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120 results for “fitness for use”
Dataset of report "A.2.2.6: Validation of the fitness of purpose of the performance assessment protocol developed in A2.1.4 by demonstrating its applicability for 2 terpenes using TD-GC/MS/FID and the static standards produced in A1.1.2."
<p>Dataset of report "A.2.2.6: Validation of the fitness of purpose of the performance assessment protocol developed in A2.1.4 by demonstrating its applicability for 2 terpenes using TD-GC/MS/FID and the static standards produced in A1.1.2."</p>
Supplementary Data: Axion global fits with Peccei-Quinn symmetry breaking before inflation using GAMBIT
<p><strong>Description of Supplementary Data</strong></p> <p>This record contains the samples used to create the figures (excluding validation and prior dependence plots) and to derive most of the results in Hoof et al., <em>“Axion global fits with Peccei-Quinn symmetry breaking before inflation using GAMBIT”</em> (available on the <a href="https://arxiv.org/abs/1810.07192">arXiv</a>). Please contact the authors if you are interested in other samples, YAML files or plotting scripts.<br> <br> This record consists of</p> <ul> <li>21 <code>YAML</code> files (6 for <code>T-Walk</code>, 15 for <code>Diver</code>). Running <code>./gambit -f path/to/YAML/file.yaml</code> in the GAMBIT directory will start the scan. However, most users might want to adjust the output file name and directory as well as the settings for the samplers to their systems.</li> <li>21 <code>hdf5</code> files (6 for <code>T-Walk</code>, 15 for <code>Diver</code>). These files contain the actual samples and were compressed using the <code>tar</code> format.</li> <li>Two example <code>pip</code> files (<code>2_QCDAxion_10M1.pip</code> for <code>Diver</code> samples, <code>2_QCDAxion_3041.pip</code> for <code>T-Walk</code> samples) for producing plots from the corresponding <code>hdf5</code> files, using <a href="https://github.com/patscott/pippi"><code>pippi</code></a> and <code>functions.py</code>.</li> </ul> <p>The files follow the naming scheme <code>V_ModelName_[S][C][I][R][E]</code> plus one of the extensions <code>.yaml</code>, <code>.hdf5.tar.gz</code>, or <code>.pip</code>.</p> <ul> <li><code>V</code>: This internal version number can be ignored, but should be quoted when asking for help with the plotting scripts</li> <li><code>ModelName</code>: Corresponds to the axion models in the paper (<em>GeneralALP</em>, <em>QCDAxion</em>, <em>DFSZAxion_I</em>, <em>DFSZAxion_II</em>, <em>KSVZAxion</em>)</li> <li><code>S</code>: Scanner (<code>S=1</code>: <code>Diver</code>, <code>S=3</code>: <code>T-Walk</code>)</li> <li><code>C</code>: Switch to include (<code>C=1</code>) or exclude (<code>C=0</code>) the White Dwarf cooling hints</li> <li><code>I</code>: Setting for the initial misalignment angle <em>θ<sub>i</sub></em> (<code>I=4</code>: flat prior on <em>θ<sub>i</sub></em> with values in [-3.1415, 3.1415]). <code>I=M</code> is used to indicate that the file includes merged samples from other scans in addition to the corresponding <code>I=4</code> scan.</li> <li><code>R</code>: Setting for the DM relic density likelihood (<code>R=1</code>: upper limit, <code>R=2</code>: matching the DM density)</li> <li><code>E</code>: Extra digit for the anomaly ratio <em>E/N</em>; only for <em>KSVZAxion</em> models (<code>E=1</code>: 0, <code>E=2</code>, 2/3, <code>E=3</code>: 5/3, <code>E=4</code>: 8/3), <em>DFSZAxion-I</em> models (<code>E=1</code>: 8/3), <em>DFSZAxion-II</em> models (<code>E=2</code>: 2/3), or some <em>GeneralALP</em> files (<code>E=a</code>: “QCD-like setting” with <em>β</em> = 7.94, <em>T<sub>crit</sub></em> = 147 MeV; <code>E=b</code>: “Simple ALP-like setting” with <em>β</em> = 0, <em>T<sub>crit</sub></em> irrelevant)</li> </ul> <p>For convenience, we provide a mapping between the figures in the paper and the <code>hdf5</code> files:</p> <ul> <li>Fig. 1: none</li> <li>Figs 2 - 11: Validation plots</li> <li>Figs 12 + 13: 2_GeneralALP_10M2</li> <li>Fig. 14: 2_GeneralALP_10M2a, 2_GeneralALP_10M2b</li> <li>Fig. 15: 2_QCDAxion_10M1, 2_QCDAxion_10M2</li> <li>Fig. 16: 2_QCDAxion_3041, 2_QCDAxion_3042</li> <li>Figs 17 + 18: 2_QCDAxion_10M1, 