PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 7Citation - Scopus: 9A Holistic Overview of the Applications of Grace-Observed Terrestrial Water Storage in Hydrology and Climate Science(Springer, 2025) Khorrami, Behnam; Gunduz, OrhanTerrestrial 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.Article Vision Transformers-Based Deep Feature Generation Framework for Hydatid Cyst Classification in Computed Tomography Images(Springer, 2025) Sagik, Metin; Gumus, AbdurrahmanHydatid 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.Editorial Editorial: Advancing Biotechnology in Turkiye: a Dedication To All Women(Springer, 2025) Cadirci, Bilge Hilal; Buyukkileci, Ali Oguz; Binay, BarisArticle Citation - WoS: 1Citation - Scopus: 1Studies on the Probiotic, Adhesion, and Induction Properties of Artisanal Lactic Acid Bacteria: To Customize a Gastrointestinal Niche To Trigger Anti-Obesity Functions(Springer, 2024) Kamber, A.; Albayrak, C. Bulut; Harsa, H. S.The primary goals of this work are to explore the potential of probiotic lactic acid bacteria's (LAB) mucin/mucus layer thickening properties and to identify anti-obesity candidate strains that improve appropriate habitat for use with the Akkermansia group population in the future. The HT-29 cell binding, antimicrobial properties, adhesion to the mucin/mucus layer, growth in the presence of mucin, stability during in vitro gastrointestinal (GI) conditions, biofilm formation, and mucin/mucus thickness increment abilities were all assessed for artisanal LAB strains. Sixteen LAB strains out of 40 were chosen for further analysis based on their ability to withstand GI conditions. Thirteen strains remained viable in simulated intestinal fluid, while most showed high viability in gastric juice simulation. Furthermore, 35.9-65.4% of those 16 bacteria adhered to the mucin layer. Besides, different lactate levels were produced, and Streptococcus thermophilus UIN9 exhibited the highest biofilm development. In the HT-29 cell culture, the highest mucin levels were 333.87 mu g/mL with O. AK8 at 50 mM lactate, 313.38 mu g/mL with Lactobacillus acidophilus NRRL-B 1910 with initial mucin, and 311.41 mu g/mL with Lacticaseibacillus casei NRRL-B 441 with initial mucin and 50 mM lactate. Nine LAB strains have been proposed as anti-obesity candidates, with olive isolates of Lactiplantibacillus plantarum being particularly important due to their ability to avoid mucin sugar consumption. Probiotic LAB's attachment to the colonic mucosa and its ability to stimulate HT-29 cells to secrete mucus are critical mechanisms that may support the development of Akkermansia.Article Citation - WoS: 1Citation - Scopus: 2<i>tubg1</I> Somatic Mutants Show Tubulinopathy-Associated Neurodevelopmental Phenotypes in a Zebrafish Model(Springer, 2024) Cark, Ozge; Katkat, Esra; Aydogdu, Ipek; Iscan, Evin; Oktay, Yavuz; Ozhan, GunesDevelopment of the multilayered cerebral cortex relies on precise orchestration of neurogenesis, neuronal migration, and differentiation, processes tightly regulated by microtubule dynamics. Mutations in tubulin superfamily genes have been associated with tubulinopathies, encompassing a spectrum of cortical malformations including microcephaly and lissencephaly. Here, we focus on gamma-tubulin, a pivotal regulator of microtubule nucleation encoded by TUBG1. We investigate its role in brain development using a zebrafish model with somatic tubg1 mutation, recapitulating features of TUBG1-associated tubulinopathies in patients and mouse disease models. We demonstrate that gamma-tubulin deficiency disrupts neurogenesis and brain development, mirroring microcephaly phenotypes. Furthermore, we uncover a novel potential regulatory link between gamma-tubulin and canonical Wnt/beta-catenin signaling, with gamma-tubulin deficiency impairing Wnt activity. Our findings provide insights into the pathogenesis of cortical defects and suggest that gamma-tubulin could be a potential target for further research in neurodevelopmental disorders, although challenges such as mode of action, specificity, and potential side effects must be addressed.Article Citation - WoS: 4Citation - Scopus: 4Estimation of Heat Production Rate Using Thermal Data During Exercise in Indoor Environments: a Study of Heat Storage Rate in Male Athletes(Springer, 2024) Balci, Gorkem Aybars; Avci, Ali Berkay; Colakoglu, Muzaffer; Basaran, Tahsin; Balcı, Görkem Aybars; Avcı, Ali Berkay; Çolakoğlu, Muzaffer; Başaran, TahsinThe increasing preference for indoor exercise spaces highlights the relationship between indoor thermal environments and physiological responses, particularly concerning thermal comfort during physical activity. Determining the metabolic heat production rate during exercise is essential for optimizing the thermal comfort, well-being, and performance of individuals engaged in physical