Araştırma Çıktıları | TR-Dizin | WoS | Scopus | PubMed

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Citation - WoS: 1
Citation - Scopus: 1
3-State Protein Secondary Structure Prediction Based on Scope Classes
(Inst Tecnologia Parana, 2021) Atasever, Sema; Azginoglu, Nuh; Erbay, Hasan; Aydin, Zafer; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
Improving 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.
Citation - WoS: 6
Citation - Scopus: 6
3-Sulfopropyl Methacrylate Based Cryogels as Potential Tissue Engineering Scaffolds
(Taylor & Francis Ltd, 2020) Durukan, Adile Yuruk; Isoglu, Ismail Alper; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
In 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.
A Comparative Study of Existing and Current On-Site Documentation of Anatolian Seljuk Kümbets
(Elsevier Ltd, 2025) Güzelci, O.Z.; Türel, A.; 01. Abdullah Gül University
During the Anatolian Seljuk period (1077–1307), monumental tombs known as kümbets emerged as a distinct architectural typology in present-day Türkiye. 2D drawings of these structures, produced since the early 20th century, contain inconsistencies that necessitate verification and accurate documentation. This study digitally documents Anatolian Seljuk kümbets in 3D to generate updated 2D sections reflecting their current condition and compares these with previously published drawings. The methodology includes collecting available 2D sections, digitally documenting kümbets through field studies, generating new 2D sections from 3D models, and systematically comparing these datasets. Two image-based metrics are employed in the comparison: the Exact Pixel Match Ratio (EPMR), which evaluates pixel-level alignment, and the Structural Similarity Index Measure (SSIM), a standard indicator for visual similarity. The results provide a comparative framework for assessing previous drawings and present a verified, up-to-date dataset of kümbet sections for future research. © 2025 Elsevier B.V., All rights reserved.
A Comprehensive Review on the Extraction and Recovery of Lithium from Primary and Secondary Sources: Advances Toward Battery-Grade Materials
(Wiley, 2025) Top, Soner; Kursunoglu, Sait; Altiner, Mahmut; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
Lithium-ion battery (LIB) technologies have become indispensable to modern energy systems, driving global demand for high-purity lithium compounds. This review focuses on lithium recovery and purification strategies for battery-grade lithium carbonate (Li2CO3) and lithium hydroxide (LiOH), addressing both primary sources (brines and minerals) and secondary sources (waste materials). Industrially established processes, such as evaporation-based brine treatment and conventional metallurgical methods, are discussed alongside emerging techniques, including membrane separation, solvent extraction, and CO2-assisted precipitation. Particular attention is given to lithium precipitation mechanisms, the behaviour of co-existing ions during extraction, and the specific quality requirements for cathode material synthesis. By evaluating process scalability, environmental impact, and product purity, this review provides a comprehensive understanding of current practices and future directions. Additionally, it highlights the growing importance of lithium in the context of accelerating electric vehicle (EV) adoption, underscoring the bright and expanding future of the lithium industry.
Citation - WoS: 3
Citation - Scopus: 3
Ab Initio Simulation of Amorphous BC3
(Elsevier, 2020) Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
We report the structural and electrical properties of an amorphous BC3 model based on ab initio molecular dynamics simulations. The amorphous network is achieved from the melt and has a layer-like structure consisting of mainly hexagonal (six membered) rings as in the crystal. However, the distribution of boron atoms in the noncrystalline configuration appears to differ significantly from that of boron atoms in the crystal. The network is a solid solution and has randomly distributed nanosized graphene-like domains at each layer. Boron atoms have a tendency to form more overcoordinated defects involving with boron-boron homopolar bond(s). The mean coordination of boron and carbon atoms is 3.2 and 3.0, respectively. Interestingly the amorphous configuration is found to have a slightly higher density and bulk modulus than the crystal, which are attributed to the existence of overcoordinated units in the amorphous state. Based on the localization of the band tail states, noncrystalline BC3 is speculated to be a semiconducting material.
