bluuebunny/crossref_metadata_2025_split huggingface dataset:
When is warmer better? Disentangling within- and between-generation effects of thermal history on survival
Authors: Rebolledo Adriana P. , Sgrò Carla M. , Monro Keyne 
Published: February 2023

AbstractUnderstanding the fitness consequences of thermal history is necessary to predict organismal responses to global warming. This is especially challenging for ectotherms with complex life cycles, since distinct life stages can differ in thermal sensitivity, acclimate to different thermal environments, and accrue responses to acclimation within and between generations.Although acclimation is widely hypothesized to benefit organisms by helping them (or their offspring) to compensate for negative impacts of environmental change, equivocal support for this hypothesis highlights the need to assess alternatives. However, assessments that do so in ways that explicitly dissect responses across life stages and generations remain limited.We assess alternative hypotheses for acclimation responses (none, beneficial, colder-is-better, and warmer-is-better) within and between generations of an externally-fertilizing marine tubeworm whose vulnerability to warming rests on survival at early planktonic stages (gametes, embryos, and larvae). We start by acclimating parents, gametes, and embryos to ambient and projected warmer temperatures (17 °C and 22 °C) factorially by life stage. We then rear individuals with differing acclimation histories to the end of larval development at test temperatures from 10 °C to 28 °C (upper and lower survival limits) to estimate thermal survival curves for development, and compare curves among acclimation histories.We show that survival curves are most responsive to parental acclimation followed by acclimation at embryogenesis, but are buffered against acclimation at fertilization. Moreover, curves respond independently to acclimation within and between generations, and respond largely as predicted by the warmer-is-better hypothesis, despite the semblance of beneficial acclimation after successive acclimations to warmer temperature.Our study demonstrates the varied nature of thermal acclimation, and the importance of considering how acclimation responses aggregate across complex life cycles when predicting vulnerability to warming.
Vulture: Cloud-enabled scalable mining of microbial reads in public scRNA-seq data
Authors: Chen Junyi , Yin Danqing , Wong Harris Y.H. , Duan Xin , Yu Ken H.O. , Ho Joshua W. K. 
Published: February 2023

AbstractThe rapidly growing collection of public single-cell sequencing data have become a valuable resource for molecular, cellular and microbial discovery. Previous studies mostly overlooked detecting pathogens in human single-cell sequencing data. Moreover, existing bioinformatics tools lack the scalability to deal with big public data. We introduce Vulture, a scalable cloud-based pipeline that performs microbial calling for single-cell RNA sequencing (scRNA-seq) data, enabling meta-analysis of host-microbial studies from the public domain. In our scalability benchmarking experiments, Vulture can outperform the state-of-the-art cloud-based pipeline Cumulus with a 40% and 80% reduction of runtime and cost, respectively. Furthermore, Vulture is 2-10 times faster than PathogenTrack and Venus, while generating comparable results. We applied Vulture to two COVID-19, three hepatocellular carcinoma (HCC), and two gastric cancer human patient cohorts with public sequencing reads data from scRNA-seq experiments and discovered cell-type specific enrichment of SARS-CoV2, hepatitis B virus (HBV), andH. pyloripositive cells, respectively. In the HCC analysis, all cohorts showed hepatocyte-only enrichment of HBV, with cell subtype-associated HBV enrichment based on inferred copy number variations. In summary, Vulture presents a scalable and economical framework to mine unknown host-microbial interactions from large-scale public scRNA-seq data. Vulture is available via an open-source license athttps://github.com/holab-hku/Vulture.
Goal-Directed Learning is Multidimensional and Accompanied by Diverse and Widespread Changes in Neocortical Signaling
Authors: Marrero Krista , Aruljothi Krithiga , Delgadillo Christian , Kabbara Sarah , Swatch Lovleen , Zagha Edward 
Published: February 2023

AbstractNew tasks are often learned in stages with each stage reflecting a different learning challenge. Accordingly, each learning stage is likely mediated by distinct neuronal processes. And yet, most rodent studies of the neuronal correlates of goal-directed learning focus on individual outcome measures and individual brain regions. Here, we longitudinally studied mice from naïve to expert performance in a head-fixed, operant conditioning whisker discrimination task. In addition to tracking the primary behavioral outcome of stimulus discrimination, we tracked and compared an array of object-based and temporal-based behavioral measures. These behavioral analyses identify multiple, partially overlapping learning stages in this task, consistent with initial response implementation, early stimulus-response generalization, and late response inhibition. To begin to understand the neuronal foundations of these learning processes, we performed widefield Ca2+imaging of dorsal neocortex throughout learning and correlated behavioral measures with neuronal activity. We found distinct and widespread correlations between neocortical activation patterns and various behavioral measures. For example, improvements in sensory discrimination correlated with target stimulus evoked activations of licking-related cortices along with distractor stimulus evoked global cortical suppression. Our study reveals multidimensional learning for a simple goal-directed learning task and generates hypotheses for the neuronal modulations underlying these various learning processes.
Viral proteogenomic and expression profiling during fully productive replication of a skin-tropic herpesvirus in the natural host
Authors: Volkening Jeremy , Spatz Stephen J. , Ponnuraj Nagendraprabhu , Akbar Haji , Arrington Justine V. , Jarosinski Keith W. 
Published: February 2023

