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Data in the analysis of Comparative Study of the Impact of Dummy Variables on Regression Coefficients and Canonical Correlation Indices: an Empirical perspective

This data is used in the analysis related to the article Comparative Study of the Impact of Dummy Variables on Regression Coefficients and Canonical Correlation Indices: an Empirical perspective. The data contain Crude Oil Prices, Exchange Rates, and Dummy variables coded 1 for the era before the Covid-19 outbreak and 0 for the era of Covid-19.

opencc-zeroJan 2021View details →

Relative impacts of gypsy moth outbreaks and insecticide treatments on forest resources and ecosystem: An experimental approach

Gypsy moth outbreaks cause severe defoliation in Holarctic forests, both in North America where it is invasive, and in its native range in Eurasia. Severe defoliation can hamper timber production and impact ecological communities and processes. Aerial insecticide applications are regularly performed in outbreak areas to mitigate economic losses. These operations can be financially costly and harmful to non-target species and may disrupt species interaction networks. However, replicated studies of the relative impacts of gypsy moth outbreaks and insecticide application on forest growth and animal communities are rare and have yet to be carried out in the species' indigenous range. Here, we review the pathways in which gypsy moth outbreaks and the chemical control of these outbreaks affect forest ecosystems. We then present an experimental design established in South Central Germany in early 2019, aiming to study the ecological and economic consequences of gypsy moth eruptions and insecticide application in oak forests. The study's full factorial design comprises forest stands with high and low defoliation risk, either treated with tebufenozide or left unsprayed, within 12 experimental blocks. Measurements of forest growth and structure, tree mortality, gypsy moth density, and composition of lepidopteran, bird, bat, ground beetle, and canopy arthropod communities will be conducted for several years. One-year intensive monitoring of gypsy moth populations and damage across the selected sites showed substantial differences in population density between plots with high and low defoliation risk and high efficacy of tebufenozide in suppressing gypsy moth populations in treated plots. In the first year of the experiment, gypsy moth density and defoliation in predicted outbreak plots differed strongly, confirming the importance of using many replicates and blocking to control spatial heterogeneity. The experiment will be running continuously during the coming years to produce short- and medium-term economic and ecological data to improve our understanding and management of gypsy moth outbreaks.

opencc-zeroJan 2021View details →

Natural toxic impact and thyroid signaling interplay orchestrates riverine adaptive divergence of salmonid fish

Abstract 1. Adaptive radiation in fishes has been actively investigated over the last decades. Along with numerous well-studied cases of lacustrine radiation, some examples of riverine sympatric divergence have been recently discovered. In contrast to the lakes, the riverine conditions do not provide evident stability in the ecological gradients. Consequently, external factors triggering the radiation, as well as developmental mechanisms underpinning it, remain unclear. 2. Herein, we present the comprehensive study of external and internal drivers of the riverine adaptive divergence of the salmonid fish Salvelinus malma. In the Kamchatka River, N-E Asia, this species splits in the reproductively isolated morphs that drastically differ in ecology and morphology: the benthivorous Dolly Varden (DV) and the piscivorous Stone charr (SC). 3. To understand why and how these morphs originated, we performed a series of field and experimental work, including common-garden rearing, comparative ontogenetic, physiological and endocrinological analyses, hormonal "engineering" of phenotypes, and acute toxicological tests. 4. We revealed that the type of spawning ground acts as the main external factor driving the radiation of S. malma. In contrast to DV spawning in the leaf krummholz zone, SC reproduces in the zone of coniferous forest, which litter has a toxic impact on developing fishes. SC enhances resistance to the toxicants via metabolism acceleration provided by the elevated thyroid hormone content. These physiological changes lead to the multiple heterochronies resulting in a specific morphology and SC's expansion into a piscivorous niche. 5. Salvelinus malma represents a notable example of how the thyroid axis contributes to the generation of diverse phenotypic outcomes underlying the riverine sympatric divergence. Our findings, along with the paleoecology data concerning spruce forest distribution during the Pleistocene, provide an opportunity to reconstruct a scenario of S. malma divergence. Taken together, obtained results with the data of the role of thyroid hormones in the ontogeny and diversification of fishes contribute a resource to consider the thyroid axis as a prime director orchestrating the phenotypic plasticity promoting evolutionary diversification under the changing environmental conditions. 06-Jan-2021

opencc-zeroJan 2021View details →

Impact of Helicoverpa zea salivary GOX on stomatal conductance and volatile emission of host plants

