Find research datasets worth reusing

opencc-by-4.0Apr 2022View details →

Supplemental Material to Article "Validation of crack initiation model by means of cyclic full-scale blade test"

This set supplements the figure data to the article "Validation of crack initiation model by means of cyclic full-scale blade test", DOI: <a href="https://doi.org/10.1088/1742-6596/2265/3/032045">https://doi.org/10.1088/1742-6596/2265/3/032045</a>.

Amazonian epiphytic bryophytes: community matrix and tools to assess diversity across scales

Aim: Tropical forests are highly diverse at many spatial scales. In these forests, epiphytic bryophyte communities can be species-rich already within a few cm2, and their species numbers increase when expanding the sampling along the tree and the forest. Understanding how this diversity increase depends on scale and position within the tree is critical to evaluate the processes that maintain biodiversity. We, therefore, studied vertical zonation and alpha and beta diversity of epiphytic bryophytes across spatial scales ranging from 100-cm2 quadrats to 24 trees up to 10 km apart. Location: Tropical lowland forest in Yasuní National Park (Amazonian Ecuador). Methods: We sampled epiphytic bryophytes in 100-cm2 quadrats on 24 trees (15-22 sampling quadrats per tree), using a spatially hierarchical design. We applied ordination, indicator species analysis, linear mixed models, and beta partitioning to study alpha and beta diversity at different spatial grains and extents. Results: At the scale of quadrats, tree crowns held more bryophyte species than trunks. Contrastingly, all crown quadrats together held fewer species than all trunk quadrats together (77 vs. 93 species), as species turnover among trunk quadrats exceeded that among crown quadrats. Across spatial extents, species turnover consistently dominated beta diversity over nestedness. Beta diversity was higher between crowns and trunks within trees than among crowns of different trees at all studied scales, while beta diversity among trunks exceeded vertical diversity when considering all 24 trees. Main conclusions: These bryophyte communities experience two distinct vertical zones, trunks and crowns, which differ more among them than trees up to 10 km apart. Still, high species turnover makes their species composition highly unpredictable, especially on trunks. Chance processes appear to play an important role in shaping these communities, although analyses at even finer spatial grains may identify the importance of fine-scale habitat filters and species interactions.

Data for "Physically Based Deep Learning Framework to Model Intense Precipitation Events at Engineering Scales"

The dataset consists of high resolution (250 m) and low resolution (0.025 degree) climate model outputs in netCDF format. Each file contains data for one variable and one month. Low resolution files follow the naming scheme: montrealC_0025deg_200x200_ERA5_1m_YYYYMM_VAR.nc High resolution files follow the naming scheme: montrealC_250m_324x324_ERA5_TEB_100_noconv_YYYYMM_VAR.nc YYYYMM stands for the year (first 4 digits) and month (last 2 digits). _VAR indicates the variable contained in the file: <ul> <li>_UU700 stands for the east-west component of wind at a pressure level of 700 hPa (hourly frequency)</li> <li>_VV700 stands for the north-south component of wind at a pressure level of 700 hPa (hourly frequency)</li> <li>When _VAR is omitted, the variable is precipitation at 1-minute temporal resolution</li> </ul>

Cross-scale drivers of woody plant species commonness and rarity in the Brazilian drylands

