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?' ---------------------------------------------------------- 61 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 7297 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 4 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 60 pathogen 8 virus 8 human 8 dna 8 disease 7 host 4 detection 4 cell 4 Salmonella 4 PCR 3 water 3 vaccine 3 transmission 3 specie 3 respiratory 3 protein 3 plant 3 infection 3 immune 3 genomic 3 Ebola 2 virulence 2 study 2 response 2 patient 2 indoor 2 genome 2 animal 2 air 2 SARS 2 O157 2 Fig 2 Escherichia 1 wetland 1 wastewater 1 syndrome 1 surveillance 1 spillover 1 spa 1 soil 1 site 1 simulation 1 sequencing 1 selection 1 sample 1 riboflavin 1 result 1 reservoir 1 removal 1 receptor Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 4924 pathogen 1915 disease 1748 virus 1509 host 1386 infection 1096 study 1084 cell 995 vaccine 851 transmission 797 plant 784 response 745 system 744 protein 723 datum 720 animal 702 risk 646 health 640 population 618 analysis 606 bacteria 603 specie 595 gene 579 time 574 case 571 water 569 % 568 human 567 method 536 effect 533 detection 527 genome 515 factor 515 approach 501 model 482 patient 476 exposure 467 outbreak 458 number 458 example 443 level 442 use 421 treatment 415 condition 403 sample 393 result 393 development 393 activity 388 type 381 agent 378 rate Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1790 al 1478 et 1023 . 222 Salmonella 207 SARS 183 E. 170 Fig 169 HIV 168 Health 163 Escherichia 161 PCR 158 RNA 141 Ebola 128 O157 112 der 110 L. 107 T 103 ME 102 von 102 Yersinia 99 B 97 CFS 94 A 92 Africa 91 S. 91 DNA 89 Europe 87 United 87 Disease 84 World 84 C 83 H7 82 MDD 78 Table 77 Water 77 States 75 • 75 Y. 75 Pathogen 74 NGS 68 Study 64 Mycobacterium 63 M. 62 US 60 CFD 58 Listeria 58 CoV 57 Zika 55 Global 55 Control Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 878 it 689 we 529 they 111 them 97 i 36 itself 35 us 29 themselves 29 one 20 you 12 he 6 me 4 she 3 il-1-β 2 oneself 1 yourself 1 ourselves 1 mine 1 https://thebest.shinyapps.io/seasonalpathogen/.authors 1 himself 1 him 1 her 1 cord-257802-vgizgq2y 1 bbg100 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 12332 be 2869 have 1475 use 876 include 623 increase 579 base 524 provide 521 associate 504 identify 498 cause 488 show 451 emerge 445 do 401 develop 358 reduce 348 detect 338 require 321 find 320 produce 286 infect 278 give 277 know 262 follow 255 lead 252 report 251 make 249 involve 246 induce 244 consider 243 result 225 occur 222 suggest 214 compare 213 describe 203 demonstrate 203 affect 202 transmit 202 control 199 relate 198 represent 187 need 187 allow 183 improve 182 bind 181 predict 179 target 175 estimate 174 reveal 173 contain 171 determine Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1349 human 1135 not 1038 such 948 also 840 high 738 infectious 724 more 722 other 665 immune 650 - 578 respiratory 543 viral 535 well 528 most 524 however 522 bacterial 514 new 485 specific 430 many 418 different 397 environmental 396 low 387 only 387 genetic 375 clinical 370 microbial 357 airborne 327 public 326 as 322 important 321 several 321 large 298 molecular 283 pathogenic 280 first 263 recent 247 multiple 247 major 247 likely 245 novel 241 e.g. 240 potential 236 common 229 early 224 often 221 zoonotic 221 effective 220 non 217 available 215 natural Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 166 most 58 Most 57 least 41 good 34 high 31 great 15 large 11 strong 8 low 7 postharv 7 late 7 early 7 close 6 simple 6 big 4 old 4 common 3 small 2 preharv 2 poor 2 fast 2 deadly 2 broad 2 bad 1 wide 1 slight 1 safe 1 rich 1 mighty 1 long 1 few 1 -I Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 362 most 29 least 27 well 2 hard 1 slowest 1 festgestellt 1 -just Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 3 doi.org 2 www.who.int 2 www 1 www3 1 www.vereduslabs 1 www.ridom.de 1 www.r-project.org 1 www.niaid.nih.gov 1 www.mammalparasites.org 1 www.istm.org 1 www.inforsense.com 1 www.healthmap.org 1 www.ejustice.just.fgov.be 1 www.ebi.ac.uk 1 www.dnastar.com 1 www.boldsystems 1 www.aphl.org 1 www.akonni 1 wishart.biology 1 thebest.shinyapps.io 1 taverna.sf.net 1 sites.google.com 1 sedac.ciesin.columbia.edu 1 pubs.acs.org 1 pfgrc.tigr.org 1 gmod.org 1 gel.ahabs.wisc.edu 1 galaxy.psu.edu 1 chromas-lite.software.informer.com Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 2 http://www 1 http://www3 1 http://www.who.int/mediacentre/ 1 http://www.who.int/csr/disease/plague/Plague-map-2016.pdf 1 http://www.vereduslabs 1 http://www.ridom.de/traceedit/ 1 http://www.r-project.org/ 1 http://www.niaid.nih.gov/dmid/genomes 1 http://www.mammalparasites.org/ 1 http://www.istm.org/geosentinel/main.html 1 http://www.inforsense.com 1 http://www.healthmap.org/en 1 http://www.ejustice.just.fgov.be/mopdf/2014/05/16_1 1 http://www.ebi.ac.uk/interpro/ 1 http://www.dnastar.com/products/lasergene.php 1 http://www.boldsystems 1 http://www.aphl.org/fellowships/pages/bioinformatics.aspx 1 http://www.akonni 1 http://wishart.biology 1 http://thebest.shinyapps.io/seasonalpathogen/.Authors' 1 http://taverna.sf.net 1 http://sites.google.com/site/ 1 http://sedac.ciesin.columbia.edu/gpw/ 1 http://pubs.acs.org/doi/10.1021/acs.est.0c02421 1 http://pfgrc.tigr.org 1 http://gmod.org 1 http://gel.ahabs.wisc.edu/mauve/download 1 http://galaxy.psu.edu 1 http://doi.org/10.1016/j.fm.2018.01.003 1 http://doi.org/10.1007/s40806-020-00256-8 1 http://doi.org/10 1 http://chromas-lite.software.informer.com/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 mahesh@dso.org.sg 1 f.balloux@ucl.ac.uk Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 8 pathogens are not 5 vaccines do not 4 pathogens are likely 4 pathogens are more 4 pathogens is not 3 diseases are infections 3 diseases is still 3 infection does not 3 pathogen does not 3 pathogen is not 3 pathogens are often 3 pathogens infecting humans 3 vaccines are currently 3 virus infected cells 3 viruses are not 3 viruses having high 2 bacteria are very 2 bacteria do not 2 bacteria using phage 2 cells are also 2 cells do not 2 cells provide molecular 2 data are available 2 disease is endemic 2 disease is often 2 diseases are more 2 diseases is not 2 diseases is very 2 host is often 2 host is only 2 humans are best 2 humans is often 2 humans is rarely 2 infection is not 2 infections are not 2 infections were common 2 pathogen was slightly 2 pathogens are able 2 pathogens are capable 2 pathogens are critically 2 pathogens are disproportionately 2 pathogens are mainly 2 pathogens are most 2 pathogens are organisms 2 pathogens cause diseases 2 pathogens causing diseases 2 pathogens do not 2 pathogens have high 2 pathogens including bacteria 2 pathogens were also Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 pathogen is not present 2 pathogens are not strongly 2 pathogens were not sufficiently 1 % had no pathogens 1 animals are not always 1 animals is not sufficient 1 cases had no pathogen 1 cases showed no evidence 1 cells have no need 1 diseases are not limited 1 diseases is not new 1 diseases is not simple 1 hosts do not yet 1 human are not important 1 infection does not typically 1 infections are not applicable 1 infections do not typically 1 infections have no available 1 pathogen does not necessarily 1 pathogen is not well 1 pathogens are not highly 1 pathogens are not likely 1 pathogens are not new 1 pathogens are not shortterm 1 pathogens are not unusual 1 pathogens is not as 1 pathogens is not complete 1 pathogens is not only 1 pathogens is not typically 1 plant causing no visible 1 population has not only 1 response including not only 1 response is not always 1 response is not sufficient 1 responses are not usually 1 species are no longer 1 species is not well 1 studies are not ethical 1 studies reported no appreciable 1 studies reported no significant 1 study are not yet 1 study found no difference 1 study was not medical 1 transmissions is not always 1 vaccines are not currently 1 vaccines do not currently 1 vaccines do not totally 1 vaccines is not always 1 viruses are not capable 1 viruses do not normally A rudimentary bibliography -------------------------- id = cord-297203-f3f31h4r author = Afrough, B. title = Emerging viruses and current strategies for vaccine intervention date = 2019-04-16 keywords = Ebola; dna; pathogen; vaccine; virus summary = While classic approaches to vaccine development are still amenable to emerging viruses, the application of molecular techniques in virology has profoundly influenced our understanding of virus biology, and vaccination methods based on replicating, attenuated and non‐replicating virus vector approaches have become useful vaccine platforms. Modified vaccinia virus Ankara (MVA) is licensed as a third-generation vaccinia type vaccine against smallpox and serves as a potent vector system for the development of new candidate vaccines against a range of infectious diseases, including those caused by emerging pathogens. Additionally, MVA elicits a strong immunological response against a range of other orthopoxviruses (OPXVs) (including Variola), and vaccines based on this platform can be considered as providing added value, as human immunity to OPXVs is low (after the cessation of the smallpox vaccination campaign) opening a gap for OPXV emergence, as evidenced by the recent occurrence of monkeypox virus in West Africa and onward cross boarder transmissions [39, 40] . doi = 10.1111/cei.13295 id = cord-301767-1jv20em8 author = Alegbeleye, Oluwadara Oluwaseun title = Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review date = 2018-02-03 keywords = Escherichia; O157; Salmonella; Typhimurium; coli; pathogen; produce; soil; water summary = Primarily, pathogens may contaminate produce ''on-field'' via various routes including; atmospheric deposition, uptake from contaminated soils and groundwater (Harris et al., 2003; Lynch et al., 2009; Mei Soon et al., 2012) , use of raw (or poorly treated) manure and compost, exposure to contaminated water (irrigation or flooding), transfer by insects, or by fecal contamination generated by livestock or wild Table 1 The most commonly implicated etiological agents in fresh produce borne illnesses (Brackett, 1994; Buck et al., 2003; Heaton and Jones, 2008; Jung et al., 2014; Callej on et al., 