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376 results for “contemporary”
Chamaecrista fasciculata Survival and Biomass in Response to Microbe Stress History and Contemporary Stress, 2018-2019
This dataset includes Chamaecrista fasciculata biomass and survival data collected as part of a greenhouse experiment that took place at Indiana University in 2018. Rhizosphere soil was collected from Chamaecrista fasciculata plants at the end of a field experiment in which plants were treated with four stress treatments: salt, herbicide, herbivory, and no stress. These field soils were used to inoculate a greenhouse experiment in which Chamaecrista fasciculata individuals from 50 manternal families were treated with these same four stress treatments in a full factorial design (4 microbe histories x 4 contemporary stress environments), plus a sterile microbial control treatment. We measured the days to first flower, noted when plants never flowered (i.e., did not survive to flower), and measured aboveground biomass.
Contemporary phenotypic change in plant quantitative traits
<p>This is a new version of the Gorné & Díaz 2017 database (doi:10.5281/zenodo.580095). We cheked the categorization of each case, fixed of some mistakes. Also, we disambiguated the trait type moderator and add a new (mean based) measure of change.</p> <p>This database included studies that provide data of changes in quantitative traits of angiosperms within a known temporal framework (<300 years). The search was performed by Scopus (www.scopus.com), up to 22 December 2015 (search strings in Gorné and Díaz 2017). The database includes studies that measured intraspecific change in a quantitative trait and which report the elapsed time when the phenotypic change occurred. The studies recorded a single population before and after a change in the environment or compared two (or more) populations by measuring a quantitative trait across two situations, where one of them was a new condition of known age. Both, by measuring change directly in the field or by performing common condition experiments (e.g. common garden experiments or reciprocal transplants). Studies reporting results from artificial selection or interspecific hybridization were excluded. The environmental changes included expansions of distributional range, soil or air pollution, exposure to herbicides, changes in salinity, pH, climate, disturbance or irrigation regime, and addition or loss of species in the local community. All data available in each study were recorded, including several observations of the same species. These procedures resulted in a database containing 1716 observations from 128 studies, with changes in populations of 152 species from 34 families, in elapsed times of < 260 years, and covering a wide range of traits, lifespan, growth forms and environmental situations.</p> <p>All data points were categorized according to biological properties of the study system (lifespan, growth form, trait type) and methodological ones. The amount and rate of phenotypic change is expresed as the standardized mean difference Hedges <em>g</em> (Hedges 1981, 1982), a rate of change which is the Hedges <em>g</em> over the elapsed time in years, and the log-transformation of both of them. The standardized mean difference is equal to the <em>haldane</em> numerator, which is a standard rate of evolution (Haldane 1949; Gingerich 1993). In addition, we upgraded the Díaz and Gorné (2017) database, computing the response ratio effect size (<em>logRR</em>) (Hedges et al. 1999) whenever possible. The response ratio is a mean-scaled metric equal to the <em>darwins</em> numerator (Haldane 1949). So that we compute a rate of change similar to <em>darwins</em> (time expressed as years instead of million years).</p> <p> </p> <p>contact email address: gorneld@gmail.com</p>
Data and code: A Comparison of Contemporary versus Older Studies of Aspirin for Primary Prevention
<p>Data (comma-separated values format) and analytical code (Stata format) relating to: Moriarty F, Ebell MH. A Comparison of Contemporary versus Older Studies of Aspirin for Primary Prevention. 2019 (under review). Available on medRxiv at https://doi.org/10.1101/19004267</p> <p><em><strong>Abstract</strong></em></p> <p><strong>Purpose</strong>: This study compares the benefits and harms of aspirin for primary prevention before and after widespread use of statins and colorectal cancer screening.</p> <p><strong>Methods: </strong>We compared studies of aspirin for primary prevention that recruited patients from 2005 onward with previous individual patient meta-analyses that recruited patients from 1978 to 2002. Data for contemporary studies were synthesized using random-effects models. We report vascular (major adverse cardiovascular events [MACE], myocardial infarction [MI], stroke), bleeding, cancer, and mortality outcomes.</p> <p><strong>Results</strong>: The IPD analyses of older studies included 95,456 patients for CV prevention and 25,270 for cancer mortality, while the four newer studies had 61,604 patients. Relative risks for vascular outcomes for older vs newer studies follow: MACE: 0.89 (95% CI 0.83-0.95) vs 0.93 (0.86-0.99); fatal hemorrhagic stroke: 1.73 (1.11-2.72) vs 1.06 (0.66-1.70); any ischemic stroke: 0.86 (0.74-1.00) vs 0.86 (0.75-0.98); any MI: 0.84 (0.77-0.92) vs 0.88 (0.77-1.00); and non-fatal MI: 0.79 (0.71-0.88) vs 0.94 (0.83-1.08). Cancer death was not significantly decreased in newer studies (RR 1.11, 0.92-1.34). Major hemorrhage was significantly increased for both older and newer studies (RR 1.48, 95% CI 1.25-1.76 vs 1.37, 95% CI 1.24-1.53). There was no effect in either group on all-cause mortality, cardiovascular mortality, fatal stroke, or fatal MI.</p> <p><strong>Conclusions</strong>: In the modern era characterized by widespread statin use and cancer screening, aspirin does not reduce the risk of non-fatal MI or cancer death. There are no mortality benefits and a significant risk of major hemorrhage. Aspirin should no longer be recommended for primary prevention.</p> <p> </p> <p>Version 1.1 - Updated Stata code to correct name of .csv data file for import.</p>
Ensemble projections (+ uncertainties) of contemporary (2012-2031) and future (2081-2100) mean annual plankton/phytoplankton/zooplankton species diversity (and species turn-over in time) for the global surface open ocean.
