bluuebunny/crossref_metadata_2025_split huggingface dataset:
S-variant SARS-CoV-2 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-QPCR
Authors: Kidd Michael , Richter Alex , Best Angus , Mirza Jeremy , Percival Benita , Mayhew Megan , Megram Oliver , Ashford Fiona , White Thomas , Moles-Garcia Emma , Crawford Liam , Bosworth Andrew , Plant Tim , McNally Alan 
Published: December 2020

AbstractBirmingham University Turnkey laboratory is part of the Lighthouse network responsible for testing clinical samples under the UK government ‘Test & Trace’ scheme. Samples are analysed for the presence of SARS-CoV-2 in respiratory samples using the Thermofisher TaqPath RT-QPCR test, which is designed to co-amplify sections of three SARS-CoV-2 viral genes.Since more recent information became available regarding the presence of SARS-CoV-2 variants of concern (S-VoC), which can show a suboptimal profile in RT-QPCR tests such as the ThermoFisher TaqPath used at the majority of Lighthouse laboratories, we analysed recently published data for trends and significance of the S-gene ‘dropout’ variant.Results showed that:the population of S-gene dropout samples had significantly lower median Ct values of ORF and N-gene targets compared to samples where S-gene was detectedon a population basis, S-gene dropout samples clustered around very low Ct values for ORF and N targetslinked Ct values for individual samples showed that a low Ct for ORF and N were clearly associated with an S-dropout characteristicwhen conservatively inferring relative viral load from Ct values, approximately 35% of S-dropout samples had high viral loads between 10 and 10,000-fold greater than 1 × 106, compared to 10% of S-positive samples.This analysis suggests that patients whose samples exhibit the S-dropout profile in the TaqPath test are more likely to have high viral loads at the time of sampling. The relevance of this to epidemiological reports of fast spread of the SARS-CoV-2 in regions of the UK is discussed.
Financial Hardship and Social Assistance as Determinants of Mental Health and Food and Housing Insecurity During the COVID-19 Pandemic in the United States
Authors: Kim Daniel 
Published: December 2020

AbstractBackgroundWhile social assistance through the United States (U.S.) federal Coronavirus Aid, Relief, and Economic Security (CARES) Act provided expanded unemployment insurance benefits during the coronavirus disease 2019 (COVID-19) pandemic until the summer of 2020, it is unclear whether subsequent social assistance has been or will be sufficient to meet everyday spending needs and to curb the adverse health-related sequelae of financial hardship.MethodsThis study estimated recent trends in financial hardship among working-aged Americans with job-related income loss during the pandemic. It also used multivariable logistic regression and repeated cross-sectional individual-level U.S. Household Pulse Survey data on 91,222 working-aged adults between September and December 2020 to explore the associations of financial hardship with mental health outcomes and food and housing insecurity after accounting for receipt of social assistance.ResultsExperiencing somewhat of a financial hardship (vs no hardship) was linked to 3-7 times higher odds of anxiety and depressive symptoms and a likely eviction, and 11 times higher odds of food insufficiency. Experiencing considerable financial hardship (vs no hardship) predicted 5-7 fold higher odds of anxiety and depressive symptoms, 34-fold higher odds of a likely housing eviction, and 37-fold higher odds of food insufficiency (all P values <.001). Across outcomes, these relationships were stronger at each successively higher level of financial hardship (all P values for linear trend <.001), and more than offset any corresponding benefits from social assistance.ConclusionsEven after accounting for receipt of social assistance, working-aged adults experiencing financial hardship had markedly greater odds of anxiety and depressive symptoms, food insufficiency, and an anticipated housing eviction. These findings point to the urgent need for direct and sustained cash relief well in excess of current levels of social assistance, and provide a critical baseline assessment for evaluating the impacts of federal public policy responses to economic hardships during the pandemic. It is essential that the U.S. Congress and the new Biden administration provide adequate and needs-based social policy relief measures in order to mitigate the pandemic’s adverse impacts on the physical, mental, and social well-being of millions of Americans.
In vivo coupling of dendritic complexity with presynaptic density in primary tauopathies
Authors: Mak Elijah , Holland Negin , Jones P. Simon , Savulich George , Low Audrey , Malpetti Maura , Kaalund Sanne S , Passamonti Luca , Rittman Timothy , Romero-Garcia Rafael , Manavaki Roido , Williams Guy B. , Hong Young T. , Fryer Tim D. , Aigbirhio Franklin I. , O’Brien John T , Rowe James B 
Published: December 2020

