus [6, 7, 208] . doi = 10.3390/v11030215 id = cord-284845-on97zu6w author = Falcinelli, Shane D. title = Integration of Global Analyses of Host Molecular Responses with Clinical Data To Evaluate Pathogenesis and Advance Therapies for Emerging and Re-emerging Viral Infections date = 2016-07-29 keywords = EBOV; Ebola; MERS; MPXV; infection; response summary = doi = 10.1021/acsinfecdis.6b00104 id = cord-340357-gyvvcnuf author = Fallahi, Hamid Reza title = Being a front-line dentist during the Covid-19 pandemic: a literature review date = 2020-04-24 keywords = SARS; coronavirus; infection; transmission summary = This article addresses all information collected to date on the virus, in accordance with the guidelines of international health care institutions, and provides a comprehensive protocol for managing possible exposure to patients or those suspected of having coronavirus. The purpose of this protocol is to protect the entire dental care team, prevent any cross-infection in the office, inform health authorities active in the field of controlling and managing the disease, and ultimately provide the optimal medical and dental care for patients affected by the virus according to the CDC and the ADA guidelines. Due to close face-to-face contact with patients and frequent utilization of sharp devices, dental personnel are repeatedly exposed to respiratory tract secretions, blood, saliva, and other contaminated body fluids and are always at risk for 2019-nCoV infection. 2019-nCoV transmission in dental settings occurs through four major routes: (1) direct exposure to respiratory secretions containing droplets, blood, saliva, or other patient materials; doi = 10.1186/s40902-020-00256-5 id = cord-281249-89eycq64 author = Falsey, Ann R title = Utility of serum procalcitonin values in patients with acute exacerbations of chronic obstructive pulmonary disease: a cautionary note date = 2012-02-23 keywords = AECOPD; bacterial; infection summary = doi = 10.2147/copd.s29149 id = cord-009860-qebenhxz author = Falsey, Ann R. title = Viral Respiratory Infections in the Institutionalized Elderly: Clinical and Epidemiologic Findings date = 2015-04-27 keywords = RSV; infection; respiratory summary = doi = 10.1111/j.1532-5415.1992.tb01929.x id = cord-292871-vgposxom author = Falsey, Ann R. title = The “Common Cold” in Frail Older Persons: Impact of Rhinovirus and Coronavirus in a Senior Daycare Center date = 2015-04-27 keywords = illness; infection; respiratory summary = doi = 10.1111/j.1532-5415.1997.tb01474.x id = cord-328795-rs1sd42z author = Falsey, Ann R. title = Rhinoviruses date = 2016-10-24 keywords = HRV; PCR; Turner; infection summary = The incidence of HRV infection in children during the first 2 years of life was noted to be 0.7-2 infections per year in older studies using cell culture for viral detection (Brownlee and Turner, 2008) . Although symptoms associated with ''the common cold'' syndrome are often attributed to HRV disease, the clinical findings of rhinovirus infections are indistinguishable from those of other viral pathogens. Currently, there are no antiviral drugs approved for clinical use in HRV infections although a few agents have been advanced to clinical trials and shown modest results in decreasing either symptom severity or viral activity. Conversely, monoclonal antibody blockade of the ICAM-1 receptor, the site of cellular attachment for the majority of HRV-A and HRV-B serotypes, has also been studied and demonstrated a reduction in the severity of symptoms and viral shedding but failed to prevent infection in the rhinovirus challenge model (Greenberg, 2003) . doi = 10.1016/b978-0-12-803678-5.00386-6 id = cord-314841-b5l6epy3 author = Falsey, Ann Regina title = Respiratory viral infections date = 2019-08-15 keywords = H1N1; HRV; RSV; infection; respiratory summary = Analysis of the host transcriptional response during respiratory viral infection using in-vitro, animal models and natural and experimental human challenge have furthered the understanding of the mechanisms and predictors of severe disease and may identify potential therapeutic targets to prevent and ameliorate illness. In addition to sensitive and rapid diagnostic testing, new molecular techniques allow an understanding of viral evolution, mechanisms and predictors of severe disease, interrogation of vaccine responses, improved bacterial and viral diagnostics and associations of viral infections with non-respiratory medical events. A number of candidate genes influencing respiratory virus susceptibility have been identified in animal and human studies and involve host virus interactions, innate immune signaling, interferon related pathways and cytokine responses (Table 1) [49] [50] [51] [69] [70] [71] [72] [73] [74] [75] . In addition, two compartments, the respiratory epithelium and blood can be sampled in human studies and interrogated using different viruses or viral strains to develop gene signatures for prognosis, as indicators of severity and to identify potential therapeutic targets. doi = 10.1016/b978-0-12-801496-7.00009-5 id = cord-300815-1vy787md author = Fang, Li-Qun title = Travel-related infections in mainland China, 2014–16: an active surveillance study date = 2018-07-20 keywords = China; Taiwan; infection summary = We integrated the data from all entry-exit ports in mainland China to characterise travel-related infections, define the demographic features of imported cases, identify risk groups and exposure countries or regions, and assess the effectiveness of surveillance for further improvement. However, hepatitis B and C virus infections, syphilis, HIV, malaria, and dengue were substantially more common in the international group, whereas respiratory infections with rhinovirus, para influenza virus and metapneumovirus, and hand, foot, and mouth disease were more common in travellers from Hong Kong, Macau, and Taiwan ( figure 3) . Our findings, which are based on surveillance data for 45 infections among 22 797 travellers who arrived at the 272 entry-exit ports to the mainland, are helpful for increasing public health awareness about the potential risk of imported infections. doi = 10.1016/s2468-2667(18)30127-0 id = cord-346318-d8oq3dyw author = Fang, Yeqing title = Reply: Practical experiences on the prevention and treatment strategies to fight against COVID-19 in hospital date = 2020-05-05 keywords = infection summary = regarding our recent article, Shenzhen'' Experience on Containing 2019 Novel Coronavirus-Infected Pneumonia Transmission [1] , which was published on April 3, 2020. The author of the letter described their treatment strategies to contain the epidemic and improve clinical outcomes: increase the medics'' protective gear to ensure double-zero infection: no nosocomial infection, no developed into critical or death case; timely control and regulate the inpatient area by adopting the AI and infection control observing system; "Two early, three changes and three strictness"; early use of traditional Chinese medicine according to characteristics of different persons, etc. Next, during the outbreak, hospitals need to redeploy the working arrangement of healthcare workers, suspend or close non-emergency departments and selective operations to add staff to supplementary emergency, fever clinic and infection wards, so that there are sufficient medical workers to respond to the increasing coronavirus patients efficiently. Shenzhen'' experience on containing 2019 novel coronavirus-infected pneumonia transmission doi = 10.1093/qjmed/hcaa158 id = cord-294568-12eyo13f author = Fernandes-Matano, Larissa title = Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico date = 2017-05-03 keywords = HRSV; infection; respiratory; virus summary = Influenza viruses are one of the main causative agents of ARIs worldwide; however, many other respiratory viruses for which insufficient epidemiological information is available can also cause ARIs. Studies performed at the international level have frequently identified human respiratory syncytial virus (HRSV), human parainfluenza virus (HPIV), influenza virus (flu), human mastadenovirus (HMdV), rhinovirus (RV), and enterovirus (EV) and less frequently identified human metapneumovirus (HMPV), primate bocaparvovirus (PBpV), and human coronavirus (HCoV) [12] . Therefore, the objective of this study was to determine the viral aetiology of these infections and to analyse the behaviour of non-influenza respiratory viruses in the Mexican population. The importance of the differential diagnosis of other respiratory viruses in samples with negative influenza results becomes apparent when we observe the prevalence of the three main viruses identified in this study as well as their associations with severe cases and deaths, especially in the child population. doi = 10.1371/journal.pone.0176298 id = cord-271130-6s79q1c1 author = Filoni, Claudia title = Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) date = 2017-11-17 keywords = FeLV; PCR; RNA; infection; jaguarundi summary = title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) Thus, the aim of this study was to perform additional serological and molecular tests and monitor the population of jaguarundis at FPZSP for FeLV infection and development of FeLV-related diseases for 5 years (2003) (2004) (2005) (2006) (2007) . Two captive-born male jaguarundis, the geriatric #1 and the mature adult #4, presented serological and molecular FeLV test results similar to the progressive FeLV infection outcome in domestic cats [25] . Moreover, consistent with findings in domestic cats with a progressive FeLV infection, no antibodies to FeLV antigens were detected in jaguarundis #1 and #4. Two captive-born jaguarundis, #2 and #22, presented test results similar to those reported for domestic cats with abortive FeLV infection and seroconversion as the only marker of FeLV exposure [28] . doi = 10.1186/s12985-017-0889-z id = cord-022472-q2qtl26d author = Fishman, Jay A. title = Infection in Renal Transplant Recipients date = 2009-05-15 keywords = CMV; EBV; PTLD; infection; recipient; transplant summary = • Solid organ transplant recipients who are naïve (seronegative) and receive an organ from a seropositive donor (D+/R−) • Solid organ transplant recipients who are seropositive (R+) and receive antilymphocyte antibodies or other intensive immune suppression (e.g., for graft rejection) Symptoms, fever/neutropenia mo (or valacyclovir 500 bid or acyclovir 400 tid) Use of CMV-negative or leukocyte-filtered blood Status unknown with ALS Intravenous ganciclovir 5mg/kg iv for first dose and QD (corrected for renal function) until sero-status determined. • End organ damage (e.g., BK polyomavirus nephropathy, cryoglobulinemia, or cirrhosis from HCV-HBV being relatively well managed at present) • Malignancy (post-transplantation lymphoproliferative disease [PTLD] due to EBV, skin, or anogenital cancer due to papilloma viruses) • Acquired immunodeficiency syndrome (HIV/AIDS) The third group of patients (~10% of all recipients) has less than satisfactory allograft function and requires excessive amounts of immunosuppressive therapy for recurrent graft rejection. doi = 10.1016/b978-1-4160-0158-4.50041-0 id = cord-347000-zxytdb0b author = Foweraker, Juliet title = Recent advances in the microbiology of respiratory tract infection in cystic fibrosis date = 2009-01-20 keywords = Burkholderia; Pseudomonas; infection summary = The range of micro-organisms causing infection differs from those in patients without CF with the commonest pathogens being Staphylococcus aureus and Pseudomonas aeruginosa. 17 Streptococcus pneumoniae from CF respiratory samples were better at producing biofilms in vitro than blood culture isolates from non-CF patients, 18 which suggests that these organisms have the ability to persist in the CF lung. 31 The role of current methods of synergy testing is controversial, but there is a definite need for clinically validated in vitro tests to guide treatment of multi-and pan-resistant bacteria at acute exacerbation and when patients receive lung transplants. Phenotypic variability of Pseudomonas aeruginosa in sputa from patients with acute infective exacerbation of cystic fibrosis and its impact on the validity of antimicrobial susceptibility testing Hypermutation is a key factor in development of multiple-antimicrobial resistance in Pseudomonas aeruginosa strains causing chronic lung infections Evolving epidemiology of Pseudomonas aeruginosa and the Burkholderia cepacia complex in cystic fibrosis lung infection doi = 10.1093/bmb/ldn050 id = cord-016020-awanrm9u author = Fox, Julie D. title = Respiratory Pathogens date = 2007 keywords = PCR; detection; infection; respiratory summary = In addition, despite the well-recognized association of viral infections with upper and lower respiratory tract infections, the current diagnostic virology procedures do not provide an answer rapidly enough to with parainfluenza virus type 4, human coronaviruses, rhinoviruses, and some enteroviruses would not ordinarily be identified without RNA detection methods. Published diagnostic methods for detection of respiratory pathogen DNA or RNA directly from clinical specimens utilize target amplification procedures such as polymerase chain reaction (PCR) or nucleic acid sequence-based amplification (NASBA).Although direct detection methods based on nucleic acid hybridization would be theoretically possible, the amount of target nucleic acid in specimens may be minimal and such methods would lack sensitivity compared to amplification methods, unless the organism was propagated before analysis. Thus, the molecular amplification procedures reported for direct detection of respiratory pathogens in clinical samples include PCR (e.g., Reference 19 and Figure 41 assays have utilized bacterial ribosomal RNA (rRNA; e.g., Reference 22 ). doi = 10.1007/978-0-387-33227-7_41 id = cord-005902-5zuij5i3 author = Frank, Johannes title = Necrotizing Fasciitis of the Extremities date = 2008-05-30 keywords = infection; tissue; treatment summary = As a consequence, early clinical diagnoses with thorough surgical debridement of the infected liquid necrotic fascia as well as correct antibiotic treatment are needed. An amputation in the extremities is not the primary treatment, but in cases where the whole tissue is necrotic and most muscles involved, this might be the only option to stop further spreading and systemic sepsis with multiple organ failure. After primary intensive care and control of the infection and sepsis (mostly after 1 week) reconstructive procedures are initialized reaching from secondary wound closure and skin grafting to flap coverage saving viable tissue and restore function. Besides the basic treatment including intensive care medicine and surgical debridement numerous adjuvant therapies have been recommended with respect to the systemic management of these infections as well as possibilities for local wound treatment. Conclusion Necrotizing fasciitis (NF) is a life threatening soft tissue infection, characterized by foudroyant spreading necrosis of the involved fascias. doi = 10.1007/s00068-008-8074-0 id = cord-007797-toam6r5y author = Franquet, Tomás title = Imaging of Pulmonary Infection date = 2019-02-20 keywords = infection; pneumonia; pulmonary summary = Community acquired pneumonia refers to an acute infection of the lung in patients who did not meet any of the criteria for HCAP, presenting select clinical features (e.g., cough, fever, sputum production, and pleuritic chest pain) and accompanied by an acute infiltrate on a chest radiograph. Chest radiographs are of limited value in predicting the causative pathogen but are of good use to determine the extent of pneumonia and to detect complications (i.e., cavitation, abscess formation, pneumothorax, pleural effusion), to detect additional or alternative diagnoses, and, in some cases, to guide invasive diagnostic procedures. Risk factors for the development of staphylococcal pneumonia include underlying pulmonary disease (e.g., COPD, carcinoma), chronic illnesses (e.g., diabetes mellitus, renal failure), or viral infection. The lower lobes contrast-enhanced CT image shows a mixed opacity of consolidation (arrow) and ground-glass opacity (small arrows) consistent with lobar pneumonia tend to be affected, and the radiographic pattern is similar to that seen with S. doi = 10.1007/978-3-030-11149-6_7 id = cord-354068-4qlk6y7h author = Friedrich, Brian M. title = Potential Vaccines and Post-Exposure Treatments for Filovirus Infections date = 2012-09-21 keywords = EBOV; MARV; ebola; infection; vaccine; virus summary = Due to the difficulties in evaluating wild-type filovirus infection in small animals and the generally high level of immune protection correlates derived from non-human primate (NHP) models of infection, therapeutics and vaccines are ultimately evaluated in NHP species for efficacy against filovirus. In their study, a heterologous prime/boost strategy with recombinant adenovirus serotypes 26 and 35 carrying GP (Z) and GP (S/G) demonstrated complete protection among NHPs. Each of these vectors was capable of stimulating humoral and cell-mediated immune responses in the context of NHPs pre-vaccinated with rAd5 as evidenced by antibody titers reaching an order of magnitude above those achieved in rAd5 vaccinated subjects (1:32,000 compared to 1:6,800), and CD8 + intracellular cytokine staining was 4.7-fold greater among heterologous prime/boosted subjects (0.41% compared to 0.09%) [59] . This GP-Fc fusion protein induced both cell-mediated and humoral immune responses, and mice vaccinated with ZEBOVGP-Fc demonstrated 90% protection against a lethal EBOV challenge. doi = 10.3390/v4091619 id = cord-261150-cdo7y3ob author = Fthenakis, G. C. title = Interactions between parasitic infections and reproductive efficiency in sheep date = 2015-02-28 keywords = effect; ewe; infection; sheep summary = doi = 10.1016/j.vetpar.2014.12.017 id = cord-003425-c5jdp5jv author = Fu, Yangxi title = Human adenovirus type 7 infection causes a more severe disease than type 3 date = 2019-01-09 keywords = HAdV-3; adenovirus; cell; infection summary = RESULTS: Clinical characteristics revealed that HAdV-7 infection caused more severe pneumonia, toxic encephalopathy, respiratory failure, longer mean hospitalization, significantly lower white blood cell (WBC) and platelet counts, compared to those of HAdV-3. In the present study, therefore, we undertook a comprehensive analysis of the comparative clinical features of HAdV-3 and HAdV-7 infection, as well as a serial of experiments, were performed to better understand the association between severity of the disease and the serotypes of HAdVs. Participants, demographic data, clinical data analysis Patients ranging in age from 1 month to 16 years and requiring inpatient treatment due to acute respiratory tract infections (ARTI) at the Department of Respiratory Medicine, Children''s Hospital of Chongqing Medical University between June, 2009 and May, 2015, were enrolled in this study. Since type-specific adenovirus infection is known to cause different tissue tropisms and clinical manifestations as indicated before, viral loads and fitness of HAdV-3 and HAdV-7 were evaluated in several human epithelial cells to determine if there were differences. doi = 10.1186/s12879-018-3651-2 id = cord-002659-566uoozj author = Fujimoto, Yousuke title = Pulmonary inflammation and cytokine dynamics of bronchoalveolar lavage fluid from a mouse model of bronchial asthma during A(H1N1)pdm09 influenza infection date = 2017-08-22 keywords = H1N1; day; infection summary = Cytokine levels and virus titres in bronchoalveolar lavage fluid from mice with and without asthma after A(H1N1)pdm09 or seasonal H1N1 infection were examined. Virus titres in asthma/A(H1N1)pdm09 mice were highest at 3 days post-infection, and decreased by 7 days post-infection, although the levels at this time point were still higher than that in any other group. In the present study, we investigated the sequential changes in intra-tracheal cytokine production, viral loads, and pulmonary inflammation in a mouse model of bronchial asthma during the first 7 days after A(H1N1)pdm09 or seasonal H1N1 influenza infection. In contrast, the levels in control mice increased to 161.4 pg/mL by 3 days post-seasonal virus infection, which were similar to those in asthma/A(H1N1)pdm09 mice (p = 1.00), and these levels were maintained until 7 days post-infection. The notable findings in the present study were the early peak in both IL-6 and TNF-α levels, the high inflammatory cell infiltration in BAL fluids, and the severe pulmonary inflammation at 3 days post-infection in asthmatic/A(H1N1)pdm09 mice. doi = 10.1038/s41598-017-08030-w id = cord-264569-q8nq2gbz author = GRÜnberg, K. title = Rhinovirus infections: induction and modulation of airways inflammation in asthma date = 2001-12-24 keywords = airway; infection; rhinovirus summary = doi = 10.1046/j.1365-2222.1999.00011.x id = cord-256147-lfwytlj3 author = Gabriella, di Mauro title = SARS-Cov-2 infection: response of human immune system and possible implications for the rapid test and treatment date = 2020-04-16 keywords = SARS; infection summary = Considering the clinical impact of the new outbreak, it is highly important to study the potential responses of the human immune system during the SARS-CoV-2 infection as well as the role of virus-specific T cells and by B-lymphocytes. In order to apply a rapid test able to detect the presence of specific IgM and IgG for SARS-CoV-2, it is important to consider that the IgM values tend to disappear within 2 weeks since the beginning of the infection. The sensitivity and specificity of these tests were evaluated on 397 blood samples from patients who tested positive for the nasopharyngeal swab for SARS-CoV-2 infection and on 128 patients who tested negative and asymptomatic but potentially at risk of developing the infection based on epidemiological criteria [7] . The results of the study showed that out of 397 blood samples from patients with a SARS-CoV-2 infection, 352 tested positive. Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis doi = 10.1016/j.intimp.2020.106519 id = cord-323551-22v2hn3v author = Galanti, M. title = Rates of asymptomatic respiratory virus infection across age groups date = 2019-04-15 keywords = infection; respiratory; symptom summary = We enrolled 214 individuals at multiple New York City locations and tested weekly for respiratory viral pathogens, irrespective of symptom status, from fall 2016 to spring 2018. Here, we document rates of asymptomatic respiratory virus infection through a large-scale community study across multiple age groups. For the entire duration of the study, participants provided a daily report rating nine respiratory illness-related symptoms (fever, chills, muscle pain, watery eyes, runny nose, sneezing, sore throat, cough, chest pain), which were recorded on a Likert scale (0 = none, 1 = mild, 2 = moderate, 3 = severe). Pairwise comparisons between single infections and coinfections across all eight definitions showed that testing positive for multiple viruses was not associated with more severe symptoms. Figure 3 shows that while children were most frequently infected with a respiratory virus (they presented with the highest number of viral shedding events per season), they recorded (as reported by their parents) the lowest symptom scores on average. doi = 10.1017/s0950268819000505 id = cord-352433-sts48u9i author = Galanti, Marta title = Direct Observation of Repeated Infections With Endemic Coronaviruses date = 2020-07-07 keywords = OC43; SARS; infection summary = BACKGROUND: Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful reference for understanding repeat infection risk. CONCLUSIONS: This study provides evidence that reinfections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection. However, in Korea, as reported by the Korean Centers for Disease Control and Prevention, viable SARS-CoV-2 was not isolated in cell culture of respiratory samples from potentially reinfected individuals [5] ; thus, these subsequent positive results may have been due to inactive genetic material detected by molecular testing. doi = 10.1093/infdis/jiaa392 id = cord-266985-9qwttt2y author = Gale, P. title = Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study date = 2014-11-04 keywords = RNA; infection; virus summary = doi = 10.1111/jam.12656 id = cord-339578-eg19rfvi author = Garcia-Garcia, Maria Luz title = Role of viral coinfections in asthma development date = 2017-12-05 keywords = RSV; asthma; infection summary = OBJECTIVE: Our aim was to compare the frequency of asthma development at 6–8 years in children with previous admission for bronchiolitis associated with single versus double or multiple viral infection. CONCLUSIONS: Asthma at 6–8 years is more frequent and severe in those children previously hospitalized with viral coinfection-bronchiolitis compared with those with single infection. Of the 351 children previously admitted with bronchiolitis, with positive viral detection and current age between 6 and 8 years, 244 (52 coinfections and 192 single infections) could be located and agreed to participate in the study. In conclusion, asthma at the age of 6-8 is more frequent and severe in those children previously hospitalized with viral coinfection bronchiolitis compared with those with single infection. Moreover, viral coinfection, allergic rhinitis and older age at admission seem also to be strong independent risk factors for asthma development in children previously hospitalised because of bronchiolitis. doi = 10.1371/journal.pone.0189083 id = cord-301225-h178zpb3 author = Gautret, Philippe title = Fever in Returned Travelers date = 2018-11-26 keywords = Africa; dengue; fever; infection; traveler summary = 5, 9, 10 While, overall, malaria is the most common specific infection causing systemic febrile illness, dengue fever, mononucleosis, rickettsial infections, and enteric fever are also important infections. More than a third of malaria-infected travelers in a study from Israel and the United States had illness that developed >2 months after return from endemic areas. 28 In the GeoSentinel database, confirmed or probable dengue fever was the most common specific diagnosis in patients with febrile systemic illness who had traveled to tropical and subtropical areas in the Caribbean, South America, South Central and Southeast Asia. 52 In most cases the disease is acquired in Africa (not only sub-Saharan); however, in the last decade an seek medical care suggested that 2% of imported fevers are caused by rickettsioses and that 20% of these patients are hospitalized. doi = 10.1016/b978-0-323-54696-6.00056-2 id = cord-019009-3ngfv96u author = Gea-Banacloche, Juan title = Risks and Epidemiology of Infections After Hematopoietic Stem Cell Transplantation date = 2016-02-15 keywords = CMV; GVHD; HCT; cell; infection; risk summary = Several characteristics of the transplant infl uence the risk of infection: the conditioning preparative regimen, the source of stem cells, the degree of HLA identity between donor and recipient, and the prophylactic strategy adopted to prevent GVHD (use of T cell depletion or immunosuppressive medications). These factors may result in increased risk of infections associated with T cell immunodefi ciency, like CMV, Pneumocystis jirovecii pneumonia (PCP), and Epstein-Barr virus (EBV)-related posttransplant lymphoproliferative disorder (PTLD). Risk factors for recurrence of invasive fungal infection during secondary antifungal prophylaxis in allogeneic hematopoietic stem cell transplant recipients Impact of the intensity of the pretransplantation conditioning regimen in patients with prior invasive aspergillosis undergoing allogeneic hematopoietic stem cell transplantation: a retrospective survey of the infectious diseases working party of the european group for blood and marrow transplantation Infl iximab use in patients with severe graftversus-host disease and other emerging risk factors of noncandida invasive fungal infections in allogeneic hematopoietic stem cell transplant recipients: a cohort study doi = 10.1007/978-3-319-28797-3_6 id = cord-283588-j27q53oz author = Gebicki, Jerzy title = COVID-19 infection: mitohormetic concept of immune response date = 2020-07-14 keywords = infection summary = title: COVID-19 infection: mitohormetic concept of immune response 1-MNA, previously regarded as a useless metabolite of NA excreted with urine, has been shown to possess significant anti-inflammatory properties 5 . The mitohormetic concept of anti-inflammatory activity by 1-MNA is presented in Fig. 1 . As AOX expression is particularly high in respiratory tissues, it may be expected that there would be significant 1-MNA anti-inflammatory activity in the airways as well. Indeed, the excretion of 1-MNA with urine has been found to be significantly reduced in respiratory syncytial virus (RSV) infection 7 . It has been suggested that the weakened ability to fend off inflammation during RSV infection is likely due to lower levels of 1-MNA 7 . The lower levels of 1-MNA observed in some airway diseases, including viral infections, may further suggest that 1-MNA plays an important physiological role in regulation of the innate immune response. doi = 10.1038/s41420-020-00297-9 id = cord-257399-p6of5fno author = Gentry, Chris A title = Long-term hydroxychloroquine use in patients with rheumatic conditions and development of SARS-CoV-2 infection: a retrospective cohort study date = 2020-09-21 keywords = CoV-2; March; SARS; infection summary = METHODS: This retrospective cohort study included de-identified information of all veterans in the US Veterans Health Administration clinical administrative database aged 18 years or older with rheumatoid arthritis, systemic lupus erythematosus, or associated rheumatological conditions (based on International Classification of Diseases, 10th edition, diagnostic codes) who were alive on March 1, 2020. We aimed to examine whether patients with rheuma tological conditions receiving chronic hydroxy chloroquine therapy are at less risk of developing SARS-CoV-2 infection compared with a propensity-matched group of patients not receiving hydroxychloroquine. Our study takes advantage of a setting in which a specific group of patients has been receiving chronic hydroxy chloroquine over several months to years as a novel virus emerges among the population, setting up an ideal premise to test the hypothesis that hydroxychloroquine might be effective in preventing SARS-CoV-2 infection. doi = 10.1016/s2665-9913(20)30305-2 id = cord-310055-9qj8d2f7 author = Gerace, Elisabetta title = Cryptosporidium Infection: Epidemiology, Pathogenesis, and Differential Diagnosis date = 2019-10-22 keywords = cryptosporidium; infection summary = Cryptosporidiosis is a worldwide infection caused by the protozoan Cryptosporidium, a parasite that infects many species of vertebrates, including humans, causing acute gastroenteritis, abdominal pain, and diarrhea [1] . Cryptosporidiosis is transmitted primarily through the fecal-oral route, i.e., by ingesting viable oocysts of animal and/or human origin, emitted with feces that contaminated food or water [2, 3] . 9-10 μm in diameter), another coccidian protozoan parasite that infects the intestine of humans causing acute diarrhea, much attention should be given when evaluating stool samples since the oocysts of both parasites are autofluorescent and acid-fast ( Figure 2 ) [46, 47] . In addition to the above described methods, watery or mushy stools can be examined for the laboratory diagnosis of cryptosporidiosis using different techniques such as the enzyme-linked immunosorbent assay (ELISA) and immunochromatographic test, which have good sensitivity and specificity for detection of Cryptosporidium antigens [51] [52] [53] . doi = 10.1556/1886.2019.00019 id = cord-356040-qdpkidn8 author = Ghazawi, Feras M. title = Infection risk of dermatologic therapeutics during the COVID‐19 pandemic: an evidence‐based recalibration date = 2020-07-03 keywords = infection; patient; trial summary = Recommendations were made recently to limit or stop the use of oral and systemic immunotherapies for skin diseases due to potential risks to the patients during the current severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) COVID‐19 pandemic. We performed a literature review to approximate the risk of SARS‐CoV‐2 infection, including available data on the roles of relevant cytokines, cell subsets, and their mediators in eliciting an optimal immune response against respiratory viruses in murine gene deletion models and humans with congenital deficiencies were reviewed for viral infections risk and if possible coronaviruses specifically. A randomized, open-label, controlled trial for the efficacy and safety of Adalimumab Injection in the treatment of patients with severe novel coronavirus pneumonia (COVID-19) Rituximab for rheumatoid arthritis refractory to anti-tumor necrosis factor therapy: results of a multicenter, randomized, double-blind, placebo-controlled, phase III trial evaluating primary efficacy and safety at twenty-four weeks Efficacy and safety of apremilast, an oral phosphodiesterase 4 inhibitor, in patients with moderate-to-severe plaque psoriasis over 52 weeks: a phase III, randomized controlled trial (ESTEEM 2) doi = 10.1111/ijd.15028 id = cord-317198-mean7sj9 author = Giamberardin, Heloisa I.G. title = Clinical and epidemiological features of respiratory virus infections in preschool children over two consecutive influenza seasons in southern Brazil date = 2016-02-09 keywords = HRV; infection; virus summary = title: Clinical and epidemiological features of respiratory virus infections in preschool children over two consecutive influenza seasons in southern Brazil This study reports the results of a systematic screening for respiratory viruses in pediatric outpatients from an emergency department (ED) in southern Brazil during two consecutive influenza seasons. © 2016 Wiley Periodicals, Inc. Viral acute respiratory infections (ARIs) in pediatric outpatients represent a significant burden on emergency departments (EDs) and the patients'' families, mainly during influenza seasons, being associated with around 20% of all deaths in pre-school children worldwide, with 90% of these deaths due to pneumonia. This study reports, the results of a laboratory-based surveillance for respiratory viruses in preschool children who were treated in the ED of a pediatric referral hospital during two consecutive influenza seasons. doi = 10.1002/jmv.24477 id = cord-009193-244ii7e2 author = Giancane, Gabriella title = Opportunistic infections in immunosuppressed patients with juvenile idiopathic arthritis: analysis by the Pharmachild Safety Adjudication Committee date = 2020-04-07 keywords = JIA; Pharmachild; SAC; infection summary = BACKGROUND: To derive a list of opportunistic infections (OI) through the analysis of the juvenile idiopathic arthritis (JIA) patients in the Pharmachild registry by an independent Safety Adjudication Committee (SAC). With the advent of biologic disease-modifying antirheumatic drugs (DMARDs), in a chronic condition like juvenile idiopathic arthritis (JIA), regulatory authorities such as the Food and Drug Administration (FDA) and the European Medicines Agency (EMA) have demanded from pharmaceutical companies and clinical researchers to evaluate the long-term safety of drugs used in children enrolled in phase II-III clinical trials [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] . Primary objectives of the present study were to derive a consensus-based list of opportunistic pathogens for use in children with JIA and confirm its role in identifying OI through the evaluation of the infectious events reported in Pharmachild registry by an independent Safety Adjudication Committee (SAC). doi = 10.1186/s13075-020-02167-2 id = cord-276907-b855tj7x author = Giersing, Birgitte K. title = Report from the World Health Organization’s third Product Development for Vaccines Advisory Committee (PDVAC) meeting, Geneva, 8–10th June 2016 date = 2019-11-28 keywords = AMR; GBS; PDVAC; RSV; development; infection; vaccine summary = doi = 10.1016/j.vaccine.2016.10.090 id = cord-267115-6jqdi417 author = Giobbe, Giovanni Giuseppe title = SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date = 2020-06-24 keywords = CoV-2; Fig; PCW; RNA; SARS; infection summary = doi = 10.1101/2020.06.24.167049 id = cord-349647-cfjrwt44 author = Girkin, Jason title = Chapter 8 In vivo experimental models of infection and disease date = 2019-12-31 keywords = AHR; COPD; IFN; exacerbation; experimental; infection summary = However, the recognition that RV infection is associated with more severe clinical manifestations in people with chronic lung diseases such as asthma and COPD provided a new impetus to research and a new direction to human experimental infection studies. 166 These studies extend the use of RV infection in mice to new areas, including mechanisms of early life infection susceptibility, to mechanisms of secondary bacterial infection/compromised antimicrobial immunity and experimental exploration of clinical risk factors associated with increased likelihood to develop virus-induced exacerbations of respiratory diseases. 190 In the same elastase-induced model, fluticasone proprionate treatment reduced IFN responses, increased viral load, suppressed airway immune cell numbers (lymphocytes and neutrophils), suppressed inflammatory cytokines (IL-6, TNFα), and increased mucus production, following RV-A1 exacerbation. Human experimental RV challenge studies have shed light on the biology of RV infection and the mechanisms associated with RV-induced exacerbations of chronic respiratory diseases. doi = 10.1016/b978-0-12-816417-4.00008-1 id = cord-009967-fyqc5bat author = Gleckman, Richard title = Cost‐Effective Antibiotic Prescribing date = 2012-01-24 keywords = antibiotic; infection; patient; therapy; treatment summary = Recent studies have confirmed the efficacy and reduced expense of oral antibiotics prescribed for selected children with osteomyelitis and septic arthritis.1"22 In 1973, it was reported that favorable results ensued when oral antibiotic therapy was prescribed for hospitalized patients with serious infectionsz3 Fourteen patients with osteomyelitis were treated successfully with oral cephalexin after they had received a short course of parenteral cephaloridine. Adults with disseminated gonococcal infection can be effectively treated with a one week program consisting initially of 2 million units of penicillin G administered every 4 hours followed by oral ampicillin or amoxicillin prescribed as 500 mg four times daily.34,35 Hospitalization is usually recommended to establish the diagnosis of disseminated gonococcal disease since misdiagnosis occurs not infrequently with this disorder.33 Selected patients can complete the oral regimens in an outpatient setting or, alternatively, they can be treated entirely without ho~pitalization.~~ Acceptable oral regimens consist of giving amoxicillin (500 mg four times daily), tetracycline (500 mg four times daily), or erythromycin (500 mg four times daily) for at least 7 days. doi = 10.1002/j.1875-9114.1983.tb03264.x id = cord-273019-hbpfz8rt author = Glingston, R. Sahaya title = Organelle dynamics and viral infections: at cross roads date = 2018-06-25 keywords = RNA; cell; infection; protein; viral; virus summary = doi = 10.1016/j.micinf.2018.06.002 id = cord-275997-4ibeidyw author = Goldrick, Barbara A. title = The practice of infection control and applied epidemiology: A historical perspective date = 2005-10-31 keywords = Control; Infection summary = doi = 10.1016/j.ajic.2005.04.250 id = cord-006586-49btg9w7 author = Golfieri, R. title = Pulmonary complications of liver transplantation: radiological appearance and statistical evaluation of risk factors in 300 cases date = 2000 keywords = CMV; OLT; infection; pulmonary summary = doi = 10.1007/s003309900268 id = cord-009577-29u7pdpk author = Gonzalez‐Scarano, F. title = Molecular pathogenesis of neurotropic viral infections date = 2004-10-08 keywords = CNS; cell; infection; viral; virus summary = To cause systemic illness, a virus must first enter the host animal, undergo primary replication at a site near its portal of entry, and then ultimately spread to distant target tissues, such as the central nervous system (CNS). An infecting animal virus faces two main blocks to penetration of the CNS or any other specific target organ: (1) a variety of barriers prevent the free access of viruses to target cells, and (2) even when these barriers are ineffective, only certain cell types will support the internalization and replication of a particular virus. Monoclonal antibody variants have been used to map the antigenic sites of the influenza hemagglutinin 122, 76, 771 and have been used successfully to define important regions of the cellular binding proteins of rabies virus, reovirus, coronaviruses, and the California serogroup-all CNS pathogens. Viruses bind to the plasma membrane of susceptible target cells through specific receptors which may be proteins (HIV), lipids (vesicular stomatitis virus), or contain sialic acid (reovirus, influenza) [21, 641. doi = 10.1002/ana.410220502 id = cord-322899-uxvlagt3 author = Gorji, Ali title = The potential roles of micronutrient deficiency and immune system dysfunction in COVID-19 pandemic date = 2020-11-06 keywords = COVID-19; immune; infection; vitamin summary = Micronutrients play a critical role in the coordinated recruitment of innate and adaptive immune responses to viral infections, particularly in the regulation of pro-and anti-inflammatory host responses. [16] Zinc deficiency is associated with impaired immune responses and leads to a higher risk of respiratory viral infections, particularly in elderly subjects. [61] The beneficial effects of vitamin A on morbidity and mortality of some viral infections, such as measles and HIV, could be due to increased antibody production and lymphocyte proliferation as well as enhanced T-cell lymphopoiesis. [102] A modest level of vitamin E supplementation regulates the cellular free radical-antioxidant balance, enhances the antibody response, and activates the immune cells of broilers vaccinated with the infectious bronchitis virus. Micronutrient deficiencies are associated with impaired immune response and higher burden of respiratory infections in elderly Ecuadorians doi = 10.1016/j.nut.2020.111047 id = cord-267947-dnv2xl0h author = Gornet, Jean-Marc title = What do surgeons need to know about the digestive disorders and paraclinical abnormalities induced by COVID-19? date = 2020-04-24 keywords = covid-19; digestive; infection; patient summary = doi = 10.1016/j.jviscsurg.2020.04.017 id = cord-259823-ia1g5dt4 author = Gowin, Ewelina title = Assessment of the Usefulness of Multiplex Real-Time PCR Tests in the Diagnostic and Therapeutic Process of Pneumonia in Hospitalized Children: A Single-Center Experience date = 2017-01-15 keywords = PCR; child; infection summary = doi = 10.1155/2017/8037963 id = cord-259422-5ex12eun author = Graat, Judith M title = A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection date = 2003-12-11 keywords = PCR; infection; respiratory summary = doi = 10.1016/s0895-4356(03)00171-9 id = cord-332533-iqe6sdq2 author = Grant, William B. title = Evidence that Vitamin D Supplementation Could Reduce Risk of Influenza and COVID-19 Infections and Deaths date = 2020-04-02 keywords = concentration; infection; risk; vitamin summary = Evidence supporting the role of vitamin D in reducing risk of COVID-19 includes that the outbreak occurred in winter, a time when 25-hydroxyvitamin D (25(OH)D) concentrations are lowest; that the number of cases in the Southern Hemisphere near the end of summer are low; that vitamin D deficiency has been found to contribute to acute respiratory distress syndrome; and that case-fatality rates increase with age and with chronic disease comorbidity, both of which are associated with lower 25(OH)D concentration. For COPD patients, 25(OH)D inversely correlated with risk, severity, and exacerbation [88] Found at higher rates in regions with elevated air pollution Air pollution associated with lower 25(OH)D concentrations [89] Note: 25-hydroxyvitamin D ((25(OH)D); acute respiratory distress syndrome (ARDS); community-acquired pneumonia (CAP); case-fatality rate (CFR); interleukin 6 (IL-6); chronic obstructive pulmonary disease (COPD); C-reactive protein (CRP); vitamin D deficiency (VDD). doi = 10.3390/nu12040988 id = cord-295746-6e6itj3y author = Gu, Young E. title = Characteristics of human parainfluenza virus type 4 infection in hospitalized children in Korea date = 2020-01-19 keywords = infection summary = doi = 10.1111/ped.14049 id = cord-273973-3uxg97tu author = Guenette, Alexis title = Infectious Complications Following Solid Organ Transplantation date = 2019-01-31 keywords = SOT; clinical; infection; recipient; transplant summary = doi = 10.1016/j.ccc.2018.08.004 id = cord-028564-sltofaox author = Gutiérrez-Spillari, Lucia title = Obesity, Cardiovascular Disease, and Influenza: How Are They Connected? date = 2020-07-06 keywords = infection; influenza; risk summary = RECENT FINDINGS: This infection could have detrimental outcomes in obese patients with cardiovascular diseases, such as an increased risk, length of hospitalization, disease severity, morbidity, and mortality. Its low-grade chronic inflammatoryinduced state negatively impacts immune function and host defense [2] , as shown during the 2009 influenza A virus H1N1 pandemic, where obesity resulted to be an independent risk factor for severe disease, hospitalization, mechanical ventilation, and mortality upon infection [1] . It is well studied that obese patients can develop cardiovascular diseases; however, it is less known that the lowinflammatory chronic state might affect host defense and immune cell dysfunction and infections, such as influenza A, could have detrimental outcomes in such patients, such as an increased risk, length of hospitalization, disease severity, morbidity, and mortality. Cardiovascular complications associated with influenza infection include myocarditis, pericardial effusion, myopericarditis, right and left ventricle dysfunction, myocardial infarction, heart failure, stroke, and circulatory failure due to septic shock. doi = 10.1007/s40475-020-00207-0 id = cord-312803-fxuynxjd author = Gómez-Ríos, Manuel Ángel title = Preventing Infection of Patients and Healthcare Workers Should Be the New Normal in the Era of Novel Coronavirus Epidemics: Comment date = 2020-06-16 keywords = infection summary = title: Preventing Infection of Patients and Healthcare Workers Should Be the New Normal in the Era of Novel Coronavirus Epidemics: Comment Unfortunately, it has taken a coronavirus to reveal the extent of these shortcomings, and it comes as no surprise that 12,300 Spanish health professionals have so far been infected, with 2,000 infections registered today. There are two reasons for this: (1) personal protective equipment, which was scarce even at the start of the outbreak, is now entirely lacking, and (2) symptomatic healthcare workers cannot be polymerase chain reaction-tested, so the authorities have to allow them to continue working. At the start of the outbreak, hospital departments went to great lengths to draw up local protocols to ensure the highest quality of care for patients with coronavirus disease 2019 (COVID-19) . Expert recommendations for tracheal intubation in critically ill patients with novel coronavirus disease 2019 doi = 10.1097/aln.0000000000003373 id = cord-021552-6jbm869r author = HURST, CHRISTON J. title = Relationship Between Humans and Their Viruses date = 2007-05-09 keywords = host; human; infection; virus summary = Viral replication ~ at the individual host level, the primary tissue and organ tropisms are toward the cervix, conjunctiva, pharynx, small intestine, and urethra; the secondary tissue and organ tropisms are toward the brain, kidney, lungs, and lymph nodes; at the host population level, these viruses generally are endemic and initially acquired at a very early age, with the infections very often asymptomatic in young children. ~ral replication ~ at the individual host level, primary tissue and organ tropisms are toward the small intestine; secondary tissue and organ tropisms are toward the liver; at the host population level, these tend to be epidemic within human populations; for the hepatitis E virus it seems that acquisition occurs from swine, with the result being epidemics (often very widespread) of human disease; some acquisition from animals may come from eating infected animals; subsequent transmission of all caliciviruses within human populations is by fecally contaminated waste and thus can be very widespread. Alternate hosts: One species of viral family Hepadnaviridae (hepatitis B virus) is known to infect humans, and it seems naturally limited to humans. doi = 10.1016/b978-012362675-2/50015-x id = cord-016572-6fu5s89c author = Hage, Chadi A. title = Endemic mycosis date = 2005 keywords = AIDS; PDH; histoplasmosis; infection; patient summary = All three illnesses occur in normal hosts, although histoplasmosis and coccidioidomycosis are also major opportunistic mycoses in patients with depressed cell-mediated immunity, and especially in patients with acquired immunodeficiency syndrome (AIDS) [4] , [5] . Histoplasmosis, blastomycosis and coccidioidomycosis are major T-cell opportunistic infections, as demonstrated by the very aggressive course seen in patients with AIDS, in whom T-cell deficiency is most severe. The most severe form of progressive disseminated histoplasmosis (PDH) occurs in patients with AIDS with profound T-cell dysfunction [21] . By that time, most patients have either recovered or have required other more invasive methods of diagnosis because of rapidly worsening disease There are two ways to make a rapid diagnosis of PDH, sampling and examination of likely infected tissue with the use of special stains and the use of the ultrasensitive assay for fungal antigens. doi = 10.1007/0-387-23380-6_12 id = cord-253761-wjm8ju3v author = Haidopoulou, Katerina title = Human bocavirus infections in hospitalized Greek children date = 2010-03-09 keywords = infection; respiratory summary = To define the epidemiological profile and the clinical characteristics associated with HBoV infection in a population of children hospitalized with respiratory tract infection. MATERIAL AND METHODS: During a one-year period throat swab samples were collected from 370 previously healthy children, aged 14 days to 13 years, admitted to two different paediatric wards because of respiratory tract infection. The aim of the present study was to define the epidemiological profile and the clinical characteristics associated with HBoV in hospitalized children with respiratory tract infection (RTI) in Greece. One may argue that the fact that HBoV is prevalent in samples from patients with respiratory tract infection does not guarantee a causative role for the symptoms, especially when -as in this case -it is frequently detected in combination with other respiratory viruses of known pathogenic potential. Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus doi = 10.5114/aoms.2010.13515 id = cord-312797-hohzjx74 author = Hamelin, Marie-Ève title = Human Metapneumovirus: A New Player among Respiratory Viruses date = 2004-04-01 keywords = hmpv; infection; respiratory summary = Despite the fact that prospective and case-control studies have been limited, the epidemiology and clinical manifestations associated with hMPV have been found to be reminiscent of those of the human respiratory syncytial virus, with most severe respiratory tract infections occurring in infants, elderly subjects, and immunocompromised hosts. In addition, studies have shown that hMPV is not a new pathogen, with serological evidence of human infection dating from 1958 in The Netherlands [4] and viral isolation for the past 10-20 years in Europe and Canada [4, 7] . Symptoms of both upper and lower respiratory tract infections have been associated with hMPV in young children, although most reports are biased towards description of the most severe symptomatology in hospitalized subjects. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups doi = 10.1086/382536 id = cord-023698-wvk200j0 author = Hammerschlag, Margaret R. title = Chlamydia pneumoniae date = 2014-10-31 keywords = Chlamydia; PCR; dna; infection; pneumoniae summary = Because the organism has been difficult to grow and because of the lack of a commercially available other diagnostic assay, most original associations with respiratory diseases have been use of serology with the microimmunofluorescence (MIF) test. 38, 39 For an example of the complexity of this issue, consider that two multicenter pneumonia treatment studies in children showed that although 7% to 13% of the patients in the study had positive culture results and 7% to 18% met the serologic criteria with the MIF test for acute infection, they were not the same patients. pneumoniae infection is that the MIF method used to detect serum antibodies is not standardized; recent studies have shown substantial interlaboratory variation in the performance of these tests. Multicenter comparison trial of DNA extraction methods and PCR assays for detection of Chlamydia pneumoniae in endarterectomy specimens Multicenter comparison trial of DNA extraction methods and PCR assays for detection of Chlamydia pneumoniae in endarterectomy specimens doi = 10.1016/b978-1-4557-4801-3.00184-3 id = cord-289650-q2io8vgi author = Hammond, Ffion R. title = If it’s not one thing, HIF’s another: immunoregulation by hypoxia inducible factors in disease date = 2020-07-06 keywords = HIF; HIF-1α; hypoxia; infection summary = Hypoxia Inducible Factors (HIFs) are master transcriptional regulators of the cellular response to hypoxia, that have influential roles in innate immune cell behaviour during inflammation and infections [1] . All rights reserved HIF researchers were awarded the Nobel Prize in Physiology or Medicine in 2019 for their discoveries on the regulation of the cellular hypoxia response, with their medical research predominantly focusing on HIFs'' potential role as a therapeutic target to combat anaemia, due to HIF''s activating effect on red blood cell production [8] . During infection and inflammation, HIF-α is stabilised in immune cell populations, partially driven by the hypoxic tissue context of disease, alongside oxygen independent activation [10]. Promoting HIF-1α stabilisation with the hydroxylase inhibitor CoCl 2 promoted fungal death in vitro (human macrophages) and in vivo (mouse) indicating a therapeutic potential for HIF-1α manipulation in candida infection [55] . doi = 10.1111/febs.15476 id = cord-018651-phb44k66 author = Hammoud, Dima A. title = Neuroimaging date = 2017-05-26 keywords = TSPO; imaging; infection summary = A common approach is the use of recombinant viruses engineered to express a luciferase enzyme which allows performing longitudinal imaging, accurately determining the site(s) of infection, describing the temporal systemic dissemination of the virus, and eventually quantifying viral titers in various organs. More recent examples include the use of recombinant murine gammaherpesvirus 68 (MHV-68) expressing the firefly luciferase (Fluc) to monitor virus progression after CNS infection [11] and of recombinant Dengue virus, for realtime evaluation of replication kinetics in the brain of infected mice [12] . Other examples of reporter gene use include imaging of Toxoplasma gondii encephalitis with spatiotemporal demonstration of recrudescence of the infection from the CNS of immunocompromised mice [15] . More complex models such as the transgenic reporter mouse strain that expresses Fluc under the regulatory control of a concatenated Gal4 promoter [18] and the transgenic reporter mouse in which luciferase expression is driven by the nuclear factor B (NF-B)-dependent portion of the human immunodeficiency virus-1 long terminal repeat (HIV-1 LTR) [19] allowed the visualization of brain luciferase expression in response to adenovirus infection [18] and LPS intraperitoneal injection [19] , respectively. doi = 10.1007/978-3-319-54592-9_8 id = cord-286337-qk90xb3a author = Hanada, Shigeo title = Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia date = 2018-11-16 keywords = URT; bacterial; infection; respiratory; viral summary = While the effects of these alterations on risk of secondary bacterial pneumonia have not been studied, potential mechanisms by which these changes might modulate susceptibility to secondary bacterial infections include alterations in the nature and magnitude of the immune response in the host (microbiome on host effects) and facilitating growth of pathogens in the absence of normal commensals (inter-microbial effects). Given the effects of viruses on enhancing bacterial adherence to the epithelium (86) (87) (88) , it is perhaps not surprising that multiple studies of human subjects as well as in animal models have shown that viral infections are associated with increased colonization by potentially pathogenic bacteria (known as "pathobionts"). Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included; however, the authors suggested that flu is associated with an expansion of Proteobacteria (109) which is generally less abundant in healthy hosts. doi = 10.3389/fimmu.2018.02640 id = cord-007417-az8xd66p author = Hansbro, Nicole G. title = Understanding the mechanisms of viral induced asthma: New therapeutic directions date = 2008-01-29 keywords = AHR; CD8; IFN; RSV; infection; respiratory; th2; virus summary = Whether an infection induces disease depends on viral (type (E.g. RSV, RV)), host (genetic susceptibility, age, immune responses) and environmental (allergen exposure, season) factors. With respect to allergy RSV infection might only trigger defective immunity in genetically susceptible individuals or that allergic inflammatory and immune responses may promote the influx of virus-specific cells into the airways increasing inflammation and AHR (Schwarze et al., 1999c) . Nevertheless most studies suggest that Th1 responses may result in viral clearance and mild symptoms whereas an aberrant bias towards a Th2 phenotype may lead to more intense RSV-induced disease and promote the development of asthma . Animal models have been used to determine if RSV can induce the development of asthma by triggering pro-asthmatic immune responses that lead to variable airflow obstruction and airway inflammation. Further studies are required to elucidate the links between infection, immune responses and susceptibility to chronic respiratory diseases and why some individuals but not others develop persistent wheeze and asthma. doi = 10.1016/j.pharmthera.2007.11.002 id = cord-318063-bainw3d6 author = Haque, Mainul title = Health care-associated infections – an overview date = 2018-11-15 keywords = Health; Healthcare; hcai; infection; patient; study summary = Several studies suggest that simple infection-control procedures such as cleaning hands with an alcohol-based hand rub can help prevent HCAIs and save lives, reduce morbidity, and minimize health care costs. Health care-associated infections and prevention strategy About 68.6% of all bacterial isolates were resistant to cefuroxime used in the management of orthopedic SSIs. This study also found that diabetes mellitus, smoking, operations lasting more than 3 hours, the absence of antibiotic prophylaxis, and a history of previous surgery were positive risk factors associated with a significant upsurge in SSIs. 87 SSIs comprise at least 14%-22.2% of all HCAIs for abdominal surgery [88] [89] [90] and often lead to extended hospitalization and higher antimicrobial costs. Prevalence, incidence burden, and clinical impact of healthcare-associated infections and antimicrobial resistance: a national prevalent cohort study in acute care hospitals in Greece doi = 10.2147/idr.s177247 id = cord-251991-ghbpga1s author = Harcourt, Jennifer L. title = Evaluation of the Calu-3 cell line as a model of in vitro respiratory syncytial virus infection() date = 2011-03-31 keywords = Calu-3; RSV; infection summary = Respiratory syncytial virus (RSV) replication is primarily limited to the upper respiratory tract epithelium and primary, differentiated normal human bronchial epithelial cells (NHBE) have, therefore, been considered a good system for in vitro analysis of lung tissue response to respiratory virus infection and virus–host interactions. Polarized Calu-3 are susceptible to RSV infection and release infectious virus primarily from the apical surface, consistent with studies in NHBE cells. The mechanisms of cellular responses to RSV infection have been studied extensively in vitro in a variety of immortalized epithelial cell lines grown in monolayer cultures, including but not limited to Vero, Hep-2, A549, and ଝ The findings and conclusions in this report are those of the author(s) and do not necessarily represent the views of CDC. Consistent with previous studies in polarized MDCK (Roberts et al., 1995) and in differentiated NHBE, polarized Calu-3 released infectious virus primarily from the apical surface, and infection was persistent, detectable for at least 6 weeks post-infection. doi = 10.1016/j.jviromet.2011.03.027 id = cord-272052-8vvpm4tx author = Hartmann, Katrin title = Clinical aspects of feline immunodeficiency and feline leukemia virus infection date = 2011-10-15 keywords = FIV; cat; feline; infection; virus summary = doi = 10.1016/j.vetimm.2011.06.003 id = cord-343690-rafvxgx1 author = Hartmann, Katrin title = Clinical Aspects of Feline Retroviruses: A Review date = 2012-10-31 keywords = FeLV; cat; feline; fiv; infection; virus summary = Although FIV can cause an acquired immunodeficiency syndrome in cats ("feline AIDS") comparable to human immunodeficiency virus (HIV) infection in humans, with increased risk for opportunistic infections, neurologic diseases, and tumors, in most naturally infected cats, FIV does not cause a severe clinical syndrome. Experimental FIV infection also progresses through several stages, similar to HIV infection in people, including an acute phase, a clinically asymptomatic phase of variable duration, and a terminal phase sometimes called "feline acquired immunodeficiency syndrome" ("AIDS") [18, 19] . Of 8642 FeLV-infected cats presented to North American Veterinary Teaching Hospitals, various co-infections (including FIV infection, feline infectious peritonitis (FIP), upper respiratory infection, hemotropic mycoplasmosis, and stomatitis) were the most frequent findings (15%), followed by anemia (11%), lymphoma (6%), leukopenia or thrombocytopenia (5%), and leukemia or myeloproliferative diseases (4%) [20] . An early defect in primary and secondary t cell responses in asymptomatic cats during acute feline immunodeficiency virus (fiv) infection doi = 10.3390/v4112684 id = cord-277313-5f5lrn3c author = Hayakawa, Satoshi title = Covid‐19 pandemic and pregnancy date = 2020-08-10 keywords = COVID-19; China; SARS; infection summary = doi = 10.1111/jog.14384 id = cord-342915-r9kv67we author = Hayden, Frederick G. title = Advances in antivirals for non‐influenza respiratory virus infections date = 2013-11-01 keywords = RSV; SARS; infection; respiratory; virus summary = Most of the treatment data regarding antivirals for non-influenza respiratory viruses have been derived from observational studies in immunocompromised hosts, and sometimes, infants, but recent randomized, controlled trials in specific target populations have helped to address the potential value of antiviral interventions. 