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Training of aerobic fitness (VO2max) and muscle strength – a cost/benefit analysis
<p>A systematic literature search in the Ovid Medline, Web of Science and SportDiscus databases was performed, limited to randomized studies of aerobic fitness and strength training, respectively. Studies with at least three "doses" of frequency, duration or intensity of training were examined in order to find out what effect could be expected from the next highest “dose”.</p>
Networks of Swiss water governance issues. Studying fit between media attention and organizational activity
<p>Anonymized data and R code needed to replicate the analysis presented in the study "Networks of Swiss water governance issues. Studying fit between media attention and organizational activity" to be published in Society & Natural Resources.</p> <p>The study looks at how relations between Swiss water governance issues are portrayed in the media as compared to the way organizations involved in water governance reflect these relations in their activity.</p> <p>This is a paper output of the SNF funded project "Overlapping subsystems". Access to the complete, non-anonymized dataset is restricted.</p> <p>Study doi: tbd</p>
Model fits (MCMC samples) for two papers on perceptual confidence
<p>These are model fits for two papers on perceptual confidence. See <a href="https://github.com/wtadler/confidence/">github.com/wtadler/confidence</a> for more info.</p>
Fig. 8 Fitness landscape for models 7 and 8 in Modelling sympatric speciation by means of biologically plausible mechanistic processes as exemplified by threespine stickleback species pairs
Fig. 8 Fitness landscape for models 7 and 8. Relative fitness is a function of trait T1 and trait T2. Epistasis is modelled as follows:
FIG. 2 in Density-Dependent Fitness Attributes and Carry-Over Effects in Crawfish Frogs (Rana areolata), a Species of Conservation Concern
FIG. 2. Field data showing effects of juvenile density on juvenile body size (A, C) and time to metamorphosis (E), and breeding adult size (B, D) and survivorship (F). Lines reflect regression calculations. While suggestive, none of these trends is significant except for the adult SVL data shown in B.
Fig. 3 in Effects of Female and Male Density on their Mating Performance and Female Post-Mating Reproductive Fitness in Plagiodera versicolora (Laicharting) (Coleoptera: Chrysomelidae)
Fig. 3. Effect of female and male density on female post-mating fecundity and the egg hatching rate. A–B) Female fecundity, C–D) Egg hatching rate. Different letters indicate significant differences from each other at P <0.05 (n = 29–40). The top and bottom of each box represent the upper and lower Quartiles, respectively; the horizontal line represents the median; the vertical lines extend to the minimum and maximum values within 1.5 times the inter-Quartile range.
Fig. 2 in Effects of Female and Male Density on their Mating Performance and Female Post-Mating Reproductive Fitness in Plagiodera versicolora (Laicharting) (Coleoptera: Chrysomelidae)
Fig. 2. Effect of female and male density on the female post-mating duration of the egg-laying period and longevity. A–B) Female longevity, C–D) Duration of egg laying. Different letters indicate significant differences from each other at P <0.05 (n = 29–40). The top and bottom of each box represent the upper and lower Quartiles, respectively; the horizontal line represents the median; the vertical lines extend to the minimum and maximum values within 1.5 times the inter-quartile range.
Fig. 1 in Effects of Female and Male Density on their Mating Performance and Female Post-Mating Reproductive Fitness in Plagiodera versicolora (Laicharting) (Coleoptera: Chrysomelidae)
Fig. 1. Effect of female and male density on time from pairing to successful mating and mating duration of Plagiodera versicolora. A–B) Time from pairing to successful mating, C–D) Mating duration. Different letters indicate significant differences from each other at P <0.05 (n = 30–41). The top and bottom of each box represent the upper and lower Quartiles, respectively; the horizontal line represents the median; the vertical lines extend to the minimum and maximum values within 1.5 times the inter-Quartile range.
Fig. 4 in Effects of Female and Male Density on their Mating Performance and Female Post-Mating Reproductive Fitness in Plagiodera versicolora (Laicharting) (Coleoptera: Chrysomelidae)
Fig. 4. Effect of female and male density on the female post-mating number of egg clutches and the number of eggs per clutch. A–B) Number of egg clutches, C–D) Number of eggs per clutch. Different letters indicate significant differences from each other at P <0.05 (n = 29–40). The top and bottom of each box represent the upper and lower Quartiles, respectively; the horizontal line represents the median; the vertical lines extend to the minimum and maximum values within 1.5 times the inter-Quartile range.
