WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Novel Statistical Approaches for Survival Analysis of RNA-Sequencing Data(Bentham Science Publ Ltd, 2026) Cephe, Ahu; Karabulut, Erdem; Zararsız, Gözde Ertürk; Sezgin, Ahmet; Koçhan, NeclaIntroduction/Objective Accurate patient survival predictions are vital for effective cancer treatments. Precision medicine uses gene expression data to improve prognosis by considering genetic variability. Predicting survival in cancer patients using high-dimensional gene expression data, such as RNA-sequencing (RNA-seq), attracted much attention in recent years. However, the literature contains limited algorithms for survival modeling that account for the high dimensionality, heterogeneity, and correlated genes of RNA-seq data. This study aims to develop novel approaches for predicting survival and identifying biomarkers using RNA-seq data.Introduction/Objective Accurate patient survival predictions are vital for effective cancer treatments. Precision medicine uses gene expression data to improve prognosis by considering genetic variability. Predicting survival in cancer patients using high-dimensional gene expression data, such as RNA-sequencing (RNA-seq), attracted much attention in recent years. However, the literature contains limited algorithms for survival modeling that account for the high dimensionality, heterogeneity, and correlated genes of RNA-seq data. This study aims to develop novel approaches for predicting survival and identifying biomarkers using RNA-seq data.Methods Survival data of RNA-seq is first transformed into binary classification data using a stacking algorithm. Then, block-based priority-Lasso and IPF-Lasso algorithms are applied to the dataset, which includes two distinct types of variables. Additionally, sample weights obtained from the voom transformation are incorporated. Our approaches, named voomStackLasso, are tested on 12 real datasets from the TCGA database. We used Harrell's concordance index and the integrated Brier score to evaluate model performance, and the number of selected features to assess model sparsity.Results The results indicated that the voomStackLasso algorithms demonstrated comparable or superior performance compared to other existing survival algorithms. Furthermore, we have introduced an R package called MLSeqSurv, which allows for the utilization of both established survival algorithms from the literature and voomStackLasso algorithms for RNA-seq data.Conclusion This study introduces two new algorithms for the survival analysis of RNA-seq data. Additionally, this study has led to new research directions for applying both existing and newly developed classification algorithms to the survival analysis of RNA-seq data.Article Effects of Alkanolamines on Calcium Sulfoaluminate Belite Cement Hydration and Fresh Properties(Emerald Group Publishing Ltd, 2026) Uzal, Burak; Wilkinson, Angus P.; Qoku, Elsa; Nguyen, Tu-Nam; Kurtis, Kimberly E.Calcium sulfoaluminate belite cements have found widespread use in specialised applications but have not been applied broadly due to rapid setting times. Conventional set retarders such as citric and tartaric acids modify hydration kinetics, introducing ancillary effects that alkanolamines may avoid. This study examined the effects of three alkanolamines, triisopropanolamine (), triethanolamine () and diisopropanolamine (), on early hydration at 0.02% dosage; was also tested across a broader dosage range. Reaction kinetics and phase evolution were examined in pastes by calorimetry, thermogravimetric analysis () and in situ quantitative X-ray diffraction () for 72 h of hydration, along with setting time and amplitude-sweep rheometry. Calorimetry showed that and delayed and reduced the main cement hydration peak, while all alkanolamines delayed and enhanced the shoulder and secondary hydration peaks. In situ and suggested that alkanolamines decrease ettringite and alumina gel formation by 24 h and may lead to poorly crystallised ettringite that cannot be quantified by . Alkanolamine-containing samples demonstrated increased storage and loss moduli and extended linear viscoelastic ranges. A consistent grouping of similar behaviour emerged: control/TIPA versus TEA/DIPA, suggesting distinct mechanisms. Finally, among the alkanolamines, was the most effective, increasing the setting time by 18 min.Article Optimizing Nanoclay-Enhanced Membranes for Oil Rejection Using Response Surface Methodology(Wiley, 2026) Gul, Ayse; Baris, Mesut; Boyraz, Pınar; Senol-Arslan, Dilek; Alibaz, Name NurThe efficient separation of waste oil from contaminated water is critical due to its challenges in environmental and industrial applications. This study investigated the production and optimization of polysulphone (PSF) membranes using two different types of clay (nanomer clay/CN and commercial nanoclay/NC). Response Surface Methodology (RSM) was applied to optimize the basic production