bluuebunny/crossref_metadata_2025_split huggingface dataset:
Knowledge, attitude, and perceptions towards the 2019 Coronavirus Pandemic: A bi-national survey in Africa
Authors: Hager Elnadi , Odetokun Ismail A. , Bolarinwa Obasanjo , Zainab Ahmed , Okechukwu Ochulor , Ibrahim Al-Mustapha A. 
Published: May 2020

AbstractThe current Coronavirus (COVID-19) pandemic has changed and impacted lives on a global scale since its emergence and spread from China in late 2019. It has caused millions of infections, and thousands of deaths worldwide. However, the control of this pandemic still remains unachievable in many African countries including Egypt and Nigeria, despite the application of some strict preventive and control measures. Therefore, this study assessed the knowledge, attitude and perceptions of Egyptians and Nigerians towards COVID-19 pandemic.A total of 1437 respondents were included in this preliminary cross-sectional survey. The mean knowledge score was 14.7±2.3. The majority of the respondents (61.6%) had a satisfactory knowledge of the disease. Age (18-39 years), education (College/bachelors) and background of respondents were factors influencing knowledge levels. The attitude of most respondents (68.9%) towards the preventive measures was satisfactory with an average attitude score of 6.9 ± 1.2. The majority of the respondents (96%) practiced self-isolation and social-distancing but only 36% follow all health recommendations. The perception of most respondents (62.1%) on the global efforts at controlling the virus and preventing further spread was satisfactory with an average score of 10.9 ± 2.7. A satisfactory knowledge of COVID-19 was significantly associated with good attitude and perceptions (p < 0.001) of respondents. Only 22% of the respondents were satisfied with their country’s handling of the pandemic.It is imperative that to avoid Africa being the next epicenter of the pandemic. Governments need to strengthen health systems, improve their surveillance activities in detecting cases, and effectively apply standard infection prevention and control measures.
Correlation of population mortality of COVID-19 and testing coverage: a comparison among 36 OECD countries and Taiwan
Authors: Wei Chen , Lee Chien-Chang , Hsu Tzu-Chun , Hsu Wan-Ting , Chan Chang-Chuan , Chen Shyr-Chyr , Chen Chien-Jen 
Published: May 2020

ABSTRACTAlthough testing is widely regarded as critical to fighting the Covid-19 pandemic, what measure and level of testing best reflects successful infection control remains unresolved. Our aim was to compare the sensitivity of two testing metrics-population testing number and testing coverage-to population mortality outcomes and identify a benchmark for testing adequacy with respect to population mortality and capture of potential disease burden. This ecological study aggregated publicly available data through April 12 on testing and outcomes related to COVID-19 across 36 OECD (Organization for Economic Development) countries and Taiwan. All OECD countries and Taiwan were included in this population-based study as a proxy for countries with highly developed economic and healthcare infrastructure. Spearman correlation coefficients were calculated between the aforementioned metrics and following outcome measures: deaths per 1 million people, case fatality rate, and case proportion of critical illness. Fractional polynomials were used to generate scatter plots to model the relationship between the testing metrics and outcomes. Testing coverage, but not population testing number, was highly correlated with population mortality (rs= −0.79, P=5.975e-09 vs rs = − 0.3, P=0.05) and case fatality rate (rs= −0.67, P=9.067e-06 vs rs= −0.21, P=0.20). A testing coverage threshold of 15-45 signified adequate testing: below 15, testing coverage was associated with exponentially increasing population mortality, whereas above 45, increased testing did not yield significant incremental mortality benefit. Testing coverage was better than population testing number in explaining country performance and can be used as an early and sensitive indicator of testing adequacy and disease burden. This may be particularly useful as countries consider re-opening their economies.
Determinants of COVID-19 vaccine acceptance in Saudi Arabia: a web-based national survey
Authors: Padhi Bijaya Kumar , Al-Mohaithef Mohammed 
Published: May 2020