Citation - WoS: 6
Citation - Scopus: 6
Absorption Enhancement by Semi-Cylindrical Structures for an Organic Solar Cell Application
(Optical Soc Amer, 2020) Hah, Dooyoung; 01. Abdullah Gül University; 02. Mühendislik Fakültesi; 02.05. Elektrik & Elektronik Mühendisliği
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: 1
Citation - Scopus: 2
Accelerated Artificial Bee Colony Optimization for Cost-Sensitive Neural Networks in Multi-Class Problems
(Wiley, 2025) Hacilar, Hilal; Dedeturk, Bilge Kagan; Ozmen, Mihrimah; Celik, Mehlika Eraslan; Gungor, Vehbi Cagri; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
Metaheuristics are advanced problem-solving techniques that develop efficient algorithms to address complex challenges, while neural networks are algorithms inspired by the structure and function of the human brain. Combining these approaches enables the resolution of complex optimization problems that traditional methods struggle to solve. This study presents a novel approach integrating the ABC algorithm with ANNs for weight optimization. The method is further enhanced by vectorization and parallelization techniques on both CPU and GPU to improve computational efficiency. Additionally, this study introduces a cost-sensitive fitness function tailored for multi-class classification to optimize results by considering relationships between target class levels. It validates these advancements in two critical applications: network intrusion detection and earthquake damage estimation. Notably, this study makes a significant contribution to earthquake damage assessment by leveraging machine learning algorithms and metaheuristics to enhance predictive models and decision-making in disaster response. By addressing the dynamic nature of earthquake damage, this research fills a critical gap in existing models and broadens the understanding of how machine learning and metaheuristics can improve disaster response strategies. In both domains, the ABC-ANN implementation yields promising results, particularly in earthquake damage estimation, where the cost-sensitive approach demonstrates satisfactory outcomes in macro-F1 and accuracy. The best results for macro-F1, weighted-F1, and overall accuracy provides best results with the UNSW-NB15 and earthquake datasets, showing values of 64%, 72%, 68%, and 60%, 80%, and 79%, respectively. Comparative performance evaluations reveal that the proposed parallel ABC-ANN model, incorporating the novel cost-sensitive fitness function and enhanced by vectorization and parallelization techniques, significantly reduces training time and outperforms state-of-the-art methods in terms of macro-F1 and accuracy in both network intrusion detection and earthquake damage estimation.
Citation - Scopus: 49
Activation of Methane by Os+: Guided-Ion and Theoretical Studies
(2013) Armentrout, Peter B.; Parke, Laura G.; Hinton, Christopher S.; Citir, Murat; 01. Abdullah Gül University
Activation of methane by the third-row transition-metal cation Os + is studied experimentally by examining the kinetic energy dependence of reactions of Os+ with CH4 and CD4 using guided-ion-beam tandem mass spectrometry. A flow tube ion source produces Os+ in its electronic ground state and primarily in the ground spin-orbit level. Dehydrogenation to form [Os,C,2 H]++H2 is exothermic, efficient, and the only process observed at low energies for reaction of Os+ with methane, whereas OsH+ dominates the product spectrum at higher energies. The kinetic energy dependences of the cross sections for several endothermic reactions are analyzed to give 0K bond dissociation energies (in eV) of D0(Os+-C)=6.20±0. 21, D0(Os+-CH)=6.77±0.15, and D0(Os +-CH3)=3.00±0.17. Because it is formed exothermically, D0(Os+-CH2) must be greater than 4.71eV, and a speculative interpretation suggests the exothermicity exceeds 0.6eV. Quantum chemical calculations at the B3LYP/def2-TZVPP level show reasonable agreement with the experimental bond energies and with previous theoretical values available. Theory also provides the electronic structures of the product species as well as intermediates and transition states along the reactive potential energy surfaces. Notably, the structure of the dehydrogenation product is predicted to be HOsCH+, rather than OsCH2+, in contrast to previous work. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. © 2013 Elsevier B.V., All rights reserved.
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; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
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: 1
Citation - Scopus: 1
Addressing the Modern Regimes of Urban Spectacle: Revisiting the Ottoman General Exhibition of 1863 in Istanbul
(Sage Publications inc, 2024) Tozoglu, Ahmet Erdem; 01. Abdullah Gül University
One of the most spectacular events of the Ottoman experience of modernity was the inauguration of the Ottoman General Exposition in Istanbul in 1863. The ancient Hippodrome, which is one of the most prominent venues of the city and the setting of memorable celebrations and festivals for centuries, hosted the event and provided the visitors with the opportunity to become part of the modern regimes of gaze and spectacle. This article posits three observer roles to reveal the multilayered structure of urban spectacle in mid-century Istanbul, namely the sultanic gaze, spectacle of the ordinary citizens, and the mediated experience of the foreigner. To understand the particularities of each position, I utilize several visual and textual documents about the exhibition event. Though just a single case in Ottoman urban history, the exposition enables us to understand how the new manner of modern urban spectacle emerged during a spectacular public event in Istanbul.
Citation - WoS: 5
Citation - Scopus: 5
Admissible Invariants of Genus 3 Curves
(Springer Heidelberg, 2015) Cinkir, Zubeyir; 01. Abdullah Gül University; 02.02. Endüstri Mühendisliği; 02. Mühendislik Fakültesi
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.