12, [17] [18] [19] In addition, systematic reviews of the observational reports concluded that the common use of multiple agents in combination, varying dose regimens, paucity of studies with systematic data collection, complications from immunosuppressive therapy, and the lack of randomized, controlled trials meant that existing data were inconclusive with regard to putative antivirals and thus inadequate to determine appropriate management of SARS infections. In addition, one approved agent for selected parasitic infections, oral nitazoxanide, may have interferon-inducing properties, is inhibitory for various respiratory viruses including influenza and a canine CoV in vitro, 32 and has shown promising dose-related activity in a phase 2, placebo-controlled, randomized trial in treating uncomplicated influenza 33 Consequently, nitazoxanide would be an interesting agent to test alone and in combination with other antivirals for CoV infections. doi = 10.1111/irv.12173 id = cord-267531-tqqj4cy0 author = He, Ying title = A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China date = 2014-05-14 keywords = IAV; RSV; infection summary = title: A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China OBJECTIVES: To determine the viral etiology and seasonality of acute respiratory infections in hospitalized children, a 3-year study was conducted in Shenzhen, China. 3, 4 The most frequently reported viruses include respiratory syncytial virus (RSV), influenza viruses A and B (IAV, IBV), parainfluenza viruses (PIVs), human rhinovirus (HRV) and adenovirus (ADV), which are responsible for most episodes of ARTIs in children. The purpose of this study is to investigate the prevalence, seasonality and clinical characteristics of acute viral respiratory infections in hospitalized children in Shenzhen and to provide insights into etiologies of ARTIs in local infants and children. Most studies showed that RSV or HRV was the most prevalent viruses in children with viral respiratory tract infection. 9 In this study, due to the high detection rate and similar seasonality of RSV, HRV, IAV, PIV and HMPV, an overall spring-summer seasonality of viral respiratory infections in children was concluded. doi = 10.1111/irv.12257 id = cord-006261-yw5k8qkz author = Heath, Gregory W. title = Exercise and Upper Respiratory Tract Infections: Is There a Relationship? date = 2012-10-23 keywords = exercise; infection; respiratory; tract summary = Few studies have investigated the common belief that moderate physical activity is beneficial in decreasing risk of respiratory tract infections and improving immune function. Laboratory and clinical studies suggest that changes in immune parameters associated with heavy train ing lead to adverse health effects, particularly an increase in the incidence or severity of upper respiratory tract infections. During this time, the women in the exercise group experienced fewer upper respiratory tract infection symptom days, improved cardiorespiratory fitness, and increased natural killer cell numbers compared with their sedentary controls. This study indicates that intensity of exercise may playa role, and that moderate activity may actually improve immune function and associated upper respiratory tract infection symptoms. Clinical studies examining the effects of moderate levels of physical activity have shown possible enhanced immune responses with a concomitant impact on the length and severity of an upper respiratory tract infection. The effects of moderate exercise training on natural killer cells and acute upper respiratory tract infections doi = 10.2165/00007256-199214060-00003 id = cord-021571-7kbq0v9w author = Heath, Joan A. title = Infections Acquired in the Nursery: Epidemiology and Control date = 2009-05-19 keywords = CDC; Control; NICU; care; hand; infant; infection; neonatal; nosocomial; outbreak; patient summary = The fact that a hand hygiene campaign was associated with increased hand hygiene compliance and a lower rate of CONS-positive cultures supports this ~ontention.''~ Enterococcus has been shown to account for 10% of total nosocomial infections in neonates, 6% to 15% of bloodstream infections, 0% to 5% of cases of pneumonia, 17% of urinary tract infections, and 9% of surgical site Sepsis and meningitis are common manifestations of enterococcal infection during NICU outbreak^''^,^^; however, polymicrobial bacteremia and NEC frequently accompany enterococcal sepsis.77 Identified risk factors for enterococcal sepsis, after adjustment for birth weight, include use of a nonumbilical CVC, prolonged presence of a CVC, and bowel resection?'' Because Enterococcus colonizes the gastrointestinal tract and can survive for long periods of time on inanimate surfaces, the patient''s environment may become contaminated and, along with the infant, serve as a reservoir for ongoing spread of the organism. doi = 10.1016/b0-72-160537-0/50037-2 id = cord-006129-5rog0s98 author = Hemida, Maged Gomaa title = Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date = 2012-08-16 keywords = HCV; RNA; infection; viral; virus summary = [12] Answering back, certain host miRNAs alter the cell gene expression to defend the cells against the viral infection by interfering with viral proteins or other cellular factors as a type of immune response against these particular viruses. [40] These virus-encoded miRNAs play important roles in the establishment of latent infection, as well as the pathogenesis of virally induced diseases. According to the most recent studies, herpesviruses utilize their encoded miRNAs in a wide range of biologic functions, such as inhibition of apoptosis, immune evasion, control of cellular proliferation, and regulation of viral replication. [58] Downregulation of UL114 protein, using miR-UL112-1, results in inhibition of viral DNA replication and subsequently triggers the latent phase of infection, making the virus able to evade the host immune system. doi = 10.1007/bf03256383 id = cord-017030-tzuyo6tx author = Henao-Martínez, Andrés F. title = Infections in Heart, Lung, and Heart-Lung Transplantation date = 2018-12-08 keywords = CMV; aspergillus; heart; infection; lung; recipient; transplant; transplantation summary = There are several factors predisposing thoracic transplant recipients to infections: (A) factors present before transplantation: age, presence of comorbidities (e.g., chronic kidney disease, diabetes mellitus, cancer, etc.), nutrition status, latent infections, colonization with healthcare-associated organisms, and occult community-acquired infections; (B) factors during the surgery: duration of the transplant procedure, graft injury including ischemic time, colonization or latent infection of the graft, surgical instrumentation (e.g., mechanical ventilation, invasive devices such as catheters, drains, Foley catheters, etc.), ICU stay, and need for re-interventions; and (C) factors present after transplant: degree of immunosuppression, CMV infection, and rejections ( Mechanical ventilation (MV) for >5 days immediately following transplant surgery and isolation of Staphylococcus aureus (SA) from airway cultures in the recipient were considered risk factors for invasive SA infections in a retrospective study of patients with lung and heart-lung transplants [20] . doi = 10.1007/978-1-4939-9034-4_2 id = cord-267003-k7eo2c26 author = Hendaus, Mohamed A title = Virus-induced secondary bacterial infection: a concise review date = 2015-08-24 keywords = infection; respiratory; virus summary = 7 The human body is usually capable of eliminating respiratory viral infections with no sequelae; however, in some cases, viruses bypass the immune response of the airways, causing conceivable severe respiratory diseases. 49, 50 virus effect on the immune system Post-viral sustained desensitization of lung sentinel cells to TLR signals may be one possible contributor to the common secondary bacterial pneumonia associated with viral infection. Hendaus et al human-alveolar basal-epithelial cells) during a respiratory viral infection by increasing the expression of ICAM-1. It has been recommended that treatment or prevention of a viral disease may be a superior method for diminishing 62 It has also been published that live attenuated influenza vaccine is effective in reducing the incidence of all-cause AOM [86] [87] [88] and pneumonia 89 compared to placebo in children. Effects of rhinovirus infection on the adherence of Streptococcus pneumoniae to cultured human airway epithelial cells doi = 10.2147/tcrm.s87789 id = cord-298181-ypgb7uuc author = Hendaus, Mohamed A title = Why Are Children With Bronchiolitis At Risk Of Urinary Tract Infections? date = 2019-11-14 keywords = UTI; infection summary = 3 Several published studies have shown an association between acute bronchiolitis and secondary bacterial infection, including urinary tract infections (UTI). 3 Several published studies have shown an association between acute bronchiolitis and secondary bacterial infection, including urinary tract infections (UTI). Hendaus et al 8 studied the prevalence of urinary tract infection in infants and children with bronchiolitis. Multicenter RSV-SBI Study Group of the Pediatric Emergency Medicine Collaborative Research Committee of the American Academy of Pediatrics Risk of serious bacterial infection in young febrile infants with respiratory syncytial virus infections Concurrent serious bacterial infections in 2396 infants and children hospitalized with respiratory syncytial virus lower respiratory tract infections Prevalence of serious bacterial infections in febrile infants with respiratory syncytial virus infection A prospective study of the risk for serious bacterial infections in hospitalized febrile infants with or without bronchiolitis Testing for urinary tract infection in the influenza/respiratory syncytial virus-positive febrile infant aged 2 to 12 months doi = 10.2147/rmhp.s222470 id = cord-017012-yl0vanuh author = Herberg, Jethro title = Infectious Diseases and the Kidney date = 2009 keywords = BKV; CMV; HBV; HIV; HIVAN; acute; case; disease; infection; patient; renal summary = Renal involvement in infectious diseases may occur by a variety of mechanisms: direct microbial invasion of the renal tissues or collecting system may take place in conditions such as staphylococcal abscess of the kidney as a result of septicemic spread of the organism or as a consequence of ascending infection; damage to the kidney may be caused by the systemic release of endotoxin or other toxins and activation of the inflammatory cascade during septicemia or by a focus of infection distant from the kidney; ischemic damage may result from inadequate perfusion induced by septic shock; the kidney may be damaged by activation of the immunologic pathways or by immune complexes resulting from the infectious process. However, in addition to this post-infection immunologically mediated disorder, in recent years there have been increasing reports of GAS causing acute renal failure as part of an invasive infection with many features of the staphylococcal toxic shock syndrome (28) . doi = 10.1007/978-3-540-76341-3_52 id = cord-017393-kx8kmdej author = Herbers, Alexandra title = Acute Myelogenous Leukemia and Febrile Neutropenia date = 2009-08-31 keywords = antibiotic; fever; infection; neutropenic; patient; regimen; therapy; treatment summary = Despite numerous clinical studies, since the 1970s, no single empirical antibiotic regimen has been shown to be superior for initial treatment of patients who become febrile during a neutropenic episode after therapy with chemotherapy drugs for hematological malignancies (see Table 5 -2) [4, 9, [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] . Similarly, bacteremias due to Staphylococcus aureus, Pseudomonas aeruginosa, and Clostridium species as well as candidemias are more frequently encountered in patients with acute leukemia who suffer from neutropenic enterocolitis or typhlitis, the most serious disturbance of the delicate balance between mucosal damage and microbial flora in the setting of prolonged exposure to antibiotics after intermediate or high-dose cytarabine chemotherapy. In addition, if a persistently neutropenic patient has no complaints and displays no clinical, radiological, or laboratory evidence of infection, cessation of antibiotic therapy or a change to oral antimicrobials should be considered after 4 days without symptoms. doi = 10.1007/978-1-59745-415-5_5 id = cord-290674-1kdc6xk8 author = Hershenson, Marc B. title = Rhinovirus-Induced Exacerbations of Asthma and COPD date = 2013-02-21 keywords = COPD; airway; infection; rhinovirus summary = doi = 10.1155/2013/405876 id = cord-019100-rce6kyu4 author = Heymann, Peter W. title = VIRUS-INDUCED WHEEZING IN CHILDREN: Respiratory Syncytial Virus (RSV) and Rhinovirus date = 1998-02-01 keywords = RSV; infection; respiratory; rhinovirus summary = Use of the polymerase chain reaction (PCR) to measure viral nucleic acid material has provided the opportunity to study virus-induced wheezing among children in greater detail, and investigations of experimental rhinovirus infections in adults have demonstrated how this virus can augment both the early and late phase manifestations of airway hyperreactivity. When nasal washes from another study of children seen in the emergency room were tested using PCR techniques, rhinovirus was again the most common virus associated with wheezing after the age of 2.43 Once again, the combination of allergen-specific IgE antibody and viral infection increased the risk for wheezing (odds ratio = 16.4). doi = 10.1016/s0889-8561(05)70345-3 id = cord-005007-pofm8b5x author = Higgins, P. G. title = Interferons and viral infections date = 1984 keywords = infection; interferon summary = This has been shown to occur in some children who are abnormally susceptible to upper respiratory tract infections (2) and also in some instances of fulminating hepatitis, when giving exogenous interferon appears to activate the patient''s own interferon production (3). As interferon''s antiviral effect is mediated through the protection of non-infected cells and not by any direct action on the virus particle, interferon''s prophylactic effect will probably be greater than its therapeutic action. For example it is now known that there is a critical concentration of interferon and frequency of administration below which intranasal interferon fails to protect against experimental rhinovirus infection (26) and that the beneficial effect of interferon in zoster in patients with malignancies is directly related to the amount given (16, 27) . Effect of human leukocyte interferon on hepatitis B virus infection in patients with chxonic active hepatitis doi = 10.1007/bf01977473 id = cord-283792-g7wyu8pc author = Hiltunen, Raimo title = Preventing airborne infection with an intranasal cellulose powder formulation (Nasaleze Travel®) date = 2007 keywords = Nasaleze; infection summary = doi = 10.1007/bf02877720 id = cord-318826-l922zqci author = Holschbach, Chelsea L. title = Salmonella in Dairy Cattle date = 2018-03-31 keywords = Dublin; Salmonella; States; Typhimurium; United; dairy; infection summary = In large free stall dairies, it is increasingly common to encounter Salmonella infection as an endemic challenge with clinical presentations that are highly variable, ranging from the classic textbook description of reproductive losses and enteric disease in adult cattle through to lower impact problems with fevers of unknown origin, little to no diarrhea, and only modest consequences in terms of appetite and milk yield reduction. 29 Hence, if one is merely trying to obtain a yes or no answer or identify and track specific serovars, or antimicrobial susceptibility patterns over time, composite fecal samples are typically collected from areas on dairy operations where manure accumulates from a majority of adult animals, such as holding pens, alleyways, and lagoons. Prompt diagnosis, treatment, and isolation are important during an outbreak in adult cattle and environmental sampling to include bulk tank milk and high-risk housing areas should now be considered a routine part of disease prevention and surveillance. doi = 10.1016/j.cvfa.2017.10.005 id = cord-312438-zr9zx7pv author = Hoo, Regina title = Innate Immune Mechanisms to Protect Against Infection at the Human Decidual-Placental Interface date = 2020-09-10 keywords = IFN; SCT; cell; human; infection summary = Here, we outline the anatomy of the human placenta and uterine lining, the decidua, and discuss the potential capacity of pathogen pattern recognition and other host defense strategies present in the innate immune cells at the placental-decidual interface. Pathogen recognition is not only an essential component of the innate immune response against infection, but also plays an important role in bridging the innate and adaptive systems by Toll-like receptors (TLR) activation of antigen presenting cells by up-regulation of major histocompatibility complex (MHC) and co-stimulatory molecules (75) . Current evidence is only limited to in vitro TLR2/4 stimulation studies using placental explants and primary first trimester trophoblast cells, which drives the expression of FIGURE 3 | Toll-like receptors and potential inflammatory response at the decidua. In the mouse model of ZIKV infection, type I IFN-mediated signaling is essential for the control of viral replication in the placenta, but can also lead to significant placental pathology and fetal mortality (116, 117) . doi = 10.3389/fimmu.2020.02070 id = cord-004247-lagv3tp7 author = Hooft van Huijsduijnen, Rob title = Reassessing therapeutic antibodies for neglected and tropical diseases date = 2020-01-30 keywords = Cryptococcus; HIV; Pneumocystis; antibody; cell; infection summary = This mAb was protective in an in vitro, antigen-dependent, cellular cytotoxicity assay with rat macrophages or eosinophils and also in vivo during the early phase of infection Second, beyond the cell-surface proteins, schistosomes also express a large number of glycans as part of their glycoprotein and glycolipid repertoire, and an antibody response against those glycans is mounted by the infected host [80] . In addition to antibodies that directly target and inhibit the fungal pathogen, mAbs can be directed to checkpoints that control the host immune response. In addition to highlighting the potential of mAbs as therapeutics, these studies have demonstrated the diversity of inhibitory actions that mAbs can perform on cryptococcal cells, which can include opsonization and increased phagocytosis, inhibition of fungal growth, capsular polysaccharide release and biofilm formation, antibody-mediated target cleavage, and augmentation of the host response [104] [105] [106] [107] . doi = 10.1371/journal.pntd.0007860 id = cord-022399-66mzbynu author = Hopkins, Graham title = Basic microbiology date = 2009-05-15 keywords = bacteria; cause; cell; eye; infection; organism; virus summary = Bacteria are important because of their ubiquity -that is, their ability to infect and multiply in varied environments -and the ability of many types of bacteria to cause disease -their pathogenicity. To reduce problems caused by bacteria, it is important to understand something of their structure, growth, environmental and metabolic requirements, classification, relationship with disease and the particular problems they can cause to the eye. The result is that the cells tend to grow and divide at a slower rate but are more resistant to antibacterial chemicals, viruses (bacteriophages), phagocytes and other adverse agents. As causative organisms of disease, fungi are less important than bacteria and viruses. • Sterilization: the killing or removal of all viable organisms (including bacterial spores) from an object or pharmaceutical product by the use of chemical or physical agents. Developments have led to the introduction of agents that are more effective against the infecting organism and less toxic to the host. doi = 10.1016/b978-0-7506-8864-2.50005-2 id = cord-298905-c2uuvfm5 author = Horzinek, M. C. title = Molecular pathogenesis of virus infections date = 1987 keywords = RNA; cell; infection; virus summary = Using coronaviruses as examples the changes in virulence have been traced back to single mutational events; recombination, however, is likely to be an alternative mechanism by which virus-host interactions (e.g. the cell-, organor animal species-spectrum) can dramatically change. Parainfluenzaviruses, for example, attach to neuraminic acid-containing receptors; since glycolipids and glycoproteins containing neuraminic acid abound in vertebrate cell membranes the adsorption/penetration process lacks the specificity required to explain the restrictions in host range and tissue tropism of paramyxoviruses 29. Also in influenza virus infection cap structures are essential: these are cannibalized from host cell nuclear RNA precursor molecules and used as primers for viral RNA replication and synthesis 28. Autoimmune phenomena involving both the humoral and cellular limbs of the immune response have been identified in neurological conditions following infections with e.g. canine distemper virus3; invasion of brain tissue is supposed to cause changes in the molecular constitution of myelin and membrane components, making them recognizable as ''nonself''. doi = 10.1007/bf01945522 id = cord-279864-5ouuu49v author = Hou, Jing title = Children’s Respiratory Infections in Tianjin Area, China: Associations with Home Environments and Lifestyles date = 2020-06-07 keywords = China; Tianjin; infection summary = doi = 10.3390/ijerph17114069 id = cord-248301-hddxaatp author = Howard, Daniel title = Genetic Programming visitation scheduling solution can deliver a less austere COVID-19 pandemic population lockdown date = 2020-06-17 keywords = infection; number summary = A number of alternatives for this computation are presented and results of numerical experiments involving over 230 people of various ages and background health levels in over 1700 visits that take place over three consecutive days. A novel partial infection model is introduced to discuss these proof of concept solutions which are compared to round robin uninformed time scheduling for visits to places. A method of optimization, in this proof of concept this is a Genetic Programming [7] method, takes these requests and simulates the outings by means of an infection model, to discover a nearly optimal allocation of precise time slots for visits that reduce the likely hospitalization and death numbers. doi = nan id = cord-292521-tpb12dkq author = Howard, John title = Widely Disseminated Cryptococcosis Manifesting in a Previously Undiagnosed Human Immunodeficiency Virus (HIV)-Positive 18-Year-Old date = 2020-10-12 keywords = CD4; HIV; infection summary = doi = 10.12659/ajcr.924410 id = cord-286368-kdwh4hgf author = Hui, David S.C. title = A clinical approach to the threat of emerging influenza viruses in the Asia‐Pacific region date = 2017-07-05 keywords = A(H5N1; A(H7N9; China; human; infection; influenza summary = Observational studies have shown that treatment with a neuraminidase inhibitor (NAI) for adults hospitalized with severe influenza is associated with lower mortality and better clinical outcomes, especially when administered early in the course of illness. The global circulation of oseltamivir-resistant seasonal influenza, the emergence of A(H1N1)pdm09 virus in 2009 followed by its continual circulation, 6 the rising number of A(H7N9) infections in humans 2 and the ongoing spread of A(H5N8) in recent months in the poultry populations in many countries in Asia, Africa, Europe and Middle East with pandemic potential 7 all point to an urgent need for developing more effective antiviral therapies to reduce morbidity and mortality. Human infections with a novel avian influenza A (H7N9) virus were first reported in China in March 2013 in patients hospitalized with severe pneumonia. doi = 10.1111/resp.13114 id = cord-016127-tbot0fc9 author = Hurtado, F. J. title = Sepsis: Clinical Approach, Evidence-Based at the Bedside date = 2009-11-19 keywords = infection; patient; sepsis; septic summary = Since 2002 the Surviving Sepsis Campaign was introduced with the initial goal of increasing clinicians'' awareness about severe sepsis mortality and to improve outcome in this patient population. Despite the fact that most of these recommendations were not supported by high levels of evidence, they represented the international consensus on the best available standards of care for the management of sepsis. Mortality increases according to the presence of shock, and metabolic markers like arterial lactate are useful to characterize disease severity and the response to treatment [8] . The current management of severe sepsis and septic shock aims to control infection, achieve hemodynamic stabilization, modulate the immune response, and provide metabolic and organ support. The SSC is a global initiative that involves several international organizations with the common objective of elaborating evidence-based guidelines and recommendations for the management of severe sepsis and septic shock. Early goal-directed therapy in the treatment of severe sepsis and septic shock doi = 10.1007/978-88-470-1436-7_25 id = cord-285270-amh99u0j author = Husain, Shahid title = A 2010 working formulation for the standardization of definitions of infections in cardiothoracic transplant recipients date = 2011-03-17 keywords = CTTX; infection; lung; transplant summary = doi = 10.1016/j.healun.2011.01.701 id = cord-296567-six7u615 author = Hussain, Akhtar title = Clinical considerations for patients with diabetes in times of COVID-19 epidemic date = 2020-04-10 keywords = COVID-19; infection summary = doi = 10.1016/j.dsx.2020.04.002 id = cord-346836-6jyv0q5e author = Ikegami, Tetsuro title = The Pathogenesis of Rift Valley Fever date = 2011-05-06 keywords = IFN; RVFV; Rift; day; fever; infection; valley; virus summary = RVFV infection in humans usually causes a self-limiting, acute and febrile illness; however, a small number of cases progress to neurological disorders, partial or complete blindness, hemorrhagic fever, or thrombosis. This review describes the pathology of RVF in human patients and several animal models, and summarizes the role of viral virulence factors and host factors that affect RVFV pathogenesis. RVFV infection in humans primarily causes a self-limiting febrile illness; however, some patients develop hemorrhagic fever, neurological disorders, or blindness after the febrile period [5, 7, 8] . Inbred rat strains mimic the disparate human response to rift valley fever virus infection Clinical, virological and serological response of the west african dwarf sheep to experimental infection with different strains of rift valley fever virus doi = 10.3390/v3050493 id = cord-334369-xgw7o5gd author = Innes, Elisabeth A. title = A One Health Approach to Tackle Cryptosporidiosis date = 2020-01-23 keywords = cryptosporidiosis; cryptosporidium; infection; oocyst; water summary = Livestock, in particular young calves, are very vulnerable to cryptosporidiosis and a recent modelling study estimated the global load of Cryptosporidium parasites in livestock manure to be in the region of 3.2 × 10 23 oocysts per year, with cattle being the predominant source [10] . Therefore, improving our understanding of environmental transmission routes of zoonotic Cryptosporidium and oocyst survival is important in assessing and mitigating against disease risk and is essential for a One Health approach to tackle human and animal cryptosporidiosis. In addition, applying methods on farm to minimise the environmental contamination with faeces containing infective Cryptosporidium oocysts will also help to minimise risk to other animals and to people through protection of the environment and water catchments (Figure 2 ). Treatment of livestock and human faecal waste to reduce viability of Cryptosporidium oocysts would help to minimise contamination of the environment with infectious parasites and protect human and animal health. doi = 10.1016/j.pt.2019.12.016 id = cord-349821-5ykwwq75 author = Ippolito, G. title = Biological weapons: Hospital preparedness to bioterrorism and other infectious disease emergencies date = 2006-09-09 keywords = SARS; States; United; case; infection summary = The term ''highly infectious diseases'' describes infections caused by pathogens that are transmissible from person to person, cause severe or life-threatening illness; present a serious hazard in healthcare settings and in the community; and require specific control measures, which may include management of cases in a highly secure isolation unit. In Canada, where SARS ''paralysed the Greater Toronto Area healthcare system for weeks'' [27] , and the Toronto public health department investigated 2132 potential cases of SARS, identified over 23,000 contacts as requiring quarantine and logged more than 316,000 calls on its SARS hotline [28] , a national review commission identified systemic deficiencies in response capacity, including ''inadequacies in institutional outbreak management protocols, infection control and infectious disease surveillance'', and found that these deficiencies resulted at least in part from failure to implement lessons learned from earlier public health emergencies [22] . doi = 10.1007/s00018-006-6309-y id = cord-018017-c8myq6bi author = Iversen, Patrick L. title = The Threat from Viruses date = 2018-09-30 keywords = EBV; Ebola; HIV; RNA; disease; human; infection; virus summary = Numerous emerging infections caused by viral agents have imposed high impact on human survival (Table 3 .3). The apparent success of these viruses is that as they move from reservoir hosts to humans and as humans become immune to the initial infection, the population of diverse genomes offers multiple chances to adapt by finding a "fit" genome version which can propagate until the next transition requiring adaption. Human T-cell Lymphotropic Virus (HTLV-1) HTLV-1 is a single-stranded RNA retrovirus, defined by their use of reverse transcriptase, a polymerase, that makes a DNA copy of the RNA 7 kb viral genome. If we combine cardiovascular events and neoplasia caused by infection, then infectious disease is the most significant threat to human life and qualifies as the area of greatest impact. Adeno-associated Virus (AAV) is a single stranded DNA virus that infects humans but are not known to cause disease. is a 5229 base double-stranded DNA virus infecting less than 5 percent of the human population. doi = 10.1007/978-3-319-98164-2_3 id = cord-326328-9w2p3xla author = JENKINS, IAN A. title = Infections of the airway date = 2009-06-25 keywords = Lemierre; abscess; airway; child; figure; infection summary = Infectious mononucleosis (IM) can cause compromise of the airway ( Figure 2 ) and this has been reported in as many as 25-60% of children presenting with IM (7) (8) (9) . Although most authors since the 1960s have advocated the use of glucocorticoids to avert the need for surgical intervention, several series note that, despite steroids, 40-88% of patients with airway obstruction required tonsillectomy (7, 9) . Historically, epiglottitis has been associated primarily with Haemophilus influenzae infections, typically occurring in children aged 3 months to 5 years, with a peak incidence between 1 and 3 years, and characterized by a rapid onset of fever, drooling and stridor (47) . Retropharyngeal abscess in children: clinical presentation, utility of imaging, and current management Haemophilus influenzae type b epiglottitis as a cause of acute upper airways obstruction in children doi = 10.1111/j.1460-9592.2009.02999.x id = cord-007176-61e9obb3 author = Jackson, George Gee title = Viroses Causing Common Respiratory Infections in Man. III. Respiratory Syncytial Viroses and Coronavimses date = 1973-11-17 keywords = infection; respiratory; virus summary = RS virus was estimated, from sucrose density gradient centrifugation studies, to be 90-120 nm in diameter [2] ; viral particles in infected cells measured 65 nm by electron microscopy. All adults tested possessed detectable levels of neutralizing antibody to RS virus before challenge, but the titer of naturally acquired antibody had no significant effect on subsequent RS infection of volunteers and was poorly correlated with development of mild clinical illnesses. The neutralization test is more sensitive than CF when serum from infants is used, but rises in neutralizing antibody have been detected in only half of the virus-positive infections in this age group. Virus structures were detected 6-8 hr later [17] .· Infection of WI-38 cells with strain 229E resulted in a reorganization of the cytoplasm, as determined by electron microscopy. Respiratory syncytial virus infection in adult volunteers. Respiratory syncytial virus infection in adult volunteers. Morphology and development of respiratory syncytial virus in cell culture doi = 10.1093/infdis/128.5.674 id = cord-353787-24c98ug8 author = Jackson, J. A. title = Immunology in wild nonmodel rodents: an ecological context for studies of health and disease date = 2015-04-27 keywords = gata3; immune; infection; natural; study; system summary = Measurement of immune expression may help define individual heterogeneity in infectious disease susceptibility and transmission and facilitate our understanding of infection dynamics and risk in the natural environment; furthermore, it may provide a means of surveillance that can filter individuals carrying previously unknown acute infections of potential ecological or zoonotic importance. Potentiating much of this is the possibility of combining gene expression profiles with analytical tools derived from ecology and systems biology to reverse engineer interaction networks between immune responses, other organismal traits and the environment (including symbiont exposures), revealing regulatory architecture. Studies in wild field voles, briefly reviewed below, have aimed to identify distributional infection patterns associated with different antipathogen strategies in natural populations and to link these to expression signatures in immune-relevant genes. doi = 10.1111/pim.12180 id = cord-337105-jlmh79qv author = Jacob, Fadi title = Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium date = 2020-09-21 keywords = CoV-2; SARS; cell; figure; infection summary = We optimized a protocol to generate choroid plexus organoids from hiPSCs and showed that productive SARS-CoV-2 infection of these organoids is associated with increased cell death and transcriptional dysregulation indicative of an inflammatory response and cellular function deficits. QPCR analysis also showed higher levels of ACE2 and TMPRSS2 expression in CPOs at 50 DIV and 100 DIV than in hippocampal organoids ( Figure S2D ) Together, these results show that our CPOs exhibit a similar transcriptome as adult human choroid plexus tissue and express markers for choroid plexus epithelial cells and SARS-CoV-2 receptors, representing a suitable experimental model to study SARS-CoV-2 infection. Our finding that dysregulated gene expression varies widely among hepatocyte, intestinal, and choroid plexus organoids infected with SARS-CoV-2 suggests unique responses in different cell types and highlights the need for diverse human cellular model systems when studying the disease. doi = 10.1016/j.stem.2020.09.016 id = cord-009144-3slh1nbk author = Jacobs, J.W. title = RESPIRATORY SYNCYTIAL AND OTHER VIRUSES ASSOCIATED WITH RESPIRATORY DISEASE IN INFANTS date = 1971-05-01 keywords = infant; infection; virus summary = Diagnosis by virus isolation and serology was attempted in 377 cases of respiratory-tract infection in infants under one year of age admitted to hospital during two winters. THERE have been few intensive studies of respiratoryvirus infections of infants.1-5 To prevent these infections, it is necessary to know which viruses cause the most severe illness and whether maternal antibody plays any part in their prevention. We report here the results of a survey of respiratory-virus infections in infants under one year of age in hospital. In this survey, as in others, R.s. virus was the commonest cause of respiratory illness requiring admission at this age (40°0), and the illnesses were more severe than those associated with other viruses (table iv). 23 Effect of Maternal Antibody The few parainfluenza virus infections observed in this survey occurred only in infants more than four months of age. doi = 10.1016/s0140-6736(71)92440-8 id = cord-022305-uvor9rts author = Jacoby, Robert O. title = Viral Diseases date = 2013-11-17 keywords = Fig; HAI; RCV; SDAV; Sendai; infection; rat; virus summary = The number of viruses known to be naturally infectious for laboratory rats is small, and most cause inapparent infections which usually are detected by serological monitoring (Table I) . Significance: Latent, vertically-transmissible agent isolated from submaxillary gland; no signs or lesions; induces HAI antibody; unre lated antigenically to rat coronaviruses or cytomegalovirus; must dif ferentiate isolates from coronaviruses, cytomegaloviruses C. Infected rats excrete virus from the respiratory tract for about 7 days, at which time anti-SDAV antibody is first detectable in serum by either NT or CF tests ( Fig. 30 and Table V) (61) . Infections of SDAV or RCV can be diagnosed on the basis of clinical signs, lesions, and serological profiles of NT and CF antibody and confirmed by isolation of the causative virus. The pathogenesis and lesions of natural and experimental Sendai virus infection have been well described for mice (2, 132, 160) , but only limited information on rats is available. doi = 10.1016/b978-0-12-074901-0.50018-6 id = cord-277818-8w15dz20 author = Jaichenco, Andre L. title = Infectious Disease Considerations for the Operating Room date = 2018-02-09 keywords = HIV; care; hand; infection; patient; transmission summary = Hand hygiene is a well-known and effective solution to the problem of bacterial transmission within and across patients and is considered the most important and cost-effective individual intervention in the prevention of health care–associated infections in children and health care providers Compliance with the current "5 moments" World Health Organization guidelines could make a major inroad into reducing provider hand and workspace contamination. These findings have clinical implications for the risk of colonization and subsequent HCIs-for example, SSIs. This calls attention to the need to develop and enforce strict hand hygiene guidelines for personnel who are providing anesthesia care, but more importantly the need to increase compliance with environmental disinfection of the OR (between cases and terminal cleaning), and to study further the directions of the spread of pathogens in the OR and anesthesia work areas. doi = 10.1016/b978-0-323-42974-0.00050-1 id = cord-256827-tht5h1tu author = Jain, Neemisha title = Upper respiratory tract infections date = 2001 keywords = infection; respiratory summary = doi = 10.1007/bf02722930 id = cord-339328-wizu3arz author = Jain, Sanjay K. title = The Promise of Molecular Imaging in the Study and Treatment of Infectious Diseases date = 2017-02-02 keywords = imaging; infection; pet summary = Preclinical Unique insights into disease pathogenesis, e.g., assessing hideouts of infections, defining the diversity of the microbial populations (microbiome) Studying multi-compartment antimicrobial pharmacokinetics Expedite bench-to-bedside translation of new therapeutics, e.g., surrogate end points to assess antimicrobial or vaccine efficacy or predict stable cure Clinical trials Unique insights into disease pathogenesis-noninvasive visualization of processes deep inside the body Phase 0 studies to determine compartment-specific antimicrobial penetration/binding (sites of infection, necrotic/fibrotic lesions, privileged sites-CNS) to inform appropriate dosing of novel drugs; determine accumulation at non-target sites to assess potential toxicities; current US Food and Drug Administration (FDA) guidelines require tissue drug distribution studies at the infected sites Patient settings Enabling precision medicine by providing unique insights into disease pathogenesis, antimicrobial pharmacokinetics, etc. doi = 10.1007/s11307-017-1055-0 id = cord-332344-upsn0zb4 author = Jeswin, Joseph title = Proteomic analysis by iTRAQ in red claw crayfish, Cherax quadricarinatus, hematopoietic tissue cells post white spot syndrome virus infection date = 2016-02-01 keywords = Hpt; WSSV; hpi; infection; protein summary = To elucidate proteomic changes of Hpt cells from red claw crayfish, Cherax quadricarinatus, we have carried out isobaric tags for relative and absolute quantitation (iTRAQ) of cellular proteins at both early (1 hpi) and late stage (12 hpi) post white spot syndrome virus (WSSV) infection. Generally, these differentially expressed proteins include: 1) the metabolic process related proteins in glycolysis and glucogenesis, DNA replication, nucleotide/amino acid/fatty acid metabolism and protein biosynthesis; 2) the signal transduction related proteins like small GTPases, G-protein-alpha stimulatory subunit, proteins bearing PDZor 14-3-3-domains that help holding together and organize signaling complexes, casein kinase I and proteins of the MAP-kinase signal transduction pathway; 3) the immune defense related proteins such as α-2 macroglobulin, transglutaminase and trans-activation response RNA-binding protein 1. To further identify proteins or pathways altered during viral infection, here we report proteomic responses of crayfish Hpt cells by iTRAQ at both early (1 hpi) and late (12 hpi) stages post WSSV infection accordingly. doi = 10.1016/j.fsi.2016.01.035 id = cord-302379-jh6jxwyn author = Jevon, Phil title = Management of odontogenic infections and sepsis: an update date = 2020-09-25 keywords = dental; infection; sepsis summary = doi = 10.1038/s41415-020-2114-5 id = cord-201898-d1vbnjff author = Jha, Vishwajeet title = Forecasting the transmission of Covid-19 in India using a data driven SEIRD model date = 2020-06-08 keywords = India; infection summary = One of the most significant epidemiological parameter, namely the effective reproduction number of the infection is extracted from the daily growth rate data of reported infections and it is included in the model with a time variation. One of the most significant epidemiological parameter, namely the effective reproduction number of the infection is extracted from the daily growth rate data of reported infections and it is included in the model with a time variation. The results of calculations with these parameters that use the time varying β(t) parameter as determined above provide a good description of the evolution in the case numbers of reported infected, recovered and death population as shown in Fig. 2a . Calculations performed using the time dependent contact rate parameter β(t) in the SEIRD model provide a good description of the case numbers of infections, recovered and deaths. doi = nan id = cord-353214-qo98m7jx author = Jhaveri, Ravi title = Fever Without Localizing Signs date = 2017-07-18 keywords = child; febrile; infection summary = 19 Among 233 infants who were born at term with no perinatal complications or underlying diseases, who had not received antibiotics, and who were hospitalized for fever and possible septicemia, 144 (62%) were considered unlikely to have a serious bacterial infection and fulfilled all of the following criteria: no clinical evidence of infection of the ear, skin, bones, or joints; white blood cell (WBC) count between 5000 and 15,000/mm 3 ; less than 1500 band cells/mm 3 ; and normal urinalysis results. Some clinicians adhere to a protocol of treating all young infants with fever and no apparent focus of infection with broad-spectrum antimicrobial agents administered intravenously in the hospital until the results of cultures of the blood, urine, and cerebrospinal fluid (CSF) are known. 34 Studies performed in that era showed that some children 3 months of age or older with fever who did not appear to be toxic and who had no apparent focus of infection had bacteremia, most often due to S. doi = 10.1016/b978-0-323-40181-4.00014-1 id = cord-309478-yhmgopmr author = Jin, Ying-Hui title = Perceived infection transmission routes, infection control practices, psychosocial changes, and management of COVID-19 infected healthcare workers in a tertiary acute care hospital in Wuhan: a cross-sectional survey date = 2020-05-11 keywords = COVID-19; Wuhan; infection summary = title: Perceived infection transmission routes, infection control practices, psychosocial changes, and management of COVID-19 infected healthcare workers in a tertiary acute care hospital in Wuhan: a cross-sectional survey Results showed that they experienced psychological burden, especially nurses, women, those in Wuhan, and frontline healthcare workers directly engaged in the diagnosis, treatment, and care for patients with COVID-19. All 105 infected medical staff with COVID-19 in our hospital was invited, finally 103 cases agreed with the consent and finished our questionnaire was included for analysis (response rate: 98.1%), Table 1 presented their basic characteristics. Protective equipment should be upgraded in hospital at the onset of a new disease especially for staff conducting procedures involving close contact and caring for high risk patients. How to train the health personnel for protecting themselves from novel coronavirus (COVID-19) infection during their patient or suspected case care doi = 10.1186/s40779-020-00254-8 id = cord-269095-lwank6hk author = Jirru, Ermias title = Impact of Influenza on Pneumococcal Vaccine Effectiveness during Streptococcus pneumoniae Infection in Aged Murine Lung date = 2020-06-11 keywords = Pneumovax; figure; infection summary = As recent work has illustrated differential efficacy of Prevnar vaccination in modulating the immune responses of adult mice to post-influenza infection with a serotype 3 strain of Streptococcus pneumoniae, we chose to examine the impact of influenza infection on Pneumovax responses during a secondary bacterial infection [30, 40] . When compared to PBS controls, there was no significant increase in cellular recruitment or viral titers in aged adult mice vaccinated with Pneumovax on day 7 post influenza ( Figure 3B,C) . The purpose of our current study was to investigate the role of immune imprinting by influenza on pneumococcal vaccine effectiveness during Streptococcus pneumoniae infection in the aged murine lung. The purpose of our current study was to investigate the role of immune imprinting by influenza on pneumococcal vaccine effectiveness during Streptococcus pneumoniae infection in the aged murine lung. doi = 10.3390/vaccines8020298 id = cord-270294-g95skuik author = Johnstone, Jennie title = Viral Infection in Adults Hospitalized With Community-Acquired Pneumonia Prevalence, Pathogens, and Presentation date = 2008-12-31 keywords = infection; patient; viral summary = doi = 10.1378/chest.08-0888 id = cord-329904-e05ywn5e author = Jose, Merin title = Fatal Superimposed Bacterial Sepsis in a Healthy Coronavirus (COVID-19) Patient date = 2020-05-29 keywords = SARS; infection summary = We present a case of a healthy COVID positive individual, with no underlying comorbidities, who rapidly deteriorated overnight on readmission to the hospital after initial discharge and succumbed to this disease due to a superimposed bacterial infection with COVID pneumonia. This case report highlights the importance of educating COVID-19 positive patients about the precautions, as well as signs and symptoms of a superimposed bacterial infection, when their plan of care is in a home setting. It also emphasizes the potential role of checking procalcitonin levels as a part of routine laboratory investigation at initial presentation in all suspected as well as confirmed COVID-19 cases to rule out an on-going bacterial infection that can prove fatal in the course of the disease. Our emphasis from this case report is to highlight the risk of superimposed bacterial infection in COVID-19 patients. doi = 10.7759/cureus.8350 id = cord-332516-eaqpiq1o author = Joseph, Carol title = Bacterial and viral infections associated with influenza date = 2013-08-27 keywords = H1N1; bacterial; infection; influenza summary = Bacterial secondary infections or co-infections associated with cases of influenza are a leading cause of severe morbidity and mortality, especially among high-risk groups such as the elderly and young children. Thus, information on the overall range, incidence and severity of influenza co-infections and secondary infections associated with different influenza strains, aetiological agents, different age groups and their underlying risk conditions is very important contextually for clinicians and public health specialists involved in implementing policy and treatment regimes for this disease spectrum. 34 In the United States, those aged 5-19 years Influenza and co-secondary infections ª 2013 Blackwell Publishing Ltd experienced overall the largest relative increase in pneumococcal hospitalisations during the 2009 pandemic influenza period compared with seasonal baseline estimates for this age group and mirrored both temporal and geographical influenza activity across the country. 75 A study of prior influenza vaccination in relation to its effect on severity and mortality in patients with CAP during seasonal influenza periods showed that prevention of the predisposing viral illness reduced the risk for more severe secondary pneumonia. doi = 10.1111/irv.12089 id = cord-347064-ljd121no author = José, Ricardo J. title = Opportunistic bacterial, viral and fungal infections of the lung date = 2016-05-05 keywords = CMV; infection; patient summary = Conventional bacterial pathogens Although the risk of opportunistic infection is high in immunocompromised patients, most pneumonias are related to the more Key points C Knowledge of the immune defect helps to narrow down the potential pathogens C Computed tomography of the chest is better than radiographs at defining the radiological pattern of disease in immunocompromised hosts C In selected patients, early bronchoscopy increases the yield of microbiological identification of a potential pathogen C Prolonged high-dose glucocorticoids (>20 mg/day for >21 days) predispose to Pneumocystis jirovecii pneumonia (PJP) C Biological agents are associated with specific immune defects that increase the risk of opportunistic lung infections (e.g. tumour necrosis factor-a inhibitors and risk of mycobacterial disease, endemic fungi and Legionella pneumophila; anti-CD20 drugs and mycobacterial disease, cytomegalovirus pneumonitis and PJP) C Due to the increase in azole resistance of Aspergillus fumigatus, combination of an azole with an echinocandin antifungal agent is recommended in immunocompromised hosts with severe invasive pulmonary aspergillosis conventional bacterial pathogens. doi = 10.1016/j.mpmed.2016.03.015 id = cord-323311-xl2fv0qx author = Kahn, R. E. title = 6th International Conference on Emerging Zoonoses date = 2012-09-07 keywords = BSE; H1N1; H5N1; Health; Professor; States; United; University; disease; human; infection; virus summary = The three key characteristics of this integrated approach to so many infectious diseases are as follows: (i) to use cell culture, primary cells, nonhuman primate and human clinical models to study viral infection; (ii) to combine traditional histopathological, virological and biochemical approaches with functional genomics, proteomics and computational biology (Haagmans et al., 2009); and (iii) to obtain signatures of virulence and insights into mechanisms of host defense response, viral evasion and pathogenesis (Casadevaill et al., 2011) . The unity of human, animal and ecosystem health outlined by Professor Aguirre, as well as the interactions among multiple tick-borne pathogens in a natural reservoir host set out by Professor Fish and his research team, both summarized in Topic 1 above, highlight the necessity of cross-disciplinary collaboration in studying zoonotic bacterial diseases (Daszak et al., 2007, pp. doi = 10.1111/j.1863-2378.2012.01539.x id = cord-260700-u12aa739 author = Kainulainen, Leena title = Recurrent and persistent respiratory tract viral infections in patients with primary hypogammaglobulinemia date = 2010-06-10 keywords = PCR; infection; patient summary = title: Recurrent and persistent respiratory tract viral infections in patients with primary hypogammaglobulinemia OBJECTIVE: We conducted a prospective 12-month follow-up study of respiratory tract infections in 12 adult patients with primary hypogammaglobulinemia. METHODS: Nasal swab samples and induced sputum samples were taken at the onset of acute respiratory tract infection and every 3 months thereafter. CONCLUSIONS: Despite adequate immunoglobulin replacement therapy, patients with primary hypogammaglobulinemia have increased susceptibility to respiratory tract viral infections. Using modern diagnostic techniques, we wanted to study the occurrence of respiratory tract infections, especially viral infections, in patients with primary hypogammaglobulinemia who were receiving regular immunoglobulin replacement therapy. If the spouse of the patient had acute symptoms of respiratory tract infection, she or he took nasal swabs at home according to the instructions of the research nurse and sent the vials by post. First, despite adequate immunoglobulin replacement therapy, most patients with primary hypogammaglobulinemia had increased susceptibility to respiratory tract viral infections. doi = 10.1016/j.jaci.2010.04.016 id = cord-270940-acwkh6ed author = Kallio-Kokko, Hannimari title = Viral zoonoses in Europe date = 2005-06-29 keywords = Congo; Crimean; Europe; Fig; RNA; fever; human; infection; table; virus summary = doi = 10.1016/j.femsre.2005.04.012 id = cord-341987-lsvifqyo author = Kalyanasundaram, Sridhar title = Novel Corona Virus Pandemic and Neonatal Care: It’s Too Early to Speculate on Impact! date = 2020-08-03 keywords = SARS; covid-19; infection summary = We discuss the basic aspects of the infection, the approach of care to novel corona virus disease 2019 (COVID-19) in positive pregnant women, the likely presentation in newborns (as per current knowledge), and the approach to the management of neonates with infection or at risk of the infection. In this article, we discuss the basic aspects of the infection, the approach of care to novel corona virus disease 2019 in positive pregnant women, the likely presentation in newborns (as per current knowledge), and the approach to the management of neonates with infection or at risk of the infection. Another recent case study published in Nature Communication reported transplacental transmission of COVID-19 from a positive pregnant mother during the last trimester to her offspring which occurred due to maternal viremia, placental infection, and neonatal viremia following placental infection [34] . doi = 10.1007/s42399-020-00440-8 id = cord-274643-vjb2yt93 author = Kang, G. title = Viral Diarrhea date = 2008-08-26 keywords = child; diarrhea; gastroenteritis; infection; virus summary = Of the ''non-group A'' rotaviruses, group B rotavirus has been identified in epidemic outbreaks of severe diarrhea in adults in China and in symptomatic infections in children. Between 20% and 50% of cases of gastroenteritis caused by rotavirus in hospitals are considered to be of nosocomial origin, and nosocomial viral enteric infections have been documented in up to 6% of children admitted for more than 72 hours in both developed and developing countries. Rotaviruses induce a clinical illness characterized by vomiting, diarrhea, abdominal discomfort, fever, and dehydration (or a combination of some of these symptoms) that occurs primarily in infants and young children and may lead to hospitalization for rehydration therapy. Studies in adult volunteers indicate that people with detectable levels of antibodies do not develop the illness, although epidemiological observations suggest that human astrovirus infections do not induce heterotypic immunity, as an episode of astrovirus diarrhea is not associated with a reduced incidence of a subsequent episode. doi = 10.1016/b978-012373960-5.00571-2 id = cord-314390-q36ye9ff author = Kang, Gagandeep title = Viral Diarrhea date = 2016-10-24 keywords = child; diarrhea; gastroenteritis; infection; virus summary = Of the ''non-group A'' rotaviruses, group B rotavirus has been identified in epidemic outbreaks of severe diarrhea in adults in China and in symptomatic infections in children. Between 20% and 50% of cases of gastroenteritis caused by rotavirus in hospitals are considered to be of nosocomial origin, and nosocomial viral enteric infections have been documented in up to 6% of children admitted for >72 h in both developed and developing countries. Rotaviruses induce a clinical illness characterized by vomiting, diarrhea, abdominal discomfort, fever, and dehydration (or a combination of some of these symptoms) that occurs primarily in infants and young children and may lead to hospitalization for rehydration therapy. Studies in adult volunteers indicate that people with detectable levels of antibodies do not develop the illness, although epidemiological observations suggest that human astrovirus infections may not induce heterotypic immunity, as an episode of astrovirus diarrhea is not associated with a reduced incidence of a subsequent episode. doi = 10.1016/b978-0-12-803678-5.00486-0 id = cord-329263-o5e2go23 author = Kaplan, Nasser M. title = Molecular epidemiology and disease severity of respiratory syncytial virus in relation to other potential pathogens in children hospitalized with acute respiratory infection in Jordan date = 2007-11-26 keywords = HRSV; infection; respiratory summary = title: Molecular epidemiology and disease severity of respiratory syncytial virus in relation to other potential pathogens in children hospitalized with acute respiratory infection in Jordan Human respiratory syncytial virus (HRSV) is the major viral cause of acute lower respiratory tract infections in children. Human respiratory syncytial virus (HRSV) is the leading viral cause of acute respiratory infection in infants and young children in terms of prevalence and effect [Shay et al., 2001] . We also compared the disease severity of HRSV subgroups A and B and their associated genotypes in hospitalized Jordanian children set in the context of other potential respiratory pathogens. A total of 72/326 (22%) patients had no pathogens detected by PCR (Table I) , but 254 (78%) had at least one potential respiratory pathogen detected which consisted of 140/ 326 (43%) HRSV, 116/312 (37%) adenoviruses, 57/312 (18%) HBoV, 36/325 (11%) rhinovirus, 14/312 (4.5%) Chlamydia spp., 8/326 (2.5%) HMPV, 4/325 (1.2%) human coronavirus NL63, and 2/323 (0.6%) influenza A virus. doi = 10.1002/jmv.21067 id = cord-324398-68je1l3o author = Kashiwazaki, Hiromi title = Spongiform degeneration induced by neuropathogenic murine coronavirus infection date = 2011-01-23 keywords = Fig; SVZ; cell; infection summary = Even in this area with mild gliosis, astroglial foot processes around the blood vessels were an outstanding feature (Fig. 2l) , indicating that a key component of the blood brain barrier had been well-preserved in the exSpongi during the course of the disease, which conspicuously contrasts with pathologies involving an inflammatory perivascular cuff induced by infection with other strains of JHM virus, where there is a disappearance of astrocytes around blood vessels with inflammation followed by degeneration of the astrocytes with swollen cytoplasm around the blood vessels in the initial phase of cell infiltration. The distribution of spongiotic lesions showed a predilection for the brainstem and cerebellum (Figs 1,2 ) without forming spongiosis in the SVZ (Figs 2,3) , although our previous report demonstrated that the viral antigens in the brain appear in the choroid plexus and SVZ, including ependymal cells, during the early phase of infection after the initial emergence in infiltrating cells of meninges at 12 h pi, without spreading into the brain parenchyma including the site of injection. doi = 10.1111/j.1440-1827.2010.02639.x id = cord-294468-0v4grqa7 author = Kasilingam, Dharun title = Exploring the Growth of COVID‐19 Cases using Exponential Modelling Across 42 Countries and Predicting Signs of Early Containment using Machine Learning date = 2020-08-04 keywords = COVID-19; Coronavirus; country; infection summary = doi = 10.1111/tbed.13764 id = cord-017461-xw02c7u5 author = Kauffman, Carol A. title = Fungal Infections date = 2009-02-02 keywords = Candida; infection; old; patient summary = doi = 10.1007/978-1-60327-534-7_22 id = cord-024795-xa7ke70d author = Kaviani, Aaron title = Management of Antimicrobial Agents in Abdominal Organ Transplant Patients in Intensive Care Unit date = 2020-01-24 keywords = SOT; Society; infection; patient summary = PURPOSE OF REVIEW: Early diagnosis of infections and immediate initiation of appropriate antimicrobials are crucial in the management of patients before and after organ transplantation. Furthermore, liver, pancreas, and intestinal recipients are especially at risk for fatal fungal infections, primarily caused by Candida species which may occur together with bacterial infections. Recommendations regarding empirical antibiotic treatment in patient with ESLD before liver transplantation have been summarized in Table 1 [9] . For SSIs, empiric treatment should include Gram-positive organisms as well as expected flora at site of transplanted organ, with broad-spectrum agents reserved for patients with risk for multidrug-resistant organisms [63] . Urinary tract infections in solid organ transplant recipients: guidelines from the American Society of Transplantation Infectious Diseases Community of Practice Intra-abdominal infections in solid organ transplant recipients: guidelines from the American Society of Transplantation Infectious Diseases Community of Practice doi = 10.1007/s40472-020-00268-0 id = cord-018101-zd4v222b author = Kawashima, Kent title = Disease Outbreaks: Critical Biological Factors and Control Strategies date = 2016-05-31 keywords = SARS; disease; individual; infection; pathogen summary = We will briefly describe some pathogens that cause human disease and their transmission mechanisms before analyzing the SARS 2002-2003 epidemic as a case study of a modern urban epidemic. In general, fecal-oral and vector-borne diseases are infections transmitted through an environmental (water, food) or a biological (animal) carrier that extends transmission range to large distances, but other routes are also possible depending on the specific pathogen. In the following three subsections, we discuss theoretical results on three important aspect of disease outbreak: (1) the effect of "superspreaders" on the probability of outbreak, (2) the impact of control strategies such as isolation and quarantine, and (3) factors that affect the evolution of pathogen virulence. When the host population has a highly heterogeneously connected network, emergence of disease may be rare, but infections that survive stochastic extinction produce "explosive" epidemics similar to the case of SARS in 2002. doi = 10.1007/978-3-319-39812-9_10 id = cord-300187-fr6tme32 author = Kearns, Shawn title = Infectious Hepatopathies in Dogs and Cats date = 2009-11-26 keywords = Mycobacterium; cat; disease; dog; infection; liver summary = doi = 10.1053/j.tcam.2009.06.004 id = cord-288238-36hiiw91 author = Keshavarz, Mohsen title = Metabolic host response and therapeutic approaches to influenza infection date = 2020-03-05 keywords = ATP; IFN; ROS; infection; influenza; virus summary = It is also reported that influenza infection significantly increases ROS production by inducing Nox4, and the proliferation of this virus in lung epithelial cells is dependent on redox-sensitive pathways activated by Nox4-derived ROS [16] . IFN can also exert its function on metabolic changes by producing several mediators including indoleamine-2,3-dioxygenase (IDO) and nitric oxide (NO), both of which appear to have either an inducible or an inhibitory role in viral replication [33] . In addition, increased temperature of cells during infection (which could be the result of virus replication and fever) causes heat stress which in turn can considerably downregulate carnitine palmitoyltransferase II (CPT II) activity and reduce the β-oxidation and ATP levels in fibroblasts of influenza-associated encephalopathy patients and healthy volunteers [110] . Through enhancing the activity of the mTORC1 complex, the influenza virus strengthens several metabolic pathways, including glycolysis, glutaminolysis, pentose phosphate, and fatty acid synthesis, to provide more ATP and structural materials for viral replication. doi = 10.1186/s11658-020-00211-2 id = cord-331827-amg309uz author = Keske, Şiran title = Human metapneumovirus infection: Diagnostic impact of radiologic imaging date = 2019-02-01 keywords = infection; patient summary = BACKGROUND: Human metapneumovirus (hMPV) is a recently detected virus, which can cause mild to severe respiratory tract infections. MATERIALS/METHODS: Between January 2012 and November 2017, patients who had hMPV detected in nasopharyngeal or bronchoalveolar lavage by molecular respiratory pathogen tests were evaluated. Lower respiratory system infection (LRTI) was diagnosed in 44 patients with clinical findings, and in 31 patients out of 44 the radiological findings supported the diagnosis. Our study demonstrates the radiologic findings of hMPV infections in patients with LRSI (Figures 3 and 4) . In a recent review for radiologic imaging of viral agents that may cause pneumonia, the general radiologic findings of hMPV infections were followed as bilateral centrilobular nodules, GGO, and multilobar infiltrations; however, there was no information about nodular consolidation. In addition, they noted that the radiologic findings of hMPV infections were most commonly reported in patients with hematologic malignancy, but there were limited data on immunocompetent patients. Clinical characterization of human metapneumovirus infection among patients with cancer doi = 10.1002/jmv.25402 id = cord-309138-44qpk2vf author = Khanna, Kanika title = Herbal Immune-boosters: Substantial Warriors of Pandemic Covid-19 Battle date = 2020-10-03 keywords = ACE2; COVID-19; CoV-2; PAK1; SARS; infection summary = Moreover, AYUSH has recommended certain preventive and medicinal plants for prevention and prophylactic of COVID-19 including warm extracts of Tinospora cordifolia (advised for chronic fever), Andrograhis paniculata (advised for fever and cold), Cydonia oblonga, Zizyphus jujube and Cordia myxa (enhancing antioxidant, immune-modulatory, anti-allergic, smooth muscle relaxant, anti-influenza activity) and Ever since, has been elucidated that, PAK1 tends to cause cancers, viral diseases like HIV, Hepatitis, pappiloma, influenza, ebola, SARS and corona virus along with immune system suppression of hosts, henceforth, propolis would be quintessential in blocking COVID/coronavirus curbed fibrosis in respiratory tract and boosting the immunity of an individual (Maruta, 2014) . Potential Inhibitor of COVID-19 Main Protease (Mpro) From Several Medicinal Plant Compounds by Molecular Docking Study Molecular mechanism of action of repurposed drugs and traditional Chinese medicine used for the treatment of patients infected with COVID-19: A systematic review Traditional Chinese medicine in the treatment of patients infected with 2019-new coronavirus (SARS-CoV-2): a review and perspective doi = 10.1016/j.phymed.2020.153361 id = cord-023369-xwclh6ih author = Kim, Faith title = Human Herpesvirus-6 Meningitis in a Premature Infant with Fevers: A Case and Literature Review date = 2020-04-18 keywords = CSF; DNA; HHV-6; infection summary = They both had IgM antibodies in the acute phase and PCR detection of HHV-6 DNA in the serum at high copy numbers suggestive of a primary infection despite presence of preexisting maternal antibodies, which the authors isolated from both mothers. 