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?' ---------------------------------------------------------- 40 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 3018 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 48 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 9 SARS 8 COVID-19 5 patient 3 respiratory 2 influenza 2 covid-19 2 RSV 2 PCR 1 table 1 system 1 statin 1 score 1 remdesivir 1 pregnant 1 orchitis 1 lbw 1 infection 1 illness 1 home 1 hepatitis 1 hcw 1 enterovirus 1 drive 1 dna 1 disease 1 datum 1 camel 1 antibiotic 1 american 1 african 1 adult 1 Wuhan 1 VOMC 1 TTV 1 Sibu 1 SEIR 1 Rickettsia 1 PUI 1 PPE 1 PIV 1 NAT 1 LPV 1 Kapit 1 IPC 1 IFA 1 ICU 1 IAV 1 HRV 1 HLH 1 HKU1 Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 1223 patient 1104 % 657 study 609 infection 385 day 383 c 381 virus 376 disease 344 p 334 influenza 325 case 322 datum 308 time 293 testing 272 illness 256 t 253 treatment 241 outcome 233 year 233 group 233 age 228 test 228 adult 227 hospital 216 care 214 analysis 212 symptom 211 e 193 sample 193 result 192 risk 182 r 175 use 169 trial 165 level 164 population 156 health 155 vaccine 155 pneumonia 153 author 147 cell 144 dose 139 pandemic 139 coronavirus 137 period 137 admission 127 therapy 126 response 118 model 118 child Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 389 SARS 343 COVID-19 280 CoV-2 189 RSV 169 M 145 u 137 PCR 133 s 119 a 110 d 107 Table 91 ID 89 PIV 85 China 84 Health 84 CoV 81 CI 80 A 78 United 77 HIV 76 remdesivir 74 States 72 CTI 65 RT 65 HRV 65 ED 62 ICU 58 TTV 58 Coronavirus 57 t 55 RNA 53 HKU1 53 EBV 52 PPE 52 Open 52 Forum 51 al 51 Supplementary 50 Hospital 50 HLH 49 Wuhan 47 Disease 46 Diseases 45 Infectious 43 US 40 sha 40 c 40 PUI 40 Dis 37 MP Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 573 we 196 it 88 they 60 i 26 she 25 us 19 them 10 he 9 you 6 itself 3 themselves 3 one 2 ourselves 2 ours 2 me Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 3983 be 877 have 319 use 307 include 233 associate 230 report 200 do 172 base 158 receive 154 find 154 compare 146 hospitalize 140 test 138 identify 133 increase 118 perform 118 infect 111 require 107 follow 99 confirm 96 define 96 collect 93 demonstrate 92 evaluate 92 develop 92 consider 90 detect 88 describe 87 suggest 87 provide 87 assess 86 show 82 treat 81 reduce 76 need 75 occur 73 present 72 determine 72 conduct 65 give 65 enrol 64 remain 62 cause 61 observe 59 relate 59 obtain 53 see 52 emerge 52 control 49 decrease Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 543 respiratory 492 not 382 clinical 243 severe 233 positive 227 - 220 high 218 more 213 viral 209 other 183 acute 163 also 162 first 157 low 147 only 135 medical 120 most 119 human 117 however 115 negative 113 significant 113 potential 113 covid-19 110 such 109 well 107 available 103 likely 101 early 97 antibiotic 84 common 83 chronic 81 pregnant 81 old 79 infectious 75 similar 74 patient 72 new 72 further 70 respectively 66 median 66 large 66 important 65 public 65 overall 65 febrile 64 real 64 previously 60 non 60 additional 58 significantly Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 31 least 29 most 17 Most 14 high 11 good 7 large 4 great 2 low 2 early 2 big 1 strong 1 small 1 severe 1 new 1 near 1 easy 1 close 1 bad Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 91 most 11 least 3 hard 2 well 1 highest Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 1 youtu.be 1 www.youtube.com 1 www.wjx.cn 1 www.panfab.org 1 www.nytimes.com 1 www.medcalc.org 1 www.r-project.org 1 wsjkw.gd.gov.cn 1 weibo.com 1 rdvcu.gilead 1 flu.houstonmethodist.org 1 openforuminfectiousdiseases.oxfordjournals.org Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 1 http://youtu.be/ecPjhdVf41k 1 http://www.youtube.com/ 1 http://www.wjx.cn/ 1 http://www.panfab.org/the-team-and-the-project/consortium-members 1 http://www.nytimes.com/interactive/2020/us/wisconsin-coronavirus-cases.html#county 1 http://www.medcalc.org/ 1 http://www.R-project.org/ 1 http://wsjkw.gd.gov.cn/ 1 http://weibo.com/ 1 http://rdvcu.gilead 1 http://flu.houstonmethodist.org/ 1 http://OpenForumInfectiousDiseases.oxfordjournals.org/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 5 patients were more 5 study has several 4 infection were more 4 patients did not 4 patients had detectable 4 patients were also 3 % were male 3 outcome was antibiotic 3 patients receiving lpv 3 study has limitations 3 tests were positive 2 % are also 2 % following first 2 % had grade 2 % were able 2 case developed symptoms 2 cases was higher 2 data were not 2 disease were older 2 group was older 2 illness are not 2 infection had respiratory 2 infection has not 2 influenza testing