Find research datasets worth reusing

opencc-zeroNov 2020View details →

Combining seascape connectivity with cumulative impact assessment in support of ecosystem-based marine spatial planning

1. Cumulative impact assessment (CIA) is a promising approach to guide marine spatial planning (MSP) and management. One limitation of CIA is the neglect of seascape connectivity, which may spread the impact of localised pressures to ambient areas, e.g. through lost dispersal and recruitment of organisms. 2. We here, for the first time, incorporate seascape connectivity into a traditional CIA model using a connectivity matrix, exemplified by dispersal of propagules estimated through biophysical modelling. Two connectivity impactsare identified: the source impact represents downstream areas losing recruits because of reduced larval dispersal from sites affected by the pressure, and the sink impact represents loss of recruits originating from upstream areas prevented from settlement in the site affected by the local pressure. 3. By including seascape connectivity into the Swedish MSP-guiding CIA tool Symphony we demonstrate how to practically account for remote effects of local environmental impact. Our example on blue mussel shows how reducing mussel fitness in a given area may have impacts on mussels far from the acting pressures. Overall, results indicate that connectivity impact for blue mussels plays a minor role in most areas, less than 10% of the ordinary cumulative impact. However, in some smaller areas, e.g. on offshore banks and the Danish Straits, seascape connectivity may increase ordinary cumulative impact with 20-30%. In an example of scenario-based CIA analyses of MSP projections, we demonstrate how impacts of particular management actions, e.g. shipping rerouting and wind power developments, can be tracked far from the original area of influence. 4. Depending on the dispersal ability of ecosystem components, a local pressure may impact a considerable area through seascape connectivity, transgressing management units and national borders. Although the mean connectivity impact may be modest for a single ecosystem component, the consideration of seascape connectivity across multiple ecosystem components may significantly alter the mapping of cumulative impact and the assessment of different MSP scenarios. 5. Synthesis and applications. Our extension of Cumulative Impact Assessment offers a new method for mapping and practically integrating seascape connectivity with ecosystem-based MSP and other spatial instruments for policy making, such as marine protected areas.

Assessing seasonal demographic covariation to understand environmental-change impacts on a hibernating mammal

Natural populations are exposed to seasonal variation in environmental factors that simultaneously affect several demographic rates (survival, development, reproduction). The resulting covariation in these rates determines population dynamics, but accounting for its numerous biotic and abiotic drivers is a significant challenge. Here, we use a factor-analytic approach to capture partially unobserved drivers of seasonal population dynamics. We use 40 years of individual-based demography from yellow-bellied marmots (Marmota flaviventer) to fit and project population models that account for seasonal demographic covariation using a latent variable. We show that this latent variable, by producing positive covariation among winter demographic rates, depicts a measure of environmental quality. Simultaneous, negative responses of winter survival and reproductive-status change to declining environmental quality result in a higher risk of population quasi-extinction, regardless of summer demography where recruitment takes place. We demonstrate how complex environmental processes can be summarized to understand population persistence in seasonal environments.

Data from: Impact of a recolonizing, cross-border carnivore population on ungulate harvest in Scandinavia

Predation from large carnivores and human harvest are the two main mortality factors affecting the dynamics of many ungulate populations. We examined long-term moose (Alces alces) harvest data from two countries that share cross-border populations of wolves (Canis lupus) and their main prey moose. We tested how a spatial gradient of increasing wolf territory density affected moose harvest density and age and sex composition of the harvested animals (n = 549,310), along a latitudinal gradient during 1995-2017. In areas containing average-sized wolf territories, harvest density was on average 37% (Norway) and 51% (Sweden) lower than in areas without wolves. In Sweden, calves made up a higher proportion of the moose harvest than in Norway, and this proportion was reduced with increased wolf territory density, while it increased in Norway. The proportion of females in the adult harvest was more strongly reduced in Sweden than in Norway as a response to increased wolf territory density. Moose management in both countries performed actions aimed to increase productivity in the moose population, in order to compensate for the increased mortality caused by wolves. These management actions are empirical examples of an adaptive management in response to the return of large carnivores.

