WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7150

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  • Article
    FTIR Spectroscopy Coupled With Chemometrics for Evaluating Functional Food Efficacy in an in Vitro Model of Iron Deficiency Anemia
    (Elsevier Science Ltd, 2026) Dalyan, Eda; Cavdaroglu, Cagri; Ozen, Banu; Gulec, Sukru
    Vibrational spectroscopy offers a rapid, cost-effective approach for studying biological systems. This study employs Fourier Transform Infrared (FTIR) spectroscopy, combined with Soft Independent Modeling of Class Analogy (SIMCA), to evaluate treatment outcomes for iron deficiency anemia (IDA). The model was built using spectra from healthy and anemic cells, then validated with cells treated with commonly used iron supplements. In calibration, 9 of 10 control and all IDA samples were correctly classified; 14 of 15 validation samples were identified as healthy. The model was applied to cells treated with protein-iron complexes. All samples treated with a 60:1 protein-iron ratio matched the healthy group, while 3 of 4 treated with a 10:1 ratio matched the IDA group. These results were further supported by iron-regulated gene expression of transferrin receptor (TFR) and (Ankyrin Repeat Domain 37) ANKRD37. FTIR coupled with chemometrics enables rapid assessment of functional effects and shows potential for screening functional ingredients in anemia-targeted food products.
  • Article
    Application of 3D Cell Culture Techniques in Nanotoxicology: How Far Are We
    (Springer, 2026) Shakeri, Raheleh; Mirjalili, Seyedeh Zohreh; Karakus, Ceyda Oksel; Safavi, Maliheh
    Investigation of toxicological profile and possible side effects of engineered nanomaterials (ENMs) is of high importance. Historically, two-dimensional (2D) cell culture was used to study the toxicity of the ENMs, but due to their inability to simulate in vivo cell behavior, three-dimensional (3D) cell culture systems have been developed. Nanotoxicity studies initiate with in vitro experiments and continue with in vivo studies, which are very challenging and sometimes accompanied by conflicting data due to the in vitro-in vivo gap. Thus, scientists are turning their attention to microfabrication techniques and engineered systems "called organ-on-a-chips", which act as an intermediate between in vivo and in vitro systems. The present account tries to review the classical study models and suitably cover the emerging 3D culture models including scaffold-free and scaffold-based 3D cell cultures, 3D co-culture with direct contact and without cell-cell contact methods as well as microfluidic-based tissue chips and organoids. Overall, this review aims to give readers a better insight about the ENMs' toxicology and fill the gaps between the knowledge and practical techniques. Hopefully, the presented information will resolve the issues of 2D in vitro cultures and display the clinically relevant responses to the concerns of therapeutic ENMs.
  • Article
    Disorder-Engineered Hybrid Plasmonic Cavities for Emission Control of Defects in hBN
    (American Chemical Society, 2026) Genc, Sinan; Yucel, Oguzhan; Aglarci, Furkan; Rodriguez-Fernandez, Carlos; Yilmaz, Alpay; Caglayan, Humeyra; Bek, Alpan
    Defect-based quantum emitters in hexagonal boron nitride (hBN) are promising building blocks for scalable quantum photonics due to their stable single-photon emission at room temperature. However, enhancing their emission intensity and controlling the decay dynamics remain significant challenges. This study demonstrates a low-cost, scalable fabrication approach to integrate plasmonic nanocavities with defect-based quantum emitters in hBN nanoflakes. Using the thermal dewetting process, we realize two distinct configurations: stochastic Ag nanoparticles (AgNPs) on hBN flakes and hybrid plasmonic nanocavities formed by AgNPs on top of hBN flakes supported on gold/silicon dioxide (Au/SiO2) substrates. While AgNPs on bare hBN yield up to a 2-fold photoluminescence (PL) enhancement with reduced emitter lifetimes, the hybrid nanocavity architecture provides a dramatic, up to 100-fold PL enhancement and improved uniformity across multiple emitters, all without requiring deterministic positioning. Finite-difference time-domain (FDTD) simulations and time-resolved PL measurements confirm size-dependent control over decay dynamics and cavity-emitter interactions. Our versatile solution overcomes key quantum photonic device development challenges, including material integration, emission intensity optimization, and spectral multiplexity.
