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.
920
datasets available to search
ShareScore release 0.9.0
Dataset results
920 results for “Functional analysis”
fMRI/fPACT 3D image stacks and analysis codes for function
Open the record for dataset details and reuse information.
Data from: Applications of three-dimensional box modeling to paleontological functional analysis
Open the record for dataset details and reuse information.
Global analysis of cell behavior and protein localization dynamics reveals region-specific functions for Shroom3 and N-cadherin during neural tube closure
Open the record for dataset details and reuse information.
Soil nutrient analysis:Nutrient Network. A cross-site investigation of bottom-up control over herbaceous plant community dynamics and ecosystem function.
This experiment is one implementation of a globally distributed experiment, known as the Nutrient Network. At Cedar Creek, as in over 70 other sites in grasslands around the world, the experiment aims to describe impacts of increased nutrients (nitrogen, phosphorus, potassium, sulfur and other metals) and decreased herbivory (removal of mammals by fencing). Two overarching questions are being explored with these manipulations: 1. To what extent are plant production and diversity co-limited by multiple nutrients in herbaceous-dominated communities? 2. Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? By utilizing identical protocols at diverse grassland sites around the world, NutNet aims to uncover both the generalities in ecosystem functioning, and the contingencies or differences which can obscure those common mechanisms. In addition to the standard NutNet protocol, e247 includes an additional low Nitrogen gradient (1 gram Nitrogen per meter squared per year and 5 grams Nitrogen per meter squared per year in addition to the standard 10 grams Nitrogen per meter squared per year).
Data from: An environmental impact assessment of different management regimes in eucalypt plantations in southern China using Landscape Function Analysis
<p>There are global concerns regarding the detrimental environmental impacts of industrial forest plantations developed over the past 30 years. To address this concern, the Landscape Function Analysis methodology was used to rapidly assess indices of soil stability, water infiltration, and nutrient cycling within eucalypt plantations at different growth stages and under different management regimes in Guangxi Province, China. Results showed that these plantations under both regimes were approaching an ecologically functional state by the time of harvest. However, within the plantation management that included the burning of post-harvest biomass residues, indices of water infiltration, and nutrient cycling were significantly lower than within the plantation that retained post-harvest residues. Indicators of rain splash protection, perennial vegetation cover, and litter accumulation were all lower in the plantation that practiced residue burning and pre-planting cultivation. Retention of post-harvest residues improves landscape functionality at the time of re-planting. Our results indicate that burning and extensive cultivation prior to re-planting should be minimized.</p>
Survey of metaproteomics software tools for functional microbiome analysis
<p>The dataset contains files used as input for running functional tools, and it also contains the output files generated by them. These output files were then used for data analysis to comparing them.</p>
Patient or family perceived deterioration in functional status and outcome after Intensive Care admission: a retrospective cohort analysis of routinely collected data
<p><span><span><span><span><span><span><span><span><span><span><span>Objective: To explore the association of patient or family reported functional deterioration (defined by a single question) in the preceding year, with mortality outcome for those admitted to the Intensive Care Unit (ICU).</span></span></span></span></span></span></span></span></span></span></span></p> <p> </p> <p><span><span><span><span><span><span><span><span><span><span><span>Design: Retrospective observational analysis of a routinely collected data source.</span></span></span></span></span></span></span></span></span></span></span></p> <p> </p> <p><span><span><span><span><span><span><span><span><span><span><span>Participants: Patients that were admitted to the ICU at Northwick Park Hospital, London North West University Healthcare NHS Trust between 1/10/2017 to 15/6/2019 were included. Patients were excluded if they had a prior ICU admission during the existing hospital episode or if information on functional deterioration could not be retrieved from either the patient or their advocate.</span></span></span></span></span></span></span></span></span></span></span></p> <p> </p> <p><span><span><span><span><span><span><span><span><span><span><span>Primary Outcomes: Mortality at the point of hospital discharge and 1 year following admission to the ICU.</span></span></span></span></span></span></span></span></span></span></span></p> <p> </p> <p><span><span><span><span><span><span><span><span><span><span><span>Results: Of the 1006 patients who were admitted to the ICU during the study period, information on functional deterioration was available for 621 patients who were included in the analysis. From these, 251 (40.4%) patients had patient or family reported functional deterioration in the preceding year, whilst 370 (59.6%) patients had a perceived stable functional baseline. Comparing the two groups, mortality was significantly higher in those who had functionally deteriorated compared to those with stable baseline function, at the point of hospital discharge (45.4% versus 25.9%; P<0.0001) and at 1 year (59.4% versus 33.0%; P<0.0001). </span></span></span></span></span></span></span></span></span></span></span></p> <p> </p> <p><span><span><span><span><span><span><span><span><span><span><span>Conclusion: Patient or family reported functional deterioration was significantly associated with higher mortality at the point of hospital discharge and at 1 year. The concept of functional deterioration in the lead up to ICU admission warrants further exploration.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function
