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861 results for “data comparison”
Large-scale comparison of bibliographic data sources: Scopus, Web of Science, Dimensions, Crossref, and Microsoft Academic
<p>This data set contains supplementary material for the paper 'Large-scale comparison of bibliographic data sources: Scopus, Web of Science, Dimensions, Crossref, and Microsoft Academic' by Martijn Visser, Nees Jan van Eck, and Ludo Waltman. The data set provides the statistics presented in the figures in the paper.</p>
Data from: Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii
<p>Different host species often differ considerably in susceptibility to a given pathogen, but the causes of such differences are rarely known. The natural hosts of the tick-transmitted bacterium <i>Borrelia afzelii</i>, which is one of causative agents of Lyme borreliosis in humans, include a variety of small mammals like voles and mice. Previous studies have shown that <i>B. afzelii-</i>infected bank voles (<i>Myodes glareolus</i>) have about ten times higher bacterial load than infected yellow-necked mice (<i>Apodemus flavicollis</i>), indicating that these two species differ in resistance. In this study, we compared the immune response to <i>B. afzelii </i>infection in these host species by using RNA-sequencing to quantify gene expression in spleen. Gene set enrichment analysis (GSEA) showed that several immune pathways were down-regulated in infected animals in both bank voles and yellow-necked mice. Moreover, IFNα response was up-regulated in <i>B. afzelii</i>-infected yellow-necked mice, while IL6 signaling and the complement pathway were down-regulated in infected bank voles; differences in regulation of these three pathways between bank voles and yellow-necked mice could thus contribute to the difference in resistance to <i>B. afzelii</i> between the species. This study provides knowledge of gene expression induced by a zoonotic pathogen in its natural host, and possible species-specific regulation of immune responses associated with resistance.</p>
Data from: Unraveling hierarchical genetic structure in a marine metapopulation: a comparison of three high-throughput genotyping approaches
<p>Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high-throughput sequencing, an emerging question is whether various genetic approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish <i>Elacatinus lori</i> using a high-resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative <i>E. lori</i> populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 non-repetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high-throughput genotyping data can elucidate subtle genetic structure at previously-undetected scales in a dispersive marine fish.</p>
Data from: Impact of agricultural weathering on physicochemical properties of biodegradable plastic mulch films: comparison of two diverse climates over four successive years
<p><span><span><span>Biodegradable plastic mulch films (BDMs) are essential in </span><span><span>the</span></span><span> production of vegetable and specialty crops due to their promotion of increased crop yield and quality. Unlike conventional polyethylene (PE) mulches, BDMs can be tilled into the soil after crop harvest to undergo biodegradation, thereby leading to minimal environmental impact. Agricultural weathering impacts both the performance of BDMs during crop production as a barrier to weeds and biodegradability of BDMs in the soil. To better understand the relative importance of climatic factors, the change of physicochemical properties of BDMs during single-season, 3-4 month, field trials for vegetable production at two diverse climates (Knoxville, TN and Mount Vernon, WA) across four successive years (2015-2018) was evaluated. Mulch treatments consisted of four commercially available BDMs composed primarily of polybutylene co-adipate- co-terephthalate (PBAT) that differed in color and polymeric feedstock</span><span><span>, a</span></span><span> black experimental BDM prepared from polylactic acid/polyhydroxybutyrate (PLA/PHA) blend, and conventional PE mulch. </span></span></span></p> <p><span><span><span>Mulch deterioration did not vary extensively between </span><span><span>years. </span></span><span><span>Solar</span></span><span> radiation, an important factor to degradation of mulches, was higher in WA than TN in most sampling years. Yet, degradation occurred </span><span><span>more greatly for</span></span><span> BDMs in TN</span><span><span>,</span></span><span> which </span><span><span>is attributable</span></span><span> to higher temperatures in TN. </span><span><span>Loss of</span></span><span> mechanical properties and color </span><span><span>was greater</span></span><span> than chemical </span><span><span>property changes.</span></span><span> </span><span><span>Differences in the extent of molecular weight decrease</span></span><span> between years correlated significantly with solar radiation </span><span><span>exposure at the two locations.</span></span><span> A black-colored PBAT-based BDM was less susceptible to degradation than equivalent clear and white-on-black films, due to carbon black acting as a photostabilizer. The impact of weathering also differed between </span><span><span>three commercially available PBAT-based films.</span></span><span> The PLA/PHA mulch was more susceptible to degradation than PBAT-based BDMs, particularly in the warmer location, TN, partially due to a leaching out of PHA and lower-molecular weight polymer molecules. The extent of change for physicochemical properties </span><span><span>of</span></span><span> BDMs due to agricultural weathering is greatly affected by polymeric composition, </span><span><span>and is greater in warmer climates.</span></span></span></span></p>
