Find research datasets worth reusing

opencc-by-4.0Dec 2021View details →

Impact of CD4 T cells on intratumoral CD8 T cell exhaustion and responsiveness to PD-1 blockade therapy in mouse brain tumors

scRNA-seq data (Cellranger filtered feature-barcode matrices) and scVDJ-seq data (Cellranger filtered_contig_annotations.csv files) for publication listed above.

opencc-zeroDec 2021View details →

Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth, and microbial communities

Plastic mulch film residues have been accumulating in agricultural soils for decades, but so far, little is known about its consequences on soil microbial communities and functions. Here, we tested the effects of plastic residues of low-density polyethylene and biodegradable mulch films on soil suppressiveness and microbial community composition. We investigated how plastic residues in a Fusarium culmorum suppressive soil affect the level of disease suppressiveness, plant biomass, nutrient status, and microbial communities in rhizosphere using a controlled pot experiment. The addition of 1% plastic residues to the suppressive soil did not affect the level of suppression and the disease symptoms index. However, we did find that plant biomasses decreased, and that plant nutrient status changed in the presence of plastic residues. No significant changes in bacterial and fungal rhizosphere communities were observed. Nonetheless, bacterial and fungal communities closely attached to the plastisphere were very different from the rhizosphere communities with overrepresentation of potential plant pathogens. The plastisphere revealed a high abundance of specific bacterial phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) and fungal genera (Rhizoctonia and Arthrobotrys). Our work revealed new insights and raises emerging questions for further studies on the impact of microplastics on the agroecosystems.

opencc-by-4.0May 2022View details →

FOCI model output used in the study by Ivanciu et al. - On the ridging of the South Atlantic Anticyclone over South Africa: the impact of Rossby wave breaking and of climate change

This dataset contains the model output used in the analysis presented in the study by Ivanciu et al., 2022 - On the ridging of the South Atlantic Anticyclone over South Africa: the impact of Rossby wave breaking and of climate change. Four ensembles of three simulations each were performed with the global coupled climate model FOCI (Flexible Ocean and Climate Infrastructure, Matthes et al., 2020). Details about the ensembles can be found in the above-mentioned publication. The files containing "past" in their name belong to the ensemble "PAST", the files containing "future" in their name belong to the ensemble "FUTURE", the files containing "future_GHG" in their name belong to the ensemble "GHG" and the files containing "future_Ozone" in their name belong to the ensemble "OZONE" from the publication.

opencc-by-4.0May 2022View details →

Additional data for "Tissue-specific impacts of aging and genetics on gene expression patterns in humans"

Additional files for paper "Tissue-specific impacts of aging and genetics on gene expression patterns in humans" by Yamamoto and Chung et al. 2021. Contains file of results from joint age and genetics model.

opencc-zeroMay 2022View details →

Behavioral and postural analyses establish sleep-like states for mosquitoes that can impact host landing and blood feeding

Sleep is an evolutionarily conserved process that has been described in different animal systems. For insects, sleep characterization has been primarily achieved using behavioral and electrophysiological correlates in a few systems. Sleep in mosquitoes, which are important vectors of disease-causing pathogens, has not been directly examined. This is surprising as circadian rhythms, which have been well studied in mosquitoes, influence sleep in other systems. In this study, we characterized sleep in mosquitoes using body posture analysis and behavioral correlates and quantified the effect of sleep deprivation on sleep rebound, host landing and blood-feeding propensity. Body and appendage position metrics revealed a clear distinction between the posture of mosquitoes in their putative sleep and awake states for multiple species, which correlate with a reduction in responsiveness to host cues. Sleep assessment informed by these posture analyses indicated significantly more sleep during periods of low activity. Nighttime and daytime sleep deprivation resulting from the delivery of vibration stimuli induced sleep rebound in the subsequent phase in day and night active mosquitoes, respectively. Lastly, sleep deprivation suppressed host landing in both laboratory and field settings, and impaired blood-feeding of a human host when mosquitoes would normally be active. These results suggest that quantifiable sleep states occur in mosquitoes and highlight the potential epidemiological importance of mosquito sleep.

opencc-by-4.0Feb 2022View details →

Dataset: Impact of GST thickness on GST-loaded silicon waveguides for optimal optical switching

The following files provide the dataset of the work "Impact of GST thickness on GST-loaded silicon waveguides for optimal optical switching". The description and organization of the files are explained in the file README.txt.

opencc-by-4.0Apr 2022View details →

Dataset for "Quantifying the physical impact of bottom trawling based on high-resolution bathymetric data"

