Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
Browse
1304 results
Search Results
Article Citation - WoS: 5Citation - Scopus: 5Π-Conjugated Donor-Acceptor Small Molecule Thin-Films on Gold Electrodes for Reducing the Metal Work-Function(Elsevier Science SA, 2016-10) Azum, Naved; Taib, Layla Ahmad; Al Angari, Yasser Mohammed; Asiri, Abdullah M.; Denti, Mitchel; Zhao, Wei; Facchetti, AntonioThis paper reports the design, facile synthesis and purification of four pi-conjugated donor-acceptor small molecules comprising heteroaromatic units, DA-1-DA-4, for surface and electronic structure modification of gold thin film. These molecules were characterized by H-1/C-13 nuclear magnetic resonance spectroscopy, cyclic voltammetry, UV-Vis spectroscopy, and single-crystal X-ray diffraction. Morphologically smooth thin-films (similar to 5 nm) of DA-1-DA-4 were deposited onto Au thin films via thermal evaporation and characterized by atomic force microscopy, theta-2 theta X-ray diffraction and ultraviolet photoelectron spectroscopy. The work functions of the small molecule coated Au electrodes are shifted to lower energies by similar to 0.1-03 eV, compared to that of the bare Au film measured as a reference. The vapor-deposition of structurally,simple small molecules developed here shows great promise as a facile approach to reduce gold work function for electron injection/extraction between organic semiconductors and Au contacts in various opto-electronic devices. (C) 2016 Elsevier B.V. All tights reserved.Article Citation - WoS: 38Citation - Scopus: 38pH- and Temperature-Responsive Amphiphilic Diblock Copolymers of 4-Vinylpyridine and Oligoethyleneglycol Methacrylate Synthesized by RAFT Polymerization(Elsevier Sci Ltd, 2014-01) Topuzogullari, Murat; Bulmus, Volga; Dalgakiran, Eray; Dincer, SevilDiblock copolymers of 4-vinylpyridine (4VP) and oligoethyleneglycol methyl ether methacrylate (OEGMA) were synthesized for the first time using RAFT polymerization technique as potential drug delivery systems. Effects of the number of ethylene glycol units in OEGMA, chain length of hydrophobic P4VP block, pH, concentration and temperature on the solution behavior of the copolymers were investigated comprehensively. Copolymer chains formed micelles at pH values higher than 5 whereas unimeric polymers were observed to exist below pH 5, owing to the repulsion between positively charged P4VP blocks. The size of the micelles was dependent on the relative length of blocks, P4VP and POEGMA. Thermo-responsive properties of copolymers were investigated depending on the pH and length of P4VP block. The increase in the length of P4VP block decreased the LCST substantially at pH 7. At pH 3, LCST of copolymers shifted to higher temperatures due to the increased interaction of copolymers with water through positively charged P4VP block. (C) 2013 Elsevier Ltd. All rights reserved.Article Citation - WoS: 26Citation - Scopus: 33miRmoduleNet: Detecting miRNA-mRNA Regulatory Modules(Frontiers Media S.A., 2022-04-12) Yousef, Malik; Goy, Gokhan; Bakir-Gungor, BurcuIncreasing evidence that MicroRNAs (miRNAs) play a key role in carcinogenesis has revealed the need for elucidating the mechanisms of miRNA regulation and the roles of miRNAs in gene-regulatory networks. A better understanding of the interactions between miRNAs and their mRNA targets will provide a better understanding of the complex biological processes that occur during carcinogenesis. Increased efforts to reveal these interactions have led to the development of a variety of tools to detect and understand these interactions. We have recently described a machine learning approach miRcorrNet, based on grouping and scoring (ranking) groups of genes, where each group is associated with a miRNA and the group members are genes with expression patterns that are correlated with this specific miRNA. The miRcorrNet tool requires two types of -omics data, miRNA and mRNA expression profiles, as an input file. In this study we describe miRModuleNet, which groups mRNA (genes) that are correlated with each miRNA to form a star shape, which we identify as a miRNA-mRNA regulatory module. A scoring procedure is then applied to each module to further assess their contribution in terms of classification. An important output of miRModuleNet is that it provides a hierarchical list of significant miRNA-mRNA regulatory modules. miRModuleNet was further validated on external datasets for their disease associations, and functional enrichment analysis was also performed. The application of miRModuleNet aids the identification of functional relationships between significant biomarkers and reveals essential pathways involved in cancer pathogenesis.Article Citation - WoS: 20Citation - Scopus: 24miRdisNET: Discovering MicroRNA Biomarkers That Are Associated With Diseases Utilizing Biological Knowledge-Based Machine