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13,587 results for “specification”
Longitudinal Data on the Specific and Universal Interventions Received / Datos Longitudinales sobre las Intervenciones Específicas y Universales Recibidas // SUJ-2_Data_CC-IC_T1toT6
<p>This is a longitudinal file that provides information on the interventions received by the participant in each grade, from first to fourth grade of primary education. Interventions can be universal or specific. Both types of interventions are organized according to the focus and/or area of intervention (teacher, child, peers, parents). The file reports the types of interventions that the participant has received in each grade in each focus and their breakdown into concrete interventions. It also reports in which courses the participant meets the criteria to be a candidate for specific interventions and the variables used to identify the candidates (variables of concern to the teacher and sociometric status variables). The information was provided by the researchers. Data were collected in public schools in Castellón (Spain) mostly in the spring of each school year, but many variables were also measured in the fall, from the first grade of primary education to the sixth grade, from the 2009-10 school year to the 2015-16 school year. To learn more about our research and access to other datasets of this or other measures, follow the link <a href="https://www.uji.es/departaments/psi/base/opengrei/">GREI Longitudinal Project</a></p> <p> </p> <p>Se trata de un fichero longitudinal que aporta información sobre las intervenciones que ha recibido el participante en cada curso, de primero a cuarto. Las intervenciones pueden ser universales o específicas. Ambos tipos de intervenciones se organizan en función del foco y/o área de intervención (profesor, niño-a, iguales, padres). En el fichero se informa de los tipos de intervenciones que el participante ha recibido en cada foco durante cada curso y de su desglose en intervenciones concretas. También se informa de en qué cursos el participante cumple criterios para ser candidato a recibir intervenciones específicas y de las variables que se han utilizado para identificar a los candidatos (variables preocupa al profesor y variables de estatus sociométrico). La información ha sido proporcionada por los investigadores. Los datos fueron recogidos en centros públicos de Castellón (España) mayoritariamente en la primavera de cada curso, pero muchas variables también fueron medidas en otoño, desde el primer curso de educación primaria a sexto, desde el curso escolar 2009-10 al curso escolar 2015-16. Para saber más sobre nuestra investigación y acceder a otros ficheros de datos de esta medida o de otras, siga el enlace <a href="https://www.uji.es/departaments/psi/base/opengrei/">Proyecto Longitudinal GREI</a></p>
Low Emission Oil and Gas Open (LEOGO) platform specification
<p>This dataset describes the integrated energy system of a hypothetical but realistic offshore oil and gas platform referred to as the LEOGO reference platform. It reflects what would be considered a typical installation on the Norwegian Continental Shelf.</p> <p>Included with the dataset is</p> <ul> <li>input data for analysis with the open-source Oogeso (https://github.com/oogeso/oogeso) operational optimisation/simulation tool, including simplified links between electricity and heat demand and the gas/oil/water flow rates through the processing system.</li> <li>A detailed electrical model implemented in the Digsilent PowerFactory tool</li> </ul> <p> </p>
MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids
<p>This tar-Archives hold the complete collection of n=7,506 metagenome-assembled genomes presented in the preprint "Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids" by Rühlemann <em>et al., <a href="https://www.biorxiv.org/content/10.1101/2023.03.01.530589v1">bioRxiv</a>, </em>2023.</p> <p>Article Summary</p> <p>Characterizing trajectories of the composition and function of hominid gut microbiota across diverse environments and host species can help reveal specific properties of the human microbiota, with possible implications for host evolution and health. Using shotgun metagenomic sequencing, we investigated taxonomic and functional diversity in the gut microbiota of wild-living great apes, including two gorilla subspecies (<em>Gorilla gorilla gorilla, Gorilla beringei beringei</em>), three chimpanzee subspecies (<em>Pan troglodytes verus, P.t. troglodytes, P.t. schweinfurthii</em>), and bonobos (<em>Pan paniscus</em>), together with human samples from Africa and Europe. We identified microbial taxonomic and functional adaptations convergent with host phylogeny at both the community and microbial genomic levels. We could show that repeated horizontal gene transfer and gene loss are processes involved in these adaptations. We hypothesize, that these adaptation processes and changes in the microbiome predispose the host to chronic inflammatory disorders, such as type 2 diabetes via altered histidine metabolism and inflammatory bowel disease indicated by adaptation of microbes to aerobic conditions. Additionally, we find multiple lines of evidence suggesting a widespread loss of microbial diversity and evolutionary conserved clades in the human microbiota, especially in the European population. Lastly, we observed patterns consistent with codivergence of hosts and microbes, particularly for the bacterial family <em>Dialisteraceae</em>, though we find that overall, co-phylogeny patterns are frequently disrupted in humans.</p>
