WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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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.Article Dayım: Bir İnsanoğlunun Portresi(TURKISH LIBRARIANS ASSOC, YENISEHIR, NECATIBEY CAD, ELGIN SOK, PO BOX 175, ANKARA, 06440, TURKEY, 2019) Donmez, Rasim OzgurThis is a memoir written by his nephew about our colleague Ali Can, who passed away in last July.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 - 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.Article Citation - WoS: 100Citation - Scopus: 138Transformation of Microgrid to Virtual Power Plant – A Comprehensive Review(Inst Engineering Technology-IET, 2019-02-28) Yavuz, Levent; Onen, Ahmet; Muyeen, S. M.; Kamwa, InnocentTo provide continuity of balancing demand and generation, renewable sources will be more active than today in near future due to the tendency of massive investment on renewable energy sources (RESs) by countries. However, due to the uncertain and intermittent nature of RESs, RESs would create problems on power system operations such as power quality, efficiency, stability and reliability. Owing to having problems with RESs integration, virtual power plant (VPP) has introduced to make this integration smooth without compromising the grid stability and reliability along with offering many other techno-economic benefits. This study reviews structures, types, architecture and operations of VPP along with the status of present implementations worldwide. The types of VPP are introduced in details with the optimisation algorithm used with each type. In addition, VPP is linked with the most of the components in power systems such as distributed generation, active prosumers, transmission system operator and distribution system operator, grid services such as fault ride through, reactive power control as well as with the help of technology such as communications, control and optimisations. This study gives a comprehensive outline of transforming microgrid to VPP that is useful for researchers, consumers, prosumers and utility operators.Conference Object Citation - WoS: 9Citation - Scopus: 10The Relationship of Surface Roughness and Wettability of 316L Stainless Steel Implants With Plastic Deformation Mechanisms(Elsevier Science Bv, 2019) Cicek, S.; Karaca, A.; Torun, I.; Onses, M. S.; Uzer, B.The wettability of the implant plays significant role in successful tissue-implant integration and shows strong dependence on the surface topography of the material. Recent studies showed that the plastic deformation mechanisms can improve cell response, and increase surface roughness and energy. In order to understand the effect of these mechanisms on wettability, 316L stainless steel samples were subjected to tensile test and deformed up to 15% to 35% of strain levels. Atomic force microscopy (AFM) presented approximately 22-fold greater average surface roughness on the 35% deformed sample compared to undeformed one. On the other hand, sessile drop test showed contact angle decrease from 82 degrees to 52 degrees as the deformation increased. This finding is significant since much higher contact angle value at similar surface roughness was presented in the literature. This demonstrates that the plastic deformation mechanisms can play significant role in enhancing the surface wettability without a need for a surface treatment technique. Hence, through the activation of these mechanisms, wettability and surface energy of the implant materials could be further increased which would result with enhanced cell response and lessened post-surgical complications. (C) 2018 Elsevier Ltd. All rights reserved.