bluuebunny/crossref_metadata_2025_split huggingface dataset:
CHOIR improves significance-based detection of cell types and states from single-cell data
Authors: Sant Cathrine , Mucke Lennart , Corces M. Ryan 
Published: January 2024

AbstractClustering is a critical step in the analysis of single-cell data, as it enables the discovery and characterization of putative cell types and states. However, most popular clustering tools do not subject clustering results to statistical inference testing, leading to risks of overclustering or underclustering data and often resulting in ineffective identification of cell types with widely differing prevalence. To address these challenges, we present CHOIR (clusteringhierarchyoptimization by iterative random forests), which applies a framework of random forest classifiers and permutation tests across a hierarchical clustering tree to statistically determine which clusters represent distinct populations. We demonstrate the enhanced performance of CHOIR through extensive benchmarking against 14 existing clustering methods across 100 simulated and 4 real single-cell RNA-seq, ATAC-seq, spatial transcriptomic, and multi-omic datasets. CHOIR can be applied to any single-cell data type and provides a flexible, scalable, and robust solution to the important challenge of identifying biologically relevant cell groupings within heterogeneous single-cell data.
Investigation of neural functional connectivity in thick acute mouse brain slices with novel multi-region 3D neural probe arrays
Authors: Smith Wesley Charles , Naumkina Zoia , Shin Hyo Geun , Chae Ui Kyu , Lee SeungHun , Park Jung-Hoon , Cho Yak Dol , Woo Ji Wan , Kwon Seok Kyu , Oh Soo Jin , Nam Min-Ho , Kim Tae Song , Cho Il Joo 
Published: January 2024

AbstractThere are significant limitations in investigating complex neural circuitsin vivo, including drawbacks to midline-adjacent surgeries, limited accessibility to deep brain regions and number of feasible regional targets for simultaneous recordings, and analytical or experimental biases from recording one columnar plane. On the other hand, recording extracellular neural signalsex vivoorin vitrousing planar microelectrode arrays (MEAs) only permits slice surface recordings, and since conventional slices under 400 μm-thick or dissociated cultures are used, no experiments contain a physiological multi-region circuit, drastically limiting conclusions about connectivity and pharmacology. Using thick, tract-preserving acute brain slices to record otherwise unassailable neural circuitsex vivocombines the strengths of both types of experiments, but is assumed to precipitate ischemic injury due to oxygen scarcity within the slice. Here, we report the first application of custom, multi-region silicon neural probe arrays to record spontaneous activity & optogenetically-induced functional connectivity acrosshe mesocorticolimbic pathway within tract-preserving 800 μm sagittal mouse brain slices, compared with 400 μm slices, among three brain regions: the ventral tegmental area (VTA), ventral striatum (VS), & medial prefrontal cortex (mPFC). We show that most single-unit signals are an order of magnitude below the noise floor seen using silicon probesin vivo, providing unit yields far higher than previously assumed, allowing for a deep functional understanding of acute slice condition compared to the assumed deterioration due to ischemia. Overall, our method allows for acute circuit manipulations beyond what is available in vivo, with far more information than conventional slice preparations.
Extracellular RNA induce neutrophil recruitment via endothelial TLR3 during venous thrombosis after vascular injury
Authors: Najem Maria Y. , Rys Ryan N. , Laurance Sandrine , Bertin François-René , Gourdou-Latyszenok Virginie , Gourhant Lénaïck , Le Gall Lauriane , Le Corre Rozenn , Couturaud Francis , Blostein Mark D. , Lemarié Catherine A. 
Published: January 2024