18 Infants with congenital infection due to ciHHV6 had evidence of high viral loads in the cord blood and detection of HHV-6 DNA in hair follicles in both the infants and at least one parent. In summary, we present a case of a premature infant with multiple anomalies who acquired acute HHV-6 viral meningitis in the setting of intermittent high fevers, elevated inflammatory markers, and diagnostic testing from her CSF that confirmed the diagnosis. Transplacental human herpesvirus 6 (HHV-6) congenital infection caused by maternal chromosomally integrated virus doi = 10.1177/1179547620912952 id = cord-345381-9cckppk2 author = Klimek, Ludger title = Use of biologicals in allergic and type-2 inflammatory diseases during the current COVID-19 pandemic: Position paper of Ärzteverband Deutscher Allergologen (AeDA)(A), Deutsche Gesellschaft für Allergologie und Klinische Immunologie (DGAKI)(B), Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)(C), Österreichische Gesellschaft für Allergologie und Immunologie (ÖGAI)(D), Luxemburgische Gesellschaft für Allergologie und Immunologie (LGAI)(E), Österreichische Gesellschaft für Pneumologie (ÖGP)(F) in co-operation with the German, Austrian, and Swiss ARIA groups(G), and the European Academy of Allergy and Clinical Immunology (EAACI)(H) date = 2020-09-07 keywords = CoV-2; SARS; covid-19; disease; infection; patient summary = title: Use of biologicals in allergic and type-2 inflammatory diseases during the current COVID-19 pandemic: Position paper of Ärzteverband Deutscher Allergologen (AeDA)(A), Deutsche Gesellschaft für Allergologie und Klinische Immunologie (DGAKI)(B), Gesellschaft für Pädiatrische Allergologie und Umweltmedizin (GPA)(C), Österreichische Gesellschaft für Allergologie und Immunologie (ÖGAI)(D), Luxemburgische Gesellschaft für Allergologie und Immunologie (LGAI)(E), Österreichische Gesellschaft für Pneumologie (ÖGP)(F) in co-operation with the German, Austrian, and Swiss ARIA groups(G), and the European Academy of Allergy and Clinical Immunology (EAACI)(H) Conclusion: The use of biologicals for the treatment of bronchial asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps, and spontaneous urticaria should be continued as usual in patients without suspected infection or proven SARS-CoV-2 infection. Conclusion: The use of biologicals for the treatment of bronchial asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps, and spontane-ous urticaria should be continued as usual in patients without suspected infection or proven SARS-CoV-2 infection. doi = 10.5414/alx02166e id = cord-003099-a0acr28o author = Koch, R. M. title = The endotoxin-induced pulmonary inflammatory response is enhanced during the acute phase of influenza infection date = 2018-07-05 keywords = LPS; infection; influenza summary = In vitro studies in which influenza-infected alveolar macrophages were subsequently stimulated with bacterial lipopolysaccharide (LPS), a bacterial compound that induces a profound innate immune response, revealed increased levels of pro-inflammatory cytokines tumor necrosis factor (TNF) α, interleukin (IL)-1β, and IL-6 [4] [5] [6] [7] [8] , indicative of a priming effect on these cells by influenza. Likewise, murine influenza infection resulted in increased levels of pro-inflammatory cytokines in both plasma and lungs, and enhanced pulmonary neutrophil influx upon pneumococcal infection 7 days later [10] . In the present study, we demonstrate that a systemic LPS challenge in the acute phase of influenza infection (4 days post-infection) results in an enhanced pulmonary, but not systemic pro-inflammatory cytokine response. Our results are in accordance with in vitro data reporting a cellular priming effect of influenza observed upon secondary stimulation with LPS [4] [5] [6] [7] [8] , as well as with other murine in vivo studies that report increased inflammation and pulmonary neutrophil influx or sequestration upon a secondary bacterial infection or LPS challenge in the acute phase of influenza infection [9, 10] . doi = 10.1186/s40635-018-0182-5 id = cord-277539-xt2nt11e author = Kochhar, Anuraj Singh title = Dentistry during and after COVID-19 Pandemic: Pediatric Considerations date = 2020 keywords = COVID-19; SARS; dental; infection; patient summary = doi = 10.5005/jp-journals-10005-1782 id = cord-022383-pz0htccp author = Kohn, Dennis F. title = Biology and Diseases of Rats date = 2013-11-17 keywords = Fig; SDAV; Sendai; animal; colony; disease; infection; lesion; rat; strain; tumor; virus summary = The severity and prevalence of clinical disease within an infected colony are associated with environmental conditions that induce stress (e.g., experimental manipulation, overcrowding, fluctuations in ambient temperature and humid ity, and copathogens). Salmonellosis, which was once a major cause of disease in laboratory rat and mouse colonies, is rarely reported in either species today. Mycoplasma pulmonis recently has become recognized as an important pathogen in the female genital tract of rats, and thus is being treated here as a distinct disease rather than as a sequella to MRM. Sendai virus commonly infects laboratory rats, but its clinical significance is less than in mice. Infection is usually diagnosed retrospectively in rats, where pulmonary lesions are observed following seroconversion to PVM in the absence of other respiratory pathogens. This disease, which occurs more fre quently in females, has been reported in numerous strains of rats. doi = 10.1016/b978-0-12-263620-2.50010-0 id = cord-315304-pge45105 author = Kotton, C.N. title = Organ Transplantation, Risks date = 2015-03-06 keywords = CMV; HHV-6; infection; transplantation summary = Viral infection is associated with both direct (invasive disease) and indirect (immune modulation) effects affecting susceptibility to other infections and promoting allograft rejection. The risk for viral infection is a function of the intensity of exposure and virulence of the specific virus, the intensity of immune suppression used to prevent graft rejection or graft-versus-host disease, underlying immune deficits, and factors affecting host susceptibility. Multiple factors contribute to viral reactivation after transplantation, including graft rejection and therapy, immune suppression (especially reduction of T-cell mediated, cytotoxic immunity), inflammation, and tissue injury. The clinical presentation of CMV (HHV-5) can range from a ''CMV syndrome'' including fever, malaise, leukopenia, to a ''flu-like'' illness with myalgias and fatigue, to a more significant end-organ disease with pneumonitis, colitis, encephalitis, hepatitis, or chorioretinitis. The treatment of viral infections in the renal transplantation recipient includes: the reduction of immunosuppression, antiviral therapy, diagnosis and treatment of co-infections (such as CMV, EBV, HHV-6, or À7), and use of adjunctive therapies such as immunoglobulins or colony stimulating factors. doi = 10.1016/b978-0-12-801238-3.02629-5 id = cord-268830-8li6xhbu author = Kozak, Robert title = Severity of coronavirus respiratory tract infections in adults admitted to acute care in Toronto, Ontario date = 2020-03-29 keywords = HKU1; OC43; infection summary = doi = 10.1016/j.jcv.2020.104338 id = cord-021413-1ht1xm88 author = Kraft, Lisbeth M. title = Viral Diseases of the Digestive System date = 2013-10-21 keywords = EDIM; Kraft; MHV; hepatitis; infection; mouse; reovirus; virus summary = Runner and Palm (1953) , studying C3H mice, indicated that there was a higher incidence of diarrhea in December/January (Kraft, 1961; Blackwell et al., 1966) , complement fixation (Wilsnack et al., 1969; Kapikian et al, 1976; Thouless et al., 1977b) , direct immunofluorescent staining or precipitin (Wilsnack et al., 1969; Spence et al., 1975; Foster α/., 1975; Peterson α/., 1976) , immune electron microscopy (Kapikian et al., 1974; Bridger and Woode, 1975) , immunoelectroosmophoresis (Tufvesson and Johnsson, 1976; Middleton et al., 1976) , enzyme-linked im munosorbent assay (ELISA) (Scherrer and Bernard, 1977; El lens etal., 1978; Yolken etal., 1978a,b,c) , radioimmunoas say (Acres and Babiuk, 1978; Kalica et al., 1977; Middleton et al., 1977) , immunodiffusion (Woode et al., 1976) , hemagglutination inhibition (Fauvel et al., 1978) , enzymelinked fluorescence assay (ELISA) (Yolken and Stopa, 1979) , an unlabeled soluble enzyme peroxidase-antiperoxidase method , plaque reduction test (Estes and Graham, 1980) , serologic trapping on antibody-coated electron microscope grids (Nicolaieff et al., 1980) , a solid phase system (SPACE, solid phase aggregation of coupled erythrocytes) for detection of rotaviruses in feces (Bradbume et al., 1979) , and immune electron microscopy with serum in agar diffusion (Lamontagne et al., 1980) . doi = 10.1016/b978-0-12-262502-2.50016-x id = cord-333355-ykmp4ven author = Kuchar, E. title = Pathophysiology of Clinical Symptoms in Acute Viral Respiratory Tract Infections date = 2015-03-19 keywords = Eccles; infection; respiratory summary = In this article we discuss the pathophysiology of common symptoms of acute viral respiratory infections (e.g., sneezing, nasal discharge, sore throat, cough, muscle pains, malaise, and mood changes). The development of sneezing before coughing in patients with a common cold may be partly explained by the involvement of the upper airways first and the infection subsequent spread to the lower respiratory tract (Eccles 2005) . We focused on the most significant symptoms of acute viral respiratory infections: sneezing, nasal discharge and obstruction, sore throat, coughing, muscle pains, malaise and mood changes, fever, and febrile seizures in children. Macrophages play a key role in triggering an acute phase response with the production of cytokines (Beutler 2003) , while the release of proinflammatory cytokines and other mediators cause upper respiratory tract infection symptoms (Eccles 2000a, b) . doi = 10.1007/5584_2015_110 id = cord-321756-a7eh4dkb author = Kwofie, Theophilus B title = Respiratory viruses in children hospitalized for acute lower respiratory tract infection in Ghana date = 2012-04-10 keywords = infection; respiratory; virus summary = The study was done to identify viruses associated with acute lower respiratory tract infection among children less than 5 years. Majority of acute lower respiratory tract infections (ALRTI) in developed countries have been reported to be often due to viral pathogens of which most common are RSV, PIV, influenza viruses, Adv, human Coronaviruses and Bocaviruses [5] [6] [7] . This study was done to determine the burden of respiratory viruses among children hospitalized at the Komfo Anokye Teaching Hospital for acute lower respiratory illness using the Real Time Polymerase Chain Reaction (RT-PCR). The overall prevalence is comparable to previous studies done in other developing countries [24] and the predominance of RSV is in accordance with the assertion that this virus is the single most frequent lower respiratory tract pathogen in infants and young children worldwide [25] [26] [27] . doi = 10.1186/1743-422x-9-78 id = cord-327493-v2iatbol author = Kwon, Hyo Jin title = Clinical manifestations of respiratory adenoviral infection among hospitalized children in Korea date = 2013-08-05 keywords = child; infection; respiratory summary = BACKGROUND: The objective of our study was to understand the epidemiological and clinical features of respiratory adenoviral infections among children at a single institution over the course of several years. CONCLUSION: Our study demonstrates that respiratory adenovirus infections are an important cause of hospitalization in young children, and contribute to a significant morbidity. The study was performed to more fully characterize the epidemiological pattern, clinical features and complications associated with hospitalization for adenoviral infection in Korean children. Adenovirus was associated with a wide variety of diagnoses, ranging from upper respiratory tract infections (URTI) to severe pneumonia and encephalitis ( Table 1 ). 22 reported that 70% of hospitalized children with adenoviral infection had pneumonia, while our results revealed a significant proportion of patients (45.4%) with URTI. Lower respiratory tract infections due to adenovirus in hospitalized Korean children: epidemiology, clinical features, and prognosis doi = 10.1111/ped.12108 id = cord-298227-av1ev8ta author = Kähler, Christian J. title = Fundamental protective mechanisms of face masks against droplet infections date = 2020-06-28 keywords = SARS; droplet; filter; infection; mask summary = doi = 10.1016/j.jaerosci.2020.105617 id = cord-001542-f089bs8r author = Lai, Kang Yiu title = Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus date = 2014-11-28 keywords = EBOV; Ebola; GP1,2; IFN; RNA; cell; infection; virus summary = These may include monoclonal antibody (mAbs)-based therapies (e.g. ZMapp), anti-sense phosphorodiamidate morpholino oligomers (PMO AVI-6002), lipid nanoparticle small interfering RNA (LNP-siRNA: TKM-Ebola), and an EBOV glycoprotein-based vaccine using live-attenuated recombinant vesicular stomatitis virus (rVSV-EBOGP) or a chimpanzee adenovirus (rChAd-EBOGP)-based vector. The GP2 of the EBOV is able to counter the interferon (IFN)-inducible antiviral protein tetherin which restricts the VP40-dependent budding of the progeny viral particles from infected cells [16] [17] [18] . Currently available therapeutic agents that are effective in targeting the EBOV infection in cell or animal studies may include convalescent plasma, favipiravir, chloroquine, amiodarone, dronedarone, verapamil, clomiphene, toremifene, IFN-β, Na + /K + exchangers, Na + /K + -ATPase pump inhibitors, and antioxidants. The anti-EBOV activity of clomiphene and toremifene is dependent not on its estrogen receptor antagonistic action but upon the ability of both drugs to induce a Niemann-Pick C-like phenotype to inhibit viral entry at late endosome. doi = 10.1186/2049-9957-3-43 id = cord-011968-abd891ej author = Lai, Yen-Chung title = Roles of Macrophage Migration Inhibitory Factor in Dengue Pathogenesis: From Pathogenic Factor to Therapeutic Target date = 2020-06-12 keywords = DENV; MIF; dengue; infection summary = Macrophage migration inhibitory factor (MIF) is a pleiotropic proinflammatory cytokine that mediates diverse immune responses, and the serum level of MIF positively correlates with disease severity in patients with dengue. In another study, it was demonstrated that live DENV2-induced endoplasmic reticulum (ER) stress is required for autophagy activation, viral replication and pathogenesis in HuH-7 and A549 cells [57] . In our study, since UV-inactivated viral particles could not induce MIF secretion or expression, it is possible that DENV infection triggered RNA sensing or pattern recognition receptor (PRR) activation, which was followed by the release of preformed MIF from the cytosol through the vesicle trafficking secretory pathway. Macrophage migration inhibitory factor induced by dengue virus infection increases vascular permeability Minocycline suppresses dengue virus replication by down-regulation of macrophage migration inhibitory factor-induced autophagy Dengue virus nonstructural protein 1 induces vascular leakage through macrophage migration inhibitory factor and autophagy doi = 10.3390/microorganisms8060891 id = cord-017831-anadq4j9 author = Lai, Yi-Horng title = Network Analysis of Comorbidities: Case Study of HIV/AIDS in Taiwan date = 2015-07-30 keywords = AIDS; HIV; infection summary = The results show that there is a high correlation in the following pairs/triad of diseases: human immunodeficiency virus infection with specified conditions (042) and pneumocystosis pneumonia (1363), human immunodeficiency virus infection with specified malignant neoplasms (0422) and kaposi''s sarcoma of other specified sites (1768), human immunodeficiency virus acquired immunodeficiency syndrome, and unspecified (0429) and progressive multifocal leukoencephalopathy (0463), and lastly, human immunodeficiency virus infection with specified infections (0420), meningoencephalitis due to toxoplasmosis (1300), and human immunodeficiency virus infection specified infections causing other specified infections (0421). In PDNs for females (Figure 4 ), human immunodeficiency virus infection with specified conditions (042) and cryptococcal meningitis (3210), kaposi''s sarcoma of unspecified (1769), and pneumocystosis (1363) are highly correlated. Human immunodeficiency virus infection with specified infections (0420) and specified infections causing other specified infections (0421), meningoencephalitis due to toxoplasmosis (1300), pneumocystosis (1363), kaschin-beck disease (7160), kaposi''s sarcoma of other specified sites (1768), with specified malignant neoplasms (0422), and falciparum malaria (0840) are highly correlation. doi = 10.1007/978-3-662-48319-0_14 id = cord-350618-rtilfnzi author = Lambelet, Valentine title = Sars‐CoV‐2 in the context of past coronaviruses epidemics: Consideration for prenatal care date = 2020-05-26 keywords = COVID-19; SARS; infection; pregnancy; pregnant; woman summary = College of Obstetricians and Gynaecologists (RCOG), pregnant women with moderate symptoms should self-isolate, unless they attend a maternity unit where patients in the 2 nd or 3 rd trimester meeting PHE criteria ( ≥ 1 of: (1) Clinical/radiological evidence of pneumonia, (2) Acute Respiratory Distress Syndrome (ARDS), (3) Fever ≥37.8 and at least one of acute persistent cough, hoarseness, nasal discharge/congestion, shortness of breath, sore throat, wheezing or sneezing) should be tested for COVID-19 and treated as infected until results are available. Past coronavirus epidemics were associated with adverse outcomes for the fetus and/or newborns including miscarriages (57%), preterm birth, fetal distress and FGR with SARS-CoV-1 infection during the 2 nd and 3 rd trimesters. In this review, we found that of 142 cases of SARS-CoV-2 infections in pregnancy, 28% experienced preterm birth and 14% had adverse fetal/neonata l outcomes (FGR, fetal/neonatal demise, severe symptoms at birth). doi = 10.1002/pd.5759 id = cord-315794-se0sq3c3 author = Lamps, L W title = Infective disorders of the gastrointestinal tract date = 2006-12-14 keywords = Crohn; disease; infection summary = Diagnostic histological features of selected enteric infections will be emphasized, including those that mimic other inflammatory conditions of the gut (such as ischaemia or idiopathic inflammatory bowel disease), along with available diagnostic methods that can aid in diagnosis. 2 Those producing a non-specific acute self-limited ⁄ infectious colitis (ASLC) pattern (e.g. Campylobacter jejuni); this is one of the most common inflammatory patterns in enteric infections. As these features can also be seen in smoldering Crohn''s disease and lymphocytic colitis, it is important to know the patient''s symptoms and, ideally, culture results as this differential diagnosis may be difficult to resolve on histological grounds alone. Selected specific food-and ⁄ or water-borne gastrointestinal infective disorders Escherichia coli, Campylobacter, Salmonella, Yersinia, Shigella and enteric viruses represent the most common food-borne pathogens worldwide. In addition, many of the food-and water-borne gastrointestinal infective diseases discussed below mimic other entities that are commonly encountered in surgical pathology practice, such as ischaemic colitis or idiopathic inflammatory bowel disease. doi = 10.1111/j.1365-2559.2006.02544.x id = cord-336045-8qcj5uiy author = Langlois, Isabelle title = Viral diseases of ferrets date = 2005-03-01 keywords = ADV; aleutian; disease; ferret; infection; virus summary = A tentative diagnosis of canine distemper is based on the presence of typical clinical signs, severe leukopenia, a history of potential exposure to the virus, and questionable vaccination. The severity of disease depends on the origin (mink or ferret) of the ADV strain that is involved as well as the immune status and genotype of the infected individual [25] . Ferrets are used extensively as an animal model for influenza virus pathogenesis and immunity studies because their biologic response to influenza infection is similar to that of humans [53, 54] . Neurologic symptoms, including ataxia, hind-limb paresis, and torticollis, were reported in ferrets that were infected experimentally with avian influenza A (H5N1) viruses that were isolated from the 1997 outbreaks of disease in domestic poultry markets in Hong Kong [50, 65] . Detection of Aleutian disease virus DNA in tissues of naturally infected mink doi = 10.1016/j.cvex.2004.09.008 id = cord-263749-bbhh5xb1 author = Larenas-Linnemann, Désirée title = Enhancing innate immunity against virus in times of COVID-19: trying to untangle facts from fictions date = 2020-10-09 keywords = COVID-19; infection; respiratory; vitamin summary = doi = 10.1016/j.waojou.2020.100476 id = cord-283779-mudwcypl author = Lauretani, Fulvio title = Assessment and treatment of older individuals with COVID-19 multi-system disease: clinical and ethical implications date = 2020-05-11 keywords = ARDS; COVID-19; SARS; clinical; infection; old; patient; phase summary = The chronic increase in inflammatory cytokines, augmented by COVID-19 infection, may explain the higher tendency for "the cascade leading to pulmonary fibrosis and insufficiency and activation of clotting" and poorer clinical prognosis, especially in multimorbid older persons (4) . In case of persistent fever, higher than 37.5°C for a time longer than 3 days and peripheral oxygen level lower than 95% after starting therapy, we should consider and proceed to hospitalization especially in multimorbid older patients with cardiac, respiratory diseases and diabetes. First, patients at risk for poor outcomes and higher mortality following infection with SARS-CoV-2, namely older adults and multimorbid individuals, should be checked for malnutrition through screening and assessment. Older patients infected by COVID-19 often experience atypical and less severe symptoms in older persons, side-effects of the drugs and require specific nutritional and motor treatment for avoiding disability and death. doi = 10.23750/abm.v91i2.9629 id = cord-305085-bv7udg9k author = Lawrence, Robert M. title = Chapter 13 Transmission of Infectious Diseases Through Breast Milk and Breastfeeding date = 2011-12-31 keywords = CMV; HBV; HCV; HIV; HTLV; MRSA; Nile; West; breast; infant; infection; milk; mother; transmission summary = Postnatal exposure of susceptible infants to CMV, including premature infants without passively acquired maternal antibodies against CMV, infants born to CMV-seronegative mothers, and immunodeficient infants, can cause significant clinical illness (pneumonitis, hepatitis, thrombocytopenia).* In one study of premature infants followed up to 12 months, Vochem et al 430 found CMV transmission in 17 of 29 infants (59%) exposed to CMV virolactia and breastfed compared with no infants infected of 27 exposed to breast milk without CMV. 38, 104, 121 Laboratory reports demonstrate the presence of cell-free virus and cell-associated virus in breast milk as well as various immunologic factors that could block or limit infection.* A dose-response relationship has been observed, correlating the HIV viral load in human milk as well as a mother'' s plasma viral load with an increased transmission risk for the breastfed infant. 76 No case of transmission of yellow fever virus from an infected mother to her infant via breastfeeding or breast milk has been reported. doi = 10.1016/b978-1-4377-0788-5.10013-6 id = cord-019089-oots4fe4 author = Laya, Bernard F. title = Infections date = 2013-08-31 keywords = Fig; child; infection; pneumonia summary = Imaging can also help evaluate complications to pneumonia and exclude other causes of respiratory distress including underlying developmental anomalies, foreign body, gastroesophageal reflux disease, and aspiration. Viruses are the most frequent cause of community-acquired pneumonia in infants older than 4 months and in preschool-aged children, with respiratory syncytial virus (RSV) being the most common. For school-aged children (6-16 years old), the incidence of bacterial infections from Streptococcus increases, although viral disease remains the most common cause (Condon 1991 ; Ostapchuk et al. Mycoplasma pneumoniae causes 30 % of lower respiratory tract infections in school-aged children (Condon 1991 ; Donnelly 2001 ) . However, lung parenchymal, pleural, and lymph node infl ammatory abnormalities can be visualized and characterized by MRI in children with pulmonary infections. Swine-origin infl uenza A (H1N1) viral infection in children: initial chest radiographic fi ndings doi = 10.1007/978-3-642-35573-8_13 id = cord-318852-gouz6tth author = Lee, J.S.E. title = Considerations and strategies in the organisation of obstetric anaesthesia care during the 2019 COVID-19 outbreak in Singapore date = 2020-04-20 keywords = infection; risk summary = It is in this context that local health authorities mandated that healthcare staff performing aerosol-generating procedures (AGP) such as tracheal intubation and extubation, bag-mask ventilation, orogastric tube insertion and bronchoscopy, don full personal protective equipment (PPE) regardless of risk status. Management in the labour ward ''High infection-risk'' parturients are placed in negative pressure ( -2.5 Pa) rooms and are asked to wear a surgical mask. When possible, we prefer to proceed with caesarean delivery in the ''high infection-risk'' patient only after she has been de-isolated or has tested ''negative'' for COVID-19 from the first nasopharyngeal swab. Highlights Identifying ''high-infection risk'' parturients is challenging in the COVID-19 outbreak A multidisciplinary approach is required to provide obstetric anaesthesia services Protocols for labour analgesia and caesarean delivery allow safe provision of care Infection control resource management allows for the allocation of finite resources Organisational changes are doi = 10.1016/j.ijoa.2020.04.003 id = cord-309274-2npxrrhr author = Lee, M.K. title = Prevalence of hospital infection and antibiotic use at a University Medical Center in Hong Kong date = 2007-02-02 keywords = infection; prevalence summary = authors: Lee, M.K.; Chiu, C.S.; Chow, V.C.; Lam, R.K.; Lai, R.W. title: Prevalence of hospital infection and antibiotic use at a University Medical Center in Hong Kong Hospital infection prevalence surveys were performed in our 1400-bed University medical centre in Hong Kong from 1985 to 1988. We investigated the rates of four major hospital-acquired infections (HAIs) (pneumonia, symptomatic urinary tract infection, surgical site infection and laboratory-confirmed bloodstream infection) in order to identify current distribution and any changes after 15 years. Demographic information, admission diagnosis, use of medical device and antibiotic were recorded by the ward nursing staff who had attended briefing sessions on each ward on the point prevalence survey with instructions on correct filling of a data collection form. The last survey in our hospital was performed over 15 years ago and some interesting changes in nosocomial infection rate and antibiotic use were found. doi = 10.1016/j.jhin.2006.12.013 id = cord-324333-huris8br author = Lee, Na Hyun title = Clinical usefulness of serum procalcitonin level in distinguishing between Kawasaki disease and other infections in febrile children date = 2017-04-25 keywords = PCT; infection summary = PURPOSE: The aims of this study were to compare serum procalcitonin (PCT) levels between febrile children with Kawasaki disease (KD) and those with bacterial or viral infections, and assess the clinical usefulness of PCT level in predicting KD. The proportion of patients in the KD group with PCT levels of >1.0 ng/mL was significantly higher in the nonresponders to the initial intravenous immunoglobulin treatment than in the responders (36% vs. The present study also showed similar results: (1) The mean PCT level in patients with KD and in those with bacterial infection was significantly higher than that in patients with viral infection. A combination of disease markers including ESR, CRP, and PCT may be useful for differentiating between KD and viral or bacterial infections. A combination of disease markers including ESR, CRP, and PCT may be useful for differentiating between KD and viral or bacterial infections. doi = 10.3345/kjp.2017.60.4.112 id = cord-347039-eap592i7 author = Lee, Seung-Hwan title = Maneuvering for advantage: the genetics of mouse susceptibility to virus infection date = 2003-08-31 keywords = MHC; cell; infection; mouse; virus summary = Receptors are recognized as important determinants of virus host range and tissue tropism; and some host resistance/susceptibility loci encode molecules that are expressed on the cell surface. Another example of natural host resistance is the restriction of ecotropic Murine LEUKEMIA VIRUS (MuLV) infection by the mouse Fv4 gene. The effort to understand the genetic basis of susceptibility to viral disease is driven by three considerations: (1) the increased public awareness of the toll imposed by viruses on the host; (2) the increase in susceptible human populations because of longer life expectancy, frequently accompanied by chronic illness, and the consequences of advances in medical technology, including immunosuppressive therapies for organ transplantation or treatment of malignancy; and (3) the need to develop new therapies for infections caused by multidrug-resistant Human killer-cell immunoglobulin-type receptor (KIR) is considered to be a functional homolog of mouse Ly49. Mouse genetics has also demonstrated that recognition and destruction of virus-infected cells by NK cells is mediated by specific interactions between activating NKcell receptors and viral target molecules. doi = 10.1016/s0168-9525(03)00172-0 id = cord-343074-dsubeaso author = Lee, Wan‐Ji title = Molecular epidemiology of a post‐influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3 date = 2014-06-01 keywords = Korea; infection; respiratory summary = title: Molecular epidemiology of a post‐influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3 An outbreak of upper respiratory tract infections associated with human adenovirus (HAdV) occurred on a national scale in Korea from September to December 2010, following a major H1N1 influenza pandemic. To determine the principal cause of the outbreak, direct polymerase chain reaction (PCR) amplification followed by sequence analysis targeting parts of the hexon gene of HAdV was performed. Serotypes of 1,007 PCR‐diagnosed HAdV‐positive samples from patients with an acute upper respiratory tract illness were determined and epidemiological characteristics including major aged group and clinical symptoms were analyzed. Epidemiological and molecular data presented in this study confirmed that the outbreak in 2010 was not associated with genetic alterations causing a change in the pathology of the major causative agent, HAdV-3, nor with multiple infections with other respiratory viruses. doi = 10.1002/jmv.23984 id = cord-333286-lr32e0w4 author = Lehtoranta, Liisa title = Role of Probiotics in Stimulating the Immune System in Viral Respiratory Tract Infections: A Narrative Review date = 2020-10-16 keywords = IFN; infection; probiotic; respiratory summary = We searched PubMed, Google Scholar, and Web of Knowledge for pre-clinical and clinical studies investigating the effect of probiotics on respiratory virus infections, immune response, and the course of upper and lower respiratory tract illness. Similar effects have been demonstrated in several mouse studies with the ability to reduce virus titers in lung tissues and modulation of antiviral and pro-inflammatory gene expression before and after viral infection. The upregulation of IFN response seems to prime cells for better resistance against virus infection as probiotics were shown effective in inhibiting the replication of various respiratory viruses, including influenza viruses and RSV. Similar effects have been demonstrated in mice with the ability of the probiotics to reduce virus titers in lung tissues and to modulate antiviral and pro-inflammatory gene expression before and after viral infection. Similar effects have been demonstrated in mice with the ability of the probiotics to reduce virus titers in lung tissues and to modulate antiviral and pro-inflammatory gene expression before and after viral infection. doi = 10.3390/nu12103163 id = cord-258336-zs04l3s0 author = Leotte, Jaqueline title = Impact and seasonality of human rhinovirus infection in hospitalized patients for two consecutive years date = 2017-06-30 keywords = HRV; infection; respiratory summary = doi = 10.1016/j.jped.2016.07.004 id = cord-016782-aods92rf author = Lessenger, James E. title = Diseases from Animals, Poultry, and Fish date = 2006 keywords = animal; disease; farm; human; infection summary = Workers, visitors, inspectors, veterinarians, and people who live on or adjacent to farms, ranches, feedlots, processing plants, and other agricultural endeavors are at risk for contracting diseases from animals, poultry, or fish. Methods of preventing the transmission of infectious material from animals and poultry to agricultural workers mirror in many ways the safety techniques for protection from chemicals, trauma and other hazards (see Chapter 6) . Key to the prevention of the transmission of animal disease to humans is the proper processing of food products. Diseases from Animals, Poultry, and Fish 369 Protective physical barriers in farm, ranch, or plant design allow for the raising or processing of food products without actual contact of humans with the animals or products. Production animals include cattle, pigs, goats, sheep, horses, dogs, deer, and other animals grown in small to large farms and ranches for human consumption. doi = 10.1007/0-387-30105-4_27 id = cord-286328-ap0wfjhq author = Lewis, Toby C. title = Nasal cytokine responses to natural colds in asthmatic children date = 2012-11-26 keywords = IFN; asthma; infection; viral summary = doi = 10.1111/cea.12005 id = cord-321132-xdpb3ukt author = Lhomme, Sebastien title = Influence of Polyproline Region and Macro Domain Genetic Heterogeneity on HEV Persistence in Immunocompromised Patients date = 2014-01-15 keywords = HEV; infection summary = We investigated the association between the genetic heterogeneity of HEV quasispecies in ORF1 and the outcome of infection in solid-organ transplant patients. Both sequence entropy and genetic distances during the hepatitis E acute phase were higher in patients whose infection became chronic than in those who cleared the virus. Both sequence entropy and genetic distances during the hepatitis E acute phase were higher in patients whose infection became chronic than in those who cleared the virus. We therefore analysed the characteristics of HEV quasispecies at the acute phase of hepatitis E in 2 groups of SOT patients, one whose infection became chronic and the other who cleared the virus. Both the complexity and diversity of the PPR and the macro domain were higher in viral population of the patients whose infection became chronic than in those who cleared the virus. doi = 10.1093/infdis/jit438 id = cord-016690-3gsq724l author = Li, Hongjun title = HIV/AIDS Related Respiratory Diseases date = 2013-09-30 keywords = AIDS; CD4; CDC; HIV; PCP; infection; lung; pulmonary summary = Its difference from the clinical manifestations of non-HIV infected patients is as the following: (1) More common pulmonary infi ltration with multiple involvements and rare cavities; (2) Higher incidence of dissemination (87-96 %) commonly along with blood fl ow and higher incidence of extrapulmonary tuberculosis (60-70 %); (3) More common lymph node tuberculosis, such as hilar, mediastinal and extrapleural lymphadenectasis; (4) Lower positive rate of tuberculin test (PPD); (5) More patients with no expectoration, with sputum smear for acid-fast bacilli staining is negative; (6) Higher incidence of resistant strains, high recurrence rate, and higher mortality (Table 17 .1 ). Based on the course of the disease, the diagnostic imaging demonstrations of Rhodococcus equi pulmonary infection can be divided into early stage, showing round liked fl aky blurry shadows surrounding unilateral hilum that has blurry boundary; middle stage (parenchymal change), showing central sphere liked high density shadow surrounding unilateral hilum, in parenchymal changes and with clear boundary; advanced stage (necrosis) showing secondary cavity of the pulmonary mass, possibly with hydropneumothorax and pleurisy. doi = 10.1007/978-94-007-7823-8_17 id = cord-288494-6qybdxc4 author = Liao, Qiaohong title = A clinical prediction rule for diagnosing human infections with avian influenza A(H7N9) in a hospital emergency department setting date = 2014-08-05 keywords = A(H7N9; China; infection; risk summary = We analyzed two databases that contained clinical and basic laboratory data from two groups of patients presenting similarly with acute respiratory infections to hospitals in China, including 121 laboratory-confirmed A(H7N9) cases and 2,603 patients who suffered from acute respiratory infections other than A(H7N9) influenza. A two-step regression model was used to develop the prediction rule, so as to simulate the decision making process in the setting of a clinic or hospital emergency room where a patient first presents [12, 13] . We had chosen the model with the best performance in terms of both the high sensitivity and area under the ROC curve, which were also maintained in the validation samples, to identify patients having a high risk for the infection at their initial clinical presentation so as to optimize resources during an epidemic. doi = 10.1186/s12916-014-0127-0 id = cord-271653-4q2olzx1 author = Libby, Peter title = The Heart in COVID19: Primary Target or Secondary Bystander? date = 2020-04-10 keywords = COVID-19; infection summary = Fulminant myocarditis due to direct viral infection can certainly occur, but patients with increased oxygen demands due to tachycardia and fever, and reduced oxygen delivery due to hypotension and hypoxemia can cause myocardial injury indirectly. Fulminant myocarditis due to direct viral infection can certainly occur, but patients with increased oxygen demands due to tachycardia and fever, and reduced oxygen delivery due to hypotension and hypoxemia can cause myocardial injury indirectly. Dealing with the immense challenge of COVID-19 disease, confronted with severely ill patients in dire straits with virtually no rigorous evidence base to guide our therapy, we must call upon our clinical skills and judgment. Dealing with the immense challenge of COVID-19 disease, confronted with severely ill patients in dire straits with virtually no rigorous evidence base to guide our therapy, we must call upon our clinical skills and judgment. doi = 10.1016/j.jacbts.2020.04.001 id = cord-288930-h13cxuh3 author = Lim, Faye J title = Viral Etiology and the Impact of Codetection in Young Children Presenting With Influenza-Like Illness date = 2016-07-20 keywords = child; infection; virus summary = doi = 10.1093/jpids/piw042 id = cord-260679-tm1s6wvj author = Lim, Wei Shen title = Pneumonia—Overview date = 2020-05-20 keywords = CAP; infection; pathogen; patient; pneumonia summary = doi = 10.1016/b978-0-12-801238-3.11636-8 id = cord-268553-2o4k24og author = Lin, Chun title = Etiology and characteristics of community-acquired pneumonia in an influenza epidemic period date = 2019-03-08 keywords = Yeast; cap; infection summary = doi = 10.1016/j.cimid.2019.03.004 id = cord-263744-zrzwhu0j author = Lin, Sheng-Wen title = Potential Trends of Point-of-Care Diagnostics—The Next Generation of the Laboratory Diagnosis date = 2020-09-30 keywords = bacterial; infection summary = Both of these issues underscore the need for the development and use of POC diagnostics using host biomarkers to distinguish between bacterial and viral infections in pediatric patients. Current biochemical analyses based on biomarkers, such as procalcitonin (PCT) and C-reactive protein (CRP) methods, can provide some clues for the differential diagnosis of bacterial and viral infections, but their low sensitivity and specificity means that they cannot be relied upon in and of themselves for treatment. Current biochemical analyses based on biomarkers, such as procalcitonin (PCT) and C-reactive protein (CRP) methods, can provide some clues for the differential diagnosis of bacterial and viral infections, but their low sensitivity and specificity means that they cannot be relied upon in and of themselves for treatment. Both of these issues underscore the need for the development and use of POC diagnostics using host biomarkers to distinguish between bacterial Diagnostics 2020, 10, 774 3 of 4 and viral infections in pediatric patients. doi = 10.3390/diagnostics10100774 id = cord-264159-e9071tyv author = Lin, Weikang Nicholas title = The Role of Single-Cell Technology in the Study and Control of Infectious Diseases date = 2020-06-10 keywords = HIV; RNA; cell; immune; infection; response; single summary = doi = 10.3390/cells9061440 id = cord-007796-zggk0x2q author = Lindemans, Caroline A. title = The Immune Response to Viral Lower Respiratory Tract Infection date = 2005 keywords = IFN-; RSV; infection; respiratory; virus summary = doi = 10.1007/0-387-25342-4_4 id = cord-017959-g0nf1iwm author = Lipkin, W. Ian title = Diagnosis, Discovery and Dissection of Viral Diseases date = 2014-02-27 keywords = PCR; assay; detection; infection; virus summary = Nested PCR tests that can employ consensus or specifi c primers in two sequential amplifi cation reactions with either one (hemi-nested) or two (fully nested) primers located 3′ with respect to the fi rst primer set may both accommodate sequence variation and be more sensitive than fl uorescent or beacon-based singleplex assays. Whereas multiplex PCR systems support rapid highthroughput diagnosis with highest sensitivity for a limited number of agents, microarray-based systems provide detection of all known pathogens for which sequence information is available, but at the expense of some degree of sensitivity. Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fl uid microbead-based assay MassTag polymerasechain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused infl uenza-like illness in New York State during doi = 10.1007/978-1-4899-7448-8_2 id = cord-336663-fawcn6em author = Liu, Chunyan title = Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012 date = 2015-10-01 keywords = hadv; infection summary = Here, HAdV types are characterized in children in the Beijing area with acute lower respiratory tract infections (ALRTIs) and the clinical features and laboratory findings of hospitalized HAdV-infected cases are described. However, because most clinical laboratories do not type the isolates, there is little published information about epidemiologic and clinical features of HAdV infections by type in children with ALRTIs. To identify HAdV types and species in children with ALRTIs in Beijing area and to characterize clinical features and laboratory findings of hospitalized HAdVinfected cases, respiratory specimens were collected from hospital-admitted pediatric patients with ALRTIs and typed HAdV positive samples using PCR and sequencing. This may also suggest that schoolage children are exposed to the most common endemic types of HAdV early in life, thereby establishing a protective immunity resulting only in mild clinical symptoms, such that upper respiratory tract infection does not require care in an emergency department or hospital in this age group. doi = 10.1186/s12879-015-1126-2 id = cord-023463-vr6uaw3a author = Liu, Wei title = Risk factors for SARS infection among hospital healthcare workers in Beijing: a case control study date = 2009-06-05 keywords = SARS; infection summary = Objective To evaluate possible severe acute respiratory syndrome (SARS) infection associated risk factors in a SARS affected hospital in Beijing by means of a case control study. Results Multivariate analysis confirmed the strong role of performing chest compression (or intubation, which is highly correlated), contact with respiratory secretion, and emergency care experience as risk factors to acquire SARS infection. Measures to prevent nosocomial infection included establishing isolation wards for triage SARS patients; training and monitoring hospital staff in infection-control procedures; active and passive screening of HCWs; enforcement of droplet and contact precautions; and compliance with the use of PPE. In summary, this study identified exposure to high-risk procedures (such as chest compression), and contact with respiratory secretions to be significant risk factors for SARS infection among HCWs in a hospital in Beijing. doi = 10.1111/j.1365-3156.2009.02255.x id = cord-274763-i6e3g3te author = Liu, Wen-Kuan title = Epidemiology of HBoV1 infection and relationship with meteorological conditions in hospitalized pediatric patients with acute respiratory illness: a 7-year study in a subtropical region date = 2018-07-16 keywords = hbov1; infection; respiratory summary = title: Epidemiology of HBoV1 infection and relationship with meteorological conditions in hospitalized pediatric patients with acute respiratory illness: a 7-year study in a subtropical region BACKGROUND: Human bocavirus 1 (HBoV1) is an important cause of acute respiratory illness (ARI), yet the epidemiology and effect of meteorological conditions on infection is not fully understood. METHODS: Samples from 11,399 hospitalized pediatric patients (≤14 years old), with ARI were tested for HBoV1 and other common respiratory pathogens using real-time PCR, between July 2009 and June 2016. We collected meteorological data for Guangzhou, including monthly mean temperature, mean relative humidity, rainfall, mean wind speed, mean air pressure, mean vapor pressure and sunshine duration for a 7-year period, to explore the correlation between meteorological conditions and prevalence of HBoV1. Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China doi = 10.1186/s12879-018-3225-3 id = cord-006523-zxn4oqly author = Lodha, Rakesh title = Nosocomial infections in pediatric intensive care units date = 2001 keywords = catheter; infection; nosocomial; patient summary = The common nosocomial infections in PICU are bloodstream infections (20–30% of all infections), lower respiratory tract infections (20–35%), and urinary tract infections (15–20%); there may be some differences in their incidence in different PICUs. The risk of nosocomial infections depends on the host characteristics, the number of interventions, invasive procedures, asepsis of techniques, the duration of stay in the PICU and inappropriate use of antimicrobials. 3 In the same study, it was observed that 91% of all nosocomial bloodstream infections occurred in children with central venous lines, 95% of nosocomial pneumonias occurred in those on mechanical ventilation and 77% of UTIs in children with urinary catheters. Transtracheal aspiration in non-intubated patients, percutaneous thin needle lung aspirations, bronchoalveolar lavage (bronchoscopic or blind), and protected bronchoscopic samples of the lower airways have all been suggested as methods for diagnosis, where contamination of lower respiratory secretions with upper airway flora is prevent-ed29~~ In the absence of gold standard criteria for the diagnosis of ventilator-associated pneumonia, quantitative cultures and microscopic examination of the lower respiratory tract secretions are the diagnostic tests of choice. doi = 10.1007/bf02722358 id = cord-025155-ow3r3469 author = Lokida, Dewi title = Underdiagnoses of Rickettsia in patients hospitalized with acute fever in Indonesia: observational study results date = 2020-05-24 keywords = Indonesia; Rickettsia; infection summary = title: Underdiagnoses of Rickettsia in patients hospitalized with acute fever in Indonesia: observational study results METHODS: Acute and convalescent blood from 975 hospitalized non-dengue patients was tested for Rickettsia IgM and IgG by ELISA. For the 103/975 (10.6%) non-dengue patients diagnosed with acute rickettsial infection, presenting symptoms included nausea (72%), headache (69%), vomiting (43%), lethargy (33%), anorexia (32%), arthralgia (30%), myalgia (28%), chills (28%), epigastric pain (28%), and rash (17%). Clinicians should include rickettsioses in their differential diagnosis of fever to guide empiric management; laboratories should support evaluation for rickettsial etiologies; and public policy should be implemented to reduce burden of disease. To characterize the epidemiology of rickettsioses in Indonesia, we performed Rickettsia diagnostic panels on blood from subjects in the Acute Fever Requiring Hospitalization (AFIRE) study [13] . Patients found to have rickettsial infection by reference laboratory testing were identified from INA-RESPOND''s [14] AFIRE observational cohort study conducted in Indonesia from 2013 to 2016. doi = 10.1186/s12879-020-05057-9 id = cord-324148-bllyruh8 author = Loubet, Paul title = Characteristics of human metapneumovirus infection in adults hospitalized for community-acquired influenza-like illness in France, 2012-2018: a retrospective observational study date = 2020-04-10 keywords = infection; patient summary = title: Characteristics of human metapneumovirus infection in adults hospitalized for community-acquired influenza-like illness in France, 2012-2018: a retrospective observational study OBJECTIVES: To describe the prevalence, clinical features and complications of human metapneumovirus (hMPV) infections in a population of adults hospitalized with influenza-like illness (ILI). METHODS: This was a retrospective, observational, multicenter cohort study using prospectively collected data from adult patients hospitalized during influenza virus circulation, for at least 24h, for community-acquired ILI (with symptom onset <7 days). The most frequent viruses seen in primary care are influenza 75 viruses A/B, rhinovirus, coronavirus, respiratory syncytial virus (RSV) and human 76 metapneumovirus (hMPV) [1, 2] . Baseline 275 characteristics and clinical symptoms related to respiratory viruses identified among patients 276 presenting with influenza-like illness in primary care Clinical 340 characteristics and outcome of respiratory syncytial virus infection among adults hospitalized 341 with influenza-like illness in France doi = 10.1016/j.cmi.2020.04.005 id = cord-267132-nb0j6k3h author = Loveday, H.P. title = epic3: National Evidence-Based Guidelines for Preventing Healthcare-Associated Infections in NHS Hospitals in England date = 2013-12-10 keywords = ABHR; BSI; CAUTI; HCAI; Health; catheter; hand; infection; patient; study summary = Clinical effectiveness (i.e. using prevention measures that are based on reliable evidence of efÀ cacy) is a core component of an effective strategy designed to protect patients from the risk of infection, and when combined with quality improvement methods can account for signiÀ cant reductions in HCAI such as meticillin-resistant Staphylococcus aureus (MRSA) and Clostridium difÀ cile. Full text conÀ rms that the article: relates to infections associated with hospital hygiene; is written in English; is primary research (randomised controlled trials, prospective cohort, interrupted time series, controlled before-after, quasi-experimental, experimental studies answering speciÀ c questions), a systematic review or a meta-analysis including the above designs; and informs one or more of the review questions. 