bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulations of co-axial jet flows on graphics processing units: the flow and noise analysis
Authors: Markesteijn A. P. , Karabasov S. A. 
Published: October 2019

Large-eddy simulations (LES) are performed for a range of perfectly expanded co-axial jet cases corresponding to conditions of the computation of coaxial jet noise (CoJeN) experiment by QinetiQ. In all simulations, the high-resolution Compact Accurately Boundary-Adjusting high-REsolution Technique (CABARET) is used for solving the Navier–Stokes equations on unstructured meshes. The Ffowcs Williams–Hawkings method based on the penetrable integral surfaces is applied for far-field noise predictions. To correctly model the turbulent flow downstream of the complex nozzle that includes a central body, a wall modelled LES approach is implemented together with a turbulent inflow condition based on synthetic turbulence. All models are run on graphics processing units to enable a considerable reduction of the flow solution time in comparison with the conventional LES. The flow and noise solutions are validated against the experimental data available with 1–2 dB accuracy being reported for noise spectra predictions on the fine grid. To analyse the structure of effective noise sources of the jets, the covariance of turbulent fluctuating Reynolds stresses is computed and their characteristic scales are analysed in the context of the generalized acoustic analogy jet noise models. Motivated by self-similarity of single-stream axi-symmetric jet flows, a suitable non-dimensionalization of the effective jet noise sources of the CoJeN jets is tested, and its implications for low-order jet noise models are discussed.
This article is part of the theme issue ‘Frontiers of aeroacoustics research: theory, computation and experiment’.
RNAseq studies reveal distinct transcriptional response to vitamin A deficiency in small intestine versus colon, uncovering novel vitamin A-regulated genes
Authors: Chai Zhi , Lyu Yafei , Chen Qiuyan , Wei Cheng-Hsin , Snyder Lindsay M. , Weaver Veronika , Sebastian Aswathy , Albert István , Li Qunhua , Cantorna Margherita T. , Ross A. Catharine 
Published: October 2019

AbstractVitamin A (VA) deficiency remains prevalent in resource limited countries, affecting over 250 million preschool aged children. Vitamin A deficiency is associated with reduced intestinal barrier function and increased risk of mortality due to mucosal infection. UsingCitrobacter rodentium(C. rodentium) infection in mice as a model for diarrheal diseases in humans, previous reports showed reduced pathogen clearance and survival in vitamin A deficient (VAD) mice compared to their vitamin A sufficient (VAS) counterparts.ObjectivesTo characterize and compare the impact of preexisting VA deficiency on gene expression patterns in the small intestine (SI) and the colon, and to discover novel target genes in VA-related biological pathways.MethodsVAD mice were generated by feeding VAD diet to pregnant C57/BL6 dams and their post-weaning offspring. RNAseq were performed using the total mRNAs extracted from SI and colon. Differentially Expressed Gene (DEG), Gene Ontology (GO) enrichment, and Weighted Gene Co-expression Network Analysis (WGCNA) were performed to characterize expression and co-expression patterns.ResultsDEGs compared between VAS and VAD groups detected 49 SI and 94 colon genes. By GO information, SI DEGs were significantly enriched in categories relevant to retinoid metabolic process, molecule binding, and immune function. Immunity related pathways, including “humoral immune response” and “complement activation” were positively associated with VA in SI. Three co-expression modules showed significant correlation with VA status in SI; these modules contained four known retinoic acid targets. In addition, other SI genes of interest (e.g.Mbl2,Cxcl14, andNr0b2) in these modules were suggested as new candidate genes regulated by VA. Furthermore, our analysis showed that markers of two cell types in SI, mast cells and Tuft cells, were significantly altered by VA status. In colon, “cell division” was the only enriched category and was negatively associated with VA. Thus, comparison of co-expression modules between SI and colon indicated distinct networks under the regulation of dietary VA and suggest that preexisting VAD could have a significant impact on the host response to a variety of disease conditions.
Effect of number and placement of EEG electrodes on measurement of neural tracking of speech
Authors: Montoya-Martínez Jair , Vanthornhout Jonas , Bertrand Alexander , Francart Tom 
Published: October 2019

