bluuebunny/crossref_metadata_2025_split huggingface dataset:
singletCode: synthetic barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms
Authors: Zhang Ziyang , Melzer Madeline E. , Kiani Karun , Goyal Yogesh 
Published: August 2023

AbstractSingle-cell RNA sequencing datasets comprise true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in single-cell RNA sequencing is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed to infer true singlets and doublets, they typically rely on datasets being highly heterogeneous. Here we develop and apply singletCode, a computational framework that leverages datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground truth singlets. We demonstrate the feasibility of singlets extracted via singletCode to evaluate the performance and robustness of existing doublet detection methods. We find that existing doublet detection methods are not as sensitive as expected when tested on doublets simulated from experimentally realistic ground truth singlets. As DNA barcoded datasets are being increasingly reported, singletCode can identify singlets and inform rational choice of doublet detecting algorithms and their associated limitations.
A pro-inflammatory stem cell niche drives myelofibrosis through a targetable galectin 1 axis
Authors: Li Rong , Colombo Michela , Wang Guanlin , Rodriguez-Romera Antonio , O’Sullivan Jennifer , Clark Sally-Ann , Pérez Sáez Juan M. , Meng Yiran , Khan Abdullah O. , Wen Sean , Dong Pengwei , Zhou Wenjiang , Sousos Nikolaos , Murphy Lauren , Clarke Matthew , Jooss Natalie J. , Olijnik Aude-Anais , Wong Zoë C. , Karali Christina Simoglou , Sirinukunwattana Korsuk , Ryou Hosuk , Norfo Ruggiero , Cheng Qian , Brierley Charlotte K. , Carrelha Joana , Ren Zemin , Thongjuea Supat , Rathinam Vijay A , Krishnan Anandi , Royston Daniel , Rabinovich Gabriel A. , Mead Adam J , Psaila Bethan 
Published: August 2023

AbstractMyeloproliferative neoplasms are stem cell-driven cancers associated with a large burden of morbidity and mortality. The majority of patients present with early-stage disease, but a substantial proportion progress to myelofibrosis and/or secondary leukemia, advanced cancers with a poor prognosis and high symptom burden. Currently, it remains difficult to predict progression, and we lack therapies that reliably prevent or reverse fibrosis development. A major bottleneck to the discovery of disease-modifying therapies has been an incomplete understanding of the interplay between perturbed cellular and molecular states. Several cell types have individually been implicated, but a comprehensive analysis of myelofibrotic bone marrow is lacking. We therefore mapped the crosstalk between bone marrow cell types in myelofibrotic bone marrow. We found that inflammation and fibrosis are orchestrated by a ‘quartet’ of immune and stromal cell lineages – with basophils and mast cells creating a TNF signaling hub, communicating with megakaryocytes, mesenchymal stromal cells and pro-inflammatory fibroblasts. We identified the ý-galactoside binding protein galectin 1 as a striking biomarker of progression to myelofibrosis and poor survival in multiple patient cohorts, and as a promising therapeutic target, with reduced myeloproliferation and fibrosisin vitroandin vivoand improved survival following galectin 1 inhibition. In human bone marrow organoids, TNF increased galectin 1 expression, suggesting a feedback loop wherein the pro-inflammatory MPN clone creates a self-reinforcing niche, fueling progression to advanced disease. This study provides a valuable resource for studying hematopoietic cell-niche interactions, with broad relevance for cancer-associated inflammation and disorders of tissue fibrosis.
An engineered culture vessel and flow system to improve thein vitroanalysis of volatile organic compounds
Authors: Eshima Jarrett , Pennington Taylor R. , Abdellatif Youssef , Olea Angela Ponce , Lusk Joel F. , Ambrose Benjamin D. , Marschall Ethan , Miranda Christopher , Phan Paula , Aridi Christina , Smith Barbara S. 
Published: August 2023

