Find research datasets worth reusing

opencc-zeroDec 2016View details →

Data from: Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence

Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), thus contributing to the evolution of endogenous genetic barriers and eventually cause population divergence. We investigated differential TE abundance among conspecific populations of the non-biting midge Chironomus riparius and evaluated their potential role in causing endogenous genetic incompatibilities between these populations. We focussed on a Chironomus-specific TE, the minisatellite-like Cla-element, whose activity is associated with speciation in the genus. Using a newly generated and annotated draft genome for a genomic study with five natural C. riparius populations, we found highly population-specific TE insertion patterns with many private insertions. A significant correlation of the pairwise FST estimated from genome-wide single nucleotide polymorphisms (SNPs) and the FST estimated from TEs, is consistent with drift as the major force driving TE population differentiation. However, the significantly higher Cla-element FST level due to a high proportion of differentially fixed Cla-element insertions also indicates selection against segregating (i.e. heterozygous) insertions. With reciprocal crossing experiments and fluorescent in-situ hybridisation of Cla-elements to polytene chromosomes, we documented phenotypic effects on female fertility and chromosomal mispairings. We propose that the inferred negative selection on heterozygous Cla-element insertions may cause endogenous genetic barriers and therefore acts as DMI among C. riparius populations. The intrinsic genomic turnover exerted by TEs may thus have a direct impact on population divergence that is operationally different from drift and local adaptation.

opencc-by-4.0Jun 2021View details →

Immunotherapy-mediated thyroid dysfunction: genetic risk and impact on outcomes with PD-1 blockade in non-small cell lung cancer

Polygenic risk score weights derived using LDpred for hypothyroidism and thyroid medication use.

opencc-zeroJun 2021View details →

Impacts of additional noise on the social interactions of a cooperatively breeding fish

Anthropogenic noise is a global pollutant known to affect the behaviour of individual animals in all taxa studied. However, there has been relatively little experimental testing of the effects of additional noise on social interactions between conspecifics, despite these forming a crucial aspect of daily life for most species. Here we use established paradigms to investigate how white-noise playback affects both group defensive actions against an intruder and associated within-group behaviours in a model fish species, the cooperatively breeding cichlid Neolamprologus pulcher. Additional noise did not alter defensive behaviour, but did result in changes to within-group behaviour. Both dominant and subordinate females, but not the dominant male, exhibited less affiliation and showed a tendency to produce more submissive displays to groupmates when there was additional noise compared to control conditions. Our experimental results therefore indicate the potential for anthropogenic noise to affect social interactions between conspecifics and that there can be intraspecific variation in the impacts of this global pollutant.

opencc-by-4.0Jun 2021View details →

Ryugu's observed volatile loss did not arise from impact heating alone

Descriptions of Supplementary Data   File Name: Supplementary Data 1 Description: The data supporting Figure 1. The time variations of the ion currents. The selected mass number of each row is described in the top column.   File Name: Supplementary Data 2 Description: The data supporting Figure 4a. The cumulative mass at a given peak pressure as a function of the peak pressure. The key information of the calculation settings for each row is described in the top column.   File Name: Supplementary Data 3 Description: The data supporting Figure 4b. The same as panel (a), except the cumulative mass at a given entropy is shown as a function of entropy. The key information of the calculation settings for each row is described in the top column.

Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization

Assembled sequence alignments and phylogenetic trees for plastomes and nuclear loci for 24 samples of Crataegus.

Data for manuscript ''The Impact of Ammonium on the Distillation of Organic Carbon in PM2.5''

Data for manuscript ''The Impact of Ammonium on the Distillation of Organic Carbon in PM2.5'' submitted to Geophysical Research Letters

Impacts of City Shape on Rainfall in Contrasting Environments

WRF-LES simulation of rainfall over inland and costal environment. Results here are under the quasi-equilibrium state.

