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18,658 results for “impacts”
Analysis scripts and PFLOTRAN input files for "Impacts of permeability heterogeneity and background flow on supercritical CO2 dissolution in the deep subsurface"
<p>Supporting files for manuscript <em>Impacts of permeability heterogeneity and background flow on supercritical CO2 dissolution in the deep subsurface </em>(preprint published at https://arxiv.org/abs/2305.12575).</p> <p>Contents:</p> <ul> <li>PFLOTRAN input files (*.in) for the simulations that were used in the manuscript.</li> <li>The corresponding heterogeneous permeability fields for those simulations (*.h5).</li> <li>The CO2 property database for use with the PFLOTRAN MPHASE module.</li> <li>Python scripts for generation of the random fields and quantification of uptake rate.</li> <li>Jupyter notebooks for generation of summary figures.</li> <li>Excel spreadsheet summarizing the output of each of the simulations.</li> </ul>
The Impact of Climate Change on Extreme Winds over Northern Europe According to CMIP6: data and codes
<p>Data and codes for the paper submitted to WES "The Impact of Climate Change on Extreme Winds over Northern Europe According to CMIP6"</p> <p>Data:</p> <p>1. U50*.nc: 50-year wind with spectral correction method from 18 CMIP6 models</p> <p>2. annual_max*.nc: annual wind maxima from 18 CMIP6 models</p> <p>3. spe*.dat: example of power spectrum from the original wind speed time series from a CMIP6 model and power spectrum with spectral correction</p> <p>Codes:</p> <p>1. AnnualMax*.py : calculate extreme winds from 18 CMIP6 models</p> <p>2. XFuture-code-sharing.nb: Mathematca code for analysis of data on the effect of climate change, and pack data for plotting using MATLAB</p> <p>3. *.m: MATLAB codes for plotting figures on climate change </p> <p> </p> <p> </p>
Data for: How do harvesting methods applied in continuous-cover forestry and rotation forest management impact soil carbon storage and degradability in boreal Scots pine forests?
<p>Forest management affects soil carbon (C) storage through forest composition, microclimate and litter inputs. How two major forest management systems, continuous-cover forestry (CCF) and clear-cut-based rotation forest management (RFM), differ in their impact on soil C in boreal forests is still poorly understood, however. We compared their effects on soil organic carbon (SOC) storage and quality in boreal Scots pine <span>(<em>Pinus sylvestris</em></span> L.) dominated forests in eastern Finland. We tested the hypotheses that (1) colder microclimates and continuous litter inputs will lead to higher SOC stocks in CCF plots than in clear-cuts and (2) the more labile litter in clear-cuts with varying ground vegetation will enhance SOC decomposition rates. We sampled uncut mature forests, clear-cuts, retention-cuts and gap-cuts, in which we analysed SOC concentrations and calculated the stocks. We measured stand characteristics such as diameter-at-breast height, basal area, dominant tree height, and understorey species coverage of the various treatments and modelled the above- and belowground litter inputs based on these parameters. We used laboratory incubation and sequential fractionation of SOC to assess its degradability under standardized conditions. To estimate the decomposition rate in the various environments we incubated cellulose bags in situ. We assessed the impact of microclimate on SOC decomposition, using data from soil-temperature and soil-moisture field measurements. We quantified the microbial biomass C pool, using chloroform fumigation extraction to gain insight on the impact of forest management practice on soil microbes. The SOC concentrations and SOC stocks did not differ significantly between the treatments, despite the presence of a warmer microclimate and lower litter inputs in the clear-cut plots. However, we found differences in the quality of the SOC. Soils in clear-cut sites showed lower proportions of labile SOC compounds than did the other treatments. As hypothesized, the decomposition rates were elevated in clear-cuts, but were equally as high within the canopy gaps on gap-cut stands. Our work highlights that forest management affects the quality, degradability, long-term accumulation and storage of SOC. We conclude that the accumulation of labile compounds in uncut forests and retention-cuts, combined with the decreased decomposition rates, indicate a higher potential for future C accumulation in the soil than in clear-cuts.</p>
Data from: Hidden demographic impacts of fishing and environmental drivers of fecundity in a sea turtle population