alone 2 outcomes were not 2 patients had severe 2 patients received antibiotics 2 patients received cti 2 patients requiring imv 2 patients were eligible 2 study did not 2 study does not 2 study is consistent 2 study using real 2 study were not 2 testing was only 1 % developed chronic 1 % developed symptomatic 1 % did not 1 % had at 1 % had coinfections 1 % had exposure 1 % had higher 1 % had low 1 % is similar 1 % require intensive 1 % required icu 1 % were at 1 % were familiar 1 % were males Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 1 adults was not statistically 1 case were not fully 1 cov-2 is not present 1 data are not available 1 data suggesting no advantage 1 day was not available 1 group had no abnormalities 1 groups were not significantly 1 illness are not well 1 illness does not necessarily 1 infections are no longer 1 influenza were not laboratory 1 outcomes is not well 1 outcomes were not mutually 1 patient were not available 1 patients had no detectable 1 study were not normally 1 testing is not routinely A rudimentary bibliography -------------------------- id = cord-305512-p5qchjva author = Alghamdi, Abdulaziz title = Molecular Evidence of Influenza A Virus Circulation in African Dromedary Camels Imported to Saudi Arabia, 2017–2018 date = 2019-09-30 keywords = H1N1; camel summary = doi = 10.1093/ofid/ofz370 id = cord-350767-6kc4hyzo author = Beh, Darius L L title = The Pandemic Academy: Reflections of Infectious Diseases Fellows During COVID-19 date = 2020-06-25 keywords = COVID-19 summary = doi = 10.1093/ofid/ofaa256 id = cord-322524-bq9ok8h1 author = Belongia, Edward A title = Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old date = 2018-11-27 keywords = PCR; RSV; respiratory summary = doi = 10.1093/ofid/ofy316 id = cord-303091-jky6jlrl author = Cellai, Michele title = Characterization of prolonged COVID-19 symptoms in an outpatient telemedicine clinic date = 2020-09-12 keywords = COVID-19; VOMC summary = We identified patients with coronavirus disease 2019 (COVID-19) in a telemedicine clinic who requested ongoing follow-up calls 6 weeks after symptom onset. We seek to describe the persistent symptoms experienced by patients with mild COVID-19 by reviewing records of those who requested follow-up VOMC care for greater than the planned 21 days and more than 6 weeks beyond symptom onset. Chart review included: (1) verification of patient demographics and comorbidities documented at VOMC intake visit, (2) verification of symptom onset dates, (3) review of follow-up notes during the 6 th week of symptoms, (4) review of return to work advice/disability letters, and (5) review of final notes for health status at time of VOMC discharge. For patients who required additional medical evaluation after the acute period (defined as an in-person or telemedicine visit at least 3 weeks into illness), we reviewed evaluation notes, diagnostics, and final diagnoses (including "alternate diagnoses" and "contributing diagnoses" based on provider documentation). doi = 10.1093/ofid/ofaa420 id = cord-311082-sspcz9t6 author = Chen, Shi title = Four Challenges Associated With Current Mathematical Modeling Paradigm of Infectious Diseases and Call for a Shift date = 2020-08-07 keywords = SEIR; covid-19 summary = We identified 4 major challenges associated with the current modeling paradigm (SEIR) that hinder the efforts to accurately characterize the emerging COVID-19 and future epidemics. These challenges included (1) lack of consistent definition of "case"; (2) discrepancy between patient-level clinical insights and population-level modeling efforts; (3) lack of adequate inclusion of individual behavioral and social influence; and (4) allowing little flexibility of including new evidence and insights when our knowledge evolved rapidly during the pandemic. Researchers, clinicians, and public health officials rely on mathematical models to characterize and predict the COVID-19 epidemic, derive critical epidemiological metrics (eg, the basic reproduction number R 0 ), evaluate various intervention strategies, and optimize resource needs [2] . The SEIR modeling paradigm is less practical to handle the complicated clinical, public health, and social system of the COVID-19 pandemic. doi = 10.1093/ofid/ofaa333 id = cord-270703-c8mv2eve author = Christensen, Paul A title = Real-time Communication With Health Care Providers Through an Online Respiratory Pathogen Laboratory Report date = 2018-11-30 keywords = datum; influenza summary = We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. To address these local needs in a major US metropolitan area, our clinical microbiology laboratory implemented an online dashboard to