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750 results for “heterogeneous data”
Subtyping of common complex diseases and disorders by integrating heterogeneous data. Identifying clusters among women with lower urinary tract symptoms in the LURN study
<p>We present a methodology for subtyping of persons with a common clinical symptom complex by integrating heterogeneous continuous and categorical data. We illustrate it by clustering women with lower urinary tract symptoms (LUTS), who represent a heterogeneous cohort with overlapping symptoms and multifactorial etiology. Data collected in the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN), a multi-center observational study, included self-reported urinary and non-urinary symptoms, bladder diaries, and physical examination data for 545 women. Heterogeneity in these multidimensional data required thorough and non-trivial preprocessing, including scaling by controls and weighting to mitigate data redundancy, while the various data types (continuous and categorical) required novel methodology using a weighted Tanimoto indices approach. Data domains only available on a subset of the cohort were integrated using a semi-supervised clustering approach. Novel contrast criterion for determination of the optimal number of clusters in consensus clustering was introduced and compared with existing criteria. Distinctiveness of the clusters was confirmed by using multiple criteria for cluster quality, and by testing for significantly different variables in pairwise comparisons of the clusters. Cluster dynamics were explored by analyzing longitudinal data at 3- and 12-month follow-up. Five clusters of women with LUTS were identified using the developed methodology. None of the clusters could be characterized by a single symptom, but rather by a distinct combination of symptoms with various levels of severity. Targeted proteomics of serum samples demonstrated that differentially abundant proteins and affected pathways are different across the clusters. The clinical relevance of the identified clusters is discussed and compared with the current conventional approaches to the evaluation of LUTS patients. The rationale and thought process are described for the selection of procedures for data preprocessing, clustering, and cluster evaluation. Suggestions are provided for minimum reporting requirements in publications utilizing clustering methodology with multiple heterogeneous data domains.</p>
Data and code from: Cooperation and coordination in heterogeneous populations
<p>One landmark application of evolutionary game theory is the study of social dilemmas. This literature explores why people cooperate even when there are strong incentives to defect. Much of this literature, however, assumes that interactions are symmetric. Individuals are assumed to have the same strategic options and the same potential payoffs. Yet many interesting questions arise once individuals are allowed to differ. Here, we study asymmetry in simple coordination games. In our setup, human participants need to decide how much of their endowment to contribute to a public good. If a group's collective contributions reach a pre-defined threshold, all group members receive a reward. To account for possible asymmetries, individuals either differ in their endowments or their productivities. According to our theoretical equilibrium analysis, such games tend to have many possible solutions. In equilibrium, group members may contribute the same amount, different amounts, or nothing at all. According to the behavioral experiment, however, humans favor the equilibrium in which everyone contributes the same proportion of their endowment. We use these experimental results to highlight the nontrivial effects of inequality on cooperation, and we discuss to which extent models of evolutionary game theory can account for these effects.</p>
Data from: Interactions of wood accumulations, channel dynamics, and geomorphic heterogeneity within a river corridor
<p>Natural rivers are inherently dynamic. Spatial and temporal variations in water, sediment, and wood fluxes both cause and respond to an increase in geomorphic heterogeneity within the river corridor. We analyze 16 two-kilometer river corridor segments of the Swan River in Montana, USA to examine relationships between wood accumulations (wood accumulation distribution density, count, and persistence), channel dynamism (total sinuosity and average channel migration), and geomorphic heterogeneity (density, aggregation, interspersion, and evenness of patches in the river corridor). We hypothesize that i) more dynamic river segments correlate with a greater presence, persistence, and distribution of wood accumulations; ii) years with higher peak discharge correspond with greater channel dynamism and wood accumulations; and iii) all river corridor variables analyzed play a role in explaining river corridor spatial heterogeneity. Our results suggest that decadal-scale channel dynamism, as reflected in total sinuosity, corresponds to greater numbers