Adult Zebrafish Brain as a Demyelination Model and Role of WNF Signaling in Remyelination
(Wiley, 2024) Bora, U.; Demirbasoglu, E. S.; Turhanlar-Sahin, E.; Guner, H.; Ozhan, G.; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.02. Moleküler Biyoloji ve Genetik
Citation - WoS: 34
Citation - Scopus: 38
Advances in Micelle-Based Drug Delivery: Cross-Linked Systems
(Bentham Science Publ Ltd, 2017) Isoglu, Ismail Alper; Ozsoy, Yildiz; Isoglu, Sevil Dincer; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
There are several barriers that drug molecules encounter in body beginning from kidney filtration and reticulo-endothelial system (RES) clearance to cellular trafficking. Multifunctional nanocarriers have a great potential for the delivery of drugs by enhancing therapeutic activity of existing methodologies. A variety of nanocarriers are constructed by different material types, which have unique physicochemical properties for drug delivery applications. Micelles formed by amphiphilic polymers are one of the most important drug/nanocarrier formulation products, in which the core part is suitable for encapsulation of hydrophobic agent whereas the outer shell can be utilized for targeting the drug to the disease area. Micelles as self-assembled nanostructures may encounter difficulties in biodistribution of encapsulated drugs because they have a tendency to be dissociated in dilution or high ionic strength. Therefore, therapeutic efficiency is decreased and it requires high amount of drug to be administered to achieve more efficient result. To overcome this problem, covalently stabilized structures produced by cross-linking in core or shell part, which can prevent the micelle dissociation and regulate drug release, have been proposed. These systems can be designed as responsive systems in which cross-links are degradable or hydrolysable under specific conditions such as low pH or reductive environment. These are enhancing characteristics in drug delivery because their cleavage allows the release of bioactive agent encapsulated in the carrier at a certain site or time. This review describes the chemical methodologies for the preparation of cross-linked micelles, and reports an update of latest studies in literature.
Citation - WoS: 3
Citation - Scopus: 3
Alantolactone Ameliorates Graft Versus Host Disease in Mice
(Elsevier, 2024) Odabas, Gul Pelin; Aslan, Kubra; Suna, Pinar Alisan; Kendirli, Perihan Kader; Erdem, Serife; Cakir, Mustafa; Unal, Ekrem; 01. Abdullah Gül University
The anti-inflammatory and immunosuppressive drugs which are used in the treatment of Graft-versus-Host Disease (GVHD) have limited effects in controlling the severity of the disease. In this study, we aimed to investigate the prophylactic effect of Alantolactone (ALT) in a murine model of experimental GVHD. The study included 4 BALB/c groups as hosts: Naive (n = 7), Control GVHD (n = 16), ALT-GVHD (n = 16), and Syngeneic transplantation (n = 10). Busulfan (20 mg/kg/day) for 4 days followed by cyclophosphamide (100 mg/kg/day) were administered for conditioning. Allogeneic transplantation was performed with cells collected from mismatched female C57BL/6, and GVHD development was monitored by histological and flow cytometric assays. Additionally, liver biopsies were taken from GVHD patient volunteers between ages 2-18 (n = 4) and non-GVHD patients between ages 2-50 (n = 5) and cultured ex vivo with ALT, and the supernatants were used for ELISA. ALT significantly ameliorated histopathological scores of the GVHD and improved GVHD clinical scores. CD8+ T cells were shown to be reduced after ALT treatment. More importantly, ALT treatment skewed T cells to a more naive phenotype (CD62L+ CD44-). ALT did not alter Treg cell number or frequency. ALT treatment appears to suppress myeloid cell lineage (CD11c+). Consistent with reduced myeloid lineage, liver and small intestine levels of GM-CSF were reduced in ALT-treated mice. IL-6 gene expression was significantly reduced in the intestinal tissue. Ex vivo ALT-treated liver biopsy samples from GVHD patients showed a trend of decrease in proinflammatory cytokines but there was no statistical significance. Collectively, the data indicated that ALT may have immunomodulatory actions in a preclinical murine GVHD model.