AbstractVolatile organic compounds (VOCs) are a biologically important subset of an organism’s metabolome, yetin vitrotechniques for the analysis of these small molecules vary substantially in practice, restricting the interpretation and reproducibility of study findings. Here, we present an engineered culture tool, termed the “Biodome”, designed to enhance analyte sensitivity by integrating dynamic headspace sampling methodology for the recovery of VOCs from viable biological cultures. We validate the functionality of the device forin vitrovolatile metabolomics utilizing computational modeling and fluorescent imaging of mammalian cell culture. We then leverage comprehensive two-dimensional gas chromatography coupled with a time-of-flight mass spectrometer and the enhanced sampling capabilities afforded by our tool to identify seven VOCs not found in the media or exogenously derived from the sampling method (typical pitfalls within vitrovolatilome analysis). We further work to validate the endogenous production of these VOCs using two independent approaches: (i) glycolysis-mediated stable isotopic labeling techniques using13C6–D-glucose and (ii) RNA interference (RNAi) to selectively knockdown β-oxidation via silencing ofCPT2. Isotope labeling reveals 2-Decen-1-ol as endogenously derived with glucose as a carbon source and, through RNAi, we find evidence supporting endogenous production of 2-ethyl-1-hexene, dodecyl acrylate, tridecanoic acid methyl ester and a low abundance alkene (C17) with molecular backbones likely derived from fatty acid degradation. To demonstrate applicability beyond mammalian cell culture, we assess the production of VOCs throughout the log and stationary phases of growth in ampicillin-resistant DH5αEscherichia coli. We identified nine compounds with results supporting endogenous production, six of which were not previously associated withE. coli. Our findings emphasize the improved capabilities of the Biodome forin vitrovolatile metabolomics and provide a platform for the standardization of methodology.
Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver events of human cancer
Authors: Besedina Elizaveta , Supek Fran 
Published: August 2023

ABSTRACTCancer driver genes can be under positive selection for various types of genetic alterations, including gain-of-function or loss-of-function point mutations (single-nucleotide variants, SNV), small indels, copy number alterations (CNA) and other structural variants. We studied the landscape of interactions between these different types of alterations affecting the same gene by a statistical method, MutMatch, which can test for significant differences in selection, while accounting for various causes of mutation risk heterogeneity. Analyzing ∼18,000 cancer exomes and genomes, we found that known oncogenes simultaneously exhibit signatures of positive selection and also negative selection, where the latter can mask the former. Consistently, focussing on known positively selected regions identifies additional tumor types where an oncogene is relevant. Next, we characterized the landscape of CNA-dependent selection effects, revealing a general trend of increased positive selection on oncogene mutations not only upon CNA gains but also upon CNA deletions. Conversely, we observe a positive interaction between mutations and CNA gains in tumor suppressor genes. Thus, two-hit events involving point mutations and CNA are universally observed on driver genes regardless of the type of CNA, and may signal new therapeutic opportunities that have been overlooked. An explicit focus on the somatic CNA two-hit events can identify additional driver genes relevant to a tumor type. By a global analysis of CNA-selection effects across many driver genes and tissues, we identified at least four independently varying signatures, and thus generated a comprehensive, data-driven classification of cancer genes by mechanisms of (in)activation by genetic alterations.
Appelmans Protocol forin vitro Klebsiella pneumoniaephage host range expansion leads to induction of a novel temperate linear plasmid prophagevB_KpnS-KpLi5
Authors: Jakob Nadine , Hammerl Jens A , Swierczewski Brett E , Würstle Silvia , Bugert Joachim J 
Published: August 2023

AbstractAdjuvant therapy with bacteriophage (phage) cocktails in combination with antibiotics is a therapeutic approach currently considered for treatment of infections with encapsulated, biofilm forming, and multidrug-resistantKlebsiella pneumoniae(Kp).Klebsiellaphage are highly selective in targeting a bacterial capsule type. Considering the numerous Kp capsule types and other Kp host restriction factors, phage treatment could be facilitated when generating phages with a broad host range A modified ‘Appelmans protocol’ was used to create phages with an extended host range viain vitroforced DNA recombination. Three T7-like Kp phages with highly colinear genomes were subjected to successive propagation on their susceptible host strains representing the capsule types K64, K27, and K23, and five Kp isolates of the same capsule types initially unsusceptible for phage lysis. After 30 propagation cycles, five phages were isolated via plaque assay. Four output phages represented the original input phages, while the fifth lysed a previously non-permissible Kp isolate, which was not lysed by any of the input phages. Surprisingly, sequence analysis revealed a novel N15/phiKO2-like phage genome (vB_KpnS_KpLi5) lacking substantial homologies to any of the used T7-like phages. This temperate phage was only induced in the presence of all input phages (cocktail), but not by any of them individually. Induction of temperate phages may be a stress response caused by using multiple phages simultaneously. Successive use of different phages for therapeutic purposes may be preferable over simultaneous application in cocktail formulations to avoid undesired induction of temperate phages. (243)
The Effects of Improved Housing on Malaria Transmission in Different Endemic Zones: A Systematic Review and Meta-Analysis
Authors: Nawa Mukumbuta , Adetokunboh Olatunji 
Published: August 2023

