bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging Ultrasound Assessment of Exercise-Induced Endothelial Shear Stress of the Brachial and Carotid Arteries
Authors: Gurovich Alvaro N. , Rodriguez Lisa , Gomez Manuel , Caraveo Paulina , Ochoa Luis , Morales-Acuna Francisco 
Published: December 2020

Abstract
Endothelial shear stress (ESS) has a possible effect on regulation of gene expression in the protection against atherosclerosis. During exercise, ESS should increase as systolic blood pressure and heart rate (HR) increase too; however, it is hard to determine ESS changes during exercise. Imaging ultrasound assessment of the brachial and the carotid arterial blood flow during exercise might help to estimate exercise-induced ESS. We present here the methodology at the Clinical Applied Physiology Laboratory to estimate exercise-induced ESS. We normally perform 2 exercise tests in 2 different visits. First, a cardiopulmonary exercise test with serial microblood sampling to determine blood lactate (La) levels on a stationary cycle ergometer to determine maximal oxygen consumption, maximal exercising HR, and lactate threshold curve. The second exercise test includes three 5-min steady state stages determined by La levels from test 1 (La <2 mmol/L, La 2–4 mmol/L, and La >4 mmol/L). During the second test, we position an ultrasound probe holder on either the arm or neck to image the brachial or carotid arteries, respectively. We obtain images and blood flow velocities through Doppler at each exercise stage and then we analyze the images using edge detection software to determine artery diameters. With these data, we are able to estimate ESS, flow direction, and the presence of turbulent flow.
Assessment of coral restoration’s contribution to reef recovery using machine learning
Authors: Morand Gaétan , Dixon Simon , Berre Thomas Le 
Published: December 2020

AbstractCoral restoration emerged globally as a form of life support for coral reefs, awaiting urgent mitigation of anthropogenic pressure. Yet its efficiency is difficult to assess, as ambitious transplantation programs handle hundreds of thousands of fragments, with survival rates inherently time-intensive to monitor. Due to limited available data, the influence of most environmental and methodological factors is still unknown.We therefore propose a new method which leverages machine learning to track each colony’s individual health and growth on a large sample size. This is the first time artificial intelligence techniques were used to monitor coralat a colony scale, providing an unprecedented amount of data on coral health and growth. Here we show the influence of genus, depth and initial fragment size, alongside providing an outlook on coral restoration’s efficiency.We show that among 77,574 fragments, individual survival rate was 31% after 2 years (21% after 4 years), which is much lower than most reported results. In the absence of significant anthropogenic pressure, we showed that there was a depth limit below whichPocilloporafragments outperformedAcroporafragments, while the opposite was true past this threshold. During the mid-2019 heatwave, our research indicates thatPocilloporafragments were 37% more likely to survive thanAcroporafragments.Overall, the total amount of live coral steadily increased over time, by more than 3,700 liters a year, as growth compensated for mortality. This supports the use of targeted coral restoration to accelerate reef recovery after mass bleaching events.
TheUstilago hordei-barley interaction is a versatile system to characterize fungal effectors
Authors: Ökmen Bilal , Schwammbach Daniela , Bakkeren Guus , Neumann Ulla , Doehlemann Gunther 
Published: December 2020

AbstractObligate biotrophic fungal pathogens, such asBlumeria graminisandPuccinia graminis, are amongst the most devastating plant pathogens, causing dramatic yield losses in many economically important crops worldwide. However, a lack of reliable tools for the efficient genetic transformation has hampered studies into the molecular basis of their virulence/pathogenicity. In this study, we present theU. hordei-barley pathosystem as a model to characterize effectors from different plant pathogenic fungi. We have generatedU. hordeisolopathogenic strains, which form infectious filaments without presence of compatible mating partner. Solopathogenic strains are suitable as heterologous expression system for fungal virulence factors. A highly efficient Crispr/Cas9 gene editing system is made available forU. hordei. In addition,U. hordeiinfection structures during barley colonization were analyzed by transmission electron microscopy, which shows thatU. hordeiforms intracellular infection structures sharing high similarity to haustoria formed by obligate rust and powdery mildew fungi. Thus,U. hordeihas high potential as a fungal expression platform for functional studies of heterologous effector proteins in barley.
The ages of zone of proximal development for retrospective time assessment and anticipation of time event
Authors: Portnova G.V. , Rebreikina A. B. , Martynova O.V. 
Published: December 2020

