bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance evaluation of the Simtomax®CoronaCheck rapid diagnostic test
Authors: Ducrest P. J. , Freymond A. , Segura J.-M. 
Published: November 2020

AbstractThe aim of this study was to evaluate the diagnostic performance of Simtomax®CoronaCheck, a serology rapid diagnostic test (RDT) for the detection of IgG and IgM against SARS-CoV-2. 48 plasma samples positive for SARS-CoV-2 based on RT-PCR and 98 negative control samples were studied. Diagnostic performance of the IgG/IgM RDT was assessed against RT-PCR and the electro-chemiluminescence immunoassay (ECLIA) Elecsys®Anti-SARS-CoV-2 total Ig. Overall, the RDT sensitivity was 92% (95% confidence interval [95%CI]: 79-97), specificity 97% (95% CI: 91-99%), PPV 94% (95% CI: 81-98) and the NPV 96% (95% CI: 89-99). When considering only samples collected ≥ 15 days post-symptoms (DPS), the sensitivity increased to 98% (95%CI: 86-100) and the specificity was 97% (95% CI: 91-99%). Two samples with 180 DPS were still positive for IgG. Globally, this IgG/IgM RDT displayed a high diagnostic accuracy for SARS-CoV-2 IgG/IgM detection in plasma samples in high COVID-19 prevalence settings. It could be effectively used, in absence of facilities for routine diagnostic serology, for samples with a DPS between 15 and 180 days.Highlights–The rapid diagnostic test Simtomax CoronaCheck displays a high sensitivity of 98% and a high specificity of 97% for SARS-CoV-2 IgG/IgM detection in plasma samples after 15 days post-symptoms.–The rapid diagnostic test Simtomax CoronaCheck can detect SARS-CoV-2 antibodies in plasma up to 180 days after symptom onset.–The rapid diagnostic test Simtomax CoronaCheck could be effectively used as an alternative to serological analysis using laboratory facilities.
Psychological and social impact of COVID-19 in Pakistan: Need for Gender Responsive Policies
Authors: Rabbani Fauziah , Khan Hyder Ali , Piryani Suneel , Khan Areeba Raza , Abid Fahad 
Published: November 2020

ABSTRACTBACKGROUNDCOVID-19 has rapidly crossed borders, infecting people throughout the world. Women may be especially vulnerable to depression and anxiety due to the pandemic,AIMSThis study attempted to assess how gender impacts risk perceptions, anxiety levels behavioral responses to the COVID 19 pandemic in Pakistan in order to recommend gender responsive health policiesMETHODSA cross-sectional online survey was conducted. Participants were asked to complete a sociodemographic data form, the Hospital Anxiety and Depression Scale (HADS), and questions on their risk perceptions, preventive behavior and information exposure. Regression analysis was used to assess effects of factors such as age, gender and household income on anxiety levels.RESULTSOf the 1390 respondents, 478 were women, and 913 were men. Women considered their chances of survival to be relatively lower than men (59 % women vs 73% men). They were also more anxious (62% women vs 50% men), and more likely to adopt precautionary behavior, such as avoiding going to the hospital (78% women vs. 71% men), not going to work (72% women and 57% men), and using disinfectants (93% women and 86% men). Men were more likely to trust friends, family and social media as reliable sources of COVID-19 information, while women were more likely to trust doctors.CONCLUSIONWomen experience a disproportion burden of the psychological and social impact of the pandemic compared to men. Involving doctors in healthcare communication targeting women, might prove effective. Social media and radio programs may be effective in disseminating information related to COVID among men.
Features of creatine-kinase in COVID-19 patients within various specific periods: A cohort study
Authors: Wan Shanshan , Qu Gaojing , Yu Hui , Zhu Haoming , Huang Guoxin , Chen Lei , Zhang Meiling , Liu Jiangtao , Pei Bin 
Published: November 2020

