WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Editorial What Does the Water Inside the Brain Tell Us? Diffusion Tensor Imaging(Sciendo, 2018-10-01) Acer, Niyazi; Dundar, Mehmet Sait; Bastepe-Gray, SerapThe brain consist of about 75 percent water. Diffusion tensor imaging (DTI) is an advanced magnetic resonance (MR) technique imaging that has been developed for diagnostic and research in medicine. It can be use DTI tractography to better understand degenerating axons of white matter lesions in some neurological diseases such as MS, AD, trauma, cerebral ischemia, epilepsy, brain tumors and metabolic disorders.Article Use of Confocal Microscopy to Monitor Structural Transformations in Nanopillars Based on DNA and CdSe/CdZnSe Quantum Dots(Springer, 2023-06-24) Motevich, I. G.; Erdem, T.; Akrema, A.; Maskevich, S. A.; Strekal, N. D.Chip system prototypes in the form of nanopillars were created from DNA complexes with CdSe/CdZnSe/ZnS quantum dots immobilized on a plasmonic gold fi lm by the use of vacuum deposition technology and inorganic synthesis. The design and presence of terminal DNA labeled with Cy3 cyanine dyes makes it possible to carry out the hybridization reaction of this terminal strand with complementary DNA and to control the process by variation of the giant Raman scattering (GRS) and the fluorescence signal. The effect of molecular recognition of complementary DNA is accompanied by a change in the GRS spectrum, a 20-fold increase in the fluorescence intensity, and a decrease in the duration of fluorescence decay.Conference Object Twist-Bend Instability of a Cantilever Beam Subjected to an End Load via Homotopy Perturbation Method(Amer Inst Physics, 2018) Yucesoy, Ahmet; Coskun, Safa Bozkurt; Atay, Mehmet Tarik; Cesoy, AhmetIn this article, twist-bend buckling analysis of a cantilever beam subjected to a concentrated end load is conducted using Homotopy Perturbation Method (HPM). Even in the linear stability analysis, obtaining an exact solution for some cases is not an easy task. However, by the use of HPM this difficulty can be overcome easily. This issue is presented with a case study and the results show that HPM can be used successfully in the analysis of twist-bend buckling of beams.Article Citation - WoS: 1Citation - Scopus: 2Tomatidine, a Steroidal Alkaloid, Synergizes With Cisplatin to Inhibit Cell Viability and Induce Cell Death Selectively on FLT3-ITD+ Acute Myeloid Leukemia Cells(Humana Press inc, 2024-07-11) Ayvaz, Havva Berre; Yenigul, Munevver; Akcok, Emel Basak Gencer; Gencer Akçok, Emel BaşakBackgroundAcute Myeloid Leukemia (AML) is a hematological cancer that frequently presents with a range of side effects and drug resistance during anticancer drug treatment. The current study aims to achieve increased efficacy by combining lower doses of cisplatin with increasing concentrations of tomatidine in AML cells to increase efficacy.MethodsAnti-proliferative effects of single and combination of cisplatin and tomatidine were assessed via MTT cell viability assay. The Annexin V/Propidium Iodide Double Staining method was used to measure the apoptotic effects of combined tomatidine and cisplatin treatment. Then, Western Blot analysis was performed to measure Poly (ADP-ribose) polymerase (PARP) and Caspase-3 protein expression levels.ResultsCisplatin treatment with lower concentrations displayed high cytotoxic effects on AML cells, compared with tomatidine. The combination of the Inhibitory Concentration (IC) 20 value of cisplatin and increasing doses of tomatidine exhibited a significant decrease in cell viability relative to single treatments. The combination index analysis revealed a mild synergistic effect of cisplatin IC20 and varying tomatidine doses. The apoptosis induced when cisplatin was combined with 500 mu M tomatidine by almost 20%, while the percentage of apoptosis in combination with 1 mM tomatidine was measured by 50% for both cell lines. The upregulation of proapoptotic cleaved-PARP (3.2 and 1.08-fold for THP-1 and MOLM-13, respectively) and downregulation in Caspase-3 (0.23 and 0.13-fold for THP-1 and MOLM-13, respectively) was detected.ConclusionsTogether, the study indicated that when tomatidine combined with cisplatin on AML cell lines, a combinatorial anti-proliferative and apoptotic effect is observed. The combination of cisplatin with tomatidine may be a promising approach.Conference Object Citation - WoS: 2Citation - Scopus: 1The Numerical Solutions for Stiff Ordinary Differential Equations by Using Interpolated Variational Iteration Method With Comparison to Exact Solutions(Amer Inst Physics, 2018) Ciftci, Cihan; Cayci, Hatice Sinem Sas; Atay, Mehmet Tarik; Toker, Batuhan; Guncan, Berkay; Yildirim, Afsin TalhaRecently proposed Interpolated Variational Iteration Method (IVIM) is used to find numerical solutions of stiff ordinary differential equations for both linear and nonlinear problems. The examples are given to illustrate the accuracy and effectiveness of IVIM method and IVIM results are compared with exact results. In recent analytical approximate methods based studies related to stiff ordinary differential equations, problems were solved by Adomian Decomposition Method and VIM and Homotopy Perturbation Method, Homotopy Analysis Method etc. In this study comparisons with exact solutions reveal that the Interpolated Variational Iteration Method (IVIM) is easy to implement. In fact, this method is promising methods for various systems of linear and nonlinear stiff ordinary differential equations as an initial value problem. Furthermore, IVIM is giving very satisfactory solutions when compared to exact solutions for nonlinear cases depending on the stiffness ratio of the stiff system to be solved.Article Citation - WoS: 3Citation - Scopus: 1The New Visual Culture in