Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,449
datasets available to search
ShareScore release 0.9.0
Dataset results
1,449 results for “stranded”
Strandings of marine mammals, sea turtles and seabirds along the northern São Paulo coast, Brazil, from 2015 to 2018.
<p><span><span><span>To assess the potential impacts on seabirds, turtles and marine mammals from oil and gas production from the oceanic Pre-Salt province at Brazil's Santos Basin, the Brazilian environmental agency (IBAMA) required PETROBRAS, the main oil company in the basin, to implement the "Programa de Monitoramento de Praias da Bacia de Santos" (Santos Basin Beach Monitoring Program - PMP-BS). Since 2015 PMP-BS has been operating along the states of Santa Catarina, Paraná, São Paulo and Rio de Janeiro, to collect biological data from live and dead stranded animals. This dataset comprises the first three years of monitoring (September 2015 to August 2018) along the northern São Paulo State coastline, from 23°22'17.366" S 44°47'0.479" W to 23°45'24.046" S 45°50'23.335" W. During this period, 5450 animals of 47 species were recorded, 82.11% of which were dead and 17.89% alive when first observed. This dataset represents the first high-intensity monitoring effort in the area and is essential to establish baselines for future work that seek to better understand the impacts of human activities on marine ecosystems.</span></span></span></p>
Strandings of marine mammals, sea turtles and seabirds along central Santa Catarina coast, Brazil, from 2015 to 2018.
<p><span><span><span>To assess the potential impacts on seabirds, turtles and marine mammals from oil and gas production from the oceanic Pre-Salt province at Brazil's Santos Basin, the Brazilian environmental agency (IBAMA) required PETROBRAS, the main oil company in the basin, to implement the "Programa de Monitoramento de Praias da Bacia de Santos" (Santos Basin Beach Monitoring Program - PMP-BS). Since 2015 PMP-BS has been operating along the states of Santa Catarina, Paraná, São Paulo and Rio de Janeiro, to collect biological data from live and dead stranded animals. This dataset comprises the first three years of monitoring (September 2015 to August 2018) along Santa Catarina state's central coast, from 27°23'7.357" S 48°26'2.519" W to 27°50'24.231" S 48°33'48.706" W. During this period, 5497 animals of 46 species were recorded, 86.90% of which were dead and 13.10% alive when first observed This dataset represents the first high-intensity monitoring effort in the area and is essential to establish baselines for future work that seek to better understand the impacts of human activities on marine ecosystems.</span></span></span></p>
Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double stranded DNA viruses
Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double stranded (ds) DNA viruses is limited. Here we sequenced the genome of a baculovirus (AcMNPV) purified from beet armyworm (Spodoptera exigua) larvae at depths >195,000X using both short-read (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total of 1,141 SVs in AcMNPV, including 464 deletions, 443 inversions, 160 duplications and 74 insertions. These variants are considered robust and unlikely to result from technical artifacts because they were independently detected in at least three long reads as well as at least three short reads. SVs are distributed along the entire AcMNPV genome and may involve large genomic regions (30,496 bp on average). We show that no less than 39.9% of genomes carry at least one SV in AcMNPV populations, that the vast majority of SVs (75%) segregate at very low frequency (<0.01%) and that very few SVs persist after 10 replication cycles, consistent with a negative impact of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we then show that populations of two iridoviruses and one herpesvirus are also full of SVs, as they contain between 426 and 1102 SVs carried by 52.4 to 80.1% of genomes. Finally, AcMNPV long reads allowed us to identify 1,757 transposable elements (TEs) insertions, 895 of which are truncated and occur at one extremity of the reads. This further supports the role of baculoviruses as possible vectors of horizontal transfer of TEs. Altogether, we found that SVs, which evolve mostly under rapid dynamics of gain and loss in viral populations, represent an important feature in the biology of large dsDNA viruses.
Strandings of marine mammals, sea turtles and seabirds along the central-south coast of São Paulo, Brazil, from 2015 to 2018.