AbstractBackgroundVenous thromboembolism is associated with endothelial cell activation that contributes to the inflammation-dependent activation of the coagulation system. Cellular damages are associated with the release of different species of extracellular RNA (eRNA) involved in inflammation and coagulation. TLR3, which recognizes (viral) double-stranded RNA, single-stranded RNA, and also self-RNA fragments might be the receptor of these eRNA during venous thromboembolism. We investigate how eRNA regulate endothelial function through TLR3 and contribute to venous thromboembolism.Methods and ResultsThrombus formation and size in WT and TLR3 deficient (-/-) mice were monitored by ultrasonography after venous thrombosis using the FeCl3and stasis models. Mice were treated with RNase1, poly(I:C) or RNA extracted from murine endothelial cells (eRNA). Gene expression and signaling pathway activation were analyzed in HEK293T cells overexpressing TLR3 in response to eRNA or in HUVECs transfected with a siRNA against TLR3. Plasma clot formation on treated HUVECs was analyzed. Thrombosis exacerbated RNA release in vivo and increased RNA content within the thrombus. RNase1 treatment reduced thrombus size compared to vehicle-treated mice. Poly(I:C) and eRNA treatments increased thrombus size in WT mice, but not in TLR3-/-mice, by bolstering neutrophil recruitment. Mechanistically, TLR3 activation in endothelial cells promotes CXCL5 secretion and neutrophil recruitment in vitro. eRNA triggered plasma clot formation. eRNA mediate these effects through TLR3-dependent activation of NFκB.ConclusionsWe show that eRNA and TLR3 activation enhance venous thromboembolism through neutrophil recruitment and secretion of CXCL5.
A Vector System Encoding Histone H3 Mutants Facilitates Manipulations of the Neuronal Epigenome
Authors: Warren Sophie , Xiong Sen , Robles Daisy , Baizabal José-Manuel 
Published: January 2024

ABSTRACTThe differentiation of developmental cell lineages is associated with genome-wide modifications in histone H3 methylation. However, the causal role of histone H3 methylation in transcriptional regulation and cell differentiation has been difficult to test in mammals. The experimental overexpression of histone H3 mutants carrying lysine-to-methionine (K-to-M) substitutions has emerged as an alternative tool for inhibiting the endogenous levels of histone H3 methylation at specific lysine residues. Here, we leverage the use of histone K-to-M mutants by creating Enhanced Episomal Vectors that enable the simultaneous depletion of multiple levels of histone H3 lysine 4 (H3K4) or lysine 9 (H3K9) methylation in projection neurons of the mouse cerebral cortex. Our approach also facilitates the simultaneous depletion of H3K9 and H3K27 trimethylation (H3K9me3 and H3K27me3, respectively) in cortical neurons. In addition, we report a tamoxifen-inducible Cre-FLEX system that allows the activation of mutant histones at specific developmental time points or in the adult cortex, leading to the depletion of specific histone marks. The tools presented here can be implemented in other experimental systems, such as humanin vitromodels, to test the combinatorial role of histone methylations in developmental fate decisions and the maintenance of cell identity.
Explorations of using a convolutional neural network to understand brain activations during movie watching
Authors: Sohn Wonbum , Di Xin , Liang Zhen , Zhang Zhiguo , Biswal Bharat B. 
Published: January 2024

AbstractNeuroimaging studies increasingly use naturalistic stimuli like video clips to trigger complex brain activations, but the complexity of such stimuli makes it difficult to assign specific functions to the resulting brain activations, particularly for higher-level content like social interactions. To address this challenge, researchers have turned to deep neural networks, e.g., convolutional neural networks (CNNs). CNNs have shown success in image recognition due to their different levels of features enabling high performance. In this study, we used pre-trained VGG-16, a popular CNN model, to analyze video data and extract hierarchical features from low-level shallow layers to high-level deeper layers, linking these activations to different levels of activation of the human brain. We hypothesized that activations in different layers of VGG-16 would be associated with different levels of brain activation and visual processing hierarchy in the brain. We were also curious about which brain regions would be associated with deeper convolutional layers in VGG-16. The study analyzed a functional MRI (fMRI) dataset where participants watched the cartoon movie Partly Cloudy. Frames of the videos were fed into VGG-16, and activation maps from different kernels and layers were extracted. Time series of the average activation patterns for each kernel were created and fed into a voxel-wise model to study brain activations. Results showed that lower convolutional layers (1stconvolutional layer) were mostly associated with lower visual regions, but some kernels (6, 19, 24, 42, 55, and 58) surprisingly showed associations with activations in the posterior cingulate cortex, part of the default mode network. Deeper convolutional layers were associated with more anterior and lateral portions of the visual cortex (e.g., the lateral occipital complex) and the supramarginal gyrus. Analyzing activation features associated with different brain regions showed the promise and limitations of using CNNs to link video content to brain functions.
Testing retrogenesis and physiological explanations for tract-wise white matter aging: links to developmental order, fibre calibre, and vascularization
Authors: Robinson Tyler D. , Chad Jordan A. , Sun Yutong L. , Chang Paul T. H. , Chen J. Jean 
Published: January 2024

