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https://www.readbyqxmd.com/read/30226484/time-lapse-confocal-imaging-datasets-to-assess-structural-and-dynamic-properties-of-subcellular-nanostructures
#1
Gianmarco Ferri, Luca Digiacomo, Francesca D'Autilia, William Durso, Giulio Caracciolo, Francesco Cardarelli
Time-lapse optical microscopy datasets from living cells can potentially afford an enormous amount of quantitative information on the relevant structural and dynamic properties of sub-cellular organelles/structures, provided that both the spatial and temporal dimensions are properly sampled during the experiment. Here we provide exemplary live-cell, time-lapse confocal imaging datasets corresponding to three sub-cellular structures of the endo-lysosomal pathway, i.e. early endosomes, late endosomes and lysosomes, along with detailed guidelines to produce analogous experiments...
September 18, 2018: Scientific Data
https://www.readbyqxmd.com/read/30226483/survey-of-local-impacts-of-biofuel-crop-production-and-adoption-of-ethanol-stoves-in-southern-africa
#2
Alexandros Gasparatos, Graham P von Maltitz, Francis X Johnson, Carla Romeu-Dalmau, Charles B L Jumbe, Caroline Ochieng, Shakespear Mudombi, Boubacar Siddighi Balde, Davies Luhanga, Paulo Lopes, Anne Nyambane, Marcin P Jarzebski, Katherine J Willis
The two datasets outlined in this paper contain information related to (a) the local impacts of biofuel feedstock production, and (b) the factors that influence the adoption and/or sustained use of ethanol stoves in southern Africa. The first dataset was generated through extensive household surveys around four operational jatropha and sugarcane production sites in Malawi, Mozambique, and Swaziland. This project aimed to examine the local impacts of the most prominent modes of existing or intended biofuel feedstock production in southern Africa...
September 18, 2018: Scientific Data
https://www.readbyqxmd.com/read/30204156/the-mount-sinai-cohort-of-large-scale-genomic-transcriptomic-and-proteomic-data-in-alzheimer-s-disease
#3
Minghui Wang, Noam D Beckmann, Panos Roussos, Erming Wang, Xianxiao Zhou, Qian Wang, Chen Ming, Ryan Neff, Weiping Ma, John F Fullard, Mads E Hauberg, Jaroslav Bendl, Mette A Peters, Ben Logsdon, Pei Wang, Milind Mahajan, Lara M Mangravite, Eric B Dammer, Duc M Duong, James J Lah, Nicholas T Seyfried, Allan I Levey, Joseph D Buxbaum, Michelle Ehrlich, Sam Gandy, Pavel Katsel, Vahram Haroutunian, Eric Schadt, Bin Zhang
Alzheimer's disease (AD) affects half the US population over the age of 85 and is universally fatal following an average course of 10 years of progressive cognitive disability. Genetic and genome-wide association studies (GWAS) have identified about 33 risk factor genes for common, late-onset AD (LOAD), but these risk loci fail to account for the majority of affected cases and can neither provide clinically meaningful prediction of development of AD nor offer actionable mechanisms. This cohort study generated large-scale matched multi-Omics data in AD and control brains for exploring novel molecular underpinnings of AD...
September 11, 2018: Scientific Data
https://www.readbyqxmd.com/read/30204155/seafloor-crustal-deformation-data-along-the-subduction-zones-around-japan-obtained-by-gnss-a-observations
#4
Yusuke Yokota, Tadashi Ishikawa, Shun-Ichi Watanabe
Crustal deformation data obtained by geodetic observation networks are foundations in the fields of geodesy and seismology. These data are essential for understanding plate motion and earthquake sources and for simulating earthquake and tsunami scenarios. Although relatively scarce, seafloor geodetic data are particularly important for monitoring the behaviour of undersea interplate boundary regions. Since the mid-1990s, we have been developing the combined Global Navigation Satellite System-Acoustic ranging (GNSS-A) technique for realizing seafloor geodesy...
