bluuebunny/crossref_metadata_2025_split huggingface dataset:
The RBD Of The Spike Protein Of SARS-Group Coronaviruses Is A Highly Specific Target Of SARS-CoV-2 Antibodies But Not Other Pathogenic Human and Animal Coronavirus Antibodies
Authors: Premkumar Lakshmanane , Segovia-Chumbez Bruno , Jadi Ramesh , Martinez David R. , Raut Rajendra , Markmann Alena , Cornaby Caleb , Bartelt Luther , Weiss Susan , Park Yara , Edwards Caitlin E. , Weimer Eric , Scherer Erin M. , Roupael Nadine , Edupuganti Sri , Weiskopf Daniela , Tse Longping V. , Hou Yixuan J. , Margolis David , Sette Alessandro , Collins Matthew H. , Schmitz John , Baric Ralph S. , de Silva Aravinda M. 
Published: May 2020

AbstractA new Severe Acute Respiratory Syndrome Coronavirus variant (SARS-CoV-2) that first emerged in late 2019 is responsible for a pandemic of severe respiratory illness. People infected with this highly contagious virus present with clinically inapparent, mild or severe disease. Currently, the presence of the virus in individual patients and at the population level is being monitored by testing symptomatic cases by PCR for the presence of viral RNA. There is an urgent need for SARS-CoV-2 serologic tests to identify all infected individuals, irrespective of clinical symptoms, to conduct surveillance and implement strategies to contain spread. As the receptor binding domain (RBD) of the viral spike (S) protein is poorly conserved between SARS-CoVs and other pathogenic human coronaviruses, the RBD represents a promising antigen for detecting CoV specific antibodies in people. Here we use a large panel of human sera (70 SARS-CoV-2 patients and 71 control subjects) and hyperimmune sera from animals exposed to zoonotic CoVs to evaluate the performance of the RBD as an antigen for accurate detection of SARS-CoV-2-specific antibodies. By day 9 after the onset of symptoms, the recombinant SARS-CoV-2 RBD antigen was highly sensitive (98%) and specific (100%) to antibodies induced by SARS-CoVs. We observed a robust correlation between levels of RBD binding antibodies and SARS-CoV-2 neutralizing antibodies in patients. Our results, which reveal the early kinetics of SARS-CoV-2 antibody responses, strongly support the use of RBD-based antibody assays for population-level surveillance and as a correlate of neutralizing antibody levels in people who have recovered from SARS-CoV-2 infections.
Pharyngeal carriage of inoculated recombinant commensal bacteria generates antigen-specific immunological memory
Authors: Laver Jay R , Gbesemete Diane , Dale Adam P , Pounce Zoe C , Webb Carl N , Roche Eleanor F , Berreen Graham , Belogiannis Konstantinos , Hill Alison R , Ibrahim Muktar M , Cleary David W , Pandey Anish K , Humphries Holly E , Allen Lauren , de Graaf Hans , Maiden Martin C , Faust Saul N , Gorringe Andrew R , Read Robert C 
Published: May 2020

ABSTRACTThe human nasopharynx is colonized by commensal bacteria and pathobionts, which comprise a complex microbial ecosystem capable of generating primary and secondary immune responses. Experimental intranasal infection of human adults with the commensal Neisseria lactamica results in safe, sustained colonization. Herein is described a novel technology to chromosomally transform N. lactamica with heterologous antigen, for the purpose of safe delivery to the mucosal surface and the generation of an antigen-specific immune response. N. lactamica was transformed to express the meningococcal vaccine antigen Neisseria Adhesin A (NadA) and was inoculated intranasally into humans at a dose of 105 colony-forming units. NadA-expressing N. lactamica colonized these individuals and was carried asymptomatically for 3 months. Colonization with NadA-expressing N. lactamica generated NadA-specific IgG-secreting plasma cells within 14 days of colonization and both NadA-specific IgG and NadA-specific IgG memory B cells within 28 days of colonization. NadA-specific IgG memory B cells circulate in the bloodstream of colonized participants for at least 90 days. Genetically transformed N. lactamica has the potential to be a safe bacterial vehicle to generate beneficial immune responses to a wide range of heterologous antigens during sustained pharyngeal carriage.
Sensitivity and specificity of a rapid test for assessment of exposure to SARS-CoV-2 in a community-based setting in Brazil
Authors: Pellanda Lucia Campos , da Ros Wendland Eliana Márcia , McBride Alan John Alexander , Tovo-Rodrigues Luciana , Ferreira Marcos Roberto Alves , Dellagostin Odir Antônio , da Silveira Mariangela Freitas , de Barros Aluisio Jardim Dornellas , Hallal Pedro Curi , Victora Cesar Gomes 
Published: May 2020

