PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Effect of Marination on the Formation of Polycyclic Aromatic Hydrocarbons in Grilled Vegetables(Wiley, 2025) Kacmaz Ozcetin, Sibel; Artok, LeventThe effect of marination on the formation of polycyclic aromatic hydrocarbons (PAH) in charcoal-grilled vegetables was studied. Various marinade ingredients, including apple cider vinegar, red grape vinegar, lemon juice, garlic powder, black pepper, and the food additive tert-butylhydroquinone (TBHQ) were applied to vegetable samples before charcoal grilling. The total phenolic content (TPC) and total antioxidant capacity (TAC) of each marinade ingredient were assessed for their contribution to PAH inhibition. A substantial decrease in PAH4 formation was observed in marinated vegetables. Red grape vinegar exhibited the strongest average inhibitory effect on total PAH4 formation (75%), followed by apple vinegar (68%), lemon juice (52%), garlic powder (34%), and black pepper (30%). Additionally, the TBHQ (67%) demonstrated a strong inhibitory effect, reducing total PAH4 formation by 67%. These findings offer valuable insights for reducing PAH levels in grilled vegetables and preventing their formation.Article Plasma Proteomic Markers of Interleukin-1β Pathway Associated With Incident Age-Related Macular Degeneration in Persons With Aids(Elsevier, 2025) Hunt, Peter W.; Olshen, Adam B.; Murad, Natalia; Ambayec, Gabrielle C.; Sezgin, Efe; Schneider, Michael F.; Jabs, Douglas A.Objective To evaluate the associations of plasma inflammatory proteins with age-related macular degeneration (AMD) in persons with the AIDS, using a discovery-based proteomics approach. Design A nested case-control study (analysis 1) and nested cohort study (analysis 2). Participants Persons with AIDS enrolled in the Longitudinal Study of the Ocular Complications with AIDS (LSOCA). Methods Cryopreserved plasma specimens obtained at baseline were assayed for inflammatory proteins using the Olink Inflammation Explore Panel 1. In analysis 1, baseline proteomic profiles for 26 persons with AIDS and incident intermediate-stage AMD 5 to 10 years after baseline and 49 matched controls (matched for age, biologic sex, race/ethnicity, and follow-up) without AMD were compared. In analysis 2, 475 persons from LSOCA with baseline plasma inflammatory proteomic profile measurements were followed for incident cataract and mortality. Main Outcome Measures Incident intermediate-stage AMD; incident cataract; and mortality. Results Of 365 measurable plasma inflammatory proteins, 118 (32%) were associated with incident intermediate-stage AMD at the false discovery rate-adjusted Q < 0.05 level after adjustment for smoking, CD4+ T count, and plasma human immunodeficiency virus RNA level. Gene ontology pathway enrichment analysis identified the interleukin (IL)-1 beta pathway and wound healing pathways, including tissue inhibitor of metalloproteinase 3, as significantly associated with incident AMD. These associations were qualitatively different from those associated with incident cataracts, where elevated levels of inflammatory proteins were associated with a decreased risk of cataracts. A much broader number of inflammatory pathways, including those related to the adaptive immune system, were associated with mortality. Conclusions Upregulation of the IL-1 beta pathway appears to be associated with an increased risk of incident AMD in persons with AIDS. Given the availability of inhibitors of this pathway, inhibition of the IL-1 beta pathway may provide a therapeutic avenue for treatment of AMD. Financial Disclosure(s) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article. Ophthalmology Science 2025;5:100794 (c) 2025 by the American Academy of Ophthalmology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Article Citation - WoS: 1Citation - Scopus: 1Improved Isolation of Ultra-High Genomic Dna Suitable for Third-Generation Sequencing(Mdpi, 2025) Ova, Ayse Oyku; Joffre, Enrique; Shafagh, Reza Zandi; Assuncao, Mariana F. G.; Sidorov, Roman Y.; Santos, Lilia M. A.; Romling, UteAlthough a variety of protocols to isolate high-molecular-weight genomic DNA exist, the isolation and preservation of ultra-high-molecular-weight genomic