bluuebunny/crossref_metadata_2025_split huggingface dataset:
An epidemiological study of season of birth, mental health, and neuroimaging in the UK Biobank
Authors: Viejo-Romero Maria , Whalley Heather C. , Shen Xueyi , Stolicyn Aleks , de Nooij Laura , Smith Daniel J. , Howard David M. 
Published: August 2023

AbstractEnvironmental exposures during the perinatal period are known to have a long-term effect on adult physical and mental health. One such influential environmental exposure is the time of year of birth which affects the amount of daylight, nutrients, and viral load that an individual is exposed to in the key developmental period. Here we investigate associations between season of birth (seasonality), four mental health traits (n=135,541) and multi-modal neuroimaging measures (n=33,815) within the UK Biobank. Summer births were associated with probable recurrent Major Depressive Disorder (β=0.024,pcorr=0.048), greater mean cortical thickness in temporal and occipital lobes and in the middle temporal, fusiform, superior temporal, and lingual gyri regions (β range=0.013 - 0.020,pcorr<0.05). Winter births were associated with greater white matter integrity globally, in the association fibers, thalamic radiations, and six individual tracts (β range=-0.010 to -0.021,pcorr<0.05). Results of sensitivity analyses that adjusted for birth weight were similar, with additional associations found between winter birth and frontal, occipital and cingulate lobe surface areas, as well as fractional anisotropy in the forceps minor. Sensitivity analyses also revealed an additional association between summer birth and greater cingulate thickness. Overall, results suggest that seasonality affects brain structure in later life and may have a role in lifetime recurrent Major Depressive Disorder. The small effect sizes observed here warrant further research to validate the results in the context of different latitudes and co-examine genetic and epigenetic measures to potentially reveal informative biological pathways.
The effect of sepsis recognition on telemedicine use and bundle completion in rural emergency department sepsis treatment
Authors: Kaldjian Anna M. , Vakkalanka J. Priyanka , Okoro Uche , Wymore Cole , Harland Karisa K. , Campbell Kalyn , Swanson Morgan B. , Fuller Brian M. , Faine Brett , Zepeski Anne , Parker Edith A. , Mack Luke , Bell Amanda , DeJong Katie , Wallace Kelli , Mueller Keith , Chrischilles Elizabeth , Carpenter Christopher R. , Jones Michael P. , Ward Marcia M. , Mohr Nicholas M. 
Published: August 2023

ABSTRACTPurposeProvider-to-provider emergency department telehealth (tele-ED) has been proposed to improve rural sepsis care. The objective of this study was to measure the association between sepsis documentation and tele-ED use, treatment guideline adherence, and mortality.Materials and MethodsThis analysis was a multicenter (n=23) cohort study of sepsis patients treated in rural emergency departments (EDs) that participated in a tele-ED network between August 2016 and June 2019. The primary exposure was whether sepsis was recognized in the local ED, and the primary outcome was rural tele-ED use, with secondary outcomes of time to tele-ED use, 3-hour guideline adherence, and in-hospital mortality.ResultsData from 1,146 rural sepsis patients were included, 315 (27%) had tele-ED used, and 415 (36%) had sepsis recognized in the rural ED. Sepsis recognition was not independently associated with higher rates of tele-ED use (adjusted odds ratio [aOR] 1.23, 95% CI 0.90–1.67). Sepsis recognition was associated with earlier tele-ED activation (adjusted hazard ratio [aHR] 1.69, 95% CI 1.34-2.13), lower 3-hour guideline adherence (aOR 0.73, 95% CI: 0.55-0.97), and lower in-hospital mortality (aOR 0.72, 95% CI: 0.54-0.97).ConclusionsSepsis recognition in rural EDs participating in a tele-ED network was not associated with tele-ED use.
Integrating genome and epigenome data to identify tissue-specific DNA methylation biomarkers for cancer risk
Authors: Yang Yaohua , Chen Yaxin , Xu Shuai , Guo Xingyi , Jia Guochong , Ping Jie , Shu Xiang , Zhao Tianying , Yuan Fangcheng , Wang Gang , Xie Yufang , Ci Hang , Liu Dan , Ye Fei , Shu Xiao-Ou , Zheng Wei , Li Li , Cai Qiuyin , Long Jirong 
Published: August 2023

