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10,801 results for “data correction”
Aquarius CAP Level 3 Sea Surface Salinity Rain Corrected Standard Mapped Image 7-Day Data V5.0
Version 5.0 Aquarius CAP Level 3 products are the fourth release of the AQUARIUS/SAC-D mapped salinity and wind speed data based on the Combined Active Passive (CAP) algorithm. CAP Level 3 standard mapped image products contain gridded 1 degree spatial resolution salinity and wind speed data averaged over 7 day and monthly time scales. This particular dataset is the 7-Day running mean sea surface salinity (SSS) rain corrected V5.0 Aquarius CAP product. CAP is a P.I. produced dataset developed and provided by JPL. The CAP algorithm utilizes data from both the onboard radiometer and scatterometer to simultaneously retrieve salinity, wind speed and direction by minimizing the sum of squared differences between model and observations. The main improvements in CAP V5.0 relative to the previous version include: updates to the Geophysical Model Functions to 4th order harmonics with the inclusion of sea surface temperature (SST) and stability at air-sea interface effects; use of the Canadian Meteorological Center (CMC) SST product as the new source ancillary sea surface temperature data in place of NOAA OI SST. The Aquarius instrument is onboard the AQUARIUS/SAC-D satellite, a collaborative effort between NASA and the Argentinian Space Agency Comision Nacional de Actividades Espaciales (CONAE). The instrument consists of three radiometers in push broom alignment at incidence angles of 29, 38, and 46 degrees incidence angles relative to the shadow side of the orbit. Footprints for the beams are: 76 km (along-track) x 94 km (cross-track), 84 km x 120 km and 96km x 156 km, yielding a total cross-track swath of 370 km. The radiometers measure brightness temperature at 1.413 GHz in their respective horizontal and vertical polarizations (TH and TV). A scatterometer operating at 1.26 GHz measures ocean backscatter in each footprint that is used for surface roughness corrections in the estimation of salinity. The scatterometer has an approximate 390km swath.
Aquarius CAP Level 3 Sea Surface Salinity Rain Corrected Standard Mapped Image Monthly Data V5.0
Version 5.0 Aquarius CAP Level 3 products are the fourth release of the AQUARIUS/SAC-D mapped salinity and wind speed data based on the Combined Active Passive (CAP) algorithm. CAP Level 3 standard mapped image products contain gridded 1 degree spatial resolution salinity and wind speed data averaged over 7 day and monthly time scales. This particular dataset is the monthly sea surface salinity (SSS) rain corrected V5.0 Aquarius CAP product. CAP is a P.I. produced dataset developed and provided by JPL. The CAP algorithm utilizes data from both the onboard radiometer and scatterometer to simultaneously retrieve salinity, wind speed and direction by minimizing the sum of squared differences between model and observations. The main improvements in CAP V5.0 relative to the previous version include: updates to the Geophysical Model Functions to 4th order harmonics with the inclusion of sea surface temperature (SST) and stability at air-sea interface effects; use of the Canadian Meteorological Center (CMC) SST product as the new source ancillary sea surface temperature data in place of NOAA OI SST. The Aquarius instrument is onboard the AQUARIUS/SAC-D satellite, a collaborative effort between NASA and the Argentinian Space Agency Comision Nacional de Actividades Espaciales (CONAE). The instrument consists of three radiometers in push broom alignment at incidence angles of 29, 38, and 46 degrees incidence angles relative to the shadow side of the orbit. Footprints for the beams are: 76 km (along-track) x 94 km (cross-track), 84 km x 120 km and 96km x 156 km, yielding a total cross-track swath of 370 km. The radiometers measure brightness temperature at 1.413 GHz in their respective horizontal and vertical polarizations (TH and TV). A scatterometer operating at 1.26 GHz measures ocean backscatter in each footprint that is used for surface roughness corrections in the estimation of salinity. The scatterometer has an approximate 390km swath.