activities. This value can be determined during the activity using several methods, including direct calorimetry measurement, indirect calorimetry that uses analysis of respiratory gases, or approximations using collected data such as speed, body mass, and heart rate. The study aimed to calculate the metabolic heat production rate by infrared thermal evaluation (ITE) based on the body's thermal balance approach and compare it with the values determined by indirect calorimetry (IC). Fourteen participants volunteered for the study, using a cycling ergometer in a controlled climatic chamber. After the familiarization sessions, maximal O-2 intake levels (VO2max) were determined through maximal graded exercise tests. Subsequently, constant work rate exercise tests were performed at 60% of VO2max for 20 min. The metabolic heat production rates were calculated by IC and ITE for each athlete individually. Respiratory gases were used to determine IC, while body skin and core temperatures, along with physical environmental data, were applied to calculate ITE using the human body thermal balance approximation of ASHRAE. According to the results, heat storage rates were misleading among the body's heat transfer modes, particularly during the first 8 min of the exercise. ITE showed a moderate level of correlation with IC (r: 0.03-0.86) with a higher level of dispersion relative to the mean (CV%: 12-84%). Therefore, a new equation (ITEnew) for the heat storage rates was proposed using the experimental data from this study. The results showed that ITEnew provided more precise estimations for the entire exercise period (p > 0.05). Correlations between ITEnew and IC values were consistently strong throughout the exercise period (r: 0.62-0.85). It can be suggested that ITEnew values can predict IC during the constant work rate steady-state exercise.Article Citation - WoS: 9Citation - Scopus: 11Experimental Investigation of Spray Characteristics of Ethyl Esters in a Constant Volume Chamber(Springer, 2024) Ulu, A.; Yildiz, G.; Özkol, Ü.; Rodriguez, A.D.Abstract: Biodiesels are mainly produced via the utilization of methanol in transesterification, which is the widespread biodiesel production process. The majority of this methanol is currently obtained from fossil resources, i.e. coal and natural gas. However, in contrast with methanol, biomass-based ethanol can also be used to produce biodiesels; this could allow the production line to become fully renewable. This study aimed to investigate the spray characteristics of various ethyl ester type biodiesels derived from sunflower and corn oils in comparison to methyl esters based on the same feedstocks and reference petroleum-based diesel. Spray penetration length (SPL) and spray cone angle (SCA) were experimentally evaluated in a constant volume chamber allowing optical access, under chamber pressures of 0, 5, 10 and 15 bar and injection pressures of 600 and 800 bar. Sauter mean diameter (SMD) values were estimated by using an analytical correlation. Consequently, ethyl esters performed longer SPL (2.8–20%) and narrower SCA (5.1–19%) than diesel under ambient pressures of 5 and 10 bar. Although the SMD values of ethyl esters were 48% higher than diesel on average, their macroscopic spray characteristics were very similar to those of diesel under 15 bar chamber pressure. Moreover, ethyl esters were found to be very similar to methyl esters in terms of spray characteristics. The differences in SPL, SCA and SMD values for both types of biodiesels were lower than 4%. When considering the uncertainty (± 0.84%) and repeatability (±5%) ratios, the difference between the spray characteristics of methyl and ethyl esters was not major. Graphical abstract: [Figure not available: see fulltext.] © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.Article Citation - WoS: 61Citation - Scopus: 60Performance of Structures in İzmir After the Samos Island Earthquake(Springer, 2022) Yakut, A.; Sucuoǧlu, H.; Binici, B.; Canbay, E.; Dönmez, C.; Ilki, A.; Ay, B.Ö.The October 30, 2020 Earthquake caused unexpectedly significant damage in İzmir considering its distance to the city. This paper evaluates the recorded ground motions, summarizes the performance of structures affected from the earthquake with emphasis on the reasons of damage. A detailed damage assessment was carried out by the Earthquake Engineering Research Center of Middle East Technical University to compile data on the damage of RC and masonry buildings. It was observed that majority of the damage was concentrated in the Bayraklı district due to its peculiar soil properties where many 7–10 story mid-rise RC buildings suffered heavy damage and collapse. The level of amplified ground motions combined with deficiencies of apparently non-code compliant buildings exacerbated the damage. The main reasons of damage were mainly attributed