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Scientific Data

Moran N Cabili, Knox Carey, Stephanie O M Dyke, Anthony J Brookes, Marc Fiume, Francis Jeanson, Giselle Kerry, Alex Lash, Heidi Sofia, Dylan Spalding, Anne-Marie Tasse, Susheel Varma, Ravi Pandya
The volume of genomics and health data is growing rapidly, driven by sequencing for both research and clinical use. However, under current practices, the data is fragmented into many distinct datasets, and researchers must go through a separate application process for each dataset. This is time-consuming both for the researchers and the data stewards, and it reduces the velocity of research and new discoveries that could improve human health. We propose to simplify this process, by introducing a standard Library Card that identifies and authenticates researchers across all participating datasets...
March 14, 2018: Scientific Data
Annina N von Allmen, Maxime G Zermatten, Kurt Leibundgut, Philipp Agyeman, Roland A Ammann
Fever in neutropenia (FN) is the most frequent potentially life threatening complication of chemotherapy for cancer. Prediction of the risk to develop FN during chemotherapy would allow for targeted prophylaxis. This retrospective, single centre cohort study in pediatric patients diagnosed with cancer before 17 years covered two decades, 1993 to 2012. The 583 (73%) of 800 patients diagnosed with cancer who had received chemotherapy were studied here. Data on 2113 observation periods was collected, defined by stable combinations of 11 predefined characteristics potentially associated with FN...
March 13, 2018: Scientific Data
Lingyan Ping, Duc M Duong, Luming Yin, Marla Gearing, James J Lah, Allan I Levey, Nicholas T Seyfried
Patients with Alzheimer's disease (AD) and Parkinson's disease (PD) often have overlap in clinical presentation and brain neuropathology suggesting that these two diseases share common underlying mechanisms. Currently, the molecular pathways linking AD and PD are incompletely understood. Utilizing Tandem Mass Tag (TMT) isobaric labeling and synchronous precursor selection-based MS3 (SPS-MS3) mass spectrometry, we performed an unbiased quantitative proteomic analysis of post-mortem human brain tissues (n=80) from four different groups defined as controls, AD, PD, and co-morbid AD/PD cases across two brain regions (frontal cortex and anterior cingulate gyrus)...
March 13, 2018: Scientific Data
Andrew D Richardson, Koen Hufkens, Tom Milliman, Donald M Aubrecht, Min Chen, Josh M Gray, Miriam R Johnston, Trevor F Keenan, Stephen T Klosterman, Margaret Kosmala, Eli K Melaas, Mark A Friedl, Steve Frolking
Vegetation phenology controls the seasonality of many ecosystem processes, as well as numerous biosphere-atmosphere feedbacks. Phenology is also highly sensitive to climate change and variability. Here we present a series of datasets, together consisting of almost 750 years of observations, characterizing vegetation phenology in diverse ecosystems across North America. Our data are derived from conventional, visible-wavelength, automated digital camera imagery collected through the PhenoCam network. For each archived image, we extracted RGB (red, green, blue) colour channel information, with means and other statistics calculated across a region-of-interest (ROI) delineating a specific vegetation type...
March 13, 2018: Scientific Data
Joanne M Bennett, Piero Calosi, Susana Clusella-Trullas, Brezo Martínez, Jennifer Sunday, Adam C Algar, Miguel B Araújo, Bradford A Hawkins, Sally Keith, Ingolf Kühn, Carsten Rahbek, Laura Rodríguez, Alexander Singer, Fabricio Villalobos, Miguel Ángel Olalla-Tárraga, Ignacio Morales-Castilla
How climate affects species distributions is a longstanding question receiving renewed interest owing to the need to predict the impacts of global warming on biodiversity. Is climate change forcing species to live near their critical thermal limits? Are these limits likely to change through natural selection? These and other important questions can be addressed with models relating geographical distributions of species with climate data, but inferences made with these models are highly contingent on non-climatic factors such as biotic interactions...
March 13, 2018: Scientific Data
Attila Kőrösi, Attila Csoma, Gábor Rétvári, Zalán Heszberger, József Bíró, János Tapolcai, István Pelle, Dávid Klajbár, Márton Novák, Valentina Halasi, András Gulyás
Humans are involved in various real-life networked systems. The most obvious examples are social and collaboration networks but the language and the related mental lexicon they use, or the physical map of their territory can also be interpreted as networks. How do they find paths between endpoints in these networks? How do they obtain information about a foreign networked world they find themselves in, how they build mental model for it and how well they succeed in using it? Large, open datasets allowing the exploration of such questions are hard to find...
