bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of hybrid learning and remote education in the implementation of the “Adopt a Microorganism” methodology
Authors: Armellini Bárbara Rodrigues Cintra , Luna Alexandre La , Bueris Vanessa , de Almeida Alisson Pinto , Tamais Alicia Moraes , Júnior Flávio Krzyzanowski , Reiter Victor Samuel Hasten , Lellis-Santos Camilo , de Cássia Café Ferreira Rita 
Published: March 2021

ABSTRACTThe Internet has changed the way teachers and students access information and build knowledge. The recent COVID-19 pandemic has created challenges for both teachers and students and a demand for new methodologies of remote learning. In the life sciences, mixing online content with practical activities represents an even greater challenge. In microbiology, the implementation of an active teaching methodology, the #Adopt project, based on the social network Facebook®, represents an excellent option for connecting remote education with classroom activities. In 2020, the version applied in high school, “Adopt a Microorganism”, was adapted to meet the demands of emergency remote education owing to the suppression of face-to-face activities caused by the pandemic. In the present study, we assessed how the change in methodology impacted the discourse richness of students from high school integrated with technical education in the Business Administration program of the Federal Institute of São Paulo, Sorocaba Campus. Three questionnaires related to the groups of microorganisms (Archaea, Bacteria, Virus, Fungi, and Protozoan) were applied. The students’ responses in the 2019 and 2020 classes were compared concerning content richness and multiplicity of concepts through the application of the Shannon diversity index, an approach that is generally used to assess biodiversity in different environments. The observed results suggest that remote learning provided students with a conceptual basis and richness of content equivalent to that achieved by students subjected to the hybrid teaching model. In conclusion, this study suggests that the #Adopt project methodology increases students’ discourse richness in microbiology even without face-to-face traditional classes.
Mapping of Quantitative Trait Locus (QTLs) that contribute to Drought Tolerance in a Recombinant Inbred Line Population of horsegram (Macrotyloma uniflorum)
Authors: Katoch Megha , Chahota R.K. 
Published: March 2021

AbstractHorsegram (Macrotyloma uniflorum) is a drought hardy legume which can be grown in varied soil and temperature regime. It is an important food legume with environmental, nutritive and medicinal benefits. But in terms of genetic improvement it still lags behind other legumes. To get insight into the genetics of tolerance to drought stress, quantitative trait loci for drought tolerance traits were identified using an intraspecific mapping population comprising of 162 F8Recombinant Inbred Lines derived from a cross between HPKM249 and HPK4. A total of 2011 markers were screened on parental lines for polymorphism survey, out of which 493 markers were found to be polymorphic and used for genotyping of the RIL population. Of these 493 polymorphic markers, 295 were assigned to ten linkage groups at LOD 3.5 spanning 1541.7cM with a mean distance of 5.20 cM between adjacent markers. This linkage map along with the phenotypic data for drought tolerance traits was used to identify regions of the horsegram genome in which the genes for the qualitative traits linked to drought tolerance located. A total of seven QTLs were identified for six different drought related traits. One QTL for malondialdehyde content on linkage group 2, two QTLs for root length on linkage group 3 & 9, one QTL each for proline content and chlorophyll content under drought stress on linkage group 4, one QTL each for root dry weight and root fresh weight on linkage group 5 were identified using composite interval mapping. The linkage map and identified QTLs will be utilized in Marker Assisted Breeding and increase our understanding on the physiology of drought stress tolerance. It will also aid in molecular breeding efforts for further genetic improvement of horsegram.
Multiple nucleotide polymorphism DNA markers for the accurate evaluation of genetic variations
Authors: Fang Zhiwei , Li Lun , Zhou Junfei , You Aiqing , Gao Lifen , Li Tiantian , Chen Hong , Han Ruixi , Cui Yehan , Chen Lihong , Xiao Huafeng , Zhang Jing , Xu Na , Fu Xiqin , Zhang Jianan , Li Xiuting , Ma Aijin , Zhang Weixiong , Peng Hai 
Published: March 2021

