ssMutPA: single-sample mutation-based pathway analysis approach for cancer precision medicine.

Background: Single-sample pathway enrichment analysis is an effective approach for identifying cancer subtypes and pathway biomarkers, facilitating the development of precision medicine. However, the existing approaches focused on investigating the changes in gene expression levels but neglected somatic mutations, which play a crucial role in cancer development.

Findings: In this study, we proposed a novel single-sample mutation-based pathway analysis approach (ssMutPA) to infer individualized pathway activities by integrating somatic mutation data and the protein-protein interaction network.

CITMIC: Comprehensive Estimation of Cell Infiltration in Tumor Microenvironment based on Individualized Intercellular Crosstalk.

The tumor microenvironment (TME) cells interact with each other and play a pivotal role in tumor progression and treatment response. A comprehensive characterization of cell and intercellular crosstalk in the TME is essential for understanding tumor biology and developing effective therapies. However, current cell infiltration analysis methods only partially describe the TME's cellular landscape and overlook cell-cell crosstalk.

Small Punch Testing of a Ti6Al4V Titanium Alloy and Simulations under Different Stress Triaxialities.

The mechanical properties of local materials subjected to various stress triaxialities were investigated via self-designed small punch tests and corresponding simulations, which were tailored to the geometry and notch forms of the samples. The finite element model was developed on the basis of the actual test method. After verifying the accuracy of the simulation, the stress, strain, and void volume fraction distributions of the Ti6Al4V titanium alloy under different stress states were compared and analyzed.

Umbilical cord mesenchymal stem cells: A novel approach to intervention of ovarian ageing.

Ovarian aging leads to endocrine disorders and systemic degeneration of tissue and organ structure and function, seriously affecting women's physical and mental health. Safe and effective treatments for this condition are lacking. Umbilical cord mesenchymal stem cells (UCMSCs), which have multidirectional differentiation potential, show strong self-renewal, secrete bioactive factors and release exosomes, can undergo homing, colonization, integration and differentiation into supporting and functional cells in tissues and organs through direct manipulation and can also improve the tissue microenvironment through paracrine action, promoting cell division, proliferation and microangiogenesis, inhibiting inflammation and apoptosis, reducing oxidative stress, and mediating two-way immune regulation.

Selected Lark Mitochondrial Genomes Provide Insights into the Evolution of Second Control Region with Tandem Repeats in Alaudidae (Aves, Passeriformes).

The control region () regulates the replication and transcription of the mitochondrial genome (mitogenome). Some avian mitogenomes possess two , and the second control region () may enhance replication and transcription; however, the in lark mitogenome appears to be undergoing loss and is accompanied by tandem repeats. Here, we characterized six lark mitogenomes from , , , and and reconstructed the phylogeny of Passerida.

IDMIR: identification of dysregulated miRNAs associated with disease based on a miRNA-miRNA interaction network constructed through gene expression data.

Micro ribonucleic acids (miRNAs) play a pivotal role in governing the human transcriptome in various biological phenomena. Hence, the accumulation of miRNA expression dysregulation frequently assumes a noteworthy role in the initiation and progression of complex diseases. However, accurate identification of dysregulated miRNAs still faces challenges at the current stage.

DrugSim2DR: systematic prediction of drug functional similarities in the context of specific disease for drug repurposing.

Background: Traditional approaches to drug development are costly and involve high risks. The drug repurposing approach can be a valuable alternative to traditional approaches and has therefore received considerable attention in recent years.

Findings: Herein, we develop a previously undescribed computational approach, called DrugSim2DR, which uses a network diffusion algorithm to identify candidate anticancer drugs based on a drug functional similarity network.

PathwayTMB: A pathway-based tumor mutational burden analysis method for predicting the clinical outcome of cancer immunotherapy.

Immunotherapy has become one of the most promising therapy methods for cancer, but only a small number of patients are responsive to it, indicating that more effective biomarkers are urgently needed. This study developed a pathway analysis method, named PathwayTMB, to identify genomic mutation pathways that serve as potential biomarkers for predicting the clinical outcome of immunotherapy. PathwayTMB first calculates the patient-specific pathway-based tumor mutational burden (PTMB) to reflect the cumulative extent of mutations for each pathway.

-Cardio: A comprehensive analysis platform for cardiovascular-relavant regulation in human and mouse.

-regulatory elements are important molecular switches in controlling gene expression and are regarded as determinant hubs in the transcriptional regulatory network. Collection and processing of large-scale -regulatory data are urgent to decipher the potential mechanisms of cardiovascular diseases from a -regulatory element aspect. Here, we developed a novel web server, -Cardio, which aims to document a large number of available cardiovascular-related -regulatory data and to provide analysis for unveiling the comprehensive mechanisms at a -regulation level.

DTSEA: A network-based drug target set enrichment analysis method for drug repurposing against COVID-19.

The Coronavirus Disease 2019 (COVID-19) pandemic is still wreaking havoc worldwide. Therefore, the urgent need for efficient treatments pushes researchers and clinicians into screening effective drugs. Drug repurposing may be a promising and time-saving strategy to identify potential drugs against this disease.

SEdb 2.0: a comprehensive super-enhancer database of human and mouse.

Super-enhancers (SEs) are cell-specific DNA cis-regulatory elements that can supervise the transcriptional regulation processes of downstream genes. SEdb 2.0 (http://www.

CRdb: a comprehensive resource for deciphering chromatin regulators in human.

