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Citation - WoS: 17
Aggregatibacter actinomycetemcomitans: GroEL protein promotes conversion of human CD4+T cells into IFNγ IL10 producing Tbet+Th1 cells
(Public Library Science, 2012) Saygili, Tahsin; Akincilar, Semih Can; Akgul, Bunyamin; Nalbant, Ayten; Akgül, Bünyamin
One of the heat shock family protein (Hsp) expressing bacteria is the gram negative, periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa). A. actinomycetemcomitans' Hsp is a 64-kDa GroEL-protein, which has been shown to influence the host cells. In this study we used recombinant A. actinomycetemcomitans GroEL (rAaGroEL) protein as a model antigen to study GroEL-mediated T cell immune response. Human peripheral mononuclear cells (PBMCs), when stimulated with recombinant rAaGroEL, expressed early activation marker CD69 and IL-2R (CD25). CD25 and CD69 expressions were higher in CD4+ T cells compared to CD8+ T cells. rAaGroEL-responding CD4+ T cells expressed IL-10, IFN gamma and TNF alpha cytokines. Interestingly, there were also IL-10 and IFN gamma double cytokine producing CD4+ T cells. Additionally, IFN gamma expressing CD4+ T cells were also T-bet positive. Altogether the results suggest that rAaGroEL protein affects CD4+ T cells to differentiate into IFN gamma IL10-secreting T-bet+ Th1 cells.
Citation - WoS: 4
Citation - Scopus: 4
Convergence analysis and numerical solution of the benjamin-bona-mahony equation by lie-trotter splitting
(Tubitak Scientific & Technological Research Council Turkey, 2018) Zurnaci, Fatma; Gucuyenen Kaymak, Nurcan; Seydaoglu, Muaz; Tanoglu, Gamze
In this paper, an operator splitting method is used to analyze nonlinear Benjamin-Bona-Mahony-type equations. We split the equation into an unbounded linear part and a bounded nonlinear part and then Lie-Trotter splitting is applied to the equation. The local error bounds are obtained by using the approach based on the differential theory of operators in a Banach space and the quadrature error estimates via Lie commutator bounds. The global error estimate is obtained via Lady Windermere's fan argument. Finally, to confirm the expected convergence order, numerical examples are studied.
Dose Enhancement Effects of Different-Sized Nanoparticles on Tumors and Surrounding Tissues Using Geant4 Track Structure Simulation
(Sciendo, 2025) Tugrul, Taylan
Free radicals, which are the most important contributors to cell death in radiotherapy, appear to increase in the presence of nanoparticles. The nanoparticles can be localized within tumor tissues, providing enhanced protection to normal tissues during radiation therapy while achieving significant dose enhancement within tumors. In our study, the dose effects of different sizes of spherical gold nanoparticles were analyzed in the tumor environment and surrounding tissues under photon radiation at various energies with the track structure code using the TOPAS interface. The nano-lattice method was used to create an environment similar to the diffusion-based distribution of nanoparticles in the medium. The Geant4-DNA code was utilized for simulations conducted in this study. Although the interaction cross-section is lower at MeV photon energy levels, the results still indicate an increase in dose due to the presence of nanoparticles (NPs) in the medium. As the size of gold nanoparticles increases, the spread in dose enhancements becomes more apparent. The lowest average dose enhancement factor (DEF) values at lateral points were observed for 28.4 nm NPs at MeV photon energy. In this study, the contribution of gold nanoparticles to dose enhancement was investigated using the Monte Carlo track structure algorithm. Additionally, the potential dose variations in the surrounding tissue resulting from the introduction of gold nanoparticles were analyzed. Even though an increase in DEF values was observed at MeV energy levels, these values might vary with a better understanding of biological effects such as cell cycle disruption, oxidative stress, and impaired DNA repair. This study offers valuable insights into nanoparticle-assisted radiation applications, including optimal nanoparticle size and applicable energy levels. By enhancing our understanding of the effects on tissues beyond the tumor and within the surrounding environment, it aims to provide critical information for researchers in the field and make a meaningful contribution to the literature.
