title: Towards a pro-silience framework: A literature review on quantitative modelling of resilient 3PL supply chain network designs

text: The increasingly dynamic and volatile market environment has elevated the importance of handling operational risks in supply chain networks. Also, black swan risks are constantly evolving and can strike from almost anywhere, including natural disaster, cyber risk, or viruses. As more companies are outsourcing their logistics to third-party logistics (3PL), at the same time, supply chain risks and uncertainties are also shifted to 3PLs. A 3PL's supply chain network capability to assure continuity can be expressed in terms of resilience, i.e., the ability of sensing and responding to disturbances or threats. Operations research/management science (OR/MS) methods have been widely applied in supply chain management. The objective of this paper is to look into research regarding the development of resilient 3PL supply chain network designs through the utilization of OR/MS methods. After extensive literature review, a so called pro-silience framework is developed aiming at improving resilience from a 3PL perspective maintaining or increasing its competitive advantage during and after major disruptions, yet also maintain competitiveness under normal operating conditions. Additionally, the framework offers insights into topics for future research.


title: Early Prediction of Disease Progression in 2019 Novel Coronavirus Pneumonia Patients Outside Wuhan with CT and Clinical Characteristics

text: Objective: To determine the predictive value of CT and clinical characteristics for short-term disease progression in patients with 2019 novel coronavirus pneumonia (NCP). Materials and Methods: 224 patients with confirmed 2019 novel coronavirus (COVID-19) infection outside Wuhan who had chest CT examinations were retrospectively screened. Clinical data were obtained from electronic medical records. CT images were reviewed and scored for lesion distribution, lobe and segment involvement, ground-glass opacities, consolidation, and interstitial thickening. All included patients with moderate NCP were observed for at least 14 days from admission to determine whether they exacerbated to severe NCP (progressive group) or not (stable group). CT and clinical characteristics between the two groups were compared, and multivariate logistic regression and sensitivity analyses were performed to identify the risk factors for developing severe NCP. Results: A total of 141 patients with moderate NCP were included, of which 15 (10.6%) patients developed severe NCP during hospitalization and assigned to the progressive group. Multivariate logistic regression analysis showed that higher neutrophil-to-lymphocyte ratio (NLR) (odds ratio [OR] and 95% confidence interval [CI], 1.26 [1.04-1.53]; P = 0.018) and CT severity score (OR and 95% CI, 1.25 [1.08-1.46]; P = 0.004) on admission were independent predictors for progression to severe NCP, and sensitivity analysis confirmed the consistent results in nonimported patients but not in imported patients. However, no significant difference in lung involvement was found on CT between imported and nonimported patients (all P > 0.05). Patients who were admitted more than 4 days from symptom onset tended to have more severe lung involvement. Spearman correlation analysis showed the close association between CT severity score and inflammatory indexes (r = 0.17~0.47, all P < 0.05). Conclusion: CT severity score was associated with inflammatory levels and higher NLR and CT severity score on admission were independent risk factors for short-term progression in patients with NCP outside Wuhan. Furthermore, early admission and surveillance by CT should be recommended to improve clinical outcomes.


title: Using input-output analysis to model the impact of pandemic mitigation and suppression measures on the workforce

text: The “flatten the curve” graphic has recently become a common tool to visualize the extent to which pandemic suppression and mitigation measures could potentially reduce and delay the number of daily infections due to a pandemic. The COVID-19 pandemic has challenged the capacity of the many healthcare systems and created cascading economic impacts on interdependent sectors of the global society. This paper specifically explores the impact of pandemics on the workforce. The model proposed in this paper comprises of three major steps. First, sources for epidemic curves are identified to generate the attack rate, which is the daily number of infections normalized with respect to the population of the affected region. Second, the model assumes that the general attack rate can be specialized to reflect sector-specific workforce classifications, noting that each economic sector has varying dependence on the workforce. Third, using economic input-output (IO) data from the US Bureau of Economic Analysis, this paper analyzes the performance of several mitigation and suppression measures relative to a baseline pandemic scenario. Results from the IO simulations demonstrate the extent to which mitigation and suppression measures can flatten the curve. This paper concludes with reflections on other consequences of pandemics such as the mental health impacts associated with social isolation and the disproportionate effects on different socioeconomic groups.


title: IL-33 expression in response to SARS-CoV-2 correlates with seropositivity in COVID-19 convalescent individuals

text: Our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still developing. We investigated seroprevalence and immune responses in subjects professionally exposed to SARS-CoV-2 and their family members (155 individuals; ages 5-79 years). Seropositivity for SARS-CoV-2 spike glycoprotein aligned with PCR results that confirmed previous infection. Anti-spike IgG titers remained high 60 days post-infection and did not associate with symptoms, but spike-specific IgM did associate with malaise and fever. We found limited household transmission, with children of infected individuals seldomly seropositive, highlighting professional exposure as the dominant route of infection in our cohort. We analyzed PBMCs from a subset of seropositive and seronegative adults. TLR7 agonist- activation revealed an increased population of IL-6+TNF-IL-1{beta}+ monocytes, while SARS-CoV-2 peptide stimulation elicited IL-33, IL-6, IFNa2, and IL-23 expression in seropositive individuals. IL-33 correlated with CD4+ T cell activation in PBMCs from convalescent subjects, and was likely due to T cell-mediated effects on IL-33- producing cells. IL-33 is associated with pulmonary infection and chronic diseases like asthma and COPD, but its role in COVID-19 is unknown. Analysis of published scRNAseq data of bronchoalveolar lavage fluid (BALF) from patients with mild to severe COVID-19 revealed a population of IL-33-producing cells that increases with disease. Together these findings show that IL-33 production is linked to SARS-CoV- 2 infection and warrant further investigation of IL-33 in COVID-19 pathogenesis and immunity.


title: Adjuvant corticosteroid therapy for critically ill patients with COVID-19

text: Addition of adjuvant corticosteroid therapy to standard antiviral treatment of patients with coronavirus disease (COVID-19) is common in clinical practice. However, evidence is scarce regarding the efficacy of adjuvant corticosteroids in patients who are critically ill. We retrospectively evaluated the effects of adjuvant corticosteroid treatment on the outcome of 244 critically ill patients with COVID-19, using a risk stratification model that adjusts for potential differences between the steroid group (n=151) and the non-steroid group (n=93). We observed that adjuvant corticosteroid therapy was independent from 28-day mortality, either in multivariate logistic regression of the entire cohort after adjustment for major mortality-associated variables (age, SpO2/FiO2, and lymphocyte count) and individual propensity score (adjusted OR: 1.05; 95% CI: -1.92-2.01), or in propensity score-matched (1:1 without replacement) case-control analysis (62 patients in 31 pairs; log-rank test P=0.17). Additionally, subgroup analyses of 147 (60%) patients who had dyspnea and 87 (36%) patients who had ARDS revealed corticosteroid treatment was not associated with clinical outcome (both, P>0.3). However, increased corticosteroids dosage was significantly associated with elevated mortality risk after adjustment for administration duration (P=0.003); every ten-milligram increase in hydrocortisone-equivalent dosage was associated with additional 4% mortality risk (adjusted HR: 1.04, 95% CI: 1.01-1.07). Our findings indicated that limited effect of corticosteroid therapy could pose to overall survival and prudent dose within effective limits may be recommended for critically ill patients under certain circumstances.


title: The Impact of School Closure for COVID-19 on the US Healthcare Workforce and the Net Mortality Effects

text: Background COVID-19 is leading to the implementation of social distancing policies around the world and in the United States, including school closures. The evidence that mandatory school closures reduce cases and ultimately mortality mostly comes from experience with influenza or from models that do not include the impact of school closure on the healthcare labor supply or the role of the healthcare labor force in reducing the per infection mortality from the pathogen. There is considerable uncertainty of the incremental effect of school closures on transmission and lives saved from school closures. The likely, but uncertain, benefits from school closure need to be weighed against uncertain, and seldom quantified, costs of healthcare worker absenteeism associated with additional child care obligations. Methods We analyze data from the US Current Population Survey to measure the potential child care obligations for US healthcare workers that will need to be addressed if school closures are employed as a social distancing measure. We account for the occupation within the healthcare sector, state, and household structure to identify the segments of the healthcare labor force that are most exposed to child care obligations from school closures. We use these estimates to identify the critical level for the importance of healthcare labor supply in increasing a patient's COVID-19 survival probability that would undo the benefits of school closures and ultimately increase cumulative mortality. Findings The US healthcare sector has some of the highest child care obligations in the United States. 29% of healthcare provider households must provide care for children 3-12. Assuming non-working adults or a sibling 13 years old or older can provide child care, leaves 15% of healthcare provider households in need of childcare during a school closure, while 7% of healthcare households are single-parent households. We document the substantial variation within the healthcare system. For example, 35% of medical assistants and 31% of nursing, psychiatric, and home health aide households have child care obligations, while only 24% of emergency medical personnel have childcare obligations. Child care obligations can vary between states by over 10 percentage points. A 15% decline in the healthcare labor force, combined with reasonable parameters for COVID-19 such as a 15% case reduction from school closings and 2% baseline mortality rate implies that a 15% loss in the healthcare labor force must decrease the survival probability per percent healthcare worker lost by 17.6% for a school closure to increase cumulative mortality. This means that the per infection mortality rate cannot increase from 2% to 2.35% when the healthcare workforce declines by 15%; otherwise, school closures will lead to a greater number of deaths than they prevent. For school closures to unambiguously provide a net reduction in COVID-19 mortality with these parameters, the school closures must reduce cases by over 25%. Conclusion School closures come with many tradeoffs. Setting aside economic costs, school closures implemented to reduce COVID-19 spread create unintended childcare obligations, which are particularly large in healthcare occupations. Detailed data are provided to help public health officials make informed decisions about the tradeoffs associated with closing schools. The results suggest that it is unclear if the potential contagion prevention from school closures justifies the potential loss of healthcare workers from the standpoint of reducing cummulative mortality.


