bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 Antibody Seroprevalence in Santa Clara County, California
Authors: Bendavid Eran , Mulaney Bianca , Sood Neeraj , Shah Soleil , Ling Emilia , Bromley-Dulfano Rebecca , Lai Cara , Weissberg Zoe , Saavedra-Walker Rodrigo , Tedrow Jim , Tversky Dona , Bogan Andrew , Kupiec Thomas , Eichner Daniel , Gupta Ribhav , Ioannidis John P.A. , Bhattacharya Jay 
Published: April 2020

AbstractBackgroundAddressing COVID-19 is a pressing health and social concern. To date, many epidemic projections and policies addressing COVID-19 have been designed without seroprevalence data to inform epidemic parameters. We measured the seroprevalence of antibodies to SARS-CoV-2 in a community sample drawn from Santa Clara County.MethodsOn April 3-4, 2020, we tested county residents for antibodies to SARS-CoV-2 using a lateral flow immunoassay. Participants were recruited using Facebook ads targeting a sample of individuals living within the county by demographic and geographic characteristics. We estimate weights to adjust our sample to match the zip code, sex, and race/ethnicity distribution within the county. We report both the weighted and unweighted prevalence of antibodies to SARS-CoV-2. We also adjust for test performance characteristics by combining data from 16 independent samples obtained from manufacturer’s data, regulatory submissions, and independent evaluations: 13 samples for specificity (3,324 specimens) and 3 samples for sensitivity (157 specimens).ResultsThe raw prevalence of antibodies to SARS-CoV-2 in our sample was 1.5% (exact binomial 95CI 1.1-2.0%). Test performance specificity in our data was 99.5% (95CI 99.2-99.7%) and sensitivity was 82.8% (95CI 76.0-88.4%). The unweighted prevalence adjusted for test performance characteristics was 1.2% (95CI 0.7-1.8%). After weighting for population demographics of Santa Clara County, the prevalence was 2.8% (95CI 1.3-4.7%), using bootstrap to estimate confidence bounds. These prevalence point estimates imply that 54,000 (95CI 25,000 to 91,000 using weighted prevalence; 23,000 with 95CI 14,000-35,000 using unweighted prevalence) people were infected in Santa Clara County by early April, many more than the approximately 1,000 confirmed cases at the time of the survey.ConclusionsThe estimated population prevalence of SARS-CoV-2 antibodies in Santa Clara County implies that the infection may be much more widespread than indicated by the number of confirmed cases. More studies are needed to improve precision of prevalence estimates. Locally-derived population prevalence estimates should be used to calibrate epidemic and mortality projections.
Is the fit of N95 facial masks effected by disinfection? A study of heat and
UV disinfection methods using the OSHA protocol fit test
Authors: Price Amy , Cui Yi , Liao Lei , Xiao Wang , Yu Xuanze , Wang Haotian , Zhao Mervin , Wang Qiqi , Chu Steven , Chu Larry 
Published: April 2020

Abstract
The current COVID-19 pandemic has highlighted global supply chain
shortcomings in the US hospital delivery system, most notably personal
protective equipment (PPE) and COVID-19 is found on these masks ∼7 days. Recent
work from our group has shown two promising disinfection methods for N95 facial
masks, dry heat (hot air (75 °C, 30 min) and UVGI which is UVGI 254 nm, 8W, 30
min. Using N95 five models of N95 masks from three different manufacturers we
determined the following: 1) Hot air treated N95 masks applied over 5 cycles did
not degrade the fit of masks (1.5% change in fit factor, p = .67), 2) UVGI
treated N95 masks applied over 10 cycles were significantly degraded in fit and
did not pass quantitative fit testing using OSHA testing protocols on a human
model (−77.4% change in fit factor, p = .0002).

NOTE
We would like to share our results with the community as
soon as possible. Be mindful that this report is a pilot study and a
work in progress. We will have more results in the coming days and
weeks.