of wood accumulations per surface area and greater persistence of these wood accumulations through time. Second, higher peak discharges correspond to greater values of wood distribution density, but not to greater channel dynamism. Third, persistent values of geomorphic heterogeneity, as reflected in the heterogeneity metrics of aggregation, interspersion, patch density, and evenness, are explained by potential predictor variables analyzed here. Our results reflect the complex interactions of water, sediment, and large wood in river corridors; the difficulties of interpreting causal relationships among these variables through time; and the importance of spatial and temporal analyses of past and present river processes to understand future river conditions</p>
Comp-het Data for "CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM"
<p>Synthetic cryo-EM datasets with simulated compositional heterogeneity and their ground truth atomic models, density maps, poses, labels, mask, and consensus volume:</p> <ul> <li>Ribosembly: 335,240 particle images (128x128, 6A/pix) containing 16 bacterial ribosome assembly states from "Cryo-em captures early ribosome assembly in action" from Qin et al. (2023)</li> <li>Tomotwin-100: 100k particle images (128x128, 9A/pix) containing a mixture of 100 different biomolecular complexes from "Tomotwin: generalized 3d localization of macromolecules in cryo-electron tomograms with structural data mining" from Rice et al. (2023)</li> </ul>
Conf-het Data for "CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM"
<p>Synthetic cryo-EM datasets with simulated conformational heterogeneity and their ground truth atomic models, density maps, poses, labels, mask, and consensus volume:</p> <ul> <li>IgG-1D: 100k particle images (128x128, 6A/pix) of IgG with conformations uniformly sampled from a simple one-dimensional continuous circular motion</li> <li>IgG-1D-noisier: The IgG-1D dataset with noise increased from SNR 0.01 to 0.005</li> <li>IgG-1D-noisiest: The IgG-1D dataset with noise increased from SNR 0.01 to 0.001</li> <li>IgG-RL: 100k particle images (128x128, 6A/pix) of IgG with conformations of its flexible linker generated by sampling backbone dihedral angles according to the Ramachandran distributions of disordered peptides</li> </ul>
Fig. 1 in Data storage and data re-use in taxonomy-the need for improved storage and accessibility of heterogeneous data
Fig. 1 (a) Sp_ci_s d_scriptions p_r d_cad_ in s_l_ct_d major groups of organisms (bas_d on data _xtract_d from th_ Int_rnational Plant Nam_s Ind_x (https://www.ipni.org/) for plants, MycoBank (http://www. mycobank.org/) for fungi, Ind_x of Organism Nam_s (http://www. organismnam_s.com/) for ins_cts, and compil_d from various databas_s for v_rt_brat_s: Eschm_y_r Catalog for fish_s (https://www.calacad_my. org/sci_ntists/proj_cts/_schm_y_rs-catalog-of-fish_s), th_ Amphibian Sp_ci_s of th_ World for amphibians (http://r_s_arch.amnh.org/vz/ h_rp_tology/amphibia/), R_ptil_ Databas_ for r_ptil_s (http://www. r_ptil_-databas_.org/), Howard and Moor_ Databas_ (https://www. howardandmoor_.org/) for birds, and ASM Mammal Div_rsity Databas_ (https://mammaldiv_rsity.org/) for mammals, all acc_ss_d in April 2019. Not_ that data for fungi and v_rt_brat_s r_f_r to curr_ntly acc_pt_d sp_ci_s nam_s only wh_r_as ins_ct data also includ_ synonyms and subsp_ci_s, and contain data gaps for s_v_ral d_cad_s in th_ nin_t__nth c_ntury; for all taxa, th_ low valu_s obtain_d for th_ last
Research data supporting "Raman spectroscopic imaging for quantification of depth-dependent and local heterogeneities in native and engineered cartilage"
<p>Research data supporting the publication: Albro M. et al., 2018, npj Regenerative Medicine, DOI: https://doi.org/10.1038/s41536-018-0042-7.</p>
Sparks et al, Heterogeneity in tumor chromatin-doxorubicin binding revealed by in vivo fluorescence lifetime imaging confocal endomicroscopy: In vitro data
<p>Data is divided into three folders:</p> <ul> <li>Sparks_et_al_FIG2_Histone_vs_free_GFP <ul> <li>data for Sparks et al Figure 2</li> <li>main text section: <em>'FRET between chromatin-bound GFP and doxorubicin'</em></li> </ul> </li> <li>Sparks_et_al_FIG3_in_vitro_dose_response <ul> <li>data for Sparks et al Figure 3#</li> <li>main text section:<em> 'FLIM endomicroscope can monitor doxorubicin cellular uptake'</em></li> </ul> </li> <li>Sparks_et_al_SuppFIG2_endoscope_spectral_cross_talk <ul> <li>data for Sparks et al Supplementary Figure 2</li> <li>Supplementary information</li> </ul> </li> </ul> <p><strong>Cell lines</strong></p> <p>IGROV-1 cell lines were cultured in CO<sub>2</sub> dependent media with 10% fetal bovine serum and 1% Pen Strep at 37 ˚C. Before experiments, cells were grown to 80% confluence. For measuring doxorubicin uptake by fluorescence an IGROV-1 cell line stably expressing GFP fused to Histone-1 (H1) was made using the PiggyBac transposon system. As a control to show that effect of doxorubicin on GFP depends on whether it is fused to H1 or not, a stable whole cell expression of GFP by lentiviral transfection and selection by Geneticin was made. For bioluminescence imaging of xenograft tumors, all IGROV-1 cell lines were made to stably express firefly luciferase.