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?' ---------------------------------------------------------- 30 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 5063 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 48 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 29 ARI 8 respiratory 5 PCR 4 RSV 2 virus 2 study 2 influenza 2 HRV 2 EMR 2 CDA 1 vitamin 1 viral 1 swab 1 self 1 rhinovirus 1 mild 1 international 1 infection 1 indigenous 1 human 1 cost 1 cat 1 asthma 1 adult 1 VP1 1 RNA 1 October 1 OLA 1 OC43 1 Niger 1 NL63 1 Lwak 1 Kenya 1 ILI 1 IFN 1 ICD-9 1 HRSV 1 HKU1 1 HIV 1 HBoV 1 FCV 1 China 1 CVEV 1 COVID-19 1 Beijing 1 BPH 1 B55 1 Ari 1 April Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 1284 virus 1094 infection 1071 study 930 % 775 child 547 influenza 501 patient 380 case 364 detection 329 year 326 disease 317 asthma 316 analysis 297 illness 292 datum 273 rhinovirus 265 pneumonia 261 symptom 247 age 239 adult 224 tract 224 time 223 swab 221 group 219 infant 214 sample 214 day 204 pathogen 195 result 189 surveillance 188 type 188 population 185 community 184 risk 177 effect 177 cell 165 author 163 rate 160 preprint 150 table 148 control 147 review 146 association 141 ari 140 p 140 hospital 139 system 136 severity 136 care 135 role Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1022 ARI 454 HRV 281 PCR 262 RSV 194 al 180 HBoV 173 et 164 . 139 HCoV 94 FCV 89 C 85 RT 83 RNA 78 Table 77 Influenza 77 A 76 NL63 76 B 69 HAdV 69 EMR 59 CI 58 ILI 56 Ari 54 OLA 54 Health 52 Human 50 CDA 49 Fig 47 T 47 SARS 47 HIV 47 China 45 COVID-19 45 B55 44 United 43 OC43 43 NC 42 April 41 States 41 CC 41 BY 39 VP1 39 ICD-9 39 H1N1 38 October 38 HRSV 37 Rhinovirus 37 PIV 37 IFN 36 HCoVs Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 416 we 257 it 105 they 26 them 22 i 20 us 9 he 6 themselves 5 one 4 you 4 she 4 myself 2 itself 2 herself 1 oneself 1 mine 1 him 1 her Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 4655 be 927 have 473 use 332 detect 328 associate 268 include 231 identify 219 do 214 report 195 base 186 compare 185 collect 175 increase 167 find 163 show 142 cause 138 hospitalize 118 relate 107 make 106 induce 105 present 103 follow 97 infect 93 describe 90 perform 90 observe 86 require 84 test 84 provide 83 obtain 83 conduct 79 display 79 age 78 reduce 78 occur 77 develop 75 see 73 post 73 determine 72 grant 71 suggest 68 remain 68 control 67 result 67 consider 66 assess 65 investigate 58 take 58 indicate 57 wheeze Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1256 respiratory 581 not 545 viral 398 clinical 368 acute 365 more 354 human 338 other 318 high 279 - 250 low 217 positive 215 also 199 most 193 severe 185 common 179 only 175 old 160 non 141 young 140 available 139 however 124 well 117 seasonal 108 such 108 significant 107 mild 107 less 105 syncytial 105 similar 96 first 94 single 94 likely 90 early 87 different 87 as 86 new 84 specific 83 previous 83 least 83 indigenous 81 further 80 same 80 bacterial 79 respectively 77 upper 77 diagnostic 75 molecular 75 healthy 75 asymptomatic Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 50 most 25 least 21 high 15 Most 9 great 9 good 5 low 4 large 3 young 3 early 2 ® 2 wet 2 strong 2 strict 2 short 2 old 2 late 1 ÀssRNA 1 small 1 simple 1 severe 1 long 1 hot 1 fast 1 close 1 big 1 -CTCTTGCAGGTAT 1 -A1b Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 149 most 58 least 3 well 1 -gagcgg Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 30 doi.org 4 orcid.org 2 www.health.qld.gov.au 1 www.picornastudygroup.com 1 www.nntonline.net 1 www.ncbi.nlm.nih.gov 1 www.nature.com 1 www.international-rhinovirus-consortium.org 1 www 1 respiratory-research.com 1 ihg.gsf.de 1 hadvwg.gmu.edu 1 form.gov.sg 1 clinicaltrials.gov 1 blast.ncbi.nlm.nih.gov 1 blast Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 13 http://doi.org/10.1101/2020.08.03.20167502 7 http://doi.org/10.1101/2020.04 6 http://doi.org/10.1101/2020.07.14.20152728 2 http://doi.org/10.1101 1 http://www.picornastudygroup.com/ 1 http://www.nntonline.net/visualrx/ 1 http://www.ncbi.nlm.nih.gov/Taxonomy/ 1 http://www.nature.com/srep 1 http://www.international-rhinovirus-consortium.org/ 1 http://www.health.qld.gov.au/ph/cdb/sru_data.asp 1 http://www.health.qld.gov.au/ph/cdb/ 1 http://www 1 http://respiratory-research.com/content/9/1/11 1 http://orcid.org/0000-0003-4395-347X 1 http://orcid.org/0000-0003-0101-9048Stefano 1 http://orcid.org/0000-0003-0044-1394 1 http://orcid.org/0000-0002-7567-3248 1 http://ihg.gsf.de/cgi-bin/hw/hwa1.pl 1 http://hadvwg.gmu.edu/ 1 http://form.gov.sg/#!