AbstractBackgroundVaccine hesitancy is a potential threat to global public health. Since, there is an unprecedented global effort to develop a vaccine against the COVID-19 pandemic, much less is known about its acceptance in the community. Understanding key determinants that influence the preferences and demands of a future vaccine by the community may help to develop strategies for improving the global vaccination program. This study aimed to assess the prevalence of the acceptance of COVID-19 vaccine, and their determinants among people in Saudi Arabia.MethodsA web-based, cross-sectional study was conducted using snowball sampling strategy under a highly restricted environment. A bilingual, self-administered anonymous questionnaire was designed and sent to 1000 study participants through social media platforms and email. Study participants were recruited across the country, including the four major cities (Riyadh, Dammam, Jeddah, and Abha) in Saudi Arabia. Associations between COVID-19 vaccine acceptance and sociodemographic profile of the respondents were explored using the chi-squared test. Key determinants that predict vaccine acceptance among respondents were modelled using logistic regression analysis.ResultsOf the 1000 survey invitees, 992 responded to the survey (response rate, 99.2%). The majority (65.8%) of the study participants were female, 29.53% were in the age group (36–45 years), and 17.9% were non-Saudi. Of the 992 respondents, 642 (64.72%) showed interest to accept the COVID-19 vaccine if it is available. Willingness to accept the future COVID-19 vaccine is relatively high among older age groups (79.2% among 45+ year old), being married (69.3%), participants with education level postgraduate degree or higher (68.8%), non-Saudi (69.1%), employed in government sector (68.9%). In multivariate model, respondents who were above 45 years (aOR: 2.15; 95% CI: 1.08-3.21), and married (aOR: 1.79; 95% CI: 1.28-2.50) were significantly associated with vaccine acceptance (p <.05). Besides, people having trust in the health system were most likely to accept the vaccine (aOR: 3.05; 95% CI: 1.13-4.92), and those having a higher perceived risk of acquiring infection were 2.13 times (95% CI: 1.35-3.85) higher odds of accepting the vaccine.ConclusionAddressing sociodemographic determinants relating to the COVID-19 vaccination may help to increase uptake of the global vaccination program to tackle future pandemics. Targeted health education interventions are needed to increase the uptake of the future COVID-19 vaccine.
A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding
Authors: Byrnes James R. , Zhou Xin X. , Lui Irene , Elledge Susanna K. , Glasgow Jeff E. , Lim Shion A. , Loudermilk Rita , Chiu Charles Y. , Wilson Michael R. , Leung Kevin K. , Wells James A. 
Published: May 2020

ABSTRACTAs SARS-CoV-2 continues to spread around the world, there is an urgent need for new assay formats to characterize the humoral response to infection. Convalescent serum is being used for treatment and for isolation of patient-derived antibodies. However, currently there is not a simple means to estimate serum bulk neutralizing capability. Here we present an efficient competitive serological assay that can simultaneously determine an individual’s seropositivity against the SARS-CoV-2 Spike protein and estimate the neutralizing capacity of anti-Spike antibodies to block interaction with the human angiotensin converting enzyme 2 (ACE2) required for viral entry. In this ELISA-based assay, we present natively-folded viral Spike protein receptor binding domain (RBD)-containing antigens via avidin-biotin interactions. Sera are then supplemented with soluble ACE2-Fc to compete for RBD-binding serum antibodies, and antibody binding quantified. Comparison of signal from untreated serum and ACE2-Fc-treated serum reveals the presence of antibodies that compete with ACE2 for RBD binding, as evidenced by loss of signal with ACE2-Fc treatment. In our test cohort of nine convalescent SARS-CoV-2 patients, we found all patients had developed anti-RBD antibodies targeting the epitope responsible for ACE2 engagement. This assay provides a simple and high-throughput method to screen patient sera for potentially neutralizing anti-Spike antibodies to enable identification of candidate sera for therapeutic use.
Clinical population genetic analysis of variants in the SARS-CoV-2 receptor ACE2
Authors: Ardeshirdavani Amin , Zakeri Pooya , Mehrtash Amirhosein , Hosseini Sayed Mostafa , Li Guangdi , Mirtavoos-Mahyari Hanifeh , Soltanpour Mohamad javad , Tavallaie Mahmoud , Moreau Yves 
Published: May 2020

