bluuebunny/crossref_metadata_2025_split huggingface dataset:
ImplemeNting SARS-CoV-2 Rapid antigen testing in the Emergency wArd of a Swiss univErsity hospital: the INCREASE study
Authors: Caruana Giorgia , Croxatto Antony , Kampouri Eleftheria , Kritikos Antonios , Opota Onya , Foerster Marylin , Brouillet René , Senn Laurence , Lienhard Reto , Egli Adrian , Pantaleo Giuseppe , Carron Pierre-Nicolas , Greub Gilbert 
Published: February 2021

BackgroundWhile facing a second wave in SARS-CoV-2 pandemic, in November 2020 the Swiss Federal Office of Public Health (FOPH) authorized the use of rapid antigen tests (RATs) in addition to the gold-standard reverse transcription-polymerase chain reaction (RT-PCR).MethodsWe implemented the use of RAT in the emergency ward of our university hospital for rapid patients’ triaging and compared performances of four different antigen tests. All results were compared to SARS-CoV-2 specific RT-PCR (reference standard).ResultsTriaging patients using RAT in association with RT-PCR allowed us to isolate promptly positive patients and to save resources, in a context of rapid RT-PCR reagents shortage. Among 532 patients with valid results, overall sensitivities were 48.3% for One Step Exdia and 41.2% for Standard Q®, Panbio−and BD Veritor. All four antigen tests exhibited specificity above 99%. Sensitivity increased up to 74.6%, 66.2%, 66.2% and 64.8% for One Step Exdia, Standard Q, Panbio, and BD Veritor respectively, when considering viral loads above 105copies/ml, up to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/ml and 100% (for all tests) when considering viral loads above 107 copies/ml. Sensitivity was significantly higher for patients presenting with symptoms onset within 4 days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with evolution of symptoms for more than 4 days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Sensitivities of all RAT assays were of only 33% among hospitalized patients without COVID-19 symptoms.ConclusionRAT might represent a useful epidemiological resource in selected clinical settings as a complementary tool to the molecular tests for rapid patients triaging, but the lower sensitivity compared to RT-PCR, especially in late presenters and subjects without COVID-19 symptoms, must be taken into account in order to correctly use RAT for triaging.
Response to Whole-Lung Low-Dose Radiation Therapy (LD-RT) Predicts Freedom from Intubation in Patients Receiving Dexamethasone and/or Remdesevir for COVID-19-Related Acute Respiratory Distress Syndrome (ARDS)
Authors: Hess Clayton B. , Eng Tony Y. , Nasti Tahseen H. , Dhere Vishal R. , Kleber Troy J. , Switchenko Jeffrey M. , Weinberg Brent D. , Rouphael Nadine , Tian Sibo , Rudra Soumon , Taverna Luisa S. , Perez Alvaro , Ahmed Rafi , Khan Mohammad K. 
Published: February 2021

