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Scientific Data

Fabio Villani, Riccardo Civico, Stefano Pucci, Luca Pizzimenti, Rosa Nappi, Paolo Marco De Martini
In the original version of the Data Descriptor the surname of author Anne Socquet was misspelled. This has now been corrected in the HTML and PDF versions of the Data Descriptor. Some authors were also not appropriately associated with their affiliations in the HTML version, due to formatting errors made by the publisher. This has now been corrected in the HTML version of the Data Descriptor, the affiliations in the PDF were correct from the time of publication.
February 19, 2019: Scientific Data
Yuyu Song, Kartik Subramanian, Matthew J Berberich, Steven Rodriguez, Isabel J Latorre, Catherine M Luria, Robert Everley, Mark W Albers, Timothy J Mitchison, Peter K Sorger
The immortalized human ReNcell VM cell line represents a reproducible and easy-to-propagate cell culture system for studying the differentiation of neural progenitors. To better characterize the starting line and its subsequent differentiation, we assessed protein and phospho-protein levels and cell morphology over a 15-day period during which ReNcell progenitors differentiated into neurons, astrocytes and oligodendrocytes. Five of the resulting datasets measured protein levels or states of phosphorylation based on tandem-mass-tag (TMT) mass spectrometry and four datasets characterized cellular phenotypes using high-content microscopy...
February 19, 2019: Scientific Data
Haroon Rashid, Pushpendra Singh, Amarjeet Singh
Efficient energy consumption at the building level is vital for sustainability. Providing energy efficient systems and solutions requires an understanding of how energy gets consumed. However, there is a general lack of large-scale open datasets about the energy consumption of buildings, which hinders the research. The recent emergence of smart energy meters makes it possible to collect such data, which can then be used for analysis. In this paper, we release I-BLEND, 52 months of electrical energy dataset at a one-minute sampling rate from commercial and residential buildings of an academic institute campus in an emerging economy, India...
February 19, 2019: Scientific Data
Hesam Dashti, Jonathan R Wedell, William M Westler, John L Markley, Hamid R Eghbalnia
Identification of discrepant data in aggregated databases is a key step in data curation and remediation. We have applied the ALATIS approach, which is based on the international chemical shift identifier (InChI) model, to the full PubChem Compound database to generate unique and reproducible compound and atom identifiers for all entries for which three-dimensional structures were available. This exercise also served to identify entries with discrepancies between structures and chemical formulas or InChI strings...
February 19, 2019: Scientific Data
Chao Tian, Lixin Wang
Stable isotopes of hydrogen and oxygen (δ2 H, δ18 O and δ17 O) serve as powerful tracers in hydrological investigations. To our knowledge, daily precipitation isotope record especially 17 O-excess is rare in the mid-latitudes. To fill such knowledge gap, daily precipitation samples (n=446) were collected from June 2014 to May 2018 in Indianapolis, Indiana, U.S. A Triple Water Vapor Isotope Analyzer (T-WVIA) based on Off-Axis Integrated Cavity Output Spectroscopy (OA-ICOS) technique was used to concurrently measure precipitation isotopic variations (δ2 H, δ18 O and δ17 O)...
February 19, 2019: Scientific Data
Huimin Cai, Qiye Li, Xiaodong Fang, Ji Li, Nicholas E Curtis, Andreas Altenburger, Tomoko Shibata, Mingji Feng, Taro Maeda, Julie A Schwartz, Shuji Shigenobu, Nina Lundholm, Tomoaki Nishiyama, Huanming Yang, Mitsuyasu Hasebe, Shuaicheng Li, Sidney K Pierce, Jian Wang
Elysia chlorotica, a sacoglossan sea slug found off the East Coast of the United States, is well-known for its ability to sequester chloroplasts from its algal prey and survive by photosynthesis for up to 12 months in the absence of food supply. Here we present a draft genome assembly of E. chlorotica that was generated using a hybrid assembly strategy with Illumina short reads and PacBio long reads. The genome assembly comprised 9,989 scaffolds, with a total length of 557 Mb and a scaffold N50 of 442 kb...
February 19, 2019: Scientific Data
Judy P Che-Castaldo, Amy Byrne, Kaitlyn Perišin, Lisa J Faust
We present life expectancy estimates for hundreds of vertebrate species based on carefully vetted studbook data from North American zoos and aquariums. These data include sex-specific median life expectancies as well as sample size and 95% confidence limits for each estimate. Existing longevity data for animals primarily consist of maximum lifespan values, which are single observations rather than statistically derived estimates of longevity. Moreover, all of our estimates are based on the same type of data and calculated using consistent, standardized methods...
February 19, 2019: Scientific Data
Rafael S Gonçalves, Mark A Musen
We present an analytical study of the quality of metadata about samples used in biomedical experiments. The metadata under analysis are stored in two well-known databases: BioSample-a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples-a repository managed by the European Bioinformatics Institute (EBI). We tested whether 11.4 M sample metadata records in the two repositories are populated with values that fulfill the stated requirements for such values. Our study revealed multiple anomalies in the metadata...
