Tissue-specific network

BACKGROUND: Intracerebral hemorrhage (ICH) is a debilitating condition characterized by the rupture of cerebral blood vessels, resulting in profound neurological deficits. A significant challenge in the treatment of ICH lies in the brain's limited capacity to regenerate damaged blood vessels. This study explores the potential synergistic effects of Ginsenoside Rh2 and Chrysophanol in promoting angiogenesis following ICH in a rat model. METHODS: Network pharmacology was employed to predict the potential targets and pathways of Ginsenoside Rh2 and Chrysophanol for ICH treatment...

Somatic evolution selects cancer cell phenotypes that maximize survival and proliferation in dynamic environments. Although cancer cells are molecularly heterogeneous, we hypothesized convergent adaptive strategies to common host selection forces can be inferred from patterns of epigenetic and genetic evolutionary selection in similar tumors. We systematically investigated gene mutations and expression changes in lung adenocarcinomas with no common driver genes (n = 313). Although 13,461 genes were mutated in at least one sample, only 376 non-synonymous mutations evidenced positive evolutionary selection with conservation of 224 genes, while 1736 and 2430 genes exhibited ≥ two-fold increased and ≥ 50% decreased expression, respectively...

Activation of quiescent hepatic stellate cells (HSCs) into proliferative myofibroblasts drives extracellular cellular matrix (ECM) accumulation and liver fibrosis; nevertheless, the transcriptional network that promotes such a process is not completely understood. ZNF469 is a putative C2H2 zinc finger protein that may bind to specific genome sequences. It is found to be upregulated upon HSC activation; however, the molecular function of ZNF469 is completely unknown. Here, we show that knockdown of ZNF469 in primary human HSCs impaired proliferation, migration, and collagen production...

BACKGROUND: Intervertebral disc degeneration (IVDD) is a common degenerative condition leading to abnormal stress distribution under load, causing intervertebral stenosis, facet joint degeneration, and foraminal stenosis. Very little is known about the molecular mechanism of eRNAs in IVDD. METHODS: Gene expression profiles of 38 annulus disc samples composed of 27 less degenerated discs (LDs) and 11 more degenerated discs (MDs) were retrieved from the GEO database...

Lung cancer staging is crucial for personalized treatment and improved prognosis. We propose a novel bimodal diagnostic approach that integrates LIBS and Raman technologies into a single platform, enabling comprehensive tissue elemental and molecular analysis. This strategy identifies critical staging elements and molecular marker signatures of lung tumors. LIBS detects concentration patterns of elemental lines including Mg (I), Mg (II), Ca (I), Ca (II), Fe (I), and Cu (II). Concurrently, Raman spectroscopy identifies changes in molecular content, such as phenylalanine (1033 cm-1 ), tyrosine (1174 cm-1 ), tryptophan (1207 cm-1 ), amide III (1267 cm-1 ), and proteins (1126 cm-1 and 1447 cm-1 ), among others...

We investigated subarachnoid haemorrhage (SAH) macrophage subpopulations and identified relevant key genes for improving diagnostic and therapeutic strategies. SAH rat models were established, and brain tissue samples underwent single-cell transcriptome sequencing and bulk RNA-seq. Using single-cell data, distinct macrophage subpopulations, including a unique SAH subset, were identified. The hdWGCNA method revealed 160 key macrophage-related genes. Univariate analysis and lasso regression selected 10 genes for constructing a diagnostic model...

BACKGROUND: Intrahepatic cholangiocarcinoma (ICC) is a highly malignant neoplasm and characterized by desmoplastic matrix. The heterogeneity and crosstalk of tumor microenvironment remain incompletely understood. METHODS: To address this gap, we performed Weighted Gene Co-expression Network Analysis (WGCNA) to identify and construct a cancer associated fibroblasts (CAFs) infiltration biomarker. We also depicted the intercellular communication network and important receptor-ligand complexes using the single-cell transcriptomics analysis of tumor and Adjacent normal tissue...

Excess abdominal fat is a sexually dimorphic risk factor for cardio-metabolic disease and is approximated by the waist-to-hip ratio adjusted for body mass index (WHRadjBMI ). Whereas this trait is highly heritable, few causal genes are known. We aimed to identify novel drivers of WHRadjBMI using systems genetics. We used two independent cohorts of adipose tissue gene expression and constructed sex- and depot-specific Bayesian networks to model gene-gene interactions from 8,492 genes. Using key driver analysis, we identified genes that, in silico and putatively in vitro, regulate many others...

In mammals, the circadian clock network drives daily rhythms of tissue-specific homeostasis. To dissect daily inter-tissue communication, we constructed a mouse minimal clock network comprising only two nodes: the peripheral epidermal clock and the central brain clock. By transcriptomic and functional characterization of this isolated connection, we identified a gatekeeping function of the peripheral tissue clock with respect to systemic inputs. The epidermal clock concurrently integrates and subverts brain signals to ensure timely execution of epidermal daily physiology...

