PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection

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Citation - WoS: 24
Effect of pH and Hydration on the Normal and Lateral Interaction Forces Between Alumina Surfaces
(2006) Polat, Mehmet; Sato, Kimiyasu; Nagaoka, Takaaki; Watari, Koji; 01. Izmir Institute of Technology; 03. Faculty of Engineering; 03.02. Department of Chemical Engineering
Normal and lateral interaction forces between alumina surfaces were measured using Atomic Force Microscopy-Colloid Probe Method at different pH. The normal force curves exhibit a well-defined repulsive barrier and an attractive minimum at acidic pH and the DLVO theory shows excellent agreement with the data. The normal forces are always repulsive at basic pH and the theory fails to represent the measurements. Lateral forces are almost an order of magnitude smaller in the basic solutions. These differences, which have important implications in the study of stability and rheology, are attributed to the hydration of the alumina surface at basic pH. © 2013 Elsevier B.V., All rights reserved.
A Green Route To Albumin/Albumin Polyelectrolyte Complex Nanoparticles in Water With High Drug Loading for Drug Delivery
(Elsevier B.V., 2025) Sozer Demirdas, Sumeyra Cigdem; Erez, Ozlem; Cakan Akdogan, Gulcin; Akdoǧan, Yaşar; 01. Izmir Institute of Technology
A polyelectrolyte complex (PEC) formation offers a simple and green approach to obtaining albumin nanoparticles (NPs) without the use of organic solvents, crosslinkers and specialized equipment. The prepared cationic albumin proteins interact with anionic albumin proteins to form albumin PEC NPs (110 nm) with +37 mV surface zeta potential. Furthermore, albumin PEC NPs preparation in water alone achieves chlorambucil (CHL) loading up to 17 times higher than the conventional desolvation method, largely due to the elimination of drug loss to organic solvents. CHL loaded albumin PEC NPs also decreased the cell viability (Huh-7) to 44 % within 24 h. This study demonstrates that high drug-loaded albumin NPs can be alternatively synthesized by using albumin polyelectrolyte properties, and applied in drug delivery applications. © 2025 Elsevier B.V., All rights reserved.
Quaternary Ammonium Functionalized Cellulose for Bromate Ion Removal: Structural Insights and Efficacy Evaluation
(John Wiley and Sons Inc, 2025) Köseoğlu, Ecem; Şenver, Buse Aleyna; Recepoğlu, Yaşar K.; Arar, Özgür; 01. Izmir Institute of Technology; 03. Faculty of Engineering; 03.02. Department of Chemical Engineering
This study evaluates the potential of quaternary ammonium-modified cellulose as a biosorbent for bromate (BrO₃−) removal from aqueous solutions. Elemental analysis and scanning electron microscopy (SEM) characterized the elemental composition and microstructural features of the biosorbent, whereas Fourier-transform infrared (FTIR) spectroscopy elucidated its molecular structure. Experimental results revealed that BrO₃− removal efficiency increased with the biosorbent dose, achieving approximately 58%, 78%, and 90% removal with 0.025, 0.05, and 0.2 g of sorbent, respectively. The removal was pH-dependent, with efficiencies of 25%, 45%, and 76% at pH 2, 4, and 10, respectively, and the optimal removal was within the pH range of 6–8. Kinetic studies demonstrated rapid sorption, achieving 91% removal within 3 min. The Langmuir sorption isotherm model provided an excellent fit to the experimental data (R2 = 0.9987), indicating a maximum sorption capacity of 9.40 mg/g. Thermodynamic analyses confirmed a spontaneous and endothermic sorption process (∆G° = −8.11 kJ/mol; ∆H° = +2.22 kJ/mol). Desorption studies showed ≥ 99.9% efficiency using 0.1-M H₂SO₄ and NaCl, with NaCl selected as the preferred regenerant to minimize acid consumption. The biosorbent retained over 90% removal efficiency across three regeneration cycles. These findings highlight the potential of quaternary ammonium-modified cellulose as a sustainable and efficient material for BrO₃− removal from water systems. © 2025 Elsevier B.V., All rights reserved.
