bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost
Authors: Ellenbogen Jared B. , Borton Mikayla A. , McGivern Bridget B. , Cronin Dylan R. , Hoyt David W. , Freire-Zapata Viviana , McCalley Carmody K. , Varner Ruth K. , Crill Patrick M. , Wehr Richard A. , Chanton Jeffrey P. , Woodcroft Ben J. , Tfaily Malak M. , Tyson Gene W. , Rich Virginia I. , Wrighton Kelly C. 
Published: July 2023

AbstractWhile wetlands are major sources of biogenic methane (CH4), our understanding of resident microbial metabolisms is incomplete, which compromises prediction of CH4emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire, in arctic Sweden. In quadrupling the genomic representation of the site’s methanogens and examining their encoded metabolisms, we revealed that nearly 20% (72) of the metagenome-assembled genomes (MAGs) encoded potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; forMethanosarcinalesandMethanobacterialesMAGs, these data indicated use of methylated oxygen compounds (e.g., methanol), while forMethanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy, and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activity. Methanogenesis across increasing permafrost thaw is thus revised from sole dominance of hydrogenotrophic production, and the appearance of acetoclastic at full thaw, to consider co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.
Age-associated alterations in thalamocortical structural connectivity in psychosis-spectrum youths
Authors: Lewis Lydia , Corcoran Mary , Cho Kang Ik K. , Kwak YooBin , Hayes Rebecca , Jalbrzikowski Maria 
Published: July 2023

AbstractObjectivePsychotic symptoms typically emerge in adolescence when connections between the thalamus and cortex are still maturing. The extent to which thalamocortical connectivity differences observed in psychosis occur as a function of age-associated alterations is not fully understood.MethodsWe analyzed diffusion-weighted imaging data from 1254 participants 8-23 years old (typically developing youth: N=626, psychosis-spectrum youth: N=329, other psychopathology: N=299) from the Philadelphia Neurodevelopmental Cohort. Using deterministic fiber tractography, we modeled eight tracts between the thalamus and cortical regions of interest. We extracted diffusion spectrum imaging (DSI) and conventional diffusion tensor imaging (DTI) measures. We used generalized additive models to determine group and age-associated differences in thalamocortical connectivity.ResultsCompared to typically developing youth and youth with other psychopathologies, psychosis-spectrum youth exhibited thalamocortical reductions in DSI global fractional anisotropy (p-values range=3.0×10−6-0.05) and DTI fractional anisotropy (p-values range=4.2×10−4-0.03). Compared to typically developing youth, psychosis-spectrum youth exhibited shallower thalamus-prefrontal age-associated increases in DSI global fractional anisotropy and DTI fractional anisotropy during middle childhood, and steeper thalamus-prefrontal age-associated increases in those measures during adolescence. Both typically developing youth and youth with other psychopathologies exhibited decreases in mean and radial diffusivity in thalamus-frontal tracts during adolescence; psychosis-spectrum youth failed to show these age-related decreases.ConclusionOur findings suggest group differences and altered age-related patterns of thalamocortical white matter connectivity in psychosis-spectrum youth. Consistent alterations present as early as middle childhood and altered age-associated patterns during adolescence and young adulthood may contribute to the disruptions in thalamocortical connectivity observed in adults with psychosis.
Comparison of blood and urine concentrations of equol by LC‒MS/MS method and factors associated with equol production in 466 Japanese men and women
Authors: Yoshikata Remi , Myint Khin Zay Yar , Taguchi Junichi 
Published: July 2023