2015) . Epidemiological investigations of food poisoning outbreaks, experimental studies examining pathogen contamination of fruits and vegetables as well as observations of increased incidence of disease in areas practicing wastewater irrigation with little or no wastewater treatment indicate that contaminated irrigation water might indeed be a source of foodborne pathogens on fresh produce (Norman and Kabler, 1953; Hern andez et al., 1997; Steele and Odumeru, 2004) . doi = 10.1016/j.fm.2018.01.003 id = cord-345583-3auz7gi6 author = Aliakbar Ahovan, Zahra title = Bacteriophage Based Biosensors: Trends, Outcomes and Challenges date = 2020-03-11 keywords = biosensor; detection; pathogen; phage summary = Consequently, the bacteriophage used like bio-probe in biosensor devises offer several advantages, such as (1) specificity to host bacteria, consequently efficient bacteria screening [15] , (2) easy to generate mass quantities of progeny phages, due to their short replication time, (3) ability to tolerate critical conditions, such as organic solvents and large range of pH and temperature [16] . Consequently, the bacteriophage used like bio-probe in biosensor devises offer several advantages, such as (1) specificity to host bacteria, consequently efficient bacteria screening [15] , (2) easy to generate mass quantities of progeny phages, due to their short replication time, (3) ability to tolerate critical conditions, such as organic solvents and large range of pH and temperature [16] . In phage-based biosensors, bacteriophage is Nanomaterials 2020, 10, 501 8 of 16 attached to the sensor surface, and consequently, it can detect the pathogen in the sample [38] . doi = 10.3390/nano10030501 id = cord-009394-3jeexu27 author = Amalaradjou, Mary Anne Roshni title = Modern Approaches in Probiotics Research to Control Foodborne Pathogens date = 2012-09-30 keywords = Escherichia; Listeria; O157; Salmonella; cell; lactobacillus; pathogen; probiotic summary = Although probiotics have been demonstrated to be effective in antagonizing foodborne pathogens, challenges exist in the characterization and elucidation of underlying molecular mechanisms of action and in the development of potential delivery strategies that could maintain the viability and functionality of the probiotic in the target organ. Those include lactose metabolism and food digestion, production of antimicrobial peptides and control of enteric infections, antimycotic effects, anticarcinogenic properties, immunologic enhancement, enhancement of short-chain fatty acid (SCFA) production, antiatherogenic and cholesterol-lowering attributes, regulatory role in allergy (Thomas et al., 2011) , protection against vaginal or urinary tract infections, increased nutritional value, maintenance of epithelial integrity and barrier, stimulation of repair mechanism in cells, and maintenance and reestablishment of a well-balanced indigenous intestinal and respiratory microbial communities. doi = 10.1016/b978-0-12-394598-3.00005-8 id = cord-312161-egwo19oc author = Aw, Tiong Gim title = Detection of pathogens in water: from phylochips to qPCR to pyrosequencing date = 2011-12-05 keywords = PCR; detection; pathogen; water summary = Microbial water quality monitoring has undergone tremendous transition in recent years, with novel molecular tools beginning to offer rapid, high-throughput, sensitive and specific detection of a wide spectrum of microbial pathogens that challenge traditional culture-based techniques. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ''molecular revolution'' are at present emerging rapidly as tools of pathogen detection and discovery. The limitations in detecting and identifying pathogens directly from environmental water samples by culture or microscopy can now be addressed by integrating concentration techniques with molecular tools to provide sensitive, specific and quantitative data on any pathogens of interest. Pyrosequencing technology is revolutionizing the study of microbial ecology as well as direct metagenomic detection Detection of pathogens in water Aw and Rose 425 High levels of several classes of resistance genes in bacterial communities exposed to antibiotic were identified. doi = 10.1016/j.copbio.2011.11.016 id = cord-307803-rlvk6bcx author = Balloux, Francois title = Q&A: What are pathogens, and what have they done to and for us? date = 2017-10-19 keywords = disease; host; human; pathogen summary = Infectious diseases have historically represented the most common cause of death in humans until recently, exceeding by far the toll taken by wars or famines. Conversely, Yersinia pestis, another intracellular obligate bacterium and the agent of plague, has a natural life cycle involving alternating infections of rodents and fleas, but can infect essentially any mammalian host. Apart from a few putative ancestral pathogens, including Helicobacter pylori [15] , that might have co-speciated with their human host, the infectious diseases afflicting us were acquired through host jumps from other wild or domesticated animal hosts or sometimes from the wider environment. We might also speculate that the evolutionary potential and high genetic diversity of most pathogens limits our ability to detect protective variants in the human genome, particularly so if these were only effective against a subset of lineages within a pathogenic species. doi = 10.1186/s12915-017-0433-z id = cord-341672-k5pa3n2l author = Barros‐Rodríguez, Adoración title = Units for vigilance of emerging diseases based on wastewater treatment plants (WWTP‐UVED) date = 2020-07-27 keywords = pathogen; wastewater summary = Here, we propose the development of Units for Vigilance of Emerging Diseases based on the screening of pathogens released to wastewater treatment plants to follow the spread of the infectious agent to determine the location of infected people. bs_bs_banner Today, we have enough culture-independent techniques for the extraction and massive sequencing of nucleic acids (e.g. Illumina or Ion Torrent) and through specific amplification of pathogen genes by qPCR, to monitor the unusual presence of pathogens at any population''s WWTPs. We therefore suggest the creation of Units for Vigilance of Emerging Diseases (UVEDs) based on the continuous analysis of pathogens in WWTPs in potentially affected areas and especially during epidemics and pandemics. Therefore, we believe that the creation of such UVEDs for WWTPs under the coordination of a central service to analyse countrywide nucleic acid samples would greatly benefit our society and should be implemented by future legislation similarly to the analysis of other pathogens in the treated wastewater. doi = 10.1111/1751-7915.13635 id = cord-348819-gq7lp931 author = Becker, Daniel J. title = Dynamic and integrative approaches to understanding pathogen spillover date = 2019-08-12 keywords = host; pathogen; reservoir; spillover summary = The second set of manuscripts focuses on in-depth analysis of each of the factors affecting cross-species transmission: infection dynamics in reservoir hosts, pathogen survival in the environment, recipient host exposure, dose -response relationships and establishment of infection in recipient hosts. The authors show how modelling cross-species transmission as a percolation process, in which pathogens move from infected reservoirs to recipient hosts along a graph representing various spillover pathways [18, 19] , reveals first principles for how such datasets will behave and how common statistical tools can produce misleading inferences and poor predictions. This inclusive approach to confronting epidemiological models with longitudinal data in poorly understood reservoir host systems holds promise for elucidating spatio-temporal risk of pathogen spillover. Through several case studies (e.g. Lyme disease [63] , Hendra virus [64] , Plasmodium knowlesi [65] ), the authors further demonstrate how ecologically focused research has facilitated predicting spillover of particular pathogens in space and time and facilitated design of intervention strategies. doi = 10.1098/rstb.2019.0014 id = cord-288170-i01pdngb author = Böhm, R. title = Chapter 9 Pathogenic agents date = 2007-12-31 keywords = Salmonella; material; pathogen; process; product summary = Nevertheless, inadequate technical design and improper management of the composting process may result in survival and transmission of the pathogens involved; therefore, only treatment in a validated process under steady supervision will lead to a hygienically safe product. The capability of a process to inactivate pathogens causing risks that depend on the raw material cannot be judged simply by analysis of presence or absence of indicators (bacterial, viral, fungal, or parasitic) in the final product. If either the thermophilic process itself or if an additional thermal treatment shall provide the inactivation of pathogens belonging to the indicated level of thermoand chemo-resistance, representative test-organisms must be exposed in a similar matrix as that being treated in a suitable test-body in a defined validation experiment. It could be demonstrated that if dealing with a moderate epidemiological risk, e.g., given in composting source-separated biowastes, Salmonella senftenberg W775 will cover the most relevant viral pathogens causing notifiable diseases in farm animals and which may be present in low concentrations in the raw material. doi = 10.1016/s1478-7482(07)80012-1 id = cord-258139-x4js9vqe author = Callan, Robert J title = Biosecurity and bovine respiratory disease date = 2005-03-04 keywords = BRDC; BVDV; disease; pathogen; respiratory summary = Alternatively, when the causative pathogens are endemic in a population and individual susceptibility is dependent on numerous interrelated factors, the management of animal resistance and risk factors may be proportionally more important for disease prevention than biosecurity practices. The authors emphasize five areas of biosecurity management that should be more rigorously applied for the reduction of respiratory disease prevalence in cattle, including (1) strategic vaccination, (2) calf biosecurity, (3) housing ventilation, (4) commingling and animal contact, and (5) bovine viral diarrhea virus control. Airborne pathogen concentration is a function of many factors, including animal type, housing system, stocking rate, bedding, humidity, dust particle density and size, and finally, elimination through ventilation. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical. doi = 10.1016/s0749-0720(02)00004-x id = cord-337219-d81v8b4j author = Cheong, Chang Heon title = Case Study of Airborne Pathogen Dispersion Patterns in Emergency Departments with Different Ventilation and Partition Conditions date = 2018-03-13 keywords = ACH; case; pathogen summary = Simulation cases for analysis were established, as shown in Table 3 , to conduct a case study that analyzed the range of airborne pathogen dispersion according to the location of diffusers in the bed area of the ED, the ventilation rate, and the installation of partitions between beds. Simulation cases for analysis were established, as shown in Table 3 , to conduct a case study that analyzed the range of airborne pathogen dispersion according to the location of diffusers in the bed area of the ED, the ventilation rate, and the installation of partitions between beds. Simulation cases for analysis were established, as shown in Table 3 , to conduct a case study that analyzed the range of airborne pathogen dispersion according to the location of diffusers in the bed area of the ED, the ventilation rate, and the installation of partitions between beds. doi = 10.3390/ijerph15030510 id = cord-279376-0x4zrfw3 author = Cherrie, Mark P. C. title = Pathogen seasonality and links with weather in England and Wales: a big data time series analysis date = 2018-08-28 keywords = England; Salmonella; Wales; pathogen summary = We aimed to systematically document the seasonality of several human infectious disease pathogens in England and Wales, highlighting those organisms that appear weather-sensitive and therefore may be influenced by climate change in the future. A systematic approach to the analysis of the potential seasonality of common pathogen serotypes and their associations with multiple weather variables is required to help narrow the focus on candidate pathogens in addition to those that have been studied in depth previously. The aim of the analysis was to use several data mining techniques to identify pathogens that display a seasonal component, and describe their associations with meteorological factors as an aid to future analytical work (including forecasting) and public health planning. In this large database of infectious diseases in England and Wales, we have provided an analysis of the seasonality of common pathogens and their correlation with meteorological data. doi = 10.1186/s12889-018-5931-6 id = cord-316999-712rit8h author = Chinchio, Eleonora title = Invasive alien species and disease risk: An open challenge in public and animal health date = 2020-10-22 keywords = IAS; pathogen; specie summary = To this aim, we provide here an overview of how animal IAS may affect local disease dynamics both directly and indirectly, i.e., acting as pathogen hosts or disrupting the recipient ecosystem structure, through real-case examples from the ecological literature, and, in the last paragraph, we propose future initiatives aimed at improving our capacity for targeted actions toward the IAS most likely to threaten human and animal health, calling for an increased involvement of people working in the fields of animal and public health in a new invasion epidemiology field. IAS may host pathogens that are absent in the area of release and cause their establishment and subsequent spillover to local species, possibly resulting in an increase of disease risk for humans, domestic animals, and native wildlife. doi = 10.1371/journal.ppat.1008922 id = cord-269607-xh1hu3k4 author = Dhir, Bhupinder title = Effective control of waterborne pathogens by aquatic plants date = 2020-02-14 keywords = pathogen; removal; wetland summary = Both dispersed growth and attached growth biological wastewater treatment systems assist in removal of pathogens but require high hydraulic retention time (HRT) (average time water molecules stay in the system) and continuous feeding of organic matter and nutrients. Biofilms present in the plant roots are believed to supply a more effective substrate for removal of bacteria through various methods such as mechanical filtration, sedimentation, adsorption, die-off, predation, and antibiotic excretion (Soto et al., 1999; Karathanasis et al., 2003) Removal (83%e94%) of pathogen especially coliform and enteric bacteria by surface flow constructed wetlands has been reported earlier (Perkins and Hunter, 2000) . Predation is another mechanism that plays an important role in the removal of bacteria, protozoan (oocysts), and fecal coliforms from wastewater in constructed wetlands (Mandi et al., 1993; Green et al., 1997) . High removal efficiency 2 to 4 log 10 (99% to 100%) of pathogens particularly bacteria, viruses, protozoa (cysts), and helminths (eggs) from wastewater has been noted in vegetated constructed wetlands. doi = 10.1016/b978-0-12-818783-8.00017-7 id = cord-308089-q2w9fb0i author = Ewald, Paul W. title = Evolution of virulence date = 2005-03-01 keywords = disease; pathogen; transmission; virulence summary = This new germ theory is emphasizing how environments and human activities influence the characteristics of infectious agents and the broader role of infection as a cause of chronic diseases. The association between vector-borne transmission and virulence explains why diseases such as malaria, yellow fever, dengue, sleeping sickness, and visceral leishmaniasis are so severe, whereas most of the respiratory-tract pathogens of humans are relatively benign. Evolutionary management of the virulence of vector-borne diseases requires interventions that elevate the immobilization of hosts more costly to the infecting pathogens. Although sexually transmitted pathogens are molded by natural selection to be benign over the short run, this long-term persistence within hosts raises the possibility of long-term damage, even though there is low probability of severe damage during any small period of time during the first years of infection. The theoretical framework for understanding the evolution of virulence of sexually transmitted pathogens provides clues about which infectious agents are the most likely causes of these illnesses. doi = 10.1016/s0891-5520(03)00099-0 id = cord-339886-th1da1bb author = Gardy, Jennifer L. title = Towards a genomics-informed, real-time, global pathogen surveillance system date = 2017-11-13 keywords = Ebola; Health; Zika; datum; genomic; pathogen; surveillance summary = Given that outbreaks of emerging infectious diseases (EIDs) most often occur in settings with minimal laboratory capacity, where routine culture and bench-top sequencing are simply not feasible, the need for a portable diagnostic platform capable of in situ clinical metagenomics and outbreak surveillance is evident. Portable genome sequencing technology and digital epidemiology platforms form the foundation for both real-time pathogen and disease surveillance systems and outbreak response efforts, all of which exist within the One Health context, in which surveillance, outbreak detection and response span the human, animal and environmental health domains. For example, genome sequences from a raccoon-associated variant of rabies virus (RRV), when paired with fine-scale geographic information and data from Canadian and US wildlife rabies vaccination programmes, demonstrated that multiple cross-border incursions were responsible for the expansion of RRV into Canada and sustained outbreaks in several provinces 70 ; this finding led to renewed concern about and action against rabies on the part of public health authorities 71 . doi = 10.1038/nrg.2017.88 id = cord-322120-wtu04r2j author = Goddard, Frederick G. B. title = Measuring Environmental Exposure to Enteric Pathogens in Low-Income Settings: Review and Recommendations of an Interdisciplinary Working Group date = 2020-08-19 keywords = Contamination; Rural; Sanitation; Water; enteric; exposure; fecal; measure; pathogen summary = Systematic reviews of water, sanitation, and hygiene (WaSH) evaluations, conducted to identify the health effects of interventions designed to reduce enteric pathogen exposure, have generally found improved WaSH to be protective against diarrhea, 24 soil-transmitted helminthiasis, 25 and malnutrition. A systematic review of the effects of sanitation interventions on fecal−oral transmission pathways identified the following approaches used: enteric pathogens or indicator bacteria in environmental samples (drinking water, hands, sentinel toys, food, household and latrine surfaces, and soil); the presence or abundance of flies; and observations of human and animal feces. 68 There are a number of factors to consider when measuring enteric pathogen prevalence in the environment, including environmental sampling strategies, the use of indicators as proxies for enteric pathogens, differentiating between human and animal sources of contamination, detection limits, and selecting which specific pathogens to target. doi = 10.1021/acs.est.0c02421 id = cord-211735-qqm4fbor author = Gulec, Fatih title = Mobile Human Ad Hoc Networks: A Communication Engineering Viewpoint on Interhuman Airborne Pathogen Transmission date = 2020-11-02 keywords = Fig; human; pathogen summary = To this end, we propose a communication engineering approach that melts different disciplines such as epidemiology, biology, medicine, and fluid dynamics in the same pot to model airborne pathogen transmission among humans. The aim of this article is to present a unified framework using communication engineering, and to highlight future research directions for modeling the spread of infectious diseases among humans through airborne pathogen transmission. By utilizing this analogy, we propose an approach to modeling interhuman airborne pathogen transmission with communication engineering perspective where mobile humans forming a group are considered as a mobile human ad hoc network (MoHANET). In this section, we present a framework with communication engineering perspective to model the spread of infectious diseases through airborne pathogen transmission. In the networking layer, the details of the MoHANET architecture are presented in order to model the spread of infectious diseases in a large scale (km) within the communication engineering framework as shown in Fig. 2. doi = nan id = cord-299790-vciposnk author = Ho, Zheng Jie Marc title = Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness date = 2015-06-09 keywords = mono; pathogen summary = Although there were observed differences in mean proportions of body temperature, nasal symptoms, sore throat, body aches and joint pains between viral and bacterial mono-pathogens, there were few differences between distinct dual-pathogen pairs and their respective mono-pathogen counterparts. For instance, one study showed that 15.3% of ambulatory patients with influenza-like illness had two viruses detected, 6 and another found that in 28.2% of children with community-acquired pneumonia, the illness was due to mixed viral-bacterial infections. 