Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Citation - WoS: 26Citation - Scopus: 31miRcorrNet: Machine Learning-Based Integration of miRNA and mRNA Expression Profiles, Combined with Feature Grouping and Ranking(PeerJ Inc., 2021-05-19) Yousef, M.; Göy, G.; Mitra, R.; Eischen, C.M.; Jabeer, A.; Bakir-Güngör, B.A better understanding of disease development and progression mechanisms at the molecular level is critical both for the diagnosis of a disease and for the development of therapeutic approaches. The advancements in high throughput technologies allowed to generate mRNA and microRNA (miRNA) expression profiles; and the integrative analysis of these profiles allowed to uncover the functional effects of RNA expression in complex diseases, such as cancer. Several researches attempt to integrate miRNA and mRNA expression profiles using statistical methods such as Pearson correlation, and then combine it with enrichment analysis. In this study, we developed a novel tool called miRcorrNet, which performs machine learning-based integration to analyze miRNA and mRNA gene expression profiles. miRcorrNet groups mRNAs based on their correlation to miRNA expression levels and hence it generates groups of target genes associated with each miRNA. Then, these groups are subject to a rank function for classification. We have evaluated our tool using miRNA and mRNA expression profiling data downloaded from The Cancer Genome Atlas (TCGA), and performed comparative evaluation with existing tools. In our experiments we show that miRcorrNet performs as good as other tools in terms of accuracy (reaching more than 95% AUC value). Additionally, miRcorrNet includes ranking steps to separate two classes, namely case and control, which is not available in other tools. We have also evaluated the performance of miRcorrNet using a completely independent dataset. Moreover, we conducted a comprehensive literature search to explore the biological functions of the identified miRNAs. We have validated our significantly identified miRNA groups against known databases, which yielded about 90% accuracy. Our results suggest that miRcorrNet is able to accurately prioritize pan-cancer regulating high-confidence miRNAs. miRcorrNet tool and all other supplementary files are available at https://github.com/ malikyousef/miRcorrNet. © 2021 Elsevier B.V., All rights reserved.Article Citation - WoS: 3Citation - Scopus: 4Tuning Optical Properties of Self-Assembled Nanoparticle Network with External Optical Excitation(American Institute of Physics Inc., 2021-04-20) Şenel, Z.; İçöz, K.; Erdem, T.; Icoez, KutayDNA-driven self-assembly enables precise positioning of the colloidal nanoparticles owing to specific Watson-Crick interactions. Another important feature of this self-assembly method is its reversibility by controlling the temperature of the medium. In this work, we study the potential of another mechanism to control the binding/unbinding process of DNA-functionalized gold nanoparticles. We employ laser radiation that can be absorbed by the gold nanoparticles to heat their network and disassociate it. Here, we show that we can actively control the optical properties of the nanoparticle network by external optical excitation. We find out that by irradiating the structure with a green hand-held laser, the total transmittance can increase by ∼30% compared to the transmittance of the sample not irradiated by the laser. Similarly, the optical microscopy images indicate the transformation of the nanoparticle network from opaque to transparent, while the nanoparticles formed a network again after the laser irradiation stopped. Our results prove that the optical excitation can be used to tailor the structure and thus the optical properties of the DNA-self-assembled nanoparticle networks. © 2021 Elsevier B.V., All rights reserved.Article Citation - WoS: 40Citation - Scopus: 49Spatio-Temporal Rich Model-Based Video Steganalysis on Cross Sections of Motion Vector Planes(Institute of Electrical and Electronics Engineers Inc., 2016-07) Taşdemir, K.; Kurugöllü, F.; Sakir Sezer, S.; Sezer, SakirA rich model-based motion vector (MV) steganalysis benefiting from both temporal and spatial correlations of MVs is proposed in this paper. The proposed steganalysis method has a substantially superior detection accuracy than the previous methods, even the targeted ones. The improvement in detection accuracy lies in several novel approaches introduced in this paper. First, it is shown that there is a strong correlation, not only spatially but also temporally, among neighbouring MVs for longer distances. Therefore, temporal MV dependency alongside the spatial dependency is utilized for rigorous MV steganalysis. Second, unlike the filters previously used, which were heuristically designed against a