Aim: Locally abundant species are typically widespread, while locally scarce species are geographically restricted – the so-called abundance-occupancy relationships (AORs). AORs help explain the drivers of species rarity and community assembly, but little is known about how variation around such relationships is driven by species traits and niche-based processes, particularly in tropical woody plants. We tested the hypothesis that AORs in tropical dryland woody plants are positive and mediated by niche and functional traits along environmental gradients. Location: The Caatinga dry forest and Cerrado savannah, Brazil. Methods: We aggregated abundance and occurrence data into grid-cells representing local (10-km) to landscape scales (50-km). We calculated species mean relative abundance at occupied grid-cells (local abundance) and the proportion of grid-cells occupied (occupancy), and estimated their niche breadth and marginality along multivariate environmental gradients. Results: AORs were positive but weak at different scales in both regions due to some locally abundant but geographically restricted species, with most species being both locally and geographically rare. Cross-species variation in local abundance was largely unpredictable, but occupancy was strongly driven by niche and functional traits, with a prominent negative effect of niche marginality. Geographically restricted species were associated with rare habitats, such as wetter and less intensively used habitats. Large seeds and abiotic dispersal favoured occupancy in Caatinga at small and large spatial scales, respectively, whereas species with conservative leaves were more widespread across scales in Cerrado. Main conclusions: Woody plants in dry tropical biotas exhibit weak AORs, likely related to low habitat availability and dispersal limitation. Caatinga and Cerrado emerge as environmentally structured at multiple spatial scales, with several habitat-specialist rare species bearing specific regenerative and resource-use traits and relying on conditions threatened by climate change and land-use intensification. Examining AORs through the lens of niche, functional traits and spatial scales enables mapping patterns and drivers of species commonness and rarity, enhancing understanding of species assembly and providing tools for biodiversity conservation.

Disentangling the impact of event- and annual-scale precipitation extremes on critical-zone hydrology in semiarid loess: A case study in apple tree plantation

The dataset is the basic data of the author's paper ' Disentangling the impact of event-and annual-scale precipitation extremes on critical-zone hydrology in semiarid loess - a case study in apple tree plantation '. The main content of this paper is to study the hydrological effect of extreme precipitation on the critical area of semi-arid loess. Taking apple plantation as an example, the data set includes the soil moisture and soil temperature data monitored in the field and the apple tree transpiration data. The measured data are used to calibrate and verify the model used in this paper. The water vapor flux, apple tree evapotranspiration and soil leakage data of the simulated soil profile are also included to analyze the hydrological effect of extreme precipitation on the critical area of loess.

Data supporting On the step type of continuous propagating positive leader in laboratory-scale long spark discharges

The data supports the manuscript entitled "On the step type of continuous propagating positive leader in laboratory-scale long spark discharges". The *.txt file contains the applied voltage waveform and discharge current waveform. The*.doc file contains the  data for Figure 5. The *.rar file contains the high-speed video frames, and can be decompressed and opened. The data can be used freely for scientific purposes with appropriate citation.

Impacts of flowering density on pollen dispersal and gametic diversity are scale dependent

Pollen dispersal is a key evolutionary and ecological process, but the degree to which variation in the density of concurrently flowering conspecific plants (i.e., co-flowering density) shapes pollination patterns remains understudied. We monitored co-flowering density and corresponding pollination patterns of the insect-pollinated palm Oenocarpus bataua in northwestern Ecuador and found that the influence of co-flowering density on these patterns was scale-dependent: high neighborhood densities were associated with reductions in pollen dispersal distance and gametic diversity of progeny arrays, whereas we observed the opposite pattern at the landscape scale. In addition, neighborhood co-flowering density also impacted forward pollen dispersal kernel parameters, suggesting that low neighborhood densities encourage pollen movement and may promote gene flow and genetic diversity. Our work reveals how co-flowering density at different spatial scales influences pollen movement, which in turn informs our broader understanding of the mechanisms underlying patterns of genetic diversity and gene flow within populations of plants.

GPR-BMP-SPI: High spatial resolution multi-scale SPI datasets over China from January 1984 to December 2020