AbstractThe relationship between tissue-specific DNA methylation and cancer risk remains inadequately elucidated. Leveraging the Genotype-Tissue Expression (GTEx) consortium, we developed genetic models to predict DNA methylation at CpG sites (CpGs) across the genome for seven tissues and applied these models to genome-wide association study (GWAS) data of corresponding cancers, namely breast, colorectal, renal cell, lung, ovarian, prostate, and testicular germ cell cancers. At Bonferroni-correctedP<0.05, we identified 2,776 CpGs significantly associated with cancer risk, of which 92.7% (2,572) were specific to a particular cancer type. Notably, 57 CpGs within 35 putative novel loci retained significant associations with cancer risk after conditioning on proximal GWAS-identified signals. Further integrative multi-omics analyses revealed 791 CpG-gene-cancer trios, suggesting that DNA methylation at 248 distinct CpGs might influence cancer risk through regulating expression of 145 uniquecis-genes. These findings substantially advance our understanding of the interplay between genetics, epigenetics, and gene expression in cancer etiology.
Candidate genes for IgA nephropathy in pediatric patients: exome-wide association study
Authors: Buianova Anastasiia A. , Proskura Mariia V. , Cheranev Valery V. , Belova Vera A. , Shmitko Anna O. , Pavlova Anna S. , Vasiliadis Iuliia A. , Suchalko Oleg N. , Rebrikov Denis V. , Petrosyan Edita K. , Korostin Dmitriy O. 
Published: August 2023

AbstractIgA nephropathy (IgAN) is an autoimmune disorder that commonly manifests during adolescence. This disease is believed to be a non-monogenic disorder related to variations in multiple genes involved in various biological pathways.We performed the exome-wide association study of 70 children with IgAN confirmed by renal biopsy and 637 healthy donors to identify gene associations responsible for the disease. The HLA allele frequencies between the patients and healthy donors from the bone marrow registry of the Pirogov University were compared. We tested 78,020 gene markers for association, performed the functional enrichment analysis and the transcription factor binding preference detection.We detected 333 genetic variants, employing three inheritance models. The most significant association with the disorder was observed for rs143409664 (PRAG1) in case of the additive and dominant models (PBONF= 1.808 × 10−15and PBONF= 1.654 × 10−15, respectively) and for rs13028230 (UBR3) in case of the recessive model (PBONF= 1.545 × 10−9). Enrichment analysis indicated the strongly overrepresented “immune system” and “kidney development” terms. The HLA-DQA1*01:01:01G allele (P = 0.0076; OR, 2.021 [95% CI, 1.322-3.048]) was significantly the most frequent among IgAN patients.Here we characterized, for the first time, the genetic background of the Russian IgAN patients identifying the risk alleles typical of the population. The most prominent signals were detected in previously undescribed loci.
From microbial communities to regional biogeography: Unraveling patterns, determinants and the influence of bottom trawling in benthic microbiota
Authors: Bonthond Guido , Beermann Jan , Gutow Lars , Neumann Andreas , Barboza Francisco Rafael , Desiderato Andrea , Fofonova Vera , Helber Stephanie , Khodami Sahar , Kraan Casper , Neumann Hermann , Rohde Sven , Schupp Peter J. 
Published: August 2023

ABSTRACTMicrobial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes that operate on different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we study how benthic microbiota vary at a regional scale in the North Sea with sediment characteristics, temperature, organic matter content, shear bed stress and bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Using 16S rDNA amplicon sequencing, we characterized benthic microbiota from the top centimeter of 349 sediment samples and used uni-and multivariate statistical models, accounting for spatial autocorrelation, to disentangle the effects of the different predictors. Fitted models demonstrate how the geographic interplay of different environmental anthropogenic drivers shapes the structure and functioning of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but at the same time increasing with mud content, highlighting different underlying processes. Alpha diversity also increased nonlinearly with total organic matter content and temperature and showed a more complex relationship with bottom shear stress but decreased with bottom trawling intensity. These trawling associated diversity changes were accompanied by shifts in functional groups related to energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying metabolism. Our findings provide first insights of benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and overall benthic metabolism at macroecological scales.
Diverse Epithelial Lymphocytes in Zebrafish Revealed Using a Novel Scale Biopsy Method
Authors: Park Gilseung , Foster Clay A. , Malone-Perez Megan , Hasan Ameera , Macias Jose Juan , Frazer J. Kimble 
Published: August 2023

