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13,587 results for “specification”
Data from: Evidence for morph-specific substrate choice in a green-brown polymorphic grasshopper
<p>Orthopteran insects are characterized by high variability in body coloration, in particular featuring a widespread green-brown color polymorphism. The mechanisms that contribute to the maintenance of this apparently balanced polymorphism are not yet understood. To investigate whether morph-dependent microhabitat choice might contribute to the continued coexistence of multiple morphs, we studied substrate choice in the meadow grasshopper <i>Pseudochorthippus parallelus.</i> The meadow grasshopper occurs in multiple discrete, genetically determined color morphs that range from uniform brown to uniform green. We tested whether three common morphs preferentially choose differently colored backgrounds in an experimental arena. We found that a preference for green backgrounds was most pronounced in uniform green morphs. If differential choices improve morph-specific performance in natural habitats via crypsis and/or thermoregulatory benefits, they could help to equalize fitness differences among color morphs and potentially produce frequency-dependent microhabitat competition, though difference appear too small to serve as the only explanation. We also measured the reflectance of the grasshoppers and backgrounds and used visual modelling to quantify the detectability of the different morphs to a range of potential predators. Multiple potential predators, including birds and spiders, are predicted to distinguish between morphs chromatically, while other species, possibly including grasshoppers themselves, will perceive only differences in brightness. Our study provides the first evidence that morph-specific microhabitat choice might be relevant to the maintenance of the green-brown polymorphisms in grasshoppers and shows that visual distinctness of color morphs varies between perceivers.</p>
Cell type specificity of glucocorticoid signaling in the adult mouse hippocampus
<p>The present study is based on the 10X scRNA-seq dataset published by the Allen Institute for Brain Science and publicly available at: <a href="https://portal.brain-map.org/atlases-and-data/RNA-seq/mouse-whole-cortex-and-hippocampus-10x">https://portal.brain-map.org/atlases-and-data/RNA-seq/mouse-whole-cortex-and-hippocampus-10x</a>. The cells from the hippocampus region were selected from the gene count expression matrix and pre-processed in R v3.6.1 according to the Seurat v3.1.5 standard pre-processing workflow for quality control, normalization, and analysis of scRNA-seq data. Here we make the final seurat object and other datasets further used in the code (<a href="https://github.com/eviho/10XHip2021_VihoEMG">https://github.com/eviho/10XHip2021_VihoEMG</a>) available for download. </p>
AA-Score: a New Scoring Function Based on Amino Acid Specific Interaction for Molecular Docking
<p>The protein-ligand scoring function plays an important role in computer-aided drug discovery, which is heavily used in virtual screening and lead optimization. In this study, we developed a new empirical protein-ligand scoring function, which is a linear combination of empirical energy components, including hydrogen bond, van der Waals, electrostatic, hydrophobic, π-stacking, π-cation, and metal-ligand interaction. Different from previous empirical scoring functions, AA-Score uses several amino acid-specific empirical interaction components. We tested AA-Score on several test sets. The resulting performance shows AA-Score performs well on scoring, docking, and ranking compared with other widely used traditional scoring functions. Our results suggest that AA-Score gains substantial improvements from using detailed protein-ligand interaction components. Besides, we developed an easy-to-use tool to analyze protein-ligand interaction fingerprint and predict binding affinity using AA-Score.</p>
Rhizogenic Agrobacterium-specific bacteriophages
<p>Raw fastq sequences (Illumina) of the phages isolated in the VIROPLANT project to control hairy roots disease in tomato.</p> <p>ST40-104 = OLIVR1</p> <p>125 = OLIVR2</p> <p>128g = OLIVR3</p> <p>128k = OLIVR4</p> <p>ST57-123 = OLIVR6</p> <p>ST95-126 = OLIVR5</p> <p> </p> <p>Finalised genbank files that were submitted in NCBI are also part of this dataset.</p> <p> </p>
Patient-specific processed data, code and visualisations for "Fluctuations in EEG band power at subject-specific timescales over minutes to days explain changes in seizure evolutions"
<p>Processed data and code for reproducing the main results and figures of the paper "<strong>Fluctuations in EEG band power at subject-specific timescales over minutes to days explain changes in seizure evolutions</strong>".</p> <p>We analysed publicly available data from subjects with drug-resistant focal epilepsy. A total of 2656 hours of long-term intracranial electroencephalography (iEEG) from 18 subjects was obtained using the "The SWEC-ETHZ iEEG Database and Algorithms" (available at <a href="http://ieeg-swez.ethz.ch">http://ieeg-swez.ethz.ch</a>) (Burrello et al., 2019).</p> <p>Reference<br> A. Burrello, L. Cavigelli, K. Schindler, L. Benini, A. Rahimi, <strong>‘‘</strong>Laelaps: An Energy-Efficient Seizure Detection Algorithm from Long-term Human iEEG Recordings without False Alarms<strong>’’</strong> <em>in proceedings of the</em> <em>ACM/IEEE Design, Automation, and Test in Europe Conference (DATE)</em>, Florence, Italy, March 25-29, 2019. </p>