distribute respiratory pathogen data for our 8-hospital system to clinicians, epidemiologists, infection control practitioners, system leadership, and the public. Development of this report began in the Fall 2017, before the respiratory virus season, during which influenza reached an epidemic status across the United States that resulted in supply shortages, testing difficulties, and a widespread public health crisis [4, 5] . In summary, our microbiology laboratory implemented a near real-time Internet report to distribute respiratory pathogen data for our 8-hospital system to clinicians, hospital epidemiologists, infection control committees, system leadership, and the public. doi = 10.1093/ofid/ofy322 id = cord-326642-kc85pev4 author = Cohen, Adam L. title = Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009–2014 date = 2015-09-19 keywords = Africa; HIV; PIV summary = doi = 10.1093/ofid/ofv139 id = cord-003565-14g33n7j author = Frey, Sharon E title = Safety and Immunogenicity of MF59-Adjuvanted Cell Culture–Derived A/H5N1 Subunit Influenza Virus Vaccine: Dose-Finding Clinical Trials in Adults and the Elderly date = 2019-03-01 keywords = H5N1 summary = We evaluated the immunogenicity and safety of an MF59adjuvanted, cell culture-derived, H5N1 subunit influenza virus vaccine in 2 phase II studies; vaccine was administered as either a full-or half-dose formulation to healthy adult or elderly subjects. In conclusion, two 7.5-μg doses of a cell culture-derived, MF59-adjuvanted H5N1 vaccine administered 3 weeks apart were well tolerated and highly immunogenic, raised no safety concerns, and induced robust antibody responses in adult and elderly subjects that met all the immunogenicity criteria required for pandemic vaccine licensure by both the US and European regulatory authorities. A randomised, single-blind, dose-range study to assess the immunogenicity and safety of a cell-culture-derived A/H1N1 influenza vaccine in adult and elderly populations Assessment of the immunogenicity and safety of varying doses of an MF59®-adjuvanted cell culture-derived A/H1N1 pandemic influenza vaccine in Japanese paediatric, adult and elderly subjects doi = 10.1093/ofid/ofz107 id = cord-314517-n1yj2zdy author = Huang, Dayong title = Social media survey and web posting assessment of the COVID-19 response in China: Health worker attitudes towards preparedness and personal protective equipment shortages date = 2020-08-31 keywords = PPE summary = title: Social media survey and web posting assessment of the COVID-19 response in China: Health worker attitudes towards preparedness and personal protective equipment shortages BACKGROUND: Understanding health worker awareness, attitudes, and self-confidence in the workplace can inform local and global responses towards emerging infectious threats, like COVID-19 pandemic response. Health workers satisfied with current preparedness to address COVID-19 were more likely to be female, to obtain knowledge about the SARS-CoV-2 outbreak from government organizations, and to consider their hospital prepared for the outbreak management. They cannot function effectively if they lack personal protective equipment (PPE), essential to ensure continuity of healthcare services during a public health emergency and to avoiding nosocomial acquisitions 5 A c c e p t e d M a n u s c r i p t 6 As of April 4, 2020, 60 Chinese health workers have died, of whom 22 (36.7%) were confirmed dead of COVID-19, according to reports by China Central Television. doi = 10.1093/ofid/ofaa400 id = cord-320511-qnxj7d9l author = Hueston, Linda title = The antibody response to SARS-CoV-2 infection date = 2020-08-27 keywords = IFA; NAT; SARS summary = doi = 10.1093/ofid/ofaa387 id = cord-256195-1hmzgwrw author = Izzy, Saef title = Characteristics and outcomes of Latinx patients with COVID-19 in comparison to other ethnic and racial groups date = 2020-09-01 keywords = COVID-19; african; american summary = 2 In the United States, where a racially and ethnically diverse population has been exposed to infection in the setting of known racial and ethnic health disparities, 14 several news reports have suggested that ethnic and racial minorities, especially Latinx and non-Latin African American individuals, may bear a higher burden of disease during the COVID-19 pandemic. We used medical records available from the largest not-for-profit healthcare system in Massachusetts to examine the association between age, race and ethnicity, reported preexisting comorbidities, and the need for hospitalization and ICU admission in a large study population of COVID-19 positive patients. First, analysis of our large study population confirmed our firsthand clinical