334 In a prospective cohort study using data from two randomised trials and a systematic review to estimate rates of PICC-related bloodstream infection in hospitalised patients, the author concluded that PICCs used in high-risk hospitalised patients are associated with a rate of CR-BSI similar to conventional CVCs placed in the internal jugular or subclavian veins (two to À ve per 1000 catheter-days). doi = 10.1016/s0195-6701(13)60012-2 id = cord-007575-5ekgabx5 author = Luby, James P. title = Southwestern Internal Medicine Conference: Pneumonias in Adults Due to Mycoplasma, Chlamydiae, and Viruses date = 2016-01-14 keywords = CMV; infection; influenza; patient; pneumonia; virus summary = Important trends and developments in the field include (1) the emergence of a Chlamydia psittaci strain (TWAR) that is passaged from human to human, causes a mycoplasma-like illness, and that is relatively resistant to erythromycin, (2) the recognition of respiratory syncytial virus as a pathogen in nursing home outbreaks and in immunosuppressed adults, (3) the continuing high lethality of fully developed influenza pneumonia, (4) the efficacy of acyclovir and adenine arabinoside in limiting the complications of varicella-zoster virus infections, and (5) the increasing frequency of pneumonia caused by cytomegalovirus and the severity of this disorder in highly immunosuppressed patients. Important trends and developments in the field include (1) the emergence of a Chlamydia psittaci strain (TWAR) that is passaged from human to human, causes a mycoplasma-like illness, and that is relatively resistant to erythromycin, (2) the recognition of respiratory syncytial virus as a pathogen in nursing home outbreaks and in immunosuppressed adults, (3) the continuing high lethality of fully developed influenza pneumonia, (4) the efficacy of acyclovir and adenine arabinoside in limiting the complications of varicella-zoster virus infections, and (5) the increasing frequency of pneumonia caused by cytomegalovirus and the severity of this disorder in highly immunosuppressed patients. doi = 10.1097/00000441-198707000-00007 id = cord-331500-l3hkn2li author = Luyt, Charles-Edouard title = Pulmonary infections complicating ARDS date = 2020-11-11 keywords = ARDS; ECMO; ICU; VAP; infection; patient summary = Whatever the initial lung injury, patients with ARDS are prone to develop secondary pulmonary infection, namely ventilator-associated pneumonia (VAP). While glucocorticoids are classically considered as immunosuppressive drugs, it has been shown that they can prevent the immune reprogramming observed after inflammatory response [16] , thus limiting the susceptibility of patients admitted to the intensive care unit (ICU) to respiratory complications such as pneumonia or ARDS and improving outcomes of patients with ARDS [17] . Peripheral blood markers have the advantage of avoiding the need for bronchoscopic sampling and are therefore easier to obtain; however, they are generally less able to discriminate pneumonia from other infections Table 1 Summary of host-based biomarkers for diagnosis of pneumonia in ARDS ARDS acute respiratory distress syndrome, RCT randomized controlled trial, sTREM soluble triggering receptor expressed on myeloid cells, VAP ventilator-associated pneumonia, HLA human leukocyte antigen doi = 10.1007/s00134-020-06292-z id = cord-023748-3kfy36hg author = Lye, Patricia S. title = Fever date = 2017-05-12 keywords = CSF; FUO; UTI; bacterial; chapter; child; diagnosis; fever; infection; meningitis summary = Although rapid testing for viral pathogens is often readily available, a detailed investigation to identify a viral pathogen is not necessary unless the confirmation of a viral infection will change the acute diagnostic plan; treatment with antivirals is an option (HSV, influenza) if the fever is prolonged and evolves into FUO or if there is end-organ involvement, as in hepatitis, myocarditis, encephalitis, or meningitis. Occult bacteremia is defined by the presence of a positive blood culture for pathogenic bacteria in a febrile patient who does not appear extremely ill and who has no focus of infection, excluding otitis media. A combination of clinical evaluation and laboratory studies can be used to define a specific population of infants aged 29-60 days who do not appear ill and are at low risk for bacterial infections. doi = 10.1016/b978-0-323-39956-2.00039-x id = cord-026005-f2khcjdy author = López, Alfonso title = Respiratory System, Mediastinum, and Pleurae date = 2017-02-17 keywords = Fig; Mannheimia; Mycobacterium; Mycoplasma; Pasteurella; alveolar; cause; cell; disease; horse; infection; lesion; lung; nasal; pneumonia; pulmonary; respiratory; type summary = Microscopic examination of properly collected, stored, and processed samples may reveal many erythrocytes and siderophages in pulmonary hemorrhage or left-sided heart failure; inclusion bodies or syncytial cells in viral pneumonias; increased number of leukocytes in pulmonary inflammation; abundant mucus in asthma or equine recurrent airway obstruction (RAO); the presence of pulmonary pathogens, such as parasites, fungi, and bacteria; or tumor cells in cases of pulmonary neoplasia. The portal of entry for the respiratory form is typically aerogenous, and the disease is generally transient; thus the primary viral-induced lesions in the nasal mucosa and lungs are rarely seen at necropsy unless complicated by secondary bacterial rhinitis, pharyngitis, or bronchopneumonia. Laryngeal edema occurs in pigs with edema disease; in horses with purpura hemorrhagica; in cattle with acute interstitial pneumonia; in cats with systemic anaphylaxis; and in all species as a result of trauma, improper endotracheal tubing, inhalation of irritant gases (e.g., smoke), local inflammation, and animal species is classified as fibrinous, catarrhal, purulent, or granulomatous (Figs. doi = 10.1016/b978-0-323-35775-3.00009-6 id = cord-022176-hprwqi4n author = Löscher, Thomas title = Emerging and Re-emerging Infectious Diseases date = 2009-07-28 keywords = Africa; Europe; United; case; country; disease; infection summary = Since the detection of the etiologic infectious agent and the subsequent development of laboratory diagnostic tests in the 1980s, the number of reported cases of Lyme disease has increased from 0 to 16,000 per year, indicating that it is an "emerging diagnosis." The reported numbers vary depending on the reproduction of the hosting rodents for ticks as well as the contacts between humans and nature (Spach et al. In recent years, norovirus infections are increasingly recognized as the cause of large outbreaks of diarrheal diseases in the general population, school classes, nursing homes, hospitals, and cruise ships in western countries with peaks in colder seasons (winter epidemics) (Centers of disease control 2006; Verhoef et al. Definition: only infections that are newly discovered in humans are listed in this chapter: HIV, new variant of Creutzfeldt-Jakob disease (vCJD), hemorrhagic uremic syndrome (HUS) caused by enterohemorrhagic Escherichia coli, viral hemorrhagic fevers like Hanta, Lassa, Ebola, and Marburg fever, Nipah virus encephalitis, monkeypox, human ehrlichiosis, severe acute respiratory syndrome (coronavirus infection, SARS), and avian influenza (H5N1) (see Fig. 3 .1 and Table 3 .2). doi = 10.1007/978-0-387-93835-6_3 id = cord-355171-oi3ezlsl author = MACINTYRE, C. R. title = Quantifying the risk of respiratory infection in healthcare workers performing high-risk procedures date = 2013-12-05 keywords = HRP; infection; risk summary = This study determined the risk of respiratory infection associated with high-risk procedures (HRPs) performed by healthcare workers (HCWs) in high-risk settings. In droplet transmission, pathogens or droplets which are larger than 5 μm, such as influenza virus and Bordetella pertussis are transmitted from an infected patient to HCWs through breathing, talking, coughing, sneezing, as well as through performing high-risk procedures (HRPs) [2, 7, 8] . Although various guidelines and policies for infection control measures are implemented in healthcare settings worldwide, the risk of transmission of infectious diseases while performing HRPs has not been well quantified. doi = 10.1017/s095026881300304x id = cord-350186-fogm1gkg author = MAMMAS, IOANNIS N. title = Current views and advances on Paediatric Virology: An update for paediatric trainees date = 2015-11-24 keywords = HPV; Medicine; Paediatric; RSV; Virology; infection summary = The Workshop on Paediatric Virology, which took place on Saturday October 10, 2015 in Athens, Greece, provided an overview of recent views and advances on viral infections occurring in neonates and children. Among the non-vaccine related topics, emphasis was given to viral infections in prematurely born infants and their long-term outcomes, new paediatric intensive care management options for bronchiolitis related to respiratory syncytial virus, the clinical implications of hepatitis B virus and cytomegalovirus genotyping, the Ebola virus threat and preparedness in Paediatric Emergency Departments, oral, oropharynx, laryngeal, nasal and ocular viral infections and Merkel cell polyomavirus as a novel emerging virus of infancy and childhood. The majority of viral conjunctivitis in children are caused by adenovirus, a DNA virus, which can cause a range of human diseases, including upper respiratory tract infection. doi = 10.3892/etm.2015.2890 id = cord-349298-8s69wprh author = MUNYWOKI, P. K. title = Influence of age, severity of infection, and co-infection on the duration of respiratory syncytial virus (RSV) shedding date = 2014-06-05 keywords = RSV; infection summary = The shedding durations were longer than previous estimates (3·9–7·4 days) based on immunofluorescence antigen detection or viral culture, and were shown to be strongly associated with age, severity of infection, and revealed potential interaction with other respiratory viruses. Respiratory syncytial virus (RSV) is a major viral cause of lower respiratory tract infection in children worldwide [1] with the key risk group being young infants [2] . The rate of RSV recovery was lower (i.e. shedding duration increased) by 65% in episodes with co-infection compared to those without (aHR 0·35, 95% CI 0·23-0·51), with a similar result for each virus individually. A community study nested within a birth cohort in coastal Kenya targeting symptomatic RSV infections by Okiro and colleagues reported a mean duration of shedding of 4·5 days [12] . doi = 10.1017/s0950268814001393 id = cord-289697-g24xib4l author = MacDowell, Ana L. title = Infectious triggers of asthma date = 2005-03-01 keywords = RSV; asthma; infection; respiratory summary = doi = 10.1016/j.iac.2004.09.011 id = cord-341827-z9r5i0ky author = Macias-Ordonez, R. title = The misleading illusion of COVID-19 confirmed case data: alternative estimates and a monitoring tool date = 2020-05-25 keywords = infection; preprint summary = Assuming that detection remains constant after Infection 34 Date, we estimated the number of deaths and the estimated percentage of the 35 population of each country expected to be immune up to 23 days into the future. Assuming that detection remains constant after Infection 34 Date, we estimated the number of deaths and the estimated percentage of the 35 population of each country expected to be immune up to 23 days into the future. . https://doi.org/10.1101/2020.05.20.20107516 doi: medRxiv preprint Introduction 50 COVID-19 confirmed case data (CCD) are the central piece of information in most 51 news, official reports, conversations, forecasting efforts, and are also probably central to 52 most decisions made by authorities worldwide since the pandemic outbreak in 53 December 2019. . https://doi.org/10.1101/2020.05.20.20107516 doi: medRxiv preprint 20 antibodies, we suggest that estimates based on reported deaths and IFR are a more 405 reliable alternative to estimate the spread of SARS-CoV-2 than CCD in any country for 406 which age structure data is available and data of reported deaths is trustworthy. doi = 10.1101/2020.05.20.20107516 id = cord-016499-5iqpl23p author = Mackay, Ian M. title = Rhinoviruses date = 2014-02-27 keywords = ARI; HRSV; HRV; IFN; PCR; RNA; human; infection; respiratory; rhinovirus; viral; virus summary = A convenience population of 15 healthy children (1-9 years old) without asthma were followed during at least three seasons, and picornaviruses were detected in 5 % of 740 specimens (21 % of infections) not associated with symptoms, The impact of HRV typing and of sampling based only on symptoms. Clinical features and complete genome characterization of a distinct human rhinovirus genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children Comparison of results of detection of rhinovirus by PCR and viral culture in human nasal wash specimens from subjects with and without clinical symptoms of respiratory illness Detection of human rhinovirus C viral genome in blood among children with severe respiratory infections in the Philippines doi = 10.1007/978-1-4899-7448-8_29 id = cord-267816-84z9fp2u author = Magdi, Mohamed title = Severe Immune Thrombocytopenia Complicated by Intracerebral Haemorrhage Associated with Coronavirus Infection: A Case Report and Literature Review date = 2019-07-12 keywords = ITP; infection summary = doi = 10.12890/2019_001155 id = cord-333950-e0hd3iuu author = Maillard, Jean-Yves title = Reducing antibiotic prescribing and addressing the global problem of antibiotic resistance by targeted hygiene in the home and everyday life settings: A Position Paper date = 2020-04-18 keywords = AMR; antibiotic; home; hygiene; infection summary = The authors call upon national and international policy makers, health agencies and healthcare professionals to further recognize the importance of targeted hygiene in the home and everyday life settings for preventing and controlling infection, in a unified quest to tackle AMR. 3, 4 The main driver is overuse and misuse of antibiotics in medicine and agriculture including unregulated over-the-counter sales, while global spread of resistant bacteria or resistance genes is attributed to poor infection prevention and control in healthcare facilities, and sub-optimal hygiene and sanitation in communities, confounded by poor infrastructure and weak governance. 94 Studies in day-care centers and schools in which hand hygiene was combined with cleaning and/or disinfection of environmental surfaces indicate a positive impact on illness rates and reduction in the use of antibiotics. The evidence set out in this paper suggests that, if combined with measures ensuring clean water and adequate sanitation, targeted hygiene practices in home and everyday life settings could make a significant contribution to tackling AMR through infection prevention and a consequential reduction in antibiotic prescribing. doi = 10.1016/j.ajic.2020.04.011 id = cord-027550-yyqsatqw author = Mammas, Ioannis N. title = Update on current views and advances on RSV infection (Review) date = 2020-06-15 keywords = RSV; bronchiolitis; child; infection; respiratory; virus summary = doi = 10.3892/ijmm.2020.4641 id = cord-297790-tpjxt0w5 author = Mandl, Judith N. title = Going to Bat(s) for Studies of Disease Tolerance date = 2018-09-20 keywords = IFN; RNA; bat; dna; infection; virus summary = Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. It is likely that differences in evolutionary history of pathogen exposure between bats and humans have led to distinct adaptations in anti-viral immune responses and the ability to tolerate certain infections without disease while being susceptible to others. We summarize this work below, but comparisons of observations made across species suggest that although a number of species appear to be capable of avoiding the pathological effects of RNA virus infection, each bat species may have achieved this through distinct pathways, possibly involving changes to both increase pathogen replication control and to mitigate any immunopathology through decreased inflammatory responses and hence increased disease tolerance. doi = 10.3389/fimmu.2018.02112 id = cord-257299-z9u12yqb author = Mansi, N. title = Ear, nose and throat manifestation of viral systemic infections in pediatric patients date = 2009-12-31 keywords = EBV; cause; child; infection; respiratory; virus summary = Common childhood viral infections, such as measles and mumps are probably an unrecognized cause of acute or progressive damage to hearing [5] . Measles infection can be avoided by administering a reduced, live-virus vaccine to children between the ages of 12 and 15 months (MMR). The etiology of the acute forms in the respiratory airways is, initially, of a viral nature in most patients, with later, secondary bacterial infections on the mucous lesions caused by the viral agents [31] . Herpangina is an extremely contagious illness caused by a coxackievirus characterized by a presence of a vesicular exanthema at the velopharyngeal mucous level and acute or croup laryngotracheitis [38] [39] [40] [41] when viral infections are associated. The most common manifestation of the primary infection of this organism is infective mononucleosis (IM), a sometimes acute, but often asymptomatic clinical syndrome which more often strikes children, adolescents, and young adults [82] . Viral etiology and epidemiology of acute lower respiratory tract infections in children doi = 10.1016/s0165-5876(09)70006-0 id = cord-017503-g2n4d0wi author = Manson, David title = Diagnostic Imaging of Neonatal Pneumonia date = 2010-05-18 keywords = infection; neonatal summary = Given the fulminant potential for some etiologic pathogens which cause neonatal pneumonia, any abnormality on the chest radiograph which may suggest a pulmonary infection warrants the initiation of broad spectrum antibiotic coverage (Dennehy 1987; Kirkpatrick and Mueller 1998; Speck et al. Furthermore, many of these neonates do not suffer from pneumonia in isolation, but may also have complicating features such as hyaline membrane disease, meconium or amniotic fl uid aspiration, persistent fl pulmonary hypertension, transient tachypnea of the newborn, secondary ARDS, patency of the ductus arteriosus, or a variety of other causes of neonatal respiratory distress. Others have suggested that air-space disease in the presence of a pleural effusion is more suggestive of bacterial pneumonia than of other causes of neonatal respiratory distress, especially when group B streptococcus is the etiologic agent (Haney et al. doi = 10.1007/978-3-540-33749-2_7 id = cord-022520-ebj51v9o author = Marini, Robert P. title = Biology and Diseases of Ferrets date = 2007-09-02 keywords = Bell; Fox; Helicobacter; Mustela; clinical; diagnosis; disease; ferret; infection; kit; sign; treatment summary = Campylobacter jejuni is a gram-negative, spirally curved microaerophilic bacterium that is recognized as a significant cause of human enteritis and is as-sociated with diarrheic illness in several animal species, including dogs, cats, cows, goats, pigs, mink, ferrets, and sheep (Carter et al., 1995) . Reports of spontaneous cases in ferrets require diagnostic confirmation and differentiation from cases of proliferative bowel disease and other infectious and noninfectious causes of diarrhea. Systemic infection with the bovine strain in ferrets results in disseminated disease with weight loss, anorexia, lethargy, death, and miliary lesions involving the lungs and other viscera (Fox, 1998a) . Clinical disease may occur in kits as young as 1-4 days old or in older animals up to 6 weeks of age. Other potential etiologies that have been considered include two infectious agents that are known to cause chronic immune stimulation in affected ferrets, the Aleutian disease virus (ADV) and Helicobacter mustelae. doi = 10.1016/b978-012263951-7/50016-8 id = cord-320663-xypg6evo author = Market, Marisa title = Flattening the COVID-19 Curve With Natural Killer Cell Based Immunotherapies date = 2020-06-23 keywords = IFN; MERS; SARS; cell; covid-19; infection; natural; patient summary = A common feature of coronavirus infections is that significant morbidity and mortality is associated with lung injury and acute respiratory distress syndrome resulting from an exaggerated immune response, of which NK cells are an important component. Natural Killer (NK) cells are a key component of the innate immune system and are critical in the response to many viral infections in humans and animal models (1) (2) (3) . Altogether these studies show that during acute CoV infection, inflammatory monocyte-macrophages and neutrophils accumulate in the lungs and produce cytokines and chemokines that induce the activation and migration of lymphocytes, including NK cells, to the lungs, where they could be one of the main producers of IFN-γ (148). Studies have reported that patients infected with SARS-CoV-2 have lower levels of circulating NK cells and these express a greater level of inhibitory receptors (e.g., NKG2A) while producing less IFN-γ (127, 129, 130) . doi = 10.3389/fimmu.2020.01512 id = cord-017021-n6rpuvwd author = Marriott, Deborah J. title = Common Infections Following Lung Transplantation date = 2018-08-31 keywords = Nocardia; infection; lung; recipient; transplant summary = • physical factors such as denervation of the allograft resulting in a reduced cough reflex and anastomotic site stenosis with distal infection • the ''net state of immunosuppression''-the result of all factors including host immune system, anti-rejection immunosuppressive therapy and concomitant viral infections such as cytomegalovirus that contribute to a patient''s risk of infection • epidemiological exposure to organisms, including donor-derived infections, community acquired infections, travel related infections and healthcare associated infections • the use of prophylactic antimicrobial agents in the post-transplant period Longer treatment is required for severe or disseminated infection or for infection involving the central nervous system and/or bone and joint and in pulmonary disease with ongoing AFB detectable in sputum (>2 months) • streptomycin should not be used in the lung transplant setting because of the associated high-risk of nephrotoxicity. doi = 10.1007/978-3-319-90933-2_15 id = cord-015922-5wwy0m2k author = Marty, Francisco M. title = Infection in the Hematopoietic Stem Cell Transplant Recipient date = 2008 keywords = CMV; GVHD; HSCT; infection; patient; therapy summary = Other prophylactic strategies commonly utilized in HSCT patients include acyclovir to prevent herpes simplex virus (HSV) and VZV reactivation, fluoroquinolones [5] to prevent gram-negative sepsis and fluconazole to prevent yeast infection. It has been suggested that EBV viral load surveillance in peripheral blood be carried out in high risk patients (those with primary EBV infection, anti-T cell antibody therapy for GVHD, HLA-mismatched or T cell-depleted HSCT recipients), with decreased immunosuppression +/− antiviral therapy (acyclovir or ganciclovir) carried out in the setting of high viral loads [1, 4, 41, 42] . Infliximab use in patients with severe graftversus-host disease and other emerging risk factors of non-Candida invasive fungal infections in allogeneic hematopoietic stem cell transplant recipients: a cohort study doi = 10.1007/978-1-59745-438-4_19 id = cord-003926-ycdaw2vh author = Maslow, Joel N. title = Zika Vaccine Development—Current Progress and Challenges for the Future date = 2019-07-14 keywords = Zika; infection; vaccine; virus summary = Of note, the first demonstration of immunoprotection was as part of a 1953 study to define the ultrastructural characteristics of Zika virus, that found intramuscular vaccination of mice with infectious viral filtrates protected against cerebral infection [36] . In pre-clinical studies, vaccinated mice and non-human primates were shown to develop B and T-cell immune responses against the Zika virus envelope and protected against development of neurologic disease and death in immunosuppressed, interferon α, β receptor deficient (IFNAR) mice [43] . A subsequent study in non-human primates vaccinated twice at four-week intervals with alum generated binding and microneutralization antibody titers of 3.54 and 3.55 log10, respectively, and complete protection against viremia and viruria following challenge with either Brazilian or Puerto Rican strains of Zika virus [47] . Guillain-Barre Syndrome outbreak associated with Zika virus infection in French Polynesia: A case-control study doi = 10.3390/tropicalmed4030104 id = cord-023669-3ataw6gy author = Masur, Henry title = Critically Ill Immunosuppressed Host date = 2009-05-15 keywords = CD4; CMV; HIV; ICU; infection; patient; therapy summary = As the population of patients with cancer, organ transplants, vasculitides, and human immunodefi ciency virus (HIV) infection has grown, intensivists are seeing more and more patients with altered immunity. For instance, if a patient presents with severe hypoxemia and diffuse pulmonary infi ltrates, a health care provider who recognizes a prior splenectomy as the major predisposition to infection would focus the diagnostic evaluation and the empiric therapy on Streptococcus pneumoniae and Haemophilus infl uenzae. Patients with HIV infection develop clinical disease as a result of three basic processes: the direct effect of HIV on specifi c organs (e.g., cardiomyopathy, enteropathy, dementia); immunologically mediated processes (e.g., glomerulonephritis, thrombocytopenia); or opportunistic infections and tumors that are enabled by HIV-induced immunosuppression. For instance, if a patient with HIV infection and a CD4+ T lymphocyte count of 700 cells/µL presents with diffuse pulmonary infi ltrates, the diagnostic evaluation and empiric antimicrobial regimen should focus on S. doi = 10.1016/b978-032304841-5.50056-x id = cord-293871-hzes7mwt author = McGuinness, Sarah L. title = Pretravel Considerations for Non-vaccine-Preventable Travel Infections date = 2018-11-26 keywords = MERS; Zika; infection summary = In this chapter, pretravel considerations for major non-vaccine-preventable infectious diseases are covered, including specific advice for dengue, chikungunya, Zika, Middle East respiratory syndrome coronavirus (MERS-CoV), and avian influenza. These include mosquito-borne infections such as dengue, chikungunya, and Zika, and regionally endemic severe respiratory infections such as Middle East respiratory syndrome (MERS) and some strains of avian influenza. These include mosquito-borne infections such as dengue, chikungunya, and Zika, and regionally endemic severe respiratory infections such as Middle East respiratory syndrome (MERS) and some strains of avian influenza. 25 Male-to-female, male-to-male, and femaleto-male transmission to unprotected sexual contacts of returning Following a short incubation period, with symptoms typically beginning 4-7 days (range 3-14 days) after exposure, dengue can present with a wide spectrum of illnesses, from asymptomatic infection to severe and fatal disease. doi = 10.1016/b978-0-323-54696-6.00007-0 id = cord-027679-89yt6fzo author = McLoud, Theresa C. title = Pulmonary Infections in the Normal Host date = 2020-06-22 keywords = Box; Fig; States; United; infection; pneumonia summary = The radiographic appearance of bronchopneumonia pneumonia is most frequently that of multiple, ill-defined nodular opacities that are patchy but that may eventually become confluent and produce consolidation with airspace opacification (Fig. 3-4) . Klebsiella pneumonia (Box 3-5) usually occurs in middle-aged or elderly patients, in those with underlying chronic lung disease, and in alcoholic individuals. Clinical features include acute febrile illness without pneumonia; systemic disease with primarily pulmonary manifestations; a peak incidence in patients older than 60 years; a predisposition in smokers and those with alcoholic liver disease; high fever, shaking chills, and cough with small amounts of mucoid sputum; pleuritic chest pain; watery diarrhea in about one half of patients; and headache. In the normal host, the most common finding is that of single or multiple pulmonary nodules that are approximately 1 to 5 cm in diameter and that usually occur in the lower lobes (Fig. 3-38) . doi = 10.1016/b978-0-323-02790-8.00003-2 id = cord-289139-5ljqnc39 author = Mengelle, C. title = The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit date = 2014-09-03 keywords = infection; respiratory summary = doi = 10.1016/j.jcv.2014.08.023 id = cord-011095-79ce5900 author = Meskill, Sarah D. title = Respiratory Virus Co-infection in Acute Respiratory Infections in Children date = 2020-01-24 keywords = RSV; infection; respiratory; viral summary = One study in children under age 5 years old found that respiratory syncytial virus (RSV), human metapneumovirus (HMPV), and parainfluenza viruses (PIV) were more likely to be causative of disease [8] . In an evaluation of children under 18 years old admitted to the hospital with a diagnosis of pneumonia, the most common cause of infection, whether bacterial or viral, was RSV quickly followed by rhinovirus [12] . While some studies do have RSV and rhinovirus as the leading cause of pneumonia in children, another important common viral contributor is influenza [15] . [55] did a systemic review of patients of all ages with respiratory illnesses and found that studies that recruited young children were more likely to report high rates of co-infection and that there were inconclusive results on risk of hospitalization or ICU admission. Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children. doi = 10.1007/s11908-020-0711-8 id = cord-354492-6r6qs4pp author = Messina, Giovanni title = Functional Role of Dietary Intervention to Improve the Outcome of COVID-19: A Hypothesis of Work date = 2020-04-28 keywords = COVID-19; IL-6; TNF; adiponectin; infection; role summary = Considering that the COVID-19 infection can generate a mild or highly acute respiratory syndrome with a consequent release of pro-inflammatory cytokines, including IL-6 and TNF-α, a dietary regimen modification in order to improve the levels of adiponectin could be very useful both to prevent the infection and to take care of patients, improving their outcomes. In human infections with highly virulent respiratory viruses-such as avian influenza H5N1, H7N9, Severe Acute Respiratory Syndrome (SARS) coronavirus, and Coronavirus Disease-19 (COVID-19)-immunopathogenesis caused by the overproduction of pro-inflammatory cytokines may play an essential role in disease progression and mortality [3] . Finally, considering that the COVID-19 infection can generate a mild or highly acute respiratory syndrome with a consequent release of pro-inflammatory cytokines, including IL-6 and TNF-α, a modification of the dietary regimen in order to improve the levels of adiponectin could be very useful both to prevent the infection and to take care of the patients, improving their outcomes. doi = 10.3390/ijms21093104 id = cord-354200-51wk3h75 author = Miller, A. C. title = Statistical deconvolution for inference of infection time series date = 2020-10-20 keywords = infection summary = In this paper, we propose a statistically robust method to infer infection time series from delayed data, which we call the Robust Incidence Deconvolution Estimator (RIDE). The first class, which we term re-convolution estimators, estimate the infection curve by sampling from an assumed delay distribution and shifting observed case reports backward in timeeffectively, applying a convolution operation in reverse. The expected value of the observed data Y is a convolution of the infection time series X with the delay distribution θ; estimation of X involves the deconvolution of Y and θ. In general, we find that the model-based approaches more accurately infer the infection time series than the re-convolution and Richardson-Lucy estimators (as measured by mean squared error). As stated in the Methods section, model-based estimators start with a likelihood model for observed case data, conditioned on the underlying incidence curve. doi = 10.1101/2020.10.16.20212753 id = cord-302403-kahi8cbc author = Miller, Robert F. title = Pulmonary Infections date = 2009-05-15 keywords = AIDS; CD4; HAART; HIV; PCP; SMX; bal; infection; patient summary = Before HAART, defined as a combination of medications that usually includes at least three potent anti-HIV agents, treatment largely consisted of specific opportunistic infection management and less effective antiretroviral therapy. In many parts of the world, the main causes of death in patients with HIV infection include bacterial pneumonia, tuberculosis, and PCP. Recent work has shown chronic obstructive pulmonary disease (COPD) and lung cancer occur more frequently among HIV-infected individuals compared with the general population. In addition to pulmonary tuberculosis, extrapulmonary disease occurs in a high proportion of HIV-infected individuals with low CD4 lymphocyte counts (<150 cells/mL). Hence, some centers advocate use of empirical therapy for HIV-infected patients who are seen with symptoms and chest radiographic and blood gas abnormalities typical of mild PCP, without the need for bronchoscopy. On the basis of current evidence, patients with CD4 counts >200 cells/mL have a low risk of HIV disease progression or death during 6 months of treatment for tuberculosis. doi = 10.1016/b978-032304825-5.10034-0 id = cord-022521-r72jtoso author = Miller, Tracie L. title = Gastrointestinal Complications of Secondary Immunodeficiency Syndromes date = 2010-12-27 keywords = AIDS; CD4; HAART; HIV; HIV-1; gastrointestinal; infection; patient summary = However, in the United States and other developed countries, severe malnutrition and new cases of perinatal HIV-1 disease are rare because of relatively high standards of living and effective highly active antiretroviral therapies (HAART) given to pregnant HIV-infected women that prevent transmission of HIV to the infants. Examination of both acute simian immunodeficiency virus (SIV) and HIV infection have documented reduced CD4 cell levels in GALT prior to a detectable reduction in T cells of the peripheral blood, highlighting the gastrointestinal tract''s role and susceptibility. Previous studies have shown that activated mucosal T cells play a role in the pathogenesis of enteropathy in the human small intestine 37 and can affect the morphology of the villi and crypts in a manner similar to that seen in patients with HIV-1 infection. Immune restoration disease after the treatment of immunodeficient HIV-infected patients with highly active antiretroviral therapy doi = 10.1016/b978-1-4377-0774-8.10042-9 id = cord-022252-9yiuuye3 author = Mims, Cedric A. title = Mechanisms of Cell and Tissue Damage date = 2013-11-17 keywords = Fig; LPS; antigen; cause; cell; damage; disease; infection; response; toxin; virus summary = A few viruses are remarkable because they cause no pathological changes at all in the cell, even during a productive infection in which infectious virus particles are produced. Primary consideration will be given to those substances which are produced under ecologically significant conditions (i.e. in the natural host or relevant animal model) and cause (also in biologically relevant systems) damage to cells or tissues thereby contributing to disease. Here we consider toxins which act on extracellular substances and are responsible for many of the main features of the diseases caused by the infecting organism. Circulating immune complexes are also deposited in the walls of small blood vessels in the skin and elsewhere, where they may induce inflammatory changes.* The prodromal rashes seen in exanthematous virus infections and in hepatitis B are probably caused in this way. doi = 10.1016/b978-0-12-498262-8.50015-1 id = cord-332747-u46xryoo author = Mingorance, Lidia title = Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation date = 2018-09-18 keywords = Fig; HCV; LPIN1; RNA; cell; infection; ns3 summary = To determine which aspects of the HCV replication cycle are limited by lipin1 silencing, single cycle infection experiments were conducted by inoculating control and lipin1-deficient cell cultures at MOI 10 with genotype 2a D183 virus. Once cultures reached >95% of HCV-positive cells, they were transduced with lentiviral vectors expressing control, HCV RNA-targeting or LPIN1-specific shRNAs. At day 7 post-transduction, cells were split and samples of the cells and supernatants were collected 24 hours later to determine infectious virus production rate by infectivity titration HCV (C) and RNA levels by RT-qPCR (D). This reduced abundance is illustrated by a significant reduction in the fraction of cells displaying vesicular structures in lipin1-deficient cell cultures (Fig 7H) despite comparable transfection efficiency and viral protein expression levels, indicating that lipin1 may be required in a critical step leading to formation of the HCV-induced vesicular compartment. doi = 10.1371/journal.ppat.1007284 id = cord-321584-4bu0lps0 author = Mitchell, Brett G. title = Nurses'' and midwives’ cleaning knowledge, attitudes and practices: An Australian study date = 2020-09-30 keywords = infection; nurse summary = BACKGROUND: As frontline providers of care, nurses and midwives play a critical role in controlling infections such as COVID-19, influenza, multi-drug resistant organisms and health care associated infections. As nurses and midwives have the most contact with patients and as an important first step in improving compliance, this study sought to explore nurses'' and midwives'' knowledge on the role of the environment in infection prevention and control and identify challenges in maintaining clean patient environments. As frontline providers of care, nurses and midwives play a vital role in prevention and control of infections such as COVID19, influenza, multi-drug resistant organisms (MDROs) and health care associated infections (HCAIs) more broadly. We asked participants to indicate who was responsible for cleaning four items, two frequently touched items (bed rails and nurse call bells) and two items of shared medical equipment (IV pole and IV pump). doi = 10.1016/j.idh.2020.09.002 id = cord-001397-nrq4ncdf author = Mlera, Luwanika title = The role of viral persistence in flavivirus biology date = 2014-05-12 keywords = IFN; JEV; Nile; RNA; WNV; West; infection; virus summary = Avenues for additional studies include determining if the multifunctional flavivirus protein NS5 has a role in viral persistence, the development of relevant animal models of viral persistence as well as investigating the host responses that allow vector borne flavivirus replication without detrimental effects on infected cells. The SL1 structure is essential for viral replication and acts as a promoter which is targeted initially by NS5 and then delivered to the 3 0 end via cyclization (Filomatori et al., 2006; Zhang et al., 2008; Lodeiro et al., 2009) Although there is low nucleotide conservation between flaviviruses and different CS homology (Hahn et al., 1987) , the 5 0 UTRs of TBFVs share the same genomic organization as the MBFVs (Kofler et al., 2006) Structural proteins Capsid (C) 11 kDa, 114 aa Cytosol/nucleus The capsid protein is a dimeric alpha-helical (Jones et al., 2003) protein and assembles into an icosahedral structure, measuring 30 nm in diameter, which initiates encapsidation of the associated genomic RNA in virus-induced membrane invaginations of the ER (Welsch et al., 2009 ). doi = 10.1111/2049-632x.12178 id = cord-018058-n3majqes author = Modrow, Susanne title = Historical Overview date = 2013-08-12 keywords = Sect; disease; infection; viral; virus summary = Many of the steps that characterize a viral infection were first discovered in experiments with bacterial viruses: such processes include attachment and penetration, the reproduction-cycledependent regulation of gene expression that results in early and late synthesized proteins, and lysogeny, which is associated with the existence of prophages. Besides the importance for tumour virus research, these observations aroused interest in the question concerning the basis of the high susceptibility of newborn animals to viral infections, and suggested investigations on the innate resistance of an organism to infections as well as the time and the causes of its formation. Between 1918 and 1920, a pandemic emerging viral disease, Spanish flu, claimed more than 20 million lives, i.e., more than in the First World War. After cultivation of the virus responsible in embryonated chicken eggs in 1933, their haemagglutinating properties were discovered in 1941 (i.e., their ability to agglutinate red blood cells), thereby laying the basis for the development of haemagglutination tests to detect viruses. doi = 10.1007/978-3-642-20718-1_1 id = cord-278364-58d8kfdf author = Mohapatra, S. title = Sterilization and Disinfection date = 2017-03-31 keywords = care; clean; infection; patient; sterilization summary = doi = 10.1016/b978-0-12-805299-0.00059-2 id = cord-307144-g8d1xkub author = Monaghan, N. P. title = Emerging infections – implications for dental care date = 2016-07-08 keywords = Ebola; infection summary = doi = 10.1038/sj.bdj.2016.486 id = cord-275795-ee7qyw5h author = Monette, Anne title = T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders date = 2018-10-24 keywords = CD4; CD8; CNS; HBV; IFN; RNA; RSV; VZV; cell; infection; virus summary = We focus on immunity generated against both natural infection and vaccination, where a steady shift in conferred vaccination immunogenicity is observed from quantifying activated and proliferating, long-lived effector memory T cell subsets, as the prominent biomarkers of long-term immunity against viruses and their associated disorders causing high morbidity and mortality rates. Since that time, the occurrence of epidemics and outbreaks are now at lower risk, following the introduction of massive vaccination programs able to induce immune system targeting of viruses causing severe disorders affecting distinct geographical locations, and with many epidemiological reports demonstrating long-term efficacy of viral control of non-naïve populations. This approach is being developed to use virus-infected cell-killing antibodies that produce an antiviral environment; these termed antibody-dependent cellular cytotoxicity (ADCC)-mediating antibodies, which are predicted to link innate and adaptive immune responses, and is becoming possible due to new technologies for rapid isolation and characterization of monoclonal antibodies targeting conserved regions of influenza virus, reviewed in Jegaskanda et al. doi = 10.1016/bs.ircmb.2018.07.006 id = cord-328287-3qgzulgj author = Moni, Mohammad Ali title = Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date = 2014-10-24 keywords = HIV; HIV-1; SARS; disease; gene; infection summary = Then based on the gene expression, PPI and signalling pathways data, we investigate the comorbidity association of these 2 infective pathologies with other 7 diseases (heart failure, kidney disorder, breast cancer, neurodegenerative disorders, bone diseases, Type 1 and Type 2 diabetes). The differential gene expression profiling strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response and statistically dysregulates a large number of genes, pathways and PPIs subnetworks in different pathologies such as chronic heart failure (21 genes), breast cancer (16 genes) and bone diseases (11 genes). To observe the association of SARS and HIV infections with other 7 important diseases (chronic heart failure, kidney disorders, breast cancer, parkinson, osteoporosis, type 1 and type 2 diabetes), we have collected mRNA microarray raw data associated with each disease from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) accession numbers are GSE9006, GSE9128, GSE15072, GSE7158, GSE8977 and GSE7621 [59] . doi = 10.1186/1471-2105-15-333 id = cord-010233-772e35kx author = Monto, Arnold S. title = Respiratory illness caused by picornavirus infection: a review of clinical outcomes date = 2002-01-03 keywords = infection; respiratory; viral summary = The search terms used were picornavirus, rhinovirus, enterovirus, viral respiratory infection, upper respiratory infection, disease burden, economic, cost, complications, asthma, COPD, immunocompromised, elderly, otitis media, and sinusitis. In fact, because rhinovirus-induced illnesses are so common, they produce more restriction of activity and physician consultations annually than respiratory illnesses caused by other viruses or bacteria.s This article reviews the clinical impact and outcomes associated with picomavirusinduced respiratory infection in specific populations at risk for complications secondary to these infections. 15 In addition, these advances in technology have confirmed the results of earlier studies, further demonstrating the significance of rhinoviruses in causing or predisposing patients to otitis media and sinusitis and exacerbating other chronic respiratory diseases such as asthma, cystic fibrosis, and chronic obstructive pulmonary disease (COPD). doi = 10.1016/s0149-2918(01)80133-8 id = cord-017252-88b3preq author = Morgan, Carrie I. title = Pneumonia date = 2014-02-20 keywords = child; infection; patient; pneumonia; respiratory summary = Despite immunizations and public health initiatives, the most common bacterial causes of CAP have remained largely unchanged over the last several decades and include: Streptococcus pneumoniae , Staphylococcus aureus , Haemophilus infl uenzae (including non-typable strains) and Moraxella catarrhalis [ 7 , 8 , 21 , 23 ] . Chest CT is helpful to further evaluate diffi cult cases, particularly immunocompromised children with ill-defi ned infi ltrates on CXR, complex empyema or effusion, or recurrent or chronic pneumonia [ 11 ] . Respiratory failure in an immunocompromised child frequently necessitates a chest CT to better visualize the pattern and extent of disease, aid in diagnosis of the etiology, determine the need for more invasive procedures, and to increase the sensitivity of assessing treatment response [ 11 ] . Etiology of community-acquired pneumonia in hospitalized school-age children: evidence for high prevalence of viral infections doi = 10.1007/978-1-4471-6356-5_6 id = cord-295873-kykyubdq author = Morikawa, Saeko title = Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children date = 2015-10-22 keywords = infection; virus summary = doi = 10.1016/j.jcv.2015.10.001 id = cord-021069-v9f9874x author = Morrison, Lynda A. title = Viral pathogenesis and central nervous system infection date = 2004-11-23 keywords = CNS; infection; virus summary = Stages in viral pathogenesis defined as (1) virus entry, (2) spread, (3) tropism, (4) virulence and injury to the host, and (5) the outcome of infection are discussed for viral infections in general and those aspects unique to infections of the central nervous system . Stages in viral pathogenesis defined as (1) virus entry, (2) spread, (3) tropism, (4) virulence and injury to the host, and (5) the outcome of infection are discussed for viral infections in general and those aspects unique to infections of the central nervous system . Genetic determinants of disease susceptibility have been found for infection of mice with strains of most neurotropic viruses, in at least one case of coronavirus reflecting lack of a gene encoding a virus receptor protein . doi = 10.1016/1044-5765(91)90002-6 id = cord-031876-v44o5shw author = Mounier, Roman title = Assessment of Bacterial Colonization of Intracranial Pressure Transducers: A Prospective Study date = 2020-09-15 keywords = ICPT; NGS; SEM; infection summary = were each identified on 3 (8%) ICPTs. Data presented are limited to the 48 ICPTs assessed by SEM Breaking of the BBB means skull depression fracture, skull base fracture, or brain surgery Data are shown as the median (25th-75th percentile) or number (%), unless otherwise indicated BBB blood brain barrier, EVD external ventricular drain, ICP intracranial pressure, ICU intensive care unit, TBI traumatic brain injury Breaking of the BBB means skull depression fracture, skull base fracture, or brain surgery BBB blood brain barrier, EVD external ventricular drain, ICPT intraparenchymal intracranial pressure transducer, ICU intensive care unit, OTU operational taxonomic units, TBI traumatic brain injury Data are shown as the median (25th-75th percentile) or number (%), unless otherwise indicated tips, suggesting that ICPT colonization may be largely underestimated using standard techniques. doi = 10.1007/s12028-020-01096-x id = cord-257644-9f30s0gy author = Mu, Xingjiang title = Comparative transcriptional analysis reveals distinct expression patterns of channel catfish genes after the first infection and re-infection with Aeromonas hydrophila date = 2013-09-12 keywords = Fig; infection summary = title: Comparative transcriptional analysis reveals distinct expression patterns of channel catfish genes after the first infection and re-infection with Aeromonas hydrophila To determine whether transcriptional levels of channel catfish (Ictalurus punctatus) genes are differentially regulated between a first infection with Aeromonas hydrophila and a re-infection, suppression subtractive hybridization (SSH) was performed in this study using anterior kidney cDNA after the re-infection as tester. Of the 96 clones isolated from the SSH library, 28 unique expressed sequence tags (ESTs) were obtained, of which eight were confirmed to be slightly but significantly (P < 0.05) more up-regulated by the re-infection at 6 h post infection (hpi). hydrophila compared to that by a first infection, a total of 96 channel catfish genes reported in literature were screened in this study, including the following: 1) 43 genes induced by Edwardsiella ictaluri [24] ; 2) 28 genes upregulated by Flavobacterium columnare [25] ; 3) 5 toll-like receptors (TLRs) up-regulated by E. doi = 10.1016/j.fsi.2013.08.027 id = cord-343728-udjjijyu author = Muggia, Victoria A. title = Nocardia ignorata Infection in Heart Transplant Patient date = 2020-11-17 keywords = Nocardia; infection summary = title: Nocardia ignorata Infection in Heart Transplant Patient To the Editor: We read with interest the recent description of pulmonary Nocardia ignorata infection (1) . The course after left ventricular assist device explantation and orthotopic heart transplant was complicated by tamponade requiring a pericardial window and an ESBL Klebsiella urinary tract infection treated with meropenem. The isolate was identified by a reference laboratory (Mycobacteria and Nocardia Laboratory, University of Texas Health Center at Tyler, Tyler, TX, USA) by partial 16S rRNA sequencing as a 99.51% match with Nocardia ignorata, with susceptibilities identical to the isolate in Rahdar et al. One year later, Trevisan characterized and termed the bacteria Nocardia farcinica, creating the genus Nocardia. Pulmonary Nocardia ignorata infection in gardener, Iran European Study Group for Nocardia in Solid Organ Transplantation. Nocardia infection in solid organ transplant recipients: a multicenter European case-control study doi = 10.3201/eid2611.202756 id = cord-259050-482nk9je author = Mätz‐Rensing, K. title = Outbreak of Streptococcus equi subsp. zooepidemicus infection in a group of rhesus monkeys (Macaca mulatta) date = 2009-06-07 keywords = animal; infection summary = doi = 10.1111/j.1600-0684.2009.00359.x id = cord-346673-kyc1wks5 author = NICKBAKHSH, S. title = Extensive multiplex PCR diagnostics reveal new insights into the epidemiology of viral respiratory infections date = 2016-03-02 keywords = infection; respiratory; virus summary = In particular, our study shows that (i) human coronavirus infections are more common during influenza seasons and in co-infections than previously recognized, (ii) factors associated with co-infection differ from those associated with viral infection overall, (iii) virus prevalence has increased over time especially in infants aged <1 year, and (iv) viral infection risk is greater in the post-2009 pandemic era, likely reflecting a widespread change in the viral population that warrants further investigation. We analysed diagnostic data generated by NHSGGC using multiplex PCR from 2005 to 2013 with the following objectives: (i) to describe testing and virus prevalence trends, (ii) to examine temporal and patient subgroup distributions for each individual virus, and (iii) to compare factors associated with overall viral infection and co-infection using statistical modelling, in order to provide robust and timely estimates of who is most at risk of viral-associated respiratory illness, and when, within a major urban UK population. doi = 10.1017/s0950268816000339 id = cord-331413-fejho1of author = Nakayama, Eiichi title = Rapid optimization of antimicrobial chemotherapy given to pediatric patients with community-acquired pneumonia using PCR techniques with serology and standard culture date = 2007-12-31 keywords = PCR; infection summary = title: Rapid optimization of antimicrobial chemotherapy given to pediatric patients with community-acquired pneumonia using PCR techniques with serology and standard culture Abstract Children (n =117; mean age 2.4 ± 2.9 years) were diagnosed as having community-acquired pneumonia (CAP) using clinical symptoms, chest X-rays, and hematological data. The causative pathogen was determined using real-time polymerase chain reaction (PCR) (6 bacteria), multiple reverse transcription-PCR (MPCR; 11 viruses), bacterial culture, and serology. [7] [8] [9] In Japan, antimicrobial chemotherapy for patients with CAP is begun empirically based on (1) chest X-rays, (2) clinical fi ndings including respiratory status, (3) age, and (4) laboratory tests such as white blood cell count (WBC) and C-reactive protein concentration (CRP). The bacteria suspected to be the causative pathogens was determined by standard culture and real-time PCR for six pathogens: Streptococcus pneumoniae, Haemophilus infl uenzae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Streptococcus pyogenes, and Legionella pneumophila (Table 3) In the patients suspected of having an infection caused by S. doi = 10.1007/s10156-007-0535-6 id = cord-003387-82573enr author = Nam, Gyu-Hwi title = Gene expression profiles alteration after infection of virus, bacteria, and parasite in the Olive flounder (Paralichthys olivaceus) date = 2018-12-24 keywords = Paralichthys; flounder; gene; infection; olive summary = title: Gene expression profiles alteration after infection of virus, bacteria, and parasite in the Olive flounder (Paralichthys olivaceus) In this study, we carried out transcriptome analysis using the olive flounder gill tissues after infection of three types of pathogens (Virus; Viral hemorrhagic septicemia virus, Bacteria; Streptococcus parauberis, and Parasite; Miamiensis avidus), respectively. Our goals are to provide plenty of genomic knowledge about olive flounder transcripts for further research and report genes, which were changed in their expression after specific pathogen infection. To profile gene expression after infection of three pathogens (VHSV, Streptococcus parauberis, and Miamiensis avidus), transcriptome analysis was conducted using gill tissues of olive flounders, respectively. In this study, we understood the relation between three types of pathogen infection and differential gene expression in the olive flounder genome through transcriptome analysis, respectively. cDNA microarray analysis of viral hemorrhagic septicemia infected olive flounder, Paralichthys olivaceus: immune gene expression at different water temperature doi = 10.1038/s41598-018-36342-y id = cord-018785-tcr5xlf8 author = Nambiar, Puja title = Infection in Kidney Transplantation date = 2018-06-27 keywords = Blumberg; CMV; HCV; HIV; infection; transplant summary = The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. The risk factors for development of CMV disease include donor seropositivity/recipient seronegativity(Dþ/RÀ), use of induction immunosuppression (antilymphocyte antibodies), donor age >60 years, simultaneous kidney-pancreas transplantation, treatment for acute rejection, impaired transplant function, and concurrent infection from other viruses (like EBV and HHV-6 and 7) (De Keyzer et al. The risk factors for PTLD include EBV naïve recipients who receive EBV seropositive organs, active primary EBV infection, younger recipient, coinfection by CMV and other viruses, prior splenectomy, second transplant, acute or chronic graft versus host disease, immunosuppressive drug regimen (OKT3 or polyclonal antilymphocyte antibody), and the type of organ transplanted. doi = 10.1007/978-3-319-19617-6_22 id = cord-322380-udjoghr6 author = Nash, Anthony A. title = Early Stages of Infection After Pathogen Entry date = 2015-02-06 keywords = cell; chapter; infection; tissue summary = In the basal layer of the epidermis, adjacent to the antibodies and immune cells that arrive from dermal blood vessels, the virus infection is incomplete; in this layer of the epidermis, only a subset of virus genes are transcribed, no virus structural proteins are produced and no virus DNA replication occurs, therefore no virus particles are produced. This means gaining access to the lumen of a subepithelial lymphatic or blood vessel, either as a free microorganism, or alternatively after entering a mobile cell (leucocyte) that will carry it to other parts of the body. Thus, rotaviruses and rhinoviruses replicate at the epithelial surface but cannot infect leucocytes, and in any case would be unlikely to find susceptible cells elsewhere in the body if they entered blood or lymphatic vessels. Indeed, bacteria and other microorganisms that are capable of extracellular replication generally advertise their presence by releasing a variety of products into surrounding fluids, many of which cause inflammation and thus bring antibacterial agents such as immunoglobulins, complement and leucocytes to the site of the infection. doi = 10.1016/b978-0-12-397188-3.00003-2 id = cord-344009-hm36pepp author = Nathanson, N. title = Virus perpetuation in populations: biological variables that determine persistence or eradication date = 2005 keywords = infection; population; virus summary = However, small animal populations can turnover significantly each year, permitting the perpetuation of some viruses that cause acute infections. Measles has several attributes that -in the aggregate -are not seen for other common viral diseases: (i) There are longterm records of measles incidence, collected by many health departments in the United States and other countries; (ii) 95% of all measles infections manifest as illness (in contrast to 1% for poliomyelitis for example); (iii) the symptoms of measles are sufficiently pathognomonic so that it can be distinguished from other viral infections by clinical observers; and (iv) population-wide reports can be corrected for under-reporting (about 15% of measles cases were reported in most cities in the United States prior to the introduction of measles vaccine in 1963). Vaccine-induced reduction of susceptible individuals in such a population can be guesstimated to reduce the number of new infections per trough generation period below the threshold for virus perpetuation. doi = 10.1007/3-211-29981-5_2 id = cord-022254-8y5sq72c author = Nathanson, Neal title = IMMUNOSUPPRESSION AND VIRUS INFECTION OF RODENTS date = 2012-12-02 keywords = infection; virus summary = One example of specific deletion is the use of anti-mu antiserum to delete IgM bearing B cells from neonatal animals, thus blocking the B cell arm of the immune response (43-46). Complement plays an important ancillary role as a host defense, since in conjunction with specific antiviral antibody, it can lyse either virions or virus-infected cells (60). The recent development of methods for the cloning of T cells and the culture of T cell lines (88) (89) (90) (91) (92) , has made it possible to study the effect of specific T cell subsets upon virus infection (93) (94) (95) (96) . I. Comparative effectiveness of antibody and reconstitution of immune spleen cells on immunosuppressed mice Protection of mice from fatal herpes simplex virus type 1 infection by adoptive transfer of cloned virusspecific and H-2-restricted cytotoxic T lymphocytes Dual role of the immune response in street rabies virus infection of mice doi = 10.1016/b978-0-12-095785-9.50036-6 id = cord-320909-p93gxjm2 author = Natoli, S. title = Does SARS‐Cov‐2 invade the brain? Translational lessons from animal models date = 2020-05-22 keywords = CNS; MERS; SARS; infection summary = Animal models of SARS and Middle East respiratory syndrome, caused by structurally similar CoVs during the 2002 and 2012 epidemics, have provided valuable data on nervous system involvement by CoVs and the potential for central nervous system spread of SARS‐CoV‐2. The expression of this receptor in neurons and endothelial cells hints that SARS‐CoV‐2 may have higher neuroinvasive potential compared with previous CoVs. However, it remains to be determined how such invasiveness might contribute to respiratory failure or cause direct neurological damage. Highly pathogenic coronavirus (CoV) infections are well-established sources of previous epidemics in humans, i.e. severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV). Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice doi = 10.1111/ene.14277 id = cord-355906-yeaw9nr8 author = Nedjadi, Taoufik title = Tackling dengue fever: Current status and challenges date = 2015-12-09 keywords = Aedes; DENV; dengue; infection; vaccine; virus summary = Recent advances in molecular biology have revealed that the genetic makeup of the three elements of dengue infection (the virus, the vector, and the host) plays a primordial role in the pathogenesis of the disease and could potentially contribute to the DHF progression [19, 24, 35] . Dengue virus serotype-1 antigen was expressed in a vector based on pediatric live-attenuated Schwarz measles vaccine (MV) by using the envelope domain III (EDIII) fused with the ectodomain of the membrane protein (ectoM). The Centers for Disease Control and Prevention (USA) have also developed a live-attenuated vaccine named DENVax, which was found to be highly immunogenic in both children and adults and has currently entered phase I clinical trial in the United States [96, 97] . doi = 10.1186/s12985-015-0444-8 id = cord-293151-g3758oes author = Nemzek, Jean A. title = Biology and Diseases of Dogs date = 2015-07-10 keywords = Animal; Ferguson; Peterson; Swaim; canine; clinical; complication; diagnosis; disease; dog; infection; laboratory; research; sign; treatment; tumor; wound summary = This provides the necessary background to discuss the spontaneous diseases, including infectious and neoplastic conditions, prevalent in purpose bred as well as random source dogs used in biomedical research. Several factors that increase pressure at the site and/or affect the integrity of the skin will predispose an individual to develop pressure sores, including poor hygiene, self-trauma, low-protein diet, preexisting tissue damage, muscle wasting, inadequate bedding, and ill-fitting coaptation devices (Swaim and Angarano, 1990) . Chronic or recurrent corneal ulcers may also be associated with infection or hereditary causes in some breeds of dogs; however, these would be rare in the laboratory setting. Research Complications Treatment of early-stage or low-grade mammary tumors may be rewarding, allowing dogs to continue on study. doi = 10.1016/b978-0-12-409527-4.00012-2 id = cord-023367-ujflw19b author = Newcomer, Benjamin W. title = Diseases of the hematologic, immunologic, and lymphatic systems (multisystem diseases) [Image: see text] date = 2020-04-17 keywords = States; United; animal; cause; chapter; clinical; clostridium; disease; goat; infection; sheep; sign summary = The cause of transformation is usually unknown; in rare cases, especially in flock outbreaks in sheep, it can be linked to exposure to the bovine leukemia virus, which has occurred experimentally and as a result of the administration of whole blood Anaplasma vaccines. C. perfringens type C in older sheep causes the disease known as "struck." Affected animals usually are found dead or with signs of toxemia. The course of the disease is usually very short (0.5-12 hours), so sudden or spontaneous death is a common clinical sign across affected small ruminant species. Additional evidence of systemic toxemia (metabolic acidosis, azotemia, and increases in liver and muscle enzymes) also may be seen; however, diagnosis of black disease is based on characteristic history (endemic liver fluke areas), clinical signs, and postmortem findings and testing. doi = 10.1016/b978-0-323-62463-3.00025-6 id = cord-282668-bs634hti author = Niang, Mbayame Ndiaye title = Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses date = 2017-03-22 keywords = ILI; Senegal; infection; respiratory summary = doi = 10.1371/journal.pone.0174287 id = cord-016704-99v4brjf author = Nicholson, Felicity title = Infectious Diseases: The Role of the Forensic Physician date = 2005 keywords = HBV; HIV; Health; Kingdom; United; disease; infection; risk summary = The risk of exposure to infections, particularly blood-borne viruses (BBVs), can be minimized by adopting measures that are considered good practice in the United Kingdom, the United States, and Australia (1) (2) (3) . Studies of prisoners in western countries have shown a higher prevalence of antibodies to HBV and other BBVs than the general population (12) (13) (14) ; the most commonly reported risk factor is intravenous drug use. HBIG is given in conjunction with the first dose of vaccine to individuals who are deemed at high risk of acquiring disease and the incident occurred within 72 hours of presentation. In 1998, 56% of reported cases were from people born outside the United Kingdom and 3% were associated with HIV infection (70, 71) . Those in contact with disease (either through exposure at home or from an infected detainee) should receive prophylactic treatment as soon as possible (see Subheading 8.3.7.). doi = 10.1385/1-59259-913-3:235 id = cord-353190-7qcoxl81 author = Nicklas, Werner title = Viral Infections of Laboratory Mice date = 2012-05-17 keywords = ELISA; IFA; LCMV; LDV; MHV; MPV; PCR; TMEV; infection; mouse; strain; virus summary = This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler''s murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi''s sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine. doi = 10.1016/b978-0-12-382008-2.00019-2 id = cord-015487-iugrhyaq author = Nicolson, Garth L. title = Chronic Bacterial and Viral Infections in Neurodegenerative and Neurobehavioral Diseases date = 2008-05-01 keywords = Alzheimer; Chlamydia; infection summary = doi = 10.1309/96m3bwyp42l11bfu id = cord-322104-f1dukpso author = Niederman, M.S. title = PNEUMONIA | Community Acquired Pneumonia, Bacterial and Other Common Pathogens date = 2006-05-13 keywords = CAP; gram; infection; organism; patient; pneumonia summary = Community-acquired pneumonia (CAP) is the number one cause of death from infectious diseases in the US, and the patient population that is affected is becoming increasingly more complex due to the presence of chronic illness which is commonly managed in outpatients who are at risk for pneumonia. Other common pathogens include atypical organisms (Chlamydophila pneumoniae, Legionella pneumophila, Mycoplasma pneumoniae), Hemophilus influenzae, enteric Gram-negatives (especially in those with chronic illness and aspiration risk factors), and Staphylococcus aureus. Today, the number of etiologic pathogens has mushroomed to include not only bacteria, but also viruses (influenza, severe acute respiratory syndrome (SARS)), fungi, and a number of other recently identified organisms (such as Legionella, Chlamydophila pneumoniae). Patients with severe CAP may have a slightly different spectrum of organisms than less severely affected individuals, being commonly infected with pneumococcus, atypical pathogens, enteric Gram-negatives (including P. doi = 10.1016/b0-12-370879-6/00310-0 id = cord-024188-d7tnku8z author = Nissen, Michael D. title = Respiratory Infections date = 2010-03-27 keywords = RSV; infection; respiratory; virus summary = For example, recent findings from the New Vaccine Surveillance Network in the United States show that despite respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), and human coronaviruses (HCoVs) all being common in early childhood; RSV and PIVs are more common causes of hospital admission with acute febrile and respiratory illness than HCoVs [33, 41] . A review of healthy adult human volunteer studies showed that viral shedding increased sharply between 0.5 and 1 day after influenza virus challenge, peaking on day two; shedding can be detected 24 to 28 h before clinical onset, and has a mean duration of 4.8 days; two-thirds of subjects had symptomatic infection, and total symptom scores peaked on day three [11] . Infections due to common viruses that result in disease severe enough to warrant laboratory testing, notification, or hospitalisation occur in the young, the very old, or both, such as with RSV and influenza [9, 14] . doi = 10.1007/978-90-481-9039-3_5 id = cord-267023-w5ig7mrl author = Nori, Priya title = Developing Interactive Antimicrobial Stewardship and Infection Prevention Curricula for Diverse Learners: A Tailored Approach date = 2017-07-20 keywords = IPC; antibiotic; infection summary = doi = 10.1093/ofid/ofx117 id = cord-025495-udz9i0fw author = Nowak, Jan K. title = Lithium and coronaviral infections. A scoping review. date = 2020-04-03 keywords = infection; lithium; study summary = The available evidence comes only from studies of cell cultures and indicates that lithium effectively inhibits coronaviral infections when administered at concentrations that are toxic to humans. "The available evidence comes only from studies of cell cultures and indicates that lithium effectively inhibits coronaviral infections when administered at concentrations that are toxic to humans." The prescription of lithium in the context of the current epidemic thus appears not to be supportable by the findings. Lithium also seemed to bring improvement in a proof-of-concept randomized double-blind placebo-controlled trial involving eleven healthy adults with recurrent HSV infections and in a randomized study of ten women with genital herpes conducted by the same research group from Philadelphia." Therefore it seems that in some instances lithium exhibits antiviral activity at concentrations, which are safe and maintained long-term (for years) in patients with affective disorders. The latter study gives hope that lithium may indeed be efficient at clinically relevant levels." In terms of discussion, the authors reviewed some existing literature and suggested a potential mechanism of reduced apoptosis by lithium, the glycogen synthase kinase 3-beta (GSK-3β) inhibitor. doi = 10.12688/f1000research.22299.2 id = cord-118119-it3q17rp author = Odagaki, Takashi title = Self-organized wavy infection curve of COVID-19 date = 2020-10-16 keywords = infection summary = Exploiting the SIQR model for COVID-19, I show that the wavy infection curve in Japan is the result of fluctuation of policy on isolation measure imposed by the government and obeyed by citizens, Assuming the infection coefficient be a 2-valued function of the number of infected individuals, I show that when the removal rate of infected individuals is between these two values, the wavy infection curve is self-organized. On the basis of the infection curve, I classify the outbreak of COVID-19 in each country into five types and show that these differences can be related to the relative magnitude of the transmission coefficient and the quarantine rate of infected individuals. The observed data for the outbreak of COVID-19 is the daily confirmed new cases ∆Q(t) ≡ qI, which is given by a convolution of the incubation period distribution function ψ(t) and the number of infecteds I(t). doi = nan id = cord-276348-vr5fit8r author = Ogra, Pearay L. title = Respiratory syncytial virus: The virus, the disease and the immune response date = 2004-01-31 keywords = RSV; infection; respiratory; virus summary = Premature babies born at 30–35 weeks of gestation, infants with cyanotic congenital heart disease, HIV-infected subjects, and patients on intensive immunosuppressive therapy especially after bone marrow transplant are considered to be at risk for increased mortality and morbidity during RSV infection. Recurrent wheezing for up to 5 to 7 years of age and established airway disease has been observed in a significant number of children with a strong family history of allergy, after primary infection or reinfection with RSV. Children at increased risk from RSV infection include young infants with prematurity, bronchopulmonary dysplasia, congenital heart disease, congenital or acquired immunodeficiency, subjects with hematologic malignancies, patients with bone-marrow or organ transplants, and cystic fibrosis. 6 It is important to recognise that virtually all children who get infected with RSV develop virus-specific IgE homocytotropic antibody in the respiratory tract. doi = 10.1016/s1526-0542(04)90023-1 id = cord-305207-fgvbrg8d author = Ohara, Hiroshi title = Fact-finding Survey of Nosocomial Infection Control in Hospitals in Kathmandu, Nepal—A Basis for Improvement date = 2013-06-29 keywords = control; hospital; infection summary = In the healthcare setting, particularly in developed countries, various measures including the organization of infection control teams (ICTs), preparation of manuals, strengthening of surveillance systems, and training of staff have been taken to assure effective control. The form consisted of the following items: "general information of the hospitals, control system including manual and infection control committees (ICC), equipment and facility preparedness, training conditions, surveillance conditions, expectation for international cooperation and current problems. Among the problems observed in the study were weak ICC function, few training opportunities among the hospital staff, inadequate use of antibiotics, shortage of infection control staff, shortage of doctors and nurses and their overload in daily medical practice, shortage of fundamental equipment including PPE, inadequate practice of basic techComparison of nosocomial infection control conditions between 2003 and 2011 at five national hospitals showed an improvement trend. Appropriate nosocomial infection control is a key strategy in providing high quality medical care, and effective measures are particularly required in developing countries, where the frequency of infectious diseases is high and environmental conditions of hospitals are poor [14, 15] . doi = 10.2149/tmh.2013-03 id = cord-146391-jlu7nv6r author = Ohsawa, Yukio title = COVID-19 Should be Suppressed by Mixed Constraints -- from Simulations on Constrained Scale-Free Networks date = 2020-04-20 keywords = infection summary = A scale-free network has been adopted for modeling on-line communities so far but is employed here for the aim to represent peoples'' social behaviors where the generated communities are restricted reflecting the spatiotemporal constraints in the real life. Second, if we adopt the constraint on m0, the number of all other people one meets separately each at a time, to the range between 2 and 8, its effect on the suppression of infections may be weak as far as we allow group meetings of size W of 8 or larger. This is an extension of SFN supposed to result in having each new node connected to "rich" people linked to a large number of "poor" people of low degrees by choosing link destination nodes by the probability estimated to be inverse of the harmonic mean (IHM). doi = nan id = cord-002222-rgqwm3vb author = Olarte-Castillo, Ximena A. title = Divergent Sapovirus Strains and Infection Prevalence in Wild Carnivores in the Serengeti Ecosystem: A Long-Term Study date = 2016-09-23 keywords = RNA; Serengeti; african; infection; sapovirus summary = By screening a large number of predominantly fecal samples (n = 631) obtained from five carnivore species in the Serengeti ecosystem, East Africa, sapovirus RNA was detected in the spotted hyena (Crocuta crocuta, family Hyaenidae), African lion (Panthera leo, family Felidae), and bat-eared fox (Otocyon megalotis, family Canidae), but not in golden or silver-backed jackals (Canis aureus and C. Long-term monitoring of sapovirus in a population of individually known spotted hyenas from 2001 to 2012 revealed: i) a relatively high overall infection prevalence (34.8%); ii) the circulation of several genetically diverse variants; iii) large fluctuations in infection prevalence across years, indicative of outbreaks; iv) no significant difference in the likelihood of infection between animals in different age categories. A total of 20 partial RdRp gene sequences (16 from spotted hyenas, 3 from African lions and 1 from bat-eared foxes) were obtained and used for the phylogenetic analysis, together with publically available sequence data from 25 representatives of all sapovirus genogroups, divergent unclassified sapoviruses, and other genera in the Caliciviridae family, including Norovirus and Vesivirus. doi = 10.1371/journal.pone.0163548 id = cord-317028-f3bpwm5j author = Olmsted, Russell N. title = Prevention by Design: Construction and Renovation of Health Care Facilities for Patient Safety and Infection Prevention date = 2016-08-09 keywords = FGI; care; construction; infection; patient summary = The built environment encompasses a broad range of physical design elements, including spaces for care of patients, support services, electronics, and major technical equipment; building systems that provide air and water; and surfaces and finishes. Use of an ICRA has been incorporated into design standards as well as Healthcare Infection Control Practices Advisory Committee guidelines that address construction and renovation. Design elements that support infection prevention and control Proactive planning for mitigating sources of infection both within and external to the construction project that will be affected Identify potential risk for transmission of airborne and waterborne pathogens during construction, renovation, and commissioning Develop ICRMRs to mitigate identified risks (see Appendix A for a stepwise approach to developing ICRMRs) There is evidence that an effective ICRA process can prevent HAIs. 25 Fig. 1 provides examples of effective containment methods. doi = 10.1016/j.idc.2016.04.005 id = cord-103893-p9ul6k5m author = Omame, A. title = A co-infection model for Oncogenic HPV and TB with Optimal Control and Cost-Effectiveness Analysis date = 2020-09-18 keywords = hpv; infection summary = A co-infection model for oncogenic Human papillomavirus (HPV) and Tuberculosis (TB), with optimal control and cost-effectiveness analysis is studied and analyzed to assess the impact of controls against incident infection and against infection with HPV by TB infected individuals as well as optimal TB treatment in reducing the burden of the co-infection of the two diseases in a population. Numerical simulations of the optimal control model reveal that the intervention strategy which combines and implements control against HPV infection by TB infected individuals as well as TB treatment control for dually infected individuals is the most cost-effective of all the control strategies for the control and management of the burden of oncogenic HPV and TB co-infection. In this section, we shall use the Pontryagin''s Maximum Principle to determine the necessary conditions for the optimal control of the oncogenic HPV-TB co-infection model. doi = 10.1101/2020.09.15.20195297 id = cord-265699-0socw0hp author = Ortega, Miguel Ángel title = Dendrimers and Dendritic Materials: From Laboratory to Medical Practice in Infectious Diseases date = 2020-09-14 keywords = EV71; HIV; PAMAM; dendrimer; disease; drug; figure; infection summary = doi = 10.3390/pharmaceutics12090874 id = cord-286683-mettlmhz author = Ortiz-Prado, Esteban title = Clinical, molecular and epidemiological characterization of the SARS-CoV2 virus and the Coronavirus disease 2019 (COVID-19), a comprehensive literature review date = 2020-05-30 keywords = COVID-19; China; CoV-2; Coronavirus; MERS; SARS; Wuhan; infection; patient; severe summary = doi = 10.1016/j.diagmicrobio.2020.115094 id = cord-022119-bzd9e1q6 author = Orzell, Susannah title = Pharyngitis and Pharyngeal Space Infections: fever, sore throat, difficulty swallowing date = 2018-10-15 keywords = infection; neck; patient; space summary = Deep neck space infections can also extend directly into the mediastinum or the lungs causing life-threatening mediastinitis or pneumonia, underscoring the importance of early recognition and treatment. The initial approach to a patient with suspected pharyngitis or parapharyngeal space infection, however, should always include a careful assessment for signs of airway compromise. Patients with persistent symptoms, who do not respond to empiric therapy based on the suspected diagnosis of infection, should undergo additional diagnostic testing to evaluate for the presence of the more unusual infectious and noninfectious entities. Deep neck space infections can present as discrete organized abscesses within specific neck spaces, as a soft tissue phlegmons without clearly forming collections of pus, or rarely, as a very rapidly destructive life-threatening process called necrotizing fasciitis. Complications of bacterial pharyngitis and deep neck space infections are uncommon, particularly if appropriate antibiotic therapy has been instituted and immediate surgical concerns have been addressed; however direct extension and invasion into surrounding structures or spaces are always a risk. doi = 10.1007/978-3-319-91080-2_5 id = cord-356188-rwf78stz author = Oshansky, Christine M. title = The human side of influenza date = 2012-07-01 keywords = H1N1; cell; infection; influenza; virus summary = Few studies have examined the role of monocytes during influenza infection in humans, particularly regarding the specific subsets mentioned above, but comparison of IFN-␥ production from T cells cocultured with CD64 ϩ CD16 Ϫ and CD64 Ϫ CD16 ϩ monocytes [119, 120] Cellular immunity Class I HLA presents peptides from internal and external viral proteins. As influenza primarily infects epithelial cells lining the respiratory tract, lung-resident DCs and macrophages are particularly important for efficient development of an adaptive immune response. [189] ), and in vitro studies suggest that activated human V␥9V␦2 T cells may have a role in the antiviral response by killing influenza-infected, monocyte-derived macrophages and producing high levels of IFN-␥ [190, 191] . Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection Characterization of the human CD8ϩ T cell response following infection with 2009 pandemic influenza H1N1 virus doi = 10.1189/jlb.1011506 id = cord-318061-xe8lljz0 author = Overgaauw, Paul A.M. title = A One Health Perspective on the Human–Companion Animal Relationship with Emphasis on Zoonotic Aspects date = 2020-05-27 keywords = Health; Toxocara; animal; cat; disease; dog; human; infection; pet; risk summary = For the human, there may be a higher risk of the transmission of zoonotic infections due to trends such as sleeping with pets, allowing pets to lick the face or wounds, bite accidents, keeping exotic animals, the importation of rescue dogs, and soil contact. A literature search was conducted through 2 March 2020, using the National Library of Medicine''s PubMed for the terms "One Health" and "companion animals"; "pet ownership"; "households" and "pets"; "dogs" or "cats" or "pets" and "mental" or "physical health" or "children"; "animal assisted therapy"; "dogs" or "cats" and "nutritional problems" or "overweight" or "obesity" or "homemade" or "raw meat diets"; "dogs" or "cats" and "behavior problems" or "aggression" or "fear" or "anxiety" or "abnormal repetitive behavior"; "dogs" or "cats" and "breeding" or "genetic problems"; "dogs" or "cats" and "zooanthroponoses"; "pets" and "anthropomorphism"; "dogs" or "cats" or "exotic animals" or "rescue dogs" or "soil" and zoonoses. Anthropomorphism, also resulting in behavioral problems and breeding on appearance rather than health, and trends such as keeping exotic animals and importing rescue dogs may result in an increased risk of contracting zoonotic infections. doi = 10.3390/ijerph17113789 id = cord-018555-3lta1tbp author = Overstreet, Robin M. title = Host–Symbiont Relationships: Understanding the Change from Guest to Pest date = 2016-01-06 keywords = Litopenaeus; Overstreet; fish; host; infection; shrimp; symbiont; virus summary = We provide examples involving multiple triggers for organisms associated with termites, for an endemic virus being affected by multiple factors and having multiple effects on its commercial penaeid shrimp hosts, and for contrasting variables associated with two exotic viruses in wild and cultured commercial penaeid shrimps with an emphasis on hypothesizing how the pathogenicity developed in these two viruses. Atypical temperatures, such as warm water associated with power plants, can cause infections of a specific parasite during periods when the hosts are more likely to be consumed by predators, more susceptible to disease, or more susceptible to interactions among parasites that can occur and result in unusual pathogenic conditions. The transformation triggers phenotypic and behavioral changes specifically attracting infective specimens to predatory birds in which the trematode matures considerable detail the host-symbiont relationships affecting the outcome of pathogenic viruses in populations of commercial penaeid shrimp. doi = 10.1007/978-3-319-28170-4_2 id = cord-023767-rcv4pl0d author = O’Ryan, Miguel L. title = Microorganisms Responsible for Neonatal Diarrhea date = 2009-05-19 keywords = Campylobacter; EAEC; EPEC; Escherichia; Salmonella; Shigella; States; United; cause; child; coli; diarrhea; human; infant; infection; neonatal; outbreak; rotavirus summary = doi = 10.1016/b0-72-160537-0/50022-0 id = cord-340629-1fle5fpz author = O’Shea, Helen title = Viruses Associated With Foodborne Infections date = 2019-05-21 keywords = Nipah; SARS; human; infection; virus summary = In infants, prior to the introduction of rotavirus vaccines, RVAs could be detected in up to 50%-60% of all childhood hospitalisations due to acute gastroenteritis each year, were estimated to cause 138 million cases of gastroenteritis annually, and 527,000 deaths in children o5 years of age living in developing countries. Recent emerging epidemic and pandemic virus infections that cause severe disease in humans and that are associated with food production, preparation and food contamination include the coronavirus, severe acute respiratory syndrome (SARS-CoV), Nipah virus, Ebola virus and some of the highly pathogenic influenza virus strains, such as the H5N1 subtype. Infections by Severe Acute Respiratory Syndrome (SARS) virus, Nipah virus (NiV), H5N1 virus, Hepatitis A virus (HAV), Hepatitis E virus (HEV), Adenovirus, Astrovirus, Norovirus (NoV) and Rotavirus (RVA) in humans and animals are detected by nucleic acid amplification tests and serologic tests. doi = 10.1016/b978-0-12-809633-8.90273-5 id = cord-021465-2pj26fmv author = PERDUE, MICHAEL L. title = Impact of Avian Viruses date = 2007-05-09 keywords = NDV; Newcastle; avian; bird; disease; host; infection; virus summary = Although there is variation in the economic or ecological impact of various viral groups from year to year and among geographic sites, the "Top Ten" list of virus groups exhibiting routine significant impact on commercial poultry worldwide (not necessarily in order of impact) are paramyxoviruses (Newcastle disease); coronaviruses (infectious bronchitis); herpesviruses (infectious laryngotracheitis; Marek''s disease; duck enteritis); reoviruses (viral arthritis); picornaviruses (avian encephalomyelitis); adenoviruses (egg drop syndrome); retroviruses (lymphoid leukosis); orthomyxoviruses (avian influenza); poxviruses (fowlpox); and birnaviruses (infectious bursal disease). With the recent documented transmission of a lethal avian influenza virus from commercial poultry to humans, these ecological relationships take on new significance. Lymphomas caused by MDV and retroviruses are still the most common viral neoplastic diseases of poultry, and a recent increase in mortality and evolution of more virulent MDV strains indicates that the impact of these viruses will continue to be felt (Witter, 1996) . doi = 10.1016/b978-012362675-2/50016-1 id = cord-333041-69n2wwn3 author = Pal, Anandita title = Obesity-Driven Deficiencies of Specialized Pro-resolving Mediators May Drive Adverse Outcomes During SARS-CoV-2 Infection date = 2020-08-11 keywords = DHA; SARS; SPM; infection summary = Obesity is a major independent risk factor for increased morbidity and mortality upon infection with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2), which is responsible for the current coronavirus disease pandemic (COVID-19). We further discuss how the effects of obesity upon SARS-CoV-2 infection are likely exacerbated with environmental exposures that promote chronic pulmonary inflammation and augment SPM deficits. Obesity is an independent risk factor for increased morbidity and mortality upon infection with the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) responsible for the current COVID-19 pandemic. The SPM precursor 17-hydroxydocosahexaenoic acid (17-HDHA) increased antibody levels and improved survival upon pH1N1 influenza vaccination and infection in lean mice by promoting B cell differentiation toward the formation of CD138 + long-lived antibody secreting cells (18) . Taken together, these data suggest that the susceptibility of obese individuals to environmental lung diseases may drive an altered pulmonary immune response and a state of SPM deficiency that increases the morbidity and mortality to respiratory infections, including COVID-19. doi = 10.3389/fimmu.2020.01997 id = cord-350749-ihkxouz8 author = Panda, Aditya K title = Plasmodium falciparum Infection May Protect a Population from Severe Acute Respiratory Syndrome Coronavirus 2 Infection date = 2020-07-29 keywords = infection summary = title: Plasmodium falciparum Infection May Protect a Population from Severe Acute Respiratory Syndrome Coronavirus 2 Infection The authors have suggested that prior exposure of children to coronavirus OC43 offers protection against severe COVID-19 phenotype by possible crossimmunity. These observations encouraged us to investigate the possible role of Plasmodium infection on coronavirus disease 2019 (COVID-19) infection or severity. Based on these observations on Plasmodium infection and positive-strand RNA viruses, we hypothesized that there could be a possible association between malaria and SARS-CoV-2 infection. To validate our observation, we investigated the prevalence of COVID-19 in the Plasmodium falciparum-endemic area of Odisha, India, Odisha is highly endemic for P. falciparum for the last 10 years (2010-2019) from the National Vector Borne Disease Control Program and COVID-19 infection status in Odisha from the government of Odisha website (see https://health. Naturally-occurring anti-alphagalactosyl antibodies in human Plasmodium falciparum infections-a possible role for autoantibodies in malaria doi = 10.1093/infdis/jiaa455 id = cord-022380-49oti4zg author = Panlilio, Adelisa L title = Occupational Infectious Diseases date = 2009-05-15 keywords = HCV; HIV; States; Table; United; infection; person summary = Because infectious diseases may represent the most common cause of time lost from work, it is important for the clinician concerned with occupational medicine to understand the relationship of specific infections to specific work environments and practices, and to give at least as much attention to prevention as to diagnosis and treatment. Susceptible household contacts of infected adults and children pose a transmission risk in the workplace during the period of virus shedding, beginning about 10 days before the development of rash (about 1 week after exposure) until 7 days after rash appears. Varicella vaccination is also recommended for susceptible adolescents and adults who will have close contact with persons at high risk for serious complications of acquired varicella, including healthcare personnel and susceptible family contacts of immunocompromised individuals. The ACIP recommends that all healthcare personnel be immune to varicella, either from a reliable history of prior varicella infection or vaccination, to reduce the risk of infection and its complications, and to decrease the possibility of transmission of varicella zoster virus to patients (Table 22. doi = 10.1016/b978-0-7216-8974-6.50026-9 id = cord-016962-8vjaot6i author = Pantanowitz, Liron title = Microbiology date = 2011-07-04 keywords = Fig; cause; form; infection summary = Bacteriology covers important bacterial causes of infection including those due to mycobacteria and filamentous bacteria. Bacteria, along with some fungi (mainly • • Candida spp.) and archaea (single-celled microorganisms), make up the normal human flora of the skin, mouth, gastrointestinal tract, conjunctiva, and vagina (lactobacilli). Infection causes lung disease but may also disseminate to involve the hematopoietic system, gastrointestinal tract, as well as skin and soft tissue. These morphological features are helpful in differentiating the zygomycetes from other fungal agents of infection that may be seen in cytologic specimens (Table 4 .5). Infection may involve virtually any organ including the lungs, skin, bones, and brain ( Fig. 4.15 ). Budding is characterized by a central yeast with multiple surrounding daughter buds, that morphologically resembles a "ship''s wheel." Infection (paracoccidioidomycosis) is caused by Paracoccidioides brasiliensis, typically found in Brazil and elsewhere in South America. Other species that cause human disease include C. doi = 10.1007/978-1-4614-0242-8_4 id = cord-260472-xvvfguht author = Papadopoulos, Nikolaos G. title = Antimicrobial strategies: An option to treat allergy? date = 2007-01-31 keywords = asthma; infection; respiratory; virus summary = doi = 10.1016/j.biopha.2006.10.004 id = cord-104317-t30dg6oj author = Parker, Michael T. title = An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery date = 2016-09-30 keywords = host; human; infection; interaction; pathogenic; virome; virus summary = However, the obvious importance of viruses in the composition of all biomes has not (yet) been met with an appropriate fervor for the characterization of the viral REVIEW Recent advances in sequencing technologies have opened the door for the classification of the human virome. The discovery of intimate interactions of viruses with humans, like the role of endogenous retrovirus (ERV †) syncytins in placentation [27] , are categorically dissimilar to the classical view of viruses only as parasites and brings to issue how scientists are approaching the study of the virome. The application of this scaffold will not only deepen the understanding of known virus-host interactions in the ecological context of the virome, but will also identify logical next steps and gaps in current knowledge that are tantalizing areas for future exploration. Additionally, further characterization of the human virome is likely to uncover more viruses that persistently infect humans [31] , and such discoveries could pave the way for the treatment of diseases of currently unknown etiology. doi = nan id = cord-271076-436nxsua author = Paul-Pierre, Pastoret title = Emerging diseases, zoonoses and vaccines to control them date = 2009-10-30 keywords = infection; specie; virus summary = In Northern America, the spectacular spread of West Nile virus infection, another vector transmitted disease, in humans and horses, was rapidly followed by the development of several vaccines, including a DNA-based vaccine for horses. To prevent Nipah virus (Henipavirus) infection in pigs a vaccine has recently been developed but, unfortunately, in countries like Bangladesh, humans are directly infected by the reservoir, a fruit bat species. The changes following globalisation, climatic change [6, 7] , and the opening of previously closed ecosystems, have considerably modified the pattern of endemic (or enzootic) infections/diseases, and contributed to the emergence of new agents that are pathogenic for humans and domestic animals. It is even more true when facing a really emerging disease that moreover is zoonotic such as Nipah virus infection [27] for which no vaccine was available yet, because the causative agent was previously unknown; the only solution is once again to kill and destroy the infected and in-contact animals. doi = 10.1016/j.vaccine.2009.06.021 id = cord-303490-rixuuytu author = Pazos, Michael A. title = Estrogen Mediates Innate and Adaptive Immune Alterations to Influenza Infection in Pregnant Mice date = 2012-07-05 keywords = CD8; cell; figure; infection summary = doi = 10.1371/journal.pone.0040502 id = cord-263927-hnsyas9q author = Peci, Adriana title = Community‐acquired respiratory viruses and co‐infection among patients of Ontario sentinel practices, April 2009 to February 2010 date = 2012-08-09 keywords = infection; respiratory summary = Objectives To describe respiratory viruses, including co‐infection and associated attributes such as age, sex or comorbidity, in patients presenting with influenza‐like illness to a community sentinel network, during the pandemic A(H1N1)pdm09 in Ontario, Canada. In multinomial logistic regression analyses adjusted for age, sex, comorbidity, and timeliness of sample collection, single infection was less often detected in the elderly and co‐infection more often in patients <30 years of age. Co‐infection, but not single infection, was more likely detected in patients who had a sample collected within 2 days of symptom onset as compared to 3–7 days. [8] [9] [10] [11] [12] [13] Higher proportions of influenza A, respiratory syncytial virus (RSV), parainfluenza viruses, and rhinovirus, compared with other circulating viruses have been detected in patients with co-infections. 9, 15, 16, 20, 21 This study enrolled community patients presenting with (ILI) to a community sentinel network, during the influenza pandemic A(H1N1)pdm09 in Ontario, Canada and documented the profile of respiratory viruses causing ILI symptoms. doi = 10.1111/j.1750-2659.2012.00418.x id = cord-315730-fzgxuak7 author = Penman, Sophie L. title = Safety perspectives on presently considered drugs for the treatment of COVID‐19 date = 2020-07-17 keywords = COVID-19; Health; IFN; SARS; clinical; infection; patient; treatment summary = Owing to their efficacy against viruses (mostly demonstrated in vitro) including influenza, HIV, coronavirus OC43, and SARS-CoV, a large number of clinical trials (>230) have been registered worldwide using chloroquine/hydroxychloroquine alone, or in combination with other drugs (e.g. azithromycin) for the treatment of COVID-19. At the time of writing, the RECOVERY trial (clinical trial identifier NCT04381936) which is the largest randomised control trial so far conducted for the treatment of COVID, has stopped recruiting to the hydroxychloroquine arm (1542 patients compared with 3132 on standard care) because of no beneficial effect either in terms of mortality or hospital stay (P. Assessment of QT Intervals in a Case Series of Patients With Coronavirus Disease 2019 (COVID-19) Infection Treated With Hydroxychloroquine Alone or in Combination With Azithromycin in an Intensive Care Unit Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial doi = 10.1111/bph.15204 id = cord-332379-340wczmq author = Pennington, Matthew R. title = Disparate Entry of Adenoviruses Dictates Differential Innate Immune Responses on the Ocular Surface date = 2019-09-13 keywords = D37; EKC; adenovirus; cell; corneal; dna; human; infection summary = These findings suggest that adenoviruses may stimulate specific pattern recognition receptors in an entry/trafficking-dependent manner, leading to distinct immune responses dependent on the virus/cell type combination. Additional work is needed to understand the specific connections between adenoviral entry and the stimulation of innate immune responses by the various cell types present on the ocular surface. Innate immune responses to adenoviruses rely on the detection of pathogen-associated molecular patterns (PAMPs): distinct ligands present on the external surfaces, and nucleic acids of pathogens (but absent in the host) that feature molecular signatures able to be recognized by pattern recognition receptors (PRR) on or in infected host cells [43] [44] [45] [46] . Innate immune responses to adenoviruses rely on the detection of pathogen-associated molecular patterns (PAMPs): distinct ligands present on the external surfaces, and nucleic acids of pathogens (but absent in the host) that feature molecular signatures able to be recognized by pattern recognition receptors (PRR) on or in infected host cells [43] [44] [45] [46] . doi = 10.3390/microorganisms7090351 id = cord-269181-1h3wbhq4 author = Perelmutter, L. title = Immunoglobulin E response during viral infections date = 1979-08-31 keywords = IgE; infection summary = Abstract One hundred and three patients (90 nonatopics and 13 atopics) with respiratory infections to various viral agents were studied retrospectively with respect to IgE immunoglobulin levels during acute (1 to 7 days) and convalescent (8 to 30 days) phases of infection. One hundred and three patients (90 nonatopics and 13 atopics) with respiratory i!fections to curious viral ugents were studied retrospectively with respect to IgE immunoglobulin levels during acute (I to 7 days) and convalescent (8 to 30 days) phases of infection. Clinical studies dating back almost 40 yr have suggested that upper respiratory tract infections are associated with bronchial asthma and can precipitate or potentiate attacks of bronchial asthma'', '' and wheezing in asthmatic patients. In the present study, it was found that naturally occurring viral respiratory infections modulated serum IgE levels in both nonatopic as well as atopic individuals. doi = 10.1016/0091-6749(79)90046-0 id = cord-344093-3bniy5b5 author = Peteranderl, Christin title = The Impact of the Interferon/TNF-Related Apoptosis-Inducing Ligand Signaling Axis on Disease Progression in Respiratory Viral Infection and Beyond date = 2017-03-22 keywords = IAV; IFN; TRAIL; cell; infection; type; virus summary = A prominent regulator of disease outcome, especially in-but not limited to-respiratory viral infection, is the IFN-dependent mediator TRAIL (TNF-related apoptosis-inducing ligand) produced by several cell types including immune cells such as macrophages or T cells. (73) Cell death induction, e.g., Bcl-2-associated X protein, caspase-8, Fas-associated protein with death domain, Fas ligand, and TNF-related apoptosis-inducing ligand (TRAIL) dsRNA, polyI:C (4, 110) IAV (4, 5, 10, 115) Sendai virus (110) TRAIL Virus control by apoptosis induction in infected cells IAV (6, 170, 171) Tissue injury by apoptosis of both infected and non-infected alveolar epithelial cells, lung macrophages IAV (5, 7, 10) RSV (137) Necrosis of fibroblasts, dendritic cells, and epithelial cells IAV (146, 147, 168) Increased cellular infiltration CoV (175) Decreased expression of Na,K-ATPase, impaired epithelial fluid reabsorption IAV (11) iNTRODUCTiON In 1957, Isaacs and Lindenmann (1) first recognized the potential of a soluble and probably cell-derived factor to combat influenza virus infection and named this factor interferon [(IFN) from latin interferre, to interfere]. doi = 10.3389/fimmu.2017.00313 id = cord-303320-3tjhisfg author = Petersen, Eskild title = Reflections on travel-associated infections in Europe date = 2015-01-31 keywords = hpv; infection summary = doi = 10.1016/s1473-3099(14)71055-2 id = cord-255623-qdpdsye9 author = Pham, Hien T. title = Clinical and Pathogenic Characteristics of Lower Respiratory Tract Infection Treated at the Vietnam National Children's Hospital date = 2020-03-11 keywords = infection; respiratory; virus summary = doi = 10.1155/2020/7931950 id = cord-021977-yu0hrg6h author = Pham, Phuong-Thu T. title = Medical Management of the Kidney Transplant Recipient: Infections and Malignant Neoplasms date = 2010-12-27 keywords = CMV; PTLD; infection; transplantation summary = Despite prophylactic therapy against common bacterial, viral, and opportunistic pathogens in the perioperative and postoperative period, infections are the second most common cause of death after cardiovascular disease (CVD) in renal transplant recipients. In the setting of immunosuppression, such viral infections may lead to the development of progressive liver disease or cirrhosis (HBV, HCV), BK nephropathy, post-transplantation lymphoproliferative disease (EBV), or squamous cell carcinoma (papillomavirus). 1 Sources of infections specific to recipients of renal transplant: perinephric fluid collections (e.g., lymphoceles, wound hematomas, urine leaks), indwelling urinary stents, or anatomic or functional genitourinary tract abnormalities (e.g., ureteral stricture, vesicoureteric reflux, neurogenic bladder blood, such as CMV DNA polymerase chain reaction (PCR) or pp65 antigenemia during surveillance studies. A suggested CMV prophylaxis protocol is shown in Figure 101 Clinical CMV disease is treated with intravenous ganciclovir (5 mg/kg twice daily for 3 weeks, dose adjusted for renal dysfunction) with reduction of immunosuppression, such as withholding of MMF. doi = 10.1016/b978-0-323-05876-6.00101-5 id = cord-003915-kje8lvgl author = Pigeyre, Laetitia title = Interaction of a Densovirus with Glycans of the Peritrophic Matrix Mediates Oral Infection of the Lepidopteran Pest Spodoptera frugiperda date = 2019-09-17 keywords = Calcofluor; JcDV; PBS; figure; infection summary = As orally transmitted viruses, densoviruses, are also challenged by the complexity of the insect gut barriers, more specifically by the chitinous peritrophic matrix, that lines and protects the midgut epithelium; how capsids stick to and cross these barriers to reach their final cell destination where replication goes has been poorly studied in insects. In addition, we showed that JcDV early infection results in (i) an arrest of N-Acetylglucosamine (GlcNAc) secretion by epithelial cells associated with a disorganization of the PM structure mimicking the effect of chitin-binding plant lectin; (ii) substantial changes in the expression of gut genes, which may also contribute to an early gut dysfunction and participate to viral pathogenesis. Results presented here show that JcDV capsids display carbohydrate-binding properties that insure recognition of the peritrophic matrix and determines caterpillars oral infection. doi = 10.3390/v11090870 id = cord-268133-obwo7741 author = Ponce, José Burgos title = Overlapping findings or oral manifestations in new SARS‐CoV‐2 infection? date = 2020-06-10 keywords = infection summary = doi = 10.1111/odi.13478 id = cord-309642-wwaa6ls0 author = Potgieter, Leon N.D. title = Pathogenesis of Viral Infections date = 1986-11-30 keywords = cell; dna; host; infection; result; viral; virus summary = 7 · 18 · 84 · 133 Such restrictions function at the cellular level either as the presence or absence of appropriate cell surface receptors (in some instances, they have been shown to be inherited as dominant alleles in a Mendelian manner) 9 · 18 · 26 · 46 · 68 · 97 ·u 9 · 120 or the intracellular hospitality of the cell (several genetic host restrictions on virus replication have been identified).18·32·59·80·82·108·109·120·126 Restricted growth of several DNA viruses in some cells results in transformation without production of progeny viruses. 112 The phenomenon appears to be mediated by virus-induced receptors on the surface membrane of cells and may be one mechanism of the often-encountered secondary bacterial infections associated with viral diseases. 51 · 52 · 104 Viral respiratory tract disease is a consequence of mechanical and biochemical injury to epithelial cells and alveolar macrophages, which can, in the most severe instances, result in secondary bacterial infection, pneumonia, and death. doi = 10.1016/s0195-5616(86)50129-7 id = cord-022582-2e9i3m4b author = Potsic, William P. title = Otolaryngologic Disorders date = 2012-03-21 keywords = airway; child; ear; infection; middle; nasal; neck; present; treatment summary = When fluid persists in the middle ear for 3 to 4 months, causing a hearing loss or is associated with ASOM, myringotomy and tympanostomy tube placement is helpful to resolve the hearing loss and reduce the frequency and severity of infection. In addition to antibiotics, treatment should include a wide field myringotomy from the anterior inferior quadrant to the posterior inferior quadrant, a tympanostomy tube placement for middle ear drainage, and a postauricular mastoidectomy to drain the subperiosteal abscess and the mastoid. These infections may be caused by a variety of viral and bacterial pathogens; and in addition to sore throat, symptoms include fever, mucopurulent nasal drainage, nasal obstruction, and facial pain. Symptoms typically appear at birth or soon thereafter and include inspiratory stridor, feeding difficulties, and, rarely, apnea or signs of severe airway obstruction. Children afflicted with recurrent respiratory papillomatosis present initially with hoarseness but may also have symptoms and signs of airway obstruction, including stridor. doi = 10.1016/b978-0-323-02842-4.50055-3 id = cord-271172-y48dovux author = Potter, Christopher William title = Chapter 25 Respiratory tract viruses date = 1998-12-31 keywords = cell; infection; influenza; respiratory; virus summary = doi = 10.1016/s1569-2582(97)80009-8 id = cord-023942-vrs3je1x author = Powers, Karen S. title = Acute Pulmonary Infections date = 2011-12-16 keywords = MRSA; RSV; child; disease; infant; infection; pneumonia; respiratory summary = Acute lower respiratory infection is a common cause of morbidity in infants and children, and at times, requires intensive care and mechanical ventilation. Acute lower respiratory infection is a common cause of morbidity in infants and children, and at times, requires intensive care and mechanical ventilation. Viral bronchiolitis remains the leading cause for hospital admission in infancy and the most frequent cause of acute respiratory failure in children admitted to pediatric intensive care units in North America. In a study of hospitalized infants with congenital heart disease infected with RSV, 33% required intensive care, 19% received mechanical ventilation, and 3.4% died. In the 1990s, fi ve randomized trials involving 225 infants, evaluating the effect of nebulized adrenaline (epinephrine) on bronchiolitis showed clinical improvement, with reductions in oxygen requirement, respiratory rate, wheezing, and decrease in pulmonary vascular resistance. High incidence of pulmonary bacterial co-infection in children with severe respiratory syncytial virus (RSV) bronchiolitis doi = 10.1007/978-0-85729-923-9_25 id = cord-103342-stqj3ue5 author = Prakash, Meher K title = A minimal and adaptive prediction strategy for critical resource planning in a pandemic date = 2020-04-10 keywords = infection; number summary = We propose a strategy for estimating the number of infections and the number of deaths, that does away with time-series modeling, and instead makes use of a ''phase portrait approach''. Using our model, we predict the number of infections and deaths in Italy and New York State, based on an adaptive algorithm which uses early available data, and show that our predictions closely match the actual outcomes. Our approach can be summarized as follows: The COVID-19 data from most countries suggests that, especially in the growing phase of the pandemic, the number of active cases and the number of hospitalizations are both proportional to the total number of infections: approximately around 70-90 % and 20-30%, respectively. Thus, using the data from South Korea as a reference standard, the deaths versus infections curve has been readjusted as seen in Figure:3A CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. doi = 10.1101/2020.04.08.20057414 id = cord-252691-757mh2mh author = Pratt, R. J. title = epic2: National Evidence-Based Guidelines for Preventing Healthcare-Associated Infections in NHS Hospitals in England date = 2007-02-28 keywords = BSI; CVAD; HCAI; HICPAC; Health; catheter; evidence; infection; study summary = Following extensive consultation, they were published in January 2001.1 These guidelines describe the precautions healthcare workers should take in three areas: standard principles for preventing HCAI, which include hospital environmental hygiene, hand hygiene, the use of personal protective equipment, and the safe use and disposal of sharps; preventing infections associated with the use of short-term indwelling urethral catheters; and preventing infections associated with central venous catheters. epic2: Guidelines for Preventing Healthcare-Associated Infections in NHS Hospitals S15 Current evidence-based guidelines conclude that in both outbreak and non-outbreak situations contaminated hands are responsible for crosstransmission of microorganisms and that effective and effective hand decontamination can significantly reduce both cross-transmission and crossinfection rates for the majority of HCAI in all healthcare settings. 1, 85 The decision to use or wear personal protective equipment must be based upon an assessment of epic2: Guidelines for Preventing Healthcare-Associated Infections in NHS Hospitals S19 the level of risk associated with a specific patient care activity or intervention and take account of current health and safety legislation. doi = 10.1016/s0195-6701(07)60002-4 id = cord-342133-khrljehj author = Principi, Nicola title = Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease date = 2015-08-12 keywords = child; infection; respiratory; viral summary = To evaluate the role of human bocavirus (hBoV) as a causative agent of respiratory disease, the importance of the viral load in respiratory disease type and severity and the pathogenicity of the different hBoV species, we studied all hBoV-positive nasopharyngeal samples collected from children who attended an emergency room for a respiratory tract infection during three winters (2009–2010, 2011–2012, and 2013–2014). To evaluate the circulation of the different hBoV types and the possible relationships between viral load, virus genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children attending the emergency room of the Fondazione IRCCS Ca'' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection arising between November 1 and March 31 during 3 winters (2009-2010, 2011-2012, and 2013-2014) . Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children doi = 10.1371/journal.pone.0135640 id = cord-317548-ft7lkpzq author = Proud, David title = Upper airway viral infections date = 2007-07-05 keywords = COPD; HRV; infection summary = Despite the major health care consequences associated with these complications, our understanding of how URI trigger upper airway symptoms and cause exacerbations of lower airway diseases remains limited. Given that HRV is the major viral pathogen associated with colds and exacerbations of asthma and COPD, we will focus on the current status of our knowledge of the response to HRV infection as representative of viral pathogenesis, indicating differences with other viral types when appropriate. Several factors are likely to play a role in determining the severity of the clinical outcome to upper airway viral responses, including the susceptibility of patients with asthma or COPD to experience lower airway exacerbations. Influenza vaccine is clearly effective in reducing upper airway symptoms, and in preventing lower disease exacerbations, induced by this virus during the winter months. Nitric oxide inhibits rhinovirus-induced cytokine production and viral replication in a human respiratory epithelial cell line doi = 10.1016/j.pupt.2007.06.004 id = cord-312795-0e4esl2o author = Puig-Domingo, M. title = COVID-19 and endocrine diseases. A statement from the European Society of Endocrinology date = 2020-04-11 keywords = covid-19; infection; patient summary = People with diabetes in particular are among those in high-risk categories who can have serious illness if they get the virus, according to the data published so far from the Chinese researchers, but other endocrine diseases such as obesity, malnutrition, and adrenal insufficiency may also be impacted by COVID-19. Contacting the healthcare provider team by telephone, email, or videoconference is also mandatory in case of possible symptoms of COVID-19 infection in order to seek advice concerning the measures to avoid risk of deterioration of diabetes control or the possibility to be referred to another specialist (pneumologist or infectious disease doctor) or in the Emergency Services of the referral hospital to avoid the most serious systemic complication of the viral infection itself. For all these reasons, patients with adrenal insufficiency may be at higher risk of medical complications and eventually at increased mortality risk in the case of COVID-19 infection. doi = 10.1007/s12020-020-02294-5 id = cord-271752-h05sten7 author = Pérez-Arellano, José Luis title = Executive summary of imported infectious diseases after returning from foreign travel: Consensus document of the Spanish Society for Infectious Diseases and Clinical Microbiology (SEIMC) date = 2018-03-31 keywords = III; infection; traveler summary = doi = 10.1016/j.eimc.2017.02.009 id = cord-026595-imn2jxcu author = Qamar, Mariam Khan title = What Do the Dental Students Know about Infection Control? A Cross-Sectional Study in a Teaching Hospital, Rawalpindi, Pakistan date = 2020-06-01 keywords = infection; student summary = Several studies have been conducted to assess the practices and knowledge of dental students and have demonstrated poor compliance of the students to infection control measures. A study conducted in India to assess the infection control practices among dental students showed that only one-tenth of the respondents adhere to the infection control measures [1] . Similar studies have been conducted worldwide to investigate the knowledge and practices of dental students on infection control [6] [7] [8] [9] [10] [11] [12] [13] [14] , and a general consensus is that students need awareness and must be protected in the unsafe environment. Knowledge, attitudes, and practice regarding infection control measures among dental students in Central India Knowledge, attitudes, and practice of infection control among dental students at Sana''a University Knowledge, attitude and practices about hepatitis B and infection control measures among dental students in Patiala doi = 10.1155/2020/3413087 id = cord-018208-sc8j1ate author = Qu, Bo title = The Accuracy of Mean-Field Approximation for Susceptible-Infected-Susceptible Epidemic Spreading with Heterogeneous Infection Rates date = 2016-11-09 keywords = NIMFA; infection summary = Moreover, given the same actual prevalence, NIMFA performs better in the cases: 1) when the variance of the i.i.d. infection rates is smaller (while the average is unchanged); 2) when the correlation between the infection rate and the nodal degree is positive. Our work suggests the conditions when the mean-field approach, in particular NIMFA, is more accurate in the approximation of the SIS epidemic with heterogeneous infection rates. In particular, we compare the average fraction y ∞ of infected nodes as a function of the effective infection rate τ computed by NIMFA to that obtained by the continuous-time simulations of the exact SIS model when the infection rates are heterogeneous but the recovery rate is the same for all nodes. In this paper, we aim to understand how the correlation influences the accuracy of NIMFA by comparing the average fraction y ∞ of infected nodes obtained by NIMFA and the simulations of the exact SIS model. doi = 10.1007/978-3-319-50901-3_40 id = cord-280184-91d8i6ix author = Querido, Micaela Machado title = Self-disinfecting surfaces and infection control date = 2019-06-01 keywords = Staphylococcus; antimicrobial; bacteria; contamination; hospital; infection; microorganism; surface summary = doi = 10.1016/j.colsurfb.2019.02.009 id = cord-291711-usvvad21 author = Radermecker, M. title = Atopie et infections date = 2000-01-31 keywords = infection summary = doi = 10.1016/s0335-7457(00)80034-9 id = cord-302833-6kntd89t author = Radonovich, Lewis J. title = The Respiratory Protection Effectiveness Clinical Trial (ResPECT): a cluster-randomized comparison of respirator and medical mask effectiveness against respiratory infections in healthcare personnel date = 2016-06-02 keywords = N95; infection; respiratory; study summary = doi = 10.1186/s12879-016-1494-2 id = cord-285467-uxfk6k3c author = Ragni, Enrico title = Management of osteoarthritis during COVID‐19 pandemic date = 2020-05-21 keywords = COVID-19; SARS; infection; osteoarthritis; patient summary = Since an effective immune response against viral infections depends on cytotoxic T cells activation (25) , experimental evidence supports the observation that overexpression of inflammatory cytokines like IL-6 during the viral immune response might be associated with a decreased viral clearance by impairing the polarization and functionality of Th1 and CD8 cells (26), contributing to the worsening of the COVID-19 symptoms, and their management may appear an intriguing therapeutical approach. Overall, the administration of drugs for the control of inflammation, inhibiting the response of the immune system, may be detrimental in the initial phases of the viral infection, reducing the ability of the body to react to the presence of SARS-CoV-2, as observed in patients chronically treated for rheumatoid arthritis (27) . All rights reserved This shall prompt orthopaedics and clinicians in general to evaluate with extreme care the clinical conditions of OA patients not only under the perspective of OA symptoms management but also for undercurrent comorbidities, naturally occurring or OA-treatment-related, that, in the era of COVID-19 pandemic, may strongly affect patients outcomes more than the net combination of SARS-CoV-2 infection and OA. doi = 10.1002/cpt.1910 id = cord-352222-zq9o66i4 author = Rajatonirina, Soatiana title = Outcome Risk Factors during Respiratory Infections in a Paediatric Ward in Antananarivo, Madagascar 2010–2012 date = 2013-09-12 keywords = child; infection; respiratory summary = BACKGROUND: Acute respiratory infections are a leading cause of infectious disease-related morbidity, hospitalisation and mortality among children worldwide, and particularly in developing countries. MATERIALS AND METHODS: We conducted a prospective study in a paediatric ward in Antananarivo from November 2010 to July 2012 including patients under 5 years old suffering from respiratory infections. CONCLUSION: Co-mordidity, low-income and age under 6 months increase the risk of severe outcome for children infected by numerous respiratory pathogens. Our study aimed to evaluate the risk factors associated with the evolution and outcome of respiratory illnesses in patients aged under 5 years old hospitalised in one of the four main public hospitals in Antananarivo. In our study, Streptococcus pneumoniae was the most common bacterial pathogen as in other studies of hospitalised patients with acute respiratory illness, and Haemophilus influenzae type B was the next most frequent [16] [17] [18] [19] . doi = 10.1371/journal.pone.0072839 id = cord-001455-n7quwr4s author = Rapin, Noreen title = Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans date = 2014-11-12 keywords = PCR; bat; infection summary = title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans Using tissue samples collected at the termination of an experiment to explore the pathogenesis of White Nose Syndrome in Little Brown Bats, we determined if hibernating bats infected with the fungus Pseudogymnoascus destructans could respond to infection by activating genes responsible for innate immune and stress responses. We found that bats responded to infection with a significant increase in lungs of transcripts for Cathelicidin (an anti-microbial peptide) as well as the immune modulators tumor necrosis factor alpha and interleukins 10 and 23. We used samples collected during the experiment to address the question: Can hibernating bats respond to infection by activating genes responsible for innate immune and stress responses? We determined levels of transcripts for several immune and stress response genes (Table 1) in lungs from infected and control bats. doi = 10.1371/journal.pone.0112285 id = cord-278873-x6i5tiju author = Reddy, Vidhatha title = Management guidelines for pregnant healthcare workers exposed to infectious dermatoses date = 2020-04-18 keywords = B19; infection summary = doi = 10.1016/j.ijwd.2020.04.004 id = cord-331673-xv1tcugl author = Reina, Giacomo title = Hard Nanomaterials in Time of Viral Pandemics date = 2020-07-15 keywords = HIV; Nanoparticles; ROS; SARS; Virus; antiviral; cell; infection; viral summary = For instance, in the case of Herpesviridae and Paramyxoviridae viruses (both enveloped viruses with embedded viral-encoded glycoproteins), AgNPs can effectively reduce their infectivity, by blocking the interaction between the viral particles and the host cells with an antiviral activity strictly dependent on the size and ζ potential of the AgNPs. As a general observation, it was reported that smaller nanoparticles have better antiviral effect. cAgNPs could reduce cytopathic effects induced by RSV and showed efficient antiviral activity against infection by directly inactivating the virus prior to entry into the host cells. have reported that porous AuNPs are able to inhibit influenza A infection more efficiently than nonporous AuNPs. 39 This effect has been associated with the higher surface area of the porous material that favors their interaction with capsids and thus increases their antiviral activity ( Figure 4 ). doi = 10.1021/acsnano.0c04117 id = cord-280060-gzby85u9 author = Rello, Jordi title = Management of infections in critically ill returning travellers in the intensive care unit—II: clinical syndromes and special considerations in immunocompromised patients() date = 2016-04-28 keywords = ESCMID; infection; patient; risk summary = doi = 10.1016/j.ijid.2016.04.020 id = cord-260267-nau9kayk author = Ren, Lili title = Human parainfluenza virus type 4 infection in Chinese children with lower respiratory tract infections: A comparison study date = 2011-06-01 keywords = HPIV-4; infection summary = title: Human parainfluenza virus type 4 infection in Chinese children with lower respiratory tract infections: A comparison study Background: Human parainfluenza viruses (HPIVs) are a leading cause of acute respiratory tract infections (ARTIs). Background: Human parainfluenza viruses (HPIVs) are a leading cause of acute respiratory tract infections (ARTIs). Objectives: To characterize the role of HPIV-4 and its clinical features in children with acute lower respiratory tract infections (ALRTIs) in Beijing, China. Objectives: To characterize the role of HPIV-4 and its clinical features in children with acute lower respiratory tract infections (ALRTIs) in Beijing, China. Human parainfluenza viruses (HPIVs) are a leading cause of acute respiratory tract infections (ARTIs). [10] [11] [12] [13] [14] However, the prevalence and clinical characteristics of HPIV-4 in Chinese paediatric patients with acute lower respiratory tract infections (ALRTIs) have not been addressed fully. doi = 10.1016/j.jcv.2011.05.001 id = cord-018302-lmly43rd author = Renaud, Christian title = Respiratory Syncytial Virus and Human Metapneumovirus Infection in Transplant Recipients date = 2016-02-15 keywords = HSCT; RSV; infection; recipient; respiratory; virus summary = Respiratory viral infections due to respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause infections in immunocompromised transplant patients ranging from mild upper respiratory infections to severe lower respiratory tract disease with respiratory failure. Surveillance studies of respiratory viruses from transplant centers have established the high frequency and the signifi cant clinical impact of respiratory viral infections in HSCT recipients overall [ 8 -15 , 46 , 47 ] as well as the relative importance of RSV in terms of morbidity and mortality (Table 31 -2 ). A retrospective MDACC study of confi rmed RSV infections in 280 allogeneic HSCT recipients from 1996 to 2009 utilized multivariable logistic regression to demonstrate that lack of ribavirin aerosol therapy at the upper respiratory tract disease stage was an important risk factor associated with RSV LRTI and all-cause mortality [ 99 ] . doi = 10.1007/978-3-319-28797-3_31 id = cord-000457-e50a0suk author = Rhim, Jung-Woo title = Epidemiological and clinical characteristics of childhood pandemic 2009 H1N1 virus infection: an observational cohort study date = 2011-08-24 keywords = H1N1; infection; patient summary = METHODS: We evaluated the epidemiologic characteristics of all the subjects infected with the 2009 H1N1 influenza A virus (2,971 patients, ≤ 15 years of age), and the clinical and laboratory findings of the inpatients (217 patients, 80 had pneumonia) between 1 September 2009 and 31 January 2010 in a single hospital throughout the epidemic. In addition, during the study period we observed a dramatic effect of early treatment with corticosteroids and oseltamivir for patients with severe pneumonia including rapidly progressive pneumonia [9, 10] . We retrospectively evaluated all patients with 2009 H1N1 virus infection during the pandemic (2,971 patients) for epidemiologic characteristics, and for clinical characteristics, we reviewed the medical records and chest radiographic findings of 217 children admitted to The Catholic University of Korea, Daejeon St Mary''s Hospital between 1 September 2009 and 31 January 2010. In pandemic 2009 H1N1 virus infections, children of all ages were evenly affected, and males were predominant in pneumonia patients. doi = 10.1186/1471-2334-11-225 id = cord-016882-c9ts2g7w author = Ribeiro, Edna title = Viruses Present Indoors and Analyses Approaches date = 2017-06-12 keywords = PCR; Rosa; infection; respiratory; virus summary = It''s well known that approximately 60% of total human respiratory and gastrointestinal infections are acquired indoor, since viruses have a rapid spread in the community and can be transmitted easily, especially in crowded and poorly ventilated environments, causing high morbidity and decline in quality of life and productivity. Viruses'' inductors of Severe Acute Respiratory Syndrome (SARS), influenza and norovirus are transmitted from patients primarily by contact and/or droplet routes, while airborne transmission occurs over a limited distance (Srikanth et al., 2008) . It is well-known that viruses are shed in large numbers, with transmission routes extraordinary diverse, including direct contact with infected persons, faecal-oral transmission (through contaminated food and water), droplet and airborne transmission, and can survive for long periods on surfaces or fomites, emphasizing the possible role of surfaces in the transmission of viruses (Barker et al., 2001; La Rosa et al., 2013) . doi = 10.1007/978-3-319-61688-9_7 id = cord-254580-nhpjvgt4 author = Ricardo, Jose W. title = Considerations for Safety in the Use of Systemic Medications for Psoriasis and Atopic Dermatitis during the COVID‐19 pandemic date = 2020-05-27 keywords = infection; psoriasis summary = In this review, we discuss overall infection risks of non‐biologic and biologic systemic medications for psoriasis and atopic dermatitis, and provide therapeutic recommendations. In this review, we summarize the current literature regarding overall infection risks with systemic immunomodulating agents for psoriasis and AD, and provide evidence-based treatment recommendations during the COVID-19 pandemic. 