WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Design, Synthesis, and Biological Evaluation of Novel Water-Soluble Quinoline-Based Conjugates with Antioxidant, Antimicrobial, and DNA-Binding Activities(Society of Chemists and Technologists Madeconia, 2025) Gumus, Aysegul; Okumus, Veysi; Emrullahoglu, Mustafa; Gumus, SelcukConsidering the extremely valuable biological and pharmaceutical properties of quinolines, novel water-soluble quinoline-based conjugates were designed and synthesized. In vitro antioxidant activities, such as free radical scavenging, metal chelating, and reducing-power activities, of the newly synthesized compounds (WQ-1, WQ-2, WQ-3, WQ-4, and WQ-5) were determined. Although the highest scavenging activity (41.21 +/- 1.18%) and chelating activity (23.53 +/- 0.97%) at a concentration of 500.0 mu g/ml were observed in WQ-4, it was determined that WQ-5 had the highest reducing-power ability (0.417 +/- 0.0116). The synthesized compounds were also tested for their antimicrobial activities against two Grampositive and two Gram-negative bacteria, and it was determined that only WQ-3 showed low activity against Enterococcus hirae and Staphylococcus aureus. DNA-binding activities of the compounds were also studied using calf thymus DNA (CT-DNA). Additionally, the three-dimensional geometries and some electronic properties of the synthesized compounds were investigated with the density functional theory approach at B3LYP/6-31++G(d,p) level of theory.Article Seismic Risk Prioritization of Stone Masonry Building Stock in Urla Peninsula Based on Rapid Assessment Techniques(Turkish Chamber of Civil Engineers, 2026) Karavin, Y.S.; Akdag, N.; Demir, U.This study aims to investigate seismic risk of stone masonry buildings in the Urla Peninsula, a region of historical and architectural significance within İzmir, Türkiye. A total of 100 stone masonry buildings were surveyed and documented with a focus on their architectural characteristics, including construction techniques, material types, structural configurations, and age. Data on the properties of all surveyed buildings are provided in an open-access database. Based on the survey, multiple rapid seismic performance assessment methods were applied to evaluate the vulnerability of these structures. These included: i) FEMA P-154 Rapid Visual Screening, ii) Provisions for the Seismic Risk Evaluation of Existing Buildings under Urban Renewal Law (RBTE-2019), iii) Seismic Vulnerability Index for Vernacular Architecture (SVIVA), and iv) the Masonry Quality Index (MQI). The comparative use of different methods is intended to investigate the relative influence of parameters shaping the seismic performance of the masonry building stock rather than to align their scores. The outcomes of this research are expected to contribute to the current risk mitigation efforts for stone masonry buildings in İzmir, thereby supporting regional seismic resilience planning. © 2026, Turkish Chamber of Civil Engineers. All rights reserved.Article Dissecting the Metabolic Landscape of Breast Cancer Subtypes via Elastic Net Modeling and Examining Its Immune Correlates(Walter de Gruyter GmbH, 2026) Kus, M.E.; Ekiz, H.A.Objectives: Breast cancer is a heterogeneous disease, and the estrogen receptor (ER) status is a key factor in disease classification and treatment planning. While metabolomic profiling has revealed subtype-specific differences, cross-study comparisons have been limited, posing challenges for data extrapolation. This study aims to investigate metabolites that differentiate ER-positive and ER-negative tumors via integrative analyses of multi-omics data. Methods: We jointly analyzed two untargeted metabolomics datasets via elastic net modeling using consistent analysis pipelines tuned for low sample sizes, namely multiple bootstrapping and stability selection. Significant metabolite predictors from two studies were cross-examined to reveal distinctions and commonalities. We also performed differential gene expression analysis using RNA sequencing data from matching samples to link metabolic patterns with transcriptomic signatures and intratumoral immune cell signatures. Results: This study identified unique