Corrigendum to "Identification of gene regulatory networks associated with breast cancer patient survival using an interpretable deep neural network model" [Expert Syst. Appl. 262 (2025) 125632].

[This corrects the article PMC11643596.].

Sirtuin1 mitigation of calcium oxalate nephropathy via enhancing itaconate abundance through reduction of histone trimethylation.

Background: Clinical therapeutic approaches to prevent and treat renal injury in patients with acute kidney injury (AKI) and chronic kidney disease (CKD) induced by calcium oxalate (CaOx) are limited. As a pivotal deacetylase, Sirtuin1 (Sirt1) exhibits notably anti-inflammatory effects, but its metabolic mechanism in regulating CaOx nephropathy remains unexplored.

Methods: We analysed organic acid metabolism in kidney using the nontargeted metabolome and identified key targets by RNA-seq.

Exploring Severe Fear of Childbirth in China: An In-depth Systematic Review of Prevalence, Risk Factors, and Interventions.

Objectives: Fear of childbirth (FOC) is a psychological symptom, prevalent among pregnant women, which negatively impacts women's health and well-being. The objective of this study is to analyze existing literature regarding pregnant women in China, evaluating the prevalence, risk elements, and interventions to alleviate severe childbirth fear.

Methods: A comprehensive search was done across nine bibliographic databases to retrieve published research from their earliest records to August 2023.

Knowledge Discovery in Databases of Proteomics by Systems Modeling in Translational Research on Pancreatic Cancer.

Background: Knowledge discovery in databases (KDD) can contribute to translational research, also known as translational medicine, by bridging the gap between and studies, and clinical applications. Here, we propose a 'systems modeling' workflow for KDD.

Methods: This framework includes the data collection of a composition model (various research models), processing model (proteomics) and analytical model (bioinformatics, artificial intelligence/machine leaning and pattern evaluation), knowledge presentation, and feedback loops for hypothesis generation and validation.

Translational studies on pancreatic cancer and gastric cancer: a methodology in PhD thesis.

Pancreatic ductal adenocarcinoma (PDAC) and gastric adenocarcinoma (GA) are aggressive cancers with poor prognoses, demanding innovative approaches to advance treatment strategies and prevention efforts. This article presents a methodology in connection with PhD thesis on PDAC and GA, including motivation and knowledge in literature (Paper I), various research models (Paper II), knowledge discovery (Papers III and IV), and thesis assessment and evaluation (dissertation). The four studies aimed to address the gaps between patients and researchers and between basic and clinical research.

Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data.

This study benchmarks the robustness and resilience of computational deconvolution methods for estimating cell-type proportions in bulk tissues, with a focus on comparing reference-based and reference-free methods. Robustness is evaluated by generating in silico pseudo-bulk tissue RNA sequencing data from cell-level gene expression profiles derived from four different tissue types, with simulated cellular composition at varying levels of heterogeneity. To assess resilience, we intentionally alter single-cell RNA profiles to create pseudo-bulk tissue RNA-seq data.

Ancient DNA reveals a two-clanned matrilineal community in Neolithic China.

Studies of ancient DNA from cemeteries provide valuable insights into early human societies, and have strongly indicated patrilocality. Here, we analysed ancient DNA alongside archaeological contexts and multiple stable isotopic data from 60 individuals in 2 separate cemeteries at the Fujia archaeological site in eastern China, dating between 2750 and 2500 BCE. Our findings suggest the existence of an early-described matrilineal community in the Neolithic period, characterized by high endogamy and a population practicing millet agriculture near the coast.

An augmented GSNMF model for complete deconvolution of bulk RNA-seq data.

Performing complete deconvolution analysis for bulk RNA-seq data to obtain both cell type specific gene expression profiles (GEP) and relative cell abundances is a challenging task. One of the fundamental models used, the nonnegative matrix factorization (NMF), is mathematically ill-posed. Although several of complete deconvolution methods have been developed and their estimates compared to ground truth for some datasets appear promising, a comprehensive understanding of how to circumvent the ill-posedness and improve solution accuracy is still lacking.