11 While methotrexate and cyclosporine are associated with decreased infection rates and favored over treatment with systemic corticosteroids, 12 their impact on susceptibility to/severity of COVID-19 is unknown and, if essential, precautions should be taken to avoid infection. In a phase III, double-blinded, placebo-controlled study on 837 psoriasis patients randomized to treatment with guselkumab, adalimumab or placebo, overall, candida, and serious infections, occurred at comparable rates across treatment groups. Efficacy and safety of guselkumab, an anti-interleukin-23 monoclonal antibody, compared with adalimumab for the treatment of patients with moderate to severe psoriasis with randomized withdrawal and retreatment: Results from the phase III, double-blind, placebo-and active comparator-controlled VOYAGE 2 trial doi = 10.1111/dth.13687 id = cord-302247-moor7dfc author = Richards, James title = Feline Vaccination Guidelines date = 2001-05-31 keywords = cat; feline; infection; vaccine summary = Kittens younger than 16 weeks of age are generally more susceptible to infection than are adult cats and typically develop more severe disease. 47 Immunity conferred by feline panleukopenia vaccines is considered to be excellent, and most vaccinated animals are completely protected from infection and clinical disease. If a susceptible cat is born into or is entering an environment in which viral upper respiratory tract disease is endemic (e.g., some catteries, boarding facilities, shelters), the use of a topical product may be advantageous. Manufacturers are required by the US Department of Agriculture to establish, by means of experimental challenge exposure studies, the minimum duration of immunity for the rabies virus vaccines that they sell, and products approved for use every year or every 3 years are available. Vaccination may be considered for cats in multiple-cat environments, where infections associated with clinical disease have been confirmed. doi = 10.1016/s0195-5616(01)50602-6 id = cord-346539-kxnrf5g5 author = Riggioni, Carmen title = A compendium answering 150 questions on COVID‐19 and SARS‐CoV‐2 date = 2020-06-14 keywords = ACE2; COVID-19; CoV-2; SARS; cell; clinical; figure; infection; patient; respiratory; severe summary = This paper answers pressing questions, formulated by young clinicians and scientists, on SARS‐CoV‐2, COVID‐19 and allergy, focusing on the following topics: virology, immunology, diagnosis, management of patients with allergic disease and asthma, treatment, clinical trials, drug discovery, vaccine development and epidemiology. The first cases of the coronavirus disease 2019 (COVID19) , caused by the novel severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), were reported in China in December 2019 1 and rapidly led to pandemic. 40, 41 A seroconversion study in COVID-19 patients has found and association between disease severity and SARS-CoV-2-specific IgA levels. Mesenchymal stem cell therapy may potentiate the low IFN-I and -III levels and moderate IFN-stimulated gene response reported in SARS-CoV-2-infected ferrets and COVID-19 patients. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial doi = 10.1111/all.14449 id = cord-017040-4zajnrsf author = Rihana, Nancy title = Skin Infections date = 2019-08-11 keywords = Pseudomonas; cutaneous; infection; lesion; patient; skin summary = doi = 10.1007/978-3-030-21859-1_5 id = cord-008499-tl3i7uzd author = Robb, James A. title = Intrauterine latent herpes simplex virus infection(): I. Spontaneous abortion date = 2007-11-06 keywords = HSV; cent; infection; positivity summary = Herpes simplex virus (HSV, probably type 2) antigen was detected in nonpregnant and pregnant endometria, placentae, umbilical cords, and neonatal tissues (companion paper) by avidinbiotin complex immunohistochemical studies. Spontaneous and therapeutic abortion material, endometrial curettage tissue, full-term placentae and umbilical cords, and stillborn and liveborn neonatal tissues were studied by HSV-specific immunohistochemical methods to evaluate the prevalence and distribution of these HSV antigens in cases in which HSV infection was not suspected or detectable as HSV cytologic abnormalities by light microscopy, virus particles by transmission electron microscopy, or infectious HSV by direct cultnre. T h e following findings strongly support our hypothesis that the staining detected in the target and patient tissues with the Dako rabbit anti-HSV 2 IgG (lot 1188, our screening antibody) is specific for HSV and, probably, for type 2 infection in t h e products of conception, placentae, umbilical cords, and endometrial curettage specimens: doi = 10.1016/s0046-8177(86)80561-5 id = cord-304720-0lgup7yj author = Robbins, R.C. title = Swine Diseases and Disorders date = 2014-08-21 keywords = PCR; PRRS; cause; disease; infection; pig; result; sign; swine summary = The industry significance, etiology, epidemiology, pathogenesis, clinical signs, postmortem and histpathologic lesions, diagnostic testing, and generic treatment, control, and prevention are described. Important history to understand from caretakers includes: age of pigs affected, duration of clinical signs, morbidity rate, mortality rate, treatments administered, response to treatments, and any other important information regarding previous diagnoses or disease in the affected group of animals. Records include but are not limited to: where the animals originated from; number in the herd; age; daily mortality; number treated; name of treatment, route of delivery and dose; feed and water usage; high-low temperatures; and vaccinations received or administered. Postweaning infections result in a high morbidity but low mortality; most significant economic losses at this time are caused by reduced average daily gain, market weights, and overall system efficiency. Postweaning infections result in a high morbidity but low mortality; most significant economic losses at this time are caused by reduced average daily gain, market weights, and overall system efficiency. doi = 10.1016/b978-0-444-52512-3.00134-0 id = cord-288505-v4dbswyk author = Roberts, M.T.M. title = An analysis of imported infections over a 5-year period at a teaching hospital in the United Kingdom date = 2003-11-30 keywords = infection summary = A 5-year analysis of cases seen in a large teaching and district general hospital in the Eastern Region of the UK was performed using ward records correlated with Hospital coding data and Hospital Episode Statistics from the Department of Health. The analysis includes all imported infections seen on the infectious diseases ward as recorded in the ward data book, at Addenbrooke''s hospital in Cambridge, UK over a 5-year period 1998 -2002. The number of imported infections necessitating hospital admission is surprisingly high, yet it is likely that this is ''the tip of an iceberg'' with many cases treated by general practitioners or non-specialist hospital physicians in this and other local hospitals and some not seeking medical attention. In conclusion, this local analysis illustrates the surprising number and diversity of imported infections seen at a hospital away from major ports of entry despite which it largely mirrors the national situation. doi = 10.1016/j.tmaid.2003.10.002 id = cord-017622-aqhyt7jg author = Robertson, Lucy J. title = Cryptosporidiosis in Farmed Animals date = 2013-08-17 keywords = Giardia; calf; cryptosporidiosis; cryptosporidium; infection; oocyst; parvum; prevalence summary = Cryptosporidiosis was first identified as a disease of veterinary, rather than human medical, importance, and infection of farmed animals with different species of Cryptosporidium continues to be of veterinary clinical concern. This chapter provides insights into Cryptosporidium infection in a range of farmed animals – cattle, sheep, goats, pigs, cervids, camelids, rabbits, water buffalo and poultry – presenting not only an updated overview of the infection in these animals, but also information on clinical disease, infection dynamics and zoonotic potential. Although extensive data have been accrued on, for example, Cryptosporidium parvum infection in calves, and calf cryptosporidiosis continues to be a major veterinary concern especially in temperate regions, there remains a paucity of data for other farmed animals, despite Cryptosporidium infection causing significant clinical disease and also, for some species, with the potential for transmission of infection to people, either directly or indirectly. doi = 10.1007/978-3-7091-1562-6_4 id = cord-270892-ycc3csyh author = Rollinger, Judith M. title = The human rhinovirus: human‐pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery date = 2010-12-13 keywords = Echinacea; Fig; HRV; RNA; Table; activity; antiviral; human; infection; rhinovirus summary = doi = 10.1002/med.20176 id = cord-264408-vk4lt83x author = Ruiz, Sara I. title = Animal Models of Human Viral Diseases date = 2017-06-23 keywords = H5N1; HIV; HIV-1; MPXV; Mers; NHP; Nipah; West; animal; disease; human; infection; model; mouse; virus summary = Well-developed animal models are necessary to understand disease progression, pathogenesis, and immunologic responses to viral infections in humans. NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus are monitored for the extent of viral shedding; however, no clinical disease is observed in these models. Intracerebral and IN routes of infection resulted in a fatal disease that was highly dependent on dose while intradermal (ID) and subQ inoculations caused only 50% fatality in mice regardless of the amount of virus (liu et al., 1970) . Ferrets infected with Hendra or Nipah virus display the same clinical disease as seen in the hamster model and human cases (Bossart et al., 2009; Pallister et al., 2011) . Characterization studies with IFNAr −/− mice challenged with different routes (IP, IN, IM, and subQ) showed that CCHFV causes acute disease with high viral loads, pathology in liver and lymphoid tissues, increased proinflammatory response, severe thrombocytopenia, coagulopathy, and death, all of which are characteristics of human disease . doi = 10.1016/b978-0-12-809468-6.00033-4 id = cord-319933-yp9ofhi8 author = Ruiz, Sara I. title = Chapter 38 Animal Models of Human Viral Diseases date = 2013-12-31 keywords = Nipah; SARS; animal; clinical; day; disease; experimental; human; infection; model; mouse; virus summary = An experimental study with cell culture-adapted hepatitis Avirus in guinea pigs challenged by oral or intraperitoneal routes did not result in clinical disease, increase in liver enzymes, or seroconversion. 32 NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus can be monitored for the extent of viral shedding; however, no clinical disease is observed in these models. 66, 67 Intracerebral and intranasal routes of infection resulted in a fatal disease that was highly dependent on dose, while intradermal and subcutaneous inoculations caused only 50% fatality in mice regardless of the amount of virus. A mouse-adapted (MA) strain of Dengue virus 2 introduced into AG129 mice developed vascular leak syndrome similar to the severe disease seen in humans. [138] [139] [140] [141] [142] [143] [144] Inoculation of WNV into NHPs intracerebrally resulted in the development of either encephalitis, febrile disease, or an asymptomatic infection, depending on the virus strain and dose. doi = 10.1016/b978-0-12-415894-8.00038-5 id = cord-351490-2fx0w30u author = Russell, Clark D. title = Treatable traits and therapeutic targets: Goals for systems biology in infectious disease date = 2017-04-27 keywords = host; immune; infection; system summary = A systems medicine approach to infection has the potential to provide new solutions to old problems: to identify host traits that are potentially amenable to therapeutic intervention, and the host immune factors that could be targeted by host-directed therapies. We suggest there are two major goals for systems biology in infection medicine: (1) to identify subgroups of patients that share treatable features; and, (2) to integrate high-throughput data from clinical and in vitro sources in order to predict tractable therapeutic targets with the potential to alter disease trajectories for individual patients. A systems medicine approach to infection has the potential to combine and integrate relevant signals from clinical, genomic, transcriptomic, proteomic and pathogen biology data to draw inferences about disease pathogenesis. A more specific host-directed therapy, recombinant human activated protein C (rhAPC), was licensed for treatment of severe sepsis based on the results of a single clinical trial [20] . doi = 10.1016/j.coisb.2017.04.003 id = cord-324950-ux7shvji author = Saade, Georges title = Coinfections and their molecular consequences in the porcine respiratory tract date = 2020-06-16 keywords = PCV2; PRRSV; cell; infection; porcine; respiratory; virus summary = In pigs, the term "Porcine Respiratory Disease Complex" (PRDC) is often used to describe coinfections involving viruses such as swine Influenza A Virus (swIAV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), and Porcine CircoVirus type 2 (PCV2) as well as bacteria like Actinobacillus pleuropneumoniae, Mycoplasma hyopneumoniae and Bordetella bronchiseptica. The outcome of any coinfection or superinfection can be affected by the interactions taking place between the infectious agents, the nature of the cell/host, adverse environmental and management conditions, intestinal and respiratory microbiomes, and the triggered immune response-innate and adaptive-developed afterwards [2, 3] . It is well-known that viral infections can induce an ideal environment for a bacterial superinfection through different mechanisms such as the destruction of the epithelial barrier, the over-expression of the receptors involved in the bacterial adhesion to the cells, and the alteration of the host immune response [1, 2, 94, 95] . doi = 10.1186/s13567-020-00807-8 id = cord-010162-hfo35gsq author = Saikku, Pekka title = Atypical respiratory pathogens date = 2014-12-29 keywords = Chlamydia; infection; pneumoniae summary = The main atypical pathogens in respiratory tract infections are classified on the basis of their ability to cause atypical pneumonia. The majority of these pathogens cause upper respiratory tract infections more often than overt pneumonias. In the following sections the main bacterial agents causing atypical respiratory tract infections are discussed, with a special emphasis on the latest bacterial addition, Chlamydia pneumoniae. Respiratory tract infections caused by Chlamydia psittaci are directly dependent on exposure to birds carrying the pathogen. The role that Chlamydia pneumoniae plays in other acute respiratory tract infections is still under study. It should also be attempted in Chlamydia pneumoniae infections in order to obtain information on disease associations and strain variability of this newly recognized pathogen. A new respiratory tract pathogen: Chlamydia pnenmoniae strain TWAR Chlamydia pnenmoniae, strain TWAR, Mycoplasma pneumoniae and viral infections in acute respiratory disease in a university student health clinic population doi = 10.1111/j.1469-0691.1997.tb00464.x id = cord-273326-gmw8gl2r author = Saiz, Juan-Carlos title = Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date = 2018-08-24 keywords = RNA; ZIKV; Zika; cell; infection; virus summary = doi = 10.3390/v10090453 id = cord-017331-ru7mvfc0 author = Samanta, Indranil title = Infectious Diseases date = 2017-02-25 keywords = AIV; Amazon; Borrelia; Campylobacter; Chlamydia; Fig; Giardia; Mycobacterium; PCR; PDD; Salmonella; USUV; WNV; avian; bird; clinical; infection; parrot; pet; virus summary = The chapter includes history, etiology, susceptible hosts, transmission, pathogenesis, clinical symptoms, lesion, diagnosis, zoonosis, Treatment and control strategy of Tuberculosis, Salmonellosis, Chlamydiosis, Campylobacteriosis, Lyme disease, other bacterial infection, Newcastle disease, Avian Influenza infection, West Nile Virus infection, Usutu virus infection, Avian Borna Virus infection, Beak and feather disease, other viral infection, Toxoplasmosis, Giardiasis, Cryptosporidiosis, other parasitic infection, Cryptococcosis, Aspergillosis, Other fungal infections. Clinical samples include faeces or cloacal swabs, blood/serum of live birds and affected tissues, such as liver, spleen, heart, intestine/caeca, lung, esophagus/crop, brain and kidney in 10% buffered formalin. Non-specific clinical symptoms such as neurological signs (head between legs), depression, ruffled feathers, and standing at the bottom of the cage are observed in pet birds with AIV infection (Fig. 2.13) . The virus is detected in brain, heart, liver, kidney, lungs, and intestinal tissues of laboratory mice and naturally infected birds. doi = 10.1007/978-981-10-3674-3_2 id = cord-269652-t7ghng17 author = Santos, Roberto Parulan title = A Practical Guide to the Diagnosis, Treatment, and Prevention of Neonatal Infections date = 2015-04-30 keywords = Committee; GBS; infant; infection; neonatal summary = doi = 10.1016/j.pcl.2014.11.010 id = cord-317499-mxt7stat author = Saraya, Takeshi title = Epidemiology of virus-induced asthma exacerbations: with special reference to the role of human rhinovirus date = 2014-05-26 keywords = HRV; IFN; infection summary = Table 1 shows the frequency of HRV infection in various adult respiratory diseases such as exacerbation of asthma (Nicholson et al., 1993; Atmar et al., 1998; Tan et al., 2003) , common cold (Makela et al., 1998; van Gageldonk-Lafeber et al., 2005) , exacerbation of COPD (Seemungal et al., 2001; Rohde et al., 2003; Tan et al., 2003; Beckham et al., 2005; Papi et al., 2006; Hutchinson et al., 2007; Ko et al., 2007; McManus et al., 2008; Kherad et al., 2010; Dimopoulos et al., 2012; Perotin et al., 2013) , community acquired pneumonia (Jennings et al., 2008; Johnstone et al., 2008; Johansson et al., 2010; Lieberman et al., 2010; Fry et al., 2011; Wootton et al., 2011; Luchsinger et al., 2013; Takahashi et al., 2013; Huijskens et al., 2014) , exacerbation of idiopathic pulmonary fibrosis (Wootton et al., 2011) , and asymptomatic infection (Fry et al., 2011) . doi = 10.3389/fmicb.2014.00226 id = cord-324923-29kudfjp author = Sarma, U. title = Quantitative modeling and analysis show country-specific quarantine measures can circumvent COVID19 infection spread post lockdown date = 2020-05-26 keywords = country; figure; infection summary = Our data driven modeling and analysis of the trajectories from multiple countries thus pave a way to understand the infection dynamics during and post lockdown phases in various countries and it can help strategize the testing and quarantine processes and influence the spread of the disease in future. By quantitatively calibrating the time series data(Data from WHO [1]) for confirmed, recovered and dead population for 23 different countries with various stages of infection, we made an estimate of different important parameters like incubation time, transmission rate, rate of quarantine, recovery and death rate, that controls the infection dynamics in a given country. Immediate early lock-down and rigorous testing coupled to systematic quarantining could be the most effective way to rapidly contain the second wave of infection and hence reduce the time of lockdown as well as size of infected population in a country. doi = 10.1101/2020.05.20.20107169 id = cord-308184-w8ewm8ve author = Sarzi-Puttini, Piercarlo title = How to handle patients with autoimmune rheumatic and inflammatory bowel diseases in the COVID-19 era: An expert opinion date = 2020-05-05 keywords = COVID-19; infection; patient; risk summary = Disease activity, co-morbidities, immunosuppressive drugs including glucocorticoids (GCs), disease-modifying antirheumatic drugs (DMARDs), conventional synthetic (csDMARDs), biological (bDMARDs), targeted synthetic DMARDs (tsDMARDs), and the biological agents currently available for treating patients with IBD are all considered risk factors for infective complications. This has raised concerns about the potential risk of COVID-19 infection in IBD patients (particularly those who are taking immunosuppressants or biological drugs) because of the high morbidity and mortality rates observed in the old and frail with co-morbidities. As a result of the early warning and strict preventive measures, none of the patients developed any significant clinical manifestation of COVID-19 infection, not even those being treated with corticosteroids (12.6%), immunosuppressants (11%) and biological agents (6%), or those with co-morbidities. The first challenge for rheumatologists is to decide whether to interrupt or continue a treatment: although it is true that the treatment is designed to control disease activity, it is also undeniable that the same treatment may expose patients, such other infection, to an increased risk for COVID-19. doi = 10.1016/j.autrev.2020.102574 id = cord-352178-irjhmxsg author = Saxton-Shaw, Kali D. title = O''nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date = 2013-01-24 keywords = CHIKV; ONNV; RNA; infection; virus summary = Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Our study analyzed both structural and non-structural regions of the ONNV genome using chimeric viruses and artificially infected Anopheles gambiae mosquitoes. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from chikungunya virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Six additional non-structural chimeric viruses were also constructed using a novel type II restriction enzyme cloning strategy to examine the broader genome with respect to ONNV''s unique vector specificity for An. gambiae mosquitoes (Figure 2) . doi = 10.1371/journal.pntd.0001931 id = cord-267139-r8rg0iqq author = Scaggs Huang, Felicia A. title = Fever in the Returning Traveler date = 2018-03-31 keywords = child; fever; infection; return summary = As many as 34% of patients with recent travel history are diagnosed with routine infections, but serious infections such as malaria, enteric fever, and dengue fever should be on the differential diagnosis due the high morbidity and mortality in children. As awareness of tropical illnesses rise in parents, such as the increase in multidrug-resistant bacteria worldwide or the emergence of epidemics with Zika virus in South America, families may be more anxious about serious infections as an etiologic factor of fevers. Because the causes and clinical outcomes associated with fevers in pediatric travelers vary from self-limited to deadly, a systems-based approach can lead to prompt diagnosis and treatment that evaluates for the most likely and serious diseases early in the illness course. A European study of travelers returning from Brazil in 2013 to 2016 reported that of the 29% of patients with travel-related complaints, 6% had dengue fever, 3% had chikungunya, and 3% had Zika virus infection. doi = 10.1016/j.idc.2017.10.009 id = cord-008716-38sqkh9m author = Schmidt, Alexander C title = Current research on respiratory viral infections: Third International Symposium date = 2001-06-01 keywords = H5N1; RSV; infection; influenza; respiratory; vaccine; virus summary = Renewed efforts in vaccine development against respiratory viruses began in the 1960s with the observation that infants and young children, after having recovered from respiratory tract infection with adenoviruses, shed virus from their gastrointestinal tract for an extended period of time without experiencing gastrointestinal symptoms. Earlier studies of viral pathogens in immunocompromised adults indicated that CMV, herpes simplex, influenza, parainfluenza, rhinovirus, adenovirus, enterovirus, and RSV cause lower respiratory infection (Connolly et al., 1994) . Children with RSV, adenovirus or influenza virus infections have a 30% risk of developing AOM within 2 weeks of the onset of the respiratory tract infection (Henderson et al., 1982) , and coinfection with bacteria and viruses also adversely influences the outcome of AOM. Populations at high risk for complications resulting from respiratory viral infections are now better defined and a more targeted prophylaxis is possible, be it passive prophylaxis against RSV disease with monoclonal antibody preparations or active prophylaxis with influenza-or adenovirus vaccines. doi = 10.1016/s0166-3542(01)00136-x id = cord-226245-p0cyzjwf author = Schneble, Marc title = Nowcasting fatal COVID-19 infections on a regional level in Germany date = 2020-05-15 keywords = Germany; death; infection summary = Given that death counts generally provide more reliable information on the spread of the disease compared to infection counts, which inevitably depend on testing strategy and capacity, the proposed model and the presented results allow to obtain reliable insight into the current state of the pandemic in Germany. The data are provided by the Robert-Koch-Institute (www.rki.de) and give the cumulative number of deaths in different gender and age groups for each of the 412 administrative districts in Germany together with the date of registration of the infection. In Figure 2 we combine these different components and map the fitted nowcasted death counts related to Covid-19 for the different districts of Germany, cumulating over the last seven days before the day of analysis (here May 14, 2020). Let Y t,r,g denote the number of daily deaths due to COVID-19 in district/region r and age and gender group g with time point (date of registration) t = 0, . doi = nan id = cord-297834-me1ajoyb author = Schountz, Tony title = Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date = 2014-03-14 keywords = RNA; infection; reservoir; response; virus summary = doi = 10.3390/v6031317 id = cord-301904-mjfbvl5n author = Schultz-Cherry, S. title = Astroviruses date = 2014-11-28 keywords = HAstV; RNA; astrovirus; infection summary = doi = 10.1016/b978-0-12-801238-3.02539-3 id = cord-169428-g6k0vqrm author = Schurwanz, Max title = Infectious Disease Transmission via Aerosol Propagation from a Molecular Communication Perspective: Shannon Meets Coronavirus date = 2020-10-31 keywords = aerosol; infection summary = Recent research in combining these areas has dealt with possible use cases for aerosol communications [6] , and with channel modeling considering infectious aerosols in a point-topoint scenario [7] , [8] . The remainder of this tutorial paper is structured as follows: Section II describes the duality between communication and information theory on the one hand and the field of airborne aerosol infection on the other. In the scenario under investigation, the signal powers are modeled in terms of the parameters of the emitted aerosols and the contained viral load coming from the infected user(s). The spatially-distributed time-varying aerosol clouds that are emitted into the environment from the various users, are subject to a dynamic channel with turbulences and changing parameters. Towards this goal, dualities and similarities between macroscopic air-based MC and infected particle transmission are worked out. doi = nan id = cord-304251-dohglrm1 author = Scully, C title = Emerging and changing viral diseases in the new millennium date = 2015-08-06 keywords = HIV; infection; oral; virus summary = Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. Gradually, however, the unexpected consequences of some oral viral infections have emerged and been recognised, not without some surprise (Scully, 1983) especially the oncogenicity of some herpesviruses (Eglin et al, 1983) and human papillomaviruses (HPVs) which we (Eglin et al, 1983; Maitland et al, 1987; Cox et al, 1993 ) and many others (e.g. Lind et al, 1986) have explored, culminating in the appreciation of unanticipated transmission routes for some cancers, such as sexual (Scully, 2002) . The recent several decades have also seen a most dramatic change with the emergence globally of new viral infectionsnotably human immunodeficiency viruses (HIV)and the appearance also in resource-rich countries, of some other dangerous and sometimes lethal infections hitherto latent, unrecognised or unappreciated in resource-poor areas. doi = 10.1111/odi.12356 id = cord-306266-8qdrshz3 author = Scully, Crispian title = Respiratory medicine date = 2014-06-25 keywords = COPD; HIV; cause; disease; infection; lung; patient; respiratory; treatment summary = Other factors that have been studied include: ■ air pollution -There is an association between air pollution and aggravation of existing asthma ■ allergen avoidance -There is no consistent evidence of benefit ■ breast-feeding -There is evidence of a protective effect in relation to early asthma ■ electrolytes -There is no consistent evidence of benefit ■ fish oils and fatty acid -There is no consistent evidence of benefit ■ house dust mites -Measures to reduce the numbers of house dust mites do not affect asthma severity ■ immunotherapy -Allergenspecific immunotherapy is beneficial in allergic asthma ■ microbial exposure -There is insufficient evidence to indicate that the use of probiotics in pregnancy reduces the incidence of childhood asthma ■ modified milk formulae -There is no consistent evidence of benefit pets -There are no controlled trials on the benefits of removing pets from the home ■ tobacco -Exposure to cigarette smoke adversely affects quality of life, lung function, need for rescue medications and longterm control with inhaled steroids. doi = 10.1016/b978-0-7020-5401-3.00015-1 id = cord-345472-qrddwebe author = Sebina, Ismail title = The Contribution of Neutrophils to the Pathogenesis of RSV Bronchiolitis date = 2020-07-27 keywords = RSV; bronchiolitis; cell; infection; neutrophil; respiratory summary = A vaccine against respiratory syncytial virus (RSV), the leading cause of viral bronchiolitis in infancy, remains elusive, and hence new therapeutic modalities are needed to limit disease severity. (1), degranulation (2), respiratory oxygen species (ROS) production (3), and the release of neutrophil extracellular traps (NETosis) (4) are associated with increased lung inflammation, systemic fever, mucus hypersecretion, airway obstruction, and epithelial cell death. Excessive neutrophil-derived inflammatory cytokine production (1), degranulation (2), respiratory oxygen species (ROS) production (3), and the release of neutrophil extracellular traps (NETosis) (4) are associated with increased lung inflammation, systemic fever, mucus hypersecretion, airway obstruction, and epithelial cell death. Unlike wild-type (WT) control mice, plasmacytoid dendritic cell (pDC)-depleted, Toll-like receptor (TLR)7-deficient, or interferon regulatory factor (IRF)7-deficient neonatal mice develop severe pathology, characterised by increased neutrophilia and lung inflammation in response to acute PVM infection [80] [81] [82] . doi = 10.3390/v12080808 id = cord-301276-eer1l8vg author = Sehrawat, Sharvan title = Opinion: Does the hygiene hypothesis apply to COVID-19 susceptibility? date = 2020-07-09 keywords = covid-19; infection summary = In this commentary we argue that the hygiene hypothesis may apply to COVID-19 susceptibility and also that residence in low hygienic conditions acts to train innate immune defenses to minimize the severity of infection. In this commentary we argue that the hygiene hypothesis may apply to susceptibility and also that residence in low hygienic conditions acts to train innate immune defenses to minimize the severity of infection. We advocate that approaches, which elevate innate immune functions, should be used to minimize the consequences of COVID-19 infection at least until effective vaccines and antiviral therapies are developed. We advocate that approaches, which elevate innate immune functions, should be used to minimize the consequences of COVID-19 infection at least until effective vaccines and antiviral therapies are developed. The hygiene hypothesis has satisfactorily explained the increased frequency of some disease syndromes, but could it also explain why some individuals are more susceptible to the severe consequences of COVID-19 infection than are others? doi = 10.1016/j.micinf.2020.07.002 id = cord-316513-dbzj101e author = Sen-Crowe, Brendon title = Utilizing technology as a method of contact tracing and surveillance to minimize the risk of contracting COVID-19 infection date = 2020-07-04 keywords = infection summary = title: Utilizing technology as a method of contact tracing and surveillance to minimize the risk of contracting COVID-19 infection A call for new methods of testing and surveillance on a large scale will be important if we hope to control the spread of SARS-CoV-2 infections. On example is the Oura ring (Ooura Health Ltd.''s, Oulu, Finland) which can detect physiologic changes and alert the possibility of infection. For example, one study at West Virginia Univeristy, Rockefeller Neuroscience Institute predicted symptoms 24 hours prior to onset based on physiologic changes detected by the Oura ring, and aim to achieve a 3-day forecast in the future. In addition, early detection and contact tracing has the potential to conserve hospital resources that have become scarce throughout the pandemic. CDC Diagnostic Test for COVID-19 WVU Rockefeller Neuroscience Institute and Oura Health unveil study to predict the outbreak of COVID-19 in healthcare professionals doi = 10.1016/j.ajem.2020.07.003 id = cord-265751-q1ecpfyg author = Shahani, Lokesh title = Antiviral therapy for respiratory viral infections in immunocompromised patients date = 2017-01-16 keywords = H1N1; PIV; RSV; infection; influenza; respiratory; virus summary = doi = 10.1080/14787210.2017.1279970 id = cord-159554-50077dgk author = Shan, Fei title = Lung Infection Quantification of COVID-19 in CT Images with Deep Learning date = 2020-03-10 keywords = covid-19; infection summary = For fast manual delineation of training samples and possible manual intervention of automatic results, a human-in-the-loop (HITL) strategy has been adopted to assist radiologists for infection region segmentation, which dramatically reduced the total segmentation time to 4 minutes after 3 iterations of model updating. By reducing and combining feature map channels, not only the model size and inference time are greatly reduced, but also cross-channel features are effectively fused via convolusion, which makes VB-Net more applicable to deal with large 3D volumetric data than traditional V-Net. Training samples with detailed delineation of each infection region are required for the proposed VB-Net. However, it is a labor-intensive work for radiologists to annotate hundreds of COVID-19 CT scans. To quantitatively evaluate the accuracy of segmentation and measurement, infection regions on 300 CT scans of 300 COVID-19 patients were manually contoured by two radiologists (W.S. and F.S., with 12 and 19 years of experience in chest radiology, respectively) to serve as the reference standard. doi = nan id = cord-021424-kocwsyi7 author = Shannon, M. Frances title = Genomic Approaches to the Host Response to Pathogens date = 2009-01-30 keywords = genetic; infection; response; susceptibility summary = This activation process includes widespread changes in the gene expression profi le of the cells with hundreds of genes being either switched on or off in response to signals generated from the pathogen-detecting TLRs. The response of individual genes has been studied in minute detail for a handful of genes and while this has produced an understanding of some aspects of host response to infection it by no means gives us the total picture. Studies in both animal models and human populations have shown that infectious disease and the response of the host to a specifi c infection also has a complex genetic component ( Clementi and Di Gianantonio, 2006 ; Lipoldova and Demant, 2006 ; Marquet et al., 1996 ; Mira et al., 2004 ) . Expression profi ling studies have been used to investigate the differences in the host response to pathogenic and nonpathogenic strains of specifi c infectious agents. doi = 10.1016/b978-0-12-369420-1.00107-4 id = cord-021966-5m21bsrw author = Shaw, Alan R. title = Vaccines date = 2009-05-15 keywords = HIV; antigen; development; dna; immune; infection; pathogen; response; vaccine; virus summary = Because a number of proteins produced in isolation by recombinant methods have been observed to elicit lower immune responses than do natural infections or live attenuated vaccines, the development and use of adjuvants to optimize recombinant vaccine immunogenicity represent an important parallel area for future exploration. Modern molecular biology and biochemistry have provided numerous options for vaccine immunogen presentation, including recombinant proteins (and recombinant virus-like particles (VLPs)), synthetic proteins, protein-polysaccharide conjugates, and gene delivery systems (recombinant viral vectors, or DNA vaccines) >> Is the antigen of interest sufficiently immunogenic on its own, or is augmentation of the desired immune response by conjugation to a specific carrier or addition of an adjuvant necessary to elicit a sufficient and sufficiently durable immune response in individuals in the target population for vaccination? doi = 10.1016/b978-0-323-04404-2.10092-2 id = cord-303966-z6u3d2ec author = Shears, P. title = Poverty and infection in the developing world: Healthcare-related infections and infection control in the tropics date = 2007-10-22 keywords = Africa; hospital; infection summary = doi = 10.1016/j.jhin.2007.08.016 id = cord-262892-n38r8n70 author = Sheikh, Jamila title = Nutritional Care of the Child with Human Immunodeficiency Virus Infection in the United States: A Historical and Contemporary Perspective date = 2015-05-08 keywords = HIV; States; United; child; infection summary = doi = 10.1016/b978-0-12-800769-3.00009-3 id = cord-022103-4zk8i6qb author = Siegel, Jane D. title = Pediatric Healthcare Epidemiology date = 2017-07-18 keywords = CDC; HCP; Healthcare; IPC; Precautions; infection; patient; transmission summary = A series of IPC guidelines have been developed and updated at varying intervals by the HICPAC/CDC, IDSA, Society for Healthcare Epidemiology of America (SHEA), American Academy of Pediatrics, Association for Professionals in Infection Control and Epidemiology, and others to provide evidence-based and rated recommendations for practices that are associated with reduced rates of HAIs, especially those infections associated with the use of medical devices and surgical procedures. (2) clinical microbiology laboratory services needed to support infection control outbreak investigations, including ability to perform molecular diagnostic testing; (3) data-mining programs and information technology specialists; (4) multidisciplinary programs to ensure judicious use of antimicrobial agents and control of resistance; (5) development of effective educational information for delivery to HCP, patients, families, and visitors; and (6) local and state health department resources for preparedness. doi = 10.1016/b978-0-323-40181-4.00002-5 id = cord-276758-k2imddzr author = Siegel, Jane D. title = 2007 Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Health Care Settings date = 2007-12-07 keywords = CDC; Control; MRSA; PPE; Precautions; SARS; Standard; Staphylococcus; States; United; base; care; health; infection; outbreak; patient; transmission summary = Activities currently assigned to ICPs in response to emerging challenges include (1) surveillance and infection prevention at facilities other than acute care hospitals (eg, ambulatory clinics, day surgery centers, LTCFs, rehabilitation centers, home care); (2) oversight of employee health services related to infection prevention (eg, assessment of risk and administration of recommended treatment after exposure to infectious agents, tuberculosis screening, influenza vaccination, respiratory protection fit testing, and administration of other vaccines as indicated, such as smallpox vaccine in 2003); (3) preparedness planning for annual influenza outbreaks, pandemic influenza, SARS, and bioweapons attacks; (4) adherence monitoring for selected infection control practices; (5) oversight of risk assessment and implementation of prevention measures associated with construction and renovation; (6) prevention of transmission of MDROs; (7) evaluation of new medical products that could be associated with increased infection risk (eg, intravenous infusion materials); (8) communication with the public, facility staff, and state and local health departments concerning infection control-related issues; and (9) participation in local and multicenter research projects. doi = 10.1016/j.ajic.2007.10.007 id = cord-282204-j1slaefb author = Silva, José V.J. title = A scoping review of Chikungunya virus infection: epidemiology, clinical characteristics, viral co-circulation complications, and control date = 2018-12-31 keywords = Aedes; CHIKV; Chikungunya; DENV; infection; virus summary = doi = 10.1016/j.actatropica.2018.09.003 id = cord-285148-bch7814v author = Singanayagam, Aran title = Viruses exacerbating chronic pulmonary disease: the role of immune modulation date = 2012-03-15 keywords = COPD; IFN; infection; virus summary = doi = 10.1186/1741-7015-10-27 id = cord-009507-l74c9x0n author = Singh, Amandeep title = Clinicopathological Conference: Fever, Productive Cough, and Tachycardia in a 22‐year‐old Asian Male date = 2008-01-08 keywords = States; United; infection; patient summary = To generate the appropriate differential diagnosis in this case, there are several key features of the patient''s history and physical examination that aid in the understanding of his pathologic process: 1) symptom development occurred soon after emigration from Indonesia, 2) the patient''s primary symptoms were pulmonary in origin, and 3) secondary cardiac involvement resulted in a large, initially asymptomatic pericardial effusion. 10 Acute infection begins with sudden onset of one or more of the following: high fevers (up to 104-1058F), severe headache, general malaise, myalgia, confusion, sore throat, chills, sweats, nonproductive cough, nausea, vomiting, diarrhea, abdominal pain, and chest pain. In our patient, the most likely cause of the pericardial effusion was infection with tuberculosis. To summarize, this patient''s recent immigration, symptoms of intermittent fever and of chronic cough that failed to respond to outpatient antibiotics, and development of large pericardial effusion all are consistent with a diagnosis of tuberculosis. doi = 10.1111/j.1553-2712.2004.tb01429.x id = cord-023817-39r3a4fd author = Singh, Namita title = Rotavirus and Noro- and Caliciviruses date = 2012 keywords = child; diarrhea; infection; rotavirus summary = Rotavirus is the most common cause of severe diarrhea in infants and children of developed and developing countries worldwide. Worldwide, approximately 40% of hospitalizations for diarrhea in children younger than 5 years of age are attributable to rotavirus infection. The Center for Disease Control and Prevention (CDC) defines a confirmed case of rotavirus gastroenteritis as diarrhea (3 or more loose stools within 24 h) or vomiting (1 or more episodes in a 24 h period) in a child with a positive stool detection of rotavirus by a standard assay, such as an enzyme immunoassay (EIA). The non-bloody, watery diarrhea of rotavirus gastroenteritis is clinically indistinguishable from that caused by other enteric viruses, including norovirus and other caliciviruses, enteric adenovirus, and astrovirus. Norwalk virus carries historical import as the first confirmed viral etiology for human gastroenteritis when it was identified by electron microscopy in stools from a severe outbreak of diarrhea in Norwalk, Ohio in 1972. doi = 10.1007/978-3-642-02202-9_120 id = cord-284216-4sl8xfur author = Sinha, Anirban title = Can Measurements of Inflammatory Biomarkers Be Used to Spot Respiratory Viral Infections? date = 2020-10-17 keywords = figure; infection; summary summary = doi = 10.3390/v12101175 id = cord-258333-jmk8hdk2 author = Sivier, V title = Place des viroses respiratoires dans les hyperthermies de sujets âgés hospitalisés au cours d’une saison hivernale date = 2001-12-10 keywords = des; infection; virus summary = Sur les 129 malades ayant présenté une hyperthermie, 12 décès ont été observés, soit un taux de mortalité de 9,3 % : un décès dans le groupe « virose respiratoire » par surinfection bactérienne pulmonaire, sept décès dans le groupe « infection respiratoire non virale » (un choc septique, cinq décompensations respiratoires aiguës, une décompensation cardiaque aiguë) et quatre décès dans le groupe « autre » (deux cancers en phase terminale, un accident vasculaire cérébral et une cause indéterminée). L''épidémie nosocomiale de virus respiratoire syncytial est survenue dans un service de long séjour avec des locaux communs et exigus, chez des patients porteurs de multiples maladies et souvent déments. En conclusion, les infections respiratoires, qu''elles soient virales, bactériennes ou non documentées, apparaissent comme la principale cause d''hyperthermie chez le sujet âgé institutionnalisé pendant la saison hivernale et sont à l''origine de nombreuses complications, voire de décès. doi = 10.1016/s0248-8663(01)00489-1 id = cord-024093-5dplc9xr author = Sizun, J title = Neonatal nosocomial respiratory infection with coronavirus: a prospective study in a neonatal intensive care unit date = 2008-01-21 keywords = infection summary = The aim of this prospective study was to evaluate the incidence of viral respiratory infection in hospitalized premature newborn infants and to assess the role of coronaviruses. The aim of this prospective study undertaken from November 1, 1991 to March 1, 1993, was to evaluate, in the pediatric intensive care unit, the incidence of upper respiratory tract viral infection in hospitalized premature newborn infants, to assess the role of CV and to analyze the associated symptomatology. In a serological study carried out in infants aged less than 18 months and hospitalized for respiratory tract infection, this cause was identified in 8.2% of cases (10). On the Similarly, in a prospective study by Ray et al., based on serological analysis and cell culture from acute lower respiratory tract infections in children less than 3 years of age, human CV viruses, as initial infecting agents, were not found to be responsible (12) . doi = 10.1111/j.1651-2227.1995.tb13710.x id = cord-021770-zn7na974 author = Slifka, Mark K. title = Passive Immunization date = 2017-07-17 keywords = antibody; human; infection; monoclonal; passive; serum; treatment; virus summary = [26] [27] [28] [29] Recent studies verify these earlier results, demonstrating a 90% to 91% vaccine efficacy against whooping cough among infants younger than 2 months of nonlymphoid tissues and to penetrate mucosal sites of infection is likely to explain why it is often considered the best immunoglobulin isotype for routine passive immunization and has shown clinical benefit ranging from reduced clinical symptoms to nearly complete protection from lethal infection in a number of infectious disease models (Table 8 .3). 118 With the recent development of polyclonal and monoclonal antibodies that show protective efficacy against tularemia in animal models, [119] [120] [121] it may be possible to incorporate both passive immunotherapy and antibiotic treatment into clinical practice not only for tularemia, but for other bacterial diseases, especially in cases in which antibiotic resistance is becoming more widespread. doi = 10.1016/b978-0-323-35761-6.00008-0 id = cord-333853-p2kbjwpy author = Smee, Donald F. title = Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) date = 2011-10-13 keywords = infection; pfu; virus summary = title: Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) An adenovirus 5 vector encoding for mouse interferon alpha, subtype 5 (mDEF201) was evaluated for efficacy against lethal vaccinia virus (WR strain) respiratory infections in mice. Lung virus titers were significantly (>100-fold) lower than in the placebo group, and the other infection parameters in mDEF201 treated mice were nearly at baseline. Ad5-vectored mouse interferon (mDEF201) resulted in sustained IFN levels [16] , that completely protected mice from a lethal Western equine encephalitis virus infection when given intramuscularly at 10 7 plaque forming units (PFU)/ mouse up to 7 days prior to virus challenge [16] . The extent of inhibition of lung Intranasal treatments with mDEF201 (10 7 PFU/mouse) were given one time only on the indicated day prior to virus exposure. doi = 10.1371/journal.pone.0026330 id = cord-257467-b8o5ghvi author = Smith, Barbara A. title = Anesthesia as a Risk for Health Care Acquired Infections date = 2010-12-31 keywords = anesthesia; infection; patient; risk summary = This article further discusses the risks for HAIs apparent in intravascular cannulation, endotracheal intubation, and the development of surgical site infections, and examines occupational measures to prevent infections in the health care worker. Although endotracheal intubation during surgery is generally a controlled safe procedure, this artificial airway predisposes the body to exposure to respiratory pathogens whether from the health care provider, the environment, or equipment. 12 A recent practice advisory prepared by the American Society of Anesthesiologists (ASA) concurs with the implementation of aseptic technique when handling neuraxial needles and catheters, and states it should include "hand washing, wearing of sterile gloves, wearing of caps, wearing of masks covering both the mouth and nose, use of individual packets of skin preparation, and sterile draping of the patient." The same advisory does not make a specific recommendation regarding the type of skin antisepsis to use. doi = 10.1016/j.cpen.2010.07.005 id = cord-344297-qqohijqi author = Smith, Jacqueline title = The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds date = 2015-10-09 keywords = IBV; gene; infection; line; response summary = title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds RESULTS: Genes and biological pathways involved in the early host response to IBV infection were determined andgene expression differences between susceptible and resistant birds were identified. [18] we used Affymetrix wholegenome chicken microarrays to examine the tracheal gene expression profiles of a line of birds known to be susceptible to IBV infection (line 15I) and a line known to show resistance (line N). Gene expression differences found in the susceptible 15I line between infected and control birds over days 2, 3 and 4 post infection were analysed, with a view to examining the innate host response to infection by IBV. Gene expression seen during the host response to IBV infection in the trachea of susceptible birds. Genes found to be differentially expressed between susceptible and resistant lines in response to IBV infection in the trachea. doi = 10.1186/s12917-015-0575-6 id = cord-017862-9fkjjmvf author = Smith, Roger P. title = Respiratory Disorders date = 2007 keywords = cold; common; infection; patient; symptom summary = Only 12-25% of all "sore throats" seen by physicians have a true pharyngitis-most are simple viral upper respiratory infections such as the common cold. infl uenzae, Staphylococcus aureus, Legionella pneumophila, and Allergens such as pollens, molds, animal dander, dust mites, and cockroaches Irritants such as strong odors and sprays, chemicals, air pollutants, tobacco smoke, and cold air Viral or sinus infections including colds, pneumonia, and sinusitis Exercise, especially in cold, dry air Gastroesophageal refl ux disease (GERD), a condition in which stomach acid fl ows back up the esophagus Medication and foods Emotional anxiety others) is the most common source of infection for most patients. Infl uenza, rubeola and rubella, Mycoplasma pneumonia, group A β-hemolytic streptococcal infections, and allergic rhinitis may all be confused with the common cold and should be considered when appropriate. When a common cold has lasted for 7-10 days and is no better or worse, acute bacterial sinusitis may have developed and additional medical care may be required. doi = 10.1007/978-0-387-32328-2_19 id = cord-301677-b6mnn27h author = Soleimanian, Saeede title = Harnessing Memory NK Cell to Protect Against COVID-19 date = 2020-08-20 keywords = COVID-19; HCMV; SARS; cell; infection summary = In this regard, Natural Killer (NK) cells as essential front-line responders to many viral infections in humans have been proposed for a suitable therapeutic approach in severe COVID-19 patients, and several clinical trials have begun (Market et al., 2020) . In this line, Type I IFNs have a critical role in concert with pattern PRR signaling to prime innate and adaptive antiviral responses such as stimulating natural killer (NK) cells, macrophages, and production of proinflammatory cytokines (Samuel, 2001; Murira and Lamarre, 2016) . The detection of both SARS-CoV-2 nucleic acid and specific antibodies to viral proteins have thus far become significant for primary diagnosis infection and immunity in COVID-19 patients, respectively. in a pneumonia model of SARS in mice, mimicking features of the human disease, illustrated that mice depleted of both CD4 and CD8T cells, had the ability to control SARS-CoV replication in the lungs, suggesting an immune mechanism independent of T cells, and a role for innate antiviral response and NK cells, in viral clearance. doi = 10.3389/fphar.2020.01309 id = cord-354931-0bwf8f1i author = Song, Jae-Hyoung title = Antiviral and Anti-Inflammatory Activities of Pochonin D, a Heat Shock Protein 90 Inhibitor, against Rhinovirus Infection date = 2018-05-02 keywords = HRV1B; Hsp90; infection; pochonin summary = In the current study, we examined the effect of the Hsp90 inhibitor pochonin D, in vitro and in vivo, using a murine model of human rhinovirus type 1B (HRV1B) infection. We therefore decided to monitor the lung cytokine levels and virus titers at 8 h after HRV1B infection for evaluating the antiviral activity of pochonin D in mice. Real-time PCR analysis of viral mRNA in lung tissues revealed that the virus titer was significantly reduced in pochonin D-treated mice compared to that of vehicle-treated mice after HRV1B infection ( Fig. 2A) . A few changes in the total cell numbers in the lung and BALF were observed after treatment of HRV1B-infected mice with pochonin D (Supplementary Fig. 3) . We found that treatment with pochonin D lowered the level of pro-inflammatory cytokines in the lung and BALF of mice, which were increased by rhinovirus infection. doi = 10.4062/biomolther.2017.233 id = cord-032181-gmcugd8h author = Song, Jian-Xin title = Main Complications of AECHB and Severe Hepatitis B (Liver Failure) date = 2019-05-21 keywords = DIC; HCO; HPS; HRS; Kupffer; LPS; SBP; blood; cell; disease; endotoxin; factor; hepatitis; increase; infection; intestinal; liver; patient; severe; tip summary = 3. Hepatorenal syndrome, which is characterized by renal failure, hemodynamic changes in arterial circulation and abnormalities in the endogenous vascular system, is a common clinical complication of end-stage liver disease, and one of the important indicators for the prognosis of patients with severe hepatitis. The latest report indicated that basic laboratory examinations for coagulation function testing in common use at present, such as PT, APTT, international normalized ratio (INR) etc., have little correlation with occurrence of gastrointestinal bleeding in these patients, thereby revealing the importance to search and pay close attention to those complicating disease upregulating bleeding risk, such as bacterial infection, renal failure, hemodynamic change after portal hypertension, dysfunction of endotheliocyte as well as macrophagocyte and so on [107] . doi = 10.1007/978-94-024-1603-9_2 id = cord-267402-kca05rvz author = South, Kieron title = Preceding infection and risk of stroke: An old concept revived by the COVID-19 pandemic date = 2020-07-24 keywords = SARS; covid-19; infection; patient; stroke summary = What follows herein is a detailed summary of the current literature surrounding COVID-19, encompassing the immune and inflammatory responses to infection, thrombotic manifestations and vascular consequences of infection with a focus on possible mechanisms by which these elements may contribute to acute stroke events. 