Find research datasets worth reusing

PM_062825_F_Varengeville_sur_Mer

File Name: PM_062825_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Extérieur. Ouest. Description: Church (Église Saint-Valery) Exterior West Keywords: Cultural heritage, Europe, France, Monuments, Normandie, Seine-Maritime, Styles, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062846_F_Varengeville_sur_Mer

File Name: PM_062846_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Intérieur. La nef. Une colonne sculptée (le pilier-colonne polygonale). Description: Church (Église Saint-Valery) Interior The nave A sculpted column (le pilier-colonne polygonal) Keywords: Bas-relief, Cultural heritage, Europe, France, Monuments, Normandie, Sculpture, Seine-Maritime, Techniques, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062836_F_Varengeville_sur_Mer

File Name: PM_062836_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Intérieur. L'allée nord. Gothique. 13ème - 15ème siècle. Description: Church (Église Saint-Valery) Interior The north aisle Gothic 13th - 15th century Keywords: Cultural heritage, Europe, France, Gothic, Monuments, Normandie, Seine-Maritime, Styles, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062833_F_Varengeville_sur_Mer

File Name: PM_062833_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Intérieur. Le transept nord et le croisement. Gothique. 13ème - 15ème siècle. Description: Church (Église Saint-Valery) Interior The north transept and the crossing Gothic 13th - 15th century Keywords: Cultural heritage, Europe, France, Gothic, Monuments, Normandie, Seine-Maritime, Styles, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062839_F_Varengeville_sur_Mer

File Name: PM_062839_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Intérieur. La nef. Une colonne sculptée (le pilier-colonne polygonale). Description: Church (Église Saint-Valery) Interior The nave A sculpted column (le pilier-colonne polygonal) Keywords: Bas-relief, Cultural heritage, Europe, France, Monuments, Normandie, Sculpture, Seine-Maritime, Techniques, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062854_F_Varengeville_sur_Mer

File Name: PM_062854_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Extérieur. Nord-ouest. Description: Church (Église Saint-Valery) Exterior Northwest Keywords: Cultural heritage, Europe, France, Monuments, Normandie, Seine-Maritime, Styles, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062849_F_Varengeville_sur_Mer

File Name: PM_062849_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Intérieur. La nef. Une colonne sculptée (le pilier-colonne polygonale). Description: Church (Église Saint-Valery) Interior The nave A sculpted column (le pilier-colonne polygonal) Keywords: Bas-relief, Cultural heritage, Europe, France, Monuments, Normandie, Sculpture, Seine-Maritime, Techniques, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062821_F_Varengeville_sur_Mer

File Name: PM_062821_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Extérieur. Le site. Description: Church (Église Saint-Valery) Exterior The site Keywords: Cultural heritage, Europe, France, Monuments, Normandie, Seine-Maritime, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062824_F_Varengeville_sur_Mer

File Name: PM_062824_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Extérieur. Le site. Description: Church (Église Saint-Valery) Exterior The site Keywords: Cultural heritage, Europe, France, Monuments, Normandie, Seine-Maritime, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062826_F_Varengeville_sur_Mer

File Name: PM_062826_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Extérieur. Nord-ouest. Description: Church (Église Saint-Valery) Exterior Northwest Keywords: Cultural heritage, Europe, France, Monuments, Normandie, Seine-Maritime, Styles, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062820_F_Varengeville_sur_Mer

File Name: PM_062820_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Extérieur. Le site. Description: Church (Église Saint-Valery) Exterior The site Keywords: Cultural heritage, Europe, France, Monuments, Normandie, Seine-Maritime, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062850_F_Varengeville_sur_Mer

File Name: PM_062850_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Extérieur. Le porche d'entrée ouest. Description: Church (Église Saint-Valery) Exterior The west entrance porch Keywords: Cultural heritage, Europe, France, Monuments, Normandie, Seine-Maritime, Styles, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

PM_062830_F_Varengeville_sur_Mer

File Name: PM_062830_F_Varengeville_sur_Mer.jpg Sublocation: Église Saint-Valery Location: Varengeville-sur-Mer Province: Normandie, Seine-Maritime Country: France Header: Intérieur. La nef et le bas-côté sud. Gothique. 13ème - 15ème siècle. Description: Church (Église Saint-Valery) Interior The nave and south aisle Gothic 13th - 15th century Keywords: Cultural heritage, Europe, France, Gothic, Monuments, Normandie, Seine-Maritime, Styles, Varengeville-sur-Mer Author: Photo: Paul M.R. Maeyaert Copyright: Paul M.R. Maeyaert