ABSTRACTIntroductionImproved housing has been shown to reduce the risk of malaria infections compared to traditional houses; however, it is unclear if the effects differ in different malaria transmission settings. This study evaluated the effects of improved housing on malaria transmission among different endemic areas.Methods and AnalysisElectronic databases, clinical trial registries and grey literature were searched for randomised controlled trials, cohort studies, case-control studies, and cross-sectional surveys on housing done between 1987 and 2022. Forest plots were done, and the quality of evidence was assessed using the Grading of Recommendations, Assessments, Development and Evaluation Framework.FindingsTwenty-two studies were included; twelve were cross-sectional, four were case-control, four were cohort studies and two were RCTs. RCTs indicated that modern houses did not protect against malaria compared to traditional houses. Cohort studies showed an adjusted risk ratio of 0.68 (95% CI 0.48 – 0.96) and Cross-sectional studies indicated an adjusted odds ratio (aOR) of 0.47 (95% CI 0.31 – 0.72). By endemic transmission regions, the adjusted odds ratio in the high endemic was 0.43 (95% CI 0.29 – 0.63); in the moderate transmission regions, aOR = 0.91 (95% CI 0.91 – 1.07) and in the low transmission settings, aOR = 0.42 (95% CI 0.26 – 0.66).ConclusionThe evidence from observational studies suggests that the risk reduction associated with modern housing is comparable or higher in low malaria transmission settings compared to high transmission settings. Evidence from RCTs in high-transmission settings shows that house improvements may induce risky behaviours such as staying outside for longer hours.Key MessagesIt is known that improved housing reduces the risk of malaria compared to traditional housing; however, the effects of improved housing in different endemic settings are unclear.To the best of our knowledge, this is the first time a systematic review and meta-analysis has stratified the effect measures of improved housing on malaria transmission in different transmission settings.Our study found no literature from high-quality research designs such as RCTs and Cohort studies on improved housing in low and moderate transmission settings. We call on researchers and funders to conduct and support high-quality research designs in low and moderate-transmission areas, especially in Africa, as more countries are reducing their malaria burdens due to increased interventions. This will help to achieve and sustain malaria elimination.Piecemeal improvements, such as closing eaves, screening and iron roofing, are not necessarily associated with a reduced risk of malaria. They may induce risky behaviours due to poor ventilation and higher indoor temperatures resulting in residents staying longer outside thus exposing themselves to infective mosquito bites.
Comparability and Stability of Holotranscobalamin levels in Capillary and Venous Blood
Authors: Woolley Timothy , Rutter Emma , Staudenmaier Macarena 
Published: August 2023

AbstractIntroductionSelf-collected capillary blood has numerous advantages over venous samples taken via phlebotomy, as such the use of this finger-prick testing has increased over recent years, driven in some part by Covid antibody testing. However, there is limited evidence that venous and capillary serum is comparable for many routine analytes. In this study we aimed to determine whether capillary sampling could offer an alternative sampling method to venous for the assessment of vitamin B12 in the form of holotranscobalamin, and if this analyte was stable in unspun capillary blood for three days, thus allowing for samples to be returned by the postal system.MethodsMatched pairs of capillary and venous blood samples were collected from 25 patients for the determination of holotranscobalamin, one set being processed on day zero, the other set being stored at ambient temperature and then processed on day three to mimic postal samples. Self-collected capillary blood was compared with phlebotomist-collected venous samples using correlation, Passing-Bablock regression, and Altman-Bland analysis.ResultsPassing-Bablock and Bland-Altman analysis showed holotranscobalamin levels in capillary and venous serum to be comparable and that the analyte was stable in unspun blood for at least three days at ambient temperatures.ConclusionsWe believe this is the first published study to determine if capillary blood sampling is an acceptable alternative to venous sampling for determining holotranscobalamin concentration; our data indicates that there is no significant difference in results from unspun venous and capillary blood stored at room temperature for at least 3 days compared to venous blood tested on the same day of collection.
Matching or genetic engineering of HLA Class I and II facilitates successful allogeneic ‘off-the-shelf’ regulatory T cell therapy
Authors: McCallion Oliver , Du Weijie , Glaser Viktor , Milward Kate , Franke Clemens , Kath Jonas , Valkov Mikhail , Yang Mingxing , Künkele Annette , Polansky Julia K. , Schmueck-Henneresse Michael , Volk Hans-Dieter , Reinke Petra , Wagner Dimitrios L. , Hester Joanna , Issa Fadi 
Published: August 2023