<p><em><strong>Gridded spatial fields (raster objects) containing the species distribution models (SDMs) projections of mean annual plankton total plankton, phytoplankton and zooplankton species diversity from Benedetti et al. (2021). </strong></em></p> <p>The present .grd file ('rasterStack' object in R) contain the fields of mean annual surface plankton/phytoplankton/zooplankton species diversity for the contemporary (2012-2031) and future (2081-2100) conditions of the global open ocean (i.e., data underlying those maps in Figure 1 and Figure 3 of Benedetti et al., 2021). Layers quantifying the uncertainty (i.e., the variablity across models projections estimated through the standard deviation) in ensemble projections were also added (i.e., data underlying the maps in Supplementary Figure 4). See the Methods section of Benedetti et al. (2021) for a full description of the methodology and the ensemble SDMs forecasting framework. The raster layers follow the 1°x1° cell grid of the World Ocean Atlas (https://www.ncei.noaa.gov/).</p> <p>In short, we empirically modelled the monthly and mean annual diversity patterns stemming from the distribution of 860 plankton species (336 phytoplankton, 524 zooplankton) spanning 13 phyla, 71 orders and 324 genera through an ensemble approach based on SDMs. The considered species cover a wide range of traits and functions, representing 10 major plankton functional groups (PFGs; three phytoplankton and seven zooplankton groups). We compiled the species occurrence records from various data sources (available here: https://zenodo.org/record/5101349#.YO7Dqm469lM) and aggregated them onto a monthly-resolved 1°x1° grid, excluding observations from regions where the seafloor is shallower than 200 m. We matched these binned open ocean records with observation-based climatologies of environmental predictors (temperature, dissolved oxygen concentration, solar irradiance, macronutrients concentration, chlorophyll a concentration) that reflect the climatic and biogeochemical conditions of the surface open ocean. Four types of SDMs (generalized linear models, generalized additive models, artificial neural networks, and random forests) were fitted to model the species’ current environmental habitat suitability patterns. For each SDMs, we used four alternative pools of predictors. Assuming niche conservatism, we projected each of the 16 resulting species-level habitat suitability models into the future using outputs from five ESMs belonging to the Coupled Model Intercomparison Project 5 (CMIP5) that were forced by the Representative Concentration Pathway 8.5 (RCP8.5) scenario of high greenhouse gas concentrations. To this end, we first computed the modelled monthly climatologies of the selected predictors for the 2012-2031 and 2081-2100 periods, and derive the future monthly anomalies from the differences between these two time periods. These anomalies were added to the observation-based monthly climatologies (i.e., those used to train the SDMs) to estimate the future environmental conditions of the ocean, and projected the SDMs in these future conditions. Finally, we estimated the mean annual present and future alpha diversity (species richness; SR) and beta diversity (species turnover through time) patterns for both trophic levels, for each cell, from the ensemble of SDMs. SR ensembles are estimated as the sum of all species’ habitat suitability patterns averaged across all 80 possible combinations (i.e., "ensemble members") of SDMs (n = 4), ESMs (n = 5) and predictor pools (n = 4). To assess the uncertainties of our diversity projections based on the ensemble members, we compute the interquartile range of the 80 ensemble members SR projections. We calculate species turnover as the change in mean annual species composition between present and future time based on Jaccard’s dissimilarity index and by decomposing this total turnover into the true species turnover (ST, also known as species replacement) and the nestedness (SR change) components. Numerous tests are conducted to ensure the robustness of the results with regard to the spatially and temporally highly uneven sampling effort as well as with regard to the relative role of different predictors.</p> <p><strong>This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862923. This output reflects only the author’s view, and the European Union cannot be held responsible for any use that may be made of the information contained therein.</strong></p>
Information Needs in Contemporary Code Review - Appendix