/5e5b6857130b0100115f3e93 1 http://doi.org/10.1101/2020.04.22.20069781 1 http://doi.org/10.1016/j.ijid.2018.08.001 1 http://clinicaltrials.gov/show/ 1 http://blast.ncbi.nlm.nih.gov/Blast.cgi 1 http://blast Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 d.a.jolliffe@qmul.ac.uk Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 7 pneumonia requiring hospitalization 4 virus is strongly 3 children using parent 3 hrv were more 3 study did not 2 ari is ongoing 2 ari was not 2 asthma had more 2 asthma were similar 2 cases were more 2 children is supportive 2 children requiring emergency 2 data are scarce 2 detection is not 2 group was older 2 groups were almost 2 illness is not 2 infection causes asthma 2 infections are frequently 2 infections are mild 2 infections are more 2 influenza was significantly 2 patients are akathisia 2 patients are constipation 2 patients were co 2 patients were cough 2 pcr did not 2 studies are not 2 studies did not 2 studies do not 2 studies have not 2 study are available 2 study is not 2 study using population 2 swab was then 2 swabs had at 2 time is not 2 virus is not 2 viruses are often 2 viruses is relatively 2 viruses was similar 1 % had ics 1 % increased risk 1 % was influenza 1 adults detected hcov-229e 1 adults did not 1 adults had evidence 1 adults have greater 1 adults is substantially 1 adults is unclear Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 1 ari had no beneficial 1 children reporting no differences 1 data are not available 1 data were not normally 1 detection is not always 1 detection is not fully 1 infection is not routinely 1 infections are not commonly 1 infections is not well 1 infections showed no therapeutic 1 pcr does not always 1 pcr is not necessarily 1 samples showed no consistent 1 samples were not available 1 studies are not comparable 1 studies showed no correlation 1 study reported no difference 1 time is not sufficient A rudimentary bibliography -------------------------- id = cord-317912-v2wovcqd author = Akmatov, Manas K. title = Equivalence of Self- and Staff-Collected Nasal Swabs for the Detection of Viral Respiratory Pathogens date = 2012-11-14 keywords = ARI; self; swab summary = found similar detection rates for respiratory pathogens between self-and staffcollected midturbinate swabs when one staff-collected and one selfcollected swab were taken from opposite nostrils during the same visit to a campus health center [5] . In the study center, a trained staff member (A.G.) obtained a nasal swab (regular flocked swab, Copan, Brescia, Italy, product number 359C) from the participant''s left nostril and instructed him/her how to perform a self-swab. Sensitivity and specificity of self-collected swabs, obtained in the study center, to detect viral respiratory pathogens (compared to staff-collected swabs)*. The detection of a viral pathogen was independent of the amount of b-actin DNA in both staff-and self-swabs collected on day 1 (Fig. 4) . This prospective study comparing staff-and self-collected nasal swabs for the detection of ARI pathogens clearly demonstrated the validity of self-swabbing; specifically, self-swabbing was not inferior in terms of acceptance, satisfaction, sample adequacy, and viral detection rate. doi = 10.1371/journal.pone.0048508 id = cord-330819-vfagxsdz author = Althouse, Benjamin M title = Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam date = 2018-08-14 keywords = ARI; RSV summary = Using enhanced hospital based surveillance of childhood ARI we identify seasonal patterns in hospitalizations as a proxy for transmission and explore the relationship of hospitalizations associated with virus detection with rainfall, temperature, and dew point, to try and identify contributing factors to observed seasonality. To examine the relationship between monthly average rain, temperature, and dew point and incidence hospitalized childhood ARI infections, we estimated the cross-wavelet transform between the z-standardized time series (we subtracted the mean of the time series and divided by the standard deviation) of weather and viral detections (Cazelles et al., 2008) . We evaluated seasonal patterns and associations with weather of hospitalizations for several respiratory viruses using three lines of evidence: 1) Poisson regression examining the relative incidence across months of virus detections adjusted for weather covariates, 2) cross-wavelet transforms of hospitalizations with viral detections, and 3) a sensitivity analysis with a logistic regression model finding odds ratio of hospitalizations with viral detections and weather variables. doi = 10.1016/j.ijid.2018.08.001 id = cord-288821-nalulzfo author = Bastien, Nathalie title = Human Coronavirus NL63 Infection in Canada date = 2005-02-15 keywords = ARI; NL63 summary = Although, in a study like this one, the inclusion of a control group of healthy individuals is necessary to clearly demonstrate a causal relationship, the detection of HCoV-NL63 in respiratory-tract specimens from patients suffering from ARI of unknown causes strongly suggests that it is associated with respiratory illness. We detected the presence of HCoV-NL63 in 19 (3.6%) of the 525 analyzed specimens that were negative for (1) influenza viruses A and B; (2) PIV 1, 2, and 3; (3) adenovirus; (4) RSV; and (5) hMPV; and these results provide further evidence of the contribution of HCoV-NL63 to ARI-and of the significant burden that it therefore may present to health-care systems. Thus, the systematic detection of HCoV-NL63 in respiratory specimens may improve the understanding of the etiology of ARI; however, the possibility of dual infection cannot be excluded, because the present study utilized samples from patients with ARI who were tested-and found to be negative-for only (1) influenza viruses A and B; (2) PIV 1, 2, and 3; (3) adenovirus; (4) RSV; and (5) hMPV. doi = 10.1086/426869 id = cord-281051-i229xv0o author = Bishop-Williams, Katherine E. title = A protocol for a systematic literature review: comparing the impact of seasonal and