bluuebunny/crossref_metadata_2025_split huggingface dataset:
The timing of one-shot interventions for epidemic control
Authors: Lauro Francesco Di , Kiss István Z. , Miller Joel C. 
Published: March 2020

AbstractThe apparent early success in China’s large-scale intervention to control the COVID-19 epidemic has led to interest in whether other countries can replicate it as well as concerns about a resurgence of the epidemic if or when China relaxes the interventions. In this paper we look at the impact of a single short-term intervention on an epidemic. We see that if an intervention cannot be sustained long-term, it has the greatest impact if it is imposed once infection levels have become large enough that there is an appreciable number of infections present. For minimising the total number infected it should start close to the peak so that there is no rebound once the intervention is stopped, while to minimise the peak prevalence, it should start earlier, allowing two peaks of comparable size rather than one very large peak. In populations with distinct subgroups, synchronized interventions are less effective than targeting the interventions in each sub-population separately.We do not attempt to clearly determine what makes an intervention sustainable or not. We believe that is a policy question. If an intervention is sustainable, it should be kept in place. Our intent is to offer insight into how best to time an intervention whose impact on society is too great to maintain.
Validity of Wrist and Forehead Temperature in Temperature Screening in the General Population During the Outbreak of 2019 Novel Coronavirus: a prospective real-world study
Authors: Chen Ge , Xie Jiarong , Dai Guangli , Zheng Peijun , Hu Xiaqing , Lu Hongpeng , Xu Lei , Chen Xueqin , Chen Xiaomin 
Published: March 2020

AbstractAimsTemperature screening is important in the population during the outbreak of 2019 Novel Coronavirus (COVID-19). This study aimed to compare the accuracy and precision of wrist and forehead temperature with tympanic temperature under different circumstances.MethodsWe performed a prospective observational study in a real-life population. We consecutively collected wrist and forehead temperatures in Celsius (°C) using a non-contact infrared thermometer (NCIT). We also measured the tympanic temperature using a tympanic thermometers (IRTT) and defined fever as a tympanic temperature ≥37.3°C.ResultsWe enrolled a total of 528 participants including 261 indoor and 267 outdoor participants. We divided outdoor participants into four types according to their means of transportation to the hospital as walk, bicycle, electric vehicle, car, and inside the car. Under different circumstance, the mean difference ranged from −1.72 to −0.56°C in different groups for the forehead measurements, and −0.96 to −0.61°C for the wrist measurements. Both measurements had high fever screening abilities in inpatients (wrist: AUC 0.790; 95% CI: 0.725-0.854, P <0.001; forehead: AUC 0.816; 95% CI: 0.757-0.876, P <0.001). The cut-off value of wrist measurement for detecting tympanic temperature ≥37.3°C was 36.2°C with a 86.4% sensitivity and a 67.0% specificity, and the best threshold of forehead measurement was also 36.2°C with a 93.2% sensitivity and a 60.0% specificity.ConclusionsWrist measurement is more stable than forehead measurement under different circumstance. Both measurements have great fever screening abilities for indoor patients. The cut-off value of both measurements was 36.2°C. (ClinicalTrials.gov number: NCT04274621)
Estimating the burden of United States workers exposed to infection or disease: a key factor in containing risk of COVID-19 infection
Authors: Baker Marissa G. , Peckham Trevor K. , Seixas Noah S. 
Published: March 2020