Background: Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancreas, particularly with respect to their "unusual" energy metabolism (where ketone bodies and amino acids are the main oxidative fuel source) and their paradoxical ability to both maintain stable blood glucose levels and tolerate extensive periods of hypoglycemia. In order to shed light on some of these processes, we carried out the first large-scale comparative transcriptomic survey of multiple cartilaginous fish tissues: the pancreas, brain and liver of the lesser spotted catshark, Scyliorhinus canicula. Results: We generated a mutli-tissue assembly comprising 86,006 contigs, of which 44,794 were assigned to a particular tissue or combination of tissues based on mapping of sequencing reads. We have characterised transcripts encoding genes involved in insulin regulation, glucose sensing, transcriptional regulation, signaling and digestion, as well as many peptide hormone precursors and their receptors for the first time. Comparisons to mammalian pancreas transcriptomes reveals that mechanisms of glucose sensing and insulin regulation used to establish and maintain a stable internal environment are conserved across jawed vertebrates and likely pre-date the vertebrate radiation. Conservation of pancreatic hormones and genes encoding digestive proteins support the single, early evolution of a distinct pancreatic gland with endocrine and exocrine functions in jawed vertebrates. In addition, we demonstrate that chondrichthyes lack pancreatic polypeptide (PP) and that reports of PP in the literature are likely due cross-reaction with PYY and/or NPY in the pancreas. A three hormone islet organ is therefore the ancestral jawed vertebrate condition, later elaborated upon only in the tetrapod lineage. Conclusions: The cartilaginous fish are a great untapped resource for the reconstruction of patterns and processes of vertebrate evolution and new approaches such as those described in this paper will greatly facilitate their incorporation into the rank of "model organism".
Data from: Biochemical and functional analysis of Cyanobacterium Oscillatoria sp. LPS on human monocytes
Cyanobacterial blooms are an increasing source of environmental toxins that affect both human and animals. After ingestion of cyanobacteria, such as Geitlerinema sp., toxins and lipopopolysaccharide (LPS) from this organism induce fever, gastro-intestinal illness, and even death. However, little is known regarding the effects of cyanobacterial LPS on human monocytes after exposure to LPS upon ingestion. Based on our previous data using Geitlerinema sp. LPS (which was previously named Oscillatoria sp., a genus belonging to the same order as Geitlerinema), we hypothesized that Geitlerinema sp. LPS would activate human monocytes to proliferate, phagocytose particles and produce cytokines that are critical for promoting pro-inflammatory responses in the gut. Our data demonstrate that Geitlerinema sp. LPS induces monocyte proliferation and TNF-α, IL-1, and IL-6 production at high concentrations. In contrast, Geitlerinema sp. LPS is equally capable of inducing monocyte-mediated phagocytosis of FITC-Latex beads when compared to E. coli LPS, which was used as a positive control for our experiments. In order to understand the mechanism responsible for the difference in efficacy between Geitlerinema sp. LPS and E. coli LPS, we performed biochemical analysis and identified that Geitlerinema sp. LPS is comprised of significantly different sugars and fatty-acid side chains in comparison to E. coli LPS. The lipid A portion of Geitlerinema sp. LPS contains longer fatty acid side chains, such as C15:0, C16:0, and C18:0, instead of C12:0 found in E. coli LPS which may explain the decreased efficacy and toxicity of Geitlerinema sp. LPS in comparison to E. coli LPS.
Data from: Auditory functional magnetic resonance imaging in dogs – normalization and group analysis and the processing of pitch in the canine auditory pathways
Background: Functional magnetic resonance imaging (fMRI) is an advanced and frequently used technique for studying brain functions in humans and increasingly so in animals. A key element of analyzing fMRI data is group analysis, for which valid spatial normalization is a prerequisite. In the current study we applied normalization and group analysis to a dataset from an auditory functional MRI experiment in anesthetized beagles. The stimulation paradigm used in the experiment was composed of simple Gaussian noise and regular interval sounds (RIS), which included a periodicity pitch as an additional sound feature. The results from the performed group analysis were compared with those from single animal analysis. In addition to this, the data were examined for brain regions showing an increased activation associated with the perception of pitch. Results: With the group analysis, significant activations matching the position of the right superior olivary nucleus, lateral lemniscus and internal capsule were identified, which could not be detected in the single animal analysis. In addition, a large cluster of activated voxels in the auditory cortex was found. The contrast of the RIS condition (including pitch) with Gaussian noise (no pitch) showed a significant effect in a region matching the location of the left medial geniculate nucleus. Conclusion: By using group analysis additional activated areas along the canine auditory pathways could be identified in comparison to single animal analysis. It was possible to demonstrate a pitch-specific effect, indicating that group analysis is a suitable method for improving the results of auditory fMRI studies in dogs and extending our knowledge of canine neuroanatomy.