High functional diversity in deep-sea fish communities and increasing intra-specific trait variation with increasing latitude
<p>Variation in both inter- and intra-specific traits affect community dynamics, yet we know little regarding the relative importance of external environmental filters vs internal biotic interactions that shape the functional space of communities along broad-scale environmental gradients, such as latitude, elevation or depth. We examined changes in several key aspects of functional alpha-diversity for marine fishes along depth and latitude gradients by quantifying intra- and inter-specific richness, dispersion and regularity in functional trait space. We derived eight functional traits related to food acquisition and locomotion, and calculated seven complementary indices of functional diversity for 144 species of marine ray-finned fishes along large-scale depth (50 m – 1200 m) and latitudinal gradients (29° – 51° S) in New Zealand waters. Traits were derived from morphological measurements taken directly from footage obtained using Baited Remote Underwater Stereo-Video systems and museum specimens. We partitioned functional variation into intra- and inter-specific components for the first time using a PERMANOVA approach. We also implemented two tree-based diversity metrics in a functional distance-based context for the first time: namely, the variance in pairwise functional distance, and the variance in nearest-neighbour distance. Functional alpha diversity increased with increasing depth, and decreased with increasing latitude. More specifically, the dispersion and mean nearest-neighbour distances among species in trait space, and intra-specific trait variability all increased with depth, whereas functional hypervolume (richness) was stable across depth. In contrast, functional hypervolume, dispersion and regularity indices all decreased with increasing latitude; however, intra-specific trait variation increased with latitude, suggesting that intra-specific trait variability becomes increasingly important at higher latitudes. These results suggest that competition within and among species are key processes shaping functional multi-dimensional space for fishes in the deep sea. Increasing morphological dissimilarity with increasing depth may facilitate niche partitioning to promote coexistence, whereas abiotic filtering may be the dominant process structuring communities with increasing latitude.</p>
Raw Data to "Computational Investigation of Explicit Solvent Effects and Specific Interactions of Hydroxypyrene Photoacids in Acetone, DMSO, and Water"
<p>This data is a supplement to the publication entitled "Computational Investigation of Explicit Solvent Effects and Specific Interactions of Hydroxypyrene Photoacids in Acetone, DMSO, and Water" in <em>Physical Chemistry Chemical Physics</em> (DOI: 10.1039/D3CP00800B). It contains the structures (as '.xyz' files) and HF/DFT energies from the quantum chemical (QC) calculations using TURBOMOLE (version 7.6).</p> <p>Additional information on the file structure is given in the README file.</p>
A benchmark of gene expression tissue-specificity metrics
<p>Supplementary figures and data to the paper "A benchmark of gene expression tissue-specificity metrics"</p> <p><em>Briefings in Bioinformatics</em>, Volume 18, Issue 2, March 2017, Pages 205–214, <a href="https://doi.org/10.1093/bib/bbw008">https://doi.org/10.1093/bib/bbw008</a></p> <p>Previously published at FigShare, republishing because of access problems for some researchers.</p>
FIG. 2 in A range extension of Heterocladium flaccidum (Schimp.) A.J.E.Sm. to Africa and Asia and confirmation of its specific status
FIG. 2. — Bayesian tree from trnS-F analysis.Bayesian posterior probabilities and MP bootstrap support are shown at branches.
FIG. 1 in A range extension of Heterocladium flaccidum (Schimp.) A.J.E.Sm. to Africa and Asia and confirmation of its specific status
FIG. 1. — Bayesian tree from nrITS analysis. Bayesian posterior probabilities and MP bootstrap support are shown at branches.
APPENDIX 9 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
APPENDIX 9. — Phylogenetic reconstruction of ITS sequences from Amanita curtipes related specimens collected in worldwide locations (Appendix 10), using A. lepiotoides Barla as outgroup. The known epithets are next to the brackets, sp designating unknown taxa. Using a 75% coverage cutoff, a total of 584 aligned positions were analysed with the Maximum Likelihood method and the General Time Reversible substitution model (Nei & Kumar 2000), with a discrete Gamma distribution to model evolutionary rate differences among sites (5 categories [gamma parameter 0.4648]). Bootstrap support values above 0.66 (200 replicates) are shown next to the relevant nodes.
APPENDIX 10. — Additional ITS sequences used for Appendix 9 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
APPENDIX 10. — Additional ITS sequences used for Appendix 9, approximately in the same order. Abbreviations: MO, Mushroom Observer (https://mushroomobserver.org); iNAT, iNaturalist (https://www.inaturalist.org/observations).
APPENDIX 8 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
APPENDIX 8. — Examples of basidiospore outlines from the Spring 2015 Luzianes collections. Scale bar: 10 μm.
APPENDIX 4 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
APPENDIX 4. — Descriptive (mean ± SE) plots for basidiospore length (L), width (l) and L/l ratio (Q). Sample identifiers refer to the Ode samples (Spring 2015) and P01 (Spring 2010).