AbstractZebrafish are a compelling model to study lymphocytes because zebrafish and humans have similar adaptive immune systems. Human and zebrafish lymphocyte types are conserved, but many aspects of zebrafish lymphocyte biology remain uninvestigated, including lymphocytes in peripheral tissues, like epidermis. Here, we report the first study focused on zebrafish scale epidermal lymphocytes. Zebrafish scales represent a source to longitudinally sample live fish. We developed a novel biopsy technique, collecting scales to analyze epithelial lymphocytes from several fluorescently-labeled lines. We imaged scales via confocal microscopy and demonstrated multiple lymphocyte types in scales/epidermis, quantifying them flow cytometrically. We profiled gene expression of scale, thymic, and marrow lymphocytes from the same animals, revealing B- and T-lineage signatures. Single-cell qRT-PCR and RNA sequencing (scRNAseq) show not only canonical B and T cells, but also novel lymphocyte populations not described previously. To validate longitudinal scale biopsies, we serially sampled scales from fish treated with dexamethasone (DXM), demonstrating epidermal lymphocyte responses. To analyze cells functionally, we employed a bead-ingestion assay, showing thymic, marrow, and epidermal lymphocytes have phagocytic activity. In summary, we establish a non-lethal technique to obtain zebrafish lymphocytes, providing the first quantification, expression profiling, and functional data from epidermal lymphocytes in the zebrafish model.SummaryThis study describes a new biopsy method to acquire zebrafish lymphocytes forex vivostudies, without euthanasia. Expression profiles of individual lymphocytes from multiple zebrafish transgenic lines reveal diverse lymphocyte populations, including novel cells expressing genes of both the B- and T-lineages.
TMS provokes target-dependent intracranial rhythms across human cortical and subcortical sites
Authors: Solomon Ethan A. , Wang Jeffrey B. , Oya Hiroyuki , Howard Matthew A. , Trapp Nicholas T. , Uitermarkt Brandt D. , Boes Aaron D. , Keller Corey J. 
Published: August 2023

AbstractTranscranial magnetic stimulation (TMS) is increasingly deployed in the treatment of neuropsychiatric illness, under the presumption that stimulation of specific cortical targets can alter ongoing neural activity and cause circuit-level changes in brain function. While the electrophysiological effects of TMS have been extensively studied with scalp electroencephalography (EEG), this approach is most useful for evaluating low-frequency neural activity at the cortical surface. As such, little is known about how TMS perturbs rhythmic activity among deeper structures – such as the hippocampus and amygdala – and whether stimulation can alter higher-frequency oscillations. Recent work has established that TMS can be safely used in patients with intracranial electrodes (iEEG), allowing for direct neural recordings at sufficient spatiotemporal resolution to examine localized oscillatory responses across the frequency spectrum. To that end, we recruited 17 neurosurgical patients with indwelling electrodes and recorded neural activity while patients underwent repeated trials of single-pulse TMS at several cortical sites. Stimulation to the dorsolateral prefrontal cortex (DLPFC) drove widespread low-frequency increases (3-8Hz) in frontolimbic cortices, as well as high-frequency decreases (30-110Hz) in frontotemporal areas, including the hippocampus. Stimulation to parietal cortex specifically provoked low-frequency responses in the medial temporal lobe. While most low-frequency activity was consistent with brief evoked responses, anterior frontal regions exhibited induced theta oscillations following DLPFC stimulation. Taken together, we established that non-invasive stimulation can (1) provoke a mixture of low-frequency evoked power and induced theta oscillations and (2) suppress high-frequency activity in deeper brain structures not directly accessed by stimulation itself.
Developmental stability and segregation of Theory of Mind and Pain networks carry distinct temporal signatures during naturalistic viewing
Authors: Bhavna Km , Ghosh Niniva , Banerjee Romi , Roy Dipanjan 
Published: August 2023

