WoS İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394

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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, Bulent
This 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.
Citation - WoS: 12
Citation - Scopus: 14
4D-QSAR Investigation and Pharmacophore Identification of Pyrrolo[2,1-C][1,4]Benzodiazepines Using Electron Conformational-Genetic Algorithm Method
(Taylor & Francis Ltd, 2016) 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.
Citation - WoS: 6
Citation - Scopus: 6
Absorption Enhancement by Semi-Cylindrical Structures for an Organic Solar Cell Application
(Optical Soc Amer, 2020) Hah, Dooyoung
Organic solar cells are attractive for various applications with their flexibility and low-cost manufacturability. In order to increase their attractiveness in practice, it is essential to improve their energy conversion efficiency. In this work, semi-cylindrical-shell-shaped structures are proposed as one of the approaches, aiming at absorption enhancement in an organic solar cell. Poly(3-hexylthiophene-2,5-diyl) blended with indene-C60 bisadduct (P3HT:ICBA) is considered as the active layer. Light coupling to the guided modes and a geometrical advantage are attributed to this absorption enhancement. Finite-difference time-domain methods and finite element analysis are used to examine the absorption spectra for two types of devices, i.e., a debossed type and an embossed type. It is shown that absorption enhancement increases as the radius of the cylinder increases, but reaches a saturation at about 4-mu m radius. The average absorption enhancement with an active layer thickness of 200 nm and radius of 4 mu m, and for incidence angles between 0 degrees and 70 degrees, is found as 51%-52% for TE-polarized input and as 30%-33% for TM-polarized input when compared to a flat structure. Another merit of the proposed structures is that the range of incidence angles where the integrated absorption is at the level of the normal incidence is significantly broadened, reaching 70 degrees-80 degrees. This feature can be highly useful especially when organic solar cells are to be placed around a round object. The study results also exhibit that the proposed devices bear broadband absorption characteristics. (C) 2020 Optical Society of America
Citation - WoS: 5
Citation - Scopus: 4
Active Subnetwork Ga: A Two Stage Genetic Algorithm Approach to Active Subnetwork Search
(Bentham Science Publ Ltd, 2017) Ozisik, Ozan; Bakir-Gungor, Burcu; Diri, Banu; Sezerman, Osman Ugur
Background: A group of interconnected genes in a protein-protein interaction network that contains most of the disease associated genes is called an active subnetwork. Active subnetwork search is an NP-hard problem. In the last decade, simulated annealing, greedy search, color coding, genetic algorithm, and mathematical programming based methods are proposed for this problem. Method: In this study, we employed a novel genetic algorithm method for active subnetwork search problem. We used active node list chromosome representation, branch swapping crossover operator, multicombination of branches in crossover, mutation on duplicate individuals, pruning, and two stage genetic algorithm approach. The proposed method is tested on simulated datasets and Wellcome Trust Case Control Consortium rheumatoid arthritis genome-wide association study dataset. Our results are compared with the results of a simple genetic algorithm implementation and the results of the simulated annealing method that is proposed by Ideker et al. in their seminal paper. Results and Conclusion: The comparative study demonstrates that our genetic algorithm approach outperforms the simple genetic algorithm implementation in all datasets and simulated annealing in all but one datasets in terms of obtained scores, although our method is slower. Functional enrichment results show that the presented approach can successfully extract high scoring subnetworks in simulated datasets and identify significant rheumatoid arthritis associated subnetworks in the real dataset. This method can be easily used on the datasets of other complex diseases to detect disease-related active subnetworks. Our implementation is freely available at https://www.ce.yildiz.edu.tr/personal/ozanoz/file/6611/ActSubGA.
Citation - WoS: 6
Citation - Scopus: 5
Admissible Invariants of Genus 3 Curves
(Springer Heidelberg, 2015) Cinkir, Zubeyir
Several invariants of polarized metrized graphs and their applications in Arithmetic Geometry are studied recently. In this paper, we explicitly calculated these admissible invariants for all curves of genus 3. We find the sharp lower bound for the invariants phi, lambda and epsilon for all polarized metrized graphs of genus 3. This improves the lower bound given for Effective Bogomolov Conjecture for such curves.