AbstractEquol is produced from daidzein by the action of gut bacteria on soy isoflavones. However, not all people can produce equol, and metabolism differs even among the producers. We aimed to examine the equol producer status in both men and women, and investigate the relationships among the serum and urinary isoflavones as well as to other biomedical parameters. In this study, we measured the equol and daidzein concentrations from the blood and urine of 292 men and 174 women aged between 22 and 88 years by liquid chromatography/tandem mass spectrometry (LC/MS/MS).We then analysed the cut-off value for equol producers in both sexes, the relationship of serum and urinary equol concentrations, and other parameters, such as sex, age, endocrine function, glucose metabolism, lipid metabolism, and renal function with regards to equol-producing ability, among the different age groups. Equol producers were defined as those whose log ratio of urinary equol and daidzein concentration or log (equol/daidzein) was -1.42 or higher. Among 466 participants, 195 were equol producers (42%). The proportion of equol producers was larger in women. The cut-off value for equol producers was consistent in both sexes. Positive relationships were noted between serum and urinary equol levels in equol producers of both sexes; however, such an association was not detected in nonproducers. PSA levels in men were significantly lower in equol producers (0.8 v.s. 1.0 ng/ml, p=0.004), especially in those in their 40 s (0.82 vs. 1.13 ng/ml, p<0.001) and 60 s (0.64 vs. 1.02 ng/ml, p<0.001).
Carbapenem-resistantAcinetobacter baumanniiat a hospital in Botswana: Detecting a protracted outbreak using whole genome sequencing
Authors: Strysko Jonathan , Thela Tefelo , Feder Andries , Thubuka Janet , Machiya Tichaona , Mkubwa Jack , Mochankana Kagiso , Tiroyakgosi Celda , Kgomanyane Kgomotso , Ntereke Tlhalefo Dudu , Zankere Tshiamo , Lechiile Kwana , Gatonye Teresia , Tembo Chimwemwe Viola , Vurayai Moses , Mannathoko Naledi , Mokomane Margaret , Moustafa Ahmed M , Goldfarb David M , Richard-Greenblatt Melissa , McGann Carolyn , Coffin Susan E , Cancedda Corrado , Lautenbach Ebbing , Bogoshi Dineo , Smith Anthony M , Planet Paul J 
Published: July 2023

AbstractCarbapenem-resistantAcinetobacter baumannii(CRAb) has emerged as a major and often fatal cause of bloodstream infections among hospitalized patients in low- and middle-income countries (LMICs). CRAb outbreaks are hypothesized to arise from reservoirs in the hospital environment, but outbreak investigations in LMICs are seldom able to incorporate whole genome sequencing (WGS) due to resource limitations. We performed WGS at the National Institute for Communicable Diseases (Johannesburg, South Africa) on storedA. baumanniiisolates (n=43) collected during 2021–2022 from a 530-bed referral hospital in Gaborone, Botswana where CRAb infection incidence was noted to be rising. This included blood culture isolates from patients (aged 2 days – 69 years), and environmental isolates collected at the hospital’s 33-bed neonatal unit. Multilocus sequence typing (MLST), antimicrobial/biocide resistance gene identification, and phylogenetic analyses were performed using publicly accessible analysis pipelines. Single nucleotide polymorphism (SNP) matrices were used to assess clonal lineage. MLST revealed 79% of isolates were sequence type 1 (ST1), including all 19 healthcare-associated blood isolates and three out of five environmental isolates. Genes encoding for carbapenemases (blaNDM-1,blaOXA-23) and biocide resistance (qacE) were present in all 22 ST1 isolates. Phylogenetic analysis of the ST1 clade demonstrated spatial clustering by hospital unit. Nearly identical isolates spanned wide ranges in time (>1 year), suggesting ongoing transmission from environmental sources. One highly similar clade (average difference of 2.3 SNPs) contained all eight neonatal blood isolates and three environmental isolates from the neonatal unit. These results were critical in identifying environmental reservoirs (e.g. sinks) and developing remediation strategies. Using a phylogenetically informed approach, we also identified diagnostic genes useful for future tracking of outbreak clones without the need for WGS. This work highlights the power of South-South and South-North partnerships in building public health laboratory capacity in LMICs to detect and contain the spread of antimicrobial resistance.
Species distribution modeling for disease ecology: a multi-scale case study for schistosomiasis host snails in Brazil
Authors: Singleton Alyson L. , Glidden Caroline K. , Chamberlin Andrew J. , Tuan Roseli , Palasio Raquel G. S. , Pinter Adriano , Caldeira Roberta L. , Mendonça Cristiane L. F. , Carvalho Omar S. , Monteiro Miguel V. , Athni Tejas S. , Sokolow Susanne H. , Mordecai Erin A. , De Leo Guilio A. 
Published: July 2023