AbstractThe potential to harness regulatory T cells (Tregs) for the treatment of autoimmune diseases and transplant rejection has been restricted by several barriers: donor variability, manufacturing complications, and time-consuming expansion processes. These issues further complicate the use of autologous Tregs during acute disease phases or when Tregs are low in number or dysfunctional. Here we explore the potential of ‘off-the-shelf’ allogeneic Tregs, from healthy donors or universal sources, to provide a more practical solution. We discover that the efficacy of these cells is undermined by the recipient’s immune response, and that that rigorous matching of HLA classes I and II overcomes this barrier. Importantly, genetically manipulating HLA expression enables the use of unmatched allogeneic Tregs within vivoefficacy. Our findings underscore the transformative potential of HLA-engineered Tregs, offering a novel, ready-to-use therapeutic avenue for treating a wide array of inflammatory diseases.One-Sentence SummaryMatching or engineering of HLA-I and HLA-II facilitates allogeneic ‘off-the-shelf’ regulatory T cells for immunoregulation.
Reversal of Biological Age in Multiple Rat Organs by Young Porcine Plasma Fraction
Authors: Horvath Steve , Singh Kavita , Raj Ken , Khairnar Shraddha , Sanghavi Akshay , Shrivastava Agnivesh , Zoller Joseph A. , Li Caesar Z. , Herenu Claudia B. , Canatelli-Mallat Martina , Lehmann Marianne , Habazin Siniša , Novokmet Mislav , Vučković Frano , Solberg Woods Leah C. , Martinez Angel Garcia , Wang Tengfei , Chiavellini Priscila , Levine Andrew J. , Chen Hao , Brooke Robert T , Gordevicius Juozas , Lauc Gordan , Goya Rodolfo G. , Katcher Harold L. 
Published: August 2023

ABSTRACTYoung blood plasma is known to confer beneficial effects on various organs in mice and rats. However, it was not known whether plasma from young pigs rejuvenates old rat tissues at the epigenetic level; whether it alters the epigenetic clock, which is a highly accurate molecular biomarker of aging. To address this question, we developed and validated six different epigenetic clocks for rat tissues that are based on DNA methylation values derived from n=613 tissue samples. As indicated by their respective names, the rat pan-tissue clock can be applied to DNA methylation profiles from all rat tissues, while the rat brain-, liver-, and blood clocks apply to the corresponding tissue types. We also developed two epigenetic clocks that apply to both human and rat tissues by adding n=1366 human tissue samples to the training data. We employed these six rat clocks to investigate the rejuvenation effects of a porcine plasma fraction treatment in different rat tissues. The treatment more than halved the epigenetic ages of blood, heart, and liver tissue. A less pronounced, but statistically significant, rejuvenation effect could be observed in the hypothalamus. The treatment was accompanied by progressive improvement in the function of these organs as ascertained through numerous biochemical/physiological biomarkers and behavioral responses to assess cognitive functions. An immunoglobulin G (IgG) N-glycosylation pattern shift from pro-to anti-inflammatory also indicated reversal of glycan aging. Overall, this study demonstrates that a young porcine plasma-derived treatment markedly reverses aging in rats according to epigenetic clocks, IgG glycans, and other biomarkers of aging.
HEARTSVG: a fast and accurate method for spatially variable gene identification in large-scale spatial transcriptomic data
Authors: Yuan Xin , Ma Yanran , Gao Ruitian , Cui Shuya , Wang Yifan , Fa Botao , Ma Shiyang , Wei Ting , Ma Shuangge , Yu Zhangsheng 
Published: August 2023