AbstractDNA markers are an essential tool for the detection and evaluation of genetic variations, a central theme in genetics and biology. Effective markers must be highly reproducible, polymorphic, accurate and efficient to profile. We developedmultiple dispersed nucleotide polymorphism(MNP) DNA marker and an efficient MNP genotyping method calledMNP-Seq. The MNP marker was 17.48% more polymorphic than the highly polymorphic marker of microsatellites on a collection of hybrid rice plants. When applied to genotype more than 80,000 individual MNP markers of diploid rice and polyploidy hybrid cotton varieties which were notoriously difficult to genotype accurately, MNP-Seq finished in two days and achieved accuracies of 99.999% and 99.988%, respectively. We adopted MNP-Seq to reveal the ubiquitous, albeit subtle and neglected, genetic heterogeneities in homonyms of Nipponbare rice, a popular model organism for plant biology. This result raised a question on the consistency of the published results using the model plant. We also used MNP-Seq to accurately and efficiently determine the identities of plant varieties, a key but difficult problem for the protection of plant intellectual property rights. While being applied to plants in the current study, the MNP marker and MNP-Seq are general and readily applicable to similar problems in animals and micro-organisms.
Integrative genomics reveals paths to sex dimorphism inSalix purpureaL.
Authors: Hyden Brennan , Carlson Craig H. , Gouker Fred E. , Schmutz Jeremy , Barry Kerrie , Lipzen Anna , Sharma Aditi , Sandor Laura , Tuskan Gerald A. , Feng Guanqiao , Olson Matthew S. , DiFazio Stephen P. , Smart Lawrence B. 
Published: March 2021

AbstractSex dimorphism and gene expression were studied in developing catkins in 159 F2individuals from the bioenergy cropSalix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination inSalix purpureais likely different from that observed in the related genusPopulus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.
Task switching costs contribute to the apparent speeding of multisensory reaction times
Authors: Albat Miriam , Hautmann Jasmin , Kayser Christoph , Molinski Josefine , Ülkü Soner 
Published: March 2021

AbstractFaster reaction times for the detection of multisensory compared to unisensory stimuli are considered a hallmark of multisensory integration. While this multisensory redundant signals effect (RSE) has been reproduced many times, it has also been repeatedly criticized as confounding multisensory integration and general task switching effects. When unisensory and multisensory conditions are presented in random order, some trials repeat the same sensory-motor association (e.g. an auditory followed by an auditory trial), while others switch this association (e.g. an auditory followed by a visual trial). This switch may slow down unisensory reaction times and inflate the observed RSE. Following this line of ideas, we used an audio-visual detection task and quantified the RSE for trials derived from pure unisensory blocks and trials from mixed blocks involving a repeat or switch of modalities. The RSE was largest for switch trials and smallest for unisensory trials. In fact, during unisensory blocks the multisensory reaction times did not differ from predictions by the race model, speaking against a genuine multisensory benefit. These results confirm that the observed multisensory RSE can be easily confounded by task switching costs, and suggest that the true benefit of multisensory stimuli for reaction speed may often be overestimated.
Integrated bioinformatics analysis reveals novel key biomarkers and potential candidate small molecule drugs in gestational diabetes mellitus
Authors: Vastrad Basavaraj , Vastrad Chanabasayya , Tengli Anandkumar 
Published: March 2021

AbstractGestational diabetes mellitus (GDM) is one of the metabolic diseases during pregnancy. The identification of the central molecular mechanisms liable for the disease pathogenesis might lead to the advancement of new therapeutic options. The current investigation aimed to identify central differentially expressed genes (DEGs) in GDM. The transcription profiling by array data (E-MTAB-6418) was obtained from the ArrayExpress database. The DEGs between GDM samples and non GDM samples were analyzed with limma package. Gene ontology (GO) and REACTOME enrichment analysis were performed using ToppGene. Then we constructed the protein-protein interaction (PPI) network of DEGs by the Search Tool for the Retrieval of Interacting Genes database (STRING) and module analysis was performed. Subsequently, we constructed the miRNA-hub gene network and TF-hub gene regulatory network by the miRNet database and NetworkAnalyst database. The validation of hub genes was performed through receiver operating characteristic curve (ROC). Finally, the candidate small molecules as potential drugs to treat GDM were predicted by using molecular docking. Through transcription profiling by array data, a total of 869 DEGs were detected including 439 up regulated and 430 down regulated genes. Biological process analysis of GO enrichment analysis showed these DEGs were mainly enriched in reproduction, nuclear outer membrane-endoplasmic reticulum membrane network, identical protein binding, cell adhesion, supramolecular complex and signaling receptor binding. Signaling pathway enrichment analysis indicated that these DEGs played a vital in cell surface interactions at the vascular wall and extracellular matrix organization. Ten genes, HSP90AA1, EGFR, RPS13, RBX1, PAK1, FYN, ABL1, SMAD3, STAT3, and PRKCA in the center of the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network were associated with GDM, according to ROC analysis. Finally, the most significant small molecules were predicted based on molecular docking. Our results indicated that HSP90AA1, EGFR, RPS13, RBX1, PAK1, FYN, ABL1, SMAD3, STAT3, and PRKCA could be the potential novel biomarkers for GDM diagnosis, prognosis and the promising therapeutic targets. The current might be essential to understanding the molecular mechanism of GDM initiation and development.
Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes
Authors: Sun Dapeng , Sang Zhe , Kim Yong Joon , Xiang Yufei , Cohen Tomer , Belford Anna K. , Huet Alexis , Conway James F. , Sun Ji , Taylor Derek J. , Schneidman-Duhovny Dina , Zhang Cheng , Huang Wei , Shi Yi 
Published: March 2021

