bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cortical ripples during NREM sleep and waking in humans
Authors: Dickey Charles W. , Verzhbinsky Ilya A. , Jiang Xi , Rosen Burke Q. , Kajfez Sophie , Eskandar Emad N. , Gonzalez-Martinez Jorge , Cash Sydney S. , Halgren Eric 
Published: May 2021

AbstractHippocampal ripples index the reconstruction of spatiotemporal neuronal firing patterns essential for the consolidation of memories in the cortex during non-rapid eye movement sleep (NREM). Recently, cortical ripples in humans have been shown to enfold the replay of neuron firing patterns during cued recall. Here, using intracranial recordings from 18 patients (12 female), we show that cortical ripples also occur during NREM in humans, with similar density, oscillation frequency (∼90 Hz), duration, and amplitude to waking. Ripples occurred in all cortical regions with similar characteristics, unrelated to putative hippocampal connectivity, and were less dense and robust in higher association areas. Putative pyramidal and interneuron spiking phase-locked to cortical ripples during NREM, with phase delays consistent with ripple generation through pyramidal-interneuron feedback. Cortical ripples were smaller in amplitude than hippocampal ripples, but were similar in density, frequency, and duration. Cortical ripples during NREM typically occurred just prior to the upstate peak, often during spindles. Upstates and spindles have previously been associated with memory consolidation, and we found that cortical ripples grouped co-firing between units within the window of spike-timing-dependent plasticity. Thus, human NREM cortical ripples are: ubiquitous and stereotyped with a tightly focused oscillation frequency; similar to hippocampal ripples; associated with upstates and spindles; and associated with unit co-firing. These properties are consistent with cortical ripples possibly contributing to memory consolidation and other functions during NREM in humans.Significance StatementIn rodents, hippocampal ripples organize replay during sleep to promote memory consolidation in the cortex, where ripples also occur. However, evidence for cortical ripples in human sleep is limited, and their anatomical distribution and physiological properties are unexplored. Here, using human intracranial recordings, we demonstrate that ripples occur throughout the cortex during waking and sleep with highly stereotyped characteristics. During sleep, cortical ripples tend to occur during spindles on the down-to-upstate transition, and thus participate in a sequence of sleep waves that is important for consolidation. Furthermore, cortical ripples organize single unit spiking with timing optimal to facilitate plasticity. Therefore, cortical ripples in humans possess essential physiological properties to support memory and other cognitive functions.
A graphical, interactive and GPU-enabled workflow to process long-read sequencing data
Authors: Reddy Shishir , Hung Ling-Hong , Sala-Torra Olga , Radich Jerald , Yeung Cecilia CS , Yeung Ka Yee 
Published: May 2021

ABSTRACTWe present a graphical cloud-enabled workflow for fast, interactive analysis of nanopore sequencing data using GPUs. Users customize parameters, monitor execution and visualize results through an accessible graphical interface. To facilitate reproducible deployment, we use Docker containers and provide an Amazon Machine Image (AMI) with all software and drivers pre-installed for GPU computing on the cloud. We observe a 34x speedup and a 109x reduction in costs for the rate-limiting basecalling step in the analysis of blood cancer cell line data. The graphical interface and greatly simplified deployment facilitate the adoption of GPUs for rapid, cost-effective analysis of long-read sequencing.
Research gaps and new insights in the intriguing evolution of Drosophila seminal proteins
Authors: Hurtado J , Almeida FC , Belliard SA , Revale S , Hasson E 
Published: May 2021