FIB-tomography data of Ni-YSZ anodes for Solid Oxide Fuel Cells (SOFC): Comparison of pristine and degraded materials (before/after redox cycling)
<p><em>Contents: </em></p> <p>This dataset contains 3D image stacks acquired with FIB-tomography from Ni-YSZ cermet anodes for Solid Oxide Fuel Cells (SOFC).</p> <p>The data was collected from three different Ni-YSZ anodes (fine-, medium- and coarse-grained). Each of these anodes was investigated first in pristine state (after sintering and reduction) and then also in degraded state (after exposure to 8 redox cycles).</p> <p>The 6 tomographs are then presented as stacks of 2D-tiff-images in 2 different versions: as gray-scale images (raw data) and as segmented images (Ni=white, YSZ=gray and pores=black). In total this gives 12 image stacks.</p> <p><strong>Further details</strong>, such as the voxel resolutions and image window sizes are listed in the downloadable excel file (<strong>2_3D_Data_Info.xlsx</strong>).</p> <p> </p> <p><em>Scientific Context: </em></p> <p>The microstructures of the cermet anodes were investigated for the purpose of optimizing the anode performance, which depends on effective transport properties (i.e. conductivity of ions in YSZ and of electrons in Ni, as well as diffusivity of fuel/gas in the pores). Furthermore the anode performance also depends on the catalytic/electrochemical activity (i.e. Ni-surface area and three phase boundary length TPBL). The microstructure characteristics have a strong influence on effective properties, electrochemical activity and associated anode performance. Furthermore, microstructure degradation (e.g. by Ni-coarsening) may lead to performance loss over time.</p> <p>Hence, the investigations focus on a fundamental, quentitative understanding of the relationships between microstructure characteristics and effective properties. The study reveals quantitative descriptions of all relevant microstructure characteristics (porosity, tortuosity, constrictivity, surface/interface areas, TPBL) and of the corresponding effective transport porperties (electric and ionic.conductivities). The corresponding anode performance was characterized by impedance spectroscopy.</p> <p>The quantitative <strong>results of the microstructure investigation were published</strong> in:</p> <p><strong>Pecho et al</strong> 2015a (doi:10.3390/ma8095265),</p> <p><strong>Pecho et al</strong> 2015b (doi:10.3390/ma8105370),</p> <p><strong>Holzer et al</strong> 2013 (doi: 10.1016/j.jpowsour.2013.05.047),</p> <p><strong>Holzer et al</strong> 2011a (doi: 10.1016/j.jpowsour.2010.08.017) and</p> <p><strong>Holzer et al</strong> 2011b (doi: 10.1016/j.jpowsour.2010.08.006).</p>
Data from: Are acute and acclimated thermal effects on metabolic rate modulated by cell size? A comparison between diploid and triploid zebrafish larvae
Being composed of small cells may carry energetic costs related to maintaining ionic gradients across cell membranes as well as benefits related to diffusive oxygen uptake. Here we test the hypothesis that these costs and benefits of cell size in ectotherms are temperature dependent. To study the consequences of cell size for whole-organism metabolic rate we compared diploid and triploid zebrafish larvae differing in cell size. A fully factorial design was applied combining three different rearing and test temperatures that allowed us to distinguish acute from acclimated thermal effects. Individual oxygen consumption rates of diploid and triploid larvae across declining levels of oxygen availability were measured. We found that both acute and acclimated thermal effects affected the metabolic response. In comparison to triploids, diploids responded more strongly to acute temperatures, especially when reared at the highest temperature. These observations support the hypothesis that animals composed of smaller cells (i.e. diploids) are less vulnerable to oxygen limitation in warm aquatic habitats. Furthermore, we found slightly improved hypoxia tolerance in diploids. By contrast, warm-reared triploids had higher metabolic rates when they were tested at acute cold temperature, suggesting that being composed of larger cells may provide metabolic advantages in the cold. We offer two mechanisms as a potential explanation of this result, related to homeoviscous adaptation of membrane function and the mitigation of developmental noise. Our results suggest that being composed of larger cells provides metabolic advantages in cold water, while being composed of smaller cells provides metabolic advantages in warm water.