Chromatin regulators (CRs) regulate epigenetic patterns on a partial or global scale, playing a critical role in affecting multi-target gene expression. As chromatin immunoprecipitation sequencing (ChIP-seq) data associated with CRs are rapidly accumulating, a comprehensive resource of CRs needs to be built urgently for collecting, integrating, and processing these data, which can provide abundant annotated information on CR upstream and downstream regulatory analyses as well as CR-related analysis functions. This study established an integrative CR resource, named CRdb (http://cr.

Efficient Adsorption-Assisted Photocatalysis Degradation of Congo Red through Loading ZIF-8 on KI-Doped TiO.

Zeolitic imidazolate framework-8 (ZIF-8) was evenly loaded on the surface of TiO doped with KI, using a solvent synthesis method, in order to produce a ZIF-8@TiO (KI) adsorption photocatalyst with good adsorption and photocatalytic properties. The samples were characterized by XRD, SEM, EDX, XPS, BET and UV-Vis. The photocatalytic efficiency of the material was obtained by photocatalytic tests.

Characterization and Validation of ceRNA-Mediated Pathway-Pathway Crosstalk Networks Across Eight Major Cardiovascular Diseases.

Pathway analysis is considered as an important strategy to reveal the underlying mechanisms of diseases. Pathways that are involved in crosstalk can regulate each other and co-regulate downstream biological processes. Furthermore, some genes in the pathways can function with other genes the relationship of the competing endogenous RNA (ceRNA) mechanism, which has also been demonstrated to play key roles in cellular biology.

Prognostic Role of Long Noncoding RNAs in Oral Squamous Cell Carcinoma: A Meta-Analysis.

Long noncoding RNAs (lncRNAs) have emerged as critical regulators of tumor progression, and lncRNA expression levels could serve as a potential molecular biomarker for the prognosis and diagnosis of some cancers. However, the prognostic value of lncRNAs in oral squamous cell carcinoma (OSCC) remains unclear. Thus, a meta-analysis was conducted to explore the potential prognostic value of lncRNAs in OSCC.

Kirsten rat sarcoma viral oncogene homolog G12C mutant advanced non-small-cell lung cancer treated with MEK1/2 inhibitor trametinib: a case report.

No targeted therapies are approved for non-small-cell lung cancer (NSCLC) with Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation to date. Trametinib, a selective allosteric inhibitor of the MEK1/2, demonstrated debatable clinical activity in KRAS-mutant NSCLC. In this case, we present a recurrent advanced NSCLC with KRAS G12C mutation successfully treated with single-agent trametinib therapy.

Genotoxicity detection of oil-containing drill cuttings by Comet assay based on a demersal marine fish Mugilogobius chulae.

An enormous amount of oil-containing drill cuttings have been produced by the marine oil and gas industry. The environmental impacts of discharged drilling waste have been extensively studied. However, there is still an urgent need to develop alternative methods to identify the genotoxicity of untreated and treated drill waste in a timely manner before it is discharged.

An interobserver reproducibility analysis of size-set semiautomatic counting for Ki67 assessment in breast cancer.

Purpose: The proliferation marker Ki67 has prognostic and predictive values in breast cancer, and the cutoff of the Ki67 label index (LI) is a key index for chemotherapy. However, poor interobserver consistency in Ki67 assessment has limited the clinical use of Ki67, especially in luminal cancers. Here, we reported a modified Ki67 assessment method, size-set semiautomatic counting (SSSAC) and investigated its interobserver reproducibility.

[Establishment and clinical application of modified endoscopic freka trelumina placement].

Objective: To establish a modified endoscopic Freka Trelumina placement (mEFTP) for modifying or substituting the traditional endoscopic Freka Trelumina placement (EFTP) and to explore the safety and feasibility of mEFTP in patients requiring enteral nutrition and gastrointestinal decompression in general surgery.

Methods: A retrospective cohort study was conducted to analyze the clinical data of patients undergoing EFTP or mEFTP at General Surgery Department of 920 Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army from January 2016 to January 2018.

Inclusion Criteria: the function of lower digestive tract was normal; patients who could not eat through mouth or nasogastric tube needed to have enteral nutrition and gastrointestinal decompression; the retention time of Freka Trelumina (FT) was not expected to exceed 2 months.

ARL4C stabilized by AKT/mTOR pathway promotes the invasion of PTEN-deficient primary human glioblastoma.

Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) deficiency in primary human glioblastoma (GBM) is associated with increased invasiveness and poor prognosis with unknown mechanisms. Therefore, how loss of PTEN promotes GBM progression remains to be elucidated. Herein, we identified that ADP-ribosylation factor like-4C (ARL4C) was highly expressed in PTEN-deficient human GBM cells and tissues.

RAS mutations in acute myeloid leukaemia patients: A review and meta-analysis.

RAS oncogene mutations frequently occur in acute myeloid leukaemia (AML), but the prognostic significance of RAS mutations in AML is inconclusive. We searched the databases of PubMed, Web of Science, EMBASE, and Cochrane from 1990 to 2018. In this study, 24 eligible studies were included, and the meta-analysis was conducted with the Comprehensive Meta-Analysis Version 2 software program.

Microbial diversity and ecotoxicity of sediments 3 years after the Jiaozhou Bay oil spill.

In 2013, the "Qingdao oil pipeline explosion" released an estimated 2000 tons of oil into the environment. Sediment samples were collected from ten sites in Jiaozhou Bay and Shilaoren Beach to evaluate the influence of the spilled oil on the benthic environment 3 years after the oil spill accident. The compositions of oil, bacterial diversity and biotoxicity were examined in this study.