</p> <p>To investigate the effect of doxorubicin on other histones, IGROV-1 cells were transiently transfected with a Histone-2B-GFP plasmid (gift from Kurt Anderson) using the Lipofectamine® 2000 reagent.</p> <p>IGROV-1 cells were obtained from Crick institute cell services and confirmed as IGROV-1 by Short Tandem Repeats (STR) profiling and no mycoplasma was detected.</p> <p><strong>In vitro experiments</strong></p> <p>IGROV-1 cells were grown to 80% confluence in 75 ml flasks before being re-plated in 12 or 24 well plates or 35 ml glass bottomed dishes and allowed to attach to the surface for 24 hours before experiments.</p> <p>To study how the fluorescence of GFP labelled H1 labelled IGROV-1 cells changes with doxorubicin treatment, fluorescence intensity and lifetime distributions were measured from cells after 3 hours of incubation with doxorubicin of varying concentrations (0, 0.18, 0.9, 1.8, 9, 18 µM) by serial dilutions of a stock solution with PBS. After 3 of hours, cells were washed in PBS then fixed for 20 minutes in 4% PFA. Cells were then imaged in PBS. Doxorubicin hydrochloride (Sigma-Aldrich, D1515-10 mg) was dissolved in PBS to a concentration of 9 mM and stored at -20˚C.</p>
Sparks et al, Heterogeneity in tumor chromatin-doxorubicin binding revealed by in vivo fluorescence lifetime imaging confocal endomicroscopy: in vivo data
<p>Data is divided into three folders:</p> <ul> <li>Sparks_et_al_FIG_6_IP_intranodule_heterogeneity <ul> <li>data for Sparks et al Figure 6</li> <li>main text section: <em>'FRET between chromatin-bound GFP and doxorubicin'</em></li> </ul> </li> <li>Sparks_et_al_FIG4_5_6_IP_IV_chemo_comparison <ul> <li>data for Sparks et al Figures 4,5 & 6</li> <li>main text section:<em> 'FLIM endomicroscope can monitor doxorubicin cellular uptake'</em></li> </ul> </li> <li>Sparks_et_al_FIG6_IP__internodule_heterogeneity <ul> <li>data for Sparks et al Figure 6</li> <li>main text section: <em>'Intra-tumor heterogeneity'</em></li> </ul> </li> </ul> <p><strong>In vivo experiments</strong></p> <p>Murine xenografts were prepared by intraperitoneal (IP) injection of IGROV-1 cancer cells. IGROV-1 cells were grown to 80% confluence before being trypsinized and re‑suspended in PBS at a concentration of cells per ml. cells were injected into ICRF nude mice. After 14 days post-injection, the presence of intraperitoneal tumors was confirmed by bioluminescence imaging. Briefly, an IVIS bioluminescence imaging system was used to image isoflurane anesthetized mice. 100 µl of D-luciferin (luciferase substrate) at 30mg ml<sup>-1</sup> was injected IP 10 minutes before recording of bioluminescence images. The presence of peritoneal tumors was confirmed if bioluminescence signals from the peritoneum were above background noise 10-30 minutes after D‑luciferin injections. Following confirmation of tumors, in vivo fluorescence imaging experiments were carried out after 21 days. To study differences in drug uptake between intravenous or intraperitoneal delivery, prior to imaging mice were subject to IP or IV doxorubicin-based chemotherapy for 1.5, 3 or 24 hours. Imaging involved terminal procedures, mice were anesthetized then peritoneal tumors were exposed by minor surgery and inspected with the CEM.</p> <p>All animal model procedures were approved by The Francis Crick Institute Biological Ethics Committee and UK Home Office authority provided by Project License 70/8380.</p> <p> </p> <p> </p>
Supplementary data for manuscript: "Characterizing dynamic heterogeneities during nanogel degradation"
<p>Contains data files and code (python Jupyter notebook) to reconstruct plots for manuscript: "Characterizing dynamic heterogeneities during nanogel degradation"<br><br>Contact: zmira@g.clemson.edu<br><br><br>This work is supported by the National Science Foundation under NSF Award No. 2110309.</p>
Research Data for the Journal Article: Efficient DMF-assisted synthesis of formamides from amines using CO2 catalyzed by heterogeneous metal-free imidazolium-hypercrosslinked polymers
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Improving triaging from primary care into secondary care using heterogeneous data-driven hybrid machine learning: A real-world case study of decision support system using blood test & GP referral letters - Bing Wang and Prof Weizi (Vicky) Li (University of Reading)
