bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development
Authors: Joglekar Anoushka , Hu Wen , Zhang Bei , Narykov Oleksandr , Diekhans Mark , Balacco Jennifer , Ndhlovu Lishomwa C , Milner Teresa A , Fedrigo Olivier , Jarvis Erich D , Sheynkman Gloria , Korkin Dmitry , Ross M. Elizabeth , Tilgner Hagen U. 
Published: April 2023

AbstractRNA isoforms influence cell identity and function. Until recently, technological limitations prevented a genome-wide appraisal of isoform influence on cell identity in various parts of the brain. Using enhanced long-read single-cell isoform sequencing, we comprehensively analyze RNA isoforms in multiple mouse brain regions, cell subtypes, and developmental timepoints from postnatal day 14 (P14) to adult (P56). For 75% of genes, full-length isoform expression varies along one or more axes of phenotypic origin, underscoring the pervasiveness of isoform regulation across multiple scales. As expected, splicing varies strongly between cell types. However, certain gene classes including neurotransmitter release and reuptake as well as synapse turnover, harbor significant variability in the same cell type across anatomical regions, suggesting differences in network activity may influence cell-type identity. Glial brain-region specificity in isoform expression includes strong poly(A)-site regulation, whereas neurons have stronger TSS regulation. Furthermore, developmental patterns of cell-type specific splicing are especially pronounced in the murine adolescent transition from P21 to P28. The same cell type traced across development shows more isoform variability than across adult anatomical regions, indicating a coordinated modulation of functional programs dictating neural development. As most cell-type specific exons in P56 mouse hippocampus behave similarly in newly generated data from human hippocampi, these principles may be extrapolated to human brain. However, human brains have evolved additional cell-type specificity in splicing, suggesting gain-of-function isoforms. Taken together, we present a detailed single-cell atlas of full-length brain isoform regulation across development and anatomical regions, providing a previously unappreciated degree of isoform variability across multiple scales of the brain.
Genome-wide association study in 404,302 individuals identifies 7 significant loci for reaction time variability
Authors: Wootton Olivia , Shadrin Alexey A. , Mohn Christine , Susser Ezra , Ramesar Raj , Gur Ruben C. , Andreassen Ole A. , Stein Dan J. , Dalvie Shareefa 
Published: April 2023

AbstractReaction time variability (RTV), reflecting fluctuations in response time on cognitive tasks, has been proposed as an endophenotype for many neuropsychiatric disorders. There have been no large-scale genome wide association studies (GWAS) of RTV and little is known about its genetic underpinnings. Here, we used data from the UK Biobank to conduct a GWAS of RTV in participants of white British ancestry (n= 404,302) as well as a trans-ancestry GWAS meta-analysis (n= 44,873) to assess replication. We found 161 genome-wide significant single nucleotide polymorphisms (SNPs) distributed across 7 genomic loci in our discovery GWAS. Functional annotation of the variants implicated genes involved in synaptic function and neural development. The SNP-based heritability (h2SNP) estimate for RTV was 3%. We investigated genetic correlations between RTV and selected neuropsychological traits using linkage disequilibrium score regression, and found significant correlations with several traits, including a positive correlation with schizophrenia. We assessed the predictive ability of a polygenic score (PGS) for RTV, calculated using PRSice and PRS-CS, and found that the RTV-PGS significantly predicted RTV in independent cohorts, but that the generalizability to other ancestry groups was poor. These results identify genetic underpinnings of RTV, and support the use of RTV as an endophenotype for neurological and psychiatric disorders.
Validation of a polygenic risk score for Frailty in the Lothian Birth Cohort and English Longitudinal Study of Ageing
Authors: Flint J P , Welstead M , Cox S R , Russ T C , Marshall A , Luciano M 
Published: April 2023