Dose Enhancement Effects of Different-Sized Nanoparticles on Tumors and Surrounding Tissues Using Geant4 Track Structure Simulation
(Sciendo, 2025) Tugrul, Taylan
Free radicals, which are the most important contributors to cell death in radiotherapy, appear to increase in the presence of nanoparticles. The nanoparticles can be localized within tumor tissues, providing enhanced protection to normal tissues during radiation therapy while achieving significant dose enhancement within tumors. In our study, the dose effects of different sizes of spherical gold nanoparticles were analyzed in the tumor environment and surrounding tissues under photon radiation at various energies with the track structure code using the TOPAS interface. The nano-lattice method was used to create an environment similar to the diffusion-based distribution of nanoparticles in the medium. The Geant4-DNA code was utilized for simulations conducted in this study. Although the interaction cross-section is lower at MeV photon energy levels, the results still indicate an increase in dose due to the presence of nanoparticles (NPs) in the medium. As the size of gold nanoparticles increases, the spread in dose enhancements becomes more apparent. The lowest average dose enhancement factor (DEF) values at lateral points were observed for 28.4 nm NPs at MeV photon energy. In this study, the contribution of gold nanoparticles to dose enhancement was investigated using the Monte Carlo track structure algorithm. Additionally, the potential dose variations in the surrounding tissue resulting from the introduction of gold nanoparticles were analyzed. Even though an increase in DEF values was observed at MeV energy levels, these values might vary with a better understanding of biological effects such as cell cycle disruption, oxidative stress, and impaired DNA repair. This study offers valuable insights into nanoparticle-assisted radiation applications, including optimal nanoparticle size and applicable energy levels. By enhancing our understanding of the effects on tissues beyond the tumor and within the surrounding environment, it aims to provide critical information for researchers in the field and make a meaningful contribution to the literature.
Effect of Geometry and Fiber Type on Energy Absorption in Polymer Based Composite Crash Boxes: An Experimental Study
(Wiley, 2025) Kosedag, Ertan; Araz, Zumray; Erkek, Baran
Vehicle crash boxes, mounted on the chassis before the bumper, absorb impact energy to protect passengers, but their metal construction adds weight, prompting increased research into lightweight composite alternatives with comparable strength. In this study, energy absorption values (EA), specific energy absorption (SEA), peak forces (PF) and crashing force efficiency (CFE) of carbon fiber, glass fiber, and aramid fiber reinforced composite crash boxes with epoxy resin matrix were compared. Composite crash boxes with different geometries were fabricated using vacuum infusion method in three different geometries: hexagonal, circle, and square. Unlike hand lay-up and prepreg winding methods, vacuum infusion method was chosen because it provides homogeneous distribution of epoxy resin. The crashworthiness of the samples was evaluated through quasi-static compression tests. The best energy absorption performance was obtained with the hexagonal carbon fiber-reinforced composite crash box (246.17 J), corresponding to a specific energy absorption of 8.57 J/g. Although aramid fiber-reinforced specimens showed lower energy absorption, they exhibited the highest crash force efficiency among all tested configurations. These results confirm the significant influence of both fiber type and geometry on the crashworthiness of polymer-based composite crash boxes. The study highlights that hexagonal geometry consistently provided superior energy absorption across all fiber types, while carbon fiber-reinforced composites demonstrated the best overall mechanical performance, making them strong candidates for lightweight crashworthiness applications.
Effect of Geometry and Fiber Type on Energy Absorption in Polymer Based Composite Crash Boxes: An Experimental Study
(Wiley, 2025) Kosedag, Ertan; Araz, Zumray; Erkek, Baran
Vehicle crash boxes, mounted on the chassis before the bumper, absorb impact energy to protect passengers, but their metal construction adds weight, prompting increased research into lightweight composite alternatives with comparable strength. In this study, energy absorption values (EA), specific energy absorption (SEA), peak forces (PF) and crashing force efficiency (CFE) of carbon fiber, glass fiber, and aramid fiber reinforced composite crash boxes with epoxy resin matrix were compared. Composite crash boxes with different geometries were fabricated using vacuum infusion method in three different geometries: hexagonal, circle, and square. Unlike hand lay-up and prepreg winding methods, vacuum infusion method was chosen because it provides homogeneous distribution of epoxy resin. The crashworthiness of the samples was evaluated through quasi-static compression tests. The best energy absorption performance was obtained with the hexagonal carbon fiber-reinforced composite crash box (246.17 J), corresponding to a specific energy absorption of 8.57 J/g. Although aramid fiber-reinforced specimens showed lower energy absorption, they exhibited the highest crash force efficiency among all tested configurations. These results confirm the significant influence of both fiber type and geometry on the crashworthiness of polymer-based composite crash boxes. The study highlights that hexagonal geometry consistently provided superior energy absorption across all fiber types, while carbon fiber-reinforced composites demonstrated the best overall mechanical performance, making them strong candidates for lightweight crashworthiness applications.
