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Li, X.

Publications and source records attributed to Li, X..

At least 217 records · Page 12Linked to original sources

Robust Inference of Individualized Treatment Effect in Mendelian Randomization

Mendelian randomization (MR), leveraging genetic variants as instrumental variables (IVs), is widely used to draw causal conclusions in the presence of unmeasured confounding, but most MR analyses focus on average treatment effects and rely on strong assumptions. For precision medicine, the primary target is instead the individualized treatment effect (ITE); yet in MR, such effects are not point-identified under core IV assumptions, and valid inference for identifiable bounds of the ITEs is particularly challenging. In this work, we propose a robust partial identification inference framework for the identifiable bounds of the ITEs under MR allowing multiple IVs. Under minimal causal assumptions, we derive a sharp inference procedure for the bounds of ITE by adopting a multiplier bootstrap procedure with data-adaptive bootstrap distribution shifting and heterogeneous variance adjustment. In theory, we prove that the proposed method achieves nominal coverage and asymptotic sharpness. Further, we extend the procedure to tolerate possible invalid IVs under a minimal proportion rule assumption by aggregating over plausible IV subsets while preserving coverage. Simulation studies demonstrate that the proposed methods attain nominal coverage and substantially shorter intervals than existing procedures. We illustrate the framework using data from the Alzheimers Disease Neuroimaging Initiative to assess heterogeneous causal effects of TREM2 expression on Alzheimers disease risk across education-defined subgroups.

genetics↗

Student-Driven Microbiome Exploration: A Low-Cost 16S rRNA Sequencing Curriculum for Undergraduate Biology Education

Microbiome science is increasingly important in modern biology education because microbial communities influence human health, ecosystems, and environmental processes. However, undergraduate microbiome instruction is often limited by the high cost and technical complexity of sequencing-based workflows, restricting opportunities for authentic student-driven research. To address this challenge, we developed a low-cost, inquiry-based curriculum that enables undergraduate students to conduct complete microbiome studies using 16S rRNA gene sequencing. The module integrates project design, environmental sample collection, microbial cell processing, PCR amplification, sequencing, and bioinformatic analysis using open-source tools such as QIIME 2. Cost-reduction strategies included centrifugation-based cell collection and a surfactant-assisted direct PCR workflow that eliminated the need for commercial DNA extraction kits. Students designed independent research projects investigating microbial communities in local environments, including campus water sources and gym equipment surfaces. Assessment data from post-course surveys, knowledge checks, and student research products demonstrated strong learning gains in microbiome concepts, molecular biology techniques, scientific communication, and computational analysis. Students reported high confidence in PCR, experimental design, and microbiome interpretation, while also identifying bioinformatics as the most challenging yet rewarding component of the curriculum. All participants expressed increased interest in future research in microbiology or bioinformatics. Overall, this curriculum provides an accessible, scalable framework for integrating next-generation sequencing into undergraduate education while promoting inquiry-driven learning, student ownership, and engagement in authentic scientific research.

microbiology↗

An fMRI dataset of verbalized spontaneous thought with annotated transcripts and self-report trait measures

Spontaneous thought is pervasive in everyday human cognition, yet datasets capturing its neural dynamics under minimally interrupted conditions remain limited. The current dataset was acquired from a think-aloud functional MRI experiment in which 118 participants continuously verbalized their spontaneous thoughts during 10-minute scanning sessions. The raw MRI data and verbal transcripts with sentence-level timestamps were previously released and analyzed in our prior study examining neural activity associated with thought transitions. Building on that release, we additionally provide preprocessed MRI data, speech transcriptions with word-level timestamps aligned to image acquisition, large language model-generated ratings of transcribed thoughts across emotional and sensory dimensions, and self-report survey measures assessing personality, mental health, and cognitive abilities. Validation analyses demonstrated activation in expected cortical regions associated with speech production and sensory content identified from transcript annotations, agreement between language model and human ratings, and adequate internal consistency of survey measures, supporting the datasets overall quality. This dataset enables reuse for investigations of spontaneous thought, speech generation, and individual differences using naturalistic functional MRI data.

