bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Imaging Method (FIM-ID) Reveals that Myofibrillogenesis Plays a Major Role in the Mechanically Induced Growth of Skeletal Muscle
Authors: Jorgenson Kent W. , Hibbert Jamie E. , Sayed Ramy K. A. , Lange Anthony N. , Godwin Joshua S. , Mesquita Paulo H. C. , Ruple Bradley A. , McIntosh Mason C. , Kavazis Andreas N. , Roberts Michael D. , Hornberger Troy A. 
Published: September 2023

AbstractAn increase in mechanical loading, such as that which occurs during resistance exercise, induces radial growth of muscle fibers (i.e., an increase in cross-sectional area). Muscle fibers are largely composed of myofibrils, but whether radial growth is mediated by an increase in the size of the myofibrils (i.e., myofibril hypertrophy) and/or the number of myofibrils (i.e., myofibrillogenesis) is not known. Electron microscopy (EM) can provide images with the level of resolution that is needed to address this question, but the acquisition and subsequent analysis of EM images is a time- and cost-intensive process. To overcome this, we developed a novel method for visualizing myofibrils with a standard fluorescence microscope (FIM-ID). Images from FIM-ID have a high degree of resolution and contrast, and these properties enabled us to develop pipelines for automated measurements of myofibril size and number. After extensively validating the automated measurements, we used both mouse and human models of increased mechanical loading to discover that the radial growth of muscle fibers is largely mediated by myofibrillogenesis. Collectively, the outcomes of this study offer insight into a fundamentally important topic in the field of muscle growth and provide future investigators with a time- and cost-effective means to study it.
Engineering heterothallic strains in fission yeast
Authors: García-Ruano Daniel , Hsu Ian , Leray Baptiste , Billard Bénédicte , Liti Gianni , Coudreuse Damien 
Published: September 2023

ABSTRACTIn poor nitrogen conditions, fission yeast cells mate, undergo meiosis and form spores that are resistant to deleterious environments. Natural isolates ofSchizosaccharomyces pombeare homothallic. This allows them to naturally switch between the twoh-andh+mating types with a high frequency, thereby ensuring the presence of both mating partners in a population of cells. However, alteration of the mating type locus can abolish mating type switching or reduce it to a very low frequency. Such heterothallic strains have been isolated and are common in research laboratories due to the simplicity of their use for Mendelian genetics. In addition to the standard laboratory strains, a large collection of naturalS. pombeisolates is now available, representing a powerful resource for investigating the genetic diversity and biology of fission yeast. However, most of these strains are homothallic, and only tedious or mutagenic strategies have been described to obtain heterothallic cells from a homothallic parent. Here, we describe a simple approach to generate heterothallic strains. It takes advantage of an alteration of the mating type locus that was previously identified in a mating type switching-deficient strain and the CRISPR-Cas9 editing tool, allowing for a one-step engineering of heterothallic cells with high efficiency.Take away points-Conventional methods for obtaining heterothallic fission yeast strains are inefficient-We implemented a streamlined genetic editing approach to engineer heterothallism-All fission yeast isolates reported in Jeffares et al. 2015 can be engineered-This method enhances the exploration of genetic diversity in wild fission yeast
Attenuated incubation of ethanol-induced conditioned taste aversion in a model of dependence
Authors: Ramirez Lindsey A , Przybysz Kathryn R , Pitock Joseph R , Starr E Margaret , Yang Hyerim , Glover Elizabeth J 
Published: September 2023

AbstractRationalePreclinical studies report attenuated ethanol-induced conditioned taste aversion (CTA) following chronic ethanol exposure, suggesting that tolerance develops to the aversive properties of ethanol. However, these studies are confounded by pre-exposure to the unconditioned stimulus (US; ethanol), which is well known to hinder conditioning.ObjectivesThis study was designed to determine whether chronic ethanol exposure produces tolerance to the aversive properties of ethanol in the absence of a US pre-exposure confound.MethodsCTA was performed in adult male and female Long-Evans rats by pairing 0.1% ingested saccharin with an intraperitoneal injection of ethanol (1.5 or 2.0 g/kg) or saline. Rats were then rendered ethanol dependent using chronic intermittent ethanol (CIE) vapor exposure. Controls were exposed to room air (AIR). The effect of chronic ethanol on CTA expression and reconditioning were examined following vapor exposure.ResultsPrior to vapor exposure, both sexes developed CTA to a comparable degree with 2.0 g/kg producing greater CTA than 1.5 g/kg ethanol. Following vapor exposure, AIR controls exhibited an increase in CTA magnitude compared to pre-vapor levels. This effect was absent in CIE-exposed rats. These group differences were eliminated upon re-conditioning after vapor exposure.ConclusionsThese data suggest that chronic ethanol does not facilitate tolerance to the aversive properties of ethanol but rather, attenuates incubation of ethanol-induced CTA. Loss of CTA incubation suggests that CIE exposure disrupts circuits encoding aversion.
After the Infection: A Survey of Pathogens and Non-communicable Human Disease
Authors: Lape Michael , Schnell Daniel , Parameswaran Sreeja , Ernst Kevin , O’Connor Shannon , Salomonis Nathan , Martin Lisa J. , Harnett Brett M. , Kottyan Leah C. , Weirauch Matthew T. 
Published: September 2023