ABSTRACTTo understand the consistently observed spatial distribution of white-matter (WM) aging, developmentally driven theories termed “retrogenesis” have gained traction, positing that the order of WM tract development predicts the order of declines. Regions that develop first are expected to deteriorate the last, i.e. “last-in-first-out”. Alternatively, regions which develop most rapidly may also decline most rapidly in aging, or “gains-predict-loss”. The validity of such theories remains uncertain, in part due to lack of clarity on the definition of developmental order. Importantly, our recent findings suggest that WM aging is also associated with physiological parameters such as perfusion, which may be linked to fibre metabolic need, which in turn varies with fibre size. Here we address the extent to which the degree of WM aging is determined by development trajectory (i.e. retrogenesis) and/or by physiological state. We obtained microstructural and perfusion measures using data from the Human Connectome Project in Aging (HCP-A), complemented by a meta-analysis involving maps of fibre calibre and macrovascular volume. Our results suggest that (1) while tracts that appear last or finish myelinating first in development display the slowest aging, the pattern of aging is not fully explained by retrogenesis; in fact, time courses of tract emergence and myelination give rise to opposite associations with WM decline; (2) tracts that appear earlier also have higher mean axon calibre and are also associated with lower degrees of WM microstructural aging; (3) such tracts also tend to exhibit relatively sustained CBF with a higher rate of lengthening of the arterial transit times (ATT), suggestive of collateral blood supply. These findings were also sex dependent in a tract-specific manner. Future work will investigate whether these are ultimately influenced by each tract’s metabolic demand and the role of macrovascular collateral flow.
Structural determinants of co-translational protein complex assembly
Authors: Mallik Saurav , Venezian Johannes , Lobov Arseniy , Heidenreich Meta , Garcia-Seisdedos Hector , Yeates Todd O. , Shiber Ayala , Levy Emmanuel D. 
Published: January 2024

ABSTRACTThe assembly of proteins into functional complexes is critical to life’s processes. While textbooks depict complex assembly as occurring between fully synthesized proteins, we know today that thousands of proteins in the human proteome assemble co-translationally during their synthesis. Why this process takes place, however, remains unknown. We show that co-translational assembly is governed by biophysical and structural characteristics of the protein complex, and involves mutually stabilized, intertwined subunits. Consequently, these subunits are also co-regulated across the central dogma, from transcription to protein degradation. Leveraging structural signatures with AlphaFold2-based predictions enables us to accurately predict co-translational assembly on a proteome-wide scale, which we validated by ribosome profiling, genetic perturbations, and smFISH experiments. Notably, the latter showed that co-translationally assembling subunits exhibit co-localized mRNAs. This work unveils a fundamental connection between protein structure and the translation process, highlighting the overarching impact of three-dimensional structure on gene expression, mRNA localization, and proteostasis.One Sentence SummaryProtein complexes with topologically intertwined subunits require co-translational assembly and synchronized proteostasis of subunits, with implications in protein stability, mRNA localization, and evolution.Graphical Abstract
SOX9-regulated matrix proteins predict poor outcomes in patients with COVID-19 and pulmonary fibrosis
Authors: Pearmain Laurence , Jokl Elliot , Simpson Kara , Birchall Lindsay , Ou Yaqing , Lawless Craig , Simpson Angela , Mann Lizzie , Scott Nick , Shah Rajesh , Venkateswaran Rajamiyer , Stanel Stefan , Hayton Conal , Rivera-Ortega Pilar , Hansbro Phil , Hanley Neil A , Blaikley John F , Hanley Karen Piper 
Published: January 2024

