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https://www.readbyqxmd.com/read/27922632/a-phenome-wide-examination-of-neural-and-cognitive-function
#1
R A Poldrack, E Congdon, W Triplett, K J Gorgolewski, K H Karlsgodt, J A Mumford, F W Sabb, N B Freimer, E D London, T D Cannon, R M Bilder
This data descriptor outlines a shared neuroimaging dataset from the UCLA Consortium for Neuropsychiatric Phenomics, which focused on understanding the dimensional structure of memory and cognitive control (response inhibition) functions in both healthy individuals (130 subjects) and individuals with neuropsychiatric disorders including schizophrenia (50 subjects), bipolar disorder (49 subjects), and attention deficit/hyperactivity disorder (43 subjects). The dataset includes an extensive set of task-based fMRI assessments, resting fMRI, structural MRI, and high angular resolution diffusion MRI...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27922631/dataset-of-eye-disease-related-proteins-analyzed-using-the-unfolding-mutation-screen
#2
Caitlyn L McCafferty, Yuri V Sergeev
A number of genetic diseases are a result of missense mutations in protein structure. These mutations can lead to severe protein destabilization and misfolding. The unfolding mutation screen (UMS) is a computational method that calculates unfolding propensities for every possible missense mutation in a protein structure. The UMS validation demonstrated a good agreement with experimental and phenotypical data. 15 protein structures (a combination of homology models and crystal structures) were analyzed using UMS...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27922630/spatial-and-temporal-analysis-of-extreme-sea-level-and-storm-surge-events-around-the-coastline-of-the-uk
#3
Ivan D Haigh, Matthew P Wadey, Thomas Wahl, Ozgun Ozsoy, Robert J Nicholls, Jennifer M Brown, Kevin Horsburgh, Ben Gouldby
In this paper we analyse the spatial footprint and temporal clustering of extreme sea level and skew surge events around the UK coast over the last 100 years (1915-2014). The vast majority of the extreme sea level events are generated by moderate, rather than extreme skew surges, combined with spring astronomical high tides. We distinguish four broad categories of spatial footprints of events and the distinct storm tracks that generated them. There have been rare events when extreme levels have occurred along two unconnected coastal regions during the same storm...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27922629/a-collection-of-european-sweet-cherry-phenology-data-for-assessing-climate-change
#4
Bénédicte Wenden, José Antonio Campoy, Julien Lecourt, Gregorio López Ortega, Michael Blanke, Sanja Radičević, Elisabeth Schüller, Andreas Spornberger, Danilo Christen, Hugo Magein, Daniela Giovannini, Carlos Campillo, Svetoslav Malchev, José Miguel Peris, Mekjell Meland, Rolf Stehr, Gérard Charlot, José Quero-García
Professional and scientific networks built around the production of sweet cherry (Prunus avium L.) led to the collection of phenology data for a wide range of cultivars grown in experimental sites characterized by highly contrasted climatic conditions. We present a dataset of flowering and maturity dates, recorded each year for one tree when available, or the average of several trees for each cultivar, over a period of 37 years (1978-2015). Such a dataset is extremely valuable for characterizing the phenological response to climate change, and the plasticity of the different cultivars' behaviour under different environmental conditions...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27922628/a-chromosome-level-genome-assembly-of-the-asian-arowana-scleropages-formosus
#5
Jia Li, Chao Bian, Yinchang Hu, Xidong Mu, Xueyan Shen, Vydianathan Ravi, Inna S Kuznetsova, Ying Sun, Xinxin You, Ying Qiu, Xinhui Zhang, Hui Yu, Yu Huang, Pao Xu, Ruobo Gu, Junmin Xu, László Orbán, Byrappa Venkatesh, Qiong Shi
Asian arowana (Scleropages formosus), an ancient teleost belonging to the Order Osteoglossomorpha, has been a valuable ornamental fish with some varieties. However, its biological studies and breeding germplasm have been remarkably limited by the lack of a reference genome. To solve these problems, here we report high-quality genome sequences of three common varieties of Asian arowana (the golden, red and green arowana). We firstly generated a chromosome-level genome assembly of the golden arowana, on basis of the genetic linkage map constructed with the restriction site-associated DNA sequencing (RAD-seq)...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27922621/sharing-brain-mapping-statistical-results-with-the-neuroimaging-data-model
