Find research datasets worth reusing

opencc-zeroDec 2023View details →

Data from: harnessing the power of regional baselines for broad-scale genetic stock identification: a multistage, integrated, and cost-effective approach

In mixed-stock fishery analyses, genetic stock identification (GSI) estimates the contribution of each population to a mixture and is typically conducted at a regional scale using genetic baselines specific to the stocks expected in that region. Often these regional baselines cannot be combined to produce broader geographical baselines due to non-overlapping populations and genetic markers. In cases where the mixture contains stocks spanning across a wide area, a broad-scale baseline is created, but often at the cost of resolution. Here, we introduce a new GSI method to harness the resolution capabilities of baselines developed for regional applications in the analysis of mixtures containing individuals from a broad geographic range. This method employs a multistage framework that allows disparate baselines to be used in a single integrated process that produces estimates along with the propagated errors from each stage. All individuals in the mixture sample are required to be genotyped for all genetic markers in the baselines used by this model, but the baselines do not require overlap in genetic markers or populations representing the broad-scale or regional baselines. We demonstrate our integrated multistage GSI model using a synthesized data set made up of Chinook salmon, Oncorhynchus tshawytscha, from the North Bering Sea of Alaska. The data set is designed to be run using R package, Ms.GSI, and it does not represent the composition of the real fishery. The results show an improved accuracy for estimates using an integrated multistage framework, compared to the conventional framework of using separate hierarchical steps. The integrated multistage framework allows GSI of a wide geographic area without first developing a large scale, high-resolution genetic baseline or dividing a mixture sample into smaller regions beforehand. This approach is more cost-effective than updating range-wide baselines with all regionally important markers.

opencc-zeroDec 2023View details →

Data from: The interactive effects of heat stress, parasitism, and hostplant quality in a host-parasitoid system

Species interactions are expected to change in myriad ways as the frequency and magnitude of extreme temperature events increase with anthropogenic climate change. The relationships between endosymbionts, parasites, and their hosts are particularly sensitive to thermal stress, which can have cascading effects to other trophic levels. We investigate the interactive effects of heat stress and parasitism on a terrestrial tritrophic system consisting of two hostplants (one common, high-quality plant and one novel, low-quality plant), a caterpillar herbivore, and a specialist parasitoid wasp. We used a fully-factorial experiment to determine the bottom-up effects of the novel hostplant on both the caterpillars' life history traits and the wasps' survival, and the top-down effects of parasitism and heat shock on caterpillar developmental outcomes and herbivory levels. Hostplant identity interacted with thermal stress to affect wasp success, with wasps performing better on the low-quality hostplant under constant temperatures but worse under heat shock conditions. Surprisingly, caterpillars consumed less leaf material of the low-quality hostplant to reach the same final mass across developmental outcomes. In parasitized caterpillars, heat shock reduced parasitoid survival and increased both caterpillar final mass and development time on both hostplants. These findings highlight the importance of studying community-level responses to climate change from a holistic and integrative perspective and provide insight into potential substantial interactions between thermal stress and diet quality in plant-insect systems.

opencc-by-4.0Dec 2023View details →

On effect of chloroform on electrical activity of proteinoids

Within the scope of this study, titled "On the effect of chloroform on the electrical activity of proteinoids," we present a comprehensive investigation and characterization of various electro-physical parameters. These include impedance, capacitance, resistance, and voltage. These metrics were determined over time to comprehensively understand the system's temporal response, particularly in the presence of chloroform. Furthermore, time-dependent voltage outputs were carefully analyzed to distinguish regular voltage spike trains, which are vital to understanding the system's electrical signal propagation properties.

opencc-by-4.0Jul 2023View details →

Probabilistic classification of Fermi LAT gamma-ray sources (effect of covariate shift)

