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526 results for “compensation”
Manipulating a host-native microbial strain compensates for low microbial diversity by increasing weight gain in a wild bird population
<h1>Manipulating a host-native microbial strain compensates for low microbial diversity by increasing weight gain in a wild bird population</h1> <h1> </h1> <p>These files contain data on bacteria present in the guts of wild great tit (Parus major) obtained from faecal samples and sequenced using Illumina MiSeq. These data resulted from an experiment which provided supplementary mealworms at the nest during the breeding season at number of woodland sites in Cork, Ireland. Approximately half of these nests were given mealworms covered in a freeze dried bacterial powder containing the bacteria Lactobacillus kimchicus, which had been isolated from great tit faeces from the previous season. This treatment aimed to disrupt the gut microbiota of the treatment birds in order to provide evidence for the gut microbiotas role in birds health and fitness. Included here are the 3 elements necessary to create a 'phyloseq object' containing the sample metadata, ASV (Amplicon Sequence Variant) count table and a taxonomy table. The metadata file includes the alpha diversity scores for each individual. The data include all negative control samples taken during sample collection and library preparation, which were removed before the main analyses. All analyses, except for the beta-diversity analyses, were conducted in R. All R code is available on GitHub (https://github.com/shan-e-s\). Raw Sequence data are available in the European Nucleotide Archive under access number PRJEB74941, and ERS18960426-ERS18960697.</p> <h2> </h2> <h2>## Description of the data and file structure </h2> <p>Taxonomy, ASV and metadata files required to create a phyloseq object in R. metadata.csv file contains data on individual birds (i.e. individual samples). The metadata includes descriptions of the bird itself and it's environment, namely:</p> <ul> <li>Rownames: unique sample ID for each sample, corresponds with asvTable.csv. </li> <li>Nest: unique identifier for the nest box associated with the bird being sampled. </li> <li>Sample.ID: unique identifier for the faecal sample or control sample.</li> <li>Bird.ID: Identity of the bird the sample came from, note some individuals sampled twice so some bird.ID's may reoccur in metadata with different Sample.ID.</li> <li>Date: Date the sample was taken dd/mm/yyyy.</li> <li>Day: Date the sample was taken, in days since 1st March.</li> <li>Ring.Mark: British Trust for Ornithology (BTO) metal ring ID where applicable. Birds only ringed at D15 so some young birds do not have IDRings.</li> <li>Site: ID of woodland site that bird was sampled at.</li> <li>Chick.LetterID: ID letter differentiates between different birds from the same nest. Either 'A'-'F' for nestlings, 'Fe' for females or 'M' for males.</li> <li>Age.code: BTO age code.</li> <li>Age.category: Age category that bird is in. D8 = 8 days post hatching, D15 = 15 days post hatching, adult = 1+ years post hatching.</li> <li>Sex: Bird's sex, only determined for adult birds. Fe = Female, M = Male.</li> <li>Wing_mm: Wing length in mm.</li> <li>Tarsus_mm: minimum tarsus length of bird in mm.</li> <li>Weight_g: bird's weight in grams.</li> <li>Faecal.Sample: bird's age at sampling.</li> <li>newRing: whether bird was fitted with a new BTO ring. Only relevant to adults.</li> <li>Treatment: the experimental treatment group that the bird was in. Either 'Treatment' when nest given L. kimchicus treated mealworms or 'Control' when nest given plain mealworms.</li> <li>Notes: field notes.</li> <li>Main.sample: indicates whether this sample was the main sample to be used for analysis, an alternative sample taken as a backup.</li> <li>Plate: the ID of the PCR plate which the sample was amplified on.</li> <li>Azenta_noPeriod: sample ID given to sequencing facility without special characters. Corresponds to fastq files and ASV table counts.</li> <li>Qubit_prePool: samples qubit score before pooling.</li> <li>Date_extracted: date the sample was extracted on dd/mm/yyyy.</li> <li>SampleType: whehther the sample was a 'main' sample intended for downstream analysis, a 'control' sample for detecting contamination during library preparation, a 'duplicate' for detecting PCR issues, a 'label_error' where sample was suspected of being mislabelled at some point, a 'repeat' sample intended to detect errors or issues, a 'contam' sample which was suspected of being contaminated, a 'common' sample used across different PCR plates to detect issues. Extraction_notes: notes regarding the DNA extraction of the sample. </li> <li>LibPrep_notes: notes regarding the library preparation of the sample.