bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive double-mutant analysis of theBacillus subtilisenvelope using double-CRISPRi
Authors: Koo Byoung-Mo , Todor Horia , Sun Jiawei , van Gestel Jordi , Hawkins John S. , Hearne Cameron C. , Banta Amy B. , Huang Kerwyn Casey , Peters Jason M. , Gross Carol A. 
Published: August 2024

SUMMARYUnderstanding bacterial gene function remains a major biological challenge. Double-mutant genetic interaction (GI) analysis addresses this challenge by uncovering the functional partners of targeted genes, allowing us to associate genes of unknown function with novel pathways and unravel connections between well-studied pathways, but is difficult to implement at the genome-scale. Here, we develop and use double-CRISPRi to systematically quantify genetic interactions at scale in theBacillus subtilisenvelope, including essential genes. We discover > 1000 known and novel genetic interactions. Our analysis pipeline and experimental follow-ups reveal the distinct roles of paralogous genes such as themreBandmblactin homologs, and identify new genes involved in the well-studied process of cell division. Overall, our study provides valuable insights into gene function and demonstrates the utility of double-CRISPRi for high-throughput dissection of bacterial gene networks, providing a blueprint for future studies in diverse bacterial species.
The Changing Immune Landscape of Innate-like T Cells and Innate Cells Throughout Life
Authors: Taheri Marziyeh , Menne Christopher , Anderson Jeremy , Li Shuo , Berzins Stuart P , Licciardi Paul V , Ashhurst Thomas M , Jalali Sedigheh , Pellicci Daniel G 
Published: August 2024

ABSTRACTSpectral flow cytometry is an advanced immunological tool that enables comprehensive analysis of the immune system by simultaneously comparing innate and adaptive immune cells. Here, using a 40-colour antibody panel we advance our knowledge of innate and innate-like T cells by investigating chemokine receptors, activation and maturation markers not usually assessed on these populations and examine age-related effects to these immune cell subsets. We characterised phenotypic changes of peripheral blood mononuclear cells (PBMC) in three age groups: newborn (cord blood), adults aged 20-30 years, and adults aged 70-80 years, focusing on innate-like T cells and innate cells, including MAIT cells, NKT cells, γδ T cells, ILCs, and Natural Killer (NK) cells. We identify subsets of double-negative (DN) T cells (CD4-CD8-) and CD161+T cells that increase in an age-related manner and exhibit a phenotype similar to innate-like T cells, MAIT cells and γδ T cells. Innate-like T cell subsets express similar patterns of the chemokine receptors and maturation markers CCR4, CCR6, CD27, CD38, CD57 and CD45RA, and resemble memory subsets of conventional CD4+T cells and CD8+T cells. We could detect ILCs in all age ranges, although the frequency of ILC1, ILC2, and ILC3 subsets decreased with age. Notably, we identify the NK maturation marker, CD57, as a universal marker that defines ageing populations of innate and adaptive immune cells. This study enhances our understanding of the ontogeny of human immune cells, highlighting significant age-related changes in the frequency and phenotype of immune cells.
Development of the FitBack online platform: enhancing global child fitness assessment, health-related interpretation, and surveillance
Authors: Sorić Maroje , Morrison Shawnda A. , Ortega Francisco B. , Carraro Attilio , Csányi Tamás , Leskošek Bojan , Mäestu Jarek , Radisavljević-Janić Snežana , Sardinha Luís B. , Scheuer Claude , Starc Gregor , Tammelin Tuija H. , Jurak Gregor 
Published: August 2024

ABSTRACTIntroductionPhysical fitness is an important indicator of health in children. Accurately monitoring child and adolescent physical fitness is critical when designing effective public health interventions and strategies. This article aims to provide an overview of the FitBack platform and the health-related criteria that support the reporting system.MethodsFour methodological phases were used to create the FitBack platform. First, a review of existing European fitness databases was conducted to identify common fitness tests and methodologies within a European framework. Second, investigators collated data to create European-level fitness norms, health-related criteria, and health-oriented educational resources dedicated to improving child fitness levels. Third, guidance on how to create one’s own fitness monitoring and surveillance system was created based on good practice examples. The FitBack platform was then piloted and launched based on data received from stakeholders who responded to ≥2 rounds of consultation dialogues.ResultsThe final version of online platform, with special focus on newly developed Fitback health-related fitness criteria, are communicated herein.DiscussionThe FitBack web platform is a first-step towards creating a standardised, person-centred, multi-national fitness surveillance system for children, bridging existing gaps between European political recommendations, individual member states, and harmonious cooperation between sectors. This article also provided the detailed age- and sex-specific health-related fitness cut-points that are used by the FitBack platform, and that could be useful for researchers, practitioners as well as fitness monitoring systems.
Linking Adiponectin Gene Variants (+45T>G and +276G>T) to Adipokine Levels and Metabolic Syndrome in a North Indian Adult Women
Authors: Gupta Abhishek , Singh Arun Kumar , Gupta Priyanka , Gupta Vani 
Published: August 2024