89 This is not the case in COVID-19 (and the previous SARS outbreak) and a recent retrospective cohort study has suggested an incidence of stroke 7-8 times higher in patients hospitalized with COVID-19 infection compared with those hospitalized by influenza, 90 supporting the possibility of a SARS-CoV-2-driven hyper-coagulant state. [91] [92] [93] Obesity, in particular, is emerging as a prominent risk factor in the development of severe COVID-19 disease and is generally associated with increased incidence and increased severity of respiratory viral infection. Notably, the cytokine IL-33 is persistently elevated in obese individuals and is capable of stimulating endothelial cells to release pro-coagulant tissue factor 97 which may expose them to more severe COVID-19 disease and/or stroke. doi = 10.1177/1747493020943815 id = cord-288945-c9ow1q5c author = Spengler, Ulrich title = Liver Disease Associated with Non-Hepatitis Viruses date = 2019-11-01 keywords = CMV; EBV; infection; virus summary = doi = 10.1016/b978-0-12-801238-3.65782-3 id = cord-320454-dhfl92et author = Srivastava, S. title = Healthcare-associated infections in neonatal units: lessons from contrasting worlds date = 2007-03-12 keywords = HAI; NICU; infection; neonatal; neonate; outbreak summary = Neonatal intensive care units are vulnerable to outbreaks and sporadic incidents of healthcare-associated infections (HAIs). Summary Neonatal intensive care units are vulnerable to outbreaks and sporadic incidents of healthcare-associated infections (HAIs). We reviewed 125 articles regarding HAIs from both advanced and resource-limited neonatal units in order to study risk factors, aetiological agents, antimicrobial susceptibility patterns and reported successes in infection control interventions. We reviewed 125 articles regarding HAIs from both advanced and resource-limited neonatal units in order to study risk factors, aetiological agents, antimicrobial susceptibility patterns and reported successes in infection control interventions. This review on healthcare-associated neonatal infections studies the definitions, associated risk factors and the aetiological agents involved with their antimicrobial susceptibility patterns in two contrasting worlds. Risk factors for hospital-acquired infections in the neonatal intensive care unit Outbreak of Candida bloodstream infections associated with retrograde medication administration in a neonatal intensive care unit doi = 10.1016/j.jhin.2007.01.014 id = cord-303741-1ou0cy5k author = Stafstrom, Carl E. title = COVID-19: Neurological Considerations in Neonates and Children date = 2020-09-10 keywords = CNS; COVID-19; CoV-2; SARS; child; infection summary = An especially apropos case demonstrated maternal viremia, placental infection shown by immunohistochemistry, and high placental viral load with subsequent neonatal viremia, implying transplacental transfer of SARS-CoV-2 from pregnant mother to fetus [24] ; this newborn presented with neurological symptoms as discussed in Section 3. The lack of unequivocal reports of SARS-CoV-2 being recovered from the CSF of individuals affected with presumed neurological involvement nor in brain tissue from the limited number of autopsied cases strengthens the possibility that the virus does not often directly cause the symptoms but rather, that the neurological sequelae are secondary to hypoxia, cytokine involvement, or some other non-direct mechanism (see Section 6). Finally, 4 of 27 children with COVID-19 associated MIS-C developed new neurologic symptoms including encephalopathy, headache, weakness, ataxia, and dysarthria [81] ; two patients had lumbar punctures and CSF was negative for SARS-CoV-2 in both. doi = 10.3390/children7090133 id = cord-314505-7qh8dsew author = Stegelmeier, Ashley A. title = Myeloid Cells during Viral Infections and Inflammation date = 2019-02-19 keywords = IFN; cell; infection; monocyte; neutrophil summary = The induction of the IFN response following viral infections fundamentally changes the bone marrow microenvironment ( Figure 1B) , leading to the enhanced differentiation of myeloid cells [24] and emigration of neutrophils and monocytes to the site of infection, which is facilitated by chemokine gradients interacting with their cognate receptors ( Figure 1A ) [25] . TLR stimulation after phagocytosis activates the NF-κB signaling cascade, resulting in the release of inflammatory cytokines such as TNF-α, IL-1, and IL-6 from monocytes [4] to control virus infections by direct antiviral mechanisms and the recruitment of other leukocytes. Taken together, these findings suggest that type I IFN signaling drives a balance of pro-and anti-inflammatory effects on the functions of monocytes and neutrophils in response to viral infections; providing protective immunity while simultaneously limiting immunopathology. Importantly, viruses and virus-mediated tissue damage stimulate both neutrophils and monocytes, triggering a cascade of cytokine/chemokine-mediated innate immune responses. doi = 10.3390/v11020168 id = cord-345339-kyboibtq author = Steiner, Israel title = Infection and the etiology and pathogenesis of multiple sclerosis date = 2001 keywords = CNS; infection; multiple summary = Our goal here is to review the data supporting the possibility that infection has a critical role in the disease, examine the list of potential candidates that have been suggested, and outline an approach regarding the potential role of infectious agents in the etiology and pathogenesis of MS. Our goal here is to review the data supporting the possibility that infection has a critical role in the disease, examine the list of potential candidates that have been suggested, and outline an approach regarding the potential role of infectious agents in the etiology and pathogenesis of MS. Clinical relapses and disease activity on magnetic resonance imaging associated with viral upper respiratory tract infections in multiple sclerosis A combined serologic/molecular analysis of possible human herpes virus-6 infection in multiple sclerosis patients The association between multiple sclerosis and infection with Epstein-Barr virus and retrovirus Multiple sclerosis associated with Chlamydia pneumoniae infection of the CNS doi = 10.1007/s11910-001-0030-x id = cord-017420-tjwxec77 author = Stephens, R. Scott title = Neutropenic Fever in the Intensive Care Unit date = 2019-07-09 keywords = fever; infection; neutropenic; patient; sepsis summary = Neutropenic patients with septic shock tend to have more frequently positive blood cultures, more fungal infections, more multidrug-resistant bacterial infections, and higher mortality rates than immunocompetent patients. Accordingly, current guidelines for the management of neutropenic fever and sepsis recommend monotherapy with an antipseudomonal beta-lactam unless otherwise dictated by circumstances such as patient allergies, the presence of resistant organisms, or refractory hemodynamic instability [28, 57, 61] . The use of surveillance rectal cultures, performed pre-transplant and then weekly after HSCT, to identify patients with MDR infections and allow immediate initiation of antibiotic therapy targeted against MDR organisms may result in better outcomes [26] . Patients with neutropenia and sepsis are at high risk of developing multi-organ failure, particularly the acute respiratory distress syndrome (ARDS) [4, 5] . Neutropenic sepsis continues to confer a poor prognosis, with recent data suggesting an approximate 46% mortality rate in patients with hematologic malignancies who develop septic shock [7, 39, 47] . doi = 10.1007/978-3-319-74588-6_118 id = cord-316894-zhmuzv7z author = Stetzenbach, L.D. title = Airborne Infectious Microorganisms date = 2009-02-17 keywords = SARS; disease; infection; virus summary = Viral diseases presented are influenza, severe acute respiratory syndrome (SARS), Norwalk-like viruses (NLVs) and hantavirus disease, measles, and varicella. Exposure to some Gram-negative and Gram-positive bacteria, endotoxin, and actinomycetes when dispersed through the air can result in disease following inhalation. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. Inhalation of microbial aerosols can elicit adverse human health effects including infection, allergic reaction, inflammation, and respiratory disease. The illnesses resulting from avian influenza infection in humans range from typical mild influenza-like symptoms (e.g., fever, sore throat, cough, and muscle aches) and conjunctivitis to more serious cases of pneumonia, acute respiratory distress, and other severe and life-threatening complications. Disease is spread by aerosol dissemination of the virus during coughing and sneezing by an infected person or it may become airborne directly from the skin lesions. doi = 10.1016/b978-012373944-5.00177-2 id = cord-006578-wv3wc0ct author = Stevens, D. L. title = Invasive streptococcal infections date = 2001 keywords = M-1; SPEA; group; infection; streptococcus summary = The risk for secondary cases is likely related to close or intimate contact and crowding, as well as host factors such as: (1) active viral infections such as varicella or influenza; (2) recent surgical wounds and childbirth (author''s unpublished observations); (3) absence of type specific opsonic antibody against the group A streptococcus causing the index case; and (4) absence of neutralizing antibody against pyrogenic exotoxin A or B. 17 Streptococcal pyrogenic exotoxins A and B induce human mononuclear cells to synthesize not only TNFα 75 but also IL-1 76 and IL-6, [76] [77] [78] suggesting that TNF could mediate the fever, shock, and organ failure observed in patients with StrepTSS. Multi-locus enzyme electrophoresis demonstrates two patterns, which correspond to M-1 and M-3 type organisms that produce pyrogenic exotoxin A, a finding that fits epidemiologic studies implicating these strains in invasive group A streptococcal infections 54 in the United States. doi = 10.1007/s101560100012 id = cord-283826-lgyc3sro author = Stiehm, E. Richard title = Therapeutic Use of Immunoglobulins date = 2010-11-05 keywords = CMV; IGIV; IVIG; antibody; immunoglobulin; infection; patient summary = medical science and thereby placed in the hands of the physician a victorious weapon against illness and death.'' '' Since then antibodies in multiple forms (animal and human serums, immune globulins and monoclonal antibodies) have been developed, primarily for prevention of infectious diseases, and less commonly for their treatment. Thus regular use of IVIG in antibody-deficient patients in doses of 400 to 600 mg/kg every 3 to 4 weeks or an equivalent amount given subcutaneously decreases the frequency and severity of otitis and other respiratory tract infections [27, 28] . High-dose IVIG (sufficient to increase the serum IgG levels to 1000 mg/mL) has been used successfully in immunodeficient patients with enteroviral encephalomyelitis [80] [81] [82] [83] . Because IgG represents the major defense of humoral immunity against infection, these patients also require immunoglobulin replacement therapy. Individualizing the dose of intravenous immune serum globulin for therapy of patients with primary humoral immunodeficiency doi = 10.1016/j.yapd.2010.08.005 id = cord-302619-3hbbpmnt author = Strausbaugh, L. J. title = Emerging health care-associated infections in the geriatric population. date = 2001 keywords = care; health; infection summary = TB is the most The increasing number of persons >65 years of age form a special population at risk for nosocomial and other health care-associated infections. TB is the most The increasing number of persons >65 years of age form a special population at risk for nosocomial and other health care-associated infections. As a health care-associated infection in this age group, TB comes to the fore in hospital and nursing home outbreaks (11) . Adult daycare centers and home care services, which have proliferated under medical auspices in recent years, provide additional avenues for geriatric populations to acquire health careassociated infections. For example, in a 2-year serologic study of selected pathogens causing respiratory tract infections and febrile episodes in two Canadian long-term care facilities, Orr and colleagues identified a positive serologic response to Chlamydia pneumoniae in 9.4% of 224 Health care-associated infections caused by antimicrobial drug-resistant bacteria have caused both endemic infections and outbreaks in nursing homes in the United States. doi = nan id = cord-009101-376snefs author = Strodtbeck, Frances title = Viral Infections of the Newborn date = 2015-12-16 keywords = Strodtbeck; infection; viral summary = The fetus and newborn are particularly vulnerable to viral infection for numerous reasons, including a developing immune system that is inadequate for preventing infection and containing the spread of viruses, lack of immunologic experience with viruses, and the presence of rapidly growing cells and tissues (Strodtbeck, 1986) . Because of the affinity of viruses for rapidly growing cells, newborn infection results in multiple outcomes that are determined by the specific virus and the gestational age at the onset of infection. Clinical viral infection in newborns usually results in a more rapid progression to full-blown disease and earlier onset of symptomatic organ involvement than would be seen in adults with the same infection (Overall, 1992; Smith, 1993; Strodtbeck, 1986) . Until such time, the major thrusts of management of neonatal viral disease are prevention of the infection and supportive care for the acutely ill newborn. doi = 10.1111/j.1552-6909.1995.tb02548.x id = cord-285628-36gyix12 author = Stull, Jason W. title = Hospital-Associated Infections in Small Animal Practice date = 2015-03-31 keywords = Staphylococcus; animal; infection; risk; veterinary summary = The routine use of simple infection prevention practices can likely dramatically reduce HAIs. Infection control is the term best suited to the goal in small animal veterinary medicine of preventing (or, more practically speaking, limiting) the introduction and/or spread of pathogens with a group of patients and caregivers. The US Centers for Disease Control and Prevention has recently assessed domestic antibiotic resistance threats for people based on Box 1 Pathogens of concern in a small animal clinic Hospital-Associated Infections clinical and economic impact, incidence, transmissibility, availability of effective antimicrobials, and barriers to prevention. Staphylococcus S pseudintermedius and to a lesser extent S aureus are common causes of veterinary HAIs. 30 Both are frequently carried on the skin and mucosal surfaces of dogs and people (respectively), creating the potential for both endogenous infection (infection caused by bacteria the animal was harboring at the time of hospital admission) and acquisition of the pathogen during hospitalization directly or indirectly from other patients, the environment, or human caregivers. doi = 10.1016/j.cvsm.2014.11.009 id = cord-002757-upwe0cpj author = Sullivan, Kathleen E. title = Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date = 2017-08-07 keywords = Africa; CNS; Europe; HIV; Leishmania; PCR; PIDD; USA; disease; infection; patient; severe; virus summary = The first section addresses general considerations, the second section profiles specific infections organized according to mechanism of transmission, and the third section focuses on unique phenotypes and unique susceptibilities in patients with PIDDs. This review does not address most parasitic diseases. In developing countries where polio is still endemic and oral polio vaccine is essential for eradicating the disease, it is of utmost importance that all PIDD patients and family members should not receive live oral polio (OPV) because of the reported prolonged excretion of the virus for months and even years [24] . As for host factors, although severe and fatal cases have been described in healthy immunocompetent hosts [129, 130] , there is evidence to suggest that children under the age of 10 [130] and immunocompromised hosts either secondary to hematologic malignancies, immunosuppressant treatment for organ transplantation, or HIV infection are at a greater risk to develop more severe disease with higher case fatality rates [131, 132] . doi = 10.1007/s10875-017-0426-2 id = cord-009169-hzxgi1t0 author = Sun, Bingwei title = Nosocomial infection in China: Management status and solutions date = 2016-07-01 keywords = infection; nosocomial summary = Investigations revealed a severe nosocomial infection resulting in deaths attributed to negligence by staff with poor infection prevention and control standards. Second, the under-reporting of nosocomial infection and the number of full-time staff experienced in infection control have been highlighted by health administrators during the performance appraisal of health care institutions. Failure to comply with standard regulations of hand hygiene or even handwashing after examining patients with infections, lack of standardized or complete disinfection of surgical instruments, failure to implement surgical standards, failure to consider oxygen humidifiers as an important source of lower respiratory infection, and inappropriate measures of disinfection and isolation are some of the factors that artificially increase nosocomial infection. • To improve environmental hygiene, a national system of sanitation should be created to provide population access to adequate sanitation measures given the current unsanitary conditions in hospitals sustainable care and development and nosocomial infection management. doi = 10.1016/j.ajic.2016.01.039 id = cord-273536-h7mzqef2 author = Surpure, J. S. title = Pediatric emergencies: newsletter 9 date = 1989 keywords = CAS; infection summary = However, the new cephalosporins have been used recently for initial empiric treatment of mening gitis because of their increased activity against the common meningeal pathogens or because some of these compounds can be adminiIn several recent controlled, prospective studies, some newer cephalosporins did not sterilize CSF cultures more rapidly nor did they improve case4atality rates compared with conventional antibiotic regimens in neonates and older children (providing that the pathogens were susceptible to the antibiotic used). Yates and Sullivan (J Pediatr Orthop, 1987; 7 : 54) 3 studied 36"children under 8 years of age with elbow injuries to evaluate the diagnostic accuracy and clinical efficacy of elbow arthrograms. Weisse et al (Pediatric Infect Dis J 1987; 6 : 1091) 1 studied the effect of acetaminophen on fever in bacterial vs viral infections in 100 children (ages 9 days to 17 years) with rectal or oral temperature of 1020 F (38.90 C) or greater. doi = 10.1007/bf02726635 id = cord-014540-27hnlu5v author = Sutthiruk, Nantanit title = Abstracts from the 8th International Congress of the Asia Pacific Society of Infection Control (APSIC): Bangkok, Thailand. 12-15 February 2017 date = 2017-02-22 keywords = CPE; Chen; Control; Infection; Lee; MRSA; Resistance; SSI; VAP; hygiene; patient; study summary = A secondary questionnaire was sent to determine whether any cases showed a positive blood or cerebral spinal fluid culture for Extended Spectrum Beta-lactamase (ESBL) producing GNB, AmpC β-lactamases producing GNB, or carbapenem-resistant enterobacteriacae (CRE) between April 2012 and March 2015.The following data were collected; demographic data pertaining to both the care facilities and patients, clinical diagnosis, and outcomes. Utilization of diagnosis-procedure combination data for advancing the antimicrobial stewardship program Haruo Nakayama, Toshiko Ota, Naoko Shirane, Chikako Matuoka, Kentaro Kodama, Masanobu Ohtsuka Toho University Ohashi medical center, Tokyo, Japan Background Infection with antibiotic-resistant bacteria results in increased morbidity, mortality and economic burden. The purpose of this study was to test the effectively of the Infection Control Risk Assessment (ICRA) monitoring tool developed by the Infection Prevention and Control Unit (IPCU) of Asian Hospital and Medical Center with the aim to increase the compliance of construction workers to recommended infection prevention and control measures during construction, renovation and demolition in the hospital. doi = 10.1186/s13756-017-0176-1 id = cord-328196-fpk9elm8 author = Sykes, Jane E. title = Immunodeficiencies Caused by Infectious Diseases date = 2010-05-13 keywords = CDV; cell; infection summary = Other important causes include canine distemper virus; canine parvovirus 2; feline infectious peritonitis virus; rickettsial organisms that infect leukocytes; Leishmania; and fungal pathogens, such as Cryptococcus. Impairment of normal host barrier function or the function of granulocytes is generally associated with a broad spectrum of bacterial infections and sometimes infection with opportunistic fungi, such as Aspergillus spp Impairment of cell-mediated immunity (CMI) results in infections with opportunistic pathogens, such as Nocardia spp, Mycobacterium spp, Toxoplasma gondii, and a variety of fungal pathogens. Dogs mounting a partial immune response may undergo recovery from acute illness but fail to eliminate the virus completely, leading to a spectrum of more chronic disease manifestations that often involve the uvea, lymphoid organs, footpads, and especially the CNS. 8 CDV infection of ferrets leads to dramatic reduction in cell-mediated immune function with markedly depressed lymphocyte proliferative activity, and to some extent delayed type hypersensitivity responses. doi = 10.1016/j.cvsm.2010.01.006 id = cord-009773-pbm2vs5h author = TRIGG, C. J. title = Bronchial inflammation and the common cold: a comparison of atopic and non‐atopic individuals date = 2006-04-27 keywords = HRV; atopic; bronchial; infection; subject summary = The aim of this study was to examine bronchial epithelial tissue in naturally acquired cold virus infections, in order to determine whether there are differences between the lower airway infiammatory response and ICAM-1 expression in atopic and nonatopic subjects. Wilcoxon''s signed rank test was used to compare baseline and acute phase results and the Mann-Whitney {/-test to compare changes in T-cell infiltration during colds between atopic and non-atopic subjects, between viral diagnostic groups and between symptom groups. There was a greater increase in bronchial responsiveness in non-atopic subjects and those without diagnosed viral infection but the difference between groups was not significant. (Paired /-test: geometric mean 1.53-fold increase, confidence interval 1.04 2.25-fold, P = 0.02.) The effect of atopy and viral diagnosis on changes in infiammatory cell infiltration of the bronchial mucosa is shown in Table 4 . The table shows the change from baseline in numbers of inflammatory cells in atopic and non-atopic subjects and in those with and without positive viral diagnoses. doi = 10.1111/j.1365-2222.1996.tb00593.x id = cord-015967-kqfyasmu author = Tagore, Somnath title = Epidemic Models: Their Spread, Analysis and Invasions in Scale-Free Networks date = 2015-03-20 keywords = epidemic; individual; infection; network summary = For instance, hub individuals of such high-risk individuals help in maintaining sexually transmitted diseases (STDs) in different populations where majority belong to long-term monogamous relationships, whereas in case of SARS epidemic, a significant proportion of all infections are due to high risk connected individuals. Likewise, models for epidemic spread in static heavy-tailed networks have illustrated that with a degree distribution having moments resulted in lesser prevalence and/or termination for smaller rates of infection [14] . Generally, epidemic models consider contact networks to be static in nature, where all links are existent throughout the infection course. But, in cases like HIV, which spreads through a population over longer time scales, the course of infection spread is heavily dependent on the properties of the contact individuals. Likewise, for a wide range of scale-free networks, epidemic threshold is not existent, and infections with low spreading rate prevail over the entire population [10] . doi = 10.1007/978-3-319-15916-4_1 id = cord-018808-h2zb87oa author = Tantawichien, Terapong title = Dengue date = 2018-03-20 keywords = Asia; DHF; DSS; dengue; infection summary = After an incubation period of 4-8 days, infection by any dengue virus can produce a wide spectrum of illnesses ranging from asymptomatic or subclinical infection to undifferentiated fever, dengue fever (DF), and severe forms of the disease associated with plasma leakage (dengue hemorrhage fever: DHF), dengue shock syndrome (DSS), severe bleeding, encephalopathy, and multi-organ failure [35] . The clinical spectrum of dengue infection ranges from mild illness (undifferentiated fever, non-severe DF) to the life-threatening severe forms of the disease with plasma leakage (DHF/DSS), severe bleeding, or multi-organ failure, which may be fatal. The unusual manifestations of dengue infection have been recognized including severe internal hemorrhage, fulminant hepatic failure, encephalopathy, cardiomyopathy, cardiac arrhythmia, adult respiratory distress syndrome (ARDS), rhabdomyolysis, pancreatitis, appendicitis, coinfection with other viruses or tropical infectious diseases, and neurological complications (e.g., altered consciousness, seizures, paresis, and coma resulting from encephalitis and encephalopathy) [91] [92] [93] [94] [95] [96] [97] [98] . The clinical spectrum of dengue ranges from mild illness (undifferentiated fever and DF) to the life-threatening infection (DHF/DSS, severe bleeding, and multi-organ failure), which may be fatal. doi = 10.1007/978-3-319-68493-2_10 id = cord-007367-e31zhty6 author = Tassier, Troy title = Network position and health care worker infections date = 2015-09-07 keywords = agent; contact; group; infection summary = We estimate, using an agent-based model, the effect of network position of different hospital worker groups on the spread of infectious diseases in a hospital. Following the theoretical discussion, we use our newly collected data on healthcare worker and patient contacts to model the spread of an infectious disease in a hospital setting. The model allows us to identify the healthcare worker groups that would be expected to play the largest role in the spread of infectious diseases, in terms of network position, in this hospital setting. Because of these difficulties we use a simulation approach to help us measure the average and marginal effects of individuals belonging to different worker groups in our hospital contact data. We discuss the data and use agent-based models to identify the healthcare workers whose position in the hospital contact network has the potential to create large numbers of infections in the hospital. doi = 10.1007/s11403-015-0166-4 id = cord-254766-585iu5ey author = Tauro, Sharyn title = Molecular and cellular mechanisms in the viral exacerbation of asthma date = 2008-08-13 keywords = RSV; asthma; infection; respiratory summary = This review summarizes the evidence associated with factors that may contribute to the development or exacerbation of asthma including age, host factors, genetic polymorphisms, altered immune responses, and aspects of viral antigen expression. These observations suggest that respiratory viral infections lead to a prolonged period of increased antigen presentation in the airways resulting in de novo and memory T-cell responses not only to the virus but also to unrelated antigens including allergens. In addition to studies of primary infections, models studying the interactions between respiratory viral infections and allergen sensitization are essential in understanding the mechanisms of virus induced asthma exacerbations. These studies show that the immune responses to allergen sensitization and respiratory viral infections interact to cause persistent inflammation and AHR, symptomatic of the asthmatic response (Fig. 2) [53] . Recurrent respiratory syncytial virus infections in allergen sensitized mice lead to persistent airway inflammation and hyperresponsiveness doi = 10.1016/j.micinf.2008.07.037 id = cord-269734-u43gt8fh author = Teijaro, J.R. title = Pleiotropic Roles of Type 1 Interferons in Antiviral Immune Responses date = 2016-09-20 keywords = IFN; ifnar1; infection; type summary = (A) Viral infection in the lung with Influenza or SARS-CoV promotes the induction of delayed IFN-I production which enhances cytokine/chemokine production, recruitment of NK cells, and neutrophils and inflammatory macrophage/monocytes all which contribute to lung immune-mediated pathology. Collectively, the studies above suggest that IFN-I signaling is essential to cytokine and chemokine amplification and innate immune cell recruitment and can promote excessive immunopathology during acute respiratory viral infections (Fig. 1) . Importantly, that IFN-I production and signaling can be blunted without enhancing virus propagation following acute respiratory viral infection suggests that this pathway can be modulated without compromising host antiviral responses. Inhibition of IFN-I signaling by antibody blockade of IFNAR1 results in elevated virus replication early following LCMV Cl13 infection and treatment of mice with IFN-I during the early stages of persistent LCMV infection promotes rapid virus control (Wang et al., 2012) . doi = 10.1016/bs.ai.2016.08.001 id = cord-020560-jnemlabp author = Tewari, Hemant title = Severe Tropical Infections date = 2012-03-09 keywords = infection summary = Close monitoring and supportive therapy is the mainstay of treatment in most of these infections, but some of them have specific therapies. Close monitoring and supportive therapy is the mainstay of treatment in most of these infections, but some of them have speci fi c therapies. Close monitoring and general organ • support in the initial days or weeks of viremia or parasitemia will salvage many patients. Step 6: Initiate empirical therapy based on initial presentation Speci fi c therapy is available only for a few tropical infections. Step 7: Start speci fi c treatment once the diagnosis is con fi rmed Dengue • A protocol for intravenous fl uid therapy has been developed by the World -Health Organization (WHO). Close clinical observation is essential, even after normal blood volume is restored, because patients can develop shock for 1-2 days after initial fl uid resuscitation, which represents the period of increased vascular permeability in dengue hemorrhagic fever. doi = 10.1007/978-81-322-0535-7_51 id = cord-023168-cd7adns8 author = Thachil, Jecko title = Haematological Diseases in the Tropics date = 2013-10-21 keywords = Africa; G6PD; HIV; SCD; anaemia; blood; cell; deficiency; disease; haemoglobin; infection; iron; patient; transfusion; treatment summary = The most useful laboratory measure of iron status Low value is diagnostic in the presence of anaemia Very high values (>100 µg/L) usually exclude iron deficiency'' Being an acute-phase protein, it increases in inflammatory conditions, and certain malignancies, making it unreliable Also increased in tissue damage especially of the liver Levels are falsely decreased in vitamin C deficiency and hypothyroidism Erythrocyte zinc protoporphyrin An intermediate in haem biosynthesis and elevated concentrations indicate interrupted haem synthesis due to iron deficiency when zinc is incorporated in place of iron Can be measured on a drop of blood with a portable haematofluorometer Small sample size makes it very useful as a screening test in field surveys, particularly in children, and pregnant women where inflammatory states may not co-exist Red cells should be washed before measurement (serum bilirubin and fluorescent compounds like some drugs can give falsely high values) although not often done Lead poisoning can give falsely high values Rarely acute myeloid leukaemia and sideroblastic anaemia give slightly high values Useful in that it is not increased in thalassaemias WHO recommends normal level >70 µmol/mol haem Iron studies Serum iron concentration represents the iron entering and leaving the circulation. doi = 10.1016/b978-0-7020-5101-2.00066-2 id = cord-339852-9rq7zzqs author = Theamboonlers, Apiradee title = Human Coronavirus Infection among Children with Acute Lower Respiratory Tract Infection in Thailand date = 2006-11-30 keywords = OC43; infection; respiratory summary = In addition, we performed this study in order to delineate the prevalence, the potential clinical impacts and evaluation of the genetic characterization of this pathogen in young children who presented with acute lower respiratory tract infections (ALRI). In this study we applied molecular biology techniques to identify hCoV in nasopharyngeal secretions (NPs) for the study on the prevalence of molecular characterization and clinical correlation of coronavirus infections in hospitalized infants and young children with acute lower respiratory tract infection (ALRI). In this study, we have identifi ed human coronavirus hCoV-OC43 and hCoV-229E infection in infants and young children presenting with ALRI. hCoV-229E and hCoV-OC43 have previously been proven responsible for infecting people of all age groups and causing severe lower respiratory tract infection primarily in frail patients such as young children and elderly individuals [17] [18] [19] . The clinical features associated with coronavirus infection appear to be similar to those observed with other respiratory viruses, such as RSV, parainfl uenza virus and human metapneumovirus. doi = 10.1159/000097392 id = cord-269627-mx1mjdqc author = Thiry, Etienne title = Feline herpesvirus infection. ABCD guidelines on prevention and management date = 2009-07-31 keywords = FHV; PCR; feline; infection summary = Passive immunity acquired via colostrum Maternally derived antibodies protect kittens against disease during the first weeks of life, but in general levels are low in FHV infections. Feline herpesvirus infection typically causes acute upper respiratory and ocular disease (Table 1) , which can be particularly severe in young kittens. 18 Viral DNA has also been detected in the aqueous humour of a larger proportion of cats suffering from uveitis, as compared with 19 Chronic rhinosinusitis, a frequent cause of sneezing and nasal discharge, has been associated with FHV infection. However, when quantitative real-time PCR is used, the virus concentration measured may provide additional information: high viral loads in nasal secretion or tears suggest active replication and FHV involvement in the clinical signs [EBM grade II]. Evaluation of serologic and viral detection methods for diagnosing feline herpesvirus-1 infection in cats with acute respiratory tract or chronic ocular disease Quantification of feline herpesvirus 1 DNA in ocular fluid samples of clinically diseased cats by real-time TaqMan PCR doi = 10.1016/j.jfms.2009.05.003 id = cord-253197-9hjvk7p5 author = Thomas, Evan title = Urinary Tract Infection with Atypical Mycobacteria date = 1980-11-30 keywords = atypical; infection summary = Abstract We present a case of disseminated atypical mycobacterial (Mycobacterium intracellularis) infection of the urinary tract. A review of the literature revealed only 13 previous cases of atypical mycobacterial infection of the urinary tract. intracellularis developed, as evidenced by positive cultures of the urine, bone marrow, liver, lymph nodes, cerebrospinal fluid, stool and blood. In 1970 Klotz noted 306 cases of urinary colonization with atypical mycobacteria, none of which was reportedly associated with observable urinary tract disease.8 Thus, we believe that adequate documentation of atypical mycobacterial infection must include either positive culture of genitourinary tissue specimens and/ or positive urine cultures in conjunction with some combination of radiologic, pathologic or laboratory evidence compatible with granulomatous genitourinary disease. Lattimer and Boyes referred to 2 children in whom urine culture yielded group I atypical mycobacteria but no supporting evidence of genitourinary disease was found. 7 In no other reported case was a patient <27 years old. doi = 10.1016/s0022-5347(17)55642-6 id = cord-174036-b3frnfr7 author = Thomas, Loring J. title = Spatial Heterogeneity Can Lead to Substantial Local Variations in COVID-19 Timing and Severity date = 2020-05-20 keywords = SIR; covid-19; infection; model summary = Based on simulations of unrestricted COVID-19 diffusion in 19 U.S cities, we conclude that heterogeneity in population distribution can have large impacts on local pandemic timing and severity, even when aggregate behavior at larger scales mirrors a classic SIR-like pattern. These results demonstrate the potential for spatial network structure to generate highly non-uniform diffusion behavior even at the scale of cities, and suggest the importance of incorporating such structure when designing models to inform healthcare planning, predict community outcomes, or identify potential disparities. In this paper, we examine the potential impact of local spatial heterogeneity on COVID-19, modeling the diffusion of SARS-CoV-2 in populations whose contacts are based on spatially plausible network structures. The disease diffuses through the contact network, with currently infectious individuals infecting susceptible neighbors as a continous time Poisson process with a rate estimated from mortality data (see supplement); recovered or deceased individuals are not considered infectious for modeling purposes. doi = nan id = cord-265005-e6rpryrh author = Tomasello, Elena title = Harnessing Mechanistic Knowledge on Beneficial Versus Deleterious IFN-I Effects to Design Innovative Immunotherapies Targeting Cytokine Activity to Specific Cell Types date = 2014-10-30 keywords = CD4; CD8; HCV; IFN; cell; figure; infection; type summary = doi = 10.3389/fimmu.2014.00526 id = cord-015640-zdwmxaz3 author = Tong, C. Y. W. title = Clinical Virology in NICU, PICU and AICU date = 2011-08-10 keywords = H1N1; ICU; RSV; infection; patient summary = Viruses are significant causes of nosocomial infections, particularly in intensive care unit (ICU) where seriously ill and vulnerable patients are being cared for. Adherence to effective infection control measures (hand hygiene, enteric precautions; Table 20 .3), as well as adequate staffing and patient cohorting/ isolation can therefore help prevent or manage an outbreak [41] . Neonates and immunocompromised patients can shed the virus for a prolonged time over months, which emphasises the need for rigorous adherence to effective infection control measures (Table 20. Postexposure prophylaxis (PEP) should therefore be offered to all health care workers who have significant exposure to blood or body fluid from a patient known to be at high risk of or to have HIV infection. Preliminary estimation of risk factors for admission to intensive care units and for death in patients infected with A(H1N1)2009 influenza virus doi = 10.1007/978-88-470-1601-9_20 id = cord-333730-qsx0m68e author = Tsai, Y. C. title = Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date = 2020-09-03 keywords = HIV; SARS; infection; treatment; virus summary = However, some immunosuppressants or disease-modifying antirheumatic drugs (DMARDs) show antiviral activity and may be safely used or even beneficial in patients with selected concomitant viral infections. In vitro anti-CMV properties of leflunomide were not through blocking the replication of viral DNA, so it is effective even in patients with direct antiviral drug-resistance history. The combination of MMF and highly active antiretroviral therapy improved the control of viral replication and delayed viral-load rebound in a randomized pilot study (n = 17 The effectiveness of thalidomide for KS might be related to anti-angiogenesis, and experts hypothesized the modulation of the immune system to trigger an antiviral action. Although in most instances, the antiviral activity of DMARDs is based on in vitro or small-scale controlled studies, this property would be useful in the choice of DMARDs for patients with concomitant viral infections. Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial doi = 10.1177/1759720x20947296 id = cord-349396-a6zyioc1 author = Tsurumi, Amy title = Multi-biomarker Prediction Models for Multiple Infection Episodes Following Blunt Trauma date = 2020-10-07 keywords = MIIE; infection; patient summary = Applying machine learning algorithms to genome-wide transcriptome data from 128 adult blunt trauma patients'' (42 MIIE cases and 85 non-cases) leukocytes collected ≤48 hours of injury and ≥3 days before any infection, we constructed a 15-transcript and a 26-transcript multi-biomarker panel model with the least absolute shrinkage and selection operator (LASSO) and Elastic Net, respectively, which accurately predicted MIIE (AUROC [95% CI]: 0.90 [0.84-0.96] and 0.92 [0.86-0.96]), and significantly outperformed clinical models. In a previous study among burn trauma patients, we developed a blood transcriptomic multi-biomarker panel for predicting multiple independent infection episodes (MIIE) outcome during the course of recovery (Yan et al., 2015) . Our study shows that employing novel prognostic models based on early blood transcriptome profiling following severe trauma is an effective method for identifying patients who are particularly at high risk for MIIE and thus, hypersusceptible to infections. doi = 10.1016/j.isci.2020.101659 id = cord-007445-2folsh35 author = Tuffaha, Amjad title = THE ROLE OF RESPIRATORY VIRUSES IN ACUTE AND CHRONIC ASTHMA date = 2000-06-01 keywords = RSV; infection; respiratory; virus summary = To more comprehensively evaluate the relationships among virus infection, atopy (cytokine dysregulation of Thl / Th2 imbalance), and immune system or lung developmental components, a rat model of virus-induced airway dysfunction has been studied extensively.''l'' In this model, infection with PIV type 1 during a critical developmental time period (when the animals are weaning [ 3 4 weeks of age] as opposed to when they are neonates [4-5 days] or adults) produces chronic (8-12 weeks fol-lowing infection), episodic, reversible airway inflammation and remodeling with associated alterations in airway physiology (increased resistance and rnethacholine responsiveness) that resemble human asthma in high (brown Norway strain) but not low (F344 strain) IgEantibody producing rats.62 The temporal progression of this asthma-like syndrome is associated with a Thl / Th2 imbalance within the lung, and its development can be significantly attenuated by the exogenous administration of IFN-8 just prior to and during the viral infection in the brown Norway responder strain.lo2 This model further supports the concept of both genetic (atopy; cytokine dysregulation or imbalance) and environmental factors (virus infection) being important in the inception of the asthmatic phenotype, as well as a developmental component contributing. doi = 10.1016/s0272-5231(05)70267-7 id = cord-265964-cnp5bwet author = Tumala, Regie B. title = Assessment of nursing students perceptions of their training hospital's infection prevention climate: A multi-university study in Saudi Arabia date = 2019-10-31 keywords = Saudi; infection; prevention summary = doi = 10.1016/j.nedt.2019.07.003 id = cord-274824-kaefedl1 author = Turski, Waldemar A. title = AhR and IDO1 in pathogenesis of Covid-19 and the “Systemic AhR Activation Syndrome:” a translational review and therapeutic perspectives date = 2020-09-24 keywords = IDO1; SARS; ahr; covid-19; infection summary = doi = 10.3233/rnn-201042 id = cord-317661-v93mde6l author = Vaid, Shashank title = Using Machine Learning to Estimate Unobserved COVID-19 Infections in North America date = 2020-05-07 keywords = Canada; infection summary = CONCLUSIONS: We have identified 2 key findings: (1) as of April 22, 2020, the United States may have had 1.5 to 2.029 times the number of reported infections and Canada may have had 1.44 to 2.06 times the number of reported infections and (2) even if we assume that the fatality and growth rates in the unobservable population (undetected infections) are similar to those in the observable population (confirmed infections), the number of undetected infections may be within ranges similar to those described above. We have identified 2 key findings: (1) as of April 22, 2020, the United States may have had 1.5 to 2.029 times the number of reported infections and Canada may have had 1.44 to 2.06 times the number of reported infections and (2) even if we assume that the fatality and growth rates in the unobservable population (undetected infections) are similar to those in the observable population (confirmed infections), the number of undetected infections may be within ranges similar to those described above. doi = 10.2106/jbjs.20.00715 id = cord-029032-s9geepsc author = Vargas-García, Cesar title = Parasite-Guest Infection Modeling: Social Science Applications date = 2020-06-22 keywords = host; infection summary = This theory states that natural selection maximizes the number of secondary infections resulting from infection of a susceptible host through free channels that do not involve direct contact between infected and susceptible hosts [7] . The proposed section reviews the classical and recent models that try to explain this phenomenon It has been suggested that infection channels between infected and susceptible hosts may provide an advantage, either by allowing parasites to evade the host''s immune response [10] , reducing antiviral drug activity [11] , or simply having a more efficient mode of infection. In the second section, a novel model of parasite-host interactions is proposed that accounts for transmission, both through free channels (not involving contact between infected and susceptible hosts), and through infections produced by contact between hosts. This shielding effect can be incorporated into the previous model, assuming the number of parasites released by the death of an infected host as a function of the infection rate [14] . doi = 10.1007/978-3-030-53956-6_55 id = cord-303054-s1clwunc author = Velly, Lionel title = Guidelines: Anaesthesia in the context of COVID-19 pandemic date = 2020-06-05 keywords = COVID-19; N95; SARS; infection; patient; risk; surgery summary = Operating theatre 12 R1.3.1 -Experts suggest that healthcare professionals involved in airway management (intubation, extubation, supraglottic airway insertion and/or removal…), or those who could be brought to do so in some given situations, wear a fit tested respirator mask (Respirator N95 or FFP2 standard, or equivalent) in addition to a disposable face shield or at least, in the absence of the latter, safety goggles, regardless of the patient''s COVID-19 status (Table 1) The presence of major (i.e., very frequent or relatively characteristic) and/or minor (i.e. more inconsistent and/or less specific) symptoms allows to orient the preoperative COVID-19 status assessment, and then to estimate the benefit/risk balance of maintaining or postponing the surgery, taking into account the risk of contamination of health personnel and others patients within the care structure. doi = 10.1016/j.accpm.2020.05.012 id = cord-016966-b23o5roz author = Verhoef, Jan title = Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites date = 2005 keywords = antibody; cell; immune; infection summary = Effective treatment, however, was not possible at that time; prevention and spread of infectious diseases depended solely on proper hygienic means.At the beginning of the 20th century, passive and active vaccination procedures were developed against a number of these pathogenic micro-organisms in order to prevent the diseases in question (rabies, diphtheria, tetanus, etc.) and due to the discovery of antimicrobial chemicals (Ehrlich) and antibiotics (Fleming), the threat of infectious diseases seemed to be minimized. CYTOKINES, such as IL-2 (INTERLEUKIN-2), GM-CSF (granulocyte-macrophage colony-stimulating factor), and TNF-α (TUMOR NECROSIS FACTOR α), stimulate non-specifically the proliferation, maturation, and Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites Jan Verhoef and Harm Snippe A7 function of the cells involved in defence (see Chapter A.4). doi = 10.1007/3-7643-7408-x_7 id = cord-023925-qrr7jcwe author = Verhoef, Jan title = A8 Immune response in human pathology: Infections caused by bacteria, viruses, fungi, and parasites date = 2011-07-12 keywords = HIV; cell; gram; infection; virus summary = 128 Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites Micro-organisms that succeed in penetrating the first line of defence are ingested, killed, and degraded by phagocytic cells [polymorphonuclear leukocytes (PMN) or neutrophils, monocytes, and macrophages], which are attracted to a microbial infection through chemotaxis. Intracellular signalling involves several kinases depending on 132 Immune response in human pathology: infections caused by bacteria, viruses, fungi, and parasites Genotypical characteristics: chromosomal DNA fragment analysis, nucleic acid sequence analysis, probes Phenotypical characteristics: morphology, biotyping, serotyping, antibiotic resistance Analytical characteristics: cell-wall analysis, lipid and protein analysis, enzyme typing (catalase) Gram staining positive or negative Aerobic, anaerobic: Fermentation of different sugars Naming and classification of viruses according to: Structure: size, morphology (naked, enveloped), nucleic acid (RNA, DNA) Molecular aspects: mode of replication, assembly and budding Disease: encephalitis, hepatitis Means of transmission: droplets, water, blood, insects Host range: animal, plant, bacteria Classification of fungi according to: Structure: macroscopic morphology of hyphae (mycelium); microscopic morphology of hyphae, conidophores and conidia (spores); and shape and size Cell features: nucleus, cytosol, plasmalemma (cell membrane which contains cholesterol), physiology, staining properties Sexual characteristics: sexual and /or asexual reproduction, extended dikaryotic phase, basidium formation Genotypical characteristics: chromosomal DNA fragment analysis, nucleic acid sequence analysis, probes doi = 10.1007/978-3-0346-0136-8_8 id = cord-283405-aozxvxxs author = Vermillion, Meghan S. title = Pregnancy and infection: using disease pathogenesis to inform vaccine strategy date = 2018-02-01 keywords = ZIKV; infection; maternal; pregnant; vaccine; virus summary = Pregnant women, unborn fetuses, and neonates represent three populations of high-risk individuals that can all be simultaneously protected from vaccine-preventable infectious disease with strategic maternal immunization protocols. Third are neonatal and infant infections, which are not considered to pose significant risk to pregnant women or unborn fetuses, but can cause severe, and sometimes fatal disease in neonates and infants that lack protective maternal immunity following birth. Studies in pregnant nonhuman primates have been instrumental for the identification of CD4 + T cell responses as critical for early control of CMV infection and transmission during pregnancy, 100 and studies in guinea pigs have demonstrated that a single-cycle infectious CMV vaccine induces immune responses similar to natural infection and protects against congenital infection. 125 Vaccine candidates have been developed using diverse platforms, including DNA, mRNA, and purified inactivated and live-attenuated virus, many of which have been tested in non-pregnant mouse and nonhuman primate models for their ability to generate immune responses that mimic responses to natural infection and protected against ZIKV challenge. doi = 10.1038/s41541-017-0042-4 id = cord-260605-smkr7b15 author = Vestby, Lene K. title = Bacterial Biofilm and its Role in the Pathogenesis of Disease date = 2020-02-03 keywords = IBC; bacterial; biofilm; chronic; infection; patient; study summary = However, the biofilm lifestyle of microorganisms were of no interest to medical microbiologists until the early 1970s when Nils Høiby observed a link between the etiology of a persistent infection and aggregates of bacteria in cystic fibrosis patients [1] . This is consistent with the experiments showing that many bacteria causing acute gallbladder infections do not form biofilms on gallstones in the presence of bile [73, 80] . This is consistent with the experiments showing that many bacteria causing acute gallbladder infections do not form biofilms on gallstones in the presence of bile [73, 80] . Several studies have detected higher incidence of Escherichia coli in patients with IBD compared to healthy individuals [90] and although biofilms were not demonstrated in vivo, the isolates were isolated from biopsies after removal of the mucosal layer, indicating adherence to the colonic epithelium and the isolates displayed biofilm forming capacity in vitro [90] . doi = 10.3390/antibiotics9020059 id = cord-255479-yd5cbwnx author = Vu, David M. title = Chikungunya Virus date = 2017-06-30 keywords = CHIKV; chikungunya; infection; virus summary = Anti-CHIKV antibodies directed against the envelope protein that neutralize the virus in vitro also protect neonatal mice from lethal CHIKV infection in vivo, suggesting that these proteins may be important antigenic lethal targets for development of naturally acquired, or vaccine-elicited protection. Stedman, who reported this "anomalous disease" called "dandy fever" by local residents, noted that the illness "attacked almost every individual in the town," had "extremely low mortality," and was associated with "pains in the joints for weeks after recovery from the acute stage," which were key differences between the 1827 and 1828 West Indies epidemic and previous descriptions of a "break-bone fever" (referring to modern-day dengue fever). For diagnostic confirmation of current and recent infection, a molecular test (typically polymerase chain reaction [PCR]) for the virus and an assay for the presence of specific IgM antibody are required. doi = 10.1016/j.cll.2017.01.008 id = cord-323112-e78zpa9c author = WATERER, Grant title = Respiratory infections: A current and future threat date = 2009-07-16 keywords = infection; pneumonia; respiratory summary = This review will focus on the human, pathogen and environmental factors that contribute to the continued global burden or respiratory diseases with a particular focus on areas where we might hope to see some progress in the coming decades. 14 While it is clear that strict infection control can reduce nosocomial infection rates, 15 the practical necessity of pooling vulnerable hosts together combined with the inevitable ageing of health-care facilities will ensure that nosocomial outbreaks continue to be a problem. In recent years the marked increase in tumour necrosis factor antagonists and monoclonal antibodies targeting specific lymphoid populations in patients with inflammatory arthritis (and especially rheumatoid disease) has significantly over taken patients on immunosuppressant therapy after solid organ transplantation as the major cause of iatrogenic immunosuppression. New therapeutic and diagnostic approaches coupled with clinical vigilance, strict infection control and solid public health measures are the hopes for reducing the burden of pulmonary infectious disease over the coming decades. doi = 10.1111/j.1440-1843.2009.01554.x id = cord-272596-yxvg8357 author = WU, Jian Jun title = Detection of Human Bocavirus in Children with Acute Respiratory Tract Infections in Lanzhou and Nanjing, China date = 2014-11-30 keywords = infection; respiratory; tract summary = title: Detection of Human Bocavirus in Children with Acute Respiratory Tract Infections in Lanzhou and Nanjing, China In our study, 72.34% of HBoV1-positive patients had co-infection with 10 different respiratory viruses, which is similar to previous reports [12] [13] [14] [46] [47] [48] . Detection of human bocavirus in children with upper respiratory tract infection by polymerase chain reaction Detection of bocavirus in children suffering from acute respiratory tract infections in Saudi Arabia Detection of human bocavirus from children and adults with acute respiratory tract illness in Guangzhou, southern China Clinical relevance of human bocavirus with acute respiratory tract infection and diarrhea in children: a prospective case-control study Frequent detection of bocavirus DNA in German children with respiratory tract infections Human bocavirus infection in children with acute respiratory tract infection in India Human bocavirus in children with acute respiratory infections in Vietnam Human bocavirus infection in young children with acute respiratory tract infection in Lanzhou doi = 10.3967/bes2014.110 id = cord-281417-z6k30y1m author = Waggoner, Stephen N title = Roles of natural killer cells in antiviral immunity date = 2016-02-29 keywords = cell; infection summary = doi = 10.1016/j.coviro.2015.10.008 id = cord-018421-wy3mtafh author = Waghmare, Alpana title = Rhinovirus, Coronavirus, Enterovirus, and Bocavirus After Hematopoietic Cell Transplantation or Solid Organ Transplantation date = 2016-02-15 keywords = D68; HRV; infection; respiratory summary = Human rhinoviruses are the most common respiratory viruses detected in the upper respiratory tract of hematopoietic cell transplant and lung transplant recipients, and evidence on the impact on clinical outcomes is mounting. Due to the development of polymerase chain reaction (PCR) assays for viral detection, HRVs are now known to be the most common viruses detected from respiratory specimens in HCT recipients and can account for 25-40% of cases of viral respiratory infections in these patients [ 2 -4 ] (Figure 32-1 ). In that study, approximately one third of the adult HCT recipients who developed symptomatic HRV infections prior to engraftment had progression of upper respiratory tract symptoms to LRTI, and all cases with pneumonias were fatal. Rhinovirus as a cause of fatal lower respiratory tract infection in adult stem cell transplantation patients: a report of two cases Human Rhinovirus RNA Detection in the Lower Respiratory Tract of Hematopoietic Cell Transplant recipients: Association with Mortality. doi = 10.1007/978-3-319-28797-3_32 id = cord-012484-c9ajmbw2 author = Wahlund, Martina title = The Feasibility of Host Transcriptome Profiling as a Diagnostic Tool for Microbial Etiology in Childhood Cancer Patients with Febrile Neutropenia date = 2020-07-26 keywords = RNA; infection summary = doi = 10.3390/ijms21155305 id = cord-167157-z0lvcb3z author = Wang, Xiubin Bruce title = Controlling the Hidden Growth of COVID-19 date = 2020-05-19 keywords = infection; rate summary = A major result indicates an existing infections estimate at about 10-50 times the daily confirmed new cases, with the stringent social distancing policy tipping to the upper end of this range. However, our method to estimate the undetected number of currently latent and active infections is based on the publicized numbers of the daily confirmed cases without having to resort to the epidemic process simulation. Day by day over a period of time, newly confirmed cases are reported by the number N 1 , N 2 , ..., and N n .The study is to use the daily confirmed numbers of infections to estimate the hidden infections and their trend of growth or declination. The above example scenarios, all assuming the epidemic is under control by having the total newly confirmed cases flat over a period of days, indicate a large number of currently active and latent infections in the population ranging from 6 to 50/60 times of the daily confirmations. doi = nan id = cord-001972-1zisomq5 author = Wang, Xue title = Pandemic Influenza A (H1N1) Virus Infection Increases Apoptosis and HIV-1 Replication in HIV-1 Infected Jurkat Cells date = 2016-02-02 keywords = H1N1; HIV-1; Jurkat; infection summary = These data indicate that HIV-1 replication can be activated by pH1N1 virus in HIV-1-infected cells resulting in induction of cell death through apoptotic pathways. Cells treated with pH1N1 had higher level of NF-kB phosphorylation and increased protein expression of NFAT and AP-1 ( Figure 3B ) relative to HIV-1 infection alone, suggesting pH1N1 infection can activate host transcription factors required for HIV-1 replication in Jurkat cells. These data indicate that pandemic influenza A (H1N1) infection can increase accumulation of CD4 protein and induce T cell signaling and activate host transcription factors required for HIV-1 replication. In conclusion, our results demonstrate that pandemic influenza A (H1N1) virus infection can induce cell death through apoptotic signaling pathways and promote HIV-1 replication through the MAPK and TCR-related signaling pathways in HIV-1-infected Jurkat cells. Pandemic influenza A (H1N1) virus infection is also able to reactivate HIV-1 replication from its state of latent infection through activating apoptosis and TCR-signaling pathways. doi = 10.3390/v8020033 id = cord-002043-z1b7pj3s author = Wang, Xue-Yang title = Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains date = 2016-05-11 keywords = BC9; BmNPV; Bombyx; Fig; P50; infection summary = obtained numerous differentially expressed genes (DEGs) involved in metabolism, immunity, and inflammatory responses in Microtus fortis following infection with Schistosoma japonicum based on comparative transcriptome analysis [20] . reported that several genes related to physical barriers, immune response, proteolytic/metabolic enzymes, heat-shock proteins, and hormonal signaling were possibly involved in silkworm resistance against Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection; although these genes might be induced by the virus in order to increase infectivity [21] . After BmNPV infection, the expression levels of 4 genes were down-regulation in BC9 and A35 (resistant strain) (Fig 6) , which was consistent with the transcriptome data. Based on their role in apoptosis activation, hosts need to increase the expression level of these genes to promote apoptosis when exposed to a virus; this supposition explains the up-regulation of genes involved in apoptosis in the transcriptome following BmNPV infection. doi = 10.1371/journal.pone.0155341 id = cord-003357-4qrg6lqu author = Wang, Yingchen title = Prevalence of Common Respiratory Viral Infections and Identification of Adenovirus in Hospitalized Adults in Harbin, China 2014 to 2017 date = 2018-11-27 keywords = China; Harbin; infection; respiratory summary = Conclusion: This study demonstrated that common respiratory viruses were partially responsible for hospitalized lower respiratory tract infections in adult patients from Harbin, China, with parainfluenza virus as the dominant viral pathogen. Viral infections played an important role in pediatric lower respiratory tract infections, and the corresponding common viral pathogens were influenza A and B virus (IAV and IBV), parainfluenza virus (PIV, type 1 to 3), respiratory syncytial virus (RSV) and human adenovirus (ADV) (Pavia, 2011) . In this report, the prevalence of common viruses in the lower respiratory tract infection of hospitalized adult patients from Harbin, China was explored in hopes of revealing the clinical and pathogenic features of respiratory viruses. The overall detection rate of viral infection among hospitalized adult patients in this report is 14.5%, which was consistent with the result of 16.8% in the age group above 14 years old by a national survey from 2009 to 2013 in China (Feng et al., 2014) . doi = 10.3389/fmicb.2018.02919 id = cord-282142-76jr4p7n author = Wang, Yun title = Potential Effect of COVID-19 on Maternal and Infant Outcome: Lesson From SARS date = 2020-08-07 keywords = COVID-19; CoV-2; SARS; infection summary = doi = 10.3389/fped.2020.00511 id = cord-321481-vrfwczve author = Watashi, Koichi title = NTCP and Beyond: Opening the Door to Unveil Hepatitis B Virus Entry date = 2014-02-19 keywords = HBV; NTCP; infection; virus summary = Recently, sodium taurocholate cotransporting polypeptide (NTCP) was identified as an HBV entry receptor and enabled the establishment of a susceptible cell line that can efficiently support HBV infection. HBV infection into host hepatocytes follows a multiple step process: (1) initially, HBV reversibly attaches to host cell surface proteoglycans with a low affinity; (2) this is followed by the process involving more specific receptor(s) with high affinity to mediate the early entry step; and (3) after endocytosis-mediated internalization, the virus fuses with the cellular membrane compartment, probably in an endosomal compartment, although the mechanisms are not fully understood. A myristoylated peptide encompassing amino acids 2-48 of the preS1 region turned out to be the most efficient in infection inhibition of HBV and also the envelope protein-related hepatitis D virus (HDV) [30, 31] . Cyclosporin A and its analogs inhibit hepatitis B virus entry into cultured hepatocytes through targeting a membrane transporter NTCP doi = 10.3390/ijms15022892 id = cord-271122-3fsl5589 author = Wathes, D. Claire title = Importance of Viral Disease in Dairy Cow Fertility date = 2019-07-24 keywords = BVDV; bovine; effect; infection; virus summary = doi = 10.1016/j.eng.2019.07.020 id = cord-336456-wg8vfh6w author = Webb, Glynn W. title = Hepatitis A and Hepatitis E: Clinical and Epidemiological Features, Diagnosis, Treatment, and Prevention date = 2020-11-01 keywords = HAV; HEV; hepatitis; infection summary = However, HAV and HEV, which are isolated from the serum of individuals suffering an acute infection, are wrapped in a hijacked layer of host cell membrane, similar to those found on classical enveloped viruses but distinguished by the lack of any virusencoded proteins at the surface [8] . A recent large prospective study in Hong Kong identified both acute and chronic HEV-C1 infection in both immunocompetent and immunocompromised patients [24] . There is significant heterogeneity in the clinical picture of acute infection in these areas; only a small minority of patients present with typical viral hepatitis as described above. One of the most important public health