AbstractPulmonary fibrosis is an increasing and major cause of death worldwide. Understanding the cellular and molecular mechanisms underlying the pathophysiology of lung fibrosis may lead to urgently needed diagnostic and prognostic strategies for the disease. SOX9 is a core transcription factor that has been associated with fibrotic disease, however its role and regulation in acute lung injury and/or fibrosis have not been fully defined. In this study we apply a hypothesis based approach to uncover unique SOX9-protein signatures associated with both acute lung injury and fibrotic progression. Usingin vivomodels of lung injury in the presence or absence of SOX9, our study shows SOX9 is essential to the damage associated response of alveolar epithelial cells from an early time-point in lung injury. In parallel, as disease progresses, SOX9 is responsible for regulating tissue damaging ECM production from pro-fibrotic fibroblasts. In determining thein vivorole of SOX9 we identified secreted ECM components downstream of SOX9 as markers of acute lung injury and fibrosis. To underscore the translational potential of our SOX9-regulated markers, we analysed serum samples from acute COVID19, post COVID19 and idiopathic pulmonary fibrosis (IPF) patient cohorts. Our hypothesis driven SOX9-panels showed significant capability in all cohorts at identifying patients who had poor disease outcomes. This study shows that SOX9 is functionally critical to disease in acute lung injury and pulmonary fibrosis and its regulated pathways have diagnostic, prognostic and therapeutic potential in both COVID19 and IPF disease.
An unconventional autophagic pathway that inhibits ATP secretion during apoptotic cell death
Authors: Terraza-Silvestre Elena , Villamuera Raquel , Bandera-Linero Julia , Letek Michal , Ramón-Barros Cristina , Moyano-Jimeno Clara , Oña-Sánchez Daniel , Pimentel-Muiños Felipe X. 
Published: January 2024

SUMMARYMobilization of Damage-Associated Molecular Patterns (DAMPs) determines the immunogenic properties of apoptosis, but the mechanisms that control DAMP exposure are still unclear. Here we describe an unconventional autophagic pathway that inhibits the release of ATP, a critical DAMP in immunogenic apoptosis, from dying cells. Mitochondrial BAK activated by BH3-only molecules interacts with prohibitins and stomatin-1 through its latch domain, indicating the existence of an interactome specifically assembled by unfolded BAK. This complex engages the WD40 domain of the critical autophagic effector ATG16L1 to induce unconventional autophagy, and the resulting LC3-positive vesicles contain ATP. Functional interference with the pathway increases ATP release during cell death, reduces ATP levels remaining in the apoptotic bodies, and improves phagocyte activation. These results reveal that an unconventional component of the autophagic burst that often accompanies apoptosis sequesters intracellular ATP to prevent its release, thus favoring the immunosilent nature of apoptotic cell death.
A dynamic functional connectivity toolbox for multiverse analysis
Authors: Burkhardt Micha , Gießing Carsten 
Published: January 2024

ABSTRACTVarious methods for estimating dynamic functional connectivity from fMRI data and subsequent analyses through graph theoretic approaches have been introduced in recent years. But with many of the ground truths unknown, researchers are often faced with arbitrary yet defensible decisions for their analyses, which raises concerns about the reproducibility of results. We here aim to address this issue through the implementation of a wide array of dynamic functional connectivity methods in a unified Python software package, facilitating a diverse exploration of brain dynamics. Anchored in the framework of multiverse analysis, the present work further introduces a workflow for the systematic examination of various methodological decisions. The developed toolbox is supplemented by a graphical user interface for easy usability and accessibility if usage outside of a script-based Python analysis pipeline is desired. Further, extensive demo scripts are provided for researchers to easily adapt this approach for their own analyses.
Giardia Antagonizes Beneficial Functions of Indigenous and Therapeutic Intestinal Bacteria during Malnutrition
Authors: Bhatt Aadra P. , Arnold Jason W. , Awoniyi Muyiwa , Sun Shan , Santiago Verônica Feijoli , Quintela Pedro Henrique , Walsh Kenneth , Ngobeni Renay , Hansen Brenna , Gulati Ajay , Carroll Ian M. , Azcarate-Peril M. Andrea , Fodor Anthony A. , Swann Jonathan , Bartelt Luther A. 
Published: January 2024

