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Wu, X.

Publications and source records attributed to Wu, X..

At least 73 records · Page 4Linked to original sources

BiomniBench: Process-level Evaluation of LLM Agents for Real-world Biomedical Research

LLM agents now perform real biomedical research, but evaluating them rigorously is hard. Outcome-only benchmarks fail in two ways. First, a correct final answer can come from memorization, reward hacking, or wrong reasoning that produces the right number by chance. Second, valid alternative analyses are marked wrong simply because they differ from the reference. We introduce BiomniBench, a process-level evaluation framework that scores the full agent trajectory against expert-designed, task-specific rubrics. Our first release, BiomniBench-DA, contains 100 data-analysis tasks across 17 task types, 5 disease areas, and a general-biology category, each based on a paper from journals such as Nature, Cell, and Science and co-developed with an original author or a domain expert. Benchmarking frontier and open-weight models across four agent harnesses reveals three findings. Frontier and open-weight bases cluster within a few points of each other, with substantial headroom for all models. The agent harness shifts scores by more than the gap between successive model generations. Agents reliably ground claims in real sources yet consistently fall short on method selection, biological interpretation, and scientific reasoning. BiomniBench is the first process-level benchmark for LLM agents in biomedical research, providing the dimension-level diagnostics that outcome scoring cannot. Datasethuggingface.co/datasets/phylobio/BiomniBench-DA

bioinformatics↗

AI platform for CRISPR functional mapping and function-based drug design

Conventional structure-based drug design has high clinical failure rates due to the disconnect where binding affinity does not guarantee safe functional modulation. To bridge this gap, we present CRISPRtile, a cloud-based platform for function-based drug design. By deriving library coverage optimization equations and leveraging AI to correct CRISPR guide biases, we generated toxicity and functional landscapes with over threefold error reduction compared to conventional methods. These maps bypass error and orders of magnitude higher computational cost in structure-based pipelines by enabling AI prediction of drug interaction directly from nontoxic functional sequences, while predicting brain penetration with benchmark leading performance. We demonstrate CRISPRtile by mapping the NLRP3 inflammasome and identifying FDA approved drugs with previously unrecognized ability to modulate it, revealing strategies to amplify or inhibit our immune response to homeostatic perturbations. These advances establish a generalizable strategy for the systematic discovery of safe functional modulators.

genetics↗

An 80-channel receive array for 10.5T neuroimaging: Key considerations for SNR optimization

PurposeHigh-density RF receive arrays are required to realize the inherently available SNR and parallel imaging advantages at ultrahigh field strengths, which are essential for high-resolution functional and anatomical brain MRI. This study aims to systematically assess the impacts of often-overlooked parasitic losses associated with various RF coil components, as these losses can degrade the realized SNR and cause significant deviation from the ultimate intrinsic SNR (uiSNR; the theoretical upper bound of available SNR). In addition, we seek to detail engineering solutions to each of these loss mechanisms in pursuit of achieving a higher fraction of the uiSNR limit. MethodsA 16-channel loop-folded dipole transceiver array was developed for 10.5T human head applications and paired with a fully-updated 64-channel receive-only loop array. The optimization of the receive array considered several factors, including (but not limited to) coil dimensions to accommodate a larger population, the size and number of loops to enhance SNR and parallel imaging performance, and circuit design strategies to minimize parasitic losses. The SNR and parallel imaging performance of the receive array were quantitatively assessed by comparison with the uiSNR, as well as existing high-channel-count receive arrays at 7T and 10.5T. Finally, the complete 16-channel transmit, 80-channel receive coil array was safety validated for human use and employed for high-resolution functional and anatomical MRI at 10.5T. ResultsInitial results show that the 80-channel array, featuring larger loops in an overlapped layout with optimized circuitry, significantly improves the SNR and approaches the uiSNR limit in a large fraction of the head, while maintaining or enhancing the parallel imaging performance compared to previously used non-overlap layout. ConclusionThis study suggests that, although the traditionally used high-channel-count loop receive array technology can approach the uiSNR limit in the >10T regime, meticulous design optimization--including systematic assessment and minimization of parasitic losses--has become increasingly critical for achieving this goal in this new field-strength territory.

neuroscience↗

A suture-specific oocyst wall protein COWP4 is essential for excystation and infectivity, while COWP6 links wall architecture to host interaction in Cryptosporidium parvum