AbstractTemporally stable large-scale functional brain connectivity among distributed brain regions is crucial during brain development. Recently, many studies highlighted an association between temporal dynamics during development and their alterations across various time scales. However, systematic characterization of temporal stability patterns of brain networks that represent the bodies and minds of others in children remains unexplored. To address this, we apply an unsupervised approach to reduce high-dimensional dynamic functional connectivity (dFC) features via low-dimensional patterns and characterize temporal stability using quantitative metrics across neurodevelopment. This study characterizes the development of temporal stability of the Theory of Mind (ToM) and Pain networks to address the functional maturation of these networks. The dataset used for this investigation comprised 155 subjects (children (n=122, 3–12 years) and adults (n=33)) watching engaging movie clips while undergoing fMRI data acquisition. The movie clips highlighted cartoon characters and their bodily sensations (often pain) and mental states (beliefs, desires, emotions) of others, activating ToM and Pain network regions of young children. Our findings demonstrate that ToM and pain networks display distinct temporal stability patterns by age 3 years. Finally, the temporal stability and specialization of the two functional networks increase with age and predict ToM behavior.
Single-cell transcriptional profiling of clear cell renal cell carcinoma reveals an invasive tumor vasculature phenotype
Authors: Zvirblyte Justina , Nainys Juozas , Juzenas Simonas , Kubiliute Raimonda , Kincius Marius , Ulys Albertas , Jarmalaite Sonata , Mazutis Linas 
Published: August 2023

ABSTRACTClear cell renal cell carcinoma (ccRCC) is the most prevalent form of renal cancer, accounting for over 75% of cases. The asymptomatic nature of the disease contributes to late-stage diagnoses and poor survival. Highly vascularized and immune infiltrated microenvironment are prominent features of ccRCC, yet the interplay between vasculature and immune cells, disease progression and response to therapy remains poorly understood. Using droplet-based single-cell RNA sequencing we profiled 50,236 transcriptomes from paired tumor and healthy adjacent kidney tissues. Our analysis revealed significant heterogeneity and inter-patient variability of the tumor microenvironment. Notably, we discovered a previously uncharacterized vasculature subpopulation associated with epithelial-mesenchymal transition. The cell-cell communication analysis revealed multiple modes of immunosuppressive interactions within the tumor microenvironment, including clinically relevant interactions between tumor vasculature and stromal cells with immune cells. The upregulation of the genes involved in these interactions was associated with worse survival in the TCGA KIRC cohort. Our findings demonstrate the role of tumor vasculature and stromal cell populations in shaping the ccRCC microenvironment and uncover a subpopulation of cells within the tumor vasculature that is associated with an invasive phenotype.
Signatures of internal feedback and trajectory control during goal-directed finger and whole-arm reaching movements
Authors: Chakrabhavi Niranjan , Varadhan SKM , Ghosal Ashitava , Murthy Aditya 
Published: August 2023