ABSTRACTUnderstanding the cellular underpinnings of neurodegeneration remains a challenge; loss of synapses and dendritic arborisation are characteristic and can be quantified in vivo, with [11C]UCB-J PET and MRI-based Orientation Dispersion Imaging (ODI), respectively. We aimed to assess how both measures are correlated, in 4R-tauopathies of Progressive Supranuclear Palsy (PSP-RS; n = 22) and amyloid-negative (determined by [11C]PiB PET) Corticobasal Degeneration (CBD; n =14), as neurodegenerative disease models, in this proof-of-concept study. Compared to controls (n = 27), PSP-RS and CBD patients had widespread reductions in cortical ODI, and [11C]UCB-J non-displaceable binding potential (BPND) in excess of atrophy. In PSP-RS and CBD separately, regional cortical ODI was significantly associated with [11C]UCB-J BPND in disease-associated regions (p < 0.05, FDR corrected). Our findings indicate that reductions in synaptic density and dendritic complexity in PSP-RS and CBD are more severe and extensive than atrophy. Furthermore, both measures are tightly coupled in vivo, furthering our understanding of the pathophysiology of neurodegeneration, and applicable to studies of early neurodegeneration with a safe and widely available MRI platform.
The prevalence of burnout, risk factors and job-related stressors in gastroenterologists: a systematic review
Authors: Ong John , Swift Carla , Bath Michael , Ong Sharon , Lim Wanyen , Al-Naeeb Yasseen , Shankar Arun , Dan Yock Young 
Published: December 2020

ABSTRACTBackground and aimsClinician burnout is an important occupational hazard and the scale of the problem within gastroenterology remains poorly understood. The primary objective of this study was to identify the prevalence of burnout and its symptoms in gastroenterologists. The secondary objective was to identify risk factors and job-related stressors that commonly contribute to burnout in gastroenterologists.MethodsSystematic searches were conducted in PubMed, Scopus, Cochrane and PsycINFO by two reviewers independently for articles published to 1 September 2020. The primary outcome measure was the reported prevalence of burnout in gastroenterologists. The secondary outcome measures were (i) the prevalence of burnout symptoms (emotional exhaustion, depersonalisation and low personal accomplishment) and (ii) the frequency of risk factors and stressors reported in studies. Data were tabulated and meta-analyses were presented as Funnel and Forest plots.ResultsData were extracted from 11 studies. 54.5% (6/11) of these studies reported the prevalence of burnout in gastroenterologists; this ranged from 18.3% to 64.4%. Similar to burnout prevalence, burnout symptoms showed geographical variation and were common in gastroenterologists (up to 63.9%). Factors associated with work volume, age, and female gender were the three most frequently reported risk factors for increased levels of anxiety, stress or burnout in 72.7% (8/11), 54.5% (6/11), and 45.5% (5/11) of studies respectively. Significant methodological and clinical heterogeneity was observed.ConclusionsBurnout and its symptoms are common in gastroenterologists but the syndrome is understudied within the field. Further research and good quality data are needed to help address the problem.Disclose StatementJO is funded by the British Society of Gastroenterology to conduct burnout research in the UK, and the Journal of Gastroenterology and Hepatology Foundation (Australia) to conduct burnout research in Southeast Asia.
Comprehensive analysis and genome-wide association studies of biomass, chlorophyll, seed and salinity tolerance related traits in rice highlight genetic hotspots for crop improvement
Authors: Ul Alam Md Nafis , Azad Jewel G.M. Nurnabi , Azim Tomalika , Seraj Zeba I. 
Published: December 2020