AbstractBackgroundPhase I/II clinical trials have explored whole-lung low-dose radiotherapy (LD-RT) as a potential treatment for patients with COVID-19-related acute respiratory distress syndrome (ARDS). Initial findings require reproduction. Concomitant LD-RT administration with existing therapies requires safety evaluation.MethodsPatients with COVID-19-related pneumonia receiving dexamethasone and/or remdesevir were treated with 1.5 Gy whole-lung LD-RT, followed for 28 days or until hospital discharge, and compared to controls blindly matched by age, comorbidity, and disease severity. Eligible patients were hospitalized, SARS-CoV-2 positive, had radiographic consolidations, and required supplemental oxygen. Endpoints included safety, clinical recovery, intubation, radiographic changes, and biomarker response.Findings20 patients received whole-lung LD-RT between Jun 11 and Dec 7, 2020 and were compared to controls. Freedom from intubation improved from 68% in controls to 86% following LD-RT (p=0.09) as did C-reactive protein (CRP) (p=0.02) and creatine kinase (CK) (p<0.01) levels, consistent with prior report. Eighty percent of LD-RT patients experienced rapid decline in CRP within 3 days and were classified as LD-RT responders. Intubation-free survival (100% vs 66%, p=0.01) and oxygenation loads were lower in LD-RT responders compared to matched controls: 32% lower per individual (p=0.03) and 56% lower for the cohort (p=0.06). No patient whose CRP declined following LD-RT died or required intubation, whereas all LD-RT non-responders died. Observed reduction of prolonged recoveries and hospitalization times did not reach significance. Radiographic changes were equivalent.InterpretationA cohort of patients with COVID-19-related ARDS treated with LD-RT demonstrated superior freedom from intubation compared to matched controls, especially LD-RT responders (p=0.01). LD-RT appears safe to deliver with concurrent drugs. LD-RT lowered CRP and CK biomarkers. CRP response predicted favorable outcome. Optimal timing for LD-RT after oxygen dependence but before intubation may extinguish immunopathology prior to systemic spread. Confirmatory clinical trials are warranted. Clinical Trial Registration: NCT04366791.FundingNone
C-reactive protein guided use of procalcitonin in COVID-19
Authors: Houghton Rebecca , Moore Nathan , Williams Rebecca , El-Bakri Fatima , Peters Jonathan , Mori Matilde , Vernet Gabrielle , Lynch Jessica , Lewis Henry , Tavener Maryanna , Durham Tom , Bowyer Jack , Saeed Kordo , Pollara Gabriele 
Published: February 2021

AbstractLow procalcitonin (PCT) concentrations (<0.5ng/mL) can facilitate exclusion of bacterial co-infection in viral infections, including COVID-19. However, costs associated with PCT measurement preclude universal adoption, indicating a need to identify settings where PCT provides clinical information beyond that offered by other inflammatory markers, such as C-reactive protein (CRP) and white cell count (WCC). In an unselected cohort of 299 COVID-19 patients, we tested the hypothesis that PCT<0.5ng/mL was associated with lower levels of CRP and WCC. We demonstrated that CRP values below the geometric mean of the entire patient population had a negative predictive value for PCT<0.5ng/mL of 97.6% and 100% at baseline and 48 hours into admission respectively, and that this relationship was not confounded by intensive care admission or microbiological findings. CRP-guided PCT testing algorithms can reduce costs and support antimicrobial stewardship strategies in COVID-19.
COVID-19 and Influenza: Vaccination Before and During the Pandemic among the Lebanese Adult Population
Authors: Elia Anthony , Taha Nedal , Tokajian Sima 
Published: February 2021

AbstractInfluenza is a common respiratory tract disease that has been around for years. Vaccination remains the most cost-effective measure to avoid infection. Influenza vaccination rates in Lebanon, like elsewhere in the world, are known to be suboptimal. The emergence and spread of SARS-CoV-2 led to a global health crisis. This study aimed at assessing the impact of the COVID-19 pandemic on the tendency of the general adult population residing in Lebanon to vaccinate against influenza. A quantitative cross-sectional study was conducted between November and December 2020 using a structured questionnaire passed on 1055 individuals to determine factors influencing vaccination habits prior to and during the COVID-19 pandemic. The factors were analyzed using univariate, bivariate, and multivariate analyses. The majority (69.7%) of the study participants never received the influenza vaccine within the last 5 years, 20% vaccinated occasionally, and only 10.3% were yearly vaccinated. Among individuals who never got the influenza vaccine within the last 5 years, 20.7% reported their willingness to vaccinate this winter significantly increasing the vaccination percentage. Participants concerned about the COVID-19 pandemic showed an enhanced willingness to vaccinate against both. Influenza and COVID-19 vaccination rates, nevertheless, are still considerably lower than the recommended coverage. The COVID-19 pandemic caused a significant increase in the tendency to vaccinate against influenza. Yet, urgent vaccination strategies should be implemented to boost vaccine uptake across all demographics to consequently diminish the burden conflicted by influenza, COVID-19, and ultimately other infectious diseases.
Human liver organoid derived intra-hepatic bile duct cells support SARS-CoV-2 infection and replication and its comparison with SARS-CoV
Authors: Lui Vincent Chi-Hang , Hui Kenrie Pui-Yan , Babu Rosanna Ottakandathil , Yue Haibing , Chung Patrick Ho-Yu , Tam Paul Kwong-Hang , Chan Michael Chi-Wai , Wong Kenneth Kak-Yuen 
Published: February 2021

