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1,157 results for “Limited data”
Data from: Genomic, ecological, and morphological approaches to investigating species limits: a case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes
A wide variety of species are distinguished by slight color variations. However, molecular analyses have repeatedly demonstrated that coloration does not always correspond to distinct evolutionary histories between closely related groups, suggesting that this trait is labile and can be misleading for species identification. In the present study, we analyze the evolutionary history of sister species of Prionurus surgeonfishes in the Tropical Eastern Pacific (TEP), which are distinguished by the presence or absence of dark spots on their body. We examined the species limits in this system using comparative specimen-based approaches, a mitochondrial gene (COI), more than 800 nuclear loci (Ultraconserved Elements), and abiotic niche comparisons. The results indicate there is a complete overlap of meristic counts and morphometric measurements between the two species. Further, we detected multiple individuals with intermediate spotting patterns suggesting that coloration is not diagnostic. Mitochondrial data recovered a single main haplotype shared between the species and all locations resulting in a complete lack of structure (ST = 0). Genomic analyses also suggest low levels of genetic differentiation (FST = 0.013), and no alternatively fixed SNPs were detected between the two phenotypes. Furthermore, niche comparisons could not reject niche equivalency or similarity between the species. These results suggest that these two phenotypes are conspecific and widely distributed in the TEP. Here we recognize Prionurus punctatus Gill 1862 as a junior subjective synonym of P. laticlavius (Valenciennes 1846). The underlying causes of phenotypic variation in this species is unknown. However, this system gives insight into general evolutionary dynamics within the TEP.
COLOURATION IN 2.5D LOCAL WAVE FIELD SYNTHESIS USING SPATIAL BANDWIDTH-LIMITATION -- Data
<p>This data set contains stimuli and results from an experiment for human perception of colouration in Stereophonics, Wave Field Synthesis, Near-Field-Compensated Higher-Order Ambisonics and Local Wave Field Synthesis simulated via binaural synthesis using head related impulse responses (HRIRs). The corresponding binaural room scanning (BRS) files for the binaural simulation can be found in the directory `brs`. The employed stimuli is contained in `stimuli`. The Multiple Stimulus with Hidden Reference and Anchor (MUSHRA) ratings are stored in `results` together with a text file to describe the content in more detail. The `analysis` directory includes scripts for the statistical evaluation in the publication. The source code is licensed under GPL v3.</p> <p>Abstract of the Publication:</p> <p>Sound Field Synthesis techniques, such as Wave Field Synthesis aim at a physically accurate reproduction of a desired sound field inside an extended listening area. This area is surrounded by loudspeakers individually driven by their respective driving signals. Due to practical limitations, artefacts impair the synthesis accuracy resulting in a perceivable change in timbre compared to the desired sound field. Recently, an approach for so-called Local Wave Field Synthesis was published which enhances the reproduction accuracy in a limited region by applying a spatial bandwidth limitation in the circular/spherical harmonics domain to the desired sound field. This paper reports on a listening experiment comparing conventional Sound Field Synthesis techniques with the mentioned approach. Also the influence of the different parametrisations for Local Wave Field Synthesis is investigated. The results show that the enhanced reproduction accuracy in Local Wave Field Synthesis leads to an improvement with regard to the perceived colouration.</p>
Scenario data, model source code and plotting routine for manuscript: Separating CO2 emission from removal targets comes with limited cost impacts