title: Elucidating the differences in the molecular mechanism of receptor binding between 2019-nCoV and the SARS-CoV viruses using computational tools

text: The outbreak of the 2019-nCoV coronavirus causing severe acute respiratory syndrome which can be fatal, especially in elderly population, has been declared a pandemic by the World Health Organization. Many biotechnology laboratories are rushing to develop therapeutic antibodies and antiviral drugs for treatment of this viral disease. The viral CoV spike (S) glycoprotein is one of the main targets for pharmacological intervention. Its receptor-binding domain (RBD) interacts with the human ACE2 receptor ensuring the entry of the viral genomes into the host cell. In this work, we report on the differences in the binding of the RBD of the previous coronavirus SARS-CoV and of the newer 2019-nCoV coronavirus to the human ACE2 receptor using atomistic molecular dynamics techniques. Our results show major mutations in the 2019-nCoV RBD with respect to the SARS-CoV RBD occurring at the interface of RBD-ACE2 complex. These mutations make the 2019-nCoV RBD protein backbone much more flexible, hydrophobic interactions are reduced and additional polar/charged residues appear at the interface. We observe that higher flexibility of the 2019-nCoV RBD with respect to the SARS-CoV RBD leads to a bigger binding interface between the 2019-nCoV RBD and ACE2 and to about 20% more contacts between them in comparison with SARS-CoV. Taken together, the 2019-nCoV RBD shows more stable binding interface and higher binding affinity for the ACE2 receptor. The mutations not only stabilize the binding interface, they also lead to overall more stable 2019-nCoV RBD protein structure, even far from the binding interface. Our results on the molecular differences in the binding between the two viruses can provide important inputs for development of appropriate antiviral treatments of the new viruses, addressing the necessity of ongoing pandemics.


title: Management of an Organ Donation Process in COVID-19 Pandemic: First Case of Turkey

text: The first case of coronavirus disease 2019 (COVID-19) was defined as unexplained pneumonia on December 8, 2019, and then it rapidly caused a pandemic and affected transplantation rates negatively. Organ donation processes got more complex because the exclusion of the disease in a short period became more difficult than normal. The exclusion of the disease is vital not only for recipients but also for the medical staff, transplantation teams, and intensive care professionals to reduce the transmission risk. The main steps for diagnosis of COVID-19 are investigation of symptoms, recollection of travel and physical contact history, and testing using the real time polymerase chain reaction (RT-PCR) test. Although it has limitations such as false negative results, RT-PCR is the most accurate method to detect COVID-19, and it is mandatory before donation processes in many countries. In this case report, we aim to share our experience about the first organ donation during the COVID-19 pandemic in Turkey.


title: Cohort-based approach to understanding the roles of generation and serial intervals in shaping epidemiological dynamics

text: Generation intervals and serial intervals are critical quantities for characterizing outbreak dynamics. Generation intervals characterize the time between infection and transmission, while serial intervals characterize the time between the onset of symptoms in a chain of transmission. They are often used interchangeably, leading to misunderstanding of how these intervals link the epidemic growth rate r and the reproduction number R. Generation intervals provide a mechanistic link between r and R but are harder to measure via contact tracing. While serial intervals are easier to measure from contact tracing, recent studies suggest that the two intervals give different estimates of R from r. We present a general framework for characterizing epidemiological delays based on cohorts (i.e., a group of individuals that share the same event time, such as symptom onset) and show that forward-looking serial intervals, which correctly link R with r, are not the same as "intrinsic" serial intervals, but instead change with r. We provide a heuristic method for addressing potential biases that can arise from not accounting for changes in serial intervals across cohorts and apply the method to estimating R for the COVID-19 outbreak in China using serial-interval data --- our analysis shows that using incorrectly defined serial intervals can severely bias estimates. This study demonstrates the importance of early epidemiological investigation through contact tracing and provides a rationale for reassessing generation intervals, serial intervals, and R estimates, for COVID-19.


title: China’s chemical industry shadowed by the coronavirus

text: With its escalating infections, city shutdowns, and nationwide transportation halts, the epidemic of the novel coronavirus is starting to strain China’s chemical industry But experts see the impact as manageable and—they hope—short lived By the afternoon of Feb 6, more than 28,000 people in China were confirmed infected with the virus, almost 20,000 of them in the central Chinese province of Hubei The death toll in China was 564, compared with 349 deaths in all of China from the severe acute respiratory syndrome (SARS) virus in 2003 The government shut down travel in and out of all cities in Hubei and extended the Lunar New Year holiday until Feb 9 or 10 for most factories nationwide Even if the epidemic is controlled in the next few months, frozen consumption, reduced factory output, and disturbed supply chains will cut 0 1 to 0 2 percentage points from global economic growth in 2020, according


title: LOCKDOWN AS A PANDEMIC MITIGATING POLICY INTERVENTION IN INDIA

text: Abstract. We use publicly available timeline data on the Covid-19 outbreak for nine indian states to calculate the important quantifier of the outbreak, the sought after Rt or the time varying reproduction number of the outbreak. This quantity can be measured in in several ways, e.g. by application of Stochastic compartmentalised SIR (DCM) model, Poissonian likelihood based (ML) model & the exponential growth rate (EGR) model. The third one is known as the effective reproduction number of an outbreak. Here we use, mostly, the second one. It is known as the instantaneous reproduction number for an outbreak. This number can faithfully tell us the success of lockdown measures inside indian states, as containment policy for the spread of Covid-19 viral disease. This can also, indirectly yield notional value of the generation time inteval in different states. In doing this work we employ, pan India serial interval of the outbreak estimated directly from data from January 30th to April 19th, 2020. Simultaneously, in conjunction with the serial interval data, our result is derived from incidences data between March 14th, 2020 to June 1st, 2020, for the said states. We find the lockdown had marked positive effect on the nature of time dependent reproduction number in most of the Indian states, barring a couple. The possible reason for such failures have been investigated.


title: Structure of the full SARS-CoV-2 RNA genome in infected cells

text: SARS-CoV-2 is a betacoronavirus with a single-stranded, positive-sense, 30-kilobase RNA genome responsible for the ongoing COVID-19 pandemic. Currently, there are no antiviral drugs or vaccines with proven efficacy, and development of these treatments are hampered by our limited understanding of the molecular and structural biology of the virus. Like many other RNA viruses, RNA structures in coronaviruses regulate gene expression and are crucial for viral replication. Although genome and transcriptome data were recently reported, there is to date little experimental data on predicted RNA structures in SARS-CoV-2 and most putative regulatory sequences are uncharacterized. Here we report the secondary structure of the entire SARS-CoV-2 genome in infected cells at single nucleotide resolution using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq). Our results reveal previously undescribed structures within critical regulatory elements such as the genomic transcription-regulating sequences (TRSs). Contrary to previous studies, our in-cell data show that the structure of the frameshift element, which is a major drug target, is drastically different from prevailing in vitro models. The genomic structure detailed here lays the groundwork for coronavirus RNA biology and will guide the design of SARS-CoV-2 RNA-based therapeutics.


The COVID-19 crisis: Opportunities for sustainable and proximity tourism


title: Compositional Cyber-Physical Epidemiology of COVID-19

text: COVID-19 pandemic has posed significant challenges globally. Countries have adopted different strategies with varying degrees of success. Epidemiologists are studying the impact of government actions using scenario analysis. However, the interactions between the government policy and the disease dynamics are not formally captured. We, for the first time, formally study the interaction between the disease dynamics, which is modeled as a physical process, and the government policy, which is modeled as the adjoining controller. Our approach enables compositionality, where either the plant or the controller could be replaced by an alternative model. Our work is inspired by the engineering approach for the design of Cyber-Physical Systems (CPSs). Consequently, we term the new framework Compositional Cyber-Physical Epidemiology (CCPE). We created different classes of controllers and applied these to control the disease in New Zealand and Italy. Our controllers closely follow government decisions based on their published data. We not only reproduce the pandemic progression faithfully in New Zealand and Italy but also show the tradeoffs produced by differing control actions.


title: Interleukin-3 is a predictive marker for severity and outcome during SARS-CoV-2 infections

text: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a worldwide health threat. Here, we report that low plasma interleukin-3 (IL-3) levels were associated with increased severity and mortality during SARS-CoV-2 infections. IL-3 promoted the recruitment of antiviral circulating plasmacytoid dendritic cells (pDCs) into the airways by stimulating CXCL12 secretion from pulmonary CD123+ epithelial cells. This study identifies IL-3 as a predictive disease marker and potential therapeutic target for SARS-CoV-2 infections.


title: The Impact of COVID-19 on Adjusted Mortality Risk in Care Homes for Older Adults in Wales, United Kingdom: A retrospective population-based cohort study for mortality in 2016-2020

text: Background: Mortality in care homes has had a prominent focus during the COVID-19 outbreak. Multiple and interconnected challenges face the care home sector in the prevention and management of outbreaks of COVID-19, including adequate supply of personal protective equipment, staff shortages, and insufficient or lack of timely COVID-19 testing. Care homes are particularly vulnerable to infectious diseases. Aim: To analyse the mortality of older care home residents in Wales during COVID-19 lockdown and compare this across the population of Wales and the previous 4-years. Study Design and Setting: We used anonymised Electronic Health Records (EHRs) and administrative data from the Secure Anonymised Information Linkage (SAIL) Databank to create a cross-sectional cohort study. We anonymously linked data for Welsh residents to mortality data up to the 14th June 2020. Methods: We calculated survival curves and adjusted Cox proportional hazards models to estimate hazard ratios (HRs) for the risk of mortality. We adjusted hazard ratios for age, gender, social economic status and prior health conditions. Results: Survival curves show an increased proportion of deaths between 23rd March and 14th June 2020 in care homes for older people, with an adjusted HR of 1.72 (1.55, 1.90) compared to 2016. Compared to the general population in 2016-2019, adjusted care home mortality HRs for older adults rose from 2.15 (2.11,2.20) in 2016-2019 to 2.94 (2.81,3.08) in 2020. Conclusions: The survival curves and increased HRs show a significantly increased risk of death in the 2020 study periods.