This data set contain raw data associated with the manuscript titled "Silencing the alarm: An insect salivary enzyme closes plant stomata and inhibits volatile release". Herbivore-induced plant volatiles (HIPVs) are widely recognized as ecologically important to plant. While the majority of studies focused on the induction of this "cry for help", little is known about whether insect herbivores have evolved mechanisms to reduce the release of HIPVs. Here we show that a caterpillar (Helicoverpa zea) salivary enzyme, glucose oxidase (GOX), commonly secreted on plant leaves causes stomatal closure and reductions in emissions of several HIPVs involved in plant defenses. We found that application of GOX to wounded regions of leaves led to reductions in stomatal conductance on tomato (Solanum lycopersicum) and soybean (Glycine max) for at least two days. The role of GOX in reducing stomatal aperture was confirmed using GOX knockout lines of H. zea (CRISPR-Cas9 mutagenesis), and microscopic observations of stomata. In addition, GOX reduced the emission of several HIPVs during feeding by H. zea, including (Z)-3-hexenol, (Z)-jasmone, and (Z)-3-hexenyl acetate, which are important air borne signals in plant defenses. Our findings highlight a novel mechanism where insect herbivore reduces the release of HIPVs during feeding by targeting fundamental plant structure (i.e. stomata), and the link between of stomatal dynamics and releases of HIPVs. We demonstrate the existence of HIPVs-interfering mechanisms as a potential evolutionary strategy for insect herbivores to interfere with plant air borne signals.

Impact of Different Nesting Methods on the Simulation of a Severe Convective Event Over South Korea Using the Weather Research and Forecasting Model

The data from various platforms (NCEP FNL, TRMM, ERA5, AWS) and WRF Model output utilised to generate the figures in the current study (https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020JD033084) are available at this Zenodo data repository.

Data for "Impacts of ozone-vegetation interactions on ozone pollution episodes in North China and the Yangtze River Delta"

Data for "Impacts of ozone-vegetation interactions on ozone pollution episodes in North China and the Yangtze River Delta"

The Impact of Tool Configuration Spaces on the Evaluation of Configurable Taint Analysis for Android

The data accompanying our ISSTA'2021 submission, Rethinking Android Taint Analysis Evaluations: A Study of the Impact of Tool Configuration Spaces   Structure: results: contains the raw results output by AQL for the runs on Fossdroid and Google Play. Note that we wrote DroidBench results directly to CSV, so there are no "raw" results for them. Instead, see the summaries package. The collection of APKs for both datasets are also in this package. summaries: contains CSV summaries of the three replications of our experiments on all three datasets (including examples of Amandroid's nondetermism on non-default configurations). datasets: contains our FossDroid classified results and justifications. Please see the README.md in that package for more information. diagrams: contains the graphs detailing the FlowDroid and DroidSafe configuration spaces, including their partial orders and disablement relationships. violations: contains the records of violations of our partial orders.

opencc-by-4.0Dec 2020View details →

The Impacts of Sentiments and Tones in Community-Generated Issue Discussions

The dataset, data analysis code, and complete results accompanying the paper published in CHASE2021, titled The Impacts of Sentiments and Tones in Community-Generated Issue Discussions.

opencc-by-4.0Feb 2021View details →

Impact of Clean Energy on CO2 Emissions and Economic Growth within the Phases of Renewables Diffusion in Selected European Countries

