bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-read genome assemblies reveals acis-regulatory landscape associated with phenotypic divergence in two sisterSinipercafishes
Authors: Tu Guangxian , Chen Qi , Zhang Xinshuang , Jiang Ruirun , Zhang Long , Lai Chengjun , Yan Zhuyue , Lv Yanrong , Weng Shaoping , Zhang Li , He Jianguo , Wang Muhua 
Published: November 2022

AbstractBackgroundDissecting the genetic basis of variation in the regulation of gene expression is essential for understanding phenotypic evolution. Structural variants intersecting thecis-regulatory elements are found to cause gene expression variation in several developmental genes, resulting in morphological divergence between species. Due to the difficulty of identifying structural variants accurately across the genome, a comprehensive study of impacts of structural variants incis-regulatory divergence of closely related species, especially fish species, is still scarce. Recently identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological processes. However, the role of broad H3K4me3 domains in phenotypic divergence remain poorly understood.Siniperca chuatsiandS. scherzeriare two closely related fish species diverge in several phenotypic traits, making them an ideal model to studycis-regulatory evolution in closely related species.ResultsWe generated chromosome-level genomes ofS. chuatsiandS. scherzeri. The evolutionary histories ofS. chuatsiandS. scherzeriwere studied by inferring the dynamic changes in the ancestral population sizes. The genetic basis of adaptation inS. chuatsiandS. scherzeriwas dissected by performing gene family expansion and contraction analysis and identifying positively selected genes (PSGs). To investigate the role of SVs incis-regulatory divergence of closely related fish species, we identified high-quality SVs betweenS. chuatsiandS. scherzeri, as well as H3K27ac and H3K4me3 domains. Integrated analysis revealed thatcis-regulatory divergence caused by SVs played an essential role in the differentiation of metabolism, skin pigmentation, and immunity betweenS. chuatsiandS. scherzeri. Additionally, divergent broad H3K4me3 domains were found to mostly associate with cancer-related genes inS. chuatsiandS. scherzeriand contribute to their phenotypic divergence.ConclusionsOur analysis reveals SVs play an essential role incis-regulatory variation between the two sister fish species, which in turn contributes to their phenotypic divergence. The divergence of broad H3K4me3 domains contributes to phenotypic divergence between closely related species. Additionally, the association of broad H3K4me3 domains and cancer-related genes has an ancient origin.
Cryo-EM structures of kalium channelrhodopsins KCRs
Authors: Zhang Mingfeng , Shan Yuanyue , Xiao Li , Zhao Liping , Pei Duanqing 
Published: November 2022

SummaryH. catenoideskalium channelrhodopsins (HcKCR1 andHcKCR2) are potassium-selective light-gated ion channels with unique properties for optogenetics. Here we report cryo-electron microscopy (cryo-EM) structures ofHcKCR1 andHcKCR2 with endogenous retinal. Strikingly, one structure of HcKCR1 represents the conducting state with continuous potassium ion flow in the lumen, while another in non-conducting state with discontinuous potassium ion flow. Further electrophysiological studies identified extracellular side of ion permeation region as the major element for channel potassium selectivity and retinal binding region for channel gating. Our results uncover the unprecedented potassium selectivity and light-gating mechanism, and may facilitate the rational design of new optogenetic tools.
Grad-seq analysis ofEnterococcus faecalisandEnterococcus faeciumprovides a global view of RNA and protein complexes in these two opportunistic pathogens
Authors: Michaux Charlotte , Gerovac Milan , Hansen Elisabeth E. , Barquist Lars , Vogel Jörg 
Published: November 2022