2_QCDAxion_10M2, 2_QCDAxion_30M1, 2_QCDAxion_30M2</li> <li>Fig. 19: 3_KSVZAxion_10M11, 3_KSVZAxion_10M12, 3_KSVZAxion_10M13, 3_KSVZAxion_10M14, 3_DFSZAxion_I_10M11, 3_DFSZAxion_II_10M12</li> <li>Fig. 20: 2_QCDAxion_10M1, 3_KSVZAxion_10M11, 3_KSVZAxion_10M12, 3_KSVZAxion_10M13, 3_KSVZAxion_10M14, 3_DFSZAxion_I_10M11, 3_DFSZAxion_II_10M12</li> <li>Fig. 21: 2_QCDAxion_11M1, 2_QCDAxion_11M2</li> <li>Fig. 22: 2_QCDAxion_3141, 2_QCDAxion_3142</li> <li>Figs 23 + 24: 2_QCDAxion_3041, 2_QCDAxion_3042, 2_QCDAxion_3141, 2_QCDAxion_3142</li> <li>Fig. 25: 2_QCDAxion_3141, 2_QCDAxion_3142</li> <li>Fig. 26: 2_QCDAxion_11M1, 3_DFSZAxion_I_11M11, 3_DFSZAxion_II_11M12</li> <li>Fig. 27: 2_QCDAxion_3141, 3_DFSZAxion_I_31411, 3_DFSZAxion_II_31412</li> <li>Fig. 28: Validation plot</li> <li>Fig. 29: Prior dependence plot</li> </ul> <p>A few caveats to keep in mind:</p> <ul> <li>The YAML files are designed to work with <code>GAMBIT 1.3.1</code>, and the pip files are tested with <code>pippi 2.1</code>, commit 1a08644. They may or may not work with later versions of either software (these working versions/commits can always be obtained via the <code>git</code> history).</li> <li>The <code>pip</code> files will produce an approximately complete, but very basic version of plots in the paper. Re-creating all the plots in the paper requires various manual, undocumented interventions such as additions, deletions and combination of the plotting scripts created by <code>pippi</code>. Users wishing to reproduce the more advanced plots in the paper should contact the authors for tips, scripts, or experiment for themselves.</li> </ul>
Science ready spectra of star clusters and their best-fitting models described in the research paper "Using Star Clusters as Tracers of Star Formation and Chemical Evolution: the Chemical Enrichment History of the Large Magellanic Cloud" by Chilingarian & Asa'd
<p>Science ready spectra of star clusters in the Large Magellanic Cloud and their best-fitting templates (alpha-enhanced MILES based simple stellar population models) obtained using the NBursts full spectrum fitting code. Each spectrum is presented as a binary FITS table, which contains a spectrum (wavelength, flux, uncertainties), best-fitting template, best-fitting parameters (radial velocity, age, metallicity), and a pixel mask used in the fitting procedure. For each cluster, 5 spectra are provided, which correspond to [alpha/Fe] values from 0.0 to 0.4 dex with a step of 0.1 dex. The only exception is NGC2249, for which only 3 models are provided. The alpha-enhancement value of a model grid used in the fitting procedure is given in the FITS keyword MGFEGRID.</p>
Sample FITS file with non-linear wavelength solution using a Chebyshev model
<p>This file was wavelength calibrated using IRAF and written to a FITS file using a non-linear wavelength solution using a Chebyshev model.</p> <p>This data is in its original shape.</p>
Sample FITS file with non-linear wavelength solution using a cubic spline model
<p>This file was wavelength calibrated using IRAF and written to a FITS file using a non-linear wavelength solution using a cubic spline model.</p> <p>This data is in its original shape.</p>
Sample FITS file with non-linear wavelength solution using a Legendre model
<p>This file was wavelength calibrated using IRAF and written to a FITS file using a non-linear wavelength solution using a Legendre model.</p> <p>This data is in its original shape.</p>
Sample FITS file with non-linear wavelength solution using a linear spline model
<p>This file was wavelength calibrated using IRAF and written to a FITS file using a non-linear wavelength solution using a linear spline model.</p> <p>This data is in its original shape.</p>
Datasets used for the manuscript: "Sibling competition, dispersal and fitness outcomes in humans"
<p>Datasets used for the manuscript: “Sibling competition, dispersal and fitness outcomes in humans”, 10.1038/s41598-023-33700-3</p>
Standard Model effective field theory global fit using electroweak data
<p>These are files that can be used to reproduce the fit results in 10.1007/JHEP09(2016)157 and arXiv:1610.01783<strong>.</strong></p> <p> </p>
Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet.