meteorological parameters on acute respiratory infections in Indigenous and non-Indigenous peoples date = 2017-01-26 keywords = ARI; indigenous; respiratory; study summary = This protocol outlines our process for conducting a systematic review to investigate whether associations between ARI and seasonal or meteorological parameters differ between Indigenous and non-Indigenous groups residing in the same geographical region. This paper outlines a protocol for conducting a systematic review to investigate whether associations between ARI and seasonal or meteorological parameters differ between Indigenous and non-Indigenous groups residing in the same geographical region. This research builds from the United Nations Declaration of the Rights of Indigenous Peoples [13] understanding of the term Indigenous peoples, which states that an Indigenous person self-identifies as Indigenous; has historical continuity Table 1 Inclusion and exclusion criteria for a systematic literature review investigating the impact of seasonal and meteorological parameters on acute respiratory infection (ARI) in Indigenous and non-Indigenous peoples doi = 10.1186/s13643-016-0399-x id = cord-287063-kheek4lx author = Carroll, Kecia N. title = Influence of maternal asthma on the cause and severity of infant acute respiratory tract infections date = 2012-02-14 keywords = ARI; HRV; RSV summary = In this investigation that included mother-infant dyads enrolled in the Tennessee Children''s Respiratory Initiative (TCRI), we tested the hypothesis that a familial atopic predisposition was associated with viral cause and increased severity of viral acute respiratory tract infection (ARI) during infancy. In our next set of analyses we examined whether having a mother with asthma (first defined by maternal self-report and then using the atopic asthma and nonatopic asthma classifications) was associated with increased severity of the infant''s HRV-or RSV-induced ARI. [5] [6] [7] 12, 22 Because of the known differential risk of early childhood asthma after RSV-and HRV-induced infant infections, we were interested in studying whether a familial predisposition to asthma and allergies was associated with the viral cause of the infant''s ARI and the severity of the ARI. doi = 10.1016/j.jaci.2012.01.045 id = cord-288332-y15g1yak author = Choi, Eunjin title = Clinical and laboratory profiles of hospitalized children with acute respiratory virus infection date = 2018-06-25 keywords = ARI; RSV summary = PURPOSE: Despite the availability of molecular methods, identification of the causative virus in children with acute respiratory infections (ARIs) has proven difficult as the same viruses are often detected in asymptomatic children. METHODS: Multiplex reverse transcription polymerase chain reaction assays were performed to detect 15 common respiratory viruses in children under 15 years of age who were hospitalized with ARI between January 2013 and December 2015. Nasopharyngeal aspirates from all patients were obtained within 48 hours of admission for multiplex RT-PCR assay to detect the following 15 common respiratory viruses: influenza virus A and B (IFA, IFB), respiratory syncytial virus A and B (RSV A, RSV B), parainfluenza virus 1-4 (PIV 1, PIV 2, PIV 3, PIV 4), human coronavirus 229E and OC43 (hCV-229E, hCV-OC43), human rhinovirus (hRV), human enterovirus (hEV), adenovirus (AdV), human bocavirus (hBV), and human metapneumovirus (hMPV). doi = 10.3345/kjp.2018.61.6.180 id = cord-001045-jm60nxc2 author = DeLisle, Sylvain title = Using the Electronic Medical Record to Identify Community-Acquired Pneumonia: Toward a Replicable Automated Strategy date = 2013-08-13 keywords = ARI; CDA; EMR summary = METHODS: A manual EMR review of 2747 outpatient ARI visits with associated chest imaging identified x-ray reports that could support the diagnosis of pneumonia (kappa score = 0.88 (95% CI 0.82∶0.93)), along with attendant cases with Possible Pneumonia (adds either cough, sputum, fever/chills/night sweats, dyspnea or pleuritic chest pain) or with Pneumonia-in-Plan (adds pneumonia stated as a likely diagnosis by the provider). The ARI CDA flagged an outpatient visit if the provider assigned it an ARI-related International Disease Classification, 9 th Revision, Clinical Modification (ICD-9) diagnostic code OR issued a prescription for a cough remedy OR documented at least two symptoms from the above ARI case definition in his/her clinical note, as retrieved by computerized text analysis [10] . Discussion Automated text analyses of chest imaging reports improved the performance of EMR-based CDAs that included structured data elements and free-text search for ARI symptoms. doi = 10.1371/journal.pone.0070944 id = cord-303845-y6ws3u6x author = DeLisle, Sylvain title = Combining Free Text and Structured Electronic Medical Record Entries to Detect Acute Respiratory Infections date = 2010-10-14 keywords = ARI; CDA; EMR; ICD-9 summary = Several factors, some of which have already been mentioned, may limit the generalizability of our results: 1) factors related to the performance of our study at the VA health care system: a) the veterans study population is mostly male and excludes the pediatric population, a key target for ARI surveillance [44] ; b) veterans health care utilization may differ from that observed in