A meta-analysis of natural selection on plant functional traits
<p>A common assumption in plant physiological ecology is that variation in functional traits reflects the adaptation of organisms to their abiotic environment. This assumption can be tested by estimating natural selection as the relationship between a functional trait and a fitness component (i.e. survival or reproduction) within a population. To understand how natural selection operates on plant functional traits, we compiled directional selection gradients (<i>β</i><span><span></span></span>), which estimate direct selection, and differentials (<i>S</i><span><span></span></span>), which estimate both direct and indirect selection, from studies conducted in manipulated and unmanipulated environments. We found that relative to manipulating biotic factors, manipulating abiotic factors had a ~5.7´ larger effect on <i>β </i><span><span></span></span>and a ~16´ larger effect on <i>S</i><span><span></span></span>, suggesting that functional traits primarily evolve in response to the abiotic environment. We found that the strength of selection on functional traits <i>(</i><span></span><i>β</i><i>)</i><span><span></span></span> did not vary with trait type, performance/fitness component, or measurement context (i.e. common garden vs. natural population). However, the direction of selection did differ between some trait types: <i>β</i><span><span></span></span> was positive for plant size traits, but negative for phenology traits. Lastly, we found that the absolute value of selection differentials (<span></span><i>S</i><span><span></span></span>) was ~2´ larger than the absolute value of selection gradients (<span></span><i>β</i><span><span></span></span>), indicating that there was indirect selection on functional traits. Overall, our meta-analysis illustrates that natural selection on plant functional traits is common, and that estimates of selection on these traits in experimentally manipulated environments can be used effectively to test hypotheses about the causes of adaptation.</p>
Data from: The use of functional data analysis to evaluate activity in a spontaneous model of degenerative joint disease associated pain in cats
Accelerometry is used as an objective measure of physical activity in humans and veterinary species. In cats, one important use of accelerometry is in the study of therapeutics designed to treat degenerative joint disease (DJD) associated pain, where it serves as the most widely applied objective outcome measure. These analyses have commonly used summary measures, calculating the mean activity per-minute over days and comparing between treatment periods. While this technique has been effective, information about the pattern of activity in cats is lost. In this study, functional data analysis was applied to activity data from client-owned cats with (n=83) and without (n=15) DJD. Functional data analysis retains information about the pattern of activity over the 24-hour day, providing insight into activity over time. We hypothesized that 1) cats without DJD would have higher activity counts and intensity of activity than cats with DJD; 2) that activity counts and intensity of activity in cats with DJD would be inversely correlated with total radiographic DJD burden and total orthopedic pain score; and 3) that activity counts and intensity would have a different pattern on weekends versus weekdays. Results showed marked inter-cat variability in activity. Cats exhibited a bimodal pattern of activity with a sharp peak in the morning and broader peak in the evening. Results further showed that this pattern was different on weekends than weekdays, with the morning peak being shifted to the right (later). Cats with DJD showed different patterns of activity from cats without DJD, though activity and intensity were not always lower; instead both the peaks and troughs of activity were less extreme than those of the cats without DJD. Functional data analysis provides insight into the pattern of activity in cats, and an alternative method for analyzing accelerometry data that incorporates fluctuations in activity across the day.
Data from: Convergence analysis of a finite element skull model of Herpestes javanicus (Carnivora, Mammalia): implications for robust comparative inferences of biomechanical function
Predictions of skull biomechanical capability based on virtual models constitute a valuable data source for testing hypotheses about craniodental form and feeding behavior. Such comparative analyses also inform dietary reconstruction in extinct species. 3D modeling using Finite Element (FE) methods is a common technique applied to the comparative analysis of craniodental function in extinct and extant vertebrates. However, taxonomically diverse skull models in the literature often are not directly comparable to each other, in part because of distinctions in how boundary conditions are defined, but also because of substantial differences in the number of FEs composing the models. In this study, we test whether a conventional convergence test is adequate in identifying the minimum number of FEs needed to achieve internally stable results for a single species. We constructed a series of skull models of Herpestes javanicus, and simulated unilateral biting across the dentition; the models differed in the number of FEs, degrees of freedom at the joint and bite point constraints, and type of tetrahedral FEs used. We found that convergence patterns differed across constraint types, FE quantities, and bite position simulated. Four-noded tetrahedral (tet-4) FE models with relaxed constraints produced the most stable measurements compared to over-constrained tet-4 models and to relaxed tet-10 models. In absence of an optimal FE quantity from convergence testing, we propose a broadly applicable sub-sampling protocol, whereby average measurement values across multiple models per specimen are used for among-species comparisons. A regime of sampling three low FE quantity models produced the closest estimates of mean measurement values relative to larger model sets, being within the 95% bootstrap estimated confidence intervals. Future studies should focus on identifying sources of variation associated with other FE modeling protocols, so that they can be accounted for before biomechanical attributes from these simulations are used to infer form–function linkage.
