bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model
Authors: Richie Tanner G. , Heeren Leah , Kamke Abigail , Pogranichniy Sophia , Monk Kourtney , Summers Trey , Wiechman Hallie , Ran Qinghong , Sarkar Soumyadev , Plattner Brandon L. , Lee Sonny T. M. 
Published: October 2022

SummaryMembers of the Enterobacteriaceae family includingEscherichia coliare associated with persistent gut inflammation during disorders like inflammatory bowel disease. This is due to rapid microbial colonization during dysbiosis combined with pathogenic tendencies. We characterized the dysbiotic gut community, defined potential functional pathways, and investigated crosstalk between host gene expression and microbial detections in an intestinal inflammation murine model. Members of Enterobacteriaceae family and theEnterococcusgenus were highly detected in dysbiotic mice. These metagenome assembled genomes (MAGs) contained several virulence factors and metabolic pathways necessary to drive perpetual inflammation. Two Enterobacteriaceae MAGs with L-cysteine and L-taurine dioxygenases were strongly correlated with upregulation of the host gene CSAD, responsible for cysteine metabolism. Suggesting these bacteria compete with the host to utilize essential amino acids. We observed that bacterial isolates from dysbiotic mice displayed increased growth rates supplemented with L-cysteine, confirming that these microbes can utilize host nutrients to sustain inflammation.In BriefInflammatory bowel disease is associated with an increase in Enterobacteriaceae andEnterococcusspecies, however the mechanisms are unclear. Richieet al. show that these bacterial populations use sulfur metabolism and tolerate host-derived immune-response, to drive host inflammation and fuel growth in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize these essential host nutrients.HighlightsMice receiving native microbial FMT showed lower colon inflammation scores, higher microbial diversity, detections and gene expression similar to control mice.Dysbiotic mice displayed increased colon inflammation, higher detection of potential pathogenic MAGs, and upregulation of cysteine dioxygenase and other inflammation response genesMAGs assigned toEnterococcusand Enterobacteriaceae species were more frequently detected in dysbiotic mice, while almost absent in mice receiving FMT or control mice, they also contain several virulence factors and antibiotic resistance genes.These MAGs also display potential functions of utilizing host products and nutrients including nitrate, cysteine, and taurine to further fuel their growth and metabolism, which results in persistent host intestinal inflammation.Isolates in the Enterobacteriaceae family from dysbiotic mice utilize L-cysteine for growth, whereas isolates from FMT and control mice show no significant difference, indicating these bacteria can utilize the host derived cysteine.
Human hippocampal ripples signal encoding of episodic memories
Authors: Sakon John J. , Halpern David J. , Schonhaut Daniel R. , Kahana Michael J. 
Published: October 2022

AbstractRecent human electrophysiology work has uncovered the presence of high frequency oscillatory events, termed ripples, during awake behavior. This prior work focuses on ripples in the medial temporal lobe (MTL) during memory retrieval. Few studies, however, investigate ripples during item encoding. Many studies have found neural activity during encoding that predicts later recall, termed subsequent memory effects (SMEs), but it is unclear if ripples during encoding also predict subsequent recall. Detecting ripples in 116 neurosurgical participants (n = 61 male) performing an episodic memory task, we find insignificant ripple SMEs in any MTL region, even as these regions exhibit robust high frequency activity (HFA) SMEs. Instead, hippocampal ripples increase during encoding of items leading to recall of temporally or semantically associated items, a phenomenon known as clustering. This subsequent clustering effect (SCE) arises specifically when hippocampal ripples occur during both encoding and retrieval, suggesting that ripples mediate the encoding and future reinstatement of episodic memories.
Polycomb Repressive Complex 1 subunit Cbx4 positively regulates effector responses in CD8 T cells
Authors: Melo G.A. , Xu T. , Calôba C. , Schutte A. , Brum G. , Passos T.O. , Higa L. , Gonçalves A. , Tanuri A. , Viola J.P.B. , Werneck M.B.F. , Nakaya H.I. , Pipkin M.E. , Martinez G.J. , Pereira R.M 
Published: October 2022