<p>This video is the sixth talk from our two day Future Blood Testing: Challenges & Opportunities Event that took place on the 13/09/2022.</p> <p>Improving triaging from primary care into secondary care using heterogeneous data-driven hybrid machine learning: A real-world case study of decision support system using blood test & GP referral letters - Bing Wang and Prof Weizi (Vicky) Li (University of Reading)</p> <p>Bio: Dr Weizi (Vicky) Li is the PI of the Future Blood Testing Network, an Associate Professor of Informatics and Digital Health, Deputy Director in Informatics Research Centre, Henley Business School, University of Reading. She is an interdisciplinary researcher focusing on using informatics, data science, machine learning, and digital information systems to solve real-world healthcare challenges. She is the academic lead of a large collaborative project of Improving the Quality of Healthcare through an Integrated Clinical Pathway Management Approach and Cloud based Digital Data Integration Platform, which was awarded ESRC O2RB Excellence in Impact Award in 2018 for her research impact on healthcare quality improvement. She is the academic lead of machine learning based decision support system for outpatient management which has successfully been implemented in Royal Berkshire NHS Foundation Trust and has received Research Engagement and Impact award in 2020. She has been PI on projects funded by ESRC, EPSRC, The Health Foundation, NHS and companies, working on data-driven decision support systems that use real-world data (under privacy preserving framework) from multiple sources including Electronic Patient Record in acute, community hospital and primary care settings, remote health monitoring and patient reported outcomes to develop novel technologies (including AI based methods) to support clinical and operational decision makings in patient pathway. Bing Wang is currently a PhD candidate in informatics and system science at the Informatics Research Center, Henley Business School, University of Reading. Bing’s research interests are Natural Language Processing, Machine Learning and Graph Machine Learning. Bing been working as a data scientist at Royal Berkshire NHS Foundation Trust since December 2019 during his PhD.</p> <p>Further details on this event can be found at: https://futurebloodtesting.org/event/13-14-09-2022/</p> <p>This video is an output from the Future Blood Testing Network which is funded by EPSRC under Grant Number EP/W000652/1</p> <p>YouTube Link: https://youtu.be/W6EH5l80NmU</p>
Data from: Tall, heterogenous forests improve prey capture, delivery to nestlings, and reproductive success for Spotted Owls in southern California
<p>Predator-prey interactions can be profoundly influenced by vegetation conditions, particularly when predator and prey prefer different habitats. Although such interactions have proven challenging to study for small and cryptic predators, recent methodological advances substantially improve opportunities for understanding how vegetation influences prey acquisition and strengthen conservation planning for this group. The California Spotted Owl (<em>Strix</em> <em>occidentalis</em> <em>occidentalis</em>) is well-known as an old-forest species of conservation concern, but whose primary prey in many regions – woodrats (<em>Neotoma</em> spp.) – occurs in a broad range of vegetation conditions. Here, we used high-resolution GPS tracking coupled with nest video monitoring to test the hypothesis that prey capture rates vary as a function of vegetation structure and heterogeneity, with emergent, reproductive consequences for Spotted Owls in Southern California. Foraging owls were more successful capturing prey, including woodrats, in taller multilayered forests, in areas with higher heterogeneity in vegetation types, and near forest-chaparral edges. Consistent with these findings, Spotted Owls delivered prey items more frequently to nests in territories with greater heterogeneity in vegetation types and delivered prey biomass at a higher rate in territories with more forest-chaparral edge. Spotted Owls had higher reproductive success in territories with higher mean canopy cover, taller trees, and more shrubby vegetation. Collectively, our results provide additional and compelling evidence that a mosaic of large tree forests with complex canopy and shrubby vegetation increases access to prey with potential reproductive benefits to Spotted Owls in landscapes where woodrats are a primary prey item. We suggest that forest management activities that enhance forest structure and vegetation heterogeneity could help curb declining Spotted Owl populations while promoting resilient ecosystems in some regions.</p>
Data for Automated Generation of Microkinetics for Heterogeneously Catalyzed Reactions Considering Correlated Uncertainties
<p>Data for the manuscript "Automated Generation of Microkinetics for Heterogeneously Catalyzed Reactions Considering Correlated Uncertainties". The data set contains all the generated mechanisms, DFT data used for the construction of the RMG library, a backup of the RMG-database, all results and scripts for the evaluation of the results. </p>
Data from: Evaluating the importance of individual heterogeneity in reproduction to Weddell seal population dynamics using integral projection models