AbstractPurposeSARS-CoV-2 infects cells via the human Angiotensin-converting enzyme 2 (ACE2) protein. The genetic variation of ACE2 function and expression across populations is still poorly understood. This study aims at better understanding the genetic basis of COVID-19 outcomes by studying association between genetic variation in ACE2 and disease severity in the Iranian population.MethodsWe analyzed two large Iranian cohorts and several publicly available human population variant databases to identify novel and previously known ACE2 exonic variants present in the Iranian population and considered those as candidate variants for association between genetic variation and disease severity. We genotyped these variants across three groups of COVID-19 patients with different clinical outcomes (mild disease, severe disease, and death) and evaluated this genetic variation with regard to clinical outcomes.ResultsWe identified 32 exonic variants present in Iranian cohorts or other public variant databases. Among those, 11 variants are novel and have thus not been described in other populations previously. Following genotyping of these 32 candidate variants, only the synonymous polymorphism (c.2247G>A) was detected across the three groups of COVID-19 patients.ConclusionGenetic variability of known and novel exonic variants was low among our COVID-19 patients. Our results do not provide support for the hypothesis that exonic variation in ACE2 has a sizeable impact on COVID-19 severity across the Iranian population.
Assessment of Individual- and Community-level Risks for COVID-19 Mortality in the US and Implications for Vaccine Distribution
Authors: Jin Jin , Agarwala Neha , Kundu Prosenjit , Harvey Benjamin , Zhang Yuqi , Wallace Eliza , Chatterjee Nilanjan 
Published: May 2020

AbstractReducing COVID-19 illness and mortality for populations in the future will require equitable and effective risk-based allocations of scarce preventive resources, including early available vaccines. To aid in this effort, we develop a risk calculator for COVID-19 mortality based on various socio-demographic factors and pre-existing conditions for the US adult population by combining information from the UK-based OpenSAFELY study, with mortality rates by age and ethnicity available across US states. We tailor the tool to produce absolute risks for individuals in future time frames by incorporating information on pandemic dynamics at the community level as available from forecasting models. We apply this risk calculation model to available data on prevalence and co-occurrences of the risk-factors from a variety of data sources to project risk for the general adult population across 477 US cities (defined as Census Places) and for the 65 years and older Medicare population across 3,113 US counties, respectively. Validation analyses based on these projected risks and data on tens of thousands of recent deaths show that the model is well calibrated for the US population. Projections show that the model can identify relatively small fractions of the population (e.g. 4.3%) which will lead to a disproportionately large number of deaths (e.g. 49.8%), and thus will be useful for effectively targeting individuals for early vaccinations, but there will be wide variation in risk distribution across US communities. We provide a web-based tool for individualized risk calculations and interactive maps for viewing the city-, county- and state-level risk projections.
Cell clusters adopt a collective amoeboid mode of migration in confined non-adhesive environments
Authors: Pagès Diane-Laure , Dornier Emmanuel , De Seze Jean , Wang Li , Luan Rui , Cartry Jérôme , Canet-Jourdan Charlotte , Raingeaud Joel , Voituriez Raphael , Coppey Mathieu , Piel Matthieu , Jaulin Fanny 
Published: May 2020

AbstractCell migration is essential to most living organisms. Single cell migration involves two distinct mechanisms, either a focal adhesion- and traction-dependent mesenchymal motility or an adhesion-independent but contractility-driven propulsive amoeboid locomotion. Cohesive migration of a group of cells, also called collective cell migration, has been only described as an adhesion- and traction-dependent mode of locomotion where the driving forces are mostly exerted at the front by leader cells. Here, by studying primary cancer specimens and cell lines from colorectal cancer, we demonstrate the existence of a second mode of collective migration which does not require adhesion to the surroundings and relies on a polarised supracellular contractility. Cell clusters confined into non-adhesive microchannels migrate in a rounded morphology, independently of the formation of focal adhesions or protruding leader cells, and lacking internal flow of cells, ruling-out classical traction-driven collective migration. Like single cells migrating in an amoeboid fashion, the clusters display a supracellular actin cortex with myosin II enriched at the rear. Using pharmacological inhibitors and optogenetics, we show that this polarised actomyosin activity powers migration and propels the clusters. This new mode of migration, that we named collective amoeboid, could be enabled by intrinsic or extrinsic neoplasic features to enable the metastatic spread of cancers.One Sentence SummaryClusters organise as polarised and contractile super-cells to migrate without adhesion.
Sox9EGFPdefines biliary epithelial heterogeneity downstream of Yap activity
Authors: Tulasi Deepthi Y , Martinez Castaneda Diego , Wager Kortney , Alcedo Karel P , Raab Jesse R , Gracz Adam D 
Published: May 2020