Citation - WoS: 7
Citation - Scopus: 7
Amorphous Boron Nitride at High Pressure
(Taylor & Francis Ltd, 2016) Durandurdu, Murat
The pressure-induced phase transformation in hexagonal boron nitrite and amorphous boron nitrite is studied using ab initio molecular dynamics simulations. The hexagonal-to-wurtzite phase transformation is successfully reproduced in the simulation with a transformation mechanism similar to one suggested in experiment. Amorphous boron nitrite, on the other hand, gradually transforms to a high-density amorphous phase with the application of pressure. This phase transformation is irreversible because a densified amorphous state having both sp(3) and sp(2) bonds is recovered upon pressure release. The high-density amorphous state mainly consists of sp(3) bonds and its local structure is quite similar to recently proposed intermediate boron nitrite phases, in particular tetragonal structure (P4(2)/mnm), rather than the known the wurtzite or cubic boron nitrite due to the existence of four membered rings and edge sharing connectivity. On the basis of this finding we propose that amorphous boron nitrite might be best candidate as a starting structure to synthesize the intermediate phase(s) at high pressure and temperature (probably below 800 degrees C) conditions.
Citation - WoS: 5
Citation - Scopus: 5
Amorphous Silicon Hexaboride at High Pressure
(Taylor & Francis Ltd, 2020) Durandurdu, Murat
We investigate the pressure-induced structural phase transformation of amorphous silicon hexaboride (a-SiB6) using a constant pressure first principles approach. a-SiB6 is found to undergo a gradual phase transformation to a high-density amorphous phase (HDA) in which the average coordination number of both B and Si atoms is about 6. The HDA phase consists of differently coordinated motifs ranging from 4 to 8. B-12 icosahedra are found to persist during compression of a-SiB6 and the structural modifications primarily occur around Si atoms and in the regions linking pentagonal pyramid-like configurations to each other. Upon pressure release, an amorphous structure, similar to the uncompressed one, is recovered, indicating a reversible amorphous-to-amorphous phase change in a-SiB6. When the electronic structure is considered, the HDA phase is perceived to have a wider forbidden band gap than the uncompressed one.
Citation - WoS: 3
Citation - Scopus: 3
Amorphous Silicon Hexaboride: A First-Principles Study
(Taylor & Francis Ltd, 2018) Durandurdu, Murat
We report for the first time the atomic structure, electronic structure and mechanical properties of amorphous silicon hexaboride (a-SiB6) based on first-principles molecular dynamics simulation. The a-SiB6 model is generated from the melt and predominantly consists of pentagonal pyramid-like configurations and B-12 icosahedral molecules, similar to what has been observed in most boron-rich materials. The mean coordination number of B and Si atoms are 5.47 and 4.55, respectively. The model shows a semiconducting behaviour with a theoretical bandgap energy of 0.3eV. The conduction tail states are found to be highly localised and hence the n-type doping is suggested to be more difficult than the p-type doping for a-SiB6. The bulk modulus and Vickers hardness of a-SiB6 are estimated to be about 118 and 13-17GPa, respectively.
Citation - WoS: 1
Amorphous to Amorphous Phase Transformation in Boron-Rich Amorphous Silicon Borides: An Ab Initio Study
(Taylor & Francis Ltd, 2024) Karacaoglan, Aysegul Ozlem Cetin; Durandurdu, Murat
This study employs a constant-pressure ab initio approach to investigate the high-pressure behavior of five distinct boron-rich amorphous silicon borides. A unique amorphous-to-amorphous phase transition is exposed, providing insights into the structural resilience of these materials under extreme conditions. Our results reveal a gradual increase in the coordination number of both B and Si atoms under pressure, with subsequent densification upon pressure release. Yet the recovered amorphous phases closely resemble the uncompressed states, highlighting the reversibility of these phase changes. Significant structural modifications around Si atoms are observed, emphasizing their pivotal role in the observed phase transitions. Additionally, pressure-induced metallization is witnessed in these materials, indicating their distinctive electronic behavior under high pressure. This work significantly contributes to a deeper understanding of the high-pressure behavior of boron-rich amorphous silicon borides and opens avenues for exploring their potential applications in fields requiring exceptional structural stability and unique pressure-dependent properties.
Citation - WoS: 10
Citation - Scopus: 10
Amorphous Zirconia: Ab Initio Molecular Dynamics Simulations
(Taylor & Francis Ltd, 2017) Durandurdu, Murat
We investigate the short-range order of the liquid and amorphous zirconia using an ab initio molecular dynamics technique. Both forms of zirconia are projected to be structurally close to each other. The amorphous network has predominantly seven-fold coordinated Zr atoms (similar to% 65), and three-fold and four-fold coordinated O atoms (similar to 46%), and hence it resembles locally the monoclinic zirconia phase. Within the known limitations of the DFT-GGA calculation, the liquid state is predicted to be semi-metal, whereas the amorphous form is projected to be semiconductor having a band gap energy of similar to 3.5 eV. We find an asymmetry in localisation of the band tail states. On the basis of this finding, we discuss possible distinctions in n-type and p-type doping in amorphous zirconia.