Data for article: Normative drift and self-correction and self-regulation in scholarly publishing: The case of scholarly books published by academics at Makerere University
<p>University academics face multiple pressures to publish. These pressures emanate from contexts with different, often competing, social norms which result in academics publishing for reasons that may run counter to accepted scientific practice. This paper asks what decisions are being taken by academics when it comes to their choice of scholarly book publisher. An analysis of books selected from more than 2,500 self-reported scholarly publications produced by academics at Makerere University in Uganda from 2011 to 2017, reveals that 31 scholarly books were published. Of these books, more than half (54%) were published by publishers that do not follow accepted scholarly publishing practice. Findings also show that there was a sharp decline in books published with suspect publishers in the second half of the seven-year period. The article discusses possible reasons for the selection of suspect publishers and considers four factors that may account for the observable decline: (1) a cyclical downturn; (2) improved research management and reporting; (3) explication of the norms of science; and (4) self-correction.</p> <p><strong>METHODS</strong></p> <p>The specific interest of this study is the publication of scholarly books by academics at Makerere University. </p> <p>The sources of the publications data were the lists of research outputs published in Makerere University’s annual reports from 2011 to 2017. Digital copies of the annual reports in PDF format were downloaded from the university’s website. Data were scraped from the annual report PDFs by exporting the publication lists from the PDFs to MSWord, removing unnecessary line breaks and spacing to create a single publication per line, and copying the publication lists into MSExcel for cleaning and analysis. Data were cleaned to remove (1) duplicate entries (e.g. identical publications in the same annual report or a publication listed as ‘under review’ or ‘in press’ in one year and listed again as a publication in a following year); (2) publications listed as ‘submitted’, unpublished masters and PhD theses, speeches, lectures, responses or retractions; (3) incomplete entries (e.g. no article, book or journal title); and (4) publications prior to 2011 (e.g. a 2008 publication listed in the 2011 annual report).</p> <p>The cleaned data were then coded for ‘year of publication’ (2011 to 2017 inclusive), ‘college’ (any of the colleges at Makerere University to which the authors were affiliated), and ‘publication type’ (book chapter, journal article, edited volume, working paper, policy brief, monograph, conference paper, textbook, report, popular article, poster presentation, newsletter, essay, catalogue, poetry, handbook). Books or parts of books (i.e. ‘book chapter’, ‘edited volume’, ‘monograph’, ‘textbook’, ‘catalogue’, ‘poetry’ and ‘handbook’) were further coded for ‘publisher’ (name); ‘publisher location’ (city, country as indicated on the imprint page of the publication); and ‘URL’ (online reference to publisher or publication). In some cases, publications were listed by type in the annual reports. Where publication lists were not presented in this way, indicators such as ‘journal of’, ‘volume’, ‘issue’ and ISSNs were used to identify journals; conference names, ‘proceedings of’, dates and cities were used to identify conference papers and presentations; ‘news’, ‘magazine’, ISSNs and the absence of ‘journal of’ were used to identify periodicals; and place of publication, publisher and ISBNs were used to identify books. Where these indicators were insufficient to determine a publication type, an online search was done to find the missing data. </p> <p>A limitation of the adopted method is that it relies on self-reporting by the university colleges and the list can therefore not be assumed to be comprehensive. Without knowledge of the reporting guidelines, it is also not possible to know whether all colleges and schools used the same criteria when selecting what to submit for reporting purposes. For example, some colleges may have decided to include working papers, policy briefs or papers presented at conferences, while others may have decided not to do so. </p>
