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3,139 results for “fitting”
Social effects on annual fitness in red squirrels
<p>When resources are limited, mean fitness is constrained and competition can cause genes and phenotypes to enhance an individual's own fitness while reducing the fitness of their competitors. Negative social effects on fitness have the potential to constrain adaptation, but the interplay between ecological opportunity and social constraints on adaptation remains poorly studied in nature. Here, we tested for evidence of phenotypic social effects on annual fitness (survival and reproductive success) in a long-term study of wild North American red squirrels (Tamiasciurus hudsonicus) under conditions of both resource limitation and super-abundant food resources. When resources were limited, populations remained stable or declined, and there were strong negative social effects on annual survival and reproductive success. That is, mean fitness was constrained and individuals had lower fitness when other nearby individuals had higher fitness. In contrast, when food resources were super-abundant, populations grew and social constraints on reproductive success were greatly reduced or eliminated. Unlike reproductive success, social constraints on survival were not significantly reduced when food resources were super-abundant. These findings suggest resource-dependent social constraints on a component of fitness, which have important potential implications for evolution and adaptation.</p>
Genomic shifts, phenotypic clines and fitness costs associated with cold-tolerance in the Asian tiger mosquito
<p>Climatic variation is a key driver of genetic differentiation and phenotypic traits evolution, and local adaptation to temperature is expected in widespread species. We investigated phenotypic and genomic changes in the native range of the Asian tiger mosquito, <em>Aedes</em> <em>albopictus</em>. We first refine the phylogeographic structure based on genome-wide regions (1,901 double-digest restriction-site associated DNA single nucleotide polymophisms [ddRAD SNPs]) from 41 populations. We then explore the patterns of cold adaptation using phenotypic traits measured in common garden (wing size and cold tolerance) and genotype–temperature associations at targeted candidate regions (51,706 exon-capture SNPs) from nine populations. We confirm the existence of three evolutionary lineages including clades A (Malaysia, Thailand, Cambodia, and Laos), B (China and Okinawa), and C (South Korea and Japan). We identified temperature-associated differentiation in 15 out of 221 candidate regions but none in ddRAD regions, supporting the role of directional selection in detected genes. These include genes involved in lipid metabolism and a circadian clock gene. Most outlier SNPs are differently fixed between clades A and C, whereas clade B has an intermediate pattern. Females are larger at higher latitudes yet produce no more eggs, which might favor the storage of energetic reserves in colder climates. Nondiapausing eggs from temperate populations survive better to cold exposure than those from tropical populations, suggesting they are protected from freezing damages but this cold tolerance has a fitness cost in terms of egg viability. Altogether, our results provide strong evidence for the thermal adaptation of <em>A</em>. <em>albopictus</em> across its wide temperature range.</p>
Data from: No evidence for impaired solitary bee fitness following pre-flowering sulfoxaflor application alone or in combination with a common fungicide in a semi-field experiment
<p class="MsoNormal"><span>Pesticide exposure is considered a major driver of pollinator decline and the use of neonicotinoid insecticides has been restricted by regulatory authorities due to their risks for pollinators. Impacts of new alternative sulfoximine-based compounds on solitary bees and their potential interactive effects with other commonly applied pesticides in agriculture remain unclear. Here, we conducted a highly replicated full-factorial semi-field experiment with the solitary bee <em>Osmia bicornis</em>, an important pollinator of crops and wild plants in Europe, and <em>Phacelia tanacetifolia</em> as a model crop. We show that spray applications of the insecticide sulfoxaflor (product Closer) and the fungicide azoxystrobin (product Amistar), both alone and combined, had no significant negative impacts on adult female survival or the production, mortality, sex ratio and body size of offspring when sulfoxaflor was applied five days before crop flowering. Our results indicate that for <em>O. bicornis</em> (1) the risk of adverse impacts of sulfoxaflor (Closer) on fitness is small when applied at least five days before crop flowering and (2) that azoxystrobin (Amistar) has a low potential of exacerbating sulfoxaflor effects under field-realistic conditions.</span></p>
Biomass data to accompany Inter-chromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance
<ul> <li>The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance.</li> <li>Here, using herbicide-resistant populations of the common morning glory (<em>Ipomoea</em> <em>purpurea</em>), we perform a multi-level analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations.</li> <li>We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost.</li> <li>Overall, our work suggests that NTSR glyphosate resistance in<em> I. purpurea</em> is conferred by multiple genes which are potentially maintained through generations <em>via</em> ILD and that the fitness cost associated with resistance in this species is likely a by-product of genetic-hitchhiking.</li> </ul>
Fitting and evaluating univariate and multivariate models of within-lineage evolution
<p><span>The nature of phenotypic evolution within lineages is central to many unresolved questions in paleontology and evolutionary biology. Analyses of evolutionary time-series of ancestor-descendant populations in the fossil record are likely to make important contributions to many of these debates. However, the limited number of models that have been applied to these types of data may restrict our ability to interpret phenotypic evolution in the fossil record. </span>Using uni- and multivariate models of trait evolution <span>that make different assumptions regarding</span> <span>the </span>dynamic<span>s of the</span> adaptive landscape, I evaluate contrasting hypotheses to explain evolution of size in the radiolarian <em><span>Eucyrtidium calvertense</span></em> and armor in the stickleback <em>Gaserosteus doryssus</em>. Body size evolution in <span><em>E. calvertense</em> </span><span>is best explained by a model where the lineage evolves as a consequence of a shift in the adaptive landscape that coincides with the initiation of neosympatry with its sister lineage. Multivariate evolution of armor traits in a stickleback lineage (<em>Gasterosteus</em> <em>doryssus</em>) shows evidence of adaptation towards independent optima on the adaptive landscape at the same time as traits change in a correlated fashion. The fitted models are available in an R package evoTS, which builds on the commonly used paleoTS framework.</span></p>
Supplementary data for "The fitness of beta-lactamase mutants depends nonlinearly on resistance level at sublethal antibiotic concentrations."
<p>Supplementary data files and scripts, notes and figures accompanying the manuscript with working title "The fitness of beta-lactamase mutants depends nonlinearly on resistance level at sublethal antibiotic concentrations". The figures and tables this dataset underpins is indicated in the name of each file of the dataset, or in the section "Code and data accessibility" of the manuscript.</p>
MM-Fit Dataset - physical exercise workout sessions (video)
<p>This repository contains the video recording of 20 physical exercise workout sessions, which is part of the <strong>MM-Fit Dataset. </strong>Further details about our dataset and other time synchronised sensor data modalities (accelerometer, gyroscope, heart rate) collected with wearable devices during these workout sessions can be found on the project page: https://mmfit.github.io/</p> <p>If you find our dataset useful and use it in your work please cite our paper:</p> <p>David Strömbäck, Sangxia Huang, Valentin Radu, <strong>MM-Fit: Multimodal Deep Learning for Automatic Exercise Logging Across Sensing Devices</strong>, ACM Interactive, Mobile, Wearable and Ubiquitous Technologies (IMWUT): Volume 4 Issue 4, December 2020.</p> <pre>@article{stromback2020mm, title={Mm-fit: Multimodal deep learning for automatic exercise logging across sensing devices}, author={Str{\"o}mb{\"a}ck, David and Huang, Sangxia and Radu, Valentin}, journal={Proceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous Technologies}, volume={4}, number={4}, pages={1--22}, year={2020}, publisher={ACM New York, NY, USA} }</pre>
FIG. 3 in Body Color and Morphological Correlates of Fitness in Eastern Fence Lizards (Sceloporus undulatus): A Spectrophotometric Approach
FIG. 3.—Significant regressions of abdominal body color against morphometric traits for female Eastern Fence Lizards (Sceloporus undulatus) collected in 2013 from Dauset Trails Nature Center (Butts County, GA). (A) Ventral UV chroma X snout-vent length (SVL), (B) ventral UV chroma X body condition, (C) ventral blue chroma X body condition, (D) dorsal hue X SVL, (E) dorsal UV chroma X SVL. Female dorsal hue was not normally distributed and did not normalize following transformation. Data for dorsal UV chroma were normalized using reciprocal transformations (see Methods), but the untransformed data are presented here for simplicity.
FIG. 2 in Body Color and Morphological Correlates of Fitness in Eastern Fence Lizards (Sceloporus undulatus): A Spectrophotometric Approach
FIG. 2.—Significant regressions of abdominal body color against morphometric traits for male Eastern Fence Lizards (Sceloporus undulatus) collected in 2013 from Dauset Trails Nature Center (Butts County, GA). (A) Ventral UV chroma X snout-vent length (SVL), (B) ventral blue chroma X SVL, (C) ventral blue chroma X patch area, (D) dorsal UV chroma X SVL. Values for UV chroma in panels A and D are depicted following a natural logarithmic transformation.