AbstractEfficient transmission of herpesviruses is essential for dissemination in host populations; however, little is known about the viral genes that mediate transmission, mostly due to their close relationship to their natural host. Marek’s disease is a devastating herpesviral disease of chickens caused by Marek’s disease virus (MDV) and an excellent natural model to study skin- tropic herpesviruses and transmission. Similar to varicella zoster virus that causes chicken pox in humans, the only site where fully productive replication occurs is in epithelial skin cells and this is required for host to host transmission. Here, we enriched for actively replicating virus in feather follicle epithelial skin cells of live chickens to measure both viral transcription and protein expression using combined RNA sequencing and LC/MS-MS bottom-up proteomics. Enrichment produced a previously unseen breadth and depth of viral peptide sequencing. We confirmed protein translation for 84 viral genes at high confidence (1% FDR) and correlated relative protein abundance with RNA expression levels. Using a proteogenomic approach, we confirmed translation of most well-characterized spliced viral transcripts and identified a novel, abundant isoform of the 14 kDa transcript family via both intron-spanning sequencing reads as well as a high-quality junction-spanning peptide identification. We identified peptides representing alternative start codon usage in several genes and putative novel microORFs at the 5’ ends of two core herpesviral genes, pUL47 and ICP4, along with evidence of transcription and translation of the capsid scaffold protein pUL26.5. Using a natural animal host model system to examine viral gene expression provides a robust, efficient, and meaningful way of validating results gathered from cell culture systems.Author SummaryIn the natural host, the transcriptome and proteome of many herpesviruses are poorly defined. Here, we evaluated the viral transcriptome and proteome in feather follicle epithelial skin cells of chickens infected with Marek’s disease virus (MDV), an important poultry pathogen as well as an excellent model for skin-tropic human alphaherpesvirus replication in skin cells. Using fluorescently tagged virus, we significantly enriched the number of infected cells sampled from live chickens, greatly enhancing the detection of viral transcripts and proteins within a host background. Based on this, we could confirm the translation of most transcripts using deep MS/MS-based proteomics and identify novel expressed peptides supportive of an increasingly complex translational and regulatory viral landscape. The demonstrated deep peptide sequencing capability can serve as a template for future work in herpesviral proteomics.
Delirium, Confusion, or Altered mental status as a risk for abnormal head computed tomogram findings in older adults in the emergency department: A systematic review and meta-analysis
Authors: Lee Sangil , Cavalier Faithe R. , Hayes Jane M. , Doering Michelle , Lo Alexander X. , Khoujah Danya , Howard Matthew A. , de Wit Kerstin , Liu Shan W. 
Published: February 2023

AbstractBackgroundDelirium, confusion, and altered mental status are common presentations among older adults to the emergency department (ED). We aimed to report the association between delirium, confusion or altered mental status in older ED patients and acute abnormal findings on head computed tomogram (CT).MethodsA systematic review was conducted using Ovid Medline, Embase,Clinicaltrials.gov, Web of Science, and Cochrane Central from conception to April 8th, 2021. We included citations if they described patients aged 65 years or older who received head imaging at the time of ED assessment, and reported whether or not patients had delirium, confusion, or altered mental status. Screening, data extraction, and bias assessment were performed in duplicate. We estimated the odds ratios (OR) for abnormal neuroimaging in patients with altered mental status.ResultsThe search strategy identified 3,014 unique citations, of which two studies reporting on 909 patients with delirium, confusion or altered mental status were included. No study formally assessed for delirium. The OR for abnormal head CT findings in patients with delirium, confusion or altered mental status was 0.35 (95% CI 0.031 to 3.97) compared to patients without delirium, confusion or altered mental status.ConclusionWe did not find a statistically significant association between delirium, confusion or altered mental status and abnormal CT findings in older ED patients.
Types of Arrhythmias and the risk of sudden cardiac death in dialysis patients: A Systematic Review and Meta-analysis
Authors: Chander Subhash , Lohana Sindhu , Sadarat FNU , Kumari Roopa 
Published: February 2023

