bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the Yields of Species Occupying a Single Trophic Level with Incomplete Information: Two Approximations Based on the Lotka-Volterra Generalized Equations
Authors: Fort Hugo 
Published: January 2021

AbstractThe linear Lotka-Volterra generalized equations (LLVGE) serve for describing the dynamics of communities of species connected by negative as well as positive interspecific interactions.Here we particularize these LLVGE to the case of a single trophic level community withS>2 species, either artificial or natural. In this case, by estimating the LLVGE parameters from the yields in monoculture and biculture experiments, the LLVGE are able to produce quite accurate predictions for species yields.However, a common situation we face is that we don’t know all the parameters appearing in the LLVGE. Indeed, for large values ofS, only a fraction of the experiments necessary for estimating the model parameters is commonly carried out.We then analyze which quantitative predictions are possible with an incomplete knowledge of the parameters. We discuss two approximations that allow using these LLVGE as a quantitative tool. First, when we only know a fraction of the model parameters, the mean field approximation allows making predictions on aggregate or average quantities. Second, for cases in which all the interaction parameters involving a particular species are available, we have the focal species approximation for predicting the yield of this focal species.
Identification of Cognitive Impairment in Cardiovascular Rehabilitation: A Cross-Sectional Study Protocol
Authors: Jamali Qutub , Karim Salman , Beg Mirza Najiullah , Raja Muhammad Shoaib , Solanki Kalpesh , Oraegbunam Chukwuma 
Published: January 2021

AbstractIntroductionCardiac Rehabilitation is a multidisciplinary intervention for people after an adverse cardiac event to improve their physical, psychological and social functioning. The risk factors of cardiac disease and dementia are similar. This cross sectional study aims to determine whether adding memory assessment to a cardiac rehabilitation program would improve early detection of cognitive impairment.Methods and AnalysisParticipants will undergo cognitive assessment by using Addenbrooke’s Cognitive Examination (ACE-III). The data obtained will be divided into: - 1- Participants who had a history of memory problems before and after the adverse cardiac event. 2-Participants with no history of memory problems before and currently presents with cognitive impairment. 3-Participants with no memory problems before and after the adverse cardiac event.Ethics and disseminationStudy ethical approval has been granted by Sheffield Research Ethics Committee (reference 20/YH/0146) and the NHS Health Research Authority (project reference 273763).
LocusZoom.js: Interactive and embeddable visualization of genetic association study results
Authors: Boughton Andrew P. , Welch Ryan P. , Flickinger Matthew , VandeHaar Peter , Taliun Daniel , Abecasis Gonçalo R. , Boehnke Michael 
Published: January 2021

AbstractLocusZoom.js is a JavaScript library for creating interactive web-based visualizations of genetic association study results. It can display one or more traits in the context of relevant biological data (such as gene models and other genomic annotation), and allows interactive refinement of analysis models (by selecting linkage disequilibrium reference panels, identifying sets of likely causal variants, or comparisons to the GWAS catalog). It can be embedded in web pages to enable data sharing and exploration. Views can be customized and extended to display other data types such as phenome-wide association study (PheWAS) results, chromatin co-accessibility, or eQTL measurements. A new web upload service harmonizes datasets, adds annotations, and makes it easy to explore user-provided result sets.AvailabilityLocusZoom.js is open-source software under a permissive MIT license. Code and documentation are available at:https://github.com/statgen/locuszoom/. Installable packages are also distributed via NPM. Additional features are provided as standalone libraries to promote reuse. Use with your own GWAS results athttps://my.locuszoom.org/.Contactlocuszoom@googlegroups.com
Moment-based approximations for the Wright-Fisher model of population dynamics under natural selection at two linked loci
Authors: He Zhangyi , Lyu Wenyang , Beaumont Mark , Yu Feng 
Published: January 2021