AbstractBackgroundWhile the recommended laboratory diagnosis of COVID-19 is a molecular based assay, population-based studies to determine the prevalence of COVID-19 usually use serological assays.ObjectiveTo evaluate the sensitivity and specificity of a rapid diagnostic test for COVID-19 compared to quantitative reverse transcription polymerase chain reaction (qRT-PCR).MethodsWe evaluated the sensitivity using a panel of finger prick blood samples from participants >18 years of age that had been tested for COVID-19 by qRT-PCR. For assessing specificity, we used serum samples from the 1982 Pelotas (Brazil) Birth Cohort participants collected in 2012 with no exposure to SARS-CoV-2.ResultsThe sensitivity of the test was 77.1% (95% CI 66.6 - 85.6), based upon 83 subjects who had tested positive for qRT-PCR at least 10 days before the rapid diagnostic test (RDT). Based upon 100 sera samples, specificity was 98.0% (95% CI 92.9 - 99.8). There was substantial agreement (Kappa score 0.76) between the qRT-PCR results and the RDT.InterpretationThe validation results are well in line with previous assessments of the test, and confirm that it is sufficiently precise for epidemiological studies aimed at monitoring levels and trends of the COVID-19 pandemic.
Mathematical Modeling & the Transmission Dynamics of SARS-CoV-2 in Cali, Colombia: Implications to a 2020 Outbreak & public health preparedness
Authors: Rojas Jorge Humberto , Paredes Marlio , Banerjee Malay , Akman Olcay , Mubayi Anuj 
Published: May 2020

AbstractIntroductionAs SARS-COV-2 and the disease COVID-19 is sweeping through countries after countries around the globe, it is critical to understand potential burden of a future outbreak in cities of Colombia. This pandemic has affected most of the countries in the world because the high global movement of individuals and excessive cost in interventions.ObjectiveUsing demographic data from city of Cali, disease epidemiological information from affected countries and mathematical models, we estimated the rate of initial exponential growth of new cases and the basic reproductive rate for a potential outbreak in city of Cali in Colombia.Materials and methodsWe used dynamical models with different modeling assumptions such as use of various types of interventions and/or epidemiological characteristics to compare and contrast the differences between Colombian cities and between Latin American countries.ResultsUnder the assumption of homogeneously mixing population and limited resources, we predicted expected number of infected, hospitalized, in Intensive Care Units (ICU) and deaths during this potential COVID-19 outbreak. Our results suggest that on a given day in Cali there may be up to around 73000 cases who might need hospitalization under no intervention. However, this number drastically reduces if we carry out only-isolation intervention (with 16 days of symptomatic infection; ~13,000 cases) versus both quarantining for 6 days and isolation within 16 days (~3500 cases). The peak in Cali will reach in 2-3 months.ConclusionsThe estimates from these studies provides different scenarios of outbreaks and can help Cali to be better prepared during the ongoing COVID-19 outbreak.
Rapidly Measuring Spatial Accessibility of COVID-19 Healthcare Resources: A Case Study of Illinois, USA
Authors: Kang Jeon-Young , Michels Alexander , Lyu Fangzheng , Wang Shaohua , Agbodo Nelson , Freeman Vincent L , Wang Shaowen 
Published: May 2020

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the coronavirus disease 2019 (COVID-19) pandemic, has infected millions of people and caused hundreds of thousands of deaths. While COVID-19 has overwhelmed healthcare resources (e.g., healthcare personnel, testing resources, hospital beds, and ventilators) in a number of countries, limited research has been conducted to understand spatial accessibility of such resources. This study fills this gap by rapidly measuring the spatial accessibility of COVID-19 healthcare resources with a particular focus on Illinois, USA. Specifically, the rapid measurement is achieved by resolving computational intensity of an enhanced two-step floating catchment area (E2SFCA) method through a parallel computing strategy based on cyberGIS (cyber geographic information science and systems). The study compared the spatial accessibility measures for COVID-19 patients to those of general population, identifying which geographic areas need additional healthcare resources to improve access. The results also help delineate the areas that may face a COVID-19-induced shortage of healthcare resources caused by COVID-19. The Chicagoland, particularly the southern Chicago, shows an additional need for resources. Our findings are relevant for policymakers and public health practitioners to allocate existing healthcare resources or distribute new resources for maximum access to health services.
Sudden death in patients with sleep apnea: a systematic review and meta-analysis
Authors: Heilbrunn Emily S. , Ssentongo Paddy , Chinchilli Vernon M. , Ssentongo Anna E. 
Published: May 2020