uninsured or privately insured individuals; c) clinical practices, documentation and coding habits by VA practitioners may differ from those observed in solo or group practices or in health systems subject to different financial or quality-control incentives; 2) factors related to our study period: optimal CDAs could differ outside the respiratory infection season, or during periods of heightened apprehension for an influenza epidemic; 3) factors related to our iterative CDA development process, which may have over adapted CDAs to VA''s particular EMR implementation and to our sample dataset in particular, this despite our efforts to maintain a separation between development and validation data subsets; 4) factors related to our text mining approach: a) we did not employ a spell checker prior to applying the NegEx algorithm. doi = 10.1371/journal.pone.0013377 id = cord-268977-hcg2rrhl author = Feikin, Daniel R. title = Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date = 2012-08-24 keywords = ARI; HIV; Kenya; Lwak; PCR summary = METHODOLOGY/PRINCIPAL FINDINGS: From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0°C or oxygen saturation <90% or hospitalization). CONCLUSIONS/SIGNFICANCE: Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings. Compared with other regions, the mortality rate among older children and adults remains several-fold higher in sub-Saharan Africa, where acute respiratory infections (ARI) are a leading cause of this high mortality, as well as associated morbidity [1] . doi = 10.1371/journal.pone.0043656 id = cord-259338-q3kw6n9o author = Jean, Sim Xiang Ying title = Utilizing the Electronic Health Records to Create a Syndromic Staff Surveillance System During the COVID-19 outbreak date = 2020-11-04 keywords = ARI; COVID-19 summary = We aimed to create a prototype staff surveillance system for the detection of acute respiratory infection (ARI) clusters amongst our healthcare workers (HCWs) and describe its effectiveness. Conclusion The use of syndromic surveillance to detect ARI clusters amongst HCWs in the COVID-19 pandemic may enable early case detection and prevent onward transmission. Utilizing the electronic health records, we have created a prototypic surveillance system in the detection of acute respiratory infection (ARI) clusters amongst staff and aim to describe its effectiveness in this study. The aim of this descriptive analytic study is to describe the effectiveness of a prototypic staff syndromic surveillance system in identifying acute respiratory infection (ARI) clusters amongst the staff population in the hospital. This initial feasibility study shows that the use of a syndromic surveillance system has the ability to identify ARI clusters amongst staff populations that would initiate downstream investigation and active screening. doi = 10.1016/j.ajic.2020.11.003 id = cord-305473-w30hsr4m author = Jiang, Lili title = Detection of viral respiratory pathogens in mild and severe acute respiratory infections in Singapore date = 2017-02-20 keywords = ARI; ILI; PCR summary = To investigate the performance of laboratory methods and clinical case definitions in detecting the viral pathogens for acute respiratory infections (ARIs) from a prospective community cohort and hospital inpatients, nasopharyngeal swabs from cohort members reporting ARIs (community-ARI) and inpatients admitted with ARIs (inpatient-ARI) were tested by Singleplex Real Time-Polymerase Chain Reaction (SRT-PCR), multiplex RT-PCR (MRT-PCR) and pathogen-chip system (PathChip) between April 2012 and December 2013. Our study concurrently assessed the role of routine laboratory diagnostics, and usefulness of the novel PathChip platform as well as ILI case definitions in identifying respiratory virus infection in a community cohort and hospital inpatients from a broad range of age groups (6 to 81, and 20 to 89 years respectively), to reflect what may be encountered in either community or primary care (mild-ARI) as well as tertiary care settings (severe-ARI) in a tropical environment with less distinct seasonal patterns. doi = 10.1038/srep42963 id = cord-262773-mfta0emi author = Jolliffe, D. title = Vitamin D supplementation to prevent acute respiratory infections: systematic review and meta-analysis of aggregate data from randomised controlled trials date = 2020-07-17 keywords = ARI; vitamin summary = title: Vitamin D supplementation to prevent acute respiratory infections: systematic review and meta-analysis of aggregate data from randomised controlled trials Design: We conducted a systematic review and meta-analysis of data from randomised controlled trials (RCTs) of vitamin D for ARI prevention using a random effects model. We previously meta-analysed individual participant data from 25 RCTs and showed a protective overall effect that was stronger in those with lower baseline 25(OH)D levels, and in trials where vitamin D was administered daily or weekly rather than in more widely spaced bolus doses. Randomised, double-blind, trials of supplementation with vitamin D 3 , vitamin D 2 or 25(OH)D of any duration, with a placebo or low-dose vitamin D control, were eligible for inclusion if they had been approved by a Research Ethics Committee and if data on incidence of ARI were collected prospectively and pre-specified as an efficacy outcome. doi = 10.1101/2020.07.14.20152728 id = cord-103657-php6aj1r author = Koller, D. title = Safety and cardiovascular effects of multiple-dose administration of aripiprazole and olanzapine in a randomised clinical trial date = 2020-08-07 keywords = ARI; OLA summary = On the contrary, the most common ADRs to OLA in schizophrenic patients are constipation, weight gain, dizziness, personality disorder, akathisia, postural hypotension, sedation, headache, increased appetite, fatigue, dry mouth and abdominal pain (R. ADRs were classified using system organ class allocation as general (asthenia, fatigue, tiredness and gait alterations), cardiovascular (palpitations), gastrointestinal (constipation, nausea, vomiting, hyposalivation, hypersalivation, dry mouth and diarrhea), nervous system (akathisia, headache, difficulties with concentration, dizziness, paraesthesia, presyncope, syncope, tremor, somnolence and restless legs), psychiatric (restlessness, insomnia, anxiety, abnormal orgasm and nightmares), respiratory (epistaxis, hiccups, cough and sore throat), endocrine (galactorrhea), metabolic (lack of appetite, increased appetite and hyporexia), reproductive (dysmenorrhea, mastalgia and menstrual irregularity), skin (hair loss, pruritus, rash and sweating), musculoskeletal (shoulder pain, knee pain, neck pain, upper limb weakness, lumbalgia, cramps, back pain and leg pain), infections (cold), eye (photophobia) and doi = 10.1101/2020.08.03.20167502 id = cord-287167-rc9a5xs5 author = Kyaw, Win Mar title = Healthcare worker acute respiratory illness cluster in 2020: Could it be from COVID-19? date = 2020-07-23 keywords = ARI summary = To the Editor-Since the emergence of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in China, >45,000 confirmed cases including >60 healthcare workers (HCWs) have been reported in Singapore. 4 After the SARS nosocomial outbreak, web-based staff sickness surveillance systems have been established at TTSH for the early detection of HCW clusters of acute respiratory infection (ARI). 7 During the COVID-19 pandemic, a team of public healthtrained personnel maintained close monitoring of staff sickness reporting to identify ARI clusters among the 12,000 HCWs working at the 1,600-bed TTSH and its collocated 330-bed National Centre for Infectious Diseases, the national referral centre for COVID-19 response. Compared to the first 27 weeks of 2019 (n = 28), the number of ARI clusters identified among staff working in inpatient wards in 2020 (n = 39) was significantly lower: 49% versus 78%, respectively (OR, 0.26; 95% CI, 0.09-0.78; P = .016). doi = 10.1017/ice.2020.364 id = cord-337747-7sb03moe author = Lagare, Adamou title = Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger date = 2019-10-11 keywords = ARI; Niger; respiratory summary = title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger This study aims to describe viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two hospitals in Niamey, Niger''s capital city, and the reported clinical procedures. 14 This study aims to describe the viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two national hospitals of Niamey, the capital city of Niger, and the reported clinical procedures. In this 1-year prospective study, both viral and bacterial pathogens were detected in high proportion among hospitalized children aged younger than 5 years with febrile ARI in Niamey, Niger. Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger doi = 10.1002/hsr2.137 id = cord-288487-hs3wfffs author = Lambert, Stephen B title = The cost of community-managed viral respiratory illnesses in a cohort of healthy preschool-aged children date = 2008-01-24 keywords = ARI; cost; influenza; study summary = The point estimate of the mean cost of community-managed influenza illnesses in healthy preschool aged children is three times greater than those illnesses caused by RSV and other respiratory viruses. Even for influenza, the most studied of all respiratory viruses, cost-of-illness and vaccine cost-effectiveness evaluations in children have tended to rely on assumptions or use retrospectively collected estimates, often from surveys, for resource utilisation, such as carer time away from work in seeking healthcare or caring for an ill child [6] [7] [8] [9] . Despite overlapping confidence intervals, the finding of most note in this study was the dramatically higher point estimate of the mean cost of influenza A ARIs, being three times higher than illnesses caused by RSV and the other common respiratory viral infections of childhood. Further studies that collect primary, integrated epidemiologic and economic data, particularly indirect costs, directly from families about community-managed ARIs in children, are required. doi = 10.1186/1465-9921-9-11 id = cord-320808-taj5swwc author = Lu, Guilan title = An outbreak of acute respiratory infection at a training base in Beijing, China due to human adenovirus type B55 date = 2020-07-23 keywords = ARI; B55; Beijing; China summary = title: An outbreak of acute respiratory infection at a training base in Beijing, China due to human adenovirus type B55 To isolate HAdV, we inoculated Hep-2 cells with the human adenovirus (HAdV)-positive samples and then carried out sequencing and phylogenetic analysis of the hexon, fiber, and penton genes of the