AbstractWe aimed to investigate the ability of children aged 5–14 years old (preschoolers, primary schoolers, and preteens) to assess and anticipate time intervals. 287 Russian children aged 5–14 years old and 26 adults of control group participated in our study. The neuropsychological assessment, Wechsler Intelligence Scale for Children and a battery of time-related tests were applied. All groups of children overestimated the event’s duration, although the accuracy of the second estimations increased among the participants aged 6–8 years after a prompt was offered. A zone of proximal development for time anticipation task was detected for children aged 9-11 years, when the prompt could significantly improve the accuracy of time perception. The participants overestimated the duration of both upcoming and past events, with the degree of overestimation being found to be negatively correlated with age. Further, a higher degree of accuracy in terms of time estimation was found to be correlated with higher scores on the attention and memory tests, and accuracy of time anticipation was associated with scores of praxis test.
A broad exome study of the genetic architecture of asthma reveals novel patient subgroups
Authors: Cameron-Christie Sophia , Mackay Alex , Wang Quanli , Olsson Henric , Angermann Bastian , Lassi Glenda , Lindgren Julia , Hühn Michael , Ohne Yoichiro , Gavala Monica , Wang Jingya , Povysil Gundula , Deevi Sri V. V. , Belfield Graham , Dillmann Inken , Muthas Daniel , Cohen Suzanne , Young Simon , Platt Adam , Petrovski Slavé 
Published: December 2020

AbstractIntroductionAsthma risk is a complex interplay between genetic susceptibility and environment. Despite many significantly-associated common variants, the contribution of rarer variants with potentially greater effect sizes has not been as extensively studied. We present an exome-based study adopting 24,576 cases and 120,530 controls to assess the contribution of rare protein-coding variants to the risk of early-onset or all-comer asthma.MethodsWe performed case-control analyses on three genetic units: variant-, gene- and pathway-level, using sequence data from the Scandinavian Asthma Genetic Study and UK Biobank participants with asthma. Cases were defined as all-comer asthma (n=24,576) and early-onset asthma (n=5,962). Controls were 120,530 UK Biobank participants without reported history of respiratory illness.ResultsVariant-level analyses identified statistically significant variants at moderate-to-common allele frequency, including protein-truncating variants inFLGandIL33.Asthma risk was significantly increased not only by individual, commonFLGprotein-truncating variants, but also among the collection of rare-to-privateFLGprotein-truncating variants (p=6.8×10−7). This signal was driven by early-onset asthma and did not correlate with circulating eosinophil levels. In contrast, a single splice variant inIL33was significantly protective (p=8.0×10−10), while the collection of remainingIL33protein-truncating variants showed no class effect (p=0.54). A pathway-based analysis identified that protein-truncating variants in loss-of-function intolerant genes were significantly enriched among individuals with asthma.ConclusionsAccess to the full allele frequency spectrum of protein-coding variants provides additional clarity about the potential mechanisms of action forFLGandIL33.Beyond these two significant drivers, we detected a significant enrichment of protein-truncating variants in loss-of-function intolerant genes.
Choosing priors in Bayesian ecological models by simulating from the prior predictive distribution
Authors: Wesner Jeff S. , Pomeranz Justin P.F. 
Published: December 2020