experience and showed indeed that Latinx and African American patients are at higher risk of being hospitalized and admitted to ICU level of care with COVID-19, than White patients. doi = 10.1093/ofid/ofaa401 id = cord-032268-oj94e8wo author = Kaeuffer, Charlotte title = The BAS²IC score: a useful tool to identify patients at high risk of early progression to severe COVID-19 date = 2020-09-01 keywords = COVID-19; score summary = We developed a score, based on easily accessible data (age, sex, BMI, dyspnea and inflammatory parameters), to predict the risk of rapid progression to severe disease in hospitalized patients with COVID-19. In a previous multicenter study involving 1,045 hospitalized patients with confirmed COVID-19, we identified several independent risk factors, such as advanced age, obesity and inflammation, associated with the early development of severe disease [3] . In the present study, we aimed to develop a practical score for estimating the risk of rapid progression to severe disease in a cohort of patients hospitalized for COVID-19. [SD], 16), and 612 patients (58.6%) were men (supplementary Table 1 Based on previously identified prognostic factors [3] , we then defined a prognostic BAS²IC score including BMI, age, sex, shortness of breath and inflammatory parameters to screen patients at a risk of developing early severe disease (Table 1 ). doi = 10.1093/ofid/ofaa405 id = cord-252751-prock3co author = Kalligeros, Markos title = Remdesivir Use Compared to Supportive Care in Hospitalized Patients with Severe COVID-19: A Single-Center Experience date = 2020-08-06 keywords = patient; remdesivir summary = To be considered eligible for trial inclusion, patients had to meet the following criteria: 1) Currently hospitalized, aged ≥ 18 years, 2) SARS-CoV-2 infection confirmed by PCR test ≤ 4 days before trial enrollment 3) SpO2 ≤ 94% on room air or requiring supplemental oxygen at screening 4) Presence of radiographic evidence of pulmonary infiltrates. For each patient we extracted the following information: age, sex, race, ethnicity, days from onset of symptoms, imaging results, weight, vital signs and laboratory values (both on admission and during hospitalization), preexisting medical conditions, admission to the intensive care unit (ICU), use of mechanical ventilation, use of systemic corticosteroids [12] , hospitalization outcome (death or discharge) and incidence of acute kidney injury (AKI) using the KDIGO criteria [13] . In order to provide a cohesive assessment of the efficacy of remdesivir, we compared the clinical outcomes of patients who were hospitalized with severe COVID-19 (requiring supplemental oxygen and having abnormal imaging findings) and received either remdesivir or supportive care. doi = 10.1093/ofid/ofaa319 id = cord-310807-p5cb6idp author = Kanwar, Anubhav title = Human Coronavirus-HKU1 Infection Among Adults in Cleveland, Ohio date = 2017-03-25 keywords = CoV; HKU1; adult summary = doi = 10.1093/ofid/ofx052 id = cord-321000-3jd2gn73 author = Karra, Nour title = A Case of Hemophagocytic Lymphohistiocytosis Associated With Mediterranean Spotted Fever in a Healthy 29-Year-Old Female date = 2020-08-13 keywords = HLH; Rickettsia; table summary = doi = 10.1093/ofid/ofaa355 id = cord-259969-q65k590s author = Kösters, Katrin title = Cutaneous Vasculitis in a Patient With COVID-19 date = 2020-10-05 keywords = patient summary = We describe a 43-year-old patient with coronavirus disease 2019 who developed a bullous hemorrhagic rash that progressed to necrotic lesions. Small blood vessel occlusion by microthrombi, which has been described in patients with coronavirus disease 2019 (COVID-19) [1] , could not be demonstrated. Under suspicion of a SARS-CoV-2-induced cutaneous vasculitis, the patient was treated with prednisolone at 0.5 mg per kilogram. Variable and heterogenous skin manifestations in patients with COVID-19 have been described that appear before, during, and after the disease [2] . However, other groups have described skin manifestations in up to 20% of COVID patients [4, 5] . However, our case demonstrates a small/medium-sized vessel vasculitis with involvement of mucous membranes as the cause of skin manifestations in a patient with COVID-19 that appeared late in the disease. Cutaneous manifestations in patients with COVID-19: a preliminary review of an emerging issue doi = 10.1093/ofid/ofaa474 id = cord-001654-o2zfilcl author = Laidler, Matthew R. title = Statin Treatment and Mortality: Propensity Score-Matched Analyses of 2007–2008 and 2009–2010 Laboratory-Confirmed Influenza Hospitalizations date = 2015-03-04 keywords = disease; influenza; statin summary = The use of immunomodulatory agents