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7,370 results for “supplementation”
Supplemental Material for Z. S. Cooper Dissertation Chapter 4 - Marinobacter Pangenomics
<p>This dataset contains main and supplemental data tables for a chapter of the doctoral dissertation by Zachary S. Cooper at the University of Washington School of Oceanography. The chapter is titled "Chapter 4: Evolutionary divergence of <em>Marinobacter </em>strains in cryopeg brines as revealed by pangenomics". Briefly, this chapter contains pangenomic analyses of novel genomes of the bacterial genus <em>Marinobacter</em> that are compared with representative species of the genus to discern evolutionary history and functional capabilities of this species in the extreme cryopeg environment. The main data tables include lists of genomes used in the analyses and their characteristics as described in the dissertation chapter. The supplemental data tables include gene cluster annotations with COGs (S1), functional frequencies across the pangenome (S2), functional enrichment analysis (S3), KEGG annotations (S4), KEGG pathway completion values (S5), average nucleotide identity values (S6), alignment coverage values (S7), and horizontal gene transfer analysis summaries (S8). The tables were produced from the combination of outputs of the bioinformatic programs Anvi'o, KEGG KofamKOALA, KEGG Decoder, PyANI, and HGTector2. Details on the methods and interpretations of this data are included in the dissertation.</p>
Supplemental Code and Data for https://gmd.copernicus.org/articles/14/7255/2021/
<p>This directory includes the final accepted version of model code and model output used in the accepted version of the manuscript<br> Kvale et al. GMDD (2020) Explicit silicate cycling in the Kiel Marine Biogeochemistry Model, version 3 (KMBM3) embedded in the UVic ESCM version 2.9, https://gmd.copernicus.org/articles/14/7255/2021/</p> <p>Please contact Karin Kvale (kkvale@geomar.de) for details</p> <p>The complete model code used to produce the output used in the writing of the manuscript can be found in the "code" directory. This is preprocessed code includes only .f and .h files, which are all that is needed to compile the model version used in the writing of the manuscript. For modification of model options, the unprocessed .F and .h files are required. These can be obtained by contacting the corresponding author.</p> <p>The data files used to run the model are found in the "data" directory.</p> <p>The model output is tavg.01775.01.01.nc and tsi.01766.01.01.nc for the annually-averaged output. Model seasonal output is provided in the "diatom_seasonal" directory.<br> <br> Data files are provided in netcdf format with metadata included in the files. </p> <p>Simulation details are described in the manuscript, as well as in the control.in model configuration file.</p> <p>Final_fig_scripts contains the Ferret scripts used to generate manuscript figures.</p> <p>The code is provided under the terms of the Apache 2.0 license.</p>
Glyco Atlas Supplemental Tables (Leo Alexander Dworkin) PhD Thesis
<p>The complex multi-step process of glycosylation occurs in a single cell, yet current analytics generally cannot measure the output (the glycome) of a single cell. Here, we addressed this discordance by testing usage of single cell transcriptomics to break this barrier. We investigated how single cell RNA-seq data can be used to characterise the state of the glycosylation machinery and metabolic network in single cell. The metabolic network involves 214 glycosylation and modification enzymes with their contributions to the glycome outlined in our previously built atlas of cellular glycosylation pathways. We studied differential mRNA regulation of enzymes at the organ and single cell level, finding that most of the general protein and lipid oligosaccharide scaffolds are produced by enzymes exhibiting limited transcriptional regulation among cells. We predict key enzymes within different glycosylation pathways to be highly transcriptionally regulated as regulatable hotspots of the cellular glycome. We designed the Glycopacity software that enables investigators to extract and interpret glycosylation information from transcriptome data and define hotspots of regulation.</p>
Data Supplement for ApJ Paper: Stumbling over planetary building blocks: AU Microscopii as an exampleof the challenge of retrieving debris-disk dust properties
<p>Computational data set underlying a manuscript analyzing visible to near infrared wavelength Hubble-STIS spectrographic coronagraph observations of the AU Microscopii debis disk. To interpret this multi-wavelength data set, we calculated light scattering properties of three different debris disk dust grain shape models: spheres, porous spheres, and more realistic irregular agglomerated debris particles. Calculations of scattering efficiency and phase function were done over a range of dust grain sizes and material refractive indices.</p> <p>This bundle contains three .hdf table files. Each table file contains a size parameter array (1D), complex refractive index array (1D), scattering efficiency array (1D), and scattering phase function array (2D). The 1st dimension of each array is the same size. The 2nd dimension of the scattering phase function is 60, the number of scattering angles calculated at an angular resolution of 3 degrees.</p>
Supplemental material: Operative videos on application of microscope-based augmented reality with intraoperative computed tomography-based navigation for resection of skull base meningiomas
<p>Supplemental material</p> <p>Operative videos:</p> <p>Patient number 9: Microsurgical resection of medial sphenoid wing meningioma using microscope-based augmented reality and intraoperative computed tomography-based navigation</p> <p>Pt 28:Microsurgical resection of right clinoidal meningioma via fronto-temporal craniotomy with microscope-based augmented reality</p> <p>Pt 31:Microsurgical resection of recurrent sphenoid wing meningioma using microscope-based augmented reality with intraoperative computed tomography</p> <p>Pt 36: Microsurgical resection of giant olfactory meningioma via bifrontal approach with use of augmented reality and intraoperative CT-based navigation</p>
Figs 23-29 in Supplement to the knowledge of the Scaphidiinae (Coleoptera: Staphylinidae) of the Moluccas
Figs 23-29. Scaphisoma donati sp. nov. (23) Parameres in ventral view, scale bar = 0.2 mm. Figs 24-27. Scaphobaeocera plana sp. nov. (24, 25) Aedeagus in dorsal and lateral views, scale = 0.1 mm. (26) Paramere in ventral view, scale = 0.05 mm. (27) Apical part of median lobe, in lateral view, scale = 0.05 mm. Figs 28, 29. Scaphoxium lobatum sp. nov. (28) Aedeagus in ventral view, scale = 0.1 mm. (29) Apex of median lobe with extruded internal sac and right paramere, in dorsal view, scale = 0.05 mm.