opencc-by-4.0Sep 2020View details →

Life Cycle Environmental Impact of Houston METRO System – Evaluation of Electric Alternatives

In the Greater Houston Area, mobile sources (on- and off-road vehicles) contribute the highest share of nitrogen oxide (NOx) emissions and second-highest share of volatile organic (VOC) emissions. The Houston METRO system is a key element in Houston's infrastructure that can be expanded to lower emissions of criteria air pollutants (CAPs) and greenhouse gases (GHGs) and improve regional air quality. Currently, there is no comparative study for relative emissions and environmental impacts between passenger automobiles and METRO routes in Houston. Our research addressed this critical gap and developed environmental life cycle assessment for conventional diesel buses, diesel hybrid buses, and alternative electric buses in Houston using the GREET model. The life cycle GHG emissions of electric buses are slightly lower than the other two types of buses. However, all the other major emissions such as CO, NOx, PM10, PM2.5, VOCs, SOx, N2O, CH4, black carbon and primary organic carbon associated with electric buses are higher than diesel buses, thus causing higher environmental cost of electric buses than diesel buses. The life cycle costs of buses are very sensitive to future diesel and electricity prices. The results from this project would serve as a guiding framework to evaluate the effects of the decision to expand the METRO system and estimate the contribution of the METRO system in realizing the Greater Houston Area's environmental objectives.

The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.)

Model-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP dataset involving North American box turtles (Terrapene spp.). Our filtering strategies included: (A) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (=none), and (B) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (=none). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discord can seriously impact M-L-classification.

Impacts of speciation and extinction measured by an evolutionary decay clock

The hypothesis that destructive mass extinctions enable creative evolutionary radiations (creative destruction) is central to classic concepts of macroevolution[1,2]. However, the relative impacts of extinction and radiation on the co-occurrence of species have not been directly quantitatively compared across the Phanerozoic eon. Here we apply machine learning to generate a spatial embedding (multidimensional ordination) of the temporal co-occurrence structure of the Phanerozoic fossil record, covering 1,273,254 occurrences in the Paleobiology Database for 171,231 embedded species. This facilitates simultaneous comparison of macroevolutionary disruptions, using measures independent of secular diversity trends. Among the 5% most significant periods of disruption, we identify the 'big five' mass extinction events[2], seven additional mass extinctions, two combined mass extinction–radiation events and 15 mass radiations. In contrast to narratives that emphasize post-extinction radiations[1,3], we find that the proportionally most comparable mass radiations and extinctions (such as the Cambrian explosion and the end-Permian mass extinction) are typically decoupled in time, refuting any direct causal relationship between them. Moreover, in addition to extinctions[4], evolutionary radiations themselves cause evolutionary decay (modelled co-occurrence probability and shared fraction of species between times approaching zero), a concept that we describe as destructive creation. A direct test of the time to over-threshold macroevolutionary decay[4] (shared fraction of species between two times ≤ 0.1), counted by the decay clock, reveals saw-toothed fluctuations around a Phanerozoic mean of 18.6 million years. As the Quaternary period began at a below-average decay-clock time of 11 million years, modern extinctions further increase life's decay-clock debt.

Supplementary material for: Exploring the impact of unstable terminals on branch support values in paleontological data

The dataset consists of a PDF file and two plain-text TNT scripts (*.run files). The PDF includes supporting Figures for the additional analyses conducted by Flores et al. on paleontological datasets. The TNT scripts conduct two complementary sets of analyses: (a) evaluation of taxon instability relative to the incompleteness ("mc.run"), and (b) changes in branch support values after pruning unstable taxa ("avmc.run"). To properly run these files in TNT, the name of the matrix files should be given as arguments (see the TNT documentation webpage for details on the usage of script files). The scripts generate CSV-formatted output for being subsequently read into any other software. Script files are provided as "ready-for-use", and are freely distributable and modifiable. We request that you cite the respective paper and dataset.