FIG. 1 in Body Color and Morphological Correlates of Fitness in Eastern Fence Lizards (Sceloporus undulatus): A Spectrophotometric Approach
FIG. 1.—Body coloration in adult Eastern Fence Lizards (Sceloporus undulatus) at 36°C. (A) Photographs of representative examples of male and female body color. (B) Mean spectral reflectance curves (males, n ¼ 28; females, n ¼ 12) of dorsal and ventral abdominal coloration. Solid brown line ¼ male dorsum; solid blue line ¼ male venter; dotted brown line ¼ female dorsum; dotted black line ¼ female venter. Spectral reflectance data from Stephenson et al. (2017). Republished with permission of the Linnean Society of London.
Training simulations for emulator fitting in study of landslide-generated tsunamis in the Makassar Strait
<p><strong>Training simulations used in the study titled 'Probabilistic landslide tsunami estimation in the Makassar Strait, Indonesia, using statistical emulation'</strong></p> <p>Description:</p> <ul> <li>'dem' directory - Bathymetric/Topographic data required to run simulations</li> <li>'Simulation{1..50}' directories: <ul> <li>eta.mp4 - video animation of wave propagation</li> <li>{1..50}.c and topics.h - code and header file for simulation</li> <li>etamax.dat - XYZ file of maximum surface elevation for simulation</li> <li>gauges directory - .dat files containing timeseries outputs for each gauge</li> </ul> </li> </ul>
Fitness costs and oviposition choice of C. nenuphar on blueberry and peach
<p>In phytophagous insects, adult attraction and oviposition preference for a host plant is often positively correlated with their immature performance; however, little is known how this preference-performance relationship changes within insect populations utilizing different host plants. Here, we investigated differences in the preference and performance of two populations of a native North American frugivorous insect pest, the plum curculio (Conotrachelus nenuphar) ‒ one that utilizes peaches and another that utilizes blueberries as hosts ‒ in the Mid-Atlantic United States. For this, we collected C. nenuphar adult populations from peach and blueberry farms and found that they exhibited a clear preference for the odors of, as well as an ovipositional preference for, the hosts they were collected from, laying 67-83% of their eggs in their respective natal hosts. To measure C. nenuphar larval performance, a fitness index was calculated using data on larval weights, development, and survival rate from egg to fourth instars when reared on the parent's natal and novel hosts. Larvae of C. nenuphar adults collected from peach had high fitness on peach but low fitness when reared on blueberry. In contrast, larvae from C. nenuphar adults collected in blueberry had high fitness regardless of the host they were reared on. In this study, we show that utilizing a novel host such as blueberry incurs a fitness cost for C. nenuphar from peaches, but this cost was not observed for C. nenuphar from blueberries, indicating that the preference-performance relationship depends on the particular insect population-host plant association.</p>
Data from: Integrated species distribution models fitted in INLA are sensitive to mesh parameterisation
<p class="MsoNormal">The ever-growing popularity of citizen science, as well as recent technological and digital developments, have allowed the collection of data on species' distributions at an extraordinary rate. In order to take advantage of these data, information of varying quantity and quality needs to be integrated. Point process models have been proposed as an elegant way to achieve this for estimates of species distributions. These models can be fitted efficiently using Bayesian methods based on integrated nested Laplace approximations (INLA) with stochastic partial differential equations (SPDE). This approach uses an efficient way to model spatial autocorrelation using a Gaussian random field and a triangular mesh over the spatial domain. The mesh is constructed by user-defined variables, so effectively represents a free parameter in the model. However, there is a lack of understanding about how to set these mesh parameters, and their effect on model performance. Here, we assess how mesh parameters affect predictions and model fit to estimate the distribution of the serotine bat, <em><span>Eptesicus serotinus</span></em><span>,<em> </em>in Great Britain. A Bayesian INLA model was fitted using five meshes of varying densities to a dataset comprising both structured observations from a national monitoring programme and opportunistic records. We demonstrate that mesh density impacted spatial predictions with a general loss of accuracy with increasing mesh coarseness</span>. However, we also show that the finest mesh was unable to overcome spatial biases in the data. In addition, the magnitude of the covariate effects differed markedly between meshes. This confirms that mesh parameterisation is an important and delicate process with implications for model inference. We discuss how species distribution modellers might adapt their use of INLA in light of these findings.</p>
FIG. 4. Individual growth model fits for 36 in Hoplodactylus duvaucelii
FIG. 4. Individual growth model fits for 36 male Diamondback Terrapins. Blue lines represent the individual von Bertalanffy model fits for the corresponding plastron-at-age observations, which are represented with black dots. The 95% credible regions are show in the pink-shaded region.