March 13, 2018: Scientific Data
Wasco Wruck, James Adjaye
Induced pluripotent stem cells (iPSCs) and human embryonic stem cells (hESCs) differentiated into hepatocyte-like cells (HLCs) provide a defined and renewable source of cells for drug screening, toxicology and regenerative medicine. We previously reprogrammed human fetal foreskin fibroblast cells (HFF1) into iPSCs employing an episomal plasmid-based integration-free approach, this iPSC-line and the hESC lines H1 and H9 were used to model hepatogenesis in vitro. Biochemical characterisation confirmed glycogen storage, ICG uptake and release, urea and bile acid production, as well as CYP3A4 activity...
March 13, 2018: Scientific Data
Zenab F Mchaourab, Andrea A Perreault, Bryan J Venters
The human K562 chronic myeloid leukemia cell line has long served as an experimental paradigm for functional genomic studies. To systematically and functionally annotate the human genome, the ENCODE consortium generated hundreds of functional genomic data sets, such as chromatin immunoprecipitation coupled to sequencing (ChIP-seq). While ChIP-seq analyses have provided tremendous insights into gene regulation, spatiotemporal insights were limited by a resolution of several hundred base pairs. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq that overcomes this limitation by providing higher precision mapping of protein-DNA interactions...
March 6, 2018: Scientific Data
Giorgio Giurato, Giovanni Nassa, Annamaria Salvati, Elena Alexandrova, Francesca Rizzo, Tuula A Nyman, Alessandro Weisz, Roberta Tarallo
The nuclear receptor estrogen receptor 2 (ESR2, ERβ) modulates cancer cell proliferation and tumor growth, exerting an oncosuppressive role in breast cancer (BC). Interaction proteomics by tandem affinity purification coupled to mass spectrometry was previously applied in BC cells to identify proteins acting in concert with ERβ to control key cellular functions, including gene transcription, RNA splicing and post-transcriptional mRNA regulation. These studies revealed an involvement of RNA in ERβ interactome assembly and functions...
March 6, 2018: Scientific Data
Konstantinos Tzioumis
We introduce a list that offers information on the relation between first names and race or ethnicity. Drawing information from mortgage applications, the list includes 4,250 first names and information on their respective count and proportions across six mutually exclusive racial and Hispanic origin groups. These six categories are consistent with the categories used in the Census Bureau's list on surnames' demographic information. Also, just like the Census Bureau's list of surnames, the list of first names is highly aggregated, so as to not identify any specific individuals...
March 6, 2018: Scientific Data
Zsolt Balázs, Dóra Tombácz, Attila Szűcs, Michael Snyder, Zsolt Boldogkői
This corrects the article DOI: 10.1038/sdata.2017.194.
March 6, 2018: Scientific Data
Laura F Grogan, Jason Mulvenna, Joel P A Gummer, Ben C Scheele, Lee Berger, Scott D Cashins, Michael S McFadden, Peter Harlow, David A Hunter, Robert D Trengove, Lee F Skerratt
The fungal skin disease chytridiomycosis has caused the devastating decline and extinction of hundreds of amphibian species globally, yet the potential for evolving resistance, and the underlying pathophysiological mechanisms remain poorly understood. We exposed 406 naïve, captive-raised alpine tree frogs (Litoria verreauxii alpina) from multiple populations (one evolutionarily naïve to chytridiomycosis) to the aetiological agent Batrachochytrium dendrobatidis in two concurrent and controlled infection experiments...
March 6, 2018: Scientific Data
Marta Seco-Cervera, Dayme González-Rodríguez, José Santiago Ibáñez-Cabellos, Lorena Peiró-Chova, Federico V Pallardó, José Luis García-Giménez
Friedreich's ataxia (FRDA; OMIM 229300), an autosomal recessive neurodegenerative mitochondrial disease, is the most prevalent hereditary ataxia. In addition, FRDA patients have shown additional non-neurological features such as scoliosis, diabetes, and cardiac complications. Hypertrophic cardiomyopathy, which is found in two thirds of patients at the time of diagnosis, is the primary cause of death in these patients. Here, we used small RNA-seq of microRNAs (miRNAs) purified from plasma samples of FRDA patients and controls...