specific MV steganography, a diverse set of many filters, which can capture aberrations introduced by various MV steganography methods is used. The variety and also the number of the filter kernels are substantially more than that of used in the previous ones. Besides that, filters up to fifth order are employed whereas the previous methods use at most second order filters. As a result of these, the proposed system captures various decorrelations in a wide spatio-Temporal range and provides a better cover model. The proposed method is tested against the most prominent MV steganalysis and steganography methods. To the best knowledge of the authors, the experiments section has the most comprehensive tests in MV steganalysis field, including five stego and seven steganalysis methods. Test results show that the proposed method yields around 20% detection accuracy increase in low payloads and 5% in higher payloads. © 2016 Elsevier B.V., All rights reserved.Conference Object Quasi-Static Operation of 2-Axis Microscanners With AlN Piezoelectric Quad-Actuators(Institute of Electrical and Electronics Engineers Inc., 2021-08-25) Hah, D.Aluminum nitride (AlN) started to draw attentions as a material for piezoelectric actuation owing to its CMOS process compatibility and safeness for biomedical applications. Due to its relatively low piezoelectric coefficients, AlN-based piezoelectric actuators have been mostly operated in resonance modes, especially in optical scanning. This paper presents a novel design of a 2-axis-tilt microscanner with AlN piezoelectric quad-actuators and meander-shaped hinges for reasonable quasi-static operation. Through finite-element-method simulation, it is shown that the proposed device can have about 9 degree of optical scan angle in two dimensions with the voltage amplitude of 50 V. Lissajous scanning operation of the device is demonstrated as well via simulation. © 2021 Elsevier B.V., All rights reserved.Article Citation - WoS: 14Citation - Scopus: 12Chaos in PID Controlled Nonlinear Systems(Korean Institute of Electrical Engineers jeet@kiee.or.kr, 2015-07-01) Ablay, G.Controlling nonlinear systems with linear feedback control methods can lead to chaotic behaviors. Order increase in system dynamics due to integral control and control parameter variations in PID controlled nonlinear systems are studied for possible chaos regions in the closed-loop system dynamics. The Lur’e form of the feedback systems are analyzed with Routh’s stability criterion and describing function analysis for chaos prediction. Several novel chaotic systems are generated from second-order nonlinear systems including the simplest continuous-time chaotic system. Analytical and numerical results are provided to verify the existence of the chaotic dynamics. © 2017 Elsevier B.V., All rights reserved.Article Citation - Scopus: 1A Laser-Assisted Cellular Electrophysiology Measurement System(Institute of Electrical and Electronics Engineers Inc., 2021-02-01) Seymen, A.A.; Özgür, E.; Soran-Erdem, Z.; Ortaç, B.Patch-clamp technique is the gold standard for cellular electrophysiological measurements, which is capable of measuring single ion transport events across the cell membrane. However, the measurement possesses significant complexities, and it requires a high level of expertise, while its experimental throughput is nevertheless considerably low. Here, we suggest and experimentally demonstrate a laser-Assisted method for performing cellular electrophysiological measurements. Femtosecond laser pulses, coupled to an optical microscope, are used to form a sub-micrometer hole on a thin polymer membrane separating two electrodes, where a nearby cell is subsequently placed onto the hole by negative pressure. Afterwards, the cell is punctured using subsequent laser exposure, revealing the cell membrane over the hole for electrophysiological recording. This system could be used to increase the output amount of the electrophysiological measurements substantially. © 2021 Elsevier B.V., All rights reserved.Article Citation - WoS: 5Citation - Scopus: 5Formation of a Very High-Density Amorphous Phase of Carbon and Its Crystallization into a Simple Cubic Structure at High Pressure(Elsevier B.V., 2021) Durandurdu, M.We report a direct computational evidence of a two-step transformation sequence for tetrahedral amorphous carbon (ta-C) with increasing pressure. First, ta-C gradually transforms into a very high-density amorphous phase (VHDA) phase. Second, the VDHA phase converts into a simple cubic (SC) crystal. The structural defects formed during the high-pressure treatment play important roles for the formation and stabilization of the SC structure, rather than favorable the SC4 crystal. These phase transformations are reversible. © 2021 Elsevier B.V., All rights reserved.