This study explores the impact of clean energy and non-renewable energy consumption on CO2 emissions and economic growth within two phases (formative and expansion) of renewable energy diffusion for three selected countries (France, Spain, and Sweden). The vector autoregression (VAR) model is estimated on the basis of annual data disaggregated into quarterly data. The Granger causality results reveal distinctive differences in the causality patterns across countries and two phases of renewables diffusion. Clean energy consumption contributes to a decline of emissions more clearly in the expansion phase in France and Spain. However, this effect seems to be counteracted by the increases in emissions due to economic growth and non-renewable energy consumption. Therefore, clean energy consumption has not yet led to a decoupling of economic growth from emissions in France and Spain; in contrast, the findings for Sweden evidence such a decoupling due to the neutrality between economic growth and emissions. Generally, the findings show that despite the enormous growth of renewables and active mitigation policies, CO2 emissions have not substantially decreased in selected countries or globally. Focused and coordinated policy action, not only at the EU level but also globally, is urgently needed to overhaul existing fossil-fuel economies into low-carbon economies and ultimately meet the relevant climate targets.

Data from: Ocean acidification impacts spine integrity but not regenerative capacity of spines and tube feet in adult sea urchins

Increasing atmospheric carbon dioxide (CO2) has resulted in a change in seawater chemistry and lowering of pH, referred to as ocean acidification. Understanding how different organisms and processes respond to ocean acidification is vital to predict how marine ecosystems will be altered under future scenarios of continued environmental change. Regenerative processes involving biomineralization in marine calcifiers such as sea urchins are predicted to be especially vulnerable. In this study, the effect of ocean acidification on regeneration of external appendages (spines and tube feet) was investigated in the sea urchin Lytechinus variegatus exposed to ambient (546 µatm), intermediate (1027 µatm) and high (1841 µatm) partial pressure of CO2 (pCO2) for eight weeks. The rate of regeneration was maintained in spines and tube feet throughout two periods of amputation and regrowth under conditions of elevated pCO2. Increased expression of several biomineralization-related genes indicated molecular compensatory mechanisms; however, the structural integrity of both regenerating and homeostatic spines was compromised in high pCO2 conditions. Indicators of physiological fitness (righting response, growth rate, coelomocyte concentration and composition) were not affected by increasing pCO2, but compromised spine integrity is likely to have negative consequences for defence capabilities and therefore survival of these ecologically and economically important organisms.

opencc-zeroJan 2020View details →

Data for: The impacts of bioenergy pine plantation management practices on bee communities

1. Cultivation of bioenergy feedstocks is a growing land-use worldwide, yet we have a poor understanding of how bioenergy crop management practices affect biodiversity. This knowledge gap is particularly acute for candidate cellulosic bioenergy feedstocks, such as tree plantations, and for organisms that provide important ecosystem services, such as pollinators. 2. We examined bee communities in 83 sites across three states in the southeastern USA—Alabama, Florida and Georgia. We compared bee abundance and diversity in 66 pine plantation sites that reflect management with and without potential bioenergy feedstock production. At least three bioenergy feedstock production methods have been proposed for this region: 1) converting conventional timber stands to short-rotation bioenergy plantations; 2) harvesting feedstock by thinning conventional plantations; and 3) harvesting of woody debris residues after plantations have been clear-cut. 3. We found that bioenergy-associated management practices including younger plantations (relative to older) and woody debris removal (relative to debris unremoved) in clear-cut plantations were associated with reduced bee diversity. Removing ground debris in clear-cut plantations also drastically increased bee abundance, though this effect was largely driven by strong dominance of just two bee species. Clear-cut plantations had lower beta diversity than standing plantations. 4. Synthesis and applications. Management practices associated with bioenergy feedstock production can have negative effects on bee community diversity. In particular, harvesting of debris in clear-cut plantations dramatically reduces bee diversity. Large-scale bioenergy feedstock production that increases the prevalence of young and clear-cut stands may cause landscape-level beta diversity to decline. Nevertheless, bioenergy pine plantations likely support higher bee diversity than corn fields, an alternative bioenergy feedstock.