  • Article
    AI-Supported Seismic Performance Evaluation of Structures: Challenges, Gaps, and Future Directions at Early Design Stages
    (Elsevier Sci Ltd, 2026) Ak, Fatma; Ekici, Berk; Demir, Ugur
    This study reviews 91 journal articles that intersect with earthquake-resistant building design and artificial intelligence (AI)- based modeling, utilizing machine learning, deep learning, and metaheuristic optimization algorithms. Previous reviews on AI applications have examined engineering problems without considering the impact of architectural design parameters and structural irregularities on seismic performance. This review discusses the role of AI in integrating architectural design variables and seismic performance objectives, highlighting challenges, gaps, and future directions in the early design phase. The reviewed articles demonstrate that AI is successful in addressing seismic performance objectives; however, a holistic framework for assessing architectural and structural variables has not been presented. The review highlights key findings, gaps, and future directions for those involved in earthquake-resistant building design utilizing AI.
  • Article
    Sustainable Recovery of Critical Raw Materials From Geothermal Igneous Systems: Geochemical, Mineralogical, and Techno-Economic Insights from the Dikili-Bergama Field (Western Anatolia, Turkiye)
    (Elsevier, 2026) Ayzit, Tolga; Baba, Alper
    The sustainable co-extraction of critical raw materials (CRMs) with renewable geothermal energy offers a dual pathway to support the circular economy and low-carbon transition. In this study, an integrated geochemical and mineralogical approach is used to comprehensively assess the recoverable lithium (Li) boron (B), strontium (Sr) and other critical raw materials in the geothermal reservoirs of the Dikili-Bergama region Turkiye. A geochemical analysis was carried out by systematic sampling and multi-element testing of geothermal water and reservoir rock. Hydrogeochemical studies of the geothermal fluids indicated the presence of remarkable concentrations of B (4.6 ppm), Sr (2.8 ppm) and Li (1.2 ppm), suggesting the possibility of active leaching processes in the deposit. Mineralogical studies using X-ray diffraction (XRD) have revealed a number of secondary mineral phases, such as quartz and labradorite, indicating the interaction between water and rock. These interactions affect not only the permeability and porosity of the deposit, but also the mobilization and precipitation of CRMs. A techno-economic analysis will be used to identify potential synergies that could improve the economic feasibility of geothermal projects in the region. The Monte Carlo simulation has shown that the Dikili-Bergama geothermal reservoirs have a potential of similar to 712 tons of Li. In this study, the CRM potential that emerged during the geothermal energy exploitation process in the region was calculated. The temporality and the process of obtaining are completely related to the extraction technology. This offers the dual benefit of renewable energy and strategic mineral extraction, contributing to sustainable resource management in volcanic environments.
  • Article
    The Effect of Layered Cover Plate Material on the Ballistic Performance of Ceramic Armors: Experimental and Numerical Study
    (Pergamon-Elsevier Science Ltd, 2026) Cellek, Seven Burcin; Tasdemirci, Alper; Cimen, Gulden; Yildiztekin, Faki Murat; Toksoy, Ahmet Kaan; Guden, Mustafa
    This study investigates the ballistic performance of silicon carbide (SiC) ceramic armor systems reinforced with single and hybrid metallic cover plates composed of Ti-6Al-4V (Ti64) and copper. Controlled ballistic experiments combined with validated LS-DYNA simulations were conducted to examine how cover-plate material, thickness, and stacking sequence influence penetration resistance, energy dissipation, and failure mechanisms. The experimental results revealed that metallic cover plates significantly enhance protection by improving projectile erosion and extending dwell time. While both Ti64 and copper single layers increased the antipenetration capability (APC) compared with bare SiC, hybrid configurations achieved the highest performance. The optimal design, consisting of a 2 mm Ti64 plate placed in front of a 1 mm copper plate, produced the greatest reduction in penetration depth and the highest APC value. Numerical analyses closely replicated the experimental trends and provided insight into stress-wave interactions, pressure evolution, and damage progression within the ceramic. The findings demonstrate that hybrid Ti64-Cu systems not only improve initial impact resistance but also redistribute energy toward the front layers, reducing stress transmission to the backing and mitigating catastrophic ceramic failure. The combined experimental and numerical results establish a clear design framework for developing lightweight, high-efficiency ceramic armor through tailored hybrid layering strategies.