Staying connected and informed: Online resources and virtual communities of practice supporting palliative care during the novel coronavirus pandemic


title: Split ventilation with pressure regulators for patient-specific tidal volumes

text: As a measure of last resort during the COVID-19 pandemic, single mechanical ventilators have been repurposed to support multiple patients. In existing split-ventilator configurations using FDA-approved tubing adaptors, each patient receives the same inspiratory pressure, requiring careful matching of patients to avoid barotrauma. Progression of disease may cause tidal volumes to diverge from desired targets, and routine interventions (eg. suctioning) in one patient may adversely affect other patients. To overcome these limitations, we demonstrate a split-ventilator configuration that enables individualized patient management by incorporating a commonly available pressure regulator used for gas appliances. We validate this method by achieving various combinations of tidal volume in each of two synthetic lungs using a standard ventilator machine in combination with two gas flow analyzers. With further safety testing and instrumentation, pressure regulators may represent a viable path to substantially augment the capacity for ventilation in resource-constrained settings.


title: Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study

text: Background Coronavirus disease 2019 (COVID-19) is now a global pandemic with Europe and the USA at its epicenter. Little is known about risk factors for progression to severe disease in Europe. This study aims to describe the epidemiology of COVID-19 patients in a Swiss university hospital. Methods This retrospective observational study included all adult patients hospitalized with a laboratory confirmed SARS-CoV-2 infection from March 1 to March 25, 2020. We extracted data from electronic health records. The primary outcome was the need to mechanical ventilation at day 14. We used multivariate logistic regression to identify risk factors for mechanical ventilation. Follow-up was of at least 14 days. Results 200 patients were included, of whom 37 (18.5%) needed mechanical ventilation at 14 days. The median time from symptoms onset to mechanical ventilation was 9.5 days (IQR 7.00, 12.75). Multivariable regression showed increased odds of mechanical ventilation in males (3.26, 1.21-9.8; p=0.025), in patients who presented with a qSOFA score [≥]2 (6.02, 2.09-18.82; p=0.001), with bilateral infiltrate (5.75, 1.91-21.06; p=0.004) or with a CRP of 40 mg/l or greater (4.73, 1.51-18.58; p=0.013). Conclusions This study gives some insight in the epidemiology and clinical course of patients admitted in a European tertiary hospital with SARS-CoV-2 infection. Male sex, high qSOFA score, CRP of 40 mg/l or greater and a bilateral radiological infiltrate could help clinicians identify patients at high risk for mechanical ventilation.


title: Correlation analysis of risk factors and GSI score of a medical team assisting Wuhan city during the epidemic of COVID-19 in China -A cohort study

text: Importance: There are few studies on the psychological status of medical staff during the COVID-19 outbreak. This study is the first in the world about the psychological status of the medical team during the COVID-19 outbreak. Objective: To study the correlation between risk factors and general symptom index (GSI) score of medical team members who support Wuhan against COVID-19. Design: Cohort study. Setting: Population-based. Participants: Anhui Province sent a total of eight medical teams,including 1382 members,to support Hubei Province. We adopted a stratified sampling method and selected the fourth team sent by Anhui Provincial Hospital, with a total of 137 members as our subjects. Exposures: Four main exposures were collected, including basic information, preparations before going to Wuhan, life issues and working issues after going to Wuhan. Main Outcomes and Measures: The GSI score of SCL-90 scale was used to reflect the frequency and intensity of psychological symptoms. We made the hypothesis of this study before data collection. Results: 110(80.29%) members completed the questionnaire, of which, 77(70.00%) female and 33(30.00%) male. When adjusted age, gender and covariates, DC, LCWT had a positive correlations with GSI score(beta was 10.17, 95%CI was 3.30 to 17.04 for DC, P=0.00<0.05;beta was 11.55, 95%CI was 0.40 to 22.71 for LCWT, P =0.04<0.05;respectively), RBT had a negative positive correlation with GSI score (beta was -28.09, 95%CI was -45.79 to -10.40, P=0.00<0.05), AoBI did not had a correlation with GSI score (beta was 11.55, 95%CI was 0.40 to 22.71, P=0.16>0.05). When adjusted covariates, DC had a positive and RBT had a negative correlation with GSI score of female (beta was 13.20, 95%CI was 4.55 to 21.85, P=0.00<0.05; beta was -57.85, 95%CI was -94.52 to -21.18, P=0.00<0.05; respectively), but for male was not (P=0.59>0.05, P=0.08>0.05, respectively), LCWT and AoBI didn't had correlation with GSI score between genders (P>0.05). Conclusions and Relevance: Improving DC, RBT and decreasing LCWT can reduce the GSI score. AoBI didn't affect the psychological status; male members have a more stable mood than female. Whether other countries medical team has the same result still needs further research.


title: Triage tool for suspected COVID-19 patients in the emergency room: AIFELL score

text: Clinical prediction scores support the assessment of patients in the emergency setting to determine the need for further diagnostic and therapeutic steps. During the current COVID-19 pandemic, physicians in emergency rooms (ER) of many hospitals have a considerably higher patient load and need to decide within a short time frame whom to hospitalize. Based on our clinical experiences in dealing with COVID-19 patients at the University Hospital Zurich, we created a triage score with the acronym AIFELL consisting of clinical, radiological and laboratory findings. The score was then evaluated in a retrospective analysis of 122 consecutive patients with suspected COVID-19 from March until mid-April 2020. Descriptive statistics, Student's t-test, ANOVA and Scheffe's post hoc analysis confirmed the diagnostic power of the score. The results suggest that the AIFELL score has potential as a triage tool in the ER setting intended to select probable COVID-19 cases for hospitalization in spontaneously presenting or referred patients with acute respiratory symptoms.


title: Knowledge, attitude, and practice regarding COVID-19 outbreak in Bangladeshi people: An online-based cross-sectional study

text: Objectives: In Bangladesh, remarkable measures have been adopted to control the rapid spread of the ongoing COVID-19 epidemic. Adherence to control measures in general populations significantly influences on their perception, knowledge, attitudes, and practices (KAP) towards COVID-19. This study aimed to investigate KAP towards COVID-19 immediately after the locked down and during the rapid rise period of the outbreak. Study design: Cross-sectional study. Methods: This online-based cross-sectional study was conducted from March 29 to April 19, 2020, involving 2017 Bangladeshi residents aged (12-64) years. The sample was successfully recruited via the social media. After consenting, participants completed an online survey assessing socio-demographic variables, perception, and KAP towards COVD-19. Results: Of the 2017 survey participants, 59.8% and 40.2% were male and female, respectively. A majority of the participants were students (71.2%), aged 21-30 years (57.9%), having a bachelor's degree (61.0%), having family income >30000 in BDT (50.0%), and living urban area (69.8). The findings revealed that 48.3% of participants had more accurate knowledge, 62.3% had more positive attitudes, and 55.1% had more frequent practices for COVID-19 prevention. Majority (96.7%) of the participants agreed COVID-19 is a dangerous disease and almost all (98.7%) of the participants wore a face mask in the crowded place, (98.8%) agreed to report a suspected case to health authorities, and (93.8%) good practicing of washing hands with soap and water. In multiple logistic regression analyses, the COVID-19 more accurate knowledge was associated with age, and residence. Whereas, the results reported that sociodemographic factors such as being older, having higher education, being unemployment, having a joint family, having monthly family income >30,000 BDT, and having more frequent prevention practices were the more positive attitudes factors; and the more frequent prevention practices factors were associated to being female, being older, having higher education, having monthly family income more than 30,000 BDT, urban area and having more positive attitudes. Conclusion: To improve the knowledge, attitudes, and practices of general populations are crucial during the rapid rise period of the COVID-19 outbreak. Therefore, an effective health education program must be initiated.


title: Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations

text: In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variant sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 38 recurrent non-synonymous mutations, including ten hotspot mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed certain genotypes specific to the geographic location. We also found co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets We have also created an inclusive unified database (http://genoma.ma/covid-19/) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.


title: 25 Years of Pathway Figures

text: Background Pathway diagrams are fundamental tools for describing biological processes in all aspects of science, including training, generating hypotheses, describing new knowledge and ultimately as communication tools in published work. Thousands of pathway diagrams are published each year as figures in papers. But as static images the pathway knowledge represented in figures is not accessible to researchers for computational queries and analyses. In this study, we aimed to identify pathway figures published in the past 25 years, to characterize the human gene content in figures by optical character recognition, and to describe their utility as a resource for pathway knowledge. Approach To identify pathway figures representing 25 years of published research, we trained a ma-chine learning service on manually-classified figures and applied it to 235,081 image query results from PubMed Central. Our previously described pipeline 1 was utilized to extract hu-man genes from the pathway figure images. These figures were characterized in terms of their parent papers, human gene content and enriched disease terms. Diverse use cases were explored for this newly accessible pathway resource. Results We identified 64,643 pathway figures published between 1995 and 2019, depicting 1,112,551 instances of human genes (13,464 unique NCBI Genes) in various interactions and contexts. This represents more genes than found in the text of the same papers, as well as genes not found in any pathway database. We developed an interactive web tool to explore the results from the 65k set of figures, and used this tool to explore the history of scientific discovery of the Hippo Signaling pathway. We also defined a filtered set of 32k pathway figures useful for enrichment analysis.


title: Elite athletes and COVID-19 lockdown: Future health concerns for an entire sector

text: In this editorial, we focused our attention on elite athletes during the COVID-19 lockdown. A high level of physical fitness is required by elite athletes irrespective of the specific type of sport. Generally speaking, elite athletes avoid long periods of rest during and at the end of the competitive season. Normally, elite athletes stop training or reduce training volume and intensity for a period that ranges from two weeks to a maximum of four weeks.


