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101 results for “levels of selection”
Global Human Settlement Layer per zoom-level 18 Quadtree tile for selected countries as Spatialite database with OpenStreetMap building completeness assessment
<p>This Spatialite database contains the built-up area of the Global Human Settlement Layer (GHSL) per zoom-level 18 Quadtree tile. Additionally, it provides a comparison of the GHSL with buildings in OpenStreetMap: For each tile the built-up ratio between the building footprints and the GHSL is given and a binary completeness assessment (buildings complete, not complete) is provided for easy use. This dataset was created using the obmgapanalysis tool: https://git.gfz-potsdam.de/dynamicexposure/openbuildingmap/obmgapanalysis</p>
3-hourly water level records (selected high flow events) for the River Garry at Invergarry (Inverness-shire), Scotland
<p>3-hourly records of stage (water level) for the River Garry at Invergarry (Inverness-shire), Gauge A2, for selected high-flow events 1936-1940. Extracts from a record spanning the period 1936-10-01 to 1944-09-30.</p> <p>Data collected by Capt. W. N. McClean via his organisation River Flow Records and with the assistance of local observers.</p> <p>We acknowledge the sponsorship of Scottish Hydro-Electric and the Scottish Environment Protection Agency in suporting the costs of creating digital time series.</p> <p>Subsequent to the colletion of these records, the River Garry was developed by the construction of dams and hydro power stations below Loch Quoich and Loch Garry.</p> <p>The Scottish Environment Protection Agency (SEPA) subsequently opened a river flow gauging station on the River Garry at Craigard in 1997, approximately 3 km upstream of McClean's gauge, operated until 2011.</p>
Accompnaying Dataset for: Chemical Heredity as Group Selection at the Molecular Level
<p>Accompnaying Dataset for: Chemical Heredity as Group Selection at the Molecular Level. File descriptions are provided in the Appendix of [Markovitch, Witkowski and Virgo; Chemical Heredity as Group Selection at the Molecular Level, arXiv (2018)] (https://arxiv.org/abs/1802.08024).</p>
Primary production estimates from 14C uptake (in situ), determined by the incorporation of inorganic carbon into particulate organic carbon (POC) due to photosynthesis at selected light levels from CCE LTER process cruises in the California Current System, 2006 - 2021 (ongoing).
Primary productivity samples of seawater are taken each day shortly before noon on the CTD rosette up-cast during the CCE Process crusies (since 2006, ongoing). Light penetration below the surface is estimated from the Secchi disk depth. Niskin bottles from depths with ambient light intensities corresponding to light levels simulated by on-deck incubators are identified and sampled. Primary production is estimated from 14C uptake using this simulated in situ technique (followed by filtering) by which the assimilation of dissolved inorganic carbon by phytoplankton yields a measure (in µg/L/day) of the rate of photosynthetic primary production (particulate organic carbon, POC) at selected light levels in the euphotic zone within the CCE study area.
Code and data for: Is habitat selection in the wild shaped by individual-level cognitive biases in orientation strategy?
<p>This repository is a companion to the manuscript "<em>Is habitat selection in the wild shaped by individual-level cognitive biases in orientation strategy?</em>" and is linked to <a href="https://github.com/CBeardsworth/Pheasant_OrientStrat_Habitat">Github</a>.</p> <p>For any questions about the code please contact Christine at <a href="mailto:c.e.beardsworth@gmail.com">c.e.beardsworth@gmail.com</a></p> <p>To use any data contained in this repository contact Joah at <a href="mailto:j.r.madden@exeter.ac.uk">j.r.madden@exeter.ac.uk</a> for permission.</p> <p>In this repository, we have included a run-through of the R analysis <a href="https://cbeardsworth.github.io/Pheasant_OrientStrat_Habitat/">here</a> to show the outputs of the analysis without the need to run the code. For those that might want to run the code themselves, we have included three R scripts (<a href="https://github.com/CBeardsworth/NavigationHabitat/blob/master/R">/R</a>) and their accompanying datasets (<a href="https://github.com/CBeardsworth/NavigationHabitat/blob/master/Data">/Data</a>). A description of the code and the data needed to run them is below:</p> <p><em>Cognition analysis and figs.R</em> = Run the cognition analysis for the first section of the manuscript and create the figures. For this, the datasets mazeData.csv (the learning trials) and mazeRotationResults.csv (the probe trial) are required. </p> <p><em>iSSA analysis and bootstrapping.R</em> = Run iSSA models and bootstrapping. This produces the datasets required for the next stage of analysis. For this code, the datasets habitat.grd (habitat information), atlas2018-strategy.csv (atlas data + id and strategy data for each bird) and FeederCoords2017_27700.csv (coordinates of feeder locations from 2017-2018) are required. The produced datasets are included in <a href="https://github.com/CBeardsworth/NavigationHabitat/blob/master/Data">/Data</a> therefore to run subsequent analyses, this code does not need to be run. To develop this code we relied heavily on the code included in the supplementary material of <a href="https://doi.org/10.1002/ece3.4823">Signer et al. (2019)</a> as well as an <a href="https://bsmity13.github.io/log_rss">online tutorial</a> from Brian J. Smith for calculating log-RSS.</p> <p><em>Habitat analysis and Figs.R</em> = Run the statistical models for the final section of the manuscript and create the figures. For this code, the datasets produced in the previous R script are required (habitatOrientation_coefs.csv and habitatOrientation_avail.csv). We have included <a href="https://github.com/CBeardsworth/NavigationHabitat/blob/master/Data">these datasets</a> so users do not need to run the iSSA analysis and bootstrapping.R script themselves. </p>
