Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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  • Article
    Trna Wobble Base Modifications and Boric Acid Resistance in Yeast: Boron-Resistant Deletion Mutants Induce the General Amino Acid Control Mechanism and Activate Boron Efflux
    (NLM (Medline), 2020) Uluisik, I.; С Karakaya, H.; Koc, A.
    Boric acid is essential for plants and has many vital roles in animals and microorganisms. However, its high doses are toxic to all organisms. We previously screened yeast deletion collections to identify boric acid-resistant and susceptible mutants to identify genes that play a role in boron tolerance. Here, we analyzed boron resistant mutants (elplΔ, elp3Δ, elp6Δ, ncs2Δ, ncs6Δ and ktil2Δ) for their abilities to modulate the general amino acid control system (GAAC) and to induce boron efflux pump ATR1. The mutants analyzed in this study lack the genes that play roles in tRNA Wobble base modifications. We found that all of the boron resistant mutants activated Gcn4-dependent reporter gene activity and increased the transcript level of the ATR1 gene. Additionally, boron resistant cells accumulated less boric acid in their cytoplasm compared to the wild type cells upon boron exposure. Thus, our findings suggested that loss of wobble base modifications in tRNA leads to GAAC activation and ATR1 induction, which in turn reduced intracellular boron levels and caused boron resistance.
  • Article
    Citation - WoS: 3
    Citation - Scopus: 3
    Two Decades of Research on Roma in Türkiye: Socioeconomic Exclusion, Identity, and State Policies
    (Liverpool Univ Press, 2024) Celik, Faika; Uştuk, Ozan; Ustuk, Ozan
    The scholarly investigation of Roma communities in Turkiye has intensified since the 2000s, largely driven by Turkiye's EU accession candidacy and subsequent adaptation process. This alignment, along with internal developments, prompted governments to prioritize Roma issues, implement projects, and issue action plans. The Roma Civil Society Movement in the 1990s further highlighted Roma challenges, resulting in a diverse body of literature. This study critically examines academic literature to map prevailing trends and thematic foci. Key areas of scholarly engagement include the various dimensions of socio-economic exclusion faced by Roma in education, employment, housing, and health. Additionally, scholars analyze how Roma negotiate and resist pejorative representations, construct their identities, and organize to address contemporary challenges. State policies affecting Roma, from past to present, also receive considerable attention. By critically engaging with this scholarship, the present study highlights significant progress and ongoing challenges in Romani Studies in Turkiye, offering insights into future research directions.
  • Article
    Effect of Random Structural Variations on the Optical Properties of Honeycomb Photonic Crystals
    (Taylor & Francis Ltd, 2024) Tuncturk, Yigit; Sozuer, H. Sami
    Periodic dielectric structures called photonic crystals are being used in various sensors and devices. Since photonic crystals are designed to operate within certain frequency ranges, accuracy in structure becomes important. In this work, we investigate the effects of two types of randomness, surface roughness and positional randomness, on the optical properties of the honeycomb photonic crystal. We employed the plane wave expansion method to investigate the effects of random perturbations of the shape and the position of the structure on the density of states. We also employ the finite-difference time-domain method to calculate the transmission spectrum as a consistency check. We find that both surface roughness and positional imperfections cause significant changes in the DOS. As the degree of randomness is increased, transverse electric and transverse magnetic gaps are narrowed and complete gaps totally disappear at $ 45\% $ 45% of surface roughness.
  • Article
    Citation - Scopus: 27
    Apoptotic Effects of Resveratrol, a Grape Polyphenol, Onimatinib-Sensitive and Resistant K562 Chronic Myeloid Leukemia Cells
    (2012) Can,G.; Cakir,Z.; Kartal,M.; Gunduz,U.; Baran,Y.