AbstractBackgroundAlthough the main route of infection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the respiratory tract, liver injury is also commonly seen in many patients, as evidenced by deranged parenchymal liver enzymes. Furthermore, patients with severe liver disease have been shown to have higher mortality. Overall, the mechanism behind the liver injury remains unclear.Approach and resultsWe showed that intra-hepatic bile duct cells could be grown using a human liver organoid platform. The cholangiocytes were not only susceptible to SARS-CoV-2 infection, they also supported efficient viral replication. We also showed that SARS-CoV-2 replication was much higher than SARS-CoV.ConclusionOur findings suggested direct cytopathic viral damage being a mechanism for SARS-CoV-2 liver injury.
Anti-nuclear matrix protein 2 antibody-positive idiopathic inflammatory myopathies represent extensive myositis without dermatomyositis-specific rash
Authors: Ichimura Yuki , Shobo Miwako , Inoue Sae , Okune Mari , Maeda Akemi , Tanaka Ryota , Kubota Noriko , Matsumoto Isao , Ishii Akiko , Tamaoka Akira , Shimbo Asami , Mori Masaaki , Morio Tomohiro , Kishi Takayuki , Miyamae Takako , Tanboon Jantima , Inoue Michio , Nishino Ichizo , Fujimoto Manabu , Nomura Toshifumi , Okiyama Naoko 
Published: February 2021

AbstractObjectiveMyositis-specific autoantibodies (MSAs) define distinct clinical subsets of idiopathic inflammatory myopathies (IIMs). The anti-nuclear matrix protein 2 (NXP2) antibody, a MSA detected in juvenile/adult IIMs, has been reported to be associated with a high risk of subcutaneous calcinosis, subcutaneous edema, and internal malignancies. The study aimed to clarify the clinical features of anti-NXP2 antibody-positive IIMs in detail.MethodsThis multi-center retrospective observational study on 76 anti-NXP2 antibody-positive patients. The antibody was detected via a serological assay using immunoprecipitation and western blotting. The patients were selected from 162 consecutive Japanese patients with IIMs.ResultsThe cohort of anti-NXP2 antibody-positive IIMs included 29 juvenile patients and 47 adult patients. Twenty-seven (35.5%) patients presented with polymyositis phenotype without dermatomyositis-specific skin manifestations (heliotrope rash and Gottron sign/papules); this was more common in the adults than children (48.9% vs. 15.8%, P < 0.01). Nine (11.8%) patients had subcutaneous calcinosis, and 20 (26.3%) patients had subcutaneous edema. In addition, the proportion of patients with muscle weakness extending to the distal limbs was high (36 patients [47.4%]) in this cohort. Adult patients had a higher prevalence of malignancy than the general population (age-standardized incidence ratio of malignancies: 22.4).ConclusionAnti-NXP2 antibody-positive IIMs, which include dermatomyositis sine dermatitis, are characterized by atypical skin manifestations and extensive muscular involvement.
A participatory modelling approach for investigating the spread of COVID-19 in countries of the Eastern Mediterranean Region to support public health decision-making
Authors: Adib Keyrellous , Hancock Penelope A. , Rahimli Aysel , Mugisa Bridget , Abdulrazeq Fayez , Farag Noha , Aguas Ricardo , White Lisa , Hajjeh Rana , Ariqi Lubna Al , Nabeth Pierre 
Published: February 2021