<p><span><span><span>To assess the potential impacts on seabirds, turtles and marine mammals from oil and gas production from the oceanic Pre-Salt province at Brazil's Santos Basin, the Brazilian environmental agency (IBAMA) required PETROBRAS, the main oil company in the basin, to implement the "Programa de Monitoramento de Praias da Bacia de Santos" (Santos Basin Beach Monitoring Program - PMP-BS). Since 2015 PMP-BS has been operating along the states of Santa Catarina, Paraná, São Paulo and Rio de Janeiro, to collect biological data from live and dead stranded animals. This dataset comprises the first three years of monitoring (September 2015 to August 2018) along the central-south São Paulo state coastline, from 24°1'1.248" S 46°23'52.026" W to 24°26'49.147" S 47°4'49.505" W. During this period, 3790 animals of 47 species were recorded, 94.88% of which were dead and 5.12% alive when first observed. This dataset represents the first high-intensity monitoring effort in the area and is essential to establish baselines for future work that seek to better understand the impacts of human activities on marine ecosystems.</span></span></span></p>
Microscopy image data of a titration series with DNA surface strands and condensate-forming DNA nanomotifs (repeat)
<p>The dataset contains microscopy image data of DNA-nanomotifs (color channel 2) that can form liquid-like condensates, especially in association with target DNA strands that can act as condensation surfaces (color channel 1). The data were recorded on a VisiTech iSIM microscopy with a 40X water immersion objective (Apo LWD 40x WI λS DIC N2, NA 1.15). Images were recorded using dual ORCA-Flash4.0 V3 cameras with simultaneous two-channel acquisition to avoid displacement of objects due to consecutive acquisition of color channels. The file names contain the flow channel number, the presence of condensation surfaces (SX4), and the amount of added nanomotif solution in microliters (NX in µl).</p> <p>The image files are in the .nd2 Nikon proprietary format, but can be read with the OME bioformats libraries.</p> <p>Scripts for the analysis of these data are available via a GitHub repository: <a href="https://github.com/lhilbert/SurfacesAndCondensates" target="_blank" rel="noopener">https://github.com/lhilbert/SurfacesAndCondensates</a></p> <p>This repository contains data recorded on 10 March, 2023</p> <p>The file size of data were too large, so additional repositories were opened. The complete date need to be also downloaded from these additional repositories:</p> <p>EXTRA DATA 1/2: 10.5281/zenodo.13788977</p> <pre><a href="https://doi.org/10.5281/zenodo.13788977" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13788977</a></pre> <p>EXTRA DATA 2/2: 10.5281/zenodo.13789555</p> <pre><a href="https://doi.org/10.5281/zenodo.13789555" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13789555</a></pre> <pre> </pre> <p>There is another data set that contains a repeat of the same conditions, recorded on 13 March, 2023, under the following link</p> <pre><a href="https://doi.org/10.5281/zenodo.13788484" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13788484</a></pre> <p><br>From these data sets, two concentration conditions were excluded from further analysis, as described in the file <a href="https://zenodo.org/api/records/15231478/draft/files/Zenodo_Titration_Exclusions.pdf/content" target="_blank" rel="noopener noreferrer">Zenodo_Titration_Exclusions.pdf</a></p>
Dataset for Simulation-guided engineering of split GFPs with efficient β-strand photodissociation
<p>Files associated with performed experiments and simulations, including source data from experimental measurements and simulations, starting structures, parameters, simulation input files, and short videos of simulation trajectories. </p><p>Simulation files include:</p><ul><li>Initial coordinates of the GFP chromophore for geometry optimization and RESP calculations in GAUSSIAN</li><li>Parameter and starting files for QM/MM calculations around the conical intersection in TeraChem</li><li>Parameter, coordinate and input files for regular MD and simulated annealing simulations in AMBER</li><li>Parameter, coordinate and input files for umbrella sampling simulations of isomerization in AMBER</li><li>Results files from TeraChem</li></ul><p>Additionally, short videos are included of simulations of the <i>cis</i> and <i>trans</i> conformations.</p><p>Experimental source data include: </p><ul><li>UV-vis data from strand-exchange experiments</li><li>Mass spectrometry data</li><li>Fluorescence data</li></ul>
Figs 1–4 in THREE NEW SPECIES OF THE GENUS CASIGNETELLA STRAND, 1928 (LEPIDOPTERA: COLEOPHORIDAE) FROM SOUTHERN SIBERIA
Figs 1–4. Casignetella pseudohelgada sp. n., holotype. 1 – imago; 2 – spine plates on
Figs 8–11 in THREE NEW SPECIES OF THE GENUS CASIGNETELLA STRAND, 1928 (LEPIDOPTERA: COLEOPHORIDAE) FROM SOUTHERN SIBERIA