APPENDIX 2 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
APPENDIX 2. — Example of a matched comparison of Amanita ponderosa Malençon & R.Heim (ApoIf2-ITS4) and A. pseudovalens comb. nov., stat. nov. (ITS3- ApsIr3) for the same set of samples representing these two species, along with others of A. curtipes E.-J.Gilbert and A. lepiotoides Barla, and an unknown sample (SM-DB 61). The whole contents of each 20 µL PCR reactions were loaded, to help detect faint signals. Negative controls (neg.) with water instead of DNA. Amanita ponderosa is represented by the valens type (G73) and three samples from Spring 2010 (B07, P08, B10). Amanita pseudovalens is represented by the pseudovalens type (G74), the two MPU samples, Ode05 and Ode07. The Amanita curtipes samples (M03, M04 and M05) may produce a weak co-migrating band with the ITS3-ApsIR3 primer pair, and the A. lepiotoides samples (G08 and Eusk) were negative in both cases. Positive control reactions were not attempted because herbaria materials may be contaminated with other fungi.
FIG. 6 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
FIG. 6. — Results of PCR amplifications using discriminant probes for Amanita pseudovalens comb. nov., stat. nov.: A, ITS region: ITS3-ApsIr3 (all samples positive with concurring control with primers ITS3-ITS4, not shown); B, LSU region: NLC2R-ApsLr2 (all positive with control NLC2R-LR5); Ode15 and Ode16 were negative and positive, respectively, in another amplification (not shown); M, molecular marker; neg. designates the negative control (water); pos. designates the positive control (the P01 extract).
FIG. 1 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
FIG. 1. — Locations of the collections used in this study (see Table 1 for details). The letters designate Landscape Units: P, Alto Alentejo; R, Alentejo Central; S, Baixo Alentejo; U, Serras do Algarve e do Litoral Alentejano. The area is outlined on the inset with a yellow rectangle. Source: DGT, Carta de Unidades de Paisagem (CUP), https://www.dgterritorio.gov.pt/dados-abertos
FIG. 2 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
FIG. 2. — Phylogenetic placement of the type nrDNA sequences, in relation to ITS + LSU sequences from european Amanita Pers. taxa belonging to the Amidella clade (only the terminal epithets are shown). Using a 70% coverage cutoff, a total of 1121 aligned positions were analysed with the Maximum Likelihood method and the Tamura-Nei (Tamura & Nei 1993) substitution model, with a discrete Gamma distribution to model evolutionary rate differences among sites (five categories [gamma parameter 0.7526]), allowing for some sites to be evolutionarily invariable (40.90% sites). The percentage bootstrap support for each node (1000 replicates) is shown next to the branches. The support for each species clade is 99% (Amanita pseudovalens comb. nov., stat. nov.), 100% (Amanita curtipes E.-J.Gilbert), 100% (Amanita lepiotoides Barla) and 100% (Amanita ponderosa Malençon & R.Heim). The scale indicates 0.02 substitutions per site.
FIG. 3 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
FIG. 3. — Photographs of Amanita pseudovalens var. tartessiana var. nov. specimens from Odemira. Some images taken in the field are matched with corresponding ones taken in the laboratory: A, grouped basidiomes (Ode12) and their appearance upon arrival at the laboratory; B, outcropping away from the vegetation, showing the coarse soil texture in this case (Ode02); inset shows squamulose inner cuticle remains; C, another specimen with cuticle squamules (Ode11); D, specimen with cracked cuticle (Ode05); E, example with stipe squamules (Ode06); F, side view of an emerging basidiome (Ode03) and the same specimen showing the darkened squamules on the stipe; G, view of the hymenophore and the appendiculate pileus margin (Ode02, specimen different from B); H, details of an immature basidiome (Ode06, specimen different from E) showing the annulus and insertion of the lamellae (left), and longitudinal section (right).
FIG. 5 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
FIG. 5. — Ground view of the Luzianes locations, showing the Cistus ladanifer L. dominance: A, Luzianes A; B, Luzianes B. Both photos were taken in spring 2015 by Ana C. Silva.
FIG. 4 in The Amidella clade in Europe (Basidiomycota: Amanitaceae): clarification of the contentious Amanita valens (E.-J.Gilbert) Bertault and the importance of taxon-specific PCR primers for identification
FIG. 4. — Plotting of the measurements summarised in Table 5 (dots), comparing with the limits of the sporographs, based on the descriptions in Neville & Poumarat (2004) for Amanita curtipes f. pseudovalens Neville & Poumarat (continuous line) and A. ponderosa f. ponderosa Malençon & R.Heim (dashed line).
Data for: Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution in Arabidopsis thaliana
<p>Differential gene expression between environments often underlies phenotypic plasticity. However, environment-specific expression patterns are hypothesized to relax selection on genes, and thus limit plasticity evolution. We collated over 27 terabases of RNA-sequencing data on <em>Arabidopsis thaliana</em> from over 300 peer-reviewed studies and 200 treatment conditions to investigate this hypothesis. Consistent with relaxed selection, genes with more treatment-specific expression have higher levels of nucleotide diversity and divergence at nonsynonymous sites but lack stronger signals of positive selection. This result persisted even after controlling for expression level, gene length, GC content, the tissue specificity of expression, and technical variation between studies. Overall, our investigation supports the existence of a hypothesized trade-off between the environment specificity of a gene's expression and the strength of selection on said gene in <em>A. thaliana</em>. Future studies should leverage multiple genome-scale datasets to tease apart the contributions of many variables in limiting plasticity evolution.</p>
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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.