AbstractCD8 T cell differentiation is controlled by the crosstalk of various transcription factors and epigenetic modulators. Uncovering the different players in regulating this process is fundamental to improving immunotherapy and designing novel therapeutic approaches. Here, we show that Polycomb Repressive Complex (PRC)1 subunit Chromobox (Cbx)4 favors differentiation to effector CD8 T cells. Cbx4 deficiency in CD8 T cells induced transcriptional signature and phenotype of memory cells, increasing the formation of memory population during acute viral infection. It has been previously shown that besides chromodomain-mediated binding to H3K27me3, Cbx4 function as a SUMO E3 ligase in a SUMO interacting motifs (SIM)-dependent way. The overexpression of Cbx4 mutants in distinct domains showed that this protein regulates CTL differentiation primarily in a SIM-dependent way and partially through its chromodomain. Our data revealed a novel role of a Polycomb group protein Cbx4 controlling CD8 T lymphocyte differentiation and indicates the SUMOylation process as a key molecular mechanism connected to chromatin modification in this process.SummaryUnderstanding the epigenetic control of CTL differentiation is critical for the manipulation of these cells in immunotherapy protocols. This article demonstrates a novel role for Cbx4, a Polycomb-group protein, in supporting CD8 T cell commitment to an effector cell phenotype.
Reconstructing Monosynaptic Connectivity fromin vivoSpike Trains Using Deep Domain-Adaptive Matching
Authors: Sheng Kaiwen , Zhang Shanghang , Zhang Shenjian , He Yutao , Beau Maxime , Qu Peng , Liu Xiaofei , Zhang Youhui , Ma Lei , Du Kai 
Published: October 2022

AbstractInferring the monosynaptic connectivity of neural circuits fromin vivoexperimental data is essential for understanding the neural architecture that underpins behavior and cognition. However, advanced machine learning (ML) methods, especially deep learning, face significant challenges becausein vivoobservation is limited and incomplete, making it impractical to obtain ground-truth labeling. As a result, researchers typically rely on synthetic data generated by biophysical neural models for initial training. However, this reliance introduces the well-known “model mismatch” problem, whereby synthetic neural dynamics do not accurately reflect the complexity of real neural activity. To address these challenges, we introduce DeepDAM (Deep Domain Adaptive Matching), a flexible and robust framework that combines cutting-edge ML techniques with biophysical modeling. DeepDAM utilizes both synthetic data and unlabeledin vivorecordings to fine-tune deep neural networks (DNNs), so that the feature space of the DNNs is adaptively aligned with real neural dynamics, thus effectively mitigating the model mismatch problem and dramatically improving inference performance. We validated DeepDAM using extracellular recordings in the hippocampal CA1 region of freely behaving mice. Surprisingly, the framework achieved a Matthews correlation coefficient of 0.97–1.0 for monosynaptic connectivity inference, significantly outperforming existing methods (∼0.6–0.7). Additionally, our framework demonstrates robust adaptability to diverse experimental conditions and a broad range of neural properties and scales, including inference of single-neuron biophysics, synaptic dynamics, and microcircuit dynamics in multipleex vivoscenarios. This work marks a significant step towards the accurate and comprehensive reconstruction of functional mammalian brains by integrating data-driven ML techniques with first-principles insights.
A novel therapeutic approach of ultrasound stimulation to restore forelimb functions following cervical cord injury in rats
Authors: Ahmed Rakib Uddin , Alam Monzurul , Li Shuai , Palanisamy Poornima , Zhong Hui , Zheng Yong-Ping 
Published: October 2022