7 Others also previously described respiratory viral 8, 9 and bacterial co-infections 10, 11 in various settings, although most focus on specific pathogen combinations, especially of the synergism between influenza and Streptococcus pneumoniae (S. Mean proportion for dual infections with nasal symptoms lay in between at 0.748, statistically different from both viral (P = 0.002) and bacterial (P < 0.001) mono-pathogen levels. doi = 10.1111/irv.12312 id = cord-295469-5an7836u author = Ijaz, M. Khalid title = Generic aspects of the airborne spread of human pathogens indoors and emerging air decontamination technologies date = 2016-09-02 keywords = air; airborne; indoor; pathogen summary = The following groups of human pathogens are covered because of their known or potential airborne spread: vegetative bacteria (staphylococci and legionellae), fungi (Aspergillus, Penicillium, and Cladosporium spp and Stachybotrys chartarum), enteric viruses (noroand rotaviruses), respiratory viruses (influenza and coronaviruses), mycobacteria (tuberculous and nontuberculous), and bacterial spore formers (Clostridium difficile and Bacillus anthracis). The following groups of human pathogens are covered because of their known or potential airborne spread: vegetative bacteria (staphylococci and legionellae), fungi (Aspergillus, Penicillium, and Cladosporium spp and Stachybotrys chartarum), enteric viruses (noro-and rotaviruses), respiratory viruses (influenza and coronaviruses), mycobacteria (tuberculous and nontuberculous), and bacterial spore formers (Clostridium difficile and Bacillus anthracis). 71 Based on our considerable experience in the study of airborne human pathogens, 13, 25, 39, 43, 72 we have built an aerobiology chamber (Fig 2) designed to meet the requirements of the EPA guidelines and have used this to study the effects that a variety of air decontamination technologies have on the airborne survival and inactivation of vegetative bacteria, viruses (bacteriophage), and bacterial spore-formers (Sattar et al, unpublished data) . doi = 10.1016/j.ajic.2016.06.008 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-294585-dl5v9p50 author = Klein, H. G. title = Pathogen‐reduction methods: advantages and limits date = 2009-02-13 keywords = blood; pathogen; plasma; virus summary = However, because blood contains numerous labile proteins and fragile cells, and because there is a wide array of potentially infectious agents, no single method of pathogen-inactivation will likely preserve all blood components, yet effectively remove all viruses, bacteria, spores, protozoa and prions. Riboflavin/ultraviolet light treatment has been evaluated in preclinical studies and found to result in reduction of infectivity by many pathogens including west Nile virus, intracellular HIV, bacteria and protozoa. Therapeutic efficacy and safety of platelets treated with a photochemical process for pathogen inactivation: the SPRINT Trial Clinical safety of platelets photochemically treated with amotosalen HCl and ultraviolet A light for pathogen inactivation: the SPRINT trial Fresh frozen plasma prepared with amotosalen HCl (S-59) photochemical pathogen inactivation: transfusion of patients with congenital coagulation factor deficiencies Therapeutic efficacy and safety of red blood cells treated with a chemical process (S-303) for pathogen inactivation: a Phase III clinical trial in cardiac surgery patients doi = 10.1111/j.1751-2824.2009.01224.x id = cord-345799-i0j6tctr author = Koon, Kassi title = Co-detection of Pandemic (H1N1) 2009 Virus and Other Respiratory Pathogens date = 2010-12-17 keywords = pathogen summary = From May through October 2009, a total of 10,624 clinical samples from 23 US states were screened for multiple respiratory pathogen gene targets. The main fi nding of this large-scale clinical study was the co-detection of multiple pathogens with the pandemic infl uenza virus strain. Pandemic (H1N1) 2009 virus and multiple other pathogens are often detected during autopsy (1,2), indicating that co-infection may play a major role in the disease process. Our fi ndings suggest that multiplex screening for respiratory pathogens is useful for providing rapid surveillance information to inform physicians who would otherwise base decisions on clinical signs and symptoms alone. Electronic reporting of empirical laboratory respiratory pathogen detection provided by a Clinical Laboratory Improvement Amendments-approved laboratory can greatly enhance surveillance data collection (10) . Development and evaluation of a novel multiplex PCR technology for molecular differential detection of bacterial respiratory disease pathogens doi = 10.3201/eid1612.091697 id = cord-348841-qxkmngyk author = Kozakiewicz, Christopher P. title = Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics date = 2018-07-28 keywords = genetic; host; landscape; pathogen; study summary = Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. We excluded reviews (n = 15), meeting abstracts (n = 1), purely methods-based papers (n = 6) and articles that identified as or mentioned landscape genetics but did not sufficiently incorporate landscape factors or genetic data into the study (n = 32), studies that referred to any of our pathogen-related search terms without it being a primary motivation for the study (n = 21), and studies that used words like "transmit" or "parasite" outside of the context of infectious agents (such as the transmission of behaviours) (n = 6). Spatial variation in pathogen prevalence or infection risk can be represented in much the same way as any landscape variable , making spatial data relating to presence of an infectious agent well-suited for incorporation into host landscape genetic models. doi = 10.1111/eva.12678 id = cord-263484-afcgqjwq author = Ladner, Jason T. title = Precision epidemiology for infectious disease control date = 2019-02-06 keywords = Ebola; genomic; pathogen; virus summary = With sufficient sampling, relevant metadata (such as location and date) and an appropriate statistical framework, pathogen genomes can reveal patterns of epidemic transmission at a fine-scale resolution, thus enabling the design of targeted interventions that are more precise than those based on traditional epidemiological data alone. Through near-real-time genome sequencing and public data deposition of clinical, environmental, and foodrelated bacterial isolates, this network is streamlining the process of recognizing, investigating, and reducing the impact of foodborne disease outbreaks 42, 43 . This includes changes to research practice regarding the benefits for rapid and open sharing of data and results as well as a focus on building capacity for sequencing and analysis within public health agencies and the regions most severely impacted by infectious disease 57, 58 . One important approach to accelerating responses in the future is to build genome sequencing and analysis capabilities within public health agencies and hospitals as well as in developing countries disproportionately impacted by infectious disease outbreaks. doi = 10.1038/s41591-019-0345-2 id = cord-255351-vp19ydce author = Lanata, Claudio F. title = Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review date = 2013-09-04 keywords = child; pathogen; study summary = We present the results of a systematic literature review of studies of diarrhea etiology in hospitalized children and use these results to estimate the global burden of diarrhea mortality by pathogen for children under 5 years of age for 2011. From 22 643 citations identified in the electronic search, 1 003 articles were selected for further evaluation (Fig. 1) ; 840 articles were excluded because they had one or more of the exclusion criteria (About 35% because they were not longitudinal studies or inappropriate laboratory methods were used, 31% because no data was given for children ,5 years of age, 23% for studies that lasted less than 12 months of duration, and the rest because data were reported after rotavirus vaccine introduction, duplicate publications or reporting results on a pathogen not included in our list). doi = 10.1371/journal.pone.0072788 id = cord-260679-tm1s6wvj author = Lim, Wei Shen title = Pneumonia—Overview date = 2020-05-20 keywords = CAP; infection; pathogen; patient; pneumonia summary = Within the grouping of hospital-acquired pneumonia (HAP), further distinction is usually made according to whether the patient was on an intensive care unit, or intubated (ventilator-acquired pneumonia (VAP)) at the time of infection (Torres et al., 2017; Kalil et al., 2016) . A definitive diagnosis of pneumonia comprises four aspects: (i) symptoms and signs of a respiratory tract infection, (ii) radiological changes, (iii) identification of a putative pathogen and (iv) a treatment response, or clinical course, consistent with pneumonia. A meta-analysis of individual participant data from 26 RCTs found that PCT-directed treatment in the management of acute respiratory tract infections (of varying types and severity, including CAP and HAP) was associated with a reduction in antibiotic exposure (5.0 vs. The respiratory pathogens commonly implicated in patients with CAP remain important aetiological agents in all other types of pneumonia, including HAP and pneumonia in the immunocompromised host (Table 8 ). doi = 10.1016/b978-0-12-801238-3.11636-8 id = cord-255230-i6q73bhs author = Makhanova, Anastasia title = Capturing Fluctuations in Pathogen Avoidance: the Situational Pathogen Avoidance Scale date = 2020-08-13 keywords = Study; avoidance; pathogen; spa summary = Across