AbstractGoal-directed behaviors involve the execution of a variety of eye, hand, and finger movements that follow invariant kinematics consisting of straight-line trajectories and bell-shaped velocity profiles. Despite the presence of neuromotor noise and distinct biomechanics such motions are performed with ease and reasonable accuracy. A fundamental unresolved issue in the field is to determine and delineate the extent to which these trajectories are planned or whether they are a consequence of trajectory-free online control. In this study, we address this question using Spearman’s rank correlation, zero-crossing rate andz-scores and analyze within-trial variability to investigate differences in the time evolution of trajectories during the presence or absence of a goal in finger and whole-arm reaching movements. We found that the central nervous system (CNS) implements control to follow an average trajectory, where goal-directed movements show an enhanced degree of trajectory control. Further, by performing the analysis on the actual timing, we found behavioral signatures of rapid control that might operate on these planned trajectories as early as 30 ms in finger movements and 16.67 ms in whole-arm reaching movements which are too early for trajectory control to be derived from delayed sensory feedback. The analysis also revealed that the controller gains varied along the movement and peaked distinctly at an early (20 %) and a late (90 %) phases of movement, suggesting that trajectory control may be accomplished through virtual way-point objectives during the execution of the movement.Significance StatementThe extent to which reaching movements reflect the unfolding of a prespecified trajectory plan or whether they arise from a trajectory-free online control has remained a vexing issue for motor theorists. Using novel measures of control during the movement such as Spearman’s rank correlation, zero-crossing rate and trends inz-scores, we investigated goal-directed finger and whole-arm reaching movements and demonstrated that the CNS implements rapid control to follow a planned trajectory, especially during early and late phases of movement. Our results provide novel constraints for computational theories of motor control.
Resting-state EEG recorded with gel-based versus consumer dry electrodes: spectral characteristics and across-device correlations
Authors: Kleeva Daria , Ninenko Ivan , Lebedev Mikhail 
Published: August 2023

AbstractRecordings of electroencephalographic (EEG) rhythms and their analyses have been instrumental in basic Neuroscience, clinical diagnostics, and the field of brain-computer interfaces (BCIs). While in the past such measurements have been conducted mostly in laboratory settings, recent advancements in dry electrode technology pave way to a broader range of consumer and medical application because of their greater convenience compared to gel-based electrodes. Here we conducted resting-state EEG recordings in two groups of healthy participants using three dry-electrode devices, the Neiry Headband, the Neiry Headphones and the Muse Headband, and one standard gel electrode-based system, the NVX. We examined signal quality for various spatial and spectral ranges which are essential for cognitive monitoring and consumer applications. Distinctive characteristics of signal quality were found, with the Neiry Headband showing sensitivity in low-frequency ranges and replicating the modulations of delta, theta and alpha power corresponding to the eyes-open and eyes-closed conditions, and the NVX system performing well in capturing high-frequency oscillations. The Neiry Headphones were more prone to low-frequency artifacts compared to the Neiry Headband, yet recorded modulations in alpha power and had a strong alignment with the NVX at higher frequencies. The Muse Headband had several limitations in signal quality. We suggest that while dry-electrode technology appears to be appropriate for the EEG rhythm-based applications the potential benefits of these technologies in terms of ease of use and accessibility should be carefully weighted against the capacity of each concrete system.
DiPPI: A curated dataset for drug-like molecules in protein-protein interfaces
Authors: Cankara Fatma , Senyuz Simge , Sayin Ahenk Zeynep , Gursoy Attila , Keskin Ozlem 
Published: August 2023

AbstractProteins interact through their interfaces, and dysfunction of protein-protein interactions (PPIs) has been associated with various diseases. Therefore, investigating the properties of the drug-modulated PPIs and interface-targeting drugs is critical. Here, we present a curated large dataset for drug-like molecules in protein interfaces. We further present DiPPI (Drugs in Protein-Protein Interfaces), a two-module website to facilitate the search for such molecules and their properties by exploiting our dataset in drug repurposing studies. In the interface module of the website, we extracted several properties of interfaces, such as amino acid properties, hotspots, evolutionary conservation of drug-binding amino acids, and post-translational modifications of these residues. On the drug-like molecule side, we curated a list of drug-like small molecules and FDA-approved drugs from various databases and extracted those that bind to the interfaces. We further clustered the drugs based on their molecular fingerprints to confine the search for an alternative drug to a smaller space. Drug properties, including Lipinski’s rules and various molecular descriptors, are also calculated and made available on the website to guide the selection of drug molecules. Our dataset contains 534,203 interfaces for 98,632 proteins, of which 55,135 are detected to bind to a drug-like molecule. 2,214 drug-like molecules are deposited on our website, among which 335 are FDA-approved. DiPPI provides users with an easy-to-follow scheme for drug repurposing studies through its well-curated and clustered interface and drug data; and is freely available athttp://interactome.ku.edu.tr:8501.