Beykent University

Aim: This study aimed to investigate the genetic variations, protein-protein interactions, and functional involvement of HTRA2 in mitochondrial homeostasis and apoptosis, with a focus on its potential contribution to Parkinson's disease (PD) pathology. Methods: Genetic variations in HTRA2 were identified using dbSNP, SWISS-Prot, and ClinVar. Protein-protein interaction (PPI) analysis was performed using STRING and GeneMANIA. Gene expression data were obtained from UniProt, BioXpress, and GTEx, and pathway analysis was conducted using KEGG. Disease associations were identified through the DISEASES database. Results: HTRA2 was found to interact strongly with apoptosis-related proteins, including DIABLO, XIAP, BIRC2, and BIRC3. It exhibited high expression in brain regions crucial for neuronal survival. Nine missense mutations were identified as potentially pathogenic. KEGG pathway analysis linked HTRA2 to mitochondrial dysfunction and apoptosis. Additionally, associations with Alzheimer's disease, essential tremor, and cancer were observed. Conclusion: HTRA2 plays a critical role in maintaining mitochondrial quality control and regulating apoptosis. Its dysfunction may contribute to PD pathogenesis by promoting neuronal death. These findings suggest that HTRA2 may represent a promising therapeutic target for PD and related neurodegenerative disorders.

To critically examine the structural limitations of the classical Decayed-Missing-Filled Teeth (DMFT) index and to propose a biologically structured, severity-adjusted conceptual framework through the Weighted DMFT (W-DMFT) model. This study presents a conceptual-analytic framework without quantitative field data. The methodological constraints of the DMFT index were examined across four domains: biological progression, functional impact, radiographic detectability, and restorative assessment. Based on the enamel-dentin-pulp hierarchy, a structured weighting system (0-3) was developed to reflect increasing biological invasion and functional consequences.The W-DMFT score is expressed as a severity-adjusted mean value per tooth. The classical DMFT index applies uniform scoring that does not differentiate lesion depth or functional severity. In contrast, the W-DMFT model introduces hierarchical weighting to capture biological progression, incorporates radiographically detectable dentinal involvement, and numerically represents functional impairment. The model provides a theoretically enhanced framework for severity-sensitive caries assessment. The W-DMFT model offers a structured conceptual extension of the classical DMFT by integrating lesion depth and functional considerations into epidemiological scoring. While biologically grounded, empirical validation studies are required to assess reliability, reproducibility, and population-level performance.

Abstract Objective As Industry 4.0 reshapes the labor market, the concept of occupational risk has evolved from purely physical hazards to complex psychosocial and ergonomic challenges. This study aims to evaluate the safety culture perception levels of vocational school students and to investigate the “interdisciplinary gap” between Technical and Social programs regarding the tangibility of risk. Method Employing a retrospective cross-sectional survey design, data were collected from a stratified random sample of 420 students (210 Technical, 210 Social) enrolled at Istanbul Beykent University Vocational School during the Fall Semester of the 2025–2026 Academic Year. The “Occupational Health and Safety Competence Perception Scale” developed by Kocaay (Yükseköğretim Kurulu Ulusal Tez Merkezi, 2020) was utilized to measure students’ risk perception, safety compliance, and safety communication. Results The analysis revealed a significant interdisciplinary dissociation. Technical students scored significantly higher in “Risk Perception” (X̄ = 4.28) and “Safety Compliance” (X̄ = 4.30). Conversely, Social students exhibited a distinct “Knowledge-Attitude Gap,” demonstrating moderate theoretical communication but alarmingly low behavioral compliance (X̄ = 2.90). Furthermore, female students demonstrated significantly higher safety rule compliance than male students (p < .05). Conclusion The findings suggest that the tangible nature of technical risks may facilitate better internalization, whereas social students often perceive office-based risks as “invisible” or distant. To bridge this gap, a paradigm shift from a uniform curriculum to a sector-specific, simulation-based OHS education integrating “Risk Science” principles is strongly recommended.