Bathymetric point cloud data and ship log data used for the article "Quantifying the physical impact of bottom trawling based on high-resolution bathymetric data" by Mischa Schönke, David Clemens and Peter Feldens (<a href="https://doi.org/10.3390/rs14122782">https://doi.org/10.3390/rs14122782</a>)

opencc-by-4.0Feb 2022View details →

Wheat stem rust back in Europe: Diversity, prevalence and impact on host resistance

SSR genotypes of European Puccinia graminis isolates based on 17 SSR markers, updated version

opencc-zeroMay 2022View details →

Impacts of oil well drilling and operating noise on abundance and productivity of grassland songbirds

Anthropogenic noise from natural resource extraction may negatively impact many species, particularly those reliant on acoustic communication. To compare impacts of several types of noise resulting from oil extraction operations on habitat use and productivity of grassland songbirds, we designed and implemented a novel large-scale, spatially and temporally replicated experiment. We recreated soundscapes produced by drilling and operating oil well noise, and compared impacts of noise-producing and quiet playback infrastructure, in twenty-nine 64.7-ha native prairie sites in Alberta, Canada, from 2013–2015. Drilling noise recordings played 24 hours/day for 10 days, twice during each breeding season, while oil well operating noise played continuously, 24 hours/day, throughout each ~90-day breeding season. Despite the much shorter duration of drilling noise playbacks, drilling noise negatively impacted three of our four focal species, and had a much greater impact on habitat use and productivity than did well operating noise. Infrastructure also impacted Vesper Sparrows and Sprague's Pipits, even in the absence of noise. Synthesis and applications: Acute oil drilling noise had a greater negative impact on breeding migratory birds when compared to chronic oil well noise, perhaps because drilling noise is unpredictable. While this study demonstrates that noise alone can negatively impact habitat use, nesting success, and nestling quality, it is also clear that effective mitigation strategies require both noise and above-ground infrastructure management to reduce impacts on wildlife.

opencc-by-4.0Dec 2022View details →

Climate Impacts of Parameterizing Subgrid Partitioning of Land Surface Heat Fluxes to the Atmosphere with the NCAR CESM1.2

The modified code as well as the CAM5 output for all the simulations in this study (V0 for the CTL run, CON1 for the EXP run, and PCON1R for EXP_COR run). The CESM1.2.1-CAM5.3 source code can be downloaded through the CESM official website https://www.cesm.ucar.edu/models/cesm1.2/cesm/doc/usersguide/x290.html#download_ccsm_code. Its output files are named in V0*.nc. The modified code for the EXP run in the study is in CON1.tar, with its CAM5 output files named in CON1*.nc. The modified code for the EXP_COR run in the study is in PCON1R.tar, with its CAM5 output files named in PCON1R*.nc

Resolved EXiobase (REX II) with regionalized biodiversity loss impact assessment of global mining – second version of a highly-resolved MRIO database for the year 2014

This repository provides a new version of the highly-resolved global multi-regional input-output database called REX II (Resolved EXiobase) for the year 2014 with improved data quality for all mining and metals processing sectors, including a regionalized biodiversity impact assessment for all mining sectors. This regionalized impact assessment is based on the global mining area data set of Maus et al (2020). The database REX II is described in the study "Hotspots of mining-related biodiversity loss in global supply chains and the potential for reduction by renewable electricity". Study: <a href="https://doi.org/10.1021/acs.est.2c04003">https://doi.org/10.1021/acs.est.2c04003</a> Open-access preprint: <a href="https://doi.org/10.31223/X5T064">https://doi.org/10.31223/X5T064</a>   An earlier version of this database (REX I) with time series from 1995–2015 is provided under: <a href="http://doi.org/10.5281/zenodo.3993659">http://doi.org/10.5281/zenodo.3993659</a> and described here: <a href="https://doi.org/10.1016/j.scitotenv.2020.142587">https://doi.org/10.1016/j.scitotenv.2020.142587</a>   The repository REXIA_2014 contains the following files (*.mat-files) referring to the year 2014: T_REXIA: transaction matrix Y_REXIA: final demand matrix Ext_REXIA and Ext_hh_REXIA: the satellite matrices of the economy and the final demand The labels of all matrices are described in the excel file Labels_REXIA.xlsx

Impact of mountains in Southern China on the Eocene climates of East Asia

These files contain the model outputs from Noresm1-F that are used to draw the main parts of Figures in our paper entitled "Impact of mountains in Southern China on the Eocene climates of East Asia".

