Find research datasets worth reusing

opencc-by-4.0Jan 2024View details →

Integrated Lysimeter Study (Deep Percolation) Data from Saint-Nicéphore, Quebec

This dataset results from a study on various landfill final covers constructed at a landfill site in Saint-Nicéphore, Quebec. The study involved three large experimental plots, each containing drainage lysimeters and sensors to measure soil moisture, temperature, and suction. For detailed construction information, please consult the construction report included in this dataset and the references.  The dataset is intended to facilitate future research on deep percolation in cold regions, providing comprehensive data for the development and validation of hydrological models. The dataset includes: <ol> <li>Hourly deep percolation rates, measured by four drainage lysimeters within the soil enclosures.</li> <li>Half-hourly measurements of soil moisture, temperature, and suction at various depths.</li> <li>Hourly and daily meteorological data for the duration of the study period.</li> <li>Laboratory-estimated soil parameters, including saturated hydraulic conductivity, dry density, and soil texture.</li> </ol> Important: Please be aware that the timestamps in these datasets may not be evenly spaced. This means that some data points might be missing or irregularly collected. Before performing any time-series analysis or data visualization, you may need to preprocess the data to ensure consistent time intervals. For further information or inquiries, please contact the creators.

Figure 6 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 6. Variation of the live adult male paratype GZNU20220705001 of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. A. Dorsolateral view; B. Dorsal view; C. Ventral view.

Figure 1 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 1. Sampling localities of Rana zhijinensis Luo, Xiao & Zhou, sp. nov., R. culaiensis, R. hanluica, and R. omeimontis in Guizhou Province, China. A. Guiguo Town, Zhijin County; B. Supu Town, Qianxi County; C. Zhujianshan Nature Reserve, Huangping County; D. Leigongshan National Nature Reserve, Leishan County.

Figure 2 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 2. Phylogenetic tree based on three mitochondrial genes and six nuclear genes. A. Maternal tree; B. Nuclear gene tree. In both phylogenetic tree, ultrafast bootstrap support (UFB) values from ML analyses/Bayesian posterior probabilities (BPP) from BI analyses are given beside nodes. Scale bars denote nucleotide substitutions per sites for mitochondrial and nuclear genes.

Figure 5 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 5. Morphological features of the live adult male holotype GZNU2018081606 of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. A. Dorsolateral view; B. Dorsal view; C. Ventral view; D. Egg cluster; E. Ventral view of hand and dark gray-blackish nuptial pad; F. Ventral view of foot.

Figure 4 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 4. Haplotype networks of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. and its related species constructed based on the nuclear gene sequences. Different species of the R. japonica group are shown as different colors.

Figure 3 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 3. Phylogenetic tree based on four mitochondrial genes and six nuclear genes. In this phylogenetic tree, UFB from ML analyses/ BPP from BI analyses are given beside nodes. The scale bar represents 0.03 nucleotide substitutions per site. Red lines represent species delimitation results of bPTP and BPP.

opencc-zeroApr 2024View details →

Scripts and data for: Integrating different facets of diversity into food web models: how adaptation among and within functional groups shape ecosystem functioning

Adaptation of communities to environmental fluctuations can emerge from different facets of biodiversity, which may impact ecosystem functioning differently. Previous work examined how ecosystem functions can be influenced by two sources of adaptive potential: sorting (i.e., changes in community composition due to fitness differences) can occur when multiple species or groups are present (richness), and trait adaptability (i.e., trait adjustments within species or functional groups) can emerge from genetic or phenotypic diversity. However, their effect is typically studied separately, and often in the context of only one trophic level. Therefore, we used a bitrophic trait-based model varying in richness and in the presence of trait adaptability at each trophic level, to investigate how sorting and trait adaptability, at one or two trophic levels, separately or jointly shape ecosystem functions. We found that the adaptive potential emerging from any facet of diversity-induced changes in trophic interactions, in turn, affects biomass distributions within and across trophic levels, dynamical behaviour, and synchrony of biomass dynamics within a trophic level. Particularly, sorting and trait adaptability could contribute to a similar degree and at a similar time to temporal changes in ecosystem functions, but their respective contribution depended on the speed of trait adaptation, the trait range between similar functional groups, and trophic interactions. We thus suggest to consider multiple facets of diversity and their corresponding sources of adaptive potential to deepen our mechanistic understanding of ecosystem functioning, especially in a context of rapid biodiversity change.

