WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article AI-Driven Drug Repositioning: A Diffusion Model Approach on Knowledge Graphs(Elsevier, 2026) Erkantarci, Betul; Şen, Tarık Üveys; Bakal, GokhanDrug repositioning - discovering new therapeutic applications for existing drugs - offers a promising pathway to accelerate cancer treatment development. This study proposes a diffusion model-driven framework that leverages biomedical knowledge graphs and graph-based learning to enhance drug repositioning predictions. The framework integrates data from the Semantic MEDLINE Database (SemMedDB), the Unified Medical Language System (UMLS), and the Repurposing Drugs Database (RepoDB) to construct a comprehensive therapeutic knowledge graph. Drug embeddings are generated using a one-layer Relational Graph Convolutional Network (R-GCN) incorporating semantic type-guided structural perturbations. These embeddings are refined through a flow-matching algorithm to denoise and reconstruct biologically meaningful representations. To evaluate the model's effectiveness, we apply a consensus strategy using Cosine Similarity, Euclidean Distance, and Manhattan Distance as proximity metrics. The model successfully identified, on average, 74 candidate drugs for repositioning in the context of leukemia. Qualitative analysis using t-distributed stochastic neighbor embedding (t-SNE) revealed enhanced clustering of pharmacologically relevant drugs in the denoised embedding space. Trastuzumab, in particular, emerged as a strong repositioning candidate for leukemia, supported by 156 co-mentions in PubMed. These findings demonstrate that the proposed framework improves embedding robustness and semantic fidelity, offering a powerful artificial intelligence (AI)-driven approach for precision oncology. Integrating structural noise modeling with diffusion-based denoising advances the discovery of novel drug-disease associations and holds potential for translational research and clinical hypothesis generation in drug repurposing.Article Views on Climate Change, Climate Action and Mental Health, in Young People with and without Existing Depression Symptoms: A Qualitative Study(Elsevier, 2026-01) Kaya, M. Siyabend; Hawkins, Ed; McCabe, CiaraBackground: Youth mental health is in crisis. Climate change has the potential to tip more young people into depression and anxiety. Knowing how young people with and without depression symptoms view climate change could guide interventions to mitigate against climate induced mental health issues. Materials and Methods: We carried out in-depth, semi-structured interviews with (N = 27) young people aged 18-25 (M-age = 20.3 years). Participants were grouped as healthy controls (C, N = 16, < 16 score on Mood and Feelings Questionnaire, MFQ) or had high depression symptoms (HD, N = 11, >= 27, MFQ). Using thematic analysis, we explored participants views on climate change, climate action, climate messaging, climate agency and mental health. Results: From the interviews, eight key themes emerged: (1) Negative environmental events - Climate change was understood as ranging from weather changes to natural disasters. (2) Mental health impacts - Most participants reported increased anxiety and depression, with the HD group being more pessimistic about climate change prevention. (3) Benefits of action - Focus on individual efforts. (4) Non-disruptive vs. disruptive actions - Preference for non-disruptive solutions. (5) Hope and Fear in climate messaging - balance is needed. (6) Local and global action - Emphasis on combining both approaches. (7) Leadership - Responsibility placed on politicians, institutions, and environmentalists. (8) Shared responsibility - Families, educators, governments, and celebrities all have a role in climate action. Conclusion: These findings offer valuable insights into the perspectives of young people with and without existing symptoms of depression. Notably, identifying differences-such as varying levels of climate pessimism-based on depression status highlights the importance of climate communication strategies that not only effectively address climate change but also safeguard youth mental health. This is important as those with existing depression symptoms may be more vulnerable to the psychological impacts of climate change.Article Densification-Induced Chemical Reorganization and Mechanical Enhancement in Amorphous Si2BC3N(Elsevier, 2026-02) Durandurdu, MuratThe atomistic mechanisms that govern the mechanical performance of amorphous silicon-boron carbonitride (SiBCN) ceramics remain insufficiently understood, particularly regarding the role of density. Here, we employ ab initio molecular dynamics simulations to elucidate the structural evolution and mechanical