We recommend that hospital
policy and
procedures be respected
and adhered to. Do not use anything in your home to disinfect contaminated
equipment. Please do not heat your masks in a home oven!
Egg cannibalism by passion vine specialistDisonychaChevrolat beetles (Coleoptera: Chrysomelidae: Galerucinae: Alticini)
Authors: Morrison Colin R. , Armstrong Wyatt , Gilbert Lawrence 
Published: April 2020

AbstractCannibalistic behavior is now recognized to be an important component of nutritional ecology in both carnivorous and herbivorous species, including many beetle families (Englert and Thomas 1970; Beaver 1974; Dickinson 1992; Bartlett 1987; Alabiet al.2008). This habit was historically viewed by an incidental outcome of unnaturally crowded laboratory situations with little ecological importance (Fox 1975), but it is increasingly acknowledged that cannibalism represents a potentially advantageous behavior (Richardsonet al.2010). Here we report on multiple cases of egg cannibalism, or conspecific oophagy, by adults of two species of passion vine (PassifloraLinnaeus: Passifloraceae) specialist flea beetles in the genusDisonychaChevrolat (Coleoptera: Chrysomelidae: Galerucinae: Alticini). This is the first report of egg cannibalism from the Galerucinae, and to our knowledge, only the fourth report of egg cannibalism by adults in the Chrysomelidae; the other three reports are of adult Chrysomelinae species eating conspecific eggs (Dickinson 1992; McCauley 1992; Schrodet al.1996). We conclude this note with several questions raised by our observations, followed by a discussion that may contribute to explanations of this behavior.
Performance Evaluation of Markerless 3D Skeleton Pose Estimates with Pop Dance Motion Sequence
Authors: Labuguen Rollyn T. , Ingco Wally Enrico M. , Negrete Salvador Blanco , Kogami Tonan , Shibata Tomohiro 
Published: April 2020

AbstractThe evaluation of markerless pose estimation performed by OpenPose has been getting much attention from researchers of human movement studies. This work aims to evaluate and compare the output joint positions estimated by the OpenPose with a marker-based motion-capture data recorded on a pop dance motion. Although the marker-based motion capture can accurately measure and record the human joint positions, this particular set-up is expensive. The framework to compare the outputs of the markerless method to the ground truth marker-based joint remains unknown, especially for complex body motion. Synchronization, camera calibration, and 3D reconstruction by fusing the outputs of the markerless method (OpenPose) are discussed. In this case study, the comparison results illustrate that even if the markerless method expects to fail when the subject’s body parts are self-occluded, the average magnitude errors for each key points are less than 700 mm.
Exome sequencing identifies ARID2 as a novel tumor suppressor in early-onset sporadic rectal cancer
Authors: Bala Pratyusha , Singh Anurag Kumar , Kavadipula Padmavathi , Kotapalli Viswakalyan , Sabarinathan Radhakrishnan , Bashyam Murali Dharan 
Published: April 2020

AbstractEarly-onset sporadic rectal cancer (EOSRC) is a unique and predominant colorectal cancer (CRC) subtype in India. In order to understand the tumorigenic process in EOSRC, we performed whole exome sequencing of 47 microsatellite stable EOSRC samples. Signature 1 was the predominant mutational signature in EOSRC, as previously shown in other CRC exome studies. More importantly, we identifiedTP53, KRAS, APC, PIK3R1andSMAD4as significantly mutated (q<0.1) andARID1AandARID2as near-significantly mutated (restricted hypothesis testing; q<0.1) candidate drivers. Unlike the other candidates, the tumorigenic potential ofARID2, encoding a component of the SWI/SNF chromatin remodeling complex, is largely unexplored in CRC. shRNA mediatedARID2knockdown performed in two different CRC cell lines resulted in significant alterations in transcript levels of cancer-related target genes. More importantly,ARID2knockdown promoted several tumorigenic features including cell viability, proliferation, ability to override contact inhibition of growth, and migration besides significantly increasing tumor formation ability in nude mice. The observed gain in tumorigenic features were rescued upon ectopic expression ofARID2. Analyses of the TCGA CRC dataset revealed poorer survival in patients withARID2alterations. We therefore proposeARID2as a novel tumor suppressor in CRC.
Deciphering cellular transcriptional alterations in Alzheimer’s disease brains
Authors: Wang Xue , Allen Mariet , Li Shaoyu , Quicksall Zachary S. , Patel Tulsi A. , Carnwath Troy P. , Reddy Joseph S. , Carrasquillo Minerva M. , Lincoln Sarah J. , Nguyen Thuy T. , Malphrus Kimberly G. , Dickson Dennis W. , Crook Julia E. , Asmann Yan W. , Ertekin-Taner Nilüfer 
Published: April 2020