AbstractFarmland is on the decline and worldwide food security is at risk. Rice is the staple of choice for over half the Earth’s people. To sustain current demands and ascertain a food secure future, substandard farmland affected by abiotic stresses must be utilized. For rapid crop improvement, a broader understanding of polygenic traits like stress tolerance and crop yield is indispensable. To this end, the hidden diversity of resilient and neglected wild varieties must be traced back to their genetic roots. In this study, we separately assayed 15 phenotypes in a panel of 176 diverse accessions predominantly comprised of local landraces from Bangladesh. We compiled high resolution sequence data for these accessions. We collectively studied the ties between the observed phenotypic differences and the examined additive genetic effects underlying these variations. We applied a sophisticated fixed effect model to associate phenotypes with genotypes on a genomic scale. Discovered QTLs were mapped to known genes. Candidate genes were sorted by tissue specific gene expression profiles and protein level consequence of existing polymorphisms. Our explorations yielded 17 QTLs related to various traits in multiple trait classes. 12 identified QTLs were equivalent to findings from previous studies. Integrative analysis assumes novel functionality for 21 candidate genes on multiple evidence levels. These findings will usher novel avenues for the bioengineering of high yielding crops of the future fortified with genetic defenses against abiotic stressors.
Black Rice Developed Through Interspecific Hybridization (O. sativaxO. rufipogon): Origin of Black Rice Gene from Indian Wild Rice
Authors: Roy Subhas Chandra , Shil Pankaj 
Published: December 2020

AbstractRice (Oryza sativaL.) is a most important staple food grain consumed by more than half of the world’s population. Wild rice (O. rufipogonGriff.) is considered as the immediate ancestral progenitor of cultivated riceO. sativa, evolved through the process of domestication. Most of the cultivated rice produced grains with white pericarp, but can also produce grains with brown, red and black (or purple rice) pericarp. Red rice pericarp accumulates proanthocyanidin whereas black rice contains anthocyanin, both have antioxidant activity and health benefits. Black pericarp is predicted to be regulated by alleles of three genetic loci- Kala1, Kala3, and Kala4. Recombinational and insertional genetic rearrangement in the promoter region of Kala4 is crucial for the development of black pericarp in rice grain. In the present study, we report first time in the breeding history that aromatic black rice lines were developed through interspecific hybridization and introgression in the genetic background ofO. sativacv.Badshabhog, Chenga and Ranjit. Badshabhog and Ranjit is white grain rice but Chenga is red rice category. Common Asian wild riceO. rufipogonis used as donor parent (red grain) and source of black rice gene. Several possible genetic explanations have come up for the creation of black rice pericarp in the progeny lines. Possible reason may be the rearrangement and insertion of LINE1 in the promoter region of Kala4 allele through recombination mechanism leading to ectopic expression of Kala4 gene for the accumulation of anthocyanin and resulted in black rice formation. Other genes and regulatory factors may be induced and become functional to produce black pericarp. Black pericarp colour appeared in F2 populations in the wide crosses (Badshabhog xO. rufipogonand Chenga xO. rufipogon) but not in the cross with (Ranjit xO. rufipogon). Black pericarp trait inherited in F4 and F5 population with segregation phenotypes.This is a first report in the history of rice genetics and pre-breeding research, that black rice has been created through wide crossing and introgression by combining wild riceO. rufipogonin the genetic background ofO. sativa. Present experimental evidence provides a new model of black rice origin. Thus, black rice (indica type) of Indian subcontinent originated independently through natural out crossing and artificial selection in the course of domestication.
Disruption of nasal bacteria enhances protective immune responses to influenza A virus and SARS-CoV-2 infection in mice
Authors: Nagai Minami , Moriyama Miyu , Ichinohe Takeshi 
Published: December 2020

AbstractGut microbiota plays a critical role in the induction of adaptive immune responses to influenza virus infection. However, the role of nasal bacteria in the induction of the virus-specific adaptive immunity is less clear. Here we demonstrate that while intranasal administration of influenza virus hemagglutinin vaccine alone was insufficient to induce the vaccine-specific antibody responses, disruption of nasal bacteria by lysozyme or addition of culturable oral bacteria from a healthy human volunteer rescued inability of the nasal bacteria to generate antibody responses to intranasally administered the split-virus vaccine. Myd88-depdnent signaling in the hematopoietic compartment was required for adjuvant activity of intranasally administered oral bacteria. In addition, we found that the oral bacteria-combined intranasal vaccine induced protective antibody response to influenza virus and SARS-CoV-2 infection. Our findings here have identified a previously unappreciated role for nasal bacteria in the induction of the virus-specific adaptive immune responses.
Reconstructing Great Basin Butterfly-Pollen Interaction Networks over the Past Century
Authors: Balmaki Behnaz , Christensen Tara , Dyer Lee A. 
Published: December 2020