ABSTRACTBackgroundCoronavirus disease 2019 (COVID-19) has been declared as a threat to the global. Due to the lack of efficient treatments, indicators were urgently needed during the evolvement of disease to analyze the illness and prognosis, and prevent the aggravation of COVID-19.MethodsPatients’ general information, clinical type, all CK values and outcome were collected. CK value of all cases during disease course started from different initial time were analyzed.ResultsAll cases underwent 504 tests of CK since symptom onset and the median value was 51.7 (35.0-91.5) U/L. The first median value on the day 8 from exposure onset was 78.1 (69.1-85.8) U/L then showed an upward trend from the day 8 to the day 12 (reaching a peak of 279.3 U/L), finally showed a fluctuation decline after the day 12. The CK median value in critical cases reached the peak (625.5 U/L) on the transforming date, and then decreased rapidly to the normal range. Before death, the CK median value in dead cases firstly increased until the day −14 with a peak as 470.0 U/L, then decreased with fluctuation until day −2, and finally increased again on the day 0.ConclusionsCK reached its peak on the day when it became critical type, dynamic detection of CK can guide clinical judgment of prognosis. The increase of CK is a high risk factor of death. Severe cell damage 2 weeks before death might determines the outcome of the disease even if CK drops to the normal range afterward.
The characteristics of HIV-positive patients with mild/asymptomatic and moderate/severe course of COVID-19 disease – a report from Central and Eastern Europe
Authors: Kowalska Justyna D. , Kase Kerstin , Vassilenko Anna , Harxhi Arjan , Lakatos Botond , Lukić Gordana Dragović , Verhaz Antonija , Yancheva Nina , Dumitrescu Florentina , Jilich David , Machala Ladislav , Skrzat-Klapaczyńska Agata , Matulionyte Raimonda 
Published: November 2020

AbstractBackgroundThere is currently no evidence suggesting that COVID-19 takes a different course in HIV-positive patients on antiretroviral treatment compared to the general population. However, little is known about the relation between specific HIV-related factors and the severity of the COVID-19 disease.MethodsWe performed a retrospective analysis of cases collected through an on-line survey distributed by the Euroguidelines in Central and Eastern Europe Network Group. In statistical analyses characteristics of HIV-positive patients asymptomatic/moderate and moderate/severe course were compared.ResultsIn total 34 HIV-positive patients diagnosed with COVID-19 were reported by 12 countries (Estonia, Czech Republic, Lithuania, Albania, Belarus, Romania, Serbia, Bosnia and Herzegovina, Poland, Russia, Hungary, Bulgaria). Asymptomatic courses of COVID-19 were reported in four (12%) cases, 11 (32%) patients presented with mild disease not requiring hospitalization, moderate disease with respiratory and/or systemic symptoms was observed in 14 (41%) cases, and severe disease with respiratory failure was found in five (15%) patients. The only HIV-related characteristics differentiating a moderate/severe course of the disease from asymptomatic/mild disease course was the use of or PI or NNRTI as part of the cART regimen (40.0% vs. 5.3%, p=0.0129 for PI and 31.6 % vs. 0.0%, p= 0.0239 for NNRTI).ConclusionsIn our analyses HIV viral suppression and immunological status were not playing a role in the course of COVID-19 disease. On the contrary the cART regimen could contribute to severity of SARS-CoV-2 infection. Large and prospective studies are necessary to further investigate this relations.
A possible stimulus to induce SPAWNING in Ezo abaloneHaliotis discus hannaiduring stormy weather: Fenton reaction induces spawning behavior
Authors: Matsumoto Yukio , Yatsuya Kousuke 
Published: November 2020

AbstractSynchronous spawning is an important behavior to increase fertilization success of invertebrates with external fertilization. Previous work has shown that it is possible to induce spawning behavior using free radicals in tank experiments, but the stimulus for spawning in the wild is not fully understood. Ezo abaloneHaliotis discus hannaimainly spawn during stormy weather. Rainwater contains H2O2and iron (II) ions (Fe2+). We propose that during stormy weather water layers in the ocean are mixed and the surface layer containing H2O2and Fe2+interacts with the ocean bottom; this leads to conditions suitable for the Fenton reaction to occur. Hydroxyl radicals (·OH) are generated during the oxidization of Fe2+by H2O2and we hypothesized these induce spawning behavior of abalone in the wild. This study observed thatH. discus hannaireleased eggs after salinity decreased due to the rainfall during stormy conditions. In addition, our tank experiment demonstrated that ·OH generated by the Fenton reaction induced synchronous spawning behavior between the sexes. This study provides a new hypothesis about control of synchronous spawning inH. discus hannaiand the results could be applicable to other invertebrates.
Genome ARTIST_v2 software – a support for annotation of class II natural transposons in new sequenced genomes
Authors: Ecovoiu Alexandru Al. , Ghita Iulian Cristian , Chifiriuc David Ioan Mihail , Ghionoiu Iulian Constantin , Ciuca Andrei Mihai , Bologa Alexandru Marian , Ratiu Attila Cristian 
Published: November 2020