AbstractThere is an urgent need to develop effective interventions resistant to the evolving variants of SARS-CoV-2. Nanobodies (Nbs) are stable and cost-effective agents that can be delivered by novel aerosolization route to treat SARS-CoV-2 infections efficiently. However, it remains unknown if they possess broadly neutralizing activities against the prevalent circulating strains. We found that potent neutralizing Nbs are highly resistant to the convergent variants of concern that evade a large panel of neutralizing antibodies (Abs) and significantly reduce the activities of convalescent or vaccine-elicited sera. Subsequent determination of 9 high-resolution structures involving 6 potent neutralizing Nbs by cryoelectron microscopy reveals conserved and novel epitopes on virus spike inaccessible to Abs. Systematic structural comparison of neutralizing Abs and Nbs provides critical insights into how Nbs uniquely target the spike to achieve high-affinity and broadly neutralizing activity against the evolving virus. Our study will inform the rational design of novel pan-coronavirus vaccines and therapeutics.
A conversion from slow to fast memory in response to passive motion
Authors: Javidialsaadi Mousa , Albert Scott T. , Wang Jinsung 
Published: March 2021

AbstractWhen the same perturbation is experienced consecutively, learning is accelerated on the second attempt. This savings is a central property of sensorimotor adaptation. Current models suggest that these improvements in learning are due to changes in the brain’s sensitivity to error. Here, we tested whether these increases in error sensitivity could be facilitated by passive movement experiences. In each experimental group, a robot moved the arm passively in the direction that solved the upcoming rotation, with no visual feedback provided. Following that, participants adapted to a visuomotor rotation. Prior passive movements substantially improved motor learning, increasing total compensation in each group by approximately 30%. Similar to savings, a state-space model suggested that this improvement in learning was due to an increase in error sensitivity, but not memory retention. When we considered the possibility that learning was supported by parallel fast and slow adaptive processes, a striking pattern emerged: whereas initial improvements in learning were driven by a slower adaptive state, increases in error sensitivity gradually transferred to a faster learning system with the passage of time. These findings suggest that passive errors engage motor learning systems, but the resulting behavioral patterns migrate between slow and fast adaptive circuits as the passive memory is consolidated.
Mapping Complex Brain Torque Components and Their Genetic and Phenomic Architecture in 24,112 healthy individuals
Authors: Zhao Lu , Matloff William , Shi Yonggang , Cabeen Ryan P. , Toga Arthur W. 
Published: March 2021

AbstractThe mechanisms determining the development and individual variability of brain torque (BT) remain unclear. Here, all relevant components of BT were analyzed using neuroimaging data of up to 24,112 individuals from 6 cohorts. Our large-scale data confirmed the population-level predominance of the typical anticlockwise torque and suggested a “first attenuating, then enlarging” dynamic across the lifespan primarily for frontal, occipital and perisylvian BT features. Sex/handedness differences in BT were found and were related to cognitive sex/handedness differences in verbal-numerical reasoning. We observed differential heritability of up to 56% for BT, especially in temporal language areas, and identified numerous genome- and phenome-wide significant associations pointing to neurodevelopment, cognitive functions, lifestyle, neurological and psychiatric disorders, sociodemographic, cardiovascular and anthropometric traits. This study provides a comprehensive description of BT and insights into biological and other factors that may contribute to the development and individual variations of BT.
A role for the Erk MAPK pathway in modulating SAX-7/L1CAM-dependent locomotion inCaenorhabditis elegans
Authors: Moseley-Alldredge Melinda , Sheoran Seema , Yoo Hayoung , O’Keefe Calvin , Richmond Janet E. , Chen Lihsia 
Published: March 2021

AbstractL1CAMs are immunoglobulin cell adhesion molecules that play important roles in the development and function of the nervous system. In addition to being associated with autism and schizophrenia spectrum disorders, impaired L1CAM function also underlies the X-linked L1 syndrome, which encompasses a group of neurological conditions, including spastic paraplegia and congenital hydrocephalus. Previous studies on both vertebrate and invertebrate L1CAMs established conserved roles that include axon guidance, dendrite morphogenesis, synapse development, and maintenance of neural architecture. We previously identified a genetic interaction between theC. elegansL1CAM encoded by thesax-7gene and RAB-3, a GTPase that functions in synaptic neurotransmission;rab-3; sax-7animals exhibit synthetic locomotion abnormalities and neuronal dysfunction. In this study, we examine the significance of this genetic interaction and show that this synergism also occurs when loss of SAX-7 is combined with mutants of other genes encoding key players of the synaptic vesicle cycle. In contrast,sax-7does not interact with genes that function in synaptogenesis. These findings suggest a post-developmental role forsax-7in the regulation of synaptic activity. To further assess this possibility, we conducted electrophysiological recordings and ultrastructural analyses at neuromuscular junctions. Lastly, we performed a forward genetic screen for suppressors of therab-3; sax-7synthetic phenotypes, uncovering a role for the Mitogen-activated Protein Kinase (MAPK) pathway in promoting coordinated locomotion.
Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations
Authors: Schmid Sonja , Stömmer Pierre , Dietz Hendrik , Dekker Cees 
Published: March 2021

