Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
Browse
528 results
Search Results
Now showing 1 - 10 of 528
Article Cryofixation Strategy for Fabrication of Robust Gelatin-Polyester Conductive Biocomposites(Taylor & Francis Inc, 2026) Koksal, Busra; Onder, Ahmet; Yildiz, Umit HakanThe development of mechanically robust and electroconductive biomaterials is critical for advancing tissue engineering strategies, particularly in neural, cardiac and musculoskeletal applications. Here, we report a polycaprolactone (PCL)-gelatin conductive polymer (poly(3,4-ethylenedioxythiophene):polystyrene sulfonate, PEDOT:PSS) biocomposite with tunable mechanical and electrical properties, fabricated via the cryofixation process relying on rapid reaction between isocyanate-terminated PCL, gelatin and PEDOT:PSS. Two isocyanate sources, hexamethylene diisocyanate (HDI) or isophorone diisocyanate (IPDI) were employed to obtain reactive end-functionalized PCLHDI and PCLIPDI. The cryofixation (at -18 degrees C) of PCLHDI or PCLIPDI, gelatin and PEDOT:PSS was found to occur in unfrozen microdomains and enabled the resultant gel with an inherited network of ice, thereby increasing porosity. Electroconductivity was introduced via the incorporation of PEDOT:PSS, yielding conductive cryogels with porous morphology. The resulting scaffolds exhibited a Young's modulus of 637 Pa and electrical conductivity of 197 mu S/cm, alongside biocompatible nature of gelatin-based gels. This multifunctional platform offers significant promise for the engineering of electrically active tissues.Article FW-S3PFCM: Feature-Weighted Safe-Semi Possibilistic Fuzzy C-Means Clustering(Springer, 2026) Khezri, Shirin; Aghazadeh, Nasser; Hashemzadeh, Mahdi; Golzari Oskouei, AminThe safe semi-supervised fuzzy c-means clustering (S3FCM) method is a well-known clustering method that can produce successful results by incorporating prior knowledge of the class distribution. Its process is fast and simple but still has two limitations. The first issue is that it gives equal weight to all data features, while in real-world applications, different features usually have different importance. Secondly, S3FCM is very sensitive to noise and outliers. This paper proposes an extension of the S3FCM, entitled FW-S3PFCM, to mitigate these shortcomings. The proposed method uses a local feature weighting scheme to consider the different feature weights in the clustering process. Additionally, a possibilistic version of the S3FCM is designed to reduce the sensitivity to noise and outliers. The effectiveness of the proposed method is comprehensively evaluated on various benchmark datasets, and its performance is compared with the state-of-the-arts methods. To practically asses the FW-S3FCM, a real-world dataset of brain MRI images and its segmentation performance are analyzed as well. The average Accuracy, F1-score, Sensitivity, and Precision measures obtained by FW-S3FCM are 0.9682, 0.9826, 0.9743, and 0.9925, respectively, which are better than the competitors' performance.Article Alterations in Secondary Lipids Are Associated with Neuroinflammation in the Brain of Neu1-Deficient Mice(Springer, 2026) Ada, Ebru; Seyrantepe, VolkanNeu1 (lysosomal sialidase 1) is essential for removing sialic acid from oligosaccharides and glycoconjugates. Neu1 deficiency impairs lysosomal digestion, leading to sialidosis and sialoglycoprotein accumulation. It also increases lipids, including gangliosides GM3, GD3, GM4, and LM1, in the kidney, liver, and spleen. Neu1-/- mice display symptoms resembling Type II sialidosis, including enlarged spleen and liver, kidney issues, neurological problems, spinal defects, and oligosaccharide buildup. The study examined secondary lipid alterations and inflammation in the cortex and cerebellum of these mice. Lipidomic, molecular, and immunohistochemical analyses of tissues from 2 and 5 M Neu1-/- mice revealed reduced levels of lipids, including PC, PE, PS, and CL, along with increased pro-inflammatory cytokines and loss of oligodendrocytes and neurons. Signs of astrogliosis and microgliosis emerged in specific brain regions. These results indicate that reduced levels of glycerophospholipids could serve as an indicator of inflammation in sialidosis mice. Future research should investigate therapies targeting these lipid changes, as modulating glycerophospholipids might slow disease progression in sialidosis patients.Article Triple Helix Spaces: A Tale of Three Helices(Routledge Journals, Taylor & Francis Ltd, 2025) Kose, Suheda; Elburz, Zeynep; Velibeyoglu, Koray; Oner, Asli CeylanIn recent years, the Triple Helix model has gained prominence within academic circles. This study, situated in the field of city planning, aims to clarify the model's theoretical foundations, evaluate its measurement techniques, and explore the relationship between the Triple Helix and urban space. By examining 231 Triple Helix-related publications from the past 40 years (up to 12 July 2024, sourced from the Web of Science Core Collection), we propose a framework of three distinct generations for understanding Triple Helix spaces in