Mechanisms of Neuronal Differentiation and Notch Signaling as a Potential Therapeutic Target in Olfactory Dysfunction of Allergic Rhinitis.

Purpose: Olfactory dysfunction (OD) in allergic rhinitis (AR) significantly diminishes quality of life, yet its pathophysiology remains unclear. The Notch signaling pathway is known to regulate olfactory epithelium proliferation and differentiation in murine models, but its role in AR with OD (AR+OD) is yet to be elucidated. This study aims to explore neuronal expression patterns and the involvement of Notch signaling in AR+OD.

Impact of fixed-point rotational reduction of the spine on pain scores and lower limb motor function in patients with lumbar facet joint disorder.

Objective: This study explores the relieving effect of spinal fixed-point rotation reduction method on pain scores of patients with lumbar facet joint disorder, and analyzes its impact on lower limb motor function.

Methods: Ninety patients diagnosed with lumbar facet joint disorder and admitted to our hospital between February 2022 and February 2024 were selected for this study. Patients were randomly divided into two groups: the intervention group and the control group, each comprising 45 individuals.

Trans-ancestry GWAS identifies 59 loci and improves risk prediction and fine-mapping for kidney stone disease.

Kidney stone disease is a multifactorial disease with increasing incidence worldwide. Trans-ancestry GWAS has become a popular strategy to dissect genetic structure of complex traits. Here, we conduct a large trans-ancestry GWAS meta-analysis on kidney stone disease with 31,715 cases and 943,655 controls in European and East Asian populations.

SMYD3 Activates Fatty Acid β-Oxidation to Promote Self-Renewal of Leukemia Stem Cells.

The development of BCR-ABL tyrosine kinase inhibitors has revolutionized disease management of chronic myeloid leukemia (CML). However, the persistence of leukemia stem cells (LSC) remains a major barrier to curing CML, highlighting the urgent need to identify the regulators supporting LSCs. In this study, we validated the critical role of the histone methyltransferase SET and MYND domain-containing 3 (SMYD3) in the maintenance of LSCs in CML.

Knowledge Discovery in Datasets of Proteomics by Systems Modeling in Translational Research on Pancreatic Cancer.

Knowledge discovery in databases (KDD) can contribute to translational research, also known as translational medicine, by bridging the gap between and studies and clinical applications. Here, we propose a 'systems modeling' workflow for KDD. This framework includes data collection of composition model (various research models) and processing model (proteomics) and analytical model (bioinformatics, artificial intelligence/machine leaning and pattern evaluation), knowledge presentation, and feedback loops for hypothesis generation and validation.

Nociceptive neurons promote gastric tumour progression via a CGRP-RAMP1 axis.

Cancer cells have been shown to exploit neurons to modulate their survival and growth, including through the establishment of neural circuits within the central nervous system. Here we report a distinct pattern of cancer-nerve interactions between the peripheral nervous system and gastric cancer. In multiple mouse models of gastric cancer, nociceptive nerves demonstrated the greatest degree of nerve expansion in an NGF-dependent manner.

Preparation and application evaluation of monoclonal antibodies against Monkeypox virus A29 protein.

Monkeypox virus (MPXV) is a DNA virus belonging to the Orthopoxvirus genus of the Poxviridae family. It causes symptoms similar to Smallpox virus and is a zoonotic virus with widespread prevalence. Antigen detection is a fast and effective detection method.

Proteomics profiling of research models for studying pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies, with a five-year survival rate of 10-15% due to late-stage diagnosis and limited efficacy of existing treatments. This study utilized proteomics-based systems modelling to generate multimodal datasets from various research models, including PDAC cells, spheroids, organoids, and tissues derived from murine and human samples. Identical mass spectrometry-based proteomics was applied across the different models.

Advancements in sacroiliac joint reduction for enhancing lumbosacral pain relief and achieving balanced gait: A literature review.