The datasets include standard precipitation index (SPI) at 1-month, 3-month, 6-month, 9-month and 12-month scales over the main terrestrial lands of China from January 1984 to December 2020. The SPI datasets were produced by blending the information from meteorological stations, and precipitation products, as well as topographical and geographical variables based on Gaussian process regression (GPR) models. The meteorological station data are from the China Meteorological Data Service Centre. Five precipitation products are used: (1) CHIRPS Daily: Climate Hazards Group InfraRed Precipitation With Station Data (Version 2.0 Final); (3) ERA5-Land Monthly Averaged by Hour of Day - ECMWF Climate Reanalysis; (3) FLDAS: Famine Early Warning Systems Network (FEWS NET) Land Data Assimilation System; (4) PERSIANN-CDR: Precipitation Estimation From Remotely Sensed Information Using Artificial Neural Networks-Climate Data Record; (5) TerraClimate: Monthly Climate and Climatic Water Balance for Global Terrestrial Surfaces. The maps of the difference of the confidence intervals (the upper prediction limit minus the lower prediction limit) at a significance level of 95% are also provided to show the spatial uncertainty of every single SPI map. The drought events were counted during 1984-2020 at annual and seasonal scales. The variables related to the drought events are presented in “Drought_Event.zip”. Reference: He, Q., Wang, M., Liu, K., Li, B., & Jiang, Z. (2023). Spatiotemporal analysis of meteorological drought across China based on the high-spatial-resolution multiscale SPI generated by machine learning. Weather and Climate Extremes, 40, 100567.

Origin, diversity, and biogeography of Antarctic scale worms (Polychaeta: Polynoidae): a wide-scale barcoding approach

Aim: The Antarctic marine environment hosts diversified and highly endemic benthos owing to its unique geologic and climatic history. Current warming trends have increased the urgency of understanding Antarctic species history to predict how environmental changes will impact ecosystem functioning. Antarctic benthic lineages have traditionally been examined under three hypotheses: 1) high endemism and local radiation, 2) emergence of deep-sea taxa through thermohaline circulation, 3) species migrations across the Polar Front. In this study, we investigated which hypotheses best describe benthic invertebrate origins by examining Antarctic scale worms. Location: Southern Ocean, Kerguelen archipelago, South American peninsula, Indian Ocean, New Zealand. Taxon: Scale worm polychaetes (Polynoidae). Methods: We amassed 670 polynoids from the Southern Ocean and neighbouring areas and performed phylogenetic reconstructions to identify lineages across geographic regions, aided by mitochondrial markers Cytochrome c oxidase subunit I (Cox1) and 16S ribosomal RNA (16S). Additionally, we produced haplotype networks at the species scale to examine genetic diversity, biogeographic separations, and past demography. Results: The Cox1 dataset provided the most illuminating insights into the evolution of polynoids. Eunoe sp. was present at South America and Kerguelen, in favour of the latter acting as a migration crossroads. Harmothoe fuligineum, widespread around the Antarctic continent, was also present but isolated at Kerguelen, possibly resulting from historical freeze-thaw cycles. The genus Polyeunoa appears to have diversified prior to colonizing the continent, leading to the cooccurrence of at least three cryptic species around the Southern and Indian Oceans. Analyses identified that nearly all populations are presently expanding following a bottleneck event, possibly caused by habitat reduction from the last glacial episodes. Main Conclusions: This study details the largest phylogenetic dataset assembled to date for Antarctic polynoids. These findings provide insight into past demographic events experienced by Antarctic marine benthos and identify multiple origin scenarios for contemporary polynoids.

opencc-by-4.0Dec 2022View details →

Orbital effect on millennial-scale East Asian summer monsoon variability during the Holocene

Data for reproducing figures in journal article submitted to JGR: Atmospheres in June 2022. Data generated from hosing simulations of the 8.2 ka BP and 4.2 ka BP events using the CESM1.2.

An ordinal severity scale for COVID-19 retrospective studies using electronic health record data

Objectives: Although the World Health Organization (WHO) Clinical Progression Scale for COVID-19 is useful in prospective clinical trials, it cannot be effectively used with retrospective Electronic Health Record (EHR) datasets. Modifying the existing WHO Clinical Progression Scale, we developed an ordinal severity scale (OS) and assessed its usefulness in the analyses of COVID-19 patient outcomes using retrospective EHR data. Results: The data set used in this analysis consists of 2,880,456 patients. PCA of the day-to-day variation in OS levels over the totality of the 28-day period revealed contrasting patterns of variation in disease severity within the first and second 14 days and illustrated the importance of evaluation over the full 28-day period. Discussion: An OS with well-defined, robust features, based on discrete EHR data elements, is useful for assessments of COVID-19 patient outcomes, providing insights on progression of COVID-19 disease severity over time. Conclusion: The OS provides a framework which can facilitate better understanding of the course of acute COVID-19, informing clinical decision-making and resource allocation.