metabolite signatures in distinct datasets and a limited overlap of discriminating metabolites that can be broadly generalizable for subtyping. Nevertheless, several glycolysis and fatty acid metabolism intermediates exhibited variation depending on the tumor ER status. Consistently, genes related to fatty acid metabolism and glycolysis were enriched in ER-positive and ER-negative tumors respectively. Furthermore, we used multiple immune cell deconvolution algorithms to correlate various immune cell types with the metabolite levels within the tumor microenvironment. Conclusions: Together, these findings highlight the metabolic and immunological diversity of breast cancer and establish a reproducible machine-learning framework for integrating multi-omics data to interrogate tumor complexity. © 2025 the author(s), published by De Gruyter, Berlin/Boston.Article N-Formylation of Amines Over a Protonic Zeolite Socony Mobil (H-Zsm-5) and Ion-Exchanged Zeolite: Catalytic Performance and Reusability(Sciendo, 2025) Mekkas, Nadia; Azizi, Soulef; Yilmaz, Selahattin; Benbouzid, Mohammed; Dizoglu, Gunsev; Taib, Hana; Gherraf, NoureddineAn efficient and sustainable method was developed for the N-formylation of primary and secondary amines using formic acid in dichloromethane at room temperature over zeolite H-ZSM-5 and ion-exchanged forms (Zn-ZSM-5, Cu-ZSM-5, Ag-ZSM-5, and Cd-ZSM-5). The catalysts were characterised by X-ray diffraction (XRD), scanning electron microscopy (SEM), Brunauer-Emmett-Teller (BET) surface area, ammonia temperature-programmed desorption (NH3-TPD), and inductively coupled plasma-optical emission spectrometry (ICP-OES) analyses, revealing a regular hexagonal plate-like morphology and high surface area. H-ZSM-5 exhibited the largest surface area (248.2 m2/g) and total acidity (0.109 mmol NH3/g), while ion exchange slightly modified these properties. The catalytic system achieved excellent yields (up to 99 %) for various amines, demonstrating high efficiency and reusability. This study highlights the potential of zeolite-based catalysts as effective, recyclable materials for N-formylation processes.Article Determining Area Affected by Corona in Lung Computed Tomography Images by Three-Phase Level Set and Shearlet Transform(Wolters Kluwer Medknow Publications, 2025) Aghazadeh, Nasser; Noras, Parisa; Moghaddasighamchi, SevdaBackground:The COVID-19 pandemic has created a critical global situation, causing widespread challenges and numerous fatalities due to severe respiratory complications. Since lung involvement is a key factor in COVID-19 diagnosis and treatment, accurate identification of infected regions in lung images is essential.Methods:We propose a multiphase segmentation method based on the level set framework to determine lunginvolved areas. The shearlet transform, a high-precision directional multiresolution transform, is employed to guide the gradient flow in the level set formulation. Additionally, the phase stretch transform (PST) is applied to enhance the contrast between infected and healthy regions, improving convergence speed during segmentation.Results:The proposed algorithm was tested on 500 lung images. The method accurately identified infected areas, enabling precise calculation of the percentage of lung involvement. The use of the shearlet transform also allowed clear delineation of ground-glass opacity boundaries.Conclusion:The proposed multiphase level set method, enhanced with shearlet and phase stretch transforms, effectively segments COVID-19-infected lung regions. This approach improves segmentation accuracy and computational efficiency, offering a reliable tool for quantitative lung involvement assessment.Editorial A Thin Film Micro-Extraction Based Salivary Metabolomics and Chemometric Strategy for Rapid Lung Cancer Diagnosis(Galenos Publ House, 2025) Pelit, Levent; Basbinar, Yasemin; Goksel, Ozlem; Goksel, Tuncay; Erbas, İlknur; Pelit, Fusun; Ozdemir, DurmusINTRODUCTION: Lung cancer (LC) remains one of the leading causes of cancer-related mortality worldwide, largely due to the lack of reliable biomarkers for early detection.1 Despite advances in di-agnostic imaging and targeted therapies, the five-year