AbstractBackgroundOver 1 billion individuals across the globe experience some form of sleep apnea, and this number is steadily rising. Obstructive sleep apnea (OSA) can negatively influence one’s quality of life and potentially increase the risk of mortality. However, this association between OSA and mortality has not been comprehensively and thoroughly explored. This meta-analysis was conducted to conclusively estimate the risk of death for all-cause mortality and cardiovascular mortality in OSA patients.Study Design4,613 articles from databases including PUBMED, OVID & Joana Briggs, and SCOPUS were comprehensively assessed by two reviewers (AES & ESH) for inclusion criteria. 28 total articles were included, with 22 of them being used for quantitative analysis. Pooled effects of all-cause mortality, cardiac mortality, and sudden death were calculated by utilizing the metaprop function in R Statistical Software and the random-effects model with appropriate 95% confidence intervals.ResultsAnalysis on 42,032 individuals revealed that those with OSA were twice as likely to die from cardiac mortality compared to those without sleep apnea (HR= 1.94, 95%CI 1.39-2.70). Likewise, individuals with OSA were 1.7 times as likely to die from all-cause sudden death compared to individuals without sleep apnea (HR= 1.74, 95%CI 1.40-2.10). There was a significant dose response relationship between severity of sleep apnea and incidence risk of death, where those with severe sleep apnea wereConclusionsIndividuals with obstructive sleep apnea are at an increased risk for all-cause mortality and cardiac mortality. Further research related to appropriate interventions and treatments are necessary in order to reduce this risk and optimize survival in this population.Key MessagesWhat is the key question?Are individuals with sleep apnea at an increased risk for cardiovascular mortality and sudden death?What is the bottom Line?Sleep apnea is associated with an increased risk of cardiovascular mortality and sudden death, with a dose response relationship, where those with severe sleep apnea are at the highest risk of mortality.Why read on?This is the first systematic review and meta-analyses to synthesize and quantify the risk of mortality in those with sleep apnea, highlighting important directions for future research.Prospero Registration IDCRD42020164941
TAMING COVID-19 EPIDEMIC IN SÃO PAULO WITH A LOGISTIC MODEL AND NON-PHARMACEUTICAL MEASURES
Authors: Marchesin Marcelo 
Published: May 2020

Abstract.In this paper I use the simple logistic mathematical model to represent the development of COVID-19 epidemic in São Paulo city under quarantine regime and I estimate the total amount of time it is necessary to decrease the number of seriously ill patients in order to reduce the demand for hospital beds of Intensive Care Units (ICU) to tolerable levels. Clearly the same reasoning and mathematical methods used in here can be used for any other city in similar conditions of social isolation.
Prepared and highly committed despite the risk of COVID-19 infection: A cross-sectional survey of primary care physicians’ concerns and coping strategies in Singapore
Authors: Lau Jerrald , Tan David Hsien-Yung , Wong Gretel Jianlin , Lew Yii-Jen , Chua Ying-Xian , Low Lian-Leng , Ho Han-Kwee , Kwek Thiam-Soo , Toh Sue-Anne Ee-Shiow , Tan Ker-Kan 
Published: May 2020