<ol> <li>Identifying and accounting for unobserved individual heterogeneity in vital rates in demographic models is important for estimating population-level vital rates and identifying diverse life-history strategies, but much less is known about how this individual heterogeneity influences population dynamics.</li> <li>We aimed to understand how the distribution of individual heterogeneity in reproductive and survival rates influenced population dynamics using vital rates from a Weddell seal population by altering the distribution of individual heterogeneity in reproduction, which also altered the distribution of individual survival rates through the incorporation of our estimate of the correlation between the two rates and assessing resulting changes in population growth.</li> <li>We constructed an integral projection model (IPM) structured by age and reproductive state using estimates of vital rates for a long-lived mammal that has recently been shown to exhibit large individual heterogeneity in reproduction. Using output from the IPM, we evaluated how population dynamics changed with different underlying distributions of unobserved individual heterogeneity in reproduction.</li> <li>Results indicate that the changes to the underlying distribution of individual heterogeneity in reproduction cause very small changes in the population growth rate and other population metrics. The largest difference in the estimated population growth rate resulting from changes to the underlying distribution of individual heterogeneity was less than 1%.</li> <li>Our work highlights the differing importance of individual heterogeneity at the population level compared to the individual level. Although individual heterogeneity in reproduction may result in large differences in the lifetime fitness of individuals, changing the proportion of above- or below-average breeders in the population results in much smaller differences in annual population growth rate. For a long-lived mammal with stable and high adult-survival that gives birth to a single offspring, individual heterogeneity in reproduction has a limited effect on population dynamics. We posit that the limited effect of individual heterogeneity on population dynamics may be due to canalization of life-history traits.</li> </ol>
Raw, processed and merged Data for Swiss Cat+ East A1 project related to the automated and high-throughput Bayesian Optimization of CO2 hydrogenation heterogeneous catalysts
<p> All files generated during the fully digitalized automated and high-throughput experimentally-guided Bayesian Optimization project, which led to the synthesis of 144 heterogeneous catalysts with a Chemspeed unit (6 generations of 24) and their testing under CO2 hydrogenation conditions with Avantium fixed bed units. Below are some indication to understand the naming of the files.</p> <ul> <li>A1 stands for the internal project number.</li> <li>G1 to G5 stands for the catalyst generation number and G2NC for the alternative second generation suggested by the Bayesian Optimizer without considering the cost of catalyst as an objective (No_Cost).</li> <li>Three fixed bed units have been used, named XDB4x (a 4 parallel reactors unit), XDC4x (another 4 parallel reactors unit) and XR16x (a 16 parallel reactors unit).</li> <li>Individual fixed bed testing raw files (FB_RawData) generated by each unit are then processed to extract the mean and standard deviation (std) values (e.g conversion, selectivity) and to compute reactions rates.</li> <li>Then the processed files for each individual reactor (XDB, XDC, XR) are combined into one file (All_FBData), and finally aggregated with the synthesis details, viathe catalyst barcodes (AllData_Processed).</li> <li>Finally, the processed file for each generation are merged together (AllGen_Merged) and a condensed file is generated for a given reaction temperature (AllGen_275CDataProcessed_Merged)</li> </ul>
Replication data for: The Effect of IS-Innovation Strategy Alignment on Corporate Performance: Investigating the Role of Environmental Uncertainty by Heterogeneity
<p>A base de dados técnico-científica de 856 empresas brasileiras examinou o alinhamento entre sistemas de informação estratégicos (ISS), na abordagem da estratégia como prática, e inovação de exploration e exploitation, e seu impacto no desempenho corporativo (CP) sobre incerteza ambiental. Os resultados mostram que todos os tipos de alinhamento entre ISS e inovação influenciam positivamente o CP. O alinhamento com inovação ambidestra teve um impacto 62% maior no CP do que o alinhamento com inovações incrementais. Além disso, inovações disruptivas tiveram efeitos positivos em ambientes hostis, enquanto inovações exploratórias e ambidestras tiveram impactos fortes em ambientes altamente dinâmicos.</p>
Data from: Heterogeneous palaeo-ecogeography of brachiopods during the Late Ordovician mass extinction in South China
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Data for: Evaluating heterogeneity in household travel response to carbon pricing: a study focusing on small and rural communities
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Data from: Homogeneous selection and stochasticity overrule heterogeneous selection across biotic taxa and ecosystems
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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.