AbstractFrailty is a complex trait. Twin studies and a high-powered Genome Wide Association Study (GWAS) conducted in the UK Biobank have demonstrated a strong genetic basis of frailty. The present study utilized summary statistics from this GWAS to create and test the predictive power of frailty polygenic risk scores (PRS) in two independent samples – the Lothian Birth Cohort 1936 (LBC1936) and the English Longitudinal Study of Ageing (ELSA) aged 67-84 years. Multiple regression models were built to test the predictive power of frailty PRS at five time points. Frailty PRS significantly predicted frailty at all-time points in LBC1936 and ELSA, explaining 2.1% (β= 0.15, 95%CI, 0.085-0.21) and 1.6% (β= 0.14, 95%CI, 0.10-0.17) of the variance, respectively, at age ∼68/∼70 years (p < 0.001). This work demonstrates that frailty PRS can predict frailty in two independent cohorts, particularly at early ages (∼68/∼70). PRS have the potential to be valuable instruments for identifying those at risk for frailty and could be important for controlling for genetic confounders in epidemiological studies.
Exploring the adoption of digital pathology in clinical settings - Insights from a cross-continent study
Authors: Pinto Daniel Gomes , Bychkov Andrey , Tsuyama Naoko , Fukuoka Junya , Eloy Catarina 
Published: April 2023

ABSTRACTThe last seventy years have been characterized by rapid advancements in computer technology, and the healthcare system has not been immune to this trend. However, anatomic pathology has remained largely an analog discipline. In recent years, this has been changing with the growing adoption of digital pathology, partly driven by the potential of computer-aided diagnosis. As part of an international collaboration, we conducted a comprehensive survey to gain a deeper understanding of the status of digital pathology implementation in Europe and Asia. A total of 127 anatomic pathology laboratories participated in the survey, including 75 from Europe and 52 from Asia, with 72 laboratories having established digital pathology workflow and 55 without digital pathology. Laboratories using digital pathology were thoroughly questioned about their implementation strategies and institutional experiences, including details on equipment, storage, integration with laboratory information system, computer-aided diagnosis, and the costs of going digital. The impact of the digital pathology workflow was also evaluated, focusing on turnaround time, specimen traceability, quality control, and overall satisfaction. Laboratories without access to digital pathology were asked to provide insights into their perceptions of the technology, expectations, barriers to adoption, and potential facilitators. Our findings indicate that while digital pathology is still the future for many, it is already the present for some. This decade may be a time when anatomic pathology finally embraces the digital revolution on a large scale.HIGHLIGHTSLarger labs adopt digital pathology moreFull digital transition is still rare nowadaysMany initial concerns have not materialized after implementationMost non-digital laboratories plan to go digital soon
The effects of a dietary supplement on brain function and structure in Junior A ice hockey players: a prospective randomized trial
Authors: Breuer Logan T. , Fickling Shaun D. , Krause David A. , D’Arcy Ryan C.N. , Frizzell Tory O. , Gendron Tania , Stuart Michael J. 
Published: April 2023

AbstractBackgroundNeurocognitive impairment linked to head impact exposure in otherwise healthy, non-concussed athletes may be associated with adverse long-term outcomes. The primary purpose of this study was to evaluate whether a dietary supplement, SynaquellTM, supports brain function and structure in male Junior A ice hockey players over the course of a season.MethodsPlayers underwent pre-season testing, were randomized into a placebo or dietary supplement group, then were retested after the season. Objective tests included: NeuroCatch®portable evoked potential platform, King-Devick Test of rapid number naming, and blood biomarker assay for neurofilament light chain (NfL).ResultsMultivariate analysis revealed significant differences in neurocognitive changes between groups from pre to postseason after controlling for covariates related to head impact exposure. Post-hoc tests showed significant within-subject differences between groups from pre- to post-season in both N100 latency (p = 0.005) and King-Devick score (p = 0.043). Univariate tests of the NeuroCatch results replicated prior findings of a N400 amplitude decrease (p = 0.017) and N100 latency increase (p = 0.049) in the placebo group, but not in the dietary supplement group.ConclusionsThis prospective, randomized trial showed that, compared to the placebo group, a multi-ingredient dietary supplement significantly affected objective measures of brain function and structure in Junior A ice hockey players from pre- to post-season. Further investigation into the effects of dietary supplementation on the contact athlete’s brain is warranted.
A hybrid CNN-Random Forest algorithm for bacterial spore segmentation and classification in TEM images
Authors: Qamar Saqib , Öberg Rasmus , Malyshev Dmitry , Andersson Magnus 
Published: April 2023

