bluuebunny/crossref_metadata_2025_split huggingface dataset:
A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection
Authors: Huang Weiren , Yu Lei , Wen Donghua , Wei Dong , Sun Yangyang , Zhao Huailong , Ye Yu , Chen Wei , Zhu Yongqiang , Wang Lijun , Wang Li , Wu Wenjuan , Zhao Qianqian , Xu Yong , Gu Dayong , Nie Guohui , Zhu Dongyi , Guo Zhongliang , Ma Xiaoling , Niu Liman , Huang Yikun , Liu Yuchen , Peng Bo , Zhang Renli , Zhang Xiuming , Li Dechang , Liu Yang , Yang Guoliang , Liu Lanzheng , Zhou Yunying , Wang Yunshan , Hou Tieying , Gao Qiuping , Li Wujiao , Chen Shuo , Hu Xuejiao , Han Mei , Zheng Huajun , Weng Jianping , Cai Zhiming , Zhang Xinxin , Song Fei , Zhao Guoping , Wang Jin 
Published: June 2020

AbstractHigh Ct-values falling in the grey zone are frequently encountered in SARS-CoV-2 detection by real-time reverse transcription PCR (rRT-PCR) and have brought urgent challenges in diagnosis of samples with low viral load. Based on the single-stranded DNA reporter trans-cleavage activity by Cas12a upon target DNA recognition, we create a Specific Enhancer for detection of PCR-amplified Nucleic Acids (SENA) to confirm SARS-CoV-2 detection through specifically targeting its rRT-PCR amplicons. SENA is highly sensitive, with its limit of detection being at least 2 copies/reaction lower than that of the corresponding rRT-PCR, and highly specific, which identifies both false-negative and false-positive cases in clinic applications. SENA provides effective confirmation for nucleic acid amplification-based molecular diagnosis, and may immediately eliminate the uncertainty problems of rRT-PCR in SARS-CoV-2 clinic detection.One Sentence SummaryCRISPR-Cas12a-based COVID-19 diagnosis.
Overview on COVID-19 outbreak indicators across Brazilian federative units
Authors: Guerra-Shinohara Elvira Maria , Weber Simone Schneider , Paniz Clóvis , Gomes Guilherme Wataru , Shinohara Eduardo Jun , Gandra Tiago Borges Ribeiro , Pereira Indiara Correia , Jarcem Karine Gomes , de Almeida Zanre Renato Ferreira , Barreto Acácia Gimenez , De Carli Alessandro Diogo 
Published: June 2020

AbstractBackgroundThe 2019 coronavirus disease pandemic (COVID-19) spread rapidly across Brazil. The country has 27 federative units, with wide regional differences related to climate, lifestyle habits, socioeconomic characteristics and population density. Therefore, we aimed to document and monitor the increase in COVID-19 cases across each federative unit in Brazil, by tracking its progression from inception to 15 May 2020.MethodsObservational study.ResultsThe first confirmed COVID-19 case in the country was notified in São Paulo on 26 February, while the first death occurred on 17 March, in Rio de Janeiro. Since then, there has been a dramatic increase in both confirmed cases and deaths from the disease. São Paulo, in the Southeast region, was initially considered the COVID-19 epidemic epicentre in Brazil. However, 10 states in the North and Northeast regions were ranked among the 14 highest incidences (over 100 cases per 100,000 people) observed on 15 May. Higher incidence rates (>100 cases per 100,000) were associated to higher rates of inadequate water supply and sewerage (OR, 5.83 (95% CI, 1.08–29.37, P=0.041)). North and Northeast states with the highest social vulnerability index scores had higher increases in the incidence rate between 14 April and 15 May. States with medium human development index (HDI) showed higher incidence increases from 14 April to 15 May, being seven of them with ratios in the range from 27.49 to 63.73 times.ConclusionSpreading of COVID-19 in Brazil differs across both regions and federative units, being influenced by different socioeconomic contexts.
Obesity and Race Alter Gene Expression in Skin
Authors: Walker Jeanne M. , Garcet Sandra , Aleman Jose O. , Mason Christopher E. , Danko David , Zuffa Simone , Swann Jonathan R. , Krueger James , Breslow Jan L. , Holt Peter R. 
Published: June 2020