AbstractLow-intensity pulsed ultrasound (LIPUS) stimulation has shown promising results in neurorehabilitation following a traumatic injury in brain and peripheral nerves. However, the effects of LIPUS stimulation in the injured neural circuit after spinal cord injury (SCI) are still unknown. We investigated the effects of LIPUS on forelimb functions in chronic cervical cord injured rats with and without a serotonergic agonist drug, Buspirone treatment. Twenty-six rats were trained for forelimb reaching and grasping followed by C4 dorsal funiculi crush injury. To deliver LIPUS, a silicon-coated ultrasound disc was implanted above the cervical cord and EMG electrodes were implanted into forelimb muscles. In two cohorts (LIPUS and LIPUS + Buspirone) rats were tested pre-, with- and post-ultrasound stimulation. In LIPUS group rats, fore-limb reaching and grasping success rates first increased and then dropped after 3 weeks while for combination of drug and LIPUS stimulation the score continued to increase. Furthermore, LIPUS stimulation alone did not result in any significant improvement of grip strength compared to the control and combined groups. The findings of this study indicated the potential of LIPUS in SCI recovery and offer a future research direction of a new neuromodulation method.
Optic radiations representing different eccentricities age differently
Authors: Kruper John , Benson Noah C. , Caffarra Sendy , Owen Julia , Wu Yue , Lee Aaron Y. , Lee Cecilia S. , Yeatman Jason , Rokem Ariel 
Published: October 2022

AbstractThe white matter pathways that carry information from the foveal, macular, and peripheral visual fields have distinct biological properties. The optic radiations (OR) carry foveal and peripheral information from the thalamus to the primary visual cortex (V1) through adjacent but separate pathways in the white matter. Here, we perform white matter tractometry using pyAFQ 1 on a large sample of diffusion MRI (dMRI) data from the UK Biobank dataset (UKBB; N=6021; age 45-81). We use pyAFQ to characterize white matter tissue properties in parts of the OR that transmit information about the foveal, macular, and peripheral visual fields, and to characterize the changes in these tissue properties with age. We find that (1) independent of age there is higher fractional anisotropy, lower mean diffusivity, and higher mean kurtosis in the foveal and macular OR than in peripheral OR, consistent with denser, more organized nerve fiber populations in foveal/parafoveal pathways, and (2) age is associated with increased diffusivity and decreased anisotropy and kurtosis, consistent with decreased density and tissue organization with adulthood aging. However, anisotropy in foveal OR decreases faster with age than in peripheral OR, while diffusivity increases faster in peripheral OR, suggesting foveal/peri-foveal OR and peripheral OR differ in how they age.
The impact of elevated aestivation temperatures on the behaviour of Bogong Moths (Agrotis infusa)
Authors: Lownds Rose M , Turbill Christopher , White Thomas E , Umbers Kate DL 
Published: October 2022

AbstractBogong moths are an iconic Australian insect that migrates annually in spring from low elevation locations in southern and eastern Australia to the Australian Alps where they aestivate during summer. As summer ends they make their return journey to the breeding grounds where they mate, lay eggs and die. Given the moth’s extreme behaviour in seeking out cool alpine habitat and with the knowledge that average temperatures at their aestivation sites are rising because of climate change, we assessed whether increased temperatures affect Bogong moth activity during aestivation. Our first hypothesis was that moth activity would be affected by temperature, and we found that moths were more active at higher temperatures, especially during the day, with near-constant activity at 15 °C at all times of day. Our second hypothesis was that moth mass would be different after aestivating at different temperatures for a week due to dehydration or consumption of body energy reserves. We found that moth wet mass loss increased with increasing temperature, but found no difference in dry mass among temperature treatments. Overall, our results suggest that Bogong moth activity will increase with increasing temperatures at their aestivation sites. The impact of warming on the success of individuals to complete their aestivation and journey back to their lowlands to breed should be investigated as a matter of priority to better understand the impact of changes in aestivation behaviour on population dynamics.
Hearing the World Differently: Examining Predictive Coding Accounts of Autism Using MEG
Authors: Rapaport Hannah , Pellieano Elizabeth , Seymour Robert A. , Benikos Nicholas , He Wei , Sun Yanan , Brock Jon , Sowman Paul F. 
Published: October 2022