Airborne and Dust-Bound PBDEs Indoors and Outdoors in İzmir, Türkiye: A Multi-Route Exposure – Risk Assessment
(Elsevier Ltd, 2025) Genisoglu, Mesut; Edebali, Özge; Sofuoglu, Aysun; Turgut, Cafer; Sofuoglu, Sait C.; 01. Izmir Institute of Technology; 03. Faculty of Engineering; 03.02. Department of Chemical Engineering; 03.07. Department of Environmental Engineering
Phased-out flame retardants, e.g., polybrominated diphenyl ethers (PBDEs), persist in environmental media due to their resistance to degradation and ongoing emissions from PBDE containing materials and industrial activities. This study addresses a notable data gap in a unique setting, i.e., İzmir, Türkiye, by investigating PBDE levels at homes, schools, and café/bar/restaurants, and assessing exposure and associated health risks. Indoor and outdoor air and dust samples were collected from rural, suburban, and urban areas. Exposure through ingestion, dermal absorption, and inhalation routes, and associated chronic-toxic and carcinogenic risks were estimated with Monte Carlo Simulation. Despite having been phase-out, house-dust ƩBDE concentrations remained prevalent with average levels of >2000 ng/g in schools and homes, while outdoors they were <500 ng/g. BDE-209 was the predominant congener with an indoor air concentration of 486 pg/m3 in schools and 56.7 pg/m3 in homes. BDE-209 contributed 83.5–90.4 % of the indoor air ƩBDE concentration in schools, while in homes this contribution ranged from 70.8 to 75.8 %. Aggregate exposure estimates show the predominant PBDE congener, BDE-209, was primarily exposed by accidental ingestion (58.6 %) followed by dermal absorption (21.9 %) and inhalation (19.5 %). Chronic-toxic risk (CTR, for BDE-47, BDE-99, BDE-153, and BDE-209) and carcinogenic risk (CR, for BDE-209) for the ingestion and dermal absorption routes indicated that house-dust and indoor-air PBDE exposures are not found to be considerable for human health. However, the contribution of inhalation route to the aggregate exposure of BDE-28, BDE-47, BDE-100, BDE-99 (87.0 %, 60.5 %, 54.3 %, and 57.3 %, respectively) may indicate the evermore PBDE exposure by inhalation for lower brominated congeners as they become more significant through environmental debromination of the predominant BDE-209. © 2025 Elsevier B.V., All rights reserved.
Integrated Spectroscopic and Morphological Analyses Reveal Cellular Shifts in Gene-Silenced Melanoma CSCs
(Nature Research, 2025) Özdil, Berrin; Güler, Günnur; Ataman, Evren; Aktuǧ, Hüseyin; 01. Izmir Institute of Technology; 04. Faculty of Science; 04.05. Department of Pyhsics
Intratumoral heterogeneity remains a major barrier to durable cancer therapies, largely driven by the persistence of cancer stem cells (CSCs). In this study, we employed an integrated, multi-scale approach to investigate how melanoma CSCs respond to siRNA-mediated silencing of three key regulatory genes: KLF4, SHH, and HIF1α. Using a combination of morphological, molecular, spectroscopic, and elemental analyses, we explored structural and biochemical consequences of gene knockdown. Gene silencing resulted in significant changes in cell shape and size, reduced F-actin organization, and decreased PFN1 expression, indicating a loss of stem-like properties. ATR-FTIR spectroscopy revealed shifts in biomolecular composition, notably a reduction in amide III intensity and an increase in lipid ester content. SEM-EDS point-based elemental analysis revealed SEM-EDS point-based elemental analysis revealed relative differences in carbon and nitrogen levels between selected central and peripheral regions of silenced and control cells, at the micron-scale working depth, reflecting broader elemental distribution trends rather than precise subcellular compartmentalization. XPS analysis further confirmed these differences, providing additional insights into the elemental composition of the cellular surface. The integration of FTIR spectroscopy into this study highlights the potential of infrared spectroscopy as a powerful tool in cancer research. These findings demonstrate that targeting critical regulatory pathways induces cytoskeletal and biochemical remodelling in melanoma CSCs, offering a multi-dimensional perspective on cellular plasticity. © 2025 Elsevier B.V., All rights reserved.