ABSTRACTObesity is accompanied by dysfunction of many organs, but effects on the skin have received little attention. We studied differences in epithelial thickness by histology and gene expression by Affymetrix gene arrays and PCR in the skin of 10 obese (BMI 35-50) and 10 normal weight (BMI 18.5-26.9) postmenopausal women paired by age and race. Epidermal thickness did not differ with obesity but the expression of genes encoding proteins associated with skin blood supply and wound healing were altered. In the obese, many gene expression pathways were broadly downregulated and subdermal fat showed pronounced inflammation. There were no changes in skin microbiota or metabolites. African American subjects differed from Caucasians with a trend to increased epidermal thickening. In obese African Americans, compared to obese Caucasians, we observed altered gene expression that may explain known differences in water content and stress response. African Americans showed markedly lower expression of the gene encoding the cystic fibrosis transmembrane regulator characteristic of the disease cystic fibrosis. The results from this preliminary study may explain the functional changes found in the skin of obese subjects and African Americans.
Instantaneous amplitude and shape of postrhinal theta oscillations differentially encode running speed
Authors: Ghosh Megha , Shanahan Benjamin E. , Furtak Sharon C. , Mashour George A. , Burwell Rebecca D. , Ahmed Omar J. 
Published: June 2020

ABSTRACTHippocampal theta oscillations have a temporally asymmetric waveform shape, but it is not known if this theta asymmetry extends to all other cortical regions involved in spatial navigation and memory. Here, using both established and improved cycle-by-cycle analysis methods, we show that theta waveforms in the postrhinal cortex are also temporally asymmetric. On average, the falling phase of postrhinal theta cycles lasts longer than the subsequent rising phase. There are, however, rapid changes in both the instantaneous amplitude and instantaneous temporal asymmetry of postrhinal theta cycles. These rapid changes in amplitude and asymmetry are very poorly correlated, indicative of a mechanistic disconnect between these theta cycle features. We show that the instantaneous amplitude and asymmetry of postrhinal theta cycles differentially encode running speed. Although theta amplitude continues to increase at the fastest running speeds, temporal asymmetry of the theta waveform shape plateaus after medium speeds. Our results suggest that the amplitude and waveform shape of individual postrhinal theta cycles may be governed by partially independent mechanisms and emphasize the importance of employing a single cycle approach to understanding the genesis and behavioral correlates of cortical theta rhythms.
Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage
Authors: Rad Ramin , Li Jiaming , Mintseris Julian , O’Connell Jeremy , Gygi Steven P. , Schweppe Devin K 
Published: June 2020

AbstractAccurate assignment of monoisotopic peaks is essential for the identification of peptides in bottom-up proteomics. Misassignment or inaccurate attribution of peptidic ions leads to lower sensitivity and fewer total peptide identifications. In the present work we present a performant, open-source, cross-platform algorithm, Monocle, for the rapid reassignment of instrument assigned precursor peaks to monoisotopic peptide assignments. We demonstrate that the present algorithm can be integrated into many common proteomics pipelines and provides rapid conversion from multiple data source types. Finally, we show that our monoisotopic peak assignment results in up to a two-fold increase in total peptide identifications compared to analyses lacking monoisotopic correction and a 44% improvement over previous monoisotopic peak correction algorithms.
RoboCOP: Jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data
Authors: Mitra Sneha , Zhong Jianling , MacAlpine David M. , Hartemink Alexander J. 
Published: June 2020