The oocyst of Cryptosporidium is a highly resilient transmission stage that protects sporozoites in the environment and mediates infection through a specialized opening known as the suture. While recent studies have identified Cryptosporidium oocyst wall proteins (COWPs) as structural components of the oocyst wall, the functional roles of individual COWPs and the molecular basis of suture biology remain poorly understood. Here, we performed a detailed characterization of two COWP family members, COWP4 and COWP6, combining immunolocalization, ultrastructural analysis, protein interaction assays, and genetic manipulation. We show that COWP4 is strictly localized to the oocyst suture, whereas COWP6 is distributed throughout the oocyst wall inner layer and enriched at the suture. COWP6 is additionally present in sporozoites and is secreted during parasite motility and host cell invasion, where it exhibits high-affinity binding to host cells. Structural analyses indicate that both proteins are cysteine-rich and likely form disulfide-stabilized architectures consistent with roles in wall assembly. Functional analyses reveal that COWP4 is essential for proper suture formation, excystation, and parasite infectivity, establishing the suture as a genetically defined gatekeeper for parasite transmission. In contrast, COWP6 functions as a multifunctional protein linking oocyst wall architecture to host interaction. We further demonstrate that COWP4 and COWP6 interact, suggesting coordinated assembly within the oocyst wall. Together, these findings provide a functional dissection of the Cryptosporidium oocyst suture and reveal distinct, non-redundant roles for individual COWPs. This work advances our understanding of oocyst wall biology and identifies COWP4 as an essential determinant of parasite transmission that may be targeted to disrupt the infectious cycle. Author summaryCryptosporidium is a major cause of diarrheal disease worldwide and is transmitted through environmentally resistant oocysts that protect infectious stages of the parasite. A defining feature of the oocyst is a specialized seam-like structure, called the suture, through which parasites exit to initiate infection. Although oocyst wall proteins (COWPs) have been identified, how individual proteins contribute to the structure and function of the oocyst wall, particularly the suture, has remained unclear. In this study, we investigated two oocyst wall proteins, COWP4 and COWP6, and uncovered distinct roles for each. We found that COWP4 is specifically localized to the suture and is essential for its proper formation, enabling parasites to exit the oocyst and establish infection. In contrast, COWP6 is distributed more broadly in the oocyst wall and also functions beyond it, being secreted during parasite movement and interacting with host cells. These findings reveal that the oocyst wall is composed of specialized proteins with non-redundant functions and identify the suture as a critical control point for parasite transmission. Understanding these mechanisms may help guide the development of new strategies to block infection by disrupting oocyst integrity or parasite release. HighlightsO_LICOWP4 is a suture-specific protein essential for oocyst excystation and infectivity C_LIO_LIGenetic disruption of COWP4 produces non-infectious oocysts with impaired viability C_LIO_LIThe oocyst suture is a genetically defined gatekeeper for parasite transmission C_LIO_LICOWP6 localizes to the wall inner layer and is enriched at the suture C_LIO_LICOWP6 is secreted by sporozoites and binds host cells with nanomolar affinity C_LIO_LI{middle dot} COWP4 and COWP6 directly interact, linking wall architecture to host interaction C_LI

microbiology↗

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↗

NEURA: An agentic system for autonomous neuroimaging workflows

Neuroimaging research depends on heterogeneous software, multimodal data and multistage statistical workflows. Large language model (LLM)-based agents offer a route to automate these workflows, but their susceptibility to hallucination limits their credibility in scientific use. Here we introduce NEURA, a proof-carrying framework for hallucination-resistant neuroimaging automation. NEURA converts free-text research questions and neuroimaging datasets into executable analysis plans, validated outputs and structured reports. The system combines disease- and tool-aware planning with a deterministic verification layer inspired by formal proof: before any claim is retained for reporting, it must be checked against tool-derived evidence and domain axioms. On NeuroEval, an expert-curated benchmark of 110 neuroimaging tasks, NEURA achieved 89.5% planning accuracy, a 30.5% improvement over direct LLM queries. In a controlled hallucination-injection experiment, the verification layer detected all the injected error classes under the specified axiom bank and trust assumptions, with no false positives. In case studies of spinocerebellar ataxia type 3, NEURA reproduced cerebellar atrophy and abnormal diffusion patterns consistent with established pathology and independent expert analyses. Together, these findings show that coupling domain-grounded agency with proof-carrying verification can turn LLM-driven workflow automation from probabilistic self-checking into auditable scientific computation.

neuroscience↗

A new species of Rana from Anhui, China (Anura, Ranidae)