Version 1: These are data products connected to <a href="https://arxiv.org/abs/2307.09584">https://arxiv.org/abs/2307.09584</a>, where an analysis of the effect of covariate shift on the probabilistic classification of the Fermi LAT gamma-ray sources from the 4FGL-DR3 catalog is performed. The files  4FGL-DR3_6class_GMM_nmin100_prob_cat.csv 4FGL-DR3_6class_GMM_nmin100_weighted_prob_cat.csv contain probabilistic classification into 6 classes (determined in <a href="https://arxiv.org/abs/2307.09584">https://arxiv.org/abs/2301.07412</a>) with random forest and neural networks methods. The catalog in "4FGL-DR3_6class_GMM_nmin100_weighted_prob_cat.csv" is constructed including weights for associated sources used in training in order to account for the difference in the distribution of associated (training dataset) and  unassociated (target dataset) sources. The catalog in "4FGL-DR3_6class_GMM_nmin100_prob_cat.csv" is constructed with unweighted training samples. The files 4FGL-DR3_6class_GMM_nmin100_summary.csv 4FGL-DR3_6class_GMM_nmin100_weighted_summary.csv contain the corresponding summaries of the definition of classes and predicted numbers of sources for the RF and NN algorithms for associated sources (averaged over cases when the sources are in the testing samples) and unassociated sources. Detailed description of the construction of the catalogs can be found in <a href="https://arxiv.org/abs/2307.09584">https://arxiv.org/abs/2307.09584</a>. Version 2: update for the Fermi LAT 4FGL-DR4 catalog. The filenames slightly change. Probabilistic catalogs with unweighted and weighted training respectively: 4FGL-DR4_6classes_GMM_prob_cat.csv 4FGL-DR4_6classes_GMM_weighted_prob_cat.csv The corresponding summary files: 4FGL-DR4_6classes_GMM_summary.csv 4FGL-DR4_6classes_GMM_weighted_summary.csv Version 3: catalogs corresponding to the published version of the paper. The filenames and the format are the same as in Version 2.

Data from: A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus), and Panthera species, using targeted bisulfite sequencing and machine learning models

Knowledge of individual age can help both in-situ and ex-situ conservation programs to design more efficient and suitable management plans for targeted wildlife species. DNA methylation is one of the epigenetic aging markers that has emerged as a promising tool that can estimate age with high accuracy using only a tiny amount of biological material, which can be collected in a minimally invasive way. Here, we sequenced five targeted genetic regions and used 8–23 selected CpG sites to build age estimation models with machine learning methods with about only $3–7 per sample, using blood samples of seven Felidae species—ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples), and five Panthera species (96 samples). The models built achieved satisfactory accuracy—the mean absolute error of the best models was 1.966, 1.348, and 1.552 years in domestic cats, Tsushima leopard cats, and Panthera spp., respectively. Our models in domestic cats and Tsushima leopard cats were applicable to individuals regardless of health conditions, indicating the high applicability of our models to samples collected from diverse situations, e.g., rescued individuals in the context of conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using two of the five genetic regions, suggesting an even lower cost to use our models for future applications.

Data from: Promoting success in thin layer sediment placement: effects of sediment grain size and amendments on salt marsh plant growth and greenhouse gas exchange

Thin layer sediment placement (TLP) is a method to mitigate factors resulting in loss of elevation and severe alteration of hydrology, such as sea level rise and anthropogenic modifications, and prolong the lifespan of drowning salt marshes. However, TLP success may vary due to plant stress associated with reductions in nutrient availability and hydrologic flushing or through the creation of acid sulfate soils. This study examined the influence of sediment grain size and soil amendments on plant growth, soil and porewater characteristics, and greenhouse gas exchange for three key US salt marsh plants: Spartina alterniflora, Spartina patens, and Salicornia pacifica. We found that bioavailable nitrogen concentrations (measured as extractable NH4+-N) and porewater pH and salinity were found to have an inverse relationship with grain size, while soil redox was more reducing in finer sediments. This suggests that utilizing finer sediments in TLP projects will result in a more reduced environment with higher nutrient availability, while larger grain-sized sediments will be better flushed and oxidized. We further found that grain size had a significant effect on vegetation biomass allocation and rates of gas exchange, although these effects were species-specific. We found that soil amendments (biochar and compost) did not subsidize plant growth but were associated with increases in soil respiration and methane emissions. Biochar amendments were additionally ineffective in ameliorating acid sulfate conditions. This study uncovers complex interactions between sediment type and vegetation, emphasizing limitations of soil amendments. The findings aid restoration project managers in making informed decisions regarding sediment type, target vegetation, and soil amendments for successful TLP projects.