Land surface modeling over the Dry Chaco: the impact of model structures, and soil, vegetation and land cover parameters

The datasets archived here include simulation results shown in the paper, “Land surface modeling over the Dry Chaco: the impact of model structures, and soil, vegetation and land cover parameters”, published in Hydrology and Earth System Sciences (Maertens et al., 2021). The simulations were conducted over the South-American Dry Chaco and output on the different water budget components was produced with three land surface models (CLM2.0, CLSM-F2.5, and Noah3.6) embedded in the NASA Land Information System (LIS). The default LIS parameters were revised with (i) improved soil parameters, (ii) satellite-based interannually varying vegetation indices (leaf area index and green vegetation fraction), and (iii) yearly land cover information. For each experiment described in the manuscript, we provide daily netcdf files (0.125° resolution, period Jan 1992 – Dec 2015). The conducted experiments are simulations with (i) default LIS parameters (BL), (ii) updated soil parameters (REVs) and (iii) interannualy varying vegetation and land cover parameters (REVSV). For details, please refer to Maertens, M., De Lannoy, G. J. M., Apers, S., Kumar, S. V., and Mahanama, S. P. P.: Land Surface modeling over the Dry Chaco: the impact of model structures, and soil, vegetation and land cover parameters, Hydrology and Earth System Sciences. Please contact Michiel Maertens (michiel.maertens@kuleuven.be) or Gabriëlle De Lannoy (gabrielle.delannoy@kuleuven.be) for any questions.

opencc-zeroOct 2019View details →

Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide

Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 130 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms were genotyped using double-digest, restriction site-associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic diversity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic diversity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more admixture in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome-scale markers to document subtle impacts of urbanization on a wide-ranging carnivore living near a large urban center.

opencc-zeroDec 2018View details →

Data from: Impacts of salt stress on locomotor and transcriptomic responses in the intertidal gastropod Batillaria attramentaria

Salinity is one of the most crucial environmental factors that structures biogeographic boundaries of aquatic organisms, affecting distribution, abundance, and behavior. However, the association between behavior and gene regulation underlying acclimation to changes in salinity remains poorly understood. In this study, we investigated the effects of salinity stress on behavior (movement distance) and patterns of gene expression (using RNA-seq) of the intertidal gastropod Batillaria attramentaria. We examined responses to short- (1 hour) and long-term (30 day) acclimation to a range of salinities (43, 33 (control), 23, 13, and 3 Practical Salinity Units (PSU)). We found that the intertidal B. attramentaria is able to tolerate a broad range of salinity from 13 to 43 PSU, but not the acute low salinity of 3 PSU. Behavioral experiments showed that salt stress significantly influenced snails' movement, with lower salinity resulting in shorter movement distance. Transcriptomic analyses revealed critical metabolic pathways and genes potentially involved in acclimation to salinity stress, including ionic and osmotic regulation, signal and hormonal transduction pathways, water exchange, cell protection, and gene regulation or epigenetic modification. In general, our study presents a robust, integrative laboratory-based approach to investigate the effects of salt stress on a non-model gastropod, which is facing detrimental consequences of environmental change. The current genetic results provide a wealth of reference data for further research on mechanisms of ionic and osmotic regulation and adaptive evolution of this coastal gastropod.

On the impact of different templates on creating and understanding user stories - Supplemental Material

Here we include the supplementary material that may be used as a replication package for the quasi-experiment reported in the paper "On the impact of different templates on creating and understanding user stories", submitted to RE 2021 (International Requirements Engineering Conference).