Nanoencapsulation of Hydroxytyrosol Extract of Fermented Olive Leaf Brine Using Proniosomes
(Wiley, 2025) Kadiroglu, Pinar; Kilincli, Betul; Ilgaz, Ceren; Bayindir, Zerrin Sezgin; Kelebek, Hasim; Helvacioglu, Selin; Ozhan, Gunes
BACKGROUND: Olive leaves are rich in bioactive compounds with potential health benefits; however, their limited bioavailability and stability hinder their effective utilization. Emerging technologies, nanocarrier-based delivery systems, have shown promise in enhancing these properties. RESULTS: The optimal conditions for proniosome formulation were 50 rpm rotational speed and 35 degrees C, achieving 81.20 +/- 0.80% encapsulation efficiency. Particle sizes ranged from 188.6 to 248.9 nm, with a zeta potential of similar to-30 mV, indicating high stability and resistance to aggregation. Advanced instrumental analysis confirmed interactions between the extract and proniosome components. After 30 days at 4 degrees C, extract-loaded proniosomes maintained better homogeneity and lower polydispersity index. Cytotoxicity studies showed that both the extract and its proniosomal form were nontoxic to HEK293T cells up to 200 mu g mL(-1). In zebrafish assays, minimal larval mortality was observed up to 3200 mu g mL(-1) for the extract, while no mortality occurred up to 1600 mu g mL(-1) for the proniosomal extract, highlighting its improved safety profile. CONCLUSION: The findings from this research could contribute to the advancement of sustainable and health-promoting food innovations by integrating cutting-edge nanotechnology-driven encapsulation strategies into plant-based food formulations. (c) 2025 Society of Chemical Industry.
Silver-Loaded Titania-Based Metal-Organic Frameworks as a Platform for Silver Ion Release for Antibacterial Applications
(American Chemical Society, 2025) Mazare, Anca; Goldmann, Wolfgang Heinrich; Kocak, Esra; Osuagwu, Benedict; Qin, Shanshan; Cao, Ran; Schmuki, Patrik; 01. Izmir Institute of Technology
Conventional Ag-decorated TiO2coatings suffer from low adsorption capacity and burst release kinetics, limiting long-term antibacterial efficacy and risking cytotoxicity. An entirely different payload release approach can be based on metal–organic frameworks (MOFs), which offer tunable porosity, high surface area, and internal diffusion channels. Here, we report a thermally stabilized Ti-based MOF [NH2-MIL-125(Ti)] functionalized with Ag+via reactive deposition, enabling high Ag loading (∼14.7 wt %) and sustained release. Annealing at 250 °C enhances aqueous stability, allowing diffusion-governed Ag+delivery over >48 h, with 77% of the Ag still present in the MOF after a 24 h release. The system exhibits dose-dependent antibacterial activity in powders and comparable efficacy in coatings, with a more gradual release profile. This scalable platform is promising for long-acting coatings, wound interfaces, and implantable materials. © 2025 Elsevier B.V., All rights reserved.
A Comprehensive MicroRNA-Seq Transcriptomic Analysis of Tay-Sachs Disease Mice Revealed Distinct MiRNA Profiles in Neuroglial Cells
(Springernature, 2025) Kaya, Beyza; Orhan, Mehmet Emin; Yanbul, Selman; Demirci, Muserref Duygu Sacar; Demir, Secil Akyildiz; Seyrantepe, Volkan
Tay-Sachs disease (TSD) is a rare lysosomal storage disorder marked by the progressive buildup of GM2 in the central nervous system (CNS). This condition arises from mutations in the HEXA gene, which encodes the alpha subunit of the enzyme beta-hexosaminidase A. A newly developed mouse model for early-onset TSD (Hexa-/-Neu3-/-) exhibited signs of neurodegeneration and neuroinflammation, evidenced by elevated levels of pro-inflammatory cytokines and chemokines, as well as significant astrogliosis and microgliosis. Identifying disease-specific microRNAs (miRNAs) may aid the development of targeted therapies. Although previous small-scale studies have investigated miRNA expression in some regions of GM2 gangliosidosis mouse models, thorough profiling of miRNAs in this innovative TSD model remains to be done. In this study, we employed next-generation sequencing to analyze the complete miRNA profile of neuroglial cells from Hexa-/-Neu3-/- mice. By comparing KEGG and Reactome pathways associated with neurodegeneration, neuroinflammation, and sphingolipid metabolism in Hexa-/-Neu3-/- neuroglial cells, we discovered new microRNAs and their targets related to the pathophysiology of GM2 gangliosidosis. For the first time, our findings showed that miR-708-5p, miR-672-5p, miR-204-5p, miR-335-5p, and miR-296-3p were upregulated, while miR-10 b-5p, miR-615-3p, miR-196a-5p, miR-214-5p, and miR-199a-5p were downregulated in Hexa-/-Neu3-/- neuroglial cells in comparison to age-matched wild-type (WT). These specific changes in miRNA expression deepen our understanding of the disease's neuropathological characteristics in Hexa-/-Neu3-/- mice. Our study suggests that miRNA-based therapeutic strategies may improve clinical outcomes for TSD patients.