<p>This data archive contains REMIND model setup, results data and data analysis files for manuscript:<br><strong>Separating CO2 emission reduction from removal targets comes with limited cost impact.<br><br>plotting</strong>(directory) contains results data, manuscript specific data analysis and plotting routine scripts used to generate the figures of the manuscript.<br><strong>remind</strong>(directory) contains REMIND model source code and scenario set-up. Detailed scenario configurations are set in remind/config/scenario_config_SepMark.csv.<br><strong>remind2</strong>(directory) contains the slightly modified R-library package used for post-processing of REMIND output.<br><br>AMENDMENT<br><strong>Plots_SeparateMarkets_afterReviewProcess.Rmd</strong> After the review process, the new plotting script was added including the additional figures in the Supplementary Material. This file should replace the previous R-markdown file SepMark_essential/plotting/Plots_SeparateMarkets.Rmd.</p>
Data from: Limiting burrowing activity and overland dispersal of the invasive alien red swamp crayfish Procambarus clarkii by sophisticated design of watercourses
<p>Two datasets belonging to the paper "Limiting burrowing activity and overland dispersal of the invasive alien red swamp crayfish <i>Procambarus clarkii</i> by sophisticated design of watercourses" published in Ecological Engineering (https://doi.org/10.1016/j.ecoleng.2022.106787), are provided here. </p><p> </p><p>The first dataset "Burrow data from Limiting burrowing activity and overland dispersal P. clarkii.csv" contains data from an inventory of crayfish burrows in three watercourses in the municipality of Horssen (Province of Gelderland), the Netherlands. These data were collected during a lowering of the water level in these watercourses, which takes place annually in the winter period to prevent nuisance from excessively high phreatic groundwater in agricultural areas. The sites were located up to 5 km apart. On each bank, red swamp crayfish burrows with tunnel openings in banks below the shoreline were counted from the opposite bank of the watercourse using binoculars. This field survey was performed in March 2019 when the water level was lowered for the maintenance of the watercourses. The chance of overlooking burrows was very low as the vegetation cover was low in this period. Three sites with 'natural-like' banks (banks rehabilitated to a natural profile during rehabilitation projects, in the dataset referred to as 'natural' banks) were chosen in the area with a lowered water level and presence of red swamp crayfish. At site 1, 2 and 3, a total of 125, 46 and 18 bank transects respectively, each one 10 metres long, were surveyed. Banks were categorized as follows: (a) non-natural (steep, <i>viz</i>. > 40°, and barely vegetated; n = 77), (b) semi-natural (steep with some vegetation; n = 50), and (c) natural (gentle sloping, <i>viz</i>. < 25°, with a diverse, well-developed submerged and emergent vegetation; n = 62). See the paper for schematic cross-sections of three bank types.</p><p>The second dataset "Inclination experiment data from Limiting burrowing activity and overland dispersal P. clarkii.csv" contains data of an inclination experiment to relate frequencies of overland movement of the red swamp crayfish to several inclinations and substrate types. For this purpose, a wooden plate of 120 x 180 cm with a 10 cm thick layer of soil was used as a base on which three lanes of 40 cm wide and 180 cm long were constructed with one substrate type each: a) bare sandy soil, b), species-poor grassland with low (2-5 cm) vegetation and c) tall (40-50 cm) herbaceous-rich grassland. Inclinations applied for this experiment were 0°, 10°, 20° and 30°. Individuals were randomly selected for each treatment and placed in the middle of a lane and oriented perpendicular to the lane. After each trial, the crayfish was placed back in the water container and replaced by another crayfish. There was a minimum period of at least one hour between each trial for each crayfish. Each crayfish was used once for each substrate type and inclination test, and the treatment order was randomised for each animal. A crayfish was placed in the middle of the lane and could freely move around for a period of three minutes. Hereafter, by the change of its position on the lane after 3 minutes it was recorded whether an individual moved up (or left in case of 0°), down (or right in case of 0°), or did not move. In total, 273 trials were conducted. Trial numbers differ between treatments due to mortality of three animals during storage.