parameters and nanoclay concentrations systematically to maximize oil rejection and permeability flow. The experimental results showed that NC and CN significantly increased the hydrophilicity, permeability, and fouling resistance of the membrane compared to pure PSF membranes. The contact angle significantly decreased from 64.34 degrees (pristine PSF) to 36.23 degrees (2% NC), indicating highly improved hydrophilicity. Consequently, the pure water flux increased from 177.2 L/m2 h to a maximum of 248.6 L/m2 h (1% NC). Furthermore, the modified membranes exhibited outstanding anti-fouling properties; the flux recovery ratio (FRR) improved from 88.09% to 96.20% (1% CN), while the decline ratio (DR) drastically dropped from 60.89% to 32.14%. The optimized condition for maximum removal efficiency using a modified quadratic model revealed that 2572 mg/L oil can be treated with a PSF membrane containing 2.0% CN to remove 98.271% of the oil. The model also suggests superiority of CN over NC with desirability factors of 0.978 and 0.900, respectively, while both demonstrated high efficiency. This theoretically modeled experimental comparative study highlights the importance of PSF membrane technology for efficient and sustainable oil-water separation and demonstrates the promising potential of nanoclay modifications.Article Identification of Potential Dual HDAC6 and HSP90 Inhibitors for the Treatment of Cancer Using Molecular Docking, Molecular Dynamics and MM/PBSA Studies: A Comprehensive In Silico Study(Bentham Science Publ Ltd, 2026) Yucel, Muhsin Samet; Akcok, IsmailBackground Histone deacetylase 6 (HDAC6) and heat shock protein 90 (Hsp90) are crucial therapeutic targets in cancer research with their interconnected roles in regulating protein homeostasis and cellular processes. The interaction of these proteins within the cytosolic complex plays a critical role in regulating cancer cell survival and progression. Notably, current studies highlight that the simultaneous inhibition of HDAC6 and Hsp90 can produce synergistic effects and offer a promising therapeutic potential for combating malignant cancers.Objective The objective of this study was to explore potential compounds that can inhibit both HDAC6 and Hsp90 proteins.Methods In this study, a number of in-silico computational techniques were employed. A total of 791 molecules, sharing at least 30% similarity with previously identified four HDAC inhibitors, were obtained from the ZINC15 database and subjected to docking on HDAC6 and Hsp90 proteins. The top eight ligands demonstrating the best binding scores against both targets, with panobinostat and ganetespib serving as reference compounds for HDAC6 and Hsp90, respectively, were selected for further analysis. Subsequently, ADME prediction and molecular dynamics simulations were conducted on the selected ligands.Results A detailed molecular docking, molecular dynamics simulations and ADME studies have revealed that ZINC27653366 exhibited the highest inhibitory potential against both Hsp90 and HDAC6 target proteins, making it the most promising inhibitor.Conclusion In conclusion, although additional in vitro and in vivo studies are required for the validation, in silico evaluation of ZINC27653366 may position it as a promising candidate for the treatment of different types of cancers.Article Minimization of Thermal Stresses in Instrumented Cutting Tools with Embedded Thin Film Thermocouples(Korean Society of Mechanical Engineers, 2026-04) Kesriklioglu, Sinan; Sivesoglu, AbdurrahmanThis study investigates the optimization of multilayer coatings on cutting tools to minimize thermal stress and temperature differences between the tool-chip interface and embedded thermocouples. The novelty of this study lies in directly linking coating architecture to temperature measurement accuracy, revealing that coatings not only affect heat dissipation and stress development but may also distort the apparent temperature recorded by embedded sensors. The types and thickness ranges of thin film layers in instrumented cutting tools were determined, and multi-physics finite element simulations were then used to evaluate coating configurations under thermal loading, assessing both stress distribution and temperature variance in the multilayer coating system. The Taguchi method, coupled with desirability analysis, identified optimal coating parameters that simultaneously minimize thermal stresses and temperature disparities, which are critical for accurate temperature measurements and extending the lifespan of cutting inserts. This framework enables a controllable trade-off between mechanical reliability and thermal measurement fidelity. The results reveal significant interactions among coating configurations (settings) and between thermal and mechanical properties of the materials used, demonstrating that careful selection of layer materials and thicknesses optimizes stress and temperature responses yielding