Data for fitness analyses used in: Environmentally-induced DNA methylation is inherited across generations in water fleas (Daphnia magna)
<p><span>Data of</span> fitness effects of environmental stressors on <em>Daphnia magna</em> over multiple generations. Ages of first and second reproduction, and sizes of first and second brood were measured and used to calculate replacement rate. This data is part of a study on whole-genome bisulphate sequencing on individual <em>Daphnia magna</em> to assess whether environmentally-induced DNA methylation can persist for up to four generations.</p>
Fig. 1 in Can the choice behavior and fitness of Tamarixia radiata (Hymenoptera: Eulophidae) be affected by the citrus (Sapindales: Rutaceae) variety used to rear the Asian citrus psyllid (Hemiptera: Liviidae)?
Fig. 1. Mean percentage (± SE) of parasitism of Tamarixia radiata on nymphs of Diaphorina citri reared on 4 citrus varieties. Means do not differ by Tukey's test (P> 0.05).
Fig. 4. A multinomial regression fit using natural splines with 3 in Fig. 1 in Positive association between PTN polymorphisms and schizophrenia in Northeast Chinese Han population.
Fig. 4. A multinomial regression fit using natural splines with 3 degrees of freedom. 95% confidence bands are constructed by bootstrapping. Records from years with asterisks (*) are excluded from the model. The dotted white lines correspond to a model with no dependence on year.
Influence of endosymbionts on the reproductive fitness of the tick Ornithodoros moubata tested through elimination of the microbiota using antibiotic treatments
<p class="MsoNoSpacing">Over the past ten years, many studies demonstrated the crucial role of the tick microbiome in tick biology. The soft tick <em>Ornithodoros moubata</em> is a hematophagous ectoparasite of Suidae particularly known to transmit the African swine fever virus. Its bacterial microbiota is characterized by a high prevalence of <em>Francisella</em>-like and <em>Rickettsia</em> endosymbionts. The present study aims to better understand the potential influence of the microbiota on the reproductive fitness of <em>O. moubata</em>. A total of 132 adult female ticks were treated using gentamycin or rifampicin added to the blood meal. Half of the ticks also received a supplementation with B vitamins to address the nutritional role of endosymbionts. Over two periods of 50 days, several traits related to reproductive fitness were monitored to investigate the importance of <em>Francisella</em> and <em>Rickettsia</em> for those traits. It appeared that most of the considered reproductive parameters were not affected. However, antibiotic treatments induced an increase in the tick survival indicating a potential fitness cost of harboring endosymbionts for ticks during the reproduction period. Similarly, 366 first-stage nymphs of <em>Ornithodoros moubata</em> were exposed to the same treatments for molecular quantification of both endosymbionts. Results from qPCR suggested that treatments produced a bacteriostatic effect on endosymbionts without fully eliminating <em>Francisella</em> or <em>Rickettsia</em>.</p>
Influence of endosymbionts on the reproductive fitness of the tick Ornithodoros moubata tested through elimination of the microbiota using antibiotic treatments
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Data for fitness analyses used in: Environmentally-induced DNA methylation is inherited across generations in water fleas (Daphnia magna)
Open the record for dataset details and reuse information.
