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.
211
datasets available to search
ShareScore release 0.9.0
Dataset results
211 results for “functional regionalization”
The data for "Reconnaissance with JWST of the J-region Asymptotic Giant Branch in Distance Ladder Galaxies: From Irregular Luminosity Functions to Approximation of the Hubble Constant"
<p>Data used for "Reconnaissance with JWST of the J-region Asymptotic Giant Branch in Distance Ladder Galaxies: From Irregular Luminosity Functions to Approximation of the Hubble Constant" by Siyang Li, Adam G. Riess, Stefano Casertano, Gagandeep S. Anand, Daniel M. Scolnic, Wenlong Yuan, Louise Breuval, and Caroline D. Huang. Magnitudes provided are after correcting for foreground extinction and crowding bias.</p>
Supplementary Data Files for the paper "Intrinsically disordered compositional bias in proteins: Sequence traits, region clustering, and generation of hypothetical functional associations"
<div> <div> <div> <div> <p><strong>Supplementary data files relating to <a href="https://doi.org/10.1177/11779322241287485">https://doi.org/10.1177/11779322241287485. </a></strong></p> <p><strong><span>Suppl. File 1: Protein Family Clusters.</span></strong></p> <p><strong><span>Suppl. File 2: Cluster GO enrichments/depletions. </span></strong></p> <p><strong><span>Suppl. File 3: The raw ID-CBR data with annotations. </span></strong></p> <p><strong><span>Suppl. File 4: ­ID-CBR Cluster membership.</span></strong></p> <p><strong><span>Each file has an explanatory header. </span></strong></p> <p> </p> </div> </div> </div> </div>
Divergent geographic patterns and functional characteristics: Subtle mapping for ponds in the Yangtze River Delta Region
<p>Pond water surfaces (PWS) possess diverse functional types, such as aquaculture, agriculture-water supplement, and ecosystem regulation. However, existing research often treats PWS as a homogeneous aquatic ecosystem; the absence of a comprehensive PWS classification system hinders ours understanding of PWS background characteristics and is detrimental to watershed management. Here, a comprehensive classification system of PWS, including fish aquaculture ponds (FAP), shrimp and crab aquaculture ponds (SCAP), natural ponds (NP), and landscaping ponds (LP) was proposed from remote sensing perspectives. Additionally, interpretation rules were standardized from multi-features including spectrum, shape, topography, and surrounding geographical environments. Subsequently, refined spatiotemporal data product of PWS in the Yangtze River Delta from 2016 to 2022 was generated using Sentinel-2 images with 10 m spatial resolutions. The results indicate that: (1) The spatiotemporal changes exhibited three stages, i.e., “declining – stable – recovery.” The area of PWS decreased from 5186.52 km² to 4920.90 km²in 2016-2017, stabilized at approximately 4500 km² in 2019-2021, and then rebounded to 4834.12 km² in 2022. (2) Regarding different PWS functional types, significant differences were demonstrated in terms of area, surrounding environment, and spatiotemporal changes. Firstly, FAP dominated in terms of area, accounting for 47.81% of the total. Secondly, FAP was widely around rivers and lakes. At the same time, SCAP was concentrated around lakes or along the coast, LP was primarily found in urban areas, and NP was predominantly found in rural areas and mountainous regions; Thirdly, NP decreased as land remediation work progressed continuously, while LP increased due to policy support for urban renewal. Changes in aquaculture were more complex, experiencing a sharp decline from 2016 to 2020 due to reduced market demand but rebounded in 2021-2022 with supportive policies. In summary, the system and data products developed in this study reveal the diverse relationships of "functional type-geographical environment-driving factor" regarding PWS, implicating appropriate planning for aquatic ecosystem.</p>
Fig. 1 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane
Fig. 1 Schematic diagram illustrating the origin (a) and beginning of differentiation (b) of the oncospheral tegument and hook region membrane in the preoncospheral stage of embryonic development of Echinococcus multilocularis. All structures involved in formation of the oncospheral tegument and hook region membrane are marked in orange colour. Two red arrows show direction of progressive sinking or migration of the binucleate subtegumental perikaryon which sunk deep into the central region of differentiating oncosphere. HFC hook-forming cell or oncoblast, HP hook primordium, HRC hook region cavity, IE inner envelope, m mitochondria, N1, N2 two nuclei of the binucleate complex primordium, N nucleus of hook-forming cell, PBC binucleate complex primordium, V vesicles in the outer cytoplasm, undergoing progressive fusion
Fig. 6 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane
Fig. 6 TEM micrographs of mature eggs of Echinococcus multilocularis. a Part of the oncosphere showing the high concentration of beta-glycogen particles (β-gl) in the musculature of oncospheral hooks (HM) as indicated by the cytochemical test of Thiéry. b Low-power electron micrograph illustrating the general topography of mature intrauterine egg. Note: (1) a bilateral symmetry of the oncosphere (white interrupted line) and (2) position of hook region membrane and oncospheral tegument at one pole of the hexacanth. The hook region is marked by a frame composed of interrupted black lines. EmB embryophoric blocks, GC germinative cells, GL granular layer, HRM hook region membrane, IE inner envelope, LH lateral hooks, MH median hooks, OE outer envelope, OM oncospheral membrane, PG penetration glands, SC somatic cells
Fig. 5 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane
Fig. 5 High-power TEM micrographs showing ultrastructural details of the oncospheral tegument and hook region membrane. a Note two oblique sections of blades of the oncospheral hooks (HBl), surrounded by numerous long microvilli (Mv) which protrude into large cavity situated under the hook region membrane (HRM) and oncospheral membrane (OM). b Oblique section through the hook region membrane showing hook blade exit and oncospheral tegument with numerous long microvilli at its surface. DR desmosome rings, HM hook musculature, IE inner envelope
Fig. 4 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane
Fig. 4 Consecutive stages of a tegumental perikaryon migration. a Part of an embryo in the early preoncospheral stage of development showing much infolded oncospheral membrane and the binucleate perikaryon (BSP) of the oncospheral tegument in the early stage of its migration, sunken already below the peripheral layers of oncospheral musculature. b Part of the late stage of preoncospheral differentiation showing the binucleate perikaryon of oncospheral tegument sunk deep into the central part of the embryo and surrounded by differentiating blastomeres. H oncospheral hooks, HCF hook forming cell, HRM hook region membrane, IE inner envelope, N1, N2, nucleus, OE outer envelope, OM oncospheral membrane, SC somatic cells
Fig. 3 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane
Fig. 3 Comparison of an early and advanced preoncospheral stage of embryonic development in Echinococcus multilocularis. a Ultrastructure of an embryo in the early preoncospheral stage of embryonic development. Note the binucleate complex primordium (PBC), which appears as a syncytial cap or "calotte" situated beneath the inner envelope (IE) at one pole of the developing embryo; two thick arrows mark the direction of progressive migration of both nuclei (N1, N2) surrounded by a thin layer of common cytoplasm and become transformed into the binucleate subtegumental perikaryon. b Part of the embryo in the advanced stage of preoncosphere showing the binucleate subtegumental perikaryon (BSP) of the tegumental syncytium sunk deep into the central part of the embryo and surrounded by differentiating blastomeres. Bl blastomere, C vitelline capsule, EmB embryophoric blocks, GL granular layer, H oncospheral hooks, HM hook muscles, HRM hook region membrane, KI keratin-like protein islands, MeN mesomere nucleus, OE outer envelope, OM oncospheral membrane, PG penetration gland, UW uterine wall
Fig. 2 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane
Fig. 2 Schematic diagram illustrating the general topography of the oncospheral tegument and hook region membrane in relation to the oncospheral hooks, penetration gland arms and glandular exits in the mature intrauterine eggs. All structures involved in formation of the oncospheral tegument and hook region membrane are marked in orange colour. BSP binucleate subtegumental perikaryon, HRM hook region membrane, IE inner envelope LH lateral hooks, MH median hooks, Mv microvilli, N1, N2 nucleus, OT oncospheral tegument, PGA penetration glands arms
Density functional theory calculations of 1D hybrid nanoobjects composed of alternating polycyclic hydrocarbon regions and double carbon chains
<p>It has been proposed recently based on molecular dynamics simulations that electron irradiation of graphene nanoribbons of alternating width can lead to creation of 1D hybrid nanoobjects composed of alternating double carbon chains and polycyclic hydrocarbon regions [1]. We have performed density functional theory calculations of such 1D hybrid nanoobjects using Quantum ESPRESSO [2]. Semi-local exchange and correlation functional of Perdew, Burke and Ernzerhof [3] and screened exchange hybrid density functional of Heyd, Scuseria and Ernzerhof [4] were used. The dependences of structure, magnetic and electronic properies on the length of chains and type of the polycyclic hydrocarbon region were studied.