Implementation and Results of a "Randomized Local Search for Two-Dimensional Bin Packing and a Negative Result for Frequency Fitness Assignment"
<p><strong><em>1. Introduction</em></strong></p> <p>In this archive, we provide the implementation and experimental results of a Randomized Local Search (RLS) applied to the two-dimensional bin packing problem with and without orientation. As benchmark dataset, we use the <code>beng</code>, <code>A</code>, and <code>class</code> instances from <a href="https://site.unibo.it/operations-research/en/research/2dpacklib">2DPackLib</a> as well as the four non-trivial Almost Squares in Almost Squares (<a href="https://math.vu.nl/~sbhulai/publications/data_analytics2016b.pdf"><code>Asqas</code></a>) instances</p> <p>These are the data used in the paper below, which contains the exact specification of all algorithms, objective functions, and the encoding we applied.</p> <p>Rui Zhao, Zhize Wu, Daan van den Berg, Matthias Thürer, Tianyu Liang, Ming Tan, and Thomas Weise. Randomized Local Search for Two-Dimensional Bin Packing and a Negative Result for Frequency Fitness Assignment. In <em>16th International Conference on Evolutionary Computation Theory and Applications (ECTA'24), part of the 16th International Joint Conference on Computational Intelligence (IJCCI'24)</em>. November 20-24, 2024. Porto, Portugal. Setúbal, Portugal: SciTePress.</p> <p>To run the experiments, you need <a href="https://thomasweise.github.io/moptipyapps">moptipyapps</a> and <a href="https://thomasweise.github.io/moptipy">moptipy</a>, which contain the actual algorithm implementations. Both packages are available on GitHub and on PyPI. However, we include several versions of them in the folder <code>source/packages</code>, just in case.</p> <p><strong><em>2. Directory Structure</em></strong></p> <p>This archive contains the following directories:</p> <ul> <li><code>source</code> contains the Python source codes needed to run the experiment.</li> <li><code>source/packages</code> contains the source codes of the Python packages with the actual algorithm implementations.</li> <li><code>source/experiment_execution_scripts</code> contains the scripts to run the experiments.</li> <li><code>results</code> is the directory with the results, i.e., with the log files generated by the experiment.</li> <li><code>evaluator</code> is the folder containing Python scripts that were used to evaluate these results.</li> <li><code>evaluation</code> was generated using the evaluation scripts and contains tables and figures and a result summary in CSV format.</li> </ul> <p><strong><em>3. License</em></strong></p> <p>The files in this repository are under the <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a>, with the exception of the files of <a href="https://site.unibo.it/operations-research/en/research/2dpacklib">2DPackLib</a> and other benchmark datasets included, which are under copyright of their respective owner (we believe that they are in the public domain, as they are provided by many sources, included in many software packages under various open source licenses, and on many websites). The license is contained as file <code>LICENSE.txt</code> in this archive.</p> <p><strong><em>4. Contact</em></strong></p> <p>If you have any questions or suggestions, please contact</p> <p>Mr. Rui ZHAO (赵睿) of the Institute of Applied Optimization (应用优化研究所, <a href="http://iao.hfuu.edu.cn">IAO</a>) of the School of Artificial Intelligence and Big Data (<a href="http://www.hfuu.edu.cn/aibd/">人工智能与大数据学院</a>) at <a href="http://www.hfuu.edu.cn/english/">Hefei University</a> (<a href="http://www.hfuu.edu.cn/">合肥大学</a>) in Hefei, Anhui, China (中国安徽省合肥市) via email to <a href="mailto:zr1329142665@163.com">zr1329142665@163.com</a>.</p>
Implementation and Results of a "Frequency Fitness Assignment: Optimization without Bias for Good Solution outperforms Randomized Local Search on the Quadratic Assignment Problem"
<p><strong><em>1. Introduction</em></strong></p> <p>In this archive, we provide the implementation and experimental results of a Randomized Local Search (RLS) with and without FFA applied to the Quadratic Assignment Problem. These are the data used in the paper below, which contains the exact specification of all algorithms, objective functions, and the encoding we applied.</p> <p>Jiayang Chen, Zhize Wu, Sarah L. Thomson, and Thomas Weise. Frequency Fitness Assignment: Optimization without Bias for Good Solution outperforms Randomized Local Search on the Quadratic Assignment Problem. In <em>16th International Conference on Evolutionary Computation Theory and Applications (ECTA'24), part of the 16th International Joint Conference on Computational Intelligence (IJCCI'24)</em>. November 20-24, 2024. Porto, Portugal. Setúbal, Portugal: SciTePress.