ChemCam data and corrected Li data
<p>Supplementary data for JGR manuscript "Boron and Lithium in Calcium Sulfate Veins: Tracking Precipitation of Diagenetic Materials in Vera Rubin Ridge, Gale Crater". Excel files contain all LIBS data collected by the Curiosity rover between sol 1-2311 and corrected Li data for vein targets.</p>
High-resolution gridded climate data for Europe based on bias-corrected EURO-CORDEX: the ECLIPS-2.0 dataset
<p>We developed a new climate dataset for Europe referred to as ECLIPS (European CLimate Index ProjectionS), which contains gridded data for 80 annual, seasonal, and monthly climate variables for two past (1961-1990, 1991-2010) and five future periods (2011-2020, 2021-2140, 2041-2060, 2061-2080, 2081-2100). The future data are based on five Regional Climate Models (RCMs)driven by two greenhouse gas concentration scenarios, RCP 4.5 and 8.5.</p> <p>The ECLIPS dataset has two versions; ECLIPS 1.1 contains data with spatial resolution of 0.11° × 0.11°, which is the resolution of underlying RCMs. ECLIPS1.1 is available at <a href="https://doi.org/10.5281/zenodo.1181780">https://doi.org/10.5281/zenodo.1181780</a>.</p> <p>The ECLIPS 2.0 presented here contains a subset of climate indices of ECLIPS 1.1, downscaled to the resolution of 30 arcsec by means of the delta correction approach. Both ECLIPS versions were evaluated by testing their relationship with independent station data from the European Climate Assessment (ECA) dataset. Correlations of the empirical testing data to ECLIPS 1.1 ranged from 0.63 to 0.78,and to ECLIPS 2.0 from 0.78 to 0.93. suggesting substantial improvement due to downscaling. A large number of climate projections, time periods and indices as well as the availability of these data at two different spatial resolutions can support diverse studies across a range of disciplines and thus extend our understanding of climate-sensitive dynamics of many social-ecological systems</p> <p>The zipfile ECLIPS2.0 contains 5 folders with subfolders</p> <p>File naming system for the subfolders / folder are as follows</p> <p>ECLIPS2.0_196191: past climate 1961-1990: < climate index><period></p> <p>ECLIPS2.0_199110: past climate 1991-2010 < climate index><period></p> <p>ECLIPS2.0_45 : future climate RCP4.5 <subfolder-Model name> < climate index><period></p> <p>ECLIPS2.0_85 : future climate RCP8.5 <subfolder-Model name> < climate index><period></p> <p>Incase zpfile reader 7zip is not available, please install from here: <a href="https://www.7-zip.org/">https://www.7-zip.org/</a></p>
Data from: Phage display peptide libraries: deviations from randomness and correctives
Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study we implemented Next Generation Sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon overrepresentation as well as in high G phosphoramidite abundance causing amino acid distribution biases. In this study we demonstrate that the UAG overrepresentation can be attributed to the burden imposed on the phage upon the assembly of the recombinant Protein 8 subunits. This was corrected by constructing the libraries using supE44-containing bacteria which suppress the UAG driven abortive termination. We also demonstrate that the overabundance of G stems from variant synthesis-efficiency and can be corrected using compensating oligonucleotide-mixtures calibrated by Mass Spectroscopy. Construction of libraries implementing these correctives results in markedly improved libraries that display random distribution of amino acids, thus ensuring that enriched peptides obtained in biopanning represent a genuine selection event, a fundamental assumption for phage display applications.
Data from: Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies
Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths.
Data from: Body mass-corrected molecular rate for bird mitochondrial DNA
Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species' body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.
