Find research datasets worth reusing

opencc-by-4.0Jun 2024View details →

Equilibrium chemical composition of impact-produced hot cloud during isentropic expansion. The initial temperature T0 is 4000 K, the initial pressure P0 is 5, 20, and 80 bar. Calculations are performed using the EQL program. Abundances of considered species are presented in molar fractions.The elemental composition of impact-produced cloud is taken as a mixture of CI chondrite, mare basalts, and ferroan anorthosite with a ratio of 1:25:25 by mass as in Berezhnoy (2013).

Considered species include ions, neutral gas-phase species, and condensates. Ions are written as ...(+) (for example, Al(+)). Condensates (solids and liquids) are written as ...(c) or ...(c;...). Examples of condensates are Al2O3(c) and Al2O3(c; gamma). For species marked in theirs names as (cr, l) in Gurvich et al. (1989) (for example, Al2O3(cr, l)) it is possible to determine a state of matter (liquid or solid). The content of studied species is 0 if the relative molar fraction is less than 1e-21.  The elemental composition of impact-produced cloud is taken as a mixture of CI chondrite, mare basalts, and ferroan anorthosite with a ratio of 1:25:25 by mass as in Berezhnoy (2013).   Calculations of the equilibrium chemical composition of impact-produced clouds were performed starting from an initial temperature of 4000 K at different initial pressures of 5, 20, and 80 bar, corresponding to entropies equal to 7.2, 5.56, and 4.25 kJ / (kg×K), respectively.  Berezhnoy, A.A., 2013. Chemistry of impact events on the Moon. Icarus 226, 205-211. Gurvich L.V., Veitz I.V. et al. Thermodynamic properties of individual substances. Fourth edition in 5 volumes. Hemisphere Pub Co. New York-London, 1989.

opencc-by-4.0Jul 2024View details →

Data and code for "Tree species abundance changes at the edges of their climatic distribution: an interplay between climate change, plant traits, and forest management"

## Secondary data and code to accompany the research entitled "Tree species abundance changes at the edges of their climatic distribution: an interplay between climate change, plant traits, and forest management" by Padullés Cubino et al. (2024). # There are four folders with (1) "raw data", (2) "processed data", (3) "results", and (4) "scripts". # The raw and processed data folders contain the CSV and XLSX files with all the data used for analysis and produced from them # The "results" folder contains the figures and table presented in the manuscript. # The "scripts" folder contains four scripts for the analyses described in the manuscript:    01_preparation_ClimEdge.R -> data cleaning and processing    02_script_Fig1.R -> code to produce Fig1    03_script_Fig2.R -> code to produce Fig2    04_script_Table1_Fig3.R -> code to produce Table 1 and Fig3 # If anything is unclear, please contact the corresponding author for clarification (padullesj@gmail.com).

opennotspecifiedSep 2013View details →

Fig. 5 a –d Diversity measures calculated for the replicates from Stations 325 and 346. a S Total species numbers, N abundance, Z in Community structure and species diversity of Harpacticoida (Crustacea: Copepoda) at two sites in the deep sea of the Angola Basin (Southeast Atlantic)

Fig. 5 a –d Diversity measures calculated for the replicates from Stations 325 and 346. a S Total species numbers, N abundance, Z Median, Min. minimum, Max. maximum, Q 1 quartile 1 (25 % of all measured data

opencc-by-4.0Dec 2025View details →

Relative abundance tables for bacterial species, pathways, ARGs, and VFGs in "Gut Microbial Community Structure, Metabolic Signature, and Resistome in Dyslipidemia: Insights from Metagenomic Sequencing"

Dyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. In this study, we analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and resistome in 1384 participants (895 with dyslipidemia cases and 489 controls) using shotgun metagenomic sequencing. Our results revealed that Bacteroides caccae was enriched in dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism, while Coprococcus eutactus and Coprococcus catus, known producers of short-chain fatty acids (SCFAs) in lipid regulation, and Blautia obeum, known to be positively impacted by SCFAs, were more abundant in controls. We also identified an enrichment of the dTDP-beta-D-fucofuranose biosynthesis pathway gene family, which is linked to bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris contributing strongly. Dyslipidemia cases exhibited depleted glycogen and peptidoglycan biosynthesis pathways, potentially impairing energy storage and immune function, alongside distinct metabolic profiles, including decreased pseudouridine, which may affect RNA metabolism. Furthermore, we observed a higher abundance of antibiotic-resistance genes, particularly tetQ, in dyslipidemia cases, suggesting a link between gut resistome and metabolic disorders. These findings provide new insights into how dysbiosis of the gut microbiota may contribute to the pathophysiology of dyslipidemia, offering potential avenues for microbiome-based interventions in personalized medicine.