isolated adenoviruses. Furthermore, the clinical laboratory data from this outbreak provides important reference for the clinical diagnosis and may ultimately aid in informing the development of strategies to control and prevent respiratory tract infections caused by HAdV-B55. To help identify the causative pathogen, we collected pharyngeal swab specimens from the affected students and carried out molecular detection and typing, phylogenic analysis, and whole-genome sequencing. The hexon (2841 bp), fiber (978 bp), and penton (1674 bp) sequences from the seven HAdV isolates were 100% identical, suggesting that this outbreak was caused by a single viral strain. Genome sequence of human adenovirus type 55, a re-emergent acute respiratory disease pathogen in China doi = 10.1186/s12879-020-05258-2 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-265257-p9f0pl3y author = Masoud, Khaldoun title = Viral Etiology of Acute Respiratory Infections in Pediatric Patients in Lebanon date = 2019-11-01 keywords = ARI; CVEV; respiratory summary = title: Viral Etiology of Acute Respiratory Infections in Pediatric Patients in Lebanon estimated that 111 500 deaths in children <5 years were attributable to influenza-associated lower respiratory tract infections (LRI) in 2008, the vast majority of which occurred in developing countries. Infants and children younger than 18 years of age with symptoms of ARI disease presenting to the emergency department or the departments of pediatrics of the American University of Beirut Medical Center (AUBMC), Beirut, Lebanon were prospectively recruited between September 2009 to February 2012. In our study, CVEV infection constituted 38.8% of all viral ARI cases and was independently associated with rhinorrhea. Etiology, seasonality and clinical characterization of viral respiratory infections among hospitalized children in Beirut, Lebanon Viral etiologies of lower respiratory tract infections among Egyptian children under five years of age Viral and atypical bacterial detection in acute respiratory infection in children under five years doi = 10.4084/mjhid.2019.059 id = cord-292948-1n5ej08f author = Masse, Shirley title = Epidemiology and Clinical Symptoms Related to Seasonal Coronavirus Identified in Patients with Acute Respiratory Infections Consulting in Primary Care over Six Influenza Seasons (2014–2020) in France date = 2020-06-10 keywords = ARI; HKU1; OC43 summary = title: Epidemiology and Clinical Symptoms Related to Seasonal Coronavirus Identified in Patients with Acute Respiratory Infections Consulting in Primary Care over Six Influenza Seasons (2014–2020) in France Further studies with representative samples should be conducted to provide additional insights into the epidemiology and clinical features of HCoVs. Coronaviruses (CoVs) are an enveloped, single positive-strand RNA species of viruses belonging to the Coronaviridae family, which infect birds and mammals. Here, we document the epidemiological and clinical features of HCoV patients with acute respiratory infection (ARI) observed in general practice. To study the weekly number of HCoVs detected among ILI/ARI patients seen in general practice during the six influenza seasons, we gathered all samples collected by GPs for influenza surveillance and for the IRIIS study (Table 1 and Figure 1 ). doi = 10.3390/v12060630 id = cord-252012-hdjbxah8 author = McErlean, Peter title = Viral diversity in asthma: Immunology and Allergy Clinics of North America: Asthma and Infectious Disease date = 2010-11-01 keywords = ARI; asthma; respiratory; virus summary = Traditionally associated with acute respiratory illness (ARI) or symptoms of the "common cold," the respiratory viruses implicated in asthma exacerbations predominantly possess RNA genomes with a distinct genome organization (positive [1] or negative [À] sense), virus particle (virion) morphology (enveloped or nonenveloped), host cell receptor interaction, and well-defined annual or seasonal prevalence. These "newly identified viruses" (NIVs) including human metapneumovirus (HMPV; described pre-SARS), the human rhinovirus (HRV) species C (HRV-Cs), human coronaviruses (HCoVs)-NL63 and -HKU1, human bocavirus (HBoV), and the KI and WU polyomaviruses (KIPyV and WUPyV) are now the focus of intense research, and their involvement in asthma exacerbations is slowly beginning to be determined. 34 In a retrospective study of clinical samples taken over a 20-year period from young children (median age 14.5 months), the percentage of lower respiratory tract illness (LRTI; including asthma exacerbations and bronchiolitis) associated with any HCoV, HCoV-NL63, or HCoV-OC43 was estimated to be 4.6%, 2.6%, and 1.9%, respectively. doi = 10.1016/j.iac.2010.08.001 id = cord-102515-ch6prsf3 author = Moran, Elizabeth title = Inequality in acute respiratory infection outcomes in the United States: A review of the literature and its implications for public health policy and practice. date = 2020-04-26 keywords = ARI; April; international summary = The health disparities query identifies articles evaluating disparities in health outcomes and healthcare access with inequities in dimensions of race/ethnicity, SES, gender identity and sexual orientation, insurance status, and other populations described as "vulnerable." We then screened studies