Electrically Controlled Heat Transport in Graphite Films Via Reversible Ionic Liquid Intercalation
(Amer Assoc Advancement Science, 2025) Steiner, Pietro; Adnan, Saqeeb; Ergoktas, M. Said; Barrier, Julien; Yu, Xiaoxiao; Orts, Vicente; Kocabas, Coskun
The ability to control heat transport with electrical signals has been an outstanding challenge due to the lack of efficient electrothermal materials. Previous attempts have mainly concentrated on low-thermal conductivity materials and encountered various problems such as narrow dynamic range and modest on/off ratios. Here, using high-thermal conductivity graphite films, we demonstrate an electrothermal switch enabling electrically tunable heat flow at the device level. The device uses reversible electro-intercalation of ions to modulate the in-plane thermal conductivity of graphite film by more than 13-fold via tunable phonon scattering, enabling observable modulation of the thermal conductivity at the device level. We anticipate that our results could provide a realistic pathway for adaptive thermal transport, enabling electrically driven thermal devices that would find a broad spectrum of applications in aerospace and microelectronics.
Task-Specific Dynamical Entropy Variations in EEG as a Biomarker for Parkinson's Disease Progression
(Springer, 2025) Onay, Fatih; Karacali, Bilge
Uncovering the neuronal mechanisms un-derlying optimal behavioral performance is essential to understand how the brain dynamically adapts to changing conditions. In Parkinson's disease (PD), these neuronal mechanisms are disrupted and lead to impairments in motor coordination and higher-order cognitive functions. This study investigates neuronal dynamics during a lower-limb pedaling task by analyzing the dynamical entropy of EEG signals in healthy controls (HC), PD patients, and PD patients with freezing of gait (PDFOG). We examined both average entropy changes and entropy variability across trials to characterize task-specific neural adaptations across disease progression. Results showed that PD and PDFOG patients exhibited decreased levels of permutation entropy in frontal and parietal regions, which may be associated with loss of cognitive adapta-tion due to altered information processing. Additionally, Vasicek's entropy variability in both PD groups was significantly diminished in occipital and left frontal regions, suggesting reduced cognitive capacity to dy-namically allocate neuronal resources during task engagement. We extended this analysis to the classification of groups using LDA and SVM classifiers, where entropy-derived features achieved a classification accuracy of up to 96.15% when distinguishing HC from PDFOG patients. This dynamical entropic framework provides a novel approach for capturing neural complexity changes during task performance, revealing subtle cognitive-motor impairments in PD. Understanding the maintenance of cognitive information processing and flexibility in response to motor and cognitive task demands could be a useful tool to track PD diagnosis and progression in addition to resting-state analyses.
