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15,560 results for “How long”
Draft genome assembly of a Japanese Oikopleura dioica male individual (O3), using Nanopore long reads.
<p>This draft assembly was used to validate the chrY scaffolds of the OSKA2016 reference genome in the publication “A genome database for a Japanese population of the larvacean Oikopleura dioica”, Development Growth and Differentiation, Wang and coll., 2020 (in press). It is provided as supplemental data for the reproducibility of this work; please note that no further polishing has been done to correct sequencing errors.</p> <p>Genome sequence reads were produced on a MinION sequencer (Oxford Nanopore Technologies) using high-molecular weight DNA from a male individual of the Oikopleura dioica species of zooplankton. The individual was related to the laboratory strain established from a western Japanese population that was used to produce the OSKA2016 reference genome. The raw reads were basecalled with the Guppy software version 3.3.0 using its dna_r9.4.1_450bps algorithm, and deposited in the European Nucleotide Archive (Study ID: PRJEB38559). The draft assembly was made with the Flye software version 2.7 with the options --genome-size 65m and --min-overlap 3000.</p>
Metagenomics assemblies and high-quality MAGs for "Long-read metagenomics to retrieve high-quality metagenome-assembled genomes from canine feces"
<p>This dataset includes the different metagenomics assemblies analyzed and its summary (_info.txt file):</p> <p>- <a href="https://zenodo.org/api/files/3a502803-82f7-4b51-ac62-7c1dfcdcb680/100_assembly.fasta">100_assembly.fasta</a> is the Flye 2.7 metagenomics assembly merging HMW and non-HMW datasets</p> <p>- <a href="https://zenodo.org/api/files/3a502803-82f7-4b51-ac62-7c1dfcdcb680/75_assembly.fasta">75_assembly.fasta</a> is the Flye 2.7 metagenomics assembly including 75% of random data of the merged dataset.</p> <p>- <a href="https://zenodo.org/api/files/3a502803-82f7-4b51-ac62-7c1dfcdcb680/50_assembly.fasta">50_assembly.fasta</a> is the Flye 2.7 metagenomics assembly including 50% of random data of the merged dataset.</p> <p>- <a href="https://zenodo.org/api/files/3a502803-82f7-4b51-ac62-7c1dfcdcb680/HMW_assembly.fasta?versionId=749ff6fd-2642-4ad1-971a-7f3404baa595">HMW_assembly.fasta</a> is the Flye 2.7 metagenomics assembly for HMW dataset.</p> <p>Moreover, it also includes the eight frameshift-corrected high-quality MAGs analyzed in the manuscript. </p>
Long-term triaxial test of Passwang Marl, Z-orientation
<p>This data set describes a long-term (> 3 yr) rock mechanics experiment of Psswang Marl using a triaxial apparatus. The sample is consolidated and fully saturated. The bedding orientation is 45° to the main axis of the sample (Z-orientation). Confining stress, axial stress and pore pressure are changed multiple times in order to investigate dilatancy, pressure diffusion coefficients and Young's modulus.</p>
Vortex input files -- McHugh et al. Staying Alive: Long-term success of small cetacean interventions in southwest Florida
<p>Vortex input file used to generate population level impacts in the manuscript "Staying Alive: Long-term success of small cetacean interventions in southwest Florida", by K. A. McHugh, et al. </p>
Dataset for Dual Fraunhofer interference and charge fluctuations in long quantum phase slip wires, Phys. Rev. B 102, 144509 (2020)
<p>Dataset for manuscript 'Dual Fraunhofer interference and charge fluctuations in long quantum phase slip wires', Phys. Rev. B 102, 144509 (2020). Dataset contains data from numerical simulations presented in the manuscript and generating scripts. The data describes the quantum phase slip rate and its suppression due to charge and width disorder in superconducting nanowires in the phase slip regime. This disorder leads to temporal fluctuations which affects the current-voltage characteristics of nanowires. </p>
Data and analysis scripts associated with the paper 'Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history''
<p><em>Eva Bons, Christine Leemann, Karin J. Metzner, Roland R. Regoes</em></p> <p>This repository contains all the data and analysis scripts associated with the paper 'Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history'</p> <p>See the readme after unpacking the .zip for a description of the files</p>
LSTM-REG: regional gridded runoff dataset for northwest Russia based on Long Short-Term Memory (LSTM) networks