<p><span>Fisheries bycatch is a critical threat to sea turtle populations worldwide, particularly because turtles are vulnerable to multiple gear types. The Canary Current is an intensely fished region, yet there has been no demographic assessment integrating bycatch and population management information of the globally significant Cabo Verde loggerhead turtle (<em>Caretta</em> <em>caretta</em>) population. Using Boa Vista island (Eastern Cabo Verde) subpopulation data from capture-recapture and nest monitoring (2013–2019), we evaluated population viability and estimated regional bycatch rates (2016–2020) in longline, trawl, purse-seine, and artisanal fisheries. We further evaluated current nesting trends in the context of bycatch estimates, existing hatchery conservation measures, and environmental (net primary productivity) variability in turtle foraging grounds. We projected that current bycatch mortality rates would lead to the near extinction of the Boa Vista subpopulation. Bycatch reduction in longline fisheries and all fisheries combined would increase finite population growth rate by 1.76% and 1.95%, respectively. Hatchery conservation increased hatchling production and reduced extinction risk, but alone it could not achieve population growth. Short-term increases in nest counts (2013–2021), putatively driven by temporary increases in net primary productivity, may be masking ongoing long-term population declines. When fecundity was linked to net primary productivity, our hindcast models simultaneously predicted these opposing long-term and short-term trends. Consequently, our results showed conservation management must diversify from land-based management. The masking effect we found has broad-reaching implications for monitoring sea turtle populations worldwide, demonstrating the importance of directly estimating adult survival and that nest counts might inadequately reflect underlying population trends.</span></p>
Evaluating the Impact of Third-Party Library Reuse in Java Projects: An Empirical Study
<p>Update, we have added the following:<br> - `dataset.ipynb`: Computes all the dataset used for this study. The user needs to use a call graph generator like OPAL/WALA.</p> <p>- `loc.ipynb`: Computes a dataset for LOC information given a call graph dataset</p> <p>- `called-reuse.ipynb`: Computing a dataset for all called functions and LOC in third-party libraries</p> <p>- `megamorphic.ipynb`: Empirically decide the megamorphic call sites. <br> <br> This part of the submission related to the paper "Evaluating the Impact of Third-Party Library Reuse in Java Projects: An Empirical Study". Here is a table of contents:</p> <ul> <li>`census.csv`: extracted data from the Census-II</li> <li>`releases_all.csv`: all releases available from Maven Coordinates in Census-II</li> <li>`releases_jar.csv`: dataset of all releases with a POM and JAR file</li> <li>`releases_jar_6_months.csv`: releases selected when studiying the 6-month interval</li> <li>`releases_jar_6_months.csv`: releases selected when comparing consecutive versions per artefactid and groupid</li> <li>`loc_composition.csv`: data on the ratio of insourced and outsourced code in project releases</li> <li>`loc_desc_without_lambdas.csv`: mined data on LOC information and class information.</li> <li>`loc_reuse_lower_bound.csv`: data on the ratio of reused LOC and functions of outsourced code, lower-bound</li> <li>`loc_reuse_upper_bound.csv`: data on the ratio of reused LOC and functions of outsourced code, upper-bound</li> </ul>
BIG DATA ANALYTICS IN DIGITAL HUMAN RESOURCES MANAGEMENT: IMPACT ON THE RECRUITMENT PROCESS
<p>This study investigates how HR employees experience the big data phenomenon in the recruitment function of HRM and how their perceptions of the phenomenon have evolved. This study also examines how BD will affect organizational and HRM and how it can be improved in other functions of HR. In this exploratory study, which comprehensively addresses the BD phenomenon in HRM, the phenomenological design approach, one of the qualitative research methods, was applied to test the research questions and a semi-structured interview form was used for research data. Using the snowball sampling method, in-depth interviews were conducted with 10 HR employees working in large and semi-structured organizations in Turkey and the interviews were analyzed with MAXQDA 20. The findings show that HRM employees are aware of BD. On the other hand, it is understood that BD technologies provide easy accessibility in recruitment, offer a strategic competitive advantage, and enable more effective management of information management, which saves HR employees' work in a facilitating way. They benefit from technology as a decision support assistant. Finally, the research results provide theoretical and practical implications for future researchers and practitioners for the development and effective use of BD technology in the field of HRM.</p>
Low- and high-intensity fire in the riparian savanna: demographic impacts in an avian model species and implications for ecological fire management