Eighteenth-Century Istanbul: Building Up New Shore Kiosks and Gardens on the Outskirts of the Royal Palace(Routledge Journals, Taylor & Francis Ltd, 2019-11-14) Tozoglu, Ahmet ErdemThis article examines the construction and expansion of a less-known royal shore kiosk complex in Istanbul, namely the Shore Palace near the Cannon Gate (Topkapisi Sahil Sarayi) or Summer Harem, which was built on the outskirts of the royal palace complex in the eighteenth century, to interpret the changing features of royal residential culture and spatial practices. In this article, I aim to propose a new thematic frame based on the central role of the issue of visuality to examine the shifting cultural paradigm of eighteenth-century royal patronage. The eighteenth century witnessed the physical expansion of the complex and renovation of the furnishings several times and the official records of these activities provide us with invaluable information for the visual construction of these buildings, which were torn down after a devastating fire in 1862. Furthermore, the choice of location and all physical changes in the interiors and gardens demonstrate the spatial results of the changing codes of visual culture in the cityscape. In this respect, examination of this case enables us to discuss how the new visual culture was adopted and exercised in and around the royal palace gardens by the royal court members.Conference Object Citation - WoS: 3Citation - Scopus: 3Template Scoring Methods for Protein Torsion Angle Prediction(Springer-Verlag Berlin, 2015) Aydin, Zafer; Baker, David; Noble, William StaffordPrediction of backbone torsion angles provides important constraints about the 3D structure of a protein and is receiving a growing interest in the structure prediction community. In this paper, we introduce a three-stage machine learning classifier to predict the 7-state torsion angles of a protein. The first two stages employ dynamic Bayesian and neural networks to produce an ab-initio prediction of torsion angle states starting from sequence profiles. The third stage is a committee classifier, which combines the ab-initio prediction with a structural frequency profile derived from templates obtained by HHsearch. We develop several structural profile models and obtain significant improvements over the Laplacian scoring technique through: (1) scaling templates by integer powers of sequence identity score, (2) incorporating other alignment scores as multiplicative factors (3) adjusting or optimizing parameters of the profile models with respect to the similarity interval of the target. We also demonstrate that the torsion angle prediction accuracy improves at all levels of target-template similarity even when templates are distant from the target. The improvement is at significantly higher rates as template structures gradually get closer to target.Article Target Attractor Formed via Fractional Feedback Control(Yildiz Technical Univ, 2021) Borisenok, SergeyWe discuss here the stabilization problem for an ordinary differential equation (ODE) dynamical model. To make such a control, one can form a Kolesnikov's subset attracting the phase trajectories to its neighborhood in the phase space via defining the appropriate feedback signal. Kolesnikov's target attractor algorithm provides the exponential convergence, but at the same time it demands the permanent power supply pumping the energy to the system even if the control goal is achieved. To decrease the power cost of Kolesnikov's control, we re-formulate the feedback in the form of Caputo's fractional derivative. In this case the solution to the ODE together with the feedback control signal could be found with the Rida-Arafa method based on the generalized Mittag-Leffler function. We prove that for the certain constraints over the initial condition and the target stabilization level, the integer-dimensional Kolesnikov algorithm can be replaced with the fractional target attractor feedback to provide the minimal power cost.Conference Object Target Attractor Tracking of Relative Phase in Bosonic Josephson Junction(Amer Inst Physics, 2016) Borisenok, SergeyThe relative phase of Bosonic Josephson junction in the Josephson regime of Bose-Hubbard model is tracked via the target attractor ('synergetic') feedback algorithm with the inter-well coupling parameter presented as a control function. The efficiency of our approach is demonstrated numerically for Gaussian and harmonic types of target phases.Article Citation - WoS: 2Citation - Scopus: 2Structural Profile Matrices for Predicting Structural Properties of Proteins(World Scientific Publ Co Pte Ltd, 2020-07-10) Azginoglu, Nuh; Aydin, Zafer; Celik, MetePredicting structural properties of proteins plays a key role in predicting the 3D structure of proteins. In this study, new structural profile matrices (SPM) are developed for protein secondary structure, solvent accessibility and torsion angle class predictions, which could be used as input to 3D prediction algorithms. The structural templates employed in computing SPMs are detected by eight alignment methods in LOMETS server, gap affine alignment method, ScanProsite, PfamScan, and HHblits. The contribution of each template is weighted by its similarity to target, which is assessed by several sequence alignment scores. For comparison, the SPMs are also computed using Homolpro, which uses BLAST for target template alignments and does not assign weights to templates. Incorporating the SPMs into DSPRED classifier, the prediction accuracy improves significantly as demonstrated by cross-validation experiments on two difficult benchmarks. The most accurate predictions are obtained using the SPMs derived by threading methods in LOMETS server. On the other hand, the computational cost of computing these SPMs was the highest.