AbstractPredictive coding accounts of autism suggest that autistic perception is characterised by divergent precision weighting. The precise nature of this divergence, however, is debated. Here, we sought to disentangle competing predictive coding accounts of autism by testing them at a neural level. To this end, we used paediatric magnetoencephalography to record the auditory evoked fields of 10 young autistic children (M = 6.2 years, range = 4.2– 8.6) and 63 neurotypical children (M = 6.1 years, range = 3.0– 9.8) as they listened to a roving auditory oddball paradigm. For each participant, we subtracted the evoked responses to the ‘standard’ from the ‘deviant’ pure tones to calculate the mismatch field ‘MMF’: an electrophysiological component that is widely interpreted as a neural signature of predictive coding. We found no significant differences between the two groups’ MMF amplitudes, p > .05. An exploratory analysis indicated larger MMF amplitudes in most of the autistic children compared to their average-age-matched neurotypical counterparts, p < .05. We interpret these findings as preliminary evidence in support of the ‘inflexibly high prior and sensory precision’ account, and against the ‘inflexibly low prior-relative-to-sensory precision’ accounts of autistic perception.HighlightsWe used paediatric MEG to compare autistic and neurotypical MMFs amplitudes.Exploratory case-cohort analyses revealed mostly larger MMFs in autistic cases.Larger MMFs support the notion of precise, inflexible prediction errors in autism.
Simple scaling laws control the genetic architectures of human complex traits
Authors: Simons Yuval B. , Mostafavi Hakhamanesh , Smith Courtney J. , Pritchard Jonathan K. , Sella Guy 
Published: October 2022

AbstractGenome-wide association studies have revealed that the genetic architectures of complex traits vary widely, including in terms of the numbers, effect sizes, and allele frequencies of significant hits. However, at present we lack a principled way of understanding the similarities and differences among traits. Here, we describe a probabilistic model that combines mutation, drift, and stabilizing selection at individual sites with a genome-scale model of phenotypic variation. In this model, the architecture of a trait arises from the distribution of selection coefficients of mutations and from two scaling parameters. We fit this model for 95 diverse, highly polygenic quantitative traits from the UK Biobank. Notably, we infer similar distributions of selection coefficients across all these traits. This shared distribution implies that differences in architectures of highly polygenic traits arise mainly from the two scaling parameters: the mutational target size and heritability per site, which vary by orders of magnitude across traits. When these two scale factors are accounted for, the architectures of all 95 traits are nearly identical.
Anesthesia-related brain microstructure modulations detected by diffusion MRI
Authors: Lindhardt Thomas Beck , Østergaard Leif , Liang Zhifeng , Hansen Brian 
Published: October 2022

AbstractBrain clearance has been found to be greatly enhanced during sleep and anesthesia. Studies using optical microscopy have attributed this to an anesthesia-related expansion of the brain’s extra-cellular space. These results, however, have been based on invasive experiments with a limited field of view. Here, we employ diffusion kurtosis magnetic resonance imaging to assess brain microstructure in the awake and anesthetized mouse brain. We find both mean diffusivity and mean kurtosis to be significantly decreased in the anesthetized mouse brain compared to the awake state. This effect is observed in both gray matter and white matter. Our findings are consistent with the reports of brain ECS volume increase in sleep and anesthesia. Based on simple simulations, we discuss how an ECS volume increase (cell shrinkage) during sleep and anesthesia can coexist with other aspects of brain physiology. Our study demonstrates that diffusion kurtosis MRI can be used in the study of the glymphatic system. Importantly, our study shows an overlooked effect of anesthesia on brain microstructure which is relevant to preclinical MRI as a whole.
From Genomics to Integrative Taxonomy? The Case Study of Pocillopora Corals
Authors: Oury Nicolas , Noël Cyril , Mona Stefano , Aurelle Didier , Magalon Helene 
Published: October 2022

