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134 results for “integrative biology”
Different facets of the same niche: integrating citizen science and scientific survey data to predict biological invasion risk under multiple global change drivers
<p>Raw data (occurrences and environmental predictors) used in the manuscript "Different facets of the same niche: integrating citizen science and scientific survey data to predict biological invasion risk under multiple global change drivers"</p>
Measurements from CalCOFI cruises in the California Current System, including log of station information, weather, sea conditions as well as physical, chemical and biological measurements including including temperature, salinity, oxygen, density, sigma theta, phosphate, silicate, nitrite, nitrate, ammonia, chlorophyll a, integrated chlorophyll a, primary productivity, and integrated primary production. 1949 - January 2020
Since 1949, hydrographic and biological data of the California Current System have been collected on quarterly CalCOFI cruises. The 59+ year hydrographic time-series includes weather, temperature, salinity, oxygen and phosphate observations. In 1961, nutrient analysis expanded to include silicate, nitrate and nitrite; in 1973, chlorophyll was added; in 1984, C14 primary productivity incubations were added. These data are being provided here in collaboration with CalCOFI-SIO in order to provide an additional queriable interface to the data. The data are updated on a regular basis from the CalCOFI hydrographic database.
Supplementary data to *Benchmarking of numerical integration methods for ODE models of biological systems*
<p>This archive contains supplementary data and code for the manuscript <strong>Benchmarking of numerical integration methods for ODE models of biological systems </strong>by<strong> Städter et al. 2020</strong>. It contains</p> <ul> <li>scripts to automatically download and install all required packages and models,</li> <li>scripts to compile the models and to perform the study,</li> <li>value files containing all data underlying the analyses in the manuscript,</li> <li>scripts to generate the manuscript figures.</li> </ul> <p>There is a <strong>README.md </strong>file with further information, in particular on what scripts to execute to reproduce the study.</p>
Screening routine for integrative dynamic structural biology using SAXS and intramolecular FRET and DEER-EPR on hGBP1 (human guanalyte binding protein 1)
<p>Initial and selected ensemble for major and minor species of the human guanalyte binding protein 1 with scripts for the reading routine to combine and analyse jointly SAXS, EPR and FRET data.</p>
Fig. 2 in Biology of snakes of the genus Tretanorhinus: an integrative review
Fig. 2. Map showing the current distribution of the four species of Tretanorhinus based on specimens from scientific collections.
Fig. 1 in Biology of snakes of the genus Tretanorhinus: an integrative review
Fig. 1. Number of specimens of the four species of Tretanorhinus according to (A) decade and (B) month of collection.
Fig. 4 in Integrated characterisation of Daubaylia burnupiae n. sp. (Nematoda: Daubayliidae) from a freshwater gastropod in South Africa, with comments on the biology of Daubaylia spp.
Fig. 4. Light (A–C) and scanning electron (D,E) micrographs of Daubaylia burnupiae n. sp. female. A, ovary anterior end; B, uterus and vulvular region; C, caudal region; D, ventral view of vulva and D, lateral view of anus. Abbreviations: a, anus; gz, germinal zone; k, knob-like protrusion; l, larva; o, oocyte; pvs, post-vulvular sac; tt, tail tip and v, vulva.
Fig. 1 in Integrated characterisation of Daubaylia burnupiae n. sp. (Nematoda: Daubayliidae) from a freshwater gastropod in South Africa, with comments on the biology of Daubaylia spp.
Fig. 1. Map showing Southern Africa (A) and the study area (B). S1: below Vaal Dam (26.872364 ◦S, 28.117173 ◦E) and S2: below Vaal Barrage (26.734854 ◦S, 27.634372 ◦E).
Fig. 6 in Integrated characterisation of Daubaylia burnupiae n. sp. (Nematoda: Daubayliidae) from a freshwater gastropod in South Africa, with comments on the biology of Daubaylia spp.
