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Scientific Data

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https://www.readbyqxmd.com/read/28291266/spatial-and-quantitative-datasets-of-the-pancreatic-%C3%AE-cell-mass-distribution-in-lean-and-obese-mice
#1
Saba Parween, Maria Eriksson, Christoffer Nord, Elena Kostromina, Ulf Ahlgren
A detailed understanding of pancreatic β-cell mass distribution is a key element to fully appreciate the pathophysiology of models of diabetes and metabolic stress. Commonly, such assessments have been performed by stereological approaches that rely on the extrapolation of two-dimensional data and provide very limited topological information. We present ex vivo optical tomographic data sets of the full β-cell mass distribution in cohorts of obese ob/ob mice and their lean controls, together with information about individual islet β-cell volumes, their three-dimensional coordinates and shape throughout the volume of the pancreas between 4 and 52 weeks of age...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291265/t1-weighted-in-vivo-human-whole-brain-mri-dataset-with-an-ultrahigh-isotropic-resolution-of-250-%C3%AE-m
#2
Falk Lüsebrink, Alessandro Sciarra, Hendrik Mattern, Renat Yakupov, Oliver Speck
We present an ultrahigh resolution in vivo human brain magnetic resonance imaging (MRI) dataset. It consists of T1-weighted whole brain anatomical data acquired at 7 Tesla with a nominal isotropic resolution of 250 μm of a single young healthy Caucasian subject and was recorded using prospective motion correction. The raw data amounts to approximately 1.2 TB and was acquired in eight hours total scan time. The resolution of this dataset is far beyond any previously published in vivo structural whole brain dataset...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291248/a-curated-collection-of-tissue-microarray-images-and-clinical-outcome-data-of-prostate-cancer-patients
#3
Qing Zhong, Tiannan Guo, Markus Rechsteiner, Jan H Rüschoff, Niels Rupp, Christian Fankhauser, Karim Saba, Ashkan Mortezavi, Cédric Poyet, Thomas Hermanns, Yi Zhu, Holger Moch, Ruedi Aebersold, Peter J Wild
Microscopy image data of human cancers provide detailed phenotypes of spatially and morphologically intact tissues at single-cell resolution, thus complementing large-scale molecular analyses, e.g., next generation sequencing or proteomic profiling. Here we describe a high-resolution tissue microarray (TMA) image dataset from a cohort of 71 prostate tissue samples, which was hybridized with bright-field dual colour chromogenic and silver in situ hybridization probes for the tumour suppressor gene PTEN. These tissue samples were digitized and supplemented with expert annotations, clinical information, statistical models of PTEN genetic status, and computer source codes...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291247/enhancing-studies-of-the-connectome-in-autism-using-the-autism-brain-imaging-data-exchange-ii
#4
Adriana Di Martino, David O'Connor, Bosi Chen, Kaat Alaerts, Jeffrey S Anderson, Michal Assaf, Joshua H Balsters, Leslie Baxter, Anita Beggiato, Sylvie Bernaerts, Laura M E Blanken, Susan Y Bookheimer, B Blair Braden, Lisa Byrge, F Xavier Castellanos, Mirella Dapretto, Richard Delorme, Damien A Fair, Inna Fishman, Jacqueline Fitzgerald, Louise Gallagher, R Joanne Jao Keehn, Daniel P Kennedy, Janet E Lainhart, Beatriz Luna, Stewart H Mostofsky, Ralph-Axel Müller, Mary Beth Nebel, Joel T Nigg, Kirsten O'Hearn, Marjorie Solomon, Roberto Toro, Chandan J Vaidya, Nicole Wenderoth, Tonya White, R Cameron Craddock, Catherine Lord, Bennett Leventhal, Michael P Milham
The second iteration of the Autism Brain Imaging Data Exchange (ABIDE II) aims to enhance the scope of brain connectomics research in Autism Spectrum Disorder (ASD). Consistent with the initial ABIDE effort (ABIDE I), that released 1112 datasets in 2012, this new multisite open-data resource is an aggregate of resting state functional magnetic resonance imaging (MRI) and corresponding structural MRI and phenotypic datasets. ABIDE II includes datasets from an additional 487 individuals with ASD and 557 controls previously collected across 16 international institutions...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291243/a-standard-database-for-drug-repositioning
#5
Adam S Brown, Chirag J Patel