Learning(Frontiers Media S.A., 2023-01-12) Jabeer, Amhar; Temiz, Mustafa; Bakir-Gungor, Burcu; Yousef, MalikDuring recent years, biological experiments and increasing evidence have shown that MicroRNAs play an important role in the diagnosis and treatment of human complex diseases. Therefore, to diagnose and treat human complex diseases, it is necessary to reveal the associations between a specific disease and related miRNAs. Although current computational models based on machine learning attempt to determine miRNA-disease associations, the accuracy of these models need to be improved, and candidate miRNA-disease relations need to be evaluated from a biological perspective. In this paper, we propose a computational model named miRdisNET to predict potential miRNA-disease associations. Specifically, miRdisNET requires two types of data, i.e., miRNA expression profiles and known disease-miRNA associations as input files. First, we generate subsets of specific diseases by applying the grouping component. These subsets contain miRNA expressions with class labels associated with each specific disease. Then, we assign an importance score to each group by using a machine learning method for classification. Finally, we apply a modeling component and obtain outputs. One of the most important outputs of miRdisNET is the performance of miRNA-disease prediction. Compared with the existing methods, miRdisNET obtained the highest AUC value of .9998. Another output of miRdisNET is a list of significant miRNAs for disease under study. The miRNAs identified by miRdisNET are validated via referring to the gold-standard databases which hold information on experimentally verified MicroRNA-disease associations. miRdisNET has been developed to predict candidate miRNAs for new diseases, where miRNA-disease relation is not yet known. In addition, miRdisNET presents candidate disease-disease associations based on shared miRNA knowledge. The miRdisNET tool and other supplementary files are publicly available at: .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 - Scopus: 1eTNT: Enhanced Textnettopics With Filtered LDA Topics and Sequential Forward / Backward Topic Scoring Approaches(Science and Information Organization, 2024) Voskergian, Daniel; Jayousi, Rashid; Bakir-Güngör, BurcuTextNetTopics is a novel text classification-based topic modelling approach that focuses on topic selection rather than individual word selection to train a machine learning algorithm. However, one key limitation of TextNetTopics is its scoring component, which evaluates each topic in isolation and ranks them accordingly, ignoring the potential relationships between topics. In addition, the chosen topics may contain redundant or irrelevant features, potentially increasing the feature set size and introducing noise that can degrade the overall model performance. To address these limitations and improve the classification performance, this study introduces an enhancement to TextNetTopics. eTNT integrates two novel scoring approaches: Sequential Forward Topic Scoring (SFTS) and Sequential Backward Topic Scoring (SBTS), which consider topic interactions by assessing sets of topics simultaneously. Moreover, it incorporates a filtering component that aims to enhance topics' quality and discriminative power by removing non-informative features from each topic using Random Forest feature importance values. These integrations aim to streamline the topic selection process and enhance classifier efficiency for text classification. The results obtained from the WOS-5736, LitCovid, and MultiLabel datasets provide valuable insights into the superior effectiveness of eTNT compared to its counterpart, TextNetTopics. © 2024 Elsevier B.V., All rights reserved.Conference Object Citation - WoS: 49Citation - Scopus: 54You May Not Reap What You Sow: How Employees' Moral Awareness Minimizes Ethical Leadership's Positive Impact on Workplace Deviance(Springer, 2017-08-02) Gok, Kubilay; Sumanth, John J.; Bommer, William H.; Demirtas, Ozgur; Arslan, Aykut; Eberhard, Jared; Yigit, AhmetAlthough a growing body of research has shown the positive impact of ethical leadership on workplace deviance, questions remain as to whether its benefits are consistent across all situations. In this investigation, we explore an important boundary condition of ethical leadership by exploring how employees' moral awareness may lessen the need for ethical leadership. Drawing on substitutes for leadership theory, we suggest that when individuals already possess a heightened level of moral awareness, ethical leadership's role in reducing deviant actions may be reduced. However, when individuals lack this strong moral disposition, ethical leadership may be instrumental in inspiring them to reduce their deviant actions. To enhance the external validity and generalizability of our findings, the current research used two