Abstract:BACKGROUNDPrimary care physicians (PCPs) play a crucial role as first points-of-contact between suspected cases and the healthcare system in the current Coronavirus Disease 2019 (COVID-19) pandemic. An overlooked angle is the potential psychosocial impact on PCPs as they place themselves at increased risk of infection. This study examines PCPs’ concerns, impact on personal lives and work, and level of pandemic preparedness in the context of COVID-19 in Singapore. We also examine factors and coping strategies that PCPs have used to manage stress during the outbreak.METHODS216 PCPs actively practicing in either a public or private clinic were convenience sampled from three primary care organizations in Singapore. Participants completed an online questionnaire consisting of items on work- and non-work-related concerns, impact on personal and work life, perceived pandemic preparedness, stress-reduction factors, and personal coping strategies related to COVID-19.RESULTSA total of 158 questionnaires were usable for analyses. PCPs perceived themselves to be at high risk of COVID-19 infection, and a source of risk and concern to loved ones. PCPs reported acceptance of these risks and the need to care for COVID-19 patients. Overall perceived pandemic preparedness was extremely high. PCPs prioritized availability of personal protective equipment, strict infection prevention guidelines, accessible information about COVID-19, and well-being of their colleagues and family as the most effective stress management factors.CONCLUSIONSPrimary care will continue to be crucial in outbreak management efforts. Healthcare organizations should continue to support PCPs by managing their psychosocial and professional needs.
A survey of the Loureedia genus (Araneae, Eresidae) with a new species from Iran and the first assessment of illegal wildlife trade as a threat to the group
Authors: Henriques Sérgio 
Published: May 2020

AbstractWe describe and illustrate a new species of velvet spider from Iran,L. venaticasp. n., the first species of this genus outside of the Mediterranean region. We also resurrectEresus jerbaefrom synonym, as a distinct and valid Loureedia species,L.jerbaecomb.n, and record this genus to Jordan for the first time.We map the distribution of all available observations ofL.venatica sp.n. andL.jerbaecomb.n, based on museum specimens and on photographic records, using these observations, and the uncertainty therein, to estimate the species range and how it would be classified under the IUCN Red List. Addressing two of the obstacles to the conservation of poorly known taxa, the Linnaean shortfall, by increasing the number of described species, and the Wallacean shortfall, by increasing current knowledge of species distribution as well as their range.We also found thatLoureedia jerbaecomb.n. from Tunisia is been sold as an exotic pet, and that photos of IranianLoureedia venaticasp.n. are being used to advertise the sale of this genus in the pet trade. We discuss the impacts this likely causes to these species, as well these species extinction risk under the IUCN Red List.
Pre-treatment of the clinical sample with Proteinase K allows detection of SARS-CoV-2 in the absence of RNA extraction
Authors: Mallmann Larissa , Schallenberger Karoline , Demolliner Meriane , Antunes Eisen Ana Karolina , Hermann Bruna Saraiva , Heldt Fágner Henrique , Hansen Alana Witt , Spilki Fernando Rosado , Fleck Juliane Deise 
Published: May 2020

AbstractCOVID-19 (Coronavirus Disease 2019) outbreak was declared a pandemic, by World Health Organization, on March 11, 2020. Viral detection using RT-qPCR has been among the most important factors helping to control local spread of SARS-CoV-2 and it is considered the “gold standard” for diagnosis. Nevertheless, the RNA extraction step is both laborious and expensive, thus hampering the diagnosis in many places where there are not laboratory staff of funds enough to contribute for diagnosis efforts. Thus, the need to simplify procedures, reduce costs of the techniques used, and expand the capacity of the number of diagnostics of COVID-19 is imperative. In this study, detection of SARS-CoV-2 in the absence of RNA extraction has been successfully achieved through pre-treatment of the clinical sample with Proteinase K. The results show that only the use of proteinase K, without the need to perform the whole standard protocol for sample extraction and purification, can be an efficient technique for the diagnosis of COVID-19, since 91% of the samples matched the results with the standard procedure, with an average increase of 5.64 CT in the RT-qPCR.
Robust and Gradient Thickness Porous Membranes forIn VitroModeling of Physiological Barriers
Authors: Gholizadeh Shayan , Allahyari Zahra , Carter Robert , Delgadillo Luis F. , Blaquiere Marine , Nouguier-Morin Frederic , Marchi Nicola , Gaborski Thomas R. 
Published: May 2020

AbstractPorous membranes are fundamental elements for tissue-chip barrier and co-culture models. However, the exaggerated thickness of commonly available membranes impedes an accuratein vitroreproduction of the biological multi-cellular continuum as it occursin vivo. Existing techniques to fabricate membranes such as solvent cast, spin-coating, sputtering and PE-CVD result in uniform thickness films. To understand critical separation distances for various barrier and co-culture models, a gradient thickness membrane is needed. Here, we developed a robust method to generate ultrathin porous parylene C (UPP) membranes not just with precise thicknesses down to 300 nm, but with variable gradients in thicknesses, while at the same time having porosities up to 25%. We also show surface etching and increased roughness lead to improved cell attachment. Next, we examined the mechanical properties of UPP membranes with varying porosity and thickness and fit our data to previously published models, which can help determine practical upper limits of porosity and lower limits of thickness. Lastly, we validate a straightforward approach allowing the successful integration of the UPP membranes into a prototyped 3D-printed scaffold enablingin vitrobarrier modeling and investigation of cell-cell interplay over variable distances using thickness gradients.
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
Authors: Gao Yan , Liu Yongzhuang , Ma Yanmei , Liu Bo , Wang Yadong , Xing Yi 
Published: May 2020