#6
Camille Maumet, Tibor Auer, Alexander Bowring, Gang Chen, Samir Das, Guillaume Flandin, Satrajit Ghosh, Tristan Glatard, Krzysztof J Gorgolewski, Karl G Helmer, Mark Jenkinson, David B Keator, B Nolan Nichols, Jean-Baptiste Poline, Richard Reynolds, Vanessa Sochat, Jessica Turner, Thomas E Nichols
Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community. This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses. In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment. NIDM-Results provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27922593/corrigendum-a-database-of-marine-phytoplankton-abundance-biomass-and-species-composition-in-australian-waters
#7
Claire H Davies, Alex Coughlan, Gustaaf Hallegraeff, Penelope Ajani, Linda Armbrecht, Natalia Atkins, Prudence Bonham, Steve Brett, Richard Brinkman, Michele Burford, Lesley Clementson, Peter Coad, Frank Coman, Diana Davies, Jocelyn Dela-Cruz, Michelle Devlin, Steven Edgar, Ruth Eriksen, Miles Furnas, Christel Hassler, David Hill, Michael Holmes, Tim Ingleton, Ian Jameson, Sophie C Leterme, Christian Lønborg, James McLaughlin, Felicity McEnnulty, A David McKinnon, Margaret Miller, Shauna Murray, Sasi Nayar, Renee Patten, Tim Pritchard, Roger Proctor, Diane Purcell-Meyerink, Eric Raes, David Rissik, Jason Ruszczyk, Anita Slotwinski, Kerrie M Swadling, Katherine Tattersall, Peter Thompson, Paul Thomson, Mark Tonks, Thomas W Trull, Julian Uribe-Palomino, Anya M Waite, Rouna Yauwenas, Anthony Zammit, Anthony J Richardson
No abstract text is available yet for this article.
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27922592/distributed-solar-photovoltaic-array-location-and-extent-dataset-for-remote-sensing-object-identification
#8
Kyle Bradbury, Raghav Saboo, Timothy L Johnson, Jordan M Malof, Arjun Devarajan, Wuming Zhang, Leslie M Collins, Richard G Newell
Earth-observing remote sensing data, including aerial photography and satellite imagery, offer a snapshot of the world from which we can learn about the state of natural resources and the built environment. The components of energy systems that are visible from above can be automatically assessed with these remote sensing data when processed with machine learning methods. Here, we focus on the information gap in distributed solar photovoltaic (PV) arrays, of which there is limited public data on solar PV deployments at small geographic scales...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27874852/a-global-gas-flaring-black-carbon-emission-rate-dataset-from-1994-to-2012
#9
Kan Huang, Joshua S Fu
Global flaring of associated petroleum gas is a potential emission source of particulate matters (PM) and could be notable in some specific regions that are in urgent need of mitigation. PM emitted from gas flaring is mainly in the form of black carbon (BC), which is a strong short-lived climate forcer. However, BC from gas flaring has been neglected in most global/regional emission inventories and is rarely considered in climate modeling. Here we present a global gas flaring BC emission rate dataset for the period 1994-2012 in a machine-readable format...
November 22, 2016: Scientific Data
https://www.readbyqxmd.com/read/27874850/a-microarray-whole-genome-gene-expression-dataset-in-a-rat-model-of-inflammatory-corneal-angiogenesis
#10
Anthony Mukwaya, Jessica M Lindvall, Maria Xeroudaki, Beatrice Peebo, Zaheer Ali, Anton Lennikov, Lasse Dahl Ejby Jensen, Neil Lagali
In angiogenesis with concurrent inflammation, many pathways are activated, some linked to VEGF and others largely VEGF-independent. Pathways involving inflammatory mediators, chemokines, and micro-RNAs may play important roles in maintaining a pro-angiogenic environment or mediating angiogenic regression. Here, we describe a gene expression dataset to facilitate exploration of pro-angiogenic, pro-inflammatory, and remodelling/normalization-associated genes during both an active capillary sprouting phase, and in the restoration of an avascular phenotype...