Disruption of Glutamine Transport Uncouples the NUPR1 Stress-Adaptation Program and Induces Prostate Cancer Radiosensitivity
(BMC, 2025) Kahya, Ugur; Lukiyanchuk, Vasyl; Gorodetska, Ielizaveta; Weigel, Matthias M.; Koeseer, Ayse Sedef; Alkan, Berke; Dubrovska, Anna
BackgroundMetabolic and stress response adaptations in prostate cancer (PCa) mediate tumor resistance to radiation therapy (RT). Our study investigated the roles of glutamine (Gln) transporters SLC1A5, SLC7A5, and SLC38A1 in regulating NUPR1-mediated stress response, PCa cell survival, metabolic reprogramming, and response to RT.MethodsThe radiosensitizing potential of GLS inhibition with CB-839 was analyzed in prostate cancer xenograft models. The level of gene expression was analyzed by RNA sequencing and RT-qPCR in the established cell lines or patient-derived tumor and adjacent non-cancerous tissues. Phosphoproteomic analysis was employed to identify the underlying signaling pathways. The publicly available PCa patient datasets, and a dataset for the patients treated with RT were analyzed by SUMO software. The key parameters of mitochondrial functions were measured by Seahorse analysis. Analysis of the general oxidative stress level and mitochondrial superoxide detection were conducted using flow cytometry. gamma H2A.X foci analysis was used to assess the DNA double strand break. Relative cell sensitivity to RT was evaluated by radiobiological clonogenic assays. Aldefluor assay and sphere-forming analysis were used to determine cancer stem cell (CSC) phenotype.ResultsA siRNA-mediated knockdown of Gln transporters SLC1A5, SLC7A5, and SLC38A1 resulted in significant radiosensitization of PCa cells. Consistently, the first-in-clinic glutaminase (GLS) inhibitor CB-839, combined with RT, demonstrated a synergistic effect with radiotherapy in vivo, significantly delaying tumor growth. Inhibition of Gln metabolism or knockdown of Gln transporters SLC1A5, SLC7A5, or SLC38A1 induces expression of NUPR1, a stress response transcriptional regulator, but simultaneously uncouples the NUPR1-driven metabolic stress-adaptation program. Similarly to the effect from NUPR1 knockdown, depletion of these Gln transporters led to reduced cell viability, accumulation of mitochondrial ROS, and increased PCa radiosensitivity. This effect is more pronounced in PCa cells with high dependency on OXPHOS for energy production.ConclusionsOur work underscores the role of Gln transporters and the NUPR1-mediated stress response in PCa cell survival, oxidative stress, mitochondrial functions, and radioresistance. Our findings provide a potential therapeutic in vivo strategy to enhance the efficacy of RT and suggest a potential synergism between the depletion of Gln transporters or NUPR1 and OXPHOS inhibition.
Comparative Proteomic Analysis of Dental-Origin Stem Cells: Insights Into Regenerative Potential
(Springer, 2025) Tez, Banu Cicek; Durukan, Sebahat Melike; Yildir, Selin Kubra; Cokkececi, Murat; Boyvat, Dudu; Altinsoy, Nilay; Ozcan, Servet
Teeth are a significant source of stem cells and have clinical importance for regenerative medicine. A human tooth harbors different kinds of stem cells in the dental pulp (DPSC) or the periodontal ligament (PDLSC). Also exfoliated teeth in childhood contain a special type of stem cells in their pulp called Stem cells from Human Exfoliated Deciduous teeth (SHED). All these stem cells have features and capacities that vary depending on their niche. Here we investigated the proteomic properties of three types of stem cells that originated from human teeth. We isolated and cultured the DPSCs, PDLSCs, and SHED cells. After validating MSC populations via immunophenotyping, we performed a mass spectrometry-based proteomic approach to identify and relatively quantify whole cell and secreted proteins. Identified proteins were evaluated by using Gene Ontology and Reactome pathway analysis tools. Our data reveal that SHED cells represented inflammation, hypoxia, and nutrient deficiency-associated ontologies in both their secretome and whole-cell proteomes. The whole-cell proteome of PDLSCs consisted of differentiation and proliferation-associated molecules while their secretory molecules were mainly associated with inflammation, ECM organization, and immune response. Among dental-originated stem cells, DPSCs appeared to be the healthiest and clinically relevant in terms of proteomic properties with their proliferation, growth factor signaling, and stemness-associated molecules in their secretome and whole-cell proteome. Obtained results demonstrated that every type of stem cell from dental origin has unique proteomic features that are altered by their location and physiological conditions. The findings may help researchers improve the dental stem-cell-based regenerative medicine approaches.