March 6, 2018: Scientific Data
Antonio García-Alix, Francisco J Jiménez-Espejo, Gonzalo Jiménez-Moreno, Jaime L Toney, María J Ramos-Román, Jon Camuera, R Scott Anderson, Antonio Delgado-Huertas, Francisca Martínez-Ruiz, Ignasi Queralt
Here we provide the geochemical dataset that our research group has collected after 10 years of investigation in the Sierra Nevada National Park in southern Spain. These data come from Holocene sedimentary records from four alpine sites (ranging from ∼2500 to ∼3000 masl): two peatlands and two shallow lakes. Different kinds of organic and inorganic analyses have been conducted. The organic matter in the bulk sediment was characterised using elemental measurements and isotope-ratio mass spectrometry (EA-IRMS)...
February 27, 2018: Scientific Data
Armin Sorooshian, Alexander B MacDonald, Hossein Dadashazar, Kelvin H Bates, Matthew M Coggon, Jill S Craven, Ewan Crosbie, Scott P Hersey, Natasha Hodas, Jack J Lin, Arnaldo Negrón Marty, Lindsay C Maudlin, Andrew R Metcalf, Shane M Murphy, Luz T Padró, Gouri Prabhakar, Tracey A Rissman, Taylor Shingler, Varuntida Varutbangkul, Zhen Wang, Roy K Woods, Patrick Y Chuang, Athanasios Nenes, Haflidi H Jonsson, Richard C Flagan, John H Seinfeld
Airborne measurements of meteorological, aerosol, and stratocumulus cloud properties have been harmonized from six field campaigns during July-August months between 2005 and 2016 off the California coast. A consistent set of core instruments was deployed on the Center for Interdisciplinary Remotely-Piloted Aircraft Studies Twin Otter for 113 flight days, amounting to 514 flight hours. A unique aspect of the compiled data set is detailed measurements of aerosol microphysical properties (size distribution, composition, bioaerosol detection, hygroscopicity, optical), cloud water composition, and different sampling inlets to distinguish between clear air aerosol, interstitial in-cloud aerosol, and droplet residual particles in cloud...
February 27, 2018: Scientific Data
Masood A Akram, Sumit Nanda, Patricia Maraver, Rubén Armañanzas, Giorgio A Ascoli
NeuroMorpho.Org was launched in 2006 to provide unhindered access to any and all digital tracings of neuronal morphology that researchers were willing to share freely upon request. Today this database is the largest public inventory of cellular reconstructions in neuroscience with a content of over 80,000 neurons and glia from a representative diversity of animal species, anatomical regions, and experimental methods. Datasets continuously contributed by hundreds of laboratories worldwide are centrally curated, converted into a common non-proprietary format, morphometrically quantified, and annotated with comprehensive metadata...
February 27, 2018: Scientific Data
Denis Torre, Patrycja Krawczuk, Kathleen M Jagodnik, Alexander Lachmann, Zichen Wang, Lily Wang, Maxim V Kuleshov, Avi Ma'ayan
Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly, resources such as OMICtools, index bioinformatics tools that can extract knowledge from these digital data objects. However, systematic access to pre-generated 'canned' analyses applied by bioinformatics tools to biomedical digital data objects is currently not available. Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets...
February 27, 2018: Scientific Data
Yongbo Liang, Zhencheng Chen, Guiyong Liu, Mohamed Elgendi
Open clinical trial data provide a valuable opportunity for researchers worldwide to assess new hypotheses, validate published results, and collaborate for scientific advances in medical research. Here, we present a health dataset for the non-invasive detection of cardiovascular disease (CVD), containing 657 data segments from 219 subjects. The dataset covers an age range of 20-89 years and records of diseases including hypertension and diabetes. Data acquisition was carried out under the control of standard experimental conditions and specifications...
February 27, 2018: Scientific Data
Susanna-Assunta Sansone, Patricia Cruse, Mark Thorley
Resources for data management, discovery and (re)use are numerous and diverse, and more specifically we need data resources that enable the FAIR principles1 of Findability, Accessibility, Interoperability and Reusability of data.
February 27, 2018: Scientific Data
Sanchita Bhattacharya, Patrick Dunn, Cristel G Thomas, Barry Smith, Henry Schaefer, Jieming Chen, Zicheng Hu, Kelly A Zalocusky, Ravi D Shankar, Shai S Shen-Orr, Elizabeth Thomson, Jeffrey Wiser, Atul J Butte
Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components-Private Data, Shared Data, Data Analysis, and Resources-for data archiving, dissemination, analyses, and reuse...
February 27, 2018: Scientific Data
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