Riverine truly dissolved, colloidal, and operationally dissolved ferric iron, dissolved organic carbon, UV-vis absorbance at 254 and 412 nm, and specific UV absorbance (SUVA) at 254 nm
<p>This dataset is attached to the following article:</p> <p>Logozzo, L.A., Martin, J.W., McArthur, J., Raymond, P.A. Contributions of Fe(III) to UV-vis absorbance in river water: A case study on the Connecticut River and argument for the systematic tandem measurement of Fe(III) and CDOM. <em>Biogeochemistry</em> <strong>160</strong>: 17–33 (2022). https://doi.org/10.1007/s10533-022-00937-5</p> <p>This dataset includes concentrations of ferric iron, Fe(III), and dissolved organic carbon (DOC) along with UV-vis absorbance at 254 nm and 412 nm on the operationally dissolved size fraction (<0.22 μm), as well as the truly dissolved (<0.02 μm) and colloidal (0.02-0.22 μm) size fractions. Samples were collected every two weeks at five sites along the Connecticut River mainstem from 2018 to 2020 and at 7 sites in the Connecticut River watershed sampled once synoptically during the summer 2019.</p>
CCG Starter Kits - Technology-specific data for Base SAND file
<p>These files contain the Capacity Factors and Residual Capacity values for all countries needed for filling in the information in the base SAND file.</p> <p>This is published as part of the MethodsX paper titled <strong>How to put together a Starter Data Kit from scratch? An extensive methodology to compile zero-order energy transition models. </strong>The main goal of the files published for this paper is to develop a set of credible data and an initial investment model for several developing countries.</p>
Gene expression and splicing counts from 49 tissues from GTEx v8 genome build hg38 - non-strand specific
<p><strong>Dataset description:</strong></p> <p>49 folders, each corresponding to one tissue from GTEx v8 and containing the following files:</p> <ol> <li> <p>geneCounts: gene-level counts </p> </li> <li> <p>k_j: split counts spanning from one exon to another.</p> </li> <li> <p>k_theta: non-split counts covering a splice site</p> </li> <li> <p>n_psi3: total split counts from a given acceptor site</p> </li> <li> <p>n_psi5: total split counts from a given donor site</p> </li> <li> <p>n_theta: total split and non-split counts for a given splice site</p> </li> <li> <p>Sample annotation describing each sample from the dataset</p> </li> <li> <p>Description file with global information from the dataset</p> </li> </ol> <p>The gene counts were originated using the GTF file from <a href="https://www.gencodegenes.org/human/release_29.html">release 29 of GENCODE</a>, and the split and non-split counts contain only the annotated junctions from the same release. Statistics are reported only for GENCODE-annotated introns and splice sites, in compliance with the regulations of the GTEx consortium. For a description of the samples, methods, and protocols, see the GTEx publication specified below.</p> <p><strong>Use: </strong>The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired-end specifications match. Afterwards, the <a href="https://github.com/gagneurlab/drop">Detection of RNA outliers Pipeline (DROP) </a> can be used to compute gene expression and splicing outliers.<br> <strong>Organism:</strong> Homo sapiens<br> <strong>Genome assembly:</strong> hg38<br> <strong>Gene annotation:</strong> gencode29<br> <strong>Strand specific: </strong>FALSE<br> <strong>Paired end: </strong>TRUE<br> <strong>Protocol: </strong>poly(A) enrichment</p> <p><strong>Contact:</strong> Vicente A. Yepez, yepez at in.tum.de; Christian Mertes, mertes at in.tum.de; Julien Gagneur, gagneur at in.tum.de</p> <p><strong>Citation:</strong> Write the following in the "Data availability" section of the manuscript or similar replacing the three citations by the ones from the References section below:</p> <blockquote> <p><strong>The count matrices for the GTEx samples <cite GTEx publication, see below> were downloaded from Zenodo (doi: 10.5281/zenodo.6078397) and were generated through DROP <cite DROP, see below> using the release 29 of the GENCODE annotation <cite GENCODE, see below>. </strong></p> </blockquote> <p>Also, write the following in the Acknowledgements section:<br> </p> <blockquote> <p><strong>The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The raw data used for the analyses described in this manuscript were obtained from the GTEx Portal on June 12, 2017, under accession number dbGaP phs000424.v8.p2.</strong></p> </blockquote> <p> </p>
Dataset related to aticle "Additive Fabrication of a Vascular 3D Phantom for Stereotactic Radiosurgery of Arteriovenous Malformations"The database contains 3D models in STL file format of a patient-specific brain arteriovenous malformation phantom reconstructed from computed tomography scans.