Data for PNASnexus article Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell phenotype

Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to self-renew in order to maintain tissue architecture and homeostasis. Adult salivary glands have been documented to harbor SSPC, which have been shown to play a vital role in the regeneration of the glandular structures post radiation damage. We have previously demonstrated that activation of aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde accumulation in SSPC, leading to less apoptosis and improved salivary function. We subsequently found that sustained pharmacological ALDH3A1 activation is critical to enhance regeneration of murine submandibular gland after radiation damage. Further investigation shows that ALDH3A1 function is crucial for SSPC self-renewal and survival even in the absence of radiation stress. Salivary glands from Aldh3a1-null mice have fewer acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological inhibition in SSPC leads to a decrease in mitochondrial DNA copy number, lower expression of mitochondrial specific genes and proteins, structural abnormalities, lower membrane potential, and reduced cellular respiration. Loss or inhibition of ALDH3A1 also elevates ROS levels and accumulation of ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product), leading to decreased survival of murine SSPC that can be rescued by treatment with 4-HNE specific carbonyl scavengers. Our data indicate that ALDH3A1 activity protects mitochondrial function and is important for the regeneration activity of SSPC. This knowledge will help to guide our translational strategy of applying ALDH3A1 activators in the clinic to prevent radiation-related hyposalivation in head and neck cancer patients.

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.

Impact of host demography and evolutionary history on endosymbiont molecular evolution: a test in carpenter ants (Genus Camponotus) and their Blochmannia endosymbionts

Obligate endosymbioses are tight associations between symbionts and the hosts they live inside. Hosts and their associated obligate endosymbionts generally exhibit codiversification, which has been documented in taxonomically diverse insect lineages. Host demography (e.g., effective population sizes) may impact the demography of endosymbionts, which may lead to an association between host demography and the patterns and processes of endosymbiont molecular evolution. Here, we used whole-genome sequencing data for carpenter ants (Genus Camponotus; subgenera Camponotus and Tanaemyrmex) and their Blochmannia endosymbionts as our study system to address whether Camponotus demography shapes Blochmannia molecular evolution. Using whole-genome phylogenomics, we confirmed previous work identifying codiversification between carpenter ants and their Blochmannia endosymbionts. We found that Blochmannia genes have evolved at a pace ~30× faster than that of their hosts' molecular evolution and that these rates are positively associated with host rates of molecular evolution. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. Host demography was associated with Blochmannia shifts toward increased selection strengths, but not associated with Blochmannia selection relaxation, positive selection, genetic drift rates, or genome size evolution. Mixed support for relationships between host effective population sizes and Blochmannia molecular evolution suggests weak or uncoupled relationships between host demography and Blochmannia population genomic processes. Finally, we found that Blochmannia genome size evolution was associated with genome-wide estimates of genetic drift and number of genes with relaxed selection pressures. --

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.

Complementary dataset of Overton metadata on citing policy-related documents for the study "From intent to impact: Investigating the effects of open sharing commitments"

This document provides the underlying dataset for the bibliometric component for the 2022 study "From intent to impact: Investigating the effects of open sharing commitments" by Research Consulting and Science-Metrix. Before reproducing the study findings or re-using the underlying datasets for other purposes, please cautiously review their limitations in the study's technical annex and main report, available at: https://zenodo.org/communities/data-sharing-in-public-health-emergencies/  Special thanks from the Science-Metrix / Elsevier teams to Euan Adie and Overton for this exceptional public release of Overton metadata, and for conducting extraordinary data collection to retrieve citations towards arXiv preprints.   Scope: note that this file combines cited journal publications and preprints from the Covid19, HVRD, Zika and HVVD thematic sets. Data treatment: this data is intend foremost to provide manual validation or qualitative triangulation of our findings. No special efforts have been made to process and clean the data for its eventual re-use in secondary analysis or text mining approaches. Definitions used in this table: <table> <tbody> <tr> <td>Column name </td> <td>Definition</td> </tr> <tr> <td>document_type</td> <td>preprint or journal publication</td> </tr> <tr> <td>doi</td> <td>digital object identifier</td> </tr> <tr> <td>arxiv_id</td> <td>arXiv preprint server's unique identifier for its preprints</td> </tr> <tr> <td>ssrn_id</td> <td>SSRN preprint server's unique identifier for its preprints. Note that some of these IDs are contained within the DOIs also assigned to some (but not all) SSRN preprints , in the form of "10.2139/ssrn." + 'ssrn_id'</td> </tr> <tr> <td>coalesce_id</td> <td>coalesce function applied to the DOI, arxiv_id and ssrn_id. Redundant for journal publications.</td> </tr> <tr> <td>policy_source_title</td> <td>name of the policy-related organization</td> </tr> <tr> <td>published_on</td> <td>publication date of the citing policy-related document</td> </tr> <tr> <td>title</td> <td>title of the citing policy-related document</td> </tr> <tr> <td>pdf_url</td> <td>URL for the online version of the policy-related document</td> </tr> <tr> <td>snippet</td> <td>Where available, excerpt of the text immediatly before and after the citation to a journal publication or preprint found in the citing policy-related document</td> </tr> </tbody> </table>

