WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Developing a Label Propagation Approach for Cancer Subtype Classification Problem(Tubitak Scientific & Technological Research Council Turkey, 2022-01-01) Guner, Pinar; Bakir-Gungor, Burcu; Coskun, MustafaCancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches.Article Theoretical Investigation of Steric Effects on the S1 Potential Energy Surface of O-Carborane Derivatives(Tubitak Scientific & Technological Research Council Turkey, 2023-01-01) Alkan, FahriTDDFT scan calculations were performed for s-carborane-anthracene derivatives (o-CB-X-Ant where X=-H,-CH3,-C2H5 and tert-butyl or-tBu) in order to understand the interplay between the steric effects, S1 potential energy surface (PES) and photophysical properties. The results show that all systems exhibit three local minima on the S1 PES, which correspond to the emissive LE and TICT state, along with the nonemissive CT state respectively. In the case of the unsubstituted system (o-CB-H-Ant), and-CH3 and-C2H5 substituted cases, S1 PES is predicted to be quite flat for certain conformations indicating that it is possible for these systems to reach the nonemissive CT state without a large energy penalty. In comparison, conformational pathways for the nonemissive CT state are predicted to be energetically unfavorable for o-CB-tBu-Ant as a result of both steric and electronic effects. These results provide a mechanism for the enhanced emission of cr-CB-fluorophore molecules with bulky ligands.Article Citation - WoS: 1Citation - Scopus: 1Study of Helical Antenna Endowing Short Wire Length and Compact Structure for High-Frequency Operations and Its Exclusive Manufacturing Process(Tubitak Scientific & Technological Research Council Turkey, 2023-03-01) Aslan, Melih; Sik, Kaan; Güzelkara, Izzet; Özdür, Ibrahim Tuna; Kilic, Veli TayfunIn this paper a study of a helical antenna resonating at high-frequency (HF) band with a very compact structure is reported. The designed antenna's S11 parameter magnitude change with frequency was calculated for different geometrical parameters. For each case, first, only a single parameter was changed. Then for a fair comparison, multiple parameters were changed simultaneously while the total wire length was set to be constant. Also, shifts in resonance frequencies and variations in -10 dB bandwidths were investigated. Our results show that resonance behaviour changes distinctively with the geometrical parameters and it allows shortening of the antenna wire length. For the designed antenna, the resonances shift to lower frequencies and -10 dB bandwidths around the resonances decrease as the winding wire thickness, number of turns, and turn radius increase. Whereas as the turn spacing increases the resonances shift to higher frequencies and -10 dB bandwidths widen, although the total wire length of the antenna increases. To verify the simulation results, the designed antenna was fabricated with an exclusive manufacturing process and characterized. The measurement results are in good agreement with the simulation results. It demonstrates the feasibility of the proposed manufacturing technique, which is new in the literature and enables accurate and rigid antenna fabrication with simple and low-cost steps.Article Solutions to Nonlinear Second-Order Three-Point Boundary Value Problems of Dynamic Equations on Time Scales(Tubitak Scientific & Technological Research Council Turkey, 2019-05-29) Dogan, AbdulkadirIn this paper, we consider existence criteria of three positive solutions of three-point boundary value problems for p-Laplacian dynamic equations on time scales. To show our main results, we apply the well-known Leggett-Williams fixed point theorem. Moreover, we present some results for the existence of single and multiple positive solutions for boundary value problems on time scales, by applying fixed point theorems in cones. The conditions we used in the paper are different from those in [Dogan A. On the existence of positive solutions for the one-dimensional p-Laplacian boundary value problems on time scales. Dynam Syst Appl 2015; 24: 295-304].Article Citation - WoS: 6Citation - Scopus: 6Sex Effect on the Correlation of Immunoglobulin G Glycosylation With Rheumatoid Arthritis Disease Activity(Tubitak Scientific & Technological Research Council Turkey, 2020-12-14) Ercan, AltanRheumatoid arthritis (RA) is a chronic autoimmune disease which affects females more than males with a presence of autoantibodies. Immunoglobulin G (IgG) produced by adaptive arm has 2 functional domains, Fc and Fab. The Fc domain binds Fc gamma receptors and C1q proteins of the innate arm. Therefore, the IgG Fc domain serves as a bridge between the innate and adaptive arms and is regulated by an evolutionarily conserved N-glycosylation with variable structures. These glycans are classified as agalactosylated G0, monogalactosylated G1, and digalactosylated G2, which are further modified by core-fucosylation (F) and bisecting N-acetylglucosamine (B) moieties such as G0F and G0FB. Interestingly, proinflammatory G0F is shown to be regulated by estrogen in vivo. Here, it is hypothesized that the regulation of G0F by estrogen contributes to sex dichotomy in RA by setting up the level of IgG-dependent inflammation and therefore, RA disease activity (Das28-CRP3). To investigate this hypothesis, IgG glycosylation was characterized in serum samples from active RA patients (n = 232) and healthy controls (n = 232) by serum N-glycan analysis using the high performance liquid chromatography. According to the results, the IgG Fc glycan phenotype originates predominantly from the structure of G0F, and both G0F and G0FB correlate with Das28-CRP3 in females, but not in males. In conclusion, IgG G0F-dependent inflammation differs in males and females, and these differences point to the differential regulation of inflammation by sex hormone estrogen via IgG glycosylation.Article Citation - WoS: 1Citation - Scopus: 1RPI-1 (Human DCDC2) Displays Functional Redundancy With Nephronophthisis 4 in Regulating Cilia Biogenesis in C. Elegans(Tubitak Scientific & Technological Research Council Turkey, 2023-01-01) Kaplan, Oktay I.Projecting from most cell surfaces, cilia serve as important hubs for sensory and