bluuebunny/crossref_metadata_2025_split huggingface dataset:
CellExplorer: a graphical user interface and a standardized pipeline for visualizing and characterizing single neurons
Authors: Petersen Peter C. , Siegle Joshua H. , Steinmetz Nicholas A. , Mahallati Sara , Buzsáki György 
Published: May 2020

AbstractThe large diversity of neuron types of the brain, characterized by a unique set of electrophysiological characteristics, provides the means by which cortical circuits perform complex operations. To quantify, compare, and visualize the functional features of single neurons, we have developed the open-source framework, CellExplorer. It consists of three components: a processing module that calculates standardized physiological metrics, performs neuron type classification and detects putative monosynaptic connections, a flexible data structure, and a powerful graphical interface. The graphical interface makes it possible to explore any combination of pre-computed features at the speed of a mouse click. The CellExplorer framework allows users to process and relate their data to a growing collection of “ground truth” neurons from different genetic lines, as well as to tens of thousands of single neurons collected across our labs. We believe CellExplorer will accelerate the linking of physiological properties of single neurons in the intact brain to genetically identified types.
Pharyngeal pouches provide a niche microenvironment for arch artery progenitor specification
Authors: Mao Aihua , Li Linwei , Liu Jie , Zhang Mingming , Ning Guozhu , Cao Yu , Wang Qiang 
Published: May 2020

AbstractThe paired pharyngeal arch arteries (PAAs) are transient blood vessels connecting the heart with the dorsal aorta during embryogenesis. Although PAA malformations often occur along with pharyngeal pouch defects, the functional interaction between these adjacent tissues remains largely unclear. Here we report that the ablation of pouches in zebrafish embryos impairs PAA progenitor specification and leads to the absence of PAA structures. Through time-lapse imaging studies, we reveal that the segmentation of pharyngeal pouches coincides spatiotemporally with the emergence of PAA progenitor clusters. These pouches physically associate with pharyngeal mesoderm in discrete regions and provide a niche microenvironment for PAA progenitor commitment by expressing BMP proteins. Specifically, tissue specific knockdown experiments demonstrate that pouch-derived BMP2a and BMP5 are the primary niche cues responsible for activating the BMP/Smad pathway in pharyngeal mesoderm, thereby promoting progenitor specification. In addition, BMP2a and BMP5 play a primary inductive function in the expression of theclochegenenpas4lin PAA progenitors. Mutation of theclochelocus represses the specification of PAA progenitors and generates ectopic muscle precursors in the pharyngeal mesoderm. Therefore, our results support a critical role of pharyngeal pouches in establishing a progenitor niche for PAA morphogenesis via BMP2a/5 expression.
Decreased Stroke, Acute Coronary Syndrome, and Corresponding Interventions at 65 US Hospitals Following COVID-19
Authors: de Havenon Adam , Ney John P. , Callaghan Brian , Delic Alen , Hohmann Samuel , Shippey Ernie , Yaghi Shadi , Anadani Mohammad , Esper Gregory J. , Majersik Jennifer J. 
Published: May 2020

AbstractBackgroundFollowing the emergence of coronavirus disease 2019 (COVID-19), early reports suggested a decrease in stroke and acute coronary syndrome (ACS). We sought to provide descriptive statistics for stroke and ACS from a sample of hospitals throughout the United States, comparing data from March 2020 to similar months pre-COVID.MethodsWe performed a retrospective analysis of 65 academic and community hospitals in the Vizient Clinical Data Base. The primary outcome is monthly count of stroke and ACS, and acute procedures for both, from February and March in 2020 compared to the same months in 2018 and 2019. Results are aggregated for all hospitals and reported by Census Region.ResultsWe identified 51,246 strokes (42,780 ischemic, 8,466 hemorrhagic), 1,043 mechanical thrombectomies (MT), 836 tissue plasminogen activator (tPA) administrations, 36,551 ACS, and 3,925 percutaneous coronary interventions (PCI) for ACS. In February 2020, relative to February 2018 and 2019, hospitalizations with any discharge diagnosis of stroke and ACS increased by 9.8% and 12.1%, respectively, while in March 2020 they decreased 18.5% and 7.5%, relative to March 2018 and 2019. When only including hospitalizations with the primary discharge diagnosis of stroke or ACS, in March 2020 they decreased 17.6% and 25.7%, respectively. In March 2020, tPA decreased 3.3%, MT increased 18.8%, although in February 2020 it had increased 36.8%, and PCI decreased 14.7%. These decreases were observed in all Census regions.ConclusionsFollowing greater recognition of the risks of COVID-19, hospitalizations with stroke and ACS were markedly diminished in a geographically diverse sample of United States hospitals. Because the most likely explanation is that some patients with stroke and ACS did not seek medical care, the underlying reasons for this decrease warrant additional study to inform public health efforts and clinical care during this and future pandemics.
Creation of a Clinical Decision-Support Tool for Assigning Occupational Disability to United States Air Force Personnel
Authors: Uptegraft Maj Colby C. , Witkop Catherine T. 
Published: May 2020