title: Future scenarios for the SARS-CoV-2 epidemic in Switzerland: an age-structured model

text: The recent lifting of COVID-19 related restrictions in Switzerland causes uncertainty about the future of the epidemic. We developed a compartmental model for SARS-CoV-2 transmission in Switzerland and projected the course of the epidemic until the end of year 2020 under various scenarios. The model was age-structured with three categories, children (0-17), adults (18-64) and seniors (65- years). Lifting all restrictions according to the plans disclosed by the Swiss federal authorities by mid-May resulted in a rapid rebound in the epidemic, with the peak expected in July. Measures equivalent to at least 90% reduction in all contacts were able to eradicate the epidemic; 56% reduction in contacts could keep the intensive care unit occupancy under the critical level, and delay the next wave until October. Scenarios where strong contact reductions were only applied in selected age groups could not suppress the epidemic, increasing the risk of a next wave in July, and another stronger wave in September. Future interventions need to cover all age groups to keep the SARS-CoV-2 epidemic under control.


title: DEMO: Extracting Physical-Layer BLE Advertisement Information from Broadcom and Cypress Chips

text: Multiple initiatives propose utilizing Bluetooth Low Energy (BLE) advertisements for contact tracing and SARS-CoV-2 exposure notifications. This demo shows a research tool to analyze BLE advertisements; if universally enabled by the vendors, the uncovered features could improve exposure notifications for everyone. We reverse-engineer the firmware-internal implementation of BLE advertisements on Broadcom and Cypress chips and show how to extract further physical-layer information at the receiver. The analyzed firmware works on hundreds of millions of devices, such as all iPhones, the European Samsung Galaxy S series, and Raspberry Pis.


title: COVID-19 and first trimester spontaneous abortion: a case-control study of 225 pregnant patients

text: Background Evidence for the impact of COVID-19 during the second and the third trimester of pregnancy is limited to a relatively small series, while data on the first trimester are scant. With this study we evaluated COVID-19 infection as a risk factor for spontaneous abortion in first trimester of pregnancy. Methods Between February 22 and May 21, 2020, we conducted a case-control study at S. Anna hospital, Torino, among first trimester pregnant women, paired for last menstruation. The cumulative incidence of COVID-19 was compared between women with spontaneous abortion (case group, n=100) and those with ongoing pregnancy (control group, n=125). Current or past infection was determined by detection of SARS-CoV-2 from nasopharingeal swab and SARS-CoV-2 IgG/IgM antibodies in blood sample. Patient demographics, COVID-19-related symptoms, and the main risk factors for abortion were collected. Findings Twenty-three (10.2%) of the 225 women tested positive for COVID-19 infection. There was no difference in the cumulative incidence of COVID-19 between the cases (11/100, 11%) and the controls (12/125, 9.6%) (p=0.73). Logistic regression analysis confirmed that COVID-19 was not an independent predictor of abortion (1.28 confidence interval 0.53-3.08). Interpretation COVID-19 infection during the first trimester of pregnancy does not appear to predispose to abortion; its cumulative incidence did not differ from that of women with ongoing pregnancy.


title: Pediatric Asthma & Coronavirus (COVID-19)-Clinical Presentation in an Asthmatic Child—Case Report

text: Pandemic coronavirus (COVID-19) is a novel virus that causes severe pneumonia. Elderly people with co-morbidities are at risk of severe disease. Symptoms are generally milder in children. We present an asthmatic 12-year old girl with cough, wheeze, and mild pneumonia due to COVID-19. Reverse transcription (RT) polymerase chain reaction (PCR) confirmed COVID-19 on nasopharyngeal sample. Chest radiograph revealed bronchopneumonia. Frequent salbutamol inhalers were administered for treatment. Case was discharged home 2 days following hospitalization. COVID-19 may present with mild pneumonia in children or with an exacerbation of asthma in asthmatic children. Additional observations of clinical presentations of COVID-19 in children are recommended.


title: Clinical evaluation of an immunochromatographic IgM/IgG antibody assay and chest computed tomography for the diagnosis of COVID-19

text: Background: We evaluated the clinical performance of an immunochromatographic (IC) IgM/IgG antibody assay for severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) and chest computed tomography (CT) for the diagnosis of Coronavirus disease 2019 (COVID-19). Methods: We examined 139 serum specimens collected from 112 patients with COVID-19 and 48 serum specimens collected from 48 non-COVID-19 patients. The presence of IgM/IgG antibody for SARS-CoV2 was determined using the One Step Novel Coronavirus (COVID-19) IgM/IgG Antibody Test. Chest CT was performed in COVID-19 patients on admission. Findings: Of the 139 COVID-19 serum specimens, IgM was detected in 27.8%, 48.0%, and 95.8% of the specimens collected within 1 week, 1-2 weeks, and >2 weeks after symptom onset and IgG was detected in 3.3%, 8.0%, and 62.5%, respectively. Among the 48 non-COVID-19 serum specimens, 1 generated a false-positive result for IgM. Thirty-eight of the 112 COVID-19 patients were asymptomatic, of whom 15 were positive for IgM, and 74 were symptomatic, of whom 22 were positive for IgM and 7 were positive for IgG. The diagnostic sensitivity of CT scan alone and in combination with the IC assay was 57.9 % (22/38) and 68.4% (26/38) for the asymptomatic patients and 74.3% (55/74) and 82.4% (61/74) for the symptomatic patients, respectively. Conclusion: The IC assay had low sensitivity during the early phase of infection, and thus IC assay alone is not recommended for initial diagnostic testing for COVID-19. If RT-qPCR is not available, the combination of chest CT and IC assay may be useful for diagnosing COVID-19.


title: Hydroxychloroquine is associated with slower viral clearance in clinical COVID-19 patients with mild to moderate disease: A retrospective study

text: Background: There is conflicting data regarding the use of hydroxychloroquine (HCQ) in COVID-19 hospitalized patients Objective: To assess the efficacy of HCQ in increasing SARS-CoV-2 viral clearance Design: Retrospective observational study Setting: Cleveland Clinic Abu Dhabi Participants: Hospitalized adult patients with confirmed SARS-CoV-2 infection Intervention: None Measurements: The primary outcome was the time from a confirmed positive nasopharyngeal swab to turn negative. A negative nasopharyngeal swab conversion was defined as a confirmed SARS-CoV-2 case followed by two negative results using RT-PCR assay with samples obtained 24 hours apart Results: 34 confirmed COVID-19 patients were included. Nineteen (55.9%) patients presented with symptoms, and 14 (41.2%) had pneumonia. Only 21 (61.8%) patients received HCQ. The time to SARS-CoV-2 negativity nasopharyngeal test was significantly longer in patients who received HCQ compared to those who did not receive HCQ (17 [13-21] vs. 10 [4-13] days, p=0.023). HCQ was independently associated with time to negativity test after adjustment for potential confounders (symptoms, pneumonia or oxygen therapy) in multivariable linear regression analysis. On day 14, 47.8% (14/23) patients tested negative in the HCQ group compared to 90.9% (10/11) patients who did not receive HCQ (p=0.016). Limitations: Small sample size and retrospective design with a potential risk of selection bias Conclusion: HCQ was associated with a slower viral clearance in COVID-19 patients with mild to moderate disease. Data from ongoing randomized clinical trials with HCQ should provide a definitive answer regarding the efficacy and safety of this treatment.


COVID-19 Pandemic: A New Chapter in the History of Infectious Diseases


title: Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes

text: The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these variations, some bat SARSr-CoVs can utilize the orthologs of human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), for entry. It is speculated that the interaction between bat ACE2 and SARSr-CoV spike proteins drives diversity. Here, we have identified a series of R. sinicus ACE2 variants with some polymorphic sites involved in the interaction with the SARS-CoV spike protein. Pseudoviruses or SARSr-CoVs carrying different spike proteins showed different infection efficiency in cells transiently expressing bat ACE2 variants. Consistent results were observed by binding affinity assays between SARS- and SARSr-CoV spike proteins and receptor molecules from bats and humans. All tested bat SARSr-CoV spike proteins had a higher binding affinity to human ACE2 than to bat ACE2, although they showed a 10-fold lower binding affinity to human ACE2 compared with their SARS-CoV counterpart. Structure modeling revealed that the difference in binding affinity between spike and ACE2 might be caused by the alteration of some key residues in the interface of these two molecules. Molecular evolution analysis indicates that these residues were under strong positive selection. These results suggest that the SARSr-CoV spike protein and R. sinicus ACE2 may have coevolved over time and experienced selection pressure from each other, triggering the evolutionary arms race dynamics. It further proves that R. sinicus is the natural host of SARSr-CoVs. Importance Evolutionary arms race dynamics shape the diversity of viruses and their receptors. Identification of key residues which are involved in interspecies transmission is important to predict potential pathogen spillover from wildlife to humans. Previously, we have identified genetically diverse SARSr-CoV in Chinese horseshoe bats. Here, we show the highly polymorphic ACE2 in Chinese horseshoe bat populations. These ACE2 variants support SARS- and SARSr-CoV infection but with different binding affinity to different spike proteins. The higher binding affinity of SARSr-CoV spike to human ACE2 suggests that these viruses have the capacity of spillover to humans. The positive selection of residues at the interface between ACE2 and SARSr-CoV spike protein suggests a long-term and ongoing coevolutionary dynamics between them. Continued surveillance of this group of viruses in bats is necessary for the prevention of the next SARS-like disease.