  • Article
    Hydrogeochemical Assessment and Health Risks of Groundwater in Sahand Volcanic Foreland (NW Iran): Arsenic Speciation and Heavy Metal Risk Indicators
    (Academic Press Inc Elsevier Science, 2026) Ghayurdoost, Farhad; Zarghami, Mahdi; Sadeghfam, Sina; Jabraili-Andaryan, Nasser; Nikmaram, Sara; Baba, Alper; Mosaferi, Mohammad
    Due to the toxic nature of arsenic (As) and its elevated concentrations in many water resources, numerous studies have focused on understanding its origin, distribution, and impacts. This study aimed to identify the dominant As species in groundwater of the Sahand Volcanic Foothills, assess water quality indices, and examine heavy metal (HM) concentrations to address rising concerns about groundwater contamination. A total of 21 groundwater samples were collected and analyzed in accordance with world health organization (WHO) guidelines. Although most samples fell within acceptable ranges, several (notably S10, S20, and S21) exhibited elevated levels of total dissolved solids (TDS), electrical conductivity (EC), and HMs, particularly iron (Fe) and As. Hydrochemical assessments using Piper, Gibbs, Stiff, and Schoeller diagrams indicated that geochemical processes resulting from rock dissolution were the main factors controlling groundwater chemistry, with limited influence from anthropogenic pollution. According to the groundwater quality index (GWQI), most samples were categorized as "good" to "excellent," though some areas ranged from "moderate" to "very poor." HM pollution indices revealed that As concentrations exceeded permissible limits. Health risk assessments further showed that both oral and dermal exposure posed significant carcinogenic and non-carcinogenic risks, especially for children. Speciation analysis indicated that arsenate (As V) was the dominant form of As, consistent with oxidizing aquifer conditions, and is less biologically hazardous than arsenite (As III). The study highlights the necessity of continuous groundwater monitoring, effective pollution source management, and implementation of protective regulations to mitigate environmental and health risks in the region.
  • Article
    Encapsulation of IR783 in UiO-66 MOFs for Improved Photodynamic Efficacy Against Breast Cancer Cells
    (OICC Press, 2025) Sahinoglu, Sinem; Sanli-Mohamed, Gulsah
    Breast cancer remains the most prevalent malignancy among women worldwide, underscoring the need for innovative therapeutic strategies beyond conventional modalities. Photodynamic therapy (PDT) offers a non-invasive approach that leverages light-activated photosensitizers to induce reactive oxygen species (ROS)-mediated tumor cell death. IR783, a near-infrared fluorescent (NIRF) heptamethine cyanine dye, has shown promise as a theranostic agent in cancer therapy due to its tumor-selective uptake and pro-apoptotic effects. However, its clinical potential is hindered by poor stability, rapid dissociation in polar environments, low quantum yield, and suboptimal tumor accumulation. In this study, we developed a multifunctional nanoplatform by encapsulating IR783 into UiO-66, a zirconium-based metal-organic framework (MOF), to enhance the delivery and photodynamic performance of the dye (IR783@UiO-66). The system was structurally characterized, and its biocompatibility and drug release profiles were evaluated. In vitro experiments were conducted to assess the cytotoxic and phototoxic effects of IR783, UiO-66, and IR783@UiO-66 on breast cancer cell lines (MCF-7, MDA-MB-231) and normal breast epithelial cells (MCF-10A), under LED irradiation at varying light intensities (18-144 J/cm2) and exposure durations (7.5-60 min). The results demonstrated that IR783@UiO-66 significantly reduced cancer cell viability in a dose-and light-dependent manner while sparing normal cells. Free IR783 showed slightly higher phototoxicity, attributed to differences in release kinetics and loading efficiency. UiO-66 alone exhibited negligible cytotoxicity under irradiation, confirming its safety profile. This study highlights the potential of UiO-66 as a promising nanocarrier for enhancing IR783-mediated PDT, offering a synergistic strategy for targeted and efficient breast cancer therapy.