The Impact of Drying and Rehydration on the Structural Properties and Quality Attributes of Pre-Cooked Dried Beans

The data used for the figures of the journal article is uploaded here.

opencc-by-4.0Feb 2021View details →

Submission to Special Issue of Quantitative Science Studies "Scientific Knowledge Graphs and Research Impact Assessment"

To be added

opencc-zeroJul 2021View details →

No impact of neonicotinoids on male solitary bees Osmia cornuta under semi-field conditions

The ubiquitous use of agrochemicals is one driver for the ongoing loss of insect biomass and diversity. Data show that field-realistic concentrations of neonicotinoid insecticides can negatively affect both population density and the fitness of solitary bees. However, the underlying mechanisms for these effects remain poorly understood. Here, using an established semi-field experimental set-up and Osmia cornuta as a solitary bee model, we examined the effects of field-realistic concentrations of a common neonicotinoid insecticide (clothianidin) on male larvae and adults. Besides measuring lethal (i.e., overwintering success and adult survival) and sub-lethal endpoints (i.e., emergence mass and emergence duration), we examined, for the first time, potential effects on the male reproductive physiology of a solitary bee (i.e., sperm quantity and viability). The data revealed no significant effects on any of the measured response variables. This may be due to the low degree of clothianidin exposure (0.56 ng g−1) and/or the apparent low susceptibility of solitary bee larvae to neonicotinoids. Furthermore, it is conceivable that ideal foraging conditions, combined with optimal weather and lack of other environmental stressors, may have improved the ability of bees to cope with the insecticide. To reliably assess and understand the environmental hazards of agrochemicals, a holistic approach, including laboratory, semi-field, and field data is required. Knowledge of underlying mechanisms will help to mitigate the current global declines of insect populations.

opencc-by-4.0Nov 2020View details →

Global process-based characterization factors of soil carbon depletion for life cycle impact assessment

The dataset includes all the Life Cycle Impact Assessment (LCIA) Characterization Factors (CFs) for the Soil Organic Carbon (SOC) depletion indicator produced by Teixeira, R.F.M., Morais, T.G., Domingos, T. 2021. Global process-based characterization factors of soil carbon depletion for life cycle impact assessment.   The dataset is divided by type of CF. The results (files) included in each file is: <ul> <li>SOC_dynamics.zip: includes all the used SOC dynamics for calculate the CFs (it includes transitions for crop, forest, grassland and urban LU classes).</li> </ul> <ul> <li>Raster_Background_Occupation.zip: includes spatial data (rasters at “tif” format) for Occupation CFs per aggregated land use flow according Table 1 of the paper at country-level.</li> </ul> For example, the raster “Occ_background_Agriculture.tif” has the CFs for the land use class “Agriculture”. <ul> <li>Raster_background_Transformation.zip: includes spatial data (rasters at “tif” format) for Transformation CFs per aggregated land use flow according Table 1 of the paper at country-level.</li> <li>Table_CFs_background.xlsx: Includes, at Excel table, the Occupation and Transformation Characterization Factors that were included in “Raster_background_ Occupation.zip” and “Raster_background_Transformation.zip”</li> <li>Raster_Foreground_Occupation.zip: includes spatial data (rasters at “tif” format) for Occupation CFs per unique land use flow according Table 2 of the paper at unique homogenous territorial unit (about 17,200 unique region).</li> </ul> For example, the raster “Occ_foreground_Irrigated_Potatoes.tif” has the CFs for the land use class “Irrigated potatoes”. <ul> <li>Raster_ Foreground _Transformation.zip: includes spatial data (rasters at “tif” format) for Transformation CFs per unique land use flow according Table 2 of the paper at unique homogenous territorial unit (about 17,200 unique region).</li> <li>Table_CFs_foreground.xlsx: Includes, at Excel table, the Occupation and Transformation Characterization Factors that were included in “Raster_Foreground_Occupation.zip” and “Raster_ Foreground _Transformation.zip”</li> <li>LCIA_OpenLCA_file.zip: includes the Background Characterization Factors to be imported as an LCIA methods for the Product Environmental Footprint database in OpenLCA software</li> </ul>

Incipient speciation and the impact on taxonomic decision: a case study using a sky island sister species pair of stag beetle (Lucanus; Lucanidae)

