Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Conference Object Citation - WoS: 2Citation - Scopus: 194.8 Km-Range Direct Detection Fiber Optic Distributed Acoustic Sensor(Optica Publishing Group (Formerly OSA), 2019) Uyar, F.; Onat, T.; Unal, C.; Kartaloǧlu, T.; Ozdur, I.; Özbay, E.This work demonstrates an ultra-long range direct detection fiber optic distributed acoustic sensor which can detect vibrations at a distance of 94.8 km with 10 m resolution along the sensing fiber. © 2023 Elsevier B.V., All rights reserved.Conference Object In-silico Identification of Papillary Thyroid Carcinoma Molecular Mechanisms(IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2019-04) Ersoz, Nur Sebnem; Guzel, Yasin; Bakir-Gungor, BurcuRepresenting approximately 70% to 80% of thyroid cancers, papillary thyroid cancer (PTC) is the most common type of thyroid cancers. PTC is seen in all age groups, but it is seen more frequently in women than in men. Detection of biomarker proteins of papillary thyroid cancinoma plays an important role in the diagnosis of the disease. In this study, we aim to find target genes and pathways that are associated with papillar thyroid carcinoma, by integrating different bioinformatics methods. For this purpose, usingin-silico methodologies, candidate genes and pathways that could explain disease development mechanisms are identified. Throughout this study, firstly we identified differentially expressed genes as the amount of their protein product differ between patient and healthy groups. Secondly, by using active subnetworks search algorithms, topologic analyses and functional enrichment tests, candidate proteins,which could be thought as PTC biomarkers, and affected pathways are identified.Conference Object In-Silico Methods to Identify Common MicroRNAs and Pathways of Neuromuscular Diseases(IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2019-04) Yazici, Miray Unlu; Menges, Evrim Aksu; Ulum, Yeliz Z. Akkaya; Hayta, Burcu Balci; Bakir-Gungor, Burcu; Balcihayta, Burcu; Akkaya Ulum, Yeliz Z.Neuromuscular disorders (NMD) are a heterogeneous group of diseases characterized by the loss of function of the peripheral nerves and muscles. However, there are no effective and widespread therapeutic approaches to prevent or delay the progression of these disease types. microRNAs (miRNAs) which cause significant changes in gene expression by binding to target messenger RNAs (mRNAs), are known to have an effect on disease mechanisms. In this study, by integrating different bioinformatics methods, we aim to find miRNAs, target genes and pathways related to a group of neuromuscular diseases. For this purpose, we determined 17 miRNAs that show significant expression changes between patient and healthy groups; predicted target genes of these miRNAs; and identified affected pathways using subnetwork discovery, functional enrichment based algorithms. In our study, we integrated different in-silico approaches that proceed in top-down manner or bottom-up manner. The identified candidate miRNAs, genes and pathways, which could help to explain neuromuscular disease development mechanisms, are now under investigation in wet-lab.Master Thesis Centella asiatica extract containing bilayered electrospun wound dressing(Abdullah Gül Üniversitesi, 2019) KOÇ, NURAY; İşoğlu, İsmail AlperInnovative and bioactive wound dressings prepared by electrospinning mimicking the native structure of the extracellular matrix (ECM) have gained significant interest as an alternative to conventional wound care applications. In this study, bilayered wound dressing material was produced by sequential electrospinning of quaternized poly(4- vinyl pyridine) (upper layer) on the Centella Asiatica (CA) extract containing electrospun poly(D, L-lactide-co-glycolide) (PLGA)/poly(3-hydroxybutyrate-co-3- hydroxy valerate) (PHBV) blend membrane (lower layer). Scanning electron microscopy (SEM) was utilized to show a uniform and bead-free fiber structure of electrospun membranes. The average diameter of CA extract containing electrospun PLGA/PHBV blend membrane was calculated 0.471±0.11 µm, whereas the average fiber diameter of electrospun poly(Q-VP) membranes was in the range of 0.460±0.057 µm. Chemical, thermal, mechanical properties, and adsorption capacity of electrospun membranes, as well as the cumulative release of CA from the electrospun PLGA/PHBV membrane, were investigated. Viability, adhesion, and attachment of human fibroblast cells on the electrospun membranes on pre-set days were evaluated by the colorimetric