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3,481 results for “data set”
Data from: PMSeeker: A Scheme for paternity marker set mining
<p>The paternity test is a genetic test that analyzes genetic characteristics (mostly molecular markers) to identify whether two individuals have a parent-child relationship. It is frequently employed in judicial identification and economic species breeding. Because a single marker's discriminability is restricted, numerous markers are typically utilized to produce an accurate result. Obviously, having an excessive number of redundant markers wastes time and resources, and adequate approaches are required to screen reduced and efficient paternity marker sets (PMS). This study established a non-redundant PMS-screening scheme based on the exhaustive algorithm and greedy algorithm. When screening PMS, the greedy algorithm selects markers based on the parental dispersity index (PDI), a uniquely defined metric that outperforms polymorphic information content (PIC) and probability of exclusion (PE). With the conjunctive use of the two algorithms the optimal solutions were found for more than 99.7% of solvable cases in three groups of random sample experiments in this study. This scheme effectively reduces the number of markers in PMS, so conserving people and experimental resources and laying the groundwork for the widespread implementation of paternity assignment technology in economic species breeding.</p>
Experimental data set of manuscript
<p>All experimental data of a manuscript submitted to GRL</p>
Data set for combined influence of food availability and agricultural intensification on a declining aerial insectivore
<p>Aerial insectivores show worldwide population declines coinciding with shifts in agricultural practices. Increasing reliance on certain agricultural practices is thought to have led to an overall reduction in insect abundance that negatively affects aerial insectivore fitness. The relationship between prey availability and the fitness of insectivores may thus vary with the extent of agricultural intensity. It is therefore imperative to quantify the strength and direction of these associations. Here we used data from an 11-year study monitoring the breeding of Tree Swallows (<em>Tachycineta bicolor</em>) and the availability of Diptera (their main prey) across a gradient of agricultural intensification in southern Québec, Canada. This gradient was characterized by a shift in agricultural production, whereby landscapes composed of forage and pastures represented less agro-intensive landscapes and those focusing on large-scale arable row crop monocultures, such as corn (<em>Zea mays</em>) or soybean (<em>Glycine max</em>) that are innately associated with significant mechanization and agro-chemical inputs, represented more agro-intensive landscapes. We evaluated the landscape characteristics affecting prey availability, and how this relationship influences the fledging success, duration of the nestling period, fledgling body mass, and wing length as these variables are known to influence the population dynamics of this species. Diptera availability was greatest within predominately forested landscapes, while within landscapes dominated by agriculture, it was marginally greater in less agro-intensive areas. Of the measured fitness and body condition proxies, both fledging success and nestling body mass were positively related to prey availability. The impact of prey availability varied across the agricultural gradient as fledging success improved with increasing prey levels within forage landscapes yet declined in more agro-intensive landscapes. Finally, after accounting for prey availability, fledging success was lowest, nestling periods were the longest, and wing length of fledglings were shortest within more agro-intensive landscapes. Our results highlight the interacting roles that aerial insect availability and agricultural intensification have on the fitness of aerial insectivores, and by extension how food availability may interact with other aspects of breeding habitats to influence the population dynamics of predators.</p>
Data Sets and plotting scripts supporting Kirsten et al. 2022, DOI: 10.1038/s41586-021-04354-w
<p>Data Sets and plotting scripts supporting Kirsten et al. 2022, DOI: 10.1038/s41586-021-04354-w</p>
MPAS-Seaice v1.0.0 data set
<p>MPAS-Seaice v1.0.0 data set</p>
Data set for EMPIR project MeDDII Report D2
<p>Data set for the D2 of project MeDDII - Comparison on microflow</p>
Data set for hydraulic fracture interactions with discontinuities study
<p>Data set used to generate results for hydraulic fracture interaction with discontinuities study</p>
Darwin's Hawkmoth (Xanthopan praedicta) responds to bat ultrasound at sonar-jamming rates: Acoustic data set
<p>This paper reveals that <em>Xanthopan praedicta</em> (Lepidoptera: Sphingidae) is part of the bat-moth coevolutionary dynamic. I played recordings of bat echolocation to live <em>X. praedicta</em> and found that males respond with such dense ultrasound they can likely jam bat sonar. Female <em>X. praedicta</em> and two other sphingid species do not produce ultrasonic responses.</p>