AbstractThere are many well-established relationships between pathogens and human disease, but far fewer when focusing on non-communicable diseases (NCDs). We leverage data from The UK Biobank and TriNetX to perform a systematic survey across 20 pathogens and 426 diseases, primarily NCDs. To this end, we assess the association between disease status and infection history proxies. We identify 206 pathogen-disease pairs that replicate in both cohorts. We replicate many established relationships, includingHelicobacter pyloriwith several gastroenterological diseases and connections between Epstein-Barr virus with multiple sclerosis and lupus. Overall, our approach identified evidence of association for 15 pathogens and 96 distinct diseases, including a currently controversial link between human cytomegalovirus (CMV) and ulcerative colitis (UC).We validate this connection through two orthogonal analyses, revealing increased CMV gene expression in UC patients and enrichment for UC genetic risk signal near human genes that have altered expression upon CMV infection. Collectively, these results form a foundation for future investigations into mechanistic roles played by pathogens in NCDs. All results are easily accessible on our website,https://tf.cchmc.org/pathogen-disease.
Comparing the Performance of ChatGPT and GPT-4 versus a Cohort of Medical Students on an Official University of Toronto Undergraduate Medical Education Progress Test
Authors: Meaney Christopher , Huang Ryan S. , Lu Kevin (Jia Qi) , Fischer Adam W. , Leung Fok-Han , Kulasegaram Kulamakan , Tzanetos Katina , Punnett Angela 
Published: September 2023

AbstractBackgroundLarge language model (LLM) based chatbots have recently received broad social uptake; demonstrating remarkable abilities in natural language understanding, natural language generation, dialogue, and logic/reasoning.ObjectiveTo compare the performance of two LLM-based chatbots, versus a cohort of medical students, on a University of Toronto undergraduate medical progress test.MethodsWe report the mean number of correct responses, stratified by year of training/education, for each cohort of undergraduate medical students. We report counts/percentages of correctly answered test questions for each of ChatGPT and GPT-4. We compare the performance of ChatGPT versus GPT-4 using McNemar’s test for dependent proportions. We compare whether the percentage of correctly answered test questions for ChatGPT or GPT-4 fall within/outside the confidence intervals for the mean number of correct responses for each of the cohorts of undergraduate medical education students.ResultsA total of N=1057 University of Toronto undergraduate medical students completed the progress test during the Fall-2022 and Winter-2023 semesters. Student performance improved with increased training/education levels: UME-Year1 mean=36.3%; UME-Year2 mean=44.1%; UME-Year3 mean=52.2%; UME-Year4 mean=58.5%. ChatGPT answered 68/100 (68.0%) questions correctly; whereas, GPT-4 answered 79/100 (79.0%) questions correctly. GPT-4 performance was statistically significantly greater than ChatGPT (P=0.034). GPT-4 performed at a level equivalent to the top performing undergraduate medical student (79/100 questions correctly answered).ConclusionsThis study adds to a growing body of literature demonstrating the remarkable performance of LLM-based chatbots on medical tests. GPT-4 performed at a level comparable to the best performing undergraduate medical student who attempted the progress test in 2022/2023. Future work will investigate the potential application of LLM-chatbots as tools for assisting learners/educators in medical education.
Pre-stroke physical activity matters for functional limitations: A longitudinal case-control study of 12,860 participants
Authors: van Allen Zack , Orsholits Dan , Boisgontier Matthieu P. 
Published: September 2023