to the presence of soft stories, lack of proper detailing, poor construction quality, presence of heavy overhangs, and hence significant lack of code-compliance in essence. The influence of infill walls on seismic performance of deficient and inadequate buildings was clearly seen in this earthquake. This paper also discusses seismic code requirements in effect and their influence on the observed building performance. The recorded ground motions were compared with the code spectra to evaluate the performance of the buildings. The code response spectra were found to be well above the recorded ground motion spectra at the sites where significant damage was observed. © 2021, The Author(s), under exclusive licence to Springer Nature B.V.Article Citation - WoS: 5Citation - Scopus: 5Differences and Similarities in Biophysical and Biological Characteristics Between U87 Mg Glioblastoma and Astrocyte Cells(Springer, 2023) Özdil, Berrin; Çalık Kocatürk, Duygu; Altunayar Ünsalan, Çisem; Açıkgöz, Eda; Oltulu, Fatih; Görgülü, Volkan; Uysal, Ayşegül; Öktem, Gülperi; Ünsalan, Ozan; Güler, Günnur; Aktuğ, HüseyinCurrent cancer studies focus on molecular-targeting diagnostics and interactions with surroundings; however, there are still gaps in characterization based on topological differences and elemental composition. Glioblastoma (GBM cells; GBMCs) is an astrocytic aggressive brain tumor. At the molecular level, GBMCs and astrocytes may differ, and cell elemental/topological analysis is critical for identifying potential new cancer targets. Here, we used U87 MG cells for GBMCS. U87 MG cell lines, which are frequently used in glioblastoma research, are an important tool for studying the various features and underlying mechanisms of this aggressive brain tumor. For the first time, atomic force microscopy (AFM), scanning electron microscopy (SEM) accompanied by energy-dispersive X-ray spectroscopy (EDS), and X-ray photoelectron spectroscopy (XPS) are used to report the topology and chemistry of cancer (U87 MG) and healthy (SVG p12) cells. In addition, F-actin staining and cytoskeleton-based gene expression analyses were performed. The degree of gene expression for genes related to the cytoskeleton was similar; however, the intensity of F-actin, anisotropy values, and invasion-related genes were different. Morphologically, GBMCs were longer and narrower while astrocytes were shorter and more disseminated based on AFM. Furthermore, the roughness values of these cells differed slightly between the two call types. In contrast to the rougher astrocyte surfaces in the lamellipodial area, SEM-EDS analysis showed that elongated GBMCs displayed filopodial protrusions. Our investigation provides considerable further insight into rapid cancer cell characterization in terms of a combinatorial spectroscopic and microscopic approach.Article Citation - WoS: 21Citation - Scopus: 21Remote Sensing-Based Monitoring and Evaluation of the Basin-Wise Dynamics of Terrestrial Water and Groundwater Storage Fluctuations(Springer, 2023) Khorrami, Behnam; Gündüz, OrhanThe recent dynamics of terrestrial water storage (TWS) and groundwater storage (GWS) fluctuations were investigated based on the Gravity Recovery And Climate Experiment (GRACE) observations over 25 basins of Türkiye. Coarse-resolution GRACE estimates were downscaled based on the Random Forest algorithm. The impacts of precipitation (P) and evapotranspiration (ET) on the variations of water storage were also assessed. The findings demonstrated good performance for the RF model in simulating finer resolution estimates of TWS. The results indicated a diminishing trend of TWS and its hydrologic components over all the basins from 2003 to 2020. The Doğu Akdeniz Basin with the annually decreasing TWS and GWS of 1.15cm/yr and 1.10cm/yr was the most critical basin of Türkiye. The least storage loss was observed in the Batı Karadeniz Basin with the annual TWS and GWS loss of 0.38cm/yr and 0.45cm/yr , respectively. Based on the results, Türkiye has lost, on average, an estimated 5.16km3/yr and 4.09km3/yr of its TWS and GWS, respectively, which are equivalent to the total storage loss of 92.88km3 and 73.62km3 of TWS and GWS during the last 18 years. The results also indicated that P and ET interact differently with the variations of TWS and GWS. The net water flux was revealed to be partially correlated with the total water storage fluctuations, suggesting the governing role of other deriving forces particularly the anthropogenic factors in the spatiotemporal variations of Türkiye’s water storage; therefore, a sector-specific analysis of the water storage variations is crucial for the country, particularly by concentrating more on the dynamics of GWS. Graphical Abstract: [Figure not available: see fulltext.]. © 2023, The Author(s), under exclusive licence to Springer Nature Switzerland AG.