A chromosome-scale genome assembly of the okapi (Okapia johnstoni)

The okapi (Okapia johnstoni), or forest giraffe, is the only species in its genus and the only extant sister group of the giraffe within the family Giraffidae. The species is one of the remaining large vertebrates surrounded by mystery because of its elusive behavior as well as the armed conflicts in the region where it occurs, making it difficult to study. Deforestation puts the okapi under constant anthropogenic pressure, and it is currently listed as "Endangered" on the IUCN Red List. Here, we present the first annotated de novo okapi genome assembly based on PacBio continuous long reads, polished with short reads, and anchored into chromosome-scale scaffolds using Hi-C proximity ligation sequencing. The final assembly (TBG_Okapi_asm_v1) has a length of 2.39 Gbp, of which 98% are represented by 28 scaffolds >3.9 Mbp. The contig N50 of 61 Mbp and scaffold N50 of 102 Mbp, together with a BUSCO score of 94.7%, and 23,412 annotated genes, underline the high quality of the assembly. This chromosome-scale genome assembly is a valuable resource for future conservation of the species and comparative genomic studies among the giraffids and other ruminants.

opencc-by-4.0Feb 2022View details →

Dataset of the research article "A semi-automated analysis of displacement-to-length scaling of the grabens affecting lunar Floor-Fractured craters"

This dataset includes all the raster data (DEM, orthoimage, slope) and vectors (shapefiles) used in our research, investigating the relationships between displacement and length of the faults affecting Lunar Floor-Fractured craters.

Supplementary data - "Learning Reduced Models for Large-Scale Agent-Based Systems"

This repository contains supplementary data on my PhD thesis "Learning Reduced Models for Large-Scale Agent-Based Systems". Chapters 1-3, 7 and A do not have supplementary data. Chapter 4 <ul> <li>Large_deviation_example.zip contains the trajectory for Figure 4.8.</li> <li>mean_exit_time* contains the raw data to compute the mean exit time and standard deviation for the ABM process (JP) and SDE process (CLE). It contains additionally a precomputed mean and standard deviation as well as the corresponding numbers of agents.</li> <li>transition_matrix* contain the computed box discretizations as MATLAB and Numpy files as used for Figures 4.2-4.4, 4.6 and Tables 4.1 and 4.2.</li> </ul> Chapter 5 <ul> <li>CVM_2021-07-09-15-53_training_data.npz contains the training data for Figure 5.7 a and b.</li> <li>CVM_2021-09-29-07-13_distribution.npz contains the raw data for Figure 5.7 c.</li> <li>The remaining data for Chapter 5 can be found in the related dataset <a href="https://doi.org/10.5281/zenodo.4522119">doi.org/10.5281/zenodo.4522119</a>.</li> </ul> Chapter 6 <ul> <li>CVM_pareto_estimate contains trajectory data required for Figure 6.6 b to estimate points in the Pareto Front using the civil violence model. </li> <li>CVM_training_data contains the training data to construct the surrogate model. Each data set consists of CVM_*_cops_train.npz as training set, CVM_*_cops_trajectory.npz as sample trajectory and CVM_*_cops.pkl to compute the training data.</li> <li>CVM_covering_iterations_8.mat Pareto set covering after 8 iterations for the civil violence model. Required for Figure 6.6 a.</li> <li>CVM_pareto_set+front.npz is required for Figure 6.6 b. </li> <li>CVM_surrogate_model.mat contains the surrogate model for the civil violence model</li> <li>Expl_iterations_* contains Pareto set coverings after 8 and 12 iterations for Example 6.1.4 and Figure 6.1.</li> <li>VM_covering_iterations_12.mat contains the Pareto set covering depicted in Figure 6.4 a.</li> <li>VM_ODE_covering_iterations_12_subset_front.mat contains the Pareto set covering depicted in Figure 6.5 and 6.5 c.</li> <li>VM_ODE_covering_iterations_12_subset.mat contains the Pareto set covering depicted in Figure 6.5 and 6.5 d.</li> <li>VM_ODE_covering_iterations_12.mat contains the Pareto set covering depicted in Figure 6.4 b.</li> <li>VM_surrogate_model.mat contains the surrogate model for the extended voter model.</li> <li>VM_test_points_non_pareto.npz contains Non-Pareto points in Figure 6.5 and 6.5 d.</li> <li>VM_test_points_pareto.npz contains Pareto points in Figure 6.5 and 6.5 c.</li> </ul>