</p><p> </p><p>Abstract</p><p> </p><p>Invasive alien crayfish species pose major ecological and hydrological risks globally. The red swamp crayfish (<i>Procambarus clarkii</i>) is one of the most widespread crayfish species worldwide. Its impacts arise from burrowing activities and lead to mobilization of soil nutrients, water safety risks by instability of dikes and erosion of banks. Increased sediment load demands additional dredging of drainage ditches and canals to ensure their water discharge capacity. Sustainable methods for limiting burrowing in banks and dispersal behaviour of crayfish were not yet available. Therefore, a field study was performed to determine whether the number of burrows and overland movement of crayfish were related to a particular bank type. Burrows were counted in three watercourses during a water-level decline. The number of burrows was significantly lower in natural banks than in non-natural and semi-natural banks. The construction of natural-like banks along watercourses may significantly reduce sediment load, erosion and the collapse of banks by burrowing activities of crayfish. An inclination experiment mimicking various types of terrestrial dispersal barriers elucidated that steepness, soil type and vegetation structure of small embankments near watercourses were significant factors for manipulating overland movement of crayfish. Crayfish were taken out of the water for this purpose and placed on small experimental embankments varying in slope and types of vegetation. The lowest frequencies of upward movement were recorded at inclinations of 20° and 30° on bare sandy soil and short and species-poor grassland substrates. This implies that crayfish crawling out of the water will return to the watercourse when encountering such a dispersal barrier. Therefore, a sophisticated design of embankments along watercourses can be a tool to reduce colonization risk of nearby located, hydrologically isolated water bodies with high nature values. </p>
Data for The role of halogens in Au-S bond cleavage for energy-differentiated catalysis at the single-bond limit
<p>The source data for figures in <strong>The role of halogens in Au-S bond cleavage for energy-differentiated catalysis at the single-bond limit </strong></p>
Data from: Limited convergence in the postcranium of aquatic crocodylomorpha
<p>Thalattosuchia (Early Jurassic–Early Cretaceous) and Dyrosauridea (Late Cretaceous–Early Eocene) are crocodylomorph archosaurs which diversified in fluvial and marine environments and endured extinction events (i.e. Jurassic–Cretaceous boundary for Thalattosuchia; Cretaceous–Paleogene for Dyrosauridea). Their postcrania remain globally undervalued in anatomical descriptions and diagnoses, shrouding the locomotive adaptations that possibly underpinned their radiations and longevity. We thoroughly surveyed the postcranial morphology of Dyrosauridea and Thalattosuchia, recreated their girdles in three-dimensions using tens of high-precisions 3D scans, and analysed their shape using geometric morphometrics. Dyrosauridea and Thalattosuchia have clearly distinct postcrania, even when found within similar environments, suggesting the existence of clade-specific features limiting the strength of evolutionary convergence. Moreover, the range of postcranial morphologies evolved by dyrosaurids and thalattosuchians is large compared to extant crocodylians, making the latter unsatisfactory functional analogues for every group of extinct crocodylomorphs. Our work reveals the previously unsuspected potential of postcranial anatomy as an abundant source of phylogenetic and taxonomic characters to assess the relationships within Crocodylomorpha. Incorporation of postcranial anatomy therefore appears crucial to fully assess the ecology, disparity, and relationships of crocodylomorphs.</p>
Data from: pollinators limit seed production in an early blooming rare plant: evidence of a mismatch between plant phenology and pollinator emergence
<p>The reproductive ecology of rare plants is seldom studied, yet the persistence of plant populations depends on successful mutualisms with pollinators. As atmospheric temperatures rise, phenology of plants and pollinators may become mismatched. We investigated the reproduction of <em>Trifolium barnebyi</em> (Barneby's Clover), a mat-forming perennial endemic to central Wyoming, USA that grows in the crevices of sandstone bedrock. Our objectives were to evaluate a method for monitoring changes in cover as well as assess the pollination and seed-set of <em>T. barnebyi</em>. We established five monitoring transects using a divided frame to estimate percent cover. We conducted seed-set experiments at three locations to measure self-pollination and the degree to which pollinating insects limited seed production. We used vane traps and bee bowls to capture pollinators, and examined