    Aim: To examine the antiproliferative and apoptotic effects of resveratrol on imatinib-sensitive and imatinib-resistant K562 chronic myeloid leukemia cells. Materials and Methods: Antiproliferative effects of resveratrol were determined by the 3-Bis[2-methoxy-4-nitro-5-sulphophenyl]-2H-tetrazolium-5- carboxanilide inner salt (XTT) cell proliferation assay. Apoptotic effects of resveratrol on sensitive K562 and resistant K562/IMA-3 cells were determined through changes in caspase-3 activity, loss of mitochondrial membrane potential (MMP), and apoptosis by annexin V-(FITC). Results: The concentrations of resveratrol that inhibited cell growth by 50% ( IC50) were calculated as 85 and 122 μM for K562 and K562/IMA-3 cells, respectively. There were 1.91-, 7.42- and 14.73-fold increases in loss of MMP in K562 cells treated with 10, 50, and 100 μM resveratrol, respectively. The same concentrations of resveratrol resulted in 2.21-, 3.30- and 7.65-fold increases in loss of MMP in K562/IMA-3 cells. Caspase-3 activity increased 1.04-, 2.77- and 4.8-fold in K562 and 1.02-, 1.41- and 3.46-fold in K562/IMA- 3 cells in response to the same concentrations of resveratrol, respectively. Apoptosis was induced in 58.7%-and 43.3% of K562 and K562/IMA-3 cells, respectively, in response to 100 μM resveratrol. Conclusion: Taken together these results may suggest potential use of resveratrol in CML, as well as in patients with primary and/or acquired resistance to imatinib.
  • Article
    Citation - WoS: 1
    Citation - Scopus: 1
    Identification of Flood Hazard Zones in Afghanistan Using Gis and Multi-Criteria Decision Approach
    (Inderscience Publishers, 2024) Tani, H.; Tayfur, G.
    This study assessed Afghanistan’s potential flood hazard zones using the geographic information systems (GIS) and the analytical hierarchy process (AHP). Six different thematic layers were selected, and the AHP was applied to estimate the influence weights of each parameter. The final flood hazard zones map (FHZM) was reclassified into five zones. Sensitivity analysis was employed to create the flood hazard sensitivity map (FHSM) based on ‘effective weights’. It was found that the land use land cover (LULC) and rainfall are less sensitive compared to the other parameters. The FHZM and FHSM comparatively indicate the same regions regarding flood hazard levels. The methodology was tested against the recorded flood events in the region. The results showed that about 44% of the study area is under low and very low flood hazards, whereas 56% is subjected to high and very high. Low-lying areas are highly prone to flooding. Copyright © 2024 Inderscience Enterprises Ltd.
  • Article
    Citation - Scopus: 1
    Performance Indices of Soft Computing Models To Predict the Heat Load of Buildings in Terms of Architectural Indicators
    (Yildiz Technical University, 2016) Turhan,C.; Kazanasmaz,T.; Akkurt,G.G.
    This study estimates the heat load of buildings in Izmir/Turkey by three soft computing (SC) methods; Artificial Neural Networks (ANNs), Fuzzy Logic (FL) and Adaptive Neuro-based Fuzzy Inference System (ANFIS) and compares their prediction indices. Obtaining knowledge about what the heat load of buildings would be in architectural design stage is necessary to forecast the building performance and take precautions against any possible failure. The best accuracy and prediction power of novel soft computing techniques would assist the practical way of this process. For this purpose, four inputs, namely, wall overall heat transfer coefficient, building area/ volume ratio, total external surface area and total window area/total external surface area ratio were employed in each model of this study. The predicted heat load is evaluated comparatively using simulation outputs. The ANN model estimated the heat load of the case apartments with a rate of 97.7% and the MAPE of 5.06%; while these ratios are 98.6% and 3.56% in Mamdani fuzzy inference systems (FL); 99.0% and 2.43% in ANFIS. When these values were compared, it was found that the ANFIS model has become the best learning technique among the others and can be applicable in building energy performance studies. © 2016. All Rights Reserved.
  • Conference Object
    Citation - WoS: 5
    Citation - Scopus: 7
    Modeling Leakage of Ephemeral Secrets in Tripartite/Group Key Exchange
    (Institute of Electronics, Information and Communication, Engineers, IEICE, 2013) Manulis, Mark; Suzuki, Koutarou; Ustaoglu, Berkant
    We propose a security model, referred as g-eCK model, for group key exchange that captures essentially all non-trivial leakage of static and ephemeral secret keys of participants, i.e., group key exchange version of extended Canetti-Krawczyk (eCK) model. Moreover, we propose the first one-round tripartite key exchange (3KE) protocol secure in the g-eCK model under the gap Bilinear Diffie-Hellman (gap BDH) assumption and in the random oracle model.