neuroscience↗

Pathway-informed Universal Domain Adaptation for Single-cell RNA-seq Data

The rapid accumulation of single-cell atlases has yielded datasets of unprecedented scale, encompassing samples across diverse platforms, locations and laboratories. This multidimensional complexity drives an urgent need for universal domain adaptation methods capable of achieving precise cell-type annotation. However, existing methods lack computational scalability and fail to integrate biological priors. Here, we develop scPathOT, a pathway-informed universal domain adaptation framework that leverages pathway activation transformations to harmonize single-cell datasets across disparate conditions. We demonstrate the versatility of scPathOT across diverse technological platforms, tissues, disease contexts, cellular senescence and treatment conditions. Crucially, this pathway-informed alignment not only accurately resolves cellular identities but also uncovers functional mechanism. In pancreatic islets, scPathOT delineates a shared stress-repair axis traversed by {beta}-cells prior to their divergence into type 1 and type 2 diabetes-specific states. In aging bone marrow, scPathOT disentangles lineage-specific senescence modules that unexpectedly converge onto unified inflammatory and oxidative-stress programs. Furthermore, application to an in-house pancreatic ductal adenocarcinoma cohort uncovers the mechanistic basis underlying the neoadjuvant chemotherapy-induced reorganization of stromal-immune crosstalk. By coupling biological priors with universal domain adaptation, scPathOT provides a scalable, mechanistically interpretable framework to accelerate biological discovery from atlas-level single-cell data.

bioinformatics↗

Alternative organelle targeting of OPA1 mediates fatty acid release from lipid droplets

Mitochondria and lipid droplets (LDs) are functionally coupled to coordinate fatty acid utilization and storage. However, a comprehensive understanding of mitochondria-LD alliances remains elusive. We have identified a previously unrecognized role for optical atrophy 1 (OPA1), a mitochondrial fusion factor, in the regulation of fatty acid release from LDs. We demonstrated that OPA1s exon 4 adapts an amphipathic helix to target OPA1 to LDs. OPA1 localized to LDs promote fatty acid release by facilitating the recruitment of lipases to LDs. In addition, OPA1s residence on LDs competes with its mitochondrial entry, influencing mitochondria fusion and connectivity. Furthermore, the S158N polymorphism within OPA1s exon 4 exhibiting attenuated fatty acid release from LDs is associated with changes in metabolic traits in pediatric cancer survivors. Altogether, our findings reveal that OPA1 actively mediates fatty acid release from LDs and provide a mechanistic link between OPA1 and human metabolism.

cell biology↗

NFIC-mediated CaSR endocytosis defines a hyperactive TOMM20highCHGAhigh oxyphil cell state as a pathological driver of autonomous secondary hyperparathyroidism

Secondary hyperparathyroidism (SHPT) is a debilitating complication of chronic kidney disease. Its clinical management is frequently compromised by calcimimetic resistance, a refractory state primarily driven by the progressive downregulation of the membrane calcium-sensing receptor (CaSR). Despite the centrality of CaSR as a therapeutic target, the mechanisms governing its aberrant expression and membrane localization remain incompletely elucidated. Here, we generated a single-cell transcriptomic atlas of human parathyroid tissues from SHPT and primary hyperparathyroidism (PHPT) patients, uncovering a unique stromal-immune niche that is specifically induced by uremic stress in SHPT. Our data also observed a striking dissociation between CaSR mRNA and its abundance as a membrane protein in SHPT tissues. Pseudotime trajectory analysis showed a progressive decline in CaSR pathway activity and a concomitant increase in endo-lysosomal activity along the trajectory, terminating in pathological oxyphil cells as the endpoint of chief cell differentiation in SHPT. Mechanistically, Nuclear Factor I C (NFIC) transcriptionally activated clathrin light chain B (CLTB) and Ras-related protein Rab7a (RAB7A) to trigger clathrin-mediated endocytosis and lysosomal degradation of CaSR, thus reducing its membrane abundance. This degradative program was further validated by multiplex immunofluorescence in TOMM20highCHGAhigh pathological oxyphil cells in human SHPT tissues. To translate these mechanistic findings into a clinically actionable strategy, we repurposed the clinically approved lysosomal inhibitor hydroxychloroquine (HCQ) to block this CaSR degradation pathway. In patient-derived xenograft (PDX) mouse models, co-administration of HCQ and cinacalcet acted synergistically to restore membrane CaSR expression, normalize serum PTH and calcium levels and suppress parathyroid tumor growth more effectively than monotherapies. Collectively, our single-cell-guided study identifies an NFIC-driven endo-lysosomal program as a previously unrecognized mechanism underlying CaSR downregulation and calcimimetic resistance in SHPT, and establishes HCQ repurposing as a clinically tractable therapeutic strategy for patients with refractory SHPT.