title: Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection

text: The CRISPR/Cas12a RNA-guided complexes have a tremendous potential for nucleic acid detection due to its ability to indiscriminately cleave ssDNA once bound to a target DNA. However, the current CRISPR/Cas12a systems are limited to detecting DNA in a picomolar detection limit without an amplification step. Here, we developed a platform with engineered crRNAs and optimized conditions that enabled us to detect DNA, DNA/RNA heteroduplex and methylated DNA with higher sensitivity, achieving a limit of detection of in femtomolar range without any target pre-amplification step. By extending the 3’- or 5’-ends of the crRNA with different lengths of ssDNA, ssRNA, and phosphorothioate ssDNA, we discovered a new self-catalytic behavior and an augmented rate of LbCas12a-mediated collateral cleavage activity as high as 3.5-fold compared to the wild-type crRNA. We applied this sensitive system to detect as low as 25 fM dsDNA from the PCA3 gene, an overexpressed biomarker in prostate cancer patients, in simulated urine over 6 hours. The same platform was used to detect as low as ~700 fM cDNA from HIV, 290 fM RNA from HCV, and 370 fM cDNA from SARS-CoV-2, all within 30 minutes without a need for target amplification. With isothermal amplification of SARS-CoV-2 RNA using RT-LAMP, the modified crRNAs were incorporated in a paper-based lateral flow assay that could detect the target with up to 23-fold higher sensitivity within 40-60 minutes.


title: Invasion of novel corona virus (COVID-19) in Indian territory

text: Coronavirus (COVID-19) started its invasion as an epidemic from the Wuhan district in China and propagated to become the scary pandemic that reached more than 200 countries all over the world High number of infected people and unfortunately high mortality are the result of this invasion The Indian scenario is no exception to this deadly infection attack, though it started a bit late The first case in India came into notice in January and the number of cases showed an enormous growth in mid March and still continue to grow This timely report focuses on the current invasion scenario in India as of 11th May, 2020;with total cases of 67,152, active cases of 44, 029, deaths totaling to 2206 and over-all recoveries of ∼20,917 patients


title: Estimating the Final Epidemic Size for COVID-19 Outbreak using Improved Epidemiological Models

text: Final epidemic sizes of different geographical regions due to COVID-19 are estimated using logistic, SIR and generalized SEIR models. These models use different parameters which are estimated using non-linear fits from the available data. It is found that both SIR and generalized SEIR models give similar estimations for regions where curves show signs of flattening. A study of these models with data from China indicates that in such cases these estimates may be more reliable. The estimates are presented for the most affected countries due to COVID-19. According to these models, the final epidemic size in the US, Italy, Spain, and Germany could be 0.8, 0.16, 0.18 and 0.14 million respectively. Also, curves for most of the geographical regions will flatten by the middle of May 2020.


title: Effects of hypertension, diabetes and coronary heart disease on COVID-19 diseases severity: a systematic review and meta-analysis

text: Background: COVID-19 patients with chronic diseases such as hypertension, diabetes and coronary heart diseases is more likely to worsen, but with mixed results for COVID-19 severity. This meta-analysis is to analyze the correlation between hypertension, diabetes, coronary heart disease and COVID-19 disease severity. Methods: Available data from PubMed, Web of Science, China National Knowledge Infrastructure Database, WanFang Database and VIP Database, were analyzed using a fixed effects model meta-analysis to derive overall odds ratios (OR) with 95% CIs. Funnel plots and Begg's were used to assess publication bias. Findings: Of 182 articles found following our initial search, we assessed 34 full-text articles, of which 9 articles with 1936 COVID-19 patients met all selection criteria for our meta-analysis. No significant heterogeneity between studies. There were significant correlations between COVID-19 severity and hypertension [OR=2.3 [95% CI (1.76, 3.00), P<0.01], diabetes [OR=2.67, 95% CI (1.91, 3.74), P<0.01], coronary heart disease [OR=2.85 [95% CI (1.68, 4.84), P<0.01]. Most of the studies in the funnel plot are on the upper part and few on the base part, and are roughly symmetrical left and right. Begg's test: hypertension (Z=-0.1, P=1.0), diabetes (Z=0.73, P=0.466), coronary heart disease (Z=0.38, P=0.707), all found no publication bias. Interpretation: Hypertension, diabetes, and coronary heart disease can affect the severity of COVID-19. It may be related to the imbalance of angiotensin-converting enzyme 2 (ACE2) and the cytokine storm induced by Glucolipid metabolic disorders (GLMD).


title: Distributed manufacturing of open source medical hardware for pandemics

text: Distributed digital manufacturing offers a solution to medical supply and technology shortages during pandemics. To prepare for the next pandemic, this study reviews the state-of-the-art of open hardware designs needed in a COVID-19-like pandemic. It evaluates the readiness of the top twenty technologies requested by the Government of India. The results show that the majority of the actual medical products have some open source development, however, only 15% of the supporting technologies required to produce them are freely available. The results show there is still considerable research needed to provide open source paths for the development of all the medical hardware needed during pandemics. Five core areas of future research are discussed, which include (i) technical development of a wide-range of open source solutions for all medical supplies and devices, (ii) policies that protect the productivity of laboratories, makerspaces, and fabrication facilities during a pandemic, as well as (iii) streamlining the regulatory process, (iv) developing Good-Samaritan laws to protect makers and designers of open medical hardware, as well as to compel those with knowledge that will save lives to share it, and (v) requiring all citizen-funded research to be released with free and open source licenses.


title: High frequency of cerebrospinal fluid autoantibodies in COVID-19 patients with neurological symptoms

text: COVID-19 intensive care patients occasionally develop neurological symptoms. The absence of SARS-CoV-2 in most cerebrospinal fluid (CSF) samples suggests the involvement of further mechanisms including autoimmunity. We therefore determined whether anti-neuronal or anti-glial autoantibodies are present in eleven consecutive severely ill COVID-19 patients presenting with unexplained neurological symptoms. These included myoclonus, cranial nerve involvement, oculomotor disturbance, delirium, dystonia and epileptic seizures. Most patients showed signs of CSF inflammation and increased levels of neurofilament light chain. All patients had anti-neuronal autoantibodies in serum or CSF when assessing a large panel of autoantibodies against intracellular and surface antigens relevant for central nervous system diseases using cell-based assays and indirect immunofluorescence on murine brain sections. Antigens included proteins well-established in clinical routine, such as Yo or NMDA receptor, but also a variety of specific undetermined epitopes on brain sections. These included vessel endothelium, astrocytic proteins and neuropil of basal ganglia, hippocampus or olfactory bulb. The high frequency of autoantibodies targeting the brain in the absence of other explanations suggests a causal relationship to clinical symptoms, in particular to hyperexcitability (myoclonus, seizures). While several underlying autoantigens still await identification in future studies, presence of autoantibodies may explain some aspects of multi-organ disease in COVID-19 and can guide immunotherapy in selected cases.


title: Increased Detection coupled with Social Distancing and Health Capacity Planning Reduce the Burden of COVID-19 Cases and Fatalities: A Proof of Concept Study using a Stochastic Computational Simulation Model

text: Objective: In absence of any vaccine, the Corona Virus Disease 2019 (COVID-19) pandemic is being contained through a non-pharmaceutical measure termed Social Distancing (SD). However, whether SD alone is enough to flatten the epidemic curve is debatable. Using a Stochastic Computational Simulation Model, we investigated the impact of increasing SD, hospital beds and COVID-19 detection rates in preventing COVID-19 cases and fatalities. Research Design and Methods: The Stochastic Simulation Model was built using the EpiModel package in R. As a proof of concept study, we ran the simulation on Kasaragod, the most affected district in Kerala. We added 3 compartments to the SEIR model to obtain a SEIQHRF (Susceptible-Exposed-Infectious-Quarantined-Hospitalised-Recovered-Fatal) model. Results: Implementing SD only delayed the appearance of peak prevalence of COVID-19 cases. Doubling of hospital beds could not reduce the fatal cases probably due to its overwhelming number compared to the hospital beds. Increasing detection rates could significantly flatten the curve and reduce the peak prevalence of cases (increasing detection rate by 5 times could reduce case number to half). Conclusions: An effective strategy to contain the epidemic spread of COVID-19 in India is to increase detection rates in combination with SD measures and increase in hospital beds.


title: Local computational methods to improve the interpretability and analysis of cryo-EM maps

text: Cryo-electron microscopy (cryo-EM) maps usually show heterogeneous distributions of B-factors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions. However, ‘over-sharpening’ due to the application of a single global B-factor can distort processed maps causing connected densities to appear broken and disconnected. This issue limits the interpretability of cryo-EM maps, i.e. ab initio modelling. In this work, we propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local B-factors and electron density occupancy maps. These algorithms have as common link the use of the spiral phase transformation and are called LocSpiral, LocBSharpen, LocBFactor and LocOccupancy. Our results, which include improved maps of recent SARS-CoV-2 structures, show that our methods can improve the interpretability and analysis of obtained reconstructions.


title: Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents

text: Coronaviruses can become zoonotic as in the case of COVID-19, and hunting, sale, and consumption of wild animals in Southeast Asia facilitates an increased risk for such incidents. We sampled and tested rodents (851) and other mammals, and found Betacoronavirus RNA in 12 rodents. The sequences belong to two separate genetic clusters, and relate closely to known rodent coronaviruses detected in the region, and distantly to human coronaviruses OC43 and HKU1. Considering close human-wildlife contact with many species in and beyond the region, a better understanding of virus diversity is urgently needed for the mitigation of future risks.


title: Full-spectrum dynamics of the coronavirus disease outbreak in Wuhan, China: a modeling study of 32,583 laboratory-confirmed cases

text: Vigorous non-pharmaceutical interventions have largely suppressed the COVID-19 outbreak in Wuhan, China. We developed a susceptible-exposed-infectious-recovered model to study the transmission dynamics and evaluate the impact of interventions using 32,583 laboratory-confirmed cases from December 8, 2019 till March 8, 2020, accounting for time-varying ascertainment rates, transmission rates, and population movements. The effective reproductive number R0 dropped from 3.89 (95% credible interval: 3.79-4.00) before intervention to 0.14 (0.11-0.28) after full-scale multi-pronged interventions. By projection, the interventions reduced the total infections in Wuhan by 96.5% till March 8. Furthermore, we estimated that 79% (lower bound: 60%) of the total infections were unascertained, potentially including asymptomatic and mild-symptomatic cases. The probability of resurgence was 0.22 and 0.10 based on models with 79% and 60% infections unascertained, respectively, assuming interventions were lifted after a 14-day period of no new ascertained infections. These results provide important implications for continuing surveillance and interventions to eventually contain the outbreak.