AbstractSpecies distribution models (SDMs) are increasingly popular tools for profiling disease risk in ecology, particularly for infectious diseases of public health importance that include an obligate non-human host in their transmission cycle. SDMs can create high-resolution maps of host distribution across geographical scales, reflecting baseline risk of disease. However, as SDM computational methods have rapidly expanded, there are many outstanding methodological questions. Here we address key questions about SDM application, using schistosomiasis risk in Brazil as a case study. Schistosomiasis—a debilitating parasitic disease of poverty affecting over 200 million people across Africa, Asia, and South America—is transmitted to humans through contact with the free-living infectious stage ofSchistosomaspp. parasites released from freshwater snails, the parasite’s obligate intermediate hosts. In this study, we compared snail SDM performance across machine learning (ML) approaches (MaxEnt, Random Forest, and Boosted Regression Trees), geographic extents (national, regional, and state), types of presence data (expert-collected and publicly-available), and snail species (Biomphalaria glabrata,B. tenagophilaandB. straminea). We used high-resolution (1km) climate, hydrology, land-use/land-cover (LULC), and soil property data to describe the snails’ ecological niche and evaluated models on multiple criteria. Although all ML approaches produced comparable spatially cross-validated performance metrics, their suitability maps showed major qualitative differences that required validation based on local expert knowledge. Additionally, our findings revealed varying importance of LULC and bioclimatic variables for different snail species at different spatial scales. Finally, we found that models using publicly-available data predicted snail distribution with comparable AUC values to models using expert-collected data. This work serves as an instructional guide to SDM methods that can be applied to a range of vector-borne and zoonotic diseases. In addition, it advances our understanding of the relevant environment and bioclimatic determinants of schistosomiasis risk in Brazil.
Physiological costs of prospecting in a resident cooperative breeder, the Florida scrub-jay
Authors: Suh Young Ha , Taff Conor , Bowman Reed , Fitzpatrick John W 
Published: July 2023

ABSTRACTProspecting is an understudied yet pivotal information-gathering process often preceding natal dispersal. While prospecting may enable individuals to optimise dispersal outcomes and obtain high quality territories, it is also likely to incur costs stemming from energy expenditure and predation risks. This trade-off may drive individual differences in prospecting effort. We tested for evidence of costs of prospecting behaviour in a wild population of Florida scrub-jays,Aphelocoma coerulescens, which prospect as nonbreeding helpers. Using random sampling across all helpers, we compared prospecting effort—approximated by frequency, distance, and activity level—with body mass changes and oxidative stress levels. We tested if prospecting incurred costs and if early-life body condition predicted subsequent prospecting effort. Prospecting frequency was positively linked to oxidative damage but not to any loss in body mass during the breeding season, suggesting that extra-territorial movement costs manifest unevenly. Early-stage body condition did not affect subsequent prospecting effort across a large set of helpers, but early-stage body condition and morphometric measures did correlate with subsequent oxidative status of those sampled. Our results suggest that prospecting movement carries some physiological costs, perhaps contributing to individual differences in prospecting. This research highlights how body condition plays a role in trade-offs between information gathering movement and physiological costs of movement itself, ultimately providing insight on the evolution of prospecting in social species.HIGHLIGHTSProspecting prior to breeding enables informed dispersal but incurs costWe tested whether prospecting by nonbreeding Florida scrub-jays results in physiological costs or varies with initial conditionWe measured oxidative status using assays testing antioxidant capacity and oxidative damageFrequent prospecting was linked to subsequent oxidative damageEarly-stage body condition and wing length affected subsequent oxidative status
Investigating the effects of radiation, T cell depletion, and bone marrow transplantation on murine gut microbiota
Authors: Kreisinger Jakub , Dooley James , Singh Kailash , Čížková Dagmar , Schmiedová Lucie , Bendová Barbora , Liston Adrian , Moudra Alena 
Published: July 2023