AbstractIntroductionWith the global spread of COVID-19, there is a compelling public health interest in quantifying who is at increased risk of disease. Occupational characteristics, such as interfacing with the public and being in close quarters with other workers, not only put workers at high risk for disease, but also make them a nexus of disease transmission to the community. This can further be exacerbated through presenteeism, the term used to describe the act of coming to work despite being symptomatic for disease. Understanding which occupational groups are exposed to infection and disease in the workplace can help to inform public health risk response and management for COVID-19, and subsequent infectious disease outbreaks.MethodsTo estimate the burden of United States workers exposed to infection and disease in the workplace, national employment data (by Standard Occupational Classification) maintained by the Bureau of Labor Statistics (BLS) was merged with BLS O*NET survey data, which ranks occupations with particular physical, ergonomic, and structural exposures. For this analysis, occupations reporting exposure to infection or disease more than once a month was the focus.ResultsBased on our analyses, approximately 10% (14.4 M) of United States workers are employed in occupations where exposure to disease or infection occurs at least once per week. Approximately 18.4% (26.7 M) of all United States workers are employed in occupations where exposure to disease or infection occurs at least once per month. While the majority of exposed workers are employed in healthcare sectors, other occupational sectors also have high proportions of exposed workers. These include protective service occupations (e.g. police officers, correctional officers, firefighters), office and administrative support occupations (e.g. couriers and messengers, patient service representatives), education occupations (e.g. preschool and daycare teachers), community and social services occupations (community health workers, social workers, counselors), and even construction and extraction occupations (e.g. plumbers, septic tank installers, elevator repair).ConclusionsThe large number of persons employed in a wide variety of occupations with frequent exposure to infection and disease underscore the importance of all workplaces developing risk response plans for COVID-19. This work also serves as an important reminder that the workplace is a key locus for public health interventions, which could protect both workers and the communities they serve.
Partial RdRp sequences offer a robust method for Coronavirus subgenus classification
Authors: Wilkinson David A , Joffrin Lea , Lebarbenchon Camille , Mavingui Patrick 
Published: March 2020

AbstractThe recent reclassification of theRiboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (familyCoronaviridae, subfamilyOrthocoronavirinae) represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardisation for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a partial region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with genome-scale analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses is sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, “MyCoV”, which provides a method for attributing subgenus and assessing the reliability of the attribution.Importance StatementThe analysis of polymerase chain reaction amplicons derived from biological samples is the most common modern method for detection and classification of infecting viral agents, such as Coronaviruses. Recent updates to the official standard for taxonomic classification of Coronaviruses, however, may leave researchers unsure as to whether the viral sequences they obtain by these methods can be classified into specific viral taxa due to variations in the sequences when compared to type strains. Here, we present a plausible method for defining genetic dissimilarity cut-offs that will allow researchers to state which taxon their virus belongs to and with what level of certainty. To assist in this, we also provide the R package ‘MyCoV’ which classifies user generated sequences.
Transmission interval estimates suggest pre-symptomatic spread of COVID-19
Authors: Tindale Lauren C. , Coombe Michelle , Stockdale Jessica E. , Garlock Emma S. , Lau Wing Yin Venus , Saraswat Manu , Lee Yen-Hsiang Brian , Zhang Louxin , Chen Dongxuan , Wallinga Jacco , Colijn Caroline 
Published: March 2020

AbstractBackgroundAs the COVID-19 epidemic is spreading, incoming data allows us to quantify values of key variables that determine the transmission and the effort required to control the epidemic. We determine the incubation period and serial interval distribution for transmission clusters in Singapore and in Tianjin. We infer the basic reproduction number and identify the extent of pre-symptomatic transmission.MethodsWe collected outbreak information from Singapore and Tianjin, China, reported from Jan.19-Feb.26 and Jan.21-Feb.27, respectively. We estimated incubation periods and serial intervals in both populations.ResultsThe mean incubation period was 7.1 (6.13, 8.25) days for Singapore and 9 (7.92, 10.2) days for Tianjin. Both datasets had shorter incubation periods for earlier-occurring cases. The mean serial interval was 4.56 (2.69, 6.42) days for Singapore and 4.22 (3.43, 5.01) for Tianjin. We inferred that early in the outbreaks, infection was transmitted on average 2.55 and 2.89 days before symptom onset (Singapore, Tianjin). The estimated basic reproduction number for Singapore was 1.97 (1.45, 2.48) secondary cases per infective; for Tianjin it was 1.87 (1.65, 2.09) secondary cases per infective.ConclusionsEstimated serial intervals are shorter than incubation periods in both Singapore and Tianjin, suggesting that pre-symptomatic transmission is occurring. Shorter serial intervals lead to lower estimates of R0, which suggest that half of all secondary infections should be prevented to control spread.
Epidemiological and clinical features of 291 cases with coronavirus disease 2019 in areas adjacent to Hubei, China: a double-center observational study
Authors: Chen Xu , Zheng Fang , Qing Yanhua , Ding Shuizi , Yang Danhui , Lei Cheng , Yin Zhilan , Zhou Xianglin , Jiang Dixuan , Zuo Qi , He Jun , Lv Jianlei , Chen Ping , Chen Yan , Peng Hong , Li Honghui , Xie Yuanlin , Liu Jiyang , Zhou Zhiguo , Luo Hong 
Published: March 2020