AbstractChromatin is the tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and level of occupancy of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. On the other hand, epigenomic accessibility data like ATAC-seq, DNase-seq, and MNase-seq provide insight into the chromatin landscape of all factors bound along the genome, but with minimal insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin information from epigenomic accessibility data with nucleotide sequence to compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors at once. We apply RoboCOP to MNase-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome. Using available protein-binding datasets from the literature, we show that our model predicts the binding of these factors genome-wide more accurately than existing methods.
Detection dogs as a help in the detection of COVID-19 Can the dog alert on COVID-19 positive persons by sniffing axillary sweat samples ? Proof-of-concept study
Authors: Grandjean Dominique , Sarkis Riad , Tourtier Jean-Pierre , Julien-Lecocq Clothilde , Benard Aymeric , Roger Vinciane , Levesque Eric , Bernes-Luciani Eric , Maestracci Bruno , Morvan Pascal , Gully Eric , Berceau-Falancourt David , Pesce Jean-Luc , Lecomte Bernard , Haufstater Pierre , Herin Gregory , Cabrera Joaquin , Muzzin Quentin , Gallet Capucine , Bacqué Hélène , Broc Jean-Marie , Thomas Leo , Lichaa Anthony , Moujaes Georges , Saliba Michele , Kuhn Aurore , Galey Mathilde , Berthail Benoit , Lapeyre Lucien , Méreau Olivier , Matteï Marie-Nicolas , Foata Audrey , Bey Louisa , Philippe Anne-Sophie , Abassi Paul , Pisani Ferri , Delarbre Marlène , Orsini Jean-Marc , Capelli Anthoni , Renault Steevens , Bachir Karim , Kovinger Anthony , Comas Eric , Stainmesse Aymeric , Etienne Erwan , Voeltzel Sébastien , Mansouri Sofiane , Berceau-Falancourt Marlène , Leva Brice , Faure Frederic , Dami Aimé , Costa Marc Antoine , Tafanelli Jean-Jacques , Luciani Jean-Benoit , Casalot Jean-Jacques , Charlet Lary , Ruau Eric , Issa Mario , Grenet Carine , Billy Christophe , Desquilbet Loic 
Published: June 2020

AbstractThe aim of this study is to evaluate if the sweat produced by COVID-19 persons (SARS-CoV-2 PCR positive) has a different odour for trained detection dogs than the sweat produced by non COVID-19 persons. The study was conducted on 3 sites, following the same protocol procedures, and involved a total of 18 dogs. A total of 198 armpits sweat samples were obtained from different hospitals. For each involved dog, the acquisition of the specific odour of COVID-19 sweat samples required from one to four hours, with an amount of positive samples sniffing ranging from four to ten. For this proof of concept, we kept 8 dogs of the initial group (explosive detection dogs and colon cancer detection dogs), who performed a total of 368 trials, and will include the other dogs in our future studies as their adaptation to samples scenting takes more time.The percentages of success of the dogs to find the positive sample in a line containing several other negative samples or mocks (2 to 6) were 100p100 for 4 dogs, and respectively 83p100, 84p100, 90p100 and 94p100 for the others, all significantly different from the percentage of success that would be obtained by chance alone.We conclude that there is a very high evidence that the armpits sweat odour of COVID-19+ persons is different, and that dogs can detect a person infected by the SARS-CoV-2 virus.
Automated Detection of Ripple Oscillations in Long-Term Scalp EEG from Patients with Infantile Spasms
Authors: McCrimmon Colin M. , Riba Aliza , Garner Cristal , Maser Amy L. , Shrey Daniel W. , Lopour Beth A. 
Published: June 2020