<p>LSTM-REG: regional gridded runoff dataset for northwest Russia.</p> <p>Model: LSTM.</p> <p>Geographical domain: 25–57°E; 55–70°N.</p> <p>Spatial resolution: 0.5°x0.5°.</p> <p>Temporal resolution: daily.</p> <p>Period: 1980-2016.</p>
Long-Term Global Satellite Soil Moisture from Maximized Temporal Correlations (1998-2015)
<p>A long-term merged satellite soil moisture product spanning 1998 to 2015. An existing combination approach that maximizes temporal correlations is used to combine six passive microwave satellite soil moisture products within the period. These include the Special Sensor Microwave Imagers (SSM/I), the Tropical Rainfall Measuring Mission (TRMM/TMI), the Advanced Microwave Scanning Radiometer-Earth Observing System (AMSR-E) sensor on the National Aeronautics and Space Administration’s (NASA) Aqua satellite, the WindSAT radiometer, onboard the Coriolis satellite and the soil moisture retrievals from the Advanced Microwave Scanning Radiometer 2 (AMSR2) sensor onboard the Global Change Observation Mission on Water (GCOM-W). The sixth is the microwave radiometer imager (MWRI) onboard China’s Fengyun-3B (FY3B) satellite, which is being used for the first time in a merging scheme. </p> <p>For more details on the quality of the data and the methodology used, please refer to the references listed:</p> <p>Hagan, D.F.T.; Wang, G.; Kim, S.; Parinussa, R.M.; Liu, Y.; Ullah, W.; Bhatti, A.S.; Ma, X.; Jiang, T.; Su, B. Maximizing Temporal Correlations in Long-Term Global Satellite Soil Moisture Data-Merging. Remote Sens. 2020, 12, 2164.</p> <p>Kim, S.; Parinussa, R.M.; Liu, Y.Y.; Johnson, F.M.; Sharma, A. A framework for combining multiple soil moisture retrievals based on maximizing temporal correlation. Geophys. Res. Lett. 2015, 42, 6662–6670.</p>
Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes - Database of Physical gene-gene Interactions in young adult C.elegans.
<p>This repository contains Supplementary Information for manuscript Suriyalaksh et al Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes corresponding to the curation of physical gene-gene interactions for young adult C elegans worms </p> <p>We manually curated 239,001 regulatory interactions from 289 young adult wild-type (WT) C.elegans datasets, consisting of 126 genes and 495 unique transcription factors (see TableS1_datasets_for_prior.csv for references). </p> <p>This repository contains 3 different files:</p> <p>TableS1_datasets_for_prior.csv - contains datasets used as sources for physical gene-gene or TF-gene interactions</p> <p>TableS2_physical_priors.xlsx - contains three tabs:<br> ChIPATAC - contains physical TF-gene interactions from 115 L4 or young-adult ChIP-seq datasets from modERN (Kudron et al., 2018) + ChIP-seq datasets (GSE28350, GSE81521) from (Hochbaum et. al, 2011, Li et. al, 2016).</p> <p>eY1HATAC- contains 3,501 TF-gene interactions from eY1H assay by Fuxman Bass et al. (2016).</p> <p>motifATAC - contains 202 unique TF DNA recognition motifs using “direct evidence” option from CiS-BP motif database (Weirauch et al., 2014), obtained through RTFBSDB R package (Wang et al., 2016) - see TableS1</p> <p>TableS3_WT_functional_priors.csv - contains functional knockdown data that we use as gold standard to validate inferred networks in Suriyalaksh et al. (see TableS1_datasets_for_prior.csv for sources)</p> <p>---</p> <p>Description of methodology to obtain regulatory interactions in TableS2:</p> <p>Regulatory sequences for each gene were acquired from ENSEMBL (Aken et al., 2017), obtained using biomaRt R package (accessed on 31st Oct 2017). This study used WBcel235/ce11 version of the C. elegans genome, and WormBase WS260 genome annotations.</p> <p>For motifs, TFs whose motifs overlapped with an open ATAC-seq region by at least one base pair were kept. For ChIP-seq, TF binding sites that overlapped with an open ATAC-seq region by at least one base pair were kept using bedtools intersect and bedtools merge commands.</p> <p>An interaction from a TF to a gene was inferred by aligning transcription start sites (TSS) using bedtools window commands with 1000 bp window size to the TF-binding locations from ChIP-seq and motifs.</p> <p>For eY1H data, an interaction is included if the TSS site of the target gene overlaps with an open ATAC-seq region by at least one base pair.</p> <p>For gene-gene interactions, of the 298 studies compiled in WormExp v1.0 database (Yang et al, 2016, updated 27/07/16), 98 studies were included in the database spanning 126 different genes (see Table S1 in this repository).</p>