</li> <li>Ring.Mark.lab: the ring or sample ID written on the sample tube, recorded to help detect mislabelling.</li> <li>Post_lab_notes: notes regarding issues found post sequencing.</li> <li>NumberOfReads: number of sequence reads associated with the sample. </li> <li>DistanceToEdge: distance between nest and woodland edge in metres. </li> <li>BroodSize.D8: number of nestlings in the nest at day-8 post hatching. </li> <li>BroodSize.D15: number of nestlings in the nest at day-15 post hatching.</li> <li>firstEggLayDate: Date the first egg in the clutch was laid, in days since 1st March.</li> <li>lastEggLayDate: Date the last egg in the clutch was laid, in days since 1st March.</li> <li>Observed: number of unique ASV's (or taxa) detected in the sample.</li> <li>Chao1: Chao1 diversity of the sample.</li> <li>Shannon: Shannon diversity of the sample.</li> </ul> <p>The file 'taxonomy.csv' contains the taxonomic breakdown of each bacterial Amplicon Sequence Variant (ASV) found in the dataset from Phylum to Species. Obtained by using the Naive Bayes Classifier against the Silva (v138) taxonomic database.</p> <p>The file 'asvTable.csv' contains counts of each amplicon sequence variant's occurrence for each individual sample. Samples are rows and taxa are columns.</p> <p> </p> <h2>Sharing/Access information </h2> <p>All R code is available on GitHub (https://github.com/shan-e-s\). Raw Sequence data are available in the European Nucleotide Archive under access number PRJEB74941, and ERS18960426-ERS18960697.</p>
Dataset for manuscript "During haptic communication, the central nervous system compensates distinctly for delay and noise"
<p>Data relating to the manuscript "Dataset for manuscript "During haptic communication, the central nervous system compensates distinctly for delay and noise". This includes the experiment dataset (in file experiment_dataset.csv) as well as the MATLAB functions used for the development of the simulation model (with main function main_delay.m)</p>
Fig. 2. Species accumulation curves for 45 in Mammal inventories in Seasonal Neotropical Forests: traditional approaches still compensate drawbacks of modern technologies
Fig. 2. Species accumulation curves for 45 sampling days for each method used to sample mammals in Serra do Japi Biological Reserve, JundiaÍ, State of SÃo Paulo, Brazil in July and August 2009 and January and February 2010.
Fig. 1 in Mammal inventories in Seasonal Neotropical Forests: traditional approaches still compensate drawbacks of modern technologies
Fig. 1. Serra do Japi Biological Reserve location (SÃo Paulo, Brazil), and camera trap (white circles) and transect placement within the reserve limits. Thin line: limits of REBIO Serra do Japi. Satellite image from Google Earth®.
Dataset for 'Intraocular scatter compensation with spatial light amplitude modulation for improved vision in simulated cataractous eyes'
<p>Dataset for the manuscript entitled: Intraocular scatter compensation with spatial light amplitude modulation for improved vision in simulated cataractous eyes</p> <p>includes:</p> <p>1) PSF from numerical simulations</p> <p>2) CSF measured in subjects</p> <p>3) Michelson contrast from numerical simulations</p>
Dataset for Using Your Beam Efficiently: Reducing Electron-dose in the STEM via Flyback Compensation
<p>Experimental scanning transmission electron microscopy dataset for the paper "Using Your Beam Efficiently: Reducing Electron-dose in the STEM via Flyback Compensation"</p>
Data from: Looking for compensation at multiple scales in a wetland bird community
<p>Compensatory dynamics, during which community composition shifts despite a near-constant total community size, are usually rare: synchronous dynamics prevail in natural communities. This is a puzzle for ecologists, because of the key role of compensation in explaining the relation between biodiversity and ecosystem functioning. However, most studies so far have considered compensation in either plants or planktonic organisms, so that evidence for the generality of such synchrony is limited. Here, we extend analyses of community-level synchrony to wetland birds. We analyse a 35-year monthly survey of a community where we suspected that compensation might occur due to potential competition and changes in water levels, favouring birds with different habitat preferences. We perform both year-to-year analyses by season, using a compensation/synchrony index, as well as multiscale analyses using a wavelet-based measure, which allows for both scale- and time-dependence. We analyse synchrony both within and between guilds, with guilds defined either as tightknit phylogenetic groups or larger