AbstractBayesian data analysis is increasingly used in ecology, but prior specification remains focused on choosing non-informative priors (e.g., flat or vague priors). One barrier to choosing more informative priors is that priors must be specified on model parameters (e.g., intercepts, slopes, sigmas), but prior knowledge often exists on the level of the response variable. This is particularly true for common models in ecology, like generalized linear mixed models, which may have a link function and dozens of parameters, each of which needs a prior distribution. We suggest that this difficulty can be overcome by simulating from the prior predictive distribution and visualizing the results on the scale of the response variable. In doing so, some common choices for non-informative priors on parameters can easily be seen to produce biologically impossible values of response variables. Such implications of prior choices are difficult to foresee without visualization. We demonstrate a workflow for prior selection using simulation and visualization with two ecological examples (predator-prey body sizes and spider responses to food competition). This approach is not new, but its adoption by ecologists will help to better incorporate prior information in ecological models, thereby maximizing one of the benefits of Bayesian data analysis.
Fast and effective protein model refinement by deep graph neural networks
Authors: Jing Xiaoyang , Xu Jinbo 
Published: December 2020

AbstractProtein structure prediction has been greatly improved, but there are still a good portion of predicted models that do not have very high quality. Protein model refinement is one of the methods that may further improve model quality. Nevertheless, it is very challenging to refine a protein model towards better quality. Currently the most successful refinement methods rely on extensive conformation sampling and thus, take hours or days to refine even a single protein model. Here we propose a fast and effective method that may refine protein models with very limited conformation sampling. Our method applies GNN (graph neural networks) to predict refined inter-atom distance probability distribution from an initial model and then rebuilds the model using the predicted distance as restraints. On the CASP13 refinement targets our method may refine models with comparable quality as the two leading human groups (Feig and Baker) and greatly outperforms the others. On the CASP14 refinement targets our method is only second to Feig’s method, comparable to Baker’s method and much better than the others (who worsened instead of improved model quality). Our method achieves this result by generating only 5 refined models for an initial model, which can be done in ∼15 minutes. Our study also shows that GNN performs much better than convolutional residual neural networks for protein model refinement when conformation sampling is limited.AvailabilityThe code will be released once the manuscript is published and available athttp://raptorx.uchicago.eduContactjinboxu@gmail.com
Plasmodesmata-dependent intercellular movement of bacterial effectors
Authors: Li Zhongpeng , Variz Haris , Chen Yani , Liu Su-Ling , Aung Kyaw 
Published: December 2020

AbstractPathogenic microorganisms deliver protein effectors into host cells to suppress host immune responses. Recent findings reveal that phytopathogens manipulate the function of plant cell-to-cell communication channels plasmodesmata (PD) to promote diseases. Several bacterial and filamentous pathogen effectors have been shown to regulate PD in their host cells. A few effectors of filamentous pathogens have been reported to move from the infected cells to neighboring plant cells through PD; however, it is unclear whether bacterial effectors can traffic through PD in plants. In this study, we systemically determined the intercellular movement ofPseudomonas syringaepv.tomato(Pst) DC3000 effectors between adjoining plant cells inNicotiana benthamiana. We observed that at least 16PstDC3000 effectors move from transformed cells to the surrounding plant cells. The movement of the effectors is largely dependent on their molecular weights. The expression of PD regulators, Arabidopsis PD-located protein PDLP5 and PDLP7, lead to PD closure and inhibits the PD-dependent movement of a bacterial effector inN. benthamiana. Similarly, a 22-amino acid peptide of bacterial flagellin (flg22) treatment induces PD closure and suppresses the movement of a bacterial effector inN. benthamiana. Together, our findings demonstrated that bacterial effectors are able to move intercellularly through PD in plants.
Manual Annotation of Genes withinDrosophilaSpecies: the Genomics Education Partnership protocol
Authors: Rele Chinmay P. , Sandlin Katie M. , Leung Wilson , Reed Laura K. 
Published: December 2020