Data from: Individual and population fitness consequences associated with large carnivore use of residential development
<p><span>Large carnivores are negotiating increasingly developed landscapes, but little is known about how such behavioral plasticity influences their demographic rates and population trends. Some investigators have suggested that the ability of carnivores to behaviorally adapt to human development will enable their persistence, and yet, others have suggested that such landscapes are likely to serve as population sinks or ecological traps. To understand how plasticity in black bear (<i>Ursus americanus</i>) use of residential development influences their population dynamics, we conducted a 6 year study near Durango, Colorado, USA. </span>Using space-use data on individual bears, we examined the influence of use of residential development on annual measures of bear body fat, cub productivity, cub survival and adult female survival, after accounting for variation in natural food availability and individual attributes (e.g., age). We then used our field-based vital rate estimates to parameterize a matrix model that simulated asymptotic population growth for bears using residential development to different degrees. We found that bear use of residential development was highly variable within and across years, with bears increasing their foraging within development when natural foods were scarce. Increased bear use of development was associated with increased body fat and cub productivity, but reduced cub and adult survival.<span> When these effects were simultaneously incorporated into a matrix model </span>we found that the population was projected to decline as bear use of development increased, given that the costs of reduced survival outweighed the benefits of enhanced productivity. Our results provide a mechanistic understanding of how black bear use of residential development exerts opposing effects on different bear fitness traits and a negative effect on population growth, with the magnitude of those effects mediated by variation in environmental conditions. They also highlight the importance of monitoring bear population dynamics, particularly as shifts in bear behavior are likely to drive increases in human-bear conflicts and the perception of growing bear populations. Finally, our work emphasizes the need to consider the demographic viability of large carnivore populations when promoting the coexistence of people and carnivores on shared landscapes.</p>
Data used to produce figures in "Monotonicity of Fitness Landscapes and Mutation Rate Control"
<p>Data used in Figures 2, 3, 4, 6, 7, 8, 9 and 10 of the manuscript "Monotonicity of Fitness Landscapes and Mutation Rate Control"</p>
Datasets for fitting trajectories of elementary particles using deep learning
<p>Training and testing datasets of simulated elementary particles, used for fitting the trajectories of elementary particles in dense materials immersed in a magnetic field using deep learning. Once decompressed, the directory structure is the following:<br><br><em>datasets.zip:</em></p> <ul> <li><strong>training</strong> (1,762,327 particles in total): <ul> <li><strong>proton</strong>: 414,824 particles.</li> <li><strong>pion</strong>: 432,855 particles.</li> <li><strong>muon</strong>: 446,858 particles (muons and antimuons).</li> <li><strong>electron</strong>: 467,790 particles (electrons and positrons).</li> </ul> </li> <li><strong>testing</strong> (1,759,491): <ul> <li><strong>proton</strong>: 412,092 particles.</li> <li><strong>pion</strong>: 432,807 particles.</li> <li><strong>muon</strong>: 447,003 particles (muons and antimuons).</li> <li><strong>electron</strong>: 467,589 particles (electrons and positrons).</li> </ul> </li> </ul> <p><em>checkpoints.zip:</em></p> <ul> <li> <p><strong>checkpoint_rnn.pth</strong>: PyTorch weights of the RNN trained model.</p> </li> <li> <p><strong>checkpoint_transformer_encoder.pth</strong>: PyTorch weights of the RNN trained model.</p> </li> </ul>
Fitness effects of mutations: An assessment of PROVEAN predictions using mutation accumulation data
<p><span><span><span><span>Predicting fitness in natural populations is a major challenge in biology. It may be possible to leverage fast-accumulating genomic datasets to infer the fitness effects of mutant alleles, allowing evolutionary questions to be addressed in any organism. In this paper, we investigate the utility of one such tool, called PROVEAN. This program compares a query sequence with existing data to provide an alignment-based score for any protein variant, with scores categorized as neutral or deleterious based on a preset threshold. PROVEAN has been used widely in evolutionary studies, e.g., to estimate mutation load in natural populations, but has not been formally tested as a predictor of aggregate mutational effects on fitness. Using three large, published datasets on the genome sequences of laboratory mutation accumulation lines, we assessed how well PROVEAN predicted the actual fitness patterns observed, relative to other metrics. In most cases, we find that a simple count of the total number of mutant proteins is a better predictor of fitness than the number of variants scored as deleterious by PROVEAN. We also find that the sum of all mutant protein scores explains variation in fitness better than the number of mutant proteins in one of the datasets. We discuss the implications of these results for studies of populations in the wild.</span></span></span></span></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.