Are offspring begging levels exaggerated beyond the parental optimum? Evidence from a bidirectional selection experiment
Parental care involves elaborate behavioural interactions between parents and their offspring, with offspring stimulating their parents via begging to provision resources. Thus, begging has direct fitness benefits as it enhances offspring growth and survival. It is nevertheless subject to a complex evolutionary trajectory, because begging may serve as a means for the offspring to manipulate parents in the context of evolutionary conflicts of interest. Furthermore, it has been hypothesized that begging is coadapted and potentially genetically correlated with parental care traits as a result of social selection. Further experiments on the causal processes that shape the evolution of begging are therefore essential. We applied bidirectional artificial selection on begging behaviour, using canaries (Serinus canaria) as a model species. We measured the response to selection, the consequences for offspring development, changes in parental care traits, here the rate of parental provisioning, as well as the effects on reproductive success. After three generations of selection, offspring differed in begging behaviour according to our artificial selection regime: nestlings of the high begging line begged significantly more than nestlings of the low begging line. Intriguingly, begging less benefitted the nestlings, as reflected by on average significantly higher growth rates, and increased reproductive success in terms of a higher number of fledglings in the low selected line. Begging could thus represent an exaggerated trait, possibly because parent-offspring conflict enhanced the selection on begging. We did not find evidence that we co-selected on parental provisioning, which may be due to the lack of power, but may also suggest that the evolution of begging is probably not constrained by a genetic correlation between parental provisioning and offspring begging.
Code and data for Bayesian joint species distribution model selection for community-level prediction
<p>Code and data for reproducing the analysis in the manuscript "Bayesian joint species distribution model selection for community-level prediction." Provided data include percent cover observations for 39 modeled vascular plant species within boreal forest understory communities and environmental model covariates. R code is provided to generate model inputs, apply alternative models, generate out-of-sample predictions, and calculate associated community and species log scores and alternative model evaluation metrics. Further, R source code is provided to implement the multinomial joint species distribution model defined in the manuscript. Details on the data, its processing, and the alternative model definitions and structure can be found in the main text of the manuscript. Provided data are currently being used in ongoing analyses and coordination with authors may be warranted to avoid duplicate publication. Potential users are encouraged to consider collaboration with authors when useful and appropriate. Misinterpretation of data may occur if used outside the context of the original analysis. All data are made available in their current state. While significant efforts have been made to ensure data accuracy, complete accuracy cannot be guaranteed. Data may be updated periodically. It is the responsibility of the data user to check for updated versions of the data.</p>
Associated code and data for "Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization (doi: 10.3389/fcell.2021.74635)"
<p>This deposit contains the data, code, and analysis to reproduce the results in the manuscript - Lai X, Keller C, Santos-Rosales G, Schaft N, Dörrie J, Vera J. Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization. Frontiers in Cell and Developmental Biolology. 2022; 9:746359; <a href="https://www.researchgate.net/publication/358461035_Multi-Level_Computational_Modeling_of_Anti-Cancer_Dendritic_Cell_Vaccination_Utilized_to_Select_Molecular_Targets_for_Therapy_Optimization">doi:10.3389/fcell.2021.746359</a>.</p> <p>If you have used the code for your research, please cite the original publication. Thank you very much.</p> <p> </p>
Text-fig. 6. Stratigraphic and phylogenetic placement inferred for fossil Fraxinus fruits. Only Fraxinus fossil fruits identified on the section level are included. The black color represents selected fossil fruits from published literature (excluding some Eocene North American occurrences not assigned to section), the red color represents the fossil fruits from the Lühe flora, Yunnan, Southwest China. The phylogenetic relationships are based on Hinsinger et al. (2013). in Fraxinus L. (Oleaceae) Fruits From The Early Oligocene Of Southwest China And Their Biogeographic Implications
Text-fig. 6. Stratigraphic and phylogenetic placement inferred for fossil Fraxinus fruits. Only Fraxinus fossil fruits identified on the section level are included. The black color represents selected fossil fruits from published literature (excluding some Eocene North American occurrences not assigned to section), the red color represents the fossil fruits from the Lühe flora, Yunnan, Southwest China. The phylogenetic relationships are based on Hinsinger et al. (2013).