Comprehensive Context-specific Genome-scale Metabolic Models for Mus Musculus

Comprehensive Context-specific Genome-scale Metabolic Models for  Mus Musculus. The data consists of 28 models for the combination 2 mouse strains (WT and Ob/Ob), 2 diets (WT and HFD) and 7 tissues (Aorta, Heart, Liver, Skeletal Muscle, Hippocampus, Hypothalamus and Epididymal fat).

Data for "Suppressing quantum errors by scaling a surface code logical qubit"

Includes the circuits that were executed, the samples that were collected, the corrections predicted by several decoders, as well as other intermediate files. See the README.txt file at the root of the ZIP archive for a more detailed overview.

Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales

Purpose: Nitrogen deposition due to human activities is known to have a substantial impact on arbuscular mycorrhizal fungi (AMF) community in plant roots. However, the influence of elevated nitrogen on the phylogenetic structure of AMF across fine spatial scales, as well as the mechanisms behind such alterations, are remained poorly understood. Results: Nitrogen addition significantly increased the phylogenetic alpha diversity (diversity within a plot) and the 'within-treatment' phylogenetic beta diversity (dissimilarity among replicate plots) of AMF communities, which resulted in an increased 'within-treatment' phylogenetic gamma diversity (overall diversity among all the replicate plots within a treatment). These changes were caused by the relative abundance decline of a dominant genus (Glomus) and an increase in non-dominant genera. Mechanically, nitrogen addition affected phylogenetic alpha diversity mainly by influencing soil properties. Likewise, the increased 'within-treatment' dissimilarity of plant community composition and changes in soil properties caused by nitrogen addition and plot distance contributed to an increase in within-treatment phylogenetic beta diversity. Conclusions: We conclude that deterministic environmental filtering (both abiotic and biotic) and dispersal limitation effect played critical roles in AMF community assembly under global change scenarios. Insightfully, this study provides a mechanistic understanding of the response of AMF to nitrogen addition across fine scales.

Fine-scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones

Analyses of the factors shaping genetic variation in widespread plant species are important for understanding evolutionary history and local adaptation and have applied significance for guiding conservation and restoration decisions. Thurber's needlegrass (Achnatherum thurberianum) is a widespread, locally abundant grass that inhabits heterogeneous arid environments of western North America and is of restoration significance. It is a common component of shrubland steppe communities in the Great Basin Desert, where drought, fire, and invasive grasses have degraded natural communities. Using a reduced representation sequencing approach, we generated SNP data at 5,677 loci across 246 individuals from 17 A. thurberianum populations spanning five previously delineated seed zones from the western Great Basin. Analyses revealed pronounced population genetic structure, with individuals forming consistent geographical clusters across a variety of population genetic analyses and spatial scales. Low levels of genetic diversity within populations, as well as high population estimates of linkage disequilibrium and relatedness, were consistent with self-fertilization as a contributor to population differentiation. Variance partitioning and partial redundancy analysis (pRDA) indicated local adaptation to environment as additionally influencing the spatial distribution of genetic variation. The environmental variables driving these results were similar to those implicated in recent genecological work which inferred local adaptation for seed zone delineation. Our analyses also revealed a complex evolutionary history of A. thurberianum in the Great Basin, where previously delineated seed zones contain distantly related populations. Our results indicate evolutionary history, mating system, and differentiation across distinct geographic and environmental scales have shaped genetic variation in A. thurberianum and illustrate how numerous aspects of population genetic variation might require consideration for restoration planning.