AbstractSummaryPartial order alignment, which aligns a sequence to a directed acyclic graph, is now frequently used as a key component in long-read error correction and assembly. We present abPOA (adaptivebandedPartialOrderAlignment), a Single Instruction Multiple Data (SIMD) based C library for fast partial order alignment using adaptive banded dynamic programming. It can work as a stand-alone multiple sequence alignment and consensus calling tool or be easily integrated into any long-read error correction and assembly workflow. Compared to a state-of-the-art tool (SPOA), abPOA is up to 15 times faster with a comparable alignment accuracy.Availability and implementationabPOA is implemented in C. A stand-alone tool and a C/Python software interface are freely available athttps://github.com/yangao07/abPOA.Contactydwang@hit.edu.cnorXINGYI@email.chop.edu
Demonstration of Patient-Specific Simulations To Assess Left Atrial Appendage Thrombogenesis Risk
Authors: García-Villalba Manuel , Rossini Lorenzo , Gonzalo Alejandro , Vigneault Davis , Martinez-Legazpi Pablo , Flores Oscar , Bermejo Javier , McVeigh Elliot , Kahn Andrew M. , del Álamo Juan C. 
Published: May 2020

AbstractAtrial fibrillation (AF) alters left atrial (LA) hemodynamics, which can lead to thrombosis in the left atrial appendage (LAA), systemic embolism and stroke. A personalized risk-stratification of AF patients for stroke would permit improved balancing of preventive anticoagulation therapies against bleeding risk. We investigated how LA anatomy and function impact LA and LAA hemodynamics, and explored whether patient-specific analysis by computational fluid dynamics (CFD) can predict the risk of LAA thrombosis. We analyzed 4D-CT acquisitions of LA wall motion with an in-house immersed-boundary CFD solver. We considered six patients with diverse atrial function, three without a LAA thrombus (LAAT/TIA-neg), and three with either a LAA thrombus (removed digitally before running the simulations) or a history of transient ischemic attacks (LAAT/TIA-pos). We found that blood inside the left atrial appendage of LAAT/TIA-pos patients had marked alterations in residence time and kinetic energy when compared with LAAT/TIA-neg patients. In addition, we showed how the LA conduit, reservoir and booster functions distinctly affect LA and LAA hemodynamics. While the flow dynamics of fixed-wall and moving-wall simulations differ significantly, fixed-wall simulations risk-stratified our small cohort for LAA thrombosis only slightly worse than moving-wall simulations.
Spiny mice (Acomys) exhibit attenuated hallmarks of aging and rapid cell turnover after UV exposure in the skin epidermis
Authors: Wong Wesley , Kim Austin , Seifert Ashley W. , Maden Malcolm , Crane Justin D. 
Published: May 2020

AbstractThe study of long-lived and regenerative animal models has revealed diverse protective responses to stressors such as aging and tissue injury. Spiny mice (Acomys) are a unique mammalian model of skin regeneration, but their response to other types of physiological skin damage have not been investigated. In this study, we examine how spiny mice skin responds to acute UVB damage or chronological aging compared to non-regenerative C57Bl/6 mice (M. musculus). We find that, compared toM. musculus, the skin epidermis inA. cahirinusexperiences a similar UVB-induced increase in basal cell proliferation but exhibits increased epidermal turnover. Notably,A. cahirinusuniquely form a suprabasal layer co-expressing Keratin 14 and Keratin 10 after UVB exposure concomitant with reduced epidermal inflammatory signaling and reduced markers of DNA damage. In the context of aging, oldM. musculusanimals exhibit typical hallmarks including epidermal thinning, increased inflammatory signaling and senescence. However, these age-related changes are absent in oldA. cahirinusskin. Overall, we find thatA. cahirinushave evolved novel responses to skin damage that reveals new aspects of its regenerative phenotype.