<ol> <li><span>Climate change is driving changes in fire frequency and intensity, making it more urgent for conservation managers to understand how species and ecosystems respond. In tropical monsoonal savannas – Earth's most fire-prone landscapes – ecological fire management aims to prevent intense wildfires late in the dry season through prescribed low-intensity burns early in the dry season. Riparian habitats embedded within tropical savannas represent critical refuges for biodiversity, yet are particularly fire-sensitive. Better understanding of the impact of fire – including prescribed burns – on riparian habitats is therefore key but requires long-term detailed post-fire monitoring of species' demographic rates, as effects may persist and/or be delayed.</span></li> <li><span>We analyse impacts of (prescribed) low-intensity and (prescribed but escaped) high-intensity fire in northern Australian riparian and adjacent savanna habitat. We quantify multi-year impacts on density, survival, reproduction and dispersal of an Endangered riparian bird, the western purple-crowned fairy-wren (<em>Malurus coronatus coronatus</em>), in a well-studied individually-marked population.</span></li> <li><span>Following low-intensity fire, bird density was reduced by >20% in burnt compared to adjacent unburnt riparian habitat for ≥2.5 years. This was a result of reduced breeding success and recruitment for two years immediately following fire, rather than mortality or dispersal of adults.</span></li> <li><span>In contrast, high-intensity fire (in a dry year) resulted in a sharp decline in population density by 50% 2–8 months after fire, with no signs of recovery after 2.5 years. The decline in density was due to post-fire adult mortality, rather than dispersal. Breeding success of the (few) remaining individuals was low but not detectably lower than in unburnt areas, likely because breeding success was poor overall due to prevailing dry conditions.</span></li> <li> <span><em>Synthesis and applications</em>. </span><span>Even if there is no or very low mortality during fire, and no movement of birds away from burnt areas, both low- and high-intensity fire in the riparian zone reduce population density. However, the mechanism by which this occurs, and recovery time, differs with fire intensity. To minimise impacts of fire on riparian zones in tropical savannas, we suggest employing low-intensity prescribed burns under optimal conditions shortly after the breeding season.</span> </li> </ol>
Age specific impacts of vegetation functional traits on gastro-intestinal nematode parasite burdens in a large herbivore
<ol> <li>Gastro-intestinal nematode (GIN) parasites play an important role in the ecological dynamics of many animal populations. Recent studies suggest fine-scale spatial variation in GIN infection dynamics is important in wildlife systems, but the environmental drivers underlying this variation remain poorly understood.</li> <li>We used data from over two decades of GIN parasite egg counts, host space use, and spatial vegetation data from a long-term study of Soay sheep on St Kilda to test how spatial autocorrelation and vegetation in an individual's home range predict parasite burden across three age groups. We developed a novel approach to quantify the plant functional traits present in a home range to describe the quality of vegetation present. </li> <li>Effects of space and vegetation varied between age classes. In immature lambs, strongyle parasite faecal egg counts (FEC) were spatially structured, being highest in the north and south of our study area. Independent of host body weight and spatial autocorrelation, plant functional traits predicted parasite egg counts. Higher egg counts were associated with more digestible and preferred plant functional traits, suggesting the association could be driven by host density and habitat preference.</li> <li>In contrast, we found no evidence that parasite FEC were related to plant functional traits in the host home range in yearlings or adult sheep. Adult FEC were spatially structured, with highest burdens in the north-east of our study area, while yearling FEC showed no evidence of spatial structuring.</li> <li>Our findings support the importance of fine-scale environmental variation for wildlife disease ecology and provide new evidence that such effects may vary across demographic groups within a population. Parasite burdens in immature individuals appear more readily influenced by fine-scale spatial variation in the environment, highlighting the importance of such heterogeneity for our understanding of wildlife epidemiology and health.</li> </ol>
Impact of household bulky waste collection on the presence of dengue-transmitting mosquito breeding sites_dataset