opencc-zeroDec 2017View details →

Data from: Selection past impacts the strength of an aquatic trophic cascade

1. In complex food webs, interactions among species in different trophic levels can generate cascading indirect effects that couple top predators with primary producers, thereby affecting ecosystem functioning. Natural selection imposed by top predators on intermediate predators may play a role in shaping the strength of these trophic cascades, but this conjecture remains largely untested. 2. To determine the effects of natural selection on the strength of trophic cascades we conducted a two-part experiment in a four-level aquatic trophic system involving a top predator (fish), an intermediate predator (damselflies), herbivores (zooplankton), and primary producers (algae). We first quantified how predation by fish generated selection on damselfly activity levels after controlling for phenotypic plasticity. We then measured the indirect effects of this selection on primary production (phytoplankton biomass). In both experiments we varied the density of predators, allowing us to elucidate both trait-mediated and density-mediated indirect effects. 3. We found that as fish density increased, damselfly survivorship declined, which generated natural selection favoring less active damselflies. These results are robust after taking into account latent effects of plasticity in response to fish predator cues. The surviving damselflies likely foraged less, freeing herbivores from predation, which in turn reduced primary production. This selection driven trait-mediated indirect effect was only apparent at low damselfly densities, because the consumptive effect of damselflies at high densities overwhelmed the effects of past selection. 4. These results demonstrate that the past action of natural selection can affect the strength of a trophic cascade. Natural selection can therefore act as a mechanism coupling ecological dynamics across trophic levels, which ultimately influences ecosystem functioning.

opencc-zeroOct 2019View details →

Data from: Hare pseudo-reference genome from: the genomic impact of historical hybridization with massive mitochondrial DNA introgression

Background: The extent to which selection determines interspecific patterns of genetic exchanges enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA. Results: Although the average nuclear and mtDNA introgression patterns are strongly contrasted, they fit a single neutral model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X-chromosome and in low recombining regions. Conclusion: General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.

opencc-zeroDec 2017View details →

Data from: Impact of involvement of non-formal health providers on TB case notification among migrant slum-dwelling populations in Odisha, India

Background: Migrant labourers living in the slums of urban and industrial patches across India make up a key sub-population so far controlling Tuberculosis (TB) in the country is concerned. This is because many TB patients from these communities remain under reached by the Revised National Tuberculosis Control Programme (RNTCP) of India. This marginalized community usually seeks early-stage healthcare from "friendly neighbourhood" non-formal health providers (NFHPs). Because, RNTCP has limited capacity to involve the NFHPs, an implementation research project was conceived, whereby an external partner would engage with the NFHPs to enable them to identify early TB symptomatics from this key sub-population who would be then tested using Xpert MTB/RIF technology. Diagnosed TB cases among them would be referred promptly to RNTCP for treatment. This paper aimed to describe the project and its impact. Methods: Adopting a quasi-experimental before-after design, four RNTCP units from two major urban-industrial areas of Odisha were selected for intervention, which spanned five quarters and covered 151,400 people, of which 30% were slum-dwelling migrants. Two similar units comprised the control population. The hypothesis was, reaching the under reached in the intervention area through NFHPs would increase TB notification from these traditionally under-notifying units. RNTCP notification data during intervention was compared with pre-intervention era, adjusted for contemporaneous changes in control population. Results: The project detected 488 Xpert+ TB cases, of whom 466 were administered RNTCP treatment. This translated into notification of additional 198 new bacteriologically positive cases to RNTCP, a 30% notification surge, after adjustment for 2% decline in control. This meant an average quarterly increase in notification of 41.20(20.08, 62.31; p<0.001) cases. The increase was immediate, evident from the rise in level in the time series analysis by 50.42(10.28, 90.55; p=0.02) cases. Conclusion: Engagement with NFHPs contributed to an increase in TB notification to RNTCP from key under reached, slum-dwelling migrant populations.

