Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Measuring Disaster Resilience in MENA Countries and Its Impact on Disaster Losses(Nature Portfolio, 2025-12-08) Demir, Abdullah; Dincer, Ali Ersin; Dincer, Nazire NergizDisaster resilience is a protective feature aimed at reducing the effects of natural disaster events and losses resulting from these events. This study develops a Disaster Resilience Index (DRI) for MENA countries to assess resilience across ten dimensions, including economic, social, institutional, infrastructural, and environmental factors. Unlike most prior studies, which focus on individual countries or use narrower sets of indicators, this study provides a multi-country, region-specific framework tailored to MENA's socio-economic and environmental heterogeneity. The index integrates geospatial data on disaster risk from geographic information systems (GIS) and a natural hazard risk dimension. Validation using disaster-related fatalities, supported by a dual PCA-based sensitivity analysis, confirms the robustness of the DRI and reveals that countries with stronger governance, higher human capital, and robust infrastructure tend to exhibit greater resilience, while fragile states and resource-dependent economies are more vulnerable. Notably, the DRI calculated using both dimension-specific and all-indicator PCA produces closely aligned values, indicating the choice of conducting PCA at the dimension level does not significantly alter the overall assessment of disaster resilience. These insights provide a foundation for targeted disaster risk reduction strategies and highlight areas where international cooperation and policy interventions can strengthen resilience in the region.Article Vim-Polyp: Multimodal Colon Polyp Dataset with Video, Histopathology, and Protein Expression(Nature Portfolio, 2025-12-03) Dogan, Refika Sultan; Akay, Ebru; Dogan, Serkan; Yilmaz, BulentThe dataset in this study includes 202 videos with a total of 422 minutes, reaching Kayseri City Hospital's gastroenterology department as colonoscopy videos and 1903 microscopy images between 2019 and 2021. It includes 399 colonoscopy, microscopy images, and pathological diagnoses of polyps, as well as immunohistochemical staining results for proteins that play an important role in the assessment of cancerous cells, such as staining results for p53 (clone: bp53-11), Ki-67 (clone: 30-9), CD34 (clone: QBend/10), PD-L1 (clone: SP142), BRAF (clone: V600E) and VEGF (clone: SP125). By sharing the data openly, we aim to facilitate benchmarking, exploratory analysis and transfer-learning studies on colorectal polyps and cancer. In combination with external datasets or pretrained models, the resource can help advance data-driven detection and characterisation work. The diverse range of polyps assigned to cancer stages from 201 patients makes this tool valuable for researchers and clinicians in furthering diagnosis and treatment.Article Citation - WoS: 11Citation - Scopus: 10UV Light Promoted Dihydrolipoic Acid and Its Alanine Derivative Directed Rapid Synthesis of Stable Gold Nanoparticles and Their Catalytic Activity(Nature Portfolio, 2024-10-21) Temur, Nimet; Dadi, Seyma; Nisari, Mustafa; Ucuncuoglu, Neslihan; Avan, Ilker; Ocsoy, IsmailIn general, colloidal gold nanoparticles (AuNPs) have been synthesized in heated or boiling water containing HAuCl4 precursor with sodium citrate as reducing stabilizing reagent. Although temperature plays a driving for synthesis of AuNPs, elevated temperature in thermal reduction method causes aggregation of the AuNPs. The preferential, rapid and strong binding of dihydro-lipoic acid and its derivatives on surface of AuNPs via thiol - Au chemistry promote the production of very stable AuNPs. In this study, we have developed citric acid (CA), dihydrolipoic acid (DHLA) and DHLA-Alanine (DHLA-Ala) directed rapid synthesis of ultra-stable AuNPs, DHLA@AuNPs and DHLA-Ala@AuNPs, under the UV (311 nm) irradiation at room temperature (RT: 25 degrees C) in around 10 min (min). CA is used as a potential reducing agent to expedite both reduction of Au3+ ion and AuNP formation, DHLA and DHLA-Ala act as stabilizing agents by replacing CA molecules on surface of AuNPs