AbstractTransposon annotation is a very dynamic field of genomics and various tools assigned to support this bioinformatics endeavor were reported. Genome ARTIST (GA) software was initially developed for mapping artificial transposons mobilized during insertional mutagenesis projects. Now, the new functions of GA_v2 qualify it as an effective companion for mapping and annotation of class II natural transposons in assembled genomes, contigs or sequencing reads.Tabular export of mapping and annotation data for subsequent high-throughput data analysis, the export of a list of flanking sequences around either the coordinates of insertion or around the target site duplications (TSDs) and generation of a consensus sequence for the respective flanking sequences are all key assets of GA_v2.Additionally, we developed two accompanying short scripts that enable the user to annotate transposons existent in assembled genomes and to use various annotation offered by FlyBase forDrosophila melanogastergenome.Herein, we present the applicability of GA_v2 for a preliminary annotation of the class II transposon P-element in the genome ofD. melanogasterstrain Horezu, Romania, which was sequenced with Nanopore technology in our laboratory. Our results point that GA_v2 is a reliable tool to be integrated in pipelines designed to perform transposon annotation in new sequenced genomes.GA_v2 is open source software compatible with Ubuntu, Mac OS and Windows and is available athttps://github.com/genomeartist/genomeartistand atwww.genomeartist.ro.
The unbiased estimation of the fraction of variance explained by a model
Authors: Pospisil Dean A. , Bair Wyeth 
Published: November 2020

AbstractThe correlation coefficient squared,r2, is often used to validate quantitative models on neural data. Yet it is biased by trial-to-trial variability: as trial-to-trial variability increases, measured correlation to a model’s predictions decreases; therefore, models that perfectly explain neural tuning can appear to perform poorly. Many solutions to this problem have been proposed, but some prior methods overestimate model fit, the utility of even the best performing methods is limited by the lack of confidence intervals and asymptotic analysis, and no consensus has been reached on which is the least biased estimator. We provide a new estimator,, that outperforms all prior estimators in our testing, and we provide confidence intervals and asymptotic guarantees. We apply our estimator to a variety of neural data to validate its utility. We find that neural noise is often so great that confidence intervals of the estimator cover the entire possible range of values ([0, 1]), preventing meaningful evaluation of the quality of a model’s predictions. We demonstrate the use of the signal-to-noise ratio (SNR) as a quality metric for making quantitative comparisons across neural recordings. Analyzing a variety of neural data sets, we find ~ 40% or less of some neural recordings do not pass even a liberal SNR criterion.Author SummaryQuantifying the similarity between a model and noisy data is fundamental to the verification of advances in scientific understanding of biological phenomena, and it is particularly relevant to modeling neuronal responses. A ubiquitous metric of similarity is the correlation coefficient. Here we point out how the correlation coefficient depends on a variety of factors that are irrelevant to the similarity between a model and data. While neuroscientists have recognized this problem and proposed corrected methods, no consensus has been reached as to which are effective. Prior methods have wide variation in their precision, and even the most successful methods lack confidence intervals, leaving uncertainty about the reliability of any particular estimate. We address these issues by developing a new estimator along with an associated confidence interval that outperforms all prior methods.
Occurrence but not intensity of mortality rises towards the climatic trailing edge of tree species ranges in European forests
Authors: Changenet Alexandre , Ruiz-Benito Paloma , Ratcliffe Sophia , Fréjaville Thibaut , Archambeau Juliette , Porte Annabel J. , Zavala Miguel A. , Dahlgren Jonas , Lehtonen Aleksi , Garzón Marta Benito 
Published: November 2020