functional groups. We find that abundance and biomass compensation are rare, likely due to the synchronizing influence of climate (and other drivers) on birds, even after considering several temporal scales of covariation (during either cold or warm seasons, above or below the annual scale). Negative covariation in abundance at the guild or community level did only appear at the scale of a few months or several years. We also found that synchrony varies with taxonomic and functional scale: the rare cases where compensation appeared consistently in year-to-year analyses were between rather than within functional groups. Our results suggest that abundance compensation may have more potential to emerge between broad functional groups rather than between species, as well as at relatively long temporal scales (multiple years for vertebrates), above that of the dominant synchronizing driver.</p>
Increases in vein length compensate for leaf area lost to lobing in grapevine
<p><span></span></p> <p>There is considerable variation in leaf lobing and leaf size, including among grapevines, some of the most well-studied leaves. We examined the relationship between leaf lobing and leaf size across grapevine populations which varied in extent of leaf lobing. We used homologous landmarking techniques to measure 2,632 leaves across two years in 476 unique, genetically distinct grapevines from 5 biparental crosses which vary primarily in the extent of lobing. We determined to what extent leaf area could explain variation in lobing, vein length, and vein to blade ratio. Although lobing was the primary source of variation in shape across the leaves we measured, leaf area varied only slightly as a function of lobing. Rather, leaf area increases as a function of total major vein length, total branching vein length, and decreases as a function of vein to blade ratio. These relationships are stronger for more highly lobed leaves, with the residuals for each model differing as a function of distal lobing. For a given leaf area, more highly lobed leaves have longer veins and higher vein to blade ratios, allowing them to maintain similar leaf areas despite increased lobing. These findings show how more highly lobed leaves may compensate for what would otherwise result in a reduced leaf area, allowing for increased photosynthetic capacity through similar leaf size.</p>
Supplementary Data for "The history of Cenozoic carbonate flux in the Atlantic Ocean constrained by multiple regional carbonate compensation depth reconstructions"
<p>The files on this site accompany the paper:</p> <p>Dutkiewicz, A. And Müller, R.D., in review, The history of Cenozoic carbonate flux in the Atlantic Ocean constrained by multiple regional carbonate compensation depth reconstructions, Geochemistry, Geophysics, Geosystems.</p> <p>There are two zipped file archives:</p> <p>1) backtracked_sites.zip</p> <p>This archive contains two directories of backtrack site files, one for the North Atlantic and one for the South Atlantic.</p> <p>Each directory contains a set of files listing, by site:</p> <p>age(Ma), compacted_depth (observed)(mbsf), compacted_thickness (observed)(m), decompacted_thickness(m), decompacted_density(g/cm3), water_depth(m), tectonic_subsidence (since formation of crust)(m), decompacted_depth(mbsf) dynamic_topography(m) lithology</p> <p>The lithology classification follows the lithology classes defined in Muller et al. (2018).</p> <p>A second set of files contains:</p> <p>age(Ma), depth(mbsf), paleowaterdepth(m), dry_bulk_density(g/cm3), DLSR(m/my), carbonate(weight_%) CAR(mg/cm2/kyr)</p> <p>DLSR=decompacted linear sedimentation rate<br> CAR=carbonate accumulation rate</p> <p>2) regional_Cenozoic_carbonate_thickness_grids.zip</p> <p>This archive contains 3 folders with grids for modelled Cenozoic carbonate thicknesses for the South Atlantic, central North Atlantic and northern North Atlantic. They can be viewed with netcdf viewers like panoply, or plotted using the Generic Mapping Tools. The workflow for creating these grids can be found on GitHub:</p> <p>https://github.com/EarthByte/CarbonateSedimentThickness</p> <p><br> This site also contains a spreadsheet entitled "Dutkiewicz_Muller_G3_2022_model_data_summary.xlsx"</p> <p>It contains our model outputs including regional decompacted carbonate sediment volumes and thicknesses, depositional areas, carbonate carbon fluxes and carbonate compensation depths for the northern and central North Atlantic and South Atlantic.</p> <p>A video entitled "compacted_carb_thick_atlantic_66-0Ma.mp4" shows the Cenozoic evolution of carbonate sediment thickness in the Atlantic Ocean.</p> <p><br> References:</p> <p>Spasojevic, S., & Gurnis, M. (2012). Sea level and vertical motion of continents from dynamic earth models since the Late Cretaceous. AAPG bulletin, 96(11), 2037-2064. https://doi.org/10.1306/03261211121</p> <p>Müller, R. D., Cannon, J., Williams, S. and Dutkiewicz, A., 2018, PyBacktrack 1.0: A Tool for Reconstructing Paleobathymetry on Oceanic and Continental Crust, Geochemistry, Geophysics, Geosystems, 19, 1898-1909, https://doi.org/10.1029/2017GC007313.</p> <p><br> </p>