ABSTRACTEnterococcus faecalisandEnterococcus faeciumare major nosocomial pathogens. Despite their relevance to public health and their role in the development of bacterial antibiotic resistance, relatively little is known about gene regulation in these species. RNA–protein complexes serve crucial functions in all cellular processes associated with gene expression, including post-transcriptional control mediated by small regulatory RNAs (sRNAs). Here, we present a new resource for the study of enterococcal RNA biology, employing the Grad-seq technique to comprehensively predict complexes formed by RNA and proteins inE. faecalisV583 andE. faeciumAUS0004. Analysis of the generated global RNA and protein sedimentation profiles led to the identification of RNA-protein complexes and putative novel sRNAs. Validating our data sets, we observe well-established cellular RNA-protein complexes such as the 6S RNA-RNA polymerase complex, suggesting that 6S RNA-mediated global control of transcription is conserved in enterococci. Focusing on the largely uncharacterized RNA-binding protein KhpB, we use the RIP-seq technique to predict that KhpB interacts with sRNAs, tRNAs, and untranslated regions of mRNAs, and might be involved in the processing of specific tRNAs. Collectively, these datasets provide departure points for in-depth studies of the cellular interactome of enterococci that should facilitate functional discovery in these and related Gram-positive species. Our data are available to the community through a user-friendly Grad-seq browser that allows interactive searches of the sedimentation profiles (https://resources.helmholtz-hiri.de/gradseqef/).
Mimicking seasonal changes in light-dark cycle and ambient temperature modulates gut microbiome in mice under the same dietary regimen
Authors: Matsumoto Shoko , Ren Liang , Iigo Masayuki , Murai Atsushi , Yoshimura Takashi 
Published: November 2022

AbstractTo better adapt to seasonal environmental changes, physiological processes and behaviors are regulated seasonally. The gut microbiome interacts with the physiology, behavior, and even the diseases of host animals, including humans and livestock. Seasonal changes in gut microbiome composition have been reported in several species under natural environments. Dietary content significantly affects the composition of the microbiome, and, in the natural environment, the diet varies between different seasons. Therefore, understanding the seasonal regulatory mechanisms of the gut microbiome is important for understanding the seasonal adaptation strategies of animals. Herein, we examined the effects of changing day length and temperature, which mimic summer and winter conditions, on the gut microbiome of laboratory mice. Principal coordinate analysis and analysis of the composition of microbiomes of 16S rRNA sequencing data demonstrated that the microbiomes of the cecum and large intestine showed significant differences between summer and winter mimicking conditions. Similar to previous studies, a daily rhythm was observed in the composition of the microbiome. Furthermore, the phylogenetic investigation of communities by reconstruction of unobserved states predicted seasonal changes in several metabolic pathways. Changing day length and temperature can affect the composition of the gut microbiome without changing dietary contents.
Hybran: Hybrid Reference Transfer and ab initio Prokaryotic Genome Annotation
Authors: Elghraoui Afif , Gunasekaran Deepika , Radecke Sarah M. , Bishop Emma , Valafar Faramarz 
Published: November 2022

AbstractDe novo assembly has become commonplace for microbial organisms, increasing the demand for reliable genome annotation. Ab initio annotation is not an ideal approach for closely related strains due to suboptimal matching of the short or hypervariable genomic features that reference-based annotation transfer can overcome through identification of conserved synteny. At the same time, reference-based annotation methods leave gaps in the annotation where structural variations introduce unique sequence. We present Hybran, a hybrid reference-based and ab initio prokaryotic genome annotation pipeline that transfers features from a curated reference annotation and supplements unannotated regions with ab initio predictions. It builds on existing tools to create initial annotations using both approaches, then compares and resolves them to produce the hybrid annotation. With this pipeline, full advantage is taken of the community’s experimental efforts on reference strains to propagate as many known features as possible without sacrificing best-effort ab initio predictions for the remaining unannotated loci. Genome annotation performed in this way can facilitate comparative genomics and the investigation of evolutionary dynamics in microbial populations.Hybran is freely available athttps://lpcdrp.gitlab.io/hybran
Sleep-dependent engram reactivation during hippocampal memory consolidation is associated with subregion-specific biosynthetic changes
Authors: Wang Lijing , Park Lauren , Wu Weisheng , King Dana , Medina Alexis Vega , Raven Frank , Martinez Jessy , Ensing Amy , McDonald Katherine , Yang Zhongying , Jiang Sha , Aton Sara J. 
Published: November 2022