opencc-by-4.0Dec 2023View details →

Data and literature repository for "Climate Futures are Political Futures: Integrating Political Development Into the Shared Socioeconomic Pathways (SSPs)"

The datasets provided in the repository (listed in Table 1 of the manuscript): <ul> <li>Governance (Andrijevic et al., 2020)*</li> <li>Government effectiveness (Andrijevic et al., 2020)*</li> <li>Violent conflict (Hegre et al., 2016)</li> <li>Rule of law (update to the Soergel et al., 2021)</li> </ul> *Please note that these two variables can be found in the same data file. The indicators can also be retrieved through the <a href="https://ssp-extensions.apps.ece.iiasa.ac.at/">SSP Extensions Explorer.</a>  For applications of the projections of political indicators in further analyses, please consult the following references:   Brutschin, E., Pianta, S., Tavoni, M., Riahi, K., Bosetti, V., Marangoni, G., & Van Ruijven, B. J. <a href="https://iopscience.iop.org/article/10.1088/1748-9326/abf0ce/meta">A multidimensional feasibility evaluation of low-carbon scenarios.</a> Environmental Research Letters 2021, 16(6), 064069. Gidden MJ, Brutschin E, Ganti G, Unlu G, Zakeri B, Fricko O, et al. <a title="https://iopscience.iop.org/article/10.1088/1748-9326/acd8d5" href="https://iopscience.iop.org/article/10.1088/1748-9326/acd8d5">Fairness and feasibility in deep mitigation pathways with novel carbon dioxide removal considering institutional capacity to mitigate</a>. Environmental Research Letters 2023, 18(7): 074006.   Hoch JM, de Bruin SP, Buhaug H, Von Uexkull N, van Beek R, Wanders N. <a title="https://iopscience.iop.org/article/10.1088/1748-9326/ac3db2" href="https://iopscience.iop.org/article/10.1088/1748-9326/ac3db2">Projecting armed conflict risk in Africa towards 2050 along the SSP-RCP scenarios: a machine learning approach</a>. Environmental Research Letters 2021, 16(12): 124068.   Joshi DK, Hughes BB, Sisk TD. <a title="https://www.sciencedirect.com/science/article/abs/pii/S0305750X15000145" href="https://www.sciencedirect.com/science/article/abs/pii/S0305750X15000145">Improving governance for the Post-2015 Sustainable Development Goals: Scenario forecasting the next 50 years</a>. World Development 2015, 70: 286-302.   Moyer JD. <a title="https://www.sciencedirect.com/science/article/pii/S0305750X23000062" href="https://www.sciencedirect.com/science/article/pii/S0305750X23000062">Blessed are the peacemakers: The future burden of intrastate conflict on poverty</a>. World Development 2023, 165: 106188.   Moyer JD, Turner SD, Meisel CJ. <a title="https://journals.sagepub.com/doi/abs/10.1177/0022343320929740" href="https://journals.sagepub.com/doi/abs/10.1177/0022343320929740">What are the drivers of diplomacy? Introducing and testing new annual dyadic data measuring diplomatic exchange</a>. Journal of Peace Research 2021, 58(6): 1300-1310.   Petrova, K, Olafsdottir, G, Hegre, H, Gilmore, EA (2023). <a title="https://iopscience.iop.org/article/10.1088/1748-9326/acb163" href="https://iopscience.iop.org/article/10.1088/1748-9326/acb163">The ‘conflict trap’ reduces economic growth in the shared socioeconomic pathways</a>. Environmental Research Letters, 2023, 18(2), 024028.

opencc-by-4.0Nov 2024View details →

Data for fitting a statistical global burned area model for seamless integration into Dynamic Global Vegetation Models

The dataset is a large R data.table object saved in RDS format. It contains global, monthly data spanning the period from 2002 to 2018, with a 0.5 degrees spatial resolution. The dataset is utilized to develop and validate statistical models for predicting global burnt areas resulting from wildfires.

opencc-by-4.0Sep 2024View details →

Supporting data for "Benchmarking the integration of hexagonal boron nitride crystals and thin films into graphene-based van der Waals heterostructures"