AbstractBackgroundThe clinical outcomes of COVID-19 patients in Hubei and other areas are different. We aim to investigate the epidemiological and clinical characteristics of patient with COVID-19 in Hunan which is adjacent to Hubei.MethodsIn this double-center, observational study, we recruited all consecutive patients with laboratory confirmed COVID-19 from January 23 to February 14, 2020 in two designated hospitals in Hunan province, China. Epidemiological and clinical data from patients’ electronic medical records were collected and compared between mild, moderate and severe/critical group in detail. Clinical outcomes were followed up to February 20, 2020.Findings291 patients with COVID-19 were categorized into mild group (10.0%), moderate group (72.8%) and severe/critical group (17.2%). The median age of all patients was 46 years (49.8% were male). 86.6% patients had an indirect exposure history. The proportion of patients that had been to Wuhan in severe/critical group (48.0% vs 17.2%, p=0.006) and moderate group (43.4% vs 17.2%, p=0.007) were higher than mild group. Fever (68.7%), cough (60.5%), and fatigue (31.6%) were common symptoms especially for severe and critical patients. Typical lung imaging finding were bilateral and unilateral ground glass opacity or consolidation. Leukopenia, lymphopenia and eosinopenia occurred in 36.1%, 22.7% and 50.2% patients respectively. Increased fibrinogen was detected in 45 of 58 (77.6%) patients with available results. 29 of 44 (65.9%) or 22 of 40 (55.0%) patients were positive in Mycoplasma pneumonia or Chlamydia pneumonia antibody test respectively. Compared with mild or moderate group, severe/critical group had a relative higher level of neutrophil, Neutrophil-to-Lymphocyte Ratio, h-CRP, ESR, CK, CK–MB, LDH, D-dimer, and a lower level of lymphocyte, eosinophils, platelet, HDL and sodium (all p<0.01). Most patients received antiviral therapy and Chinese Medicine therapy. As of February 20, 2020, 159 (54.6%) patients were discharged and 2 (0.7%) patients died during hospitalization. The median length of hospital stay in discharged patients was 12 days (IQR: 10-15).InterpretationThe epidemiological and clinical characteristics of COVID-19 patients in Hunan is different from patients in Wuhan. The proportion of patients that had been to Wuhan in severe/critical group and moderate group were higher than mild group. Laboratory and imaging examination can assist in the diagnosis and classification of COVID-19 patients.
Restoration of leukomonocyte counts is associated with viral clearance in COVID-19 hospitalized patients
Authors: Chen Xiaoping , Ling Jiaxin , Mo Pingzheng , Zhang Yongxi , Jiang Qunqun , Ma Zhiyong , Cao Qian , Hu Wenjia , Zou Shi , Chen Liangjun , Yao Lei , Luo Mingqi , Chen Tielong , Deng Liping , Liang Ke , Song Shihui , Yang Rongrong , Zheng Ruiying , Gao Shicheng , Gui Xien , Ke Hengning , Hou Wei , Lundkvist Åke , Xiong Yong 
Published: March 2020