AbstractBackgroundAdiponectin, an adipocyte-derived adipokine, is often downregulated in obesity-related disorders. This study aimed to explore the association between adiponectin gene variants (+45T>G, rs2241766, and +276G>T, rs1501299) and circulating adipokine levels as well as metabolic syndrome in North Indian adult women.MethodsWe genotyped single nucleotide polymorphisms (SNPs) in 541 adult women, comprising 269 with metabolic syndrome (MetS) according to NCEP-ATP III criteria and 272 without MetS (wMetS; control). We assessed circulating levels of adiponectin, leptin, lipid profile, glucose, insulin, and HOMA-IR.ResultsSignificant differences (p<0.01) were observed in circulating adipokines (adiponectin and leptin), lipid profile, glucose, insulin, HOMA-IR, and waist-to-hip ratio (WHR) between wMetS and MetS women. The frequency of the combined mutant genotype (TG+GG) at +45T>G was significantly lower (p=0.017) in MetS women, while the mutant G allele was higher (p=0.008) compared to the wild type. For the +276G>T variant, the frequency of the mutant T allele was significantly lower (p=0.027) in MetS women compared to wMetS women. The mutant genotypes GG of +45T>G and TT of +276G>T were significantly associated with lower adiponectin levels, higher leptin levels, and increased HOMA-IR (all p<0.001) in MetS women.ConclusionsThe findings suggest that adiponectin gene variants (+45T>G and +276G>T), along with reduced adiponectin levels and elevated HOMA-IR, may contribute significantly to the development of metabolic syndrome.
Clinical validation of RNA sequencing for Mendelian disorder diagnostics
Authors: Zhao Sen , Macakova Kristina , Sinson Jefferson C. , Dai Hongzheng , Rosenfeld Jill , Zapata Gladys E. , Li Shenglan , Ward Patricia , Wang Christiana , Qu Chunjing , Maywald Becky , Network Undiagnosed Diseases , Lee Brendan , Eng Christine , Liu Pengfei 
Published: August 2024

SummaryDespite rapid advancements in clinical sequencing, over half of diagnostic evaluations still lack definitive results. RNA-seq has shown promise in research settings for bridging this gap by providing essential functional data for accurate interpretation of diagnostic sequencing results. However, despite advanced research pipelines, clinical translation of diagnostic RNA-seq has not yet been realized. We have developed and validated a clinical diagnostic RNA-seq test in a CLIA laboratory for individuals with suspected genetic disorders who have existing or concurrent comprehensive DNA diagnostic testing. This diagnostic RNA-seq test processes patient RNA samples from fibroblasts or blood and derives clinical interpretations based on the analytical detection of outliers in gene expressions and splicing patterns. The clinical validation involves 150 samples, including benchmark, negative, and positive samples. We developed provisional expression and splicing benchmarks using short-read and long-read RNA-seq data from the HG002 lymphoblastoid sample produced by the Genome in a Bottle Consortium. Our validation data achieved analytical sensitivity and specificity higher than 99% against the benchmarks. For clinical validation, we first established reference ranges for each gene and junction based on expression distributions from our control data. We then evaluated the clinical performance of our outlier-based pipeline using positive samples with previously identified diagnostic findings from the Undiagnosed Diseases Network project. Our pipeline identified 19 of 20 positive findings in both fibroblast and blood samples and highlighted the limitations of the test. Our study provides a paradigm and necessary resources for independent laboratories to validate a clinical RNA-seq test.
The level of HAND1 controls the specification of multipotent cardiac and extraembryonic progenitors
Authors: Lynch Adam T , Phillips Naomi , Douglas Megan , Dorgnach Marta , Lin I-Hsuan , Adamson Antony D , Darieva Zoulfia , Whittle Jessica , Hanley Neil A , Bobola Nicoletta , Birket Matthew J 
Published: August 2024