An Extension of Lucas's Theorem
(indian Nat Sci Acad, 2025) Cinkir, Zubeyir; Ozturkalan, Aysegul
We give elementary proofs of some congruence criteria to compute binomial coefficients modulo a prime number. These criteria are analogues to the symmetry property of binomial coefficients. We give extended version of Lucas's Theorem by using those criteria. We give applications of these criteria by describing a method to derive identities and congruences involving sums of binomial coefficients.
Citation - WoS: 1
Citation - Scopus: 2
Analysis of Mosaic Mortars From the Roman, Byzantine and Early Islamic Periods Sourced From Gerasa's Northwest Quarter
(Springer, 2024) Ball, Richard J.; Ansell, Martin P.; Su-Cadirci, Tugce Busra; Baki, Vahiddin Alperen; Fletcher, Philip J.; Lichtenberger, Achim; Wootton, Will
This study analyses and compares around 650 years of mosaic mortar production spanning the Roman, late Roman and Umayyad periods, at Gerasa/Jerash in Jordan, offering a better understanding of composition, structural features, and manufacturing processes. It assesses the value of optical and electron microscopy examination of morphological and textural features, pore structure using MIP, and composition studies using EDX, XRD, FTIR, TGA, and Raman spectroscopy. The study indicated high density lime adhesive was used compared to other mortars. Wood was used as a fuel when producing the lime and natural fibres were incorporated when manufacturing mortars. Aggregates were primarily calcitic with a small proportion of silica-based aggregates. Key outcomes of the study conclude that early Roman mortars were of highest quality, which was demonstrated through the careful selection of materials including different stone for lime and tesserae, and differences between layers. Late Roman mortars used the same slaked lime plus fibres and charcoal. Mortars dating from the Umayyad period also had the same higher lime content than late Roman, but higher porosity with fibres and charcoal. In general, the mortars showed slight differences in content and aggregate; different stone for lime and tesserae. The research attests to underlying traditions as well as changes in mortar mixes and methods according to context and time. The resulting data is contextualized within local and regional approaches.
Citation - WoS: 9
Citation - Scopus: 10
An Answer to Colon Cancer Treatment by Mesenchymal Stem Cell Originated from Adipose Tissue
(Mashhad Univ Med Sciences, 2018) Iplik, Elif Sinem; Ertugrul, Baris; Kozanoglu, Ilknur; Baran, Yusuf; Cakmakoglu, Bedia
Objective(s): Colon cancer is risen up with its complex mechanism that directly impacts on its treatment as well as its common prevalence. Mesenchymal stem cells (MSCs) have been considered as a therapeutic candidate for conventional disease including cancer. In this research, we have focused on apoptotic effects of adipose tissue-derived MSCs in colon cancer. Materials and Methods: MSCs were obtained from adipose tissue and characterized by Flowcytometer using suitable antibodies. MSCs, HT-29, HCT-116, RKO and healthy cell line MRC5 were cultured by different seeding procedure. After cell viability assay, changes in caspase 3 enzyme activity and the level of phosphatidylserine were measured. Results: For cell viability assay, a 48 hr incubation period was chosen to seed all cells together. There was a 1.36-fold decrease in caspase 3 enzyme activity by co-treatment of RKO and MSCs in addition to 2.02-fold decrease in HT-29 and MSCs co-treatment, and 1.103-fold increase in HCT-116 and MSCs. The results demonstrated that HCT-116 led to the highest rate of apoptotic cell death (7.5%) compared with other cells. Conclusion: We suggest that MSCs might remain a new treatment option for cancer by its differentiation and repair capacity.