Modelling the carbon balance in bryophytes and lichens: Presentation of PoiCarb 1.0, a new model for explaining distribution patterns and predicting climate-change effects

Premise Bryophytes and lichens have important functional roles in many ecosystems. Insight into how their CO2 exchange responds to climatic conditions is essential for understanding current and predicting future productivity and biomass patterns, but responses are hard to quantify at time-scales beyond instantaneous measurements. We present PoiCarb 1.0, a model to study how CO2 exchange rates of these poikilohydric organisms change through time as a function of weather conditions. Methods PoiCarb simulates diel fluctuations of CO2 exchange and estimates long-term carbon balances, identifying optimal and limiting climatic patterns. Modelled processes are net photosynthesis, dark respiration, evaporation and water uptake. Measured CO2-exchange responses to light, temperature, atmospheric CO2 concentration, and thallus water content (calculated in a separate module) are used to parameterise the model's carbon module. We validated the model by comparing modelled diel courses of net CO2 exchange to such courses from field measurements on the tropical lichen Crocodia aurata. To demonstrate the model's usefulness, we simulated potential climate-change effects. Results Diel patterns were reproduced well and modelled and observed diel carbon balances were strongly positively correlated. Simulated warming effects via changes in metabolic rates were consistently negative, while effects via faster drying were variable, depending on the timing of hydration. Conclusions Being able to reproduce the weather-dependent variation in diel carbon balances is a clear improvement compared to simple extrapolations of short-term measurements or potential photosynthetic rates. Apart from predicting climate-change effects, future uses of PoiCarb include testing hypotheses about distribution patterns of poikilohydric organisms and guiding species' conservation.

opencc-zeroDec 2023View details →

An inbreeding perspective on the effectiveness of wildlife population defragmentation measures: A case study on wild boar (Sus scrofa) of Veluwe, The Netherlands

Pervasive inbreeding is a major genetic threat of population fragmentation and can undermine the efficacy of population connectivity measures. Nevertheless, few studies have evaluated whether wildlife crossings can alleviate the frequency and length of genomic autozygous segments. Here, we provided a genomic inbreeding perspective on the potential effectiveness of mammal population defragmentation measures. We applied a SNP-genotyping case study on the ~2500 wild boar Sus scrofa population of Veluwe, The Netherlands, a 1000-km2 Natura 2000 protected area with many fences and roads but also, increasingly, fence openings and wildlife crossings. We combined a 20K genotyping assessment of genetic status and migration rate with a simulation that examined the potential for alleviation of isolation and inbreeding. We found that Veluwe wild boar subpopulations are significantly differentiated (FST-values of 0.02-0.07) and have low levels of gene flow. One noteworthy exception was the Central and Southeastern subpopulation, which were nearly panmictic and appeared to be effectively connected through a highway wildlife overpass. Estimated effective population sizes were at least 85 for the meta-population and ranging from 31 to 52 for the subpopulations. All subpopulations, including the two connected subpopulations, experienced substantial inbreeding, as evidenced through the occurrence of many long homozygous segments. Simulation output indicated that whereas one or few migrants per generation could undo genetic differentiation and boost effective population sizes rapidly, genomic inbreeding was only marginally reduced. The implication is that ostensibly successful connectivity restoration projects may fail to alleviate genomic breeding of fragmented mammal populations. We put forward that defragmentation projects should allow for (i) monitoring of levels of differentiation, migration and genomic inbreeding, (ii) anticipation of the inbreeding status of the meta-population, and, if inbreeding levels are high and/or haplotypes have become fixed, (iii) consideration of enhancing migration and gene flow among meta-populations, possibly through translocation.