ABSTRACTObjectiveIn the chronic phase after a stroke, limitations in activities of daily living (ADLs) and instrumental ADL (IADLs) initially plateau before steadily increasing. The benefits of pre-stroke physical activity on these limitations remain unclear. To clarify this relationship, we examined the effect of physical activity on the long-term evolution of functional limitations in a cohort of stroke survivors and compared it to a cohort of matched stroke-free adults.MethodsLongitudinal data from 2,143 stroke survivors and 10,717 stroke-free adults aged 50 years and older were drawn from a prospective cohort study based on the Survey of Health, Ageing and Retirement in Europe (2004-2022; 8 data collection waves). Physical activity was assessed in the pre-stroke wave. Functional limitations were assessed in the post-stroke waves. Each stroke survivor was matched with 5 stroke-free adults who had similar propensity scores computed on the basis of key covariates, including baseline age, sex, body mass index, limitations in ADL and IADL, chronic conditions and country of residence, before any of the participants from either cohort had experienced a stroke.ResultsResults showed an interaction between stroke status and physical activity on ADL limitations (b = -0.076; 95% CI = -0.142 to -0.011), with the effect of physical activity being stronger in stroke survivors (b = -0.345, 95% CI = -0.438 to -0.252) than in stroke-free adults (b = -0.269, 95% CI = -0.269 to -0.241).ConclusionThe beneficial effect of pre-stroke physical activity on ADL limitations after stroke is stronger than its effect in matched stroke-free adults followed for a similar number of years.ImpactPhysical activity, an intervention within the physical therapist’s scope of practice, is effective in reducing the risk of functional dependence after stroke. Moreover, pre-stroke levels of physical activity can inform the prognosis of functional dependence in stroke survivors.
circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA
Authors: Okholm Trine Line Hauge , Kamstrup Andreas Bjerregaard , Nielsen Morten Muhlig , Hollensen Anne Kruse , Graversgaard Mette Laugesen , Sørensen Matilde Helbo , Kristensen Lasse Sommer , Vang Søren , Park Samuel S. , Yeo Gene W. , Dyrskjøt Lars , Kjems Jørgen , Pedersen Jakob Skou , Damgaard Christian Kroun 
Published: September 2023

AbstractCircular RNAs (circRNAs) represent a class of widespread endogenous RNAs that regulate gene expression and thereby influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses of large genomics datasets and mechanistic cell biological follow-up experiments. Specifically, we use temporal depletion of circHIPK3 or specific RNA binding proteins (RBPs) and identify several perturbed genes by RNA sequencing analyses. Using expression-coupled motif analyses of mRNA expression data from various knockdown experiments, we identify an 11-mer motif within circHIPK3, which is also enriched in genes that become downregulated upon circHIPK3 depletion. By mining eCLIP datasets, we find that the 11-mer motif constitutes a strong binding site for IGF2BP2 and validate this circHIPK3-IGF2BP2 interaction experimentally using RNA-immunoprecipitation and competition assays in bladder cancer cell lines. Our results suggest that circHIPK3 and IGF2BP2 mRNA targets compete for binding. Since the identified 11-mer motif found in circHIPK3 is enriched in upregulated genes following IGF2BP2 knockdown, and since IGF2BP2 depletion conversely globally antagonizes the effect of circHIPK3 knockdown on target genes, our results suggest that circHIPK3 can sequester IGF2BP2 as a competing endogenous RNA (ceRNA), leading to target mRNA stabilization. As an example of a circHIPK3-regulated gene, we focus on theSTAT3mRNA as a specific substrate of IGF2BP2 and validate that manipulation of circHIPK3 regulates IGF2BP2-STAT3mRNA binding and therebySTAT3mRNA levels. However, absolute copy number quantifications demonstrate that IGF2BP2 outnumbers circHIPK3 by orders of magnitude, which is inconsistent with a simple 1:1 ceRNA hypothesis. Instead, we show that circHIPK3 can nucleate multiple copies of IGF2BP2, potentially via phase separation, to produce IGF2BP2 condensates. Finally, we show that circHIPK3 expression correlates with overall survival of patients with bladder cancer. Our results are consistent with a model where relatively few cellular circHIPK3 molecules function as inducers of IGF2BP2 condensation thereby regulating STAT3 and other key factors for cell proliferation and potentially cancer progression.
Skeletal Muscle Mitochondrial Morphology Negatively Affected by Loss of Xin
Authors: Martin Grace , Al-Sajee Dhuha , Gingrich Molly , Chattha Rimsha , Akcan Michael , Monaco Cynthia M.F. , Hughes Megan C. , Perry Christopher G.R. , Rebalka Irena A. , Tarnopolsky Mark A. , Hawke Thomas J. 
Published: September 2023