AbstractWhile the striking effects that seminal fluid proteins (SFPs) exert on females are fairly conserved among Diptera, they exhibit remarkable evolutionary lability. Consequently, most SFPs lack detectable homologs among the repertoire of SFPs of phylogenetically distant species. How such a rapidly changing proteome “manages” to conserve functions across taxa is a fascinating question. However, this and other pivotal aspects of SFPs’ evolution remain elusive because discoveries on these proteins have been mainly restricted to the model D. melanogaster. Here, we provide an overview of the current knowledge on the inter-specific divergence of Drosophila SFPs and compile the increasing amount of relevant genomic information from multiple species. Capitalizing the accumulated knowledge in D. melanogaster, we present novel sets of high-confidence SFP candidates and transcription factors presumptively involved in regulating the expression of SFPs. We also address open questions by performing comparative genomic analyses that failed to support the existence of conserved SFPs shared by most dipterans and indicated that gene co-option is the most frequent mechanism accounting for the origin of Drosophila SFP-coding genes. We hope our update establishes a starting point to integrate, as more species are assayed for SFPs, further data and thus, to widen the understanding of the intricate evolution of these proteins.
Key Promoter Region of Wnt4 response to FSH and Genetic Effect on Several Production Traits of Its Mutations in Chicken
Authors: Zhong Conghao , Wang Yiya , Liu Cuiping , Jiang Yunliang , Kang Li 
Published: May 2021

AbstractThe signaling pathway of the wingless-type mouse mammary tumor virus integration site (Wnt) plays an important role in ovarian and follicular development. Wnt4 was shown in our previous study to be involved in the selection and development of chicken follicles by up-regulating the expression of follicle stimulating hormone receptors (FSHR), stimulating the proliferation of follicular granulosa cells and increasing the secretion of steroidal hormones. To further characterize cis-elements regulating chicken Wnt4 transcription, in this study we determined critical regulatory regions affecting chicken Wnt4 transcription, then identified a single nucleotide polymorphism (SNP) in this region, and finally analyzed the association of the SNP with chicken production traits. The results showed that the 5′ regulatory region from -3354 to -2689 of the chicken Wnt4 gene had the strongest activity and greatest response to FSH stimulation, and that one SNP site -3015 (G > C) in this segment was identified as affecting the binding of NFAT5 (nuclear factor of activated T cells 5). When G was replaced by C at this site, it eliminated the binding by NFAT5. Moreover, this locus was significantly associated with the keel length and comb length of hens. Individuals with the genotype CG had longer keels while those with genotype CC had longer combs. Collectively, these data suggested that the SNP-3015 (G > C) is (i) involved in the regulation of Wnt4 gene expression by affecting the binding of NFAT5, (ii) associated with chicken keel length and comb length, and (iii) is a potential DNA marker in the molecular breeding of chickens for egg laying.
Multiple ancestral and a plethora of recent gene duplications during the evolution of the green sensitive opsin genes (RH2) in teleost fishes
Authors: Musilova Zuzana , Cortesi Fabio 
Published: May 2021

AbstractVertebrates have four visual cone opsin classes that, together with a light-sensitive chromophore, provide sensitivity from the ultraviolet to the red wavelengths of light. The rhodopsin-like 2 (RH2) opsin is sensitive to the centre blue-green part of the spectrum, which is the most prevalent light underwater. While various vertebrate groups such as mammals and sharks have lost theRH2gene, in teleost fishes this opsin has continued to proliferate. By investigating the genomes of 115 teleost species, we find thatRH2shows an extremely dynamic evolutionary history with repeated gene duplications, gene losses and gene conversion affecting entire orders, families and species. At least four ancestral duplications provided the substrate for today’sRH2diversity with duplications occurring in the common ancestors of Clupeocephala, Neoteleostei, and Acanthopterygii. Following these events,RH2has continued to duplicate both in tandem and during lineage specific genome duplications. However, it has also been lost many times over so that in the genomes of extant teleosts, we find between zero to eightRH2copies. Using retinal transcriptomes in a phylogenetic representative dataset of 30 species, we show thatRH2is expressed as the dominant green-sensitive opsin in almost all fish lineages. The exceptions are the Osteoglossomorpha (bony tongues and mooneyes) and several characin species that have lostRH2, and tarpons, other characins and gobies which do not or only lowly express the gene. These fishes instead express a green-shifted long-wavelength-sensitiveLWSopsin. Our study highlights the strength of using modern genomic tools within a comparative framework to elucidate the detailed evolutionary history of gene families.
Social selection within aggregative multicellular development drives morphological evolution
Authors: Fortezza Marco La , Velicer Gregory J. 
Published: May 2021