September 11, 2018: Scientific Data
https://www.readbyqxmd.com/read/30204154/the-eicu-collaborative-research-database-a-freely-available-multi-center-database-for-critical-care-research
#5
Tom J Pollard, Alistair E W Johnson, Jesse D Raffa, Leo A Celi, Roger G Mark, Omar Badawi
Critical care patients are monitored closely through the course of their illness. As a result of this monitoring, large amounts of data are routinely collected for these patients. Philips Healthcare has developed a telehealth system, the eICU Program, which leverages these data to support management of critically ill patients. Here we describe the eICU Collaborative Research Database, a multi-center intensive care unit (ICU)database with high granularity data for over 200,000 admissions to ICUs monitored by eICU Programs across the United States...
September 11, 2018: Scientific Data
https://www.readbyqxmd.com/read/30204153/single-cell-rna-sequencing-of-adult-mouse-testes
#6
Soeren Lukassen, Elisabeth Bosch, Arif B Ekici, Andreas Winterpacht
Spermatogenesis is an efficient and complex system of continuous cell differentiation. Previous studies investigating the transcriptomes of different cell populations in the testis relied either on sorting cells, cell depletion, or juvenile animals where not all stages of spermatogenesis have been completed. We present single-cell RNA sequencing (scRNA-Seq) data of 2,500 cells from the testes of two 8-week-old C57Bl/6J mice. Our dataset includes all spermatogenic stages from preleptotene to condensing spermatids as well as individual spermatogonia, Sertoli and Leydig cells...
September 11, 2018: Scientific Data
https://www.readbyqxmd.com/read/30204152/whole-genome-sequencing-data-for-two-individuals-of-pakistani-descent
#7
Shahid Y Khan, Firoz Kabir, Oussama M'Hamdi, Xiaodong Jiao, Muhammad Asif Naeem, Shaheen N Khan, Sheikh Riazuddin, J Fielding Hejtmancik, S Amer Riazuddin
Here we report next-generation based whole genome sequencing of two individuals (H1 and H2) from a family of Pakistani descent. The genomic DNA was used to prepare paired-end libraries for whole-genome sequencing. Deep sequencing yielded 706.49 and 778.12 million mapped reads corresponding to 70.64 and 77.81 Gb sequence data and 23× and 25× average coverage for H1 and H2, respectively. Notably, a total of 448,544 and 470,683 novel variants, not present in the single nucleotide polymorphism database (dbSNP), were identified in H1 and H2, respectively...
September 11, 2018: Scientific Data
https://www.readbyqxmd.com/read/30179235/a-new-dataset-of-computed-tomography-angiography-images-for-computer-aided-detection-of-pulmonary-embolism
#8
Mojtaba Masoudi, Hamid-Reza Pourreza, Mahdi Saadatmand-Tarzjan, Noushin Eftekhari, Fateme Shafiee Zargar, Masoud Pezeshki Rad
The lack of publicly available datasets of computed-tomography angiography (CTA) images for pulmonary embolism (PE) is a problem felt by physicians and researchers. Although a number of computer-aided detection (CAD) systems have been developed for PE diagnosis, their performance is often evaluated using private datasets. In this paper, we introduce a new public dataset called FUMPE (standing for Ferdowsi University of Mashhad's PE dataset) which consists of three-dimensional PE-CTA images of 35 different subjects with 8792 slices in total...
September 4, 2018: Scientific Data
https://www.readbyqxmd.com/read/30179234/hisdac-us-historical-settlement-data-compilation-for-the-conterminous-united-states-over-200-years
#9
Stefan Leyk, Johannes H Uhl
Human settlement plays a key role in understanding social processes such as urbanization and interactions between human and environmental systems but not much is known about the landscape evolution before the era of operational remote sensing technology. In this study, housing and property databases are used to create new gridded settlement layers describing human settlement processes at fine spatial and temporal resolution in the conterminous United States between 1810 and 2015. The main products are a raster composite layer representing the year of first settlement, and a raster time series of built-up intensity representing the sum of building areas in a pixel...
September 4, 2018: Scientific Data
https://www.readbyqxmd.com/read/30179233/transcriptomic-analysis-of-left-right-differences-in-human-embryonic-forebrain-and-midbrain
#10
Carolien G F de Kovel, Steven N Lisgo, Clyde Francks
Left-right asymmetry is subtle but pervasive in the human central nervous system. This asymmetry is initiated early during development, but its mechanisms are poorly known. Forebrains and midbrains were dissected from six human embryos at Carnegie stages 15 or 16, one of which was female. The structures were divided into left and right sides, and RNA was isolated. RNA was sequenced with 100 base-pair paired ends using Illumina Hiseq 4000. After quality control, five paired brain sides were available for midbrain and forebrain...