AbstractLarge-scale brain bulk-RNAseq studies identified molecular pathways implicated in Alzheimer’s disease (AD), however these findings can be confounded by cellular composition changes in bulk-tissue. To identify cell intrinsic gene expression alterations of individual cell types, we designed a bioinformatics pipeline and analyzed three AD and control bulk-RNAseq datasets of temporal and dorsolateral prefrontal cortex from 685 brain samples. We detected cell-proportion changes in AD brains that are robustly replicable across the three independently assessed cohorts. We applied three different algorithms including our in-house algorithm to identify cell intrinsic differentially expressed genes in individual cell types (CI-DEGs). We assessed the performance of all algorithms by comparison to single nucleus RNAseq data. We identified consensus CI-DEGs that are common to multiple brain regions. Despite significant overlap between consensus CI-DEGs and bulk-DEGs, many CI-DEGs were absent from bulk-DEGs. Consensus CI-DEGs and their enriched GO terms include genes and pathways previously implicated in AD or neurodegeneration, as well as novel ones. We demonstrated that the detection of CI-DEGs through computational deconvolution methods is promising and highlight remaining challenges. These findings provide novel insights into cell-intrinsic transcriptional changes of individual cell types in AD and may refine discovery and modeling of molecular targets that drive this complex disease.
Cholinergic modulation of membrane properties of calyx terminals in the vestibular periphery
Authors: Ramakrishna Yugandhar , Manca Marco , Sadeghi Soroush G. 
Published: April 2020

ABSTRACTVestibular nerve afferents are divided into regular and irregular groups based on the variability of interspike intervals in their resting discharge. Most afferents receive inputs from bouton terminals that contact type II hair cells as well as from calyx terminals that cover the basolateral walls of type I hair cells. Calyces have an abundance of different subtypes of KCNQ (Kv7) potassium channels and muscarinic acetylcholine receptors (mAChRs) and receive cholinergic efferent inputs from neurons in the brainstem. We investigated whether mAChRs affected membrane properties and firing patterns of calyx terminals through modulation of KCNQ channel activity. Patch clamp recordings were performed from calyx terminals in central regions of the cristae of the horizontal and anterior canals in 13 – 18 day old Sprague-Dawley rats. KCNQ mediated currents were observed as voltage sensitive currents with slow kinetics (activation and deactivation), resulting in spike frequency adaptation so that calyces at best fired a single action potential at the beginning of a depolarizing step. Activation of mAChRs by application of oxotremorine methiodide or inhibition of KCNQ channels by linopirdine dihydrochloride decreased voltage activated currents by ∼30%, decreased first spike latencies by ∼40%, decreased spike thresholds by ∼50%, and resulted in continuous firing during depolarizing steps. Interestingly, some of the calyces showed spontaneous discharge in the presence of these drugs. Together, these findings suggest that cholinergic efferents can modulate the response properties and encoding of head movements by afferents.
Invasion of homogeneous and polyploid populations in nutrient-limiting environments
Authors: Kimmel Gregory J. , Dane Mark , Heiser Laura , Altrock Philipp M. , Andor Noemi 
Published: April 2020

AbstractBreast cancer progresses in a multistep process from primary tumor growth and stroma invasion to metastasis. Progression is accompanied by a switch to an invasive cell phenotype. Nutrient-limiting environments promote chemotaxis with aggressive morphologies characteristic of invasion. It is unknown how co-existing cells differ in their response to nutrient limitations and how this impacts invasion of the metapopulation as a whole. We integrate mathematical modeling with microenvironmental perturbation-data to investigate invasion in nutrient-limiting environments inhabited by one or two cancer cell subpopulations. Hereby, subpopulations are defined by their energy efficiency and chemotactic ability. We estimate the invasion-distance traveled by a homogeneous population. For heterogeneous populations, our results suggest that an imbalance between nutrient efficacy and chemotactic superiority accelerates invasion. Such imbalance will spatially segregate the two populations and only one type will dominate at the invasion front. Only if these two phenotypes are balanced do the two subpopulations compete for the same space, which decelerates invasion. We investigate ploidy as a candidate biomarker of this phenotypic heterogeneity to discern circumstances when inhibiting chemotaxis amplifies internal competition and decelerates tumor progression, from circumstances that render clinical consequences of chemotactic inhibition unfavorable.SignificanceA better understanding of the nature of the double-edged sword of high ploidy is a prerequisite to personalize combination-therapies with cytotoxic drugs and inhibitors of signal transduction pathways such as MTOR-Is.
A facile method of mapping HIV-1 neutralizing epitopes using chemically masked cysteines and deep sequencing
Authors: Datta Rohini , Chowdhury Rohan Roy , Manjunath Kavyashree , Hanna Luke Elizabeth , Varadarajan Raghavan 
Published: April 2020