challenges related to acute hepatitis E infection, which most commonly occurs in developing countries, is the excess morbidity and mortality seen among pregnant women (Table 1 ). Hepatitis E virus (HEV) infection in patients with cirrhosis is associated with rapid decompensation and death doi = 10.1016/j.clinmicnews.2020.10.001 id = cord-019051-gtruu1op author = Weber, Olaf title = The role of viruses in the etiology and pathogenesis of common cold date = 2009-11-10 keywords = RNA; RSV; infection; respiratory; virus summary = Viruses with an established role in common cold are rhinoviruses, adenoviruses, parainfluenza viruses, coronaviruses and the respiratory syncytial virus, and these are reviewed in greater detail here. Therefore, the viral etiology and the role of viruses in the pathogenesis of common cold is complex and it is safe to say, not fully understood for each and every virus that is linked to respiratory tract infection. RSV infection is assumed to be frequently misdiagnosed, particularly in adults [56] , because the symptoms are similar to those caused by other respiratory viruses like influenza. Human parainfluenza viruses (HPIV) are important causes of respiratory diseases in infants and children. HMPV is thought to be the second or third cause of severe acute respiratory tract infection in children, just ranking behind RSV and influenza virus [146, 148] . Retinoic acid-inducible gene I mediates early Antiviral Response and Toll-like receptor 3 expression in respiratory syncytial virus-infected airway epithelial cells doi = 10.1007/978-3-7643-9912-2_5 id = cord-332737-iclruwmx author = Webley, Wilmore C. title = Infection-mediated asthma: etiology, mechanisms and treatment options, with focus on Chlamydia pneumoniae and macrolides date = 2017-05-19 keywords = COPD; Chlamydia; asthma; infection summary = Another recent study concluded that the nasopharyngeal microbiome within the first year of life was a determinant for infection spread to the lower airways and predicted the severity of accompanying inflammatory symptoms, as well as risk for future asthma development. Factors that predict risk in non-asthmatics for developing the "infectious asthma" syndrome include a previous history of self-limited lower respiratory tract illnesses such as acute bronchitis (often with wheezing) and/or pneumonia [35, 38, 39] . A 2013 metaanalysis of 12 randomized, controlled trials (RCTs) of macrolides for the long term management of asthma in both adults and children found positive effects on peak expiratory flow rate (PEFRa measure of pulmonary function), asthma symptoms, asthma quality of life (AQL), and airway hyper responsiveness (AHR), but not on forced expiratory flow rate in 1 s (FEV1) [77] . doi = 10.1186/s12931-017-0584-z id = cord-326138-16kpn9db author = Weinstein, Robert A. title = Laboratory-Acquired Infections date = 2009-07-01 keywords = United; infection; laboratory summary = Although the precise risk of infection after an exposure remains poorly defined, surveys of laboratory-acquired infections suggest that Brucella species, Shigella species, Salmonella species, Mycobacterium tuberculosis, and Neisseria meningitidis are the most common causes. Surveys of diagnostic laboratory workers in the United Kingdom conducted since 1971 have reported that tuberculosis and enteric infections (especially shigellosis) were the most common laboratory-acquired infections [7, 8] . Similar results were obtained from a survey of clinical microbiology laboratories in Utah from the period 1978-1992, with shigellosis reported to be the most common laboratory-acquired infection [10] . Although no controlled studies have been performed to assess the benefit of postexposure prophylaxis (PEP), it should be considered for laboratory workers who have high-risk exposure to Brucella species (e.g., because of direct manipulation of Brucella cultures outside of laminar-flow BSCs). Viral agents transmitted through blood and bodily fluids cause most of the laboratory-acquired infections in diagnostic laboratories and among health care workers [1] . doi = 10.1086/599104 id = cord-300793-tuq8z6gm author = Weiss, Robin A title = Social and environmental risk factors in the emergence of infectious diseases date = 2004 keywords = AIDS; HIV; SARS; disease; human; infection summary = doi = 10.1038/nm1150 id = cord-348844-4rpbsj48 author = Wessel, Lindsay title = Public health interventions for epidemics: implications for multiple infection waves date = 2011-02-25 keywords = infection summary = METHODS: We develop mean-field and stochastic epidemiological models for disease transmission, and perform simulations to show how control measures, such as drug treatment and isolation of ill individuals, can influence the epidemic profile and generate sequences of infection waves with different characteristics. In this study, we consider the occurrence of multiple infection waves of a pathogen from a public health perspective, and develop mathematical models to investigate how intervention measures may affect the transmission dynamics in a population. These parameters may reflect the effectiveness of intervention strategies (e.g., treatment or isolation of infected cases) in reducing disease transmission, or their epidemiological consequences (e.g., emergence of drug resistance), and may therefore play an important role in determining the outcome of disease control activities. For the purpose of this investigation, we develop both mean-field and stochastic epidemiological models that describe the transmission dynamics of a disease in the population, and incorporate treatment and isolation of infected cases as control measures. doi = 10.1186/1471-2458-11-s1-s2 id = cord-267671-ys43n672 author = Whary, Mark T. title = Biology and Diseases of Mice date = 2015-07-10 keywords = BALB; C57BL/6; Control; Fig; Helicobacter; LCMV; MHV; PCR; SCID; animal; cell; complication; diagnosis; disease; dna; infection; laboratory; medicine; mouse; sign; strain; virus summary = Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases. doi = 10.1016/b978-0-12-409527-4.00003-1 id = cord-354720-fu19u2b0 author = White-Dzuro, Gabrielle title = Multisystem effects of COVID-19: a concise review for practitioners date = 2020-11-04 keywords = ACE2; COVID-19; SARS; infection; patient summary = It is important that clinicians managing critically ill COVID-19 patients be aware of the multisystem impact of the disease so that care can be focused on the prevention of end-organ injuries to potentially improve clinical outcomes. It is important that clinicians managing these critically ill patients be aware of the multisystem impact of the disease so that care can be focused on the prevention of end-organ injuries to potentially improve clinical outcomes. The indirect effects of the virus result from the host''s response to the viral infection, and are associated with a cytokine storm characterized by very high circulating levels of pro-inflammatory cytokines, including tumor necrosis factor (TNF)-α, interleukins, granulocyte-colony stimulating factor, and chemokines [9] . include direct viral damage of nervous tissue, injury resulting from the excessive inflammatory response, unintended host immune response effects after the acute infection (e.g., Guillain-Barré syndrome as reported in a case series of four patients [24] ), and injury resulting from the effects of systemic illness. doi = 10.1080/00325481.2020.1823094 id = cord-272194-h7xnr389 author = Wiegers, Hanke M. G. title = Bacterial co-infection of the respiratory tract in ventilated children with bronchiolitis; a retrospective cohort study date = 2019-11-06 keywords = PICU; infection summary = doi = 10.1186/s12879-019-4468-3 id = cord-023528-z9rc0ubj author = Wilkins, Pamela A. title = Disorders of Foals date = 2009-05-18 keywords = HIE; Rhodococcus; blood; cause; clinical; disease; effect; equine; foal; increase; infection; neonatal; pas; respiratory; result; therapy; treatment summary = doi = 10.1016/b0-72-169777-1/50021-4 id = cord-010175-p2py9wau author = Winter, Harland title = GASTROINTESTINAL AND NUTRITIONAL PROBLEMS IN CHILDREN WITH IMMUNODEFICIENCY AND AIDS date = 1996-04-01 keywords = AIDS; HIV; child; infection summary = The observations that transmission is increased in women who were symptomatic or who had more advanced AIDS27 and that zidovudine therapy given during pregnancy reduces perinatal transmission3 suggest that viral burden is an important factor in vertical transmission; however, the effects of maternal nutritional status, micronutrient deficiency, or acute infection on viral replication are difficult to evaluate. Gastrointestinal bleeding is unusual in HIV-infected children, but, when present, it may be caused by focal ulcerations in the colon, stomach, small intestine, or esophagus from cytomegalovirus-induced disease. Many of the medications used to treat complications of HIV disease cause hepatocellular injury or cholestasis; however, infectious agents, such as hepatitis B, that cause hepatocellular injury by immune mechanisms have milder clinical courses in immunodeficient hosts.Z4 Preservation of immune function in HIV-infected children could account for the apparent increase in chronic active hepatitis in the pediatric population compared with the incidence in Although abnormalities in liver function tests are not diagnostic, they are beneficial as screening procedures. doi = 10.1016/s0031-3955(05)70421-1 id = cord-268729-n7slf5tx author = Wissinger, E L title = Manipulation of acute inflammatory lung disease date = 2008-05-07 keywords = CD8; cell; immune; infection; lung; respiratory summary = doi = 10.1038/mi.2008.16 id = cord-016426-aw3wirmb author = Wohrley, Julie D. title = The Role of the Environment and Colonization in Healthcare-Associated Infections date = 2018-07-16 keywords = MRSA; Staphylococcus; aureus; infection summary = Studies have failed to show benefit for a combination of AST and isolation in reducing VRE infection or colonization; however, outbreaks of VRE have been successfully controlled in hospital settings with use of active surveillance, contact precautions, patient isolation, and cohorting [57] . A cluster randomized trial in intensive care units found that universal gown and glove use did not reduce overall acquisition of multidrug-resistant organisms (MDRO); there was, however, a small reduction in MRSA transmission noted as a secondary outcome [59] . Methicillin-resistant Staphylococcus aureus colonization and its association with infection among infants hospitalized in neonatal intensive care units Contamination of hands with methicillin-resistant Staphylococcus aureus after contact with environmental surfaces and after contact with the skin of colonized patients Analysis of data from the German Nosocomial Infection Surveillance System regarding the placement of patients with methicillin-resistant Staphylococcus aureus in private rooms in intensive care units Role of decolonization in a comprehensive strategy to reduce methicillin-resistant Staphylococcus aureus infections in the neonatal intensive care unit: an observational cohort study doi = 10.1007/978-3-319-98122-2_2 id = cord-279483-gwikyux2 author = Wong, Joshua Guoxian title = Risk prediction models to guide antibiotic prescribing: a study on adult patients with uncomplicated upper respiratory tract infections in an emergency department date = 2020-11-02 keywords = antibiotic; infection; patient summary = doi = 10.1186/s13756-020-00825-3 id = cord-333724-a3dufzxt author = Wong, T. E. title = Evaluating the Sensitivity of SARS-CoV-2 Infection Rates on College Campuses to Wastewater Surveillance date = 2020-10-11 keywords = Fig; infection; wastewater summary = Through a Monte Carlo risk analysis, we find that surveillance testing that relies solely on wastewater sampling can be fragile against scenarios with high viral reproductive numbers and high rates of infection of campus community members by outside sources. Such a global analysis would quantify how the variation in infection rates is attributable to each uncertain model parameter and potential decision lever, including, for example, the viral reproduction rate and the rate at which screening tests are administered to the campus population. Similarly to our modification of the traditional individual surveillance testing, the false and true positive results from the wastewater-based screenings are modulated by a noncompliant proportion parameter, fnc. We evaluate the sensitivity of these eight testing strategies, corresponding to the eight values of Ts,ww above, to our assumptions about three critical parameters: the effective reproductive rate, Rt, the number of new infections from exogenous sources each week, Nexo, and the fraction of individuals who are not compliant with quarantine/isolation procedures, fnc. doi = 10.1101/2020.10.09.20210245 id = cord-022592-g7rmzsv5 author = Wynn, James L. title = Pathophysiology of Neonatal Sepsis date = 2016-07-06 keywords = PMN; cell; increase; infant; infection; neonatal; neonate; response; sepsis summary = 14, 15, [27] [28] [29] [30] [31] [32] [33] Prematurity, low birth weight (especially infants weighing less than 1,000 g), male sex, a maternal vaginal culture positive for group B streptococcus (GBS), prolonged rupture of membranes, maternal intrapartum fever, and chorioamnionitis are strongly associated with an increased risk for early-onset sepsis. In addition to the initial inflammatory response including complement activation, molecular detection of PAMPs promotes IL-1β and IL-6 production, which in turn increases the production of multiple other innate proteins that possess valuable immune function and serve to reduce pathogen load. Very low birth weight preterm infants with early onset neonatal sepsis: the predominance of gram-negative infections continues in the National Institute of Child Health and Human Development Neonatal Research Network Very low birth weight preterm infants with early onset neonatal sepsis: the predominance of gram-negative infections continues in the National Institute of Child Health and Human Development Neonatal Research Network doi = 10.1016/b978-0-323-35214-7.00152-9 id = cord-298131-zolwjl9u author = Xiao, Shuqi title = Understanding PRRSV Infection in Porcine Lung Based on Genome-Wide Transcriptome Response Identified by Deep Sequencing date = 2010-06-29 keywords = IFN; PRRSV; figure; gene; infection summary = Upregulation expression of virus-induced pro-inflammatory cytokines, chemokines, adhesion molecules and inflammatory enzymes and inflammatory cells, antibodies, complement activation were likely to result in the development of inflammatory responses during N-PRRSV infection processes. To investigate the regulation of the host response to the N-PRRSV virus, we considered the global gene expression profiles in lungs using Solexa/Illumina''s DGE system, a tag-based transcriptome sequencing method. From the data presented in the paper, a model for the relationship between pulmonary gene expression profiles and infection pathology can be surmised in Figure 7 , N-PRRSV virus replicates and spreads by subverting host innate immune response and hijacking host lipid metabolism as well as inducing an antiapoptotic and anti-inflammatory state, as indicated by suppression expression of SPI IFN, IFN-a, down-regulation expression of proapoptotic genes for BAK, APR-1, SARP3, high levels expression of genes involved in lipid metabolism, such as APOE, LDLB, PIK3C3, anti-apoptotic genes for MCL1, BCL2A1, CHFR, ADM, NFKB, IL10, and anti-inflammatory molecule PGE2 as well as CD163. doi = 10.1371/journal.pone.0011377 id = cord-324880-s1oqkqef author = Xu, Lili title = A fatal case associated with respiratory syncytial virus infection in a young child date = 2018-05-11 keywords = RSV; infection; patient summary = RSV-related encephalitis with acute encephalopathic symptoms such as seizure, severe sequelae and even death following RSV infection in children without underlying disease has sporadically been reported [5] . In this report, we present the case of a 2-year-old girl who was not born prematurely and had no underlying disease whose sudden death may have been related to an RSV infection identified by conventional methods and metagenomic analyses. Viral antigen detection based on both an immunofluorescence assay and the Luminex xTAG respiratory viral panel assay was positive for RSV in the patient''s nasopharyngeal aspirates (which were collected on 14 Nov, the 5th day of disease onset and the 2nd day of admission) and negative for adenovirus, influenza A and B viruses, parainfluenza virus 1-4, human metapneumovirus, enteroviruses and rhinoviruses, human coronavirus HKU1, 229E, NL63 and OC43, and human bocavirus. reported that influenza virus RNA was detected in the CSF of 71.4% (5/7) of patients who developed influenza-associated acute encephalopathy/encephalitis [17] . doi = 10.1186/s12879-018-3123-8 id = cord-335614-qh98622y author = Xu, Puzhi title = A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus date = 2019-11-16 keywords = Dis; NIBV; RNA; figure; infection; pathway summary = These genes and metabolites were linked to NIBV-infection related processes, including immune response, signal transduction, peroxisome, purine, and amino acid metabolism. Taken together, our research comprehensively describes the host responses during NIBV infection and provides new clues for further dissection of specific gene functions, metabolite affections, and the role of gut microbiota during chicken gout. The results of PCA and OPLA-DA analysis showed that there was an obvious separation between the content of the Con and Dis groups, revealing significant changes in the concentrations of metabolites in the kidney induced by NIBV infection. In addition, the transcriptomic analysis showed that NIBV infection also activated the RIG-I-like receptor signalling pathway (Figure 3f , signal 2), which included the transcriptional upregulation of genes such as MDA5, IPS-1, TRAF3, and IκB. In the present study, the ABCG2 mRNA was downregulated in the model group chicken kidneys, partially explaining the significantly increased uric acid levels caused by NIBV infection. doi = 10.3390/v11111070 id = cord-003053-5sucu1cg author = Yang, Liu title = Risk factors for infectious complications of ANCA-associated vasculitis: a cohort study date = 2018-06-14 keywords = AAV; ANCA; infection summary = In this study, we retrospectively analysed the epidemiological and clinical characteristics of Chinese patients with ANCA-associated vasculitis and discussed major infection episodes occurring during immunosuppressive therapy in a single centre. All clinical and laboratory data were collected retrospectively at diagnosis and during the follow-up period, including the patients'' age, gender, medical history, routine blood analysis, 24-h urine protein excretion, urinary sediment red blood cell count, serum albumin and serum creatinine (SCr), liver enzymes, immunoglobulin and T lymphocyte counts, serum ANCAs, lung involvement, Birmingham Vasculitis Activity Score (BVAS) [16] , the usage of immunosuppressive agents, methlyprednisone pulse therapy, plasma exchange, and adverse events including major infection. Single factor analysis revealed that risk factors for complicated infection in patients with AAV included age, smoking, pulmonary involvement, hemoglobulin, albumin, SCr level, CD4 + T cell count, BVAS, and immunosuppressive therapy with MMF, CYC and TW. doi = 10.1186/s12882-018-0933-2 id = cord-323668-evzzfu04 author = Yin, Zhixin title = lncRNA expression signatures in response to enterovirus 71 infection date = 2013-01-11 keywords = EV71; RNA; infection summary = To identify the cellular long noncoding RNAs (lncRNAs) involved in the host response to EV71 infection, we performed comprehensive lncRNA and mRNA profiling in EV71-infected rhabdomyosarcoma cells through microarray. These findings suggest the widespread differential expression of lncRNAs in response to 0006 virus infection and their involvement in regulating the host response, including innate immunity [19] . Further analysis resulted in 313 differentially expressed lncRNAs and nearby coding gene pairs (distance < 300 kb) for each comparison between mock-and EV71-infected cells (Table S7) . In the present study, using Arraystar microarray analysis, we identified the differentially expressed lncRNAs in RD cells after EV71 infection, together with nearby differentially expressed mRNA pairs. They also observed the down-regulation of several genes encoding proteins involved in host RNA synthesis in EV71-infected SF268 cells. [19] performed functional enrichment analysis on the nearby protein-coding genes of differentially expressed lncRNAs in SARS-CoV infected mouse. doi = 10.1016/j.bbrc.2012.11.101 id = cord-325172-a8ntxnmm author = Yip, Ming Shum title = Antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus date = 2014-05-06 keywords = ADE; SARS; cell; infection; spike summary = More recently, we demonstrated that anti-Spike antibody potentiates infection of both monocytic and lymphoid immune cell lines, not only by SARS-CoVpp but also by replication-competent SARS-coronavirus [16] , thus providing evidence for a novel and versatile mechanism by which SARS-CoV can enter into target cells that do not express the conventional ACE2 virus receptor and are otherwise refractory to the virus. Finally, we have provided evidence that the intracellular signaling motifbut not the IgG binding motifof the FcγR is the key molecular determinant for triggering ADE of SARS-CoVpp. Our findings conclusively demonstrate that anti-spike serum promotes internalization of SARS-CoV by human macrophages. All the endodomain-truncated constructs (FcγRIIA-H.ΔIC, FcγRIIA-R.ΔIC and FcγRIIB.ΔIC, corresponding to constructs 2, 6, 11 respectively) were not susceptible to ADE of infection, indicating that binding of anti-Spike IgG-SARS-CoVpp immune complexes was not sufficient to mediate entry and that the signaling-competent endodomain was required. doi = 10.1186/1743-422x-11-82 id = cord-307813-elom30nx author = Yip, Tsz-Fung title = Advancements in Host-Based Interventions for Influenza Treatment date = 2018-07-10 keywords = IAV; IFN; TNF; cell; infection; influenza; viral; virus summary = Besides controlling virus replication, potential targets for drug development include controlling virus-induced host immune responses such as the recently suggested involvement of innate lymphoid cells and NADPH oxidases in influenza virus pathogenesis and immune cell metabolism. Besides controlling virus replication, potential targets for drug development include controlling virus-induced host immune responses such as the recently suggested involvement of innate lymphoid cells and NADPH oxidases in influenza virus pathogenesis and immune cell metabolism. A recent study using RNAi also demonstrated that cholesterol homeostasis can be regulated via acid phosphatase 2 (ACP2)-mediated Niemann-Pick C2 activity and impaired the membrane fusion of IAV and influenza B virus (IBV) (52) , further suggesting the importance of controlling cholesterol homeostasis in the release of viral genome to cytoplasm. Furthermore, FPR2 antagonists have been described to possess antiviral activity against not only IAV but also IBV infection (111) , promoting the idea that antagonizing FPR2 to suppress Raf/MEK/ERK signaling cascade could potentially be a novel approach for the treatment of a broad spectrum of influenza viruses. doi = 10.3389/fimmu.2018.01547 id = cord-327888-4g3x5dje author = Yuan, C. T. title = Perceptions of hand hygiene practices in China date = 2009-02-28 keywords = hand; hygiene; infection summary = Our study suggests that a pivotal issue for improving hand hygiene practice in China is providing infection control departments adequate attention, priority, and influence within the hospital, with a clear line of authority to senior management. Findings from this study suggest that the primary challenges in improving hand hygiene in China are the limited authority of infection control departments in hospitals, the lack of essential resources, and the ineffective use of data monitoring and feedback to hospital staff. Elevating the place of infection control on the hospital organisational chart and changing the paradigm of surveillance to continuous monitoring and effective data feedback are central to achieving improved hand hygiene practices and quality of care. Elevating the place of infection control on the hospital organisational chart and changing the paradigm of surveillance to continuous monitoring and effective data feedback are central to achieving improved hand hygiene practices and quality of care. doi = 10.1016/j.jhin.2008.09.017 id = cord-016990-ot1wi3xi author = Zaki, Sherif R. title = Viral Infections of the Lung date = 2008 keywords = CMV; Fig; HSV; Nipah; SARS; cell; human; infection; pneumonia; respiratory; virus summary = 105, [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] The pathology is more prominent in larger bronchi, and inflammation may vary in intensity in individual patients, Viral inclusions cannot be identified by light microscopy (Fig, 11 .8D), Secondary bacterial infections with organisms such as Streptococcus pneumoniae (group A streptococcus [GAS]), Staphylococcus aureus, and Haemophilus influenzae may occur as a complication in about 50% to 75% of fatal cases and make it difficult to recognize the pathologic changes associated with the primary viral infec-445 tion ,190,192,193 The histopathologic features in other organs may include myocarditis, cerebral edema, rhabdomyolysis, and hemophagocytosis (Figs, 11.8H and 11.9E,F), Immunohistochemistry and ISH assays demonstrate that viral antigens and nucleic acids are usually sparse and are primarily seen in the bronchioepithelial cells of larger bronchioles (Figs. doi = 10.1007/978-0-387-68792-6_11 id = cord-324301-bzrh2fni author = Zambon, Maria title = Influenza, respiratory syncytial virus and SARS date = 2005-05-01 keywords = RSV; infection; influenza summary = The recent emergence of the SARS coronavirus in the human population in 2003, with an ensuing global epidemic affecting more than 8000 individuals with a case fatality of about 10%, underlines the fact that respiratory viral infections of humans may originate in animals, and that many different influenza A viruses also occur naturally in animal reservoirs, representing a constant threat of zoonotic infections of humans and ensuing global pandemics. About 30-50% of acute LRTIs are viral in origin; of these, influenza and respiratory syncytial virus (RSV) are associated with the greatest disease burden in humans. About 30-50% of acute LRTIs are viral in origin; of these, influenza and respiratory syncytial virus (RSV) are associated with the greatest disease burden in humans. Seasonal illness, epidemics and pandemics -influenza viruses circulating in humans (A H1N1, H3N2, B and C) cause respiratory tract disease. doi = 10.1383/medc.33.5.130.64960 id = cord-027860-s97hdhh6 author = Zeimet, Anthony title = Infectious Diseases date = 2020-06-22 keywords = HBV; HCV; HIV; HSV; PPD; SOR; States; UTI; United; antibiotic; cause; infection; patient; treatment summary = Although common upper respiratory bacterial pathogens, such as Moraxella (Branhamella) catarrhalis, Streptococcus pneumoniae, and Haemophilus influenzae, may be isolated from patients with acute bronchitis, their relevance is questionable because these bacteria can be present in the respiratory tract of healthy individuals. In the treatment of Bordetella pertussis, early administration of a macrolide antibiotic and patient isolation will likely decrease coughing paroxysms and limit spread of disease (Braman, 2006) (SOR: A). Risk factors for Pseudomonas infection include severe structural lung disease (e.g., bronchiectasis) and recent antibiotic therapy, health care-associated exposures or stay in hospital (especially in the ICU). Patients who present with severe infection or whose infection is progressing despite empiric antibiotic therapy should be treated more aggressively; the treatment strategy should be based on results of appropriate Gram stain, culture, and drug susceptibility analysis. For suspected MRSA skin infections, oral treatment options include trimethoprim-sulfamethoxazole, clindamycin, and doxycycline of purulent material when performing incision and drainage in the event that the patient fails to improve and antibiotic coverage becomes necessary. doi = 10.1016/b978-1-4377-1160-8.10016-8 id = cord-305457-t7qw1oy2 author = Zhang, Youhong title = Baculovirus transit through insect cell membranes: A mechanistic approach date = 2020-09-21 keywords = cell; infection; virion summary = The production of recombinant proteins in BEVS is greatly affected by the characteristics and kinetics of the viral infection process-including, for instance, the multiplicity of infection (MOI), time of infection (TOI), cell cycle, cell line selection, and culture state [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] , but the early events of viral infection, such as the attachment of virions to their receptors and the kinetics of their entry into the cell, are still not entirely understood. Mathematical modeling and simulations may serve as effective predictive tools in pursuing this goal [8, [14] [15] 27] , as they allow dynamical simulation of the process and estimating variables that are hard to measure directly, such as the rate of virion internalization after its attachment to the cell. doi = 10.1016/j.ces.2020.115727 id = cord-011438-imbpgsub author = Zhang, Yun title = Host–Virus Interaction: How Host Cells Defend against Influenza A Virus Infection date = 2020-03-29 keywords = IAV; IFN; Influenza; infection; virus summary = Upon IAV infection, host innate immune system is triggered and activated to restrict virus replication and clear pathogens. In the current review, we present a general description on recent work regarding different host cells and molecules facilitating antiviral defenses against IAV infection and how IAVs antagonize host immune responses. Host innate immunity, including phagocytic cells, interferons (IFNs), proinflammatory cytokines, etc., applies multiple mechanisms in defending IAV infection [105] . Influenza A virus nucleoprotein induces apoptosis in human airway epithelial cells: Implications of a novel interaction between nucleoprotein and host protein Clusterin Antiviral response elicited against avian influenza virus infection following activation of toll-like receptor (TLR)7 signaling pathway is attributable to interleukin (IL)-1β production The human interferon-induced MxA protein inhibits early stages of influenza A virus infection by retaining the incoming viral genome in the cytoplasm Cell death regulation during influenza A virus infection by matrix (M1) protein: A model of viral control over the cellular survival pathway doi = 10.3390/v12040376 id = cord-257392-u6jy6w1m author = Zhao, Yanfeng title = Proteomic analysis of primary duck hepatocytes infected with duck hepatitis B virus date = 2010-06-07 keywords = DHBV; infection; protein summary = In this report, we explored global changes in cellular protein expression in DHBV infected PDHs by two-dimension gel electrophoresis (2-DE) combined with MALDI-TOF/TOF tandem mass spectrometry (MS/MS). The down-regulated expression of beta-actin and annexin A2 was confirmed by Western blot analysis, and potential roles of some differentially expressed proteins in the virus-infected cells have been discussed. CONCLUSIONS: Differentially expressed proteins of DHBV infected PDHs revealed by 2-DE, are involved in carbohydrate metabolism, amino acid metabolism, stress responses and cytoskeleton processes etc, providing the insight to understanding of interactions between hepadnavirus and hepatocytes and molecular mechanisms of hepadnavirus pathogenesis. Expression levels of annexin A2, beta-actin, Hsp70, destrin, and lamin A were validated by Western blot analysis to confirm the dynamic alterations of protein expression during DHBV infection. In summary, the present study explored global changes in cellular protein expression of hepadnavirus infection by 2-DE analysis, using a natural DHBV-PDHs infection system. doi = 10.1186/1477-5956-8-28 id = cord-340028-6oicmeam author = Zhavoronkov, Alex title = Geroprotective and senoremediative strategies to reduce the comorbidity, infection rates, severity, and lethality in gerophilic and gerolavic infections date = 2020-03-31 keywords = COVID-19; NAD; SARS; age; clinical; infection summary = Here we compare the expected benefit of treatments for elderly populations (60 years and older) that are currently in development, including standard preventative strategies such as vaccines and antivirals targeting SARS-CoV-2, and the potential added benefit of speculative geroprotective strategies such as rapalogs, NAD+ boosters, senolytics, and stem cell treatment. People >60 years of age with chronic medical conditions, such as type 2 diabetes or cardiovascular disease, direct immunosuppression from HIV, posttransplant or biologic treatment, pregnant individuals, or those with BMI>40, are believed to be at higher risk for influenza infection due to a weakened immune response [31] . As discussed in this paper, small clinical studies have shown that several geroprotective and senoremediative interventions, such as treatment with AGING sirolimus and rapalogs, can induce immunopotentiation, increase resistance to infection, and reduce disease severity in the elderly, without severe side effects. doi = 10.18632/aging.102988 id = cord-350715-x92g6bnk author = Zheng, Yutong title = Analysis of the application value of serum antibody detection for staging of COVID‐19 infection date = 2020-07-23 keywords = acid; infection summary = We conducted a retrospective analysis to explore the clinical characteristics of COVID‐19 patients at different infection stages and to characterize the characteristics of specific serum antibodies at each stage. In this study we explored the clinical value of specific serum antibody detection in COVID-19 patients. According to the biological characteristics of nucleic acids and specific serum IgM and IgG antibodies, the 723 COVID-19 cases were classified into infection stages ( Table 1) . (2) the convalescent stage in which the nucleic acid turned negative, the IgM antibody disappeared and the IgG antibody began to appear but was still below the detection limit. IgM+IgG-May be in the acute stage of infection, consider the possibility of false negative nucleic acid. Consider the possible active stage of infection with false negative nucleic acid. doi = 10.1002/jmv.26330 id = cord-325613-oamw57gx author = Zhong, Peipei title = Clinical characteristics of the lower respiratory tract infection caused by a single infection or coinfection of the human parainfluenza virus in children date = 2019-05-29 keywords = HPIV; infection summary = title: Clinical characteristics of the lower respiratory tract infection caused by a single infection or coinfection of the human parainfluenza virus in children BACKGROUND: Human parainfluenza virus (HPIV), usually combined with other pathogens, causes lower respiratory tract infection (LRTI) in children. This study aimed to investigate the viral and atypical bacterial etiology of LRTI in children and compare the clinical characteristics of HPIV single infection with those of coinfection. Therefore, this study aimed to investigate the viral and HPIV-positive patients were divided into three groups based on the test results: HPIV single infection, coinfection with other viruses, and coinfection with atypical bacteria. Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children. Clinical characteristics of the lower respiratory tract infection caused by a single infection or coinfection of the human parainfluenza virus in children doi = 10.1002/jmv.25499 id = cord-304088-xkg0ylz8 author = Zhu, Han title = Cardiovascular Complications in Patients with COVID-19: Consequences of Viral Toxicities and Host Immune Response date = 2020-04-21 keywords = ACE2; COVID-19; SARS; infection summary = While limited data exist, potential mechanisms of cardiac injury include direct viral entry through the angiotensin-converting enzyme 2 (ACE2) receptor and toxicity in host cells, hypoxia-related myocyte injury, and immune-mediated cytokine release syndrome. The increased incidence of cardiac injury among those with severe systemic inflammatory response syndromes (SIRS) and shock in the setting of COVID-19 also highlights an important relationship between the immune response to the virus and the cardiovascular system. Of note, SARS-CoV-2 also contains an RNA-dependent RNA polymerase which is the target of the anti-viral agent remdesivir, currently being studied randomized clinical trials for use against COVID-19 disease [26] . A recent retrospective, multi-center study of 150 patients confirmed that inflammatory markers, including elevated ferritin (mean 1297.6 ng/ml in non-survivors vs 614.0 ng/ml in survivors, p < 0.001) and IL-6 (p < 0.0001) were associated with more severe COVID-19 infection, suggesting that systemic inflammation may be a significant driver of multi-organ damage [18, 64] . doi = 10.1007/s11886-020-01292-3 id = cord-264916-c4n0kyog author = Zimmerman, Keith title = Natural protection of ocular surface from viral infections – a hypothesis date = 2020-07-09 keywords = SARS; infection; ocular; virus summary = doi = 10.1016/j.mehy.2020.110082 id = cord-320548-oigyut2k author = Zumla, Alimuddin title = Emerging novel and antimicrobial-resistant respiratory tract infections: new drug development and therapeutic options date = 2014-09-01 keywords = H1N1; MERS; infection; infl; treatment; uenza summary = 19 In patients admitted to hospital with severe infl uenza A H7N9 infection, reduction of viral load after treatment with oseltamivir correlated with improved outcome, whereas the emergence of virus resistant to neuraminidase inhibitors that harbours an Arg292Lys substitution is associated with poor outcomes and poor response to oseltamivir and peramivir. Several observational studies show that systemic corticosteroids given for 2009 pandemic infl uenza A H1N1-associated viral pneumonia increased the risk of mortality and morbidity (eg, secondary infections), especially when there was a delay in initiation, or absence of, eff ective antiviral therapy. Several observational studies have shown that systemic corticosteroids given for 2009 pandemic infl uenza A H1N1-asssociated viral pneumonia or acute respiratory distress syndrome increased the risk of mortality and morbidity (eg, secondary bacterial or fungal infections), especially if there is delay or lack of eff ective antiviral therapy. doi = 10.1016/s1473-3099(14)70828-x id = cord-308816-nux087gc author = de Graaf, Dirk C title = A review of the importance of cryptosporidiosis in farm animals date = 2000-01-10 keywords = calf; cryptosporidiosis; cryptosporidium; diarrhoea; infection summary = Cryptosporidium parvum is considered to be an important agent in the aetiology of the neonatal diarrhoea syndrome of calves, lambs and goat kids, causing considerable direct and indirect economic losses. In the following years methods to free the infective oocysts from other contaminating pathogens became available, which permitted the experimental demonstration that Cryptosporidium was capable of causing clinical diarrhoea in calves [27, 28] . Since then, Cryptosporidium has been attributed an increasingly important role in neonatal diarrhoea syndrome in this domestic species and is currently associated with high morbidity rates and, depending on environmental conditions and the presence of other intestinal pathogens, mortality [46, 75, 76] . Cryptosporidium parvum is the most commonly found enteropathogen during the ®rst weeks of the life of calves, lambs and goat kids and is considered to be an important agent in the aetiology of the neonatal diarrhoea syndrome. doi = 10.1016/s0020-7519(99)00076-4 id = cord-001521-l36f1gp7 author = nan title = Oral and Poster Manuscripts date = 2011-04-08 keywords = A(H1N1; CDC; China; ELISA; H1N1; H3N2; H5N1; H9N2; HAI; Health; Hong; ILI; Influenza; Kong; LAIV; MDCK; PB1-F2; PCR; RNA; TCID; USA; cell; figure; infection; ns1; pandemic; table; virus summary = The IC 50 values determined in functional NI assays provide valuable information for detection of resistant viruses, but should not be used to draw direct correlations with drug concentrations needed to inhibit virus replication in the infected human host, as clinical data to support such inferences are inadequate. • Standardized reagents and protocols • Choice of detection technology • Simple instrumentation requirements • High sensitivity for use with low virus concentrations • Compatibility with batch-mode processing and largescale assay throughput • Broad specificity of influenza detection • Flexibility in assay format • Additional NA assay applications -cell-based viral assays, screening for new NIs, detection of NA from other organisms Functional neuraminidase inhibition assays enable detection of any resistance mutation and are extremely important in conjunction with sequence-based screening assays for global monitoring of virus isolates for NI resistance mutations, including known and new mutations. Such new assays need to include methods to measure local antibodies and virus-specific lymphocytes, especially in the case of live attenuated influenza vaccines, because of their potential to induce such broad-based immune responses. doi = 10.1111/j.1750-2659.2011.00209.x id = cord-004586-i8tacj63 author = nan title = Empfehlung zur Prävention nosokomialer Infektionen bei neonatologischen Intensivpflegepatienten mit einem Geburtsgewicht unter 1500 g: Mitteilung der Kommission für Krankenhaushygiene und Infektionsprävention beim Robert Koch-Institut date = 2007-10-05 keywords = Frühgeborenen; Kategorie; Staphylococcus; care; die; infection; intensive; neonatal; outbreak; unit summary = F Die Reinigung der Innenseite des belegten Inkubators kann mit Wasser von Trinkwasserqualität erfolgen (siehe oben), wobei für jeden Inkubator (patientenbezogen) ein frisches, keimarmes Tuch verwendet werden muss (Kategorie IB). Transmission of community-associated methicillin-resistant Staphylococcus aureus from breast milk in the neonatal intensive care unit Outbreak of nosocomial sepsis and pneumonia in a newborn intensive care unit by multiresistant extended-spectrum beta-lactamase-producing Klebsiella pneumoniae: high impact on mortality Nosocomial Klebsiella pneumoniae infection: clinical and hygienic measures in a neonatal intensive care unit Nosocomial outbreak of gentamicin-resistant Klebsiella pneumoniae in a neonatal intensive care unit controlled by a change in antibiotic policy Coronavirus-related nosocomial viral respiratory infections in a neonatal and paediatric intensive care unit: a prospective study Eradication of methicillin-resistant Staphylococcus aureus from a neonatal intensive care unit by active surveillance and aggressive infection control measures Clinical and molecular biological analysis of a nosocomial outbreak of vancomycin-resistant enterococci in a neonatal intensive care unit doi = 10.1007/s00103-007-0337-0 id = cord-004675-n8mlxe7p author = nan title = 2019 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date = 2019-02-26 keywords = ADA; CD3; CD4; CD8; CGD; CMV; CVID; EBV; HLH; HSCT; IFN; IVIG; PCR; PID; PIDD; RAG1; SCID; TCL; age; case; cell; disease; dna; dock8; infection; mutation; patient; report; result; year summary = However, the mean infusion rate per site was similar between patients aged <18 years ( XMEN disease (X-linked Immunodeficency with Magnesium defect, Epstein-Barr virus infection and Neoplasia) is a primary immune deficiency caused by mutations in MAGT1 and characterized by chronic infection with Epstein-Barr virus (EBV), EBV-driven lymphoma, CD4 T-cell lymphopenia, and dysgammaglobulinemia. We present the case of a 1-year old Hispanic infant with a pathogenic variant in MAGT1 gene that clinically manifested with early Pneumocystis jirovecii and cytomegalovirus (CMV) interstitial pneumonia, and EBV chronic infection with good response to intravenous immunoglobulins supplementation without hematopoietic stem cell transplantation or gene therapy. Chief, Laboratory of Clinical Immunology and Microbiology, IDGS, DIR, NIAID, NIH, Bethesda, MD, USA Hypomorphic Recombination Activating Gene 1 (RAG1) mutations result in residual T-and B-cell development in both humans and mice and have been found in patients presenting with delayed-onset combined immune deficiency with granulomas and/or autoimmunity (CID-G/AI). doi = 10.1007/s10875-019-00597-5 id = cord-006466-e1phpqes author = nan title = 2018 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date = 2018-04-23 keywords = ADA; Background; CD3; CD4; CD8; CGD; CMV; CTLA4; CVID; EBV; GVHD; HSCT; IGRT; IVIG; Immunology; Introduction; PID; SCID; TREC; cell; conclusion; disease; dna; hct; infection; method; mutation; patient; result summary = Whole exome sequencing revealed a heterozygous mutation, previously reported (c.1425+1G>T) Conclusions: In summary, this report emphasizes the suspicion of a combined immunodeficiency in the presence of multiple abscesses by Mycoplasma, the usefulness of rDNA 16s in order to achieve proper Objectives: We describe a 15-year-old male patient with novel heterozygous mutation of EP300 gene; his first manifestations were initially characterized by infections, cytopenia and hypogammaglobulinemia suggesting a Common Variable Immunodeficiency (CVID), but later on, persisting lymphopenia was suggestive of a combined immunodeficiency. Conclusions: Close monitoring of immune function in early life for patients with CHH and CID as well as the availability of suitable donors assists in determining management, including HSCT Introduction/Background: Leukocyte Adhesion Deficiency (LAD) represents a group of distinct inherited disorders, which inhibit the normal extravasation of neutrophils and their recruitment to sites of infection or inflammation. doi = 10.1007/s10875-018-0485-z id = cord-009664-kb9fnbgy author = nan title = Oral presentations date = 2014-12-24 keywords = CDI; CTX; Candida; ESBL; Europe; MRSA; PCR; PFGE; PVL; clinical; dna; gene; gram; infection; isolate; method; objective; patient; resistance; result; strain; study summary = Because of the conflicting reports and lack of published data from paediatric patients, we sought to assess possible MIC change over time and to compare results generated by using different methodologies including Etest, agar dilution, and broth microdilution (MicroScan) methods. Recently, in vitro and in vivo studies have shown that NO plays a key role in the eradication of the leishmania parasite Objective: To determine whether a NO donor patch (developed by electrospinning technique) is as effective as meglumine antimoniate in the treatment of CL while causing less adverse events Methods: A double-blind, randomised, placebo-controlled clinical trial was conducted with 178 patients diagnosed with CL in Santander, Colombia, South-America. To follow the development and spread of the resistance among these strains is difficult, as antibiotic susceptibility testing of clinically relevant anaerobes in different routine laboratories in Europe is less and less frequently carried out due to the fact, that clinicians treat many presumed anaerobic infections empirically. doi = 10.1111/j.1469-0691.2009.02857.x id = cord-014712-5u4e00q6 author = nan title = Selected Abstracts from the 100th J Project Meeting, Antalya, Turkey, March 12-14, 2014 date = 2014-08-02 keywords = BCG; CGD; CVID; HSCT; Hospital; IVIG; Immunology; PID; SCID; University; case; cell; deficiency; disease; dna; infection; patient; year summary = Ege University Faculty of Medicine, Dept of Pediatric Immunology, Izmir, Turkey Ig class switch recombination deficiencies are rare PIDs (1:500,000 births) with normal or elevated serum IgM and low IgG, IgA and IgE levels, defective or normal somatic hypermutation, defective T/B cooperation (50%), intrinsic B cell defect (50%), susceptibility to bacterial infections begining from the first year of age (impaired B cell immunity) and lack of germinal centres in secondary lymphoid organs. Great North Children''s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, and Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK Even following the introduction of biologic disease modifying antirheumatic drugs (DMARDs), a small number of children suffering from severe, refractory autoimmune (AI), rheumatic and/or autoinflammatory disorders will not get into clinical remission (CR) and will potentially further suffer from multiple side-effects of combined and long-term immunosuppressive and anti-inflammatory therapies, in particular severe infections (Marodi L, Casanova JL. doi = 10.1007/s10875-014-0065-9 id = cord-014965-efmozngq author = nan title = Infectious diseases other than CMV (1st Section) date = 2001-06-11 keywords = ELISA; PCR; SCT; infection; patient summary = To evaluate the influence of the helicobacter pylori (h.p.) infection on gastrointestinal complications after high-dose chemotherapy and stem cell transplantation (STX) we tested 114 patients (54 female, 60 male) by the 13C-urea breath test prior to initiation of conditioning therapy. 26 immunocompromised patients (15-70 y, median 44; 17 leukemia, 7 myeloma, 2 lymphoma) received 32 courses of ABLC at the median daily dose of 2 mg/kg rounded off to the nearest vial size (range, 1.3-2.7 mg/kg) after autologous (n=7) or allogeneic (n=8) stem cell transplantation or chemotherapy (n=17). Seven of the 12 allogeneic transplanted patients with at least one positive PCR-result had a VZV-disease. All (n=2) of the autologous transplanted patients with a positive PCR-result developed a VZV-disease. Background: Severe acute graft-versus-host-disease (aGvHD) of the gut is still a major complication after allogeneic stem-cell transplantation (SCT) as response rates to treatment (tx) of intestinal GvHD (iGvHD) are lower than those observed for GvHD of the skin. doi = 10.1038/sj.bmt.1702942 id = cord-017184-1ewi3dka author = nan title = Primary Immunodeficiencies date = 2008 keywords = BMT; CD4; CD8; Fig; HLA; IFN; SCID; Table; cell; child; deficiency; infection; patient summary = In this disease, microorganism phagocytosis by polymorphonuclear (PMN) leukocytes appears annulled, and the patient is subject to severe infections supported by capsular bacteria: the deficiency, described in association with severe and recurrent infantile infections [175, 485, 487] , depends on the lack of mannose-binding lectin (MBL) [487] , its Primary Immunodeficiencies a possible atopy dependence on IgA underproduction rather than on IgE hyperproduction ( Fig. 4.1 ): in children with levels of IgA at the minimum normal level, and followed from birth until the age of 18-23 months, a greater severity of atopic manifestations and an increased cumulative incidence of asthma, AD and otitis media with effusion (OME) were observed compared to controls. doi = 10.1007/978-3-540-33395-1_22 id = cord-019490-m1cuuehi author = nan title = Abstracts cont. date = 2015-12-28 keywords = AUC; CIP; ESBL; Enterobacteriaceae; GISA; GRN; MIC; MIC90; MRSA; NCCLS; PCR; PFGE; Staphylococcus; gram; infection; isolate; method; objective; patient; resistance; result; strain; study; test summary = Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control. doi = 10.1111/j.1469-0691.2005.clm_1134_02.x id = cord-019964-9leljj8j author = nan title = Recent research in infectious disease date = 2005-01-22 keywords = CD4; HAART; HIV; MRSA; infection; patient summary = These patients had significantly longer hospital stays (mean, 27.2 versus 19.4 days) and a higher risk of having Clostridium difficile-associated diarrhoea (8.3% versus 1.9%), infection-related death (23.3% versus 13.6%), and all-cause mortality (30.8% versus 19.4%) than patients whose empiric therapy was appropriate. Data were available from three endocervical swabs and a urine specimen collected from each of 1,412 women and tested by three different NAATs. Results from all three assays were used equally in a rotating fashion to define the infected-patient gold standard. Multiple different infectedpatient gold standards for estimating swab and urine specimen sensitivity and specificity for one NAAT method were created by varying the number and combinations of swab and urine comparator results with two different NAATs, The effect of changing the infected-patient gold standard definition was determined by constructing receiver-operator-like curves with calculated sensitivities and specificities for each test. LOUIS (MD Consult)-Some studies suggest antiretroviral therapy is a risk factor for gynecomastia in men with human immunodeficiency virus (HIV) infection. doi = 10.1016/j.jinf.2004.11.005 id = cord-019977-kj0eaw6v author = nan title = Neonatal bacterial infection: A changing scene? date = 2005-04-14 keywords = gram; infection summary = This time period coincided with the entry of paediatricians to newborn nurseries on a much larger scale than hitherto, with an increase in the use of antimicrobial drugs, and with the introduction of apparatus such as incubators, resuscitation and suction units, the humidification parts of which often harboured Gramnegative organisms, all capable of causing lethal disease in the infant. During the half century under review, mortality from neonatal bacteraemia fell from 9o per cent in the period I928-I933, ~ to z6 per cent in I966-I978 ;6 and the proportion of isolates recorded as recovered in the first 48 hours of life (early infections) increased from IO per cent to 57 per cent of the total respectively. 16 Clostridium difficile and its toxin may be present in the stools of many well newborn babies, but this organism has not been implicated in the genesis of neonatal necrotising enterocolitis as it has been with pseudomembranous colitis. doi = 10.1016/s0163-4453(82)91569-9 id = cord-020010-q58x6xb0 author = nan title = 19th ICAR Abstracts: date = 2006-03-13 keywords = CDV; Department; HCMV; HCV; HIV; HIV-1; Institute; REP; RNA; Research; ST-246; Sciences; USA; University; Virology; WNV; activity; antiviral; cell; compound; dna; infection; virus summary = doi = 10.1016/j.antiviral.2006.02.001 id = cord-022501-9wnmdvg5 author = nan title = P1460 – P1884 date = 2015-12-28 keywords = 16S; CDAD; CFU; ELISA; ESBL; Enterococcus; GRN; ICU; MIC; MRSA; PCR; Staphylococcus; TGC; dna; gram; infection; isolate; method; objective; patient; resistance; result; strain; study summary = Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing). doi = 10.1111/j.1470-9465.2006.12_4_1431.x id = cord-022555-a7ie82fs author = nan title = Digestive System, Liver, and Abdominal Cavity date = 2011-12-05 keywords = EPI; FIP; Giardia; IBD; cat; cause; clinical; diarrhea; disease; feline; figure; gastrointestinal; infection; intestinal; liver; pancreatic; sign; small; treatment summary = One study found that, of cats investigated for gastrointestinal disease, 9 of 33 cats (27%) had no pathology recognized proximal to the jejunum (i.e., the effective length of diagnostic endoscopes would have precluded diagnosis), and other organs were affected in 9 of 10 cats with inflammatory bowel diseases and 7 of 8 cats with intestinal small cell lymphoma. 60, 64 Quantification of serum cobalamin levels is recommended in cats with clinical signs of small bowel diarrhea, ones suspected to have an infiltrative disease of the small intestine (inflammatory bowel disease or gastrointestinal lymphoma), or ones with pancreatic dysfunction. Survey radiographs may be normal in cats with esophagitis and strictures, but are useful to rule out other causes for the clinical signs, such as a foreign body, or to detect related problems, such as aspiration pneumonia. 8, 29 Other non-neoplastic causes reported for gastric or gastroduodenal ulceration in cats include parasites (e.g., Ollulanus tricuspis, Toxocara cati, Aonchotheca putorii, Gnathostoma spp.), bacterial infections, toxins, inflammatory bowel disease, and foreign bodies. doi = 10.1016/b978-1-4377-0660-4.00023-5 id = cord-022583-9lmudxrh author = nan title = Antimikrobielle und antiinfektiöse Maßnahmen date = 2016-07-29 keywords = Anforderungen; Antibiotika; Antibiotikaprophylaxe; Anwendung; Aufbereitung; CHX; Desinfektion; Desinfektionsmittel; Eingriffen; Einsatz; Erreger; Haut; Infektionen; Kramer; Patienten; Prophylaxe; Risiko; SSI; Sterilisation; Studien; Tab; Verfahren; Wirksamkeit; Wirkung; auch; auf; bei; der; des; die; durch; eine; für; infection; ist; mit; nicht; oder; pap; rate; sind; und; von; werden; wird; zur summary = Wenn auch je nach eingesetzter Technologie und chemisch-physikalischen Möglichkeiten der beteiligten Komponenten (Material, Wirkstoff, Imprägnierungsverfahren) eine Wirksamkeit von Objekten durch Beschichtung oder Imprägnierung mit antimikrobiellen Stoffen gegen bestimmte Mikroorganismenspezies erzielt werden kann, ist die Bezeichnung "antimikrobiell" weder mit einer spezifischen Infektionsprävention verknüpft, noch liegen ihr einheitliche Kriterien zugrunde. Die immense sozioökonomische Bedeutung der sogenannten "Surgical Site Infections" (SSI) wird anhand bundesweit erhobener epidemiologischer Daten deutlich: In der nationalen Prävalenzstudie (2011) konnte zwar gezeigt werden, dass in Deutschland die Rate an nosokomialen Infektionen (NI) mit 3,4 % im europäischen Vergleich stabil niedrig ist (in Vergleichsstudien international zwischen 6,1 % und 9,3 %), letztlich aber doch bei 18 Mio. stationär behandelten Patienten im Jahr dementsprechend 400 000 NI auftreten. Die SSI-Rate wird für geschlossene Frakturen mit 1-5 % angegeben und erreicht bei offenen Frakturen abhängig vom Ausmaß der Gewebezerstörung eine Häufigkeit von bis zu 43 %. doi = 10.1016/b978-3-437-22312-9.00002-0 id = cord-023143-fcno330z author = nan title = Molecular aspects of viral immunity date = 2004-02-19 keywords = CD4; CD8; CNS; CTL; HIV; HIV-1; HLA; IFN; LCMV; MHC; cell; infection; mouse; protein; response; viral; virus summary = Based on a variety of experimental evidence, it is clear that demyelination induced in SJUJ mice by infection with the BeAn strain of TMEV is a Thl-mediated event: (a) disease induction is suppressed in T cell-deprived mice and by in vivo treatment with anti-I-A and anti-CD4 antibodies; (b) disease susceptibility correlates temporally with the development of TMEV-specific, MHC-class Il-restricted DTH responses and with a predominance of anti-viral lgG2a antibody; (c) activated (Le., lL-2RC) T cells infiltrating the CNS are exclusively of the CD4+ phenotype, and (d) proinflammatory cytokines (IFNq and TNF-p) are predominantly produced in the CNS. These results have important implications for a possible viral trigger in MS as they indicate that chronic demyelination in TMEV-infected mice is initiated in the absence of demonstrable neuroantigen-specific autoimmune responses and are consistent with a model wherein early myelin damage is mediated via primarily by mononuclear phagocytes recruited to the CNS and activated by pro-inflammatory cytokines produced by TMEV-specific Thl cells. doi = 10.1002/jcb.240591009 id = cord-024651-578c9ut5 author = nan title = 2020 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date = 2020-05-11 keywords = ALPS; Abstract; Background; CD4; CD8; CGD; CVID; Case; EBV; GOF; HIES; HLH; HSCT; Hospital; IFN; IVIG; Immunology; National; PID; Report; SCID; STAT3; Text; cell; disease; figure; infection; introduction; mutation; patient; result summary = Abstract/Case Report Text Introduction: Mutations in the gene encoding signal transducer and activator of transcription 3 (STAT3) cause autosomal dominant hyperimmunoglobulin E syndrome (AD-HIES) characterized by recurrent skin and sinopulmonary infections, atopic dermatitis, and elevated serum immunoglobulin E (IgE) levels. Objective: The purpose of this study is to increase awareness and improve diagnosis of primary immune deficiency (PID) in the heterogenous group of patients with autoimmune cytopenia (AIC) by identifying clinical characteristics and laboratory biomarkers that distinguish those with underlying PID, disease activity and guide mechanism-based targeted therapy. 7 Chief, Laboratory of Clinical Immunology and Microbiology/National Institute of Allergy and Infectious Diseases, NIAID/National Institutes of Health, NIH Abstract/Case Report Text We have previously used the artificial thymic organoid (ATO) system, based on the 3D aggregation and culture of a delta-like canonical Notch ligand 4-expressing stromal cell line (MS5-Dll4) with CD34+ cells, to study T cell differentiation from CD34+ cells obtained from patients carrying defects that are intrinsic to hematopoietic cells (RAG1-2, AK2, IL2RG) or that affect thymus development (DiGeorge syndrome). doi = 10.1007/s10875-020-00764-z id = cord-286574-t9z2ynt5 author = nan title = Speaker presentations date = 2017-09-30 keywords = AMR; Asia; HIV; Korea; MRSA; SFTS; antibiotic; infection; patient; resistance summary = doi = 10.1016/s0924-8579(17)30340-0 id = cord-333024-1yrmun3z author = von Lilienfeld-Toal, Marie title = Community acquired respiratory virus infections in cancer patients—Guideline on diagnosis and management by the Infectious Diseases Working Party of the German Society for haematology and Medical Oncology date = 2016-09-25 keywords = CRV; LRTI; RSV; infection; patient summary = METHODS: A panel of 18 clinicians from the Infectious Diseases Working Party of the German Society for Haematology and Medical Oncology have convened to assess the available literature and provide recommendations on the management of CRV infections including influenza, respiratory syncytial virus, parainfluenza virus, human metapneumovirus and adenovirus. Usually, orthomyxoviridae (influenza A, B and C), paramyxoviridae (including parainfluenza 1e4 [PIV], respiratory syncytial virus A and B [RSV] , and human metapneumovirus [hMPV]), coronaviridae, picornaviridae (including >100 different serotypes of rhinovirus and enterovirus), adenoviridae, polyomavirus type 1 and bocavirus are regarded as potential causes of CRV infection. Despite some reports with a good outcome without treatment, we believe the available evidence justifies a recommendation for the use of ribavirin in cancer patients with RSV infection (B II, Table 4 ). An outbreak of respiratory syncytial virus infection in hematopoietic stem cell transplantation outpatients: good outcome without specific antiviral treatment doi = 10.1016/j.ejca.2016.08.015