SAXS calculations for Refinement of 𝛼-synuclein ensembles against SAXS data: Comparison of force fields and methods
<p>SAXS curves calculated from MD simulations used as input to reweighting as described in preprint Refinement of 𝛼-synuclein ensembles against SAXS data: Comparison of force fields and methods</p>
Data for the article "Quantitative comparison of spin and orbital Hall and Rashba-Edelstein effects in heavy-metal/3d-metal bilayers"
<p>Data for the article "Quantitative comparison of spin and orbital Hall and Rashba-Edelstein effects in heavy-metal/3d-metal bilayers" (<a href="https://arxiv.org/abs/2004.11942">[2004.11942] Quantitative comparison of spin and orbital Hall and Rashba-Edelstein effects in heavy-metal/3d-metal bilayers (arxiv.org)</a>)</p>
Training data for "From small to large-scale genome comparison", a tutorial for the Galaxy Training Network
<p>This dataset comprises two sequence pairs in FASTA format, one including two mycoplasmas (<em>Hyopneumoniae</em> 232 and 7422) and the other including the first chromosome of two plant genomes (<em>Aegilops tauschii</em> and <em>Triticum aestivum</em>).</p>
Data from: Comparison of rapid biodiversity assessment of meiobenthos using MALDI-TOF MS and metabarcoding
<p>Nowadays, most biodiversity assessments involving meiofauna are mainly carried out using very time-consuming, specimen-wise morphological identifications, which demands comprehensive taxonomic knowledge. Animals have to be examined for minor differences of setae compositions, mouthpart morphology or number of segments for various extremities. DNA-based methods such as metabarcoding as well as recently emerged rapid analyses using MALDI-TOF mass spectrometry to identify specimens based on a proteome fingerprint could vastly accelerate the process of specimen identification in biodiversity assessments. However, these techniques depend on reference libraries to connect collected data to morphologically described species. In this study the success rate of both approaches have been tested based on reference libraries constructed using part of the samples from a new study area to identify unknown samples. Using MALDI-TOF MS we found, that species which do not exist in an incomplete mass spectra reference library only have minor impact on the results, when employing a post hoc test for Random Forest classifications. This test reveals specimens that demand morphological re-examination for the final species assignment. Metabarcoding however strongly demands a rich reference library to provide correct MOTU assessments in congruence with morphological determination. Nevertheless, with a complete library and a suitable data transformation [herein log(x + 1)], the number of reads per MOTU reflects relative species abundances in metabarcoding inference. The results of this study facilitate specimen identification by using MALDI-TOF MS, which is incomparably cheap for specimen-by specimen identification, but when it comes to sample-wise analyses, metabarcoding outperforms other techniques by far.</p>
Data from: Effects of soil type and light on height growth, biomass partitioning, and nitrogen dynamics on 22 species of tropical dry forest tree seedlings: comparisons between legumes and nonlegumes
PREMISE OF THE STUDY: The seedling stage is particularly vulnerable to resource limitation, with potential consequences for community composition. We investigated how light and soil variation affected early growth, biomass partitioning, morphology, and physiology of 22 tree species common in tropical dry forest, including eight legumes. Our hypothesis was that legume seedlings are better at taking advantage of increased resource availability, which contributes to their successful regeneration in tropical dry forests. METHODS: We grew seedlings in a full-factorial design under two light levels in two soil types that differed in nutrient concentrations and soil moisture. We measured height biweekly and, at final harvest, biomass partitioning, internode segments, leaf carbon, nitrogen, δ 13 C, and δ 15 N. KEY RESULTS: Legumes initially grew taller and maintained that height advantage over time under all experimental conditions. Legumes also had the highest final total biomass and water-use efficiency in the high-light and high-resource soil. For nitrogen-fixing legumes, the amount of nitrogen derived from fixation was highest in the richer soil. Although seed mass tended to be larger in legumes, seed size alone did not account for all the differences between legumes and nonlegumes. Both belowground and aboveground resources were limiting to early seedling growth and function. CONCLUSIONS: Legumes may have a different regeneration niche, in that they germinate rapidly and grow taller than other species immediately after germination, maximizing their performance when light and belowground resources are readily available, and potentially permitting them to take advantage of high light, nutrient, and water availability at the beginning of the wet season.