AbstractAimTree mortality is increasing worldwide, leading to changes in forest composition and altering global biodiversity. Yet, due to the multi-faceted stochastic nature of tree mortality, large-scale spatial patterns of mortality across species ranges and their underlying drivers remain difficult to understand. Our main goal is to describe the geographical patterns and drivers of the occurrence and intensity of tree mortality in Europe. We hypothesize that the occurrence of mortality represents background mortality and is higher in the margin than the core populations, whereas the intensity of mortality could have a more even distribution according to the spatial and temporal stochasticity of die-off events.LocationEurope (Spain, France, Germany, Belgium, Sweden and Finland)Time period1981 to 2014.Major taxa studiedMore than 1.5 million trees belonging to 20 major forest tree speciesMethodsWe develop hurdle models to tease apart the occurrence and intensity of tree mortality in National Forest Inventory plots at range-wide scale. The occurrence of mortality indicates that at least one tree has died in the plot and the intensity of mortality refers to the number of trees dead per plot.ResultsThe highest mortality occurrence was found in peripheral regions and the climatic trailing edge linked with drought, whereas the intensity of mortality was driven by competition, drought and high temperatures and was uniformly scattered across species ranges.Main conclusionsOur findings provide a new perspective in our understanding of tree mortality across species ranges. We show that tree background mortality but not die-off is generally higher in the trailing edge populations, but whether other demographic traits such as growth, reproduction and regeneration would also decrease at the trailing edge of European tree populations needs to be explored.
Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer
Authors: Chauhan Lakshya , Ram Uday , Hari Kishore , Jolly Mohit Kumar 
Published: November 2020

AbstractPhenotypic (non-genetic) heterogeneity has significant implications for development and evolution of organs, organisms, and populations. Recent observations in multiple cancers have unravelled the role of phenotypic heterogeneity in driving metastasis and therapy recalcitrance. However, the origins of such phenotypic heterogeneity are poorly understood in most cancers. Here, we investigate a regulatory network underlying phenotypic heterogeneity in small cell lung cancer, a devastating disease with no molecular targeted therapy. Discrete and continuous dynamical simulations of this network reveal its multistable behavior that can explain co-existence of four experimentally observed phenotypes. Analysis of the network topology uncovers that multistability emerges from two teams of players that mutually inhibit each other but members of a team activate one another, forming a ‘toggle switch’ between the two teams. Deciphering these topological signatures in cancer-related regulatory networks can unravel their ‘latent’ design principles and offer a rational approach to characterize phenotypic heterogeneity in a tumor.
Climate influences the response of community functional traits to local conditions
Authors: Guzman Laura Melissa , Trzcinski M. Kurtis , Barberis Ignacio M. , Céréghino Régis , Srivastava Diane S. , Gilbert Benjamin , Pillar Valério D. , de Omena Paula M. , MacDonald A. Andrew M. , Corbara Bruno , Leroy Céline , Bautista Fabiola Ospina , Romero Gustavo Q. , Kratina Pavel , Debastiani Vanderlei J. , Gonçalves Ana Z. , Marino Nicholas A.C. , Farjalla Vinicius F. , Richardson Barbara A. , Richardson Michael J. , Dézerald Olivier , Piccoli Gustavo C.O. , Jocqué Merlijn , Montero Guillermo 
Published: November 2020

AbstractFunctional traits determine an organism’s performance in a given environment and as such determine which organisms will be found where. Species respond to local conditions, but also to larger scale gradients, such as climate. Trait ecology links these responses of species to community composition and species distributions. Yet, we often do not know which environmental gradients are most important in determining community trait composition at either local or biogeographical scales, or their interaction. Here we quantify the relative contribution of local and climatic conditions to the structure and composition of functional traits found within bromeliad invertebrate communities. We conclude that climate explains more variation in invertebrate trait composition within bromeliads than does local conditions. Importantly, climate mediated the response of traits to local conditions; for example, invertebrates with benthic life-history traits increased with bromeliad water volume only under certain precipitation regimes. Our ability to detect this and other patterns hinged on the compilation of multiple fine-grained datasets, allowing us to contrast the effect of climate vs. local conditions. We suggest that, in addition to sampling communities at local scales, we need to aggregate studies that span large ranges in climate variation in order to fully understand trait filtering at local, regional and global scales.
Closing the research-implementation gap using data science tools: a case study with pollinators of British Columbia
Authors: Guzman Laura Melissa , Kelly Tyler , Morandin Lora , M’Gonigle Leithen , Elle Elizabeth 
Published: November 2020