Citation - WoS: 4
Citation - Scopus: 9
End-to-end security implementation for mobile devices using TLS protocol
(Springer France, 2006) Kayayurt, Baris; Tuglular, Tugkan; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
End-to-end security has been an emerging need for mobile devices with the widespread use of personal digital assistants and mobile phones. Transport Layer Security Protocol (TLS) is an end-to-end security protocol that is commonly used on the Internet, together with its predecessor, SSL protocol. By implementing TLS protocol in the mobile world, the advantage of the proven security model of this protocol can be utilized. The main design goals of mobile end-to-end security protocol are maintainability and extensibility. Cryptographic operations are performed with a free library, Bouncy Castle Cryptography Package. The object oriented architecture of proposed end-to-end security protocol implementation makes the replacement of this library with another cryptography package easier. The implementation has been experimented with different cases, which represent use of different cryptographic algorithms.
Citation - WoS: 73
Evidence for water-tuned structural differences in proteins: an approach emphasizing variations inlocal hydrophilicity
(Public Library Science, 2012) Akdogan, Yasar; Reichenwallner, Joerg; Hinderberger, Dariush
We present experimental evidence for the significant effect that water can have on the functional structure of proteins in solution. Human (HSA) and Bovine Serum Albumin (BSA) have an amino acid sequence identity of 75.52% and are chosen as model proteins. We employ EPR-based nanoscale distance measurements using double electron-electron resonance (DEER) spectroscopy and both albumins loaded with long chain fatty acids (FAs) in solution to globally (yet indirectly) characterize the tertiary protein structures from the bound ligands' points of view. The complete primary structures and crystal structures of HSA and as of recently also BSA are available. We complement the picture as we have recently determined the DEER-derived solution structure of HSA and here present the corresponding BSA solution structure. The characteristic asymmetric FA distribution in the crystal structure of HSA can surprisingly be observed by DEER in BSA in solution. This indicates that the BSA conformational ensemble in solution seems to be narrow and close to the crystal structure of HSA. In contrast, for HSA in solution a much more symmetric FA distribution was found. Thus, conformational adaptability and flexibility dominate in the HSA solution structure while BSA seems to lack these properties. We further show that differences in amino acid hydropathies of specific structural regions in both proteins can be used to correlate the observed difference in the global (tertiary) solution structures with the differences on the primary structure level.
Citation - WoS: 23
Exact solutions of forced burgers equations with time variable coefficients
(Elsevier, 2013) Buyukasik, Sirin A.; Pashaev, Oktay K.
In this paper, we consider a forced Burgers equation with time variable coefficients of the form U-t + (mu(t)/mu(t))U + UUx = (1/2 mu(t))U-xx - omega(2)(t)x, and obtain an explicit solution of the general initial value problem in terms of a corresponding second order linear ordinary differential equation. Special exact solutions such as generalized shock and multi-shock waves, triangular wave, N-wave and rational type solutions are found and discussed. Then, we introduce forced Burgers equations with constant damping and an exponentially decaying diffusion coefficient as exactly solvable models. Different type of exact solutions are obtained for the critical, over and under damping cases, and their behavior is illustrated explicitly. In particular, the existence of inelastic type of collisions is observed by constructing multi-shock wave solutions, and for the rational type solutions the motion of the pole singularities is described. (c) 2012 Elsevier B.V. All rights reserved.
Citation - WoS: 3
Exactly solvable madelung fluid and complex burgers equations: a quantum sturm-liouville connection
(Springer, 2012) Buyukasik, Sirin A.; Pashaev, Oktay K.
Quantum Sturm-Liouville problems introduced in our paper (BuyukaAYA +/- k et al. in J Math Phys 50:072102, 2009) provide a reach set of exactly solvable quantum damped parametric oscillator models. Based on these results, in the present paper we study a set of variable parametric nonlinear Madelung fluid models and corresponding complex Burgers equations, related to the classical orthogonal polynomials of Hermite, Laguerre and Jacobi types. We show that the nonlinear systems admit direct linearazation in the form of Schrodinger equation for a parametric harmonic oscillator, allowing us to solve exactly the initial value problems for these equations by the linear quantum Sturm-Liouville problem. For each type of equations, dynamics of the probability density and corresponding zeros, as well as the complex velocity field and related pole singularities are studied in details.
Fourier analysis-based automatic test pattern generation for combinational circuits
(Ieee, 2015) Ayav, Tolga; Ayav, Tolga; Bilgisayar Mühendisliği Bölümü
Fourier analysis of boolean functions has attracted great attention from computer scientists in the last decade but it still has few application areas. This work presents a Fourier analysis-based automatic test pattern generation method for combinational circuits.