opencc-by-4.0Apr 2019View details →

YALFF's reassembled 32-mers datasets

This repository contains the reassembled 32-mers of different datasets for the software YALFF <a href="https://doi.org/10.5281/zenodo.2637919">https://doi.org/10.5281/zenodo.2637919</a> In particular: <ul> <li>hg19.reassembled.fa.gz and hg38.reassembled.fa.gz are reference fasta files containing the reassembled contigs from hg19 and hg38 respectively. Note that these two files are exactly equivalent to the original ones if used as 32-mer indices because they contain the exact same 32-mers at least once. Obviously they cannot be used for alignment, only presence/absence queries.</li> <li>affykmers.reassembled.fa.gz contains all the reassembled 32-mers from hg19 and the variants spanning the the SNPs listed in Affymetrix_6_SNPs.txt (available at <a href="http://cb.csail.mit.edu/cb/lava/">http://cb.csail.mit.edu/cb/lava/</a>).</li> <li>dbSNPkmers.reassembled.fa.gz contains all the reassembled 32-mers from hg19 and the variants spanning the the SNPs listed in SNPs142_hg19_Common.filt.txt (available at <a href="http://cb.csail.mit.edu/cb/lava/">http://cb.csail.mit.edu/cb/lava/</a>).</li> <li>dec200.reassembled.fa.gz is the reassembled database of 32-mers of Quartz (the dec200.bin file at <a href="http://cb.csail.mit.edu/cb/quartz">http://cb.csail.mit.edu/cb/quartz</a>).</li> <li>mit_all.reassembled.fa.gz is the FASTA with the contigs obtained by reassembling the hg19, dec200 and all the SNPs into a single database.</li> </ul>

zenodo44/100

Two 100 ns NVT molecular dynamics simulations of dsDNA and dsRNA "GGGG" 18-mers (GCGGGGGGGGGGGGGGGC)

Supporting information for "Molecular origin of distinct hydration dynamics in double helical DNA and RNA sequences" by E. Frezza, D. Laage and E. Duboué-Dijon, J. Phys. Chem. Lett. 2024, 15, 4351–4358 Two 100 ns-long NVT molecular dynamics simulation: one of dsDNA "GGGG" 18-mer (GCGGGGGGGGGGGGGGGC) and one of  the analogous dsRNA. The nucleic acid is explicitly solvated in water and neutralized with 0.15M KCl. Simulations were performed using the Gromacs 5 software. DNA is described with the Amber 99SB-ILDN force field with the BSC0 modifications, RNA is described with the Amber 99SB-ILDN force field with the BSC0 and χOL3 modifications, the SPC/E force field is used for water, and the Joung Cheatham paraeters for ions. The shared coordinates are saved every 500fs, twice less frequently than the original trajectories used for the publication, to reduce the size of the shared dataset below the allowed size limit.

opencc-by-4.0Feb 2024View details →

zenodo44/100

Dataset for: Pre-pandemic artificial MERS analog of polyfunctional SARS-CoV-2 S1/S2 furin cleavage site domain is unique among spike proteins of genus Betacoronavirus