  • Article
    Investigation of Earth Dam Filter Performance Under Static and Dynamic Loading Conditions
    (Amer Soc Testing Materials, 2024) Valizadeh, Hadi; Ecemis, Nurhan; Leclerc, Rabia Zeynep Sarica
    Erosion -induced piping is the primary cause of failure in embankment dams' ' bodies and foundations. The filter is a principal part of an earth dam, owing to the crucial role of this layer in protecting the clayey core from erosion. Erosion is the process by which soil particles migrate due to an interior fluid flow and is recognized as a significant hazard for earthen constructions. Designing a proper filter -soil system can regulate and seal undesirable cracks that may form in the impermeable core due to nonuniform settlements, extreme water levels, or earthquakes. In this study, a No -Erosion Filter (NEF) test device, which still seems to be the most reliable filtersoil system design, has been adapted to evaluate the performance of the filter sand of two dams under static and dynamic loading conditions. The outcomes were compared with the several filter design criteria in the literature, and it was found that the filter's design approach using the available criteria may not always align with the NEF test results. Therefore, a precise understanding of fluid-particle -particle interactions is necessary to design and operate earth dam filters. The dynamic excitation can change hole pressure distribution and cause erosion even after steady-state conditions under static situations. Consequently, the effectiveness of filters under static conditions does not necessarily translate to satisfactory performance when exposed to dynamic loading.
  • Article
    Validation of New Micro-Spectrophotometric Method To Determine Diamine Oxidase Activity in Serum
    (Springer india, 2024) Sozmen, Eser Yildirim; Sozmen, Alper Baran
    Food allergy and histamine intolerance (HI) are prevalent worldwide. Diamine oxidase (DAO) activity determination in serum is a promising approach for diagnosing HI. Despite the numerous methods that have been published for determining diamine. oxidase activity in serum, most of them have not been validated and have inherent limitations, such as interference and multi-step analysis. Our objective was to perform the analytical validation of a novel micro-spectrophotometric method for the determination of DAO activity in a routine clinical laboratory setting. In this study we determined DAO activity in serum using a 4-aminoantypirine (4-AAP) and 2,4,6 tribromo-3-hidroxybenzoic acid (TBHBA) combination as chromogen for the first time. Validation steps included determination of accuracy (recovery and linearity) and precision (within-run and between-run repeatability) following the Clinical and Laboratory Standards Institute protocols and the other guidelines. Reagent stability assessment at both 4 degrees C temperature and frozen (- 20 degrees C) after 4 h, 24 h, 72 h and a week storage were conducted. The optimum test conditions were determined as pH = 6.0, 37 degrees C, 55 mM Putrescine and 60 min. LOD and LOQ levels were found as 10.08 U/L and 30.56 U/L respectively. Coefficients of variation (CVs) for within-run and between-run precisions were 5.2%, 9.4% for the normal level and 2.6%, 2.2% for the high range, respectively. This reliable method for quantifying DAO activity in serum provides an optimal approach, offering rapid and straightforward performance in laboratories for clinical use.
  • Article
    Proliferative Effects and Cellular Uptake of Ceramic Nanoparticles in Cancer and Normal Cells
    (Univ Chemistry & Technology, Prague, 2024) Cesmeli, Selin; Tomak, Aysel; Winkler, David A.; Karakus, Ceyda Oksel
    The high biocompatibility, wear resistance, and high surface area-to-volume ratios of calcium phosphate (CaP) nanoparticles make them materials of great interest for a very broad range of medical applications, such as dentistry, drug delivery, biomedical imaging, gene transfection and silencing, biomedical imaging, immunisation, and bone substitution. While their use as an enamel remineralisation agent, a bone substitution material, an implant coating, and drug/gene delivery agents is widely approved by the regulating bodies, insufficient attention has been paid to the interactions of CaP-based nanoparticles with cells and organs once in the bloodstream and distributed through the body. Here, three different CaP-based nanoparticles (CP: calcium phosphate, TCP: tricalcium phosphate, and HAp: hydroxyapatite) were examined for the proliferative effects, oxidative damage potential, and cellular uptake in the human embryonic kidney (HEK293) and pancreatic cancer (Panc-1) cell lines. The physicochemical properties of the nanoparticles were characterised by Teller analysis, and X-ray diffraction spectroscopy. Maximum proliferative effects were generated by 400 mu g center dot ml-1 TCP (220 %) in HEK293 cells. Interestingly, although CP nanoparticles had the highest reactive oxygen species formation capacity in the HEK293 cells, they exhibited the lowest proliferative effects and a relatively low internalisation rate, suggesting a minimal correlation between the cellular uptake level and oxidative potential.