pollen carried on bees. Percent cover along transects declined over the 4 year period and was associated with spring precipitation. <em>Trifolium barnebyi</em> did not self-pollinate and relied on pollinators to produce seeds. The number and mass of viable seeds per flower, and the number of bees captured increased as the season progressed, indicating that more and larger seeds were made when more pollinators were present. Blooming of <em>T. barnebyi</em> ranged between April and June depending on the microhabitat the plant lived in and we observed much higher seed production in later-blooming plants. Pollen from <em>T. barnebyi </em>was primarily carried by Andrena bees, although we found smaller amounts of pollen on seven other bee genera. A mismatch in timing between blooming and pollinating insect emergence could limit seed production in<em> T. barnebyi </em>if plants bloom earlier over time and bee emergence does not follow the same phenology. Rare plants can be pollinated by rare pollinators showing that conserving these pollinators is crucial for rare plants and early blooming species may be higher at risk.</p>
Data from: In the social amoeba Dictyostelium discoideum, shortened stalks may limit obligate cheater success even when exploitable partners are available
<p>Cooperation is widespread across life, but its existence can be threatened by exploitation. The rise of obligate social cheaters that are incapable of contributing to a necessary cooperative function can lead to the loss of that function. In the social amoeba <em>Dictyostelium discoideum</em>, obligate social cheaters cannot form dead stalk cells and in chimeras instead form living spore cells. This gives them a competitive advantage within chimeras. However, obligate cheaters of this kind have thusfar not been found in nature, probably because they are often enough in clonal populations that they need to retain the ability to produce stalks. In this study we discovered an additional cost to obligate cheaters. Even when there are wild-type cells to parasitize, the chimeric fruiting bodies that result have shorter stalks and these are disadvantaged in spore dispersal. The inability of obligate cheaters to form fruiting bodies when they are on their own combined with the lower functionality of fruiting bodies when they are not represent limits on obligate social cheating as a strategy<em>.</em></p>
Data from: Limited evidence of biased offspring sex allocation in a cavity-nesting conspecific brood parasite
<p>Sex allocation theory predicts that mothers should bias investment in offspring toward the sex that yields higher fitness returns; one such bias may be a skewed offspring-sex ratio. Sex allocation is well-studied in birds with cooperative breeding systems, with theory on local resource enhancement and production of helpers at the nest, but little theoretical or empirical work has focused on birds with brood parasitic breeding systems. Wood ducks (<em>Aix sponsa</em>) are conspecific brood parasites, and rates of parasitism appear to increase with density. Because female wood ducks show high natal philopatry and nest sites are often limiting, local resource competition (LRC) theory predicts that females should overproduce male offspring—the dispersing sex—when competition (density) is high. However, the unique features of conspecific brood parasitism generate alternative predictions from other sex allocation theories, which we develop and test here. We experimentally manipulated the nesting density of female wood ducks in four populations from 2013-2016 and analyzed the resulting sex allocation of >2000 ducklings. In contrast to predictions we did not find overproduction of male offspring by females in high-density populations, females in better condition, or parasitic females; modest support for LRC was found in overproduction of only female parasitic offspring with higher nest box availability. The lack of evidence for sex ratio biases, as expected for LRC and some aspects of brood parasitism, could reflect conflicting selection pressures from nest competition and brood parasitism, or that mechanisms of adaptive sex ratio bias are not possible.</p>
Output data from "Emissions leakage and economic losses could limit the effectiveness of deforestation-linked oil crop import restrictions"