AbstractWith the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data due to the small number of currently available markers, coupled with difficulties in inferring gene trees and morphological incongruences, encrypts species boundaries, thereby blurring the study and conservation of these organisms. Yet, can genomics alone be used to delimit species in an integrative taxonomic context? Here, focusing on the coral genus Pocillopora, which plays key roles in Indo-Pacific reef ecosystems but has challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNPs) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to previous genetic evidences, as well as to evidences based on morphology, biogeography and symbiosis. Genomics allowed to delimit 21 species hypotheses where only seven are currently recognised based on current taxonomy. Moreover, 13 species were strongly supported by all approaches, either confirming their currently recognised species status, or supporting the presence of new species that need to be formally described. Some of the other genomic species hypotheses were supported by biogeographic or symbiosis evidences, but additional investigations are needed to state on their species status. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species limits, (2) the need to identify molecularly species prior to their study, as morphology can blur species identification on the field, (3) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, and (4) the need for a taxonomical revision in the Pocillopora genus. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora species limits and will ultimately provide helpful insights for the conservation of the species from this scleractinian genus. [biogeography; cryptic species delimitation; Indo-Pacific; microsatellites; morphology; phylogenetics; single-nucleotide polymorphism (SNP); Symbiodiniaceae]
Predicting the temperature-driven development of stage-structured insect populations with a Bayesian hierarchical model
Authors: Studens Kala , Bolker Ben , Candau Jean-Noel 
Published: October 2022

AbstractThe management of forest pests relies on an accurate understanding of the species’ phenology. Thermal performance curves (TPCs) have traditionally been used to model insect phenology; many such models have been proposed and fitted to data from both wild and laboratory-reared populations, most of which have used maximum likelihood estimation (MLE). Analyses typically present point estimates of parameters with confidence intervals, but estimates of the correlations among TPC parameters are rarely provided. Neglecting aspects of model uncertainty such as correlation among parameters may lead to incorrect confidence intervals of predictions. This paper implements a Bayesian hierarchical model of insect phenology incorporating individual variation, quadratic variation in development rates across insects’ larval stages, and non-parametric adjustment terms that allow for deviations from a parametric TPC. We use Hamiltonian Monte Carlo (HMC) for estimation; the model is fitted to a laboratory-reared spruce budworm population as a case study. We assessed the accuracy of the model using stratified, 10-fold cross-validation. Using the posterior samples, we found prediction intervals for spruce budworm development for a given year.
Epigenetics of post-operative delirium: A genome-wide DNA methylation study of neurosurgery patients
Authors: Yamanashi Takehiko , Crutchley Kaitlyn J. , Wahba Nadia E. , Nagao Takaaki , Marra Pedro S. , Akers Cade C. , Sullivan Eleanor J. , Iwata Masaaki , Howard Mathew A , Cho Hyunkeun R. , Kawasaki Hiroto , Hughes Christopher G. , Pandharipande Pratik P. , Hefti Marco M. , Shinozaki Gen 
Published: October 2022

AbstractAimsThere is no previous study demonstrating the differences of genome-wide DNA methylation (DNAm) profiles between patients with and without postoperative delirium (POD). We aimed to discover epigenetic (DNAm) markers that are associated with POD in blood obtained from patients before and after neurosurgery.MethodsPre- and post-surgical blood DNA samples from 37 patients, including 10 POD cases, were analyzed using the Illumina EPIC array genome-wide platform. We examined DNAm differences in blood from patients with and without POD. Enrichment analysis with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes terms were also conducted.ResultsWhen POD cases were tested for DNAm change before and after surgery, enrichment analyses showed many relevant signals with statistical significance in immune response related-pathways and inflammatory cytokine related-pathways such as “cellular response to cytokine stimulus”, “regulation of immune system process”, “regulation of cell activation”, and “regulation of cytokine production”. Furthermore, after excluding the potential effect of common factors related to surgery and anesthesia between POD cases and non-POD controls, the enrichment analyses showed significant signals such as “immune response” and “T cell activation”, which are same pathways previously identified from an independent non-surgical inpatient cohort. Conclusions: Our first genome-wide DNAm investigation of POD showed promising signals related to immune response, inflammatory response and other relevant signals considered to be associated with delirium pathophysiology. Our data supports the hypothesis that epigenetics are playing an important role in pathophysiological mechanism of delirium and suggest the potential usefulness of epigenetics based biomarker of POD.