The diversity of the brown frog genus Rana may be underestimated as the high similarity of morphological characters. A new species belonging to the genus Rana is delineated based on eight specimens obtained from the Tianma National Nature Reserve, Jinzhai County, Luan City, Anhui Province, China. The phylogenetic analysis based on three mitochondrial genes (12S, ND2, and Cyt b) and one nuclear gene (BDNF) showed that the new species formed an independent clade closely related to R. culainensis and received strong support. In addition, morphological differentiation confirmed the phylogenetic results, and both supported the validity of a new species (Rana tianmaensis sp. nov.) in the R. japonica species group. The discovery of this new species enhances peoples understanding of the biodiversity of Rana and can provide important foundational data for scientific decision-making on protected area construction, ecological conservation, and species diversity. With the inclusion of newly described species in this study, the distribution of Rana genus in China now includes 31 recognized species.

zoology↗

Rhizoxin and 2,4-diacetylphloroglucinol Contribute to Biocontrol of Pseudomonas protegens Pf-5 Against Pea Ascochyta Blight Pathogen Didymella pinodes

Biological control using beneficial bacteria is a promising strategy for managing pea Ascochyta blight (AB), yet the underlying mechanisms remain poorly understood. In this study, we identified ten bacterial strains from four genera, including Bacillus, Paenibacillus, Peribacillus, and Pseudomonas, that significantly reduced the severity of AB caused by Didymella pinodes under greenhouse conditions. Most strains inhibited D. pinodes in vitro, suggesting antibiosis as a primary mode of action. To further elucidate the biocontrol mechanisms, we used Pseudomonas protegens Pf-5, which produces eight known antimicrobial compounds, as a model. While wild-type Pf-5 strongly inhibited D. pinodes in cultures and controlled AB in planta, a derivative ({Delta}8-fold mutant) lacking all eight compounds showed significantly compromised biocontrol efficacy. Individual complementation of biosynthetic genes for rhizoxin, 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin, or hydrogen cyanide partially restored inhibitory activity, confirming their roles in inhibition of D. pinodes. Notably, restoring rhizoxin and DAPG biosynthesis recovered the disease control capability of the {Delta}8-fold mutant in greenhouse trials. These results demonstrate that rhizoxin and DAPG are key metabolites driving the biocontrol activity of P. protegens against D. pinodes. SIGNIFICANCEAn advanced understanding of how beneficial bacteria control plant diseases can help us better use these microorganisms in agriculture. In this study, beneficial bacteria isolated from pea roots and soils effectively mitigated damages of pea Ascochyta blight caused by the fungal pathogen Didymella pinodes. Most of the identified beneficial bacteria inhibited the fungal pathogen in cultures, indicating antimicrobial compounds were likely produced by the bacteria to control the disease. Using the soil beneficial bacterium Pseudomonas protegens Pf-5 as a model, we demonstrated that four bacteria-derived antimicrobial compounds, rhizoxin and 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin, and hydrogen cyanide play important roles in inhibiting D. pinodes growth. This study also showed that rhizoxin and DAPG produced by Pf-5 contribute to the suppression of AB development. These findings provided new insights into the molecular basis of beneficial bacteria-mediated disease suppression of pea Ascochyta blight.

microbiology↗

U-Probe: universal agentic probe design for imaging-based spatial-omics

Probe design for fluorescence in situ hybridization (FISH) underpins spatial transcriptomics, three-dimensional genome studies, and clinical diagnostics, yet remains constrained by two challenges: dependence on expert knowledge for parameter selection and quality evaluation, and the inability of existing tools to accommodate the diverse probe architectures introduced by rapidly emerging methods. Here we present U-Probe, a universal and agentic probe design platform. U-Probe employs a declarative configuration system with a directed acyclic graph (DAG)-based assembly engine that supports arbitrary probe structures from established protocols such as MERFISH, seqFISH, and MiP-seq to entirely novel architectures without code modifications. Integrated LLM-based AI agents enable conversational design workflows, allowing users to specify experimental goals in natural language and receive synthesis-ready probe sequences. We validated U-Probe in three scenarios: agent-driven MiP-seq panel design for influenza-infected mouse lung tissue, genome-tiling DNA-FISH for herpesvirus detection, and a novel RCA-based ligation probe for single-nucleotide mutation discrimination. U-Probe is available as an open-source tool with CLI, Web, and agent interfaces.

bioinformatics↗

Rete Ridge Topography as a Determinant of Epidermal Stem Cell Identity: Implications for Skin Aging