AbstractAnnotating the genomes of multiple organisms allows us to study their genes as well as the evolution of those genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP;thegep.org) has developed an annotation protocol for protein-coding genes that enables undergraduate students and other researchers to create high-quality gene annotations that can be utilized in subsequent scientific investigations. For example, this protocol has been utilized by the GEP faculty to engage undergraduate students in the comparative annotation of genes involved in the insulin signaling pathway in 28Drosophilaspecies, usingD. melanogasteras the informant genome. Students construct gene models using multiple lines of computational and experimental evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST, multiple sequence alignments), and computational gene predictions. For quality control, each gene is annotated by at least two students working independently, followed by reconciliation of the submitted gene models by a more experienced student. This article provides an overview of the annotation protocol and describes how discrepancies in student submitted gene models are resolved to produce a final, high-quality gene set suitable for subsequent analyses. This annotation protocol can be adapted to other scientific questions (e.g., expansion of theDrosophilaMuller F element) and other species (e.g., parasitoid wasps) to provide additional opportunities for undergraduate students to participate in genomics research. These student annotation efforts can substantially improve the quality of gene annotations in publicly available genomic databases.
BBrowser: Making single-cell data easily accessible
Authors: Le Tri , Phan Tan , Pham Minh , Tran Dat , Lam Loc , Nguyen Tung , Truong Thao , Vuong Hy , Luu Tam , Phung Nam , Pham Ngan , Nguyen Trang , Pham Oanh , Nguyen An , Nguyen Huy , Tran Hao , Tran Loc , Nguyen Ha An , Tran Thanh , Nguyen Nhung , Tran Ngoc , Boysen Cecilie , Nguyen Uyen , Pham Vy , Kim Theodore , Pham Ngoc , Gill Tristan , Pham Son 
Published: December 2020

AbstractBioTuring’s BBrowser is a software solution that helps scientists effectively analyze single-cell omics data. It combines big data with big computation and modern data visualization to create a unique platform where scientists can interact and obtain important biological insights from the massive amounts of single-cell data. BBrowser has three main components: a curated single-cell database, a big-data analytics layer, and a data visualization module. BBrowser is available for download at:https://bioturing.com/bbrowser/download.
Profound Treg perturbations correlate with COVID-19 severity
Authors: Galván-Peña Silvia , Leon Juliette , Chowdhary Kaitavjeet , Michelson Daniel A. , Vijaykumar Brinda , Yang Liang , Magnuson Angela , Manickas-Hill Zachary , Piechocka-Trocha Alicja , Worrall Daniel P. , Hall Kathryn E. , Ghebremichael Musie , Walker Bruce D. , Li Jonathan Z. , Yu Xu G. ,   MGH COVID-19 Collection & Processing Team, Mathis Diane , Benoist Christophe 
Published: December 2020

SummaryThe hallmark of severe COVID-19 disease has been an uncontrolled inflammatory response, resulting from poorly understood immunological dysfunction. We explored the hypothesis that perturbations in FoxP3+ T regulatory cells (Treg), key enforcers of immune homeostasis, contribute to COVID-19 pathology. Cytometric and transcriptomic profiling revealed a distinct Treg phenotype in severe COVID-19 patients, with an increase in both Treg proportions and intracellular levels of the lineage-defining transcription factor FoxP3, which correlated with poor outcomes. Accordingly, these Tregs over-expressed a range of suppressive effectors, but also pro-inflammatory molecules like IL32. Most strikingly, they acquired similarity to tumor-infiltrating Tregs, known to suppress local anti-tumor responses. These traits were most marked in acute patients with severe disease, but persisted somewhat in convalescent patients. These results suggest that Tregs may play nefarious roles in COVID-19, via suppressing anti-viral T cell responses during the severe phase of the disease, and/or via a direct pro-inflammatory role.
Distinct expression of select and transcriptome-wide isolated 3’UTRs suggests critical roles in development and transition states
Authors: Ji Shaoyi , Yang Ze , Gozali Leonardi , Kenney Thomas , Kocabas Arif , Park Carolyn Jinsook , Hynes Mary 
Published: December 2020

