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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Modelling data for predicting new iron garnet thin films with perpendicular magnetic anisotropy(Elsevier, 2020) Department of Electrical and Electronics Engineering; N/A; Onbaşlı, Mehmet Cengiz; Zanjani, Saeedeh Mokarian; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 258783; N/AThese data include detailed calculations and graphs based on our manuscript submitted to Journal of Magnetism and Magnetic Materials, entitled “Predicting New Iron Garnet Thin Films with Perpendicular Magnetic Anisotropy”. These data are organized in two parts; first, we present the calculated plots of sensitivity of magnetic anisotropy field and anisotropy energy density for 49 epitaxial rare earth iron garnet (REIG) film/substrate pairs (a total of 98 plots, Figs. 1–15). In the second part, we present in Table 1 the complete details on the calculations for total magnetic anisotropy and all material constants used for each of 50 film/substrate pairs. The comparison with the previous experimental demonstrations is also shown in Table 1 (last column) and 2 with an accompanying discussion confirming the reliability of our model.Publication Open Access Dataset of the analyzing trace elements and minerals via ICP-MS: method validation for the mammalian tissue and serum samples Dataset of the analyzing trace elements and minerals via ICP-MS: method validation for the mammalian tissue and serum samples(Elsevier, 2020) Aydemir, Duygu; Franci, Gülsu Şimşek; Ulusu, Nuriye Nuray; PhD Student; Researcher; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); School of Medicine; N/A; N/A; 6807Minerals and trace elements play vital role in the biological functions for all organisms including human and other mammals. Therefore, imbalance in the mineral and/or trace element levels may cause formation of several diseases including cancer, diabetes, cardiovascular diseases, and neurological disorders. ICP-MS (inductively coupled plasma – mass spectrometry) is described as the most sensitive and accurate method. Here we reported an effective and fast protocol as method validation to evaluate trace element and minerals via ICP-MS in the mammalian tissue and serum samples. Our data showed that minimum relative standard deviation (RSD) values with the ICP-MS were observed when we used microwave digestion with the SUPRAPUR® grade nitric acid at the lower dilution rates. Our protocol validation may help researchers to measure trace elements and minerals in the mammalian samples fast, easily and accurately. EMSURE® grade HNO3 caused cross contamination in the serum and tissue samples. Our protocol validation may help researchers to measure trace elements and minerals in the mammalian samples fast, easily and accurately.Publication Open Access Understanding gender differences in leadership(Oxford University Press (OUP), 2020) Alan, Şule; Kubilay, Elif; Loranth, Gyongyi; Department of Economics; Ertaç, Seda; Faculty Member; Department of Economics; College of Administrative Sciences and Economics; 107102Using data from a large-scale field experiment, we show that while there is no gender difference in willingness to make risky decisions on behalf of a group in a sample of children, a large gap emerges in a sample of adolescents. The proportion of girls who exhibit leadership willingness drops by 39%, going from childhood to adolescence. We explore the possible factors behind this drop and find that it is largely associated with a dramatic decline in 'social confidence', measured by willingness to perform a real effort task in public.Publication Open Access The BenBioDen database, a global database for meio-, macro- and megabenthic biomass and densities(Nature Publishing Group (NPG), 2020) Stratmann, T.; van Oevelen, D.; Martínez Arbizu, P.; Wei, C.-L.; Liao, J.-X.; Cusson, M.; Scrosati, R.A.; Archambault, P.; Snelgrove, P.V.R.; Burd, B.J.; Kenchington, E.; Gilkinson, K.; Belley, R.; Soetaert, K.; Department of Molecular Biology and Genetics; Balcı, Patricia A. Ramey; Researcher; Department of Molecular Biology and Genetics; College of Sciences; 261777Benthic fauna refers to all fauna that live in or on the seafloor, which researchers typically divide into size classes meiobenthos (32/64 µm–0.5/1 mm), macrobenthos (250 µm–1 cm), and megabenthos (>1 cm). Benthic fauna play important roles in bioturbation activity, mineralization of organic matter, and in marine food webs. Evaluating their role in these ecosystem functions requires knowledge of their global distribution and biomass. We therefore established the BenBioDen database, the largest open-access database for marine benthic biomass and density data compiled so far. In total, it includes 11,792 georeferenced benthic biomass and 51,559 benthic density records from 384 and 600 studies, respectively. We selected all references following the procedure for systematic reviews and meta-analyses, and report biomass records as grams of wet mass, dry mass, or ash-free dry mass, or carbon per m2 and as abundance records as individuals per m2. This database provides a point