Normal view
-
cs.AI, q-bio.NC updates on arXiv.org
-
Metropolis-Scale Resilient and Trustworthy Traffic Flow Inference Using Multi-Source Data
arXiv:2605.25004v1 Announce Type: cross Abstract: Inferring network-wide traffic states from sparse observations with high accuracy and trustworthy uncertainty quantification is essential for intelligent transportation systems, yet it remains challenging due to the underdetermined nature of the problem, multifaceted disturbances in sensing networks, and the inherent conflicts among multiple inference sub-tasks when modeled jointly. We propose the Task-Aware Attentive Neural Process (TA-ANP), a
-
Omics in Hepatocellular
-
Spatial transcriptomic-metabolic features of tumor foci and tumor capsule in microvascular invasion with hepatocellular carcinoma: A spatial multi-omics study
PLoS Med. 2026 May 15;23(5):e1004703. doi: 10.1371/journal.pmed.1004703. eCollection 2026 May.ABSTRACTBACKGROUND: Microvascular invasion (MVI) is closely related to the recurrence and metastasis of hepatocellular carcinoma (HCC), but the underlying cellular mechanism remains largely elusive. This study aims to elucidate the regional cellular discrepancy between MVI-positive (MVI+) and MVI-negative (MVI-) HCC by integrating Spatial transcriptomics (ST) and spatial metabolomics (SM).METHODS AND FI
Spatial transcriptomic-metabolic features of tumor foci and tumor capsule in microvascular invasion with hepatocellular carcinoma: A spatial multi-omics study
PLoS Med. 2026 May 15;23(5):e1004703. doi: 10.1371/journal.pmed.1004703. eCollection 2026 May.
ABSTRACT
BACKGROUND: Microvascular invasion (MVI) is closely related to the recurrence and metastasis of hepatocellular carcinoma (HCC), but the underlying cellular mechanism remains largely elusive. This study aims to elucidate the regional cellular discrepancy between MVI-positive (MVI+) and MVI-negative (MVI-) HCC by integrating Spatial transcriptomics (ST) and spatial metabolomics (SM).
METHODS AND FINDINGS: ST and SM were performed on six tissue samples from four patients (including 2 MVI+, 2 MVI-, and 2 paratumor tissues), with the integration of 79 public single-cell RNA sequencing datasets of HCC. Patient identity was used as a covariate in the linear equation for regional differentially expressed gene analysis with the ST data. Clinical validation was conducted through multiplex immunofluorescence staining in 79 patients, together with external validation in the cancer genome atlas (TCGA)-liver hepatocellular carcinoma (LIHC) cohort (n = 299) and an independent microarray dataset (n = 62). For cell-type-specific metabolic profiling, spatial transcriptomic-metabolic registration was performed. The functional roles of key metabolites were further validated in vitro using inflammatory cancer-associated fibroblasts (iCAFs) derived from hepatic stellate cells (HSCs) and primary CAFs through co-culture models and various functional assays assessing cell proliferation, migration, and invasion. In the tumor lesion, a malignant STMN1+HMGN2+GPC3+ cell subtype enriched in MVI+ HCC was identified, which exhibited enhanced proliferative activity and was associated with poor prognosis. This finding was further confirmed in a local cohort of 79 patients, where multiplex immunofluorescence staining for the three genes (STMN1, HMGN2, and GPC3) showed significantly higher expression in the MVI+ group than in the MVI- group (p = 0.046). Integrated SM analysis further revealed that this cell population underwent metabolic reprogramming characterized by suppressed glycerolipid metabolism. In the tumor capsule, iCAFs-related genes were downregulated in MVI+ cases, and iCAFs were located distally from the tumor boundary. Spatial metabolite mapping showed a strong correlation between taurine and iCAFs, and functional assays demonstrated that taurine promotes HCC proliferation and migration by suppressing iCAF activity. One limitation of this study is the small sample size of spatial omics data, which hinders a more complete molecular functional analysis of the STMN1+HMGN2+GPC3+ cell subtype and iCAFs in MVI+ HCC. Larger-scale ST cohorts are required to further validate and expand the findings of this study.
CONCLUSIONS: This integrative spatial atlas proposes a hypothesis that there exists a highly proliferative and metabolically reprogrammed malignant cell subtype in the tumor lesion of MVI+ HCC, and that taurine in the tumor capsule modulates iCAF activity to influence tumor progression. The exploratory results provide mechanistic insights into MVI-related HCC progression and offer potential avenues for targeted therapeutic intervention of MVI+ HCC.
PMID:42139279 | PMC:PMC13178920 | DOI:10.1371/journal.pmed.1004703
-
Nature - Issue - nature.com science feeds
-
Molecular basis for methylation-sensitive editing by Cas9
Nature, Published online: 15 April 2026; doi:10.1038/s41586-026-10384-zThermoCas9, a genome-editing enzyme that is sensitive to the DNA methylation status of the target locus, is characterized and shows promise for targeting hypomethylated DNA regions in cancer cells.
Molecular basis for methylation-sensitive editing by Cas9
Nature, Published online: 15 April 2026; doi:10.1038/s41586-026-10384-z
ThermoCas9, a genome-editing enzyme that is sensitive to the DNA methylation status of the target locus, is characterized and shows promise for targeting hypomethylated DNA regions in cancer cells.-
Cell
-
Genetically encoded fluorescent reporters to visualize α-synuclein pathology in live brain
The development of genetically encoded fluorescent reporters, along with their corresponding knock-in mouse lines for labeling α-Syn inclusions, enables diverse applications in studying the propagation and pathological effects of α-Syn inclusions in the live brain.
Genetically encoded fluorescent reporters to visualize α-synuclein pathology in live brain
-
Omics in Hepatocellular
-
Computational analysis of multi-omics data reveals CXCL10(+) DC-Treg interaction drives immunosuppressive microenvironment in AFP-positive hepatocellular carcinoma
Cell Mol Life Sci. 2026 Mar 19. doi: 10.1007/s00018-026-06167-4. Online ahead of print.NO ABSTRACTPMID:41854876 | DOI:10.1007/s00018-026-06167-4
Computational analysis of multi-omics data reveals CXCL10(+) DC-Treg interaction drives immunosuppressive microenvironment in AFP-positive hepatocellular carcinoma
Cell Mol Life Sci. 2026 Mar 19. doi: 10.1007/s00018-026-06167-4. Online ahead of print.
NO ABSTRACT
PMID:41854876 | DOI:10.1007/s00018-026-06167-4
-
cs.AI, q-bio.NC updates on arXiv.org
-
Rethinking Driving World Model as Synthetic Data Generator for Perception Tasks
arXiv:2510.19195v4 Announce Type: replace-cross Abstract: Recent advancements in driving world models enable controllable generation of high-quality RGB videos or multimodal videos. Existing methods primarily focus on metrics related to generation quality and controllability. However, they often overlook the evaluation of downstream perception tasks, which are $\mathbf{really\ crucial}$ for the performance of autonomous driving. Existing methods usually leverage a training strategy that first p