AbstractProperly modelling genetic recombination and local linkage has been shown to bring significant improvement to the inference of natural selection from time series data of allele frequencies under a Wright-Fisher model. Existing approaches that can account for genetic recombination and local linkage are built on either the diffusion approximation or a moment-based approximation of the Wright-Fisher model. However, methods based on the diffusion approximation are likely to require much higher computational cost, whereas moment-based approximations may suffer from the distribution support issue: for example, the normal approximation can seriously affect computational accuracy. In the present work, we introduce two novel moment-based approximations of the Wright-Fisher model on a pair of linked loci, both subject to natural selection. Our key innovation is to extend existing methods to account for both the mean and (co)variance of the two-locus Wright-Fisher model with selection. We devise two approximation schemes, using a logistic normal distribution and a hierarchical beta distribution, respectively, by matching the first two moments of the Wright-Fisher model and the approximating model. As compared with the diffusion approximation, our approximations enable the approximate computation of the transition probabilities of the Wright-Fisher model at a far smaller computational cost. We can also avoid the distribution support issue found in the normal approximation.
Algorithm optimization for weighted gene co-expression network analysis: accelerating the calculation of Topology Overlap Matrices with OpenMP and SQLite
Authors: Shuai Min , Chen Xin 
Published: January 2021

AbstractMotivationWeighted gene co-expression network analysis (WGCNA) is an R package that can search highly related gene modules. The most time-consuming step of the whole analysis is to calculate the Topological Overlap Matrix (TOM) from the Adjacency Matrix in a single thread. This study changes it to multithreading.ResultsThis paper uses SQLite for multi-threaded data transfer between R and C++, uses OpenMP to enable multi-threading and calculates the TOM via an adjacency matrix on a Shared-memory MultiProcessor (SMP) system, where the calculation time decreases as the number of physical CPU cores increases.Availability and implementationThe source code is available athttps://github.com/do-somethings-haha/fast_calculate_TOM_of_WGCNAContactchenxin@cdutcm.edu.cn
Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant
Authors: Singh Jasdeep , Ehtesham Nasreen Z. , Rahman Syed Asad , Hasnain Seyed E. 
Published: January 2021

AbstractThe SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus) has accumulated multiple mutations during its global circulation. Recently, a new strain of SARS-CoV-2 (VUI 202012/01) had been identified leading to sudden spike in COVID-19 cases in South-East England. The strain has accumulated 23 mutations which have been linked to its immune evasion and higher transmission capabilities. Here, we have highlighted structural-function impact of crucial mutations occurring in spike (S), ORF8 and nucleocapsid (N) protein of SARS-CoV-2. Some of these mutations might confer higher fitness to SARS-CoV-2.SummarySince initial outbreak of COVID-19 in Wuhan city of central China, its causative agent; SARS-CoV-2 virus has claimed more than 1.7 million lives out of 77 million populations and still counting. As a result of global research efforts involving public-private-partnerships, more than 0.2 million complete genome sequences have been made available through Global Initiative on Sharing All Influenza Data (GISAID). Similar to previously characterized coronaviruses (CoVs), the positive-sense single-stranded RNA SARS-CoV-2 genome codes for ORF1ab non-structural proteins (nsp(s)) followed by ten or more structural/nsps [1, 2]. The structural proteins include crucial spike (S), nucleocapsid (N), membrane (M), and envelope (E) proteins. The S protein mediates initial contacts with human hosts while the E and M proteins function in viral assembly and budding. In recent reports on evolution of SARS-CoV-2, three lineage defining non-synonymous mutations; namely D614G in S protein (Clade G), G251V in ORF3a (Clade V) and L84S in ORF 8 (Clade S) were observed [2–4]. The latest pioneering works by Plante et al and Hou et al have shown that compared to ancestral strain, the ubiquitous D614G variant (clade G) of SARS-CoV-2 exhibits efficient replication in upper respiratory tract epithelial cells and transmission, thereby conferring higher fitness [5, 6]. As per latest WHO reports on COVID-19, a new strain referred as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) had been identified as a part of virological and epidemiological analysis, due to sudden rise in COVID-19 detected cases in South-East England [7]. Preliminary reports from UK suggested higher transmissibility (increase by 40-70%) of this strain, escalating Ro (basic reproduction number) of virus to 1.5-1.7 [7, 8]. This apparent fast spreading variant inculcates 23 mutations; 13 non-synonymous, 6 synonymous and 4 amino acid deletions [7]. In the current scenario, where immunization programs have already commenced in nations highly affected by COVID-19, advent of this new strain variant has raised concerns worldwide on its possible role in disease severity and antibody responses. The mutations also could also have significant impact on diagnostic assays owing to S gene target failures.
RNA pull-down-Confocal Nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-Synuclein levels
Authors: Zhu Siran , Rooney Saul , Pham Nhan T. , Koszela Joanna , Kelly David , Auer Manfred , Michlewski Gracjan 
Published: January 2021