Citation - WoS: 20
Citation - Scopus: 23
Apoptotic Effects of Non-Edible Parts of Punica Granatum on Human Multiple Myeloma Cells
(Sage Publications Ltd, 2016) Kiraz, Yagmur; Neergheen-Bhujun, Vidushi S.; Rummun, Nawraj; Baran, Yusuf
Multiple myeloma is of great concern since existing therapies are unable to cure this clinical condition. Alternative therapeutic approaches are mandatory, and the use of plant extracts is considered interesting. Punica granatum and its derived products were suggested as potential anticancer agents due to the presence of bioactive compounds. Thus, polypenolic-rich extracts of the non-edible parts of P. granatum were investigated for their antiproliferative and apoptotic effects on U266 multiple myeloma cells. We demonstrated that there were dose-dependent decreases in the proliferation of U266 cells in response to P. granatum extracts. Also, exposure to the extracts triggered apoptosis with significant increases in loss of mitochondrial membrane potential in U266 cells exposed to the leaves and stem extracts, while the flower extract resulted in slight increases in loss of MMP. These results were confirmed by Annexin-V analysis. These results documented the cytotoxic and apoptotic effects of P. granatum extracts on human U266 multiple myeloma cells via disruption of mitochondrial membrane potential and increasing cell cycle arrest. The data suggest that the extracts can be envisaged in cancer chemoprevention and call for further exploration into the potential application of these plant parts.
Citation - WoS: 20
Citation - Scopus: 21
Application of the Collocation Method With B-Splines to the GEW Equation
(Kent State University, 2017) Zeybek, Halil; Karakoc, S. Battal Gazi
In this paper, the generalized equal width (GEW) wave equation is solved numerically by using a quintic B-spline collocation algorithm with two different linearization techniques. Also, a linear stability analysis of the numerical scheme based on the von Neumann method is investigated. The numerical algorithm is applied to three test problems consisting of a single solitary wave, the interaction of two solitary waves, and a Maxwellian initial condition. In order to determine the performance of the numerical method, we compute the error in the L-2- and L-infinity- norms and in the invariants I-1, I-2, and I-3 of the GEW equation. These calculations are compared with earlier studies. Afterwards, the motion of solitary waves according to different parameters is designed.
Citation - WoS: 4
Citation - Scopus: 9
Are We Ready for the New Normal in E-Business Education? Sentiment Analysis of Learners' Opinions on MOOCs
(Russian State Vocational Pedagogical Univ, 2021) Derindag, O. F.; Cizmeci, B.
Introduction. The new digital economy and its constantly evolving paradigm have completely transformed the model of doing business and the learning methods. MOOCs (massive-open-online-courses) and micro-credentials are the educations interfaces, have become an important teaching environment tool. Distance learning has become an indispensable alternative teaching method in updating and transferring classical education materials according to real-world settings, especially for learners in higher education. Aim. The current research is aimed to address the society's readiness and attitude direction to the concept of MOOCs and distance learning, highlighting its emergence and inevitability for educational institutions of all types in order to make a fundamental change in their curricula, especially in e-business courses, which are the most demanded training courses on MOOCs platforms. Methodology and research methods. In the study, the awareness and recognition of the online community on the MOOCs concept is examined. in this direction, Turkish people's perception and attitudes toward MOOCs have been addressed via sentiment analysis on Eksi Sozluk, the largest social communication and discussion platform in Turkey. Results. According to the sentiment analysis results, it has been determined that 52% of respondents have positive judgments on distance education and MOOCs, 29% of responses are neutral and 18% are negative. In general, distance education and MOOCs are perceived as a useful new education model by the Turkish people. Scientific novelty. This paper is the first sentiment analysis of learners' opinions on MOOCs and distance learning in Turkey. Considering the increasing awareness of MOOCs and the need for e-business education, as the most demanded type of MOOCs, this is the first study investigating the priority of these two phenomena within the context of COVID-19. Practical significance. It is thought that this study will contribute to the stakeholders in terms of showing how MOOCs and micro-credentials have a high potential to understanding trends in education especially in the new normal after the COVID-19 pandemic. The holistic education model of institutions has difficulty meeting the competitive nature and result-oriented approach of the e-business ecosystem. This market reality requires the institutions to offer more to-the-point and applied education solutions. In terms of e-business (e-commerce, digital marketing) education, the importance of MOOCs as a solution-focused on "how" rather than "what." has been comprehensively discussed in the paper.
Citation - WoS: 6
Citation - Scopus: 6
Arsenic Removal From Aqueous Solutions by Ultrafiltration Assisted With Polyacrylamide: An Application of Response Surface Methodology
(Taylor & Francis inc, 2015) Varol, Bekir; Uzal, Nigmet
The present work deals with removal of arsenic from aqueous solutions by ultrafiltration assisted with polyacrylamide as an environmental friendly complexing polymer. The system performance was evaluated in relation to quality of permeate in terms of operating variables as feed concentration of arsenic ions (C-o, gL(-1)), ratio of polymer to arsenic (r, w/w), and pH of feed solution. The effect of the operating variables and maximum arsenic removal efficiency was determined by adopting design of experiments and response surface methodology under different conditions for this polymer. The experimental data were analyzed with a second order polynomial model validated by statistical analysis. Based on the response model developed, the maximum removal efficiency, close to 100%, of arsenic ions has been obtained at optimum operating parameters as C-o: 150 gL(-1), r: 2, and pH 10.