AbstractWe present a new approach to segment and classify bacterial spore layers from Transmission Electron Microscopy (TEM) images using a hybrid Convolutional Neural Network (CNN) and Random Forest (RF) classifier algorithm. This approach utilizes deep learning, with the CNN extracting features from images, and the RF classifier using those features for classification. The proposed model achieved 73% accuracy, 64% precision, 46% sensitivity, and 47% F1-score with test data. Compared to other classifiers such as AdaBoost, XGBoost, and SVM, our proposed model demonstrates greater robustness and higher generalization ability for non-linear segmentation. Our model is also able to identify spores with a damaged core as verified using TEMs of chemically exposed spores. Therefore, the proposed method will be valuable for identifying and characterizing spore features in TEM images, reducing labor-intensive work as well as human bias.
A dirofilariasis mouse model for heartworm preclinical research
Authors: Marriott A E , Dagley J L , Hegde S , Steven A , Fricks C , DiCosty U , Mansour A , Campbell E J , Wilson C M , Gusovsky F , Ward S A , Hong W D , O’Neill P , Moorhead A , McCall S , McCall J W , Taylor M J , Turner J D 
Published: April 2023

ABSTRACTUse of experimental cats and dogs in veterinary heartworm preclinical drug research is increasing. As a potential alternative primaryin vivoheartworm preventative drug screen, we assessed lymphopenic mice with ablation of the interleukin-2/7 common gamma chain (γc) as susceptible to the larval development phase ofD. immitis. Non-obese diabetic (NOD) Severe Combined ImmunoDeficient (SCID)γc-/-(NSG / NXG) mice consistently yielded viableD. immitislarvae at 2-4 weeks post-infection across multiple experiments, different batches of infectious larvae inoculates, different isolates ofD. immitisand at independent laboratories. Mice did not display any overt clinical signs associated with infection up to 4 weeks. Developing larvae were found in subcutaneous and muscle fascia tissues, the natural site of this stage of heartworm in dogs. Larvae retrieved from NSG / NXG mice were mid-L4 stage of development. Compared with 14-dayin vitropropagated larvae,in vivoderived L4 were significantly larger and contained expandedWolbachiaendobacteria titres, determined by QPCR and Fluorescentin situHybridisation (FISH). We established anex vivo6-day L4 paralytic screening system against nematodicidal agents (moxidectin, levamisole) which highlighted discrepancies in relative drug sensitivities in comparison within vitroreared L4D. immitis.We demonstrated effective depletion ofWolbachiaby 70-90% inD. immitisL4 following 2-7 day oralin vivoexposures of NSG / NXG infected mice with doxycycline or the rapid-acting investigational anti-Wolbachiadrug, AWZ1066S. We validated the NSG / NXG mouse model as a filaricide drug screen byin vivotreatments with single injections of moxidectin, which mediated 60-88% reduction in L4 larvae at 14-28 days. Future adoption of the mouse model as a first-line efficacy screen will benefit end-user laboratories conducting research and development of novel heartworm preventatives via increased access, rapid turnaround and reduced costs whilst simultaneously decreasing need for experimental cat or dog use.
Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria
Authors: Alonso-del Valle Aida , Toribio-Celestino Laura , Quirant Anna , Tardio Pi Carles , DelaFuente Javier , Canton Rafael , Rocha Eduardo , Ubeda Carles , Peña-Miller Rafael , San Millan Alvaro 
Published: April 2023