SummaryDiverse sets of progenitors contribute to the development of the embryonic heart, but the mechanisms of their specification have remained elusive. Here, using a human pluripotent stem cell (hPSC) model, we deciphered cardiac and non-cardiac lineage trajectories in differentiation and identified transcription factors underpinning cell specification, identity and function. We discovered a concentration-dependent, fate determining function in mesodermal progenitors for the basic helix-loop-helix transcription factor HAND1 and uncovered its gene regulatory network. At low level, HAND1 directs differentiation towards multipotent juxta-cardiac field progenitors able to make cardiomyocytes and epicardial cells, whereas at high level it promotes the development of extraembryonic mesoderm. Importantly, HAND1-low progenitors can be propagated in their multipotent state. This detailed mechanistic insight into human development will accelerate the delivery of effective disease modelling, including for congenital heart disease, and cell therapy-based regenerative medicine.
IdentifiHR: predicting homologous recombination deficiency in high-grade serous ovarian carcinoma using gene expression
Authors: Weir Ashley L. , Lee Samuel C. , Li Mengbo , Tan Chin Wee , Ramus Susan J. , Davidson Nadia M. 
Published: August 2024

AbstractBackgroundApproximately half of all high-grade serous ovarian carcinomas (HGSCs) have a therapeutically targetable defect in the homologous recombination (HR) DNA repair mechanism. While there are genomic and transcriptomic methods, developed for other cancer types, to identify HR deficient (HRD) samples, there are no gene expression-based tools to predict HR repair status in HGSC specifically. We have built the first HGSC-specific model to predict HR repair status using gene expression.MethodsWe separated The Cancer Genome Atlas (TCGA) cohort of HGSCs (n = 361) into training (n = 288) and testing (n = 73) sets and labelled each case as HRD or HR proficient (HRP) based on the clinical standard for classification, being a score of HRD genomic damage. Using the training set, we performed differential gene expression analysis between HRD and HRP cases. The 2604 significantly differentially expressed genes were then used to tune and train a penalised logistic regression model.ResultsIdentifiHR is an elastic net penalised logistic regression model that uses the expression of 209 genes to predict HR status in HGSC. These genes capture known regions of HR-specific copy number alteration, which impact gene expression levels, and preserve the genomic damage signal. IdentifiHR has an accuracy of 85% in the TCGA test set and of 91% in an independent cohort of 99 samples, collected from primary tumours before (n = 74/99) and after autopsy (n = 6/99), in addition to ascites (n = 12/99) and normal fallopian tube samples (n = 7/99). Further, IdentifiHR is 84% accurate in pseudobulked single-cell HGSC sequencing from 37 patients and outperforms existing gene expression-based methods to predict HR status, being BRCAness, MutliscaleHRD and expHRD.ConclusionsIdentifiHR is an accurate model to predict HR status in HGSC using gene expression alone, that is available as an R package fromhttps://github.com/DavidsonGroup/IdentifiHR.
Distinct evolutionary trajectories following loss of RNA interference inCryptococcus neoformans
Authors: Huang Jun , Larmore Connor J. , Priest Shelby J. , Xu Ziyan , Dietrich Fred S. , Yadav Vikas , Magwene Paul M. , Sun Sheng , Heitman Joseph 
Published: August 2024