cell biology↗

An LLM-driven pipeline for proteomics-based detection and structural modeling of post-translational modifications

Post-translational modifications (PTMs) on proteins dynamically regulate their functions and subsequently cellular physiology. Significant advances have been made in their detection and modeling: mass spectrometry-based proteomics has become the cornerstone for PTM detection in complex samples, while emerging structure-prediction frameworks enable modeling of PTM-dependent conformational changes. However, the biological significance of many PTMs remains largely unexplored, in part because integrated pipelines that bridge PTM detection with structural modeling remain limited. We present a generative AI-driven pipeline that integrates PTM detection with structural modeling of their effects on protein dynamics and interactions. The pipeline comprises two complementary tools: PTMdiscoverer and PTM-Psi. First, PTMdiscoverer leverages large language models to identify, annotate, and interpret candidate PTMs from open-search proteomics results, addressing limitations of conventional proteomics tools. Next, PTM-Psi models the structural, functional, and dynamic consequences of these spatially aware modifications on protein dynamics. These two components bridge PTM discovery with mechanistic interpretation at the structural level. We demonstrate our pipeline by using cyanobacterial proteomics data to study potential molecular mechanisms of redox-regulated "dark complex" formation in carbon metabolism, advancing our ability to interpret PTM-mediated regulation in microbial systems.

bioinformatics↗

Hippocampal Glucuronyl C5-epimerase promotes stress resilience by directly engaging PI3K through a non-enzymatic mechanism

Major depressive disorder (MDD) seriously affects human physical and mental health and causes global socioeconomic burdens. Stress-induced depressive etiology is linked to dendritic atrophy in the hippocampus, however, the underlying mechanism was poorly understood. Here, we identify that glucuronyl C5-epimerase (Glce), a heparan sulfae-modifying enzyme, as a critical regulator of hippocampal dendritic integrity and stress resilience. Genetic ablation of Glce in the hippocampal excitatory neurons is sufficient to induce dendritic atrophy and depressive-like behaviors, whereas its restoration rescues these deficits. Notably, Glce levels are reduced in the plasma of depressed individuals. We further find that Glce functions independently of its enzymatic activity, instead binding directly to and activating PI3K (p85/p110), thereby triggering an Akt/CREB/BDNF signaling cascade. Together, our findings uncover a non-canonical role for Glce and establish that Glce-PI3K-BDNF axis is essential for maintaining hippocampal structure and behavioral resilience, thereby highlighting a critical role of Glce in the pathophysiology of depression.

neuroscience↗

Novel linkage disequilibrium-based genotype-by-environmental interaction method for genomic prediction of cotton yield and fibre quality traits