survival rate remains low because most cases are diagnosed at advanced stages. Consequently, the development of sensitive, non-invasive, and cost-effective diagnostic approaches is a major clinical priority. Metabolomics, the comprehensive profiling of small-molecule metabolites, has emerged as a powerful tool for uncovering cancer-associated metabolic alterations, providing insights into tumor biology and facilitating the discovery of novel biomarkers for accurate diagnosis and disease monitoring. Among biological matrices, saliva is a promising diagnostic biofluid because it can be collected non-invasively, is simple to obtain, and reflects systemic and local metabolic changes. Recent studies have demonstrated its potential for detecting various cancers, including lung cancer, highlighting its value for biomarker-based early di-agnosis.2,3 In this study, a novel thin-film microextraction (TFME) technique integrated with liquid chromatography-tandem mass spectrometry (LC-MS/MS) is introduced for the rapid, selective, and reproducible extraction of salivary metabolites. The developed TFME approach offers high throughput, reduced solvent consumption, and enhanced analytical performance, enabling the identification and quantification of key metabolic biomarkers associated with lung cancer. The objective of this workflow is to advance saliva-based metabolomics toward clinical translation, offering a promising avenue for the early and non-invasive diagnosis of lung cancer. MATERIAL AND METHODS: Synthesis of SiO2 Nanoparticles and TFME blade Preparation: SiO2 nanoparticles were synthesized using the Stöber method, followed by post-coating with tetraethyl orthosilicate, centrifugation, wash-ing with ethanol, and drying. The nanoparticles were incorporated into a polyacrylonitrile (PAN) matrix and coated onto steel TFME blades via a controlled dip-coating process to ensure uniform film thick-ness. Participants and Sample Collection: Saliva samples were collected from 40 histopathologically con-firmed lung cancer patients and 38 healthy volunteers following an overnight fast and an oral rinse. Ethical approval and informed consent were obtained (Ege University Ethics Committee, protocol: 15-11.1/46). Saliva samples were centrifuged, diluted (1:2), and stored at -80 °C until analysis. TFME Sampling and Analysis: A 96-well plate system equipped with PAN/SiO2-coated TFME blades was used for metabolite extraction (Figure 1). Blades were immersed in diluted saliva samples and rotated at 850 rpm for 150 minutes to allow analyte adsorption, followed by desorption of analytes in 0.1% formic acid for 30 minutes. Desorbed solutions were spiked with 0.5 µg/mL ornidazole as an internal standard prior to LC-MS/MS analysis. RESULTS: The TFME method was optimized to detect 18 metabolites in pre-treatment saliva samples from lung cancer patients. Chromatographic evaluation demonstrated that the Inertsil 100 column, employing isocratic elution with ornidazole as the internal standard, provided optimal separation effi-ciency and reproducibility. Extraction parameters, including desorption solution type and pH, were optimized; desorption solution type 2 at pH 8-9 yielding the highest metabolite recovery. Analytical validation indicated robust linearity (R2: 0.9841-0.9975), sensitivity (limit of detection: 0.014-0.97 μg/mL; limit of quantification: 0.046-3.20 μg/mL), precision (%relative standard deviation <20%), and accuracy (85-125% for most metabolites). Pathway analysis revealed significant alterations in the me-tabolism of phenylalanine, purine, tyrosine, histidine, and methionine. The Heatmap visualization showed increased levels of proline, hypoxanthine, phenylalanine, and tyrosine in lung cancer pa-tients. receiver operating characteristic curve analysis highlighted these metabolites as potential bi-omarkers, with proline exhibiting the highest diagnostic performance [area under the curve (AUC): 0.946], followed by hypoxanthine (AUC: 0.933) and phenylalanine (AUC: 0.905) CONCLUSION: The findings of this study demonstrate that the TFME approach is a reliable and effi-cient platform for metabolomic profiling in lung cancer. Using pre-treatment saliva samples, the method