Fig. 6. Spicules of Daubaylia spp. A, D. burnupiae n. sp.; B, D. seistanensis; C, D. potomaca; D, D. dewiti; E, D. elegans; F, D. malayanum; G, D. helicophilus; H, D. olsoni; I, D. pearsoni and J, D. bonaerensis. Abbreviations: m, manubrium; la, lamina. B-J, redrawn from Baylis and Daubney (1922), Chitwood and Chitwood (1934), Schuurmans-Stekhoven (1956), Honer and Jansen (1961), Sullivan and Palmieri (1978), Poinar and Richards (1979), Poinar (1984), Anderson and Bartlett (1993), Camino and Gonzalez (2011), respectively.
Fig. 3 in Integrated characterisation of Daubaylia burnupiae n. sp. (Nematoda: Daubayliidae) from a freshwater gastropod in South Africa, with comments on the biology of Daubaylia spp.
Fig. 3. Light (A–C) and scanning electron (D–F) micrographs of Daubaylia burnupiae n. sp. anterior end. A, oesophagus male; B, oesophagus female; C, anterior region of corpus female; D, dorsal view of cephalic end female; E, subventral view showing excretory pore; F, apical view cephalic end male, showing papillae on lateral lips (broken line circles), and on the dorso-ventral lips (solid line circles). Abbreviations: a, amphids; co, corpus; ep, excretory pore; gb, glandular basal bulb; i, isthmus; nr, nerve ring and pl, pharyngeal lobes.
Fig. 5 in Integrated characterisation of Daubaylia burnupiae n. sp. (Nematoda: Daubayliidae) from a freshwater gastropod in South Africa, with comments on the biology of Daubaylia spp.
Fig. 5. Light (A–C) and scanning electron (D,E) micrographs of Daubaylia burnupiae n. sp. male. A, testis anterior end; B, genital armature; C, paired spicules; D, caudal region, subventral view; E, cloacal region, subventral. Abbreviations: c, cloaca; g, gubernaculum; lp, latero-ventral papilla; mp, median papilla; r, reflexed part of testis; s, spicules; st, spicule tip and tt, tail tip.
Fig. 2 in Integrated characterisation of Daubaylia burnupiae n. sp. (Nematoda: Daubayliidae) from a freshwater gastropod in South Africa, with comments on the biology of Daubaylia spp.
Fig. 2. Line drawings of Daubaylia burnupiae n. sp. A, female; B, anterior end female; C, anterior end male; D, male; E, posterior end female; F, posterior end male (arrows with no fill show lateroventral genital papillae) and G, gubernaculum. A-F, lateral view; G, subventral view. Abbreviations: a, anus; co, corpus; ep, excretory pore; g, gubernaculum; gb, glandular basal bulb; i, isthmus; nr, nerve ring and s, spicule.
Integrative processing in artificial and biological vision predicts the perceived beauty of natural images
<p><em>Data, code, and materials for Nara & Kaiser (2023). </em></p> <p><em>Preprint: </em><a href="https://www.biorxiv.org/content/10.1101/2023.05.05.539579v1">https://www.biorxiv.org/content/10.1101/2023.05.05.539579v1</a></p> <p>Paper: <a href="https://doi.org/10.1126/sciadv.adi9294">https://doi.org/10.1126/sciadv.adi9294</a></p> <p>In this version (v2) of the repository, we:</p> <ul> <li>fixed an error in the fMRI data, where only the data from one participant, instead of all participants was uploaded previously - now all data are available,</li> <li>added brain masks (extracted by SPM) for each participant, and</li> <li>added realignment parameter text files (created by SPM) to the functional data for each participant.</li> </ul>
Data for: An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean
<p><span>Soybean [<em>Glycine max (L.) Merr.</em>] </span><span>serves as one of the most economically valuable crops globally, but it is sensitive to low temperatures during the crop growing season. Currently, agriculture around the world has faced more serious abiotic stresses due to climate change, so there is an urgent need to breed cold-tolerant cultivars to resist the changing environment. The cold-tolerant trait is a complex and quantitative trait controlled by multiple genes, environmental factors, and their interaction. A total of 56 soybean samples were used, including 28 resistant varieties and 28 susceptible varieties, in the field experiments. We selected 55 SNPs (which were mapped to 39 CTgenes) from the CTgenes for distinguishing cold-tolerant lines from cold-susceptible lines. The SNP data can be applied for soybean's cold-tolerant experiment, such as soybean marker-assisted selection, soybean varieties clustering, the systems biology analysis, and further validation. </span></p>
Data from: Morphological integration during postnatal ontogeny: Implications for evolutionary biology