AbstractBackgroundPatients on long-term dialysis therapy due to ESRD tend to have a high mortality rate, predominantly due to cardiovascular complications, which is associated with an increased risk of arrhythmias compared to the general population. Arrhythmia has been firmly identified as the primary cause of sudden death during dialysis, as studies have shown a correlation between the timing of dialysis sessions and episodes of sudden death, as well as relationships with serum or dialysate electrotype concentrations. It also associated with a six-fold increased risk of developing ventricular fibrillation following a first myocardial infarction.MethodsThis systematic review and meta-analysis followed the guidelines provided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The reviewers searched the Cochrane Library, MEDLINE, Europe PMC, and Google Scholar Databases for relevant data sources. We included only randomized controlled trials and cohort studies published in English. A quantitative analysis (meta-analysis) was conducted using Review Manager version 5.4 (RevMan 5.4; The Nordic Cochrane Center, The Cochrane Collaboration, 2014).ResultsThe initial database search yielded 547 studies, of which 213 duplicates were excluded. The title, abstract, and full-text screening excluded 247 studies, and the final total included 13 studies reporting the incidence of SCD mortality in this meta-analysis.ConclusionSCD remains a major public health concern, particularly in patients undergoing dialysis. Meta-analysis results show that bradyarrhythmia emerges as a common type of arrhythmia leading to SCD; however, other types of arrhythmias should also be considered.
Mortality and Mode of Dialysis
Authors: Chander Subhash , Lohana Sindhu , Sadarat FNU , Kumari Roopa 
Published: February 2023

AbstractBackgroundDialysis is an intervention used chiefly to cover poorly functioning kidneys’ ultrafiltration and diffusion functions. Dialysis can be performed using three major approaches: peritoneal dialysis, hemodialysis, and continuous renal replacement therapy, which have varying degrees of efficiency. We sought to compare the mortality rates among patients receiving different dialysis modalities.Study DesignStatistical Review and Meta-Analysis.Setting & PopulationThe investigation was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Data sources were drawn from Google Scholar, ResearchGate, PubMed (MEDLINE), Cochrane Library, and Embase databases. Eligible patients had to be ones presenting with acute or chronic kidney failure who required assistance with kidney function.Selection Criteria for StudiesThe eligibility criteria included studies with participants requiring dialysis and comparing two of the three dialysis modalities that provided outcomes on mortality rates. Inclusion criteria (underlying disease, chronic or acute kidney disease, presenting signs, age categories, subject consent, etc.), the type of dialysis modalities under investigation, and the mortality rates (% per modality group).Index Texts‘mortalities, fatalities, dialysis, hemodialysis, continuous renal replacement therapy (CRRT), Peritoneal dialysis, and comparative.’OutcomesWe sought to explore the studies’ findings by comparing the mortality rates among the three broad categories of dialysis. Therefore, we aimed to compare mortality rates in CRRT vs. Hemodialysis, mortality Rates in CRRT vs. PD, and mortality rates in patients with PD vs. HD.ResultsFifteen studies were narrowed down from the study search and were placed into three categories: PD vs. CRRT (4), PD vs. HD (5), and CRRT vs. HD (6). For the three outcomes, none recorded statistically significant differences in mortality rates between the patient categories (p= 0.92, 0.009, 0.22).ConclusionLike other interventions for patients with chronic kidney disease, dialysis is associated with detrimental effects caused by the inflammatory response and worsening progression of the condition. Mortality is a common complication among dialysis patients, independent of modality, based on the lack of statistically significant differences between the three groups.
Taste matters: Mapping expectancy-based appetitive placebo effects onto the brain
Authors: Khalid Iraj , Rodrigues Belina , Dreyfus Hippolyte , Frileux Solène , Meissner Karin , Fossati Philippe , Hare Todd Anthony , Schmidt Liane 
Published: February 2023

AbstractExpectancies, which are higher order prognostic beliefs, can have powerful effects on experiences, behavior and brain. However, it is unknown where, how, and when, in the brain, prognostic beliefs influence appetitive interoceptive experiences and related economic behavior. This study combined a placebo intervention on hunger with computational modelling and functional magnetic resonance imaging of value-based decision-making. The results show that prognostic beliefs about hunger shape hunger experiences, how much participants value food and food-value encoding in the prefrontal cortex. Computational modelling further revealed that these placebo effects were underpinned by how much and when during the decision process taste and health information are integrated into the accumulation of evidence toward a food choice. The drift weights of both sources of information further moderated ventromedial and dorsolateral prefrontal cortex interactions during choice formation. These findings provide novel insights into the neurocognitive mechanisms that translate higher order prognostic beliefs into non-aversive interoceptive sensitivity and shape decision-making.
Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype
Authors: Simonin Marie , Préveaux Anne , Marais Coralie , Garin Tiffany , Arnault Gontran , Sarniguet Alain , Barret Matthieu 
Published: February 2023