six studies, we demonstrate the reliability and validity of the SPA scale, show that the scale is influenced by situational activation of pathogen avoidance motives, and demonstrate that it mediates the association between pathogen avoidance motives (both chronic and situational) and social biases against obese and foreign targets. Study 1 is a preliminary study intended to establish the reliability and factor structure of the scale and examine predictive validity by assessing the association between the SPA scale and aversive reactions toward an obese target (a heuristic cue associated with pathogen avoidance). Study 1 provides initial evidence for the reliability and the one-factor structure of the SPA scale and examined whether SPA scores were associated with bias against a target linked to heuristic pathogen threat (an obese target). Additionally, individuals who reported higher (relative to lower) SPA scores also reported more aversive reactions toward an obese target, consistent with prior research linking pathogen avoidance to prejudice against targets heuristically associated with illness. doi = 10.1007/s40806-020-00256-8 id = cord-310439-z0bxsjug author = Martin, R. R. title = Pathogen-Tested Planting Material date = 2014-12-31 keywords = certification; pathogen; plant; program; virus summary = Buffer zone An area surrounding or adjacent to an area for production of plants in a certification scheme designed to minimize the probability of spread of the target pathogens, pollen, or seed into or out of the block, to meet phytosanitary or other control measures as defined in a certification standard. Many certification programs are based on a published standard that defines site selection and preparation, isolation distances from plants of the same species and other vegetation, number of inspections, record keeping on plant traceability so that tracebacks or traceforwards can be done if a problem should arise, a pest and disease management plan, records of all pest management activities, the conditions and protocols to be followed during plant or seed production, and types and amount of testing that needs to be done at each level in the propagation cycle. doi = 10.1016/b978-0-444-52512-3.00173-x id = cord-329149-1giy1fow author = Martinez-Martin, Nadia title = Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions date = 2017-02-22 keywords = cell; host; human; interaction; pathogen; protein; receptor summary = Despite SPR and related methods offering higher sensitivity for detection of transient Biochemical and MS PDGFR identified as a high affinity cell surface receptor for the CMV gHgLgO protein complex [21] Herpes simplex viruses (HSVs) Biophysical Secreted and plasma membrane-expressed glycoprotein G targets a specific set of human chemokines with high affinity [22] Human immunodeficiency virus type 1 (HIV) Despite the undoubted importance of the biochemical and biophysical approaches to the study of host-pathogen interactions, the aforementioned limitations have motivated the development of alternative technologies for large-scale analysis of ePPIs. From the initial utilization of microarrays for detection of PPI over a decade ago, human proteome chips containing thousands of recombinant proteins have been generated, some of which are now commercially available. doi = 10.1155/2017/2197615 id = cord-001387-2g9dc5z4 author = McIntyre, K. Marie title = A Quantitative Prioritisation of Human and Domestic Animal Pathogens in Europe date = 2014-08-19 keywords = animal; index; pathogen summary = By coupling the H-index method with the EID2, the primary aim of this study was to establish priority lists of human and domestic animal pathogens (including zoonoses) present in Europe. Its potential as a quantitative One Health indicator (i.e. a single measure applicable to both human and animal diseases) was investigated by comparing scores for human-only, zoonotic, and animal-only pathogen groups, including emerging status as this would likely drive research impact. We investigated its value as a proxy for animal disease impact by comparing domestic animal pathogen H-indices with other measures of impact including presence on the OIE list [10] , and inclusion in DISCONTOOLS [11] . The study establishes priority lists of human and domestic animal pathogens (including zoonoses) present in Europe, using the H-index as a proxy measure for impact. doi = 10.1371/journal.pone.0103529 id = cord-346053-mk1mzc5z author = Morris, Cindy E. title = Expanding the Paradigms of Plant Pathogen Life History and Evolution of Parasitic Fitness beyond Agricultural Boundaries date = 2009-12-24 keywords = evolution; factor; pathogen; plant; virulence summary = We present numerous examples of virulence traits in plant pathogenic microorganisms that also have a function in their survival and growth in nonagricultural and nonplant habitats. Adaptation to biotic and abiotic stresses, within or outside of agricultural habitats, likely plays as important a role in the evolution of parasitic fitness of plant pathogens as it does for human pathogens. As illustrated above, traits that confer fitness in response to biotic and abiotic environmental stress can have dual-use as virulence factors in human pathogens. In plant pathogens, the transport systems for toxins and antimicrobials can have broad spectrum activity, leading to resistance to agricultural fungicides and also contributing to virulence [12] . The examples listed above that describe traits that play roles in both environmental fitness and virulence to plants provide a compelling incentive to expand our paradigms concerning the forces that drive evolution of plant pathogenicity. doi = 10.1371/journal.ppat.1000693 id = cord-260420-4s7akmdp author = Mubareka, Samira title = Bioaerosols and Transmission, a Diverse and Growing Community of Practice date = 2019-02-21 keywords = MERS; bioaerosol; pathogen; virus summary = There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate interand intra-species pathogen transmission via bioaerosols. New developments have enabled progress in this domain, and one of the major turning points has been the recognition that cross-disciplinary collaborations across spheres of human and animal health, microbiology, biophysics, engineering, aerobiology, infection control, public health, occupational health, and industrial hygiene are essential. There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate inter-and intra-species pathogen transmission via bioaerosols. A network approach has proven successful in other cross-disciplinary fields, including One Health and eco-health whereby wildlife, computational and evolutionary biologists, microbiologists, virologists, epidemiologists, ecologists, environmental scientists, climatologists, and human, animal, and public health practitioners are collaborating to address challenges in zoonotic diseases research and control (17, 18) . doi = 10.3389/fpubh.2019.00023 id = cord-307874-0obomty2 author = Pardon, Bart title = Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date = 2020-05-23 keywords = PCR; pathogen; respiratory; result; sample summary = Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. However, naturally resistant to fluoroquinolones 71 Escherichia coli, Gallibacterium anatis, Enterobacter hormaechei, staphylococci, streptococci, fungi Secondary Single reports on cattle-specific strains isolated in pure culture in an outbreak of pneumonia in calves 52, [72] [73] [74] Multiple other bacterial species can be detected in the bovine respiratory tract. 10, 35, 54 However, with current knowledge on the interpretation of DNS results at the individual or group level, samples of the lower respiratory tract are likely a better option to evaluate potential involvement of opportunistic pathogens. In the example where the pathogen is causing the disease in 100% of affected calves, the risk of not finding an infected animal after sampling n cases is (1-Se)n , where Se is the test sensitivity. doi = 10.1016/j.cvfa.2020.03.005 id = cord-297440-uw263cfc author = Peacock, Sharon J title = Microbial sequencing to improve individual and population health date = 2014-11-19 keywords = pathogen; sequencing summary = Personalized anti-infective therapies and surveillance of emergent pathogen outbreaks are just two examples of the potential benefits of merging the fields of genomics and infectious diseases. Sequencing will bring improvements in the detection and control of outbreaks associated with multidrugresistant and other pathogens in hospitals and the community [1] . Passive surveillance using sequence data generated for clinical use would provide an overview of the emergence and spread of antimicrobial resistance. Active genomic surveillance of key human pathogens would provide an early warning system for outbreaks, inform vaccine strategies through tracking of vaccine escape, and detect the emergence of new clones that harbor known or novel virulence determinants. New methods to handle and process everexpanding pathogen-specific microbial genome databases will also be needed, including global and region-specific listings of gene mutations associated with drug resistance. Further technological advances are also required to reduce the turnaround time between taking a clinical sample and generating sequence data. doi = 10.1186/s13073-014-0103-5 id = cord-004914-cnz61qjy author = Pedersen, Amy B. title = Cross-Species Pathogen Transmission and Disease Emergence in Primates date = 2010-03-16 keywords = PRHS; host; pathogen; primate summary = This analysis provides the first quantitative attempt to assess the risk of pathogens host-shifting to humans from wildlife populations, a critical step toward predicting disease emergence. Following Davies and Pedersen (2008) , we derived the relationship between evolutionary divergence (representing time to most recent common ancestor from the dated phylogenetic tree of Bininda-Emonds et al., 2007) , and pathogen community similarity (as described above) between each primate pair using generalized linear modeling (GLM) with binomial errors and a logit link function in the statistical package R (R: a programming environment for data analysis and graphics, v. Next, to provide an estimate of the cross-species pathogen transmission risk from wild primates to humans, we constructed