Long document similarity datasets, Wikipedia excerptions for movies, video games and wine collections
<p>Three corpora in different domains extracted from Wikipedia.</p> <p>For all datasets, the figures and tables have been filtered out, as well as the categories and "see also" sections.</p> <p>The article structure, and particularly the sub-titles and paragraphs are kept in these datasets</p> <p> </p> <p><strong>Wines</strong></p> <p>Wikipedia wines dataset consists of 1635 articles from the wine domain. The extracted dataset consists of a non-trivial mixture of articles, including different wine categories, brands, wineries, grape types, and more. The ground-truth recommendations were crafted by a human sommelier, which annotated 92 source articles with ~10 ground-truth recommendations for each sample. Examples for ground-truth expert-based recommendations are </p> <ul> <li>Dom Pérignon - Moët & Chandon</li> <li>Pinot Meunier - Chardonnay</li> </ul> <p><strong>Movies</strong></p> <p>The Wikipedia movies dataset consists of 100385 articles describing different movies. The movies' articles may consist of text passages describing the plot, cast, production, reception, soundtrack, and more.<br> For this dataset, we have extracted a test set of ground truth annotations for 50 source articles using the "<a href="https://bestsimilar.com/">BestSimilar</a>" database. Each source articles is associated with a list of ${\scriptsize \sim}12$ most similar movies.<br> Examples for ground-truth expert-based recommendations are </p> <ul> <li>Schindler's List - The Pianist</li> <li>Lion King - The Jungle Book</li> </ul> <p><strong>Video games</strong></p> <p>The Wikipedia video games dataset consists of 21,935 articles reviewing video games from all genres and consoles. Each article may consist of a different combination of sections, including summary, gameplay, plot, production, etc. Examples for ground-truth expert-based recommendations are:</p> <ul> <li>Grand Theft Auto - Mafia</li> <li>Burnout Paradise - Forza Horizon 3</li> </ul>
Process map for casting a long-term experimental campaign on RC shrinkage cracking.
<p>This dataset presents the process map that was developed for the casting of a long-term experimental campaign on reinforced concrete (RC) slabs subjected to the combined effect of restrained shrinkage and vertical loads.<br> This experimental campaign was performed in the scope of the FCT project "IntegraCrete: A comprehensive multi-physics and multi-scale approach to the combined effects of applied loads and thermal/shrinkage deformations in reinforced concrete structures''.<br> The results from this experimental campaign are presented in Gomes et al (2020), while the conceptualization, planning and experimental procedures are described in detail in Gomes et al (2021). The latter is supported by this process map to describe the micromanagement plan that was devised for the casting day.<br> 14 people were involved in the casting of 3 slabs and 2 complementary specimens inside a highly instrumented climatic chamber, as well as 38 specimens for concrete characterization at different ages and 12 load blocks to use as vertical loads. This process map was developed with the standard Business Process Model and Notation (BPMN).</p>
Data from: Long-term, high frequency in situ measurements of intertidal mussel bed temperatures using biomimetic sensors
At a proximal level, the physiological impacts of global climate change on ectothermic organisms are manifest as changes in body temperatures. Especially for plants and animals exposed to direct solar radiation, body temperatures can be substantially different from air temperatures. We deployed biomimetic sensors that approximate the thermal characteristics of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers recorded temperatures at 10–30 min intervals nearly continuously at multiple intertidal elevations. Comparisons against direct measurements of mussel tissue temperature indicated errors of ~2.0–2.5 °C, during daily fluctuations that often exceeded 15°–20 °C. Geographic patterns in thermal stress based on biomimetic logger measurements were generally far more complex than anticipated based only on 'habitat-level' measurements of air or sea surface temperature. This unique data set provides an opportunity to link physiological measurements with spatially- and temporally-explicit field observations of body temperature.