February 19, 2019: Scientific Data
Karina Vink, Eriko Ankyu, Michihisa Koyama
Microgrids comprising renewable energy technologies are often modelled and optimised from a theoretical point of view. Verification of theoretical systems with data of actually implemented systems in the field rarely occurs in an open manner, especially on the intermediate scale of research buildings. To enable modelling of the actual microgrid performance of a research environment, we present a multiyear dataset of a microgrid with solar arrays and a battery. The main energy datasets comprise data per second supplemented by hourly solar irradiation data...
February 19, 2019: Scientific Data
Feibiao Song, Lanmei Wang, Wenbin Zhu, Zaijie Dong
As a novel IGF system member, igf3 plays an important role in gonadal development of teleost fish. Although studies have reported the unusual expression of igf3 in fish gonad, whether the igf3 affects the expression of long noncoding RNAs (lncRNAs) in gonad remains unknown. In this study, an igf3 knockdown common carp (Cyprinus carpio) model was established by RNA interference. Then RNA sequencing of C. carpio gonad after igf3 knockdown was performed. A total of 327,169,410 and 306,305,018 clean reads were identified from control and igf3-dsRNA interference group, respectively...
February 19, 2019: Scientific Data
Patrick A Curry, Nils Moosdorf
The number of online data repositories is growing and they are becoming increasingly difficult to navigate. Data are scattered among different repositories, or hidden on personal or institutional servers. To access data, users must search extensively and rely on site-specific tools. These hurdles substantially inhibit data findability and accessibility; in particular, those in the long tail of data. We developed an open source web application, Spatial Data Hub, that is a geospatial data index, connected to remote Internet sources...
February 12, 2019: Scientific Data
Peter Blattmann, Vivienne Stutz, Giulia Lizzo, Joy Richard, Philipp Gut, Ruedi Aebersold
Sequential window acquisition of all theoretical mass spectra (SWATH-MS) requires a spectral library to extract quantitative measurements from the mass spectrometry data acquired in data-independent acquisition mode (DIA). Large combined spectral libraries containing SWATH assays have been generated for humans and several other organisms, but so far no publicly available library exists for measuring the proteome of zebrafish, a rapidly emerging model system in biomedical research. Here, we present a large zebrafish SWATH spectral library to measure the abundance of 104,185 proteotypic peptides from 10,405 proteins...
February 12, 2019: Scientific Data
Hui-Zeng Sun, Yanhong Chen, Le Luo Guan
MicroRNAs (miRNAs) play essential roles in regulating gene expression involved in various biological functions. The knowledge of miRNA expression profiles across different tissues in cattle is still limited. Using the miRNAs data generated from 158 samples in three studies, we characterized the miRNA expression profiles of bovine sera, exosomes and 11 different tissues. Totally 639 miRNAs were identified and 159 miRNAs were expressed in all samples. After relative log expression normalization, four miRNA expression clusters were generated: 1) sera and exosomes; 2) liver; 3) mammary gland; 4) rumen and gut tissues...
February 12, 2019: Scientific Data
Ryan A McManamay, Christopher R DeRolph
Stream classifications are important for understanding stream ecosystem diversity while also serving as tools for aquatic conservation and management. With current rates of land and riverscape modification within the United States (US), a comprehensive inventory and evaluation of naturally occurring stream habitats is needed, as this provides a physical template upon which stream biodiversity is organized and maintained. To adequately represent the heterogeneity of stream ecosystems, such a classification needs to be spatially extensive where multiple stream habitat components are represented at the highest resolution possible...
February 12, 2019: Scientific Data
Markus Gastauer, Mabel Patricia Ortiz Vera, Kleber Padovani de Souza, Eder Soares Pires, Ronnie Alves, Cecílio Frois Caldeira, Silvio Junio Ramos, Guilherme Oliveira
Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis...
February 12, 2019: Scientific Data
Natacha Mendes, Sabine Oligschläger, Mark E Lauckner, Johannes Golchert, Julia M Huntenburg, Marcel Falkiewicz, Melissa Ellamil, Sarah Krause, Blazej M Baczkowski, Roberto Cozatl, Anastasia Osoianu, Deniz Kumral, Jared Pool, Laura Golz, Maria Dreyer, Philipp Haueis, Rebecca Jost, Yelyzaveta Kramarenko, Haakon Engen, Katharina Ohrnberger, Krzysztof J Gorgolewski, Nicolas Farrugia, Anahit Babayan, Andrea Reiter, H Lina Schaare, Janis Reinelt, Josefin Röbbig, Marie Uhlig, Miray Erbey, Michael Gaebler, Jonathan Smallwood, Arno Villringer, Daniel S Margulies
The dataset enables exploration of higher-order cognitive faculties, self-generated mental experience, and personality features in relation to the intrinsic functional architecture of the brain. We provide multimodal magnetic resonance imaging (MRI) data and a broad set of state and trait phenotypic assessments: mind-wandering, personality traits, and cognitive abilities. Specifically, 194 healthy participants (between 20 and 75 years of age) filled out 31 questionnaires, performed 7 tasks, and reported 4 probes of in-scanner mind-wandering...