a second hotspot map, weighting each primate distribution in proportion to its evolutionary distance from humans, using the nonlinear transformation determined from the GLM model coefficients described above. Population centers in close proximity to regions with high phylogenetic risk of host shifts and human population growth are likely to be foci of disease emergence. doi = 10.1007/s10393-010-0284-3 id = cord-354254-89vjfkfd author = Peng, Shanbi title = The role of computational fluid dynamics tools on investigation of pathogen transmission: Prevention and control date = 2020-08-31 keywords = CFD; method; model; pathogen; simulation; transmission summary = Inspired by the impact of COVID-19, this review summarizes research works of pathogen transmission based on CFD methods with different models and algorithms. Defining the pathogen as the particle or gaseous in CFD simulation is a common method and epidemic models are used in some investigations to rise the authenticity of calculation. The Re-Normalization Group (RNG) k-ε was used in simulation in order to solve the turbulence with the good performance of accuracy, efficiency and robustness; In Gao and Niu [45] study, RNG k-ε model including the effect of low-Reynolds-number is used to solve the airflow and the diffusion of tracer gas which can represent the contaminant transmission are calculated by the equation below: Gao, et.al [102] combined the use of experiment and CFD method to study airborne transmission in different flats of a high-rise building and to verify their simulation, the data of tracer gas experiment from Denmark Aalborg University [103] is used. doi = 10.1016/j.scitotenv.2020.142090 id = cord-023830-w218ogsk author = Perlin, David title = Rapid Detection of Bioterrorism Pathogens date = 2008-09-10 keywords = PCR; assay; detection; dna; pathogen summary = The inadequacy of phenotypic-based diagnostic assays is illustrated graphically by the ''''gold standard'''' public health laboratory-testing algorithm that was in place for positive identification of Bacillus anthracis from environmental samples during the October 2001 anthrax outbreak (Fig. 16.1a) . Genomic differences between microbes offer an alternative to culturing for detection and identification of pathogens by providing species-specific DNA targets that can be accurately resolved by molecular methodology. Polymerase chain reaction (PCR)-based amplification of highly conserved ribosomal RNA (rRNA) genes, intergenic sequences, and specific toxin genes is currently the most reliable approach for identification of bacterial, fungal and many viral pathogenic agents. Most importantly, these genetic probing systems offer rapid turn around time (1-6 h) and are suitable for high throughput, automated multiplex operations critical for use in clinical diagnostic laboratories. Rapid diagnostic assays in the genomic biology era: detection and identification of infectious disease and biological weapon agents doi = 10.1007/978-1-59745-326-4_16 id = cord-282610-zim7nond author = Proal, Amy title = Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity date = 2018-12-04 keywords = CFS; disease; dna; human; immune; microbiome; pathogen; patient summary = title: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. The gut microbiome can initiate and promote colorectal cancer at all stages of tumorigenesis by acting as an inducer of DNA damage, generating epigenetic changes, regulating cell growth, and modulating host immune responses (80) . If ME/CFS is driven by successive infection, treatments that support or activate the human immune system could improve microbiome health by allowing patients to better target persistent pathogens. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to many of these persistent microbiome pathogens. In ME/CFS, the immune response, metabolism, central nervous system, and human gene expression are all linked by the activity of the microbiome and its associated proteins/metabolites. doi = 10.3389/fped.2018.00373 id = cord-280107-tulne0v3 author = Rabaa, Maia A. title = The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases date = 2015-09-24 keywords = VIZIONS; Vietnam; human; pathogen summary = This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance understanding of viral cross-species transmission events, and identify relevant risk factors and drivers of zoonotic disease emergence. Here, we describe a project that is currently underway in communities across Vietnam in which we are collecting clinical samples and associated clinical, epidemiological, and demographic data, which will be combined with high-throughput viral genome sequences and qualitative social sciences data to address key onehealth questions with the aim of better understanding the origins, risks, and emergence of zoonotic infections. To estimate the burden of disease (focusing on viral and zoonotic diseases), and investigate the disease epidemiology in patients hospitalized with specified clinical syndromes and infections in a cohort of high-risk individuals occupationally exposed to animals; with targeted sampling from domestic animals and wildlife in association with these individuals 3. This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance the understanding of viral cross-species transmission events, and allow us to identify the relevant risk factors and drivers of zoonotic disease emergence. doi = 10.1007/s10393-015-1061-0 id = cord-347946-i6kx3n6m author = Raison, Charles L title = Pathogen–Host Defense in the Evolution of Depression: Insights into Epidemiology, Genetics, Bioregional Differences and Female Preponderance date = 2016-09-15 keywords = IFN; MDD; Raison; depression; immune; increase; inflammation; pathogen; pathos summary = Like sickness behavior, depression in response to immune activation aided in host defense both directly (ie, raised body temperature and energy conservation behaviors) and indirectly (social avoidance, energy conservation, and hypervigilance; Raison and Miller, pathogenhost defense theory of depression [PATHOS-D]) Adaptive explanations for associations between MDD and altered immune functioning are not considered (frequent unexamined assumption of researchers working on proximal mechanisms) Toll-like receptor (TLR) mRNA and protein have been reported to be elevated in both the periphery and CNS of individuals with MDD (Hung et al, 2014 (Hung et al, , 2015 Keri et al, 2014; van Dooren et al, 2016) , with some evidence suggesting that successful pharmaco-or psychotherapy reduces peripheral TLR activity (Keri et al, 2014; Hung et al, 2015) . doi = 10.1038/npp.2016.194 id = cord-292031-weiwksh6 author = Ramírez-Castillo, Flor Yazmín title = Waterborne Pathogens: Detection Methods and Challenges date = 2015-05-21 keywords = PCR; detection; dna; pathogen; water summary = Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. Molecular techniques, such as nucleic acid amplification procedures, offer sensitive and analytical tools for detecting a variety of pathogens, including new emerging strains, present the possibility of automation, and real-time analysis to provide information for microbial risk assessment purposes [33] . Limitations of DNA based methods such as PCR include the inability to discriminate between viable from non-viable cells that both contain DNA, the low concentration of several pathogens in water such as Cryptosporidium, Giardia and viruses, and the lack of data to indicate the real infectious risk to a population. Oligonucleotide microarrays are a powerful genomic technology that is widely utilized to monitor gene expression under different cell growth conditions, detecting specific mutations in DNA sequences and characterizing microorganisms in environmental samples [76] . doi = 10.3390/pathogens4020307 id = cord-276966-wmelyonk author = Roe, Kevin title = A proposed treatment for pathogenic enveloped viruses having high rates of mutation or replication date = 2020-07-08 keywords = cell; pathogen; protein summary = In targeting specific viral pathogens, dual-protein ligand masks (for brevity, henceforth called dualprotein ligands) should be able to create a quick and powerful immune memory response with existing memory immune cells against some viral pathogens or virus infected cells, without some of the practical limitations of vaccines. Dual-protein ligands could induce an immune response by mimicking the key parts of antigens that activate existing immune memory cells or innate immune cells to attack tagged viral pathogens. All rights reserved One treatment option injects dual-protein ligands into the blood stream or localized regions to mask pathogenic surface proteins used by viruses to infect mammalian cells. Targeted dual-protein ligands could mask viral surface proteins to quickly treat some untreatable virus infections by using already existing immune cells. doi = 10.1111/sji.12928 id = cord-256615-gvq8uyfk author = Rosenberg, Ronald title = Detecting the emergence of novel, zoonotic viruses pathogenic to humans date = 2014-11-22 keywords = RNA; animal; human; pathogen; virus summary = RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations. Despite the differences in clinical presentation and geographical location, these three pathogens share three characteristics: all were unknown before found infecting humans, all are RNA viruses, and all have proven or putative non-human, animal sources. A single subtropical bat species hardly represents all mammal species and indeed many viruses are known to infect more than one species; they tested for only 9 of the 25 virus families pathogenic to humans. doi = 10.1007/s00018-014-1785-y id = cord-024652-4i6kktl0 author = Santra, Hiran Kanti title = Natural Products as Fungicide and Their Role in Crop Protection date = 2020-05-12 keywords = Botrytis; Fusarium; Muscodor; Penicillium; Rhizoctonia; Streptomyces; activity; antifungal; compound; endophytic; fungus; isolate; pathogen; phytoalexin; plant summary = A large number of bioactive compounds ranging from direct plant (both cryptogams algae and moss and phanerogams)-derived natural extracts, essential oil of aromatic plants, and low-molecular-weight antimicrobial compounds known as phytoalexins to secondary metabolites that are both volatile and nonvolatile organic compounds of microbes (fungal and actinobacterial members) residing