AbstractWhile increased mutation rates typically have negative consequences in multicellular organisms, hypermutation can be advantageous for microbes adapting to the environment. Previously, we identified two hypermutatorCryptococcus neoformansclinical isolates that rapidly develop drug resistance due to transposition of a retrotransposon, Cnl1. Cnl1-mediated hypermutation is caused by a nonsense mutation in the gene encoding a novel RNAi component, Znf3, combined with a tremendous transposon burden. To elucidate adaptative mechanisms following RNAi loss, two bioinformatic pipelines were developed to identify RNAi loss-of-function mutations in a collection of 387 sequencedC. neoformansisolates. Remarkably, several RNAi-loss isolates were identified that are not hypermutators and have not accumulated transposons. To test if these RNAi loss-of-function mutations can cause hypermutation, the mutations were introduced into a non-hypermutator strain with a high transposon burden, which resulted in a hypermutator phenotype. To further investigate if RNAi-loss isolates can become hypermutators,in vitropassaging was performed. Although no hypermutators were found in twoC. neoformansRNAi-loss strains after short-term passage, hypermutation was observed in a passagedC. deneoformansstrain with increased transposon burden. Consistent with a two-step evolution, when an RNAi-loss isolate was crossed with an isolate containing a high Cnl1 burden, F1 hypermutator progeny inheriting a high transposon burden were identified. In addition to Cnl1 transpositions, insertions of a novel gigantic DNA transposon KDZ1 (∼11 kb), contributed to hypermutation in the progeny. Our results suggest that RNAi loss is relatively common (7/387, ∼1.8%) and enables distinct evolutionary trajectories: hypermutation following transposon accumulation or survival without hypermutation.Significance StatementThere is a dearth of antifungal drugs available to treatCryptococcus neoformans, a human fungal pathogen of global impact. We previously identified natural hypermutators with a loss-of-function mutation in the RNAi machinery and transposon expansion. Here, we identified several novel natural isolates with RNAi defects, none of which are hypermutators or have undergone transposon expansion. Furthermore, we demonstrate that these isolates can lie on a pathway to hypermutation following introduction of a transposon burden. In addition, a novel DNA transposon class was discovered that contributes to antifungal drug resistance. These findings highlight the importance of transposons in driving rapid adaptation in the absence of RNAi and reveal distinct evolutionary trajectories following RNAi loss, a relatively common event inC. neoformans.
Instruction-tuned large language models misalign with natural language comprehension in humans
Authors: Gao Changjiang , Ma Zhengwu , Chen Jiajun , Li Ping , Huang Shujian , Li Jixing 
Published: August 2024

AbstractTransformer-based language models have significantly advanced our understanding of meaning representation in the human brain. Prior research utilizing smaller models like BERT and GPT-2 suggests that “next-word prediction” is a computational principle shared between machines and humans. However, recent advancements in large language models (LLMs) have highlighted the effectiveness of instruction tuning beyond next-word prediction. It remains to be tested whether instruction tuning can further align the model with language processing in the human brain. In this study, we evaluated the self-attention of base and finetuned LLMs of different sizes against human eye movement and functional magnetic resonance imaging (fMRI) activity patterns during naturalistic reading. Our results reveal that increases in model size significantly enhance the alignment between LLMs and brain activity, whereas instruction tuning does not. These findings confirm a scaling law in LLMs’ brain-encoding performance and suggest that “instruction-following” may not mimic natural language comprehension in humans.
Tat_BioV: Tattoo ink exposure and biokinetics of selected tracers in a short-term clinical study of 24 subjects
Authors: Kochs Susanne , Schiewe Sandra , Foerster Milena , Hillmann Kathrin , Blankenstein Claudia , Meinke Martina C. , Kugler Josephine , Kocovic David , Luch Andreas , Blume-Peytavi Ulrike , Schreiver Ines 
Published: August 2024

AbstractBackgroundAbout one-fifth of people in industrialised countries are tattooed, potentially putting them at risk of exposure to possible carcinogenic or otherwise harmful substances. Health risks are directly correlated with the amounts of substances introduced, yet reliable data on the systemic exposure to tattoo inks are lacking.ObjectivesThis study aims to determine the exposure to soluble tattoo ink ingredients and their excretion within 24 hours after tattooing. Comparativein vivoandin vitroexperiments were conducted to determine the change in metabolite exposure between tattooing and oral exposure.MethodsIn a clinical study, 24 subjects were tattooed with black or red tattoo ink to which the tracer substances potassium iodide, 4-aminobenzoic acid (PABA) and 2-phenoxyethanol (PEtOH) had been added to mimic known hazardous substances found in tattoo inks. Tracers and their metabolites were quantified in blood, urine, ink, and consumables pre- and post-tattooing. Tattooed skin area was determined using picture analysis. PABA metabolism upon tattooing was compared to peroral administration. Skin fibroblasts and macrophages were testedin vitrofor their ability to metabolise PABA.ResultsAll tracers or their metabolites were identified in urine; iodide and the PABA metabolite 4-acetamidobenzoic acid (ACD) were identified in plasma. The worst-case scenario for systemic ink exposure was estimated to be 0.31 g of ink per tattoo session (75thpercentile). Peroral administration resulted in lower levels of ACD than tattooing. Fibroblasts and macrophages were capable of converting PABA into ACD.DiscussionOur results are the first humanin vivodata on soluble tattoo ink ingredients and suggest that the overall exposure might be lower than the estimates previously used for regulatory purposes. In addition, the first-pass effect by skin metabolism leads to an altered metabolite profile compared to oral exposure. Skin metabolism might also contribute to detoxification of certain carcinogenic substances throughN-acetylation.
The prevalence among heart failure patients and clinical profiles of patients with cor pulmonale at a tertiary center in Ethiopia
Authors: Anagaw Sewale , Fentahun Netsanet , Bayih Habtamu , Tekleab Yohannes 
Published: August 2024