Stem cell niches are dynamic microenvironments that regulate tissue homeostasis. Epidermal stem cells (EpiSC) preferentially localize to concave regions of epidermal rete ridges, which serve as primary niches for stem cell maintenance. EpiSC number and functional integrity decline during chronological aging. A defining feature of aged skin is epidermal atrophy, in which the prominent rete ridges present in young skin become flattened. Whether such topographical alterations influence EpiSC homeostasis and differentiation remains unclear. To address this, we generated anatomically accurate rete ridge structures using 3D bioprinting of collagen matrices as an ex vivo model and compared EpiSC cultured within concave topography to those maintained on a flat matrix resembling aged skin. Transcriptomic analysis revealed that concave niches promoted keratinocyte differentiation, marked by increased type I and II keratin gene expression and downregulation of cell cycle-associated genes. ATAC-seq identified topography-dependent chromatin accessibility changes enriched for transcription factors regulating epidermal differentiation, including upregulation of KLF4 and GRHL3 and downregulation of SOX9, HOXA1, and ETS1. Consistently, aged human skin showed reduced KLF4 and GRHL3 and increased SOX9 compared with young skin. Our findings demonstrate that concave niche topography imposes a spatially defined EpiSC microenvironment that promotes differentiation, alters cell cycle, and when perturbed, potentially contributes to the aging process. We conclude that spatial localization within rete ridge regions significantly affects epidermal progenitor stemness properties as fundamental differences in the physical microenvironment appear to influence cell fate decisions, thus, form shapes function of EpiSC.

cell biology↗

Dissetangling the Vine: Phylogenomics and Historical Biogeography of Vanilla (Orchidaceae)

Renowned for its aromatic fruits and economic importance, the genus Vanilla poses longstanding taxonomic and phylogenetic challenges. Despite recent molecular studies, a comprehensive species tree is lacking, and the evolutionary processes and historical patterns shaping the genus remain poorly understood. We present a new, comprehensive phylogenomic framework for Vanilla, based on 349 low-copy nuclear genes and 76 plastid loci from the Angiosperms353 probe set, which we used to infer evolutionary relationships, assess cyto-nuclear and gene-species tree discordance, and thoroughly investigate its historical distribution and diversification. Sampling 43% of the genus, our framework resolves phylogenetic uncertainties, clarifies major clades, confirms prior hypotheses, and reveals novel placements, including V. planifolia and Vanilla subg. Gondwana. Discordances are primarily driven by incomplete lineage sorting, particularly in the vanillin-producing clade, with evidence of both ancient and recent hybridization, including a natural hybrid from the Yucatan Peninsula. Biogeographic analyses indicate a Guiana Shield origin ([~]30 Mya), Amazonia as a major diversification source, the Andes as a permeable barrier, and Central America as the main diversification sink. This study provides a robust evolutionary framework for Vanilla, supporting taxonomic revisions, comparative trait analyses, and a deeper understanding of the processes shaping this economically and biologically important orchid genus.

evolutionary biology↗

A lateral linker histone binding mode scaffolds dinucleosome stacking in chromatin fibers

Linker histones are essential for chromatin compaction, yet how they contribute to higher-order fiber assembly remains poorly understood. Here, we determined cryo-electron microscopy structures of Arabidopsis dodeca-nucleosome fibers containing distinct H2A/H3 variants and linker histone H1.3, revealing a noncanonical binding mode that a laterally positioned H1.3 connects the acidic patch of one nucleosome and the DNA of the neighboring nucleosome, thereby scaffolding dinucleosomes into two-start chromatin fibers. This noncanonical binding mode is structurally conserved when H1.3 is replaced by Gallus gallus H5. Furthermore, incorporation of H2A.W and H3.3 further induces back-to-back fiber dimerization. Cryo-electron tomography and in vivo cross-linking mass spectrometry analyses support the physiological relevance of H1 lateral engagement. Our findings establish that linker histones act as active architectural scaffolds in higher-order chromatin organization.

molecular biology↗

Probiotic Lactiplantibacillus plantarum VB165 improves metabolic disorders in Insulin-Resistant Mice