<p><em>The database contains 3D models in STL file format of a patient-specific brain arteriovenous malformation phantom reconstructed from computed tomography scans.</em></p>
dataset related to article "On the evaluation of edgeless diode detectors for patient-specific QA in high-dose stereotactic radiosurgery"
<p>The database contains the comparison table between calculated doses and values actually measured by the edgeless detectors and an example of dose planar distribution as exported from the radiotherapy Treatment Planning System.</p> <p> </p>
Data from: Metabarcoding of soil environmental DNA replicates plant community variation but not specificity
<blockquote> <p>While metabarcoding of plant DNA from their environment is an exciting method that can supplement inventorying of live plant species, the accuracy and specificity has yet to be fully assessed over complex continuous landscapes. In this work, we evaluate plant community profiles produced via metabarcoding of soil by comparing them to a morphological survey. We assessed plant communities by metabarcoding of soil DNA in 130 sites along ecological gradients (nutrients, succession, moisture) in Denmark using chloroplast <i>trn</i>L region (10-143 bp) primer set and compared the resulting communities to communities produced with a longer nuclear ITS2 region (~216 bp) and a morphological survey. We found that the community variation observed within the morphological survey was well represented by molecular surveys, with significant correlation with both community composition and richness using both primer sets. While the majority of the ITS2 sequences could be assigned to species (over 80%), we had less success with the <i>trn</i>L sequences (70%), which was only possible after restricting the reference database to local species. We conclude that the community profiles produced by metabarcoding can be highly effective in performing large-scale macroecological studies. However, the discovery rates and taxonomic assignments produced via metabarcoding remained inferior to morphological surveys, but manual curation of databases improves the <i>specificity</i> of assignments made by the <i>trn</i>L primers, and improves the <i>accuracy</i> of the assignments made with the ITS2 primers. Finally, we suggest that a greater percentage of named diversity would be recovered by increasing soil sampling with the use of additional universal primer sets.</p> </blockquote>
Sub-national tailoring of malaria interventions in Mainland Tanzania: simulation of the impact of strata-specific intervention combinations using modelling
<p>Simulation dataset. </p>
Data for "Exemplifying parametric timed specifications over signals with bounded behavior"
<p>Data for "<strong>Exemplifying parametric timed specifications over signals with bounded behavior</strong>" by Étienne André, Masaki Waga, Natuski Urabe, and Ichiro Hasuo, published in the proceedings of the 14th NASA Formal Methods Symposium (NFM 2022)</p> <p>See README.md in the zipped file for explanations and instructions for reproductibility.</p>
Specific report on biscuit packaging
<p>This data was used for the redaction of the project deliverable "D2.4: Specific report on organic products". It is a Specific report on barriers and opportunities for European consumers concerning innovative packaging of organic products.</p> <p>Moreover, this data is from the scientific publications "<a href="https://www.sciencedirect.com/science/article/pii/S0166497221001723#gs1"><strong>Misalignments between users and designers as source of inspiration: A novel hybrid method for physical new product development</strong></a>" and“<a href="https://www.sciencedirect.com/science/article/pii/S0272494421001778?via%3Dihub%22%20l%20%22ack001"><strong>A meaningful reminder on sustainability: When explicit and implicit packaging cues meet</strong></a>”.</p>
Specific report on sterilized baby food packaging