Dataset for the publication "Benchmarking the integration of hexagonal boron nitride crystals and thin films into graphene-based van der Waals heterostructures"

opencc-by-4.0Nov 2024View details →

Data and figure reproduction for paper titled 'Lateral quantum-confined Stark effect for integrated quantum dot electroabsorption modulators'

The dataset contains the data behind, and instructions to reproduce, the figures in the paper titled 'Lateral quantum-confined Stark effect for integrated quantum dot electroabsorption modulators' written by the named dataset creators.

opencc-zeroOct 2021View details →

Data from: Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management

1. Species' ranges are changing at accelerating rates. Species distribution models (SDMs) are powerful tools that help rangers and decision-makers prepare for reintroductions, range shifts, reductions, and/or expansions by predicting habitat suitability across landscapes. Yet, range-expanding or -shifting species in particular face other challenges that traditional SDM procedures cannot quantify, due to large differences between a species' currently-occupied range and potential future range. The realism of SDMs is thus lost and not as useful for conservation management in practice. Here, we address these challenges with an extended assessment of habitat suitability through an integrated SDM database (iSDMdb). 2. The iSDMdb is a spatial database of predicted sites in a species' prediction range, derived from SDM results, and is a single spatial feature that contains additional, user-friendly data fields that synthesise and summarise SDM predictions and uncertainty, human impacts, restoration features, novel preferences in novel spaces, and management priorities. To illustrate its utility, we used the endangered New Zealand sea lion (Phocarctos hookeri). We consulted with wildlife rangers, decision-makers, and sea lion experts to supplement SDM predictions with additional, more realistic, and applicable information for management. 3. Almost half the data fields included in this database resulted from engaging with these end-users during our study. The SDM found 395 predicted sites. However, the iSDMdb's additional assessments showed that the actual suitability of most sites (90%) was questionable due to human impacts. >50% of sites contained unnatural barriers (fences, grazing grasslands), and 75% of sites had roads located within the species' range of inland movement. Just 5% of the predicted sites were mostly (>80%) protected. 4. Integrating SDM results with supplemental assessments provides a way to address SDM limitations, especially for range-expanding or -shifting species. SDM products for conservation applications have been critiqued for lacking transparency and interpretation support, and ineffectively communicating uncertainty. The iSDMdb addresses these issues and enhances the practical relevance and utility of SDMs for stakeholders, rangers, and decision-makers. We exemplify how to build an iSDMdb using open-source tools, and how to make diverse, complex assessments more accessible for end-users.

opencc-by-4.0Feb 2022View details →

Integrated Data of Single cell RNA sequencing for Human Pancreatic Adenocarcinoma

These data are collected and integrated from five available deposit data and one original data of single cell RNA sequencing from human pancreatic adenocarcinoma. Further analyses data for bulk transcriptomics (such as TCGA )using scRNAseq data and re-clustering for ductal epithelial cells and fibroblasts are also stored in step by step. Moreover, all R code is uploaded.

opencc-zeroMar 2022View details →

Data from: Integrating tracking and resight data enables unbiased inferences about migratory connectivity and winter range survival from archival tags

Archival geolocators have transformed the study of small, migratory organisms but analysis of data from these devices requires bias correction because tags are only recovered from individuals that survive and are re-captured at their tagging location. Data and code provided in this repository can be used to replicate the simulation and Painted Bunting case study results presented by Rushing et al. (2021) showing that integrating geolocator recovery data and mark–resight data enables unbiased estimates of both migratory connectivity between breeding and nonbreeding populations and region-specific survival probabilities for wintering locations.

opencc-zeroApr 2022View details →

Data and Rscripts from: An integrated experimental and mathematical approach to inferring the role of food exploitation and interference interactions in shaping life history