DNA of sufficient quality and length for error-free third-generation sequencing remains challenging. Inspired by the isolation of high-molecular-weight DNA in agarose plugs suitable to be separated by pulsed-field gel electrophoresis, we report the construction of an incubation chamber for DNA isolation. The chamber is flanked by semi-permeable polycarbonate membranes of variable pore size for the selective diffusion of compounds and components, which allows efficient cell lysis and the subsequent isolation of ultra-high-molecular-weight genomic DNA without shearing. The designed experimental approach is simple, but effective in isolating high-quality ultra-long genomic DNA that is suitable for third-generation sequencing by Oxford Nanopore Technology from challenging bacterial samples. We envisage that genomic DNA isolation using the incubation chamber, or variations thereof, will facilitate the regular sequencing of megabasepair-long DNA fragments, with a multitude of applications in microbiology, immunology, oncology, paleontology and forensic science.Article Citation - WoS: 4Citation - Scopus: 4Sulfonated Cellulose: a Strategy for Effective Methylene Blue Sequestration(Amer Chemical Soc, 2025) Toy, Mustafa; Recepoglu, Yasar Kemal; Arar, OzgurThis study investigates the sulfonation modification of cellulose for the removal of methylene blue (MB) from aqueous solutions. The prepared biosorbent was characterized, and its sorption capacity, kinetics, and thermodynamics were systematically evaluated. Fourier-transform infrared (FTIR) spectroscopy analyzed structural modifications, while scanning electron microscopy (SEM) examined the surface properties. The optimal sorbent dosage was determined as 0.05 g. MB removal efficiency increased from 11% at pH 1 to 70% at pH 2, reaching 99% within the pH range of 3 to 7. Kinetic studies revealed rapid sorption, achieving 99% removal within 3 min. Among various isotherm models, the Langmuir model provided the best fit (R 2 = 0.9989), indicating monolayer sorption with a maximum capacity of 37.65 mg/g. Thermodynamic analysis showed negative Delta G degrees values, confirming a spontaneous sorption process, while an enthalpy change (Delta H degrees) of -33.5 kJ/mol indicated exothermic behavior. The entropy change (Delta S degrees) of -82.6 J mol-1<middle dot>K-1 suggested decreased disorder during sorption. Regeneration studies demonstrated that 0.2 M HCl combined with ethanol achieved the highest desorption efficiency, and after three cycles, the MB removal efficiency remained above 99%. The presence of -SO3 - groups played a crucial role in MB sorption via ion exchange and may also contribute through hydrogen bonding, thereby enhancing MB sorption. These findings highlight sulfonated cellulose as an efficient and regenerable biosorbent for MB removal, offering valuable insights into its sorption mechanisms.Article Citation - WoS: 3Citation - Scopus: 4Magsity Platform: a Hybrid Magnetic Levitation-Based Lensless Holographic Microscope Platform for Liquid Density and Viscosity Measurements(Royal Soc Chemistry, 2025) Ince, Oyku Doyran; Tekin, H. CumhurThe viscosity and density of liquids are the most extensively studied material properties, as their accurate measurement is critical in various industries. Although developments in micro-viscometers have overcome the limitations of traditional bulky methods, more accessible technologies are required. Here, we introduce a novel magnetic levitation-based method to measure the viscosity and density of solutions in a microcapillary channel. This principle exploits microparticles as microsensors to correlate levitation time and height with solutions' viscosity and density, using buoyancy and drag forces. The platform has an integrated lensless holographic microscope, providing a hybrid system for in situ and precise measurements. By utilizing this hybrid technology, portable, rapid and cost-effective measurements can be conducted. This platform enables viscosity and density measurements within 7 minutes, achieving high accuracies of at least 97.7% and 99.9%, respectively, across an operation range of 0.84-5.09 cP and 1.00-1.09 g cm-3. The platform is utilized to clearly distinguish differences