BACKGROUND AND OBJECTIVE: Complete denture is a common restorative treatment in dental patients and the design of the core components (major connector and retentive mesh) of complete denture metal base (CDMB) is the basis of successful restoration. However, the automated design process of CDMB has become a challenging task primarily due to the complexity of manual interaction, low personalization, and low design accuracy. METHODS: To solve the existing problems, we develop a computer-aided Segmentation Network-driven CDMB design framework, called CDMB-SegNet, to automatically generate personalized digital design boundaries for complete dentures of edentulous patients...

The genomes of plant and animal species are influenced by ancestral whole genome duplication (WGD) events, which have profound impacts on the regulation and function of gene networks. To gain insight into the consequences of WGD events, we characterized the sequence conservation and expression patterns of ohnologs in the highly duplicated activin receptor signaling pathway in rainbow trout (RBT). The RBT activin receptor signaling pathway is defined by tissue-specific expression of inhibitors and ligands and broad expression of receptors and Co-Smad signaling molecules...

Since their invention, tissue expanders, which are designed to trigger additional skin growth, have revolutionised many reconstructive surgeries. Currently, however, the sole quantitative method to assess skin growth requires skin excision. Thus, in the context of patient outcomes, a machine learning method which uses non-invasive measurements to predict in vivo skin growth and other skin properties, holds significant value. In this study, the finite element method was used to simulate a typical skin expansion protocol and to perform various simulated wave propagation experiments during the first few days of expansion on 1,000 individual virtual subjects...

OBJECTIVES:  This in vitro study aimed to investigate the impact of bicarbonate air-abrasive powders and ultrasonic scaling with stainless steel tips on the micro- and nanotopography and roughness of three different implant-abutment junction titanium surfaces. MATERIALS AND METHODS:  Three types of sterile and decontaminated titanium surfaces (RS, UTM, XA) were used for analysis. Nine disks per surface type were subjected to micro- and nanotopography analysis, scanning electron microscopy (SEM), roughness analysis, and fibroblast cultivation...

Comparative analyses between traditional model organisms, such as the fruit fly Drosophila melanogaster, and more recent model organisms, such as the red flour beetle Tribolium castaneum, have provided a wealth of insight into conserved and diverged aspects of gene regulation. While the study of trans-regulatory components is relatively straightforward, the study of cis-regulatory elements (CREs, or enhancers) remains challenging outside of Drosophila. A central component of this challenge has been finding a core promoter suitable for enhancer-reporter assays in diverse insect species...

The present work describes a preclinical trial ( in silico , in vivo and in vitro ) protocol to assess the biomechanical performance and osteogenic capability of 3D-printed polymeric scaffolds implants used to repair partial defects in a sheep mandible. The protocol spans multiple steps of the medical device development pipeline, including initial concept design of the scaffold implant, digital twin in silico finite element modeling, manufacturing of the device prototype, in vivo device implantation, and in vitro laboratory mechanical testing...

Multicellular organisms exhibit synergistic effects among their components, giving rise to emergent properties crucial for their genesis and overall functionality and survival. Morphogenesis, the formation of an organism's shape, involves and relies upon intricate and biunivocal interactions among cells and their environment, i.e., the extracellular matrix (ECM). Cells secrete their own ECM which, in turn regulates their morphogenetic program by controlling time and space presentation of matricellular signals...

Cancer remains a formidable adversary, challenging medical advancements with its dismal prognosis, low cure rates and high mortality rates. Within this intricate landscape, long non‑coding RNAs (lncRNAs) emerge as pivotal players, orchestrating proliferation and migration of cancer cells. Harnessing the potential of lncRNAs as therapeutic targets and prognostic markers holds immense promise. The present comprehensive review delved into the molecular mechanisms underlying the involvement of lncRNAs in the onset and progression of the top five types of cancer...

Accurate determination of body segment parameters is crucial for studying human movement and joint forces using musculoskeletal (MSK) models. However, existing methods for predicting segment mass have limited generalizability and sensitivity to body shapes. With recent advancements in machine learning, this study proposed a novel artificial neural network-based method for computing subject-specific trunk segment mass and center of mass (CoM) using only anthropometric measurements. We first developed, trained, and validated two artificial neural networks that used anthropometric measurements as input to predict body shape (ANN1) and tissue mass (ANN2)...

Organ formation requires tight coordination with vascular growth. Intricate networks of blood vessels course through all organs and tissues and are composed of both endothelial cells (ECs) and associated mural cells. Despite decades of research into the biology of blood vessel formation and homeostasis, little is known about how the vasculature ensures its properly coordinated growth and intimate development with the cells of different organs. Even more mystifying is how a highly dynamic endothelium quiesces to differentiate into mature vessels, and how disruption of this mature quiescence results in pathological conditions...

Background: Understanding how cells and tissues respond to stress factors and perturbations during disease processes is crucial for developing effective prevention, diagnosis, and treatment strategies. Single-cell RNA sequencing (scRNA-seq) enables high-resolution identification of cells and exploration of cell heterogeneity, shedding light on cell differentiation/maturation and functional differences. Recent advancements in multimodal sequencing technologies have focused on improving access to cell-specific subgroups for functional genomics analysis...