February 12, 2019: Scientific Data
Anahit Babayan, Miray Erbey, Deniz Kumral, Janis D Reinelt, Andrea M F Reiter, Josefin Röbbig, H Lina Schaare, Marie Uhlig, Alfred Anwander, Pierre-Louis Bazin, Annette Horstmann, Leonie Lampe, Vadim V Nikulin, Hadas Okon-Singer, Sven Preusser, André Pampel, Christiane S Rohr, Julia Sacher, Angelika Thöne-Otto, Sabrina Trapp, Till Nierhaus, Denise Altmann, Katrin Arelin, Maria Blöchl, Edith Bongartz, Patric Breig, Elena Cesnaite, Sufang Chen, Roberto Cozatl, Saskia Czerwonatis, Gabriele Dambrauskaite, Maria Dreyer, Jessica Enders, Melina Engelhardt, Marie Michele Fischer, Norman Forschack, Johannes Golchert, Laura Golz, C Alexandrina Guran, Susanna Hedrich, Nicole Hentschel, Daria I Hoffmann, Julia M Huntenburg, Rebecca Jost, Anna Kosatschek, Stella Kunzendorf, Hannah Lammers, Mark E Lauckner, Keyvan Mahjoory, Ahmad S Kanaan, Natacha Mendes, Ramona Menger, Enzo Morino, Karina Näthe, Jennifer Neubauer, Handan Noyan, Sabine Oligschläger, Patricia Panczyszyn-Trzewik, Dorothee Poehlchen, Nadine Putzke, Sabrina Roski, Marie-Catherine Schaller, Anja Schieferbein, Benito Schlaak, Robert Schmidt, Krzysztof J Gorgolewski, Hanna Maria Schmidt, Anne Schrimpf, Sylvia Stasch, Maria Voss, Annett Wiedemann, Daniel S Margulies, Michael Gaebler, Arno Villringer
We present a publicly available dataset of 227 healthy participants comprising a young (N=153, 25.1±3.1 years, range 20-35 years, 45 female) and an elderly group (N=74, 67.6±4.7 years, range 59-77 years, 37 female) acquired cross-sectionally in Leipzig, Germany, between 2013 and 2015 to study mind-body-emotion interactions. During a two-day assessment, participants completed MRI at 3 Tesla (resting-state fMRI, quantitative T1 (MP2RAGE), T2-weighted, FLAIR, SWI/QSM, DWI) and a 62-channel EEG experiment at rest...
February 12, 2019: Scientific Data
Tomoyasu Horikawa, Shuntaro C Aoki, Mitsuaki Tsukamoto, Yukiyasu Kamitani
Achievements of near human-level performance in object recognition by deep neural networks (DNNs) have triggered a flood of comparative studies between the brain and DNNs. Using a DNN as a proxy for hierarchical visual representations, our recent study found that human brain activity patterns measured by functional magnetic resonance imaging (fMRI) can be decoded (translated) into DNN feature values given the same inputs. However, not all DNN features are equally decoded, indicating a gap between the DNN and human vision...
February 12, 2019: Scientific Data
Rossella Aversa, Mohammad Hadi Modarres, Stefano Cozzini, Regina Ciancio, Alberto Chiusole
Following further analysis of the Majority Dataset (Data Citation 3, originally ) and 100% Dataset (Data Citation 4, originally ) presented in the original version of this Data Descriptor it was revealed that a large number of duplicate images were included in both datasets. Both datasets have been corrected in updated versions, removing all replicates. The new version of the Majority Dataset (Data Citation 3) can be accessed via https://doi...
February 5, 2019: Scientific Data
Hai-Ping Liu, Shi-Jun Xiao, Nan Wu, Di Wang, Yan-Chao Liu, Chao-Wei Zhou, Qi-Yong Liu, Rui-Bin Yang, Wen-Kai Jiang, Qi-Qi Liang, Wangjiu, Chi Zhang, Jun-Hua Gong, Xiao-Hui Yuan, Zhen-Bo Mou
Animal genomes in the Qinghai-Tibetan Plateau provide valuable resources for scientists to understand the molecular mechanism of environmental adaptation. Tibetan fish species play essential roles in the local ecology; however, the genomic information for native fishes was still insufficient. Oxygymnocypris stewartii, belonging to Oxygymnocypris genus, Schizothoracinae subfamily, is a native fish in the Tibetan plateau living within the elevation from roughly 3,000 m to 4,200 m. In this report, PacBio and Illumina sequencing platform were used to generate ~385...
February 5, 2019: Scientific Data
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