in the spent cell culture medium across various cell lines. This method, as presented, can be readily applied to measure a diverse array of liquids in multiple domains, encompassing biotechnology, medicine, and engineering.Article Citation - WoS: 5Citation - Scopus: 5Nanoarchitectonics Approach To Graphite/Starch-supported Bioelectrode for Enhanced Supercapacitor Performance(Elsevier, 2025) Goren, Aysegul Yagmur; Dincer, IbrahimThere has been an increasing interest in finding suitable materials for supercapacitor applications in response to the growing need for energy, to use alternative energy sources to fossil fuels in addition to energy storage. In this regard, bio-based carbon-loaded materials can be a promising option for high-performance supercapacitors because of their abundance, diversity, and reproducibility with waste management strategies. In this study, a new graphite-loaded bioelectrode is synthesized for supercapacitor application. The electrochemical performance of the synthesized electrode is tested at room temperature using the cyclic voltammetry method, and the capacity and energy density of the electrodes are evaluated. The electrochemical performance of 1 g of graphiteloaded bioelectrode was 3.5 mA/cm2, while the specific capacitance value was 355.6 F/g at a current density of 0.5 A/g. Furthermore, the bioelectrode provided significant cyclic stability with 93.5% in specific capacitance value after 5000 charge/discharge cycles at the current density of 0.5 A/g. Consequently, the synthesized bioelectrode can be a promising option for energy storage as a sustainable electrode due to its superior conductivity, stability, and low cost.Article Citation - WoS: 1Tcgex: a Powerful Visual Interface for Exploring and Analyzing Cancer Gene Expression Data(Springernature, 2025) Kus, M. Emre; Sahin, Cagatay; Kilic, Emre; Askin, Arda; Ozgur, M. Mert; Karahanogullari, Gokhan; Ekiz, H. AtakanAnalyzing gene expression data from the Cancer Genome Atlas (TCGA) and similar repositories often requires advanced coding skills, creating a barrier for many researchers. To address this challenge, we developed The Cancer Genome Explorer (TCGEx), a user-friendly, web-based platform for conducting sophisticated analyses such as survival modeling, gene set enrichment analysis, unsupervised clustering, and linear regression-based machine learning. TCGEx provides access to preprocessed TCGA data and immune checkpoint inhibition studies while allowing integration of user-uploaded data sets. Using TCGEx, we explore molecular subsets of human melanoma and identify microRNAs associated with intratumoral immunity. These findings are validated with independent clinical trial data on immune checkpoint inhibitors for melanoma and other cancers. In addition, we identify cytokine genes that can be used to predict treatment responses to various immune checkpoint inhibitors prior to treatment. Built on the R/Shiny framework, TCGEx offers customizable features to adapt analyses for diverse research contexts and generate publication-ready visualizations. TCGEx is freely available at https://tcgex.iyte.edu.tr, providing an accessible tool to extract insights from cancer transcriptomics data.Article Citation - Scopus: 2Turkmednli: a Turkish Medical Natural Language Inference Dataset Through Large Language Model Based Translation(Peerj inc, 2025) Ogul, Iskender Ulgen; Soygazi, Fatih; Bostanoglu, Belgin ErgencNatural language inference (NLI) is a subfield of natural language processing (NLP) that aims to identify the contextual relationship between premise and hypothesis sentences. While high-resource languages like English benefit from robust and rich NLI datasets, creating similar datasets for low-resource languages is challenging due to the cost and complexity of manual annotation. Although translation of existing datasets offers a practical solution, direct translation of domain-specific datasets presents unique challenges, particularly in handling abbreviations, metric conversions, and cultural alignment. This study introduces a pipeline for translating a medical NLI dataset into Turkish, which is a low-resource language. Our approach employs fine-tuning the Llama-3.1 model with selected samples