Data from: Sex-specific effects of inbreeding in juvenile brown trout

Inbreeding depression, i.e., the reduction of health and vigour in individuals with high inbreeding coefficients, is expected to increase with environmental, social, or physiological stress. It has therefore been predicted that sexual selection and the associated stress usually lead to higher inbreeding depression in males than in females. However, sex-specific differences in life history may reverse that pattern during certain developmental stages. In some salmonids, for example, female juveniles start developing their gonads earlier than males who instead grow faster. We tested whether the sexes are differently affected by inbreeding during that time. To study the effects of inbreeding coefficients that may be typical for natural populations of brown trout (Salmo trutta), and also to control for potentially confounding maternal or paternal effects, we sampled males and females from the wild, used their gametes in a block-wise full-factorial breeding design to produce 60 full-sib families, released the offspring as yolk-sac larvae into the wild, sampled them 6 months later, identified their genetic sex, and used microsatellites to assign them to their parents. We used whole-genome resequencing to calculate the kinship coefficients for each breeding pair and hence the expected average inbreeding coefficient per family. Juvenile growth could be predicted from these expected inbreeding coefficients and the genetic sex: Females reached lower body sizes with increasing inbreeding coefficient, while no such link could be found in males. This sex-specific inbreeding depression led to the overall pattern that females were on average smaller than males by the end of their first summer.

The effect of Israeli acute paralysis infection on honey bee brood care behavior

To protect themselves from communicable diseases, social insects utilize social immunity—behavioral, phsyiological, and organizational means to combat disease transmission and severity. Within a honey bee colony, larvae are visited thousands of times by nurse bees, representing a prime environment for pathogen transmission. We investigated a potential social immune response to Israeli acute paralysis virus (IAPV) infection in brood care, testing the hypotheses that bees will respond with behaviors that result in reduced brood care, or that infection results in elevated brood care as a virus-driven mechanism to increase transmission. We tested for group-level effects by comparing three different social environments in which 0%, 50%, or 100% of bees were experimentally infected with IAPV. We investigated individual-level effects by comparing exposed bees to unexposed bees within the mixed-exposure treatment group. We found no evidence for a social immune response at the group level; however, individually, exposed bees interacted with the larva more frequently than their unexposed nestmates. While this could increase virus transmission from adults to larvae, it could also represent a hygienic response to increase grooming when an infection is detected. Together, our findings underline the complexity of disease dynamics in complex social animal systems.

opencc-by-4.0Dec 2022View details →

Effect of shade and nitrogen content on Arabidopsis Col-0 and cytokinin mutants abcg14 and cypDM mRNA-seq gene expression processed tables.

This dataset is an add-on for Gautrat et al., containing processed files for the mRNAseq data in tab delimited txt format. Here, you can obtain the raw counts file, the normalized CPM values, and the normalized logCPM values The RNA-seq raw data supporting the conclusions of this article have been deposited in ArrayExpress (Kolesnikov et al., 2015) at EMBL-EBI (www.ebi.ac.uk/arrayexpress), under accession numbers E-MTAB-13638. All relevant custom r scripts are available at https://github.com/aromanowski/shade_N_ck

opencc-by-4.0Jan 2024View details →

Data for sensitivity analysis of Hübler, M., M. Wiese, M. Braun and J. Damster (2023): The distributional effects of CO2 pricing at home and at the border on German income groups

