Database

Traditional database search methods for the analysis of bottom-up proteomics tandem mass spectrometry (MS/MS) data are limited in their ability to detect peptides with post-translational modifications (PTMs). Recently, "open modification" database search strategies, in which the requirement that the mass of the database peptide closely matches the observed precursor mass is relaxed, have become popular as ways to find a wider variety of types of PTMs. Indeed, in one study, Kong et al. reported that the open modification search tool MSFragger can achieve higher statistical power to detect peptides than a traditional "narrow window" database search...

BACKGROUND: The unprecedented emergence of the COVID-19 pandemic necessitated the development and global distribution of vaccines, making the understanding of global vaccine acceptance and hesitancy crucial to overcoming barriers to vaccination and achieving widespread immunization. OBJECTIVE: This umbrella review synthesizes findings from systematic reviews and meta-analyses to provide insights into global perceptions on COVID-19 vaccine acceptance and hesitancy across diverse populations and regions...

BACKGROUND: Digital health interventions (DHIs) have shown promising results in enhancing the management of heart failure (HF). Although health care interventions are increasingly being delivered digitally, with growing evidence on the potential cost-effectiveness of adopting them, there has been little effort to collate and synthesize the findings. OBJECTIVE: This study's objective was to systematically review the economic evaluations that assess the adoption of DHIs in the management and treatment of HF...

BACKGROUND: Disclosure of donor conception has been advocated in several jurisdictions in recent years, especially in those that practice identity-release donation. However, research on disclosure decisions has not been consolidated systematically in the last 10 years to review if parents are telling and what factors may be impacting their decisions. OBJECTIVE AND RATIONALE: Are parents disclosing to their donor-conceived children, and what factors have influenced their disclosure decisions across different contexts and family forms in the last 10 years? SEARCH METHODS: A bibliographic search of English-language, peer-reviewed journal articles published between 2012 and 2022 from seven databases was undertaken...

BACKGROUND: As an antioncogene gene, phosphataseandtensinhomolog (PTEN) is closely related to tumorigenesis. However, after mutation, PTEN will lose its function and no longer exert a tumor suppression effect. Through this research, we explored the impact of PTEN mutation on hepatic carcinoma (HCC) and the mechanism of PTEN for regulating HCC. METHODS: First, bioinformatics was used to analyze the prognosis of PTEN in HCC. PTEN-related genes were then further analyzed by the LinkedOmics database, and GO and KEGG functional enrichment analysis were performed...

BACKGROUND: Leptomeningeal metastasis (LM) is a severe lung cancer complication, with potentially fatal consequences. The use of intrathecal therapy (IT) combined with systemic therapy has shown promise as a treatment approach for LM. Thus, this study aimed to evaluate the features and responses to IT combined therapy and identify determinants affecting patients with leptomeningeal metastasis resulting from lung adenocarcinoma (LM-LA). METHODS: A retrospective analysis of medical records from our hospital database was performed, covering from April 2018 to August 2022, for 37 patients diagnosed with LM-LA and treated with IT combined therapy...

OBJECTIVE: To analyze the characteristics of retracted oncology papers from Chinese scholars and the reasons for retraction. METHODS: Data on retracted oncology papers from Chinese scholars published from 2013 to 2022 were retrieved from the Retraction Watch database. The retraction number and annual distribution, article types, reasons for retraction, retraction time delay, publishers, and journal characteristics of the retracted papers were analyzed. RESULTS: A total of 2695 oncology papers from Chinese scholars published from 2013 to 2022 had been retracted...

INTRODUCTION: There are emerging but inconsistent evidences about anti-epileptic drugs (AEDs) as radio- or chemo-sensitizers to improve survival in glioblastoma patients. We conducted a nationwide population-based study to evaluate the impact of concurrent AED during post-operative chemo-radiotherapy on outcome. MATERIAL AND METHODS: A total of 1057 glioblastoma patients were identified by National Health Insurance Research Database and Cancer Registry in 2008-2015...

The incidence of thromboembolic events (TEs) in non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICIs) has rarely been reported. The MEDLINE, EMBASE, and the Cochrane Library databases were searched. The primary outcome was the incidence of TEs, and the secondary outcome was the relationship between TEs and overall survival (OS) following ICI therapy. A subgroup analysis of TE incidents was performed according to the TE type and combination regimens. The I2 statistic was used to determine the heterogeneity, and funnel plots and Egger's test were used to assess publication bias...

Objective Allergic asthma (AA) is common in children. Excess copper is observed in AA patients. It is currently unclear whether copper imbalance can cause cuproptosis in pediatric AA. Methods The datasets about pediatric AA (GSE40732 and GSE40888) were obtained from Gene Expression Omnibus (GEO) database. The expression of cuproptosis-related genes (CRGs) and immune cell infiltration in pediatric AA samples were analyzed. Single-cell RNA sequencing (scRNA-seq) data (GSE193816) were used to evaluate the expression patterns of CRGs in AA...

