WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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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: 1Citation - Scopus: 1Targeting Cholinergic Dysfunction and Neuroinflammation through Rationally Designed Thieno[3,2-d]Pyrimidine Hybrids(Academic Press Inc Elsevier Science, 2026-07) Acar, Ozden Ozgun; Acar, Busra; Senol, Halil; Tokali, Feyzi Sinan; Sen, Alaattin; Demir, Yeliz; Cakir, FurkanNeurodegenerative diseases involve the convergence of cholinergic dysfunction, neuronal loss, and sustained neuroinflammatory responses, necessitating the development of multifunctional therapeutic agents. In this study, a series of novel thieno[3,2-d]pyrimidine-phenolic Mannich base hybrids were rationally designed, synthesized, and evaluated as dual cholinesterase inhibitors with neuroprotective and anti-neuroinflammatory potential. The synthesized compounds exhibited potent inhibition against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), with inhibition constants in the low nanomolar range. Among them, compounds 5 and 9 emerged as the most active derivatives, displaying Ki values of 8.79 and 14.11 nM for AChE and 7.04 and 11.75 nM for BChE, surpassing the reference inhibitors tacrine and donepezil. Molecular docking and molecular dynamics simulations supported the experimental findings, and Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) binding free energy calculations further confirmed their superior binding affinities compared with donepezil. Cytotoxicity profiling in SH-SY5Y neuronal cells and RAW 264.7 and THP-1 immune cells identified a narrow sub-cytotoxic concentration window (EC05-EC10 = 1.2-2.1 mu M), ensuring biological effects independent of nonspecific cell damage. Within this range, both compounds exerted pronounced antineuroinflammatory activity. Notably, compound 9 significantly downregulated pro-inflammatory mediators, reducing IL-1 beta, IL-6, and NF-kappa B1 gene expression by up to 2.78-, 3.37-, and 4.84-fold, respectively. Consistently, it suppressed nitric oxide production in LPS-stimulated macrophages to levels comparable with ascorbic acid and markedly decreased Iba1 expression in activated THP-1 cells. This integrated enzymatic, computational, and cellular investigation identifies compounds 5 and 9 as promising multifunctional lead combining dual cholinesterase inhibition with robust anti-neuroinflammatory activity. The results provide a strong foundation for future in vivo studies and further optimization toward disease-modifying agents for neurodegenerative disorders.Article Prosocial Behavior as Bridge and Buffer: Exploring Its Dual Role between Stress and Mental Health in Emerging Adults(Springer, 2026-03-16) Coskun, Muhammet; Arslan, Gokmen; Genc, Emel; Caprara, Gian VittorioThe present study investigated the dual role of prosocial behavior among emerging adults in a non-Western cultural con-text. Within this scope, first, adaptation and validation of the Adult Prosocialness Behavior Scale (PBS) was carried out for Turkish population. Then, it tested both mediating and moderating functions of prosocial behavior in the links from stress to subjective wellbeing (SWB) and quality of life. To this end, a sample of 419 emerging adults (41.3% males and 58.7% females) completed an online survey. Results revealed Turkish version of the APBS to be a reliable and valid mea-surement tool for assessing prosocial behavior. Regarding the main hypotheses, serial multiple mediation analysis revealed that perceived stress predicted quality of life through the sequential pathway of prosocial behavior and SWB. Additionally, the moderated-mediation analysis confirmed the moderating role of prosocial behavior in the relationship between stress. Nevertheless, moderated mediation index did not reveal a significant conditional indirect effect of prosocial behavior for the indirect path from stress on quality of life through SWB. Overall, findings suggest that prosocial behavior plays a dual role as both a 'bridge' (mediator) and a 'buffer' (moderator) in the relationship between stress and mental health.Article Recent 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 Sensitive Hybrid Plasmonic Refractive Index Sensor Based on Ag Cross-Grating Nanoantenna and Au Quantum Dot upon SiO2 Nanowire(IOP Publishing Ltd, 2026-04-03) Sanli, Atif Kerem; Kilic, Veli Tayfun; Tabaru, Timucin EmreThis study presents a distinctive hybrid plasmonic sensor architecture combining a silver (Ag) cross-shaped nanoantenna with a gold (Au) quantum dot (QD) for enhanced refractive index sensing applications. The structure consists of a silicon dioxide (SiO2) substrate and a cylindrically shaped SiO2 wire on it, topped with a silicon nitride (Si3N4) dielectric layer and an Ag cross grating, with an Au QD positioned at the center. Using free and open source 3D Finite-Difference Time-Domain (FDTD) simulations, exceptional electric field enhancement at the resonant wavelength of approximately 639-667 nm is demonstrated. The optimized structure achieves remarkable quality factors (Q-factors) exceeding 267 for biological media, representing among the highest