<p>Contains a .dat file with queried output from scenario runs used in the paper, Yarlagadda, B., X. Zhao, G. Iyer, T. Wild, N. Hultman and J. Lamontagne, "Emissions leakage and economic losses could limit the effectiveness of deforestation-linked oil crops". This output can be run with the workflow in <a href="https://github.com/brinday/oilcrop-trade-deforestation-leakage">https://github.com/brinday/oilcrop-trade-deforestation-leakage</a> to generate the figures presented in the paper.</p>
Source Data File – Dual role of the peptide loading complex as proofreader and limiter of MHC-I presentation – PNAS 2023-21600
<p>Source Data Files</p>
Data from: Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli
<p>Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified in vitro, the influence of interactions with other microbiome members is largely unknown. Here, we investigated the influence of three genera of lactic acid bacteria (LAB) derived from the chicken gastrointestinal microbiome on the spread of an epidemic narrow-range ESBL resistance plasmid, IncI1 carrying <em>bla<sub>CTX-M-1</sub></em>, in mixed cultures of isogenic <em>Escherichia coli </em>strains. Secreted products of LAB decreased <em>E. coli</em> growth rates in a genus-specific manner but did not affect plasmid transfer rates. Importantly, we quantified plasmid transfer rates by controlling for density-dependent mating opportunities. Parametrization of a mathematical model with our in vitro estimates illustrated that small fitness costs of plasmid carriage may tip the balance towards plasmid loss under growth conditions in the gastrointestinal tract. This work shows that microbial interactions can influence plasmid success and provides an experimental-theoretical framework for further study of plasmid transfer in a microbiome context.</p>
Data: Gradient expansions for the large-coupling strength limit of the Møller-Plesset adiabatic connection (arXiv:2111.13146)
<p>Data corresponding to the work <em>Gradient expansions for the large-coupling strength limit of the Møller-Plesset adiabatic connection</em> (https://arxiv.org/abs/2111.13146). </p> <p>The zip file contains:</p> <p>- Data for the functional E_el and W_1/2 for all the systems presented in the article (.csv files)</p> <p>- Minimising positions for all the systems presented in the article (.csv files)</p> <p>- Checkpoint Files for all the calculations done with PySCF 1.7.6.</p>
DFT Calculation Data for "Stabilized tilted-octahedra halide perovskites inhibit local formation of performance-limiting phases"
<p>Initial and optimized structures that are used for DFT simulations associated with Fig 2A-G in <em>Science</em> <strong>374</strong>, 1598 (2021) (DOI: 10.1126/science.abl4890)</p>
Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics: 35 Binding Site Data
<p>This is the original data for the manuscript "Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics" by J Bryan IV, I Sgouralis, and S Presse. This repository contains movies of DNA origami with 35 binding sites.</p>
Haptic Zoom: An interaction model for desktop haptic devices with limited workspace - Evaluation data
<p>Raw data collected in the evaluation of the new interaction technique for force feedback desktop haptic devices called Haptic Zoom.<br><br></p> <p>Gutiérrez-Fernández, A., Fernández-Llamas, C., Esteban, G. & Conde, Miguel A. (2023). Haptic Zoom: An Interaction Model for Desktop Haptic Devices with Limited Workspace. <em>International Journal of Human–Computer Interaction, 39</em>(4), 851-862. <a href="https://doi.org/10.1080/10447318.2022.2049140">https://doi.org/10.1080/10447318.2022.2049140</a></p>
Data from: Phytoplankton functional composition determines limitation by nutrients and grazers across a lake productivity gradient
<p>Functional tradeoffs among ecologically important traits govern the diversity of communities and changes in species composition along environmental gradients. A tradeoff between predator defense and resource competitive ability has been invoked as a mechanism that may maintain diversity in lake phytoplankton. Tradeoffs may promote diversity in communities where grazing- and resource-limited taxa coexist, which determines the extent to which communities are resource- or consumer-controlled. In addition, changes in temperature may alter nutrient demands and grazing pressure, changing the balance between the two regulating factors. Our study aims to understand whether a tradeoff between grazer vulnerability and nutrient limitation promotes coexistence of phytoplankton functional groups in communities that differ in trophic status, and how this tradeoff may shift with warming. We conducted multifactorial experiments manipulating grazing, nutrients, and