ABSTRACTMany strategies have been pursued to trap and monitor single proteins over time in order to detect the molecular mechanisms of these essential nanomachines. Single protein sensing with nanopores is particularly attractive because it allows label-free high-bandwidth detection based on ion currents. Here we present the Nanopore Electro-Osmotic trap (NEOtrap) that allows trapping and observing single proteins for hours with sub-millisecond time resolution. The NEOtrap is formed by docking a DNA-origami sphere onto a passivated solid-state nanopore, which seals off a nanocavity of a user-defined size and creates an electro-osmotic flow that traps nearby particles irrespective of their charge. We demonstrate the NEOtrap’s ability to sensitively distinguish proteins based on size and shape, and discriminate nucleotide-dependent protein conformations, as exemplified by the chaperone protein Hsp90. Given the experimental simplicity and capacity for label-free single-protein detection over the broad bio-relevant time range, the NEOtrap opens new avenues to study the molecular kinetics underlying protein function.
Admixed Populations Improve Power for Variant Discovery and Portability in Genome-wide Association Studies
Authors: Lin Meng , Park Danny S. , Zaitlen Noah A. , Henn Brenna M. , Gignoux Christopher R. 
Published: March 2021

AbstractGenome-wide association studies (GWAS) are primarily conducted in single-ancestry settings. The low transferability of results has limited our understanding of human genetic architecture across a range of complex traits. In contrast to homogeneous populations, admixed populations provide an opportunity to capture genetic architecture contributed from multiple source populations and thus improve statistical power. Here, we provide a mechanistic simulation framework to investigate the statistical power and transferability of GWAS under directional polygenic selection or varying divergence. We focus on a two-way admixed population and show that GWAS in admixed populations can be enriched for power in discovery by up to 2-fold compared to the ancestral populations under similar sample size. Moreover, higher accuracy of cross-population polygenic score estimates is also observed if variants and weights are trained in the admixed group rather than in the ancestral groups. Common variant associations are also more likely to replicate if first discovered in the admixed group and then transferred to an ancestral population, than the other way around (across 50 iterations with 1,000 causal SNPs, training on 10,000 individuals, testing on 1,000 in each population, p=3.78e-6, 6.19e-101, ~0 for FST= 0.2, 0.5, 0.8, respectively). While some of these FSTvalues may appear extreme, we demonstrate that they are found across the entire phenome in the GWAS catalog. This framework demonstrates that investigation of admixed populations harbors significant advantages over GWAS in single-ancestry cohorts for uncovering the genetic architecture of traits and will improve downstream applications such as personalized medicine across diverse populations.
CHIPS: A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data
Authors: Taing Len , Cousins Clara , Bai Gali , Cejas Paloma , Qiu Xintao , Herbert Zach , Brown Myles , Meyer Clifford A. , Liu X. Shirley , Long Henry W. , Tang Ming 
Published: March 2021

AbstractMotivationThe chromatin profile measured by ATAC-seq, ChIP-seq, or DNase-seq experiments can identify genomic regions critical in regulating gene expression and provide insights on biological processes such as diseases and development. However, quality control and processing chromatin profiling data involve many steps, and different bioinformatics tools are used at each step. It can be challenging to manage the analysis.ResultsWe developed a Snakemake pipeline called CHIPS (CHromatin enrichmentProcessor) to streamline the processing of ChIP-seq, ATAC-seq, and DNase-seq data. The pipeline supports single- and paired-end data and is flexible to start with FASTQ or BAM files. It includes basic steps such as read trimming, mapping, and peak calling. In addition, it calculates quality control metrics such as contamination profiles, PCR bottleneck coefficient, the fraction of reads in peaks, percentage of peaks overlapping with the union of public DNaseI hypersensitivity sites, and conservation profile of the peaks. For downstream analysis, it carries out peak annotations, motif finding, and regulatory potential calculation for all genes. The pipeline ensures that the processing is robust and reproducible.AvailabilityCHIPS is available athttps://github.com/liulab-dfci/CHIPS