This study investigated the effects of Lactiplantibacillus plantarum VB165, a probiotic strain with intrinsic -glucosidase inhibitor (AGI) activity, on metabolic disorders in high-fat diet (HFD)-induced insulin-resistant (IR) mice. Male C57BL/6 mice were divided into four groups: normal control diet (NCD), NCD supplemented with VB165, HFD, and HFD supplemented with VB165. After 16 weeks, VB165 supplementation significantly attenuated HFD-induced weight gain and reduced epididymal and inguinal white adipose tissue indices. VB165 also improved glucose intolerance and insulin resistance (IR), as demonstrated by oral glucose tolerance tests (OGTT) and insulin tolerance tests (ITT), and lowered fasting blood glucose, fasting insulin, and Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) levels. Additionally, it ameliorated dyslipidemia by reducing serum total cholesterol, triglycerides, and low-density lipoprotein cholesterol (LDL-C), while alleviating hepatic steatosis and adipocyte hypertrophy. Mechanistically, VB165 enhanced intestinal barrier function by upregulating tight junction proteins (ZO-1 and Occludin), reduced systemic inflammation by lowering LPS, IL-6, and IL-1{beta}. Gut microbiota analysis revealed that VB165 modulated community composition, suppressing HFD-enriched genera (e.g., Ileibacterium and Coriobacteriaceae_UCG_002) and promoting beneficial taxa (e.g., Faecalibaculum and Oscillibacter). These findings demonstrate that L. plantarum VB165 improves HFD-induced metabolic disorders via multi-target mechanisms, highlighting its potential as a probiotic intervention for IR and related metabolic diseases.

microbiology↗

Paternal behavior is controlled by preoptic Trpc5 neurons

Male parenting behavior is highly conserved and activated only after offspring are born. Here we show that the behavioral switch from infanticide in virgin male mice to caregiving in wild-type sires is associated with enhanced expression and activation of Transient receptor potential channel 5 (Trpc5) in estrogen receptor (Esr1)-expressing neurons in the hypothalamic medial preoptic area (MPOA). While selective deletion of Trpc5 from Esr1MPOA neurons diminishes paternal behavior in sires, overexpression of Trpc5 in these neurons converts the otherwise infanticidal virgin males to exhibit care to pups. Mechanistically, Trpc5-dependent changes in neuronal excitability underlie fatherhood-associated Esr1MPOA neuron plasticity. Notably, Trpc5 overexpression also enhances escape behavior and elicits exploratory diving behavior, suggesting that these neurons control a broader adaptive parenting response in males. These findings establish a Trpc5-dependent MPOA neural signal as a critical regulator of paternal behavior.

neuroscience↗

Donor-derived CD8+CD122+ Tregs generated in mixed donor chimeric NOD mice delete autoreactive T cells

The establishment of mixed hematopoietic chimerism is a promising way to induce immune tolerance for islet replacement therapy and to treat the underlying autoimmunity in type 1 diabetes (T1D). Mixed chimerism not only promotes effective thymic negative selection of autoreactive cells but also restores regulatory T cell (Treg) function and peripheral tolerance. In the current study, we determined that a novel class of donor-derived CD8+CD44+CD122+ Tregs (d-CD8+CD122+ Tregs) plays a crucial role in controlling autoimmunity in non-obese diabetic (NOD) mice with induced mixed chimerism. Using adoptive T cell transfer experiments, we showed that d-CD8+CD122+ Tregs abrogate autoimmunity by selectively depleting the exogenously injected diabetogenic T cells in Recombination-Activating Gene deficient NOD mice. These d-CD8+CD122+ Tregs from NOD chimeras show upregulation of Helios, Programmed cell death protein 1, perforin, granzyme-B, CD39, Folate receptor 4, and downregulation of proinflammatory markers like Scart1 and Scart2. Using in vitro assays, we show that d-CD8+CD122+ Tregs respond specifically to a Complementarity-Determining Region-3 peptide sequence derived from T cell receptors of islet antigen-specific autoreactive T cells. Similarly, we found that individuals with T1D have a deficiency in CD8+CD122+ Tregs, suggesting a potential loss of regulatory function accompanies disease onset. Revitalizing CD8+CD122+ Tregs may offer a new therapeutic strategy of restoring immune tolerance in autoimmune diabetes.

immunology↗

Adipose-driven complement-lipid reprogramming controls nociceptive vulnerability in obesity-associated osteoarthritis