<table> <tbody> <tr> <th> </th> <td> <div> <h3>Data File Descriptions and Methods</h3> <ol> <li>Data file 1 [betacov_matching_IPR042578.fasta]: Representative set of 2,465 betacoronavirus S protein overlapping homologous superfamily sequences retrieved in fasta format on 4 December 2022 from the InterPro repository at https://www.ebi.ac.uk/interpro/entry/InterPro/IPR042578/. </li> <li>Data File 2 [betacov_matching_IPR042578_motif.fasta]: With Data File 1 as input, extracted 98,122 furin cleavage site (FCS) output motifs of 20 amino acids length, including overlapping and redundant sequences, produced with the FindFur algorithm with preset parameters as described by (Gu, 2020). FindFur as used was deposited on 15 December 2020 at the GitHub software repository at https://github.com/chwisteeng/FindFur. </li> <li>Data File 3 [table_s1s2_hits_betacov_polyf.pdf]: Compiled summary table of sequence hits (PDF) of spike S1/S2 domains across genus Betacoronavirus. The compiled table of hits removed from Data File 2 sequences corresponding to spike protein fragments (incomplete length spike proteins as deposited at GenBank) and duplicates (redundant parts identically overlapping within the 20 amino acids motif windows), and then selected one sequence representative for multiple but identical sequences. Collection dates and geographical locations were retrieved from the NCBI Genbank protein database at https://www.ncbi.nlm.nih.gov/protein/. For SARS-CoV-2 spike variants, these data were also cross-validated with the SARS-CoV-2 lineage mutation tracker (Gangavarapu, 2023) available at https://outbreak.info which was based on extensive sequencing data from the global GISAID initiative (https://gisaid.org/). Solid lines (-) depict pat7 NLS, asterisks (*) O-glycosites, and circumflex (^) symbols FCS. </li> <li> Data File 4 [table_s1s2_hits_betacov_polyf.xlsx]: Compiled summary table of sequence hits (MS Excel) of spike S1/S2 domains across genus Betacoronavirus. The compiled table of hits removed from Data File 2 sequences corresponding to spike protein fragments (incomplete length spike proteins as deposited at GenBank) and duplicates (redundant parts identically overlapping within the 20 amino acids motif windows), and then selected one sequence representative for multiple but identical sequences. Collection dates and geographical locations were retrieved from the NCBI Genbank protein database at https://www.ncbi.nlm.nih.gov/protein/. For SARS-CoV-2 spike variants, these data were also cross-validated with the SARS-CoV-2 lineage mutation tracker (Gangavarapu, 2023) available at https://outbreak.info which was based on extensive sequencing data from the global GISAID initiative (https://gisaid.org/). Solid lines (-) depict pat7 NLS, asterisks (*) O-glycosites, and circumflex (^) symbols FCS. </li> <li> Data File 5 [betacov_s1s2_nls_pat7_furin_psort.txt]: Nuclear localization signal (NLS) detection output for 5 representative betacoronavirus spike sequence domains, including the positive hits for pat7 in SARS-CoV-2 and for MERS-MA30 CoV. NLS predictions used the PSORT algorithm available as a webservice at https://wolfpsort.hgc.jp/ which is based on the work of Nakai and Horton (Nakai and Horton, 1999). Numbering refers to Data File 3 and Data File 4. </li> <li> Data File 6 [betacov_s1s2_oglyc_netogly.txt]: Detection output for 5 representative betacoronavirus spike sequence domains tested for Thr/Ser O-glycosite residue pairs with the standard prediction software NetOGlyc4.0 (Steentoft et al., 2013) as available at https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/. Positive hits have scores above 0.5. Numbering refers to Data File 3 and Data File 4. </li> <li> Data File 7 [betacov_s1s2_nls_pat7_furin_blastp.txt]: Comprehensive sequence database searches using were performed using the NCBI protein BLAST (blastp) algorithm with webservice available at https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins. The following blastp search parameters and settings were used: Word size=2; Expect value=200000; Hitlist size=500; Gapcosts=9,1; Matrix=PAM30; Filter string=F; Genetic Code=1;Window Size=40; Threshold=11; Composition-based stats=0; Database Posted date=Jan 19, 2023 2:59 AM; Number of letters=17,117,563; Number of sequences=10,766; Entrez query: Includes: Betacoronavirus (taxid:694002); Excludes: SARS-CoV-2 (taxid:2697049). The six polyfunctional input query consensus motif sequences were TXXPR(K/H/R)XRSX and TXXPRX(K/H/R)RSX. </li> </ol> <h3>References</h3> Gu, C., 2020. FindFur: A Tool for Predicting Furin Cleavage Sites of Viral Envelope Substrates. Master’s Thesis, San Jose State University, CA, USA. doi: <a href="https://doi.org/10.31979/etd.4ahv-9jya">10.31979/etd.4ahv-9jya</a>  Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S; GISAID Core and Curation Team; Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nat Methods. 2023. 20(4):512-522. doi: <a href="https://doi.org/10.1038/s41592-023-01769-3">10.1038/s41592-023-01769-3</a>. Nakai, K., Horton, P., 1999. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 24, 34–36. doi: <a href="https://doi.org/10.1016/s0968-0004(98)01336-x">10.1016/s0968-0004(98)01336-x</a> Steentoft, C., Vakhrushev, S.Y., Joshi, H.J., Kong, Y., Vester-Christensen, M.B., Schjoldager, K.T.-B.G., Lavrsen, K., Dabelsteen, S., Pedersen, N.B., Marcos-Silva, L., Gupta, R., Bennett, E.P., Mandel, U., Brunak, S., Wandall, H.H., Levery, S.B., Clausen, H., 2013. Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J 32, 1478–1488. doi: <a href="https://doi.org/10.1038/emboj.2013.79">10.1038/emboj.2013.79</a> </div> </td> </tr> </tbody> </table>

opencc-by-4.0Jul 2024View details →

FIG. 11 in Entre tradition classique et imaginaire germano-celtique: les monstres anthropomorphes des mers septentrionales, au Moyen Âge et au début de l'époque moderne

FIG. 11. — Sirène. Chapiteau de la cathédrale de Bâle, avant-choeur, fin XIIe siècle (cliché P. Heman, Bâle).

FIG. 9 in Entre tradition classique et imaginaire germano-celtique: les monstres anthropomorphes des mers septentrionales, au Moyen Âge et au début de l'époque moderne

FIG. 9. — Ondine? Sirène? Psautier dit de Charlemagne, Saint-Riquier, 800. (Paris, BnF, lat. 13159,f. 13v). © Bibliothèque nationale de France, Paris.

FIG. 7 in Entre tradition classique et imaginaire germano-celtique: les monstres anthropomorphes des mers septentrionales, au Moyen Âge et au début de l'époque moderne

FIG. 7. — Monachus maris. Thomas de Cantimpré, De natura rerum. Nord de la France, 1275-1290 (Valenciennes, B.M. 320, f. 117) © Bibliothèque municipale de Valenciennes.

FIG. 4 in Entre tradition classique et imaginaire germano-celtique: les monstres anthropomorphes des mers septentrionales, au Moyen Âge et au début de l'époque moderne

FIG. 4. — Zytiron. Hortus sanitatis, Mayence, 1491 (Bruxelles, KBR, Inc. B. 229). © Bibliothèque royale de Belgique, Bruxelles.