Recent Advances in Hydrogel-Based 3D Disease Modeling and Drug Screening Platforms
(2025) Bilginer-Kartal, R.; Çoban, B.; Yildirim-Semerci, Ö.; Arslan-Yildiz, A.; 01. Izmir Institute of Technology
Three-dimensional (3D) disease modeling and drug screening systems have become important in tissue engineering, drug screening, and development. The newly developed systems support cell and extracellular matrix (ECM) interactions, which are necessary for the formation of the tissue or an accurate model of a disease. Hydrogels are favorable biomaterials due to their properties: biocompatibility, high swelling capacity, tunable viscosity, mechanical properties, and their ability to biomimic the structure and function of ECM. They have been used to model various diseases such as tumors, cancer diseases, neurodegenerative diseases, cardiac diseases, and cardiovascular diseases. Additive manufacturing approaches, such as 3D printing/bioprinting, stereolithography (SLA), selective laser sintering (SLS), and fused deposition modeling (FDM), enable the design of scaffolds with high precision; thus, increasing the accuracy of the disease models. In addition, the aforementioned methodologies improve the design of the hydrogel-based scaffolds, which resemble the complicated structure and intricate microenvironment of tissues or tumors, further advancing the development of therapeutic agents and strategies. Thus, 3D hydrogel-based disease models fabricated through additive manufacturing approaches provide an enhanced 3D microenvironment that empowers personalized medicine toward targeted therapeutics, in accordance with 3D drug screening platforms. © 2025. The Author(s), under exclusive license to Springer Nature Switzerland AG.
Tc-99m Erythromycin Lactobionate Inhalation Scintigraphy in Parenchymal Lung Diseases
(Elsevier Science inc, 1999) Durak, H; Aktogu, S; Degirmenci, B; Sayit, E; Ertay, T; Dereli, S; 01. Izmir Institute of Technology
We have investigated Technetium 99m erythromycin lactobionate (Tc 99m EL) clearance from the lungs after inhalation, in the presence of an alveolitis. Eighteen patients (6 sarcoidosis, 7 idiopathic fibrosis, and 5 miliary tuberculosis) were imaged after the patients inhaled 1,110 MBq of Tc 99m EL. Clearance half time for the first 45 min, for 24 h, and retention at 24 h correlated with percentage of lymphocytes in bronchoalveolar lavage fluid (BAL) (r =.729, r =.883, and r =.826, respectively). There was a positive correlation between peripheral penetration (PP) and forced expiratory volume in 1 s (FEV1) (r =.806) and forced vital capacity (FVC) (r =.781). Retention was more marked in sarcoidosis compared with tuberculosis (0.025 < p less than or equal to 0.05). Radioaerosol lung imaging may reflect the pulmonary function impairment in parenchymal lung diseases. Retention of Tc 99m EL may be related to number of BAL cells or presence of a lymphocytic alveolitis. Long residency time of Tc 99m EL in the lungs implies that erythromycin can also be administered by inhalation for therapeutic purposes. NUCL MED BIOL 26;6:695-698, 1999. (C) 1999 Elsevier Science Inc. All rights reserved.
Elastic and Anelastic Behavior Associated With Structural Transitions in CsPbBr3
(Amer Chemical Soc, 2025) Luo, Pingjing; He, Zhengwang; Yang, Dexin; Aktas, Oktay; Ding, Xiangdong; Zhang, Xuefeng; 01. Izmir Institute of Technology
Strain coupling and relaxation dynamics critically influence the photovoltaic and photoluminescent performances of metal halide perovskites. Here, resonant ultrasound spectroscopy is employed to study the elastic and anelastic properties associated with the octahedral tilting transitions in the optoelectronic semiconductor CsPbBr3 over the temperature range 303-468 K. The cubic-to-tetragonal transition near 405 K is marked by pronounced elastic softening accompanied by a sharp increase in acoustic loss. High anelastic loss below this transition reveals the presence of mobile ferroelastic twin walls that become pinned by lead vacancies at a temperature interval near 380 K in the tetragonal phase. The elastic softening in the cubic phase is strongly correlated to dynamic effects such as the local polar fluctuations. This local disordered effect is further verified by the anomalously high attenuation in the orthorhombic structure, in which the ferroelastic twin walls might become mobile.