achieved a sensitivity exceeding 90% for detecting newly diagnosed histopathologically con-firmed patients. Among the metabolites analyzed, proline, hypoxanthine, and phenylalanine showed strong diagnostic potential, consistent with the pathway analyses implicating purine and phenylala-nine metabolism. These results underscore the potential of salivary metabolomics as a non-invasive screening alternative in the absence of validated early lung cancer biomarkers. Additionally, TFME’s high-throughput capacity, cost-effectiveness, and environmental sustainability support its feasibility for routine clinical application.Article Soylulaştırmanın Kırsal Boyutu: Turizm, Tarım ve Sanayi(Kare Publ, 2025) Buldan, Ece; Akış, TonguçKırsal soylulaştırma, arazi özelleştirmesi ve yerinden edilme ile karakterize edilen bir süreç olup, 1990'larda devlet güdümlü mü- dahalelerin sisteme daha fazla entegre edilmesiyle yoğunlaştı. Soy- lulaştırma tarihsel referanslarını kaybederek, genelleşmiş bir olgu olarak kent merkezlerinin ötesindeki kırsal alanları da etkilemek - tedir. Bu özel gelişme, kentsel ve kırsal temeller üzerine yoğunla- şan çalışmalar üzerinden ele alınmaktadır. Günümüz söyleminde kırsal alanlar, sanayi kenti ve doğal kırsal ortamlar arasında birer hibritleşme alanı olarak tasvir edilmekte, bu alanların tüketimi, sermaye akışının etkilerini dışlamakta ve giderek daha fazla din - lenme ve turizm üzerinden şekillenmektedir. Küresel Güney ül - kelerindeki çalışmalar incelendiğinde, sanayileşme fonksiyonu da turizm ve ikincil konut sürecinin yanı sıra kırsal soylulaştırmaya katkı sağlamaktadır. Bu süreçler, hizmet ve üretim sektörlerinde ağırlıklı olarak ortaya çıkmakta, kentsel ve kırsal alanlar arasın - daki ayrımı bulanıklaştırarak araştırma ve kavramsallaştırmada zorluklar sunmaktadır. Bu boşluğu ele alarak, bu çalışma, güncel mekânsal sorunlar üzerinden kentsel-kırsal durumun bulanıklığını teorik bir katkı dahilinde bağlamsallaştırmayı amaçlamaktadır. Tu- rizm, sanayi ve tarımdaki dönüşüm süreçlerini inceleyerek, kırsal alan üretimine dair gelişmiş ve gelişmekte olan bağlamlarda tar- tışmalar sunmayı hedeflemektedir. Literatür taraması ve önemli örnekler üzerinde nitel araştırma yöntemleri kullanılarak, bu çalış- ma yeni demografik veriler aracılığıyla kentsel ve kırsal çalışmalar çerçevesinde kırsal soylulaştırmayı inceleyerek, bunun etkilerine ve uygulamalarına dair içgörüler sunacaktır. Buna uygun olarak, kırsal alana giren yeni sermaye akışının etkileri de araştırılacaktır.Article Citation - WoS: 1Citation - Scopus: 1Two Key Substitutions in the Chromophore Environment of mKate2 Produce an Enhanced FusionRed-Like Red Fluorescent Protein(Russian Federation Agency Science & innovation, 2025) Ruchkin, D. A.; Gavrikov, A. S.; Kolesov, D., V; Gorokhovatsky, A. Yu.; Chepurnykh, T., V; Mishin, A. S.; Bogdanov, A. M.Red fluorescent proteins (RFPs) are often probes of choice for living tissue microscopy and whole-body imaging. When choosing a specific RFP variant, the priority may be given to the fluorescence brightness, maturation rate, monomericity, excitation/emission wavelengths, and low toxicity, which are rarely combined in an optimal way in a single protein. If additional requirements such as prolonged fluorescence lifetime and/or blinking ability are applied, the available repertoire of probes could dramatically narrow. Since the entire diversity of conventional single-component RFPs belongs to just a few phylogenetic lines (DsRed-, eqFP578-and eqFP611-derived being the major ones), it is not unexpected that their advantageous properties are split between close homologs. In such cases, a systematic mutagenetic analysis focusing on variant-specific amino acid residues can shed light on the origins of the distinctness between related RFPs and may aid in consolidating their strengths in new RFP variants. For instance, the protein FusionRed, despite being efficient in fluorescence labeling thanks to its good monomericity and low cytotoxicity, has undergone considerable loss in fluorescence brightness/lifetime compared to the parental mKate2. In this contribution, we describe a fast-maturing monomeric RFP designed semi-rationally based on the mKate2 and