TR Dizin İndeksli Yayınlar / TR Dizin Indexed Publications Collection
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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.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 Experimental Study of Evolution of Breach Resulting From Piping at Upper Part of Earth-Fill Dam(Turkish Chamber Civil Engineers, 2025) Guney, Mehmet Sukru; Tayfur, Gokmen; Bor, Asli; Okan, Merve; Dumlu, Emre; Aklık, PelinPiping and overtopping are the most important causes of earth-fill dam failure. Such dams may erode under seepage, causing a reduction in the structural strength. The aim of this study was to investigate the temporal evolution of the breach and flow rate from the breach resulting from the piping in earth-fill dams. The experiments were carried out at Hydraulics Laboratory of Civil Engineering Department of İzmir University of Economics. The dam was constructed by using a mixture consisting of 85 % sand and 15 % fine (low plasticity clay). In the first scenario a circular tunnel with a diameter of 2 cm was created along the centreline at 6 cm below the dam crest whereas in the second one it was located at the upper edge. Six cameras at different locations recorded the evolution of the progress of the breach formation. The pump flow rate was measured by magnetic flow meter, and the continuity equation was used to calculate the flow rate values from the breach. The time-varied values of the total breach areas were determined using the Gauss Area formula. The image processing method was also applied in the determination of the breach areas. The time-dependent changes of water depth in the channel were also recorded. The obtained experimental findings are presented and commented, together with the universal dimensionless curves. The failure of the dams occurred mainly because of the head cut erosion developed from downstream to upstream. When breaching started, the orifice flow was converted to open channel flow where breach bottom behaved like a broad crested weir. In the second scenario, the rigid lateral side considerably influenced the flow rate and the development of the breach. The peak flow rate corresponding to the first scenario was found approximately 2.3 times greater than that of the second one. The maximum values of all the breach parameters were reached earlier in the case of the seepage along the centerline. The ratios between the values corresponding to the first and the second scenarios were found as 3.25 and 1.75 for maximum breach areas at downstream and at upstream sides, respectively. These ratios were 2.44 and 1.37 for the average breach widths at downstream and upstream sides, respectively. A very good agreement was found between the area values obtained from Gauss area method and image processing technique, in both scenarios. This fact demonstrated that either of these two approaches can be used to determine the time-dependent breach areas. These experimental findings provide the opportunities for the calibration and validation of the numerical models used in the relevant numerical investigations. This study also offers guidance for the strategies concerning emergency action plans related to the failure of homogeneous earth-fill dams when the piping starts at upper part of the homogeneous earth-fill dams.Article Gypsophila Eriocalyx Roots Inhibit Proliferation, Migration, and Tgf-Β Signaling in Melanoma Cells(Walter de Gruyter GmbH, 2025) Azbazdar, Yagmur; Ozhan, Gunes; Helvacioglu, SelinObjectives: Melanoma is a highly malignant and serious form of skin cancer. In addition to the standard treatments, complementary approaches, including phytotherapy, are also used to alleviate symptoms and improve patient well- being. This study aims to investigate the anticancer effects of Gypsophila eriocalyx (GE), an endemic species from Türkiye, on melanoma cells. We set out to determine the efficacy of GE in inhibiting melanoma cell proliferation, migration, and growth, and to explore its underlying mechanisms. Methods: We examined the impact of GE on the prolifera- tion of two melanoma cell lines, Malme-3M and SK-MEL-28, and assessed its developmental toxicity in zebrafish em- bryos. Next, we evaluated GE’s influence on colony forma- tion and wound healing in melanoma cells, as well as its ability to induce apoptosis and affect the TGF-β/Smad signaling pathway, by measuring pathway reporter activity and target gene expression. Results: GE inhibited cell proliferation in melanoma cell lines at concentrations 104 to 488 times lower than those required for normal non-malignant L929 fibroblast cells. In zebrafish embryos, GE demonstrated developmental toxicity only at concentrations above 50 μg/mL. GE treatment significantly impaired the colony formation and wound healing abilities of melanoma cells, indicating reduced pro- liferation and migration. Moreover, GE induced apoptosis in melanoma cells and inhibited the TGF-β/Smad