Background: This meta-analysis aimed to evaluate the effectiveness and adverse effects of specific immunotherapy (SIT) in the management of respiratory allergens, including allergic asthma, rhinitis, and related disorders, based on a review of current literature up to November 8, 2022. Methods: We conducted a search of databases, including PubMed, Embase, Cochrane, and Web of Science, to identify relevant randomized controlled trials (RCTs) assessing respiratory allergy-specific immunotherapy. We employed the Consolidated Standards of Reporting Trials (CONSORT) Statement to select RCTs that adhered to rigorous reporting standards...

Blackleg and soft rot are harmful diseases in potato (Solanum tuberosum) caused by Pectobacterium spp. and Dickeya spp. (Czajkowski et al. 2015). The occurrence of potato blackleg was serious in potato-producing areas around Xiapu County in Fujian Province, China, in 2021 (6 ha) and 2022 (7 ha), with an incidence of approximately 5%, which reached nearly 23%. Three diseased plants were collected to isolate the pathogen. Single colonies from each sampled plant were isolated and streaked onto fresh plates. DNA from three colonies from different plants was PCR amplified with primer pair 27F/1492R (Lane 1991) for the 16S rRNA gene...

BACKGROUND: Current staging systems have limitations in stratifying high-risk cases of cutaneous squamous cell carcinoma (cSCC). Tumor budding (TB) has emerged as a potential prognostic factor in various cancers. OBJECTIVES: This systematic review and meta-analysis aimed to evaluate the prognostic significance of TB in predicting lymph node metastases (NM) in cSCC. METHODS: A comprehensive search of the PubMed, Web of Science, EMBASE, and Cochrane databases was conducted...

Cancer cell lines are an important component in biological and medical research, enabling studies of cellular mechanisms as well as the development and testing of pharmaceuticals. Genomic alterations in cancer cell lines are widely studied as models for oncogenetic events and are represented in a wide range of primary resources. We have created a comprehensive, curated knowledge resource-cancercelllines.org-with the aim to enable easy access to genomic profiling data in cancer cell lines, curated from a variety of resources and integrating both copy number and single nucleotide variants data...

OBJECTIVE: The study aims to assess and compare the outcomes of modified radical surgery, preserving the nipple-areola complex, against radical mastectomy in patients with triple-negative breast cancer. Emphasis is placed on the clinical significance of this comparison, including its potential impact on patient outcomes, quality of life, and healthcare resources. METHODS: Relevant literature from January 2017 to January 2022 was searched in the following databases: PubMed, Embase, MEDLINE, Science Citation Index, Web of Science, China National Knowledge Internet, CCD, and CSPD with keywords...

OBJECTIVE: This study aimed to identify and analyze gender-specific differences in mRNA expression in the peripheral whole blood of acute ischemic stroke (AIS) patients using bioinformatics. METHODS: mRNA expression data from the peripheral whole blood of AIS patients were obtained from GEO datasets. Male stroke-related mRNAs (M-mRNAs) and female stroke-related mRNAs (F-mRNAs) were identified using GEO2R. The biological functions of M-mRNAs and F-mRNAs were evaluated using GO and KEGG databases, and protein-protein interaction networks were created...

OBJECTIVE: To explore the risk factors and predictive effects of visceral pleural invasion in lung adenocarcinoma patients with mGGN type, in order to identify high-risk groups of visceral pleural invasion early, and to provide more references for targeted intervention and individualized treatment adjustment of high-risk groups based on the analysis of risk factors. METHODS: The clinical data of 135 patients with mGGN-type lung adenocarcinoma who received surgical treatment in our hospital from January 2018 to December 2022 were selected from our hospital's medical record database for retrospective analysis...

OBJECTIVE: This meta-analysis aims to evaluate the comparative clinical efficacy of photodynamic therapy (PDT) versus other non-surgical treatments in managing peri-implantitis. METHODS: Computer searches were conducted in databases including PubMed, The Cochrane Library, Embase, China National Knowledge Infrastructure (CNKI), VIP, and Wanfang for randomized controlled trials (RCTs) on the clinical efficacy of Photodynamic Therapy (PDT) compared to other non-surgical methods in the treatment of peri-implantitis...

OBJECTIVE: Deep venous thrombosis (DVT) refers to a clot in a deep vein caused by various reasons. If such a clot becomes dislodged, it can return to the vein and lead to pulmonary embolism (PE), which can cause death in severe cases. Therefore, we aimed to evaluate the efficacy and safety of Safflower yellow combined with low molecular weight heparin (LMWH) for the prevention of DVT after orthopedic surgery. METHODS: A comprehensive search of randomized controlled studies (RCTs) of Safflower yellow combined with LMWH for the prevention of DVT after orthopedic surgery was performed in PubMed, Embase, Cochrane Library, CNKI, VIP, and Wanfang databases from January 2000 to June 2021...

OBJECTIVE: The NLRP3 inflammasome plays a dual role in the occurrence and development of tumors, and its role in lung cancer remains unclear. This study aims to investigate the impact of NLRP3 inflammasome activation on the proliferation and migration of lung cancer cells. METHODS: Data from the GEPIA, TCGA, and HPA databases were utilized to analyze the expression of NLRP3 in lung adenocarcinoma and its microenvironment. GO/KEGG enrichment analysis and GSEA analysis were employed to annotate the functions of differentially expressed genes related to NLRP3...