urban contexts. The first-generation Triple Helix space is characterized by direct interactions among the three primary actors: university, industry, and government. The second-generation expands on this by including multiple interactions among the three main actors and their facilitators. The third-generation involves the circular interaction of multiple second-generation Triple Helix spaces. Across these generations, the study provides a lens for analyzing innovative urban spaces through Triple Helix interactions and offers practical approaches for examining the Triple Helix spaces. The findings also contribute to the theoretical foundation for the sustainable development of such spaces.Article Mass Spectrometric Profiling Reveals Alterations in N-Glycans and O-Glycans in Tay-Sachs Disease Under Autophagy-Induced Conditions(Springer, 2025) Can, Melike; Basirli, Hande; Jin, Chunsheng; Karlsson, Niclas G.; Bojar, Daniel; Seyrantepe, VolkanTay-Sachs disease is a rare neurodegenerative disorder caused by mutations in the HEXA gene. The HEXA gene encodes the alpha-subunit of the enzyme beta-hexosaminidase A, which degrades GM2 ganglioside. Previously, we identified impaired autophagy in the brains of a mouse model of Tay-Sachs disease, which exhibited neuropathological and clinical abnormalities. Moreover, we demonstrated autophagosome clearance in Tay-Sachs cells under lithium-induced conditions. Here, we further aimed to evaluate N- and O-glycan changes in these cells and examine whether glycan alterations are linked to ER stress. The profiles of N- and O-glycans were analyzed using LC-MS/MS in fibroblasts and neuroglial cells from 5-month-old Hexa-/-Neu3-/- mice and neuroglial cells from Tay-Sachs patients under lithium induction and nutrient deprivation. The expression levels of ER stress-related markers were assessed using qRT-PCR and Western blot analyses. We demonstrated higher levels of high mannose and lower levels of complex types of N-glycans, along with increased O-glycan levels in Tay-Sachs cells. Compared to control groups, we observed upregulated expression of endoplasmic reticulum (ER) stress-related markers, CHOP and ATF-6, in Tay-Sachs cells. Our study demonstrated that autophagy induction causes the degradation of accumulated high-mannose N-glycans and O-glycans, which is associated with the downregulation of ER stress-related genes in Tay-Sachs cells. Our study is the first to show this phenomenon in Tay-Sachs cells and suggests the presence of ER stress-mediated autophagy. Therefore, targeting glycans through autophagy induction could offer therapeutic benefits to patients with Tay-Sachs disease in future studies.Article Dimensionality Effects in Anisotropic Single Layers TiSe5 and TiTe5: a Comparative Study of 2D Sheets and 1D Nanochains(IOP Publishing Ltd, 2026) Can Dogan, Kadir; Kutay Tamdogan, Omer; Bozkurt, Yagmur; Cetin, Zebih; Yagmurcukardes, MehmetIn this study, we present a comprehensive first-principles investigation of the structural, vibrational, and electronic properties of titanium pentachalcogenide structures in both two-dimensional (2D) and one-dimensional (1D) nanochain (NC) forms. Total energy and geometry optimizations reveal that the 2D TiX5 (X = Se, Te) structures exhibit in-plane anisotropy arising from the trigonal prismatic TiX3 units interconnected via the chalcogenide chains. Phonon band dispersions and elastic tensor elements confirm the dynamical and mechanical stability of the 2D layers, respectively. Electronically, while TiTe5 is a metal, TiSe5 possesses direct band gap semiconducting behavior. In addition, free-standing 1D NC counterparts, which are sub-units of the 2D structures, are investigated by means of their stability. Three stable 1D NCs, namely TiTe5-NC, TiSe7-NC, and TiTe7-NC, are found to be composed of edge-sharing TiX6-like units with either five- or seven-fold coordination. The dynamically stable 1D NCs are shown to be semiconductors with relatively larger band gaps as compared to 2D layers. Predicted Raman spectra reveal clear signatures of vibrational mode evaluations as a result of quantum confinement from the 2D layer to the 1D NC. Moreover, finite-temperature ab-initio quantum molecular dynamics simulations at 300 K confirm the thermal stability of both the 2D TiX5 layers and 1D NC derivatives, showing that the Ti-based systems retain their structural integrity under ambient conditions and are feasible candidates for experimental synthesis. Our findings highlight the formation of stable semiconducting 1D NCs of Ti-pentachalcogenides from their 2D counterparts.Article Interventions in Historic Urban Sites After Earthquake Disasters(MDPI, 2025) Demir, Hatice Aysegul; Turan, Mine HamamciogluEarthquakes, fires, and climate change-related hazards increasingly threaten cultural heritage. Documenting and identifying the significance of heritage sites before disasters is essential for archival purposes and for guiding post-disaster interventions such as consolidation, reconstruction, or redesign. Although various post-disaster strategies exist in the literature, they often lack consideration of pre-disaster