September 4, 2018: Scientific Data
https://www.readbyqxmd.com/read/30179232/marine-microbial-metagenomes-sampled-across-space-and-time
#11
Steven J Biller, Paul M Berube, Keven Dooley, Madeline Williams, Brandon M Satinsky, Thomas Hackl, Shane L Hogle, Allison Coe, Kristin Bergauer, Heather A Bouman, Thomas J Browning, Daniele De Corte, Christel Hassler, Debbie Hulston, Jeremy E Jacquot, Elizabeth W Maas, Thomas Reinthaler, Eva Sintes, Taichi Yokokawa, Sallie W Chisholm
Recent advances in understanding the ecology of marine systems have been greatly facilitated by the growing availability of metagenomic data, which provide information on the identity, diversity and functional potential of the microbial community in a particular place and time. Here we present a dataset comprising over 5 terabases of metagenomic data from 610 samples spanning diverse regions of the Atlantic and Pacific Oceans. One set of metagenomes, collected on GEOTRACES cruises, captures large geographic transects at multiple depths per station...
September 4, 2018: Scientific Data
https://www.readbyqxmd.com/read/30179231/single-cell-genomes-of-prochlorococcus-synechococcus-and-sympatric-microbes-from-diverse-marine-environments
#12
Paul M Berube, Steven J Biller, Thomas Hackl, Shane L Hogle, Brandon M Satinsky, Jamie W Becker, Rogier Braakman, Sara B Collins, Libusha Kelly, Jessie Berta-Thompson, Allison Coe, Kristin Bergauer, Heather A Bouman, Thomas J Browning, Daniele De Corte, Christel Hassler, Yotam Hulata, Jeremy E Jacquot, Elizabeth W Maas, Thomas Reinthaler, Eva Sintes, Taichi Yokokawa, Debbie Lindell, Ramunas Stepanauskas, Sallie W Chisholm
Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups...
September 4, 2018: Scientific Data
https://www.readbyqxmd.com/read/30179230/imaging-and-clinical-data-archive-for-head-and-neck-squamous-cell-carcinoma-patients-treated-with-radiotherapy
#13
Aaron J Grossberg, Abdallah S R Mohamed, Hesham El Halawani, William C Bennett, Kirk E Smith, Tracy S Nolan, Bowman Williams, Sasikarn Chamchod, Jolien Heukelom, Michael E Kantor, Theodora Browne, Katherine A Hutcheson, G Brandon Gunn, Adam S Garden, William H Morrison, Steven J Frank, David I Rosenthal, John B Freymann, Clifton D Fuller
Cross sectional imaging is essential for the patient-specific planning and delivery of radiotherapy, a primary determinant of head and neck cancer outcomes. Due to challenges ensuring data quality and patient de-identification, publicly available datasets including diagnostic and radiation treatment planning imaging are scarce. In this data descriptor, we detail the collection and processing of computed tomography based imaging in 215 patients with head and neck squamous cell carcinoma that were treated with radiotherapy...
September 4, 2018: Scientific Data
https://www.readbyqxmd.com/read/30179229/high-resolution-temperature-data-for-ecological-research-and-management-on-the-southern-ocean-islands
#14
Rachel I Leihy, Grant A Duffy, Erika Nortje, Steven L Chown
Southern Ocean Islands are globally significant conservation areas. Predicting how their terrestrial ecosystems will respond to current and forecast climate change is essential for their management and requires high-quality temperature data at fine spatial resolutions. Existing datasets are inadequate for this purpose. Remote-sensed land surface temperature (LST) observations, such as those collected by satellite-mounted spectroradiometers, can provide high-resolution, spatially-continuous data for isolated locations...
September 4, 2018: Scientific Data
https://www.readbyqxmd.com/read/30179228/chemotactic-responses-of-growing-neurites-to-precisely-controlled-gradients-of-nerve-growth-factor
#15
Brendan A Bicknell, Zac Pujic, Julia Feldner, Irina Vetter, Geoffrey J Goodhill
Chemotaxis plays a key role in many biological systems. In particular in the context of the developing nervous system, growing neurites can respond in vitro to shallow gradients of chemotropic molecules such as nerve growth factor (NGF). However, in such studies the gradient parameters are often not well controlled. Here we present a dataset of ~3500 images of early postnatal rat dorsal root ganglion (DRG) explants growing in 40 different precisely controlled combinations of absolute concentration and gradient steepness of NGF...