inside the host tissue, called endophyte, are widely used as agricultural bioweapons. Endophytic culture extracts are also known to be rich sources of phenolics; usually they are directly proportional to the antioxidative property of any fungal isolate, but in some particular cases, they are characterized with their antifungal potentials against phytopathogenic fungus. So it is a great opportunity to use the unique mixture of volatile organic compounds of the endophytic isolate to reduce the crop loss caused by the pathogenic infection on the commercially valuable plant of cherry tomato worldwide. doi = 10.1007/978-981-15-3024-1_9 id = cord-330463-j4cf7vzs author = Sattar, Syed A. title = Indoor air as a vehicle for human pathogens: Introduction, objectives, and expectation of outcome date = 2016-09-02 keywords = air; indoor; pathogen summary = In this international workshop, a panel of 6 experts will expound on the following: (1) the potential for indoor air to spread a wide range of human pathogens, plus engineering controls to reduce the risk for exposure to airborne infectious agents; (2) the behavior of aerosolized infectious agents indoors and the use of emerging air decontamination technologies; (3) a survey of quantitative methods to recover infectious agents and their surrogates from indoor air with regard to survival and inactivation of airborne pathogens; (4) mathematical models to predict the movement of pathogens indoors and the use of such information to optimize the benefits of air decontamination technologies; and (5) synergy between different infectious agents, such as legionellae and fungi, in the built environment predisposing to possible transmission-related health impacts of aerosolized biofilm-based opportunistic pathogens. doi = 10.1016/j.ajic.2016.06.010 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-016588-f8uvhstb author = Sintchenko, Vitali title = Informatics for Infectious Disease Research and Control date = 2009-10-03 keywords = dna; gene; genome; genomic; pathogen summary = The goal of infectious disease informatics is to optimize the clinical and public health management of infectious diseases through improvements in the development and use of antimicrobials, the design of more effective vaccines, the identification of biomarkers for life-threatening infections, a better understanding of host-pathogen interactions, and biosurveillance and clinical decision support. "New Age" infectious disease informatics rests on advances in microbial genomics, the sequencing and comparative study of the genomes of pathogens, and proteomics or the identification and characterization of their protein related properties and reconstruction of metabolic and regulatory pathways (Bansal 2005) . The figure was produced using Artemis software (The Wellcome Trust Sanger Institute, UK) 1 Informatics for Infectious Disease Research and Control evidence-based gene calling or translating alignments of the DNA sequence to known proteins; and (3) aligning cDNAs from the same or related species. doi = 10.1007/978-1-4419-1327-2_1 id = cord-289443-46w52de3 author = Sironi, Manuela title = Evolutionary insights into host–pathogen interactions from mammalian sequence data date = 2015-03-18 keywords = HIV-1; NPC1; host; pathogen; selection; site summary = Nevertheless, natural selection signatures have been described at several mammalian genes that interact with recently emerged human infectious agents (for example, HIV-1), possibly as a result of the pressure imposed by extinct pathogens or because these agents have established long-lasting interactions with non-human hosts. Thus, as observed for ACE2, MERS-CoV and related viruses (for example, coronavirus HKU4) are likely to act as drivers of molecular evolution on mammalian DPP4 genes; it will be especially interesting to evaluate the contribution of positively selected sites in ferrets because these animals are resistant to MERS-CoV infection. In the host-pathogen arms race, these molecules represent one of the foremost detection-defence systems; consistently, several studies have reported adaptive evolution at genes encoding mammalian PRRs. Analyses in primates, rodents and representative mammalian species indicate that positive selection shaped nucleotide diversity at most TLRs, with the strongest pressure acting on TLR4 (REFS 35, 48, 49) . doi = 10.1038/nrg3905 id = cord-269124-oreg7rnj author = Spyrou, Maria A. title = Ancient pathogen genomics as an emerging tool for infectious disease research date = 2019-04-05 keywords = Europe; Fig; Yersinia; ancient; dna; genome; pathogen; pestis summary = Examples of tools that have shown their effectiveness with ancient metagenomic DNA include the widely used Basic Local Alignment Search Tool (BLAST) 68 ; the MEGAN Alignment Tool (MALT) 41 , which involves a taxonomic binning algorithm that can use whole genome databases (such as the National Center for Biotechnical Information (NCBI) Reference Sequence (RefSeq) database 69 ); Metagenomic Phylogenetic Analysis (MetaPhlAn) 70 , which is also integrated into the metagenomic pipeline MetaBIT 71 and uses thousands (or millions) of marker genes for the distinction of specific microbial clades; or Kraken 72 , an alignment free sequence classifier that is based on k-mer matching of a query to a constructed database. Similar limitations can arise when the evolutionary history of a microorganism is vastly affected by recombination, as observed for HBV 44, 53 , although HBV molecular dating was recently attempted using a different genomic data set and suggested that the currently explored diversity of Old and New World pri mate lineages (including all human genotypes) may have emerged within the last 20,000 years 43 . doi = 10.1038/s41576-019-0119-1 id = cord-282628-6uoberfu author = Tiwari, Bhagyashree title = Future impacts and trends in treatment of hospital wastewater date = 2020-05-01 keywords = antibiotic; disease; emergence; human; pathogen; virus summary = The causative agent of most emerging infectious diseases is viruses; every year approximately more than two novel viral pathogens are identified, which can cause illness in a human. Factors for emergence include natural process (evolution of pathogen), infectious agents transfer from vertebrate to mammals, antimicrobial resistance (AMR), and climate change. The factors responsible for the emergence of infectious diseases such as (1) the evolution of new strain, (2) the introduction of a host to enzootic, (3) translocation of infected wildlife, (4) farming practices, and (5) others were provided. Due to emergence of antibiotic-resistant pathogens and unavoidable use of antibiotics, concomitant environmental perturbation caused by climate change might make the earth is not suitable for humans and other livings. Increasing resistance to antibiotics and the emergence of "superbugs" that are resistant to drugs of last resort have highlighted the great need for alternative treatments of bacterial disease. Furthermore, development of drug-resistant organisms and increased pathogen survival rate, only raising panic about the human, animal, and environmental health. doi = 10.1016/b978-0-12-819722-6.00017-1 id = cord-257802-vgizgq2y author = Uttamchandani, Mahesh title = Applications of microarrays in pathogen detection and biodefence date = 2008-11-12 keywords = SARS; dna; microarray; pathogen; protein summary = Advances in miniaturizing this initial PCR step, for instance the development of Review Glossary Biodefence: defensive measures against biological threats, including natural/ emerging pathogens and bioterror agents, that have significant potential to endanger public health Detection: identifying the presence of target pathogen(s) from clinical or environmental samples. (b) Antibody microarrays can be used to detect pathogen proteins or antigens that might be present in environmental samples as an indication of contamination or for diagnostic purposes to determine pathogen infection in human tissues. fabricated a customized Affymetrix microarray containing 53 660 probes to detect DNA amplified from 18 different pathogenic microorganisms simultaneously, including pathogens from the US CDC''s list of bioterrorism agents, such as Bacillus anthracis (which causes anthrax), Clostridium botulinum (which generates the botulinum toxin), Yersinia pestis (which causes bubonic plague) and the Ebola virus [17] . doi = 10.1016/j.tibtech.2008.09.004 id = cord-031017-xjnbmah5 author = Van Goethem, N. title = Perceived utility and feasibility of pathogen genomics for public health practice: a survey among public health professionals working in the field of infectious diseases, Belgium, 2019 date = 2020-08-31 keywords = NGS; WGS; health; pathogen; public summary = METHODS: In May 2019, Belgian public health and healthcare professionals were invited to complete an online survey containing eight main topics including background questions, general attitude towards pathogen genomics for public health practice and main concerns, genomic literacy, current and planned NGS activities, place of NGS in diagnostic microbiology pathways, data sharing obstacles, end-user requirements, and key drivers for the implementation of NGS. The following criteria were included (top to bottom): clinical and/or public health significance, priority with respect to preventing the spread of antimicrobial resistance, local/national/international policy surveillance priorities or obligations, importance of prevention and control programs (e.g. vaccination), utility of WGS for diagnostics and/or treatment decisions (individual patient care), utility of increased resolution to infer relatedness that would not be obtained via conventional methods, availability of high-quality/complete/standardized epidemiological and/or clinical data to provide context to the WGS results, possibility to link genomic data from different sources (food-animalhuman-environment), cost-effectiveness (e.g. replacing multiple tests), time-saving compared to conventional testing methods, impact on outcomes for patients and populations (translation into actionable results), availability of WGS typing schemes and reference databases (e.g. for antimicrobial resistance), availability of validated (quality-controlled) WGS workflows (both wet and dry laboratory), availability of expertise to