AbstractOccupational dispositions (profiles) are the top reason active duty service members are not medically ready to deploy or fulfill their job responsibilities. An audit across multiple U.S. Air Force (AF) medical treatment facilities revealed significant shortcomings in how medical providers assign profiles. We aimed to create a predictive model and a decision-support tool that estimates profile duration.Using retrospective profiles (n=1,546,805) from the Aeromedical Services Information Management System between 1 Feb 2007 and 31 Jan 2017, we built and validated a decision-support tool that estimates profile length. Multivariate quantile regressions (n=2,575) were performed across five quantiles and six levels of diagnostic specificity for every diagnostic code with 2,100 or more observations.The models universally estimated profile duration with very poor accuracy (pseudoR2 0.000 to 0.168); however, predictive ability was directly correlated with quantile level with minimal variation by diagnostic specificity. Age, O4 to O6+ ranks, very heavy job class, and co-morbid conditions were all significant in more than 25.0% of regressions down all levels of diagnostic specificity. Age, co-morbid conditions, E7-E9 ranks, O4 to O6+ ranks, and light job class all added days to profile duration while E1 to E4 ranks, heavy, and very heavy job class subtracted days.While this study failed to produce an accurate tool, several findings, the indirect correlation between profile duration and very heavy job class and the assignment of durations based on convenient calendar times, warrant further investigation. For now, providers may consult existing decision-support tools when building profiles for AF service members, heeding attention that they were built with non-representative civilian populations.DisclaimerThe views expressed are solely those of the authors and do not reflect the official policy or position of the US Army, US Navy, US Air Force, the Department of Defense, or the US Government.
Social Distancing is Effective at Mitigating COVID-19 Transmission in the United States
Authors: Badr Hamada S. , Du Hongru , Marshall Max , Dong Ensheng , Squire Marietta , Gardner Lauren M. 
Published: May 2020

AbstractCOVID-19 is present in every state and over 90 percent of all counties in the United States. Decentralized government efforts to reduce spread, combined with the complex dynamics of human mobility and the variable intensity of local outbreaks makes assessing the effect of large-scale social distancing on COVID-19 transmission in the U.S.a challenge. We generate a novel metric to represent social distancing behavior derived from mobile phone data and examine its relationship with COVID-19 case reports at the county level. Our analysis reveals that social distancing is strongly correlated with decreased COVID-19 case growth rates for the 25 most affected counties in the United States, with a lag period consistent with the incubation time of SARS-CoV-2. We also demonstrate evidence that social distancing was already under way in many U.S. counties before state or local-level policies were implemented. This study strongly supports social distancing as an effective way to mitigate COVID-19 transmission in the United States.
Monitoring the Covid-19 epidemics in Italy from mortality data
Authors: del Re Daniele , Meridiani Paolo 
Published: May 2020

AbstractThe mortality data can be used as an alternative source to monitor the status of Covid-19. We have studied a dataset including deaths up to the fourth week of April. There is a large excess, more pronounced at the beginning of the pandemic, showing a difference in age and gender compared to the Covid-19-confirmed cases. The study indicates that mortality information can be used to provide a less biased time profile of the pandemic.
Rapid and extraction-free detection of SARS-CoV-2 from saliva with colorimetric LAMP
Authors: Lalli Matthew A. , Langmade S. Joshua , Chen Xuhua , Fronick Catrina C. , Sawyer Christopher S. , Burcea Lauren C. , Wilkinson Michael N. , Fulton Robert S. , Heinz Michael , Buchser William J. , Head Richard D. , Mitra Robi D. , Milbrandt Jeffrey 
Published: May 2020

