WoS İndeksli Yayınlar Koleksiyonu
Bu koleksiyon için kalıcı URIhttps://hdl.handle.net/20.500.12573/394
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Kitap Bölümü Atıf - Scopus: 1"What if You Are a Medieval Monarch?": A Crusader Kings III Experience to Learn Medieval History(de Gruyter Oldenbourg, 2022-10-10) Tozoglu, Ahmet Erdem; Kuran, Mehmet SukruThis chapter is about the authors' experiences and observations on a blended world history course that combines classical lecture and discussion components of teaching with video game sessions. The students play strategy video games with a heavy historical focus. The course, named Playing with The Past, is designed to experiment on how to integrate video games on teaching history, especially in order to achieve a higher understanding of the contemporary social, political, economic, and technological context of a given era for different cultures and civilizations. This chapter presents the utilization of Crusader Kings, a renowned grand strategy game series, to teach medieval history, which constitutes an integral part of our course. It also examines how the game provides advantages for an immersive learning environment and how it fails to model medieval history at specific points. Our experiments and observations may be beneficial for designing a general world history course and any history course on specific periods, cultures, and nations that aims to utilize alternative tools to deliver a course.Makale Atıf - WoS: 2Atıf - Scopus: 23-State Protein Secondary Structure Prediction Based on Scope Classes(Inst Tecnologia Parana, 2021) Atasever, Sema; Azginoglu, Nuh; Erbay, Hasan; Aydin, ZaferImproving the accuracy of protein secondary structure prediction has been an important task in bioinformatics since it is not only the starting point in obtaining tertiary structure in hierarchical modeling but also enhances sequence analysis and sequence-structure threading to help determine structure and function. Herein we present a model based on DSPRED classifier, a hybrid method composed of dynamic Bayesian networks and a support vector machine to predict 3-state secondary structure information of proteins. We used the SCOPe (Structural Classification of Proteins-extended) database to train and test the model. The results show that DSPRED reached a Q(3) accuracy rate of 82.36% when trained and tested using proteins from all SCOPe classes. We compared our method with the popular PSI PRED on the SCOPe test datasets and found that our method outperformed PSI PRED.Makale Atıf - WoS: 6Atıf - Scopus: 63-Sulfopropyl Methacrylate Based Cryogels as Potential Tissue Engineering Scaffolds(Taylor & Francis Ltd, 2019-12-25) Durukan, Adile Yuruk; Isoglu, Ismail Alper; Yürük Durukan, AdileIn this study, we developed cryogels containing 3-sulfopropyl methacrylate (SPMA) and 4-vinyl pyridine (4-VP) as a potential scaffold for tissue engineering applications. Cryogels with varying monomer ratios were synthesised by chemical cross-linking under cryogelation conditions. Effect of initiators and cross-linker amount (0.025-0.15 g MBA; 0.012-0.05 g APS; 2.5-12.5 mu l TEMED) and also freezing temperature (-20 and -80oC) were investigated, and the conditions were optimised according to the morphological structures examined by SEM. The functional groups of the materials were characterised by FT-IR. Compression test and swelling were applied to investigate mechanical properties and water absorption ability, respectively. As a preliminary study, selected materials were tested for cell cytotoxicity with MTT. According to our results, the ionic and biocompatible cryogels prepared in this study possessing a highly porous and interconnective structure with good mechanical characteristics and swelling properties can be suitable as tissue scaffolds for many applications.Makale 3D Sampling of K-Space With Non-Cartesian Trajectories in MR Imaging(Gazi Univ, Fac Engineering Architecture, 2025) Dundar, Mehmet Sait; Gumus, Kazim Z.; Yilmaz, BulentThis study presents an innovative approach to 3D k-space sampling in MR imaging using non-Cartesian concentric shell trajectories. The method involves 32 concentric shells of varying radii, allowing for rapid data acquisition through undersampling techniques. Simulations using IDEA software demonstrate that this approach can fill the k-space in less than one second, a significant time reduction compared to traditional FLASH sequences that can take 3-4 minutes. The concentric shell model enhances imaging efficiency by minimizing artifacts and ensuring uniform k-space filling, leading to higher resolution and faster scans. This technique shows promise for clinical applications, particularly in dynamic imaging scenarios such as acute stroke and pediatric radiology, where speed and precision are critical. As illustrated in Figure A, the concentric shell trajectories enable uniform k-space filling, significantly reducing scan times and improving image quality. These results are based on the simulations conducted with IDEA software.Makale Atıf - WoS: 13Mont: A Multi-Omics Integrative Tool for Breast Cancer Subtype Stratification(Public Library Science, 2025) Unlu Yazici, Miray; Marron, J. S.; Bakir-Gungor, Burcu; Zou, Fei; Yousef, Malik; Yazici, Miray UnluBreast Cancer (BRCA) is a heterogeneous disease, and it is one of the most prevalent cancer types among women. Developing effective treatment strategies that address diverse types of BRCA is crucial. Notably, among different BRCA molecular sub-types, Hormone Receptor negative (HR-) BRCA cases, especially Basal-like BRCA sub-types, lack estrogen and progesterone hormone receptors and they exhibit a higher tumor growth rate compared to HR+ cases. Improving survival time and predicting prognosis for distinct molecular profiles is substantial. In this study, we propose a novel approach called 3-Multi-Omics Network and Integration Tool (3Mont), which integrates