AbstractConjugative plasmids play a key role in the dissemination of antimicrobial resistance (AMR) genes across bacterial pathogens. AMR plasmids are widespread in clinical settings, but their distribution is not random, and certain associations between plasmids and bacterial clones are particularly successful. For example, the globally spread carbapenem resistance plasmid pOXA-48 can use a wide range of enterobacterial species as hosts, but it is usually associated with a small number of specificKlebsiella pneumoniaeclones. These successful associations represent an important threat for hospitalized patients. However, knowledge remains limited about the factors determining AMR plasmid distribution in clinically relevant bacteria. Here, we combinedin vitroandin vivoexperimental approaches to analyze pOXA-48-associated AMR levels and conjugation dynamics in a collection of wild type enterobacterial strains isolated from hospitalized patients. Our results reveal significant variability in these traits across different bacterial hosts, withKlebsiellaspp. strains showing higher pOXA-48-mediated AMR and conjugation frequencies thanEscherichia colistrains. Using experimentally determined parameters, we developed a simple mathematical model to interrogate the contribution of AMR levels and conjugation permissiveness to plasmid distribution in bacterial communities. The simulations revealed that a small subset of clones, combining high AMR levels and conjugation permissiveness, play a critical role in stabilizing the plasmid in different polyclonal microbial communities. These results help to explain the preferential association of plasmid pOXA-48 withK. pneumoniaeclones in clinical settings. More generally, our study reveals that species- and strain-specific variability in plasmid-associated phenotypes shape AMR evolution in clinically relevant bacterial communities.Significance statementConjugative plasmids disseminate AMR genes across bacterial pathogens. Understanding the rules governing plasmid dynamics in bacterial communities is therefore crucial to controlling the global AMR crisis. In this study, we analyzed the dynamics of an AMR plasmid of great clinical relevance, pOXA-48, in a collection of wild type bacteria recovered from hospitalized patients. We reported a high degree of variability in two key plasmid-associated phenotypes, AMR level and conjugation ability, across the collection of clinical bacteria. Using simulations based on the experimental results, we studied how successful associations between AMR plasmids and clinical strains can arise in bacterial communities. Our results revealed that accounting for variability in plasmid-associated phenotypes help to understand the evolution of AMR in clinical settings.
Cross-species communication viaagrcontrols phage susceptibility inStaphylococcus aureus
Authors: Yang Jingxian , Bowring Janine Zara , Krusche Janes , Bejder Benjamin Svejdal , Silva Stephanie Fulaz , Bojer Martin Saxtorph , Grunert Tom , Peschel Andreas , Ingmer Hanne 
Published: April 2023

AbstractBacteria and their viruses (phages) use quorum sensing (QS) systems to coordinate group behavior. InStaphylococcus aureus, QS plays a critical role in the transition from colonization to infection and involves the accumulation of auto-inducing peptides (AIPs). Humans and animals are also colonized by non-aureus staphylococci (NAS) that produce AIPs, many of which inhibitS. aureusQS. We found that QS induction is necessary forS. aureussusceptibility to the lytic phage, Stab20 and that in mixed communities with NAS producing inhibitory AIPs,S. aureusis protected from phage infection. The primary phage receptors inS. aureusare wall teichoic acids (WTA) substituted with α- and/or β-linked N- acetylglucosamine (GlcNAc). We show that QS induction reduces α-GlcNAc substitutions and enables Stab20 infection through binding to β-glycosylated WTA. However, in the presence of inhibitory AIPs or during co-culture with NAS, QS induction and Stab20 infection are impeded. Our results highlight how cross-species communication can significantly impact bacterial susceptibility to phages and may explain occasional failures observed when phages are used as antimicrobials in for example phage therapy.
IS1-related large-scale deletion of chromosomal regions harbouring oxygen-insensitive nitroreductase genenfsBcauses nitrofurantoin heteroresistance inEscherichia coli
Authors: Wan Yu , Sabnis Akshay , Mumin Zaynab , Potterill Isabelle , Jauneikaite Elita , Brown Colin S. , Ellington Matthew J. , Edwards Andrew , Sriskandan Shiranee 
Published: April 2023