AbstractIdentifying spatially variable genes (SVGs) is crucial for understanding the spatiotemporal characteristics of diseases and tissue structures, posing a distinctive challenge in spatial transcriptomics research. We propose HEARTSVG, a distribution-free, test-based method for fast and accurately identifying spatially variable genes in large-scale spatial transcriptomic data. Extensive simulations demonstrate that HEARTSVG outperforms state-of-the-art methods with higherF1scores (averageF1score=0.903), improved computational efficiency, scalability, and reduced false positives (FPs). Through analysis of twelve real datasets from various spatial transcriptomic technologies, HEARTSVG identifies a greater number of biologically significant SVGs (average recall=0.985, average AUC=0.788) than other comparative methods without prespecifing spatial patterns. Furthermore, by clustering SVGs, we uncover two distinct tumor spatial domains characterized by unique spatial expression patterns, spatial-temporal locations, and biological functions in human colorectal cancer data, unraveling the complexity of tumors.
An Aurora kinase A-BOD1L1-PP2A B56 Axis promotes chromosome segregation fidelity
Authors: Kucharski Thomas J. , Vlasac Irma M. , Higgs Martin R. , Christensen Brock C. , Bechstedt Susanne , Compton Duane A. 
Published: August 2023

SummaryCancer cells are often aneuploid and frequently display elevated rates of chromosome mis-segregation in a phenomenon called chromosomal instability (CIN). CIN is commonly caused by hyperstable kinetochore-microtubule (K-MT) attachments that reduces the efficiency of correction of erroneous K-MT attachments. We recently showed that UMK57, a chemical agonist of MCAK (alias KIF2C) improves chromosome segregation fidelity in CIN cancer cells although cells rapidly develop adaptive resistance. To determine the mechanism of resistance we performed unbiased proteomic screens which revealed increased phosphorylation in cells adapted to UMK57 at two Aurora kinase A phosphoacceptor sites on BOD1L1 (alias FAM44A). BOD1L1 depletion or Aurora kinase A inhibition eliminated resistance to UMK57 in CIN cancer cells. BOD1L1 localizes to spindles/kinetochores during mitosis, interacts with the PP2A phosphatase, and regulates phosphorylation levels of kinetochore proteins, chromosome alignment, mitotic progression and fidelity. Moreover, theBOD1L1gene is mutated in a subset of human cancers, andBOD1L1depletion reduces cell growth in combination with clinically relevant doses of taxol or Aurora kinase A inhibitor. Thus, an Aurora kinase A-BOD1L1-PP2A axis promotes faithful chromosome segregation during mitosis. (175 words)
The impact of ZIKV infection on gene expression in neural cells over time
Authors: Rodrigues Moreno Magalhães de Souza , Júnior Antonio Marques Pereira , Fukutani Eduardo Rocha , Araújo-Pereira Mariana , Salgado Vanessa Riesz , de Queiroz Artur Trancoso Lopo 
Published: August 2023

AbstractZika virus (ZIKV) outbreak caused one of the most significant medical emergencies in the Americas due to associated microcephaly in newborns. To evaluate the impact of ZIKV infection on neuronal cells over time, we retrieved gene expression data from several ZIKV-infected samples obtained at different time point post-infection (pi). Differential gene expression analysis was applied at each time point, with more differentially expressed genes (DEG) identified at 72h pi. There were 5 DEGs (PLA2G2F, TMEM71, PKD1L2, UBD, and TNFAIP3 genes) across all timepoints, which clearly distinguished between infected and healthy samples. The highest expression levels of all five genes were identified at 72h pi. Taken together, our results indicate that ZIKV infection greatly impacts human neural cells at early times of infection, with peak perturbation observed at 72h pi. Our analysis revealed that all five DEGs, in samples of ZIKV-infected human neural stem cells, remained highly upregulated across the timepoints evaluated. Moreover, despite the pronounced inflammatory host response observed throughout infection, the impact of ZIKV is variable over time. Finally, the five DEGs identified herein play prominent roles in infection, and could serve to guide future investigations into virus-host interaction, as well as constitute targets for therapeutic drug development.