AbstractRapid, reliable, and widespread testing is required to curtail the ongoing COVID-19 pandemic. Current gold standard nucleic acid tests are hampered by supply shortages in critical reagents including nasal swabs, RNA extraction kits, personal protective equipment (PPE), instrumentation, and labor. Here we present an approach to overcome these challenges with the development of a rapid colorimetric assay using reverse-transcription loop-mediated isothermal amplification (RT-LAMP) optimized on human saliva samples without an RNA purification step. We describe our optimizations of the LAMP reaction and saliva pretreatment protocols that enabled rapid and sensitive detection of < 102 viral genomes per reaction in contrived saliva controls. Moreover, our saliva pretreatment protocol enabled sensitive viral detection by conventional quantitative reverse transcription polymerase chain reaction (qRT-PCR) without RNA extraction. We validated the high performance of these assays on clinical samples and demonstrate a promising approach to overcome the current bottlenecks limiting widespread testing.
Coronavirus Disease 2019 (COVID-19): An Evidence Map of Medical Literature
Authors: Liu Nan , Chee Marcel Lucas , Niu Chenglin , Pek Pin Pin , Siddiqui Fahad Javaid , Ansah John Pastor , Matchar David Bruce , Lam Sean Shao Wei , Abdullah Hairil Rizal , Chan Angelique , Malhotra Rahul , Graves Nicholas , Koh Mariko Siyue , Yoon Sungwon , Ho Andrew Fu Wah , Ting Daniel Shu Wei , Low Jenny Guek Hong , Ong Marcus Eng Hock 
Published: May 2020

AbstractSince the beginning of the COVID-19 outbreak in December 2019, a substantial body of COVID-19 medical literature has been generated. As of May 2020, gaps in the existing literature remain unidentified and, hence, unaddressed. In this paper, we summarise the medical literature on COVID-19 between 1 January and 24 March 2020 using evidence maps and bibliometric analysis in order to systematically identify gaps and propose areas for valuable future research. The examined COVID-19 medical literature originated primarily from Asia and focussed mainly on clinical features and diagnosis of the disease. Many areas of potential research remain underexplored, such as mental health research, the use of novel technologies and artificial intelligence, research on the pathophysiology of COVID-19 within different body systems, and research on indirect effects of COVID-19 on the care of non-COVID-19 patients. Research collaboration at the international level was limited although improvements may aid global containment efforts.
Utility of Cloth Masks in Preventing Respiratory Infections: A Systematic Review
Authors: Mondal Agnibho , Das Arnavjyoti , Goswami Rama Prosad 
Published: May 2020

AbstractBackgroundUsing face masks is one of the possible prevention methods against respiratory pathogens. A number of studies and reviews have been performed regarding the use of medical grade masks like surgical masks, N95 respirators etc. However, the use of cloth masks has received little attention.ObjectivesThe purpose of this review is to analyze the available data regarding the use of cloth masks for the prevention of respiratory infections. We intended to use data from both clinical and non-clinical studies to arrive at our conclusion.MethodsWe used PubMed, Cochrane Library and Google Scholar as our source databases. Both clinical and non-clinical studies, which had data regarding the efficacy of cloth masks, were selected. Articles not containing analyzable data including opinion articles, review articles etc. were excluded. After screening the search results, ten studies could be included in our review.Data relevant to our objective was extracted from each study including clinical efficacy, compliance, filtration efficacy etc. Data from some studies were simplified for the purpose of comparison. Extracted data was summarized and categorized for detailed analysis. Qualitative synthesis of the data was performed. But the heterogeneity between the studies did not allow for a meta-analysis.DiscussionThe review was limited by a lack of sufficient clinical studies. Lack of standardization between studies was another limitation.Although cloth masks generally perform poorer than the medical grade masks, they may be better than no masks at all. Filtration efficacy varied greatly depending on the material used, with some materials showing a filtration efficacy above 90%. However, leakage could reduce efficacy of masks by about 50%. Standardization of cloth masks and appropriate use is essential for cloth masks to be effective. However, result of a randomized controlled trial suggest that they may be ineffective in the healthcare setting.
Low testosterone and high cytokine levels correlate with lethal H7N9 infections in men: a retrospective cohort study from 98 H7N9 patients
Authors: Chen Yongkun , Bai Tian , Beck Sebastian , Stanelle-Bertram Stephanie , Chen Tao , Dong Jie , Yang Jing , Wang Lijie , Wang Dayan , Shu Yuelong , Gabriel Gülsah 
Published: May 2020