</p> <p>I.V.L acknowledges the IKUR HPC project "First-principles simulations of complex condensed matter in exascale computers" funded by MCIN and by the European Union NextGenerationEU/PRTR-C17.I1, as well as by the Department of Education of the Basque Government through the collaboration agreement with nanoGUNE within the framework of the IKUR Strategy, computer resources at MareNostrum and the technical support provided by Barcelona Supercomputing Center (RES grant nos. FI-2022-1-0023, FI-2022-2-0035, FI-2022-3-0048 and FI-2023-1-0037). A.M.P., and Y.E.L. acknowledge the support by the Russian Science Foundation grant No. 23-42-10010, https://rscf.ru/en/project/23-42-10010/. S.A.V. and N.A.P. acknowledge support by the Belarusian Republican Foundation for Fundamental Research (Grant No. F23RNF-049) and by the Belarusian National Research Program "Convergence-2025".</p> <p>[1] A. S. Sinitsa, I. V. Lebedeva, Y. G. Polynskaya, D. G. de Oteyza, S. V. Ratkevich, A. A. Knizhnik, A. M. Popov, N. A. Poklonski, and Y. E. Lozovik, “Transformation of a graphene nanoribbon into a hybrid 1D nanoobject with alternating double chains and polycyclic regions,” Phys. Chem. Chem. Phys. 23, 425–441 (2021).</p> <p>[2] P. Giannozzi et al., “Advanced capabilities for materials modelling with Quantum ESPRESSO,” J. Phys.: Condens. Matter 29, 465901 (2017).</p> <p>[3] J. P. Perdew, K. Burke, and M. Ernzerhof, “Generalized gradient approximation made simple,” Phys. Rev. Lett. 77, 3865–3868 (1996).</p> <p>[4] J. Heyd, G. E. Scuseria, and M. Ernzerhof, “Hybrid functionals based on a screened Coulomb potential,” J. Chem. Phys. 118, 8207–8215 (2003).</p>
Data from: Genetic and functional variation across regional and local scales is associated with climate in a foundational prairie grass
<ul> <li>Global change forecasts in ecosystems require knowledge of within species diversity, particularly of dominant species within communities. We assessed site-level diversity and capacity for adaptation of the dominant species of the shortgrass steppe biome of the Central US, Bouteloua gracilis.</li> <li>We quantified genetic diversity from 17 sites across regional scales, north-south from New Mexico to South Dakota, and local scales in Northern Colorado. We also quantified phenotype and plasticity within and among sites and determined the extent to which phenotypic diversity in B. gracilis was related to climate.</li> <li>Genome sequencing indicated pronounced population structure at the regional scale, and local differences indicated gene flow and/or dispersal may also be limited. Within a common environment, we found evidence for genetic divergence in biomass-related phenotypes, plasticity, and phenotypic variance, indicating functional divergence and different adaptive potential. Phenotypes differentiated according to climate, chiefly median Palmer Hydrological Drought Index and other aridity metrics.</li> <li>Our results indicate conclusive differences in genetic variation, phenotype, and plasticity in this species and suggest a mechanism explaining variation in shortgrass steppe community responses to global change. This analysis of B. gracilis intraspecific diversity across spatial scales will improve conservation and management of the shortgrass steppe ecosystem moving forward.</li> </ul>
dataset for bioRxiv preprint titled 'Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease'
<p>This data supports the Figures in the preprint titled</p> <p><strong>Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease</strong></p> <p><strong>working abstract</strong></p> <p>The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS). During the progression of the disease, some individual patients acquire -drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies. It has recently been discovered that drug-resistant mutations accumulate on the ‘flap region’ of the HIV-1 protease, which is a critical dynamic region involved in non-specific polypeptide binding during invasion and infection of the host cell. In this study, we utilize machine learning assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and polypeptide binding of the main protease. We use a multi-agent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs (SIV and FIV). We also investigate changes in dynamics due to common drug-resistant mutations in many patients. We find that a key functional site in the flap region, a solvent-exposed isoleucine (ILE50) and surrounding sites that control flap dynamics is often targeted by drug-resistance mutations, likely leading to malfunctional molecular dynamics affecting the overall flexibility of the flap region. We conclude that better long term patient outcomes may be achieved by designing drugs that target protease regions which are less dependent upon single sites with large functional binding effects.</p>
Species functional traits affect regional and local dominance across western Amazonian forests
Open the record for dataset details and reuse information.
Data from: Trade-offs among restored ecosystem functions are context-dependent in Mediterranean-type regions
Open the record for dataset details and reuse information.
Genetic and functional variation across regional and local scales is associated with climate in a foundational prairie grass
Open the record for dataset details and reuse information.