temperature in phytoplankton communities from three Dutch lakes varying in trophic status, and used a trait-based approach to classify functional groups based on grazing susceptibility. <span>We found no associations between susceptibility to grazing and response to nutrient additions in any of the communities or temperature regimes, indicating that</span> a competition-defense tradeoff is unlikely to <span>explain diversity within the tested communities. Instead, w</span>e observed a tendency towards both a higher grazing-resistance and weaker nutrient limitation <span>along with a shift in the functional composition of phytoplankton in communities across a gradient from low to high productivity.</span></p>
Data from : Limited influence of irrigation on pre-monsoon heat stress in the Indo-Gangetic Plain
<p>The dataset contains WRF-CLM4 simulation post-processed output for three experiments named CTL, AGR, and MOD for pre-monsoon (April-May) from 2004-2016. Here, CTL represents WRF-CLM4 simulation with no irrigation, AGR represents WRF-CLM4 simulation with agricultural census-based irrigation data and MOD represents WRF-CLM4 simulation with model-estimated irrigation data. Here, C1, C2, and C3 represent different parameterization scheme combinations.</p> <ul> <li>C1:Mellor-Yamada Nakanishi and Niino Level 3 - WRF Double-Moment 6-class scheme - Tiedtke scheme (MYNN3-WDM6-Tiedtke)</li> <li>C2:Mellor-Yamada Nakanishi and Niino Level 3 - WRF Single-Moment 6-classscheme - KF scheme (MYNN3-WSM6-KF)</li> <li>C3:Mellor-Yamada Nakanishi and Niino Level 3 - WRF Single-Moment 6-class scheme - Grell3D (MYNN3-WSM6 Grell3D)</li> </ul> <p>The post-processed output contains the following variables:</p> <ol> <li>Land Surface Temperature</li> <li>Mean Air Temperature</li> <li>Maximum Air Temperature</li> <li>Wet-bulb Temperature</li> <li>Specific Humidity</li> <li>Latent Heat Flux</li> <li>Sensible Heat Flux</li> <li>Planet Boundary Layer Height</li> <li>Surface Pressure</li> <li>Relative Humidity</li> </ol> <p>The dataset also contains a spreadsheet that contains the FAO monthly calendar of the percentage of crop irrigation and pre-monsoon season crop calendar based on crop production data and annual reports “Agricultural Statistics At a Glance” from the Government of India. In addition, the file contains raw pre-monsoon data (area under the crop and crop irrigated area) from 2004 to 2016 for five crops (rice, maize, gram, sugarcane, and sunflower) over Indo-Gangetic Plain (Bihar, Uttar Pradesh, Haryana, Punjab, and Rajasthan). The pre-monsoon irrigation files for WRF contain irrigation data input for the WRF-CLM4 model.</p>
Data for "Sea-level stability over geologic time owing to limited deep subduction of hydrated mantle"
<p>This repository contains data to reproduce the results displayed in the manuscript : "Sea-level stability over geologic time owing to limited deep subduction of hydrated mantle" by Cerpa, N. G., Arcay, D., & Padron-Navarta J. A.<br> The data includes the P-T paths and the slab-water retention for the 56 modeled subduction transects. </p>
Data from: Limited evidence of a genetic basis for sex determination in the common creek chub, Semotilus atromaculatus
<p>Sexual reproduction is almost universal in vertebrates of the animal kingdom; therefore, each species which use it must have a mechanism for designating sex as male or female. Fish especially have a wide range of sex determining systems. In the present study, we aimed to identify a genetic basis for sex determination in the common creek chub (<em>Semotilus atromaculatus</em>) using genotyping-by-sequencing data. No sex-associated markers were found by RADSex or a GWAS using GEMMA, however, our Weir and Cockerham locus-specific F<sub>ST</sub> analysis and discriminant analysis of principal components revealed some genetic differentiation between the sexes at several loci. While no explicit sex determination mechanism has been yet discovered in creek chub, these loci are potential candidates for future studies. Incompatible systems are thought to increase reproductive isolation but interspecific hybridization is common among groups such as cyprinid minnows; thus, studies such as ours can provide insight into hybridization and evolutionary diversification of this clade. We also highlight technical challenges involved in studying sex determination in species with extremely variable mechanisms.</p>
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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.