opencc-zeroDec 2012View details →

Data from: Environmental factors influence both abundance and genetic diversity in a widespread bird species

Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations.

opencc-zeroDec 2017View details →

Data from: Which species, how many, and from where: Integrating habitat suitability, population genomics, and abundance estimates into species reintroduction planning

Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multi-species approaches. We used an interdisciplinary, multi-species, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple-criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species-habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information-based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field.

opencc-zeroAug 2021View details →

Cannot see the diversity for all the species: evaluating inclusion criteria for local species lists when using abundant citizen science data

Abundant citizen science data on species occurrences is becoming increasingly available and enables identifying composition of communities occurring at multiple sites with high temporal resolution. However, for species displaying temporary patterns of local occurrences, i.e. that are transient to some sites, biodiversity measures are clearly dependent on the criteria used to include species into local species lists. Using abundant opportunistic citizen science data from frequently visited wetlands we investigated the sensitivity of α- and β-diversity estimates to the use raw vs. detection-corrected data and to the use of inclusion criteria for species presence reflecting alternative site use. We tested 7 inclusion criteria (with varying number of days required to be present) on time series of daily occurrence status during a breeding season of 90 days for 77 wetland bird species. We show that even when opportunistic presence-only observation data is abundant, raw data may not produce reliable local species richness estimates and rank sites very differently in terms of species richness. Furthermore, occupancy model based - and - diversity estimates were sensitive to the inclusion criteria used. Total species lists (all species observed at least once during a season) may therefore mask diversity differences among sites in local communities of species, by e.g. including vagrant species on potentially breeding communities and change the relative rank order of sites in terms of species richness. Very high sampling effort does not necessarily free opportunistic data from its inherent bias and can produce a pattern in which many species are observed at least once almost everywhere, thus leading to a possible paradox: the large amount of biological information may hinder its usefulness. Therefore, when prioritizing among sites to manage or preserve species diversity estimates need to be carefully related to relevant inclusion criteria depending on the diversity estimate in focus.

opencc-zeroJul 2022View details →

Long-term changes in occurrence, relative abundance, and reproductive fitness of bat species in relation to arrival of White-nose Syndrome in West Virginia, USA

White-nose syndrome (WNS) is a disease caused by the fungus Pseudogymnoascus destructans which has resulted in the deaths of millions of bats across eastern North America. To date, hibernacula counts have been the predominant means of tracking the spread and impact of this disease on bat populations. However, an understanding of the impacts of WNS on demographic parameters outside the winter season is critical to conservation and recovery of bat populations impacted by this disease. We used long-term monitoring data to examine WNS-related impacts to summer populations in West Virginia, where WNS has been documented since 2009. Using capture data from 290 mist-net sites surveyed from 2003–2019 on the Monongahela National Forest, we estimated temporal patterns in presence and relative abundance for each bat species. For species that exhibited a population-level response to WNS, we investigated post-WNS changes in adult female reproductive state and body mass. Myotis lucifugus (little brown bat), M. septentrionalis (northern long-eared bat), and Perimyotis subflavus (tri-colored bat) all showed significant decreases in presence and relative abundance during and following the introduction of WNS, while Eptesicus fuscus (big brown bat) and Lasiurus borealis (eastern red bat) responded positively during the WNS invasion. Probability of being reproductively active was not significantly different for any species, though a shift to earlier reproduction was estimated for E. fuscus and M. septentrionalis. For some species, body mass appeared to be influenced by the WNS invasion, but the response differed by species and reproductive state. Results suggest that continued long-term monitoring studies, additional research into impacts of this disease on the fitness of WNS survivors, and a focus on providing optimal non-wintering habitat may be valuable strategies for assessing and promoting recovery of WNS-affected bat populations.

Figure 1 in Abundance variations and life history traits of two sympatric species of Neotropical annual fish (Cyprinodontiformes: Rivulidae) in temporary ponds of southern Brazil

Figure 1. Map of South America and location of the Lagoa do Peixe National Park (LPNP) and study sites sampled in southern Brazil in 2008 and 2009.

Figure 4 in Abundance variations and life history traits of two sympatric species of Neotropical annual fish (Cyprinodontiformes: Rivulidae) in temporary ponds of southern Brazil

Figure 4. Sex ratio for Austrolebias minuano (A) and Cynopoecilus fulgens (B) sampling in temporary ponds of Lagoa do Peixe National Park, southern Brazil, in 2008 and 2009.

Figure 5 in Abundance variations and life history traits of two sympatric species of Neotropical annual fish (Cyprinodontiformes: Rivulidae) in temporary ponds of southern Brazil

Figure 5. Length–weight relationship for Austrolebias minuano (A) and Cynopoecilus fulgens (B) sampled in temporary ponds of Lagoa do Peixe National Park, southern Brazil, in 2008 and 2009.