SummaryBackgroundHuman infections with avian influenza A (H7N9) virus emerged in East China in March 2013. In contrast to seasonal influenza A viruses, H7N9 infections showed a strong sex bias. Over the five epidemic waves in China, ~70% of all H7N9 cases were observed in men. Thus, in this human cohort, we retrospectively analyzed sex hormones as well as inflammatory cytokine and chemokine levels in men and women infected with avian H7N9 influenza.MethodsWe systematically analyzed the underlying correlation based on established human cohorts of two age groups (18-49 years and ≥50 years) including laboratory-confirmed H7N9 cases as well as seasonal influenza cases, H7N9 close contacts and poultry workers as controls in dependency on sex. The level of testosterone, estradiol and cytokines/chemokines were measured in all study participants. We compared the levels of sex hormones, cytokines/chemokines by sex and disease outcome.FindingsWe included H7N9 cases (n=98), close contacts (n =71), poultry workers (n =108) and mild seasonal influenza cases (n =53) in this study. Samples were collected between 2014 and 2017. All control groups showed similar median age within H7N9 cases except for the seasonal influenza group with a younger median age. In H7N9 infected men, testosterone levels were strongly reduced compared to male H7N9 virus-negative close contacts or males with seasonal influenza. Low testosterone levels in H7N9 infected men correlated with high inflammatory cytokine levels, e.g. IL-6, and lethal outcome in those 18-49 years of age. No significant differences were detected in estradiol levels in H7N9 infected men. In H7N9 infected women (≥ 50 years), estradiol levels were significantly elevated compared to H7N9 virus-negative close contacts. However, increased estradiol levels did not significantly correlate with lethal outcome in women albeit a slight tendency towards poor outcome could be detected.InterpretationThis study provides evidence that low testosterone levels in H7N9 influenza infected men correlate with inflammatory cytokine/chemokine responses and lethal outcome. Thus, treatment of H7N9 influenza virus infected patients should consider sex-specific mitigation strategies.FundingThis study was supported by the National Key Research and Development Program of China (2016YFC1200200 to Y.L.S. and 2016YFD0500208 to D.Y.W), the Guangdong Province Science and Technology Innovation Strategy Special Fund (2018A030310337 to Y.K.C), the German Free and Hanseatic City of Hamburg (to HPI (G.G.)) as well as the German Federal Ministry of Health (to HPI (G.G.)).
Serological signatures of SARS-CoV-2 infection: Implications for antibody-based diagnostics
Authors: Rosado Jason , Pelleau Stéphane , Cockram Charlotte , Hélène Merkling Sarah , Nekkab Narimane , Demeret Caroline , Meola Annalisa , Kerneis Solen , Terrier Benjamin , Fafi-Kremer Samira , de Seze Jerome , Dejardin François , Petres Stéphane , Longley Rhea , Backovic Marija , Mueller Ivo , White Michael T 
Published: May 2020