<p>The objective was to evaluate the impact of a municipal strategy to reduce Ae. aegypti in Asunción focused on the management of household bulky waste. To estimate the result, the Difference in Difference (DID) method was used. For the baseline, a simple random sampling of 324 households was carried out. The intervention implemented by the local government in an area with 180,000 residents, contributed to the collection of the equivalent of 14 kilos of bulky waste per inhabitant, given an idea of the magnitude of the problem. For the evaluation survey, 2.5 to 4 years after the intervention, 120 households were randomly selected, of which 60% had not been intervened (control households) and 40% had been intervened. As a result, a significant reduction was achieved in the total number of large solid waste found in the homes that were the object of the intervention. The differentiated collection was used mainly by those households that had a large number of large solid waste (DID of -55%), but not to get rid of all of these objects, but only a part. The data present no evidence of change in the percentage of households with breeding containers between the intervention and control groups.</p>
Anonymized data for "The Impact of Argument Arrangement on Persuasiveness in Online Discussions"
<p>Anonymous upload of the data for the paper "The Impact of Argument Arrangement on Persuasiveness in Online Discussions" for blind review.</p>
The impact of information disclosure on consumer acceptance of genome-edited foods in Japan
<p>Genome editing is promising to accelerate the rate of genetic progress by enabling the replacement of the germ cell lineage of commercial breeding animals with cells derived from genetically elite lines. This is an efficient way to produce foods and reduce food waste. However, foods using genome editing are not very familiar in Japan. The purpose of this study is to investigate consumer acceptance of genome-edited foods and the impact of information disclosure on it. We constructed an acceptance model for genome-edited foods and investigate the amount of willingness to pay for the level of information disclosure. Genome-edited food acceptance model illustrated that information credibility and perceived usefulness were significantly related to the consumer acceptance of genome-edited foods. WTP of functional information label is 76 JPY (approx. 0.69USD), and that of genome-edited food label is 11 JPY (approx. 0.1USD). For genome editing technology description, it was 38 JPY (approx. 0.345USD). The most important factor is functional information. Since this study is an early study in the genome-edited food acceptance model, we believe that there is room for various discussions in the future.</p>
Digitalizing Europe: The promising impact of AI on Car Safety Development
<p>Video through which the ESR09 Giada Colella applied to the MSCA Science-Policy Pitch Competition and Awards.</p>
Data for: Meta analysis reveals impacts of disturbance on reptile and amphibian body condition
<p>Ecosystem disturbance is increasing in extent, severity, and frequency across the globe. To date, research has largely focused on the impacts of disturbance on animal population size, extinction risk, and species richness. However, individual responses, such as changes in body condition, can act as more sensitive metrics and may provide early warning signs of reduced fitness and population declines.</p> <p>We conducted the first global systematic review and meta-analysis investigating the impacts of ecosystem disturbance on reptile and amphibian body condition. We collated 384 effect sizes representing 137 species from 133 studies. We tested how disturbance type, species traits, biome, and taxon moderate the impacts of disturbance on body condition.</p> <p>We found an overall negative effect of disturbance on herpetofauna body condition (Hedges' <em>g =</em> -0.37, 95%CI: -0.57, -0.18). Disturbance type was an influential predictor of body condition response and all disturbance types had a negative mean effect. Drought, invasive species, and agriculture had the largest effects. The impact of disturbance varied in strength and direction across biomes, with the largest negative effects found within Mediterranean and temperate biomes. In contrast, taxon, body size, habitat specialisation, and conservation status were not influential predictors of disturbance effects.</p> <p>Our findings reveal the widespread effects of disturbance on herpetofauna body condition and highlight the potential role of individual-level response metrics in enhancing wildlife monitoring. The use of individual response metrics alongside population and community metrics would deepen our understanding of disturbance impacts by revealing both early impacts and chronic effects within affected populations. This could enable early and more informed conservation management.</p>