AbstractIdentification of specific epitopes targeted by neutralizing antibodies is essential to advance epitope-based vaccine design strategies. We report a facile methodology for rapid epitope mapping of neutralizing antibodies (NAbs) against HIV-1 Envelope (Env) at single residue resolution, using Cys labeling, viral neutralization assays and deep sequencing. This was achieved by the generation of a library of Cys mutations in Env glycoprotein on the viral surface, covalent labeling of the Cys residues using a Cys reactive label that masks epitope residues, followed by infection of the labeled mutant virions in mammalian cells in the presence of NAbs. Env gene sequencing from NAb-resistant viruses was used to accurately delineate epitopes for the NAbs VRC01, PGT128 and PGT151. These agreed well with corresponding experimentally determined structural epitopes previously inferred from NAb:Env structures. HIV-1 infection is associated with complex and polyclonal antibody responses, typically composed of multiple antibody specificities. Deconvoluting the epitope specificities in a polyclonal response is a challenging task. We therefore extended our methodology to map multiple specificities of epitopes targeted in polyclonal sera, elicited in immunized animals as well as in an HIV-1 infected elite neutralizer capable of neutralizing Tier-3 pseudoviruses with high titers. The method can be readily extended to other viruses for which convenient reverse genetics or lentiviral surface display systems are available.
Asian wild apples threatened by gene flow from domesticated apples and by their pestified pathogen
Authors: Feurtey Alice , Guitton Ellen , De Gracia Coquerel Marie , Duvaux Ludovic , Shiller Jason , Bellanger Marie-Noëlle , Expert Pascale , Sannier Mélanie , Caffier Valérie , Giraud Tatiana , Cam Bruno Le , Lemaire Christophe 
Published: April 2020

AbstractMassive gene flow between crops and their wild relatives may threaten the genetic integrity of wild species. Such threats are now well documented, but little is known about indirect consequences involving the spillover of crop pathogens to wild plants or introgression between crop and wild pathogens. To address these questions, we used population genetics approaches, demographic inference and pathogenicity tests on host-pathogen pairs composed of wild or domesticated apple trees of Central Asia and their fungal pathogen,Venturia inaequalis, itself showing differentiated agricultural-type and wild-type populations. We confirmed the occurrence of gene flow from cultivated to wild apple trees in Asian forests, threatening the Asian wild apple genetic integrity. SNP markers and demographic modeling revealed the occurrence of a secondary contact followed by hybridization between agricultural-type and wild-type fungal pathogen populations, and the dispersal of the agricultural-type pathogen in wild forests. We detected a SNP predicting the ability of the fungus to parasitize the different host populations, which induced an early stop codon in a gene coding for a small secreted protein in the agricultural-type fungal population, thus representing a putative avirulence gene which function loss would enable to parasitize cultivated apples. Pathogenicity tests in fact revealed the pestification ofV. inaequalis, with higher virulence of the agricultural-type population on both wild and domesticated trees. Our findings highlight the threat posed by cultivating a crop near its center of origin, with the invasion of a pestified pathogen on wild plants and introgression in the wild-type pathogen.
Forest production efficiency increases with growth temperature
Authors: Collalti A. , Ibrom A. , Stockmarr A. , Cescatti A. , Alkama R. , Fernández-Martínez M. , Matteucci G. , Sitch S. , Friedlingstein P. , Ciais P. , Goll D.S. , Nabel J.E.M.S. , Pongratz J. , Arneth A. , Haverd V. , Prentice I.C. 
Published: April 2020