from the Medical Abbreviation dataset (MeDAL) to extract and resolve medical abbreviations. Consequently, NLI pairs are refined with extracted abbreviations and subjected to metric correction. Later, the processed sentences are then translated using Facebook's No Language Left Behind (NLLB) translation model. To ensure quality, we conducted comprehensive evaluations using both machine learning models and medical expert review. Our results show that BERTurk achieved 75.17% accuracy on TurkMedNLI test data and 76.30% on the normalized test set, while BioBERTurk demonstrated comparable performance with 75.59% accuracy on test data and 72.29% on the normalized dataset. Medical experts further validated the translations through manual assessment of sampled sentences. This work demonstrates the effectiveness of large language models in adapting domain-specific datasets for low-resource languages, establishing a foundation for future research in multilingual biomedical NLP.Article Radially Aligned Carbon Nanotube Glass Fiber Composites as Ion-Selective Microelectrodes(Amer Chemical Soc, 2025) Onder, Ahmet; Ng, Zhi Kai; Tsang, Siu Hon; Alagappan, Palaniappan; Teo, Edwin Hang Tong; Yildiz, Umit HakanDetection of ions is challenging due to their small size, rapid diffusion, and high mobility, especially for assaying in samples of low volumes. Among the traditional analytical methods, potentiometric ion-selective electrodes (ISE) have become a popular choice for detecting ions as they are cost-effective, user-friendly and can be miniaturized, making them useful for on-site analysis. In this context, radially aligned carbon nanotubes (RACNT) directly grown on glass fibers (GF) via the chemical vapor deposition method is investigated as a solid contact material for the fabrication of ion-selective microelectrodes (mu ISE) upon incorporating specific ionophores within a polymeric encapsulation membrane. As an illustration, sensitive detection of ammonium ions is accomplished by the fabricated mu ISE (plasticized PVC membrane containing nonactin ionophores), which yielded a LOD and a linear response range between 7.5 x 10-6 and 1.0 x 10-5 to 1.0 x 10-1 M, respectively. The mu ISE fabricated with RACNT-GF as an interface material exhibited improvements in LOD and enhanced the detection selectivity as compared to a conventional ISE fabricated using planar solid contact materials such as graphite. We hypothesize that the fabricated mu ISE with a high surface area and mechanical durability maximize the accommodation of ionophores in the barrier membrane for yielding improved potentiometric responses. Experimental results illustrate that the mu ISE possesses the potential to be utilized for the fabrication of selective and sensitive ISE upon incorporation of specific ionophores with RACNT-GF composites.Article Citation - WoS: 5Citation - Scopus: 5A Microrna-Regulated Transcriptional State Defines Intratumoral Cd8+t Cells That Respond To Immunotherapy(Cell Press, 2025) Tang, William W.; Battistone, Ben; Bauer, Kaylyn M.; Weis, Allison M.; Barba, Cindy; Fadlullah, Muhammad Zaki Hidayatullah; O'Connell, Ryan M.The rising incidence of advanced-stage colorectal cancer (CRC) and poor survival outcomes necessitate new and effective therapies. Immune checkpoint inhibitors (ICIs), specifically anti-PD-1 therapy, show promise, yet clinical determinants of a positive response are suboptimal. Here, we identify microRNA-155 (miR-155) as necessary for CD8+ T cell-infiltrated tumors through an unbiased in vivo CRISPR-Cas9 screen identifying functional tumor antigen-specific CD8+ T cell-expressed microRNAs. T cell miR-155 is required for anti-PD-1 responses and for a vital intratumor CD8+ T cell differentiation cascade by repressing Ship-1, inhibiting Tcf-1 and stemness, and subsequently enhancing Cxcr6 expression, anti-tumor immunity, and effector functions. Based on an underlying miR-155-dependent CD8+ T cell transcriptional profile, we identify a gene signature that predicts ICI responses across 12 diverse cancers. Together, our findings support a model whereby miR155 serves as a central regulator of CD8+ T cell-dependent cancer immunity and ICI responses that may be leveraged for future therapeutics.