Citation - WoS: 10
Citation - Scopus: 9
Assessment of Deformation Properties of CoAl Measure Sandstones Through Regression Analyses and Artificial Neural Networks
(Polska Akad Nauk, Polish Acad Sciences, 2021) Koken, Ekin
The deformation properties of rocks play a crucial role in handling most geomechanical problems. However, the determination of these properties in laboratory is costly and necessitates special equipment. Therefore, many attempts were made to estimate these properties using different techniques. In this study, various statistical and soft computing methods were employed to predict the tangential Young Modulus (Eti, GPa) and tangential Poisson's Ratio (vti) of coal measure sandstones located in Zonguldak Hardcoal Basin (ZHB), NW Turkey. Predictive models were established based on various regression and artificial neural network (ANN) analyses, including physicomechanical, mineralogical, and textural properties of rocks. The analysis results showed that the mineralogical features such as the contents of quartz (Q, %) and lithic fragment (LF, %) and the textural features (i.e., average grain size, d50, and sorting coefficient, Sc) have remarkable impacts on deformation properties of the investigated sandstones. By comparison with these features, the mineralogical effects seem to be more effective in predicting the Eti and vti. The performance of the established models was assessed using several statistical indicators. The predicted results from the proposed models were compared to one another. It was concluded that the empirical models based on the ANN were found to be the most convenient tools for evaluating the deformational properties of the investigated sandstones.
Citation - WoS: 4
Citation - Scopus: 5
Assessment of Los Angeles Abrasion Value (LAAV) and Magnesium Sulphate Soundness (MWL) of Rock Aggregates Using Gene Expression Programming and Artificial Neural Networks
(Polska Akad Nauk, Polish Acad Sciences, 2022) Koken, Ekin
It has been acknowledged that two important rock aggregate properties are the Los Angeles abrasion value (LAAV) and magnesium sulphate soundness (Mwl). However, the determination of these properties is relatively challenging due to special sampling requirements and tedious testing procedures. In this stu-dy, detailed laboratory studies were carried out to predict the LAAV and Mwl for 25 different rock types located in NW Turkey. For this purpose, mineralogical, physical, mechanical, and aggregate properties were determined for each rock type. Strong predictive models were established based on gene expression programming (GEP) and artificial neural network (ANN) methodologies. The performance of the proposed models was evaluated using several statistical indicators, and the statistical analysis results demonstra-ted that the ANN-based proposed models with the correlation of determination (R2) value greater than 0.98 outperformed the other predictive models established in this study. Hence, the ANN-based predictive models can reliably be used to predict the LAAV and Mwl for the investigated rock types. In addition, the suitability of the investigated rock types for use in bituminous paving mixtures was also evaluated based on the ASTM D692/D692M standard. Accordingly, most of the investigated rock types can be used in bituminous paving mixtures. In conclusion, it can be claimed that the proposed predictive models with their explicit mathematical formulations are believed to save time and provide practical knowledge for evaluating the suitability of the rock aggregates in pavement engineering design studies in NW Turkey.
Assessment of the Quality of Tuffs in Central Anatolia, Turkey: A Quantitative Classification Approach
(Acad Sci Czech Republic Inst Rock Structure & Mechanics, 2025) Koken, Ekin; Ince, Ismail
The growing global demand for dimension stones necessitates efficient and accurate evaluation methods to ensure their optimal use in various industries. To assess their suitability for various dimension stone applications, this study investigates tuffs from Central Anatolia, Turkey. For this purpose, the fundamental physical and mechanical properties of the tuffs were determined in laboratory studies, and a detailed durability assessment was conducted for each rock type. The analysis results indicate that most of the examined rocks are of low quality and more suitable for non-load-bearing applications. Based on the collected data, fuzzy clustering techniques were applied to develop a new classification system, categorising the tuffs into four classes (Class A-D) according to their potential applications. Additionally, a user-friendly MATLAB-based software tool was also developed to facilitate the implementation of the proposed classification system.

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