Reproductive compensation and selection among viable embryos drive the evolution of polyembryony
<p>Simple polyembryony -- where one gametophyte produces multiple embryos with different sires but the same maternal haplotype -- is common among vascular plants. We develop an infinite-site, forward population genetics model showing that together polyembryony's two benefits -- "reproductive compensation" achieved by providing a backup for inviable embryos, and the opportunity to favor the fitter of surviving embryos, can favor its evolution. Our model tests how these factors can favor the evolution of polyembryony, and how these underlying benefits of polyembryony shape the genetic load under a range of biological parameters. While these two benefits are difficult to disentangle in nature, we construct variant models of polyembryony that either only include or only exclude the opportunity for reproductive compensation. We find that reproductive compensation strongly favors the evolution of polyembryony, and that polyembryony is favored much more weekly in its absence, suggesting that the benefit of a backup embryo is a major force favoring polyembryony. Remarkably we find nearly identical results in cases in which mutations impact either embryo or post-embryonic fitness (no pleiotropy), and in cases in which mutations have identical fitness effects embryo or post-embryonic fitness (extreme pleiotropy). Finally, we find that the consequences of polyembryony depends on its function – polyembryony results in a decrease in mean embryonic fitness when acting as a mechanism of embryo compensation, and ultimately increases mean embryonic fitness when we exclude this potential benefit.</p>
Data from: Evidence for seasonal compensation of hunting mortalities in a long-lived migratory bird
<p>Understanding whether hunting mortality is additive to or compensated by other mortality sources is at the heart of managing harvested populations. Long-lived species are expected to exhibit hunting mortality additive to other sources of mortality, making them ideal candidates for population management through sport harvest. Previous studies on these processes have focussed on density-dependent natural mortality compensating for hunting mortality, but when harvest occurs in distinct periods of the year, heterogeneity in hunting vulnerability between individuals could also lead to compensatory mortality between these periods. We explore this new idea using the case of the greater snow goose (<em>Anser caerulescens atlantica</em>), a harvested species whose population became overabundant in the late 20<sup>th</sup> century. To control this population, wildlife agencies liberalized hunting regulations with unprecedented actions such as special hunting seasons implemented in spring 1999 in Canada and in winter 2009 in the USA. To determine the relative impact of each measure on survival, we estimated survival of adult geese on a seasonal basis using 30 years of capture-mark-reencounter data in a joint live-and-dead-encounter multievent model. We also used this quasi-experimental set-up to evaluate possible compensation in hunting mortality between seasons. We found that both special hunting seasons decreased goose survival in the seasons and periods in which they were implemented. However, survival increased during the spring hunting season after the establishment of the special winter hunting season in the USA in 2009. There was a negative relationship between annual spring and winter mortalities, suggesting that the increase in hunting mortality in winter was compensated by a reduction in spring mortality after 2009.</p> <p><em>Synthesis and applications:</em> To our knowledge, we report the first documented instance of hunting mortality in one season being compensated by a reduction in hunting mortality in a subsequent season. We suggest that heterogeneity in hunting vulnerability among individuals, possibly linked to the presence of juveniles, may explain this phenomenon. A better knowledge of seasonal patterns and relationships between mortality components is needed to improve our understanding of population dynamics and management of harvested populations.</p>
Interactive map of Heat Stress Compensability Classification (HSCC) application in 96 United States cities.