SummaryBackgroundViral clearance is one important indicator for the recovery of SARS-CoV-2 infected patients. Previous studies have pointed out that suboptimal T and B cell responses can delay viral clearance in MERS-CoV and SARS-CoV infected patients. The role of leukomonocytes in viral clearance of COVID-19 patients is not yet well defined.MethodsFrom January 26 to February 28, 2020, an observational study was launched at the Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China. We enrolled 25 laboratory-confirmed COVID-19 patients, whose throat-swab specimens were tested positive for SARS-CoV-2 infection by qRT-PCR. To investigate the factors that contribute to the viral clearance, we comprehensively analyzed clinical records, counts of lymphocyte subsets including CD3+, CD4+, CD8+ T cells, B cells and NK cells in the patients who successfully cleared SARS-CoV-2, and compared to those that failed to, after a standardized treatment of 8-14 days.FindingsIn 25 enrolled COVID-19 patients, lymphopenia was a common feature. After the treatment, 14 out of the 25 enrolled patients were tested negative for SARS-CoV-2. The patients that cleared the infection had restored the numbers of CD3+, CD4+, CD8+ T cells and B cells as compared to the still viral RNA positive patients, while the recovered patients had a higher count of leukomonocytes.ConclusionsBy comparison of leukomonocytes counts in COVID-19 patients at different stages of the disease, we found that CD3+, CD4+, CD8+ T cells and B cells appear to play important roles in viral clearance. The restoration of leukomonocytes counts from peripheral blood can be used as prognosis for the recovery of an COVID-19 infection. We propose that restoration of leukomonocytes counts can be added to the COVID-19 diagnostic guidance as a criterion for releasing and discharging patients.
Increased Expression of Colonic Mucosal Melatonin in Patients with Irritable Bowel Syndrome Correlated with Gut Dysbiosis
Authors: Wang Ben , Zhu Shiwei , Liu Zuojing , Wei Hui , Zhang Lu , Pei Fei , He Meibo , Zhang Jindong , Sun Qinghua , Duan Liping 
Published: March 2020

AbstractDysregulation of the gut microbiota/gut hormone axis contributes to the pathogenesis of irritable bowel syndrome (IBS). Melatonin plays a beneficial role in gut motility and immunity. However, altered expression of local mucosal melatonin in IBS and its relationship with the gut microbiota remain unclear. Therefore, we aimed to detect the colonic melatonin levels and microbiota profiles in patients with diarrhea-predominant IBS (IBS-D) and explore their relationship in germ-free (GF) rats and BON-1 cells. Thirty-two IBS-D patients and twenty-eight healthy controls (HC) were recruited. Fecal specimens from IBS-D patients and HCs were separately transplanted into GF rats by gavage. The levels of colon mucosal melatonin were assessed by immunohistochemical methods, and fecal microbiota communities were analyzed using 16S rDNA sequencing. The effect of butyrate on melatonin synthesis in BON-1 cells was evaluated by ELISA. Melatonin levels were significantly increased in IBS-D patients compared with HC and were significantly negatively correlated with visceral sensitivity in IBS-D patients. GF rats inoculated with fecal microbiota from IBS-D patients had high colonic melatonin levels. Butyrate-producing Clostridium cluster XIVa species, such as Roseburia species and Lachnospira species, were positively related to colonic mucosal melatonin expression. Butyrate significantly increased melatonin secretion in BON-1 cells. Increased melatonin expression may be an adaptive protective mechanism in the development of IBS-D. Moreover, some Clostridium cluster XIVa species could increase melatonin expression via butyrate production. Modulation of the gut hormone/gut microbiota axis offers a promising target of interest for IBS in the future.
Key Points of Clinical and CT Imaging Features of 2019 Novel Coronavirus (2019-nCoV) Imported Pneumonia Based On 21 Cases Analysis
Authors: Xu Z.F. , Wu W.X. , Jin Y.B. , Pan A.Z. 
Published: March 2020