Allometric scaling of a superposition eye optimises sensitivity and acuity in large and small hawkmoths

Animals vary widely in body size within and across species. This has consequences for the function of organs and body parts in both large and small individuals. How these scale, in relation to body size, reveals evolutionary investment strategies, often resulting in trade-offs between functions. Eyes exemplify these trade-offs, as they are limited by their absolute size in two key performance features: sensitivity and spatial acuity. Due to their size polymorphism, insect compound eyes are ideal models for studying the allometric scaling of eye performance. Previous work on apposition compound eyes revealed that allometric scaling led to poorer spatial resolution and visual sensitivity in small individuals, across a range of insect species. Here, we used X-ray microtomography to investigate allometric scaling in superposition compound eyes – the second most common eye type in insects – for the first time. Our results reveal a novel strategy to cope with the trade-off between sensitivity and spatial acuity, as we show that the eyes of the hummingbird hawkmoth retain an optimal balance between these performance measures across all body sizes.

Results of surface hot-in place recycling (remix) of modified and alternative asphalt mixtures in Finland. Part II: Bitumen scale

The following material is included in a digital appendix. <ul> <li><a href="https://zenodo.org/api/files/a34688f2-e7e5-43a4-bcb7-a4238429f56b/Appendix%201.%20FT-IR.pdf?versionId=6ea761b1-a830-4e01-a761-f103373497ce">Appendix 1</a>: FT-IR spectra of all bitumens before and after REM/RUT.</li> <li><a href="https://zenodo.org/api/files/a34688f2-e7e5-43a4-bcb7-a4238429f56b/Appendix%202.%20Gradations.pdf?versionId=b8b1b0b0-d421-42f8-84ef-728cb1acce33">Appendix 2</a>: Gradations of the specimens before and after REM/RUT (two specimens per material).</li> <li><a href="https://zenodo.org/api/files/a34688f2-e7e5-43a4-bcb7-a4238429f56b/Appendix%203.%20DSR%20test%20results.pdf?versionId=cd3ccf9e-a264-458c-9d54-fcfbca40ec1f">Appendix 3</a>: DSR test data. Complex shear modulus (G*), phase angle (δ), and Black diagram for all materials before and after REM/RUT.</li> <li><a href="https://zenodo.org/api/files/a34688f2-e7e5-43a4-bcb7-a4238429f56b/Appendix%204a.%20DSR%20master%20curves%20(8-mm).pdf?versionId=44f9c881-912f-4f35-b4c7-193d88d5572c">Appendix 4a</a>: DSR shifted data, and master (fitted) curves, 8-mm, summary before and after REM/RUT.</li> <li><a href="https://zenodo.org/api/files/a34688f2-e7e5-43a4-bcb7-a4238429f56b/Appendix%204b.%20DSR%20master%20curves%20(4-mm).pdf?versionId=30952a8f-029b-409f-ba87-da9d9972880b">Appendix 4b</a>: DSR shifted data, and master (fitted) curves, 4-mm, summary before and after REM/RUT.</li> <li><a href="https://zenodo.org/api/files/a34688f2-e7e5-43a4-bcb7-a4238429f56b/Appendix%205.%20WLF%20and%20sigmoidal.pdf?versionId=fb826979-868d-47f4-8acd-697550000f87">Appendix 5</a>: WLF fitting constants (Table A1), and parameters for sigmoidal curves (Table A2).</li> <li><a href="https://zenodo.org/api/files/a34688f2-e7e5-43a4-bcb7-a4238429f56b/Data%20II%20-%20Read%20me.pdf?versionId=c40871da-deff-456f-b4d6-a6136e9c294a">Database</a>: Laboratory data (Excel files, brief read-me guide) of all tests at bitumen scale. </li> </ul>