AbstractAltered mitochondrial structure and function are implicated in the functional decline of skeletal muscle. Numerous cytoskeletal proteins have been reported to affect mitochondrial homeostasis, but this complex network is still being unraveled. Here, we investigated alterations to mitochondrial structure and function in mice lacking the cytoskeletal adapter protein, Xin.Xin deficient (Xin-/-) and wild-type (WT) littermate mice were fed a chow or high-fat diet (HFD; 60% kcal fat) for 8 weeks before high-resolution respirometry, histology, electron microscopy and Western blot analyses of their skeletal muscles were conducted.Immuno-electron microscopy and immunofluorescence staining indicates that Xin is present in the mitochondria and peri-mitochondrial areas, as well as the myoplasm. Intermyofibrillar mitochondria in chow-fed Xin-/- mice were notably different from WT; frequently spanning a whole sarcomere and/or swollen in appearance with abnormal cristae. Succinate Dehydrogenase and Cytochrome Oxidase IV (COX) activity staining indicated greater evidence of mitochondrial enzyme activity in Xin-/- mice. HFD did not result in a difference between cohorts with respect to body mass gains or glucose handling. However, electron microscopy revealed significantly greater mitochondrial density (∼2.1-fold) with evident structural abnormalities (swelling, reduced cristae density) in Xin-/- mice. Complex I and II-supported respiration were not different between groups per mg muscle, but when made relative to mitochondrial density, were significantly lower in Xin-/- muscles. Western blotting of fusion, fission, and autophagy proteins revealed no differences between groups.These results provide the first evidence for a role of Xin in maintaining mitochondrial morphology and function but not in regulating mitochondrial dynamics.
Prediction of Bovine coronavirus immune epitopes using selection and phylogenetic analysis
Authors: Russell Tristan , Lozano Jose Maria , Challinor Cailyn , Barry Gerald 
Published: September 2023

AbstractBovine betacoronavirus(BoCoV) is a pneumoenteric pathogen of cattle, which is closely related to Human coronavirus OC43. Vaccines are administered to protect against diseases caused by BoCoV, but knowledge gaps exist with regard to correlates of protection and the effect of immune evasion on driving evolution. In this study, immune epitopes were predicted for the BoCoV structural proteins including spike and haemagglutinin esterase (HE) and these predictions were supported through targeted gene sequencing of Irish clinical isolates and selective pressure analysis. Increased prevalence of diversifying selection and amino acid changes in some predicted immune epitopes suggests immune escape is selecting for non-synonymous mutations arising in these regions. Selection analysis and sequencing provided increased support for nAb epitopes compared to other predicted immune epitopes suggesting nAbs are an important arm of the immune response to BoCoV. Phylogenetic analysis of spike and HE sequences showed Irish isolates from this study were in the European clade except for one HE sequence that sat in the Asian/American clade, while the spike gene of this sample was in the European clade. Recombination between a European and an Asian/American isolate could give rise to such a sequence and recombination breakpoints that were detected at the 3’ end of HE and 5’ end of spike would produce such a sequence. This study presents evidence showing pressure to evade the nAb response is contributing to BoCoV evolution and for the first time, sequenced an isolate likely derived from a recombination event between European and Asian/American strains.
LinkingGba1E326K mutation to microglia activation and mild age-dependent dopaminergic Neurodegeneration
Authors: Kweon Sin Ho , Ryu Hye Guk , Park Hyeonwoo , Lee Saebom , Kim Namshik , Kwon Seung-Hwan , Ma Shi-Xun , Kim Sangjune , Ko Han Seok 
Published: September 2023