Nanostructured Ox-MWCNT-Ppy-Au Electrochemical Sensor for Ultralow Detection of Retrorsine and Evaluation of Its Cytotoxic Effects on Liver Cells
(Taylor & Francis Ltd, 2025) Akturk, Ezgi Zekiye; Njjar, Muath; Ata, Melek Tunc; Kaya, Ahmet; Akdogan, Abdullah; Onac, Canan; 01. Izmir Institute of Technology
This study presents the development of a novel retrorsine (RTS)-imprinted sensor utilizing oxidized multi-walled carbon nanotubes (Ox-MWCNTs), polypyrrole (PPy), and gold nanoparticles (AuNPs), employing square wave voltammetry for the sensitive and selective detection of RTS which causes oxidative-stress and DNA damage. The fabricated Ox-MWCNT-PPy-AuNP sensor demonstrated a surface-area of (0.218 cm2) is 4.25 times larger than a bare glassy carbon electrode, with a low charge transfer resistance (10.9 Omega), enhancing electron transfer kinetics. The sensor showed excellent sensitivity in detecting retrorsine, with a limit of detection of 0.035 nM in synthetic matrices and -0.030 nM in HepaRG cell culture medium. Toxicity assays in HepaRG cells revealed dose-dependent oxidative-stress, with glutathione levels decreasing from 23.08 +/- 0.21 mu mol/109 to 21.21 +/- 0.02 mu mol/109 at 35 mu M retrorsine. Concurrently, GSSG levels increased from 1.32 +/- 0.26 mu mol/109 to 2.22 +/- 0.02 mu mol/109. DNA-damage assessed via comet assay, showed significant increases in tail-moment (2.53 mu m) and tail-migration (16.13 mu m). Oxidative DNA-damage, indicated by 8-OHdG levels, increased significantly from 0.29 +/- 0.02 ng.mL- (control) to 0.47 +/- 0.07 ng.mL- at 35 mu M retrorsine. These findings demonstrate the sensor's effectiveness for retrorsine detection and its applicability in toxicological studies. The integration of nanomaterial engineering and molecular imprinting provides a highly sensitive, selective, and eco-friendly solution for monitoring toxic agents and assessing their biological impacts.
Citation - WoS: 1
Citation - Scopus: 2
A Holistic Overview of the Applications of Grace-Observed Terrestrial Water Storage in Hydrology and Climate Science
(Springer, 2025) Khorrami, Behnam; Gunduz, Orhan; 03.07. Department of Environmental Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
Terrestrial Water Storage (TWS) represents a vital element of the hydrological cycle, with its fluctuations significantly impacting the climate of the Earth and its ecological balance. Since its launch in 2002, the Gravity Recovery and Climate Experiment (GRACE) satellite mission has revolutionized the ability to observe and analyze large-scale mass changes within Earth's system components. This paper offers a comprehensive and current overview of GRACE satellite gravimetry, highlighting its relevance to hydrological and climate-related studies. It outlines the fundamental measurement principles of the GRACE mission, provides an in-depth explanation of GRACE data products (including spherical harmonic and mascon solutions), examines emerging trends in GRACE-based research, and reviews key applications in hydrology and climate science. Additionally, it addresses the major challenges in utilizing GRACE data and explores promising avenues for future research and applications.
Understanding the Role of a Specific Microenvironment in Personal Exposure To Semi-Volatile Organic Compounds Using Silicone Wristbands
(Royal Soc Chemistry, 2025) Akmermer, Zulfikar; Demirtepe, Hale; 03.07. Department of Environmental Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
Assessment of personal exposure to semi-volatile organic compounds was facilitated using silicone wristbands (SWBs), an easy-to-use sampler that reflects total inhalation and dermal exposure from all the microenvironments and the activities in which the user was involved. Hence, SWBs help understand exposure from various routes, activities, and microenvironments. Offices are critical microenvironments where workers spend one-third of their daily time on weekdays; hence exposure from offices should be more extensively studied. This study aimed to investigate the personal exposure of university personnel and elaborate on the contribution of the exposure due to the office air to their overall exposure using SWBs. One SWB was worn by the participant, and another was hung in their office. After seven days of sampling on the wrist, exposure to polycyclic aromatic hydrocarbons (PAHs) was found to be related to combustion activities at home or from open fire, whereas exposure to organophosphate esters and phthalates was suggested to originate from building materials, such as flooring materials and paints, and consumer products, e.g. mattresses and furniture. PAHs in the participants' offices were influenced by the transport of outdoor air and phthalates from the ceiling material. Then, we estimated the equivalent air concentrations using the SWBs sampled from the offices and previously developed sampling rates and partition coefficients. The estimated office air exposure contributions to total inhalation and dermal exposure were 83%, 51%, and 39% for fluorene, tri(n-butyl) phosphate, and tris(2-chloro isopropyl) phosphate, respectively. These findings were consistent with the statistical analysis of personal data. To conclude, this study highlighted the importance of specific microenvironments in our exposure to particular SVOCs, offering strategies for indoor air quality management and human health risk assessment.