generate, analyze and interpret WGS data, and availability of the appropriate infrastructure (sequence technology, high-performance computing, data storage, etc.). doi = 10.1186/s12889-020-09428-4 id = cord-016717-2twm4hmc author = Vourc’h, Gwenaël title = How Does Biodiversity Influence the Ecology of Infectious Disease? date = 2011-06-28 keywords = disease; host; pathogen; specie summary = To conclude, we consider that the consequences of the loss of species biodiversity on infectious diseases is still largely unknown, notably due to the lack of knowledge on the dynamics of host-pathogen relationships, especially at the population and at the community level.. To conclude, we consider that the consequences of the loss of species biodiversity on infectious diseases is still largely unknown, notably due to the lack of knowledge on the dynamics of host-pathogen relationships, especially at the population and at the community level.. In this chapter, we investigate how biodiversity influences the ecology of infectious diseases at the intraspecific level (genetic variability of pathogens and hosts) and at the level of communities (species composition). The hypothesis underlying the amplification and dilution effect is that for many diseases, the competence of reservoirs, i.e. the ability to become infected and retransmit the pathogen, varies according to the host species (Haydon et al. doi = 10.1007/978-94-007-2114-2_13 id = cord-325052-7vlxa0i7 author = Williamson, E. D. title = Vaccines for emerging pathogens: prospects for licensure date = 2019-04-11 keywords = EUA; United; disease; pathogen; vaccine summary = However, vaccines for pathogens which cause severe, but occasional, disease outbreaks in endemic pockets have suffered from a lack of commercial incentive for development to a clinical standard, encompassing Phase III clinical trials for efficacy. While approval of vaccines for diseases caused by such pathogens would Clinical and Experimental Immunology REvIEw ARtIClE Series Editor: E Diane williamson make a significant impact on disease outbreaks, taking niche vaccines into clinical development, including Phase III clinical trials for efficacy, requires a large investment in time and money. An alternative is to develop such vaccines to request US Emergency Use Authorization (EUA), or an alternative status in the United States, Canada and European Union (EU) making use of a considerable number of alternative regulatory mechanisms that are available prior to licensing, so that the products are deployable at the first indications of a disease outbreak. doi = 10.1111/cei.13284 id = cord-320295-k2i52wgs author = Woolhouse, Mark E.J. title = Host Range and Emerging and Reemerging Pathogens date = 2005-12-17 keywords = pathogen; specie summary = However, although zoonotic pathogens do represent the most likely source of emerging and reemerging infectious disease, only a small minority have proved capable of causing major epidemics in the human population. All the defined host types are potential sources of zoonotic infections, but differences occurred in their importance (ranked by number of pathogen species supported) across viruses, bacteria, fungi, protozoa, and helminths and no 1 type consistently dominates ( Figure 1A) , although ungulates are the most important overall, supporting over 250 species of human pathogen. However, when the fraction of emerging and reemerging species is compared with the breadth of host range (as the number of host types other than humans), a pattern becomes apparent (Figure 2) . Relationship between breadth of host range (as number of nonhuman host types, as listed in Figure 1 ) and the fraction of pathogen species regarded as emerging or reemerging. doi = 10.3201/eid1112.050997 id = cord-256543-7kfi2yvu author = de Graaf, Miranda title = Sustained fecal-oral human-to-human transmission following a zoonotic event date = 2016-11-23 keywords = human; pathogen; transmission summary = Using a comparative approach including parasites, bacteria and viruses that transmit via the fecal-oral route, the meeting aimed at identifying the key drivers of sustained human-to-human transmission after a zoonotic event, taking into account the host, the pathogen and the interface (transmission amplifiers). Enteric pathogens can be transmitted between humans by the fecal-oral route via direct contact or indirect contact via contaminated fluids, including surface water, food, and carriers such as fomites ( Figure 1 ). After shedding from the host enteric pathogens can be transmitted between humans by the fecal-oral route via direct contact between humans, or via indirect contact via contaminated fluids, including surface water, food, and carriers such as fomites. A human reservoir for non-typhoid Salmonella (NTS) transmission of multiple serotypes was demonstrated in a study of NTS-infected patients who continued to shed NTS for months up to years, and strains of these patients acquired antimicrobial resistance genes and virulence genes that possibly affected host-pathogen interactions [34 ] . doi = 10.1016/j.coviro.2016.11.001 id = cord-015484-t1zbpyin author = nan title = Emerging Pathogens: What Are the Sources and How Can They Be Spotted Quickly? date = 2003-05-01 keywords = CDC; pathogen summary = Top priorities of the 4 major sections include: í í Surveillance: The CDC with state health departments and other task force members began planning a coordinated surveillance system, such that all entities would use similar methodology and develop patterns of use for antimicrobial drug used in human medicine, agriculture, and other consumer products. A case in point was published in the March 2003 issue of Emerging Infectious Diseases as a letter to the editor, describing a multi-drug resistant Shigella dysenteriae type 1 organism, first seen in India in 1984, where it was sensitive to nalidixic acid. Hooper (Massachusetts General Hospital, Harvard Medical School, Boston, MA), writing in a special issue of Emerging Pathogens (Mar-April, 2001), drug resistance in Streptococcus pneumoniae, which is currently low, will require close monitoring as fluoroquinolones are used more extensively for treating respiratory tract infections. doi = 10.1309/nm113vcpd3pgvgcl id = cord-285778-80baxwgc author = nan title = Introduction to the Immune Response date = 2014-10-10 keywords = cell; pathogen; response summary = Some innate mechanisms require no induction and are completely non-specific, whereas others are inducible and involve broad receptor-mediated recognition of a limited number of pathogen-associated or damage-associated molecular patterns (PAMPs/DAMPs). When invaders breach anatomical and physiological barriers, innate leukocytes start to take action as a result of pattern recognition mediated by the binding of PRMs to PAMPs furnished by pathogens and to DAMPs emanating from damaged host cells. If the pathogen manages to enter the underlying cell layer, mechanisms mediated by complement and innate leukocytes are induced due to relatively broad recognition of PAMPs. If a more targeted, pathogen-specific response becomes necessary, elements of innate immunity then facilitate induction of highly specific adaptive responses initiated by engagement of the antigen receptors of B, Th or Tc lymphocytes. Innate leukocytes activated by the binding of PRRs to PAMPs provided by the attacking pathogen, or to DAMPs present due to host cell injury or death, work quickly to eliminate the invader using the mechanisms of inflammation, phagocytosis and target cell lysis. doi = 10.1016/b978-0-12-385245-8.00001-7 id = cord-297621-xunyqlr5 author = nan title = Pathogen-Inaktivierungssysteme für Thrombozytenkonzentrate: Stellungnahme date = 2018-06-21 keywords = MIRASOL; Pathogen; die; platelet; riboflavin summary = Die Daten aus den Hämovigilanzberichten 2013/14 und 2015 [7, 8] zeigen, dass in Deutschland sowohl das Risiko einer Übertragung von viralen Erregern als auch das Risiko einer Transfusions-bedingten bakteriellen Infektion durch TK [9] sehr gering ist. Interstrang-Reaktionen sind möglich, so dass ein breites Spektrum von Nukleinsäuren einschließlich der von Viren und anderen Pathogenen inaktiviert werden kann [10] In einem Hämostase-Globaltest (RO-TEM®) war die Gerinnungszeit nach 5 Tagen Lagerung verglichen mit den Kontrollen nur leicht verkürzt [60] . Die Wirkung von THERAFLEX auf Protozoen wurde mit Trypanosoma cruzi, Leishmania infantum, Plasmodium falciparum und Babesia divergens untersucht [135] [136] [137] . Pathogen inactivation of double-dose buffy-coat platelet concentrates photochemically treated with amotosalen and UVA light: preservation of in vitro function Pathogen reduction technology treatment of platelets, plasma and whole blood using riboflavin and UV light Pathogen inactivation of Trypanosoma cruzi in plasma and platelet concentrates using riboflavin and ultraviolet light Pathogen reduction by ultraviolet C light effectively inactivates human white blood cells in platelet products doi = 10.1007/s00103-018-2766-3 id = cord-355165-xc6ythgp author = van den Wijngaard, Cees title = Validation of Syndromic Surveillance for Respiratory Pathogen Activity date = 2008-06-17 keywords = pathogen; respiratory; syndrome summary = We defi ned syndrome data as data in health-related registries that refl ect infectious disease activity without identifying causative pathogen(s) or focusing on pathogenspecifi c symptoms (such as routine surveillance data for infl uenza-like illness [11] or surveillance of acute fl accid paralysis for polio [12] ). Six registries were selected ( Table 1 ) that collected data on work absenteeism, general practice (GP) consultations, prescription medications dispensed by pharmacies, diagnostic test requests (laboratory submissions) (13), hospital diagnoses, and deaths. As a reference for the syndrome data, we included specifi c pathogen counts for 1999-2004 from the following sources: 1) Weekly Sentinel Surveillance System of the Dutch Working Group on Clinical Virology (which covers 38%-73% of the population of the Netherlands [14] respiratory disease-related counts of Streptococcus pneumoniae (data in 2003-2004 were interpolated for 2 laboratories during short periods of missing data; total coverage 24%); and 3) national mandatory notifi cations of pertussis. doi = 10.3201/eid1406.071467