Figs 8–11. Casignetella sibirolinosyris sp. n., holotype. 8 – imago; 9 – spiny plates on
Figs 5–7 in THREE NEW SPECIES OF THE GENUS CASIGNETELLA STRAND, 1928 (LEPIDOPTERA: COLEOPHORIDAE) FROM SOUTHERN SIBERIA
Figs 5–7. Casignetella pseudoheihensis sp. n., holotype. 5 – imago; 6 – spiny plates on
California Sea Lion Stranding Records from Quantifying the linkages between California sea lion (Zalophus californianus) strandings and particulate domoic acid concentrations at piers across Southern California
<p>Pacific Marine Mammal Center (PMMC) is a member of the West Coast Marine Mammal Stranding Network, which was established under the United States Marine Mammal Protection Act by the National Oceanic and Atmospheric Administration (NOAA) to respond to stranded marine mammals. PMMC rescues, rehabilitates, and releases sick and injured marine mammals along the Orange County coastline, which is approximately 68 km of the Southern California coastline (<strong>Figure 1</strong>). All marine mammal rescue and rehabilitation activities are conducted by PMMC under a Stranding Agreement with National Marine Fisheries Service/NOAA.</p> <p>Patient case records from 2015-2019 for California sea lions (hereafter, sea lions) were reviewed and collated for each animal’s case presentation including sex, age class, seizure activity, postictal signs, comatose, abortion, and whether the sea lion was diagnosed by the attending veterinarian with domoic acid intoxication following the behavioral diagnostic criteria outlined by Gulland et al., <a href="https://www.zotero.org/google-docs/?XUrLiy">(2002)</a>. Multiple veterinarians made diagnoses during the time series based on these criteria which may have introduced some variation in the diagnosis of domoic acid intoxication during the study period. Age classes were defined following Greig et al. <a href="https://www.zotero.org/google-docs/?DGqEGG">(2005)</a> using dentition, straight length, pregnancy status, and sexual dimorphism to classify a sea lion’s age class. The following demographic categories are included in this study: juvenile/subadult male, subadult female, adult male, and adult female. Younger sea lions in the pup and yearling age classes were excluded as sea lions within these age classes are generally the most common patients at the center and often strand due to malnutrition <a href="https://www.zotero.org/google-docs/?eTzjbp">(Bejarano et al., 2008a)</a>, and rarely present with acute or chronic domoic acid intoxication during blooms. Adult and subadult age classes are the most commonly affected by domoic acid intoxication <a href="https://www.zotero.org/google-docs/?6xP9cn">(Bejarano et al., 2008a)</a>. Only live sea lions that were rescued on the Orange County coastline, brought to PMMC's facility, and assessed by the attending veterinarian were included. Adult and subadult sea lions that died on the beach were excluded from the study cohort because an attending veterinarian could not assess clinical signs to diagnosis domoic acid intoxication prior to death.</p>
Single-Stranded DNA with Internal Base Modifications Mediates Highly Efficient Gene Insertion in Primary Cells
<p>The manuscript describes the use of ssDNA with chemical modifications in internal bases to improve gene insertion. The dataset contains an excel file with the data corresponding to the figures in this manuscript. In addition, it has results from next-generation sequencing used in Figure 2B. </p>
Illumina TruSeq stranded mRNA sequences of Rhynchosporium commune isolate UK7 in plantae
<p>Transcription profiles were generated from the <em>Rhynchosporium commune</em> isolate UK7. RNA-seq experiments were conducted <em>in plantae</em> on the barley cultivar Beatrix (Viskosa 9 Pasadena, Saaten Union, breeders’ Reference NS01/2449). Leaves were collected at 9 and at 13 days post infection (dpi). All experiments were conducted in triplicates. Total RNA was extracted using TRIzol (Invitrogen Inc.) following the manufacturer’s recommendations. RNA integrity and quantity was assessed on a Bioanalyzer 2100 (Agilent) and a Qubit fluorometer (Life Technologies) and a Bioanalyzer 2100. Libraries were prepared using the TruSeq stranded mRNA sample prep kit (Illumina Inc.). Total RNA was ribosome-depleted by using polyA selection and reverse-transcribed into double-stranded cDNA.</p>
Illumina TruSeq stranded mRNA sequences of Rhynchosporium commune isolate UK7 in vitro
<p>Transcription profiles were generated from the <em>Rhynchosporium commune</em> isolate UK7. Cultures were grown either on Luria-Bertani (LBA) or Potato Dextrose Broth (PDB) media. Total RNA was extracted using TRIzol (Invitrogen Inc.) following the manufacturer’s recommendations. Experiments were conducted in triplicates. RNA integrity and quantity was assessed on a Bioanalyzer 2100 (Agilent) and a Qubit fluorometer (Life Technologies) and a Bioanalyzer 2100. Libraries were prepared using the TruSeq stranded mRNA sample prep kit (Illumina Inc.). Total RNA was ribosome-depleted by using polyA selection and reverse-transcribed into double-stranded cDNA.</p>