Data sets for Interacting effects of cold snaps, rain, and agriculture on the fledging success of a declining aerial insectivore
<p>Climate change predicts the increased frequency, duration, and intensity of inclement weather periods, such as unseasonably low temperatures (i.e., cold snaps) and prolonged precipitation. Many migratory species have advanced the phenology of important life history stages, and as a result will likely be exposed to these periods of inclement spring weather more often, thus risking reduced fitness and population growth. For declining avian species, including aerial insectivores, anthropogenic landscape changes such as agricultural intensification are another driver of population declines. These landscape changes may affect the foraging ability of food provisioning parents, and reduce the survival of nestlings exposed to inclement weather, through for example pesticide exposure impairing thermoregulation and punctual anorexia. Breeding in agro-intensive landscapes may thus exacerbate the negative effects of inclement weather under climate change. We observed that a significant reduction in the availability of insect prey occurred when daily maximum temperatures fell below 18.3°C, and thereby defined any day where the maximum temperature fell below this value as a day witnessing a cold snap. We then combined daily information on the occurrence of cold snaps and measures of precipitation to assess their impact on the fledging success of Tree Swallows (<em>Tachycineta bicolor</em>) occupying a nest box system placed across a gradient of agricultural intensification. Estimated fledging success of this declining aerial insectivore was 36.2% lower for broods experiencing four cold snap days during the 12 days post hatching period versus broods experiencing none, and this relationship was worsened when facing more precipitation. We further found that the overall negative effects of a brood experiencing periods of inclement weather was exacerbated in more agro-intensive landscapes. Our results indicate that two of the primary hypothesized drivers of many avian population declines may interact to further increase the rate of declines in certain landscape contexts.</p>
Data set for behavioural OA experiments with Caribbean Damselfish (Stegastes partitus)
<p>The neurobehavioural responses of fish exposed to ocean acidification (OA) are variable, possibly due to species-specific differences or involvement of multiple neuronal receptors. Here, we investigated behavioural responses of bicolor damselfish (Stegastes partitus) to OA and the involvement of dopamine receptors. Damselfish were exposed to control (pH 8.06; CO2 ~400 <span>μ</span>atm) or OA (pH 7.73; CO2 ~1,000 <span>μ</span>atm) seawater for five days, subjected to the open field, novel object approach, light/dark, and mirror-aggression tests, and returned to their respective aquaria. Two days later, tests were repeated upon treatment with the dopamine D1 receptor agonist SKF 38393. The D1 agonist, but not OA, altered locomotion in the open field test and boldness in the novel object approach test. Both the D1 agonist and OA increased anxiety-like behaviour in the light/dark test.</p>
Astra Memory Error and System Monitoring Data Sets
<p>Memory error events and system monitoring information gathered on Astra while it was operating from January 20, 2019 to September 14, 2019. See the dataset description files in the archive for additional details.</p>
Structural conversion of α-synuclein at the mitochondria induces neuronal toxicity; Data sets
<p>Lists of data sets included in <strong>"Structural conversion of α-synuclein at the mitochondria induces neuronal toxicity"</strong></p> <p> </p> <p>Single-molecule confocal Quantification_Images (SNCA-A53T TIRF Images)</p> <p>TIRF Image Quantification</p> <p>TIRF Emission Data</p> <p>Single Vesicle Emission Data</p> <p>DLS Emission Data</p> <p>CD Measurements</p> <p>Amyloid Fibril TIRFM Emission Data </p> <p>α-Syn WT, A53T, A30P and E46K Confirmatory LCMS </p> <p>SNCA A53T iPSC mutation confirmatory Sanger Sequencing</p> <p>ELISA</p> <p>Immunocytochemistry (MAP2 and TRB1)</p> <p>Pierce BCA Protein Assay</p> <p>Aggregation Assay</p> <p>Copy of Empiar_upload_info (CLEM quantification); metadata spreadsheet for TEM and FIB-SEM Image Quantification</p> <p>Live-cell imaging data</p> <ul> <li>Superoxide Emission Data</li> <li>MitoTracker® Red Emission Data</li> <li>MembranePotentialEmissionData (the same experiment for ' TMRM Emission data')</li> <li>Ca 2+ Emission Data</li> <li>NADH Autofluorescence and Redox Quantification</li> <li>ATP Emission Data</li> <li>mPTP Emission Data</li> <li>Cell Death Emission Data (PI & SYTOX)</li> <li>FRET Emission Data</li> <li>MitoTracker® Red Assay</li> <li>Cell Death Assay</li> </ul>
Data set on: New finds of naked amoebae in the Black Sea (Ukraine)