Drug repositioning, the process of discovering, validating, and marketing previously approved drugs for new indications, is of growing interest to academia and industry due to reduced time and costs associated with repositioned drugs. Computational methods for repositioning are appealing because they putatively nominate the most promising candidate drugs for a given indication. Comparing the wide array of computational repositioning methods, however, is a challenge due to inconsistencies in method validation in the field...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291235/metazoan-mitochondrial-gene-sequence-reference-datasets-for-taxonomic-assignment-of-environmental-samples
#6
Ryuji J Machida, Matthieu Leray, Shian-Lei Ho, Nancy Knowlton
Mitochondrial-encoded genes are increasingly targeted in studies using high-throughput sequencing approaches for characterizing metazoan communities from environmental samples (e.g., plankton, meiofauna, filtered water). Yet, unlike nuclear ribosomal RNA markers, there is to date no high-quality reference dataset available for taxonomic assignments. Here, we retrieved all metazoan mitochondrial gene sequences from GenBank, and then quality filtered and formatted the datasets for taxonomic assignments using taxonomic assignment tools...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291234/collocated-observations-of-cloud-condensation-nuclei-particle-size-distributions-and-chemical-composition
#7
Julia Schmale, Silvia Henning, Bas Henzing, Helmi Keskinen, Karine Sellegri, Jurgita Ovadnevaite, Aikaterini Bougiatioti, Nikos Kalivitis, Iasonas Stavroulas, Anne Jefferson, Minsu Park, Patrick Schlag, Adam Kristensson, Yoko Iwamoto, Kirsty Pringle, Carly Reddington, Pasi Aalto, Mikko Äijälä, Urs Baltensperger, Jakub Bialek, Wolfram Birmili, Nicolas Bukowiecki, Mikael Ehn, Ann Mari Fjæraa, Markus Fiebig, Göran Frank, Roman Fröhlich, Arnoud Frumau, Masaki Furuya, Emanuel Hammer, Liine Heikkinen, Erik Herrmann, Rupert Holzinger, Hiroyuki Hyono, Maria Kanakidou, Astrid Kiendler-Scharr, Kento Kinouchi, Gerard Kos, Markku Kulmala, Nikolaos Mihalopoulos, Ghislain Motos, Athanasios Nenes, Colin O'Dowd, Mikhail Paramonov, Tuukka Petäjä, David Picard, Laurent Poulain, André Stephan Henry Prévôt, Jay Slowik, Andre Sonntag, Erik Swietlicki, Birgitta Svenningsson, Hiroshi Tsurumaru, Alfred Wiedensohler, Cerina Wittbom, John A Ogren, Atsushi Matsuki, Seong Soo Yum, Cathrine Lund Myhre, Ken Carslaw, Frank Stratmann, Martin Gysel
Cloud condensation nuclei (CCN) number concentrations alongside with submicrometer particle number size distributions and particle chemical composition have been measured at atmospheric observatories of the Aerosols, Clouds, and Trace gases Research InfraStructure (ACTRIS) as well as other international sites over multiple years. Here, harmonized data records from 11 observatories are summarized, spanning 98,677 instrument hours for CCN data, 157,880 for particle number size distributions, and 70,817 for chemical composition data...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291232/comprehensive-rna-seq-transcriptomic-profiling-in-the-malignant-progression-of-gliomas
#8
Zheng Zhao, Fanlin Meng, Wen Wang, Zheng Wang, Chuanbao Zhang, Tao Jiang
Gliomas are the most common and lethal intracranial tumours. RNA sequencing technologies and advanced data analyses recently enabled the characterization of transcriptomic information, including protein-coding gene expression, non-coding gene expression, alternative splicing, and fusion gene detection, to facilitate detection of diseases and altered phenotypes. As a part of the Chinese Glioma Genome Atlas (CGGA) project, our aim was to delineate comprehensive transcriptome profiling in the malignant progression of human gliomas...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291231/targeted-deep-sequencing-of-flowering-regulators-in-brassica-napus-reveals-extensive-copy-number-variation
#9
Sarah Schiessl, Bruno Huettel, Diana Kuehn, Richard Reinhardt, Rod J Snowdon
Gene copy number variation (CNV) is increasingly implicated in control of complex trait networks, particularly in polyploid plants like rapeseed (Brassica napus L.) with an evolutionary history of genome restructuring. Here we performed sequence capture to assay nucleotide variation and CNV in a panel of central flowering time regulatory genes across a species-wide diversity set of 280 B. napus accessions. The genes were chosen based on prior knowledge from Arabidopsis thaliana and related Brassica species...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291230/corrigendum-transcriptome-characterisation-and-simple-sequence-repeat-marker-discovery-in-the-seagrass-posidonia-oceanica
#10
D D'Esposito, L Orrù, E Dattolo, L Bernardo, A Lamontanara, L Orsini, I A Serra, S Mazzuca, G Procaccini
No abstract text is available yet for this article.
