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305 results for “characterization model”
Improved dual-permeability model for characterizing the mass transfer process inside matrix blocks
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Multimodal mucosal and systemic immune characterization of a non-human primate trachoma model highlights the critical role of local immunity during acute phase disease
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Model for: Characterizing long‐term population conditions of the elusive red tree vole with dynamic individual‐based modeling
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Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation
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Data from: Development of an adrenocortical cancer humanized mouse model to characterize anti-PD1 effects on tumor microenvironment
Context: While the development of immune checkpoint inhibitors has transformed treatment strategies of several human malignancies, research models to study immunotherapy in ACC are lacking. Objective: To explore the effect of anti-PD1 immunotherapy on the alteration of the immune milieu in ACC in a newly generated preclinical model and correlate with the response of the matched patient. Design, Setting and Intervention: To characterize the CU-ACC2-M2B patient-derived xenograft in a humanized mouse model, evaluate the effect of a PD-1 inhibitor therapy and compare to the CU-ACC2 patient with metastatic disease. Results: Characterization of the CU-ACC2-hu-CB-BRGS model confirmed ACC origin and match with the original human tumor. Treatment of the mice with pembrolizumab demonstrated significant tumor growth inhibition (TGI = 60%) compared to controls, which correlated with increased tumor infiltrating lymphocyte activity, with an increase of human CD8+ T cells (p<0.05), HLA-DR+ T cells (p<0.05) as well as Granzyme B+ CD8+ T cells (<0.001). In parallel, treatment of the CU-ACC2 patient, who had progressive disease, demonstrated a partial response with 79%-100% reduction in the size of target lesions, and no new sites of metastasis. Pre-treatment analysis of the patient's metastatic liver lesion demonstrated abundant intra-tumoral CD8+ T cells by immunohistochemistry. Conclusions: Our study reports the first humanized ACC PDX mouse model which may be useful to define mechanisms and biomarkers of response and resistance to immune-based therapies, to ultimately provide more personalized care for patients with ACC.
Bayesian stable isotope mixing models effectively characterize the diet of an Arctic raptor
<p>1. Bayesian stable isotope mixing models (BSIMMs) for δ13C and δ15N can be a useful tool to reconstruct diets, characterize trophic relationships, and assess spatiotemporal variation in food webs. However, use of this approach typically requires a priori knowledge on the level of enrichment occurring between the diet and tissue of the consumer being sampled (i.e., a trophic discrimination factor or TDF).</p> <p>2. TDFs derived from captive feeding studies are highly variable, and it is challenging to select the appropriate TDF for diet estimation in wild populations. We introduce a novel method for estimating TDFs in a wild population: a proportionally balanced equation that uses high-precision diet estimates from nest cameras installed on a subset of nests in lieu of a controlled feeding study (TDFCAM).</p> <p>3. We tested the ability of BSIMMs to characterize diet in a free-living population of gyrfalcon (Falco rusticolus) nestlings by comparing model output to high-precision nest camera diet estimates. We analyzed the performance of models formulated with a TDFCAM against other relevant TDFs and assessed model sensitivity to an informative prior. We applied the most parsimonious model inputs to a larger sample to analyze broad-scale temporal dietary trends.</p> <p>4. BSIMMs fitted with a TDFCAM and uninformative prior had the best agreement with nest camera data, outperforming TDFs derived from captive feeding studies. BSIMMs produced with a TDFCAM produced reliable diet estimates at the nest level and accurately identified significant temporal shifts in gyrfalcon diet within and between years.</p> <p>5. Our method of TDF estimation produced more accurate estimates of TDFs in a wild population than traditional approaches, consequently improving BSIMM diet estimates. We demonstrate how BSIMMs can complement a high-precision diet study by expanding its spatiotemporal scope of inference and recommend this integrative methodology as a powerful tool for future trophic studies. </p>