Vision Transformers-Based Deep Feature Generation Framework for Hydatid Cyst Classification in Computed Tomography Images
(Springer, 2025) Sagik, Metin; Gumus, Abdurrahman; 03.05. Department of Electrical and Electronics Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
Hydatid cysts, caused by Echinococcus granulosus, form progressively enlarging fluid-filled cysts in organs like the liver and lungs, posing significant public health risks through severe complications or death. This study presents a novel deep feature generation framework utilizing vision transformer models (ViT-DFG) to enhance the classification accuracy of hydatid cyst types. The proposed framework consists of four phases: image preprocessing, feature extraction using vision transformer models, feature selection through iterative neighborhood component analysis, and classification, where the performance of the ViT-DFG model was evaluated and compared across different classifiers such as k-nearest neighbor and multi-layer perceptron (MLP). Both methods were evaluated independently to assess classification performance from different approaches. The dataset, comprising five cyst types, was analyzed for both five-class and three-class classification by grouping the cyst types into active, transition, and inactive categories. Experimental results showed that the proposed VIT-DFG method achieves higher accuracy than existing methods. Specifically, the ViT-DFG framework attained an overall classification accuracy of 98.10% for the three-class and 95.12% for the five-class classifications using 5-fold cross-validation. Statistical analysis through one-way analysis of variance (ANOVA), conducted to evaluate significant differences between models, confirmed significant differences between the proposed framework and individual vision transformer models (p<0.05\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p < 0.05$$\end{document}). These results highlight the effectiveness of combining multiple vision transformer architectures with advanced feature selection techniques in improving classification performance. The findings underscore the ViT-DFG framework's potential to advance medical image analysis, particularly in hydatid cyst classification, while offering clinical promise through automated diagnostics and improved decision-making.
A Pragmatic Grouping Model for Bone-Only De Novo Metastatic Breast Cancer (MetS Protocol MF22-03)
(MDPI, 2025) Goktepe, Berk; Demirors, Berkay; Senol, Kazim; Ozbas, Serdar; Sezgin, Efe; Lucci, Anthony; Soran, Atilla; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
De novo metastatic breast cancer (dnMBC) accounts for 3-10% of newly diagnosed cases, with 20-40% presenting as a bone-only metastatic disease, which can achieve survival outcomes exceeding 10 years with multimodal therapy. However, the role of multimodal therapy remains controversial in the guidelines. Objective: This study aims to identify dnBOMBC subgroups to develop a pragmatic staging system for guiding locoregional therapy decisions. Materials and Methods: Data from the MF07-01 phase III randomized trial (2021, median follow-up time (mFT): 40 months (range 1-131)) and the BOMET prospective multi-institutional registry trial (2021, mFT: 34 months (range 25-45)) were combined for analysis, including only patients who presented with bone-only metastases. Exclusion criteria were patients under 18 and those with a history of prior cancer or cancer metastases. Patients with missing data and positive surgical margins were excluded. Out of 770 patients, 589 were included. Survival analyses were first conducted according to molecular subgroups, after which patients were further stratified by hormone receptor status, human epidermal human epidermal growth factor receptor 2 (HER2) status, tumor grade, and clinical T (cT) stage. Group A (GrA) included hormone receptor (HR)-positive, low- or intermediate-grade tumors at any cT; HR-positive, high-grade tumors with cT0-3; or any HER2-positive tumors. Group B (GrB) included HR-positive, high-grade tumors with cT4 disease or any triple-negative (TN) tumors. Results: The hazard of death (HoD) was 43% lower in GrA than in GrB. Median OS was 65 months (39-104) for GrA patients and 44 months (28-72) for GrB patients (HR 0.57, 95% CI 0.41-0.78, p = 0.0003). Primary tumor surgery (PTS) significantly improved OS in GrA patients, regardless of the number of metastases (solitary: HR, 0.375, 95% CI 0.259-0.543, p < 0.001; multiple: HR 0.435, 95% CI 0.334-0.615, p < 0.001). Conversely, GrB patients did not experience a significant benefit from PTS. Conclusions: This study demonstrates that GrA patients have better OS than GrB patients, and PTS reduces the HoD in GrA patients compared to systemic therapy alone. These findings support using a modified staging system in dnBOBMC to identify patients who may benefit from multimodal therapy including PTS.

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