Data used in: "Impacts of predator-mediated interactions along a climatic gradient on the population dynamics of an alpine bird"

Data for: Impacts of predator-mediated interactions along a climatic gradient on the population dynamics of an alpine bird doi: 10.1098/rspb.2020.2653 Diana E. Bowler, Mikkel A. J. Kvasnes, Hans C. Pedersen, Brett K. Sandercock, Erlend B. Nilsen Questions to: diana.e.bowler@gmail.com or erlend.nilsen@nina.no

Data from: Biogeography and anthropogenic impact shape the success of invasive wasps on New Zealand's offshore islands

Aim The theory of island biogeography predicts that the susceptibility of an island to invasion is determined by its isolation and size. However, many island ecosystems have been intensely modified by humans. Here, we investigated the biogeographic, biotic and anthropogenic drivers of invasive social wasps on 36 offshore islands. Location Islands off the east coast of New Zealand's North Island. Taxa Vespula germanica (Fabricius, 1793), Vespula vulgaris (Linnaeus, 1758) and Polistes chinensis antennalis (Fabricius, 1793), Polistes humilis (Fabricius, 1781). Methods We used GIS software for in situ randomisation of plots on each island (36 islands, 409 plots) and conducted 5-minute wasp counts to estimate wasp abundance. Wasp abundance and canopy cover were recorded at each plot. Island isolation was measured using GIS software. Data on island size, human settlement and the presence of introduced rats (Rattus spp.) were collated from the literature and island managers. The number of boat docks per island was counted from satellite images. A generalised linear mixed effect model (GLMM) was fitted to identify drivers of Vespula and Polistes abundance on offshore islands. Results The abundance of Vespula was negatively correlated with island isolation and canopy cover, yet positively correlated with island size. Vespula were also more abundant on islands that have been settled by humans. The abundance of Polistes was negatively correlated with canopy cover. Finally, results did not support the notion that invasive wasps were associated with introduced rats on New Zealand's offshore islands. Conclusions Our findings highlight the importance of biogeographic factors, such as island size and isolation, for species invasions, and suggest that intact forest cover could contribute to biotic resistance to invasive wasps in island ecosystems. Studies of invasive species should consider the joint effects of biogeographic, biotic and anthropogenic factors to best inform conservation management.ealand's North Island.

Data from: Impacts of habitat on butterfly dispersal in tropical forests, parks and grassland patches embedded in an urban landscape

Dispersal distances of 17 species of butterflies in tropical Singapore were significantly greater in forest than in urban habitat. Butterflies in urban plots frequently moved within suitable habitat (park/grassland) patches but rarely crossed non-habitat patches suggesting potential isolation and a need for urban corridors.

Data from: Impact of cognitive tasks on CO2 and isoprene emissions from humans

The human body emits a wide range of chemicals, including CO2 and isoprene. To examine the impact of cognitive tasks on human emission rates of CO2 and isoprene, we conducted an across subjects, counterbalanced study in a controlled chamber involving 16 adults. The chamber replicated an office environment. In groups of four, participants engaged in 30 minutes each of cognitive tasks (stressed activity) and watching nature documentaries (relaxed activity). Measured biomarkers indicated higher stress levels were achieved during the stressed activity. Per-person CO2 emission rates were greater for stressed than relaxed activity (30.3 ± 2.1 vs. 27.0 ± 1.7 g/h/p, p = 0.0044, mean ± standard deviation). Isoprene emission rates were also elevated under stressed vs. relaxed activity (154 ± 25 µg/h/p vs. 116 ± 20 µg/h/p, p = 0.041). Chamber temperature was held constant at 26.2 ± 0.49 ◦C; incidental variation in temperature did not explain variance in emission rates. Isoprene emission rates increased linearly with salivary-alpha amylase levels (r2 = 0.6, p = 0.02). These results imply the possibility of considering cognitive tasks when determining building ventilation rates. They also present the possibility of monitoring indicators of cognitive tasks of occupants through measurement of air quality.