FusionRed templates that outperforms both its parents in terms of molecular brightness, has extended fluorescence lifetime, and displays a spontaneous blinking pattern that is promising for nanoscopy use.Article Proposal of Conservation-Based Planning Approach for Agricultural Areas Designated as Special Project Area (OPA) in Turkey; Example of Mugla Plain(Kare Publ, 2018) Yorur, Neriman; İnceköse, Ülkü; Cirak, Aysegul Altinors; Aydin, Burcu Silaydin; Incekose, Ulku; Nemutlu, Fusun Erduran; Aydin, Gonul; Yorulmaz, AlperAgricultural areas are natural areas that must be protected and maintained in order to provide food, which is the most basic necessity of man. It is observed that agricultural areas are being removed from the industrialization and urbanization processes that are developed within the framework of industrial development oriented economic development policies that started with the Industrial Revolution and then spread to global scale. Especially agricultural areas in the urban fringes are threatened to be used for non-agricultural purposes due to the demand for spatial growth and are opposed to the pressure of settlement. One of the agricultural areas under threat is the Mugla Plain. It is important to protect the Mugla Plain, which is an absolute agricultural land and at the same time constitute part of the natural and cultural landscape of the city, and to sustain the agricultural activities. Mugla Plain is designated as Special Project and Planning Area (OPA) in 1/25.000 Scale Master Plan; it was aimed to develop a project to preserve the original quality of the agricultural character of Plain in this frame. In this article, analyzes and proposals made within the scope of the idea project prepared for the section of Mugla Plain defined as "Special Project and Planning Area" are presented. In the proposals, it was aimed to protect the agricultural quality of the plains and to prevent the spread of the settlement by integrating the plain with the urban residents. Towards achieving this goal, it has been adopted to develop approaches dealt with under the heading of "urban agriculture". Strategies developed in this context include recommendations on the protection and use of agricultural land; Establishment of agricultural development cooperative of Mugla Plain agricultural operators association; reduction of urbanization impact, and integrating the city with the natural landscape of the area.Article Decision-Support Approaches for Sustainable Water Resource Management in Northwest Algeria(Polish Society of Ecological Engineering – PTIE, 2025) Meskine, Ahmed; Cherif, El Amine; Zerouali, Bilel; Ouadja, Abid; Santos, Celso Augusto Guimaraes; Bailek, Nadjem; Baba, AlperThis study investigates water resource management in the Wilaya of Mostaganem, northwest Algeria, using the water evaluation and planning (WEAP) decision support tool in combination with the analytic hierarchy process (AHP). As water scarcity becomes increasingly critical due to population growth, agricultural demands, and climate variability, effective management strategies are essential. This research employs WEAP to simulate various water demand and supply scenarios, assessing the impacts of irrigation efficiency, industrial development, and climate conditions on water availability. Under the ASI scenario, unsatisfied water demand may reach 4.3 hm3 per year by 2027. However, improving irrigation efficiency could reduce this by up to 50% compared to the reference scenario. Seasonal variations reveal deficits reaching 3.2 hm3 per month during the summer months of July through October. Additionally, the study highlights that a significant increase in water demand, exceeding 80 hm3 by 2060, can be mitigated through improved water supply initiatives, such as constructing new dams. The integration of AHP enables the prioritization of management strategies based on stakeholder preferences, demonstrating that adapting to climate change can stabilize demand below 50 million cubic meters. This integrated approach provides valuable insights for policymakers and stakeholders in developing sustainable water resource strategies that address the challenges faced by the Mostaganem region.