Genomic prediction (GP) across diverse environments has a potential to accelerate genetic gain in cotton breeding programs. A major challenge in GP is modelling genotype-by-environment interactions (GEI), which is essential for selecting stable and high-performing genotypes under variable production conditions. However, incorporating GEI into GP models increases the dimensionality and computational complexity, risking complex models that are impractical to use on commercial breeding-scale data sets because of run times and computational demands. This study addresses two primary aims. Firstly, we evaluate the practical benefits of GEI-informed GP for predicting economically important cotton traits. Second, advanced statistical modelling strategies are developed and assessed for integrating genomic and environmental data at scale. We propose a dimensionality reduction approach that combines linkage disequilibrium network analysis with principal component techniques to reduce redundancy while preserving informative variation. Using this reduced dataset, we implement Bayesian linear regression models and, for comparison, deep residual neural networks for genomic prediction. Analyses were conducted on a large multi-environment dataset from the CSIRO cotton breeding program, comprising 3,236 breeding lines, 54 environmental covariates, and 8,049 yield and fibre quality phenotype records collected over 10 years and 9 locations representing 41 year-location combinations. Results demonstrate that generally Bayesian linear regression approaches outperform BG-BLUP models, with all three linear/linear mixed methods providing clearly more reliable performance than the deep learning models. These findings highlight the value of using interpretable statistical models for integrating genomic and environmental information to support selection decisions under diverse environmental conditions.

plant biology↗

IL-36γ Drives Th9 cell Differentiation via IκBζ to Sustain Antitumor Immunity

Th9/Tc9 cells polarized with TGF-{beta} and IL-4 exhibit superior antitumor efficacy, prompting extensive efforts to optimize their differentiation protocols and augment therapeutic potency. In the current study, we identified IL-36{gamma} as a potent cytokine that synergizes with TGF-{beta} to robustly drive Th9 differentiation both in the presence and absence of IL-4. IL-36{gamma}-programmed Th9 cell subsets exhibited phenotypic and transcriptional profiles identical to classic Th9 cells. Mechanistically, IL-36{gamma} drove Th9 cell differentiation through amplifying key signaling pathways such as STAT6, STAT5, and NF-{kappa}B that are essential for classic Th9 programming. Notably, we uncovered a novel regulatory axis wherein IL-36{gamma} upregulates the transactivation factor I{kappa}B{zeta}, which directly governs Th9 lineage specification. In in adoptive cell therapy (ACT) models, IL-36{gamma}-polarized Th9 cell subsets demonstrated enhanced antitumor efficacy, attributable to their sustained persistence, reduced exhaustion markers and stem-like/memory properties. Collectively, this study elucidates a previously unrecognized I{kappa}B{zeta}-dependent mechanism underpinning Th9 differentiation and highlights the translational potential of IL-36{gamma}-engineered Th9 cells as a valuable ACT strategy for refractory tumors.

immunology↗

A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases

The BRAIN Initiative Cell Atlas Network (BICAN) is generating large-scale multimodal datasets to profile cell types in the human, non-human primate, and mouse brain. The diversity of single-cell and spatial transcriptomic and epigenomic assays, combined with varied experimental contexts, multiple data-generating laboratories and distributed infrastructure, poses substantial challenges for data integration and reuse in BICAN. To address this, we implemented a standards framework that enables layered integration of these data into knowledge-ready products for interoperable brain cell atlases. This framework organizes data based on three progressively structured layers. First, we introduced an assay-agnostic modeling layer that unifies the representation of single-cell and spatial omics data using a common set of biological entities and processes assessed by diverse experimental techniques. Second, we implemented harmonized metadata standards that capture key experimental features linked to biospecimen provenance across heterogeneous tissue sources, species, and preparations, supporting integration and validation while minimizing burden on data contributors. Third, we present an extensible representation for data-driven cell type taxonomies that integrates molecular data with annotations, ontology mappings, and evidence. Together, these contributions represent an end-to-end framework that transforms heterogeneous datasets into structured, interoperable resources that support broad community reuse via mapping algorithms, annotation systems, and visualization platforms. This approach links biospecimen provenance with cell-level outputs and embeds these in a standardized taxonomy format, enabling downstream applications such as cross-dataset integration, reference mapping, and knowledge-driven analysis. More broadly, our work demonstrates a generalizable strategy for enabling an efficient data-to-knowledge pipeline in a large-scale consortium setting.