opencc-zeroDec 2020View details →

Impact of cellulose-rich organic soil amendments on growth dynamics and pathogenicity of Rhizoctonia solani

Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable substrate for R. solani, whereas its performance on wood sawdusts varied with tree species. In two pot experiments, the effects of amendment of R. solani-infected soil with cellulose-rich materials on performance of beetroot seedlings were tested. All deciduous sawdusts and paper pulp stimulated soil fungal biomass, but only oak, elder and beech sawdusts reduced damping-off of beetroot. Oak sawdust amendment gave a consistent stimulation of saprotrophic Sordariomycetes fungi and of seedling performance, independently of the time between amendment and sowing. In contrast, paper pulp caused a short-term increase in R. solani abundance, coinciding with increased disease severity for beet seedlings sown immediately after amendment. However, damping-off of beetroot was reduced if plants were sown two or four weeks after paper pulp amendment. Cellulolytic bacteria, including Cytophagaceae, responded to paper pulp during the first two weeks and may have counteracted further spread of R. solani. The results showed that fungus-stimulating, cellulose-rich amendments have potential to be used for suppression of R. solani. However, such amendments require a careful consideration of material choice and application strategy.

opencc-zeroJan 2020View details →

Synergistic impacts of co-occurring invasive grasses cause persistent effects in the soil-plant system after selective removal

1. Human influence on the environment is so extensive that virtually all ecosystems on the planet are now affected by biological invasions. And, often, ecosystems are invaded by multiple co-occurring non-native species. Hence, it is important to understand the impacts these invasions are producing on biodiversity and ecosystem processes. 2. Here, we present results of a two-year long field experiment where we tested the effects of co-occurring invasive C4 African grasses in a Cerrado area in central Brazil. We compared plant and arthropod communities, plant biomass, and soil nitrogen dynamics and soil chemical characteristics across five experimental treatments: Urochloa decumbens removal, Melinis minutiflora removal, both U. decumbens, and M. minutiflora removal, U. decumbens and M. minutiflora invaded plots, and uninvaded Cerrado. We hypothesized that selective removal of invasive grasses would have distinct effects on the native ecosystem structure and functioning. We expected that each invasive grass would produce a different type of impact on the native ecosystem and that their impacts would be synergistic when co-occurring. 3. Removal of M. minutiflora doubled native plant diversity and biomass when compared to invaded plots, whereas removal of U. decumbens did not alter these parameters. Cerrado plots had four times more plant species than plots cleared of invasives. Removal of invasive grasses did not affect the species richness or community composition of soil epigeal fauna. Cerrado soils had lower fertility, organic matter content, and pH than invaded soils. The effects were generally higher when both invasive grasses were removed, suggesting impacts were synergistic, but M. minutiflora had greater effects on plants and soils than U. decumbens. Both invasive species produced negative impacts, but a single species was the main driver. We also detected persistent effects of the invasive grass species on the ecosystem after two years of removal. 4. We conclude that invasive species of the same functional group have similar types of effects in native ecosystems, but the magnitude of impact was largely dependent on invasive species biomass and cover. Where multiple invasive species are present, research and management of invaded ecosystems should tackle the interacting effects of co-occurring invaders.

Data from: Origins of the Greenland shark (Somniosus microcephalus): impacts of ice-olation and introgression