AbstractThe evolution of developmental systems might be shaped by both historical differences in developmental features and social selection, among other factors. In aggregative multicellularity, development is itself a social process in which unicellular organisms cooperate in carrying out complex developmental programs. In some aggregative systems, development culminates in the construction of spore-packed fruiting bodies. Fruiting body development in myxobacteria often unfolds within genetically and behaviorally diverse conspecific cellular environments that can include social defection and warfare. Here we use the bacterium Myxococcus xanthus to test whether the character of the cellular environment during aggregative development shapes morphological evolution. We manipulated the cellular composition of Myxococcus development in an experiment in which evolving populations initiated from a single ancestor repeatedly co-developed with one of several non-evolving partners - a benign cooperator, one of three cheaters or one of three antagonists. Fruiting body morphology was found to diversify as a function of developmental partners, revealing adaptation specific to distinct cellular environments. Collectively, antagonistic partners selected for higher levels of robust fruiting body formation than did cheaters or the benign cooperator. Moreover, even small degrees of genetic divergence between the distinct cheater partners were sufficient to drive treatment-level morphological divergence. Co-developmental partners not only shaped mean trait evolution but also determined the magnitude and dynamics of stochastic morphological diversification and subsequent convergence. In sum, we find that even few genetic differences affecting developmental and social features can greatly impact the morphological evolution of multicellular bodies and experimentally demonstrate that microbial warfare can promote cooperation.
Spatiotemporal specificity of correlated DNA methylation and gene expression pairs across different human tissues and stages of brain development
Authors: Wang Kangli , Dai Rujia , Xia Yan , Tian Jianghua , Jiao Chuan , Mikhailova Tatiana , Zhang Chunling , Chen Chao , Liu Chunyu 
Published: May 2021

AbstractDNA methylation (DNAm) that occurs on promoter regions is primarily considered to repress gene expression. Previous studies indicated that DNAm could also show positive correlations with gene expression. Both DNAm and gene expression profiles are known to be tissue- and development-specific. This study aims to investigate how DNAm and gene expression are coordinated across different human tissues and developmental stages, as well as the biological significance of such correlations. By analyzing 2,239 samples with both DNAm and gene expression data in the same human subjects obtained from six published datasets, we evaluated the correlations between gene and CpG pairs (GCPs) at cis-regions and compared significantly correlated GCPs (cGCPs) across different tissues and brains at different age groups. A total of 37,363 cGCPs were identified in the six datasets; approximately 38% of the cGCPs were positively correlated. The majority (>90%) of cGCPs were tissue- or development-specific. We also observed that the correlation direction can be opposite in different tissues and ages. Further analysis highlighted the importance of cGCPs for their cellular functions and potential roles in complex traits and human diseases. For instance, early developmental brain possessed a highly unique set of cGCPs that were associated with neurogenesis and psychiatric disorders. By assessing the epigenetic factors involved in cGCPs, we discovered novel regulatory mechanisms of positive cGCPs distinct from negative cGCPs, which were related to multiple factors, such as H3K27me3, CTCF, and JARD2. The catalog of cGCPs compiled can be used to guide functional interpretation of genetic and epigenetic studies.
Mycolactone enhances the Ca2+ leakage from endoplasmic reticulum by trapping Sec61 translocons in a Ca2+ permeable state
Authors: Bhadra Pratiti , Santos Scott Dos , Gamayun Igor , Pick Tillman , Ogbechi Joy , Hall Belinda S. , Zimmermann Richard , Helms Volkhard , Simmonds Rachel E. , Cavalié Adolfo 
Published: May 2021