AbstractEarly on in the COVID-19 pandemic, the WHO Eastern Mediterranean Regional Office (WHO EMRO) recognised the importance of epidemiological modelling to forecast the progression of the COVID-19 pandemic to support decisions guiding the implementation of response measures. We established a modelling support team to facilitate the application of epidemiological modelling analyses in the Eastern Mediterranean Region (EMR) countries. Here we present an innovative, stepwise approach to participatory modelling of the COVID-19 pandemic that engaged decision-makers and public health professionals from countries throughout all stages of the modelling process. Our approach consisted of first identifying the relevant policy questions, collecting country-specific data, and interpreting model findings from a decision-maker’s perspective, as well as communicating model uncertainty. We used a simple modelling methodology that was adaptable to the shortage of epidemiological data, and the limited modelling capacity, in our region. We discuss the benefits of using models to produce rapid decision-making guidance for COVID-19 control in the WHO Eastern Mediterranean Region (EMR), as well as challenges that we have experienced regarding conveying uncertainty associated with model results, synthesizing and comparing results across multiple modelling approaches, and modelling fragile and conflict-affected states.
Shared genetic aetiology between childhood intelligence and longevity
Authors: Hill W. David , Deary Ian J. 
Published: February 2021

AbstractBackgroundIntelligence and longevity are phenotypically and genetically correlated. Whereas molecular genetic data has been used to show that adult intelligence is genetically correlated with longevity, no such analysis has examined the association between childhood intelligence and longevity.Method and ResultsUsing genome wide association study data on childhood intelligence (n = 12,441) and on parental longevity (n = 389,166) we found a positive genetic correlation of rg = 0.35 (SE = 0.14, P = 0.01) between childhood intelligence and parental longevity.ConclusionThese results add to the weight of evidence that the phenotypic link between childhood intelligence and longevity is, partly, accounted for by shared genetic aetiology.
A robust phenomenological approach to investigate COVID-19 data for France
Authors: Griette Q. , Demongeot J. , Magal P. 
Published: February 2021

AbstractWe provide a new method to analyze the COVID-19 cumulative reported cases data based on a two-step process: first we regularize the data by using a phenomenological model which takes into account the endemic or epidemic nature of the time period, then we use a mathematical model which reproduces the epidemic exactly. This allows us to derive new information on the epidemic parameters and to compute the effective basic reproductive ratio on a daily basis. Our method has the advantage of identifying robust trends in the number of new infectious cases and produces an extremely smooth reconstruction of the epidemic. The number of parameters required by the method is parsimonious: for the French epidemic between February 2020 and January 2021 we use only 11 parameters in total.
County-Specific, Real-Time Projection of the Effect of Business Closures on the COVID-19 Pandemic
Authors: Yurk Dominic , Abu-Mostafa Yaser 
Published: February 2021

AbstractPublic health policies such as business closures have been one of our most effective tools in slowing the spread of COVID-19, but they also impose costs. This has created demand from policy makers for models which can predict when and where such policies will be most effective to head off a surge and where they could safely be loosened. No current model combines data-driven, real-time policy effect predictions with county-level granularity. We present a neural net-based model for predicting the effect of business closures or re-openings on the COVID-19 time-varying reproduction number Rt in real time for every county in California. When trained on data from May through September the model accurately captured relative county dynamics during the October/November California COVID-19 surge (r2 = 0.76), indicating robust out-of-sample performance. To showcase the model’s potential utility we present a case study of various counties in mid-October. Even when counties imposed similar restrictions at the time, our model successfully distinguished counties in need of drastic and immediate action to head off a surge from counties in less dire need of intervention. While this study focuses on business closures in California, the presented model architecture could be applied to other policies around world.
Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States
Authors: Alpert Tara , Brito Anderson F. , Lasek-Nesselquist Erica , Rothman Jessica , Valesano Andrew L. , MacKay Matthew J. , Petrone Mary E. , Breban Mallery I. , Watkins Anne E. , Vogels Chantal B.F. , Kalinich Chaney C. , Dellicour Simon , Russell Alexis , Kelly John P. , Shudt Matthew , Plitnick Jonathan , Schneider Erasmus , Fitzsimmons William J. , Khullar Gaurav , Metti Jessica , Dudley Joel T. , Nash Megan , Beaubier Nike , Wang Jianhui , Liu Chen , Hui Pei , Muyombwe Anthony , Downing Randy , Razeq Jafar , Bart Stephen M. , Grills Ardath , Morrison Stephanie M. , Murphy Steven , Neal Caleb , Laszlo Eva , Rennert Hanna , Cushing Melissa , Westblade Lars , Velu Priya , Craney Arryn , Fauntleroy Kathy A. , Peaper David R. , Landry Marie L. , Cook Peter W. , Fauver Joseph R. , Mason Christopher E. , Lauring Adam S. , George Kirsten St. , MacCannell Duncan R. , Grubaugh Nathan D. 
Published: February 2021