thermal stress of 1628 MPa (second lowest and only 0.4 % higher than the minimum) and temperature difference of 12.1 degrees C (third lowest and 55 % lower than average). These findings underscore the potential of precise coating design to enhance tool performance and longevity in high temperature machining applications.Article Unveiling the Therapeutic Role of 3D-Cultured Mesenchymal Stem Cells in Diabetic Foot Ulcers through Transcriptomic Integration and Fibroblast Modulation(Springer, 2026-03-31) Ozturk, Esengul; Bicer, MesudeBackground Diabetic foot ulcers (DFUs) are among the most severe complications of diabetes mellitus and remain difficult to manage due to chronic inflammation, defective angiogenesis, delayed tissue repair, which increase the risk of recurrence and limb amputation. Standard treatments, such as debridement, infection management, pressure off-loading and revascularization, are commonly used, however; these interventions often inadequate to fully restore effective wound repair. Mesenchymal stem cells (MSCs) have attracted remarkable interest due to their potential regenerative ability and paracrine activity. Nevertheless, the molecular interaction between MSCs and fibroblasts under hyperglycemic conditions has not been fully elucidated. Objective This study aimed to examine differentially expressed genes (DEGs) associated with DFUs and MSC-related regenerative mechanisms using transcriptomic datasets (such as GSE143735, GSE199939, and GSE217709). Methods and results Differentially expressed genes and protein-protein interaction (PPI) network analysis were performed to determine central regulatory genes. Four key genes including CXCL1, MMP9, THBS1, and POSTN were recognized as hub genes related to inflammatory response, extracellular matrix reorganization, and angiogenesis. For experimental validation, L929 murine fibroblasts were exposed to high-glucose conditions to set-up an in vitro diabetic model and subsequently treated with MSCs with/without a 3D platform. Hyperglycemic conditions significantly reduced fibroblast proliferation and migration downregulated the expression of the identified hub genes and enhanced apoptotic activity. MSC treatment partially increased cellular function, while MSCs embedded into 3D culture enhanced a more pronounced recovery in both gene expression patterns and functional assays. Conclusions These findings suggest that high glucose impair fibroblast functions for wound repair, while 3D-cultured MSCs enhance regenerative responses and may represent a promising strategy for diabetic wound healing.Article TEffectBayes: A Nextflow Pipeline for Exploring the Potential Effect of Transposable Elements in Gene Regulatory Network with Multi-Omic Bayesian Network Model(Springer Heidelberg, 2026-03-10) Karakülah, Gökhan; Güner, Hüseyin; Kutlu, Necati KaanTransposable elements (TEs) are critical contributors to gene regulatory networks, yet their repetitive and abundant nature complicates efforts to elucidate their precise regulatory roles. While existing computational tools facilitate systematic identification of associations between TEs and gene expression, these methods typically cannot account for confounding variables or capture causal and directional interactions. To address these limitations, we developed TEffectBayes, a Nextflow-based pipeline leveraging a multi-omic Bayesian network (BN) framework designed to systematically infer directional, probabilistic regulatory dependencies involving TEs. TEffectBayes integrates diverse omics datasets, including RNA-seq-derived gene and locus-specific TE expression, along with ChIP-seq-based histone modification data processed via custom R and Python scripts. Integrated multi-omic datasets are subsequently employed to build gene-centric Bayesian models, enabling robust inference of context-dependent, probabilistic relationships between TEs, chromatin modifications, and gene expression. TEffectBayes thus provides a reproducible and scalable computational framework for unraveling the complex regulatory landscape shaped by TEs. In summary, TEffectBayes supports systematic prioritization of TE-chromatin-gene regulatory candidates for downstream benchmarking and experimental validation, enabling hypothesis-driven follow-up studies in diverse biological contexts. The pipeline, along with comprehensive user tutorials and example datasets, is publicly accessible at https://github.com/nkaan-kutlu/TEffectBayes.Article Citation - WoS: 2Citation - Scopus: 2Recent Progress in the Beneficiation of Iron-Manganese Ores: An Overview(Pleiades Publishing Ltd, 2025) Top, SonerIron-manganese (Fe-Mn) ores are essential for steelmaking, ferroalloy production, and emerging energy technologies, yet their beneficiation is challenging due to the close association of Fe and Mn oxides and their overlapping physicochemical properties. This review assesses key processing strategies, including gravity separation, magnetic