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Supplementary material 5 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S5
Supplementary material 14 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S14
Supplementary material 13 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S13
Supplementary material 12 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S12
Supplementary material 1 from: Woodburn M, Droege G, Grant S, Groom Q, Jones J, Trekels M, Vincent S, Webbink K (2021) A Data Standard for Dynamic Collection Descriptions. Biodiversity Information Science and Standards 5: e73902. https://doi.org/10.3897/biss.5.73902
Provisional list of classes.
Supplementary material 1 from: Ingala MR, Werner IE, Fitzgerald AM, Naro-Maciel E (2021) 18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York. Metabarcoding and Metagenomics 5: e69691. https://doi.org/10.3897/mbmg.5.69691
Scripts used for metabarcoding analysis
Supplementary material 2 from: Ingala MR, Werner IE, Fitzgerald AM, Naro-Maciel E (2021) 18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York. Metabarcoding and Metagenomics 5: e69691. https://doi.org/10.3897/mbmg.5.69691
Figure S1, Tables S1, S2
Supplementary material 1 from: Eitzel M.V (2021) A modeler's manifesto: Synthesizing modeling best practices with social science frameworks to support critical approaches to data science. Research Ideas and Outcomes 7: e71553. https://doi.org/10.3897/rio.7.e71553
Modeler's Manifesto: Self-Situating Appendix
Supplementary data --The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner
<p>Supplementary data for the Cell Systems manuscript 'The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner', by Hamelin <em>et al.</em></p> <p><strong>GISAID_Authors_Recognition_2021-01-19. </strong>Metadata concerning the SARS-CoV-2 viral sequences analysed, and generously provided by GISAID. </p> <p><strong>Table S1. </strong>SARS-CoV-2 mutations identified from 330,246 GISAID entries (December 31<sup>st</sup> 2020), Related to Figure 1 and Figure 2. SARS-CoV-2 mutations at the nucleic and amino acid level are indicated. Number of genomes carrying mutation show the frequency of individual mutations among all SARS-CoV-2 variants. </p> <p><strong>Table S2. </strong>SARS-CoV-2 prevalent mutations identified from 330,246 GISAID entries (December 31<sup>st</sup> 2020) and detected in at least 100 individuals, Related to Figure 2.</p> <p><strong>Table S3.</strong> Previously validated SARS-CoV-2 CD8+ T cell epitopes and their matching mutated forms identified in this study, Related to Figure 1 and Figure 2.</p> <p><strong>Table S4.</strong> List of previously validated SARS-CoV-2 CD8+ T cell epitopes. Epitopes were downloaded from https://www.mckayspcb.com/SARS2TcellEpitopes/ (as of January 2021). This database has effectively catalogued all SARS-CoV-2 CD8+ epitopes validated by 18 separate studies. See Quadeer et al. 2021 for details, Related to Figure 1 and Figure 2. </p>
Novel associations of BST1 and LAMP3 with rapid eye movement sleep behavior disorder: supplementary data
<p><b>Objective:</b> To examine the role of genes identified through genome-wide association studies (GWASs) of Parkinson disease (PD) in the risk of isolated rapid-eye-movement (REM) sleep behavior disorder (iRBD).</p> <p><b>Methods:</b> We fully sequenced 25 genes previously identified in GWASs of PD, in a total of 1,039 iRBD patients and 1,852 controls. The role of rare heterozygous variants in these genes was examined using burden tests. The contribution of biallelic variants was further tested. To examine the potential impact of rare nonsynonymous <i>BST1</i> variants on the protein structure, we performed <i>in silico</i> structural analysis. Finally, we examined the association of common variants using logistic regression adjusted for age and sex.</p> <p><b>Results:</b> We found an association between rare heterozygous nonsynonymous variants in <i>BST1</i> and iRBD (<i>p</i>=0.0003 at coverage >50X and 0.0004 at >30X), mainly driven by three nonsynonymous variants (p.V85M, p.I101V and p.V272M) found in 22 (1.2%) controls vs. two (0.2%) patients. All three variants seem to be loss-of-function variants with a potential effect on the protein structure and stability. Rare non-coding heterozygous variants in <i>LAMP3</i> were also associated with iRBD (<i>p</i>=0.0006 at >30X). We found no association between rare heterozygous variants in the rest of genes and iRBD. Several carriers of biallelic variants were identified, yet there was no overrepresentation in iRBD.</p> <p><b>Conclusion:</b> Our results suggest that rare coding variants in <i>BST1 </i>and rare non-coding variants in<i> LAMP3 </i>are associated with iRBD. Additional studies are required to replicate these results and examine whether loss-of-function of <i>BST1 </i>could be a therapeutic target.</p>
Figures 1-6 from: Gess F (2012) A new species of Masarina Richards 1962 from southern Africa, description of the female of M. ceres Gess 1997 and supplementary data on three other species of the genus (Hymenoptera, Vespidae, Masarinae). Journal of Hymenoptera Research 25: 83-92. https://doi.org/10.3897/jhr.25.2442
Figures 1-6 - Masarina gabymariae 1 ♀, lateral view (actual length 6.7 mm) 2 ♂, lateral view (actual length 6.0 mm) 3 ♀, dorsal view 4 ♂, dorsal view 5 ♀, head, front view (actual width 2.1 mm), tongue not extended 6 ♂, head, front view (actual width 1.9 mm), tongue extended.