</p> <p>To run the experiments, you need <a href="https://thomasweise.github.io/moptipyapps">moptipyapps</a> and <a href="https://thomasweise.github.io/moptipy">moptipy</a>, which contain the actual algorithm implementations. Both packages are available on GitHub and on PyPI. However, we include several versions of them in the folder <code>source/packages</code>, just in case.</p> <p><strong><em>2. Directory Structure</em></strong></p> <p>This archive contains the following directories:</p> <ul> <li><code>source</code> contains the Python source codes needed to run the experiment.</li> <li><code>source/packages</code> contains the source codes of the Python packages with the actual algorithm implementations.</li> <li><code>source/experiment_execution_scripts</code> contains the scripts to run the experiments.</li> <li><code>results</code> is the directory with the results, i.e., with the log files generated by the experiment.</li> <li><code>evaluator</code> is the folder containing Python scripts that were used to evaluate these results.</li> <li><code>evaluation</code> was generated using the evaluation scripts and contains tables and figures and a result summary in CSV format.</li> </ul> <p><strong><em>3. License</em></strong></p> <p>The files in this repository are under the <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a>, with the exception of the benchmark datasets included, which are under copyright of their respective owner (we believe that they are in the public domain, as they are provided by many sources, included in many software packages under various open source licenses, and on many websites). The license is contained as file <code>LICENSE.txt</code> in this archive.</p> <p><strong><em>4. Contact</em></strong></p> <p>If you have any questions or suggestions, please contact</p> <p>Mr. Jiayang CHEN (陈嘉阳) of the Institute of Applied Optimization (应用优化研究所, <a href="http://iao.hfuu.edu.cn">IAO</a>) of the School of Artificial Intelligence and Big Data (<a href="http://www.hfuu.edu.cn/aibd/">人工智能与大数据学院</a>) at <a href="http://www.hfuu.edu.cn/english/">Hefei University</a> (<a href="http://www.hfuu.edu.cn/">合肥大学</a>) in Hefei, Anhui, China (中国安徽省合肥市) via email to <a href="mailto:cjy65820607@163.com">cjy65820607@163.com</a>.</p>
Implementation and Results of a "Randomized Local Search vs. NSGA-II vs. Frequency Fitness Assignment on The Traveling Tournament Problem"
<p><strong><em>1. Introduction</em></strong></p> <p>In this archive, we provide the implementation and experimental results of a Randomized Local Search (RLS) with and without FFA as well as NSGA-II applied to the Traveling Tournament Problem. These are the data used in the paper below, which contains the exact specification of all algorithms, objective functions, and the encoding we applied.</p> <p>Cao Xiang, Zhize Wu, Daan van den Berg, and Thomas Weise. Randomized Local Search vs. NSGA-II vs. Frequency Fitness Assignment on The Traveling Tournament Problem. In <em>16th International Conference on Evolutionary Computation Theory and Applications (ECTA'24), part of the 16th International Joint Conference on Computational Intelligence (IJCCI'24)</em>. November 20-24, 2024. Porto, Portugal. Setúbal, Portugal: SciTePress.</p> <p>To run the experiments, you need <a href="https://thomasweise.github.io/moptipyapps">moptipyapps</a> and <a href="https://thomasweise.github.io/moptipy">moptipy</a>, which contain the actual algorithm implementations. Both packages are available on GitHub and on PyPI. However, we include several versions of them in the folder <code>source/packages</code>, just in case.</p> <p><strong><em>2. Directory Structure</em></strong></p> <p>This archive contains the following directories:</p> <ul> <li><code>source</code> contains the Python source codes needed to run the experiment.</li> <li><code>source/packages</code> contains the source codes of the Python packages with the actual algorithm implementations.</li> <li><code>source/experiment_execution_scripts</code> contains the scripts to run the experiments.</li> <li><code>results</code> is the directory with the results, i.e., with the log files generated by the experiment.</li> <li><code>evaluator</code> is the folder containing Python scripts that were used to evaluate these results.</li> <li><code>evaluation</code> was generated using the evaluation scripts and contains tables and figures and a result summary in CSV format.</li> </ul> <p><strong><em>3. License</em></strong></p> <p>The files in this repository are under the <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a>, with the exception of the benchmark datasets included, which are under copyright of their respective owner (we believe that they are in the public domain, as they are provided by many sources, included in many software packages under various open source licenses, and on many websites). The license is contained as file <code>LICENSE.txt</code> in this archive.</p> <p><strong><em>4. Contact</em></strong></p> <p>If you have any questions or suggestions, please contact</p> <p>Mr. Xiang CAO (曹翔) of the Institute of Applied Optimization (应用优化研究所, <a href="http://iao.hfuu.edu.cn">IAO</a>) of the School of Artificial Intelligence and Big Data (<a href="http://www.hfuu.edu.cn/aibd/">人工智能与大数据学院</a>) at <a href="http://www.hfuu.edu.cn/english/">Hefei University</a> (<a href="http://www.hfuu.edu.cn/">合肥大学</a>) in Hefei, Anhui, China (中国安徽省合肥市) via email to <a href="mailto:452015026@qq.com">452015026@qq.com</a>.</p>