Data from: Coalescent models characterize sources and demographic history of recent round goby colonization of Great Lakes and inland waters
The establishment and spread of aquatic invasive species is ecologically and economically harmful and a source of conservation concern internationally. Processes of species invasion have traditionally been inferred from observational data of species presence/absence and relative abundance. However, genetic-based approaches can provide valuable sources of inference. Restriction-site associated DNA sequencing was used to identify and genotype single nucleotide polymorphism (SNP) loci for Round Gobies (Neogobius melanostomus) (N=440) from 18 sampling locations in the Great Lakes and in three Michigan, USA drainages (Flint, Au Sable, and Cheboygan River basins). Sampled rivers differed in size, accessibility, and physical characteristics including man-made dispersal barriers. Population levels of genetic diversity and inter-population variance in SNP allele frequency were used in coalescence-based Approximate Bayesian Computation (ABC) to statistically compare models representing competing hypotheses regarding source population, post-colonization dispersal, and demographic history in the Great Lakes and inland waters. Results indicate different patterns of colonization across the three drainages. In the Flint River, models indicate a strong population bottleneck (< 3% of contemporary effective population size) and a single founding event from Saginaw Bay led to the colonization of inland river segments. In the Au Sable River, analyses could not distinguish potential source populations, but supported models indicated multiple introductions from one source population. In the Cheboygan River, supported models indicated that colonization likely proceeded from east (Lake Huron source) to west among inland locales sampled in the system. Despite the recent occupancy of Great Lakes and inland habitats, large numbers of loci analyzed in an ABC framework enable statistically supported identification of source populations and reconstruction of the direction of inland spread and demographic history following establishment. Information from analyses can direct management actions to limit the spread of invasive species from identified sources and most probable vectors into additional inland aquatic habitats.
Data from: A spatially explicit hierarchical model to characterize population viability
Many of the processes that govern the viability of animal populations vary spatially, yet population viability analyses (PVAs) that account explicitly for spatial variation are rare. We develop a PVA model that incorporates autocorrelation into the analysis of local demographic information to produce spatially explicit estimates of demography and viability at relatively fine spatial scales across a large spatial extent. We use a hierarchical, spatial autoregressive model for capture-recapture data from multiple locations to obtain spatially explicit estimates of adult survival (Φad), juvenile survival (Φjuv), and juvenile-to-adult transition rates (ψ), and a spatial autoregressive model for recruitment data from multiple locations to obtain spatially explicit estimates of recruitment (R). We combine local estimates of demographic rates in stage-structured population models to estimate the rate of population change (λ), then use estimates of λ (and its uncertainty) to forecast changes in local abundance and produce spatially explicit estimates of viability (probability of extirpation, Pex). We apply the model to demographic data for the Sonoran desert tortoise (Gopherus morafkai) collected across its geographic range in Arizona. There was modest spatial variation in λ (0.94–1.03), which reflected spatial variation in Φad (0.85–0.95), Φjuv (0.70–0.89), and ψ (0.07–0.13). Recruitment data were too sparse for spatially explicit estimates, therefore we used a range-wide estimate (R = 0.32 one-year old females per female per year). Spatial patterns in demographic rates were complex, but Φad, Φjuv, and λ tended to be lower and ψ higher in the northwestern portion of the range. Spatial patterns in Pex varied with local abundance. For local abundances > 500, Pex was near zero (Pex approached one in the northwestern portion of the range and remained low elsewhere. When local abundances were Pex > 0.25). This approach to PVA offers the potential to reveal spatial patterns in demography and viability that can inform conservation and management at multiple spatial scales, provide insight into scale-related investigations in population ecology, and improve basic ecological knowledge of landscape-level phenomena.
Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed.