September 4, 2018: Scientific Data
https://www.readbyqxmd.com/read/30152814/regional-scale-management-maps-for-forested-areas-of-the-southeastern-united-states-and-the-us-pacific-northwest
#16
Matthew Marsik, Caroline G Staub, William J Kleindl, Jaclyn M Hall, Chiung-Shiuan Fu, Di Yang, Forrest R Stevens, Michael W Binford
Forests in the United States are managed by multiple public and private entities making harmonization of available data and subsequent mapping of management challenging. We mapped four important types of forest management, production, ecological, passive, and preservation, at 250-meter spatial resolution in the Southeastern (SEUS) and Pacific Northwest (PNW) USA. Both ecologically and socio-economically dynamic regions, the SEUS and PNW forests represent, respectively, 22.0% and 10.4% of forests in the coterminous US...
August 28, 2018: Scientific Data
https://www.readbyqxmd.com/read/30152813/an-acquisition-curation-and-management-workflow-for-sustainable-terabyte-scale-marine-image-analysis
#17
Timm Schoening, Kevin Köser, Jens Greinert
Optical imaging is a common technique in ocean research. Diving robots, towed cameras, drop-cameras and TV-guided sampling gear: all produce image data of the underwater environment. Technological advances like 4K cameras, autonomous robots, high-capacity batteries and LED lighting now allow systematic optical monitoring at large spatial scale and shorter time but with increased data volume and velocity. Volume and velocity are further increased by growing fleets and emerging swarms of autonomous vehicles creating big data sets in parallel...
August 28, 2018: Scientific Data
https://www.readbyqxmd.com/read/30152812/sixty-one-thousand-recent-planktonic-foraminifera-from-the-atlantic-ocean
#18
Leanne E Elder, Allison Y Hsiang, Kaylea Nelson, Luke C Strotz, Sara S Kahanamoku, Pincelli M Hull
Marine microfossils record the environmental, ecological, and evolutionary dynamics of past oceans in temporally expanded sedimentary archives. Rapid imaging approaches provide a means of exploiting the primary advantage of this archive, the vast number of fossils, for evolution and ecology. Here we provide the first large scale image and 2D and 3D shape dataset of modern planktonic foraminifera, a major microfossil group, from 34 Atlantic Ocean sediment samples. Information on more than 124,000 objects is provided, including general object classification for 4/5ths of the dataset (~ 99,000 objects)...
August 28, 2018: Scientific Data
https://www.readbyqxmd.com/read/30152811/the-first-annotated-set-of-scanning-electron-microscopy-images-for-nanoscience
#19
Rossella Aversa, Mohammad Hadi Modarres, Stefano Cozzini, Regina Ciancio, Alberto Chiusole
In this paper, we present the first publicly available human-annotated dataset of images obtained by the Scanning Electron Microscopy (SEM). A total of roughly 26,000 SEM images at the nanoscale are classified into 10 categories to form 4 labeled training sets, suited for image recognition tasks. The selected categories span the range of 0D objects such as particles, 1D nanowires and fibres, 2D films and coated surfaces as well as patterned surfaces, and 3D structures such as microelectromechanical system (MEMS) devices and pillars...
August 28, 2018: Scientific Data
https://www.readbyqxmd.com/read/30152810/computational-workflow-to-study-the-seasonal-variation-of-secondary-metabolites-in-nine-different-bryophytes
#20
Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
In Eco-Metabolomics interactions are studied of non-model organisms in their natural environment and relations are made between biochemistry and ecological function. Current challenges when processing such metabolomics data involve complex experiment designs which are often carried out in large field campaigns involving multiple study factors, peak detection parameter settings, the high variation of metabolite profiles and the analysis of non-model species with scarcely characterised metabolomes. Here, we present a dataset generated from 108 samples of nine bryophyte species obtained in four seasons using an untargeted liquid chromatography coupled with mass spectrometry acquisition method (LC/MS)...
August 28, 2018: Scientific Data
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