AbstractThe Mycobacterium ulcerans exotoxin, mycolactone, is an inhibitor of co-translational translocation via the Sec61 complex. Mycolactone has previously been shown to bind to, and alter the structure of, the major translocon subunit Sec61α, and change its interaction with ribosome nascent chain complexes. In addition to its function in protein translocation into the ER, Sec61 also plays a key role in cellular Ca2+ homeostasis, acting as a leak channel between the endoplasmic reticulum (ER) and cytosol. Here, we have analysed the effect of mycolactone on cytosolic and ER Ca2+ levels using compartment-specific sensors. We also used molecular docking analysis to explore potential interaction sites for mycolactone on translocons in various states. These results show that mycolactone enhances the leak of Ca2+ ions via the Sec61 translocon, resulting in a slow but substantial depletion of ER Ca2+. This leak was dependent on mycolactone binding to Sec61α because resistance mutations in this protein completely ablated the increase. Molecular docking supports the existence of a mycolactone-binding transient inhibited state preceding translocation and suggests mycolactone may also bind Sec61α in its idle state. We propose that delayed ribosomal release after translation termination and/or translocon “breathing” during rapid transitions between the idle and intermediate-inhibited states allow for transient Ca2+ leak, and mycolactone’s stabilisation of the latter underpins the phenotype observed.
One Cell At a Time: A Unified Framework to Integrate and Analyze Single-cell RNA-seq Data
Authors: Wang Chloe X. , Zhang Lin , Wang Bo 
Published: May 2021

1AbstractThe surge of single-cell RNA sequencing technologies gives rise to the abundance of large single-cell RNA-seq datasets at the scale of hundreds of thousands of single cells. Integrative analysis of large-scale scRNA-seq datasets has the potential of revealingde novocell types as well as aggregating biological information. However, most existing methods fail to integrate multiple large-scale scRNA-seq datasets in a computational and memory efficient way. We hereby propose OCAT,OneCellAt aTime, a graph-based method that sparsely encodes single-cell gene expressions to integrate data from multiple sources without most variable gene selection or explicit batch effect correction. We demonstrate that OCAT efficiently integrates multiple scRNA-seq datasets and achieves the state-of-the-art performance in cell type clustering, especially in challenging scenarios of non-overlapping cell types. In addition, OCAT efficaciously facilitates a variety of downstream analyses, such as differential gene analysis, trajectory inference, pseudotime inference and cell inference. OCAT is a unifying tool to simplify and expedite the analysis of large-scale scRNA-seq data from heterogeneous sources.
Lmo7 recruits myosin II heavy chain to induce apical constriction in Xenopus ectoderm
Authors: Matsuda Miho , Chu Chih-Wen , Sokol Sergei Y. 
Published: May 2021

AbstractApical constriction, or reduction of the apical domain, underlies many morphogenetic events during development, such as furrow or tube formation. Actomyosin complexes play an essential role in apical constriction, however the detailed analysis of molecular mechanisms is still pending. Here we show that Lim domain only protein 7 (Lmo7), a multidomain adaptor at apical junctions, promotes apical constriction in the Xenopus superficial ectoderm, whereas apical domain size increases in Lmo7-depleted cells. Lmo7 is localized to and promotes the formation of the circumferential actomyosin belt adjacent to apical junctions. We find that Lmo7-dependent apical constriction requires the RhoA-ROCK-Non-muscle myosin II (NMII) pathway. Strikingly, Lmo7 binds and recruits NMII heavy chains to apical junctions. Lmo7 overexpression altered the subcellular distribution of Wtip, a sensor of mechanical tension. Our findings suggest that Lmo7 serves as a scaffold organizing the actomyosin network to regulate contractility at apical junctions.
A spatially aware likelihood test to detect sweeps from haplotype distributions
Authors: DeGiorgio Michael , Szpiech Zachary A. 
Published: May 2021