AbstractMeasurement of neural tracking of natural running speech from the electroencephalogram (EEG) is an increasingly popular method in auditory neuroscience and has applications in audiology. The method involves decoding the envelope of the speech signal from the EEG signal, and calculating the correlation with the envelope of the audio stream that was presented to the subject. Typically EEG systems with 64 or more electrodes are used. However, in practical applications, set-ups with fewer electrodes are required. Here, we determine the optimal number of electrodes, and the best position to place a limited number of electrodes on the scalp. We propose a channel selection strategy based on an utility metric, which allows a quick quantitative assessment of the influence of a channel (or a group of channels) on the reconstruction error. We consider two use cases: a subject-specific case, where the optimal number and position of the electrodes is determined for each subject individually, and a subject-independent case, where the electrodes are placed at the same positions (in the 10-20 system) for all the subjects. We evaluated our approach using 64-channel EEG data from 90 subjects. In the subject-specific case we found that the correlation between actual and reconstructed envelope first increased with decreasing number of electrodes, with an optimum at around 20 electrodes, yielding 29% higher correlations using the optimal number of electrodes compared to all electrodes. This means that our strategy of removing electrodes can be used to improve the correlation metric in high-density EEG recordings. In the subject-independent case, we obtained a stable decoding performance when decreasing from 64 to 22 channels. When the number of channels was further decreased, the correlation decreased. For a maximal decrease in correlation of 10%, 32 well-placed electrodes were sufficient in 91% of the subjects.
An integrated multi-omic single cell atlas to redefine human B cell memory
Authors: Glass David R. , Tsai Albert G. , Oliveria John Paul , Hartmann Felix J. , Kimmey Samuel C. , Calderon Ariel A. , Borges Luciene , Bendall Sean C. 
Published: October 2019

AbstractTo evaluate the impact of heterogeneous B cells in health and disease, comprehensive profiling is needed at a single cell resolution. We developed a highly-multiplexed screen to quantify the co-expression of 351 surface molecules on low numbers of primary cells. We identified dozens of differentially expressed molecules and aligned their variance with B cell isotype usage, metabolism, biosynthesis activity, and signaling response. Here, we propose a new classification scheme to segregate peripheral blood B cells into ten unique subsets, including a CD45RB+ CD27- early memory population and a CD19hiCD11c+ memory population that is a potent responder to immune activation. Furthermore, we quantify the contributions of antibody isotype and cell surface phenotype to various cell processes and find that phenotype largely drives B cell function. Taken together, these findings provide an extensive profile of human B cell diversity that can serve as a resource for further immunological investigations.
Extreme storms cause rapid, context-dependent shifts in nearshore subtropical bacterial communities
Authors: Ares Ángela , Brisbin Margaret Mars , Sato Kirk N. , Martín Juan P. , Iinuma Yoshiteru , Mitarai Satoshi 
Published: October 2019

AbstractClimate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run-off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early- and late-season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment—locally known as red soil pollution—and caused moderate increases of macronutrients—especially SiO2 and PO43-. We detected shifts in relative abundances of marine bacteria and the introduction of terrestrially-derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run-off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short-lived and bacterial communities quickly recovered following both storm events. The early- and late-season storms caused different physicochemical and bacterial community changes, demonstrating the context-dependency of extreme storm responses in a subtropical coastal ecosystem.
Riboflavin Directly Mediates the Dealkylation by Microbial Cytochrome P450 Monooxygeneses
Authors: Zhang Chengchang , Lu Meiling , Lin Lin , Huang Zhangjian , Zhang Rongguang , Wu Xuri , Chen Yijun 
Published: October 2019

ABSTRACTAs a vast repertoire of enzymes in nature, microbial cytochrome P450 monooxygenases require an activated form of flavin as a cofactor for the catalytic activity. Riboflavin is the precursor of FAD and FMN that serve as indispensable cofactors for flavoenzymes. In contrast to previous notion, here we describe the identification of an electron transfer process directly mediated by riboflavin for the N-dealkylation by microbial P450 monooxygenases. The electron relay from NADPH to riboflavin and then via activated oxygen to heme was proposed based on the combination of X-ray crystallography, molecular modeling and molecular dynamics simulation, site-directed mutagenesis and biochemical analysis of representative microbial P450 monooxygenases. This study provides new insights into the electron transfer mechanism in microbial P450 enzyme catalysis and likely in plants and mammals.
Diversification of metazoan Kexin-like proprotein convertases: insights from the leechHelobdella
Authors: Tao Wei-Yu , Cheng Ya-Chih , Song Mi Hye , Weisblat David A. , Kuo Dian-Han 
Published: October 2019