response of low-density (LDA, 2.20 g/cm3) and high-density (HDA, 2.53 g/cm3) amorphous Si2BC3N prepared via melt-quench. The HDA phase exhibits markedly higher atomic packing and network connectivity, accompanied by a nontrivial chemical reorganization. Densification significantly enhances heteronuclear bonding-especially Si-C coordination-while suppressing C-C and Si-Si homopolar bonds. These changes yield substantial mechanical strengthening: the HDA phase exhibits a 48% increase in bulk modulus (130 GPa vs. 88 GPa), along with elevated Young's (266 GPa) and shear (112 GPa) moduli. Our findings reveal a clear density-structure-property relationship in amorphous SiBCN, demonstrating that densification suppresses weak self-bonded motifs and promotes a robust, interconnected atomic network. This insight provides a pathway for designing high-performance amorphous SiBCN ceramics for extreme-environment applications.Article Supervised Learning-Driven Dead Band Control of Occupant Thermostats for Energy-Efficient Residential HVAC(Elsevier, 2026-03) Savasci, Alper; Ceylan, Oguzhan; Paudyal, SumitHeating, ventilation, and air conditioning (HVAC) systems play a crucial role in demand-side management (DSM) by shaping residential electricity consumption and enabling flexible, grid-responsive operation. Thermostats in HVAC systems regulate indoor temperature as part of a closed-loop control framework, typically incorporating a fixed temperature dead band-a range around the setpoint where no action is taken-to reduce energy use and prevent frequent cycling of the HVAC system. Although essential for efficiency and equipment longevity, fixed dead bands limit adaptability, as dynamically adjusting them under varying environmental conditions remains challenging for occupants. To address this limitation, we propose a machine learning (ML)-based dead band tuning framework that optimally adjusts thermostat settings in real time. The method integrates conventional optimization with data-driven modeling: a mixed-integer linear programming (MILP) model is first used to gen erate optimal dead band values under measured outdoor temperature records (diverse seasonal weather scenarios) which are then employed to train the ML-based predictor to learn a real-time discrete dead band decision policy that approximates the MILP-optimal hysteresis-aware decisions. Among the evaluated models, Random Forest demonstrates superior predictive performance, achieving a mean squared error (MSE) of 0.0399 and a coefficient of determination (R2) of 95.75 %.Article Tuning Properties of Amorphous Boron Via Hydrogenation: An Ab Initio Study(Elsevier, 2026-01) Durandurdu, MuratAb initio simulations are employed to investigate the structural, mechanical, and electronic properties of hydrogenated amorphous boron (a-B:H) across a range of hydrogen concentrations (approximate to 6-21 at.%). The results indicate that pentagonal-like boron clusters constitute the primary structural motifs. The bonding environment consists of both B-H terminal bonds and B-H-B bridging bonds, with the fraction of bridging bonds ranging from 10 % to 16 %. Increasing the hydrogen content leads to a reduction in density and bulk modulus, accompanied by a systematic widening of the electronic band gap. These results demonstrate that hydrogen incorporation profoundly modifies the atomic structure, softens the network, and enhances the semiconducting character of a-B:H, highlighting the tunability of properties in boron-based amorphous materials.Article Development and Characterization of Starch-Fatty Acid Complexes Produced with Buckwheat Starch and Capric/Stearic Acid Using Different Reaction Conditions(Elsevier, 2025-12) Oskaybas-Emlek, Betul; Ozbey, Ayse; Aydemir, Levent Yurdaer; Kahraman, KevserThe aim of present study was to investigate the impact of reaction parameters on the complex formation between buckwheat starch and capric acid (B-Capric) or stearic acid (B-Stearic). The most effective parameters on complex formation indicator (Complex index (CI) value) were found as reaction temperature (60-90 degrees C) and pH (5-8). Additionally, the effect of these parameters on physicochemical, pasting, and in-vitro digestibility properties of complex samples were evaluated. XRD and FTIR was also used in characterize the complex samples. In general, increasing pH increased the CI values of B-Stearic samples while decreasing those of B-Capric samples. Syneresis of buckwheat starch increased after complexation while paste clarity and swelling power diminished. The pasting properties of native starch significantly changed after complex formation. The FTIR results showed that starch structure changed with complex formation. XRD revealed that buckwheat starch, having an A-type