AbstractA challenge in conservation is the gap between knowledge generated by researchers and the information being used to inform conservation practice. This gap, widely known as the research-implementation gap, can limit the effectiveness of conservation practice. One way to address this is to design conservation tools that are easy for practitioners to use. Here, we implement data science methods to develop a tool to aid in conservation of pollinators in British Columbia. Specifically, in collaboration with Pollinator Partnership Canada, we jointly develop an interactive web app, the goal of which is two-fold: (i) to allow end users to easily find and interact with the data collected by researchers on pollinators in British Columbia (prior to development of this app, data were buried in supplements from individual research publications) and (ii) employ up to date statistical tools in order to analyse phenological coverage of a set of plants. Previously, these tools required high programming competency in order to access. Our app provides an example of one way that we can make the products of academic research more accessible to conservation practitioners. We also provide the source code to allow other developers to develop similar apps suitable for their data.
Hippocampus shape across the healthy lifespan and its relationship with cognition
Authors: Bussy Aurelie , Patel Raihaan , Plitman Eric , Tullo Stephanie , Salaciak Alyssa , Bedford Saashi A. , Farzin Sarah , Béland Marie-Lise , Valiquette Vanessa , Kazazian Christina , Tardif Christine L. , Devenyi Gabriel A. , Chakravarty Mallar 
Published: November 2020

AbstractThe study of the hippocampus across the healthy adult lifespan has rendered inconsistent findings. While volumetric measurements have often been a popular technique for analysis, more advanced morphometric techniques have demonstrated compelling results that highlight the importance and improved specificity of shape-based measures. Here, the MAGeT Brain algorithm was applied on 134 healthy individuals aged 18-81 years old to extract hippocampal subfield volumes and hippocampal shape measurements, notably: local surface area (SA) and displacement. We used linear, second or third order natural splines to examine the relationships between hippocampal measures and age. In addition, partial least squares analyses were performed to relate measurements with cognitive and demographic information. Volumetric results indicated a relative preservation of the right cornus ammonis 1 with age and a global volume reduction linked with older age, female sex, lower levels of education and cognitive performance. Vertex-wise analysis demonstrated an SA preservation in the anterior hippocampus with a peak during the sixth decade, while the posterior hippocampal SA gradually decreased across lifespan. Overall, SA decrease was linked to older age, female sex and, to a lesser extent lower levels of education and cognitive performance. Outward displacement in the lateral hippocampus and inward displacement in the medial hippocampus were enlarged with older age, lower levels of cognition and education, indicating an accentuation of the hippocampal “C” shape with age. Taken together, our findings suggest that vertex-wise analyses have higher spatial specifity and that sex, education and cognition are implicated in the differential impact of age on hippocampal subregions throughout its antero-posterior and medial-lateral axes.
Oscillatory activity in alpha/beta frequencies coordinates auditory and prefrontal cortices during extinction learning
Authors: Gritton Howard J. , Nocon Jian C. , James Nicholas M. , Lowet Eric , Abdulkerim Moona , Sen Kamal , Han Xue 
Published: November 2020

AbstractCortical synchrony is theorized to contribute to communication between connected networks during executive functioning. To understand the functional role of neural synchrony in cognitive flexibility, we recorded from auditory cortex (AC) and medial prefrontal cortex (mPFC), while mice performed an auditory extinction learning task. We found that while animals gradually showed reduced responding to the unrewarded tone over hundreds of trials, the power of local field potential (LFP) oscillations (8-18 Hz, centered at alpha/beta frequencies) in AC and mPFC exhibited immediate and robust increases, prior to behavioral changes. The strength of LFP alpha/beta power in the mPFC, but not AC, was strongly correlated with the behavioral performance that mice would achieve later in the training session. Further, we found that coherence between AC and mPFC at 8-18Hz was selectively enhanced only after mice learned to suppress licking, and this LFP coherence increase coincided with a reduction in spiking rate for the unrewarded tone in AC. These results reveal that enhanced interactions between PFC and AC is an inherent property of auditory discrimination learning, and that coordinated alpha/beta oscillations contribute to cognitive flexibility.