ABSTRACTIntrahepatic bile ducts are lined by biliary epithelial cells (BECs). However, defining the genetic heterogeneity of BECs remains challenging, and tools for identifying BEC subpopulations are limited. Here, we characterize Sox9EGFPtransgene expression in the liver and demonstrate that GFP expression levels are associated with distinct cell types. BECs express “low” or “high” levels of GFP, while periportal hepatocytes express “sublow” GFP. Sox9EGFPdistribution varies by duct size, with GFPhighBECs found at greater numbers in smaller ducts. RNA-seq reveals distinct gene expression signatures for Sox9EGFPpopulations and enrichment of Notch and Yap signaling in GFPlowand GFPhighBECs. All GFP+populations are capable of forming organoids, but demonstrate interpopulation differences in organoid survival and size, dependent on media conditions. Organoids derived from Sox9EGFPpopulations also demonstrate differential activation of HNF4A protein in hepatocyte media conditions, suggesting variable potency in BEC subpopulations. We find that Yap signaling is required to maintainSox9expression in biliary organoids, and that bile acids are insufficient to induce Yap activity orSox9 in vivoandin vitro. Our data demonstrate that Sox9EGFPlevels provide a readout of Yap activity and delineate BEC heterogeneity, providing a tool for assaying subpopulation-specific cellular function in the liver.
Keratin 19 maintains E-cadherin localization at the cell surface and stabilizes cell-cell adhesion of MCF7 cells
Authors: Alsharif Sarah , Sharma Pooja , Bursch Karina , Milliken Rachel , Collins Meagan , Lam Van , Fallatah Arwa , Phan Thuc , Dohlman Priya , Nehmetallah Georges , Raub Christopher B. , Chung Byung Min 
Published: May 2020

AbstractA cytoskeletal protein keratin 19 (K19) is highly expressed in breast cancer but its effects on breast cancer cell mechanics are unclear. UsingKRT19knockout (KO) cells and cells where K19 expression was rescued, we found that K19 is required to maintain rounded epithelial-like shape and tight cell-cell adhesion of MCF7 cells. A loss of K19 resulted in a lower level of plakoglobin and internalization of E-cadherin in early and recycling endosomes. Inhibiting internalization restored cell-cell adhesion ofKRT19KO cells, suggesting E-cadherin internalization contributes to defective adhesion. Ultimately, while K19 inhibited cell migration, it was required for cells to form colonies in suspension. Our results suggest that K19 stabilizes E-cadherin complexes at the cell membrane to maintain cell-cell adhesion which inhibits cell migration but provides growth and survival advantages for circulating tumor cells. These findings provide context-dependent roles of K19 during metastasis.
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals
Authors: Bastian Frederic B. , Roux Julien , Niknejad Anne , Comte Aurélie , Fonseca Costa Sara S. , de Farias Tarcisio Mendes , Moretti Sébastien , Parmentier Gilles , de Laval Valentine Rech , Rosikiewicz Marta , Wollbrett Julien , Echchiki Amina , Escoriza Angélique , Gharib Walid H , Gonzales-Porta Mar , Jarosz Yohan , Laurenczy Balazs , Moret Philippe , Person Emilie , Roelli Patrick , Sanjeev Komal , Seppey Mathieu , Robinson-Rechavi Marc 
Published: May 2020

ABSTRACTBgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as “healthy” or not) as well as many small ones. Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression, along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available athttps://bgee.org/and through its Bioconductor R package BgeeDB.
Sample preparation and imaging conditions affect mEos3.2 photophysics in fission yeast cells
Authors: Sun Mengyuan , Hu Kevin , Bewersdorf Joerg , Pollard Thomas D. 
Published: May 2020