AbstractIntercellular communication is quintessential for multicellularity and often mediated by secreted peptide ligands. In Metazoa, proprotein convertases are a major class of endoproteases partaking in the proteolytic processing of these ligands, which is in turn required for their signaling activities. In vertebrates, the best-studied convertase substrates are neuropeptides, peptide hormones, and members of the TGFβ/BMP-family. Each ligand is processed by a particular subset of convertases. Therefore, the diversification of convertases may have contributed to the growing complexity of cellular communication in metazoan evolution. However, proprotein convertases have not been systematically explored in Metazoa. Here, we sampled the representative metazoan genomes and established that six Kexin-like proprotein convertases were present in the last common ancestor of protostomes and deuterostomes. Among these, we identified a novel PCSKX orthologous group (OG) that was lost in vertebrates. Spiralian protosomes have, in general, maintained all six OGs. Therefore, we characterized the functional divergence of the Kexin-like OGs in the leechHelobdella, an experimentally tractable spiralian. Gene expression patterns suggested that PCSK1 and PCSK2 are specialized for the processing of neuropeptides and peptide hormones in bilaterians and that the newly identified PCSKX is probably functionally similar to furin and PCSK7. Finally, we showed that, distinct from the BMP morphogen in vertebrate embryos, the convertase-mediated proteolytic cleavage is not required for the short-range BMP signaling in the dorsoventral patterning of leech ectoderm. Together, our data revealed the complexity of the Kexin-like proprotein convertase gene family and their roles in generating diverse patterns of cellular communication in Metazoa.
The Bovine Genome Variation Database (BGVD): Integrated Web-database for Bovine Sequencing Variations and Selective Signatures
Authors: Chen Ningbo , Fu Weiwei , Zhao Jianbang , Shen Jiafei , Chen Qiuming , Zheng Zhuqing , Chen Hong , Sonstegard Tad S. , Lei Chuzhao , Jiang Yu 
Published: October 2019

AbstractNext-generation sequencing has yielded a vast amount of cattle genomic data for the global characterization of population genetic diversity and the identification of regions of the genome under natural and artificial selection. However, efficient storage, querying and visualization of such large datasets remain challenging. Here, we developed a comprehensive Bovine Genome Variation Database (BGVD, http://animal.nwsuaf.edu.cn/BosVar) that provides six main functionalities: Gene Search, Variation Search, Genomic Signature Search, Genome Browser, Alignment Search Tools and the Genome Coordinate Conversion Tool. The BGVD contains information on genomic variations comprising ∼60.44 M SNPs, ∼6.86 M indels, 76,634 CNV regions and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data and resources from NCBI, the UCSC Genome Browser and AnimalQTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale.
The zebrafish dorsolateral habenula is required for updating learned behaviors
Authors: Palumbo Fabrizio , Serneels Bram , Pelgrims Robbrecht , Yaksi Emre 
Published: October 2019

ABSTRACTOperant conditioning requires multiple cognitive processes, such as learning, prediction of potential outcomes and decision making. It is less clear how interactions of these processes lead to the behavioral adaptations that allow animals to cope with a changing environment. We showed that juvenile zebrafish can perform conditioned place avoidance learning, with an improving performance across development. Ablation of the dorsolateral habenula (dlHb), a brain region involved in associative learning and prediction of outcomes, led to an unexpected improvement in performance and delayed memory extinction. Interestingly, while the control animals exhibited rapid adaptation to a changing learning rule, dlHb ablated animals failed to adapt. Altogether, our results show that the dlHb plays a central role in switching animals’ strategies while integrating new evidence with prior experience.
Brain aging comprises many modes of structural and functional change with distinct genetic and biophysical associations
Authors: Smith Stephen M. , Elliott Lloyd T. , Alfaro-Almagro Fidel , McCarthy Paul , Nichols Thomas E. , Douaud Gwenaëlle , Miller Karla L. 
Published: October 2019

AbstractBrain imaging can be used to study how individuals’ brains are aging, compared against population norms. This can inform on aspects of brain health; for example, smoking and blood pressure can be seen to accelerate brain aging. Typically, a single “brain age” is estimated per subject, whereas here we we identified 62 modes of subject variability, from 21,407 subjects’ multimodal brain imaging data in UK Biobank. The modes represent different aspects of brain aging, showing distinct patterns of functional and structural brain change, and distinct patterns of association with genetics, lifestyle, cognition, physical measures and disease. While conventional brain-age modelling found no genetic associations, 34 modes had genetic associations. We suggest that it is important not to treat brain aging as a single homogeneous process, and that modelling of distinct patterns of structural and functional change will reveal more biologically meaningful markers of brain aging in health and disease.
Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs
Authors: Arvola René M. , Chang Chung-Te , Buytendorp Joseph P. , Levdansky Yevgen , Valkov Eugene , Freddolino Peter L. , Goldstrohm Aaron C. 
Published: October 2019