AbstractPost-learning sleep is essential for hippocampal memory processing, including contextual fear memory (CFM) consolidation. We used targeted recombination in activated populations (TRAP) to label context-encoding engram neurons in the hippocampal dentate gyrus (DG) and assessed reactivation of these neurons after fear learning. Post-learning sleep deprivation (SD), which impairs CFM consolidation, selectively disrupted reactivation of inferior blade DG engram neurons. This change was linked to more general suppression of neuronal activity markers in the inferior, but not superior, DG blade by SD. To further characterize how learning and subsequent sleep or SD affect these (and other) hippocampal subregions, we used subregion-specific spatial profiling of transcripts and proteins. We found that transcriptomic responses to sleep loss differed greatly between hippocampal regions CA1, CA3, and DG inferior blade, superior blade, and hilus – with activity-driven transcripts, and those associated with cytoskeletal remodeling, selectively suppressed in the inferior blade. Critically, learning-driven transcriptomic changes, measured 6 h following contextual fear learning, were limited to the two DG blades, differed dramatically between the blades, and were absent from all other regions. These changes suggested an increase in glutamatergic receptor signaling, and a decrease in GABA receptor signaling, during CFM consolidation. Protein abundance across hippocampal subregions was also differentially impacted by learning and sleep, with most alterations to protein expression restricted to DG. Together, these data suggest that the DG is critical for sleep-dependent memory consolidation, and that the effects of sleep loss on the hippocampus are highly subregion-specific, even within the DG itself.
Adaptive preservation of orphan ribosomal proteins in chaperone-stirred condensates
Authors: Ali Asif , Garde Rania , Schaffer Olivia C , Bard Jared A M , Husain Kabir , Kik Samantha Keyport , Davis Kathleen A , Luengo-Woods Sofia , Drummond D Allan , Squires Allison H , Pincus David 
Published: November 2022

ABSTRACTRibosome biogenesis is among the most resource-intensive cellular processes, with ribosomal proteins accounting for up to half of all newly synthesized proteins in eukaryotic cells. During stress, cells shut down ribosome biogenesis in part by halting rRNA synthesis, potentially leading to massive accumulation of aggregation-prone “orphan” ribosomal proteins (oRPs). Here we show that during heat shock in yeast and human cells, oRPs accumulate as reversible condensates at the nucleolar periphery recognized by the Hsp70 co-chaperone Sis1/DnaJB6. oRP condensates are liquid-like in cell-free lysate but solidify upon depletion of Sis1 or inhibition of Hsp70. When cells recover from heat shock, oRP condensates disperse in a Sis1-dependent manner, and their ribosomal protein constituents are incorporated into functional ribosomes in the cytosol, enabling cells to efficiently resume growth.One sentence summaryDuring stress, molecular chaperones preserve “orphan” ribosomal proteins (RPs) – RPs that are not bound to rRNA – in liquid-like condensates, maintaining the RPs in a usable form and enabling cells to efficiently resume growth upon recovery from stress.
Perception of Rigidity in Three- and Four-Dimensional Spaces
Authors: He Dongcheng , Nguyen Dat-Thanh , Ogmen Haluk , Nishina Shigeaki , Yazdanbakhsh Arash 
Published: November 2022

AbstractOur brain employs mechanisms to adapt to changing visual conditions. In addition to natural changes in our physiology and those in the environment, our brain is also capable of adapting to “unnatural” changes, such as inverted visual-inputs generated by inverting prisms. In this study, we examined the brain’s capability to adapt to hyperspaces. We generated four spatial-dimensional stimuli in virtual reality and tested the ability to distinguish between rigid and non-rigid motion. We found that observers are able to differentiate rigid and non-rigid motion of tesseracts (4D) with a performance comparable to that obtained using cubes (3D). Moreover, observers’ performance improved when they were provided with more immersive 3D experience but remained robust against increasing shape variations. At this juncture, we characterize our findings as “perception” since, while we show the ability to extract and use 4D information, we do not have yet evidence of a complete phenomenal 4D experience.
Voltage-Seq: all-optical postsynaptic connectome-guided single-cell transcriptomics
Authors: Csillag Veronika , Bizzozzero Marianne Hiriart , Noble Joyce , Reinius Björn , Fuzik János 
Published: November 2022