cBioPortal for Cancer Genomics is a widely used platform for exploratory, interactive visualization and analysis of large-scale clinico-genomic datasets. cBioPortal provides a range of visualizations and analyses including interactive cohort exploration, OncoPrints, mutation “lollipop” plots, survival analysis, alteration enrichment analysis, and detailed patient-level visualizations. cBioPortal also integrates variant annotations from a variety of sources to facilitate interpretation. The public cBioPortal (https://www.cbioportal.org) is accessed by >40,000 unique visitors each month and hosts data from >460 studies. All data is also available in the cBioPortal Datahub: https://github.com/cBioPortal/datahub. In 2024 we added 76 new studies (∼30,000 samples), including data from the NCI Genomic Data Commons. In addition, >94 instances of cBioPortal are installed at academic institutions and companies worldwide. cBioPortal partners with AACR Project GENIE to provide access to the GENIE cohort in a dedicated instance (https://genie.cbioportal.org). Users can explore the full GENIE cohort of >229,000 clinically sequenced samples from 19 institutions, as well as cohorts with comprehensive clinical annotations including response, outcome, and treatment history, from the GENIE Biopharma Collaborative (BPC). BPC cohorts for NSCLC (∼2,000 samples) and colorectal cancer (∼1,500 samples) are available, with more to come. The past year has brought a variety of enhancements to cBioPortal. A new data type selector on the home page enables users to find studies with specific types of data. The interactive cohort exploration has new ways to explore data with the addition of gene-specific charts to summarize the types of mutations in a gene and the integration of the Plots tab for customizable graphs of any two data attributes. The OncoPrint can now display per group alteration frequency based on any categorical attribute. Variant interpretation is enhanced with the integration of AlphaMissense as a novel annotation source and an update to the latest MutationAssessor data. The patient page also has new visualizations, including mutational signatures and the integration of Chromoscope to visualize structural variations. We also made significant changes to the backend code to improve both the developer and user experience. The backend code was repackaged and upgraded to simplify and improve the development process. In addition, we are working on switching to an Online Analytical Processing (OLAP) database which will bring significant performance improvements. cBioPortal is open source: https://github.com/cBioPortal. Development is a collaborative effort among groups at Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children’s Hospital of Philadelphia, Princess Margaret Cancer Centre, Caris Life Sciences, Bilkent University, SE4BIO and The Hyve. We welcome open source contributions from others in the cancer research community. Ino de Bruijn,Tali Mazor,Rima AlHamad,Calla Chennault,Corey Dubin,Jeremy Easton-Marks,Zhaoyuan Fu,Benjamin Gross,Charles Haynes,David M. Higgins,Jason Hwee,Prasanna K. Jagannathan,Mirella Kalafati,Karthik Kalletla,Zeynep Karagöz,James Ko,Tim Kuijpers,Sowmiyaa Kumar,Priti Kumari,Ritika Kundra,Bryan Lai,Xiang Li,James Lindsay,Aaron Lisman,Qi-Xuan Lu,Ramyasree Madupuri,Zain-ul-Abideen Nasir,Angelica Ochoa,Yusuf Ziya Özgül,Oleguer Plantalech,Matthijs N. Pon,Baby A. Satravada,Jessica Singh,Selcuk Onur Sumer,Pim van Nierop,Floris Vleugels,Avery Wang,Manda Wilson,Hongxin Zhang,Gaofei Zhao,Ugur Dogrusoz,Allison Heath,Adam Resnick,Trevor J. Pugh,Chris Sander,Ethan Cerami,JianJiong Gao,Nikolaus Schultz. cBioPortal for cancer genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1117.

Thymol, a monoterpenoid phenolic compound, exhibits broad-spectrum antibacterial activity and is gaining increasing attention as a natural alternative to synthetic agents. Thymol appears to demonstrate high antibacterial efficacy against Gram-negative and Gram-positive bacteria, particularly resistant pathogens, through disruption of bacterial cell membranes, protein and enzyme inhibition, influencing DNA synthesis, and triggering oxidative stress mechanisms. Given these reported mechanisms and its broad-spectrum activity, thymol has been the subject of increasing research interest in recent years. The aim of this review is to comprehensively evaluate the antibacterial effects of thymol based on studies published between 2020 and 2025, identified through major databases including PubMed, Scopus, and Web of Science. Based on current literature, thymol appears to have strong potential as an antibacterial agent in diverse fields such as dermatological products, veterinary treatments, oral health formulations, food preservative systems, and agricultural biopesticide applications. In recent years, various encapsulation and controlled-release strategies have been developed to overcome the limiting characteristics of thymol, such as low water solubility, volatility, and chemical instability, which restrict its direct use in clinical and industrial applications. Studies using thymol in combination with various carrier systems, nanoparticles, and phenolic extracts have shown that the bioavailability of the compound is increased and, in some cases, synergistic antimicrobial effects can be achieved. However, the data indicates that studies have not progressed beyond the in vitro and in vivo levels. This finding reveals the need for more detailed clinical data to support the research on such valuable molecules, which are essential in today’s world where resistant pathogens are dramatically developing. Current research shows that thymol is a promising natural agent with antibacterial properties and potential applications. Despite the promising in vitro and in vivo evidence, thymol lacks clinical validation data and standardized formulation protocols. The primary bottleneck appears to be its pharmacokinetic profile, low oral bioavailability ( 16