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106 results for “relative fit”
Complete Hydrogen Column Density Fit Data for NH/AV Relation Calculation
<p>Xspec fit summaries (and graphics of fits) for multiple regions within 17 supernova remnants. Complete data is included on html pages (which make browsing the data easier). Hydrogen column density (NH) fit values were combined with published optical extinction values (AV) to determine the slope of the linear relationship between the two measurements. The NH data alone is included in a spreadsheet format.</p>
Consistent traffic noise impacts few fitness-related traits in a field cricket
<p>Anthropogenic habitat change is occurring rapidly, and organisms can respond through within-generation responses that improve the match between their phenotype and the novel conditions they encounter. But, plastic responses can be adaptive or maladaptive and are most likely to be adaptive only when contemporary conditions reasonably mimic something experienced historically to which a response has already evolved. Noise pollution is a ubiquitous anthropogenic stressor that accompanies expanding urbanization. We tested whether the amplitude of traffic noise influences a suite of fitness-related traits (e.g. survival, life history, reproductive investment, immunity) and whether that depends on the life stage at which the noise is experienced (juvenile or adult). Our treatments mimic the conditions experienced by animals living in urban roadside environments with variable vehicle types, but continuous movement of traffic. We used the Pacific field cricket, an acoustically communicating insect that was previously shown to experience some negative behavioral and life history responses to very loud, variable traffic noise, as a model system. </p>
Data and fitting script for "Direct measurement of a sin(2φ) current phase relation in a graphene superconducting quantum interference device"
<p>This repository contains data and Python analysis scripts used for the publication "Direct measurement of a sin(2\phi) current phase relation in a graphene superconducting quantum interference device (https://doi.org/10.48550/arXiv.2405.13642).</p> <p>The repository is organized as follows: the raw data are encapsulated in a QCoDes database (https://microsoft.github.io/Qcodes/) named 'D-SQUID-06.db'. Post-treated critical current data are included as .csv files and are indexed by measurement ids.</p> <p>The principal analysis is realized in the Jupyter notebook 'Fits_and_Figures.ipynb', which includes all article figures as well as fit functions for fitting both critical currents Ic- and Ic+ simulatenously, first using analytical expression from equation 3 then using numerical expression from equation 5. All fits mentionned in the article are performed there. The repository includes a generic notebook "Extract_Critical_Current.ipynb" used to explore the raw data in the Qcodes database and features an enhanced peak detection script that we used to automatically extract critical current data despite having some artifacts on raw differential conductance versus bias current and magnetic field.</p> <p>We acknowledge the contribution of R. Kerjouan for developing the Python fitting script.</p>
Phenotype, genotype and fitness data related to genetic analysis of praziquantel response in schistosome parasites.
<p>These data are related to the study of the Genetic analysis of praziquantel response in schistosome parasites implicates a Transient Receptor Potential channel.</p> <p>Mass treatment with praziquantel (PZQ) monotherapy is the mainstay for schistosomiasis treatment. This drug shows imperfect cure rates in the field and parasites showing reduced PZQ response can be selected in the laboratory, but the extent of resistance in <em>Schistosoma mansoni</em> populations is unknown. We examined the genetic basis of variation in PZQ response in a <em>S. mansoni</em> population (SmLE-PZQ-R) selected with PZQ in the laboratory: 35% of these worms survive high dose (73 µg/mL) PZQ treatment. We used genome wide association to map loci underlying PZQ response. The major chr. 3 peak contains a transient receptor potential (Sm.TRPM_PZQ) channel (Smp_246790), activated by nanomolar concentrations of PZQ. PZQ response shows recessive inheritance and marker-assisted selection of parasites at a single Sm.TRPM_PZQ SNP enriched populations of PZQ-resistant (PZQ-ER) and sensitive (PZQ-ES) parasites showing >377 fold difference in PZQ response. The PZQ-ER parasites survived treatment in rodents better than PZQ-ES. Resistant parasites show 2.25-fold lower expression of Sm.TRPM_PZQ than sensitive parasites. Specific chemical blockers of Sm.TRPM_PZQ enhanced PZQ resistance, while Sm.TRPM_PZQ activators increased sensitivity. A single SNP in Sm.TRPM_PZQ differentiated PZQ-ER and PZQ-ES lines, but mutagenesis showed this was not involved in PZQ response, suggesting linked regulatory changes. We surveyed Sm.TRPM_PZQ sequence variation in 259 parasites from the New and Old World revealing one nonsense mutation that results in a truncated protein with no PZQ-binding site. Our results demonstrate that Sm.TRPM_PZQ underlies variation in PZQ response in <em>S. mansoni</em> and provides an approach for monitoring emerging PZQ-resistance alleles in schistosome elimination programs.</p> <p>This dataset is divided in 3 folders. Each folder has a readme detailing its content.</p> <p><strong>1-Phenotyping_data</strong></p> <p>This folder includes the data tables related to the phenotyping of the worms performed during this study. The phenotype measured was the viability of worms following PZQ treatment (i.e., PZQ response). This viability was assessed microscopically or using worm lactate production released in culture media.</p> <p>The data correspond to the following experiments:</p> <ul> <li>PZQ response of single adult male worms from SmLE and SmLE-PZQ-R populations to different doses of PZQ. This data was used to determine the PZQ IC50 of each population.