in order to produce quite stable AuNP. It is worthy to mention that reduction of Au3+ ion, formation and surface stabilization of AuNPs are consequently occurred in one step. We also investigated how experimental parameters including reaction time and temperature, pH of reaction solution, affect formation of the AuNPs. The effects of salt concentration and storage temperature were studied to show stability of the AuNPs. The synthesized DHLA@AuNPs and DHLA-Alanine@AuNPs were characterized via UV-Vis spectrophotometer (UV-Vis), scanning transmission electron microscope (STEM), dynamic light scattering (DLS) and Zeta potential (ZT) devices. The reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) was efficiently catalyzed by the AuNPs in the presence of sodium borohydride in aqueous solution.Article Citation - WoS: 28Citation - Scopus: 25Quantum Dot and Electron Acceptor Nano-Heterojunction for Photo-Induced Capacitive Charge-Transfer(Nature Portfolio, 2021-01-28) Karatum, Onuralp; Eren, Guncem Ozgun; Melikov, Rustamzhon; Onal, Asim; Ow-Yang, Cleva W.; Sahin, Mehmet; Nizamoglu, SedatCapacitive charge transfer at the electrode/electrolyte interface is a biocompatible mechanism for the stimulation of neurons. Although quantum dots showed their potential for photostimulation device architectures, dominant photoelectrochemical charge transfer combined with heavy-metal content in such architectures hinders their safe use. In this study, we demonstrate heavy-metal-free quantum dot-based nano-heterojunction devices that generate capacitive photoresponse. For that, we formed a novel form of nano-heterojunctions using type-II InP/ZnO/ZnS core/shell/shell quantum dot as the donor and a fullerene derivative of PCBM as the electron acceptor. The reduced electron-hole wavefunction overlap of 0.52 due to type-II band alignment of the quantum dot and the passivation of the trap states indicated by the high photoluminescence quantum yield of 70% led to the domination of photoinduced capacitive charge transfer at an optimum donor-acceptor ratio. This study paves the way toward safe and efficient nanoengineered quantum dot-based next-generation photostimulation devices.Article Citation - WoS: 55Citation - Scopus: 53MoO3/WO3 as Electrode Material for Supercapacitor and Catalyst for Methanol and Ethanol Electrooxidation(Nature Portfolio, 2024-04-30) Askari, Mohammad Bagher; Salarizadeh, Parisa; Zadeh, Mohammad Hassan Ramezan; Ramezan zadeh, Mohammad HassanThe potential of metal oxides in electrochemical energy storage encouraged our research team to synthesize molybdenum oxide/tungsten oxide nanocomposites (MoO3/WO3) and their hybrid with reduced graphene oxide (rGO), in the form of MoO3/WO3/rGO as a substrate with relatively good electrical conductivity and suitable electrochemical active surface. In this context, we presented the electrochemical behavior of these nanocomposites as an electrode for supercapacitors and as a catalyst in the oxidation process of methanol/ethanol. Our engineered samples were characterized by X-ray diffraction pattern and scanning electron microscopy. As a result, MoO3/WO3 and MoO3/WO3/rGO indicated specific capacitances of 452 and 583 F/g and stability of 88.9% and 92.6% after 2000 consecutive GCD cycles, respectively. Also, MoO3/WO3 and MoO3/WO3/rGO nanocatalysts showed oxidation current densities of 117 and 170 mA/cm(2) at scan rate of 50 mV/s, and stability of 71 and 89%, respectively in chronoamperometry analysis, in the MOR process. Interestingly, in the ethanol oxidation process, corresponding oxidation current densities of 42 and 106 mA/cm(2) and stability values of 70 and 82% were achieved. MoO3/WO3 and MoO3/WO3/rGO can be attractive options paving the way for prospective alcohol-based fuel cells.Article Citation - WoS: 18Citation - Scopus: 17Machine Learning Based Classification of Cells into Chronological Stages Using Single-Cell Transcriptomics(Nature Portfolio, 2018-11-21) Singh, Sumeet Pal; Janjuha, Sharan; Chaudhuri, Samata; Reinhardt, Susanne; Kraenkel, Annekathrin; Dietz, Sevina; Reid, John E.; Kränkel, AnnekathrinAge-associated deterioration of cellular physiology leads to pathological conditions. The ability to detect premature