AbstractMature mRNA molecules are typically considered to be comprised of a 5’UTR, a 3’UTR and a coding region (CDS), all attached until degradation. Unexpectedly, however, there have been multiple recent reports of widespread differential expression of mRNA 3’UTRs and their cognate coding regions, resulting in the expression of isolated 3’UTRs (i3’UTRs); these i3’UTRs can be highly expressed, often in reciprocal patterns to their cognate CDS. Similar to the role of other lncRNAs, isolated 3’UTRs are likely to play an important role in gene regulation but little is known about the contexts in which they are deployed. To begin to parse the functions of i3’UTRs, here we carry outin vitro, in vivoandin silicoanalyses of differential 3’UTR/CDS mRNA ratio usage across tissues, development and cell state changes both for a select list of developmentally important genes as well as through unbiased transcriptome-wide analyses. Across two developmental paradigms we find a distinct switch from high i3’UTR expression of stem cell related genes in proliferating cells compared to newly differentiated cells. Our unbiased transcriptome analysis across multiple gene sets shows that regardless of tissue, genes with high 3’UTR to CDS ratios belong predominantly to gene ontology categories related to cell-type specific functions while in contrast, the gene ontology categories of genes with low 3’UTR to CDS ratios are similar and relate to common cellular functions. In addition to these specific findings our data provide critical information from which detailed hypotheses for individual i3’UTRs can be tested-with a common theme that i3’UTRs appear poised to regulate cell-specific gene expression and state.Significance StatementThe widespread existence and expression of mRNA 3’ untranslated sequences in the absence of their cognate coding regions (called isolated 3’UTRs or i3’UTRs) opens up considerable avenues for gene regulation not previously envisioned. Each isolated 3’UTR may still bind and interact with micro RNAs, RNA binding proteins as well as other nucleic acid sequences, all in the absence or low levels of cognate protein production. Here we document the expression, localization and regulation of i3’UTRs both within particular biological systems as well as across the transcriptome. As this is an entirely new area of experimental investigation these early studies are seminal to this burgeoning field.
16p12.1 deletion orthologs are expressed in motile neural crest cells and are important for regulating craniofacial development inXenopus laevis
Authors: Lasser Micaela , Bolduc Jessica , Murphy Luke , O’Brien Caroline , Lee Sangmook , Girirajan Santhosh , Lowery Laura Anne 
Published: December 2020

AbstractCopy number variants (CNVs) associated with neurodevelopmental disorders are characterized by extensive phenotypic heterogeneity. In particular, one CNV was identified in a subset of children clinically diagnosed with intellectual disabilities (ID) that results in a hemizygous deletion of multiple genes at chromosome 16p12.1. In addition to ID, individuals with this deletion display a variety of symptoms including microcephaly, seizures, cardiac defects, and growth retardation. Moreover, patients also manifest severe craniofacial abnormalities, such as micrognathia, cartilage malformation of the ears and nose, and facial asymmetries; however, the function of the genes within the 16p12.1 region have not been studied in the context of vertebrate craniofacial development. The craniofacial tissues affected in patients with this deletion all derive from the same embryonic precursor, the cranial neural crest, leading to the hypothesis that one or more of the 16p12.1 genes may be involved in regulating neural crest cell (NCC)-related processes. To examine this, we characterized the developmental role of the 16p12.1-affected gene orthologs,polr3e,mosmo,uqcrc2, andcdr2, during craniofacial morphogenesis in the vertebrate model system,Xenopus laevis. While the currently-known cellular functions of these genes are diverse, we find that they share similar expression patterns along the neural tube, pharyngeal arches, and later craniofacial structures. As these genes show co-expression in the pharyngeal arches where NCCs reside, we sought to elucidate the effect of individual gene depletion on craniofacial development and NCC migration. We find that reduction of several 16p12.1 genes significantly disrupts craniofacial and cartilage formation, pharyngeal arch migration, as well as NCC specification and motility. Thus, we have determined that some of these genes play an essential role during vertebrate craniofacial patterning by regulating specific processes during NCC development, which may be an underlying mechanism contributing to the craniofacial defects associated with the 16p12.1 deletion.