Frequency of diarrhea in novel coronavirus 2019 infection


title: Group testing for SARS-CoV-2 allows for up to 10-fold efficiency increase across realistic scenarios and testing strategies

text: We provide a comparison of general strategies for group testing in view of their application to medical diagnosis in the current COVID-19 pandemic. We find significant efficiency gaps between different group testing strategies in realistic scenarios for SARS-CoV-2 testing, highlighting the need for an informed decision of the pooling protocol depending on estimated prevalence, target specificity, and high- vs. low-risk population. For example, using one of the presented methods, all 1.47 million inhabitants of Munich, Germany, could be tested using only around 141 thousand tests if an infection rate up to 0.4% is assumed. Using 1 million tests, the 6.69 million inhabitants from the city of Rio de Janeiro, Brazil, could be tested as long as the infection rate does not exceed 1%. Altogether this work may help provide a basis for efficient upscaling of current testing procedures, fine grained towards the desired study population, e.g. cross-sectional versus health-care workers and adapted mixtures thereof. For comparative visualization and querying of the precomputed results we provide an interactive web application. The source code for computation is open and freely available.


title: The timing of one-shot interventions for epidemic control

text: The 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.


title: 3D-Printed Splitter for Use of a Single Ventilator on Multiple Patients During COVID-19

text: During epidemics or pandemics affecting the respiratory systems, hospital equipment such as ventilators may become insufficient and different solutions can be considered In fast spreading respiratory illnesses such as COVID-19 due to the rapidly increasing number of patients, ventilatory machine insufficiencies may appear It may be considered to use one hospital ventilator for more than one patient by dividing the airway of the machine with a specially designed splitter The aim of this study was to determine whether a ventilator can be modified to provide ventilation of two or more patients simultaneously by using 3D designed and manufactured splitters A two-port and four-port splitter were designed in Autodesk Fusion 360 computer program and manufactured by 3D printer using PolyJet technology (Stratasys J750) Two sets of splitters were used to adapt to the ventilator during trial process: one for inspiratory and one for expiratory outputs Two intensive care specialists voluntarily tried this study on themselves It was concluded from the study that 3D designed and manufactured two-port splitter can be used to separate the airway of a single ventilator to multiple patients within a very limited indication and time interval


title: Hydroxychloroquine and mortality risk of patients with COVID-19: a systematic review and meta-analysis of human comparative studies

text: Background: Global COVID-19 deaths reached at least 400,000 fatalities. Hydroxychloroquine is an antimalarial drug that elicit immunomodulatory effects and had shown in vitro antiviral effects against SRAS-CoV-2. This drug divided opinion worldwide in the medical community but also in the press, the general public and in public health policies. The aim of this systematic review and this meta-analysis was to bring a new overview on this controversial drug and to assess whether hydroxychloroquine could reduce COVID-19 mortality risk in hospitalized patients. Methods and Findings: Pubmed, Web of Science, Cochrane Library, MedRxiv and grey literature were searched until 10 June 2020. Only studies of COVID-19 patients treated with hydroxychloroquine (with or without azithromycin) compared with a comparative standard care group and with full-text articles in English were included. Studies reporting effect sizes as Odds Ratios, Hazard Ratio and Relative Risk for mortality risk and the number of deaths per groups were included. This meta-analysis was conducted following PRISMA guidelines and registered on PROSPERO (Registration number: CRD42020190801). Independent extraction has been performed by two independent reviewers. Effect sizes were pooled using a random-effects model. The initial search leaded to 112 articles, from which 16 articles met our inclusion criteria. 15 studies were retained for association between hydroxychloroquine and COVID-19 survival including 15,081 patients (8,072 patients in the hydroxychloroquine arm and 7,009 patients in the standard care arm with respectively, 1,578 deaths and 1,423 deaths). 6 studies were retained for hydroxychloroquine with azithromycin. Hydroxychloroquine was not significantly associated with mortality risk (pooled Relative Risk RR=0.82 (95% Confidence Interval: 0.62-1.07, I2=82, Pheterogeneity<0.01, n=15)) within hospitalized patients, nor in association with azithromycin (pooled Relative Risk RR=1.33 (95% CI: 0.92-1.92, I2=75%, Pheterogeneity<0.01, n=6)), nor in the numerous subgroup analysis by study design, median age population, published studies (vs unpublished articles), level of bias risk. However, stratified analysis by continents, we found a significant decreased risk of mortality associated with hydroxychlroquine alone but not with azithromycin among European (RR= 0.62 (95%CI: 0.41-0.93, n=7)) and Asian studies (RR=0.36 (95%CI:0.18-0.73, n=1)), with heterogeneity detected across continent (Pheterogeneity between=0.003). These finding should be interpreted with caution since several included studies had a low quality of evidence with a small sample size, a lack of adjustment on potential confounders or selection and intervention biases. Conclusion: Our meta-analysis does not support the use of hydroxychloroquine with or without azithromycin to reduce COVID-19 mortality in hospitalized patients. It raises the question of the hydroxychloroquine use outside of clinical trial. Additional results from larger randomised controlled trials are needed


title: UV light dosage distribution over irregular respirator surfaces. Methods and implications for safety

text: Background and Objectives: The SARS-CoV2 pandemic has lead to a global decrease in protection ware, especially facepiece filtering respirators (FFRs). Ultraviolet-C wavelength is a promising way of descontamination, however adequate dosimetry is needed to ensure balance between over and underexposed areas and provide reliable results. Our study demonstrates that UVGI light dosage varies significantly on different respirator angles, and propose a method to descontaminate several masks at once ensuring appropriate dosage in shaded zones. Methods: An UVGI irradiator was built with internal dimensions of 69.5 x55 x 33 cm with three 15W UV lamps. Inside, a grating of 58 x 41 x 15 cm was placed to hold the masks. Two different respirator models were used to assess irradiance, four of model Aura 9322 3M of dimensions 17 x 9 x 4cm, and two of model SAFE 231FFP3NR with dimensions 17 x 6 x 5 cm. A spectrometer STN-SilverNova was employed to verify wavelength spectrum and surface irradiance. A simulation was performed to find the irradiance pattern inside the box and the six masks placed inside. These simulations were carried out using the software DIALUX EVO 8.2. Results: The data obtained reveal that the dosage received inside the manufactured UVGI-irradiator depends not only on the distance between the luminaires plane and the base of the respirators but also on the orientation and shape of the masks. This point becomes relevant in order to assure that all the respirators inside the chamber receive the correct dosage. Conclusion: Irradiance over FFR surfaces depend on several factors such as distance, angle of incidence of the light source. Careful dosage measurement and simulation can ensure reliable dosage in the whole mask surface, balancing overexposure. Closed box systems might provide a more reliable, reproducible UVGI dosage than open settings.


title: Social participation and life satisfaction of peoples during the COVID-19 home confinement: the ECLB-COVID19 multicenter study

text: Abstract Background Public health recommendations and governmental measures during the COVID-19 pandemic have enforced numerous restrictions on daily living including social distancing, isolation and home confinement. While these measures are imperative to mitigate spreading of COVID-19, the impact of these restrictions on psychosocial health is undefined. Therefore, an international online survey was launched in April 2020 in seven languages to elucidate the behavioral and lifestyle consequences of COVID-19 restrictions. This report presents the preliminary results from the first thousand responders on social participation and life satisfaction. Methods Thirty-five research organisations from Europe, North-Africa, Western Asia and the Americas promoted the survey through their networks to the general society, in English, German, French, Arabic, Spanish, Portuguese, and Slovenian languages. Questions were presented in a differential format with questions related to responses before and during confinement conditions. Results 1047 replies (54% women) from Asia (36%), Africa (40%), Europe (21%) and other (3%) were included in the analysis. Preliminary findings revealed psychosocial strain during the enforced COVID-19 home confinement. In particular, large decreases in the amount of social activity through family (58%), friends/neighbors (44.9%) or entertainment (46.7%) were triggered by the enforced confinement. These negative effects on social participation were also associated with lower satisfaction (-30.5%) during the confinement period. Conversely, social contact score through digital technologies has significantly increased (p<0.001) during the confinement period with more individuals (24.8%) being socially connected through digital technology. Conclusion These preliminary findings elucidate the risk of psychosocial strain during the current home confinement period. Therefore, in order to mitigate the negative psychosocial effects of home confinement, implementation of national strategies focused on promoting social inclusion through technology-based solution is urgently needed.


title: Monitoring COVID-19 progression: Look at Us Today, See Yourself Tomorrow

text: The coronavirus disease 2019 (COVID-19) pandemic is causing public health emergency and economic crisis all over the globe. Being widely spread, the virus can make any place in the world a new epicenter of the possible second wave of outbreaks. To control the pandemic progression, monitoring of the virus spreading is imperative. This paper proposes a simple and robust approach to monitor the COVID-19 pandemic progression in many countries or regions. This data science pipeline can provide actionable insights via straightforward COVID-19 data visualization for many regions at a glance, which informs of relative time delay of the pandemic progression, projected numbers of confirmed cases in the near future, and the sizes of infections.