Data from: Characterizing neutral and adaptive genomic differentiation in a changing climate: the most northerly freshwater fish as a model
Arctic freshwater ecosystems have been profoundly affected by climate change. Given that the Arctic charr (Salvelinus alpinus) is often the only fish species inhabiting these ecosystems, it represents a valuable model for studying the impacts of climate change on species life history diversity and adaptability. Using a genotyping-by-sequencing approach, we identified 5976 neutral single nucleotide polymorphisms (SNPs) and found evidence for reduced gene flow between allopatric morphs from two high Arctic lakes, Linne´vatn (Anadromous, Normal, and Dwarf) and Ellasjøen (Littoral and Pelagic). Within each lake, the degree of genetic differentiation ranged from low (Pelagic vs. Littoral) to moderate (Anadromous and Normal vs. Dwarf). We identified 17 highly diagnostic, putative adaptive SNPs that differentiated the allopatric morphs. Although we found no evidence for adaptive differences between morphs within Ellasjøen, we found evidence for moderate (Anadromous vs. Normal) to high genetic differentiation (Anadromous and Normal vs. Dwarf) among morphs within Linne´vatn based on two adaptive loci. As these freshwater ecosystems become more productive, the frequency of sympatric morphs in Ellasjøen will likely shift based on foraging opportunities, whereas the propensity to migrate may decrease in Linne´vatn, increasing the frequency of the Normal morph. The Dwarf charr was the most genetically distinct group. Identifying the biological basis for small body size should elucidate the potential for increased growth and subsequent interbreeding with sympatric morphs. Overall, neutral and adaptive genomic differentiation between allopatric and some sympatric morphs suggests that the response of Arctic charr to climate change will be variable across freshwater ecosystems.
Characterizing the complexity of subduction zone flow with an ensemble of multiscale global convection models
<p>Parameter files and model input .txt files for ASPECT mantle convection simulations.</p>
Characterizing Code Clones from Large Language Models Dataset and Scripts
<p>characterizing_code_clones_data.zip: <br><br>This dataset contains a collection of code snippets generated by Large Language Models (LLMs) such as GPT-3.5 and GPT-4 in response to specific programming prompts derived from LeetCode. Each sub-directory within the dataset corresponds to a particular LLM version and contains code snippets, preprocessed data, and SLACC input files. </p><p>characterizing_code_clones_project.zip: </p><p>This zipped directory encompasses the core scripts and results used in the "Characterizing Code Clones of LLMs" research. It features the Python script <strong>collect_samples.py</strong> for collecting LLM-generated code snippets, as well as a suite of scripts in the <strong>slacc_scripts</strong> sub-directory for processing and analyzing the data using SLACC. The directory also includes the results of the LeetCode test suites, providing insights into the correctness and efficiency of the code generated by GPT-3.5 and GPT-4. </p>
Thermal modeling of a high-energy prismatic lithium-ion battery cell and module based on a new thermal characterization methodology
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Characterizing Design Discussions With Semi-Supervised Topic Modeling
<p><strong>Note:</strong> Please refer to the README.md file for instructions.</p> <p><strong>Abstract:</strong> Stack Overflow is a rich source of questions and answers—discussions—about software development. One topic of discussion is software design, such as the correct use of design patterns, or best practices in data access. Since design is a more abstract topic in software engineering, researchers have long sought to characterize and model design knowledge. However, these approaches typically require significant expert input in order to contextualize the abstract design information. In this study, we explore how combining expert input with Stack Overflow might serve as an effective way to identify design topics. We first perform a qualitative analysis of design-tagged Stack Overflow questions and answers to identify the design concepts developers discuss. We report on areas where agreement was a challenge, including abstraction levels. Since inductive coding is expensive, we apply a semi-supervised (Anchored CorEx) approach. We find it performs as well as LDA but offers superior interpretability and the ability to guide the topic model. We leverage CorEx to characterize how design is discussed in Stack Overflow and on GitHub. We conclude by describing how our experience using the semi-supervised CorEx approach leads us to believe that approaches like CorEx that combine domain knowledge and scalability are key for analyzing large SE text repositories.</p>