AbstractPhotoconvertible fluorescent proteins (PCFPs) are widely used in super-resolution microscopy and studies of cellular dynamics. However, our understanding of their photophysics is still limited, hampering their quantitative application. For example, we do not know the optimal sample preparation methods or imaging conditions to count protein molecules fused to PCFPs by single-molecule localization microscopy in live and fixed cells. We also do not know how the behavior of PCFPs in live cells compares with fixed cells. Therefore, we investigated how formaldehyde fixation influences the photophysical properties of the popular green-to-red PCFP mEos3.2 in fission yeast cells under a wide range of imaging conditions. We estimated photophysical parameters by fitting a 3-state model of photoconversion and photobleaching to the time course of fluorescence signal per yeast cell expressing mEos3.2. We discovered that formaldehyde fixation makes the fluorescence signal, photoconversion rate and photobleaching rate of mEos3.2 sensitive to the buffer conditions by permeabilizing the yeast cell membrane. Under some imaging conditions, the time-integrated mEos3.2 signal per yeast cell is similar in live cells and fixed cells imaged in buffer at pH 8.5 with 1 mM DTT, indicating that light chemical fixation does not destroy mEos3.2 molecules. We also discovered that some red-state mEos3.2 molecules entered an intermediate dark state that is converted back to the red fluorescent state by 561-nm illumination. Our findings provide a guide to compare quantitatively conditions for imaging and counting of mEos3.2-tagged molecules in yeast cells. Our imaging assay and mathematical model are easy to implement and provide a simple quantitative approach to measure the time-integrated signal and the photoconversion and photobleaching rates of fluorescent proteins in cells.STATEMENT OF SIGNIFICANCEMaking quantitative measurements with single-molecule localization microscopy (SMLM) has been impeded by limited understanding of the photophysics of the fluorophores, which is very sensitive to the sample preparation and imaging conditions. We characterized the photophysics of the green-to-red photoconvertible fluorescent protein mEos3.2, which is widely used in SMLM. We combined quantitative fluorescence microscopy and mathematical modeling to measure the fluorescence signal and rate constants for photoconversion and photobleaching of mEos3.2 in live and fixed cells under a wide range of illumination intensities. Our findings provide a guide to compare conditions for imaging and counting mEos3.2-tagged proteins in cells. The presented approach is generally applicable to characterize other fluorescent proteins or dyes in cells.
Atypical B cells are a normal component of immune responses to vaccination and infection in humans
Authors: Sutton Henry J. , Aye Racheal , Idris Azza H. , Vistein Rachel , Nduati Eunice , Kai Oscar , Mwacharo Jedida , Li Xi , Gao Xin , Andrews T. Daniel , Koutsakos Marios , Nguyen Thi H. O. , Nekrasov Maxim , Milburn Peter , Ethala Auda , Berry Andrea A. , Natasha KC , Chakravarty Sumana , Sim B. Kim Lee , Wheatley Adam K. , Kent Stephen J. , Hoffman Stephen L. , Lyke Kirsten E. , Bejon Philip , Luciani Fabio , Kedzierska Katherine , Seder Robert A. , Ndungu Francis M. , Cockburn Ian A. 
Published: May 2020

AbstractThe full diversity of the circulating human B cell compartment is unknown. Flow cytometry analysis suggests that in addition to naïve and memory B cells, there exists a population of CD11c+, CD27−CD21−“atypical” B cells, that are associated with chronic or recurrent infection and autoimmunity. We used single cell RNA-seq approaches to examine the diversity of both antigen-specific B cells and total B cells in healthy subjects and individuals naturally-exposed to recurrent malaria infections. This analysis revealed two B cell lineages: a classical lineage of activated and resting memory B cells, and an atypical-like lineage. Surprisingly, the atypical lineage was common in both malaria exposed individuals and non-exposed healthy controls. Using barcoded antibodies in conjunction with our transcriptomic data, we found that atypical lineage cells in healthy individuals lack many atypical B markers and thus represent an undercounted cryptic population. We further determined using antigen specific probes that atypical cells can be induced by primary vaccination in humans and can be recalled upon boosting. Collectively these data suggest that atypical cells are not necessarily pathogenic but can be a normal component of B responses to antigen.