This article provides a comprehensive review of recent research advancements in sacroiliac joint reduction therapy for addressing lumbosacral pain and gait balance issues, delving into its application efficacy, future outlook, and existing challenges. Current literatures were searched on sacroiliac joint reduction therapy, lumbosacral pain and gait balance disorders using the databases PubMed and Cochrane. There were no restrictions when conducting the literature search with regard to publication date, study language, or study type.

Identification of Gene Regulatory Networks Associated with Breast Cancer Patient Survival Using an Interpretable Deep Neural Network Model.

Artificial neural networks have recently gained significant attention in biomedical research. However, their utility in survival analysis still faces many challenges. In addition to designing models for high accuracy, it is essential to optimize models that provide biologically meaningful insights.

PRMT1 Promotes the Self-renewal of Leukemia Stem Cells by Regulating Protein Synthesis.

The application of tyrosine kinase inhibitors (TKIs) has revolutionized the management of chronic myeloid leukemia (CML). However, disease relapse and progression particularly due to persistent leukemia stem cells (LSCs) remain a big challenge in the clinic. Therefore, validation of the therapeutic vulnerability in LSCs is urgently needed.

OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers.

Alternative splicing (AS) is a crucial mechanism to regulate gene expression and protein complexity. RNA-binding proteins (RBPs) play an important role in regulating abnormal alternative splicing in cancers. However, few resources are available to identify specific RBPs responsible for regulating individual AS event.

Targeting DDX3X eliminates leukemia stem cells in chronic myeloid leukemia by blocking NT5DC2 mRNA translation.

Tyrosine kinase inhibitors (TKIs) are highly effective in the treatment of patients with chronic myeloid leukemia (CML), but fail to eliminate leukemia stem cells (LSCs), which can lead to disease relapse or progression. It is urgently need to identify the regulators specifically driving LSCs. In this study, we identified DEAD-box helicase 3 X-linked (DDX3X), a ubiquitously expressed RNA helicase, as a critical regulator for CML LSCs by using patient samples and BCR-ABL-driven CML mouse model.

Sirtuin1 Suppresses Calcium Oxalate Nephropathy via Inhibition of Renal Proximal Tubular Cell Ferroptosis Through PGC-1α-mediated Transcriptional Coactivation.

Calcium oxalate (CaOx) crystals induce renal tubular epithelial cell injury and subsequent nephropathy. However, the underlying mechanisms remain unclear. In the present study, single-cell transcriptome sequencing is performed on kidney samples from mice with CaOx nephrocalcinosis.

Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia.

Biomarkers associated with the progression from gastric intestinal metaplasia (GIM) to gastric adenocarcinoma (GA), i.e., GA-related GIM, could provide valuable insights into identifying patients with increased risk for GA.

CircSP3 encodes SP3-461aa to promote ccRCC progression via stabilizing MYH9 and activating the PI3K-Akt signaling pathway.

Clear cell renal cell carcinoma (ccRCC) is a primary kidney cancer with high aggressive phenotype and extremely poor prognosis. Accumulating evidence suggests that circular RNAs (circRNAs) play pivotal roles in the occurrence and development of various human cancers. However, the expression, clinical significance and regulatory role of circRNAs in ccRCC remain largely unclear.

IL-1β-induced epithelial cell and fibroblast transdifferentiation promotes neutrophil recruitment in chronic rhinosinusitis with nasal polyps.

Neutrophilic inflammation contributes to multiple chronic inflammatory airway diseases, including asthma and chronic rhinosinusitis with nasal polyps (CRSwNP), and is associated with an unfavorable prognosis. Here, using single-cell RNA sequencing (scRNA-seq) to profile human nasal mucosa obtained from the inferior turbinates, middle turbinates, and nasal polyps of CRSwNP patients, we identify two IL-1 signaling-induced cell subsets-LY6D club cells and IDO1 fibroblasts-that promote neutrophil recruitment by respectively releasing S100A8/A9 and CXCL1/2/3/5/6/8 into inflammatory regions. IL-1β, a pro-inflammatory cytokine involved in IL-1 signaling, induces the transdifferentiation of LY6D club cells and IDO1 fibroblasts from primary epithelial cells and fibroblasts, respectively.