<p>This repository includes the interactive map in format .html of the very first application of the <strong>Heat Stress Compensability Classification (HSCC) in 96 cities in the United States </strong>showing the proportion of days with compensable and uncompensable heat stress from the top 10th percentile of hottest days from 2005-2020 in each place.</p> <p>This map offers the detailed results of the very first application of the classification system as in the journal article: <strong>The Development of an Adaptive Heat Stress Compensability Classification Applied to the United States</strong>, published in the 4th SNP special issue in the International Journal of Biometeorology. The results of this visualization were obtained from open-source data and coding packages such as Folium, and the model results were obtained by applying the Python Human Heat Balance (PyHHB) on weather dataset freely available.</p> <p>The interactive map offers a detailed visualization of the results from each of the cities, allowing you to see 3 tabs when the icon of the pie chart from each location is clicked.</p> <p><strong>Tab statistics:</strong> Detail per city of Figure 4b of related paper.</p> <p><strong>Tab Histogram 2D: </strong>Details per city of Fig 6 of related paper</p> <p><strong>Tab How to read: </strong>Figure 2 in related paper.</p> <p>Please for questions related to this dataset/code contact Gisel Guzman-Echavarria (gguzma20@asu.edu).</p> <p>Guzman-Echavarria, G., & Vanos, J. (2023). PyHHB: Physiological-based estimations of human survivability and liveability to heat in a changing climate (Nature Communications (1.0.0)). Zenodo. https://doi.org/10.5281/zenodo.10020137</p> <p> </p> <p> </p>
Lecturer Performance: The Influence of Transformational Leadership Style, Work Environment, Compensation, and Institutional Transformation
<p>This study aims to test and analyze the influence of transformational leadership style, work environment, compensation, and institutional transformation on the performance of lecturers at the Mandala Institute of Technology and Science. This study uses a quantitative approach. Data analysis uses descriptive statistical analysis and inferential statistical analysis that describes a certain characteristic or feature of a phenomenon that occurs and makes conclusions or generalizations about the population based on sample data. The sample used was 48 lecturers at the Mandala Institute of Technology and Science. The results of the study indicate that compensation affects lecturer performance, while transformational leadership style, work environment, and institutional transformation do not affect lecturer performance. The implications of this study indicate that increasing compensation can significantly improve lecturer performance at the Mandala Institute of Technology and Science, so it is important for institutions to focus on fairer and more adequate compensation policies. Conversely, improvements in transformational leadership style, work environment, and institutional transformation need to be adjusted to the specific context and needs of lecturers in order to have a more significant impact on performance.</p>
Ray Tracing-Based Delay Model for Compensating Gravitational Deformations of VLBI Radio Telescopes (Data Set)
<p>The precision and the reliability of very long baseline interferometry (VLBI) depend on several factors. Apart from fabrication discrepancies or meteorological effects, gravity-induced deformations of the receiving unit of VLBI radio telescopes are identified as a crucial error source biasing VLBI products and obtained results such as the scale of a realized global geodetic reference frame. Gravity-induced deformations are systematical errors and yield signal path variations (SPVs). In 1988, Clark and Thomsen derived a VLBI delay model, which was adopted by the International VLBI Service for Geodesy and Astrometry (IVS) to reduce these systematic errors. However, the model parametrizes the SPV by a linear substitute function and considers only deformations acting rotationally symmetrically. The aim of this investigation is to derive the signal path variations of a legacy radio telescope and a modern broadband VGOS-specified radio telescope and to study the effect of nonrotationally symmetric deformation patterns. For that purpose, SPVs are obtained from a nonlinear spatial ray tracing approach. For the first time, a tilt and a displacement of the subreflector perpendicular to the optical axis of the feed unit is taken into account. The results prove the commonly used VLBI delay model as a suitable first-order delay model to reduce gravity-induced deformations.</p>
Data from: Earlier flowering of winter oilseed rape compensates for higher pest pressure in warmer climates