ABSTRACTRNA-protein interactions are central to all gene expression processes and contribute to variety of human diseases. Therapeutic approaches targeting RNA-protein interactions have shown promising effects on some diseases that are previously regarded as ‘incurable’. Here we developed a fluorescent on-bead screening platform: RNA pull-down-Confocal Nanoscanning (RP-CONA), to identify RNA-protein interaction modulators in eukaryotic cell extracts. Using RP-CONA, we identified small molecules that disrupt the interaction between HuR, an inhibitor of brain-enriched miR-7 biogenesis, and the conserved terminal loop of pri-miR-7-1. Importantly, miR-7’s primary target is an mRNA of α-Synuclein, which contributes to aetiology of Parkinson’s disease. Our method identified a natural product quercetin as a molecule able to upregulate cellular miR-7 levels and downregulate the expression of α-Synuclein. This opens up new therapeutic avenues towards treatment of Parkinson’s disease as well as provides novel methodology to search for RNA-protein interaction modulators.
More than expected: the abundance of yellow-legged gullsLarus michahellisbreeding in the historic centre of Venice and the initial effects of the new waste collection policy on the population
Authors: Coccon Francesca , Vanni Lorenzo , Dabalà Caterina , Giunchi Dimitri 
Published: January 2021

AbstractYellow-legged gull,Larus michahellis, has undergone widespread colonization of the urban environment in recent past. Starting in 2000 this affected the historical centre of Venice, 24 roof-nesting pairs being recorded in 2005, with this number increasing significantly in the last decade. In 2016, the waste management company of Venice established a new door to door garbage collection system to prevent the accumulation of rubbish in the streets and limit the trophic resources available for the species. The study provides an up-to-date estimate of the urban population of yellow-legged gulls, using Distance Sampling method. We also studied the effect of the new system on the species by comparing the population estimate before and after the change and by analysing the trend of individuals collected in the old town by the service of wildlife recovery during 2010-2018. Results estimate 440 breeding pairs (95s% confidence interval: 326-593) in June 2018 and show a 34% decrease of breeding pairs in 2018 with respect to 2017, as well as a decrease in number of 1-year birds andpullicollected by wildlife recovery service starting from 2016, year of the policy implementation. Our data did not show a significant decrease in the overall number of individuals, suggesting the new policy has a stronger effect on the breeding success of the species than on adult survival. This study emphasizes the importance of preventing rubbish accumulation in the streets as factor for reducing the abundance of urban yellow-legged gulls.
Do school closures and school reopenings affect community transmission of COVID-19? A systematic review of observational studies
Authors: Walsh Sebastian , Chowdhury Avirup , Braithwaite Vickie , Russell Simon , Birch Jack , Ward Joseph , Waddington Claire , Brayne Carol , Bonell Chris , Viner Russell , Mytton Oliver 
Published: January 2021