pattern, converted to V-type pattern after complexation. Complex formation of buckwheat starch with capric and stearic acid significantly increased the RS content of buckwheat starch (19.01 %) by up to 36.25 % and 30.60 %, respectively. These results highlight the possibility of using buckwheat starch-capric acid/stearic acid complexes in food formulation to enhance the RS content.Letter Citation - WoS: 18Yemen's Triple Emergency: Food Crisis Amid a Civil War and COVID-19 Pandemic(Elsevier, 2021-11) Hashim, Hashim Talib; Miranda, Adriana Viola; Babar, Maryam Salma; Essar, Mohammad Yasir; Hussain, Hasham; Ahmad, Shoaib; Basalilah, Ashraf Fhed MohammedYemen has been termed as the world's worst humanitarian crisis by the United Nations. About 20.1 million (more than 50% of population) Yemenis are facing hunger and 10 million are severely food insecure according to reports by the World Food Programme. With the spread of COVID-19, the situation in Yemen has worsened and humanitarian aid from other countries has become the basis of life for hundreds of thousands of Yemenis after the threat of famine. Yemen is practically one of the poorest countries in the world. It has structural vulnerabilities that have developed over a protracted period of conflict and poor governance and more than 50% live in starving, they suffer for getting one meal a day. To prevent a total collapse of Yemen's food crises, the government and the international community should act now more decisively.Correction Citation - Scopus: 1Understanding the Effects of Artificial Intelligence on Energy Transition: the Moderating Role of Paris Agreement(Elsevier, 2025-02) Chishti, Muhammad Zubair; Xia, Xiqiang; Dogan, EyupArticle Citation - WoS: 7Citation - Scopus: 7Unveiling the Multifaceted Properties of a 3D Covalent-Organic Framework: Pressure-Induced Phase Transition, Negative Linear Compressibility and Auxeticity(Elsevier, 2023-08) Erkartal, MustafaHigh-pressure behavior and mechanical properties of a three-dimensional covalent-organic framework (NPN-1) were investigated by using different types of first principles molecular simulations. An irreversible pressureinduced first-order isosymmetric phase transition was predicted at 0.14 GPa. The subunit of NPN-1 retains its rigidity under pressure thanks to the strong covalent bonds. However, compression leads to significant tilting of the nitrophenyl groups. The mechanical properties of frameworks are highly anisotropic. Remarkably, both phases exhibit not only negative linear compressibility along the c-axis but also negative Poisson's ratio in certain directions. Detailed structural analysis revealed that the origin of the phase transition and anomalous mechanical properties of both phases are the wine-rack motif and strut-hinge mechanism. To the best of our knowledge, this study is the first report of such behavior in COFs, opening up new avenues for the exploration of COFs as materials for many promising applications.Article Citation - WoS: 16Citation - Scopus: 22Ultrasonic-Assisted Production of Precipitated Calcium Carbonate Particles From Desulfurization Gypsum(Elsevier, 2021-04) Altiner, Mahmut; Top, Soner; Kaymakoglu, BurcinThis study aimed to investigate the effect of ultrasonic application on the production of precipitated calcium carbonate (PCC) particles from desulfurization gypsum via direct mineral carbonation method using conventional and venturi tube reactors in the presence of different alkali sources (NaOH, KOH and NH4OH). The venturi tube was designed to determine the effect of ultrasonication on PCC production. Ultrasonic application was performed three times (before, during, and after PCC production) to evaluate its exact effect on the properties of the PCC particles. Scanning electron microscope (SEM), X-ray diffraction (XRD), Atomic force microscope (AFM), specific surface area (SSA), Fourier transform infrared spectrometry (FTIR), and particle size analyses were performed. Results revealed the strong influence of the reactor types on the nucleation rate of PCC particles. The presence of Na+ or K+ ions in the production resulted in producing PCC particles containing only calcite crystals, while a mixture of vaterite and calcite crystals was observed if NH4+ ions were present. The use of ultrasonic power during PCC production resulted in producing cubic calcite rather than vaterite crystals in the presence of all ions. It was determined that ultrasonic power should be conducted in the venturi tube before PCC production to obtain PCC particles with superior properties (uniform particle size, nanosized crystals, and high SSA value). The resulting PCC particles in this study can be suitably used in paint, paper, and plastic industries according to the ASTM standards.