SummaryThe emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.
A Convex Optimization Solution for the Effective Reproduction NumberRt
Authors: Salas Joaquín 
Published: February 2021

AbstractCOVID-19 is a global infectious disease that has affected millions of people. With new variants emerging with augmented transmission rates, slowing down of vaccine rollouts, and rising new cases threatening sanitary capabilities to the brink of collapse, there is the need to continue studying more effective forms to track its spread. This paper presents a strategy to compute the effective reproduction numberRt. Our method starts with a form of the renewal equation of the birth process specially suitable to computeRt. After showing that one can express it as a linear system, we proceed to solve it, along with appropriate constraints, using convex optimization. We demonstrate the method’s effectiveness using synthetic and real sequences of infections and comparing it with a leading approach.
Virus transmission by ultrasonic scaler and its prevention by antiviral agent
Authors: Fidler Aleš , Steyer Andrej , Gašperšič Rok 
Published: February 2021

ABSTRACTDuring an ultrasonic scaler (USS) operation, droplets and aerosol are generated that may contribute to the transmission of viruses contained in saliva and gingival crevicular fluid. The purpose of this research was to develop an experimental model for testing the spread of viruses during USS instrumentation and to examining the prevention of spreading by replacing the coolant with an antiviral agent. In a virus transmission tunnel, USS operation with saline coolant and delivery of a viral suspension to the vicinity of USS tip generated droplets and aerosol containing Equine Arteritis Virus (EAV). Evaluation of droplet transmission was evaluated with adherent 48h cell culture monolayer RK13 cell lines in standard 48-well-plates positioned at a distance from 30 to 55 cm. The aerosol was collected by a cyclone aero-sampler flow of 100l/min. Antiviral activity of 0.25% sodium hypochlorite or electrolyzed water (EOW) was tested by suspension test. The two tested antiviral agents’ transmission prevention ability was evaluated by repeating the same experiment as with saline coolant. All experiments were repeated twice. With saline coolant, the cytopathic effect on cells was found in cells up to the distance of 45 cm, with the number of infected wells decreasing with distance. Viral particles were detected in only one AS in a very low concentration (≤4.2 TCID50/ml). In suspension test of 0.25% NaOCl and EOW, the TCID50/ml was below detection limit after 5s. With both antiviral agents, no cytopathic effect was found. However, the cytotoxic effect of 0.25% NaOCl was evident up to the distance of 35 cm. By USS activity, EAV could be transmitted by droplets up to a distance of 45 cm. Both antiviral agents could prevent virus droplet transmission. The transmission of EAV by aerosol yielded inconclusive results.
Latrophilin GPCR Signaling Mediates Synapse Formation
Authors: Sando Richard , Südhof Thomas C. 
Published: February 2021

ABSTRACTNeural circuit assembly in the brain requires precise establishment of synaptic connections, but the mechanisms of synapse assembly remain incompletely understood. Latrophilins are postsynaptic adhesion-GPCRs that engage in trans-synaptic complexes with presynaptic teneurins and FLRTs. In CA1-region neurons, Latrophilin-2 and Latrophilin-3 are essential for formation of entorhinal-cortex-derived and Schaffer-collateral-derived synapses, respectively. However, it is unknown whether latrophilins function as GPCRs in synapse formation. Here, we show that Latrophilin-2 and Latrophilin-3 exhibit constitutive GPCR activity that increases cAMP levels, which was blocked by a mutation interfering with G-protein and arrestin interactions of GPCRs. The same mutation impaired the ability of Latrophilin-2 and Latrophilin-3 to rescue the synapse-loss phenotype in Latrophilin-2 and Latrophilin-3 knockout neuronsin vivo. Our results suggest that Latrophilin-2 and Latrophilin-3 require GPCR signaling in synapse formation, indicating that latrophilins promote synapse formation in the hippocampus by activating a classical GPCR-signaling pathway.