signaling processes and have been linked to a variety of human disorders, including Bardet-Biedl Syndrome (BBS), Meckel-Gruber Syndrome (MKS), Nephronophthisis (NPHP), and Joubert Syndrome, and these diseases are collectively known as a ciliopathy. DCDC2 is a ciliopathy protein that localizes to cilia; nevertheless, our understanding of the role of DCDC2 in cilia is still limited. We employed C. elegans to investigate the function of C. elegans RPI-1, a Caenorhabditis elegans ortholog of human DCDC2, in cilia and found that C. elegans RPI-1 localizes to the entire ciliary axoneme, but is not present in the transition zone and basal body. We generated a null mutant of C. elegans rpi-1, and our analysis with a range of fluorescence-based ciliary markers revealed that DCDC2 and nephronophthisis 4 (NPHP-4/NPHP4) display functional redundant roles in regulating cilia length and cilia positions. Taken together, our analysis discovered a novel genetic interaction between two ciliopathy disease genes (RPI-1/DCDC2 and NPHP-4/NPHP4) in C. elegans.Article Citation - WoS: 1Citation - Scopus: 1Prediction of Preference and Effect of Music on Preference: A Preliminary Study on Electroencephalography from Young Women(Tubitak Scientific & Technological Research Council Turkey, 2019-03-01) Yilmaz, Bulent; Gazeloglu, Cengiz; Altindis, FatihNeuromarketing is the application of the neuroscientific approaches to analyze and understand economically relevant behavior. In this study, the effect of loud and rhythmic music in a sample neuromarketing setup is investigated. The second aim was to develop an approach in the prediction of preference using only brain signals. In this work, 19-channel EEG signals were recorded and two experimental paradigms were implemented: no music/silence and rhythmic, loud music using a headphone, while viewing women shoes. For each 10-sec epoch, normalized power spectral density (PSD) of EEG data for six frequency bands was estimated using the Burg method. The effect of music was investigated by comparing the mean differences between music and no music groups using independent two-sample t-test. In the preference prediction part sequential forward selection, k-nearest neighbors (k-NN) and the support vector machines (SVM), and 5-fold cross-validation approaches were used. It is found that music did not affect like decision in any of the power bands, on the contrary, music affected dislike decisions for all bands with no exceptions. Furthermore, the accuracies obtained in preference prediction study were between 77.5 and 82.5% for k-NN and SVM techniques. The results of the study showed the feasibility of using EEG signals in the investigation of the music effect on purchasing behavior and the prediction of preference of an individual.Article Citation - WoS: 5Citation - Scopus: 5Performance Analysis of Hamming Code for WSN-Based Smart Grid Applications(Tubitak Scientific & Technological Research Council Turkey, 2018) Yigit, Melike; Gungor, Vehbi Cagri; Boluk, PinarMany methods have been employed to detect, compare, and correct errors to increase communication reliability and efficiency in wireless sensor networks (WSNs). However, to the best of our knowledge, no existing study has compared the performance of error control codes by using different modulation techniques in a smart grid communication environment when multichannel scheduling is used. This paper presents a detailed performance evaluation and makes a comparison of different modulation techniques, such as frequency shift keying (FSK), differential phase shift keying (DPSK), binary phase shift keying (BPSK), and offset quadrature phase-shift keying (OQPSK), using Hamming codes in a 500-kV line-of-sight substation smart grid environment with multichannel scheduling. A link-quality-aware routing algorithm is used as a routing protocol and a log-normal shadowing channel is employed as a channel model. Simulations are performed in MATLAB and the performance of the Hamming code with various modulation techniques is compared with the results obtained without using any error correction codes for throughput, delay, and bit error rate. The results show that the performance of the Hamming code with OQPSK modulation is better than its performance with other modulation techniques. Moreover, the results show that the performance of Hamming code improves with multichannel scheduling for all modulation techniques.Article Multiple Positive Solutions of Nonlinear M-Point Dynamic Equations for P-Laplacian on Time Scales(Tubitak Scientific & Technological Research Council Turkey, 2016) Dogan, AbdulkadirIn this paper, we study the existence of positive solutions of a nonlinear m-point p-Laplacian dynamic equation (phi(p) (x(Delta)(t)))(del) w(t)f (t,x(t), x(Delta)(t)) = 0, t(1) < m-1 X(ti) - B-0 (Sigma m-1 i=2 a(i)x(Delta)(t(i))) = 0, x(Delta) (tm) = 0, or x(Delta)(t(1)) - 0, x(t(m)) + B-1(Sigma m-1 i=2 b(i)s(Delta)(t(i))) -0, where phi(p)(s) =vertical bar s vertical bar(P-2) s, p > 1. Sufficient conditions for the existence of at least three positive solutions of the problem are obtained by using a fixed point theorem. The interesting point is the nonlinear term f is involved with the first order derivative explicitly. As an application, an example is given to illustrate the result.Article Modified Self-Adaptive Local Search Algorithm for a Biobjective Permutation Flow Shop Scheduling Problem(Tubitak Scientific & Technological Research Council Turkey, 2019-07-26) Alabas Uslu, Cigdem; Dengiz, Berna; Aglan, Canan; Sabuncuoglu, Ihsan; Uslu, Çiğdem AlabaşInterest in multiobjective permutation flow shop scheduling (PFSS) has increased in the last decade to ensure effective resource utilization. This study presents a modified self-adaptive local search (MSALS) algorithm for the biobjective permutation flow shop scheduling problem where both makespan and total flow time objectives are minimized. Compared to existing sophisticated heuristic algorithms, MSALS is quite simple to apply to different biobjective PFSS instances without requiring effort or time for parameter tuning. Computational experiments showed that MSALS is either superior to current heuristics for Pareto sets or is incomparable due to other performance indicators of multiobjective problems.