signaling pathway, as evidenced by decreased pathway reporter activity and target gene expression. Conclusions: This study highlights the potential of GE as a novel therapeutic agent in melanoma treatment by demon- strating its ability to inhibit tumor growth and progressionArticle Housing Instability and Roma Children's Educational Engagement: Perspectives From Teachers and Volunteers(Istanbul Univ, Fac Letters, dept Sociology, 2024) Uştuk, OzanInequalities experienced by the Roma remain a complex challenge, particularly in education. Despite various initiatives, their impact on the Roma communities’ daily lives has been limited. This article is based on applied research aimed at reducing early school-leaving rates among Roma children in Türkiye. The study highlights that the high rates of early school leaving cannot be fully understood without considering the profound impact of housing instability on their educational experiences. By exploring the intersection of educational challenges and housing insecurity through the perspectives of elementary school teachers, preschool teachers, and volunteering university students engaged with a Roma community, the findings reveal that the constant threat of displacement and inadequate living conditions severely disrupt educational engagement, undermining the stability necessary for academic success. However, these perspectives also expose critical gaps in understanding, particularly among educators who often overlook the significance of housing insecurity in shaping educational outcomes. By situating these challenges within the broader context of systemic housing issues, this research underscores the need for comprehensive, community-based interventions that address the root causes of educational inequities among Roma students. The study advocates for a holistic approach to educational equity—one that addresses both the material and psychological dimensions of housing insecurity, thereby creating pathways for genuine social mobility and inclusion for Roma children.Article Citation - WoS: 1Citation - Scopus: 1Investigation of Flow and Heat Transfer Performance of Gyroid Structure as Porous Media(Turkish Soc Thermal Sciences Technology, 2024) Genc, Alper Mete; Karadeniz, Ziya HaktanThere are active and passive methods used to improve heat transfer. One of the passive methods is utilising porous media with high heat transfer surface area. Porous media are divided into two groups: regular and irregular structures. One of the regular structures is triply periodic minimal surfaces (TPMS), which have been studied quite frequently recently. In this study, heat transfer and flow analysis of a Gyroid geometry, one of the most used TPMS in the literature, is investigated numerically considering the conjugate heat transfer conditions. A single porosity is considered (epsilon = 0.6), and aluminium, ceramic and PLA are selected for the heat exchanger material to examine the temperature change in the heat exchanger. To understand the different flow characteristics, Reynolds numbers are assumed to be 19.12, 95.61 and 172.09. The fluid inlet temperature is assumed to be constant at 298.15 K, and the initial temperature of the heat exchanger is assumed to be constant at 278.15 K to be consistent with the regenerative heat recovery temperature difference in ventilation standards. Nusselt numbers under different operating conditions are compared, and it is the ceramic material with low thermal diffusivity is at the highest level despite its low thermal conductivity. At the highest Reynolds number, it provided approximately 6% better heat transfer than the aluminium heat exchanger.Article Citation - WoS: 10Effects of Seismic Activity on Groundwater Level and Geothermal Systems in İzmir, Western Anatolia, Turkey: the Case Study From October 30, 2020 Samos Earthquake(Tubitak Scientific & Technological Research Council Turkey, 2021) Uzelli, Taygun; Bilgic, Esra; Ozturk, Bahadir; Baba, Alper; Sozbilir, Hasan; Tatar, OrhanThe October 30, 2020 Samos earthquake (Mw 6.6) affected the Aegean Sea and environs, caused destruction and loss of life in the city of & Idot;zmir located 70 km away from the earthquake epicenter. Before this earthquake, water resources were monitored in the areas of Bayrakl & imath;, G & uuml;lbah sigma e, and Seferihisar. For this purpose, 10 groundwater monitoring wells were drilled in the Bayrakl & imath; area, where groundwater level, temperature, and electrical conductivity changes were monitored at 1-h intervals in 5 wells. Besides physical parameters such as groundwater levels, temperatures and electrical conductivities, hydrogeochemical cations, and anions measured in the study area. Change in the groundwater levels was observed before, during, and after the Samos earthquake. A trend of rising groundwater level was observed two days before the mainshock, to a height of 10 cm, and the level was maintained till the end of