AbstractAimsInsects and the plants they interact with dominate terrestrial biomes and constitute over half of the earth’s macro-organismal diversity. Their abundance in museum collections can provide a wealth of natural history data if they are collected as part of careful ecological studies or conservation programs. Here, we summarize pollen-insect quantitative networks gleaned from adult lepidopteran museum specimens to characterize these interactions and to examine how richness and frequency of butterfly-pollen associations have changed over a 100-year time series in Nevada and California. Pollen collected from well-curated butterfly specimens can provide insight into spatial and temporal variation in pollen-butterfly interactions and provide a complement to other approaches to studying pollination, such as pollinator observation networks.LocationGreat Basin and Sierra Nevada: California, NevadaTime periodThe last 100 yearsMajor Taxon studiedButterfliesMethodsWe estimated butterfly-pollen network parameters based on pollen collected from butterfly specimens from the Great Basin and Sierra Nevada. Additionally, we pooled interaction networks associated with specimens captured before and after 2000 to compare pollen-pollinator interaction variation under drought periods in California and Nevada in the last two decades versus previous years in the time series.ResultsButterfly-pollen networks indicated that most pollen-butterfly species interactions are specialized and appear to be different from observational networks. Interaction networks associated with specimens captured before and after 2000 revealed that compared to previous decades, butterfly-pollen networks over the past 20 years had higher nestedness and connectance, with high pollen richness and low pollen abundance.Main conclusionsThese findings represent another unique approach to understanding more about pollination biology, and how butterfly-pollen interactions are impacted by climate variation and ecosystem alteration.
Neuronal cascades shape whole-brain functional dynamics at rest
Authors: Rabuffo Giovanni , Fousek Jan , Bernard Christophe , Jirsa Viktor 
Published: December 2020

AbstractAt rest, mammalian brains display remarkable spatiotemporal complexity, evolving through recurrent brain states on a slow timescale of the order of tens of seconds. While the phenomenology of the resting state dynamics is valuable in distinguishing healthy and pathological brains, little is known about its underlying mechanisms. Here, we identify neuronal cascades as a potential mechanism. Using full-brain network modeling, we show that neuronal populations, coupled via a detailed structural connectome, give rise to large-scale cascades of firing rate fluctuations evolving at the same time scale of resting-state networks. The ignition and subsequent propagation of cascades depend upon the brain state and connectivity of each region. The largest cascades produce bursts of Blood-Oxygen-Level-Dependent (BOLD) co-fluctuations at pairs of regions across the brain, which shape the simulated resting-state network dynamics.We experimentally confirm these theoretical predictions. We demonstrate the existence and stability of intermittent epochs of functional connectivity comprising BOLD co-activation bursts in mice and human fMRI. We then provide evidence for the existence and leading role of the neuronal cascades in humans with simultaneous EEG/fMRI recordings. These results show that neuronal cascades are a major determinant of spontaneous fluctuations in brain dynamics at rest.1Significance StatementFunctional connectivity and its dynamics are widely used as a proxy of brain function and dysfunction. Their neuronal underpinnings remain unclear. Using connectome-based modeling, we link the fast microscopic neuronal scale to the slow emergent whole-brain dynamics. We show that cascades of neuronal activations spontaneously propagate in resting state-like conditions. The largest neuronal cascades result in the co-fluctuation of Blood-Oxygen-Level-Dependent signals at pairs of brain regions, which in turn translate to stable brain states. Thus, we provide a theoretical framework for the emergence and the dynamics of resting-state networks. We verify these predictions in empirical mouse fMRI and human EEG/fMRI datasets measured in resting states conditions. Our work sheds light on the multiscale mechanisms of brain function.
Pairs of mutually compensatory frameshifting mutations contribute to protein evolution in vertebrates and insects
Authors: Biba Dmitry , Klink Galya , Bazykin Georgii 
Published: December 2020