Following Darwin's footsteps: Evaluating the impact of an activity designed for elementary school students to link historically important evolution key concepts on their understanding of natural selection

While several researchers have suggested that evolution should be explored from the initial years of schooling, little information is available on effective resources to enhance elementary school students' level of understanding of evolution by natural selection (LUENS). For the present study, we designed, implemented and evaluated an educational activity planned for fourth graders to explore concepts and conceptual fields that were historically important for the discovery of natural selection. Observation field notes and students' productions were used to analyse how the students explored the proposed activity. Additionally, an evaluation framework consisting of a test, the evaluation criteria and the scoring process was applied in two fourth-grade classes to estimate elementary school students' LUENS before and after engaging in the activity. Our results suggest that our activity allowed students to effectively link all of the key concepts in the classroom and produced a significant increase in their LUENS. These results indicate that our activity had a positive impact on students' understanding of natural selection. They also reveal that additional activities and minor fine-tuning of the present activity are required to further support students' learning about the concept of differential reproduction. We also observed a low level of teleological predictions for both pre- and post-tests. --

Data from: Species tree estimation and the impact of gene loss following whole-genome duplication

Whole-genome duplication (WGD) has been demonstrated to occur broadly and repeatedly in the evolutionary history of eukaryotes, and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD, however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs – paralogous genes mistakenly identify as orthologs because they are present in single copes within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as result of gene extinction (or incomplete laboratory sampling) in a phylogenetic context is only recently starting to gain empirical attention. Moreover, few of these studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying levels of incomplete lineage sorting (ILS) and different patterns of gene loss following WGD. When gene loss occurs in the terminal branches of the species tree, the alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the level of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of sampled genes increases. Furthermore, pseudoorthologs can mislead species tree inference if gene loss occurs in the internal branches of the species tree, where both coalescent and concatenation methods are prone to produce inconsistent results. However, pseudoorthologs are problematic when filtering only for single-copy genes in phylogenomic data sets. Pruning orthologs or even randomly selecting a copy from multi-copy genes can avoid most of those pseudoorthologs. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era.

Size-dependent intraspecific variation in wood traits has little impact on aboveground carbon estimates in a tropical forest landscape

There is increasing evidence that intraspecific trait variation plays a role in governing rates of ecosystem functioning. While wood traits such as wood specific gravity (WSG) and wood carbon concentration (WCC) are key drivers of forest aboveground carbon (AGC) stocks, the sources of intraspecific variation in these wood traits and the consequences of this variation on AGC are poorly known, especially in the tropics. Here, we investigated intraspecific variation in wood specific gravity (WSG) and wood carbon concentration (WCC) from 556 individual trees belonging to 15 species that well characterize different successional stages of seasonal evergreen forests in Southeast Asia. Specifically, we tested the contribution of individual or species characteristics (tree size, growth rate and regeneration guilds) and local environmental conditions (topographic wetness index and successional stages) to intraspecific variation in WSG and WCC, and assessed the consequences of intraspecific variation in these wood traits on AGC estimates in 14 permanent forest plots established along a successional gradient in Khao Yai National park, Thailand. We found that tree size was the main driver of intraspecific variation in WSG and WCC as tree sizes increased from 10−100 cm in diameter, WSG increased by 7.3%, while WCC increased by 2.4% in heartwood, 1.6% and 2.7% in sapwood without and with volatile carbon included. There was no effect of the topographic wetness and other local environment condition in wood traits led to a slight overestimation of AGC in young secondary forests (+0.09 to +1.29%) and a small underestimation in older forests (-0.86 to -2.87%), but overall AGC estimates (13 of 14 forest plots) remained within error margins (the 95% interval). Our study provides evidence that tree size variation translates into intraspecific variability in wood traits, whereas local environmental conditions related to topography successional stages had no effect on wood trait variability. While size-dependent variation in WSG and WCC have largely been undocumented and thus ignored in forest carbon assessment approaches, we highlight that it has a limited impact on AGC estimates, indicating that it does not invalidate current forest carbon stock estimation approaches.