the earthquake. The water levels returned to its original height after about 7 to 10 days of the earthquake. Moreover, electrical conductivity (EC) values were changed because of the interaction with the surrounding rocks and well walls, mixing with different waters during the earthquake shaking. The essential anomalies were observed in the geothermal fields of G & uuml;lbah sigma e and Seferihisar. Due to this earthquake, new geothermal springs emerged along the NE-SW trending G & uuml;lbah sigma e and Tuzla faults, located about 50 to 20 km from the Samos earthquake epicenter, respectively. The new geothermal waters are in Na-Cl composition and similar to other geothermal springs in the region. While the recorded water temperatures in the new geothermal springs vary from 40 to 45 degrees C in Seferihisar, it was measured between 35 and 40 degrees C in G & uuml;lbah sigma e. Due to these anomalies, it is found essential to monitor the effect of the earthquake on the physical and chemical characteristics of the groundwater and its usefulness in earthquake predictions.Article Ai-Assisted Survival Prediction in Colorectal Cancer: a Clinical Decision Support Tool(Dokuz Eylul Univ inst Health Sciences, 2024) Misirlioglu, Huseyin Koray; Leblebici, Asim; Calibasi-Kocal, Gizem; Ellidokuz, Hulya; Basbinar, YaseminPurpose: This study was planned to determine the problems and affecting factors that children encounter Purpose: Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. Accurate survival prediction is crucial for advanced-stage patients to optimize treatment strategies and improve clinical outcomes. This study aimed to develop an artificial intelligence-assisted clinical decision support system (CDSS) for survival prediction in CRC patients using clinical and genomic data from the Cancer Genome Atlas Colon Adenocarcinoma Collection (TCGA-COAD) dataset. Methods: Machine learning algorithms, including C4.5 Decision Tree, Support Vector Machines (SVM), Random Forest, and Naive Bayes, were employed to create survival prediction models. Clinical parameters and genomic data from key pathways, such as glycolysis/gluconeogenesis and mTORC1, were integrated into the models. The models were evaluated based on accuracy and performance. Results: The Random Forest algorithm achieved the highest accuracy (82.3%) when only clinical parameters were used. When clinical data were combined with gene expression data, the model's accuracy increased further. The resulting models were incorporated into a user-friendly web interface, SurvCOCA, for clinical use. Conclusions: This study demonstrates the potential of AI-based tools to improve prognosis predictions in CRC patients. Further research is needed, with larger datasets and additional machine learning algorithms, to enhance clinical decision-making and optimize treatment strategies.Article Citation - Scopus: 1Anomalous Crustal Structure Beneath the Örenli-Eğiller Depression Zone, Inferred From Magnetotelluric Studies, Western Anatolia, Türkiye(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2024) Chandrasekharam, Dornadula; Raju, K.; Subba Rao, P.B.V.; Baba, AlperIn Türkiye, the prevalence of high radiogenic granites makes them ideal locations for initiating enhanced geothermal system (EGS) projects. One such occurrence of these granites is observed in the Kozak area of the Bergama region. To assess the energy potential of this site, a magnetotelluric (MT) survey was conducted, focusing on determining the depth distribution of the intrusive granite. The survey employed dimensionality analysis, utilizing Bahr skew and phase tensor analyses that denote a 2D subsurface nature up to 100 s and beyond that a 3D nature. In the present study, we interpreted MT data up to 100 s. The data collected, including rotated impedance tensors and tippers, were inverted using a nonlinear conjugate gradient algorithm integrated into the MT interpretation software of the WinG Link 2D inversion data modeling package. Multiple homogeneous half-space initial models were tested during the 2D inversion process. The findings indicate the existence of a midcrustal conductor associated with graphites and iron sulfides in the source region. This conductivity may be attributed to processes such as exsolution of metamorphic fluids, influx of mantle sources, or the entry of magmatic fluids through transcrustal fault zones. The findings indicate that the intrusive granite was emplaced along a NE–SW major fault, penetrating shallow crustal levels. The depth of this granite intrusion is determined to be 15 km, covering an outcrop area of 60 km². This detailed geological information allows a comprehensive assessment of the power-generating capacity of the intrusive granite. The results of this investigation contribute valuable insights for the development and optimization of Enhanced Geothermal System (EGS) projects in the region. © 2024, TUBITAK. All rights reserved.