In vivo transcriptome of Lactobacillus acidophilus and colonization impact on murine host intestinal gene expression

Lactobacillus acidophilus NCFM is a probiotic strain commonly used in dairy products and dietary supplements. Post-genome in vitro studies of NCFM thus far have linked potential key genotypes to its probiotic-relevant attributes including gut survival, prebiotic utilization, host interactions and immunomodulatory activities. To corroborate and extend beyond previous in vivo and in vitro functional studies, we employed a dual RNA-seq transcriptomic approach to identify genes potentially driving the gut fitness and activities of L. acidophilus NCFM in vivo, and in parallel, examine the ileal transcriptional response of its murine hosts during monocolonization. Spatial expression profiling of NCFM from the ileum through the colon revealed a set of 134 core genes that were consistently overexpressed during gut transit. These in vivo core genes are predominantly involved in the metabolism of carbohydrates, amino acids and nucleotides, along with mucus-binding proteins and adhesion factors, confirming their functionally important roles in nutrient acquisition and gut retention. Functional characterization of the highly expressed major S-layer encoding gene established its indispensable role as a cell shape determinant and maintenance of cell surface integrity, essential for viability and probiotic attributes. Host colonization by L. acidophilus resulted in significant down-regulation of several pro-inflammatory cytokines and tight junction proteins. Genes related to redox signaling, mucin glycosylation and circadian rhythm modulation were induced, suggesting impacts on intestinal development and immune functions. Metagenomic analysis of NCFM populations post-colonization demonstrated the genomic stability of L. acidophilus as a gut transient and further established its safety as a probiotic and biotherapeutic delivery platform.

opencc-by-4.0Sep 2020View details →

On The Impact of 22Ne On The Pulsation Periods of Carbon-Oxygen White Dwarfs With Helium Dominated Atmospheres

This file contains the python scripts needed to re-produce figures 2-11 in our paper.  It also contains the information to re-run our 22Ne tests and other WD mass models.  The README.md file contains a more detailed description of the data.

Data from: Differing impacts of two major plant invaders on urban plant-dwelling spiders (Araneae) during flowering season

The dataset contains spider (Araneae) specimen numbers collected from flowering invasive American goldenrod (Solidago canadensis/gigantea) and invasive Himalayan balsam (Impatiens glandulifera) stands occuring naturally in urban areas of the city of Karlsruhe, Germany. Corresponding plots with native ruderalized vegetation in direct vicinity of each invaded plot were used as a comparison plot, resulting in a fully paired design for each plant invader study. An additional column represents potential non-araneae prey items collected together with the spiders from each stand. Spider specimens were determined to the family level as well as classified into web builders and hunters without a web.

opencc-zeroJan 2021View details →

The impact of the program for medical male circumcision on HIV in South Africa: analysis using three epidemiological models

Background: South Africa began offering medical male circumcision (MMC) in 2010. We evaluated the current and future impact of this program to see if it is effective in preventing new HIV infections. Methods: The Thembisa, Goals and EMOD HIV transmission models were calibrated to South Africa's HIV epidemic, fitting to household survey data on HIV prevalence, risk behaviors, and proportions of men circumcised, and to programmatic data on intervention roll-out including program-reported MMCs over 2009-2017. We compared the actual program accomplishments through 2017 and program targets through 2021 with a counterfactual scenario of no MMC program. Results: The MMC program averted 71,000-83,000 new HIV infections from 2010 to 2017. The future benefit of the circumcision already conducted will grow to 496,000-518,000 infections (6-7% of all new infections) by 2030. If program targets are met by 2021 the benefits will increase to 723,000-760,000 infections averted by 2030. The cost would be $1,070-1,220 per infection averted relative to no MMC. The savings from averted treatment needs would become larger than the costs of the MMC program around 2034-2039. In the Thembisa model, when modelling South Africa's 9 provinces individually, the 9-provinces-aggregate results were similar to those of the single national model. Across provinces, projected long-term impacts were largest in Free State, KwaZulu-Natal and Mpumalanga (23-27% reduction over 2017-2030), reflecting these provinces' greater MMC scale-up. Conclusions: MMC has already had a modest impact on HIV incidence in South Africa and can substantially impact South Africa's HIV epidemic in the coming years.