AbstractInsertions and deletions of lengths not divisible by 3 in protein-coding sequences cause frameshifts that usually induce premature stop codons and may carry a high fitness cost. However, this cost can be partially offset by a second compensatory indel restoring the reading frame. The role of such pairs of compensatory frameshifting mutations (pCFMs) in evolution has not been studied systematically. Here, we use whole-genome alignments of protein coding genes of 100 vertebrate species, and of 122 insect species, studying the prevalence of pCFMs in their divergence. We detect a total of 619 candidate pCFM-genes; 11 of them pass stringent quality filtering, including three human genes:RAB36, ARHGAP6andNCR3LG1. In some instances, amino acid substitutions closely predating or following pCFMs restored the biochemical similarity of the frameshifted segment to the ancestral amino acid sequence, possibly reducing or negating the fitness cost of the pCFM. Typically, however, the resulting sequence bore no biochemical similarity to the ancestral one, indicating that pCFMs can uncover radically novel regions of protein space. In total, pCFMs represent an appreciable and previously overlooked source of novel variation in amino acid sequences.
Landscape configuration of an Amazonian island-like ecosystem drives population structure and genetic diversity of a habitat-specialist bird
Authors: Ritter Camila D. , Ribas Camila C. , Menger Juliana , Borges Sergio H. , Bacon Christine D. , Metzger Jean P. , Bates John , Cornelius Cintia 
Published: December 2020

AbstractContextAmazonian white-sand ecosystems(campinas)are open vegetation patches which form a natural island-like system in a matrix of tropical rainforest. Due to their clear distinction from the surrounding matrix, the spatial characteristics ofcampinapatches may affect the genetic diversity and composition of their specialized organisms such as the small and endemic passerineElaenia ruficeps.ObjectivesHere, we estimate the relative contribution of the current extension, configuration and geographical context ofcampinapatches to the patterns of genetic diversity and population structure ofE. ruficeps.MethodsWe sampled individuals ofE. ruficepsfrom three landscapes in Central Amazonia with contrastingcampinaspatial distribution, from landscapes with large and connected patches to landscapes with small and isolated patches. We estimate population structure, genetic diversity, and contemporary and historical migration within and among the three landscapes and used landscape metrics as predictor variables. Furthermore, we estimate genetic isolation by distance and resistance among individuals sampled within landscapes.ResultsWe identified three genetically distinct populations with asymmetrical gene flow among landscapes and a decreasing migration rate with distance. Within each landscape, we found low genetic differentiation without genetic isolation by distance nor by resistance. In contrast, we found differentiation and spatial correlation between landscapes.ConclusionsOur results uncover population dynamics ofE. ruficepsthrough time. Together with previous studies, this suggests that both regional context and landscape structure shape the connectivity among populations ofcampinaspecialist birds, and that Amazonian landscapes, together with their associated biota, have responded to recent climatic changes.
A benchmark of structural variation detection by long reads through a realistic simulated model
Authors: Dierckxsens Nicolas , Li Tong , Vermeesch Joris R. , Xie Zhi 
Published: December 2020

ABSTRACTDespite the rapid evolution of new sequencing technologies, structural variation detection remains poorly ascertained. The high discrepancy between the results of structural variant analysis programs makes it difficult to assess their performance on real datasets. Accurate simulations of structural variation distributions and sequencing data of the human genome are crucial for the development and benchmarking of new tools. In order to gain a better insight into the detection of structural variation with long sequencing reads, we created a realistic simulated model to thoroughly compare SV detection methods and the impact of the chosen sequencing technology and sequencing depth. To achieve this, we developed Sim-it, a straightforward tool for the simulation of both structural variation and long-read data. These simulations from Sim-it revealed the strengths and weaknesses for current available structural variation callers and long read sequencing platforms. Our findings were also supported by the latest structural variation benchmark set developed by the GIAB Consortium. With these findings, we developed a new method (combiSV) that can combine the results from five different SV callers into a superior call set with increased recall and precision. Both Sim-it and combiSV are open source and can be downloaded at https://github.com/ndierckx/.