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Using biomedical foundation models (FMs) for inference on small cohorts, represents a promising and practical route to advance drug response biomarker discovery and target identification. Here, we demonstrate this via an innovative data-driven inference workflow, …
Read PDFDuring the hair cycle and wound regeneration, various developmental transcriptomic features are reactivated. Consequently, studying skin development provides critical insights into both fundamental biology and skin regeneration. However, chromatin accessibility during skin development remains underexplored. …
Read PDFAdvanced imaging and single-cell omics technologies are fundamentally transforming developmental biology research, shifting it from static observation to dynamic, spatially resolved systems biology. Super-resolution microscopy breaks the diffraction barrier to visualize nanoscale subcellular dynamics, while …
Read PDFRecent advances in spatial omics technologies have provided unprecedented insight into tissue spatial organization, but challenges remain in aligning spatial slices and integrating complementary single-cell and spatial data. Here, we propose TOAST (topography-aware optimal alignment …
Read PDFThe progression from metabolic dysfunction-associated steatotic liver disease (MASLD) to metabolic dysfunction-associated steatohepatitis (MASH) is a critical link leading to cirrhosis and hepatocellular carcinoma. Yet the responsible cellular programs remain unclear. We integrated public single-cell, …
Read PDFAn important task in the analysis of spatially resolved transcriptomics (SRT) data is to identify spatially variable genes (SVGs), or genes that vary in a 2D space. Current approaches rank SVGs based on either $ …
Read PDFThe process of arterial atherosclerosis is characterised by accumulation of lipids and fibrous material with accompanying inflammation. As plaques progress, they restrict blood flow and cause rupture, which results in life threatening organ ischemia and …
Read PDF<h4>Introduction</h4>The objective of this study was to evaluate the fetal programming effects of removing maternal heat abatement during late gestation on offspring growth, thermotolerance, physiological responses, and liver gene expression during the backgrounding phase.<h4>Methods</h4>Fifty-six Angus-cross …
Read PDFSpatial transcriptomics (ST) facilitates the exploration of biological tissue structures and functions within spatial context. Slice alignment and integration are prevalent for analyzing ST data, and current algorithms either focus on adjacent slices or require …
Read PDFTranslating pathogen-specific molecular insights into effective treatments remains a significant challenge, particularly for drug-resistant wound infections. In this study, we develop a nitrogen-doped iron/cobalt dual-atom catalyst (FeCo-N-DAC) with high metal loading (Fe > 5.4%, Co …
Read PDF<h4>Introduction</h4>Hepatocellular carcinoma (HCC) is a common malignant tumor, is characterized by an early stage that is not easy to diagnose and a high mortality rate in the late stage, which is a serious threat to …
Read PDFLocal protein synthesis is vital for neuronal function, but its dysregulation in neurodegenerative diseases remains poorly defined. Here we applied spatial transcriptomics to adult mouse motor nerve axons and cell bodies to enable subcellular mapping. …
Read PDF<h4>Study question</h4>Does the analysis of endometrial microbes provide the same information when using DNA or RNA sequencing-based techniques?<h4>Summary answer</h4>DNA vs RNA-based microbial analysis techniques demonstrated significant microbial compositional differences and lack of transcriptionally active lactobacilli …
Read PDFFertility is a multifactorial trait and a key determinant of productivity and sustainability in beef cattle production. Identifying molecular mechanisms and biomarkers associated with fertility could improve the prediction of reproductive potential in beef heifers. …
Read PDFBACKGROUND: Neutrophil extracellular traps (NETs) facilitate hepatocellular carcinoma (HCC) progression, but the upstream cellular organizers and the histopathological correlates of NETosis-prone niches remain poorly defined. We aimed to build a pathology-to-single-cell framework to (i) quantify …
Read PDF<h4>Introduction</h4>Cancer-associated fibroblasts (CAFs) are integral components of the tumor microenvironment that modulate the response to immune checkpoint inhibitors, particularly in breast cancer. However, the specific roles of CAF subtypes in regulating the efficacy of anti-PD-1 …
Read PDF<h4>Background</h4>Pancreatic ductal adenocarcinoma (PDAC), an aggressive cancer with poor prognosis, poses major challenges owing to late diagnosis and limited response to current therapies. However, the identification of candidate drugs through multi-omics analyses and therapeutic peptides …
Read PDF<h4>Background</h4>Tertiary lymphoid structures (TLSs) promote antitumor immunity and predict favorable immunotherapy outcomes in breast cancer. The study aimed to investigate how Tryptophan 2,3-dioxygenase (TDO2)-associated tryptophan metabolism influences TLS maturation and B cell class switching in …
Read PDF<h4>Background</h4>The orbitofrontal cortex (OFC) represents a promising yet underexplored neuromodulation target for negative symptoms in schizophrenia, and the macroscale and microscale mechanisms underlying its therapeutic effects remain unclear.<h4>Methods</h4>In a randomized, double-blind, sham-controlled trial, 84 patients …
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