using title and abstract review to identify articles with a specific focus on all-cause ARI, ILI, RSV, and influenza. In 2009, a number of studies documented social race/ethnic outcome disparities [36] [37] [38] [39] [40] [41] , with lower SES 41 associated with increased exposure risk 36 , as well as overall incidence 37 , hospitalization 38, 39, 41 , complications 36 , and death 39,40 due to pandemic H1N1. The evidence turned up by our review, as well as the issues of racially and socioeconomic disparate exposure risks, coupled with unequal access to testing and treatment made clear by the COVID-19 pandemic, demonstrate that the principles underlying Link & Phelan''s theory of SES and race as fundamental causes of health and illness apply to ARIs as much as many non-communicable diseases as well as infections more classically understood has having social antecedents, such as tuberculosis and diarrheal disease. doi = 10.1101/2020.04.22.20069781 id = cord-257248-aii0tj9x author = O''Grady, K.F. title = Prevalence, codetection and seasonal distribution of upper airway viruses and bacteria in children with acute respiratory illnesses with cough as a symptom date = 2016-02-22 keywords = ARI; RSV summary = Most studies exploring the role of upper airway viruses and bacteria in paediatric acute respiratory infections (ARI) focus on specific clinical diagnoses and/or do not account for virus–bacteria interactions. Bilateral nasal swabs, demographic, clinical and risk factor data were collected at enrollment in children aged <15 years presenting to an emergency department with an ARI and where cough was a symptom. While upper airway specimens (nasopharyngeal swabs) are controversial because they cannot reliably distinguish between carriage and disease [8] , they continue to be widely used in observational and experimental studies of ARI in children, including those attempting to identify associations between organisms and clinical symptoms and/or severity. In 817 children presenting to a tertiary paediatric ED with an ARI and cough, at least one virus or bacterium was detected in nasal swab specimens from 90.6% of cases, while viruses and bacteria were codetected in 51.8%. doi = 10.1016/j.cmi.2016.02.004 id = cord-283946-ts2lyy4p author = Pedersen, N.C title = An isolated epizootic of hemorrhagic-like fever in cats caused by a novel and highly virulent strain of feline calicivirus date = 2000-05-11 keywords = Ari; FCV; October; cat summary = An isolated epizootic of a highly fatal feline calicivirus (FCV) infection, manifested in its severest form by a systemic hemorrhagic-like fever, occurred over a 1-month period among six cats owned by two different employees and a client of a private veterinary practice. The causative agent was isolated from blood and nasal swabs from two cats; the electron microscopic appearance was typical for FCV and capsid gene sequencing showed it to be genetically similar to other less pathogenic field strains. The ®fth cat in this focal epidemic was Aristotle (Ari), a 3.5-year old, neutered male, domestic, indoors-only cat and the son of Ria. There were no signi®cant past health problems; he tested negative for FeLV and FIV infections and had been parenterally vaccinated against rabies and FPHCV on 10 April 1997 Ari presented on 19 October 1998 with a history of an acute onset of lethargy and anorexia of 2 days duration. doi = 10.1016/s0378-1135(00)00183-8 id = cord-319845-oob2ktnz author = Proença-Modena, José Luiz title = Detection of Human Bocavirus mRNA in Respiratory Secretions Correlates with High Viral Load and Concurrent Diarrhea date = 2011-06-20 keywords = ARI; HBoV; PCR; VP1 summary = Therefore, in order to test whether active viral replication of human bocavirus is associated with respiratory diseases and to understand the clinical impact of this virus in patients with these diseases, we performed a 3-year retrospective hospital-based study of HBoV in outpatients and inpatients with symptoms of Acute Respiratory Infections (ARI) in Brazil. This article reports a cross-sectional study of HBoV in ARI patients from Ribeirão Preto, Brazil, in which the shedding of VP1 mRNA in respiratory secretions was used as surrogate marker for active HBoV replication, to look for correlations with viral load, and presence of particular clinical manifestations and simultaneous detection of other respiratory viruses. The results of this cross-sectional study of HBoV in ARI patients from Ribeirão Preto, Brazil, indicate that shedding of VP1 mRNA in respiratory secretions, as a marker of HBoV replication, correlates positively with high viral load, presence of diarrhea, and lack of co-infection by other respiratory viruses. doi = 10.1371/journal.pone.0021083 id = cord-300019-8vxqr3mc author = Shi, Ting title = The Etiological Role of Common Respiratory Viruses in Acute Respiratory Infections in Older Adults: A Systematic Review and Meta-analysis date = 2019-03-08 keywords = ARI; adult; respiratory summary = We aimed to identify all case-control studies investigating the potential role of respiratory viruses in the etiology of ARI in older adults aged ≥65 years. This review supports RSV, Flu, PIV, HMPV, AdV, RV, and CoV as important causes of ARI in older adults and provides quantitative estimates of the absolute proportion of