FIG. 1. Individual growth model fits for 44 in Hoplodactylus duvaucelii
FIG. 1. Individual growth model fits for 44 female Diamondback Terrapins. Red lines represent the individual von Bertalanffy model fits for the corresponding plastron-at-age observations, which are represented with black dots. The 95% credible regions are shown in the blue-shaded region.
Generated sequences and fitness data for ProGen2
<p>Sequences generated from pretrained and fine-tuned ProGen2 models. Fitness benchmark data for evaluation of ProGen2 models.</p>
Bleaching and Gaussian fitting (Inverse Photobleach Flow)
<p>Bleaching and Gaussian fitting (Inverse Photobleach Flow)</p>
Universal Dynamic Fitting of Magnetic Resonance Spectroscopy - Data
<p>Original data for the in vivo experiments included in the article Universal Dynamic Fitting of Magnetic Resonance Spectroscopy by William T Clarke, Clémence Ligneul, Michiel Cottaar, Betina Ip and Saad Jbabdi (Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, UK).</p> <p>This data accompanies the online <a href="https://git.fmrib.ox.ac.uk/wclarke/fsl-mrs-dynamic-fitting">code repository</a>. Note that this repository contains preprocessed versions of this data already.</p> <p>Two files are included:</p> <ol> <li>fmrs_invivo_unprocessed_data.zip - NIfTI-MRS formatted data relating to the fMRS in vivo example in this work. Data is originally from <a href="https://doi.org/10.1016/j.neuroimage.2017.04.030">10.1016/j.neuroimage.2017.04.030</a>.</li> <li>dwmrs_invivo_original_data.zip = matlab .mat data relating tot he dwMRS in vivo example in this work. Data is originally from <a href="https://doi.org/10.1016/j.neuroimage.2019.02.046">10.1016/j.neuroimage.2019.02.046</a>.</li> </ol> <p>If you use this data in your work please cite this work (Universal Dynamic Fitting of Magnetic Resonance Spectroscopy) once available and the originating publications.</p>
Mismatches between phenotype and environment shape fitness at hyperlocal scales (Agama atra)
<p><span>In the era of human-driven climate change, understanding whether behavioural buffering of temperature change is linked with organismal fitness is essential.</span><span> According to the "cost-benefit" model of thermoregulation, animals that live in environments with high frequencies of favourable thermal microclimates should incur lower thermoregulatory costs, thermoregulate more efficiently and shunt the associated savings in time and energy towards other vital tasks such as feeding, territory defence, and mate acquisition, increasing fitness. </span><span>Here, we explore how thermal landscapes at the scale of individual territories, physiological performance, and behaviour interact and shape fitness in the southern rock agama lizard (<em>Agama</em> <em>atra</em>). We integrated laboratory assays of whole organism performance with behavioural observations in the field, fine-scale estimates of environmental temperature, and paternity assignment of offspring to test whether fitness is predicted by territory thermal quality (i.e.,</span> <span>the number of hours that operative temperatures in a territory fall within individual's performance breadth). Male lizards that occupied territories of low thermal quality spent more time behaviourally compensating for suboptimal temperatures and displayed less. Further, display rate was positively associated with lizard fitness, suggesting that there is an opportunity cost to engaging in thermoregulatory behaviour that will increase as climate change progresses. </span></p>
Data from: The CD73 immune checkpoint promotes tumor cell metabolic fitness
<p>CD73 is an ectonucleotidase overexpressed on tumor cells that suppresses anti-tumor immunity. Accordingly, several CD73 inhibitors are currently being evaluated in the clinic, including in large randomized clinical trials. Yet, the tumor cell-intrinsic impact of CD73 remains largely uncharacterized. Using metabolomics, we discovered that CD73 significantly enhances tumor cell mitochondrial respiration and aspartate biosynthesis. Importantly, rescuing aspartate biosynthesis was sufficient to restore proliferation of CD73-deficient tumors in immune-deficient mice. Seahorse analysis of a large panel of mouse and human tumor cells demonstrated that CD73 enhanced oxidative phosphorylation (OXPHOS) and glycolytic reserve. Targeting CD73 decreased tumor cell metabolic fitness, increased genomic instability and suppressed poly ADP ribose polymerase (PARP) activity. Our study thus uncovered an important immune-independent function for CD73 in promoting tumor cell metabolism and provides the rationale for previously unforeseen combination therapies incorporating CD73 inhibition.</p>
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.