Quantifying the potential epidemiological impact of a two-year active case finding for tuberculosis in rural Nepal: A model-based analysis
<p>Includes data and codes for the manuscript entitled: <strong>Quantifying the potential epidemiological impact of a two-year active case finding for tuberculosis in rural Nepal: A model-based analysis</strong></p> <div> <div> <div> <p>doi:10.1136/ bmjopen-2022-062123</p> </div> </div> </div>
An analysis of the impact of domain debt in open-source projects
<p>Datasets related to the thesis paper:</p> <ul> <li><em>original_boa.txt</em> contains the intial output given by <a href="https://boa.cs.iastate.edu/boa/index.php">BOA</a>, while <em>filtered_boa.txt</em> comprises the set of repositories with at most five domain entity packages</li> <li><em>original_seart.txt</em> included data as returned by <a href="https://seart-ghs.si.usi.ch/">SEART</a></li> <li><em>database_structure.sql</em> is the SQL file that may be exploited to perform further analysis on the two datasets</li> <li><em>repos.json</em> contains the final list of repositories, as chosen in the study</li> </ul>
Dataset to Study Flexibility Service Providers' Gaming Potential and its Impact on TSO-DSO Coordinated Markets
<p>We publish the dataset and nomenclature table used to study the Flexibility Service Providers’ Gaming Potential and its Impact on TSO-DSO Coordinated Markets (paper published in the 2023 SEST conference).</p> <p>The dataset is composed by an interconnected system consisting of the IEEE 14-bus (TN) transmission network connected to two distribution networks: the Matpower systems 69-bus (DN_69), and 141-bus (DN_141). All systems topology and some parameters are based on the corresponding cases in Matpower [1]. Injections and loads of the nodes are adapted to create an anticipated negative imbalance (total load surpassing total generation) in the interconnected system, resolved by upward flexibility. In addition, the lines’ upper limits are adjusted to create anticipated congestion in the networks. The interconnected system is fully represented in "Network.xlsx".<br>Upward and downward flexibility bids are randomly generated and allocated to the nodes. Their quantities are aligned with the nodes’ base injection/load and their marginal values are in the range [10, 26] euro/MW for downward, and marginal costs in the range [30, 73] euro/MW for upward, totaling 536 bids. </p> <p>4 bids lists are available in this dataset, to allow the strategic behavior analysis with different levels of liquidity:</p> <p>- In the list of bids "case 0", all 536 bids are present.</p> <p>- In the list of bids "case 1", 40% of bids in the transmission list are deleted (distribution bids are the same as in case 0).</p> <p>- In the list of bids "case 2", 98% of the bids in the distribution bids are deleted (transmission bids are the same as in case 0).</p> <p>- In the list of bids "case 3", only bids needed to solve distribution systems congestions are kept (all the others are deleted) (transmission bids are the same as in case 0).</p> <p>Source of the systems' topology:</p> <p>[1] R. D. Zimmerman, C. E. Murillo-Sanchez, and R. J. Thomas, “Mat-power: Steady-state operations, planning, and analysis tools for power systems research and education,” IEEE Transactions on power systems, vol. 26, no. 1, pp. 12–19, 2010.</p> <p>Please notice that this dataset does not replace the information provided by Matpower related to the aforementioned systems. It rather uses those systems topology and some of their parameters to build a case study to investigate TSO-DSO coordination market models for the procurement of flexibility. For the full description of these systems, please visit: <a href="https://matpower.org/">MATPOWER – Free, open-source tools for electric power system simulation and optimization</a>.</p>
Data for: Drought and temperature stresses impact pollen production and autonomous selfing in a California wildflower, Collinsia heterophylla
<p>Ongoing climatic changes have altered growing conditions for plants by limiting water availability and inducing unprecedented temperature increases, eliciting plant functional responses that compromise floral trait expression, reduce pollen production but promote early self-pollination. In a controlled greenhouse study, plants of <em>Collinsia heterophylla</em>, an annual mixed-mated hermaphrodite, were grown under temperature and water stresses. Floral trait responses and related effects on plant reproductive success were recorded. Plants grown under temperature and water stresses were shorter and had fewer leaves at flowering than control plants. Temperature-stressed plants flowered earlier and had smaller flowers that produced fewer per capita pollen grains than control and water-stressed plants. While lifetime flower production in plants experiencing