large field samples of working professionals in both Turkey and the USA. Results suggest that ethical leadership's positive influence on workplace deviance is dependent upon the individual's moral awareness-helpful for those employees whose moral awareness is low, but not high. Thus, our investigation helps to build theory around the contingencies of ethical leadership and the specific audience for whom it may be more (or less) influential.Article Citation - WoS: 8Citation - Scopus: 8Writing Chemical Patterns Using Electrospun Fibers as Nanoscale Inkpots for Directed Assembly of Colloidal Nanocrystals(Royal Soc Chemistry, 2020) Kiremitler, N. Burak; Torun, Ilker; Altintas, Yemliha; Patarroyo, Javier; Demir, Hilmi Volkan; Puntes, Victor F.; Onses, M. SerdarApplications that range from electronics to biotechnology will greatly benefit from low-cost, scalable and multiplex fabrication of spatially defined arrays of colloidal inorganic nanocrystals. In this work, we present a novel additive patterning approach based on the use of electrospun nanofibers (NFs) as inkpots for end-functional polymers. The localized grafting of end-functional polymers from spatially defined nanofibers results in covalently bound chemical patterns. The main factors that determine the width of the nanopatterns are the diameter of the NF and the extent of spreading during the thermal annealing process. Lowering the surface energy of the substrates via silanization and a proper choice of the grafting conditions enable the fabrication of nanoscale patterns over centimeter length scales. The fabricated patterns of end-grafted polymers serve as the templates for spatially defined assembly of colloidal metal and metal oxide nanocrystals of varying sizes (15 to 100 nm), shapes (spherical, cube, rod), and compositions (Au, Ag, Pt, TiO2), as well as semiconductor quantum dots, including the assembly of semiconductor nanoplatelets.Article Citation - WoS: 17Citation - Scopus: 23Women's Tertiary Education Masks the Gender Wage Gap in Turkey(Springer, 2017-03-10) Tekguc, Hasan; Eryar, Deger; Cindoglu, DilekThis paper investigates the gender wage gap for full-time formal sector employees, disaggregated by education level. The gap between the labor force participation rate of women with tertiary education and those with lower levels of education is substantial. There is no such gap for men. Hence, existing gender wage gap studies for Turkey, where we observe lopsided labor force participation rates by education levels, compare two very different populations. We disaggregate the whole sample by education level to create more homogenous sub-groups. For Turkey, without disaggregation, the gender wage gap was 13% in 2011, and women are significantly over-qualified relative to men on observed characteristics. Once we disaggregate the sample by education level, we show that the gender wage gap is 24% for less educated women and 9% for women with tertiary education in full-time formal employment. Observed characteristics only explain 1 % of this gap in absolute terms. We further disaggregate the data by public and private employment. The gender gap is higher in the private sector. However, women with tertiary education in the public sector are significantly better qualified compared to men, and consequently the adjusted gender wage gap is higher for women with tertiary education in the public sector. Our estimates also indicate a rise in the gender wage gap between 2004 and 2011.Article Citation - WoS: 11Citation - Scopus: 13Wireless Sensor Network-Based Communication for Cooperative Simultaneous Localization and Mapping(Pergamon-Elsevier Science Ltd, 2015-01) Tuna, Gurkan; Gungor, Vehbi Cagri; Potirakis, Stelios M.; Zeadally, SheraliThis paper presents a novel approach of using a Wireless Sensor Network (WSN) as the communication means for Multi-Robot, Cooperative, Simultaneous Localization and Mapping (CSLAM) applications investigating the associated design challenges and suggesting corresponding solutions. Although the proposed approach brings several benefits including an increased coverage and communication range, self-organization capabilities, quick deployment, and flexible architecture, the realization is interrelated with performance in terms of energy efficiency and reliability. In this respect, the applicability of the WSNs for the presented approach is investigated. Centralized and distributed map merging methods in WSN-based CSLAM are evaluated in detail and the impacts of packet delays and losses on the performance of CSLAM algorithms are shown. Additionally, the involved network congestion and contention dynamics are presented, while the effects of observation range, speed, time intervals between observations, and odometry readings on the SLAM accuracy are shown based on an extensive set of simulation studies. (C) 2014 Elsevier Ltd. All rights reserved.