virus-associated ARI cases to which a viral cause can be attributed. Although influenza virus (Flu) is the most widely recognized viral infection associated with respiratory illness, >25 viruses have been linked to pneumonia, causing a substantial disease burden in adults and elderly individuals. Therefore, we aimed to conduct a similar systematic review to identify all case-control studies since 1996 investigating the potential role of respiratory viruses in the etiology of ARIs in older adults aged ≥65 years. doi = 10.1093/infdis/jiy662 id = cord-010170-rwf52bly author = Sutrisna, B. title = Randomised, controlled trial of effectiveness of ampicillin in mild acute respiratory infections in Indonesian children date = 1991-08-24 keywords = ARI; BPH; mild summary = The recommended treatment for mild acute respiratory infections (ARI) in children is supportive care only, but many physicians, especially in developing countries, continue to prescribe antibiotic treatment because they believe it prevents progression to more severe ARI. The recommended treatment for mild acute respiratory infections (ARI) in children is supportive care only, but many physicians, especially in developing countries, continue to prescribe antibiotic treatment because they believe it prevents progression to more severe ARI. In our previous work on ARI in Indonesia (unpublished), we observed that many children with mild ARI were being treated with ampicillin by physicians at Government clinics despite the Ministry of Health guidelines (which accord with WHO recommendations) that only supportive care is required.14 In our discussions with physicians, it became clear that many believed antibiotics were effective at preventing the progression of mild ARI to pneumonia or other forms of severe ARI, which are frequently bacterial in origin. doi = 10.1016/0140-6736(91)90544-y id = cord-349279-wbb7h2zu author = Walker, Gregory J. title = Viruses associated with acute respiratory infection in a community‐based cohort of healthy New Zealand children date = 2019-05-07 keywords = ARI; respiratory summary = The rates of infection and community epidemiology of respiratory viruses in healthy children needs further definition to assist interpretation of molecular diagnostic assays in this population. The most commonly detected viruses in samples collected during ARI were HRV (52.8%), HCoV (11.0%), parainfluenza virus (PIF) (6.0%), IFV (4.5%), RSV (3.8%), and HMPV (3.5%). Detection of any virus and codetection of viruses were both significantly associated with swabs collected during ARI episodes. While their corresponding risk ratios are not considered significant, the number of detections of these viruses is relatively small, and a larger analysis would be required to rule out the clinical significance of detecting HRV-B, AdV and HBoV in ARIs. The effect of viral coinfection on respiratory disease severity in children has not been well established. New molecular virus detection methods and their clinical value in lower respiratory tract infections in children Viruses associated with acute respiratory infection in a community-based cohort of healthy New Zealand children doi = 10.1002/jmv.25493 id = cord-326122-5m1727m1 author = Wishaupt, Jérôme O. title = PCR testing for Paediatric Acute Respiratory Tract Infections date = 2014-08-04 keywords = ARI; PCR; respiratory summary = The Pediatric Infectious Disease Society (PIDS) and the Infectious Diseases Society of America (IDSA) recommend in their guideline ''Community-Acquired Pneumonia (CAP) in Infants and Children'' the use of sensitive and specific tests for the rapid diagnosis of influenza virus and other respiratory viruses in the evaluation of children older than three months of age with CAP [19] . In another recent retrospective study of 177 children with ARI in a general hospital, antibiotic management was not influenced after detecting a viral respiratory pathogen, although the authors state that routine testing of common respiratory pathogens could lead to a better understanding of their role in disease in children with respiratory symptoms [38] . Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children doi = 10.1016/j.prrv.2014.07.002 id = cord-316217-ynh8d853 author = Yoshihara, Keisuke title = Influenza B associated paediatric acute respiratory infection hospitalization in central vietnam date = 2019-02-28 keywords = ARI; influenza summary = In Victoria lineage, Group1 ARI cases were clinically more severe compared to Group5, presenting a greater proportion of wheeze, tachypnea, and lower respiratory tract infection. With regard to the demographic and clinical characterization of overall paediatric ARI hospitalization cases enrolled in the current study (n = 4,429), 2,602 were male (58.8%), and the median age (in months) was 16.6 (IQR: 8.6-27.3). The demographic and clinical characteristics between influenza B (n = 133) and non-influenza B ARI groups (n = 4296) were compared ( Table 2 ). The proportion of paediatric ARI hospitalizations with chest X-ray abnormal findings was also greater in the non-influenza B ARI group ( Furthermore, in the comparison between influenza A and B, influenza B-associated ARI hospitalizations were slightly older with different age distribution pattern (P = 0.002) (Table S2) . doi = 10.1111/irv.12626