Data from: Functional traits and community composition: a comparison among community-weighted means, weighted correlations, and multilevel models
1. Of the several approaches that are used to analyze functional trait-environment relationships, the most popular is community-weighted mean regressions (CWMr) in which species trait values are averaged at the site level and then regressed against environmental variables. Other approaches include model-based methods and weighted correlations of different metrics of trait-environment associations, the best known of which is the fourth-corner correlation method. 2. We investigated these three general statistical approaches for trait-environment associations: CWMr, five weighted correlation metrics (Peres-Neto et al. 2017), and two multilevel models (MLM) using four different methods for computing p-values. We first compared the methods applied to a plant community dataset. To determine the validity of the statistical conclusions, we then performed a simulation study. 3. CWMr gave highly significant associations for both traits, while the other methods gave a mix of support. CWMr had inflated type I errors for some simulation scenarios, implying that the significant results for the data could be spurious. The weighted correlation methods had generally good type I error control but had low power. One of the multilevel models, that from Jamil et al. (2013), had both good type I error control and high power when an appropriate method was used to obtain p-values. In particular, if there was no correlation among species in their abundances among sites, a parametric bootstrap likelihood ratio test (LRT) gave the best power. When there was correlation among species in their abundances, a conditional parametric LRT had correct type I errors but had lower power. 4. There is no overall best method for identifying trait-environment associations. For the simple task of testing, one-by-one, associations between single environmental variables and single traits, the weighted correlations with permutation tests all had good type I error control, and their ease of implementation is an advantage. For the more complex task of multivariate analyses and model fitting, and when high statistical power is needed, we recommend MLM2 (Jamil et al. 2013); however, care must be taken to ensure against inflated type I errors. Because CWMr exhibited highly inflated type I error rates, it should always be avoided. 2. We investigated these three general statistical approaches for trait-environment associations: CWMr, five weighted correlation metrics (Peres-Neto et al. 2017), and two multilevel models (MLM) using five different methods for computing p-values. We first compared the methods applied to a plant community dataset. To determine the validity of the statistical conclusions, we then performed a simulation study. 3. CWMr gave highly significant associations for both traits, while the other methods gave a mix of support. CWMr had inflated type I errors for some simulation scenarios. The weighted correlation methods had generally good type I error control but had low power. One of the multilevel models, that from Jamil et al. (2013), had both good type I error control and high power when an appropriate method was used to obtain p-values. In particular, if there was no correlation among species in their abundances among sites, a parametric bootstrap likelihood ratio test (LRT) gave the best power. When there was correlation among species in their abundances, a conditional parametric LRT had correct type I errors but suffered from low power. 4. There is no overall best method for identifying trait-environment associations. For the simple task of testing, one-by-one, associations between single environmental variables and single traits, the weighted correlations with permutation tests all had good type I error control, and their ease of implementation is an advantage. For the more complex task of multivariate analyses and model fitting, and when high statistical power is needed, we recommend MLM2 (Jamil et al. 2013); however, care must be taken to ensure against inflated type I errors. Because CWMr exhibited highly inflated type I error rates, it should be avoided.
Data from: "Lake Metabolism: Comparison of Lake Metabolic Rates Estimated from a Diel CO2- and the Common Diel O2-Technique" in PlosOne
<p>The data file is a matlab file (MATLAB 8.2) that contains structures providing the data used in the analysis of lake metabolism in Lake Illmensee, Germany.</p> <p>Data set comprises of:</p> <p>1. Original time series on CO<sub>2</sub>, O<sub>2</sub> and Temperature</p> <p>2. Morphometric data on Lake Illmensee</p> <p>3. Time series of derived data:</p> <p>a) atmospheric fluxes of CO2 and O2</p> <p>b) vertical turbulent diffusivities</p> <p>c) mixing depth</p> <p>d) metabolic rates</p> <p>All structures provide detailed information on the data. The equations and models used can be found in the paper: Lake Metabolism: Comparison of lake Metabolic Rates Estimated from a Diel CO<sub>2</sub>- and the Common Diel-O<sub>2</sub> technique in a manuscript submitted to PlosOne in 2016.</p> <p> </p> <p> </p> <p> </p>
Final Version of the Data associated to the publication "A Benchmark for Finite Prandtl Number Convection: Comparison of Boltzmann and Navier-Stokes Solutions"