AbstractBackgroundSchool closures are associated with significant negative consequences and exacerbate inequalities. They were implemented worldwide to control SARS-CoV-2 in the first half of 2020, but their effectiveness, and the effects of lifting them, remain uncertain. This review summarises observational evidence of the effect of school closures and school reopenings on SARS-CoV-2 community transmission.MethodsThe study protocol was registered on Prospero (ID:CRD42020213699). On 07 January 2021 we searched PubMed, Web of Science, Scopus, CINAHL, the WHO Global COVID-19 Research Database, ERIC, the British Education Index, the Australian Education Index, and Google. We included observational studies with quantitative estimates of the effect of school closures/reopenings on SARS-CoV-2 community transmission. We excluded prospective modelling studies and intra-school transmission studies. We performed a narrative synthesis due to data heterogeneity. We used the ROBINS-I tool to assess risk of bias.FindingsWe identified 7,474 articles, of which 40 were included, with data from 150 countries. Of these 32 studies assessed school closures, and 11 examined reopenings. There was substantial heterogeneity between school closure studies, with half of the studies at lower risk of bias reporting reduced community transmission by up to 60%, and half reporting null findings. The majority (n=3 out of 4) of school reopening studies at lower risk of bias reported no associated increases in transmission.ConclusionsSchool closure studies were at risk of confounding and collinearity from other non-pharmacological interventions implemented around the same time as school closures, and the effectiveness of closures remains uncertain. School reopenings, in areas of low transmission and with appropriate mitigation measures, were generally not accompanied by increasing community transmission. With such varied evidence on effectiveness, and the harmful effects, policymakers should take a measured approach before implementing school closures; and should look to reopen schools in times of low transmission, with appropriate mitigation measures.
Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension
Authors: Duzdevich Daniel , Carr Christopher E. , Ding Dian , Zhang Stephanie J. , Walton Travis S. , Szostak Jack W. 
Published: January 2021

ABSTRACTNonenzymatic copying of RNA templates with activated nucleotides is a useful model for studying the emergence of heredity at the origin of life. Previous experiments with defined-sequence templates have pointed to the poor fidelity of primer extension as a major problem. Here we examine the origin of mismatches during primer extension on random templates in the simultaneous presence of all four 2-aminoimidazole-activated nucleotides. Using a deep sequencing approach that reports on millions of individual template-product pairs, we are able to examine correct and incorrect polymerization as a function of sequence context. We have previously shown that the predominant pathway for primer extension involves reaction with imidazolium-bridged dinucleotides, which form spontaneously by the reaction of two mononucleotides with each other. We now show that the sequences of correctly paired products reveal patterns that are expected from the bridged dinucleotide mechanism, whereas those associated with mismatches are consistent with direct reaction of the primer with activated mononucleotides. Increasing the ratio of bridged dinucleotides to activated mononucleotides, either by using purified components or by using isocyanide-based activation chemistry, reduces the error frequency. Our results point to testable strategies for the accurate nonenzymatic copying of arbitrary RNA sequences.
The Ricepropiconazole resistant 1-Dmutant, with activated expression of a DPb transcription factor gene, exhibits increased seed yields
Authors: Corvalán Claudia , An Gynheung , Choe Sunghwa 
Published: January 2021

SUMMARYMutants defective in brassinosteroid (BR) biosynthesis or signaling pathways often display semi-dwarfism, as do the highly productive gibberellin mutants that enabled the Green Revolution. However, reduced vegetative growth in BR mutants does not necessarily correspond to increased seed yields. To better understand the mode of action of BR, we isolated a ricepropiconazole resistant1-D(pzr1-D) mutant by screening an activation-tagging mutant population in the presence of the BR biosynthesis inhibitor propiconazole (Pcz). The expression of a putative transcription factor gene homologous to Arabidopsis Dimerization Partner (DPb) was activated inpzr1-D. pzr1-Dexhibited characteristic phenotypes such as reduced height, and increased seed yields and tiller numbers. Like ArabidopsisDPb, ricePZR1is expressed differentially in the tissues examined. Furthermore,pzr1-Ddisplayed altered cell division phenotypes, including the production of small calli. In addition, the cell number and size in mutant roots and leaves differed from those in wild-type plants of the same age. RNA sequencing revealed that the promoters of differentially expressed genes are enriched with cognate sequences for both BZR1 and EF-DPb transcription factors, suggesting that PZR1 functions in BR-mediated cell division in rice.PZR1expression may thus be manipulated to increase seed yield in economically important rice varieties.SIGNIFICANCE STATEMENTMutants defective in brassinosteroid biosynthesis or signaling pathways often display semi-dwarfism. However, in many cases these mutants do not necessarily produce increased seed yields. We show a ricepropiconazole resistant1-D(pzr1-D) mutant which exhibits reduced height phenotypes along with increase tiller number and seed yields.pzr1-Dshows activation of a putative homologous to Arabidopsis Dimerization Partner (DPb) with functions in cell division, pointing that PZR1 may function in BR-mediated cell division in rice.
Real-time respiration changes as a viability indicator for rapid antibiotic susceptibility testing in a microfluidic chamber array
Authors: Jusková Petra , Schmitt Steven , Kling André , Rackus Darius G. , Held Martin , Egli Adrian , Dittrich Petra S. 
Published: January 2021