November 22, 2016: Scientific Data
https://www.readbyqxmd.com/read/27874849/systematic-chemical-genetic-and-chemical-chemical-interaction-datasets-for-prediction-of-compound-synergism
#11
Jan Wildenhain, Michaela Spitzer, Sonam Dolma, Nick Jarvik, Rachel White, Marcia Roy, Emma Griffiths, David S Bellows, Gerard D Wright, Mike Tyers
The network structure of biological systems suggests that effective therapeutic intervention may require combinations of agents that act synergistically. However, a dearth of systematic chemical combination datasets have limited the development of predictive algorithms for chemical synergism. Here, we report two large datasets of linked chemical-genetic and chemical-chemical interactions in the budding yeast Saccharomyces cerevisiae. We screened 5,518 unique compounds against 242 diverse yeast gene deletion strains to generate an extended chemical-genetic matrix (CGM) of 492,126 chemical-gene interaction measurements...
November 22, 2016: Scientific Data
https://www.readbyqxmd.com/read/27824340/spatial-and-temporal-dynamics-of-multidimensional-well-being-livelihoods-and-ecosystem-services-in-coastal-bangladesh
#12
Helen Adams, W Neil Adger, Sate Ahmad, Ali Ahmed, Dilruba Begum, Attila N Lázár, Zoe Matthews, Mohammed Mofizur Rahman, Peter Kim Streatfield
Populations in resource dependent economies gain well-being from the natural environment, in highly spatially and temporally variable patterns. To collect information on this, we designed and implemented a 1586-household quantitative survey in the southwest coastal zone of Bangladesh. Data were collected on material, subjective and health dimensions of well-being in the context of natural resource use, particularly agriculture, aquaculture, mangroves and fisheries. The questionnaire included questions on factors that mediate poverty outcomes: mobility and remittances; loans and micro-credit; environmental perceptions; shocks; and women's empowerment...
November 8, 2016: Scientific Data
https://www.readbyqxmd.com/read/27824338/rock-signalling-induced-gene-expression-changes-in-mouse-pancreatic-ductal-adenocarcinoma-cells
#13
Nicola Rath, Gabriela Kalna, William Clark, Michael F Olson
The RhoA and RhoC GTPases act via the ROCK1 and ROCK2 kinases to promote actomyosin contraction, resulting in directly induced changes in cytoskeleton structures and altered gene transcription via several possible indirect routes. Elevated activation of the Rho/ROCK pathway has been reported in several diseases and pathological conditions, including disorders of the central nervous system, cardiovascular dysfunctions and cancer. To determine how increased ROCK signalling affected gene expression in pancreatic ductal adenocarcinoma (PDAC) cells, we transduced mouse PDAC cell lines with retroviral constructs encoding fusion proteins that enable conditional activation of ROCK1 or ROCK2, and subsequently performed RNA sequencing (RNA-Seq) using the Illumina NextSeq 500 platform...
November 8, 2016: Scientific Data
https://www.readbyqxmd.com/read/27824337/3-dimensional-electron-microscopic-imaging-of-the-zebrafish-olfactory-bulb-and-dense-reconstruction-of-neurons
#14
Adrian A Wanner, Christel Genoud, Rainer W Friedrich
Large-scale reconstructions of neuronal populations are critical for structural analyses of neuronal cell types and circuits. Dense reconstructions of neurons from image data require ultrastructural resolution throughout large volumes, which can be achieved by automated volumetric electron microscopy (EM) techniques. We used serial block face scanning EM (SBEM) and conductive sample embedding to acquire an image stack from an olfactory bulb (OB) of a zebrafish larva at a voxel resolution of 9.25×9.25×25 nm(3)...
November 8, 2016: Scientific Data
https://www.readbyqxmd.com/read/27824336/a-variant-reference-data-set-for-the-africanized-honeybee-apis-mellifera
#15
Samir M Kadri, Brock A Harpur, Ricardo O Orsi, Amro Zayed
The Africanized honeybee (AHB) is a population of Apis mellifera found in the Americas. AHBs originated in 1956 in Rio Clara, Brazil where imported African A. m. scutellata escaped and hybridized with local populations of European A. mellifera. Africanized populations can now be found from Northern Argentina to the Southern United States. AHBs-often referred to as 'Killer Bees'- are a major concern to the beekeeping industry as well as a model for the evolutionary genetics of colony defence. We performed high coverage pooled-resequencing of 360 diploid workers from 30 Brazilian AHB colonies using Illumina Hi-Seq (150 bp PE)...