CONSOLE_WP2_Task2.2_Data collection, selection and diagnosis of reasons for successes and failures of initiatives in Europe_second level diagnosis_2022.10.25
<p>This dataset contains data on the second level analysis of existing and highly potential contract solutions throughout Europe within the EU-H2020 project CONSOLE (CONtract Solutions for Effective and lasting delivery of agri-environmental-climate public goods by EU agriculture and forestry).</p> <p>The dataset is organized in one document (.rtf). The document represents the list of the 26 in-depth case studies, including data on case study ID, AECPGs addressed, performance description and evaluation. The dataset is related to the Deliverable 2.3.</p>
CONSOLE_WP2_Task2.2_Data collection, selection and diagnosis of reasons for successes and failures of initiatives in Europe_first level diagnosis_2022.10.25
<p>This dataset contains data on the first level analysis of existing and highly potential contract solutions throughout Europe within the EU-H2020 project CONSOLE (CONtract Solutions for Effective and lasting delivery of agri-environmental-climate public goods by EU agriculture and forestry).</p> <p>The dataset is organized in one document (.rtf) with two main chapters. The first part contains the information gained for the first level diagnosis based on Task 2.2 and Deliverable 2.1 and the second half of the document contains updated information on the case studies connected to Deliverable 2.6.The analyses performed with this dataset can be found in Deliverable 2.4.</p> <p>The first chapter represents the list on the 60 first level case studies and the second chapter contains the 61 updated case studies, including data on case study ID, NUTS location, short description, AECPGs addressed, main contractual features, a simplified SWOT.</p>
Are offspring begging levels exaggerated beyond the parental optimum? Evidence from a bidirectional selection experiment
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Code and data for Bayesian joint species distribution model selection for community-level prediction
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Data from: Müllerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection
<p>Hybrid zones, where distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Studying clines in genetic loci and adaptive traits across hybrid zones is a powerful method for understanding how selection drives differentiation within a single species, but can also be used to compare parallel divergence in different species responding to a common selective pressure. Here, we study parallel divergence of wing colouration in the butterflies <i>Heliconius erato</i> and <i>H</i><i>. melpomene</i>, which are distantly related Müllerian mimics that show parallel geographic variation in both discrete variation in pigmentation, and quantitative variation in structural colour. Using geographic cline analysis, we show that clines in these traits are positioned in the roughly the same geographic region for both species, which is consistent with direct selection for mimicry. However, the width of the clines varies markedly between species. This difference is explained in part by variation in the strength of selection acting on colour traits within each species, but may also be influenced by differences in the dispersal rate and total strength of selection against hybrids between the species. Genotyping-by-sequencing also revealed weaker population structure in <i>H. melpomene</i>, suggesting the hybrid zones may have evolved differently in each species; which may also contribute to the patterns of phenotypic divergence in this system Overall, we conclude that multiple factors are needed to explain patterns of clinal variation within and between these species, although mimicry has probably played a central role.</p>
Habitat complexity dampens selection on prey activity level
<p>Conspecific prey individuals often exhibit persistent differences in behavior (i.e., animal personality) and consequently vary in their susceptibility to predation. How this form of selection varies across environmental contexts is essential to predicting ecological and evolutionary dynamics, yet remains currently unresolved. Here, we use three separate predator–prey systems (sea star–snail, wolf spider–cricket, and jumping spider–cricket) to independently examine how habitat structural complexity influences the selection that predators impose on prey behavioral types. Prior to conducting staged predator–prey interaction encounters, we ran prey individuals through multiple behavioral assays to determine their average activity level. We then allowed individual predators to interact with groups of prey in either open or structurally complex habitats and recorded the number and individual identity of prey that were eaten. Habitat complexity had no effect on overall predation rates in any of the three predator–prey systems. Despite this, we detected a pervasive interaction between habitat structure and individual prey activity level in determining individual prey survival. In open habitats, all predators imposed strong selection on prey behavioral types: sea stars preferentially consumed sedentary snails, while spiders preferentially consumed active crickets. Habitat complexity dampened selection within all three systems, equalizing the predation risk that active and sedentary prey faced. These findings suggest a general effect of habitat complexity that reduces the importance of prey activity level in determining individual predation risk. We reason this occurs because activity level (i.e., movement) is paramount in determining risk within open environments, whereas in complex habitats, other behavioral traits (e.g., escape ability to a refuge) may take precedence.</p>