This dataset contains the output files used in the sensitivity analysis of the computable general equilibrium (CGE) model developed in Hübler et al. (2023). Each folder is labeled with the respective set of sector-level elasticity of substitution parameters considered in the analysis: elasticities between domestically produced versus imported goods (esubd), Armington elasticities (esubm) and elasticities between production factors (esubva). For each set of parameters, we generate 1000 random draws from a +-10 % interval around each of the sector-specific elasticities, resulting in 1000 sets of sectoral parameter values. Each .xlsx output file located in a dedicated subfolder corresponds to a model run with a specific set of parameter values. In addition, we conduct sensitivity analyses of two individual parameters, namely the CO2 target (CO2factor) considered in our policy scenarios and the elasticity of substitution in consumption (esub_cons). The sensitivity analysis is carried out using the <a href="https://snakemake.readthedocs.io/en/stable/">Snakeflow</a> workflow management system, and R code for generating parameter spaces and processing the output files is available on <a href="https://github.com/mariuslbraun/climate-trade-distribution-sensitivity">GitHub</a>.

Data from: Effects of past mating behavior versus past ejaculation on male mate choice and male attractiveness

Past reproductive effort allows males to assess their ability to acquire mates, but it also consumes resources that can reduce their future competitive ability. Few studies have examined how a male's reproductive history affects his subsequent mate choice; and, to date, no study has determined the relative contribution of past mating behavior and past ejaculate production because these two forms of investment are naturally highly correlated. Here, we disentangled the relative effects of past mating behavior and past ejaculate production in male mosquitofish (Gambusia holbrooki) by experimentally preventing some males from ejaculating when trying to mate. We assessed the effect of mating behavior on mate choice by comparing males that had previously been with or without access to females and male rivals for 16 weeks; and assessed the effect of ejaculation on mate choice by comparing males that either could or could not ejaculate when they had access to females for 16 weeks. We compared (1) time females spent with each male, (2) total distance males swam, (3) total time males spent inspecting females, (4) proportion of time males spent with the solitary females in separate models, with age (week 8, week 16) and treatment of reproductive history ("naive male", "mating only male" and "mating and ejaculation males") as fixed factors. We showed that reproductive history did not affect male attractiveness, but it did affect male mate choice. Somewhat surprisingly, in two-choice trials males from all three treatments preferred females in the vicinity of a rival over solitary females. This preference was marginally stronger for males engaging in previous mating behavior but was unaffected by past ejaculate production. This is the first study to quantify the relative influence of pre- and post-copulatory reproductive investment on male mate choice.

opencc-by-4.0Apr 2023View details →

Post-hypnotic safety suggestion improves stress coping with long-lasting effects

Effective coping with acute stress is important to promote mental health and to build stress resilience. Interventions improving stress coping usually require long training periods. In this study, we present a hypnosis-based intervention that produces long-term effects after a single hypnosis session. In that session, we established a post-hypnotic safety suggestion that participants can activate afterwards with a cue. We tested 60 participants in our study who all received the hypnosis session and a stress task. The safety group used the post-hypnotic safety cue during acute stress (Trier Social Stress Test, TSST). The control group used a neutral trigger instead. We measured subjective stress responses via self-reports and physiological stress responses via saliva and blood samples as well as heart rate. One week later, all participants filled in an online survey to measure long-term effects of the post-hypnotic safety suggestion. We found that participants using the post-hypnotic safety cue during the TSST reported significantly lower stress compared to the control group. The safety group also reported significantly fewer negative thoughts concerning their TSST performance than the control group during the stress recovery phase and one week later. All participants indicated that the post-hypnotic safety suggestion still worked one week after its establishment. Suggestibility did not affect the efficacy of the post-hypnotic safety suggestion. Our findings demonstrate that post-hypnotic safety suggestions improve stress coping with long-lasting effects, which makes it a promising intervention to promote mental health and establish stress resilience in just one hypnosis session. The manuscript is published in Scientific Reports on February 12, 2024 and available here: https://doi.org/10.1038/s41598-024-54071-3

Data for: Effective population size mediates the impact of pollination services on pollen limitation