AbstractBackgroundInfection with SARS-CoV-2 induces an antibody response targeting multiple antigens that changes over time. This complexity presents challenges and opportunities for serological diagnostics.MethodsA multiplex serological assay was developed to measure IgG and IgM antibody responses to seven SARS-CoV-2 spike or nucleoprotein antigens, two antigens for the nucleoproteins of the 229E and NL63 seasonal coronaviruses, and three non-coronavirus antigens. Antibodies were measured in serum samples from patients in French hospitals with RT-qPCR confirmed SARS-CoV-2 infection (n= 259), and negative control serum samples collected before the start of the SARS-CoV-2 epidemic (n= 335). A random forests algorithm was trained with the multiplex data to classify individuals with previous SARS-CoV-2 infection. A mathematical model of antibody kinetics informed by prior information from other coronaviruses was used to estimate time-varying antibody responses and assess the potential sensitivity and classification performance of serological diagnostics during the first year following symptom onset. A statistical estimator is presented that can provide estimates of seroprevalence in very low transmission settings.ResultsIgG antibody responses to trimeric Spike protein identified individuals with previous RT-qPCR confirmed SARS-CoV-2 infection with 91.6% sensitivity (95% confidence interval (CI); 87.5%, 94.5%) and 99.1% specificity (95% CI; 97.4%, 99.7%). Using a serological signature of IgG and IgM to multiple antigens, it was possible to identify infected individuals with 98.8% sensitivity (95% CI; 96.5%, 99.6%) and 99.3% specificity (95% CI; 97.6%, 99.8%). Informed by prior data from other coronaviruses, we estimate that one year following infection a monoplex assay with optimal anti-StriIgG cutoff has 88.7% sensitivity (95% CI: 63.4%, 97.4%), and that a multiplex assay can increase sensitivity to 96.4% (95% CI: 80.9%, 100.0%). When applied to population-level serological surveys, statistical analysis of multiplex data allows estimation of seroprevalence levels less than 1%, below the false positivity rate of many other assays.ConclusionSerological signatures based on antibody responses to multiple antigens can provide accurate and robust serological classification of individuals with previous SARS-CoV-2 infection. This provides potential solutions to two pressing challenges for SARS-CoV-2 serological surveillance: classifying individuals who were infected greater than six months ago, and measuring seroprevalence in serological surveys in very low transmission settings.
Prevalence of metabolic disorders in obese triple negative breast cancer patients
Authors: Torres-de la Roche Luz Angela , Schulte Alina Jara , Devassy Rajesh , Krentel Harald , Willborn Kay , Eidswick Jennifer , De Wilde Rudy Leon 
Published: May 2020

AbstractIntroductionObesity is a risk factor for hormone receptor positive breast cancer in postmenopausal women. However, the association between triple negative breast cancer risk and metabolic abnormalities is not yet clear. Moreover, little is known regarding the prevalence of these abnormalities in this group of women. Here we present the prevalence of metabolic abnormalities in a single cohort of obese postmenopausal triple negative breast cancer patients.MethodsMonocentric, retrospective, single cohort analysis of triple negative breast cancer patients treated between January 2008 and December 2017 at Pius Hospital Oldenburg. For quantitative or numerical variables, central tendency and dispersion measures were used. Values are presented as mean number of patients or percentage.ResultsAmong 2745 breast cancer cases, 43 obese postmenopausal patients with a mean age of 64 years (range 51 to 90) had triple negative breast cancer. Most were diagnosed with invasive ductal (n = 39; 90.7 %), high-grade carcinoma (n = 35; 81.4 %), with a tumor size between 2 and 5 cm (n = 19; 44.2 %). Half the cohort lacked lymph node involvement; 5 patients showed distant metastasis (11.6 %). The majority had no family history of breast cancer (n = 32; 74.4 %), were non-smokers (n = 37; 86 %), and had a history of pregnancy (n = 35; 81.4 %). Frequent metabolic abnormalities included hypertension (n = 31; 72.1 %) and dyslipidemia (n = 36; 83.7 %) whereas type 2 diabetes or glucose intolerance were less prevalent (n = 13; 30.2 %).ConclusionHypertension and dyslipidemia were more prevalent in the study cohort than type 2 diabetes. Moderately obese patients were most frequently affected. These findings partially align with international studies which observed an association between triple negative breast cancer and elevated levels of blood glucose and triglycerides, but not between tumor disease and hypertension.
Time-resolving the COVID-19 outbreak using frequency domain analysis
Authors: Krewer Keno L. , Bonn Mischa 
Published: May 2020

AbstractDifficulties assessing and predicting the current outbreak of the severe acute respiratory syndrome coronavirus 2 can be traced, in part, to the limitations of a static description of a dynamic system. Fourier transforming the time-domain data of infections and fatalities into the frequency domain makes the dynamics easily accessible. Defining a quantity like the “case fatality” as a spectral density allows a more sensible comparison between different countries and demographics during an ongoing outbreak. Such a case fatality informs not only how many of the confirmed cases end up as fatalities, but also when. For COVID-19, knowing this time and using the entire case fatality spectrum allows determining that an outbreak had entered a steady-state (most likely its end) about 14 days before this is obvious from time-domain data. The lag between confirmations and deaths also helps to estimate the effectiveness of contact management: The larger the lag, the less time the average confirmed person had to infect people before quarantine.