AbstractObjectiveScalp high frequency oscillations (HFOs) are a promising biomarker of epileptogenicity in infantile spasms (IS) and many other epilepsy syndromes, but prior studies have relied on visual analysis of short segments of data due to the prevalence of artifacts in EEG. Therefore, we set out to develop a fully automated method of HFO detection that can be applied to large datasets, and we sought to robustly characterize the rate and spatial distribution of HFOs in IS.MethodsWe prospectively collected long-term scalp EEG data from 13 subjects with IS and 18 healthy controls. For patients with IS, recording began prior to diagnosis and continued through initiation of treatment with adenocorticotropic hormone (ACTH). The median analyzable EEG duration was 18.2 hours for controls and 83.9 hours for IS subjects (∼1300 hours total). Ripples (80-250 Hz) were detected in all EEG data using an automated algorithm.ResultsHFO rates were substantially higher in patients with IS compared to controls. In IS patients, HFO rates were higher during sleep compared to wakefulness (median 5.5/min and 2.9/min, respectively;p=0.002); controls did not exhibit a difference in HFO rate between sleep and wakefulness (median 0.98/min and 0.82/min, respectively). Spatially, the difference between IS patients and controls was most salient in the central/posterior parasaggital region, where very few HFOs were detected in controls. In IS subjects, ACTH therapy significantly decreased the rate of HFOs.DiscussionHere we show for the first time that a fully automated algorithm can be used to detect HFOs in long-term scalp EEG, and the results are accurate enough to clearly discriminate healthy subjects from those with IS. We also provide a detailed characterization of the spatial distribution and rates of HFOs associated with infantile spasms, which may have relevance for diagnosis and assessment of treatment response.
A mathematical modelling approach to uncover factors influencing the spread ofCampylobacterin a flock of chickens
Authors: Rawson Thomas , Paton Robert , Colles Frances M. , Maiden Martin C.J. , Dawkins Marian Stamp , Bonsall Michael B. 
Published: June 2020

ABSTRACTDespite continued efforts into improving biosecurity protocol,Campylobactercontinues to be detected in the majority of commercial chicken flocks across Europe. Using an extensive data set ofCampylobacterprevalence within a chicken breeder flock for over a year, multiple Bayesian models are presented to explore the dynamics of the spread ofCampylobacterin response to seasonal variation, species-specificity, bird health and total infection prevalence. It was found that birds within the flock varied greatly in their response to bacterial challenge, and that this phenomena had a large impact in the overall prevalence of different species ofCampylobacter. Campylobacter jejuniappeared more frequently in the summer, whileCampylobacter colipersisted for a longer duration, amplified by the most susceptible birds in the flock. Our study suggests that strains ofCampylobacterthat appear most frequently likely possess no demographic advantage, but are instead amplified due to the health of the birds that ingest it.
A Genomics Resource for Genetics, Physiology, and Breeding of West African Sorghum
Authors: Faye Jacques M. , Maina Fanna , Akata Eyanawa A. , Sine Bassirou , Diatta Cyril , Mamadou Aissata , Marla Sandeep , Bouchet Sophie , Teme Niaba , Rami Jean-Francois , Fonceka Daniel , Cisse Ndiaga , Morris Geoffrey P. 
Published: June 2020

AbstractLocal landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolorL. Moench) in West Africa has diversified across a mosaic of cultures and end-uses, and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing was used to generate 159,101 high-quality biallelic SNPs, with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP (π = 0.00045), only slightly less than in a global diversity panel (π = 0.00055). Linkage disequilibrium decayed to background level (r2< 0.1) by ~50 kb in the WASAP. Genome-wide diversity was structured both by botanical type, and by populations within botanical type, with eight ancestral populations identified. Most populations were distributed across multiple countries, suggesting several potential common gene pools across the national programs. Genome-wide association studies of days to flowering and plant height revealed eight and three significant quantitative trait loci (QTL), respectively, with major height QTL at canonical height lociDw3andSbHT7.1. Colocalization of two of eight major flowering time QTL with flowering genes previously described in US germplasm (Ma6andSbCN8) suggests that photoperiodic flowering in WA sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics-enabled breeding of climate-resilient varieties in West Africa.
Annotating high-impact 5’untranslated region variants with the UTRannotator
Authors: Zhang Xiaolei , Wakeling Matthew , Ware James , Whiffin Nicola 
Published: June 2020