genomics↗

Foxp4+ Mandibular Skeletal Stem Cells Orchestrate Bone/Tooth Development and Regeneration

The identity of stem/progenitor cells that drive mandible/tooth development and regeneration remains poorly understood. Here, we show that cranial neural crest-derived Foxp4+ mesenchymal cells condense to form Meckels cartilage, and simultaneously promote mandible development and tooth germ formation. In postnatal mandibles, Foxp4+ cells localize in the endosteum, periosteum and dental pulp, which undergo osteogenesis and odontogenesis under steady state, as well as chondrogenesis during fracture repair. Importantly, transplantation of embryonic or adult Foxp4+CD200+CD105- mandibular skeletal stem cells (mdSSCs) generate ectopic bone and tooth. In contrast, genetic ablation of Foxp4+ cells severely impairs mandible/tooth development and delays fracture healing. Mechanistically, we find that primary cilia critically regulate mdSSC maintenance and differentiation into bone and tooth. FOXP4+PDPN+CADM1+ mdSSCs also exist in adult human mandible, which generate ectopic bone and intact tooth upon transplantation into immunodeficient mice. Taken together, we identify Foxp4+ mdSSCs with potential therapeutic applications in regenerating mandibular bone and tooth.

cell biology↗

Atherosclerotic plaque iron accumulation characterizes a distinct phase of intra-plaque hemorrhage and is associated with inflammation and remodeling

Intraplaque haemorrhage (IPH) is a hallmark of advanced atherosclerosis and a major risk factor for ischemic stroke and myocardial infarction. Current IPH classification focusses on extravascular erythrocyte presence as a proxy of acute bleeding, where iron detection generally indicates older haemorrhages. While often used interchangeably, a comprehensive analysis of transcriptional and metabolic context and impact of iron and erythrocyte deposition on the plaque is still lacking. Here, we investigate iron as a late-stage IPH hallmark in human atherosclerotic plaques. We analysed erythrocyte-rich, iron-rich, and non-IPH regions in human carotid endarterectomy plaques by re-analysing a published transcriptomic dataset of 43 patient samples. In addition, we performed histological and immune phenotyping to define plaque traits associated with iron versus erythrocyte accumulation. Finally, we performed spatial metabolic profiling to functionally define iron-rich regions. Although iron and erythrocyte deposits frequently co-localised, both co-related with different histological traits. While iron- and erythrocyte-rich regions shared transcriptomic features of advanced plaques compared with non-IPH regions, direct comparison showed differences in gene expression profiles. Iron deposition was associated with increased myeloid cell accumulation and a unique spatial metabolic signature distinct from erythrocyte-rich and non-IPH regions. While sharing many characteristics with IPH plaques, the molecular, cellular and metabolic landscape of iron-rich regions is marked by features of plaque remodelling and repair. This makes iron deposition a unique hallmark of late-stage IPH, extending the current erythrocyte-based definition of IPH.

pathology↗

Harnessing Human Immune Organoid model for Systemic and Comparative Analysis of Clinically Vaccine Adjuvants