Herein, we use genetic data from 277 sleeper sharks to perform coalescent-based modeling to test the hypothesis of early Quaternary emergence of the Greenland shark (Somniosus microcephalus) from ancestral sleeper sharks in the Canadian Arctic-Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus pacificus can be genetically distinguished using combined mitochondrial and nuclear DNA markers. Our data confirm the presence of genetically admixed individuals in the Canadian Arctic and sub-Arctic, and temperate Eastern Atlantic regions, suggesting introgressive hybridization upon secondary contact following the initial species divergence. Conservative substitution rates fitted to an Isolation with Migration (IM) model indicate a likely species divergence time of 2.34 Ma, using the mitochondrial sequence DNA, which in conjunction with the geographic distribution of admixtures and Pacific signatures likely indicates speciation associated with processes other than the closing of the Isthmus of Panama. This time span coincides with further planetary cooling in the early Quaternary period followed by the onset of oscillating glacial-interglacial cycles. We propose that the initial S. microcephalus–S. pacificus split, and subsequent hybridization events, were likely associated with the onset of Pleistocene glacial oscillations, whereby fluctuating sea levels constrained connectivity among Arctic oceanic basins, Arctic marginal seas, and the North Atlantic Ocean. Our data demonstrates support for the evolutionary consequences of oscillatory vicariance via transient oceanic isolation with subsequent secondary contact associated with fluctuating sea levels throughout the Quaternary period—which may serve as a model for the origins of Arctic marine fauna on a broad taxonomic scale.

Data from: Do impacts of an invasive nitrogen-fixing shrub on Douglas-fir and its ectomycorrhizal mutualism change over time following invasion?

1. Impacts of invasive species may change in magnitude and even direction with invasion age. Impacts could increase as the population increases, individuals grow in size, and ecological changes accumulate. 2. We used a chronosequence approach to characterize the development of soil impacts over time following the invasion of Cytisus scoparius, a widespread nitrogen-fixing shrub thought to limit reforestation success. In a greenhouse experiment, we evaluated how abundance of ectomycorrhizal fungi, Douglas-fir performance, and leaf nitrogen changed across a 3-31 year chronosequence of invasion. Each of the chronosequence sites were clearcuts where reforestation efforts were unsuccessful and where C. scoparius invaded. To estimate the contributions of the invasion separately from contributions of the accompanying disturbance, i.e. deforestation, we included soils from both invaded and uninvaded patches in each site of the chronosequence. In a complementary soil conditioning experiment, we examined the separate effects of host absence and invader presence on the mycorrhizal mutualism, leaf nitrogen, and seedling growth. 3. Ectomycorrhizal colonization was lower in invaded soil, but this effect did not intensify with time. Despite the suppression of the mutualism, Douglas-fir grew larger in invaded soils. This positive response is likely due to nitrogen fertilization, a conclusion supported by higher concentrations of leaf nitrogen of Douglas-fir grown in invaded soils. While leaf N concentration increased with invasion duration, Douglas-fir survival and growth did not. Synthesis. Our findings suggest that soil impacts of an invader can develop rapidly and can be surprisingly stable over time. In such systems, recently invaded areas may be as difficult to restore as long invaded areas, especially where ectomycorrhizal fungi are important drivers of reforestation success. More chronosequence studies or long time series are needed to evaluate whether this is a general pattern.

Data from: Malagasy cichlids differentially limit impacts of body shape evolution on oral jaw functional morphology

Patterns of trait covariation, like integration and modularity, are vital factors that influence the evolution of vertebrate body plans. In functional systems, decoupling of morphological modules buffers functional change in one trait by reducing correlated variation with another. However, for complex morphologies with many-to-one mapping of form to function (MTOM), resistance to functional change may also be achieved by constraining morphological variation within a functionally stable region of morphospace. For this research, we used geometric morphometrics to evaluate the evolution of body shape and its relationship to jaw functional morphology in two independent radiations of endemic Malagasy cichlid (Teleostei: Cichlidae). Our results suggested that the two subfamilies used different strategies to mitigate impacts of body shape variation on a metric of jaw function, maxillary kinematic transmission (MKT): (1) modularity between cranial and postcranial morphologies, and (2) integration of body and jaw evolution, with jaw morphologies varying in a manner that limits change in MKT. This research shows that, unlike modularity, MTOM allows traits to retain strong evolutionary covariation while still reducing impacts on functionality. These results suggest that MTOM, and its influence on the evolution of correlated traits, is likely much more widespread than is currently understood.