title: Co-infection with Influenza A and COVID-19

text: COVID-19, also called severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2), originated in Wuhan, China. It has caused significant morbidity and mortality worldwide and has been declared a global pandemic by the WHO. Influenza occurs mainly during the winter, with the burden of disease determined by several factors, including the effectiveness of the vaccine that season, the characteristics of the circulating viruses, and how long the season lasts. We describe the case of a 66-year-old woman who was diagnosed with influenza A and COVID-19 co-infection. LEARNING POINTS: COVID-19 can co-occur with other viral infections. Some of these co-infections have active treatments, while supportive treatment is the mainstay of treatment for others.


title: SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice

text: The COVID-19 pandemic continues to spread throughout the world with an urgent need for a safe and protective vaccine to effectuate herd immunity to control the spread of SARS-CoV-2. Here, we report the development of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) produced from the full-length spike (S) protein, stabilized in the prefusion conformation. Purified NVX-CoV2373 S form 27.2nm nanoparticles that are thermostable and bind with high affinity to the human angiotensin-converting enzyme 2 (hACE2) receptor. In mice and baboons, low-dose NVX-CoV2373 with saponin-based Matrix-M adjuvant elicits high titer anti-S IgG that is associated with blockade of hACE2 receptor binding, virus neutralization, and protection against SARS-CoV-2 challenge in mice with no evidence of vaccine-associated enhanced respiratory disease (VAERD). NVX-CoV2373 vaccine also elicits multifunctional CD4+ and CD8+ T cells, CD4+ T follicular helper T cells (Tfh), and the generation of antigen-specific germinal center (GC) B cells in the spleen. These results support the ongoing phase 1/2 clinical evaluation of the safety and immunogenicity of NVX-CoV2327 with Matrix-M (NCT04368988).


title: Glaucoma home-monitoring using a tablet-based visual field test (Eyecatcher): An assessment of accuracy and adherence over six months

text: Purpose: To assess accuracy and adherence of visual field (VF) home-monitoring in a pilot sample of glaucoma patients. Design: Prospective longitudinal observation. Methods: Twenty adults (median 71 years) with an established diagnosis of glaucoma were issued a tablet-perimeter (Eyecatcher), and were asked to perform one VF home-assessment per eye, per month, for 6 months (12 tests total). Before and after home-monitoring, two VF assessments were performed in-clinic using Standard Automated Perimetry (SAP; 4 tests total, per eye). Results: All 20 participants could perform monthly home-monitoring, though one participant stopped after 4 months (Adherence: 98%). There was good concordance between VFs measured at home and in the clinic (r = 0.94, P < 0.001). In 21 of 236 tests (9%) Mean Deviation deviated by more than {+/-}3 dB from the median. Many of these anomalous tests could be identified by applying machine learning techniques to recordings from the tablets' front-facing camera (Area Under the ROC Curve = 0.78). Adding home-monitoring data to 2 SAP tests made 6 months apart reduced measurement error (between-test measurement variability) in 97% of eyes, with mean absolute error more than halving in 90% of eyes. Median test duration was 4.5 mins (Quartiles: 3.9 - 5.2 mins). Substantial variations in ambient illumination had no observable effect on VF measurements (r = 0.07, P = 0.320). Conclusions: Home-monitoring of VFs is viable for some patients, and may provide clinically useful data.


title: Mortality of COVID-19 is Associated with Cellular Immune Function Compared to Immune Function in Chinese Han Population

text: In December 2019, novel coronavirus (SARS-CoV-2) infected pneumonia occurred in Wuhan, China. The number of cases has increased rapidly but information on the clinical characteristics of SARS-CoV-2 pneumonia compared to normal controls in Chinese Han population is limited. Our objective is to describe the clinical characteristics of SARS-CoV-2 pneumonia compared to normal controls in the Chinese Han population. In this case series of 752 patients, the full spectrum of cases is described. Fever was present in 86-90% of the patients. The second most common symptom was cough (49.1-51.0%), fatigue (25.2-27.1%), sputum (20.0-23.1%), and headache (9.8-11.1%). the mortality rate is 4.6% in Wuhan, 1.9% in Beijing, and 0.9% in Shanghai. Our findings showed that the levels of lymphocytes were 0.8（IQR, 0.6-1.1）109/L in Wuhan, 1.0（IQR, 0.7-1.4）109/L in Beijing, and 1.1 (IQR, 0.8-1.5) 109/L in Shanghai before admission to hospitals, respectively, indicating that cellular immune function might relate to the mortality. Based on the reference ranges of normal Chinese Han population and the data of the critically ill patients we have observed, it is recommended that reference ranges of people at high risk of COVID-19 infection are CD3+ lymphocytes below 900 cells/mm3, CD4+ lymphocytes below 500 cells/mm3, and CD8+ lymphocytes below 300 cells/mm3.


title: Nature as a treasure trove of potential anti-SARS-CoV drug leads: a structural/mechanistic rationale

text: The novel Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 is a potential factor for fatal illness and a tremendous concern for global public health The COVID-19 pandemic has entered a dangerous new phase In the context of drug discovery, the structurally-unique and chemically-diverse natural products have been valuable sources for drug leads In this review, we report for potential candidates derived from natural sources with well-reported in vitro efficacy against SARS-CoV during the last decade Additionally, a library of 496 phenolic metabolites was subjected to a computer-aided virtual screening against the active site of the recently reported SARS-CoV Main protease (M-pro) Analysis of physicochemical properties of these natural products has been carried out and presented for all the tested phenolic metabolites Only three of the top candidates, viz acetylglucopetunidin (31), isoxanthohumol (32) and ellagic acid (33), which are widely available in many edible fruits, obey both Lipinski's and Veber's rules of drug-likeness and thus possess high degrees of predicted bioavailability These natural products are suggested as potential drug candidates for the development of anti-SARS-CoV-2 therapeutics in the near future


title: World governments should protect their population from COVID-19 pandemic using Italy and Lombardy as precursor

text: The COVID-19 pandemic is spreading worldwide. Italy emerged early on as the country with the largest outbreak outside Asia. The outbreak in Northern Italy demonstrates that it is fundamental to contain the virus' spread at a very early stage of diffusion. At later stages, no containment measure, even if strict, can prevent the saturation of the hospitals and of the intensive care units in any country. Here we show that it is possible to predict when the intensive care units will saturate, within a few days from the first cases of COVID-19 intensive care patients. Using early counts of intensive care patients, we predict the saturation for Lombardy, Italy. Governments should use the Italian precursor to control the outbreak of COVID-19 and prevent the saturation of their intensive care units to protect their population.


Smart city technologies for pandemic control without lockdown


title: Coronavirus diaries: social media in an unsocial age

text: John Tregoning confronts social-media jealousy in the age of coronavirus [Figure not available: see fulltext ]


title: A Contribution to the Mathematical Modeling of the Corona/COVID-19 Pandemic

text: The responsible estimation of parameters is a main issue of mathematical pandemic models. Especially a good choice of β as the number of others that one infected person encounters per unit time (per day) influences the adequateness of the results of the model. For the example of the actual COVID-19 pandemic some aspects of the parameter choice will be discussed. Because of the incompatibility of the data of the Johns-Hopkins-University to the data of the German Robert-Koch-Institut we use the COVID-19 data of the European Centre for Disease Prevention and Control (ECDC) as a base for the parameter estimation. Two different mathematical methods for the data analysis will be discussed in this paper and possible sources of trouble will be shown. Parameters for several countries like UK, USA, Italy, Spain, Germany and China will be estimated and used in W.O. Kermack and A.G. McKendrick's SIR model. Strategies for the commencing and ending of social and economic shutdown measures are discussed. The numerical solution of the ordinary differential equation system of the modified SIR model is being done with a Runge-Kutta integration method of fourth order. At the end the applicability of the SIR model could be shown. Suggestions about appropriate points in time at which to commence with lockdown measures based on the acceleration rate of infections conclude the paper.


title: Virtual Remote Attending Supervision in an Academic Emergency Department during the COVID-19 Pandemic

text: Background: As the surge of patients with COVID-19 increased, our academic university faculty needed to explore ways to protect the more vulnerable physicians in the group from infection while maintaining the service to our patients and the educational objectives of our residency training program. Methods: We utilized telehealth carts used for other purposes in the institution and the ED to allow the replacement of one physically present supervising attending physician with a virtual remote attending physician. This physician, working from home, can be virtually present for resident history and physicals with all patients in the supervised pod. Discussions about patient care, review of studies, and decision on final disposition can also be performed. Resident teaching can also be accomplished. Results: Our innovation represents a novel use of telemedicine capabilities which allows us to protect vulnerable faculty from infection during the COVID-19 pandemic while maintaining appropriate EM resident supervision and patient care. We found some advantages of this process which allow us to more directly observe the initial resident assessment of the patient. The residents responded favorably to the degree of supervision and patient care that we can provide remotely. Conclusions: Our novel use telemedicine during the COVID-19 pandemic has allowed us to decrease the exposure of more vulnerable faculty while maintaining the ability of these faculty to continue to contribute to patient care and resident education. It is well accepted by our residents and seems to be a viable alternative to physical presence in the ED for at least one faculty member. This modality might also be utilized by an attending who fell ill and was not yet able to return to physical work. We hope our description of this process might be useful to other academic departments or community hospital groups who may have at-risk members.


title: On the progression of COVID19 in Portugal: A comparative analysis of active cases using non-linear regression

text: Portugal has been portrayed as a relatively successful case in the control of the COVID-19's March 2020 outbreak in Europe due to the timely confinement measures taken. As other European Union member states, Portugal is now preparing the phased loosening of the confinement measures, starting in the beginning of May. Even so, the current data, albeit showing at least a reduction in infection rates, renders difficult to forecast scenarios in the imminent future. Using South Korea data as scaffold, which is becoming a paradigmatic case of recovery following a high number of infected people, we fitted Portuguese data to biphasic models using non-linear regression and compared the two countries. The results, which suggest good fit, show that recovery in Portugal can be much slower than anticipated, with a very high percentage of active cases (over 50%) remaining still active even months after the projected end of mitigation measures. This, together with the unknown number of asymptomatic carriers, may increase the risk of a much slower recovery if not of new outbreaks. Europe and elsewhere must consider this contingency when planning the relief of containment measures.