AbstractSummaryCurrent tools to annotate the predicted effect of genetic variants are heavily biased towards protein-coding sequence. Variants outside of these regions may have a large impact on protein expression and/or structure and can lead to disease, but this effect can be challenging to predict. Consequently, these variants are poorly annotated using standard tools. We have developed a plugin to the Ensembl Variant Effect Predictor, the UTRannotator, that annotates variants in 5’untranslated regions (5’UTR) that create or disrupt upstream open reading frames (uORFs). We investigate the utility of this tool using the ClinVar database, providing an annotation for 30.8% of all 5’UTR (likely) pathogenic variants, and highlighting 31 variants of uncertain significance as candidates for further follow-up. We will continue to update the UTR annotator as we gain new knowledge on the impact of variants in UTRs.Availability and implementationUTRannotator is freely available on Github:https://github.com/ImperialCardioGenetics/UTRannotatorSupplementary informationSupplementary data are available at bioRxiv.
Local adaptation can cause both peaks and troughs in nucleotide diversity within populations
Authors: Jasper Russ J. , Yeaman Sam 
Published: June 2020

ABSTRACTLocal adaptation is expected to cause high FSTat sites linked to a causal locus, however this pattern can also be driven by background or positive selection. Within-population nucleotide diversity could provide a means to differentiate these scenarios, as both background and positive selection deplete diversity, whereas some theoretical studies have shown that local adaptation increases it. However, it is unclear whether such theoretical predictions generalize to more complicated models. Here, we explore how local adaptation shapes genome-wide patterns in nucleotide diversity and FST, extending previous work to study the effect of variable degrees of polygenicity and genotypic redundancy in an adaptive trait, and different levels of population structure. We show that local adaptation produces two very different patterns depending on the relative strengths of migration and selection, either markedly decreasing or increasing within-population diversity at linked sites at equilibrium. When migration is low, regions of depleted diversity can extend large distances from the causal locus, with substantially more diversity eroded than expected with background selection. With higher migration, peaks occur over much smaller genomic distances but with much larger magnitude changes in diversity. In spatially extended clinal environments both patterns can be found within a single species, with increases in diversity at the center of the range and decreases towards the periphery. Our results demonstrate that there is no universal diagnostic signature of local adaptation based on nucleotide diversity, however, given that neither background nor positive selection inflate diversity, when peaks are found they strongly suggest local adaptation.
Insights into the salivaryN-glycome ofLutzomyia longipalpis, vector of visceral leishmaniasis
Authors: Mondragon-Shem Karina , Wongtrakul-Kish Katherine , Kozak Radoslaw P. , Yan Shi , Wilson Iain , Paschinger Katharina , Rogers Matthew E. , Spencer Daniel I. R. , Acosta-Serrano Alvaro 
Published: June 2020

AbstractDuringLeishmaniatransmission sand flies inoculate parasites and saliva into the skin of vertebrates. Saliva has anti-haemostatic and anti-inflammatory activities that evolved to facilitate bloodfeeding, but also modulate the host’s immune responses. Sand fly salivary proteins have been extensively studied, but the nature and biological roles of protein-linked glycans remain overlooked. Here, we characterised the profile ofN-glycans from the salivary glycoproteins ofLutzomyia longipalpis, vector of visceral leishmaniasis in the Americas.In silicopredictions suggest half ofLu. longipalpissalivary proteins may beN-glycosylated. SDS-PAGE coupled to LC-MS analysis of sand fly saliva, before and after enzymatic deglycosylation, revealed several candidate glycoproteins. To determine the diversity ofN-glycan structures in sand fly saliva, enzymatically released sugars were fluorescently tagged and analysed by HPLC, combined with highly sensitive LC-MS/MS, MALDI-TOF-MS, and exoglycosidase treatments. We found that theN-glycan composition ofLu. longipalpissaliva mostly consists of oligomannose sugars, with Man5GlcNAc2being the most abundant, and a few hybrid-type species. Interestingly, some glycans appear modified with a group of 144 Da, whose identity has yet to be confirmed. Our work presents the first detailed structural analysis of sand fly salivary glycans.