ABSTRACTSeed-borne microorganisms can be pioneer taxa during germination and seedling emergence. Still, the identity and phenotypic effects of these taxa that constitute a primary inoculum of plant microbiota is mostly unknown. Here, we studied the transmission of bacteria from radish seeds to seedlings using the inoculation of individual seed-borne strains and synthetic communities (SynComs) underin vitroconditions. The SynComs were composed of highly abundant and prevalent, sub-dominant or rare bacterial seed taxa. We monitored the transmission of each strain alone or in communities usinggyrBgene amplicon sequencing and assessed their impacts on germination and seedling phenotype.All strains and SynComs successfully colonized seedlings and we were able to reconstruct a richness gradient (6, 8 and 12 strains) on both seeds and seedlings.Stenotrophomonas rhizophilabecame dominant on seedlings of the three SynComs but most strains had variable transmission success (i.e increasing, stable or decreasing during seed to seedling transition) that also depended on the SynCom richness.Most individual strains had no effect on seedling phenotypes, at the exception ofPseudomonas viridiflavaandPaenibacillus sp. thathad detrimental effects on germination and seedling development. Abnormal seedling morphologies were also observed with SynComs but their proportions decreased at the highest richness level. Interestingly, some bacterial strains previously identified as core taxa of radish seeds (Pseudomonas viridiflava, Erwinia persicina)were associated with detrimental effects on seedling phenotypes either in isolation or in SynComs. These results confirm that the plant core microbiome includes pathogenic and not only commensal or mutualistic taxa.Altogether, these results show that SynCom inoculation can effectively manipulate seed and seedling microbiota diversity and thus represents a promising tool to better understand the early stages of plant microbiota assembly. This study also highlights strong differences between native seed-borne taxa in the colonization and survival on plant habitats.
Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complex through fuzzy interaction and mesoscale condensation
Authors: Xie Shangqiang , Yue Congran , Ye Sheng , Li Zhenlu 
Published: February 2023

AbstractNuclear transition protein TNP1 is a crucial player mediating histone-protamine exchange in condensing spermatids. A unique combination of intrinsic disorder and multivalent properties turns TNP1 into an ideal agent for orchestrating the formation of versatile TNP-DNA assembly and endows the protein with potent value for vaccine design. Despite its significance, the physicochemical property and the molecular mechanism taken by TNP1 for histone replacement and DNA condensation are still poorly understood. In this study, for the first time, we expressed and purified in vitro human TNP1. We investigated the hierarchical dynamics of TNP1: DNA interaction by combing computational simulations, biochemical assay, fluorescence imaging, and atomic force microscopy. We analyzed fuzzy interactions between TNP1 and DNA at the atomistic level and assessed the influence of TNP1 association on the electrostatic and mechanical properties of DNA. Furthermore, the alteration of the physicochemical properties of the TNP1-DNA complex modulates its molecular assembly and phase separation. Our study sets the foundation for understanding TNP1-mediated histone replacement and sheds light on the encapsulation of genetic material by TNP1 for vaccine development.
Structural landscape of the Respiratory Syncytial Virus nucleocapsids
Authors: Gonnin Lorène , Desfosses Ambroise , Bacia-Verloop Maria , Chevret Didier , Galloux Marie , Éléouët Jean-François , Gutsche Irina 
Published: February 2023

AbstractHuman Respiratory Syncytial Virus (RSV) is a prevalent cause of severe respiratory infections in children and the elderly. The viral genome, enwrapped by the nucleoprotein N into a helical nucleocapsid (NC), is a template for the viral RNA synthesis and a scaffold for the virion assembly. Although the structures of NC filaments representative of the other major families of theMononegaviralesorder have been solved, a detailed understanding of the RSV NCs is missing. This cryo-electron microscopy (cryo-EM) analysis highlights the polymorphism of the RSV nucleocapsid-like assemblies. We reveal in particular the non-canonical arrangement of the RSV NC helix, composed of 16 N per asymmetric unit, and the resulting systematic variations in the RNA accessibility. We demonstrate that this unique helical symmetry originates from recurring longitudinal interactions by the C-terminal arm of the RSV N, whose truncation abrogates the inter-turn contacts. We report the cryo-EM structures of the full-length helical NC filaments, double-headed NCs, ring-capped NCs and double-decameric N-RNA rings, as well as those of the alternative assemblies formed by a C-terminally truncated N mutant. In addition, we demonstrate the functional importance of the interface involved in the formation of the double-headed and the ring-capped interactions. We put all these findings in the context of the RSV RNA synthesis machinery and delineate the structural basis for its further investigation.