Effective vaccine adjuvants are crucial for eliciting strong, specific, and long-lasting adaptive immune responses. However, traditional vaccine and adjuvant development is often hindered by prolonged animal testing, reliance on singular evaluation metrics, and batch variability, limiting the comparative analysis of immune responses induced by different adjuvants. To our knowledge, systematic adjuvant-focused analysis in human immune organoids remains limited, particularly across distinct antigen-conditioned immune baselines. Here, we established a matrix supported human tonsil immune organoid (M-hTIO) platform, derived from tonsil tissue for systemic adjuvant evaluation. Within 2 days, the platform replicated key germinal center (GC) features, with the potential for antigen-specific antibody production and plasmablast differentiation. Dynamic GC formation and T-B cell interactions were tracked using light-field imaging. Notably, IL-21 significantly accelerates GC-like remodeling and enhanced immune responses. Employing bulk cell transcriptomics we systematically analyzed early immune signatures and prolonged adaptive responses induced by five clinical-grade adjuvants (Alum, MnJ{beta}, AddaSO3, R848, ODN 1018) paired with influenza HA and SARS-CoV-2 RBD antigens across only adjuvant, weak and strong memory backgrounds. By integrating early and prolonged response phases, M-hTIO captured complementary dimensions of adjuvant activity, distinguishing rapid immune activation from sustained adaptive remodeling. Importantly, early activation signatures and prolonged adaptive remodeling provided complementary information, highlighting the value of temporally resolved adjuvant evaluation. AddaSO3 showed a consistent activity pattern across early and prolonged response phases, supporting both rapid immune activation and sustained adaptive remodeling. Moreover, our findings reveal shared/exclusive signaling pathways and gene networks. These results represent systematic and comparative analysis of clinically tested vaccine adjuvants in a human model, paving the way for high-throughput systems vaccinology research.

immunology↗

EnzCast: Prediction of Patient-Specific Enzymatic Kinetics through Multi-Modal Deep Learning and Isoform-Resolved Bayesian Inference based on Single-Cell Transcriptomics

Enzyme kinetic parameters underpin mechanistic biology but remain sparse in physiological context. We present EnzCast, a multi-modal framework jointly predicting Km, kcat, kcat/Km, and Ki from protein sequence, 3D structure, substrate chemistry, and experimental conditions, paired with IsoKin, an isoform-resolved Bayesian framework converting EnzCast priors into patient-specific in vivo kinetics. Trained on KinBench, the largest curated kinetics database, task-adaptive EnzCast achieved R2 = 0.413, 0.455, 0.227, and 0.105 for Km, Ki, kcat, and kcat/Km, surpassing all baselines on catalytic tasks. Systematic condition scans recovered compartment-specific pH direction inversion and pathway-level temperature responses. In a 20-patient colorectal cancer single-cell cohort, IsoKin reduced posterior uncertainty by 73.3% and 77.3%, revealing cell-type-specific rewiring. Orthogonal validation--scFEA flux, DepMap essentiality (permutation P = 0.0008) and TCGA survival-- provided mixed but directionally consistent support. Together, EnzCast and IsoKin bridge in vitro prediction, condition-aware biochemical interrogation and patient-resolved in vivo inference.

bioinformatics↗

SpaCir-VDJ: a broadly compatible circularization strategy for spatial immune repertoire profiling

Deciphering the spatial organization of immune clonal lineages is critical for understanding the evolution of adaptive immune responses. However, mainstream spatial transcriptomics platforms struggle to reconcile cost-effective short-read sequencing with the simultaneous and efficient capture of V(D)J sequences. To address this gap, we developed SpaCir-VDJ, an approach that utilizes a "multiplex PCR enrichment plus library circularization" strategy to integrate spatial barcodes and V(D)J CDR3 regions into a compact circular template optimized for standard short-read sequencing. This workflow is accompanied by an automated computational pipeline designed for circular-library data parsing, sequence reconstruction, spatial barcode deconvolution, and high-fidelity clonotype calling. In human lymphoid tissues, SpaCir-VDJ delineated germinal center (GC)-associated clonal organization and isotype-linked somatic hypermutation (SHM) patterns. Notably, lineage-based spatial analyses inferred inter-GC clonal redistribution events, suggesting that GCs in the analyzed samples may not be fully isolated reaction units. Functional perturbation provided orthogonal support for candidate SHM regulators identified by spatial analysis, with knockdown of MDM4, LYN, EAF2, and H2AFY each leading to reduced SHM. Finally, in gastric cancer, SpaCir-VDJ localized dominant BCR lineages within tertiary lymphoid structures and tumor-margin plasma cell-rich regions, with lineage patterns consistent with extension toward the tumor interior. We further observed a significant positive correlation between cumulative tumor mutations and spatial TCR diversity, consistent with a spatial association between local mutational burden and T-cell remodeling within the tumor microenvironment. Collectively, SpaCir-VDJ provides a scalable and cost-effective framework for interrogating the spatiotemporal dynamics of immune microenvironments.