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291228/high-resolution-data-on-the-impact-of-warming-on-soil-co2-efflux-from-an-asian-monsoon-forest
#11
Naishen Liang, Munemasa Teramoto, Masahiro Takagi, Jiye Zeng
This paper describes a project for evaluation of global warming's impacts on soil carbon dynamics in Japanese forest ecosystems. We started a soil warming experiment in late 2008 in a 55-year-old evergreen broad-leaved forest at the boundary between the subtropical and warm-temperate biomes in southern Japan. We used infrared carbon-filament heat lamps to increase soil temperature by about 2.5 °C at a depth of 5 cm and continuously recorded CO2 emission from the soil surface using a multichannel automated chamber system...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28291224/replication-data-collection-highlights-value-in-diversity-of-replication-attempts
#12
K Andrew DeSoto, Martin Schweinsberg
Researchers agree that replicability and reproducibility are key aspects of science. A collection of Data Descriptors published in Scientific Data presents data obtained in the process of attempting to replicate previously published research. These new replication data describe published and unpublished projects. The different papers in this collection highlight the many ways that scientific replications can be conducted, and they reveal the benefits and challenges of crucial replication research. The organizers of this collection encourage scientists to reuse the data contained in the collection for their own work, and also believe that these replication examples can serve as educational resources for students, early-career researchers, and experienced scientists alike who are interested in learning more about the process of replication...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28248931/systematic-high-content-genome-wide-rnai-screens-of-endothelial-cell-migration-and-morphology
#13
Steven P Williams, Cathryn M Gould, Cameron J Nowell, Tara Karnezis, Marc G Achen, Kaylene J Simpson, Steven A Stacker
Many cell types undergo migration during embryogenesis and disease. Endothelial cells line blood vessels and lymphatics, which migrate during development as part of angiogenesis, lymphangiogenesis and other types of vessel remodelling. These processes are also important in wound healing, cancer metastasis and cardiovascular conditions. However, the molecular control of endothelial cell migration is poorly understood. Here, we present a dataset containing siRNA screens that identify known and novel components of signalling pathways regulating migration of lymphatic endothelial cells...
March 1, 2017: Scientific Data
https://www.readbyqxmd.com/read/28248930/genome-wide-sirna-screen-of-genes-regulating-the-lps-induced-tnf-%C3%AE-response-in-human-macrophages
#14
Jing Sun, Samuel Katz, Bhaskar Dutta, Ze Wang, Iain D C Fraser
The mammalian innate immune system senses many bacterial stimuli through the toll-like receptor (TLR) family. Activation of the TLR4 receptor by bacterial lipopolysaccharide (LPS) is the most widely studied TLR pathway due to its central role in host responses to gram-negative bacterial infection and its contribution to endotoxemia and sepsis. Here we describe a genome-wide siRNA screen to identify genes regulating the human macrophage TNF-α response to LPS. We include a secondary validation screen conducted with six independent siRNAs per gene to facilitate removal of off-target screen hits...
March 1, 2017: Scientific Data
https://www.readbyqxmd.com/read/28248929/rnai-screens-for-rho-gtpase-regulators-of-cell-shape-and-yap-taz-localisation-in-triple-negative-breast-cancer
#15
Patricia Pascual-Vargas, Samuel Cooper, Julia Sero, Vicky Bousgouni, Mar Arias-Garcia, Chris Bakal
In order to metastasise, triple negative breast cancer (TNBC) must make dynamic changes in cell shape. The shape of all eukaryotic cells is regulated by Rho Guanine Nucleotide Exchange Factors (RhoGEFs), which activate Rho-family GTPases in response to mechanical and informational cues. In contrast, Rho GTPase-activating proteins (RhoGAPs) inhibit Rho GTPases. However, which RhoGEFs and RhoGAPS couple TNBC cell shape to changes in their environment is very poorly understood. Moreover, whether the activity of particular RhoGEFs and RhoGAPs become dysregulated as cells evolve the ability to metastasise is not clear...