CellTiter 96® Aqueous One Solution Cell Proliferation Assay (MTS assay) and SEM. Results revealed that CA loaded bilayered electrospun wound dressing showed promoted attachment and proliferation of fibroblasts. Hence, it can be concluded that CA extract containing bilayered electrospun wound dressing prepared in this study has a promising potential for wound healing applications.Conference Object Citation - WoS: 1Citation - Scopus: 1A New Method to Identify Affected Pathway Subnetworks and Clusters in Colon Cancer(IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2019-09) Goy, Gokhan; Yazici, Miray Unlu; Bakir-Gungor, BurenNowadays new technological developments that play an important role in the production of big data have brought about the interpretation, sharing and storage of data related to complex diseases. Combining multi-omic data in different molecular levels is potentially important for understanding the biological origin of complex diseases. One of these complex diseases is cancer of different types, which has one of the highest causes of death worldwide. The integration of multiple omic data in the framework of a comprehensive analysis and identification of relevant pathways contribute to the development of therapeutic approaches related to disease. In this study, RNA and methylation data (genes and p values) of colon adenocarcinoma were obtained from TCGA data portal and combined with Fisher's method. While protein subnetworks affected by the disease were identified by using subnetwork algorithm, pathways related to the disease and genes associated with these pathways were determined by functional enrichment analysis. Using gene-pathway relationship matrix, kappa scores of pathways were determined by similarity calculation. In this way, the pathways were clustered according to the hierarchically optimal number, as a result, the most important pathway clusters and related genes that are effective in disease formation identified.Article Citation - Scopus: 46Willingness to Pay for Renewable Electricity: A Contingent Valuation Study in Turkey(Elsevier Inc., 2019-12) Dogan, Eyup; Muhammad, IftikharRenewable energy sources are advised as an important alternative vehicle for dealing with a high rate of energy dependency and global warming. Turkey has also an ambitious national energy goal of minimizing energy import and producing 30% of electricity from renewable energy sources by 2023. However, it may not be easy to reach these goals. Willingness to Pay (WTP) thus plays a central role in directing appropriate policies for the country to realize its energy targets. This study reviews previous studies in the same literature as well as examines WTP of Turkish citizens for renewable electricity energy by using a stratified-sample and contingent valuation survey of 2500 households. The results from estimated models show that environmental conscience, membership to an environmental organization, age, education level, gender and income of households are significant determinants of WTP. In addition, the mean value of WTP for green electricity by Turkish households is estimated at around US$ 1 (with the exchange rate 5,3 TL/ US$) per month per household. A number of policy suggestions are further discussed. © 2023 Elsevier B.V., All rights reserved.Article Citation - Scopus: 1What Are the Outcomes of Emerging Markets Mergers and Acquisitions? Evidence From Turkey(Inderscience Publishers, 2019) Genç, Omer Faruk; Kalkan, BurakEmerging markets have become home to an increasing amount of acquisition activity. However, we do not know much about how domestic and international acquisitions differ in terms of their outcomes. The objective of this study is to compare these acquisitions in the context of an emerging country. To do so, we analysed all acquisitions that occurred in Turkey between 1989 and 2017. We found that domestic acquirers significantly outperformed foreign acquirers of Turkish companies. Our analysis of financial indicators suggests that foreign acquirers are larger in size, have greater leverage and intangibles, and engage in bigger deals. However, growth in leverage, capital expenditures, and administrative and staff expenses are greater in domestic acquirers. Overall, our findings suggest that domestic acquirers are affected more significantly by acquisitions compared to foreign acquirers and based on the financial outcomes of acquisitions there are several differences between these two groups of acquirers. © 2020 Elsevier B.V., All rights reserved.Article Citation - WoS: 