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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: 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: 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 - 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: 17
Citation - Scopus: 30
A Performance and profit oriented data replication strategy for cloud systems
(Ieee, 2016) Tos, Uras; Mokadem, Riad; Hameurlain, Abdelkader; Ayav, Tolga; Bora, Sebnem; Ayav, Tolga; Bilgisayar Mühendisliği Bölümü
In today's world, tenants of cloud systems expect timely responses to queries that process ever-increasing sizes of data. However, most cloud providers offer their services without any performance guarantees to their tenants. In this paper we propose a data replication strategy that aims to satisfy performance guarantees for the tenant while ensuring profitability of the cloud provider. Our strategy estimates the response time of the queries, as well as the expenditures that affect the profitability of the cloud provider. The decision of whether to perform replication is determined by the fulfillment of these two criteria. Validity of the proposed strategy is provided by means of a simulation study.
Citation - WoS: 9
Citation - Scopus: 8
Synthesis and characterization of novel high temperature structural adhesives based on nadic end capped MDA-BTDA-ODA copolyimide
(Iop Publishing Ltd, 2018) Acar, Oktay; Varis, Serhat; Isik, Tugba; Tirkes, Seha; Demir, Mustafa M.; Demir, Mustafa
A series of novel copolyimide structural adhesives were synthesized using 4,4'-diaminodiphenyl-methane (MDA), 3,4'-oxydianiline (ODA) and 3,3',4,4'-benzophenonetetracarboxylic acid dianhy-dride (BTDA) as co-monomers, and nadic anhydride as an end cap reagent. The adhesives with different MDA and ODA contents were examined in terms of their structure, thermal stability, mechanical properties, and adhesive performance. They have glass transition temperatures (T-g) about 400 degrees C, with thermal stability up to 500 degrees C. The effect of diamine monomer compositions on adhesion performance and processability of the copolyimides were studied. The copolyimides exhibited adhesion strength up to 16.3 MPa at room temperature. Nadic end capped MDA-BTDA-ODA copolyimide resins gained adjustable and controllable processability with the addition of ether bridged aromatic segments. The copolyimide adhesive with equimolar composition of MDA: ODA is distinguished form the both commercial PMR-15 and LARC RP-46 polyimides in terms of its better processability and mechanical performance.
Citation - WoS: 10
Transcriptomics analysis of circular RNAs differentially expressed in apoptotic HeLa cells
(Frontiers Media Sa, 2019) Yaylak, Bilge; Erdogan, Ipek; Akgul, Bunyamin; Akgül, Bünyamin
Apoptosis is a form of regulated cell death that plays a critical role in survival and developmental homeostasis. There are numerous reports on regulation of apoptosis by protein-coding genes as well as small non-coding RNAs, such as microRNAs. However, there is no comprehensive investigation of circular RNAs (circRNA) that are differentially expressed under apoptotic conditions. We have performed a transcriptomics study in which we first triggered apoptosis in HeLa cells through treatment with four different agents, namely cisplatin, doxorubicin, TNF-alpha and anti-Fas mAb. Total RNAs isolated from control as well as treated cells were treated with RNAse R to eliminate the linear RNAs. The remaining RNAs were then subjected to deep-sequencing to identify differentially expressed circRNAs. Interestingly, some of the dys-regulated circRNAs were found to originate from protein-coding genes well-documented to regulate apoptosis. A number of candidate circRNAs were validated with qPCR with or without RNAse R treatment as well. We then took advantage of bioinformatics tools to investigate the coding potential of differentially expressed RNAs. Additionally, we examined the candidate circRNAs for the putative miRNA-binding sites and their putative target mRNAs. Our analyses point to a potential for circRNA-mediated sponging of miRNAs known to regulate apoptosis. In conclusion, this is the first transcriptomics study that provides a complete circRNA profile of apoptotic cells that might shed light onto the potential role of circRNAs in apoptosis.
Citation - WoS: 13
Citation - Scopus: 18
Triboluminescent electrospun mats with blue-green emission under mechanical force
(American Chemical Society, 2017) Incel, Anil; Varlikli, Canan; McMillen, Colin D.; Demir, Mustafa M.; Demir, Mustafa
Fibrous mechanosensing elements can provide information about the direction of crack propagation and the mechanism of material failure when they are homogeneously dispersed into the bulk volume of materials. A fabrication strategy of fibrous systems showing triboluminescent (TL) responses is in high demand for such applications. In this work, micrometer-sized Cu(NCS) (py)(2)(PPh3) crystals were synthesized, and polymeric fibrous mats containing the TL crystals were obtained via electrospinning as a stress probe for the determination of mechanical impact. Four different polymeric systems have been employed (PMMA, PS, PU, and PVDF), and the mechano-optical sensing performance of electrospun mats of the polymer-crystal composites was measured. Photophysical properties (quantum yield, band gap, and broadness of the emission) of the TL crystal/electrospun mat composites were also studied. TL and PL emission maxima of the PU-based composite mat show identical behavior due to the chemical affinity between the two structures and the smallest fiber diameter. Moreover, the PU fiber mats exhibit long-lived bluish-green emission persisting over a large number of drops.

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