March 1, 2017: Scientific Data
https://www.readbyqxmd.com/read/28248925/genome-wide-sirna-screen-of-genes-regulating-the-lps-induced-nf-%C3%AE%C2%BAb-and-tnf-%C3%AE-responses-in-mouse-macrophages
#16
Ning Li, Samuel Katz, Bhaskar Dutta, Zachary L Benet, Jing Sun, Iain D C Fraser
The mammalian innate immune system senses many bacterial stimuli through the toll-like receptor (TLR) family. Activation of the TLR4 receptor by bacterial lipopolysaccharide (LPS) is the most widely studied TLR pathway due to its central role in host responses to gram-negative bacterial infection and its contribution to endotoxemia and sepsis. Here we describe a genome-wide siRNA screen to identify genes regulating the mouse macrophage TNF-α and NF-κB responses to LPS. We include a secondary validation screen conducted with six independent siRNAs per gene to facilitate removal of off-target screen hits...
March 1, 2017: Scientific Data
https://www.readbyqxmd.com/read/28248924/microrna-screening-identifies-mir-134-as-a-regulator-of-poliovirus-and-enterovirus-71-infection
#17
Nichole Lynn Orr-Burks, Byoung-Shik Shim, Weilin Wu, Abhijeet A Bakre, Jon Karpilow, Ralph A Tripp
MicroRNAs (miRNAs) regulate virus replication through multiple mechanisms. Poliovirus causes a highly debilitating disease and though global efforts to eradicate polio have sharply decreased polio incidence, unfortunately three countries (Afghanistan, Nigeria and Pakistan) remain polio-endemic. We hypothesize that understanding the host factors involved in polio replication will identify novel prophylactic and therapeutic targets against polio and related viruses. In this data set, employing genome wide screens of miRNA mimics and inhibitors, we identified miRNAs which significantly suppressed polio replication...
March 1, 2017: Scientific Data
https://www.readbyqxmd.com/read/28248923/image-based-sirna-screen-to-identify-kinases-regulating-weibel-palade-body-size-control-using-electroporation
#18
Robin Ketteler, Jamie Freeman, Francesco Ferraro, Nicole Bata, Dan F Cutler, Janos Kriston-Vizi
High-content screening of kinase inhibitors is important in order to identify biogenesis and function mechanisms of subcellular organelles. Here, we present a human kinome siRNA high-content screen on primary human umbilical vein endothelial cells, that were transfected by electroporation. The data descriptor contains a confocal fluorescence, microscopic image dataset. We also describe an open source, automated image analysis workflow that can be reused to perform high-content analysis of other organelles. This dataset is suitable for analysis of morphological parameters that are linked to human umbilical vein endothelial cell (HUVEC) biology...
March 1, 2017: Scientific Data
https://www.readbyqxmd.com/read/28248922/knocking-down-the-obstacles-to-functional-genomics-data-sharing
#19
Kaylene J Simpson, Jennifer A Smith
This week, Scientific Data published a collection of eight papers that describe datasets from high-throughput functional genomics screens, primarily utilizing RNA interference (RNAi). The publications explore host-pathogen dependencies, innate immune response, disease pathways, and cell morphology and motility at the genome-level. All data, including raw images from the high content screens, are publically available in PubChem BioAssay, figshare, Harvard Dataverse or the Image Data Resource (IDR). Detailed data descriptors enable use of these data for analysis algorithm design, machine learning, data comparisons, as well as generating new scientific hypotheses...
March 1, 2017: Scientific Data
https://www.readbyqxmd.com/read/28248921/development-of-improved-vaccine-cell-lines-against-rotavirus
#20
Weilin Wu, Nichole Orr-Burks, Jon Karpilow, Ralph A Tripp
Rotavirus is a major cause of severe gastroenteritis among very young children. In developing countries, rotavirus is the major cause of mortality in children under five years old, causing up to 20% of all childhood deaths in countries with high diarrheal disease burden, with more than 90% of these deaths occurring in Africa and Asia. Rotavirus vaccination mimics the first infection without causing illness, thus inducing strong and broad heterotypic immunity against prospective rotavirus infections. Two live vaccines are available, Rotarix and RotaTeq, but vaccination efforts are hampered by high production costs...
March 1, 2017: Scientific Data
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