various -omics data by applying a grouping function, detecting pro-groups, and assigning scores to each pro-group using Feature importance scoring (FIS) component. Following that, machine learning (ML) models are constructed based on the prominent pro-groups, which enable the extraction of promising biomarkers for distinguishing BRCA sub-types. Our tool allows users to analyze the collective behavior of features in each pro-group (biological groups) utilizing ML algorithms. In addition, by constructing the pro-groups and equalizing the feature numbers in each pro-group using the FIS component, this process achieves a significant 20% speedup over the 3Mint tool. Contrary to conventional methods, 3Mont generates networks that illustrate the interplay of the prominent biomarkers of different -omics data. Accordingly, exploring the concerted actions of features in pro-groups facilitates understanding the dynamics of the biomarkers within the generated networks and developing effective strategies for better cancer sub-type stratification. The 3Mont tool, along with all supporting materials, can be found at https://github.com/malikyousef/3Mont.git.Makale Atıf - WoS: 13Atıf - Scopus: 154D-QSAR Investigation and Pharmacophore Identification of Pyrrolo[2,1-C][1,4]Benzodiazepines Using Electron Conformational-Genetic Algorithm Method(Taylor & Francis Ltd, 2016-04-02) Ozalp, A.; Yavuz, S. C.; Sabanci, N.; Copur, F.; Kokbudak, Z.; Saripinar, E.In this paper, we present the results of pharmacophore identification and bioactivity prediction for pyrrolo[2,1-c][1,4]benzodiazepine derivatives using the electron conformational-genetic algorithm (EC-GA) method as 4D-QSAR analysis. Using the data obtained from quantum chemical calculations at PM3/HF level, the electron conformational matrices of congruity (ECMC) were constructed by EMRE software. The ECMC of the lowest energy conformer of the compound with the highest activity was chosen as the template and compared with the ECMCs of the lowest energy conformer of the other compounds within given tolerances to reveal the electron conformational submatrix of activity (ECSA, i.e. pharmacophore) by ECSP software. A descriptor pool was generated taking into account the obtained pharmacophore. To predict the theoretical activity and select the best subset of variables affecting bioactivities, the nonlinear least square regression method and genetic algorithm were performed. For four types of activity including the GI(50), TGI, LC50 and IC50 of the pyrrolo[2,1-c][1,4] benzodiazepine series, the r(train)(2), r(test)(2) and q(2) values were 0.858, 0.810, 0.771; 0.853, 0.848, 0.787; 0.703, 0.787, 0.600; and 0.776, 0.722, 0.687, respectively.Konferans Nesnesi Atıf - WoS: 2Atıf - Scopus: 194.8 Km-Range Direct Detection Fiber Optic Distributed Acoustic Sensor(Optica Publishing Group (Formerly OSA), 2019) Uyar, F.; Onat, T.; Unal, C.; Kartaloǧlu, T.; Ozdur, I.; Özbay, E.This work demonstrates an ultra-long range direct detection fiber optic distributed acoustic sensor which can detect vibrations at a distance of 94.8 km with 10 m resolution along the sensing fiber. © 2023 Elsevier B.V., All rights reserved.Konferans Nesnesi Atıf - WoS: 2Atıf - Scopus: 394.8 Km-Range Direct Detection Fiber Optic Distributed Acoustic Sensor(Institute of Electrical and Electronics Engineers Inc., 2019) Uyar, Faruk; Onat, Talha; Unal, Canberk; Kartaloǧlu, Tolga; Ozdur, Ibrahim T.; Özbay, EkmelThis work demonstrates an ultra-long range direct detection fiber optic distributed acoustic sensor which can detect vibrations at a distance of 94.8 km with 10 m resolution along the sensing fiber. © 2019 Elsevier B.V., All rights reserved.Makale Atıf - WoS: 5Atıf - Scopus: 9A Battery-Friendly Data Acquisition Model for Vehicular Speed Estimation(Pergamon-Elsevier Science Ltd, 2016-02) Kaya, Sevgi; Kilic, Necati; Kocak, Taskin; Gungor, CagriModeling traffic flow and gathering accurate traffic congestion information are two challenging problems in smart transportation systems. Most of the traffic flow models and velocity estimation methodologies that have been proposed so far gather the data from GPS-equipped smart phones and extract the flow model based on GPS sampling. However, these approaches tend to fail in real life scenarios due to the insufficient vehicle data and unpredictable dynamics of the flow. Furthermore, utilization of GPS sensor leads to a battery drainage and hence reduces the overall system performance. In this paper, we propose a new battery-friendly data acquisition model to obtain the raw data. We then evaluate our model under various traffic conditions to determine its feasibility in vehicle speed estimation. The proposed model results in 88% location accuracy whereas it reduces the battery consumption by half. (C) 2016 Elsevier Ltd. All rights reserved.Makale Atıf - WoS: 7Atıf - Scopus: 6A Chapter in the Modernization of Turkey: Damming the Rivers, Claiming the Natural Landscape, and Building of the Seyhan Dam in Cilicia(Routledge Journals, Taylor & Francis Ltd, 2020-03-31) Tozoglu, Ahmet ErdemThis article examines building of the Seyhan Dam (1953-1956) in Turkey. Both Turkish and American agents played significant roles for planning and implementation of the project during the Cold War era. The 1950s provided necessary conditions in Turkey for the rise of new actors and developments to facilitate transition from limited modernity, which had mostly manifested in urban areas, to a more comprehensive state of modernity extended to rural areas. This extension had irrevocable impacts on the natural landscape as well. By referring to some patterns of modernization, this article posits building of the Seyhan Dam as a significant example to demonstrate how state-led modernization extended its scope by means of taming rivers and opening of plains for agriculture in the Cilician (cukurova) region from late Ottoman to Republican periods.