AbstractBackground and ObjectiveWHO Director-General declared that the 2019-nCoV outbreak constitutes a Public Health Emergency of International Concern,and the outbreak is still on-going.Chest CT had been a key component of the diagnostic workup for patients with suspected infection. In this retrospective study, we attempt to summarize and analyze the chest CT features of 2019-nCov infections, and to identify the typical features to improved the diagnostic accuracy of new coronavirus pneumonia (NCP).MethodsChest CT scans and Clinical data of 21 patients confirmed NCP in our hospital were enrolled.These patients were divided into mild and sever group according to clinical manifestations described by the 6th clinical practice guideline of NCP in China. Main clinical and chest CT features were analyzed and identify.ResultsFever (85.7%) and cough (80.9%) were the two main symptoms of NCP patients.More significantly higher incidence (85.7%) of shortness of breath in the severe cases. Multiple lesions in both lungs and with incidence of GGO(100%),vascular enlargement (76.5%) and cobblestone/reticular pattern(70.6%) were the major feature.The incidence of consolidation, mixed pattern and vascular enlargement features were up to 100% in the severe group, significantly higher than that of patients in mild group. In addition, the incidence of air-bronchogram, dilated bronchi with thickened wall and fibrosis in the severe group was significantly higher than that in the mild group.ConclusionsFever and cough are the typical clinical features of NCP patients, and chest CT mainly manifested as multiple lesions in both lungs, often accompanied by GGO, vascular enlargement and cobblestone/reticular pattern.Changes in these main CT features can indicate development of the diseaseSummary2019 novel Coronavirus (2019-nCov) had typical clinical manifestations (fever and cough), and presented with characteristic chest CT imaging features (multiple lesions in both lungs, often accompanied by GGO, vascular enlargement and cobblestone/reticular pattern), which are helpful to the radiologist in the early detection and diagnosis of this emerging global health emergency. In addition, changes in these main CT features can indicate development of the disease.HighlightsFever (85.7%) and cough (80.9%) were the two main symptoms of NCP patients.The incidence of shortness of breath was 85.7% in the severe cases, significantly higher than 21.4% in the mild cases.Multiple lesions in both lungs and with incidence of GGO (100%), vascular enlargement (76.5%) and cobblestone/reticular pattern (70.6%) were the major features of NCP patients. 85.7% of cases in serve group displayed 4-5 lobes were involved simultaneously.Changes in these main CT imaging features can indicate development of the disease. About 19.1% of patients (4 of 21) presented with a normal CT.
Psychological impact of the coronavirus disease 2019 (COVID-19) outbreak on healthcare workers in China
Authors: Dai Yuhong , Hu Guangyuan , Xiong Huihua , Qiu Hong , Yuan Xianglin 
Published: March 2020

AbstractIntroductionSince the outbreak of coronavirus disease 2019 (COVID-19), more than 3000 (including clinical diagnosis) healthcare workers (HCWs) have been infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China. This study is aimed to investigate the risk perception and immediate psychological state of HCWs in the early stage of the COVID-19 epidemic.MethodsThis study utilized a cross-sectional survey designed on a convenient sample of 4357 HCWs in China. Its data were collected using anonymous structured questionnaires distributed through social software. 6 questions were set to evaluate the participants’ risk perception of COVID-19, and a General Health Questionnaire was used to identify the participants’ immediate psychological status. Descriptive statistics were used for data analysis. Risk perception and psychological status were compared by demographic characteristics and COVID-19 exposure experiences.ResultA total of 4,600 questionnaires were distributed, and 4,357 qualified ones (94.7%) were collected. The main concerns of HCWs are: infection of colleagues (72.5%), infection of family members (63.9%), protective measures (52.3%) and medical violence (48.5%). And 39.1% of the HCWs had psychological distress, especially working in Wuhan, participating in frontline treatments, having been isolated and having family members or colleagues infected.ConclusionsThe finding indicating that, faced with the COVID-19 epidemic, HCWs, especially in Wuhan, were worried about the risks of infection and protective measures, resulting in psychological distress, so further actions should be taken.
Influence of spatial structure on protein damage susceptibility – A bioinformatics approach
Authors: Fichtner Maximilian , Schuster Stefan , Stark Heiko 
Published: March 2020

AbstractAging research is a very popular field of research in which the gradual transformation of functional states into dysfunctional states are studied. Here we only consider the molecular level, which can also have effects on the macroscopic level. It is known that the proteinogenic amino acids differ in their modification susceptibilities and this can affect the function of proteins. For this it is important to know the distribution of amino acids between the protein surface/shell and the core. This was investigated in this study for all known structural data of peptides and proteins. As a result it is shown that the surface contains less susceptible amino acids than the core with the exception of thermophilic organisms. Furthermore, proteins could be classified according to their susceptibility. This can then be used in applications such as phylogeny, aging research, molecular medicine and synthetic biology.