aging could provide a window for preventive therapies against age-related diseases. However, the techniques for determining cellular age are limited, as they rely on a limited set of histological markers and lack predictive power. Here, we implement GERAS (GEnetic Reference for Age of Single-cell), a machine learning based framework capable of assigning individual cells to chronological stages based on their transcriptomes. GERAS displays greater than 90% accuracy in classifying the chronological stage of zebrafish and human pancreatic cells. The framework demonstrates robustness against biological and technical noise, as evaluated by its performance on independent samplings of single-cells. Additionally, GERAS determines the impact of differences in calorie intake and BMI on the aging of zebrafish and human pancreatic cells, respectively. We further harness the classification ability of GERAS to identify molecular factors that are potentially associated with the aging of beta-cells. We show that one of these factors, junba, is necessary to maintain the proliferative state of juvenile beta-cells. Our results showcase the applicability of a machine learning framework to classify the chronological stage of heterogeneous cell populations, while enabling detection of candidate genes associated with aging.Article Citation - WoS: 7Citation - Scopus: 9Green Synthesis of Silver Nanoparticles From Pomegranate Peel and Their Application in PVA-Based Nanofibers for Coating Minced Meat(Nature Portfolio, 2025-05-16) Gencag, Burcu Sari; Kahraman, Kevser; Ekici, Lutfiye; Sari Gencag, BurcuIn this study, silver nanoparticles (AgNPs) were synthesized via a green method from pomegranate peel extract and incorporated into polyvinyl alcohol (PVA) to produce AgPVA nanofibers through electrospinning. Nanofibers containing different silver concentrations (0.5, 1, and 1.5% Ag) were used as coating materials to coat minced meat, and their effects on various quality parameters during storage at 4 degrees C were evaluated. FTIR, XRD, SEM, and antibacterial analyses were conducted for the characterization of AgNPs and AgPVA nanofibers. To assess the quality characteristics of the minced meat during storage, pH, color, peroxide, TBARS, and microbiological analyses were performed. The results indicated that silver concentrations up to 1% could delay oxidation in minced meat and help preserve its quality. Compared with the other samples, the samples coated with 0.5% AgPVA (A1) and 1.0% AgPVA (A2) nanofibers exhibited a significant antimicrobial effect at the 6-day storage point (p < 0.05). The migration of AgNPs into minced meat was monitored during storage, and all migration values remained below the European food safety authority (EFSA) safety limit of 0.05 mg/kg, demonstrating the safety of the coatings. These findings suggest that AgPVA nanofibers synthesized via a green method could be a promising approach for extending the shelf life of perishable foods by reducing spoilage.Article Citation - WoS: 35Citation - Scopus: 37Glucose-Dependent Anaplerosis in Cancer Cells Is Required for Cellular Redox Balance in the Absence of Glutamine(Nature Portfolio, 2016-09-08) Cetinbas, Naniye Malli; Sudderth, Jessica; Harris, Robert C.; Cebeci, Aysun; Negri, Gian L.; Yilmaz, Oemer H.; Sorensen, Poul H.; Yllmaz, Ömer H.Cancer cells have altered metabolism compared to normal cells, including dependence on glutamine (GLN) for survival, known as GLN addiction. However, some cancer cell lines do not require GLN for survival and the basis for this discrepancy is not well understood. GLN is a precursor for antioxidants such as glutathione (GSH) and NADPH, and GLN deprivation is therefore predicted to deplete antioxidants and increase reactive oxygen species (ROS). Using diverse human cancer cell lines we show that this occurs only in cells that rely on GLN for survival. Thus, the preference for GLN as a dominant antioxidant source defines GLN addiction. We show that despite increased glucose uptake, GLN addicted cells do not metabolize glucose via the TCA cycle when GLN is depleted, as revealed by C-13-glucose labeling. In contrast, GLN independent cells can compensate by diverting glucose-derived pyruvate