Introductory paragraphWe present a global analysis of the relationship of forest production efficiency (FPE) to stand age and climate, based on a large compilation of data on gross primary production and either biomass production or net primary production. FPE is important for both forest production and atmospheric carbon dioxide uptake. Earlier findings – FPE declining with age – are supported by this analysis. However, FPE also increases with absolute latitude, precipitation and (all else equal) with temperature. The temperature effect is opposite to what would be expected based on the short-term physiological response of respiration rates to temperature. It implies top-down regulation of forest carbon loss, perhaps reflecting the higher carbon costs of nutrient acquisition in colder climates. Current ecosystem models do not reproduce this phenomenon. They consistently predict lower FPE in warmer climates, and are therefore likely to overestimate carbon losses in a warming climate.
Cancer SIGVAR: A semi-automated interpretation tool for germline variants of hereditary cancer-related genes
Authors: Li Hong , Liu Shuixia , Wang Shuangying , Zeng Quanlei , Chen Yulan , Fang Ting , Zhang Yi , Zhou Ying , Zhang Yu , Wang Kaiyue , Yan Zhangwei , Qiang Cuicui , Xu Meng , Chai Xianghua , Yuan Yuying , Huang Ming , Zhang Hongyun , Xiong Yun 
Published: April 2020

AbstractThe American College of Medical Genetics and Genomics and the Association for Molecular Pathology published guidelines in 2015 for the clinical interpretation of Mendelian disorder sequence variants based on 28 criteria. ClinGen Sequence Variant Interpretation (SVI) Working Groups have developed many adaptations or refinements of these guidelines to improve the consistency of interpretation. We combined the most recent adaptations to expand the criteria from 28 to 48 and developed a tool called Cancer SIGVAR to help healthcare workers and genetic counselors interpret the clinical significance of cancer germline variants, which is critical for the clinical diagnosis and treatment of hereditary cancer. Our tool can accept VCF files as input and realize fully automated interpretation based on 21 criteria and semi-automated interpretation based on 48 criteria. We validated our tool on the ClinVar and CLINVITAE benchmark databases for the accuracy of fully automated interpretation, achieving an average consistency for pathogenic and benign assessment up to 93.40% and 82.54%, respectively. We compared Cancer SIGVAR with a similar tool, InterVar, and analyzed the main differences in criteria and implementation. In addition, to verify the performance of semi-automated interpretation based on 48 criteria, we selected 911 variants from two benchmark databases and reached an average classification consistency of 98.35%. Our findings highlight the need to optimize automated interpretation tools based on constantly updated guidelines.
Identification of a Novel Picorna-like Virus in Coconut Rhinoceros Beetles (Oryctes rhinoceros)
Authors: Etebari Kayvan , Shelomi Matan , Furlong Michael J. 
Published: April 2020

AbstractA novel Picorna-like virus, tentatively named Oryctes rhinoceros Picorna-like virus 1 (OrPV1), was identified in coconut rhinoceros beetle (Oryctes rhinoceros) larvae in Taiwan. The complete genome sequence consisted of 9,665 nucleotides with a polyA tail and included one open reading frame. Conserved structural domains such as Picornavirus capsid protein, RNA helicase, Peptidase and RNA-dependent RNA polymerase (RdRp) were identified through Pfam domain searches. The genome shares approximately 28% identity with other unclassified picornavirals that infect honey bees (Darwin bee virus 2, Bundaberg bee virus 5, and Sacbrood virus) and a recently reported virus from Asian lady beetle (Harmonia axyridis virus 1). We did not detect this virus in any other geographical populations ofO. rhinoceroscollected from the South Pacific Islands and the Philippines. Analysis of the deduced RdRp amino acid sequences showed that the virus clustered with other Picorna-like viruses and separated from other members of family Dicistroviridae and Iflaviridae.
Insect herbivory on urban trees: Complementary effects of tree neighbours and predation
Authors: Stemmelen Alex , Paquette Alain , Benot Marie-Lise , Kadiri Yasmine , Jactel Hervé , Castagneyrol Bastien 
Published: April 2020

AbstractInsect herbivory is an important component of forest ecosystems functioning and can affect tree growth and survival. Tree diversity is known to influence insect herbivory in natural forest, with most studies reporting a decrease in herbivory with increasing tree diversity. Urban ecosystems, on the other hand, differ in many ways from the forest ecosystem and the drivers of insect herbivory in cities are still debated.We monitored 48 urban trees from five species – three native and two exotic – in three parks of Montreal (Canada) for leaf insect herbivory and predator activity on artificial larvae, and linked herbivory with both predation and tree diversity in the vicinity of focal trees.Leaf insect herbivory decreased with increasing tree diversity and with increasing predator attack rate.Our findings indicate that tree diversity is a key determinant of multitrophic interactions between trees, herbivores and predators in urban environments and that managing tree diversity could contribute to pest control in cities.This article has been peer-reviewed and recommended byPeer Community in Ecologyhttps://doi.org/10.24072/pci.ecology.100061