AbstractUnderstanding the routing of neuronal information requires the functional characterization of connections. Neuronal projections recruit large postsynaptic ensembles with distinct postsynaptic response types (PRTs). PRT is probed by low-throughput whole-cell electrophysiology and is not a selection criterion for single-cell RNA-sequencing (scRNA-seq). To overcome these limitations and target neurons based on specific PRTs for soma harvesting and subsequent scRNA-seq we created Voltage-Seq. To test our methodology, we established all-optical voltage imaging and recorded the PRT of 8347 periaqueductal gray (PAG) neurons evoked by the optogenetic activation of ventromedial hypothalamic (VMH) terminals. PRTs were classified and spatially resolved in the entire VMH-PAG connectome. We built an on-site analysis named VoltView to navigate soma harvesting towards target PRTs guided by a classifier which used the VMH-PAG connectome database as a reference. We demonstrated the agility of Voltage-Seq in locating VMH-driven GABAergic neurons in the PAG, solely guided by the on-site classification in VoltView.
Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor
Authors: Gatreddi Santhosh , Sui Dexin , Hausinger Robert P. , Hu Jian 
Published: November 2022

AbstractThe nickel-pincer nucleotide (NPN) cofactor discovered in lactate racemase fromLactiplantibacillus plantarum(LarALp) is essential for the activities of racemases/epimerases in the highly diverse LarA superfamily. Prior mechanistic studies have established a proton-coupled hydride-transfer mechanism for LarALp, but direct evidence showing that hydride attacks the C4 atom in the pyridinium ring of NPN has been lacking. Here, we show that sodium borohydride (NaBH4) irreversibly inactivates LarALpaccompanied by a rapid color change of the enzyme. The drastically altered ultraviolet-visible spectra during NaBH4titration supported hydride transfer to C4 of NPN, and the concomitant Ni loss unraveled by mass spectrometry experiments accounted for the mechanism-based inactivation. High resolution structures of LarALprevealed a substantially weakened C-Ni bond in the metastable sulfite-NPN adduct where the NPN cofactor is in the reduced state. These findings allowed us to propose a mechanism of LarALpinactivation by NaBH4that provides key insights into the enzyme-catalyzed reaction and sheds light on the reactivity of small molecule NPN mimetics.
A football debate: the future of football accountability research
Authors: Philippou Christina 
Published: November 2022

PurposeThe purpose of this paper is to provide commentary on Soccer Society debate that is used to create accountability research agenda.Design/methodology/approachThe methodology applied is thematic analysis of debate in relation to accountability research gaps.FindingsThe authors found that areas for future football accountability research include refereeing, human rights in event hosting, governance, ownership, networks and club and fan finances.Originality/valueThe study contributes to debate commentary and agenda for football accountability research.
Band gap mechanism and vibration attenuation of a quasi-zero stiffness metastructure
Authors: Li Yingli , Tijjani Muhammad Zahradeen , Jiang Xudong , Ahmed Jamiu Opeyemi 
Published: November 2022

PurposeThe main purpose of this paper is to investigate the vibration isolation performance of a quasi-zero stiffness (QZS) metastructure by employing the band gap (BG) mechanism.Design/methodology/approachThe metastructure QZS characteristic was investigated through static analysis by numerical simulation. Based on that, the BG mechanism is primarily used in this article to investigate the wave propagation characteristics of this structure. The model's dispersion relation is then examined using theoretical (perturbation method) and finite element techniques. The dynamic response of the finite-size systems and experimental analysis is used to confirm the vibration mitigation property under investigation. Finally, the model's ability to absorb energy was examined and contrasted with a traditional model.FindingsThe analytical analysis reveals the dispersion curve and the effect of the nonlinear parameter on the curve shifting. The dispersion curve in the finite element method (FEM) result depicts five complete BGs within the range of 0–1,000 Hz, and the BG width accounted for 67.4% of the frequency concerned (0–1,000 Hz). Eigenmodes of the dispersion curves were analyzed to investigate the BG formation mechanisms. The dependence of BG opening and closure on structure parameters was also studied. Finally, the energy absorption property of the QZS metastructure was evaluated by comparing it with a classical model. The QZS structure absorbs 4.08 J/Kg compared to the 3.69 J/Kg absorbed by the classical model, which reveals that the QZS demonstrates better energy absorption performance. Based on the BG mechanism, it is clear that this model is an excellent vibration isolator, and the study reveals the frequencies at which complete vibration mitigation is achieved. As a result, this model could be a promising candidate for vibration mitigation engineering structures and energy absorption.Originality/valueThe tough vibration issue, which is primarily experienced in mechanical equipment, will be resolved in this study. This study provides a precise understanding of the QZS metastructure's isolation of vibration, including the frequencies at which this isolation occurs.
The outlook of sustainability assurance in global trends: a bibliometric review and research agenda
Authors: Oware Kofi Mintah , Moulya V. Harshitha 
Published: November 2022