<p>Our research identified 12 species of naked amoebae of eight morphotypes in the Black Sea (coastal zone of Zatoka village, Odessa region). In more than half of the samples, Vannella devonica, Vannella aberdonica and Thecamoeba orbis were present. The species Saccamoeba marina, Vexillifera armata, Vannella plurinucleolus, Cochliopodium gulosum, and Stenamoeba sp. were rare and infrequent in our samples. The upper layers of the bottom sediment were inhabited by all 12 species of amoebae; two layers were inhabited by S. marina, V. armata, V. devonica, V. aberdonica, Mayorella gemmifera, T. orbis, Stenamoeba sp., Acanthamoeba griffin; three layers were colonized by V. armata, V. devonica, V. aberdonica, T. orbis, Stenamoeba sp., and A. griffini. All amoebae species and their morphotypes occurred at Black Sea water temperatures of +22 ºС to +26 ºС and salinity of 15.5 ‰ to 17.6 ‰. The species V. simplex and A. griffini, which belong to the fan–shaped and acanthopodial morphotypes, respectively, were collected in samples from the Mediterranean Sea at water temperatures of +29 ºС and salinity of 37.8 ‰. The amoebas identified belong to two classes, seven orders, eight families and eight genera.</p> <p> </p>
Patterns and drivers of the global diversity of non-native macrofungi [DATA SET]
<p>Data sets used in manuscript: <strong>Patterns and drivers of the global diversity of non-native macrofungi.</strong></p>
Training data set for inverse pyrolysis machine learning
<p>For dataset description see https://doi.org/10.5281/zenodo.6606247</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 05
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 05 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR. The recorded area shows the profiles of a few ciliated cells which are structurally impaired by vesiculation, probably due to the sampling and storage before fixation. Only few organelles are detectable, including nucleus and some of the mitochondria. The cells are surrounded by cellular debris and heterogenous material (e.g. membrane lamella, needle-like crystals, round profiles with a fine-fibrous matrix). Virus particles are not visible.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Data from: Model choice for phylogeographic inference using a large set of models
Model-based analyses are common in phylogeographic inference because they parameterize processes such as population division, gene flow and expansion that are of interest to biologists. Approximate Bayesian Computation is a model-based approach that can be customized to any empirical system and used to calculate the relative posterior probability of several models, provided that suitable models can be identified for comparison. The question of how to identify suitable models is explored using data from Plethodon idahoensis, a salamander that inhabits the North American inland northwest temperate rainforest. First, we conduct an ABC analysis using five models suggested by previous research, calculate the relative posterior probabilities, and find that a simple model of population isolation has the best fit to the data (PP = 0.70). In contrast to this subjective choice of models to include in the analysis, we also specify models in a more objective manner by simulating prior distributions for 143 models that included panmixia, population isolation, change in effective population size, migration, and range expansion. We then identify a smaller subset of models for comparison by generating an expectation of the highest posterior probability that a false model is likely to achieve due to chance and calculate the relative posterior probabilities of only those models that exceed this expected level. A model that parameterized divergence with population expansion and gene flow in one direction, offered the best fit to the P. idahoensis data (in contrast to an isolation only model from the first analysis). Our investigation demonstrates that the determination of which models to include in ABC model choice experiments is a vital component of model-based phylogeographic analysis.
Data set for "A neuronal mechanism for motivational control of behavior"
<p>Acting to achieve goals depends on the ability to motivate specific behaviors based on their predicted consequences given an individual’s internal state. However, the underlying neuronal mechanisms that encode and maintain such specific motivational control of behavior are poorly understood. Here, we used Ca2+ imaging and optogenetic manipulations in the basolateral amygdala of freely moving mice performing non-cued, self-paced instrumental goal-directed actions to receive and consume rewards. We found that distinct neuronal activity patterns sequentially represent the entire action-consumption behavioral sequence. Whereas action-associated patterns integrated the identity, value, and expectancy of pursued goals, consumption-associated patterns reflected the identity and value of experienced outcomes. Thus, the interplay between these patterns allows the maintenance of specific motivational states necessary to adaptively direct behavior toward prospective rewards.</p>
Data set used in SRDS 2020 paper
<p>Data set used in SRDS 2020 paper</p>
Biodiversity information retrieval across networked data sets
<p>Recording of presentation. An approach to integrate data through wrapping of various datasets stored in relational databases located on networked platforms. It is designed to overcome copyright problems in data sharing.</p>
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.