Data from: Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014
<p>Understanding the transition of epidemic to endemic dengue transmission remains a challenge in regions where serotypes co-circulate and there is extensive human mobility. French Polynesia, an isolated group of 72 inhabited islands, distributed among five geographically separated subdivisions, has recorded mono-serotype epidemics since 1944, with long inter-epidemic periods of circulation. Laboratory confirmed cases have been recorded since 1978, enabling exploration of dengue epidemiology under monotypic conditions in an isolated, spatially structured geographical location. A database was constructed of confirmed dengue cases, geolocated to island for a 35-year period. Statistical analyses of viral establishment, persistence and fade-out as well as synchrony among subdivisions were performed. Seven monotypic and one heterotypic dengue epidemic occurred, followed by low-level viral circulation with a recrudescent epidemic occurring on one occasion. Incidence was asynchronous among the subdivisions. Complete viral die-out occurred on several occasions with invasion of a new serotype, but also in the absence of any novel serotype. Island population size had a strong impact on the establishment, persistence and fade-out of dengue cases and endemicity was estimated achievable only at a population size in excess of 175 000. Despite island remoteness and low population size, dengue cases were observed somewhere in French Polynesia almost constantly, in part due to the spatial structuration generating asynchrony among subdivisions. Long-term persistence of dengue virus in this group of island populations may be enabled by island hopping, although could equally be explained by a reservoir of sub-clinical infections on the most populated island, Tahiti.</p>
Data from: Long-term nitrous oxide fluxes in annual and perennial agricultural and unmanaged ecosystems in the upper Midwest USA
Differences in soil nitrous oxide (N2O) fluxes among ecosystems are often difficult to evaluate and predict due to high spatial and temporal variabilities and few direct experimental comparisons. For 20 years, we measured N2O fluxes in 11 ecosystems in southwest Michigan USA: four annual grain crops (corn–soybean–wheat rotations) managed with conventional, no-till, reduced input, or biologically based/organic inputs; three perennial crops (alfalfa, poplar, and conifers); and four unmanaged ecosystems of different successional age including mature forest. Average N2O emissions were higher from annual grain and N-fixing cropping systems than from nonleguminous perennial cropping systems and were low across unmanaged ecosystems. Among annual cropping systems full-rotation fluxes were indistinguishable from one another but rotation phase mattered. For example, those systems with cover crops and reduced fertilizer N emitted more N2O during the corn and soybean phases, but during the wheat phase fluxes were ~40% lower. Likewise, no-till did not differ from conventional tillage over the entire rotation but reduced emissions ~20% in the wheat phase and increased emissions 30–80% in the corn and soybean phases. Greenhouse gas intensity for the annual crops (flux per unit yield) was lowest for soybeans produced under conventional management, while for the 11 other crop × management combinations intensities were similar to one another. Among the fertilized systems, emissions ranged from 0.30 to 1.33 kg N2O-N ha−1 yr−1 and were best predicted by IPCC Tier 1 and ΔEF emission factor approaches. Annual cumulative fluxes from perennial systems were best explained by soil inline image pools (r2 = 0.72) but not so for annual crops, where management differences overrode simple correlations. Daily soil N2O emissions were poorly predicted by any measured variables. Overall, long-term measurements reveal lower fluxes in nonlegume perennial vegetation and, for conservatively fertilized annual crops, the overriding influence of rotation phase on annual fluxes.
Dataset for "Long-term extreme response of an offshore turbine: How accurate are contour-based estimates?"