Figure 6 in Abundance variations and life history traits of two sympatric species of Neotropical annual fish (Cyprinodontiformes: Rivulidae) in temporary ponds of southern Brazil

Figure 6. Condition factor (K) ± SE of Austrolebias minuano (A) and Cynopoecilus fulgens (B) sampled in temporary ponds of Lagoa do Peixe National Park, southern Brazil, in 2008 and 2009.

Figure 2 in Abundance variations and life history traits of two sympatric species of Neotropical annual fish (Cyprinodontiformes: Rivulidae) in temporary ponds of southern Brazil

Figure 2. Mean abundances ± SE of Austrolebias minuano (A) and Cynopoecilus fulgens (B) sampled in temporary ponds of Lagoa do Peixe National Park, southern Brazil, in 2008 and 2009.

Figure 3 in Abundance variations and life history traits of two sympatric species of Neotropical annual fish (Cyprinodontiformes: Rivulidae) in temporary ponds of southern Brazil

Figure 3. Mean standard length (LS) ± SE of Austrolebias minuano (A) and Cynopoecilus fulgens (B) sampled in temporary ponds of Lagoa do Peixe National Park, southern Brazil, in 2008 and 2009.

opencc-zeroAug 2021View details →

Vegetation changes from private forestland management can increase species richness and abundance

Conservation efforts on private lands are important for biodiversity conservation. On private lands in South Carolina, forestry management practices (prescribed burning, thinning, herbicide application) are used to improve upland pine habitat for wildlife and timber harvest and are incentivized through United States Department of Agriculture Farm Bill cost-share programs. Because many forest-dependent bird species have habitat requirements created primarily through forest management, data are needed on the effectiveness of these management activities. We studied privately-owned loblolly pine (Pinus taeda) stands in the South Carolina Piedmont region. Our objective was to understand how management practices influence avian species richness and abundance at local (forest stand) and landscape levels in relatively small stands (average ~28 hectares). We surveyed 49 forest stands during two bird breeding seasons with traditional point counts and vegetation surveys. We evaluated the effects of management on pine stand characteristics, avian species richness, and abundance of state-designated bird species of concern. Repeated burning and thinning shifted stand conditions to open pine woodlands with reduced basal area and herbaceous understories. Stands with lower basal area supported greater avian species richness. Some species increased in abundance in response to active management (e.g., Brown-headed Nuthatch, Sitta pusilla, and Indigo Bunting, Passerina cyanea), but relationships varied. Some species responded positively to increases in forest quantity at a landscape scale (1–5 km, e.g., Northern Bobwhite, Colinus virginianus). We found species-rich avian communities and species of conservation concern on working timber lands, indicating that incentivized forest management on private lands can provide valuable habitat for wildlife.

opennotspecifiedNov 2008View details →

Figure 3 in Seasonality and abundance of Metamasius callizona (Coleoptera: Dryophthoridae), an invasive insect herbivore, on two species of Tillandsia (Bromeliaceae) in Florida

Figure 3. Average monthly values (¡ two standard errors) for: (A) rainfall (cm); (B) lowest temperature (°C); (C) health ratings for Tillandsia fasciculata; and (D) health ratings for Tillandsia utriculata.

opennotspecifiedNov 2008View details →

Figure 4 in Seasonality and abundance of Metamasius callizona (Coleoptera: Dryophthoridae), an invasive insect herbivore, on two species of Tillandsia (Bromeliaceae) in Florida

Figure 4. The average weevil count per fallout (wc:fo) per month (¡ two standard errors) for: (A) T. fasciculata; and (B) T. utriculata from June 2001 to June 2005. Note: The weevil count was the number of living weevil adults and living or dead weevil larvae and pupae found in fallout.

opennotspecifiedMar 2003View details →

F in Host plant utilization and population abundance of three tropical species of Cassidinae (Coleoptera: Chrysomelidae)

F. 2. Population abundance of Stolas chalybea, S. areolata and Anacassis phaeopoda at different life stages at Serra do Japi, SP.

opennotspecifiedMar 2003View details →

F in Host plant utilization and population abundance of three tropical species of Cassidinae (Coleoptera: Chrysomelidae)

F. 1. Climatic diagram of Jundiaí (where Serra do Japi is located), in São Paulo state, during the years 1997 and 1998 (according to Walter and Lieth, 1960). Original data were collected in a station at 715 m and temperature data were corrected to 1170 m (data provided by Instituto Agronômico de Campinas). Dotted region represents dry periods and dark region represents super-humid periods.