November 8, 2016: Scientific Data
https://www.readbyqxmd.com/read/27824332/cross-cultural-dataset-for-the-evolution-of-religion-and-morality-project
#16
Benjamin Grant Purzycki, Coren Apicella, Quentin D Atkinson, Emma Cohen, Rita Anne McNamara, Aiyana K Willard, Dimitris Xygalatas, Ara Norenzayan, Joseph Henrich
A considerable body of research cross-culturally examines the evolution of religious traditions, beliefs and behaviors. The bulk of this research, however, draws from coded qualitative ethnographies rather than from standardized methods specifically designed to measure religious beliefs and behaviors. Psychological data sets that examine religious thought and behavior in controlled conditions tend to be disproportionately sampled from student populations. Some cross-national databases employ standardized methods at the individual level, but are primarily focused on fully market integrated, state-level societies...
November 8, 2016: Scientific Data
https://www.readbyqxmd.com/read/27779621/a-studyforrest-extension-simultaneous-fmri-and-eye-gaze-recordings-during-prolonged-natural-stimulation
#17
Michael Hanke, Nico Adelhöfer, Daniel Kottke, Vittorio Iacovella, Ayan Sengupta, Falko R Kaule, Roland Nigbur, Alexander Q Waite, Florian Baumgartner, Jörg Stadler
Here we present an update of the studyforrest (http://studyforrest.org) dataset that complements the previously released functional magnetic resonance imaging (fMRI) data for natural language processing with a new two-hour 3 Tesla fMRI acquisition while 15 of the original participants were shown an audio-visual version of the stimulus motion picture. We demonstrate with two validation analyses that these new data support modeling specific properties of the complex natural stimulus, as well as a substantial within-subject BOLD response congruency in brain areas related to the processing of auditory inputs, speech, and narrative when compared to the existing fMRI data for audio-only stimulation...
October 25, 2016: Scientific Data
https://www.readbyqxmd.com/read/27779619/a-database-of-human-exposomes-and-phenomes-from-the-us-national-health-and-nutrition-examination-survey
#18
Chirag J Patel, Nam Pho, Michael McDuffie, Jeremy Easton-Marks, Cartik Kothari, Isaac S Kohane, Paul Avillach
The National Health and Nutrition Examination Survey (NHANES) is a population survey implemented by the Centers for Disease Control and Prevention (CDC) to monitor the health of the United States whose data is publicly available in hundreds of files. This Data Descriptor describes a single unified and universally accessible data file, merging across 255 separate files and stitching data across 4 surveys, encompassing 41,474 individuals and 1,191 variables. The variables consist of phenotype and environmental exposure information on each individual, specifically (1) demographic information, physical exam results (e...
October 25, 2016: Scientific Data
https://www.readbyqxmd.com/read/27779618/a-studyforrest-extension-retinotopic-mapping-and-localization-of-higher-visual-areas
#19
Ayan Sengupta, Falko R Kaule, J Swaroop Guntupalli, Michael B Hoffmann, Christian Häusler, Jörg Stadler, Michael Hanke
The studyforrest (http://studyforrest.org) dataset is likely the largest neuroimaging dataset on natural language and story processing publicly available today. In this article, along with a companion publication, we present an update of this dataset that extends its scope to vision and multi-sensory research. 15 participants of the original cohort volunteered for a series of additional studies: a clinical examination of visual function, a standard retinotopic mapping procedure, and a localization of higher visual areas-such as the fusiform face area...
October 25, 2016: Scientific Data
https://www.readbyqxmd.com/read/27779615/a-german-language-replication-study-analysing-the-role-of-figurative-speech-in-reasoning
#20
Ursula Christmann, Anne-Louise Göhring
According to the metaphorical framing model, the use of metaphors in discussing an issue influences recipients' understanding and assessment of that issue. In a recent study, participants read a text referring to a city's crime problem either as a beast or a virus and then proposed counter-measures for that problem. Participants' suggestions differed depending on the metaphor they had read. This replication matched the original procedure regarding the content of the rhetorical figures (beast vs virus), the topic under focus (crime) and the measurement of the dependent variable (open-end format to collect participants' proposals)...
October 25, 2016: Scientific Data
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