</li> <li>Lactate production from single SmLE-PZQ-R adult male worms and correlation with visual observation. This was a proof-of-principle that lactate production can be used to efficiently and unbiasedly phenotype schistosome adult male worms in response to PZQ drug.</li> <li>PZQ response of single SmLE-PZQ-R adult male worms. These worms were then divided in low and high producer in response to PZQ and used to perform a genome-wide association study.</li> <li>PZQ response of single adult male worms from SmLE-PZQ-ER and SmLE-PZQ-ES populations to different doses of PZQ. This data was used to determine the PZQ IC50 of each population.</li> <li>PZQ response of single adult male worms from SmLE-PZQ-ER and SmLE-PZQ-ES populations in presence of Sm.TRPM_PZQ blocker (MB2) and activator (MV1) with and without PZQ drug.</li> <li>In vivo PZQ response of schistosome worms from SmLE-PZQ-ER and SmLE-PZQ-ES populations.</li> </ul> <p><strong>2-Genotyping_data</strong></p> <p>This folder includes the data tables related to the genotyping of the worms performed during this study. Worms were genotyping using PCR-RFLP (genotyping of single nucleotide polymorphisms (SNPs) on chr2 and chr3 QTLs) or using qPCR (genotyping of a copy number variation (CNV) on chr3 QTL).</p> <p>The data correspond to the following experiment:</p> <ul> <li>Association between PZQ response of single adult male worms from SmLE-PZQ-R population and their respective genotype on chromosome 2 (SNP) and chromosome 3 (SNP and CNV) loci.</li> </ul> <p><strong>3-Fitness_data</strong></p> <p>This folder includes the data tables related to the fitness of the parasite populations. We collected data regarding:</p> <ul> <li>The number of surviving and infected snails after exposure to SmLE-PZQ-ER or SmLE-PZQ-ES miracidia.</li> <li>The number of adult worms recovered from golden Syrian female hamsters exposed to SmLE-PZQ-ER or SmLE-PZQ-ES cercariae.</li> </ul> <p>All the data were collected during 12 generations of parasites and are used to evaluate a potential impact of PZQ resistance on the parasite fitness.</p>
Consistent traffic noise impacts few fitness-related traits in a field cricket
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Data from: Fitness outcomes in relation to individual variation in constitutive innate immune function
<p>Although crucial for host survival when facing persistent parasite pressure, costly immune functions will inevitably compete for resources with other energetically expensive traits such as reproduction. Optimising, but not necessarily maximising, immune function might therefore provide net benefit to overall host fitness. Evidence for associations between fitness and immune function is relatively rare, limiting our potential to understand ultimate fitness costs of immune investment. Here, we assess how measures of constitutive immune function (haptoglobin, natural antibodies, complement activity) relate to subsequent fitness outcomes (survival, reproductive success, dominance acquisition) in a wild passerine (<i>Malurus coronatus</i>). Surprisingly, survival probability was not positively linearly predicted by any immune index. Instead, both low and high values of complement activity (quadratic effect) were associated with higher survival, suggesting that different immune investment strategies might reflect a dynamic disease environment. Positive linear relationships between immune indices and reproductive success suggest that individual heterogeneity overrides potential resource reallocation trade-offs within individuals. Controlling for body condition (size-adjusted body mass) and chronic stress (heterophil-lymphocyte ratio) did not alter our findings in a sample subset with available data. Overall, our results suggest that constitutive immune components have limited net costs for fitness and that variation in immune maintenance relates to individual differences more closely.</p>
Data from: Age-related variation in non-breeding foraging behaviour and carry-over effects on fitness in an extremely long-lived bird
1. Senescence has been widely documented in wild vertebrate populations, yet the proximate drivers of age-related declines in breeding success, including allocation trade-offs and links with foraging performance, are poorly understood. For long-lived, migratory species, the non-breeding period represents a critical time for investment in self-maintenance and restoration of body condition, which in many species is linked to fitness. However, the relationships between age, non-breeding foraging behaviour and fitness remain largely unexplored. 2. We performed a cross-sectional study, investigating age-related variation in the foraging activity, distribution and diet of an extremely long-lived seabird, the wandering albatross Diomedea exulans during the non-breeding period, and its links with subsequent reproductive performance. 3. We tracked the distributions of 82 adults aged 8 – 33 years with geolocator-immersion loggers and found an age-related decline in the number of landings (a proxy of foraging effort) during daylight hours. There was a decrease in body feather δ13C values in older males but not females, yet this did not accompany an age-related shift in distributions. Males conducted fewer landings than females, and the sexes were spatially segregated, with males foraging further south, likely due to their differential utilization of winds. 4. While younger (< 20 years) birds had higher foraging activity, all individuals went on to breed successfully the following season. In contrast, among older (20+ years) birds, individuals that landed more often were more likely to defer breeding or fail during incubation, suggesting they have lower foraging success. 5. As far as we are aware, this is the first demonstration of an age-specific carry-over effect of foraging behaviour in the non-breeding period on subsequent reproductive performance. This link between foraging behaviour and fitness in late but not early adulthood indicates that the ability of individuals to forage efficiently outside the breeding period may be an important driver of fitness differences in old age.