Figs 1-9 in Supplement to the knowledge of the Scaphidiinae (Coleoptera: Staphylinidae) of the Moluccas
Figs 1-9. Baeocera humicola sp. nov. (1, 2) Aedeagus in dorsal and lateral views, scale bar = 0.1 mm. (3) Internal sac, scale bar = 0.05 mm. Figs 4-6. Baeocera incurva sp. nov. (4, 5) Aedeagus in dorsal and lateral views, scale bar = 0.1 mm. (6) Internal sac, scale bar = 0.05 mm. Figs 7-9. Baeocera notata sp. nov. (7) Aedeagus in dorsal view, scale bar = 0.1 mm. (8) Paramere in ventral view, scale = 0.05 mm. (9) Internal sac, scale = 0.05 mm.
Figs 19-22 in Supplement to the knowledge of the Scaphidiinae (Coleoptera: Staphylinidae) of the Moluccas
Figs 19-22. Baeocera punctiventris sp. nov. (19) Aedeagus in lateral view. Figs 20-22. Scaphisoma donati sp. nov. (20, 21) Aedeagus in dorsal and lateral views, scale bars 0.2 mm. (22) Median lobe with left paramere, without internal sac.
Figs 10-18 in Supplement to the knowledge of the Scaphidiinae (Coleoptera: Staphylinidae) of the Moluccas
Figs 10-18. Baeocera notata sp. nov. (10) Aedeagus in lateral view, scale bar = 0.1 mm. Figs 11-13. Baeocera paucivestis sp. nov. (11, 12) Aedeagus in dorsal and lateral views, scale bar = 0.1 mm. (13) Internal sac, scale bar = 0.05 mm. Figs 14-16. Baeocera punctigera sp. nov. (14, 15) Aedeagus in dorsal and lateral views, scale bar = 0.1 mm. (16) Internal sac, scale bar = 0.05 mm. Figs 17, 18. Baeocera punctiventris sp. nov. (17) Aedeagus in dorsal view, internal sac extruded, scale bar = 0.1 mm. (18) Paramere in dorsal view, scale bar = 0.05 mm.
Implementation and sensitivity analysis of a Dam-Reservoir OPeration model (DROP v1.0) over Spain - Supplement
<p>Supplement of the following scientific paper submitted in GMD :</p> <p><strong>Sadki M., Munier S., Boone A., Ricci S. : Implementation and sensitivity analysis of a Dam-Reservoir OPeration model (DROP v1.0) over Spain, Geoscientific Model Development, 2022. </strong></p> <p> </p>
Occupancy model for Rattus spp. in high and low human human refuse supplementation conditions
<p>Globally, the genus <em>Rattus </em>is one of the most influential exotic species due to its high rates of competitive exclusion and large dietary breadth. However, the specific foraging strategies of urban and urban-adjacent populations remain largely unknown. We examined <em>Rattus </em>spp. dependency on human food supplementation in a peri-urban population. Through a natural experiment made possible by the COVID-19 shelter in place order in Santa Cruz California, USA, we measured changes in activity between invasive rats and native rodents with and without human supplementation. We measured invasive rat presence in normal (pre-COVID) conditions near dining halls and similar waste sources, and again under COVID lockdown conditions where all sources of human supplementation were removed. We found a decrease in <em>Rattus </em>presence after the removal of human refuse (p < 0.001), while native small mammal presence remained unchanged. These results have strong conservation implications, as they suggest that proper waste management is an effective, targeted, and less-invasive form of population control over conventional forms of poison. </p>
Supplement materials - An appraisal of Ulva (Ulvophyceae, Chlorophyta) taxonomy
<p>Sequence alignments, supplement figures and tables for the manuscript "An appraisal of <em>Ulva </em>(Ulvophyceae, Chlorophyta) taxonomy"</p>
Online Supplement for An Arabic Version of The Visual Aesthetics of Websites Inventory (AR-VisAWI): Translation and Psychometric Properties
<p>This is the online supplement for a translation of the Visual Aesthetics of Websites Inventory into Arabic (AR-VisAWI). </p> <p>In the field of human-computer interaction, the concept of visual aesthetics gained popularity after researchers started to recognize its merits and effects on user experience. Yet, no proper instrument exists to assess the visual aesthetics of websites that are intended for users who speak Arabic as their native language. As such, the aim of this study was to develop and evaluate an Arabic version of the Visual Aesthetics of Websites Inventory (VisAWI, Moshagen & Thielsch, 2010) and its short version (VisAWI-S, Moshagen & Thielsch, 2013). For this purpose, participants were asked to evaluate a randomly assigned website with the AR-VisAWI and with different validating instruments. A final sample of 223 participants was included in the analyses.</p> <p>This online supplement includes</p> <ul> <li>a codebook describing all instructions and items</li> <li>raw data (anonymised) and analysis script (Note: The raw data contains only the information of persons who have agreed to be included in the analysis. Some demographic information was deleted to ensure anonymity.)</li> <li>Questionnaire template and scoring instructions</li> </ul>
Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. Supplemental VCF file
<p>Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2 kb to 10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50 kb to 100 kb which are usual distances between markers of the medium-density chip.</p> <p> </p> <p>File submitted correspond to the supplementary data 1 of the publication (under submission) : INRAE_USDA_MAF1.vcf.gz</p>
Supplemental data for submission "Bridging between LegalRuleML and TPTP for Automated Normative Reasoning"
<p>These files are supplementary material to the submission<br> Bridging between LegalRuleML and TPTP for Automated Normative Reasoning<br> by<br> Alexander Steen and David Fuenmayor<br> submitted to the 6th International Joint Conference on Rules and Reasoning (RuleML+RR 2022), 2022.</p> <p>Files ex1.lrml.xml and ex2.lrml.xml are two example LegalRuleML files.<br> Files ex1.dsl.p and ex2.dsl.p are two examples from above translated to the NMF DSL.<br> The files ex1.output.X.p and ex2.output.X.p are the translations of the NMF files into the concrete logic X (X = SDL or X = cJ (Carmo Jones) or X = aqvist (system E)).</p> <p>Alexander Steen, <alexander.steen@uni-greifswald.de></p>
Supplement to Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination
<p>Extended Data S1-S2 and Tables S6-S9 corresponding to the publication entitled Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination. Data S1 contains the phylogeny analyzed in the aforementioned study, and Data S2 contains a table of all samples considered to be descendant of a recombinant node in the study, as well as the relevant recombinant node ID. Tables S6-S9 are acknowledgments tables corresponding to GISAID (Table S6), China National Center for Bioinformation (Table S7), COVID-19 Genomics UK (COG-UK) (Table S8), and National Center for Biotechnology Information database (Table S9) on which the study was based.</p>
Supplement to: Enhanced surveillance of monkeypox in Bas-Uélé, Democratic Republic of Congo: the limitations of symptom-based case definitions
<p>This repository contains data and R code which are supplements to:</p> <p><em>Enhanced surveillance of monkeypox in Bas-Uélé, Democratic Republic of Congo: the limitations of symptom-based case definitions</em><br> Gaspard Mande, Innocent Akonda, Anja De Weggheleire, Isabel Brosius, Laurens Liesenborghs, Emmanuel Bottieau, Noam Ross, Guy Crispin Gembue, Robert Colebunders, Erik Verheyen Ngonda Daulya, Herwig Leirsh, and Anne Laudisoit (2022).</p> <p>A data dictionary and instructions for reproducing the analysis are provided. Details can be found in the README.md file.</p>
Climate Change and 2030 Cooling Demand in Ahmedabad, India: Opportunities for Expansion of Renewable Energy and Cool Roofs (Supplemental Information)
<p>Supplemental information and analysis files for article, "Climate change and 2030 cooling demand in Ahmedabad, India: opportunities for expansion of renewable energy and cool roofs" (Original article available at: https://doi.org/10.1007/s11027-022-10019-4)</p>
Supplemental files to "A COI DNA Barcode Library for Anastrepha Schiner (Diptera: Tephritidae)"
<p>The attached files are the supplemental material from Moore et al., "A COI DNA Barcode Library for <em>Anastrepha </em>Schiner (Diptera: Tephritidae)". They contain various DNA sequence alignments, calculation tables, tree files, taxonomic information on <em>Anastrepha</em>, and a R script.</p>
Supplemental data for: Variations in the naming of malondialdehyde (MDA) in PubMed-, Scopus-, and Web of Science-indexed literature
<p>Three scientific databases (PubMed, Scopus, and Web of Science (WoS)) were consulted (July 14, 2022) to assess the frequency of eight nomenclatural forms of malondialdehyde (MDA). Due to the peculiarities of the search interface of the selected databases, PubMed was searched in the Title and Abstract fields (search query example in PubMed: "malone dialdehyde"[Title/Abstract]), Scopus was searched in the Title, Abstract, and Keywords fields (search query example in Scopus: TITLE-ABS-KEY (“malone dialdehyde”)), and WoS Core Collection was searched in the Title, Abstract, Author keywords, and Keywords Plus fields (search query example in WoS Core Collection: TS=(“malone dialdehyde”)). All types of publications for the years 2002-2021 are taken into account.</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.