Best-fit Abundances, Observed Spectra and Spectral Models for the New Sample of Ultracool Dwarf Benchmarks with Detailed Chemical Characterization
<p>Dataset associated with Fisher et al. 2024 in RNAAS <a href="https://iopscience.iop.org/article/10.3847/2515-5172/ad79f0">[link to publication]</a></p> <p><code>summary.mrt</code> is a table of identifiers, photometry, fundamental stellar parameters and detailed chemical compositions for 13 candidate wide binary systems with FGK Main Sequence primaries (5100 K < Teff < 6300 K) and ultracool dwarf companions (2500 K < Teff < 3100 K). Refer to the file header for detailed description of columns and units.</p> <p><code>stars.zip</code> contains the high-resolution spectra of primaries observed with the Automated Planet Finder (APF, program <code>2021B_A010</code>), as well as the corresponding best-fit spectral models. Each FITS file in the archive represents an individual exposure of the primary. The files are arranged in directories by identifiers of the primaries. The total number of exposures varies from source to source.</p> <p>FITS files are composed of a primary HDU and 6 extensions.</p> <ul> <li>The primary HDU contains the unmodified sky-subtracted spectrum of the object as produced by the APF pipeline and published on <a href="https://jump.caltech.edu/">Jump</a>. The spectrum is stored as a 2D array organized by Echelle orders.</li> <li>The first extension contains the corresponding air wavelengths [in A] transformed to the rest frame of the source.</li> <li>The second extension is the boolean mask of pixels included in model fitting.</li> <li>The third extension is the adopted statistical weights of each pixel, estimated as inverse variances under the assumption of Poisson noise.</li> <li>The fourth extension contains the best-fit synthetic spectrum in CGS units of surface intensity per wavelength in A.</li> <li>The fifth extension is the best-fit spline continuum correction between the model and the data.</li> <li>The final extension contains the adopted FWHM of the line spread function in each pixel, estimated by combining in quadrature a wavelength-dependent component with λ/Δλ=120,000 and a best-fit wavelength independent component (the <code>quickblur</code> parameter of the <a href="https://github.com/Roman-UCSD/chemfit">chemfit</a> package)</li> </ul> <p>This repository is for the research note "New Sample of Ultracool Dwarf Benchmarks with Detailed Chemical Characterization" by Fisher et al. It is associated with manuscript number AAS58102.</p>
Exploring zero-shot structure-based protein fitness prediction
<p>This repository contains data used in Exploring zero-shot structure-based protein fitness<br>prediction.</p> <p>Directions to use this data can be found on <a href="https://github.com/gitter-lab/benchmarking-structure-based-models">our GitHub repository</a>.</p> <ol> <li><code>experimental_struct_artifacts</code> contains the experimentally determined structures for ProteinGym assays used in our analysis along with the reference file needed to generate ESM inverse folding predictions for these structures in ProteinGym.</li> <li><code>results</code> contains the prediction results obtained by running SSEmb on the 216 ProteinGym assays being considered in this study.</li> <li><code>test.tar.gz</code> contains all the structures from ProteinGym as well as MSAs generated using mmseqs2. To use this directory: <ul> <li>Setup SSEmb as directed in its <a href="https://github.com/KULL-Centre/_2023_Blaabjerg_SSEmb">repository</a></li> <li>Download this file and extract it in the data folder.</li> </ul> </li> </ol> <p> </p> <p> </p>
Means and standard errors of fits for the l=2 spherical harmonic expansion coefficients of the radio brightness distribution on the sky using Parker Solar Probe/FIELDS/RFS data
Open the record for dataset details and reuse information.
Dataset for "Insect frass from upcycling vegetable by-products with cereals: effects on the soil properties, plant development and soil invertebrate fitness"
Open the record for dataset details and reuse information.