Inadequate pollen receipt limits flowering plant reproduction worldwide. Ecological causes of pollen limitation ('PL'), like pollinator scarcity and low plant abundance, have been a primary focus of research. The genetic diversity of plant populations could impact both quantity and quality components of PL in concert with ecological factors, yet empirical examples are lacking. We evaluated joint effects of ecological factors (flower abundance, pollinator visitation) and genetic effective population size (NE) on PL across 13 populations of a common herb. We used a histological approach with 5504 styles from 1137 flowers to separate quantity and quality components of PL, and link these to reproductive output. NE and pollinator visitation interacted to shape PL, but NE had stronger direct effects. Effectively smaller populations experienced stronger quantity PL, and controlled crosses in a pollinator-free environment revealed that pollen quantity was an intrinsic population-level attribute that increased with NE. Pollinator visitation enhanced pollen quality, but only in effectively larger populations. Quantity and quality PL negatively impacted fruit and seed set, respectively. Results highlight that PL is dictated by plant population genetic diversity in addition to commonly evaluated ecological factors. Efforts to support pollinators will only enhance plant reproduction in genetically diverse plant populations.

opencc-zeroFeb 2024View details →

Data for: Dissolved organic matter (DOM) offsets the detrimental effects of climate change in the nitrogen fixing cyanobacterium Crocosphaera

<div> <div> <div> <div> Diazotrophs provide a significant reactive nitrogen source in the ocean. Increased warming and stratification may decrease nutrient availability in the future, forcing microbial communities to use dissolved organic matter (DOM). Not depending on reactive nitrogen availability, diazotrophs may be "winners" in a nutrient depleted ocean. However, their ability to exploit DOM may influence this success. We exposed cultures of the widespread Crocosphaera to low (26°C, pH 8.1), moderate (28°C, pH 8.0), and extreme (30°C, pH 7.9) climate change scenarios, under control or DOM-amended conditions. Growth was suboptimal in the low and extreme treatments, and favoured in the moderate treatment. DOM was preferred as a carbon source regardless of the treatment, and promoted N2 fixation in extreme conditions. This was reflected in the increased expression of photosynthesis genes to obtain energy. DOM provides Crocosphaera with a key ecological advantage, possibly dictating diazotroph-derived nitrogen inputs in the future ocean. </div> </div> </div> </div>

opencc-by-4.0Feb 2024View details →

Identifying Unexpected Neurotoxicity Drivers with Acetylcholinesterase Inhibition by Virtual Effect-Directed Analysis in Nationwide Estuarine Waters

Neurotoxicity is frequently observed in the global aquatic environment, threatening aquatic ecosystems and human health. However, a very limited proportion of neurotoxic effects (~1%) has been explained by known chemicals of concern. Here, we integrated machine learning, nontargeted analysis, and in vitro biotesting to identify neurotoxic drivers of acetylcholinesterase (AChE) inhibition in estuarine waters along the coastline of China. Machine learning was used as a virtual fractionation tool to reduce the complexity of chemical mixtures, thus guiding nontargeted screening of AChE inhibitors. Ultimately, sixty chemicals with diverse known and presently unknown structures were identified, explaining 82.1% of the observed AChE inhibition in estuarine water samples. Polyunsaturated fatty acids were unexpectedly found to be neurotoxic drivers, accounting for 80.5% of the overall effect. This proof-of-concept study demonstrates that our approach enables rapid and comprehensive screening of causative organic pollutants associated with various in vitro endpoints for large-scale monitoring of water quality.

opencc-by-4.0Dec 2012View details →

Fig. 6 in Effect of abiotic variables on fish eggs and larvae distribution in headwaters of Cuiabá River, Mato Grosso State, Brazil

Fig. 6. Temporal (a) and spatial (b) frequency of occurrence of the seven most abundant taxa of fish larvae captured in the headwaters of the Cuiabá River between November 2007 and March 2008.

opencc-by-4.0Dec 2012View details →

Fig. 2 in Effect of abiotic variables on fish eggs and larvae distribution in headwaters of Cuiabá River, Mato Grosso State, Brazil

Fig. 2. Temporal (a) and spatial (b) distribution of density (individuals/10m3) of fish eggs and larvae captured in the headwaters of the Cuiabá River, in all the collection sites, between November 2007 and March 2008.