ABSTRACTUndernutrition in children commonly disrupts the structure and function of the small intestinal microbial community, leading to enteropathies, compromised metabolic health, and impaired growth and development. The mechanisms by which diet and microbes mediate the balance between commensal and pathogenic intestinal flora remain elusive. In a murine model of undernutrition, we investigated the direct interactionsGiardia lamblia,a prevalent small intestinal pathogen, on indigenous microbiota and specifically on Lactobacillus strains known for their mucosal and growth homeostatic properties. Our research reveals thatGiardiacolonization shifts the balance of lactic acid bacteria, causing a relative decrease inLactobacillus spp. and an increase inBifidobacterium spp. This alteration corresponds with a decrease in multiple indicators of mucosal and nutritional homeostasis. Additionally, protein-deficient conditions coupled withGiardiainfection exacerbate the rise of primary bile acids and susceptibility to bile acid-induced intestinal barrier damage. In epithelial cell monolayers,Lactobacillus spp. mitigated bile acid-induced permeability, showing strain-dependent protective effects.In vivo, L. plantarum,either alone or within aLactobacillusspp consortium, facilitated growth in protein-deficient mice, an effect attenuated byGiardia, despite not inhibiting Lactobacillus colonization. These results highlight Giardia’s potential role as a disruptor of probiotic functional activity, underscoring the imperative for further research into the complex interactions between parasites and bacteria under conditions of nutritional deficiency.
Effects of D3-preferring agonist PD 128907 on compulsive behaviour and decision making as assessed by the 5C-CPT
Authors: Abdulkader Sara , Gigg John 
Published: January 2024

AbstractBackgroundRepetitive rituals in OCD patients result from pathological doubt, which has been linked to dysfunction in decision-making. First-line drug treatments for OCD are selective serotonin reuptake inhibitors; however, 40% of OCD patients do not respond to these. As brain activity patterns in OCD resemble those in schizophrenic patients, this suggests a dopaminergic component, supported by data showing that the D2/D3 receptor agonist Quinpirole induces compulsive checking in male rats. OCD has proved difficult to model in rodents and the contribution of decision making to compulsive behaviour in such models has not been studied. The five-choice continuous performance task (5C-CPT) measures both decision making and compulsive behaviour, making it possible to evaluate whether OCD models show correlated changes in these two behaviours. Establishing this would provide a new model approach to help develop therapeutic agents for OCD.AimsThe role of dopaminergic D3 receptors in decision making and compulsive behaviour was determined by testing the effect of the preferential D3 agonist PD 128907 on 5C-CPT performance measures. Oldham’s method was used to determine the presence of any rate-dependent effect.MethodsFemale Lister hooded rats were trained to criterion in the 5C-CPT (>70% accuracy, < 30% omission and < 40% false alarms). The effects of PD128907 (0.25-1 mg/kg) were then investigated under challenging task conditions.ResultsOldham method revealed: a moderate positive association between baseline perseverative correct responses and the change at 0.05 mg/kg PD 128907; a strong positive association between baseline perseverative false alarm and the change at 0.2 mg/kg; a positive association between baseline total number of perseverative responses and the change at 0.05 mg/kg or 0.2 mg/kg PD 128907; a positive relationship between baseline accuracy and the change at 0.05 mg/kg PD 128907; and a moderate positive association between baseline correct response latency and the change at 0.05 mg/kg or 0.2 mg/kg PD 128907. The angle measurements and the direction of movement (clockwise or counterclockwise) showed how effective is one dose at increasing compulsive behaviour compared with other doses.ConclusionsPD 128907 effects on compulsive like behaviour and decision making in poor performing female lister hooded rats with long correct response latency and high perseveration at baseline (vulnerable population) in the 5C-CPT task matches two key features of OCD compulsions in humans (perseveration and indecision), this suggests that PD 128907 is more effective than Quinpirole in simulating the brain network conditions that underpin OCD. This model could help to develop more successful pharmacological interventions and to generate data translatable to clinical studies.