temperature stress alone or water stress alone was similar to control plants, those receiving combined temperature and water stresses had significantly lower lifetime flower production. Abiotic stress did not affect investment in female traits such as ovule number per flower but impacted male traits seen as fewer pollen grains per flower. In plants experiencing abiotic stress, an increase in autonomous self-pollination was facilitated through a compromise in herkogamy, a sexual interference mechanism to promote cross-pollination. Spatial separation between stigma and anther, a measure of herkogamy, was zero or negative in stressed plants. Thus, abiotic stress responses in plants did not compromise plant reproductive success as autonomous selfing was augmented. In nature, such responses will likely reduce available nutrition for pollinators through decreased flower and pollen production.</p>
Social interactions differ in their impact on foraging decisions
<p>Data and code for the manuscript: Social interactions differ in their impact on foraging decisions</p>
The impact of genetically controlled splicing on exon inclusion and protein structure
<p><strong>This repository contains raw and processed files used in Einson et. al 2022. </strong></p> <p>Code used to generate these files can be found here: https://github.com/jeinson/sqtl_manuscript</p> <p><strong><em>Descriptions of files contained within each sub directory</em></strong></p> <p><strong>01_raw_psi</strong></p> <ul> <li><em>{GTEx_tissue_id}_v8.psi.tsv.gz: </em>Unfiltered PSI output from IPSA-nf, per tissue. See methods for details about how files were created. </li> <li><em>gtex_v8_exon_id_map.tsv: </em>Mapping file between exon coordinates and Ensembl gene IDs, with suffix used in GTEx v8 gencode annotation. </li> </ul> <p><strong>02_qtl_results</strong></p> <ul> <li><strong>cross_tissue</strong> <ul> <li><em>top_sQTLs_MAF05.tsv: </em>List of top GTEx v8 sQTLs across tissues, with one exon and top variant per tissue. See methods for details. See matching file for column descriptions. </li> <li><em>top_sQTLs_median_psi.tsv: </em>The median, mean, and standard deviation of PSI of each significant exon from the previous file, taken across all individuals from GTEx with data available.</li> <li><em>top_sQTLs_MAF05_w_anc_allele.tsv: </em>List of top sQTLs across tissues, with additional columns for the top ψQTL ancestral and derived alleles, where available. </li> </ul> </li> <li><strong>per_tissue</strong> <ul> <li><em>{GTEx_tissue_id}_combined_sQTLs.tsv.gz: </em>Raw output of ψQTL calling using QTLtools in grouped permutational mode per tissue, with groups specified by gene. See methods for more details, and https://qtltools.github.io/qtltools/ for column descriptions. </li> </ul> </li> </ul> <p><strong>03_qtl_credible_sets</strong></p> <ul> <li> <em>GTEx_psi_{GTEx_tissue_id}.collapsed.txt.gz: </em>Output of the QTL catalog fine mapping pipeline (https://github.com/eQTL-Catalogue/qtlmap), run on all exons and tissues, and collapsed using the procedure described in Methods. </li> </ul> <p><strong>04_qtl_coloc</strong></p> <ul> <li><em>combined_coloc_results_full.tsv.gz: </em>Combined output of running coloc on ψQTLs from the 18 GTEx tissues against 87 sets of GWAS summary statistics. This file contains all results, including non-significant associations. A nominal QTLtools pass was used as input. We do not include these files in this repository due to size limitations, but contact the authors if you need access to nominal QTL calls. </li> <li><em>top_sQTLs_with_top_coloc_event.tsv: </em>The QTLs in <em>top_sQTLs_MAF05.tsv</em> with additional columns for the GWAS with the highest posterior probability of a colocalization event. Importantly, the tissue and top variant may not match the main <em>top_sQTLs_MAF05.tsv </em>file for every gene. </li> </ul> <p><strong>05_exon_features: </strong>See matching files for description of each column. </p> <ul> <li><em>cross_tissue_constitutive_exons_with_AF.tsv: </em>Detailed features of cross tissue constitutive exons. See methods for definition of constitutive exons. </li> <li><em>cross_tissue_nonsignificant_genes_with_AF.tsv: </em>Detailed features of sufficiently variable exons with no significant variant across tissues. See methods for more details. </li> <li><em>top_sQTLs_MAF05_with_AF.tsv: </em>Detailed features of top sQTLs. </li> <li><em>top_sQTLs_with_top_coloc_with_AF.tsv: </em>Detailed features of sQTLs that colocalize with at least one GWAS trait. Contains columns for Euclidean distances between PAE matrices and RMSD between isoforms, among genes with a significant GWAS colocalization event. </li> </ul> <p><strong>06_predicted_structures: </strong>Each prediction was run 5 times, and we report the best model in the