AbstractBackgroundHeart failure is a complex clinical syndrome resulting from structural and functional impairment of ventricular filling or ejection of blood. Cor pulmonale is one type of this clinical syndrome. There are only a few published studies on cor pulmonale from Ethiopia. The objective of this study was to determine the prevalence among patients with heart failure and the clinical and laboratory profiles of patients with cor pulmonale who had follow up at one of the tertiary hospitals in EthiopiaMethodsA hospital-based cross-sectional study was conducted at Felege Hiwot Referral Hospital from December 2018 to April 2019. A single population proportion formula was used to determine the number of heart failure patients that had to be included in the study to determine the prevalence of cor pulmonale. The medical records of cor pulmonale patients among the sample heart failure patients were then retrieved and data was extracted using a structured checklist. Data was entered into, cleaned, and analyzed using IBM.SPSS version 23.0. Descriptive statistics were used to report the findings.ResultsEight percent (35) of patients with heart failure had cor pulmonale. Fifty-four point three percent (19) of the patients with cor pulmonale were males and 45.7 %(16) were females. The median age of patients with cor pulmonale was 55 years. The commonest clinical features were cough and dyspnea (91.4 % and 97.1 % respectively). All patients had right ventricular dilation on echocardiography. Pulmonary Complications post-treatment for tuberculosis were the leading causes followed by interstitial lung disease. There was no identified respiratory disease in 40% of patients with cor pulmonaleConclusionCor pulmonale accounted for less than 10 % of heart failure cases. Complications post-pulmonary tuberculosis were found to be the leading respiratory conditions underlying the cor pulmonale. Programs on prevention, early detection, and treatment of pulmonary tuberculosis must be strengthened.
Deep learning-derived splenic radiomics, genomics, and coronary artery disease
Authors: Kamineni Meghana , Raghu Vineet , Truong Buu , Alaa Ahmed , Schuermans Art , Friedman Sam , Reeder Christopher , Bhattacharya Romit , Libby Peter , Ellinor Patrick T. , Maddah Mahnaz , Philippakis Anthony , Hornsby Whitney , Yu Zhi , Natarajan Pradeep 
Published: August 2024

AbstractBackgroundDespite advances in managing traditional risk factors, coronary artery disease (CAD) remains the leading cause of mortality. Circulating hematopoietic cells influence risk for CAD, but the role of a key regulating organ, spleen, is unknown. The understudied spleen is a 3-dimensional structure of the hematopoietic system optimally suited for unbiased radiologic investigations toward novel mechanistic insights.MethodsDeep learning-based image segmentation and radiomics techniques were utilized to extract splenic radiomic features from abdominal MRIs of 42,059 UK Biobank participants. Regression analysis was used to identify splenic radiomics features associated with CAD. Genome-wide association analyses were applied to identify loci associated with these radiomics features. Overlap between loci associated with CAD and the splenic radiomics features was explored to understand the underlying genetic mechanisms of the role of the spleen in CAD.ResultsWe extracted 107 splenic radiomics features from abdominal MRIs, and of these, 10 features were associated with CAD. Genome-wide association analysis of CAD-associated features identified 219 loci, including 35 previously reported CAD loci, 7 of which were not associated with conventional CAD risk factors. Notably, variants at 9p21 were associated with splenic features such as run length non-uniformity.ConclusionsOur study, combining deep learning with genomics, presents a new framework to uncover the splenic axis of CAD. Notably, our study provides evidence for the underlying genetic connection between the spleen as a candidate causal tissue-type and CAD with insight into the mechanisms of 9p21, whose mechanism is still elusive despite its initial discovery in 2007. More broadly, our study provides a unique application of deep learning radiomics to non-invasively find associations between imaging, genetics, and clinical outcomes.