values and authentic qualities, limiting their effectiveness in value-based regeneration. This study proposes a framework for managing post-disaster interventions grounded in pre-disaster documentation of heritage values, authenticity, and integrity. The methodology includes seven phases: case selection; site survey and documentation; thematic analysis and mapping; quantification of qualitative data; synthesis of pre-disaster analysis results to define values, problems, and potentials; post-disaster assessment using aerial and terrestrial imagery; and development of targeted intervention strategies. This study focuses on two areas in Antakya, T & uuml;rkiye: Kurtulu & scedil; Street and Kuyulu Neighborhood, affected by the 2023 earthquake (M 7.7). These areas represent different historical layers: a Hellenistic grid plan with French-style buildings, and an organic Ottoman settlement morphology, respectively. Conservation data collected in 2019 inform the analysis. Mapping techniques evaluate attributes such as spatial characteristics, typologies, and structural systems. The study concludes that traces of pre-disaster spatial patterns and building features should inform post-disaster designs, ensuring sustainable, earthquake-resistant, and value-based interventions.Article Contrastive Retrieval Methodology for Turkish Metaphor Detection and Identification(Assoc Computing Machinery, 2025) Inan, EmrahMetaphorical expressions, as a form of figurative language, are individually limited in their use. However, whenboth literal and non-literal meanings are considered, they are frequently used in web content. Hence, producinga balanced dataset to learn superior representations is a challenging task, and metaphor detection suffers froma limited training dataset. To alleviate this problem, we present a retrieval-based contrastive learning approachwhich first identifies candidate metaphors in the input text and then detects metaphorical expressions as aclaim verification task in the inherently unbalanced setting of this study. Furthermore, we adapt contrastivelearning to make it easier to distinguish between the literal and figurative meanings of the same expression.For the experimental setup, we extract non-literal and literal expressions along with their meanings andsample sentences from a Turkish dictionary. In the metaphor detection subtask, performance evaluation shows that sparse and dense search variations using the Turkish-e5-Large model achieve a Recall@10 (R@10) scoreof 0.614. Moreover, the SimCSE-TR-Contr-Sample-Meaning model achieves the highest Recall@10 (R@10)of 0.9739 on the generated test dataset for the metaphor identification subtask. In the real-world scenario,it achieves a competitive R@10 score of 0.8684, and these results clearly demonstrate that our model cangeneralise to this real-world scenarioArticle Design Strategies to Optimize Polymeric Vectors for mRNA Delivery(Taylor and Francis Ltd., 2025) Turhan, Z.Y.; Savaş, M.; Alakbarov, A.; Bulmus, V.mRNA holds great promise for preventing and treating a variety of diseases, from infectious diseases to diverse cancers, owing to its transient expression, lack of genomic integration, and scalable production. Among non-viral vectors, polymeric carriers are attractive due to their synthetic versatility and stability, which allow for precise tuning for efficient mRNA delivery. Their scalability further supports the applicability of polymeric vectors. Studies have addressed the room for improvement in polymeric systems for mRNA delivery and have adapted varying approaches depending on the type of polymeric structure, including but not limited to PEGylation, hydrophobic modification, and incorporation of responsive or targeting moieties. This review summarizes advances in polymeric vectors for mRNA delivery and highlights how distinct structural modifications influence toxicity, mRNA transfection efficiency, biodistribution, intracellular trafficking and immune activation, providing a framework for the rational design of next-generation polymeric vectors that can fully realize the clinical potential of mRNA therapeutics. © 2025 Taylor & Francis Group, LLC.Article Fragile Solidarity Amid Urban Exclusion: Syrian Refugees and Neighborhood Life in a Historic District of İzmir, Turkey(Routledge Journals, Taylor & Francis Ltd, 2025) Aksoy, Sadullah; Turk, AliThis article explores how Syrian refugees experience neighboring and community relations in Basmane, a marginalized district in & Idot;zmir, T & uuml;rkiye. While neighborhood ties have weakened in modern urban life, exclusionary urban zones often foster stronger solidarity. Yet, how refugees form neighborly bonds within such zones remains unclear. Drawing on ethnographic fieldwork, the study examines how neighborhood relations are shaped by spatial confinement, economic precarity, and social exclusion. Findings reveal fragmented solidarity, limited place attachment, and constrained mobility. The article contributes to urban migration research by highlighting the ambiguous nature of belonging in spaces of forced settlement and involuntary urban segregation.