<p>Pest abundance and timing of migration relative to the vulnerable crop stage influence the severity of crop damage and yield loss to insect pests in oilseed rape (OSR). Both abundance and timing are influenced by landscape composition, changes therein due to crop rotation, and temperature. The need for sustainable and temperature-adapted management strategies of OSR pests due to the environmental harm of current conventional practices and global warming calls for a better understanding of the combined effects of landscape composition and temperature on pest abundances, larval parasitism, crop damage and yield, but also of the role of crop phenology for crop damage and yield under field conditions. Here, 29 winter OSR crops were studied along a multi-annual mean temperature gradient (MAT, 1981–2010) in Bavaria, Germany. We measured pest abundances (pollen beetles, stem weevils), crop damage (bud loss, stem tunnelling), pollen beetle larval parasitism and crop yield and calculated Julian dates of flowering from biweekly observations of growth stages. Pest abundances and parasitism were analysed with regard to MAT and landscape parameters at six scales (non-crop habitat and OSR area, change in the proportion of OSR area relative to the previous year; 0.6 km, and 1–5 km in 1-km steps), while analysis of crop damage and yield also included Julian date of flowering. Pollen beetle abundance was increased under higher MAT, but less strongly when OSR proportions were high (1-km scale) and not strongly reduced relative to the previous year (5-km scale), while pollen beetle larval parasitism was overall low but exceeded 30% (considered as threshold for effective natural control) occasionally under both low and high MAT. In contrast to abundance of adult pollen beetles, stem weevil larval abundance – as well as stem damage – did not respond to landscape composition nor MAT. Despite high abundance of adult pollen beetles under high MAT, crop yield was high (and the proportion of bud loss low) under high MAT when OSR flowered early. Our results underpin the potential of targeted landscape management (e.g. through regionally coordinated crop rotations) and timing of flowering (e.g. through cultivar choice) for environment-friendly and temperature-adapted pest management in winter OSR.</p>
Dataset for the publication "Theory and Experimental Validation of Two Techniques for Compensating VT Nonlinearities"
<p>This is dataset for paper published:</p> <p>G. D’Avanzo <em>et al</em>., "Theory and Experimental Validation of Two Techniques for Compensating VT Nonlinearities," in <em>IEEE Transactions on Instrumentation and Measurement</em>, vol. 71, pp. 1-12, 2022, Art no. 9001312, doi: 10.1109/TIM.2022.3147883.</p>
Immediate neural impact and incomplete compensation after semantic hub disconnection
<p>Data repository for "Immediate neural impact and incomplete compensation after semantic hub disconnection"</p> <p>Abstract: The human brain extracts meaning using an extensive neural system for semantic knowledge. <br> Whether broadly distributed systems depend on or can compensate after losing a highly interconnected hub is controversial. <br> We report rare intracranial recordings from two patients during a speech prediction task, <br> obtained minutes before and after neurosurgical treatment requiring disconnection of the left anterior temporal lobe (ATL), <br> a candidate semantic knowledge hub. Informed by modern diaschisis and predictive coding frameworks, <br> we tested hypotheses ranging from solely neural network disruption to complete compensation by <br> the indirectly affected language-related and speech processing sites. Immediately after ATL disconnection, <br> we observed substantial neurophysiological alterations in the recorded frontal and auditory sites, <br> providing direct evidence for the importance of the ATL as a semantic hub. We also obtained evidence for rapid, albeit incomplete, <br> attempts at neural network compensation, with neural impact largely in the forms stipulated by the predictive coding framework, <br> in specificity, and the modern diaschisis framework, more generally. The overall results validate these frameworks and reveal <br> a remarkable immediate impact and capability of the human brain to adjust after losing a brain hub.</p> <p>In this dataset, you will be able to access the intracranial recordings from 2 subjects, <br> with the description of recording channels, along with event codes and times in ms. Both the raw data, <br> and the preprocessed (DBT denoised and SVD applied; matrix in times x channels format, 1000 Hz sampling rate) data are available. For further information, please consult the paper (currently in press, but will provide a DOI when available), <br> or email zsuzsanna-kocsis@uiowa.edu or zkocsis@andrew.cmu.edu<br> </p>
Reproductive compensation and selection among viable embryos drive the evolution of polyembryony
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Increases in vein length compensate for leaf area lost to lobing in grapevine
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Dosage compensation and sexual conflict in female heterogametic methylomes
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