AbstractThe inference of positive selection in genomes is a problem of great interest in evolutionary genomics. By identifying putative regions of the genome that contain adaptive mutations, we are able to learn about the biology of organisms and their evolutionary history. Here we introduce a composite likelihood method that identifies recently completed or ongoing positive selection by searching for extreme distortions in the spatial distribution of the haplotype frequency spectrum along the genome relative to the genome-wide expectation taken as neutrality. Furthermore, the method simultaneously infers two parameters of the sweep: the number of sweeping haplotypes and the “width” of the sweep, which is related to the strength and timing of selection. We demonstrate that this method outperforms the leading haplotype-based selection statistics. As a positive control, we apply it to two well-studied human populations from the 1000 Genomes Project and examine haplotype frequency spectrum patterns at theLCTand MHC loci. We also apply it to a data set of brown rats sampled in NYC and identify genes related to olfactory perception. To facilitate use of this method, we have implemented it in user-friendly open source software.
Numerical study of external explosion characteristics induced by indoor natural gas vented explosion
Authors: Pang Lei , Hu Qianran , Yang Kai 
Published: May 2021

PurposeThe purpose of this paper is to ascertain the harm to personnel and equipment caused by an external explosion during natural gas explosion venting. The external explosion characteristics induced by the indoor natural gas explosion are the focal points of the investigation.Design/methodology/approachComputational fluid dynamics technology was used to investigate the large-scale explosion venting process of natural gas in a 6 × 3 × 2.5 m room, and the characteristics of external explosion under different scaled vent size (Kv= Av/V2/3, 0.05, 0.08, 0.13, 0.18) were numerically analyzed.FindingsWhen Kv = 0.08, the length and duration of the explosion fireball are 13.39 and 450 ms, respectively, which significantly expands the degree and range of high-temperature hazards. The suitable flow-field structure causes the external explosion overpressure to be more than twice that indoors, i.e. the natural gas explosion venting overpressure may be considerably more hazardous in an outdoor environment than inside a room. A specific range for the Kvcan promote the superposition of outdoor rupture waves and explosion shock waves, thereby creating a new overpressure hazard.Originality/valueLittle attention has been devoted to investigating systematically the external explosion hazards. Based on the numerical simulation and the analysis, the external explosion characteristics induced by the indoor large-scale gas explosion were obtained. The research results are theoretically significant for mitigating the effects of external gas explosions on personnel and equipment.
MHD flow of MgO-Ag/water hybrid nanofluid past a moving slim needle considering dual solutions: an applicable model for hot-wire anemometer analysis
Authors: Dinarvand Saeed , Mousavi Seyed Mehdi , Yousefi Mohammad , Nademi Rostami Mohammadreza 
Published: May 2021

PurposeThe purpose of this paper is to study the steady laminar magnetohydrodynamics (MHD) flow of a magnesium oxide-silver/water hybrid nanofluid along a horizontal slim needle with thermal radiation by considering dual solutions.Design/methodology/approachIt is assumed that the needle can move in the same or opposite direction of the free stream. Also the solid phase and fluid phase are in thermal equilibrium. The basic partial differential equations become dimensionless using a similarity transformation method. Moreover, problem coding is accomplished using the finite difference method. The emerging parameters are nanoparticles mass (0–40 gr), base fluid mass (100 gr), needle’s size (0.001–0.2), magnetic field parameter, velocity ratio parameter, radiation parameter and Prandtl number (6.2).FindingsWith help of the stability analysis, it is shown that always the first solutions are physically stable. Results indicate that the magnetic parameter and the second nanoparticle’s mass limit the range of the velocity ratio parameter for which the solution exists. Besides, the magnetic parameter leads to decrease of quantities of engineering interest, i.e. skin friction coefficient and local Nusselt number.Originality/valueTo the best of the authors’ knowledge, no one has ever attempted to study the present problem through a mass-based model for hybrid nanofluid. Moreover, the dual solutions for the problem are new. Indeed, the results of this paper are purely original and the numerical achievements were never published up to now. Finally, the authors expect that the present investigation would be useful in hot-wire anemometer or shielded thermocouple for measuring the velocity of the wind, etc.