AbstractMicrobiome research has gained much attention in recent years as the importance of gut microbiota in regulating host health becomes increasingly evident. However, the impact of radiation on the microbiota in the murine bone marrow transplantation model is still poorly understood. In this paper, we present the major conclusions of our investigation into the effects of radiation and subsequent bone marrow transplantation with or without T cell depletion of the donor bone-marrow on the microbiota of the ileum and cecum. Our findings show that radiation has different effects on the microbiota of the two intestinal regions, with the cecum showing increased interindividual variation, suggesting an impaired ability of the host to regulate microbial symbionts, consistent with the Anna Karenina principle. Additionally, we observed changes in the ileum composition, including an increase in bacterial taxa that are important modulators of host health, such asAkkermansiaandFaecalibaculum.In contrast, radiation in the cecum was associated with an increased abundance of several common commensal taxa in the gut, includingLachnospiraceaeandBacteroides. Finally, we found that high doses of radiation had more substantial effects on the caecal microbiota of the T-cell-depleted group than that of the non-T-cell-depleted group. Overall, our results contribute to a better understanding of the complex relationship between radiation and the gut microbiota in the context of bone marrow transplantation and highlight the importance of considering different intestinal regions when studying microbiome responses to environmental stressors.
PyLabRobot: An Open-Source, Hardware Agnostic Interface for Liquid-Handling Robots and Accessories
Authors: Wierenga Rick P. , Golas Stefan , Ho Wilson , Coley Connor , Esvelt Kevin M. 
Published: July 2023

AbstractLiquid handling robots are often limited by proprietary programming interfaces that are only compatible with a single type of robot and operating system, restricting method sharing and slowing development. Here we present PyLabRobot, an open-source, cross-platform Python interface capable of programming diverse liquid-handling robots, including Hamilton STARs, Tecan EVOs, and Opentron OT-2s. PyLabRobot provides a universal set of commands and representations for deck layout and labware, enabling the control of diverse accessory devices. The interface is extensible and can work with any robot that manipulates liquids within a Cartesian coordinate system. We validated the system through unit tests and several application demonstrations, including a browser-based simulator, a position calibration tool, and a path-teaching tool for complex movements. PyLabRobot provides a flexible, open, and collaborative programming environment for laboratory automation.Figure AbstractPyLabRobot overcomes the limitations of proprietary robotic systems.(a) Scientists with access to liquid-handling robots are currently limited by proprietary interfaces that require specialized knowledge, hinder cross-platform operability, and restrict sharing of methods among different robot types. For complex tasks, many researchers need assistance from a specialist familiar with their particular system, most notably when creating or editing protocols. (b) PyLabRobot (https://github.com/PyLabRobot/pylabrobot) offers a single interface that allows any person with basic Python skills to program diverse types of liquid-handling robots and share protocols freely, fostering a more collaborative and efficient research environment. The Python API makes it easy to interact with a large scientific computing ecosystem and allows users to leverage large language models for programming assistance.
The within-person association of relative left frontal activity and vagally mediated heart rate variability not moderated by history of depression
Authors: Ding Yaohui , Allen John J.B. 
Published: July 2023

AbstractMotivated by the Neurovisceral Integration Model (NVI) of cardiac vagal control, we investigated the relationship between relative left frontal activity (rLFA) and vagally mediated heart rate variability or respiratory sinus arrhythmia (RSA) in 287 participants, half of whom had a history of depression. We hypothesized that there would be a within-person association of rLFA and RSA such that when RSA is lower rLFA would also be lower (Hypothesis I). Moreover, it was hypothesized that this within-subject association would be moderated by a history of depression (Hypothesis II). Metrics of rLFA and RSA were derived from concurrent electroencephalogram and electrocardiogram recordings. The logarithmic difference in EEG alpha power between the homologous right and left electrodes (Ln (Right/Left)) in the frontal region was used to index rLFA. A Hilbert transform was applied to the mean-centered and bandpass-filtered (0.12-.40 Hz) inter-beat interval (IBI) time series to get a fine-grained measure (in the time domain) of RSA. A linearmixed ANOVAmodel with rLFA as the dependent variable and RSA as the main fixed effect found that participants had less rLFA during epochs when they had lower RSA, which was consistent with the prediction from Hypothesis I. Contrary to the prediction from Hypothesis II, the within-person association of RSA and rLFA wasnotmoderated by a history of depression. However, the association between RSA and rLFA varied across the four pairs of frontal electrodes that we examined. Thus, more research is needed to determine the spatial extent of this association, e.g., examining the relationship between source-localized rLFA and RSA.
Hepatocyte-specific disruption of soluble epoxide hydrolase attenuates abdominal aortic aneurysm formation: novel role of the liver in aneurysm pathogenesis
Authors: Kim David , Horimatsu Tetsuo , Ogbi Mourad , Goo Brandee , Shi Hong , Veerapaneni Praneet , Chouhaita Ronnie , Moses Mary , Prasad Rosaria , Benson Tyler W. , Harb Ragheb , Aboud Ghaith , Seller Hunter , Haigh Steve , Fulton David J. , Csányi Gábor , Huo Yuqing , Long Xiaochun , Coffey Philip , Lee Richard , Guha Avirup , Zeldin Darryl , Hwang Sung Hee , Hammock Bruce D. , Weintraub Neal L. , Kim Ha Won 
Published: July 2023