Characterizing and Understanding the Behavior of Quantized Models for Reliable Deployment
<p>quantization benchmark</p>
Data and Codes of Characterizing Uncertainties of Earth System Modeling with Heterogeneous Many-core Architecture Computing
<p>These are the supporting information to verify the results in the paper, including input data, model outputs, the postprocessing scripts and the source codes.</p>
Data access - Operando characterization and theoretical modelling of metal|electrolyte interphase growth kinetics in solid-state-batteries - part I: experiments
<p>The zip file contains XPS and EIS data used in parts 1 and 2 of the publication entitled: "New insights into the kinetics of metal|electrolyte interphase growth in solid-state-batteries via an <em>operando</em> XPS analysis"</p> <p>Folders description: </p> <p>- "XPS" contains three subfolders with the XPS data and fitting models (in .vms format, CasaXPS) corresponding to the reference Na metal sample, the Na|NZSPas interface and Na|NZSPpolished interface</p> <p>- "EIS" contains two subfolders with the EIS data from the Na|NZSPas and Na|NZSPpolished symmetrical cells. The raw data is stored as .mpr files (EC-lab), and the fitted data is stored as .eis3 files (RelaxIS)</p>
Chemical and Structural In-Situ Characterization of Model Electrocatalysts by Combined Infrared Spectroscopy and Surface X-Ray Diffraction
<p>Raw and treated data</p>
Data for Characterization of cytokine response to intraperitoneally administered LPS & subdiaphragmatic branch vagus nerve stimulation in rat model
<p>These are the data files used for publication "Characterization of cytokine response to intraperitoneally administered LPS & subdiaphragmatic branch vagus nerve stimulation in rat model" to be published in PLOS ONE.</p>
Best-fit Abundances, Observed Spectra and Spectral Models for the New Sample of Ultracool Dwarf Benchmarks with Detailed Chemical Characterization
<p>Dataset associated with Fisher et al. 2024 in RNAAS <a href="https://iopscience.iop.org/article/10.3847/2515-5172/ad79f0">[link to publication]</a></p> <p><code>summary.mrt</code> is a table of identifiers, photometry, fundamental stellar parameters and detailed chemical compositions for 13 candidate wide binary systems with FGK Main Sequence primaries (5100 K < Teff < 6300 K) and ultracool dwarf companions (2500 K < Teff < 3100 K). Refer to the file header for detailed description of columns and units.</p> <p><code>stars.zip</code> contains the high-resolution spectra of primaries observed with the Automated Planet Finder (APF, program <code>2021B_A010</code>), as well as the corresponding best-fit spectral models. Each FITS file in the archive represents an individual exposure of the primary. The files are arranged in directories by identifiers of the primaries. The total number of exposures varies from source to source.</p> <p>FITS files are composed of a primary HDU and 6 extensions.</p> <ul> <li>The primary HDU contains the unmodified sky-subtracted spectrum of the object as produced by the APF pipeline and published on <a href="https://jump.caltech.edu/">Jump</a>. The spectrum is stored as a 2D array organized by Echelle orders.</li> <li>The first extension contains the corresponding air wavelengths [in A] transformed to the rest frame of the source.</li> <li>The second extension is the boolean mask of pixels included in model fitting.</li> <li>The third extension is the adopted statistical weights of each pixel, estimated as inverse variances under the assumption of Poisson noise.</li> <li>The fourth extension contains the best-fit synthetic spectrum in CGS units of surface intensity per wavelength in A.</li> <li>The fifth extension is the best-fit spline continuum correction between the model and the data.</li> <li>The final extension contains the adopted FWHM of the line spread function in each pixel, estimated by combining in quadrature a wavelength-dependent component with λ/Δλ=120,000 and a best-fit wavelength independent component (the <code>quickblur</code> parameter of the <a href="https://github.com/Roman-UCSD/chemfit">chemfit</a> package)</li> </ul> <p>This repository is for the research note "New Sample of Ultracool Dwarf Benchmarks with Detailed Chemical Characterization" by Fisher et al. It is associated with manuscript number AAS58102.</p>
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.