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Endophytic fungi residing within medicinal plants represent a rich and sustainable source of bioactive secondary metabolites with diverse pharmacological applications. These symbiotic microorganisms establish mutualistic relationships with their host plants, contributing to enhanced stress tolerance, …
Read PDF<h4>Background</h4>Breast invasive carcinoma (BRCA) remains a leading cause of female cancer mortality, necessitating novel biomarkers and therapeutic targets. Heterogeneous nuclear ribonucleoprotein A3 (HNRNPA3) emerges as a potential regulator in tumor progression and immune modulation, yet …
Read PDF<h4>Background</h4>Acute pancreatitis (AP) ranges from mild to severe, and severe disease frequently causes multi-organ damage, with intestinal injury being a major complication. The mechanisms underlying SAP-induced intestinal injury remain unclear, particularly regarding spatial cellular reorganization …
Read PDFTranscriptomics experiments are often conducted to capture changes in gene expression over time. However, time annotations may be missing, imprecise, or not reflect the same physiological state of the bacterial culture between different experiments. Assigning …
Read PDFSpatial transcriptomics and in situ hybridisation techniques have become essential for contextualising single-cell RNA sequencing (scRNA-seq) data by mapping cell type- and state-specific mRNA expression within intact tissues. Beyond validating scRNA-seq predictions, these spatial methods …
Read PDFAs a pivotal therapeutic approach following surgery, chemoradiotherapy, and molecular targeted therapy, tumor immunotherapy has revolutionized survival outcomes for cancer patients, with immune checkpoint inhibitors (ICIs) demonstrating remarkable efficacy in clinical practice. However, challenges such …
Read PDFThe lower airways are a dynamic environment where physical, microbial, and molecular factors intersect to regulate respiratory health and disease. The muco-microbiotic (MuMi) layer, composed of mucus, resident microbes, and extracellular vesicles (EVs), is not …
Read PDFSpatial transcriptomics enables in situ mapping of gene expression, offering insights into tissue organization and cell-cell interactions. However, its utility is limited by data sparsity and technical noise for decoding complex tissue microenvironments. Here, we …
Read PDFSpaFun is a novel, non-model-based method developed to address limitations in existing spatially variable gene detection techniques, particularly for large-scale spatially resolved transcriptomics datasets. These limitations include computational inefficiency, limited statistical power with increasing data …
Read PDFDuring the initial stage of gestation, precise constructions of the microenvironment at the feto-maternal interface are critical for successful embryonic development to term. It consists of the fetal placenta and the maternal decidua, contributing to …
Read PDF<h4>Background</h4>Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, with marked heterogeneity in patient survival. Conventional clinicopathologic staging provides limited individualized prognostic information. Artificial intelligence (AI) and machine learning methods have enabled survival-aware …
Read PDF<h4>Background</h4>Dementia with Lewy bodies shares clinical and pathological features with both Parkinson's disease and Alzheimer's disease, but the local biological factors that render specific cortical regions vulnerable to atrophy remain poorly defined. In particular, it …
Read PDFIdiopathic pulmonary fibrosis (IPF) increases the risk of lung squamous cell carcinoma (LUSC), yet its molecular pathogenesis remains unclear. We conducted multi-omics analysis, including single-cell RNA sequencing and digital spatial profiling, on LUSC specimens from …
Read PDFCells function within intricate three-dimensional (3D) architectures to form tissues and organs. Constructing 3D tissue structure is critical for understanding cellular states, biological processes, and intercellular interactions. Herein, we describe a comprehensive 3D spatial omics …
Read PDFNeoadjuvant therapy (NAT) is increasingly used for pancreatic ductal adenocarcinoma (PDAC); yet most patients only achieve partial response. Pathological treatment response grading focuses on assessing residual tumor burden, often overlooking changes in tumor microenvironment (TME). …
Read PDFSpatial transcriptomics enables detailed mapping of gene expression within tissues, revealing spatial organization of cellular and molecular processes. However, generating such data is costly and technically challenging, and analysis requires advanced bioinformatics skills. Although public …
Read PDFThe emergence of multidrug-resistant (MDR) in various microorganisms due to prolonged antibiotic treatment poses a growing worldwide health issue. It is essential to identify alternative, effective methods to address MDR bacterial diseases, as treating infections …
Read PDFResolving fine-grained cell subtypes in single-cell RNA sequencing (scRNA-seq) data remains challenging, as their subtle transcriptional differences are often obscured by technical noise and data sparsity. Here, we present scMagnifier, a consensus clustering framework that …
Read PDFPulmonary manifestation in malaria can be life-threatening. Using a rodent malaria model and comprehensive transcriptomics analyses to illustrate the immune landscape of malaria-associated lung pathology, we identified that IFN-γ signaling in T cells plays an …
Read PDF<h4>Summary</h4>Understanding the molecular impact of ionizing radiation exposure is essential for both biomedical research and public health. Among the possible approaches to study this phenomenon, gene expression profiling via transcriptomics assays has been a valuable …
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