<p>Contemporary code review is a widespread practice used by software engineers to maintain high software quality and share project knowledge. However, conducting proper code review takes time and developers often have limited time for review. In this paper, we aim at investigating the information that reviewers need to conduct a proper code review, to better understand this process and how research and tool support can make developers become more effective and efficient reviewers. Previous work has provided evidence that a successful code review process is one in which reviewers and authors actively participate and collaborate. In these cases, the threads of discussions that are saved by code review tools are a precious source of information that can be later exploited for research and practice. In this paper, we focus on this source of information as a way to gather reliable data on the aforementioned reviewers’ needs. We manually analyze 900 code review comments from three large open-source projects and organize them in categories by means of a card sort. Our results highlight the presence of seven high-level information needs, such as knowing the uses of methods and variables declared/modified in the code under review. Based on these results we suggest ways in which future code review tools can better support collaboration and the reviewing task. Appendix material.</p>
Data from: Contemporary and future distributions of cobia, Rachycentron canadum
<p><b>Aim:</b> Climate change has influenced the distribution and phenology of marine species, globally. However, knowledge of the impacts of climate change are lacking for many species that support valuable recreational fisheries. Cobia (<i>Rachycentron canadum</i>) are the target of an important recreational fishery along the U.S. east coast that is currently the subject of a management controversy regarding allocation and stock structure. Further, the current and probable future distributions of this migratory species are unclear, further complicating decision-making. The objectives of this study are to better define the contemporary distribution of cobia along the U.S. east coast and to project potential shifts in distribution and phenology under future climate change scenarios.</p> <p><b>Location:</b> Chesapeake Bay and the U.S. east coast.</p> <p><b>Methods:</b> We developed a depth-integrated habitat suitability model using archival tagging data from cobia that were caught and tagged in Chesapeake Bay during summer months and coupled those data with high-resolution ocean models to project the contemporary and future distributions of cobia along U.S. east coast.</p> <p><b>Results:</b> During the winter months, suitable cobia habitat currently occurs in offshore waters off North Carolina and further south, whereas during the summer months, suitable habitat occurs in waters from Florida to southern New England. In warmer years, the availability of suitable habitat increases in northern latitudes. Under continued climate change over the next 40-80 years, suitable habitat is projected to shift northward and decrease over the shelf.</p> <p><b>Main conclusions:</b> Habitat distributions suggest cobia overwinter offshore and could inhabit waters further north during warmer months, into state jurisdictions that do not have strict management regulations for cobia. When waters are warmer, distributions are projected to shift poleward and seasonal migrations may begin earlier. These results can inform resource allocation discussions between fishery managers and resource users.</p>
FIG. 2 in The skull on the hill. Anthropological and osteological investigation of contemporary horse skull ritual practices in central Mongolia (Arkhangai province)
FIG. 2. —, Distribution of the ovoos surveyed north of the Tamir River;, ovoos on which horse skulls were found;, winter encampments of the Bayantsagaan herders. Three linked figures, Sambuu's encampments (winter, spring, and summer)., Sambuu's ovoo, located just slightly higher than his winter encampment. Shaded area, summer encampments of the Bayantsagaan herders (data, C. Marchina, S. Lepetz & C. Salicis; map, S. Lepetz, based on the background map of the Musée d'Anthropologie préhistorique of Monaco, F. Burle).
FIG. 4. — A, B in The skull on the hill. Anthropological and osteological investigation of contemporary horse skull ritual practices in central Mongolia (Arkhangai province)
FIG. 4. — A, B, Skulls of three animals (one calf and two horses) placed in a tree; C, one horse skull taken down from the tree for the purposes of the picture, clearly showing a circular mark of ante-mortem stunning on the forehead.
FIG. 13 in The skull on the hill. Anthropological and osteological investigation of contemporary horse skull ritual practices in central Mongolia (Arkhangai province)
FIG. 13. — Number of horse skulls per age group (in years) and sex, on Sambuu's ovoo. While sex distribution is even, we can see that most of the slaughtered animals are either young (less than four years old) or old. The method used to determine the animals' age is based on the analysis of dental eruption and the degree of wear (Cornevin & Lesbre 1894; Lepetz 2013).
FIG. 6 in The skull on the hill. Anthropological and osteological investigation of contemporary horse skull ritual practices in central Mongolia (Arkhangai province)
FIG. 6. — Stones placed in the skull's cavities: A, skulls located west of the archaeological structure; B, stones inserted between the temporal cavity and the zygomatic arch.
FIG. 9 in The skull on the hill. Anthropological and osteological investigation of contemporary horse skull ritual practices in central Mongolia (Arkhangai province)
FIG. 9. — Repository of metallic items and various animal bones on the central mound of a khirigsuur.