A Test of the Repeatability of Measurements of Relative Fitness in the Long-Term Evolution Experiment with Escherichia coli
<p>Experimental studies of evolution using microbes have a long tradition, and these studies have increased greatly in number and scope in recent decades. Most such experiments have been short in duration, typically running for weeks or months. A venerable exception, the long-term evolution experiment (LTEE) with <i>Escherichia coli</i> has continued for 30 years and 70,000 bacterial generations. The LTEE has become one of the cornerstones of the field of experimental evolution, in general, and the BEACON Center for the Study of Evolution in Action, in particular. Science laboratories and experiments usually have finite lifespans, but we hope that the LTEE can continue far into the future. There are practical issues associated with maintaining such a long-term experiment. One issue, which we address here, is whether key measurements made at one time and place are reproducible, within reasonable limits, at other times and places. This issue comes to the forefront when one considers moving an experiment like the LTEE from one lab to another. To that end, the Barrick lab at the University of Texas at Austin, measured the fitness values of samples from the 12 LTEE populations at 2,000, 10,000, and 50,000 generations and compared the new data to data previously obtained at Michigan State University. On balance, the datasets agree very well. More generally, this finding shows the value of simplicity in experimental design, such as using a chemically defined growth medium and appropriately storing samples from microbiological experiments. Even so, one must be vigilant in checking assumptions and procedures given the potential for uncontrolled factors (e.g., water quality) to affect outcomes. This vigilance is perhaps especially important for a trait like fitness, which integrates all aspects of organismal performance and may therefore be sensitive to any number of subtle environmental influences.</p>
Data from: Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments
Assays to accurately estimate relative fitness of bacteria growing in multistrain communities can advance our understanding of how selection shapes diversity within a lineage. Here, we present a variant of the "evolve and resequence" approach both to estimate relative fitness and to identify genetic variants responsible for fitness variation of symbiotic bacteria in free-living and host environments. We demonstrate the utility of this approach by characterizing selection by two plant hosts and in two free-living environments (sterilized soil and liquid media) acting on synthetic communities of the facultatively symbiotic bacterium Ensifer meliloti. We find (i) selection that hosts exert on rhizobial communities depends on competition among strains, (ii) selection is stronger inside hosts than in either free-living environment, and (iii) a positive host-dependent relationship between relative strain fitness in multistrain communities and host benefits provided by strains in single-strain experiments. The greatest changes in allele frequencies in response to plant hosts are in genes associated with motility, regulation of nitrogen fixation, and host/rhizobia signaling. The approach we present provides a powerful complement to experimental evolution and forward genetic screens for characterizing selection in bacterial populations, identifying gene function, and surveying the functional importance of naturally occurring genomic variation.
Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity
<p>Despite its implications for population dynamics and evolution, the relationship between genetic and phenotypic variation in wild populations remains unclear. Here, we estimated variation and plasticity in life-history traits and fitness of the annual plant <em>Arabidopsis thaliana</em> in two common garden experiments that differed in environmental conditions. We used up to 306 maternal inbred lines from six Iberian populations characterized by low and high genotypic (based on whole-genome sequences) and ecological (vegetation type) diversity. Low and high genotypic and ecological diversity was found in edge and core Iberian environments, respectively. Given that selection is expected to be stronger in edge environments and that ecological diversity may enhance both phenotypic variation and plasticity, we expected genotypic diversity to be positively associated with phenotypic variation and plasticity. However, maternal lines, irrespective of the genotypic and ecological diversity of their population of origin, exhibited a substantial amount of phenotypic variation and plasticity for all traits. Furthermore, all populations harbored maternal lines with canalization (robustness) or sensitivity in response to harsher environmental conditions in one of the two experiments. Overall, we conclude that the environmental attributes of each population probably determine their genotypic diversity, but all populations maintain substantial phenotypic variation and plasticity for all traits, which represents an asset to endure in changing environments.</p>
Data for: Telomere dynamics in relation to experimentally increased locomotion costs and fitness in great tits
<p>Evidence that telomere length (TL) and dynamics can be interpreted as proxy for 'life stress' experienced by individuals stems largely from correlational studies. We tested for effects of an experimental increase of workload on telomere dynamics by equipping male great tits (Parus major) with a 0.9 gram backpack for a full year. In addition, we analysed associations between natural life-history variation, TL and TL dynamics. Carrying 5% extra weight for a year did not significantly accelerate telomere attrition. This agrees with our earlier finding that this experiment did not affect survival or future reproduction. Apparently, great tit males were able to compensate behaviourally or physiologically for the increase in locomotion costs we imposed. We found no cross-sectional association between reproductive success and TL, but individuals with higher reproductive success (number of recruits) lost fewer telomere base pairs in the subsequent year. We used the TRF method to measure TL, which method yields a TL distribution for each sample, and the association between reproductive success and telomere loss was more pronounced in the higher percentiles of the telomere distribution, in agreement with the higher impact of ageing on longer telomeres within individuals. Individuals with longer telomeres and less telomere shortening were more likely to survive to the next breeding season, but these patterns did not reach statistical significance. Whether successful individuals are characterized by losing fewer or more base pairs from their telomeres varies between species, and we discuss aspects of ecology and social organisation that may explain this variation.</p>
Transgenerational phenotypic plasticity of diapause induction and related fitness cost in a commercial strain of the parasitoid Aphidius ervi Haliday
<p>Dataset.</p> <p>Diapause is an adaptation that insects have evolved to synchronize their life cycle with that of seasonal climatic changes and resources availability. However, cues for its induction are not always clear and, in some cases, a maternal effect may be involved. At the population level, just a part of the individuals may exhibit diapause with important consequences in terms of winter survival. Moreover, clear indicators of diapause state are difficult to identify. Diapause induction was thus investigated in the aphid parasitoid species Aphidius ervi Haliday (Hymenoptera: Braconidae) developing in the aphid Sitobion avenae (Hemiptera: Aphididae) at four crossed photothermal regimes (16 °C and 8 °C, 16:8 h L:D and 8:16 h L:D), and during 2 successive generations. We analyzed the reliability of changes in mummy color to assess for the diapausing state compared to dissections, and we measured parasitoid morphological and physiological traits. We observed that the proportion of dark brown mummies increased after one generation under low photothermal regime compared to other regimes. No diapause was recorded at 16 °C, 16:8 h L:D, while we observed 16.2% and 67.5% diapause incidence at 8 °C, 8:16 h L:D, at 1st and 2nd generation, respectively. Diapause induction is thus increased by short day-length conditions and low temperatures as well as by maternal effects. All parasitoid life-history traits (weight, size, fat content, water content, egg-load, and longevity) were affected by the photothermal regime and/or the generation. These results raise new questions on the environmental thresholds needed to induce diapause and on survival and adaptation potential of commercially available parasitoid strains in different environments.</p>
Novel environments induce variability in fitness-related traits
<p class="MsoNormal">Environmental change from anthropogenic activities threatens individual organisms, the persistence of populations, and entire species. Rapid environmental change puts organisms in a double bind, they are forced to contend with novel environmental conditions but with little time to respond. Phenotypic plasticity can act quickly to promote establishment and persistence of individuals and populations in novel or altered environments. In typical environmental conditions, fitness-related traits can be buffered, reducing phenotypic variation in expression of traits, and allowing underlying genetic variation to accumulate without selection. In stressful conditions, buffering mechanisms can break down, exposing underlying phenotypic variation and permitting the expression of phenotypes that may allow populations to persist in the face of altered or otherwise novel environments. Using reciprocal transplant experiments of freshwater snails, we demonstrate that novel conditions induce higher variability in growth rates and, to a lesser degree, morphology (area of the shell opening) relative to natal conditions. Our findings suggest a potentially important role of phenotypic plasticity in population persistence as organisms face a rapidly changing, human-altered world.</p>
A Study to Evaluate the Relative Bioavailability of Subcutaneous Bepirovirsen When Delivered From a Vial or Prefilled Syringe Fitted With a Safety Syringe Device in Healthy Adult Participants
ClinicalTrials.gov study NCT06058390. IPD Sharing: YES. Countries: 1. Publications: 1.
Data from: Fitness outcomes in relation to individual variation in constitutive innate immune function
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Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity
Open the record for dataset details and reuse information.
Data from: Age-related variation in non-breeding foraging behaviour and carry-over effects on fitness in an extremely long-lived bird
Open the record for dataset details and reuse information.
A Test of the Repeatability of Measurements of Relative Fitness in the Long-Term Evolution Experiment with Escherichia coli
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Data from: Spatiotemporal variation in selection on floral traits related to abortion rate, predispersal seed predation, and fitness variance
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Data from: Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments
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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.