Obesity amplifies osteoarthritis (OA) pain disproportionately to joint damage, creating a major unmet clinical need for non-opioid interventions that act beyond the joint. Using OA as a translational model, we integrated serum multi-omics in obese mice with surgically induced OA and genetic and adipose-reconstitution models of complement factor D (FD). In humans, we analyzed longitudinal metabolomics data from the IDEA weight-loss trial and conducted functional studies in dorsal root ganglion (DRG) neurons. Adipose-derived FD emerged as a regulator of systemic immunometabolic state: FD deficiency in obese mice worsened pain sensitivity whereas restoring circulating FD normalized pain and inflammatory markers without altering joint structure. Cross-species lipid profiling identified conserved shifts in linoleic acid versus arachidonic acid-derived lipids that were associated with pain phenotypes in mice and with pain improvement in humans. Defined lipid cocktails modulated excitability and TRPV1 sensitivity in human DRG neurons, and transcriptomics of knee-innervating DRGs revealed diet and FD-dependent activation of complement and neuronal excitability pathways. Together, these findings define an adipose-complement-lipid axis that regulates nociceptive vulnerability independent of joint damage and identify extra-articular targets for translational, non-opioid OA pain therapies. One Sentence SummaryWe identify an adipose-complement-lipid axis that systemically regulates sensory neuron sensitization, providing a mechanistic basis for pain-structure discordance in obesity-associated osteoarthritis.

physiology↗

A feed-forward loop between niche adenosine and Gzmk⁺ CD8 T cells propagates systemic inflammaging

The causal link between the aging microenvironment and T cell aging remains elusive. Here, we demonstrate that adenosine within aging tissues actively reprograms CD8+ T cells into a pro-aging Granzyme K+ (Gzmk+) population. Mechanistically, senescent cells create an adenosine-rich niche via p16-dependent CD39 upregulation, triggering A2aR signaling to induce Gzmk+ T cell differentiation. Once released, Gzmk promotes systemic inflammaging through PAR1 and complement activation. Crucially, targeting this axis--either via genetic Gzmk ablation or pharmacological A2aR blockade--reverses multi-organ aging phenotypes and significantly extends healthy lifespan in mice. Human analysis reveals age-dependent Gzmk+ T cell accumulation in multi organs, while coffee intake (an A2aR antagonist) inversely correlates with plasma Gzmk levels. Our findings uncover how metabolic niche changes drive T cell aging and establish the adenosine-Gzmk axis as a pivotal therapeutic target for combating age-related diseases.

immunology↗

Convergent cortical temporal axis: common cortical oscillatory modes

Brain dynamics provide the most direct substrate for neural function and representation. Extensive prior work has demonstrated that the human brain is organized into hierarchical structures across molecular, cellular, microstructural, and macroscale network levels. However, whether these hierarchies can be directly linked through shared patterns of neural dynamics remains unresolved, and clear evidence from data-driven analyses is still lacking. A central open question is whether brain dynamics vary along a single continuous dimension, or whether they are instead composed of a limited number of reproducible coordination modes that could provide a unifying basis for cross-scale integration. Here, using source-resolved resting-state magnetoencephalography (MEG), we adopt a fully data-driven approach that imposes no a priori assumptions about cortical hierarchy or gradient structure. By characterizing full-spectrum power relationships across cortical regions, we identify a set of stable and reproducible spectral coordination modes. These modes capture how multiple frequency components jointly co-vary across space, defining distinct dynamical configurations rather than conventional band-limited oscillations or continuous gradients. The identified spectral coordination modes exhibit pronounced spatial differentiation across the cortex, distinguishing regions dominated by narrowband rhythmic activity from those characterized by broadband or multi-frequency coordination. Importantly, these modes do not correspond to predefined hierarchical axes, nor can they be reduced to existing MEG gradients or functional connectivity organizations. Instead, they emerge directly from the data, revealing a finite set of shared organizational patterns underlying cortical dynamics. Multimodal analyses further demonstrate that individual spectral coordination modes show selective associations with neurotransmitter system distributions, laminar microarchitecture, and cell-type-specific gene expression, suggesting that these dynamical patterns may serve as linking mechanisms between micro- and macroscale brain organization. Computational modeling supports this interpretation, showing that differences in local circuit parameters are sufficient to generate distinct spectral coordination states without invoking a single global dynamical hierarchy. Across the adult lifespan, these coordination modes exhibit frequency- and region-specific reorganization, indicating multiple parallel trajectories of dynamical aging. In Parkinsons disease, alterations are observed in specific spectral coordination modes, particularly within higher-order cortical regions, suggesting that the disorder preferentially disrupts distinct dynamical configurations rather than inducing a global breakdown of cortical dynamics. Together, these findings indicate that large-scale brain dynamics are not organized along a single pre-existing hierarchical axis, but instead are structured by a limited number of data-driven spectral coordination modes. This framework provides a new dynamical perspective for linking brain organization across modalities and scales, and offers a principled avenue for understanding systematic changes associated with aging and neurological disease.

neuroscience↗