ABSTRACTRapid identification of a pathogen and the measurement of its antibiotic susceptibility are key elements in the diagnostic process of bacterial infections. Microfluidic technologies offer great control over handling and manipulation of low sample volumes with the possibility to study microbial cultures on the single-cell level. Downscaling the dimensions of cultivation systems directly results in a lower number of bacteria required for antibiotic susceptibility testing (AST) and thus in a reduction of the time to result. The developed platform presented in this work allows the reading of pathogen resistance profiles within 2-3 hours based on the changes of the dissolved oxygen levels during bacterial cultivation. The platform contains hundreds of individual growth chambers prefilled with a hydrogel containing oxygen-sensing nanoprobes and different concentrations of antibiotic compounds. The performance of the microfluidic platform is tested using quality controlEscherichia colistrains (ATCC 25922 and ATCC 35218) in response to different clinically relevant antibiotics. The achieved results are in agreement with values given in clinical reference guides and independent measurements using a clinical AST protocol. Finally, the platform is successfully used for AST of anE. coliclinical isolate obtained from a patient blood culture.
Polymerase chain reaction-based assays facilitate the breeding and study of mouse models of Klinefelter syndrome
Authors: Zhang Haixia , Xu Wenyan , Zhou Yulin , Chen Xiaolu , Jiang Jiayang , Zhou Xiaoman , Wang Zengge , Ke Rongqin , Guo Qiwei 
Published: January 2021

AbstractKlinefelter syndrome (KS) is one of the most frequent genetic abnormalities and the leading genetic cause of non-obstructive azoospermia. The breeding of mouse models of KS and their study are essential to advance our knowledge of the pathologic mechanism. Karyotyping and fluorescencein situhybridization are reliable methods for identifying chromosomal contents. However, technical issues associated with these methods can decrease the efficiency of breeding KS mouse models and limit studies that require rapid identification of target mice. To overcome these limitations, we developed three polymerase chain reaction-based assays to measure the specific genetic information, including the presence or absence ofSry, copy number ofAmelx, and Xist RNA transcript levels. Through a combined analysis of the assay results, we can infer the karyotype of target mice. We confirmed the utility of our assays with the successful generation of KS mouse models. Our assays are rapid, inexpensive, high capacity, easy to perform, and require small amounts of sample. Therefore, they facilitate the breeding and study of KS mouse models and help advance our knowledge of the pathologic mechanism underlying KS.
Intracortical recordings reveal Vision-to-Action cortical gradients driving human exogenous attention
Authors: Seidel Malkinson Tal , Bayle Dimitri J. , Kaufmann Brigitte C. , Liu Jianghao , Bourgeois Alexia , Lehongre Katia , Fernandez-Vidal Sara , Navarro Vincent , Lambrecq Virginie , Adam Claude , Margulies Daniel S. , Sitt Jacobo D. , Bartolomeo Paolo 
Published: January 2021

AbstractExogenous attention, the process that makes external salient stimuli pop-out of a visual scene, is essential for survival. How attention-capturing events modulate human brain processing remains unclear. Here we show how the psychological construct of exogenous attention gradually emerges over large-scale gradients in the human cortex, by analyzing activity from 1,403 intracortical contacts implanted in 28 individuals, while they performed an exogenous attention task. The timing, location and task-relevance of attentional events defined a spatiotemporal gradient of three neural clusters, which mapped onto cortical gradients and presented a hierarchy of timescales. Visual attributes modulated neural activity at one end of the gradient, while at the other end it reflected the upcoming response timing, with attentional effects occurring at the intersection of visual and response signals. These findings challenge multi-step models of attention, and suggest that frontoparietal networks, which process sequential stimuli as separate events sharing the same location, drive exogenous attention phenomena such as inhibition of return.