Data from Schaffter, S.W. and Strychalski, E.A. "Co-transcriptionally encoded RNA strand displacement circuits" Science Advances (2022)
<p>The <strong>ctRSD_data_upload.xlsx</strong> file contains both the raw and normalized fluorescence data from this manuscript.</p> <p>In the Excel file, rows highlighted in green indicate the times when T7 RNAP was added to the samples. Plots of data in the manuscript designate this time as time = 0 min.</p> <p>The <strong>figure2D_fluorescence_data_plotting.py</strong> file is an example showing how the data was imported from the Excel file and plotted in the manuscript.</p> <p>In the script, the save_loc variable will need to be changed to the path pointing to where the ctRSD_data_upload.xlsx file (Data S1) is saved on a user’s local computer.</p>
Microscopy data from: Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli
<p>Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in <em>Escherichia coli</em>. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in <em>E. coli</em> and other bacteria. Three replication restart pathways have been identified in <em>E. coli</em>: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the <em>priB</em> replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel <em>priB </em>interactions were discovered. Far fewer connections were found with the PriA/PriC or PriC/Rep pathways, suggesting a primacy role for the PriA/PriB pathway in <em>E. coli</em>. Targeted genetic and imaging-based experiments with <em>priB</em> and its genetic partners revealed significant double-strand DNA break (DSB) accumulation in strains with mutations in <em>dam</em>, <em>rep</em>, <em>rdgC</em>, <em>lexA</em>, or <em>polA</em>. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of <em>rdgC</em> or <em>lexA</em> mutations in Δ<em>priB</em> cells. Taken together, our results highlight roles for several genes in DSB homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in <em>E. coli</em>.</p>
RBBP4 regulates the expression of Mre11-Rad50-NBS1(MRN)complex and promotes DNA double-strand breaks repair to mediate glioblastoma Chemoradiotherapy resistance
<p>Article <a>related</a> SUPPLEMENTARY data.</p> <p> </p>
Figure 3 in First record of Thiania cf. subopressa Strand 1907 (Araneae: Salticidae: Euophryini) from India with some natural history notes on the species
Figure 3 (continued on next page). Representative Thiania species from southeastern Asia. 1, Female T. bhamoensis, 10 JUN 2019, Penang, Malaysia. 2, Male T. bhamoensis, 7 MAY 2018, Penang, Malaysia. Photographs posted at iNaturalist © Richard Ong, used under a Creative Commons Attribution-NonCommercial 4.0 International License (CC-BY-NC 4.0).
Figure 2 in First record of Thiania cf. subopressa Strand 1907 (Araneae: Salticidae: Euophryini) from India with some natural history notes on the species
Figure 2. Thiania cf. subopressa in Agartala, Tripura, India. 1, Female in nest between two leaves, held together with silk rivets (upper left). 2, View of entrance to nest that contained spiderlings, with dry upper leaf. 3-4, Spiderlings near the nest. Photographs by Atanu Chakraborti.
Figure 3 in First record of Thiania cf. subopressa Strand 1907 (Araneae: Salticidae: Euophryini) from India with some natural history notes on the species
Figure 3 (continued from previous page). Representative Thiania species from southeastern Asia. 3, Female T. bhamoensis, 23 AUG 2016, feeding on a female Myrmarachne sp., Labrador Villa Road, Singapore, © budak. 4, T. cf. bhamoensis, 11 JUN 2017, Penang, Malaysia, © Robin Bad. 5, Female T. cf. subopressa, Tawau Hill, Singapore, © Nicky Bay, used with permission. 6, T. cf. subopressa feeding on ant, 1 AUG 2018, Hong Kong, © wklegend. 7, Female T. latefasciata, 6 OCT 2016, Botanic Gardens, Singapore, © budak. 8, Female T. latefasciata, 18 MAY 2019, Botanic Gardens, Singapore, © budak. Photographs 3-4, 6-8 posted at iNaturalist, used under a Creative Commons Attribution-NonCommercial 4.0 International License (CC-BY-NC 4.0).
Figure 1 in First record of Thiania cf. subopressa Strand 1907 (Araneae: Salticidae: Euophryini) from India with some natural history notes on the species
Figure 1. Adult female Thiania cf. subopressa in Agartala, Tripura, India. Note the black eye region. Legs I are also completely black except for the coxae and the tarsi. Behind the eye region the carapace is wide and flat. Photographs by Atanu Chakraborti.
ScienceDex guides
Understand access before you commit
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.