Intraspecific interactions can occur through many ways but the mechanisms can be broadly categorized as food exploitation and interference interactions. Identifying how intraspecific interactions impact life history is crucial to accurately predict how population density and structure influence dynamics. However, disentangling the effects of interference interactions from exploitation using experiments, is challenging for most biological systems. Here we propose an approach that combines experiments with modeling to infer the pathways of intraspecific interactions in a system. First, a consumer-resource model is built without intraspecific interactions. Then, the model is parameterized by fitting it to life-history data from a first experiment in which food abundance was varied. Next, hypothesized scenarios of intraspecific interactions are incorporated into the model which is then used to predict life histories with increasing competitor density. Lastly, model predictions are compared against data from a second experiment which raised groups of competitors of different densities. This comparison allows us to infer the role of interference and exploitation in shaping life history. We demonstrated the approach using the smaller tea tortrix Adoxophyes honmai across a range of temperature. We investigated five scenarios of interactions that included exploitation and three pathways for interference through some effects either on energetics to represent changes in ingestion or activity, or on mortality to model deadly interactions, or on mortality and ingestion to model cannibalism. Overall, intraspecific interactions in tea tortrix are best explained by a high level of deadly interactions along with some level of interference that acts on energy such as escaping and blocking access to food. Deadly interactions increase with temperature while interference that acts on energy is strongest close to the optimal temperature for reproduction. Interestingly, exploitation is more important than interference at low competitor density. The combination of mathematical modeling and experimentation allowed us to mechanistically characterize the intraspecific interactions in tea tortrix in a way that is readily incorporated into population-level mathematical models. The primary value of this approach, however, is that it can be applied to a much wider range of taxa than is possible with pure experimental approaches.

opencc-zeroApr 2022View details →

Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq

Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RADADOR, to mitigate the ADO in outgroups by recovering missing loci from previously published transcriptomes in our study of a gymnosperm genus Torreya. Using the supplemented RAD-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and test hypotheses on diversity anomaly in eastern Asian-North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya. Using the fossilized-birth-death model and divergence-extinction-cladogenesis method we resolved detailed biogeographic history of Torreya that suggested a Jurassic origin in the Laurasia and differential speciation and extinction among continents accounting for the modern diversity anomaly biased toward Eastern Asia (EA). The history also supported a vicariance origin of the modern Torreya from a widespread ancestor in EA and NA in the mid-Eocene, cross-Beringia exchange in the early Paleogene before the vicariant isolation, in contrast to the "Out of NA" pattern common to gymnosperms and in contrast to the "Out of EA" hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies on T. jackii, suggesting differential lineage sorting of plastid genomes among Torreya species or plastid genome capture in T. jackii.

opencc-by-4.0Apr 2022View details →

Data for "How flexible electrification can integrate fluctuating renewables"

This upload provides the files used to compile and compute the input data used in the aforementioned working paper.

opencc-by-4.0May 2022View details →

Integrated data-driven reannotation of the Kluyveromyces marxianus genome reveals an expanded protein coding repertoire

Supplementary data for Fenton et al. 2022.  <table> <tbody> <tr> <td>Supplementary Table</td> <td>ID</td> <td>Table Description</td> </tr> <tr> <td>supplementary table 1</td> <td>S1</td> <td>Transcript Start Site (TSS) metrics</td> </tr> <tr> <td>supplementary table 2</td> <td>S2</td> <td>Polyadenylation Site (PAS) metrics</td> </tr> <tr> <td>supplementary table 3</td> <td>S3</td> <td>NTE candidates </td> </tr> <tr> <td>supplementary table 4</td> <td>S4</td> <td>MTS candidates</td> </tr> <tr> <td>supplementary table 5</td> <td>S5</td> <td>iORFs candidates</td> </tr> <tr> <td>supplementary table 6</td> <td>S6</td> <td>uORFs candidates</td> </tr> <tr> <td>supplementary table 7</td> <td>S7</td> <td>ouORFs candidates</td> </tr> <tr> <td>supplementary table 8</td> <td>S8</td> <td>aORFs candidates</td> </tr> <tr> <td>supplementary table 9</td> <td>S9</td> <td>tRNA copy numbers</td> </tr> <tr> <td>supplementary table 10</td> <td>S10</td> <td>novel gene periodicity scores</td> </tr> <tr> <td>supplementary table 11</td> <td>S11</td> <td>description of novel genes</td> </tr> <tr> <td>supplementary table 12</td> <td>S12</td> <td>comparison of published genomes</td> </tr> <tr> <td>supplementary table 13</td> <td>S13</td> <td>table corrections</td> </tr> <tr> <td>supplementary table 14</td> <td>S14</td> <td>start codon corrections</td> </tr> <tr> <td>supplementary table 15</td> <td>S15</td> <td>Genes with splicing (at least one intron)</td> </tr> </tbody> </table>