<p>Final Version of V_rms and Nu for the three codes, GAIA, StreamV, TLBM, used for a benchmark manuscript titled "A Benchmark for Finite Prandtl Number Convection: Comparison of Boltzmann and Navier-Stokes Solutions", Authors: Gabriele Morra, Peter Mora, Christian Huttig, Nicola Tosi, Henri Samuel, David A. Yuen</p> <p>The Zip file contains both npy and out versions of V_rms and Nu. In the out files, time is embedded in each file. In the "npy" version, time is a separate npy file. In this final version, pdf figures for each case are also embedded.</p>
Supplementary Data for "Comparison of Ensemble-Based Data Assimilation Methods for Sparse Oceanographic Data"
<p>This data set represents the supplementary data for the paper Comparison of Ensemble-Based Data Assimilation Methods for Sparse Oceanographic Data (Section 4) by Florian Beiser, Håvard Heitlo Holm, and Jo Eidsvik.</p><p>It contains the data that is plotted in the manuscript. The code for plotting is provided in the supplementary software.</p>
Experimental raw data sets associated with certified reference material BAM-P116 (titanium dioxide) for comparison of nitrogen and argon sorption, available in the universal adsorption information format (AIF)
<p>These data sets serve as models for calculating the specific surface area (BET method) using gas sorption in accordance with ISO 9277.<br>The present measurements were carried out with nitrogen at 77 Kelvin and argon at 87 Kelvin.<br>It is recommended to use the following requirements for the molecular cross-sectional area:<br>Nitrogen: 0.1620 nm²<br>Argon: 0.1420 nm²</p> <p>Expected specific surface area for nitrogen (BET): 305 to 345 m²/g<br>Expected specific surface area for argon (BET): 300 to 310 m²/g</p> <p>Titanium dioxides certified with nitrogen sorption and additionally measured with argon for research purposes were used as sample material.<br>The resulting data sets are intended to serve as comparative data for own measurements and show the differences in sorption behaviour and evaluations between nitrogen and argon.<br>These data are stored in the universal AIF format (adsorption information format), which allows flexible use of the data.</p>
Data from: LHFPL5 is a key element to the gating spring of cochlear hair cells: comparison of mechanotransduction channel activation in presence or absence of LHFPL5
<p>During auditory transduction, sound-evoked vibrations of the hair cell stereociliary bundles open mechanotransducer (MET) ion channels via tip links extending from one stereocilium to its neighbor. How tension in the tip link is delivered to the channel is not fully understood. The MET channel comprises a pore-forming subunit, transmembrane channel-like protein (TMC1 or TMC2), aided by several accessory proteins, including LHFPL5 (lipoma HMGIC fusion partner-like 5). We investigated the role of LHFPL5 in transduction by comparing MET channel activation in outer hair cells of <em>Lhfpl5-/- </em>knockout mice with those in <em>Lhfpl5+/-</em> heterozygotes. The 10-90 percent working range of transduction in <em>Tmc1+/+; Lhfpl5+/-</em> was 52 nm, from which the single-channel gating force, Z was evaluated as 0.34 pN. However, in <em>Tmc1+/+; Lhfpl5‑/- </em>mice,<em> </em>the<em> </em>working range increased to 123 nm and Z more than halved to 0.13 pN, indicating reduced sensitivity. Tip link tension is thought to activate the channel via a gating spring, whose stiffness is inferred from the stiffness change on tip link destruction. The gating stiffness was ~40 percent of the total bundle stiffness in wild-type but was virtually abolished in <em>Lhfpl5-/-,</em> implicating LHFPL5 as a principal component of the gating spring. The mutation <em>Tmc1 </em>p.D569N reduced the LHFPL5 immunolabeling in the stereocilia and like <em>Lhfpl5-/-</em> doubled the MET working range but other deafness mutations had no effect on the dynamic range. We conclude that tip-link tension is transmitted to the channel primarily via LHFPL5; residual activation without LHFPL5 may occur by direct interaction between PCDH15 and TMC1.</p>
Simulation Data for Comparison of Plasmode and Parametric Simulation
<p>Simulation results of a study comparing Plasmode and parametric simulation for the example of estimating the MSE of the least squares estimator in linear regression. </p>
Data from: Comparison of dopamine release and uptake parameters across sex, species and striatal subregions
<p><span>Dopamine in the striatum strongly regulates behavioral output in a heterogenous across the various striatal subregions. Moreover, dopamine dynamics not only displays heterogeneity across brain structures but also within males and females. The purpose of this dataset was to evaluate the dopamine dynamics in male and female mice and rats across five subregions: the dorsolateral caudate, ventromedial caudate, nucleus accumbens core, nucleus accumbens lateral shell, and the nucleus accumbens medial shell. Fast scan cyclic voltammetry (FSCV) was employed to measure dopamine release and uptake following a single pulse electrical stimulation in each of these subregions within a single brain slice. The dopamine dynamics were also observed across a variety of stimulation amplitudes. The goal of this dataset was to produce systematic FSCV measurements of dopamine across the rodent striatum using FSCV which would be available as a </span><span>resource for further investigation of DA terminal function.</span></p>
Data for: Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny
<p>Sequence alignments and gene trees for: Braun et al. "Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny." See README file for detailed description of all files.</p>
ScienceDex guides
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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.