Characterising the Chilean megadrought using satellite data of precipitation and evapotranspiration (supplementary material)
<p>This is the supplementary material accompanying the article submitted to Remote Sensing on Environment on February 26th, 2019.</p>
Supplementary material 1 from: Zhang M, Zhang X-H, Ge C-L, Chen B-H (2022) Danxiaorchis mangdangshanensis (Orchidaceae, Epidendroideae), a new species from central Fujian Province based on morphological and genomic data. PhytoKeys 212: 37-55. https://doi.org/10.3897/phytokeys.212.91534
Appendix S1
Emergence timing and voltinism of phantom midges, Chaoborus spp., in the UK., supplementary data
<p>Supporting water quality, environmental and biological data for draft manuscript.</p>
Supplementary Data Álvaro López-Valiñas PhD
<p>Supplementary material for the thesis of Álvaro López Valiñas entitled "Evolution of swine influenza virus associated with vaccination"</p>
Supplementary material 1 from: Murray HL (2022) Florida Keys Mosquito Control District mosquito trapping data between Vaca Key and Lower Matecumbe Key, 2018-2021. Research Ideas and Outcomes 8: e96714. https://doi.org/10.3897/rio.8.e96714
Marathon Area Trap Data 2018-2021
Supplementary material 1 from: Nations JA, Giarla TC, Morni MA, William Dee J, Swanson MT, Hiller AE, Khan FAA, Esselstyn JA (2022) Molecular data from the holotype of the enigmatic Bornean Black Shrew, Suncus ater Medway, 1965 (Soricidae, Crocidurinae), place it in the genus Palawanosorex. ZooKeys 1137: 17-31. https://doi.org/10.3897/zookeys.1137.94217
GenBank Accession numbers for genetic sequences used in this study
Supplementary data of Agricultural Water Management Evaluation
<p>Supplementary data of Agricultural Water Management Evaluation</p>
Supplementary material 3 from: Nations JA, Giarla TC, Morni MA, William Dee J, Swanson MT, Hiller AE, Khan FAA, Esselstyn JA (2022) Molecular data from the holotype of the enigmatic Bornean Black Shrew, Suncus ater Medway, 1965 (Soricidae, Crocidurinae), place it in the genus Palawanosorex. ZooKeys 1137: 17-31. https://doi.org/10.3897/zookeys.1137.94217
Maximum-likelihood crocidurine mitochondrial gene tree, without CYTB, inferred in IQTree
Supplementary material 2 from: Nations JA, Giarla TC, Morni MA, William Dee J, Swanson MT, Hiller AE, Khan FAA, Esselstyn JA (2022) Molecular data from the holotype of the enigmatic Bornean Black Shrew, Suncus ater Medway, 1965 (Soricidae, Crocidurinae), place it in the genus Palawanosorex. ZooKeys 1137: 17-31. https://doi.org/10.3897/zookeys.1137.94217
Best-fitting nucleotide substitution model for each gene in the mitochondrial DNA analysis
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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.