PurposeThere is a growing interest in how firms respond to environmental degradation and societal challenges. Firms respond through their sustainability reports, but assurance of the reports gives confidence to the stakeholders. This study aims to identify the main research development in sustainability assurance which is rising in global studies.Design/methodology/approachThis study uses a bibliometric analysis to assess the global trend in sustainability assurance studies. The methodology is based on descriptive, performance and science mapping. The set is based on 655 documents from the Scopus database, covering the period from 2005 to 2022.FindingsThe findings from the study suggest that sustainability studies are relevant, and the researcher's examination of the domain has dramatically increased from 2014 to date. This is due to the rise in the concerns expressed by stakeholders in satisfying themselves about the firm's responsibility to the Sustainable Development Agenda 2030. The findings also show that most research on sustainability assurance is from Spain, the USA, the United Kingdom (UK) and Australia. However, the UK has the most collaboration in terms of co-authorship. It is suggestive that the UK has more links than Spain, which is the most productive country with more publications. This may be attributed to the influx of more international students completing a second and third degree in the UK. The study highlights intellectual foundations and emerging trends and outlines avenues for future studies.Research limitations/implicationsThis study is limited to the data obtained from the Scopus database.Originality/valueThis study is the first bibliometric study of the sustainability assurance domain.
A phase 3, randomized, double‐blind, placebo‐controlled study evaluating a single, patient‐initiated dose of amenamevir for recurrent herpes labialis
Authors: Kawashima Makoto , Watanabe Daisuke , Fujio Kosuke , Komazaki Hiroshi 
Published: November 2022

AbstractAmenamevir (ASP2151), a novel, non‐nucleoside analog, antiviral drug, inhibits the enzyme activities of helicase and primase, which are essential for replication of herpes viral genomic DNA. In this phase 3, randomized, double‐blind, placebo‐controlled, multicenter study, the authors investigated the efficacy and safety of a single patient‐initiated dose of amenamevir to treat recurrent herpes labialis. Adult immunocompetent patients with recurrent herpes labialis who had the experience and ability to recognize prodromal symptoms were randomly assigned to administer amenamevir 1200 mg or placebo as a patient‐initiated therapy within 6 hours after onset of prodromal symptoms. The primary efficacy end point was time to healing of all herpes labialis lesions in the modified intention‐to‐treat population. Secondary efficacy end points were time to crusting of all herpes labialis lesions, time to resolution of pain accompanying herpes labialis, proportion of patients with aborted lesions, and time to resolution of subjective symptoms accompanying herpes labialis. The modified intention‐to‐treat population, which excluded patients with aborted lesions, comprised 298 patients who self‐initiated amenamevir and 307 who took placebo. Amenamevir demonstrated superiority over placebo for the primary end point; the median time to all lesion healing was 5.1 days for amenamevir versus 5.5 days for placebo (hazard ratio, 1.24; 95% confidence interval, 1.06–1.46; p = 0.0085). Time to crusting of all lesions was significantly shorter with amenamevir versus placebo (p = 0.0065); there were no significant between‐group differences in other secondary outcomes. Treatment‐emergent adverse events in both groups were generally mild in severity; there were two moderate events that were judged unrelated to study treatment, and no severe or serious events. In summary, a single patient‐initiated dose of amenamevir 1200 mg taken within 6 hours of prodromal symptom onset significantly shortened the time to all lesion healing of recurrent herpes labialis compared with placebo, with no clinically important safety concerns.