Citation - WoS: 5
Heme binding constricts the conformational dynamics of the cytochrome: Heme binding cavity
(Amer Chemical Soc, 2012) Akdogan, Yasar; Anbazhagan, Veerappan; Hinderberger, Dariush; Schneider, Dirk
Cytochrome b(559)' is a transmembrane protein formed by homodimerization of the 44-residue PsbF polypeptide and noncovalent binding of a heme cofactor. The PsbF polypeptide can dimerize in the absence and presence of heme. To monitor structural alterations associated with binding of heme to the apocytochrome, we analyzed the apo- and holo-cytochrome structure by electron paramagnetic resonance spectroscopy. Spin labeling of amino acids located close to the heme binding domain of the cytochrome revealed that the structure of the heme binding domain is unconstrained in the absence of heme. Heme binding restricts the conformational dynamics of the heme binding domain, resulting in the structurally more constricted holo-cytochrome structure.
Citation - Scopus: 1
Hydrothermal Liquefaction of Sinapis Arvensis Biomass Using TiO2-Supported Metal Catalysts: A Study on Bio-Oil Yield and Composition
(Elsevier, 2026) Durak, Halil; Genel, Salih; Genel, Yasar
The development of catalytic systems for hydrothermal liquefaction (HTL) is crucial for transforming lignocellulosic biomass into biofuels with high energy density. This research investigates the HTL process of Sinapis arvensis biomass using TiO2-supported catalysts, specifically Fe, Al, and Fe-Al, at temperatures from 275-325 degrees C. The catalysts were synthesized through incipient wetness impregnation and characterized using techniques like X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), X-ray fluorescence (XRF), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX), and inductively coupled plasma optical emission spectrometry (ICP-OES) to evaluate element distribution and surface chemistry. Findings show that the Al/TiO2 catalyst boosted lighter bio-oil production via acid-catalyzed dehydration and decarboxylation, while the Fe/TiO2 catalyst favored heavier oils through redox-assisted depolymerization. The Fe-Al/TiO2 bifunctional catalyst exhibited superior biomass conversion, yielding more aliphatic hydrocarbons. Gas chromatography-mass spectrometry (GC-MS) revealed how catalysts influenced product distributions, increasing monoaromatic and aliphatic compounds and reducing oxygenated entities. Elemental analysis confirmed higher carbon content, lower oxygen levels, and improved higher heating values (HHVs) in catalyzed bio-oils, indicating enhanced fuel quality.
Citation - Scopus: 1
Hydrothermal Liquefaction of Sinapis Arvensis Biomass Using TiO2-Supported Metal Catalysts: A Study on Bio-Oil Yield and Composition
(Elsevier, 2026) Durak, Halil; Genel, Salih; Genel, Yasar
The development of catalytic systems for hydrothermal liquefaction (HTL) is crucial for transforming lignocellulosic biomass into biofuels with high energy density. This research investigates the HTL process of Sinapis arvensis biomass using TiO2-supported catalysts, specifically Fe, Al, and Fe-Al, at temperatures from 275-325 degrees C. The catalysts were synthesized through incipient wetness impregnation and characterized using techniques like X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), X-ray fluorescence (XRF), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX), and inductively coupled plasma optical emission spectrometry (ICP-OES) to evaluate element distribution and surface chemistry. Findings show that the Al/TiO2 catalyst boosted lighter bio-oil production via acid-catalyzed dehydration and decarboxylation, while the Fe/TiO2 catalyst favored heavier oils through redox-assisted depolymerization. The Fe-Al/TiO2 bifunctional catalyst exhibited superior biomass conversion, yielding more aliphatic hydrocarbons. Gas chromatography-mass spectrometry (GC-MS) revealed how catalysts influenced product distributions, increasing monoaromatic and aliphatic compounds and reducing oxygenated entities. Elemental analysis confirmed higher carbon content, lower oxygen levels, and improved higher heating values (HHVs) in catalyzed bio-oils, indicating enhanced fuel quality.