AbstractNitrofurantoin is a broad-spectrum first-line antimicrobial used for managing uncomplicated urinary tract infection. Loss-of-function mutations in chromosomal genesnfsA, nfsB, andribEofEscherichia coliare known to reduce nitrofurantoin susceptibility. Here, we report monoclonal nitrofurantoin heteroresistance inE. coliand a novel genetic mechanism associated with this phenomenon.Subpopulations with reduced nitrofurantoin susceptibility in cultures of twoE. coliblood strains were identified using population analysis profiling. Four colonies of each strain growing on agar with 0.5×MIC nitrofurantoin were sub-cultured in broth with 0.5×MIC nitrofurantoin (n=2) or without nitrofurantoin (n=2). Moreover, one colony of each strain growing without nitrofurantoin exposure was selected as a reference for genomic comparison. Whole-genome sequencing of all isolates were conducted on Illumina and Nanopore MinION systems.Both strains had a nitrofurantoin MICs of 64 mg/L. The proportion of cells grown at 0.5×MIC was two and 99 per million, respectively, which is distinct to that of a homogeneously susceptible or resistant isolate. All isolates grown at 0.5×MIC had 11–66 kbp deletions in chromosomal regions harbouringnfsB, and all these deletions were immediately adjacent to IS1-family insertion sequences.Although this study is limited toE. coliand nitrofurantoin, our findings suggest IS1-associated genetic deletion represents a hitherto unrecognised mechanism of heteroresistance that could compromise infection management and impact conventional antimicrobial susceptibility testing.Impact statementNitrofurantoin is widely used for treating and preventing urinary tract infection. Prevalence of nitrofurantoin resistance generally is low inE. coli. Here, we report nitrofurantoin heteroresistance in twoE. coliblood strains and attribute this phenotype to IS1-associated deletion of chromosomal regions harbouring oxygen-insensitive nitroreductase genenfsB. Our discoveries demonstrate a novel genetic mechanism of heteroresistance and suggest detecting nitrofurantoin heteroresistance inE. coliurinary isolates for improving prescribing.Data summaryWhole-genome sequencing reads and genome assemblies generated in this study have been deposited under BioProject PRJEB58678 in the European Nucleotide Archive (ENA). Accession numbers are listed in Supplementary Table 1. Previously generated Illumina whole-genome sequencing reads of parental isolates EC0026B and EC0880B are available under ENA accessions ERR3142418 and ERR3142524, respectively.
Assessing Brain Involvement in Fabry Disease with Deep Learning and the Brain-Age Paradigm
Authors: Montella Alfredo , Tranfa Mario , Scaravilli Alessandra , Barkhof Frederik , Brunetti Arturo , Cole James , Gravina Michela , Marrone Stefano , Riccio Daniele , Riccio Eleonora , Sansone Carlo , Spinelli Letizia , Petracca Maria , Pisani Antonio , Cocozza Sirio , Pontillo Giuseppe 
Published: April 2023

AbstractBackgroundWhile neurological manifestations are core features of Fabry disease (FD), quantitative neuroimaging biomarkers allowing to measure brain involvement are lacking. We used deep learning and the brain-age paradigm to assess whether FD patients’ brains appear older than normal and to validate brain-predicted age difference (brain-PAD) as a possible disease severity biomarker.MethodsMRI scans of FD patients and healthy controls (HC) from a single Institution were retrospectively studied. The Fabry stabilization index (FASTEX) was recorded as a measure of disease severity. Using minimally preprocessed 3D T1-weighted brain scans of healthy subjects from 8 publicly available sources (N=2160; mean age=33y[range 4-86]), we trained a model predicting chronological age based on a DenseNet architecture and used it to generate brain-age predictions in the internal cohort. Within a linear modeling framework, brain-PAD was tested for age/sex-adjusted associations with diagnostic group (FD vs HC), FASTEX score, and both global and voxel-level neuroimaging measures.ResultsWe studied 52 FD patients (40.6±12.6y; 28F) and 58 HC (38.4±13.4y; 28F). The brain-age model achieved accurate out-of-sample performance (mean absolute error=4.01y, R2=0.90). FD patients had significantly higher brain-PAD than HC (estimated marginal means: 3.1vs-0.1, p=0.01). Brain-PAD was associated with FASTEX score (B=0.10, p=0.02), brain parenchymal fraction (B=-153.50, p=0.001), white matter hyperintensities load (B=0.85, p=0.01), and tissue volume reduction throughout the brain.ConclusionsWe demonstrated that FD patients’ brains appear older than normal. Brain-PAD correlates with FD-related multi-organ damage and is influenced by both global brain volume and white matter hyperintensities, offering a comprehensive biomarker of (neurological) disease severity.Summary StatementUsing deep learning and the brain-age paradigm, we found that Fabry disease is associated with older-appearing brains. The gap between brain-predicted and chronological age correlates with multi-organ disease severity, offering a novel quantitative neuroimaging biomarker.Key PointsPatients with Fabry disease show significantly higher brain-predicted age difference values compared to healthy controls (estimated marginal means: 3.1 vs -0.1, p=0.01).Brain-predicted age difference correlates with multi-organ disease severity and is associated with brain parenchymal fraction, white matter hyperintensities load, and tissue volume throughout the brain.Brain-predicted age difference might represent a sensitive quantitative biomarker of brain involvement in Fabry disease, with potentially relevant implications for patient stratification and treatment response monitoring.