such as statins to target host inflammatory responses in influenza virus infection has been suggested as an adjunct treatment, especially during pandemics, when antiviral quantities are limited or vaccine production can be delayed. We used population-based, influenza hospitalization surveillance data, propensity score-matched analysis, and Cox regression to determine whether there was an association between mortality (within 30 days of a positive influenza test) and statin treatment among hospitalized cohorts from 2 influenza seasons (October 1, 2007 to April 30, 2008 and September 1, 2009 to April 31, 2010). A study by Vandermeer et al [23] , using data from a populationbased influenza surveillance system, found a protective effect of statin use on mortality among patients hospitalized with laboratory-confirmed influenza during the 2007-2008 influenza season. We used Cox proportional hazards models with robust standard errors, stratified on matched pairs, to determine the effect of statin treatment on mortality within 30 days of a positive influenza test. doi = 10.1093/ofid/ofv028 id = cord-334210-lhadzo7o author = Lepak, Alexander J title = Utility of Repeat Nasopharyngeal SARS-CoV-2 RT-PCR Testing and Refinement of Diagnostic Stewardship Strategies at a Tertiary Care Academic Center in a low Prevalence Area of the United States date = 2020-08-27 keywords = PUI; SARS summary = doi = 10.1093/ofid/ofaa388 id = cord-261619-31jk1vh6 author = Lindholm, David A title = Outcomes of Coronavirus Disease 2019 Drive-Through Screening at an Academic Military Medical Center date = 2020-07-17 keywords = SARS; drive summary = Drive-through coronavirus disease 2019 screening can evaluate large numbers of patients while reducing healthcare exposures and personal protective equipment use. Mitigation of the coronavirus disease 2019 (COVID-19) pandemic requires increased access to testing for its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1] . During the current pandemic, drive-through screening has processed large volumes of patients more efficiently than conventional in-clinic assessment, while reducing potential healthcare exposures and personal protective equipment (PPE) use [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] . The electronic medical record was reviewed (1) for comorbid conditions in positive cases and (2) for additional SARS-CoV-2 testing and BAMC hospital admission within 14 days of screening for all patients. Nonetheless, the median time from screening to admission suggests that some patients requiring additional medical evaluation may have reported to the drive-through. However, none of the screen-only patients later tested positive or were hospitalized for COVID-19 within 14 days. doi = 10.1093/ofid/ofaa306 id = cord-347255-fl9lur4h author = May, Larissa title = Rapid Multiplex Testing for Upper Respiratory Pathogens in the Emergency Department: A Randomized Controlled Trial date = 2019-11-05 keywords = patient; respiratory summary = Secondary outcomes included the proportion of patients with a respiratory pathogen identified by the FilmArray Respiratory Panel test or any other upper respiratory pathogen diagnostic test ordered by the physician; the proportion of patients with a laboratory-confirmed influenza diagnosis; the proportion of patients receiving appropriate anti-influenza treatment or prescription in the ED by an emergency medicine clinician (composite rate of anti-influenza treatment in positive patients and nonuse of anti-influenza treatment in negative patients); the proportion of patients discharged home from the ED vs hospital admission; the proportion of patients with all-cause or respiratory illness-related repeat ED visit, hospital or ICU admission, or death within 30 days; clinician adherence to guidelines for the treatment of patients with influenza (recommendations for use of antivirals only); length of ED stay; length of hospital stay; time to influenza test results; and time to other respiratory pathogen test results. Thus, we conducted a randomized clinical trial of the FilmArray RP vs usual care in ED patients with signs or symptoms of upper respiratory infection or influenza-like illness. doi = 10.1093/ofid/ofz481 id = cord-279334-j0i9ozsz author = McCreary, Erin K title = Coronavirus Disease 2019 Treatment: A Review of Early and Emerging Options date = 2020-03-23 keywords = COVID-19; China; LPV; SARS summary = doi = 10.1093/ofid/ofaa105 id = cord-327609-no58ucyq author = Murkey, Jamie A. title = Hepatitis E Virus–Associated Meningoencephalitis in a Lung Transplant Recipient Diagnosed by Clinical Metagenomic Sequencing date = 2017-06-13 keywords = HEV; hepatitis; patient summary = doi = 10.1093/ofid/ofx121 id = cord-256130-zhlvvuj4 author = Nordén, Rickard title = Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation date = 2018-03-06 keywords = EBV; PCR; TTV; dna summary = Here, we evaluated quantification of torque teno virus (TTV) and Epstein-Barr virus (EBV) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. The aim of the present study was to evaluate levels of TTV and EBV in relation to the frequency of infectious events and acute rejections over time in a prospective manner in a single-center cohort of lung-transplanted patients. The total nucleic acid content was isolated from serum or whole blood samples and analyzed for TTV-, EBV-, and CMV-DNA load by real-time PCR. Comparison of TTV-and EBV-DNA levels in lung transplant recipients who received either Tacrolimus-or Cyclosporinebased therapy revealed that Cyclosporine-treated patients had significantly lower TTV-DNA levels in serum at month 6 post-LTx and onwards, compared with the Tacrolimustreated patients (Figure 1 ). However, we found no association between either TTV-or EBV-DNA load and infectious events or acute rejections, which suggests a limited clinical applicability as biomarkers predicting short-term outcomes related to the net state of immunosuppression. doi = 10.1093/ofid/ofy050 id = cord-267023-w5ig7mrl author = Nori, Priya title = Developing Interactive Antimicrobial Stewardship and Infection Prevention Curricula for Diverse Learners: A Tailored Approach date = 2017-07-20 keywords = IPC; antibiotic; infection summary = We integrated case-based modules, group learning activities, smartphone applications (apps), decision support tools, and prescription audit and feedback into curricula of the medical school, medicine residency program, infectious diseases (ID) fellowship program, and hospital medicine program operations. In a 2013 follow-up multicenter survey of fourth year medical students, 90% desired further education on antimicrobial prescribing, but only 40% were familiar with the role of antimicrobial stewardship (AS) in promoting judicious antimicrobial use and preventing multidrug resistance [3, 4] . It consists of 5 educational strategies designed to bridge perceived learning gaps and lay the foundation for best practices in stewardship and infection prevention in medical students, postgraduate trainees, and mature clinicians. The majority used a quasi-experimental, before-and-after study design with preand postintervention knowledge assessment questions, surveys of learners, or chart review with post-antibiotic prescription audit as methods of evaluation. doi = 10.1093/ofid/ofx117 id = cord-282862-kve6fa49 author = Pastick, Katelyn A title = A Systematic Review of Treatment and Outcomes of Pregnant Women with COVID-19 – A Call for Clinical Trials date = 2020-08-13 keywords = COVID-19; SARS; pregnant summary = doi = 10.1093/ofid/ofaa350 id = cord-274943-fn3m14cn author = Philpott, Erin K title = Febrile Rhinovirus Illness During Pregnancy Is Associated With Low Birth Weight in Nepal date = 2017-04-06 keywords = HRV; illness; lbw summary = doi = 10.1093/ofid/ofx073 id = cord-002631-e6rc8mvu author = Piantadosi, Anne title = Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis and Orchitis date = 2017-07-28 keywords = enterovirus; orchitis summary = title: Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis and Orchitis We found that the genome belonged to the subgroup echovirus 30, which is a common cause of aseptic meningitis but has not been previously reported to cause orchitis. We found that the genome belonged to the subgroup echovirus 30, which is a common cause of aseptic meningitis but has not been previously reported to cause orchitis. Given the relatively unusual presentation of orchitis and meningitis, we performed metagenomic sequencing to obtain additional genomic information about the particular strain of enterovirus and to identify any potential copathogens including mumps virus. We performed metagenomic sequencing and enterovirus genome assembly using methods developed and validated by our group [1, 2] . We performed metagenomic analysis of all sequencing reads from this patient''s CSF and identified enterovirus; no other pathogen, including mumps virus, was found. Aseptic meningitis and orchitis associated with echovirus 6 infection doi = 10.1093/ofid/ofx138 id = cord-350557-7i7122zi author = Rawlings, Stephen A title = No Evidence of SARS-CoV-2 Seminal Shedding Despite SARS-CoV-2 Persistence in the Upper Respiratory Tract date = 2020-08-07 keywords = CoV-2; SARS summary = doi = 10.1093/ofid/ofaa325 id = cord-268662-mw8ec7u2 author = Salton, Francesco title = Prolonged low-dose methylprednisolone