opencc-zeroJan 2021View details →

Data from: The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: a global meta-analysis

Human activities are primarily responsible for habitat loss and changes in natural environments around the world. It has been suggested that populations inhabiting human-modified landscapes are subject to reduced gene flow, inbreeding depression, and loss of alleles due to genetic drift. However, empirical evidence shows contradictory effects of anthropogenic disturbances on the genetic diversity of terrestrial species. We performed a meta-analysis of 61 studies that compared the genetic diversity of plant and/or animal populations in disturbed and preserved areas (317 paired comparisons) to investigate general responses to different disturbance type. We found significant negative effects of disturbance on genetic diversity (effect size: -0.45), in which the loss of structural connectivity was the most detrimental disturbance type. The choice of the genetic parameter has an influence on the detection of the effect (direction and magnitude), and consequently the studies using number of effective alleles did not detect genetic erosion, while all other indices, especially allelic richness, revealed negative responses to disturbances. Yet, only studies performed with transferred or both transferred and specific microsatellites showed negative responses to disturbances. The general effect was more detrimental in animal than plant populations. Only plant species with biotic pollination and seed dispersal mode, self-incompatible reproductive system, and shrubs showed negative responses to disturbances. Despite all heterogeneity among studies, we found an overall negative effect of disturbance on genetic diversity of terrestrial populations, which suggests that the remaining populations inhabiting anthropogenic landscapes have a reduced evolutionary potential being more prone to local extinction.

opencc-by-4.0Jan 2021View details →

Impact of targetted health education and sensitization of family caregivers upon treatment maintenance and satisfaction among completely edentulous patients suffering from elder abuse and neglect

the following is the raw and coded data associated with the research

opencc-by-4.0Dec 2020View details →

The impact of Solar wind variability on pulsar timing

Timing models, ToA files and DM time series (UTC_start_date, UTC_center_date, MJD, DMvariation, DMvariation_error, SolarElongation) used in the article "The impact of Solar wind variability on pulsar timing" (published in A&A, part of the Veni project SOLTRAC, 016.Veni.192.086)

opencc-zeroJan 2021View details →

Synergistic impacts of aggressive species on small birds in a fragmented landscape

1. Attempts to conserve threatened species in fragmented landscapes are often challenging because factors such as habitat loss, habitat degradation and dominant species interact to reduce threatened species' capacity to survive and reproduce. Understanding how threatening and mitigating processes interact is critical if conservation measures are to be effective. 2. We used data from long-term monitoring of bird populations and multivariate latent variable models to quantify how Australian woodland birds respond to the presence of the Noisy Miner, a despotic species known to exclude other bird species. We then investigated the extent to which the presence of other aggressive species exacerbates the impacts of the Noisy Miner, and to what extent these impacts can be mitigated by dense midstorey plantings. 3. We found strong synergies between the Noisy Miner and two other aggressive species (Grey Butcherbird and Pied Butcherbird), despite weak effects of butcherbirds in isolation. 4. The impacts of aggressive birds are most pronounced for small-bodied species; but these impacts are lessened in the presence of high midstorey cover. 5. Synthesis and applications. Accounting for interactions reveals that revegetation may be capable of improving conservation outcomes even when the proximate cause of species declines (i.e. exclusion or predation by aggressive bird species) cannot be managed directly.