manuscript. </p> <ul> <li><strong>{protein.id}[_mutant].result</strong> <ul> <li><em>{protein.id}[_mutant]{_run.id}_coverage.png.gz: </em>Plot of the number of sequences per position in MSA</li> <li><em>{protein.id}[_mutant]{_run.id}_PAE.png.gz: </em>PAE matrix plots for each model</li> <li><em>{protein.id}[_mutant]{_run.id}_plddt.png.gz: </em>pLDDT plots for each model</li> <li><em>{protein.id}[_mutant]{_run.id}_predicted_aligned_error_v1.json.gz</em>: A PAE matrix for the best model using <a href="https://alphafold.ebi.ac.uk/faq#faq-7">AlphaFold-DB's format</a></li> <li><em>{protein.id}[_mutant]{_run.id}_unrelaxed_rank_{rank.num}_model_{model.num}_scores.json.gz</em>: Per model array (list of lists) with PAE, a list of the average pLDDT and the pTM score. </li> <li><em>{protein.id}[_mutant]{_run.id}_unrelaxed_rank_{rank.num}_model_{model.num}_pdb.gz: </em>Per model predicted structure in pd format</li> <li><em>{protein.id}[_mutant]{_run.id}.a3m.gz</em>: A3M formatted input MSA</li> <li><em>cite.bibtex: </em>BibTex file with citations for all used tools and databases</li> <li><em>config.json</em>: Model input parameters</li> </ul> </li> </ul> <p><strong>07_other_data</strong></p> <ul> <li><em>cross_tissue_constitutive_exons.tsv: </em>List of exons that are constitutively spliced across multiple tissues. See methods for details. </li> <li><em>cross_tissue_nonsignificant_genes.tsv</em>: List variably spliced exons with no significant sVariant in any tissue. See methods for details. </li> <li><em>gtex_v8_exon_id_map.rds: </em>rds representation of a map between exon IDs, as used in the modified version of gencode v26, and exon hg38 coordinates. </li> <li><em>gtex_v8_n_exons_per_gene.tsv: </em>Number of exons per gene, as annotated in the modified version of gencode v26 used in GTEx v8. </li> </ul> <p><strong>08_geuvadis</strong></p> <ul> <li><em>geuvadis_psi.tsv.gz: </em>Unfiltered PSI output from IPSA-nf, run on Geuvadis BAM files. See methods for details. (Raw data was downloaded from ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEUV)</li> <li><em>geuvadis_sQTLs.tsv.gz: </em>Raw output of ψQTL calling using QTLtools in grouped permutational mode for geuvadis data, with groups specified by gene. See methods for more details, and https://qtltools.github.io/qtltools/ for column descriptions. </li> <li><em>remapped_gencode.v26.GRCh37.GTEx_v8.nochr.genes.gtf.gz:</em> Lifted over version of the gencode v26 gtf file, used to define exons for PSI and qtl mapping in the geuvadis analysis. The original version that was used in the GTEx analysis is based on GRCh38, and is available here: https://storage.googleapis.com/gtex_analysis_v8/reference/gencode.v26.GRCh38.genes.gtf</li> </ul>
Impact of multiple soil microbial inoculants on biomass and biomass allocation of the legume crop field pea (Fabaceae: Pisum sativum L.)
<p>Food production is a global challenge and consequently, there is considerable interest in manipulating the rhizobiome using microbial inoculants (MI) to support sustainable agriculture. We investigated how three commercially-available types of plant growth-promoting MI, alone and in combination (B5: five species of <em>Bacillus</em> bacteria, GP: four species of <em>Trichoderma</em> fungi, N2: <em>Paenibacillus polymyxa</em> bacteria) impacted field pea (Fabales: Fabaceae, <em>Pisum sativum</em> L.) in the greenhouse and a two-year field experiment in the United States, North Dakota, NDSU Field Research station at Prosper ND. CON indicates controls that did not receive any MI and FC is the fertilizer control in the field experiment which also did not receive any MI. The dataset consists of data plant data from a 2-wk greenhouse experiment (GH 2wk), a 4-wk greenhouse experiment (GH 4wk), and a two-year field experiment (field). In the greenhouse, we found that effects of MI on plant performance varied, with positive effects of MI only apparent when plants were grown in the winter and likely under greater stress because they lacked nodules. Plants grown in the summer had nodules, and two-week-old MI plants had less root biomass and total plant weight than non-inoculated controls, but weight of four-week-old MI plants was similar to or greater than controls. In the field, the root-to-shoot biomass ratio was highest in non-inoculated controls, and positive effects of N2 on shoots and B5 on shoots and pod densities didn't translate into differences in pod weight or total plant weight. In most cases, plants inoculated with all three inoculants performed similarly to those receiving a single inoculant, while root colonization by arbuscular mycorrhizal fungi (AMF) was higher for B5 plants than plants in the other treatments. This research underscores the need to consider microbial and environmental context when evaluating MI. </p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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