<p>Datasets belonging to the paper "Long-term extreme response of an offshore turbine: How accurate are<br> contour-based estimates?" by Haselsteiner, Frieling, Mackay, Sander and Thoben.</p> <p>Available are:<br> * A 1000-year time series of hourly environmental conditions<br> * 516 1-hour time series of the mudline overturning moment, simulated using openFAST</p> <p> </p>
A survey of the sorghum transcriptome using single-molecule long reads
<p>Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyze transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single molecule real time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA of ~11,000 expressed genes and more than 2,100 novel genes. These results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyze Iso-Seq data from any organism.</p>
Lipid center-of-mass trajectory: long-time dynamics
<p>This file contains the center-of-mass coordinates of the lipid molecules in a Molecular Dynamics simulation of a hydrated lipid bilayer. The simulated system consists of 2033 POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) molecules and 57952 water beads (equivalent to 231808 water molecules), using the coarse-grained representation of the MARTINI force field. Note that the mass of a POPC molecule is significantly higher (936 g/mol) in this representation than the mass of a real POPC molecule (760 g/mol). The simulation was performed in an NVT ensemble at T = 320 K.</p> <p>This trajectory stores the long-time dynamics of the lipid centers of masses, sampled at a time step of 18 ps up to a total length of 600 ns. The short-time dynamics are available at http://dx.doi.org/10.5281/zenodo.61742.</p> <p>For a detailed description of the simulation, see the thesis of Sławomir Stachura, available at http://www.theses.fr/2014PA066239</p> <p>Two analyses of this simulation have already been published:</p> <ul> <li>S. Stachura and G.R. Kneller Anomalous lateral diffusion in lipid bilayers observed by molecular dynamics simulations with atomistic and coarse-grained force fields Mol. Sim. 40, 245-250 (2014) (http://dx.doi.org/10.1080/08927022.2013.840902)</li> <li>S. Stachura and G.R. Kneller Probing anomalous diffusion in frequency space J. Chem. Phys. 143, 191103 (2015) (http://dx.doi.org/10.1063/1.4936129)</li> </ul> <p>This work was funded by the French Agence Nationale de la Recherche (Contract No. ANR- 2010-COSI-01-001).</p> <p><strong>Trajectory data</strong></p> <p>The trajectory is stored in an HDF5 file that uses the ActivePapers conventions (http://www.activepapers.org/). Any HDF5-compatible software can be used to read the trajectory data. The ActivePapers software is only required to re-use the included conversion script.</p> <p>The trajectory is contained in the group<br /> /data/POPC_martini_nvt</p> <p>It is stored in H5MD/MOSAIC format. The positions and time labels are contained in the following datasets:<br /> /data/POPC_martini_nvt/particles/universe/position/value<br /> /data/POPC_martini_nvt/particles/universe/position/time</p> <p>For a complete specification of the H5MD/MOSAIC format, see:<br /> http://nongnu.org/h5md/index.html<br /> http://mosaic-data-model.github.io/mosaic-specification/h5md_mosaic_module.html</p> <p><strong>Plots</strong></p> <p>Two 3D plots are provided to give an overview of the lipid motions:<br /> /documentation/all_lipids.pdf<br /> shows all the lipid center-of-mass positions once every 0.3 ps.<br /> /documentation/one_lipids.pdf<br /> shows a single lipid center of mass position every 10 ps.</p>
FIGURE 4 in A new genus of longhorned caddisfly from the Amazon basin (Trichoptera: Leptoceridae: Grumichellini)
FIGURE 4. Amazonatolica hamadae, new species. Male genitalia: A—lateral; B—inferior appendage, ventral; C—segments IX & X, dorsal; D—phallus, lateral; E—apex of phallus, enlarged, lateral; F—apex of phallus, enlarged, ventral.
FIGURE 9 in A new genus of longhorned caddisfly from the Amazon basin (Trichoptera: Leptoceridae: Grumichellini)
FIGURE 9. Amazonatolica hamadae, new species. Pupa: A—abdomen, abdominal hook plates, enlarged; B—head, frontal, mandible enlarged; C—anterior silken membrane of pupal case.
FIGURE 3. Terrapotamon longitarsus n in A new species of long-legged terrestrial Terrapotamon Ng, 1986 (Crustacea: Brachyura: Potamidae) from limestone formations in Satun, southern Thailand
FIGURE 3. Terrapotamon longitarsus n. sp. Overall habitus. A, male (35.0 × 29.5 mm) (ZRC 2016.0162 a); B, paratype male (28.4 × 23.8 mm) (PSUZC 20150611 - 01.01); C, female (23.8 × 20.2 mm) (ZRC 2016.0162 b).
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.