Data from: Correction for bias in meta-analysis of little-replicated studies
1. Meta-analyses conventionally weight study estimates on the inverse of their error variance, in order to maximize precision. Unbiased variability in the estimates of these study-level error variances increases with the inverse of study-level replication. Here we demonstrate how this variability accumulates asymmetrically across studies in precision-weighted meta-analysis, to cause undervaluation of the meta-level effect size or its error variance (the meta-effect and meta-variance). 2. Small samples, typical of the ecological literature, induce big sampling errors in variance estimation, which substantially bias precision-weighted meta-analysis. Simulations revealed that biases differed little between random- and fixed-effects tests. Meta-estimation of a one-sample mean from 20 studies, with sample sizes of 3 to 20 observations, undervalued the meta-variance by ~20%. Meta-analysis of two-sample designs from 20 studies, with sample sizes of 3 to 10 observations, undervalued the meta-variance by 15-20% for the log response ratio (lnR); it undervalued the meta-effect by ~10% for the standardised mean difference (SMD). 3. For all estimators, biases were eliminated or reduced by a simple adjustment to the weighting on study precision. The study-specific component of error variance prone to sampling error and not parametrically attributable to study-specific replication was replaced by its cross-study mean, on the assumption of random sampling from the same population variance for all studies, and sufficient studies for averaging. Weighting each study by the inverse of this mean-adjusted error variance universally improved accuracy in estimation of both the meta-effect and its significance, regardless of number of studies. For comparison, weighting only on sample size gave the same improvement in accuracy, but could not sensibly estimate significance. 4. For the one-sample mean and two-sample lnR, adjusted weighting also improved estimation of between-study variance by DerSimonian-Laird and REML methods. For random-effects meta-analysis of SMD from little-replicated studies, the most accurate meta-estimates obtained from adjusted weights following conventionally-weighted estimation of between-study variance. 5. We recommend adoption of weighting by inverse adjusted-variance for meta-analyses of well- and little-replicated studies, because it improves accuracy and significance of meta-estimates, and it can extend the scope of the meta-analysis to include some studies without variance estimates.
Data from: Inconsistent use of multiple comparison corrections in studies of population genetic structure: are some type I errors more tolerable than others?
Studies of genetic population structure often involve numerous tests of Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and genetic differentiation. Tests of HWE or LD are important precursors to population structure assessments. When conducting multiple related statistical tests, type 1 error increases, e.g., familywise error rate (FWER) inflation. FWER inflation can alter the results of statistical tests and thus the conclusions. Authors are aware of the need to control for FWER inflation, but there has been low consistency of use. Furthermore, there is a potential for the choice of correction methods to be exploited to selectively use FWER corrections to avoid data exclusion or to result in increased the rejection of null hypotheses. We surveyed literature from 2011-2013 to determine if studies of population structure assess LD and HWE and if FWER corrections were applied consistently across different types of genetic differentiation, linkage disequilibrium, and Hardy-Weinberg equilibrium tests. We found a lack of documentation of FWER corrections in studies, and we advocate for authors to be more cognizant in reporting their corrections. We also found significantly inconsistent FWER corrections, with a bias towards less restrictive correction on genetic differentiation and more restrictive corrections with LD and HWE. While varied adjustments of FWER for different types of analyses might be justified, papers with inconsistent usage across tests of HWE, LD and genetic differentiation did not present rationale for their FWER corrections. We also found a lack of documentation of HWE, LD and FWER corrections in studies. We encourage authors to report statistical tests and related FWER corrections, use FWER corrections consistently or justify their different methods in the same study.
Data accompanying the publication "Quantum error correction with silicon spin qubits"
<p>Data accompanying the publication "Quantum error correction with silicon spin qubits"</p>
Data from: A pair of nonoptimal codons are necessary for the correct biosynthesis of the Aspergillus nidulans urea transporter, UreA
Both in prokaryotic and eukaryotic genomes synonymous codons are unevenly used. Such differential usage of optimal or nonoptimal codons has been suggested to play a role in the control of translation initiation and elongation, as well as at the level of transcription and mRNA stability. In the case of membrane proteins codon usage has been proposed to assist in the establishment of a pause necessary for the correct targeting of the nascent chains to the translocon. In this work, using as model UreA, the Aspergillus nidulans urea transporter, we show that the synonymous mutation of a pair of nonoptimal codons coding for amino acids situated at the limit between the N-terminus and the first transmembrane segment are necessary for its proper biogenesis at 37ºC. This effect is less relevant at 25ºC. These codons presumably regulate translation rate in order to allow for the correct interaction of UreA-translating ribosomes with factors required for the targeting and/or folding of the protein, in a very early stage of the biosynthesis process. Whether this mechanism would affect other proteins, remains to be determined.