<p>This data was used for the redaction of the project deliverable "D2.3: Specific report on sterilized baby food ". It is a Specific report on barriers and opportunities for European consumers concerning innovative packaging of sterilized baby food.</p> <p>Moreover, this data is from the scientific publications "<a href="https://www.sciencedirect.com/science/article/pii/S0166497221001723#gs1"><strong>Misalignments between users and designers as source of inspiration: A novel hybrid method for physical new product development</strong></a>" and“<a href="https://www.sciencedirect.com/science/article/pii/S0272494421001778?via%3Dihub%22%20l%20%22ack001"><strong>A meaningful reminder on sustainability: When explicit and implicit packaging cues meet</strong></a>”.</p>
Specific report on fresh-cut salad packaging
<p>This data was used for the redaction of the project deliverable "D2.2: specific report on fresh-cut vegetable products". It is a specific report on barriers and opportunities for European consumers concerning the innovative packaging of fresh-cut vegetable products.</p> <p>Moreover, this data is from the scientific publications "<a href="https://www.sciencedirect.com/science/article/pii/S0166497221001723#gs1"><strong>Misalignments between users and designers as source of inspiration: A novel hybrid method for physical new product development</strong></a>" and“<a href="https://www.sciencedirect.com/science/article/pii/S0272494421001778?via%3Dihub%22%20l%20%22ack001"><strong>A meaningful reminder on sustainability: When explicit and implicit packaging cues meet</strong></a>”.</p>
Morphological and molecular evidence support elevating Erythroxylum macrophyllum var. savannarum (Erythroxylaceae) to specific status
<p><em>Erythroxylum macrophyllum</em> is a morphologically variable and widely distributed species complex in Central and South America with several sub-specific taxa and numerous species included in its synonymy. A single variety grows in the Colombo-Venezuelan savanna region which can be distinguished from the rest of the <em>E. macrophyllum</em> complex by the size of leaves, cataphyll and stipule characteristics, and shape of calyx lobes. A molecular phylogeny reconstructed from 519 nuclear genes also reveals that the savanna variety is more closely related to <em>E. acuminatum </em>and <em>E. pauciflorum</em> than <em>E. macrophyllum</em>. This phylogenomic evidence also suggests <em>Erythroxylum </em>sect. <em>Macrocalyx</em>, to which <em>E. macrophyllum</em> belongs, is a polyphyletic taxonomic section. We thus propose elevating this variety to specific status. We provide an updated taxonomic description, information about its habitat and distribution, and justify its IUCN categorization of Near Threatened (NT).</p>
Fig. 3. Spiraea japonica L in The Spider Mite Schizotetranychus Spireafolia (Acari, Tetranychidae), Specific Pest Of Spiraea In The A. V. Fomin Botanical Garden
Fig. 3. Spiraea japonica L. infested with Sch. spireafolia mites: a — upper surface of leaf, b — lower surface of leaf.
Fig. 2 in The Spider Mite Schizotetranychus Spireafolia (Acari, Tetranychidae), Specific Pest Of Spiraea In The A. V. Fomin Botanical Garden
Fig. 2. Morphological characteristics of Sch. spireafolia from A. V. Fomin Botanical Garden, Kyiv, Ukraine: a — female x10; b — male x10; c — dorsal setae x100; d — palp tarsus of female x100; e — palp tarsus of male x100; f — empodium of tarsus I of female x100; g —
Fig. 5 in Patterns of tooth crown wear in Dryomys nitedula (Mammalia, Rodentia): age-related variation in the light of annual cycle specifics based on museum collections
Fig. 5. Changes in the external appearance of the forest dormouse during the first year of life. The animal was caught in early June 2009 near Luhansk: a — 19 of June, 1–2 weeks old, feeding exclusively with insects, mainly locusts; b — 16 of July, 1+ month of age, active motions, feeding with insects, including locusts, butterflies, and mealworms; c — 18 of August, 2+ months of age, low mobility, willingly feeding with mealworms, also began to consume nuts, honey, and cookies; d — 16 of September, 3+ months of age, low mobility, feeding almost exclusively with nuts, honey and other energy-rich products instead of insects, which became less preferred.
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.