in patients with severe COVID-19 pneumonia date = 2020-09-12 keywords = COVID-19; ICU summary = doi = 10.1093/ofid/ofaa421 id = cord-351022-8y43jhmu author = Schwartz, Carmela title = A dynamic response to exposures of healthcare workers to newly diagnosed COVID-19 patients or hospital personnel, in order to minimize cross transmission and need for suspension from work during the outbreak date = 2020-09-01 keywords = COVID-19; hcw summary = doi = 10.1093/ofid/ofaa384 id = cord-260257-phmd0u6d author = Siegler, Aaron J title = Willingness to seek laboratory testing for SARS-CoV-2 with home, drive-through, and clinic-based specimen collection locations date = 2020-06-30 keywords = SARS; covid-19; home summary = METHODS: A cross-sectional, online survey in the United States measured willingness to seek testing if feeling ill under different specimen collection scenarios: home-based saliva, home-based swab, drive-through facility swab, and clinic-based swab. 8, 9 Calls for home-based specimen collection or drive-through specimen collection models to address SARS-CoV-2 virus test scale-up have cogently argued that these approaches have the benefit of (1) avoiding burdening hospitals at a critical time, (2) avoiding potential nosocomial infections (the risk of acquiring disease from clinical or laboratory settings), (3) likely lowering costs, and (4) potentially achieving rapid scale-up due to laboratory centralization. We conducted an online survey to assess patient willingness to use the following SARS-CoV-2 testing modalities for clinical care: home-based specimen collection, drive-through testing, and clinic-based testing. Across a diverse sample of 1,435 participants, one-third more persons reported that they would be willing to collect specimens at home for SARS-CoV-2 testing if they experienced illness, compared to clinic-based testing. doi = 10.1093/ofid/ofaa269 id = cord-288044-ver1nrsz author = Sierra, Beatriz title = Association of early nasopharyngeal immune markers with COVID-19 clinical outcome: predictive value of CCL2/MCP-1 date = 2020-09-03 keywords = CCL2 summary = We found significant differences between the groups with favorable and unfavorable clinical evolution, suggesting the value of the early detection of TNFα, CCL2/MCP-1, CCL3/MIP-1 A c c e p t e d M a n u s c r i p t alpha mRNA in nasopharyngeal swab samples, and the predictive value of CCL2/MCP-1 for the COVID-19 clinical outcome. The objective of this study was to explore the early expression of TNF-alpha, CCL2/MCP-1, CCL3/MIP-1 alpha, IL-10, and TGFβ, previously associated with the uncontrolled cytokines response in the ARDS pathogenesis produced by human pathogenic coronaviruses, thereby taking advantage of the nasopharyngeal swab sample, mandatory for diagnosis of COVID-19 diagnosis in Cuban suspected cases. To determine the possible association of early gene expression of immune mediators in nasopharyngeal swab sample with the clinical evolution, we studied patients with a mild or severe COVID-19 clinical picture, and asymptomatic subjects. doi = 10.1093/ofid/ofaa407 id = cord-310872-2z1wnj63 author = Spellberg, Brad title = Alignment With Market Forces: The “Re-Whithering” of Infectious Diseases date = 2020-06-20 keywords = American; system summary = Approximately 35 years after Dr. Petersdorf first asked the question, we find ourselves once again wondering, "Whither Infectious Diseases?" To answer this question, and align with predominant US market forces, ID experts should push for the following: (1) restrictions regarding utilization of ID diagnostics and antimicrobial agents; (2) pay-for-performance measures regarding antimicrobial prescribing rates; and (3) healthcare reform as called for by the American College of Physicians to move away from fee-for-service medicine. Infectious diseases practitioners may be better at diagnosing and treating infections than those who practice other specialties, but to what financial advantage to healthcare systems that hang on by their fingernails with operating margins under 2% [16, 17] ? First, ID practitioners have unique expertise in the diagnosis and treatment of infections, which can lead to less antimicrobial resistance and superinfections, better outcomes, and lower cost for patients and health systems. doi = 10.1093/ofid/ofaa245 id = cord-296890-08kqtw8s author = Toh, Teck-Hock title = High Prevalence of Viral Infections Among Hospitalized Pneumonia Patients in Equatorial Sarawak, Malaysia date = 2019-02-13 keywords = IAV; Kapit; RSV; Sibu summary = Specimens were examined at our collaborating institutions with a panel of molecular assays for viral pathogens including influenza A (IAV), IBV, ICV, and