ABSTRACTPumilio is an RNA-binding protein that represses a network of mRNAs to control embryogenesis, stem cell fate, fertility, and neurological functions inDrosophila. We sought to identify the mechanism of Pumilio-mediated repression and find that it accelerates degradation of target mRNAs, mediated by three N-terminal Repression Domains (RDs), which are unique to Pumilio orthologs. We show that the repressive activities of the Pumilio RDs depend on specific subunits of the Ccr4-Not (CNOT) deadenylase complex. Depletion of Pop2, Not1, Not2, or Not3 subunits alleviates Pumilio RD-mediated repression of protein expression and mRNA decay, whereas depletion of other CNOT components had little or no effect. Moreover, the catalytic activity of Pop2 deadenylase is important for Pumilio RD activity. Further, we show that the Pumilio RDs directly bind to the CNOT complex. We also report that the decapping enzyme, Dcp2, participates in repression by the N-terminus of Pumilio. These results support a model wherein Pumilio utilizes CNOT deadenylase and decapping complexes to accelerate destruction of target mRNAs. Because the N-terminal RDs are conserved in mammalian Pumilio orthologs, the results of this work broadly enhance our understanding of Pumilio function and roles in diseases including cancer, neurodegeneration, and epilepsy.
Molecularly-Defined Hippocampal Inputs Regulate Population Dynamics in the Prelimbic Cortex to Suppress Context Fear Memory Recall
Authors: Hallock Henry L. , Quillian Henry M. , Maynard Kristen R. , Mai Yishan , Chen Huei-Ying , Hamersky Gregory R. , Shin Joo Heon , Maher Brady J. , Jaffe Andrew E. , Martinowich Keri 
Published: October 2019

AbstractAssociating fearful events with the context in which they occur is critical for survival. Dysregulation of context-fear memory processing is a hallmark symptom of several neuropsychiatric disorders, including generalized anxiety disorder (GAD) and post-traumatic stress disorder (PTSD). Both the hippocampus and prelimbic subregion (PrL) of the medial prefrontal cortex (mPFC) have been linked with context fear memory recall in rodents, but the mechanisms by which hippocampal-prelimbic circuitry regulates this process remains poorly understood. Spatial and genetic targeting of this circuit in mice allowed us to use molecular profiling to show that hippocampal neurons with projections to the PrL (vHC-PrL projectors) are a transcriptomically-distinct sub-population that is enriched for expression of genes associated with both GAD and PTSD. We further show that stimulation of this population of vHC-PrL projectors suppresses context fear memory recall and impairs the ability of PrL neurons to dynamically distinguish between distinct phases of fear learning. Using transgenic and circuit-specific molecular targeting approaches, we demonstrate that unique patterns of activity-dependent gene transcription within vHC-PrL projectors causally regulate excitatory/inhibitory balance in the PrL during context fear memory recall. Together, our data illuminate the molecular mechanisms by which hippocampal-prelimbic circuitry regulates the retrieval of contextually-mediated fear memories.
“Alkyladenine DNA glycosylase associates with transcription elongation to coordinate DNA repair with gene expression”
Authors: Montaldo Nicola P. , Bordin Diana L. , Brambilla Alessandro , Rösinger Marcel , Fordyce Martin Sarah L. , Bjørås Karine Øian , Bradamante Stefano , Aas Per Arne , Furrer Antonia , Olsen Lene C. , Otterlei Marit , Sætrom Pål , Bjørås Magnar , Samson Leona D. , van Loon Barbara 
Published: October 2019

AbstractBase excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG; aka MPG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases including cancer and neurological disorders. While BER is well studied on naked DNA, it remains unclear how BER efficiently operates on chromatin. Here we show that AAG binds to chromatin and forms complex with active RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation. Importantly, at co-regulated genes aberrantly methylated bases accumulate towards 3’end, in regions enriched for BER enzymes AAG and APE1, Elongator and active RNA pol II. Active transcription and functional Elongator are further crucial to ensure efficient BER, by promoting AAG and APE1 chromatin recruitment. Our findings provide novel insights to maintaining genome stability in actively transcribing chromatin, and reveal roles of aberrantly methylated bases in regulation of gene expression.
On the evolution of neural decisions from uncertain visual input to uncertain actions
Authors: Tomassini Alessandro , Price Darren , Zhang Jiaxiang , Rowe James B 
Published: October 2019

AbstractBehavior can be conceived as the result of a sequence in which the outcomes of perceptual decisions inform decisions on which action to take. However, the relationship between these processes, and spatiotemporal dynamics of the visual-to-motor transformation remains unclear. Here, we combined accumulation-to-threshold models and electro-magnetoencephalography, to trace neural correlates of sensorimotor decisions in space, time and frequency. We challenge the assumption of sequential decisions, with evidence that visuomotor processing unfolds through a continuous flow of information from sensory to motor regions. Action selection is initiated before regional visual decisions are completed. By linking behavior and physiology through theoretical decision models, we identify simultaneous forward and backward flow of information for visuomotor decisions between sensory and motor regions, in beta and gamma ranges. The model of integrated visuomotor decisions provides a powerful approach to investigate behavioral disorders that impair the ability to use sensory inputs to guide appropriate actions.