Statistical Data for The Impact of Chatbots using Concept Maps on Correction Outcomes–a Case Study of Programming Courses
<p>experiment learners' questionnaire result and test score</p>
PBE, PBE0, B86bPBE data and relative DNN-MBDQ dispersion corrections for S66x8 and S22 data sets.
<p>PBE, PB0 and B86bPBE interaction energy data for the S66x8 and/or S22<br> data sets as well as their relative DNN-MBDQ dispersion corrections for the different range-separation parameters (β) discussed.</p>
The experimental data of three-axis fluxgate instrument installation orientation error correction
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MRI Raw Data for 2024 ISMRM Workshop on Motion Correction
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Data_Effects_and_correctability_of_pile_up_distortion_using_established_figures_of_merit_in_time_domain_diffuse_optics_at_extreme_photon_rates
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scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data
<p><span>In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination for all genes globally. However, specific evaluation for different contamination levels is lacking. Here, we show that DecontX and CellBender under-correct highly-contaminating genes, while SoupX and scAR over-correct lowly-/non-contaminating genes. Here, we develop scCDC as the first method to detect the contamination-causing genes and only correct expression levels of these genes, some of which are cell-type markers. Compared with existing decontamination methods, scCDC excels in decontaminating highly-contaminating genes while avoiding over-correction of other genes.</span></p>
Data from: Corrections for rooting volume and plant size reveal negative effects of neighbour presence on root allocation in pea
Plants are able to detect the presence of their neighbours belowground. The associated root responses may affect plant performance, plant-plant interactions and community dynamics, but the extent and direction of these responses is heavily debated. Some studies suggest that plants will over-proliferate roots in response to neighbours at the expense of reproduction, which was framed as a "tragedy of the commons". Others proposed an "ideal free distribution" hypothesis, stating that plants produce roots simply as a function of the amount of available nutrients. However, experimental evidence for either hypothesis that is unbiased by confounding effects of rooting volume and plant size in their experimental setups is still lacking. We grew split-root pea plants in the presence or absence of a belowground neighbour at a range of rooting volumes, while providing equal amounts of nutrients per plant. Path analyses were used to disentangle the direct effects of neighbour presence on allocation patterns from the confounding effects of rooting volume and plant size. Within the chosen range of rooting volumes, the presence of a belowground neighbour generally reduced plant root mass by 21% and total mass by 9%. A doubling of rooting volume generally increased plant root mass by 18% and total mass by 11%. Pod mass was only directly and positively correlated with vegetative mass. The presence of a belowground neighbour induced less root allocation but more pod allocation, whereas increased rooting volume caused a reduction in reproductive allocation. A large part of these effects, however, was indirectly mediated through the influence on plant total mass. Synthesis: Not considering the effects of rooting volume and plant size may lead to misinterpretations of plant growth strategies in response to neighbours. Accounting for these factors, we found pea allocating less mass to roots in the presence of a belowground neighbour. The obtained results can help to reconcile the various responses to belowground neighbours as they are published in the literature.
Code and data for manuscript: Does ankle push-off correct for errors in anterior-posterior foot placement relative to center-of-mass states?
<p>Data and code documentation for paper: “Does ankle push-off correct for errors in anterior-posterior foot placement relative to center-of-mass states?” All code in the current study can be accessed via the link (https://drive.google.com/drive/folders/1AnL9ajMk_Q3Gwzv_OrOp7A8DNwS8lniC?usp=sharing). The code was written by Jian Jin, Sjoerd Bruijn and Moira van Leeuwen. The data was from (van Leeuwen et al., 2020)and can be accessed through the link (https://doi.org/https://doi.org/10.5281/zenodo.4229851).</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.