Citation - Scopus: 1
Alzheimer Disease Associated Loci: APOE Single Nucleotide Polymorphisms in Marmara Region
(MDPI, 2024) Ismail, Aya Badeea; Dundar, Mehmet Sait; Erguzeloglu, Cemre Ornek; Ergoren, Mahmut Cerkez; Alemdar, Adem; Sag, Sebnem Ozemri; Temel, Sehime Gulsun; 01. Abdullah Gül University
Alzheimer's disease (AD) is a major global health challenge, especially among individuals aged 65 or older. According to population health studies, Turkey has the highest AD prevalence in the Middle East and Europe. To accurately determine the frequencies of common and rare APOE single nucleotide polymorphisms (SNPs) in the Turkish population residing in the Marmara Region, we conducted a retrospective study analyzing APOE variants in 588 individuals referred to the Bursa Uludag University Genetic Diseases Evaluation Center. Molecular genotyping, clinical exome sequencing, bioinformatics analysis, and statistical evaluation were employed to identify APOE polymorphisms and assess their distribution. The study revealed the frequencies of APOE alleles as follows: epsilon 4 at 9.94%, epsilon 2 at 9.18%, and epsilon 3 at 80.68%. The gender-based analysis in our study uncovered a tendency for females to exhibit a higher prevalence of mutant genotypes across various SNPs. The most prevalent haplotype observed was epsilon 3/epsilon 3, while rare APOE SNPs were also identified. These findings align with global observations, underscoring the significance of genetic diversity and gender-specific characteristics in comprehending health disparities and formulating preventive strategies.
Citation - WoS: 6
Citation - Scopus: 5
Amorphous BC5 From First Principles Calculations
(Elsevier, 2022) Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
A boron-substituted amorphous graphite (BC5) network is generated using a first principles molecular dynamics simulation and its atomic structure and electrical and mechanical properties are discussed in details. The network has a layered structure with primarily hexagonal (six membered) rings and its average coordination is about 3.0. The material is a solid solution having a minor amount of B-B homopolar bonds. It is structurally different from the BC5 crystal or monolayers proposed in the literature. The model is a semimetal material based on a generalized gradient approximation with the Hubbard correction (GGA+U) calculation. When its mechanical properties are concerned, they are comparable with those of graphite or amorphous graphite.
Citation - WoS: 3
Citation - Scopus: 3
Amorphous Boron Arsenide
(Elsevier, 2019) Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
The short-range order and electrical properties of amorphous boron arsenide (BAs) are evaluated by means of ab initio molecular dynamics simulations. The amorphous model is obtained from the fast solidification of the BAs melt and consists of B-rich and As-rich domains. The average coordination number of B- and As-atoms are found as 4.97 and 3.34, respectively. B-atoms have a tendency to form pentagonal pyramidal-like configurations as commonly seen in boron or boron rich materials. Yet B-12 molecules do not develop in the system but the formation of a B-10 cluster is perceived in the network. On the other hand, As-atoms have a trend to structure chain-like motifs and four-membered rings. Amorphization yield about 31% volume expansion in the amorphous network. All these findings reveal that the model shows strong chemical disorder and its short-range order is considerably different than that of the crystal. Amorphization-induced metallization is proposed for BAs.
Amorphous Boron Carbide From Ab Initio Simulations
(Elsevier, 2023) Yildiz, Tevhide Ayca; Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
Citation - WoS: 5
Citation - Scopus: 5
Amorphous Boron Carbide From Ab Initio Simulations
(Elsevier, 2020) Yildiz, Tevhide Ayca; Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
An amorphous boron carbide (a-B4C) model is generated by means of ab-initio molecular dynamics calculations within a generalized gradient approximation and its structural, mechanical and electrical features are discussed in details. The mean coordination number of B and C atoms is estimated to be 5.29 and 4.17, respectively. The pentagonal pyramid-like motifs for B atoms, having sixfold coordination, are the main building units in a-B4C and some of which involve with the development of B-12 icosahedra. On the other hand, the fourfold-coordinated units are the leading configurations for C atoms. Surprisingly the formation of C-C bonds is found to be less favorable in the noncrystalline network, compared to the crystal. a-B4C is a semiconducting material having an energy band gap considerably less than that of the crystal. A noticeably decrease in the mechanical properties of B4C is observed by amorphization. Nonetheless a-B4C is categorized as a hard material due to its high Vickers hardness of about 24 GPa.
Citation - WoS: 2
Citation - Scopus: 2
Amorphous Boron Carbonitride (BC4N) From Ab Initio Simulations
(Elsevier, 2024) Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
This study utilizes ab initio molecular dynamics simulations to explore the structure and properties of amorphous boron carbonitride (a-BC4N). A 432-atom model, generated via a conventional melt-and-quench technique, exhibits a graphite-like structure with all elements possessing an average coordination number of about 3.0. C atoms dominate within individual layers, interspersed with distinct BN domains. This atomic arrangement deviates considerably from that proposed for crystalline BC4N structures. Despite this structural variation, the aBC4N model is likely a narrow band gap semiconductor (0.15 eV), similar to its crystalline counterparts. In terms of mechanical properties, a-BC4N demonstrates similarities with various layered materials while exhibiting a notably larger bulk modulus.

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