  • Article
    Notum1a Inhibition Promotes Neurogenesis in the Adult Zebrafish Brain
    (Nature Portfolio, 2025) Kocagoz, Yigit; Erdogan, Nuray Sogunmez; Ozdinc, Sevval; Ipekgil, Dogac; Katkat, Esra; Ozhan, Gunes
    Notum is a carboxylesterase enzyme that modulates extracellular signaling by hydrolyzing palmitoleoyl residues from proteins, thereby influencing key pathways involved in cell differentiation, survival, and proliferation. While notum1 expression has been identified in the brain, its role in adult neurogenesis remains poorly understood. Using the adult zebrafish brain as a model system, we demonstrate that the notum1a homolog is broadly expressed across various brain cell types but is absent in undifferentiated radial glial cells. Pharmacological inhibition of Notum activity with the small molecule inhibitor ABC99 stimulates activation of radial glial cells, leading to increased neurogenesis. A BrdU pulse-chase assay confirms that ABC99-induced proliferation enhances the production of mature neurons. Despite Notum's established role in Wnt signaling, transcriptional analysis following ABC99 treatment reveals no sustained impact on Wnt pathway targets, suggesting that Notum may regulate neurogenesis through alternative mechanisms. Our findings highlight notum1a as a potential modulator of neural progenitor cell dynamics in the adult brain and suggest that targeting Notum could represent a novel therapeutic strategy for neurodegenerative conditions characterized by impaired neurogenesis.
  • Article
    Iron Oxide Nanocube Assembly on Silver Nanowire Templates to Enhance Magnetic Hyperthermia Performance
    (Royal Society of Chemistry, 2026) Arica, Tugce A.; Tiryaki, Ecem; Sadeghi, Ehsan; Mannir, Abubakar R.; Balci, Sinan; Pellegrino, Teresa
    Iron oxide nanocubes (IONCs) represent one of the benchmark magnetic nanoparticles able to most efficiently convert magnetic energy into heat for magnetic hyperthermia cancer treatment, and their heat losses can be further increased by controlling their assembly through the synthesis of ordered structures. However, achieving the alignment of nanoparticles with one-dimensional chain or columnar structures into long arrays to then study their magnetic heat losses still remains a significant challenge. This study exploits silver nanowires as high-surface-area anisotropic templates for the controlled chaining of IONCs. The surfaces of the IONCs were purposely functionalized with polyethyleneimine (IONCs@PEI) and interacted with silver nanowire (AgNW) surfaces via electrostatic attraction. Here, alternating current (AC) magnetometry was employed to compare the heating performance expressed as specific absorption rate values between individually coated IONCs@PEI and AgNWs@IONCs@PEI composites at various magnetic field strengths and frequencies. SAR values reveal that clustering of IONCs on AgNW surfaces improves the heating efficiency at an applied magnetic field strength of 24 kA m-1, regardless of the applied frequencies, with SAR values of AgNWs@IONCs@PEI composites outperforming those of individual IONCs@PEI. Moreover, dynamic hysteresis loops showed that the coercive field of AgNWs@IONCs@PEI increased significantly at 24 kA m-1, indicating the existence of strong magnetic dipolar interactions between nanoparticles. This study shows an innovative approach for guiding the orientation of magnetic nanoparticles using one-dimensional templates to enhance their heating performance.