title: Is there an airborne component to the transmission of COVID-19? : a quantitative analysis study

text: Objectives While COVID-19 is known to be spread by respiratory droplets (which travel <2m horizontally), much less is known about its transmission via aerosols, which can become airborne and be widely distributed throughout room spaces. In order to quantify the risk posed by COVID-19 infectors exhaling respiratory aerosols in enclosed spaces, we undertook a computer modelling study to simulate transmission in an office building. Methods Respiratory droplet data from four published datasets were analysed to quantify the number and volume of droplets <100m diameter produced by a typical cough and speaking event (i.e. counting from 1 to 100). This was used in a stochastic model to simulate (10,000 simulations) the number of respiratory particles, originating from a COVID-19 infector, that would be inhaled in one hour by a susceptible individual practicing socially distancing in a 5 x 5 x 2.75m office space. Several scenarios were simulated that mimicked the presence of both symptomatic and asymptomatic COVID-19 infectors. Results On average, each cough and speaking event produced similar numbers of droplets <100 m diameter (median range = 955 - 1010). Computer simulations (at ventilation rate = 2AC/h) revealed that sharing the office space with a symptomatic COVID-19 infector (4 coughs per hour) for one hour resulted in the inhalation of 187.3 (median value) respiratory droplets, whereas sharing with an asymptomatic COVID-19 positive person (10 speaking events per hour) resulted in the inhalation of 482.9 droplets. Increasing the ventilation rate resulted in only modest reductions in particle numbers inhaled. Conclusions Given that live SARS-CoV-2 virions are known to be shed in high concentrations from the nasal cavity of both symptomatic and asymptomatic COVID-19 patients, the results suggest that individuals who share enclosed spaces with an infector may be at risk of contracting COVID-19 by the aerosol route, even when practicing social distancing.


title: Environmental Contamination of SARS-CoV-2 in a Non-Healthcare Setting Revealed by Sensitive Nested RT-PCR

text: Fomite-mediated transmission has been identified as a possible route for disease spread of the COVID-19 pandemic. In healthcare settings, evidence of environmental contamination by SARS-CoV-2 has been found in patients' rooms and toilets. Here, we investigate environmental contamination of SARS-CoV-2 in non-healthcare settings and assessed the efficacy of cleaning and disinfection in removing SARS-CoV-2 contamination. A total of 428 environmental swabs and six air samples was taken from accommodation rooms, toilets and elevators that have been used by COVID-19 cases. Through the use of a sensitive nested RT-PCR assay, we found two SARS-CoV-2 RNA positive samples from the room resided by a COVID-19 case, highlighting the risk of fomite-mediated transmission in non-healthcare settings and the importance of surface disinfection of spaces occupied by cases. Of note, we did not find evidence for air-borne transmission, nor of environmental contamination of elevators, which were transiently exposed to infected persons.


title: Transforming the Language of Life: Transformer Neural Networks for Protein Prediction Tasks

text: The scientific community is rapidly generating protein sequence information, but only a fraction of these proteins can be experimentally characterized. While promising deep learning approaches for protein prediction tasks have emerged, they have computational limitations or are designed to solve a specific task. We present a Transformer neural network that pre-trains task-agnostic sequence representations. This model is fine-tuned to solve two different protein prediction tasks: protein family classification and protein interaction prediction. Our method is comparable to existing state-of-the art approaches for protein family classification, while being much more general than other architectures. Further, our method outperforms all other approaches for protein interaction prediction. These results offer a promising framework for fine-tuning the pre-trained sequence representations for other protein prediction tasks.


title: Education in the Context of the Pandemic: A Look at the Case of Portugal

text: The COVID-19 pandemic is causing structural and irreversible changes and transformations in individuals, families, companies, countries and in the world There will be a society before and after COVID-19 Education is a pillar of sustainability and of society's future which is also being damaged by this world crisis Professionals, students and family, the government, the educational system are looking for answers in record time This brief article aims to share Portugal's experience, a country marked by a series of successive reforms of the national education system


title: Clinical features and outcomes of 197 adult discharged patients with COVID-19 in Yichang, Hubei

text: Purpose To investigate the epidemiology and clinical features of discharged adult patients with COVID-19 in Yichang. Method The retrospective study recruited 197 cases of COVID-19 discharged from Yichang Central People's Hospital and Yichang Third People's Hospital from Jan 17 to Feb 26, 2020. All cases were confirmed by real-time RT-PCR or chest computer tomography (CT).The survivors were followed up until March 4,2020. Clinical data, including demographic characteristic, presentation, exposure history, laboratory examination, radiology and prognosis were enrolled and analyzed by SPSS 19.0 software. Results There were 197 adult discharged patients with COVID-19 in this study. Statistical analysis indicated that the average age was 55.94 years, and female patients were 50.3%. Those patients mainly resided in urban with exposure history in 2 weeks. Fever, cough and weakness were the common symptoms. Leucocytes were mainly normal or decreased in 185 patents, both lymphocytes and eosinophils reduced, the ratios were 56.9% and 50.3%, respectively. On the contrary, lactate dehydrogenases raised in 65 patients. C-reactive protein elevated in the most of patients. The sensitivity of RT-PCR was 63.5%. Chest CT indicated that bilateral patchy shadows were the most common imaging manifestations.169 patients recovered and transferred to a designated hospital for observation, and the others turned worst and died of acute respiratory failure. Conclusion COIVD-19 infection have become a life-threaten public health problem, the sensitivity of RT-PCR was limited. Chest CT scan was recommended for the suspected patients. Moreover, lymphocytopenia and eosinophils declining without leukocytes increasing may be considered as a useful evidence for the diagnosis.


title: Bilanz 2019: BASF

text: AbstractBASF setzte im Jahr 2019 weniger um als im Jahr zuvor Die Ergebnisse der Basischemie sanken Künftig will das Unternehmen stärker in China als in Europa und zudem in Batteriematerialien investieren


title: Hospital-based autonomous pre-clinical screening of COVID-19: An emergency triage using a vital signs recording system, Paris-Ile de France region.

text: The COVID-19 pandemic has had a dramatic toll worldwide on the populations but also has been essentially supported by the existing public health system, particularly hospital-based emergency wards and intensive care units. In France, the first cases were identified on the 24th of January 2020. The first epidemic sprout emerged in the Eastern part of the country and spread in two weeks towards the center to the Paris-region where it peaked on the 14th of April 2020. In Paris and the region around it, the intensity of the epidemic has increased significantly to have a strong impact on all public and private hospital systems in a few weeks. During France's 2020 COVID-19 epidemic, a private hospital went into a major organizational change of its Emergency Department which mainly included the use of a Telemedicine Booth for vitals automatic recording during triage procedures. The present study describes the organizational scheme adopted by the hospital and discusses the data of 1,844 patients that attended the facility over a month. While among them, 766 patients were engaged in an automated triage process supported by a Telemedicine Booth. Patients' clinical characteristics are comparable to those found in international literature during the COVID-19 pandemic. The use of the Telemedicine Booth as a screening process facilitated patients' flow. It usefully participated in the patient rapid orientation, relieving the hospital emergency department, actively contributes in a safe and secure environment highly trusted by the hospital staff and health workers. To our knowledge, the Telemedicine Booth use as a screening process during an epidemic constitutes the first contribution to such an innovative approach.


title: Recomendaciones nutricionales para pacientes hospitalizados con infección respiratoria grave (IRAG) sospechosa o confirmada por COVID-19/ Nutritional recommendations for hospitalized patients with severe respiratory infection (SARS) suspected or confirmed by COVID-19

text: Durante estas tres décadas del cuidado continuo de pacientes hospitalizados hemos reconocido la fisiopa-tología de la respuesta metabólica al estrés y la afectación de los enfermos desde la activación molecular de la sepsis, hasta el compromiso hemodinámico y neurológico del shock, ofreciendo soporte nutricional para obtener mejores resultados para la salud y la vida de nuestros pacientes, mediante recomendaciones que han sido comprobadas en poblaciones heterogéneas con diversas presentaciones en la práctica clínica. En esta revisión de la literatura proponemos sugerencias sobre la intervención nutricional en el paciente con SARS-CoV2 o COVID-19


title: A cohort of patients with COVID-19 in a major teaching hospital in Europe

text: Background: Since the confirmation of the first patient infected with SARS-CoV-2 in Spain in January 2020, the epidemic has grown rapidly, with the greatest impact on the region of Madrid. This article describes the first 2226 adult patients with COVID-19, consecutively admitted to La Paz University Hospital in Madrid. Methods: Our cohort included all patients consecutively hospitalized who had a final outcome (death or discharge) in a 1286-bed hospital of Madrid (Spain) from 25 February (first case admitted) to 19 April 2020. The data were manually entered into an electronic case report form, which was monitored prior to the analysis. Results: We consecutively included 2226 adult patients admitted to the hospital who either died (460) or were discharged (1766). The patients’ median age was 61 years, and 51.8% were women. The most common comorbidity was arterial hypertension (41.3%), and the most common symptom on admission was fever (71.2%). The median time from disease onset to hospital admission was 6 days. The overall mortality was 20.7% and was higher in men (26.6% vs. 15.1%). Seventy-five patients with a final outcome were transferred to the intensive care unit (ICU) (3.4%). Most patients admitted to the ICU were men, and the median age was 64 years. Baseline laboratory values on admission were consistent with an impaired immune-inflammatory profile. Conclusions: We provide a description of the first large cohort of hospitalized patients with COVID-19 in Europe. Advanced age, male sex, the presence of comorbidities and abnormal laboratory values were more common among the patients with fatal outcomes.