reported values for plasmonic sensing structures. Unlike conventional red-shift sensors, our design exhibits a distinctive blue-shift sensing behavior arising from hybrid plasmonic mode coupling, achieving sensitivities ranging from 190 to 344 nm RIU-1 for various analytes, including water, blood, PDMS, body fat, ethanol, and glass. The ultrasharp resonances (FWHM similar to 2.3 nm) combined with intense field enhancement make this design highly suitable for biosensing applications.Article Production of Waste-Based Lightweight Geopolymer Concretes Using Calcined Bentonite, Fly Ash, Slag, and Expanded Polystyrene Granules(Taylor & Francis Inc, 2026-03-19) Top, Soner; Nussrat Shukur Shukur, Yasir; Vapur, HüseyinThis study investigates the production of environmentally friendly lightweight geopolymer concretes utilizing fly ash (FA) as the primary precursor with calcined calcium bentonite (CCB), ferrochrome slag (SG), and expanded polystyrene (EPS) as supplementary components. A Box-Behnken design was employed to investigate the combined effects of CCB and SG additions, along with the solid-to-liquid ratio, on the compressive strength. Moderate CCB incorporation, particularly around 10%, improved mechanical performance, achieving strengths above 48 MPa, with a maximum of 51.33 MPa at 90 degrees C for a mix containing 5% CCB and 5% SG. Higher CCB dosages (>20%) reduced strength due to matrix dilution, while SG showed limited contribution at elevated levels. Incorporation of EPS granules reduced density to as low as 1292 kg/m & sup3;, yet compressive strengths between 25 and 30 MPa were maintained in mixes with 10% CCB and 0.3% EPS. SEM-EDX analysis confirmed dense geopolymer matrices in FA-CCB composites, whereas SG particles appeared less integrated. These results confirm the potential for producing high-strength, lightweight geopolymer concretes through the effective valorization of waste. The combined use of FA, CCB, SG, and EPS offers a sustainable pathway for resource-efficient construction that supports circular resource utilization.Article Pressure-Induced Polyamorphic Transition and Stepwise Ordering to Superhard B-Doped Diamond-like BC3(Elsevier Science SA, 2026-04) Durandurdu, MuratWe employ constant-pressure ab initio molecular dynamics simulations to investigate the pressure-induced phase transformations of amorphous BC3, which initially possesses a graphite-like layered structure. Our simulations reveal a first-order polyamorphic transition marked by a significant volume collapse and an increase in atomic coordination from a predominantly sp(2) network to a dense, tetrahedrally coordinated sp(3) network. Subsequent thermal annealing of the high-pressure phase uncovers a multi-step ordering process involving a metastable paracrystalline intermediate that bridges the high-density amorphous state and a thermally induced boron-doped diamond-like phase. All high-pressure phases are quenchable to ambient conditions, importantly retaining their semiconducting electronic structures across these transformations. Mechanical characterization demonstrates substantial stiffening, with bulk moduli ranging similar to 252 to 323 GPa. These findings illuminate novel and accessible routes to superhard semiconducting BC3 phases stabilized by pressure and temperature, with the boron-doped diamond-like phase identified as a metastable superhard semiconductor that is thermodynamically favored over the amorphous precursor but kinetically accessible only via the stepwise pathway described. This offers promising directions for advanced material design under extreme conditions.Article Parametric Study on the Behavior of CFRP-Strengthened Reinforced Concrete Deep Beams with Cut Circular Web Openings in Shear Spans(Nature Portfolio, 2026-02-17) Yagmur, ErenWeb openings in reinforced concrete deep beams are often necessary for functional purposes but substantially reduce structural performance. Carbon fiber-reinforced polymer (CFRP) strengthening is commonly employed to mitigate these effects. Previous studies typically examined openings in regions without stirrups or assumed closed stirrup configurations, overlooking the frequent stirrup damage that occurs in practice due to the high shear reinforcement in deep beams. In this study, three specimens from a prior experimental program were modeled in ABAQUS, and the numerical results were validated against experimental data. Openings of varying diameters were introduced by cutting reinforcements, and the beams were subsequently strengthened with CFRP laminates, and a parametric study was conducted. Results showed that increasing opening diameter markedly reduces load-carrying capacity and energy absoption, while thicker CFRP laminates partially restore performance. For example, a 300 mm opening in a 500 mm high unstrengthened beam reduced load capacity by 56% and energy absorption by 87%. Even when the opening diameter was less than one-third of the beam height, 1.8 mm CFRP laminates provided only limited improvement. Deep beam performance was strongly influenced by web opening size, and the effectiveness of CFRP strengthening was limited when stirrup integrity was compromised.