Data from: On the link between functional traits and growth rate: meta-analysis shows effects change with plant size, as predicted
A plant's growth rate is seen as a central element of its ecological strategy, and as determined by its traits.Yet the literature is inconsistent about the empirical correlation between functional traits and growth, casting doubt on the capacity of some prominent traits to influence growth rate. We propose that traits should influence growth in a way that depends on the size of individual plants. We outline mechanisms and hypotheses based on new theoretical work, and test these predictions in tree species using a meta-analysis of 103 studies (> 500 correlations) for five traits (specific leaf area, wood density, maximum height, seed mass and maximum assimilation rate).We also recorded data for 14 other traits commonly used in the trait literature.To capture the effects of plant size, we tested for a shift in the direction of correlation between growth rates and each trait across three ontogenetic stages: seedling,sapling and adult. Results were consistent with predictions, although there were some limitations arising from unequal numbers of observation across ontogenetic stages.Specific leaf area was correlated with relative growth rate in seedlings but not in adult plants.Correlations of growth with wood density were not affected by ontogenetic stage. Seed mass, assimilation rate and maximum height were correlated with relative growth rate only in one ontogenetic stage category: seedlings,seedlings and adults,respectively. Although we were able to confirm several of our theoretical predictions,major knowledge gaps still exist in the trait literature.For example,for one third of the traits considered,the majority (> 75%) of reported correlations with growth came from the same ontogenetic stage. Synthesis: We show for some traits, how trait-growth correlations change in a predictable way with plant size.Our understanding of plant strategies should shift away from describing species as having a fixed growth strategy throughout their life (on a continuous axis from slow to fast growth), in favour of a size-dependent growth trajectories.
Raw data associated to the paper "Analysis of species pair associations combined with functional traits reveals the effects of environmental filtering and biotic interactions in an unmanaged temperate forest"
Open the record for dataset details and reuse information.
Expression Pattern and Potential Functional Sites Analysis of ALOX12B Gene in Sheep Horn
Open the record for dataset details and reuse information.
Experimental raw data for "Characterization of activated carbons for water treatment using TGA-FTIR for analysis of oxygen-containing functional groups"
<p>LICENSE: These data are made available under the Public Domain Dedication and License v1.0 whose full text can be found at: http://opendatacommons.org/licenses/pddl/1.0/</p> <p><br> This is the repository of all experimental raw data used in the Applied Water Science publication "Characterization of activated carbons for water treatment using TGA-FTIR for analysis of oxygen-containing functional groups" by Daniel Dittmann, Leon Saal, Frederik Zietzschmann, Maike Mai, Korinna Altmann, Dominik Al-Sabbagh, Pia Schumann, Aki Sebastian Ruhl, Martin Jekel, and Ulrike Braun.</p> <p>It includes<br> - Results_summary (.xlsx and .ods) containing overview tables with all numerical results for the eight selected PACs<br> - 01_N2_Adsorption_Desorption<br> - 02_Particle_Counter<br> - 03_CHNS<br> - 04_PZC<br> - 05_XPS<br> - 06_XRF<br> - 07_XRD<br> - 08_TGA-FTIR<br> - 09_PCA_all_properties<br> - 10_OMP_removals</p> <p>Subfolders are provided for<br> - "Raw_Data"<br> - "processed_for_plotting" with Origin files<br> - "easyPCA" with data for principal component analyses using Jupyter Notesbooks from https://github.com/danield5732/easyPCA</p>
Functional analysis data (AlphaMissense) for Amylase proteins
<p>Data ectracted from AlphaMissense (J. Cheng <em>et al.</em> 2023).</p>
Effects of blood cell traits on cardiovascular morpho-functional phenotypes: Evidence from Mendelian randomization analysis
Open the record for dataset details and reuse information.
Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins - Molecular dynamics trajectories and analysis scripts
Open the record for dataset details and reuse information.
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.