Citation - WoS: 4
The importance of protein profiling in the diagnosis and treatment of hematologic malignancies
(Galenos Yayincilik, 2011) Sanli-Mohamed, Gulsah; Turan, Taylan; Ekiz, Huseyin Atakan; Baran, Yusuf; Baran, Yusuf
Proteins are important targets in cancer research because malignancy is associated with defects in cell protein machinery. Protein profiling is an emerging independent subspecialty of proteomics that is rapidly expanding and providing unprecedented insight into biological events. Quantitative assessment of protein levels in hematologic malignancies seeks a comprehensive understanding of leukemia-associated protein patterns for use in aiding diagnosis, follow-up treatment, and the prediction of clinical outcomes. Many recently developed high-throughput proteomic methods can be applied to protein profiling. Herein the importance of protein profiling, its exploitation in leukemia research, and its clinical usefulness in the treatment and diagnosis of various cancer types, and techniques for determining changes in protein profiling are reviewed. (Turk J Hematol 2011; 28: 1-14)
Citation - WoS: 7
Citation - Scopus: 9
Input contract testing of graphical user interfaces
(World Scientific Publ Co Pte Ltd, 2016) Tuglular, Tugkan; Belli, Fevzi; Linschulte, Michael; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
User inputs are critical for the security, safety, and reliability of software systems. This paper proposes a new concept called user input contracts, which is an integral part of a design-by-contract supplemented development process, and a model-based testing approach to detect violations of user input contracts. The approach generates test cases from an input contract integrated with graph-based model of user interface specification and applies them to the system under consideration. The paper presents a proof-of-concept tool that has been developed and used to validate the approach by experiments. The experiments are conducted on a web-based system for marketing tourist services to analyze input robustness of system under consideration with respect to user input contracts.
Mixed Hydrogenetic-Hydrothermal Genesis of Quaternary Ferromanganese Nodules in a Tectonically Active Lacustrine Basin, Eastern Türkiye
(Pergamon-Elsevier Science Ltd, 2025) Uner, Tijen
This study presents a detailed investigation of the mineralogical, geochemical, and rare earth element (REE) characteristics of ferromanganese nodules found within Quaternary lacustrine sediments in the Agri region of Eastern Anatolia, T & uuml;rkiye. These nodules, primarily composed of goethite and manganite with minor quartz, exhibit botryoidal and colloform textures typical of low-temperature diagenetic environments. Raman and XRD analyses identified significant iron and manganese mineral phases, while SEM-EDX revealed trace amounts of Co, Ni, and Zn associated with these phases. Chondrite-normalized REE patterns demonstrate light REE enrichment, a weak negative europium anomaly (EuN/Eu* = 0.69-0.84), and variable cerium anomalies (CeN/Ce* ranging from 0.74 to 1.95, corresponding to both weak negative and positive Ce anomalies), indicating a mixed hydrogenous and hydrothermal origin under fluctuating redox conditions. These geochemical signatures, together with sedimentological evidence, suggest formation within a restricted lacustrine environment characterized by episodic anoxia and limited detrital input. The results contribute to a broader understanding of Fe-Mn mineralization in continental settings and underscore the influence of volcanic and tectonic processes on nodule genesis.
Mixed Hydrogenetic-Hydrothermal Genesis of Quaternary Ferromanganese Nodules in a Tectonically Active Lacustrine Basin, Eastern Türkiye
(Pergamon-Elsevier Science Ltd, 2025) Uner, Tijen
This study presents a detailed investigation of the mineralogical, geochemical, and rare earth element (REE) characteristics of ferromanganese nodules found within Quaternary lacustrine sediments in the Agri region of Eastern Anatolia, T & uuml;rkiye. These nodules, primarily composed of goethite and manganite with minor quartz, exhibit botryoidal and colloform textures typical of low-temperature diagenetic environments. Raman and XRD analyses identified significant iron and manganese mineral phases, while SEM-EDX revealed trace amounts of Co, Ni, and Zn associated with these phases. Chondrite-normalized REE patterns demonstrate light REE enrichment, a weak negative europium anomaly (EuN/Eu* = 0.69-0.84), and variable cerium anomalies (CeN/Ce* ranging from 0.74 to 1.95, corresponding to both weak negative and positive Ce anomalies), indicating a mixed hydrogenous and hydrothermal origin under fluctuating redox conditions. These geochemical signatures, together with sedimentological evidence, suggest formation within a restricted lacustrine environment characterized by episodic anoxia and limited detrital input. The results contribute to a broader understanding of Fe-Mn mineralization in continental settings and underscore the influence of volcanic and tectonic processes on nodule genesis.
Multimodal Prediction of Pathological Complete Response in Esophageal Cancer Using Automated Machine Learning and Variational Autoencoder-Based Synthetic Data Augmentation
(Amer Assoc Cancer Research, 2025) Dincer, Sefika; Tugrul, Taylan; Kara, Mahmut; Aldemir, Mehmet Naci
Multimodal Prediction of Pathological Complete Response in Esophageal Cancer Using Automated Machine Learning and Variational Autoencoder-Based Synthetic Data Augmentation
(Amer Assoc Cancer Research, 2025) Dincer, Sefika; Tugrul, Taylan; Kara, Mahmut; Aldemir, Mehmet Naci

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