Migratory cavity nesters (Ficedula hypoleuca) incur fitness costs from ecological traps
<p><span>When selecting a habitat for breeding and offspring rearing, it is optimal for organisms to select a stable habitat with high amounts of quality resources. However, organisms may inadvertently select a habitat for breeding that would initially appear preferential and healthy, but may in reality be detrimental to parent and/or offspring fitness. Such ecological traps may even be the result of human habitat modification and conservation efforts. In this study, we tested whether migratory European pied flycatcher (</span>Ficedula hypoleuca) offspring cavity-nesting in patches of forest affected by outbreaks of the great web-spinning sawfly (Acantholyda posticalis<span>) incurred fitness detriments characteristic of ecological traps when compared to flycatchers that nested in patches of unaffected forest. Outbreaking sawfly larvae overconsume Scots pine (Pinus sylvestris) needles and substrate, which decreases resource availability directly and indirectly–through cascading effects–for birds inhabiting the forest. In installing nest boxes to attract breeding pairs and potentially combat the outbreak, we found that flycatchers inhabiting areas of sawfly outbreaks had similar clutch sizes to pairs breeding in healthy forest patches. Contrarily, the fledgling number and body condition were significantly lower for those nesting in the damaged forests. Though larvae serve as the primary food source for nestlings, the forest patches damaged by sawflies also had lower larval biomass from rapid resource decline due to overconsumption. In provisioning nest boxes for migrating flycatcher pairs in forest patches that were subsequently impacted by a pest insect outbreak, an ecological trap arose for those pairs choosing to nest in what appeared to be an unaffected forest at first. Given the inability of breeding pairs to distinguish habitat quality on initial inspection, we suggest that nest boxes be used with caution in areas with unstable habitat conditions when attracting migratory birds given the trends of their declining global numbers.</span></p>
Data from: Paternal care in a fish: epigenetics and fitness enhancing effects on offspring anxiety
In many animals, including humans, interactions with caring parents can have long-lasting effects on offspring sensitivity to stressors. However, whether these parental effects impact offspring fitness in nature is often unclear. In addition, despite evidence that maternal care can influence offspring behaviour via epigenetic alterations to the genome, it remains unclear whether paternal care has similar effects. Here, we show in three-spined sticklebacks, a fish in which fathers are the sole provider of offspring care, that the direct care provided by fathers affects offspring anxiety and the potential for epigenetic alterations to the offspring genome. We find that families are differentially vulnerable to early stress and fathers can compensate for this differential sensitivity with the quality of their care. This variation in paternal care is also linked to the expression in offspring brains of a DNA methyltransferase (Dnmt3a) responsible for de novo methylation. We show that these paternal effects are potentially adaptive and anxious offspring are unlikely to survive an encounter with a predator. By supplying offspring care, fathers reduce offspring anxiety thereby increasing the survival of their offspring—not in the traditional sense through resource provisioning but through an epigenetic effect on offspring behavioural development.
Data from: Genetic rescue increases fitness and aids rapid recovery of an endangered marsupial population
Genetic rescue has now been attempted in several threatened species, but the contribution of genetics per se to any increase in population health can be hard to identify. Rescue is expected to be particularly useful when individuals are introduced into small isolated populations with low levels of genetic variation. Here we consider such a situation by documenting genetic rescue in the mountain pygmy possum, Burramys parvus. Rapid population recovery occurred in the target population after the introduction of a small number of males from a large genetically diverged population. Initial hybrid fitness was more than two-fold higher than non-hybrids; hybrid animals had a larger body size, and female hybrids produced more pouch young and lived longer. Genetic rescue likely contributed to the largest population size ever being recorded at this site. These data point to genetic rescue as being a potentially useful option for the recovery of small threatened populations.
Data from: No correlation between multi-locus heterozygosity and fitness in the common buzzard despite heterozygote advantage for plumage colour
Correlations between heterozygosity and fitness are frequently found but rarely well understood. Fitness can be affected by single loci of large effect which correlate with neutral markers via linkage disequilibrium, or as a result of variation in genome-wide heterozygosity following inbreeding. We explored these alternatives in the common buzzard, a raptor species in which three colour morphs differ in their lifetime reproductive success. Using 18 polymorphic microsatellite loci, we evaluated potential genetic differences among the morphs which may lead to subpopulation structuring and tested for correlations between three fitness-related traits and heterozygosity, both genome wide and at each locus separately. Despite their assortative mating pattern, the buzzard morphs were found to be genetically undifferentiated. Multilocus heterozygosity was only found to be correlated with a single fitness-related trait, infection with the blood parasite, Leucocytozoon buteonis, and this was via interactions with vole abundance and age. One locus also showed a significant relationship with blood parasite infection and ectoparasite infestation. The vicinity of this locus contains two genes, one of which is potentially implicated in the immune system of birds. We conclude that genome-wide heterozygosity is unlikely to be a major determinant of parasite burden and body condition in the polymorphic common buzzard.
ScienceDex guides
Understand access before you commit
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.