Species delimitation can be difficult when the divergence between focal taxa falls in the incipient stage of speciation, because conflicting results are expected among different data sets and the species limit may differ depending on the applied species concept. We studied the speciation history and investigated the impact on taxonomic decision when using different data types in a Taiwanese endemic sister species pair of stag beetle, Lucanus miwai and L. yulaoensis, from sky island habitats. We showed that the two geographical taxa can be diagnosed by male mandibular shape. We found two mitochondrial co1 lineages with pairwise sequence divergence > 3 %; however, L. miwai may not be monophyletic. Our multispecies coalescent based species delimitation result using five nuclear loci supported the evolutionary independence of the two sister species, but the calculated values of genealogical divergence index (gdi) corresponded to the species delimitation ambiguous zone. We further showed that post divergence gene flow is unlikely. Our study demonstrates challenges in incipient species delineation, but shows the importance of understanding the speciation history and integrative approaches to reconcile seemingly conflicting results before making evolutionarily relevant taxonomic decisions.

Supplementary information from: Species interactions have predictable impacts on diversification

A fundamental goal of ecology is to reveal generalities in the myriad types of interactions among species, such as competition, mutualism, and predation. Another goal is to explain the enormous differences in species richness among groups of organisms. Here, we show how these two goals are intertwined: we find that different types of species interactions have predictable impacts on rates of species diversification, which underlie richness patterns. Based on a systematic review, we show that interactions with positive fitness effects for individuals of a clade (e.g. insect pollination for plants) generally increase that clade's diversification rates. Conversely, we find that interactions with negative fitness effects (e.g. predation for prey, competition) generally decrease diversification rates. The sampled clades incorporate all animals and land plants, encompassing ~90% of all described species across life. Overall, we show that different types of local-scale species interactions can predictably impact large-scale patterns of diversification and richness.

opencc-by-4.0Aug 2021View details →

Impacts of concentrated seepage flow on suffusion development in cohesionless soil: insight from a theoretical model

The uploaded file is the original data of a paper submitted to the journal of " Water Resources Research"

Data from: Socio-economic impacts of energy access through off-grid systems in rural communities: A case study of South-West Nigeria

The development of resilient energy systems is important for sustainable cities and communities. However, in countries with insufficient national energy supply, electricity distributors rarely consider remote communities due to their distant settlement, low electricity demand and poor payment capabilities. The United Nations has set a goal to deliver universal energy access by 2030, hence, it has become imperative to deploy clean and affordable off-grid mini-grid solutions to previously abandoned communities. Access to energy in rural communities is expected to result in unlocking their economic potentials. This paper investigates the impact of a solar hybrid mini-grid on the socio-economic growth of local entrepreneurs in Gbamu Gbamu village, Nigeria. A total of 83 Micro and Small Enterprises has been surveyed, descriptive statistics, paired-sample t-test, cross-tabulation, and Chi-square test, were used to assess the performance of businesses before and after electrification. The outcomes include the number of business enterprises created, employment statistics, energy expenses and income generated. Regression analysis was conducted on the relationship between the average income generated by businesses and independent socio-economic variables such as gender, marital status, household size, age, education level, years of business establishment, hours of operation, building tenure, capital source, number of employees, generator ownership and the days of operation.

Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing

Studies of structural variation (SV) have been challenging due to technological contraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examime SV in the EGFR landscape of four haplotypes derived from two human samples. We analyzed the EGFR gene and its landscape (+/- 500,000 base pairs) using this sequencing approach and were able to identify regions of non-coding DNA which had relatively high similarity to the most common activating EGFR mutation in non-small cell lung cancer. We discovered that reverse complements to the exon 19 deletion mutation which had at least 60% homology to the EGFR exon 19 canonical deletion and were within ± 421,000 bp of the deletion varied across the five haploid genomes examined (4 patient landscapes and hg38). Although the sample size is limited in this study, the estimated variation observed in genomic stability between the five EGFR haplotypes examined is novel and encourages further work to examine structural variation in larger cohorts.