methods, flotation, reduction roasting, and selective reductive leaching. Physical beneficiation offers limited upgrades, being constrained by mineral liberation and ore texture. Reduction roasting with carbonaceous or hydrogen reductants exploits the different reduction stabilities of Fe and Mn oxides, creating magnetic contrasts for effective separation. Hydrometallurgical techniques based on reductive leaching also show strong potential, particularly with biomass-derived or organic reductants, achieving manganese recoveries often above 90-99%. A central focus is the use of Ellingham and Eh-pH diagrams as predictive tools for selective separation. Ellingham diagrams outline the thermodynamic stabilities of Fe and Mn oxides, guiding roasting design, while Eh-pH diagrams describe dissolution behavior under varying acidity and redox conditions, enabling leaching optimization. Integrating these frameworks with experimental evidence demonstrates how thermodynamic and electrochemical principles can improve process selectivity. No single technique universally addresses Fe-Mn beneficiation challenges; instead, hybrid flowsheets combining physical, thermal, and hydrometallurgical routes tailored to ore characteristics are most effective. Future research should prioritize low-carbon and sustainable approaches such as hydrogen roasting, bio-reductant leaching, and zero-waste systems. This review thus provides both a synthesis of current advances and a roadmap for sustainable Fe and Mn resource recovery.Article Integrative Bioinformatics Prediction of West Nile Virus-Derived microRNAs Reveals Potential Host Regulatory Interactions(Elsevier Sci Ltd, 2026-08) Demirci, Muserref Duygu Sacar; Orhan, Mehmet Emin; Erginkoc, Altay Nida; Saçar Demirci, Müşerref DuyguWest Nile virus (WNV) is a mosquito-borne flavivirus linked to severe neuroinvasive disease. Although host and vector microRNAs (miRNAs) have been implicated in viral infection, the presence and functional relevance of WNV-encoded miRNAs remain largely unexplored. Here, we developed an integrative bioinformatics pipeline that combines multiple miRNA prediction algorithms with secondary structure screening and host transcriptomic data to identify high-confidence candidate WNV-derived mature miRNAs. Overlap-based confidence scoring and differential expression support from RNA-seq datasets prioritized a small subset of putative miRNA-mRNA interactions with potential roles in infection-associated gene regulation. A competitive endogenous RNA network constructed from predicted mRNA, lncRNA, and circRNA targets highlighted pathways involving innate immunity, GPCR and Wnt signaling, RNA degradation, and viral replication. Together, these findings provide a reproducible computational workflow and nominate testable regulatory interactions for future experimental validation.Article Effects of a Period and a Contact Angle on Absorption Performance of Hemispherical-Shell-Shaped Organic Photovoltaic Cells(SPIE-Soc Photo-Optical Instrumentation Engineers, 2026-02-17) Hah, DooyoungFor wearable electronics applications, organic photovoltaic (OPV) cells are good candidates as sources of renewable energy. Many efforts have been devoted to increasing energy conversion efficiency in OPV cells, and improvement in light retention has been one of the main research directions. Within this context, our group recently proposed an OPV cell structure with a hemispherical-shell-shaped (HSS) active layer and discovered that it has high potential for substantial enhancement in absorption performance. As a continuation of the study, this paper reports an in-depth investigation of the proposed device, examining the effects of several design parameters on its absorption performance. Using finite element analysis, it is found that the absorption performance depends on the periodicity type, and that a hexagonal type results in higher absorption than a square one due to its closer shape resemblance to a circular cross-section. The absorption performance is also affected by a contact angle, i.e., the angle made between a sphere and a flat part of the structure. It is learned that the average integrated absorption generally increases along with the contact angle, which saturates at around 80 deg of contact angle. Lastly, the effects of a cell period are studied, and it turns out that the average integrated absorption decreases as the period increases. It is also observed that at high incidence angles (>similar to 75 deg ), an array with a shorter period results in lower absorption than one with a longer period owing to a partial obstruction issue. All of these results support the understanding that the primary contribution of absorption enhancement in the proposed HSS structure comes from improved light retention rather than from a simple advantage in active layer volume. It is envisaged that these study outcomes will provide important guidelines in the design of HSS OPV cells.