Wordlist of contemporary Kathmandu Newari
<p>Ulrike Kolver prepared this word list in conjunction with her work on the following dictionary.</p> <p> Kolver, Ulrike, and Iswarananda Shresthacarya. 1994. A Dictionary of Contemporary Newari, Newari-English. Bonn: VGH</p>
Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics (Dataset)
<p>Complete dataset of <em>Clock</em> and <em>Adcyap1</em> alleles, distance matrices, and migration data used in the review and meta-analysis "<strong>Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics".</strong> </p>
Figure 6 in The death adder Acanthophis antarcticus (Shaw & Nodder, 1802) in Victoria: historical records and contemporary uncertainty
Figure 6. Ventral view of the head scales of Death Adder specimens from Melbourne Museum, and close up of Gerard Krefft's illustration of the ventral head scales of the Death Adder collected at Lake Boga in 1857 (bottom right). Top left is specimen D3579. Top right is D51857. Bottom left is D4349.
Figure 1 in The death adder Acanthophis antarcticus (Shaw & Nodder, 1802) in Victoria: historical records and contemporary uncertainty
Figure 1. South-eastern Australia, showing records of the death adder Acanthophis antarcticus (black dots; Atlas of Living Australia, year) and key localities discussed in the text.
Figure 2. Specimen D4349, a in The death adder Acanthophis antarcticus (Shaw & Nodder, 1802) in Victoria: historical records and contemporary uncertainty
Figure 2. Specimen D4349, a death adder Acanthophis antarcticus in the collection of Museums Victoria.
Figure 5 in The death adder Acanthophis antarcticus (Shaw & Nodder, 1802) in Victoria: historical records and contemporary uncertainty
Figure 5. Illustration by Gerard Krefft of the death adder collected at Lake Boga in north-western Victoria on the 8 March 1857. (Photograph by Rebecca Carland; Museum of Natural History Berlin. Historical collection of pictures and writings. [Sigel: MfN, HBSB.] Bestand: Zool. Mus. Signatur: B VIII/56.)
Climate and habitat type interact to influence contemporary dispersal potential in Prairie Smoke (Geum triflorum)
<p>Understanding dispersal potential, or the probability a species will move a given distance, under different environmental conditions is essential to predicting species' ability to move across the landscape and track shifting ecological niches. Two important drivers of dispersal ability are climatic differences and variation in local habitat type. Despite the likelihood these global drivers act simultaneously on plant populations, and thus dispersal potential is likely to change as a result, their combined effects on dispersal are rarely examined. To understand the effect of climate and varying habitat types on dispersal potential, we studied <em>Geum triflorum</em> - a perennial grassland species that spans a wide range of environments, including both prairie and alvar habitats. We explored how the climate of the growing season and habitat type (prairie vs alvar) interact to alter dispersal potential. We found a consistent interactive effect of climate and habitat type on dispersal potential. Across prairie populations, an increased number of growing degree days favored traits that increase dispersal potential, or the probability of dispersing farther distances. However, for alvar populations, dispersal potential tended to decrease as the number of growing degree days increase. Our findings suggest that under continued warming, populations in prairie habitats will benefit from increased gene flow, while alvar populations will become increasingly segregated, with reduced potential to track shifting fitness optima.</p>
The excess of cool supergiants from contemporary stellar evolution models defies the metallicity-independent Humphreys-Davidson limit
<p>Input files and simulation results for stellar evolution tracks computed for the paper "The excess of cool supergiants from contemporary stellar evolution models defies the metallicity-independent Humphreys-Davidson limit", as well as synthetic populations generated and catalogues of observed cool supergiants in the Magellanic Clouds used in the analysis. Version 10398 of MESA was used for the simulations. More details in the README.txt file and in the paper.</p>
Global contemporary effective population sizes across taxonomic groups
<p>Effective population size (<em>N<sub>e</sub></em>) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum <em>N<sub>e</sub> </em>of 50 and 500 to avoid short-term inbreeding and to preserve long-term adaptive potential, respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between <em>N<sub>e</sub></em><sub> </sub>and human activities. Through a quantitative review, we generated a dataset with 4610 georeferenced <em>N<sub>e</sub></em> estimates from 3829 unique populations, extracted from 723 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal, and amphibian populations had a <54% probability of reaching = 50 and a <9% probability of reaching = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller median than unlisted populations, and this was consistent across all taxonomic groups. was reduced in areas with a greater Global Human Footprint, especially for amphibians, birds, and mammals, however relationships varied between taxa. We also highlight several considerations for future works, including the role that gene flow and subpopulation structure plays in the estimation of in wild populations, and the need for finer-scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on <em>N<sub>e</sub></em> and help prioritize assessment of populations from taxa most at risk of failing to meet conservation thresholds.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.