Value of water level class observations for parameter set selection in hydrological modelling
<p>Data corresponding to the study "<span>Value of water level class observations for parameter set selection in hydrological modelling</span>", published in the Hydrological Sciences Journal.</p>
Multi-level in vivo selection of the biocontrol agent Akanthomyces muscarius, virulence, growth, sporulation, and variant data
<p>Changes in parasite virulence are commonly expected to lead to trade-offs in other life history traits that can affect fitness. Understanding these trade-offs is particularly important if we want to manipulate the virulence of microbial biological control agents. Theoretically, selection across different spatial scales, i.e. between- and within-hosts, shapes these trade-offs. However, trade-offs are also dependent on parasite biology. Despite their applied importance the evolution of virulence in fungal parasites is poorly understood: virulence can be unstable in culture and commonly fails to increase in simple passage experiments. We hypothesized that manipulating selection intensity at different scales would reveal virulence trade-offs in a fungal pathogen of aphids, <em>Akanthomyces muscarius</em>. Starting with a genetically diverse stock we selected for speed of kill, parasite yield, or infectivity by manipulating competition within and between hosts and between populations of hosts over 7 rounds of infection. We characterized ancestral and evolved lineages by whole genome sequencing and by measuring virulence, growth rate, sporulation, and fitness. While several lineages showed increases in virulence, we saw none of the trade-offs commonly found in obligately-killing parasites. Phenotypically similar lineages within treatments often shared multiple single-nucleotide variants, indicating strong convergent evolution. The most dramatic phenotypic changes were in the timing of sporulation and spore production <em>in vitro. </em>We found that early sporulation led to reduced competitive fitness but could increase the yield of spores on media, a trade-off characteristic of social conflict. Notably, the selection regime with the strongest between-population competition and lowest genetic diversity produced the most consistent shift to early sporulation, as predicted by social evolution theory. Multi-level selection therefore revealed social interactions novel to fungi and showed that these biocontrol agents have the genomic flexibility to improve multiple traits - virulence and spore production - that are often in conflict in other parasites.</p>
Determination of Natural Radioactivity Levels and Associated Radiation Hazard Indices of Wheat Flour Samples From Selected Ethiopian Markets.
<p>Wheat flour is a nutrient-dense food that is commonly consumed by various age groups in Ethiopia. In this study, natural radioactivity levels of <sup>226</sup>Ra, <sup>232</sup>Th, and <sup>40</sup>K, as well as the related dangerous radiological characteristics, were successfully measured on 10 different brands of wheat flour samples using high-purity germanium (HPGe) gamma-ray spectrometry. Average activity concentrations of <sup>226</sup>Ra, <sup>232</sup>Th, and <sup>40</sup>K in wheat flour are found to be 0.26<strong> ±</strong>0.07 Bq.kg<sup>-1</sup>, 1.54<strong> ± </strong>0.43 Bq.kg<sup>-1</sup>, and 59.79<strong>±</strong>3.65 Bq.kg<sup>-1</sup>, respectively. Moreover, the average values of the corresponding radiological parameters, Ra<sub>eq</sub>, H<sub>int</sub>, and annual effective dose (E<sub>ave</sub>) (sum), were also found to be 7.07±0.96 Bq.kg<sup>-1</sup>, 0.019±0.003, and 0.109±0.019 mSvy<sup>-1</sup>, respectively. When the obtained results for all of the samples were compared to the internationally accepted norms, they were found to be below the permissible world average values. Furthermore, the lifetime cancer risk was discovered to be substantially below the permissible limit. According to the study, the risk of absorbing natural radionuclides from wheat flour consumption is negligible. The findings can be used to develop radiation protection rules and regulations for the use of wheat flour in food production and processing.</p>
Selective enamel etching: What level of accuracy is achievable in simulated clinical conditions?
<p>Dataset of a laboratory study assessing the accuracy of selective enamel etching</p>
Assessment of the expression level of selected genes and protein phosphorylation of the PI3K/Akt signaling pathway in patients with colorectal cancer
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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.