AbstractIntroductionInflammation is a key pathogenic feature of abdominal aortic aneurysm (AAA). Soluble epoxide hydrolase (sEH) is a pro-inflammatory enzyme that converts cytochrome P450-derived epoxides of fatty acids to the corresponding diols, and pharmacological inhibition of sEH prevented AAA formation. Both cytochrome P450 enzymes and sEH are highly expressed in the liver. Here, we investigated the role of hepatic sEH in AAA using a selective pharmacological inhibitor of sEH and hepatocyte-specific Ephx2 (which encodes sEH gene) knockout (KO) mice in two models of AAA [angiotensin II (AngII) infusion and calcium chloride (CaCl2) application].Methods and resultssEH expression and activity were strikingly higher in mouse liver compared with aorta and further increased the context of AAA, in conjunction with elevated expression of the transcription factor Sp1 and the epigenetic regulator Jarid1b, which have been reported to positively regulate sEH expression. Pharmacological sEH inhibition, or liver-specific sEH disruption, achieved by crossing sEH floxed mice with albumin-cre mice, prevented AAA formation in both models, concomitant with reduced expression of hepatic sEH as well as complement factor 3 (C3) and serum amyloid A (SAA), liver-derived factors linked to AAA formation. Moreover, sEH antagonism markedly reduced C3 and SAA protein accumulation in the aortic wall. Co-incubation of liverex vivowith aneurysm-prone aorta resulted in induction of sEH in the liver, concomitant with upregulation of Sp1, Jarid1b, C3 and SAA gene expression, suggesting that the aneurysm-prone aorta secretes factors that activate sEH and downstream inflammatory signaling in the liver. Using an unbiased proteomic approach, we identified a number of dysregulated proteins [e.g.,plastin-2, galectin-3 (gal-3), cathepsin S] released by aneurysm-prone aorta as potential candidate mediators of hepatic sEH induction.ConclusionWe provide the first direct evidence of the liver’s role in orchestrating AAA via the enzyme sEH. These findings not only provide novel insight into AAA pathogenesis, but they have potentially important implications with regard to developing effective medical therapies for AAA.
Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment
Authors: Díaz-Gay Marcos , Vangara Raviteja , Barnes Mark , Wang Xi , Islam S M Ashiqul , Vermes Ian , Narasimman Nithish Bharadhwaj , Yang Ting , Jiang Zichen , Moody Sarah , Senkin Sergey , Brennan Paul , Stratton Michael R , Alexandrov Ludmil B 
Published: July 2023

ABSTRACTAnalysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped the evolution of a cancer genome. Here we present SigProfilerAssignment, a desktop and an online computational framework for assigning all types of mutational signatures to individual samples. SigProfilerAssignment is the first tool that allows both analysis of copy-number signatures and probabilistic assignment of signatures to individual somatic mutations. As its computational engine, the tool uses a custom implementation of the forward stagewise algorithm for sparse regression and nonnegative least squares for numerical optimization. Analysis of 2,700 synthetic cancer genomes with and without noise demonstrates that SigProfilerAssignment outperforms four commonly used approaches for assigning mutational signatures. SigProfilerAssignment is freely available athttps://github.com/AlexandrovLab/SigProfilerAssignmentwith a web implementation athttps://cancer.sanger.ac.uk/signatures/assignment/.