Browsing by Type "Data article"

Now showing 1 - 11 of 11

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A nineteenth-century urban ottoman population micro dataset: data extraction and relational database curation from the 1840s pre-census bursa population registers
(Nature Portfolio, 2024) Department of History; Kabadayı, Mustafa Erdem; Erünal, Efe; Department of History; College of Social Sciences and Humanities; Graduate School of Social Sciences and Humanities
In recent decades, the "big microdata revolution" has transformed access to transcribed historical census data for social science research. However, the population records of the Ottoman Empire, spanning Southeastern Europe, Western Asia, and Northern Africa, remained inaccessible to the big microdata ecosystem due to their prolonged unavailability. This publication marks the inaugural release of complete population data for an Ottoman urban center, Bursa, derived from the 1839 population registers. The dataset presents originally non-tabulated register data in a tabular format integrated into a relational Microsoft Access database. Thus, we showcase the extensive and diverse data found in the Ottoman population registers, demonstrating a level of quality and sophistication akin to the censuses conducted worldwide in the nineteenth century. This valuable resource, whose potential has been massively underexploited, is now presented in an accessible format compatible with global microdata repositories. Our aim with this dataset is to enable historical demographic studies for the Ottoman realm and beyond, while also broadening access to the datasets constructed by our large research team.
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; 6807
Minerals 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.
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; 307350
Single 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.
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/A
This 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.
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/A
These 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.
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; 1512
The 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).
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SNAPSHOT USA 2021: a third coordinated national camera trap survey of the United States
(ESA-Ecological Society of America, 2024) Shamon H, Maor R, Cove MV, Kays R, Adley J, Alexander PD, Allen DN, Allen ML, Appel CL, Barr E, Barthelmess EL, Baruzzi C, Bashaw K, Bastille-Rousseau G, Baugh ME, Belant J, Benson JF, Bespoyasny BA, Bird T, Bogan DA, Brandt LSE, Bresnan CE, Brooke JM, Buderman FE, Buzzell SG, Cheeseman AE, Chitwood MC, Chrysafis P, Collins MK, Collins DP, Compton JA, Conner LM, Cosby OG, Coster SS, Crawford B, Crupi AP, Darracq AK, Davis ML, DeGregorio BA, Denningmann KL, Dougherty KD, Driver A, Edelman AJ, Ellington EH, Ellis-Felege SN, Ellison CN, Fantle-Lepczyk JE, Farris ZJ, Favreau J, Fernandez P, Fisher-Reid MC, Fitzpatrick MC, Flaherty EA, Forrester TD, Fritts SR, Gallo T, Gerber BD, Giery ST, Glasscock JL, Gonatas AD, Grady AC, Green AM, Gregory T, Griffin N, Hagen RH, Hansen CP, Hansen LP, Hasstedt SC, Hernández-Yáñez H, Herrera DJ, Horan RV 3rd, Jackson VL, Johnson L, Jordan MJ, Kahano W, Kiser J, Knowles TW, Koeck MM, Koroly C, Kuhn KM, Kuprewicz EK, Lafferty DJR, LaPoint SD, Lashley M, Lathrop RG, Lee TE Jr, Lepczyk CA, Lesmeister DB, Lombardi JV, Long RA, Lonsinger RC, MacKay P, Maher SP, Mason DS, Millspaugh JJ, Moll RJ, Moon JB, Mortelliti A, Mychajliw AM, Nagy CM, et al.; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Department of Molecular Biology and Genetics; College of Sciences
SNAPSHOT USA is a multicontributor, long-term camera trap survey designed to survey mammals across the United States. Participants are recruited through community networks and directly through a website application (https://www.snapshot-usa.org/). The growing Snapshot dataset is useful, for example, for tracking wildlife population responses to land use, land cover, and climate changes across spatial and temporal scales. Here we present the SNAPSHOT USA 2021 dataset, the third national camera trap survey across the US. Data were collected across 109 camera trap arrays and included 1711 camera sites. The total effort equaled 71,519 camera trap nights and resulted in 172,507 sequences of animal observations. Sampling effort varied among camera trap arrays, with a minimum of 126 camera trap nights, a maximum of 3355 nights, a median 546 nights, and a mean 656 ± 431 nights. This third dataset comprises 51 camera trap arrays that were surveyed during 2019, 2020, and 2021, along with 71 camera trap arrays that were surveyed in 2020 and 2021. All raw data and accompanying metadata are stored on Wildlife Insights (https://www.wildlifeinsights.org/), and are publicly available upon acceptance of the data papers. SNAPSHOT USA aims to sample multiple ecoregions in the United States with adequate representation of each ecoregion according to its relative size. Currently, the relative density of camera trap arrays varies by an order of magnitude for the various ecoregions (0.22–5.9 arrays per 100,000 km2), emphasizing the need to increase sampling effort by further recruiting and retaining contributors. There are no copyright restrictions on these data. We request that authors cite this paper when using these data, or a subset of these data, for publication. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US Government.
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; 261777
Benthic 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.
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The politics of Europeanisation work and family life reconciliation policy introduction
(Routledge, 2021) N/A; Department of Sociology; Kazanoğlu, Nazlı; Teaching Faculty; Department of Sociology; The Center for Gender Studies (KOÇ-KAM) / Koç Üniversitesi Toplumsal Cinsiyet ve Kadın Çalışmaları Araştırma ve Uygulama Merkezi (KOÇ-KAM); College of Social Sciences and Humanities; N/A
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The politics of Europeanisation work and family life reconciliation policy preface
(Routledge, 2021) N/A; Department of Sociology; Kazanoğlu, Nazlı; Teaching Faculty; Department of Sociology; The Center for Gender Studies (KOÇ-KAM) / Koç Üniversitesi Toplumsal Cinsiyet ve Kadın Çalışmaları Araştırma ve Uygulama Merkezi (KOÇ-KAM); College of Social Sciences and Humanities; N/A
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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; 107102
Using 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.