immunology↗

Yawning reveals energy-dynamics mismatch and neural inertia across state transitions

Yawning is a highly conserved behavior, yet its neural dynamics across arousal state transitions remain poorly understood. Classical reflex models fail to account for the precise timing of yawns during large-scale changes in brain network organization. Here, we investigated the neural signatures of yawning using simultaneous electroencephalography (EEG), electromyography (EMG), and kinematic recordings in a beagle model during wakefulness and propofol anesthesia. Propofol-associated yawning exhibited marked temporal asymmetry, with 89.2% of events occurring during emergence from anesthesia. To resolve the fast neural dynamics surrounding these events, we applied empirical mode decomposition coupled with the Hilbert-Huang transform (EMD-HHT) analyses. Across induction, recovery, and wakefulness, yawning was consistently associated with a transient decoupling between local and global network dynamics: a brief increase in local {gamma}-band power coincided with a drop in network flexibility, quantified by instantaneous frequency volatility; IFV). We termed this reproducible motif as "Energy-Dynamics Mismatch" (EDM). A machine learning classifier leveraging EDM features reliably decoded the brain state immediately preceding yawning. We further validated the presence of this signature in an independent human cohort during anesthesia induction. These findings indicate that yawning is not a passive reflex, but is tightly linked to moments of network instability during state transitions. From a computational perspective, EDG may reflect a transient "control effort" that preserves information integration in the presence of "neural inertia." This dynamic signature may provide a quantitative biomarker for monitoring arousal transitions brain-computer interface (BCI) interface state-alerting. Significance StatementYawning is a ubiquitous and evolutionarily conserved behavior, yet its neural basis remains elusive. Using high-resolution neural recordings in a cross-species model, we show that yawning is not a passive reflex, but reliably coincides with a distinct, transient brain-state signature. Specifically, yawning occurs when local high-frequency cortical activity briefly increases while global network flexibility decreases - a pattern we term an "Energy-Dynamics Mismatch" (EDM). We propose that EDM reflects a compensatory neural process engaged during moments of network instability, consistent with overcoming neural inertia to preserve information integration. By identifying this conserved neural marker, this work advances the biological understanding of yawning and suggests a potential biomarker for detecting critical brain states in future BCI.

neuroscience↗

ExMODE: A Multi-Omics Repository for Extremophile Adaptation and Bioprospecting

Extreme environments, though hostile to most life forms, host specialized extremophile communities that have redefined biological cognition and emerged as vital biotechnological resources, with their unique adaptive traits and bioactive molecules driving advances in multiple scientific and industrial fields. However, research on extremophiles is hindered by limitations in culture-based methods, fragmented multi-omics data with non-uniform annotation standards across repositories, the lack of cross-extreme comparative research in existing resources, and the singularity of data dimensionality that neglects key structural information, all of which restrict the functional interpretation of extremophile microbes and the exploitation of their bioprospecting potential. To tackle these challenges, we developed ExMODE (https://db.genomics.cn/exmode/), a comprehensive multi-omics database platform dedicated to extremophiles. It centrally integrates multi-omics data from diverse extreme habitats with a standardized annotation framework, resolving data fragmentation and enabling systematic cross-environment comparative analyses to elucidate extremophile adaptive mechanisms. Moreover, ExMODE aggregates multi-dimensional datasets including genes, genomes, secondary metabolite sequences and protein structures, overcoming the constraints of single-dimensional data and significantly improving the efficiency of biotechnological resource discovery from extreme microorganisms.

microbiology↗