IDV, human adenovirus (AdV), human enterovirus (EV), human coronavirus (CoV), respiratory syncytial virus subtype A (RSV-A) or RSV-B, and parainfluenza virus (PIV) types 1–4. One study of respiratory samples collected from children living in Kuala Lumpur under 5 years of age between 1982 and 2008 found that 26.4% of the samples were positive by immunofluorescence assays and viral cultures for viral pathogens, with a prevalence of 18.6% for respiratory syncytial virus (RSV), 3.5% for parainfluenza viruses (PIVs), 2.9% for influenza viruses, and 1.37% for adenovirus [10] . The overall objective of this study was to examine the viral etiology of and risk factors for pneumonia among patients admitted to Sibu and Kapit Hospitals between June 2017 and May 2018 and, in doing so, to assist Malaysian collaborators with setting up sustainable real-time molecular assays for viral respiratory pathogens. doi = 10.1093/ofid/ofz074 id = cord-252305-rstxyofq author = Tyan, Kevin title = Considerations for the Selection and Use of Disinfectants Against SARS-CoV-2 in a Healthcare Setting date = 2020-08-31 keywords = SARS summary = We then developed a streamlined set of guidelines to help rapidly evaluate and select suitable disinfectants from List N, including practicality, efficacy, safety, and cost/availability. While this list appears extensive, it lacks guidance or discussion of practical concerns that must be taken into consideration when selecting a disinfectant during this pandemic, including efficacy, practicality, safety profile, and availability. Some products on List N do not have an emerging viral pathogen claim but have been included because they 1) demonstrate efficacy against another human coronavirus similar to SARS-CoV-2 or 2) are EPA-approved against select viruses that are harder-to-kill [5] . The publication of the EPA List N was an important step in providing a resource for selecting disinfectants against SARS-CoV-2 and can be more easily operationalized in healthcare settings when supplemented with additional data on safety, practicality, and availability. doi = 10.1093/ofid/ofaa396 id = cord-010773-z2eogm18 author = Vora, Surabhi B title = Infectious Complications Following CD19 Chimeric Antigen Receptor T-cell Therapy for Children, Adolescents, and Young Adults date = 2020-04-09 keywords = CRS; CTI summary = Pre-CTI risk factors associated with infection included prior hematopoietic cell transplantation (HCT), immunoglobulin G (IgG) level <400 mg/dL, and lymphodepletion other than cyclophosphamide plus fludarabine; post-CTI risk factors included higher-severity CRS and IgG <400 mg/dL. Finally, these patients often develop cytokine release syndrome (CRS) following CTI, which may require treatment with anti-interleukin 6 (IL-6) therapies (eg, tocilizumab), steroids, and admission to the intensive care unit (ICU), with associated increased risk for immunosuppression and nosocomial infections [8] [9] [10] . This study is the first in-depth description of the frequency, type, severity, and risk factors for infections following CD-19 CAR T-cell therapy in children, adolescents, and young adults. In a study of adult CTI recipients, the median time to neutrophil recovery was 6 days, but prolonged cytopenias have been demonstrated previously, even in patients with MRD-negative remission after CAR T-cell therapy [3, 7, 11, 21] . doi = 10.1093/ofid/ofaa121 id = cord-258113-mnou31j3 author = Wang, Yaping title = Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China date = 2020-05-19 keywords = SARS; Wuhan; patient summary = title: Clinical Characteristics of Patients Infected With the Novel 2019 Coronavirus (SARS-Cov-2) in Guangzhou, China CONCLUSIONS: Most of the patients infected with SARS-CoV-2 in Guangzhou, China are not severe cases and patients with older age, male, and decreased albumin level were more likely to develop into severe ones. [5] studied the clinical features of 99 patients with COVID-19 and found that SARS-Cov-2 was more likely to infect older men with comorbidities and to lead to acute respiratory distress syndrome (ARDS). Among all patients, univariate analysis indicated that age, sex, imported disease, incubation period, interval between hospital admission and symptom onset, any coexisting medical condition, leukocyte count, neutrophil count, lymphocyte count, PCT, LDH, CK, ALB, AST, and D-dimer were associated with disease severity. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series doi = 10.1093/ofid/ofaa187 id = cord-303935-qdehf6rb author = Yun, Heather C. title = Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine date = 2015-09-01 keywords = respiratory summary = doi = 10.1093/ofid/ofv120