4Citation - Scopus: 4Very Low Density Amorphous Phase of Zircon(Elsevier Science Bv, 2019-06) Bolat, Suleyman; Durandurdu, MuratUsing a reliable ab initio molecular dynamics method, we investigate the rapid solidification of the zircon melt. Accompanied by amorphization, a drastic volume expansion of 27% is perceived. This value is fairly larger than 18% observed in the metamict zircon. Such a large volume swelling leads to a significant decrease in the mean coordination number of Zr atoms, which is about 5.66 and the lowest one reported so far. On the other hand, the volume expansion is found to have almost no impact on the average coordination number of Si atoms i.e., they maintain their tetragonal coordination. As suggested by earlier investigations, the polymerization of SiO4 units is witnessed but our model shows the highest polymerization with respect to the previous simulations. Based on our findings, we propose that our model does not represent the metamict zircon but a very low density amorphous phase of zircon.Article Citation - WoS: 15Citation - Scopus: 14Understanding Plasmon Coupling in Nanoparticle Dimers Using Molecular Orbitals and Configuration Interaction(Royal Soc Chemistry, 2019) Alkan, Fahri; Aikens, Christine M.We perform a theoretical investigation of the electronic structure and optical properties of atomic nanowire and nanorod dimers using DFT and TDDFT. In both systems at separation distances larger than 0.75 nm, optical spectra show a single feature that resembles the bonding dipole plasmon (BDP) mode. A configuration interaction (CI) analysis shows that the BDP mode arises from constructive coupling of transitions, whereas the destructive coupling does not produce significant oscillator strength for such separation distances. At shorter separation distances, both constructive and destructive coupling produce oscillator strength due to wave-function overlap, which results in multiple features in the calculated spectra. Our analysis shows that a charge-transfer plasmon (CTP) mode arises from destructive coupling of transitions, whereas the BDP results from constructive coupling of the same transitions at shorter separation distances. Furthermore, the coupling elements between these transitions are shown to depend heavily on the amount of exact Hartree-Fock exchange (HFX) in the functional, which affects the splitting of CTP and BDP modes. With 50% HFX or more, the CTP and BDP modes mainly merge into a single feature in the spectra. These findings suggest that the effects of exact exchange must be assessed during the prediction of CTP modes in plasmonic systems.Article Citation - WoS: 18Citation - Scopus: 18Ultrahigh Vacuum Self-Assembly of Rotationally Commensurate C8-BTBT/MoS2 Mixed-Dimensional Heterostructures(Amer Chemical Soc, 2019-02-12) Liu, Xiaolong; Balla, Itamar; Sangwan, Vinod K.; Usta, Hakan; Facchetti, Antonio; Marks, Tobin J.; Hersam, Mark C.Mixed-dimensional van der Waals heterostructures combine the advantages of nanomaterials with qualitatively distinct properties such as the extended bandstructures and high charge carrier mobilities of inorganic two-dimensional materials and the discrete orbital energy levels and strong optical absorption of zero-dimensional organic molecules. The synergistic interplay between nanomaterials of distinct dimensionality has enabled a variety of unique applications such as antiambipolar transistors, sensitized photodetectors, and gate-tunable photovoltaics. Because the performance of mixed-dimensional heterostructure devices depends sensitively on the buried interfacial structure, it is of great interest to identify materials and chemistries that naturally form highly ordered heterointerfaces. Toward this end, here we demonstrate ultrahigh vacuum self-assembly of 2,7-dioctyl[1]benzothieno [3,2-b][1]benzothiophene (C8-BTBT) monolayers onto epitaxial MoS2/graphene heterostructures. With molecular-resolution scanning tunneling microscopy and spectroscopy, the resulting C8-BTBT/MoS2/graphene mixed-dimensional heterostructures are found to be rotationally commensurate with well-defined physical and electronic structures. It is further shown that the self-assembled C8-BTBT monolayers are insensitive to the structural defects and electronic perturbations of the underlying MoS2 substrate, which provides significant processing latitude. For these reasons, this work will facilitate ongoing efforts to utilize organic/MoS2/graphene mixed-dimensional heterostructures for electronic, optoelectronic, and photovoltaic applications.