Data from: Forest loss and treeless matrices cause the functional impoverishment of sapling communities in old-growth forest patches across tropical regions
<p>Landscape-level disturbances, such as forest loss, can profoundly alter the functional composition and diversity of biotic assemblages. In fact, the landscape-moderated functional trait selection (LMFTS) hypothesis states that landscape-level disturbances may act as environmental filters that select a set of species with disturbance-adapted attributes while causing the loss of species with disturbance-sensitive attributes, ultimately compromising ecosystem functioning. However, the impact of landscape patterns on the functional composition and diversity of tropical regenerating trees (saplings) is unknown.</p> <p>Using a multiscale approach to identify the best spatial scale (i.e. the scale of effect), we tested the effect of forest cover, matrix openness and forest patch density (fragmentation) on functional composition and functional diversity of tree saplings in old-growth forest patches (n = 59) in three Mexican rainforest regions with different degree of deforestation. For 368 species and ~23,000 individuals, we compiled information from global and national databases on six functional traits related to seed dispersal and plant establishment and calculated their community abundance-weighted mean (CWMs) and three complementary functional diversity indices.</p> <p>Forest loss and matrix openness reduced functional richness and evenness, but only in the two most deforested regions. Overall, fragmentation had contrasting effects on functional diversity and composition, but correlated negatively with some functional traits in the most deforested region. Importantly, in the regions with high-to-intermediate degree of deforestation, functional composition experienced major changes: maximum height, seed mass, fruit size and wood density decreased, and SLA increased, in forest patches surrounded by open matrices in highly deforested and fragmented landscapes. This caused a shift of community traits towards more disturbed-adapted attributes.</p> <p><em>Synthesis and applications</em>. In agreement with the LMFTS hypothesis, our results confirm that landscape modifications in regions undergoing high and long-lasting deforestation greatly impoverish the functional composition and diversity of sapling communities. The shift from communities composed mainly by conservative attributes towards communities with a higher prevalence of disturbance-adapted attributes disrupts the future community structure and jeopardizes critical ecosystem functions. Management practices focused on preventing deforestation, increasing forest cover, and promoting treed matrices are necessary to preserve the functionality of these species-rich but increasingly threatened rainforests.</p>
Thallium(I) exposure perturbs the gut microbiota and metabolic profile as well as the regional immune function of C57BL/6 J mice
<p><span>Intestinal microbes</span><span> regulate the development of diseases induced by environmental exposure. Thallium (Tl) is a highly toxic heavy metal</span><span>, </span><span>and its toxicity is rarely discussed in relation to gut microbes. Herein, we showed that Tl(I) exposure (10 ppm for two weeks) affected the alpha diversity of bacteria in </span><span>the ileum, colon, and </span><span>feces, but had little effect on the beta diversity of bacteria through 16S rRNA sequencing. LEfSe analysis revealed that Tl(I) exposure changed the abundance of intestinal microbiota along the digestive tract. Cecum metabolomic detection and analysis showed that Tl(I) exposure altered the abundance and composition of metabolites. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that Tl(I) exposure impaired amino acid, lipid, purine metabolism, and G protein-coupled receptor signalling pathways. A consistency test revealed a strong correlation, and a Pearson's correlation analysis showed an extensive interaction, between microorganisms and metabolites. Analysis of the intestinal immunity revealed that Tl(I) exposure suppressed the immune responses, which also had regional differences. These results identify the perturbation of the intestinal microenvironment by Tl exposure and provide a new explanation for Tl toxicity.</span></p>
Exploiting functional regions in the viral RNA genome as druggable entities
<p><span>XML files with normalized SHAPE reactivities are provided in SHAPE_react_rep1/2.react.xml; </span></p> <p><span>WIG files with Shannon entropies are provided in SHAPE_react_rep1/2.react.xml,</span></p> <p><span>and the full secondary structure are provided in PEDV_incell_secondary structure.ct</span></p>
Supplementary material: Accuracy of finite fault slip estimates in subduction zone regions with topographic Green's functions and seafloor geodesy
<p># Code attached to the manuscript entitled "Accuracy of finite fault slip estimates in subduction zone regions with topographic Green's functions and seafloor geodesy"</p> <p>These python scripts are for producing Figure 1 (trench-perpendicular topographic profile for regions where some megathrust earthquakes occurred) and the average topographic profile that is used in the paper.</p> <p> </p>
Study Comparing Appearance and Function of Three Different Dental Implant Designs When Placed in Front Region of Upper Jaw
ClinicalTrials.gov study NCT00820235. IPD Sharing: Not stated. Countries: 2. Publications: 3.
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.