<p>How covariance patterns of phenotypes change during development is fundamental for a broader understanding of evolution. There is compelling evidence that mammalian cranium covariance patterns change during ontogeny. However, it is unclear to what extent variation in covariance patterns during ontogeny can impact the response to selection. To tackle this question we explored: i) the extent to which covariance patterns change during postnatal ontogeny; ii) in which ontogenetic stages covariance patterns differ the most, and iii) the extent to which the phenotypic covariance pattern at different ontogenetic stages can be explained by the same processes determining additive genetic covariance. We sampled postnatal ontogenetic series for both marsupials, and placentals. Within each ontogenetic series, we compared covariance matrices (<strong>P</strong>-matrices) at different ontogenetic stages. Furthermore, we compared these <strong>P</strong>-matrices to two target matrices [adult <strong>P</strong>-matrix and an additive genetic covariance matrix (<strong>G</strong>-matrix)]. Our results show that for all ontogenetic series, covariance patterns from weaning onward are conserved and probably shaped by the same processes determining the <strong>G</strong>-matrix. We conclude that irrespective of eventual differences in how selection operates during most of postnatal ontogeny, the net response to such pressures will probably not be affected by ontogenetic differences in the covariance pattern.</p>
Integrative taxonomy, larval biology and functional morphology of the little known gall-forming coral endoparasite Petrarca (Thecostraca: Ascothoracida)
<p><em><span>Petrarca</span></em><span> is an ascothoracidan endoparasite in scleratinian dendrophyllid corals</span><span>. <em>Petrarca</em> can stimulate coral growth, forming a gall chamber to house itself inside the coral skeleton. The diversity, molecular phylogeny and feeding ecology of <em>Petrarca</em> are understudied. This is the first study of Petrarca to be based on light and scanning electron microscopy to document the fine-scale external and functional morphology of its trophi and other structures. A combined molecular and morphological approach revealed at least four closely related species of <em>Petrarca</em>, <em>P. goanna</em>, <em>P. morula</em>, <em>Petrarca nozawai </em>sp. nov. and <em>Petrarca rubus</em> sp. nov in <em>Turbinaria</em> and <em>Astreopora</em> corals in Asia. Carapace shape and fine morphology, ultrastructure of the antennular aesthetasc, morphological characteristics of the trophi and the shape and size of the penis rami are diagnostic characters. Several morphological characters, </span><span>which are all probably synapomorphies, have been proposed to distinguish the genus <em>Petrarca</em> from other Ascothoracida. M</span><span>outhparts morphology of </span><span><em>Petrarca</em> </span><span>are developed for cutting and chewing, rather than for piercing and sucking as in many other Ascothoracida. </span><span>The external surface of the carapace of<em> Petrarca</em> is ornamented with densely packed secretory papillae used putatively for the chemical dissolution of the substrate necessary for the formation of the gall chamber.</span></p>
Integrated multi-omics analysis of early lung adenocarcinoma links tumor biological features with predicted indolence or aggressiveness
<p>This is a collection of datasets presented in the manuscript "Multi-omics data analysis identifies correlations between tumor biology features and predicted behaviors in early lung adenocarcinoma". This study provides a comprehensive profiling of LUAD indolence and aggressiveness at the biological bulk and single cell levels, as well as at the clinical and radiomics levels. This hypothesis generating study uncovers several potential future research avenues. It also highlights the importance and power of data integration to improve our systemic understanding of LUAD and to help reduce the gap between basic science research and clinical practice.</p>
Clarification of Abatacept Effects in SLE With Integrated Biologic and Clinical Approaches
ClinicalTrials.gov study NCT02270957. IPD Sharing: YES. Countries: 1. Publications: 2.
Phenomic data-driven biological prediction of maize through field-based high throughput phenotyping integration with genomic data
Open the record for dataset details and reuse information.
Integrative taxonomy, larval biology and functional morphology of the little known gall-forming coral endoparasite Petrarca (Thecostraca: Ascothoracida)
Open the record for dataset details and reuse information.
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.