into the TCA cycle. GLN addicted cells exhibit reduced PDH activity, increased PDK1 expression, and PDK inhibition partially rescues GLN starvation-induced ROS and cell death. Finally, we show that combining GLN starvation with pro-oxidants selectively kills GLN addicted cells. These data highlight a major role for GLN in maintaining redox balance in cancer cells that lack glucose-dependent anaplerosis.Article Citation - WoS: 23Citation - Scopus: 21Environmental Responsiveness of Tubulin Glutamylation in Sensory Cilia Is Regulated by the P38 MAPK Pathway(Nature Portfolio, 2018-05-30) Kimura, Yoshishige; Tsutsumi, Koji; Konno, Alu; Ikegami, Koji; Hameed, Saira; Kaneko, Tomomi; Setou, MitsutoshiGlutamylation is a post-translational modification found on tubulin that can alter the interaction between microtubules (MTs) and associated proteins. The molecular mechanisms regulating tubulin glutamylation in response to the environment are not well understood. Here, we show that in the sensory cilia of Caenorhabditis elegans, tubulin glutamylation is upregulated in response to various signals such as temperature, osmolality, and dietary conditions. Similarly, tubulin glutamylation is modified in mammalian photoreceptor cells following light adaptation. A tubulin glutamate ligase gene ttll-4, which is essential for tubulin glutamylation of axonemal MTs in sensory cilia, is activated by p38 MAPK. Amino acid substitution of TTLL-4 has revealed that a Thr residue (a putative MAPKphosphorylation site) is required for enhancement of tubulin glutamylation. Intraflagellar transport (IFT), a bidirectional trafficking system specifically observed along axonemal MTs, is required for the formation, maintenance, and function of sensory cilia. Measurement of the velocity of IFT particles revealed that starvation accelerates IFT, which was also dependent on the Thr residue of TTLL-4. Similarly, starvation-induced attenuation of avoidance behaviour from high osmolality conditions was also dependent on ttll-4. Our data suggest that a novel evolutionarily conserved regulatory system exists for tubulin glutamylation in sensory cilia in response to the environment.Article Citation - WoS: 47Citation - Scopus: 45Enabling Three-Dimensional Porous Architectures via Carbonyl Functionalization and Molecular-Specific Organic-SERS Platforms(Nature Portfolio, 2021-10-21) Deneme, Ibrahim; Liman, Gorkem; Can, Ayse; Demirel, Gokhan; Usta, HakanNanostructured films of organic semiconductors with low lying LUMO orbitals can enhance Raman signals via a chemical enhancement mechanism but currently the material choice is limited to fluorinated oligothiophenes. Here, the authors investigate the growth of a porous thienoacene film enabled by carbonyls and demonstrate molecular specific organic-SERS platforms. Molecular engineering via functionalization has been a great tool to tune noncovalent intermolecular interactions. Herein, we demonstrate three-dimensional highly crystalline nanostructured D(C7CO)-BTBT films via carbonyl-functionalization of a fused thienoacene pi-system, and strong Raman signal enhancements in Surface-Enhanced Raman Spectroscopy (SERS) are realized. The small molecule could be prepared on the gram scale with a facile synthesis-purification. In the engineered films, polar functionalization induces favorable out-of-plane crystal growth via zigzag motif of dipolar C = O center dot center dot center dot C = O interactions and hydrogen bonds, and strengthens pi-interactions. A unique two-stage film growth behavior is identified with an edge-on-to-face-on molecular orientation transition driven by hydrophobicity. The analysis of the electronic structures and the ratio of the anti-Stokes/Stokes SERS signals suggests that the pi-extended/stabilized LUMOs with varied crystalline face-on orientations provide the key properties in the chemical enhancement mechanism. A molecule-specific Raman signal enhancement is also demonstrated on a high-LUMO organic platform. Our results demonstrate a promising guidance towards realizing low-cost SERS-active semiconducting materials, increasing structural versatility of organic-SERS platforms, and advancing molecule-specific sensing via molecular engineering.