AbstractMutations in theGBA1gene have been identified as a prevalent genetic risk factor for Parkinson’s disease (PD).GBA1mutations impair enzymatic activity, leading to lysosomal dysfunction and elevated levels of α-synuclein (α-syn). While most research has primarily focused on GBA1’s role in promoting synucleinopathy, emerging evidence suggests that neuroinflammation may be a key pathogenic alteration caused by GBA1 deficiency. To examine the molecular mechanism underlying GBA1 deficiency-mediated neuroinflammation, we generatedGba1E326K knock-in (KI) mice using the CRISPR/Cas9 technology, which is linked to an increased risk of PD and dementia with Lewy bodies (DLB). In the ventral midbrain and hippocampus of 24-month-oldGba1E326K KI mice, we found a moderate decline in GBA1 enzymatic activity, a buildup of glucosylceramide, and an increase in microglia density. Furthermore, we observed increased levels of pro-inflammatory cytokines and formation of reactive astrocytes in primary microglia and astrocytes, respectively, cultured fromGba1E326K KI mice following treatment with pathologic α-syn preformed fibrils (PFF). Additionally, the gut inoculation of α-syn PFF inGba1E326K KI mice significantly enhanced the accumulation of Lewy bodies in the dentate gyrus of the hippocampus, accompanied by aggravated neuroinflammation and exacerbated non-motor symptoms. This research significantly enhances our understanding of theGba1E326K mutation’s involvement in neuroinflammation and the cell-to-cell transmission of pathogenic α-syn in the brain, thereby opening new therapeutic avenues.
Involvement of remote regions in sustained, but not transient, epileptic activities in the kainate mouse model of temporal lobe epilepsy
Authors: Padmasola Guru Prasad , Friscourt Fabien , Schaller Karl , Michel Christoph M , Sheybani Laurent , Quairiaux Charles 
Published: September 2023

AbstractAnimal and human studies have shown that the seizure-generating region is vastly dependent on distant neuronal hubs that can decrease duration and propagation of ongoing seizures. However, we still lack a comprehensive understanding of the impact of distant brain areas on specific interictal or ictal epileptic activities (e.g., isolated spikes, spike trains, seizures). Such knowledge is critically needed since all kinds of epileptic activities are not equivalent in terms of clinical expression and impact on the progression of the disease. We used surface, high-density EEG and multisite intracortical recordings, combined with pharmacological silencing of specific brain regions in the well-known kainate mouse model of temporal lobe epilepsy. We tested the impact of selective regional silencing on the generation of epileptic activities within a continuum ranging from very transient to more sustained and long-lasting discharges reminiscent of seizures. Silencing the contralateral hippocampus completely suppresses sustained ictal activities in the focus, as efficiently as silencing the focus itself, but while focus silencing abolishes all focal activities, contralateral silencing fails to control transient spikes. In parallel, we observed that sustained epileptic discharges in the focus are preceded by contralateral firing and more strongly phase locked to bi-hippocampal delta/theta oscillations than transient spiking activities, reinforcing the presumed dominant role of the contralateral hippocampus in promoting long-lasting, but not transient, epileptic activities. Altogether, our work provides suggestive evidence that the contralateral hippocampus is necessary for the interictal-to ictal-state transition and proposes that cross-talk between contralateral neuronal activity and ipsilateral delta/theta oscillation could be a candidate mechanism underlying the progression from short to long-lasting epileptic activities.Key PointsWe study how regions remote from the focus influence epileptic activities in the kainate mouse model of temporal lobe epilepsy.The contralateral hippocampus plays a decisive role in the initiation of sustained epileptic activitiesIntegration of contralateral activities and bi-hippocampal delta/theta oscillations precedes focal paroxysmal activitiesWe propose that a large-scale epileptic network might be necessary for the transition from interictal to ictal states
A collection of diverse bacteriophages for biocontrol of ESBL- and AmpC-β-lactamase-producingE. coli
Authors: Vitt Amira R. , Sørensen Anders Nørgaard , Bojer Martin S. , Bortolaia Valeria , Sørensen Martine C. Holst , Brøndsted Lone 
Published: September 2023

SUMMARYNovel solutions are needed to reduce the risk of transmission of extended spectrum β-lactamase and AmpC β-lactamase producingEscherichia coli(ESBL/AmpCE. coli) in livestock to humans. Since phages are promising biocontrol agents, we established a collection of 28 phages against ESBL/AmpCE. coliand showed by whole genome sequencing that all phages were unique and could be assigned to 15 different genera. Host range analysis showed that 82% of 198 strains, representing the genetic diversity of ESBL/AmpCE. coli, were sensitive to at least one phage. Identifying receptors used for initial binding experimentally as well asin silicopredictions, allowed us to combine phages into two different cocktails with broad host range targeting diverse receptors. These phage cocktails inhibit growth and kill ESBL/AmpCE. coli in vitro, thus suggesting the potential of phages as promising biocontrol agents.HIGHLIGHTS28 unique phages infecting ESBL/AmpCE. coliwere isolated and characterizedBroad host range phages targeting different receptors were used to compose phage cocktailsPhage cocktails efficiently inhibit growth of ESBL/AmpCE. coli in vitro