of reference for future studies on the distribution and biomass of benthic fauna.Publication Open Access Experimental data on novel Fe(III)-complexes containing phenanthroline derivatives for their anticancer properties(Elsevier, 2019) Matos, Cristina P.; Adıgüzel, Zelal; Yıldızhan, Yasemin; Çevik, Özge; Nunes, Patrique; Ferreira, Liliana P.; Carvalho, Maria Deus; Campos, Debora L.; Pavan, Fernando R.; Pessoa, Joao Costa; Garcia, Maria Helena; Tomaz, Ana Isabel; Correia, Isabel; Department of Molecular Biology and Genetics; Cevatemre, Buse; Önder, Tuğba Bağcı; Ayhan, Ceyda Açılan; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; N/A; 184359; N/AThis dataset is related to the research article entitled “May iron(III) complexes containing phenanthroline derivatives as ligands be prospective anticancer agents?” [1]. It includes the characterization by UV–Vis absorption spectroscopy and magnetic techniques of a group of mixed ligand Fe(III) complexes bearing a tripodal aminophenolate ligand L2−, H2L = N,N-bis(2-hydroxy-3,5-dimethylbenzyl)-N-(2-pyridylmethyl)amine, and different aromatic bases (NN = 2,2′-bipyridine [Fe(L)(bipy)]PF6 (1), 1,10-phenanthroline [Fe(L)(phen)]PF6 (2), or a phenanthroline derivative co-ligand: [Fe(L)(amphen)]NO3 (3), [Fe(L)(amphen)]PF6 (3a), [Fe(L)(Clphen)]PF6 (4), [Fe(L)(epoxyphen)]PF6 (5) (where amphen = 1,10-phenanthroline-5-amine, epoxyphen = 5,6-epoxy-5,6-dihydro-1,10-phenanthroline, Clphen = 5-chloro-1,10-phenanthroline), as well as [Fe(L)(EtOH)]NO3 (6), [Fe(phen)Cl3] (7) and [Fe(amphen)Cl3] (8). Data on their hydrolytic stability in physiological buffers is shown, as well as on their interaction with calf thymus DNA by spectroscopic tools. Additionally, the anticancer efficacy and the cellular death mechanisms activated in response to these drugs in HeLa, H1299 and MDA-MB-231 cells are provided.Publication Open Access Revisiting the complex architecture of ALS in Turkey: expanding genotypes, shared phenotypes, molecular networks, and a public variant database(Wiley, 2020) Şeker, Tuncay; Akçimen, Fulya; Coşkun, Cemre; Zor, Seyit; Kocoğlu, Cemile; Kartal, Ece; Şen, Nesli Ece; Hamzeiy, Hamid; Erimiş, Aslıhan Özoğuz; Norman, Utku; Karakahya, Oğuzhan; Olgun, Gülden; Akgün, Tahsin; Durmuş, Hacer; Şahin, Erdi; Çakar, Arman; Gürsoy, Esra Baar; Yıldız, Gülşen Babacan; İsak, Barış; Uluç, Kayıhan; Hanağası, Haşmet; Bilgiç, Başar; Turgut, Nilda; Aysal, Fikret; Ertaş, Mustafa; Boz, Cavit; Kotan, Dilcan; İdrisoğlu, Halil; Soysal, Aysun; Adatepe, Nurten Uzun; Akalın, Mehmet Ali; Koç, Filiz; Tan, Ersin; Deymeer, Feza; Taştan, Öznur; Çiçek, A. Ercüment; Kavak, Erşen; Parman, Yeşim; Tunca, Ceren; Bayraktar, Elif; Palvadeau, Robin Jerome; Oflazer, Piraye; Başak, Ayşe Nazlı; Researcher; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; N/A; N/A; N/A; N/A; 1512The last decade has proven that amyotrophic lateral sclerosis (ALS) is clinically and genetically heterogeneous, and that the genetic component in sporadic cases might be stronger than expected. This study investigates 1,200 patients to revisit ALS in the ethnically heterogeneous yet inbred Turkish population. Familial ALS (fALS) accounts for 20% of our cases. The rates of consanguinity are 30% in fALS and 23% in sporadic ALS (sALS). Major ALS genes explained the disease cause in only 35% of fALS, as compared with similar to 70% in Europe and North America. Whole exome sequencing resulted in a discovery rate of 42% (53/127). Whole genome analyses in 623 sALS cases and 142 population controls, sequenced within Project MinE, revealed well-established fALS gene variants, solidifying the concept of incomplete penetrance in ALS. Genome-wide association studies (GWAS) with whole genome sequencing data did not indicate a new risk locus. Coupling GWAS with a coexpression network of disease-associated candidates, points to a significant enrichment for cell cycle- and division-related genes. Within this network, literature text-mining highlightsDECR1, ATL1, HDAC2, GEMIN4, andHNRNPA3as important genes. Finally, information on ALS-related gene variants in the Turkish cohort sequenced within Project MinE was compiled in the GeNDAL variant browser (www.gendal.org).Publication Open Access Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source(Nature Publishing Group (NPG), 2020) Li, H.; Nazari, R.; Abbey, B.; Alvarez, R.; Aquila, A.; Ayyer, K.; Barty, A.; Berntsen, P.; Bielecki, J.; Pietrini, A.; Bucher, M.; Carini, G.; Chapman, H. N.; Contreras, A.; Daurer, B. J.; Flűckiger, L.; Frank, M.; Hajdu, J.; Hantke, M. F.; Hogue, B. G.; Hosseinizadeh, A.; Hunter, M. S.; Jönsson, H. O.; Kirian, R. A.; Kurta, R. P.; Loh, D.; Maia, F. R. N. C.; Mancuso, A. P.; Morgan, A. J.; McFadden, M.; Muehlig, K.; Munke, A.; Reddy, H. K. N.; Nettelblad, C.; Ourmazd, A.; Rose, M.; Schwander, P.; Marvin, Seibert M.; Sellberg, J. A.; Sierra, R. G.; Sun, Z.; Svenda, M.; Vartanyants, I. A.; Walter, P.; Westphal, D.; Williams, G.; Xavier, P. L.; Yoon, C. H.; Zaare, S.; Department of Molecular Biology and Genetics; Demirci, Hasan; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 307350Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.