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35 results for “EVE”
CPT-1 whole-proteome feature matrices (EVE set)
<p><strong>Cross-protein transfer learning for variant effect prediction</strong></p> <p>This repository contains the feature matrices for CPT-1 to make variant effect prediction on 3,045 human proteins within the EVE set (<a href="https://www.nature.com/articles/s41586-021-04043-8">Frazer et al., 2021</a>), initially released with the manuscript "Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects".</p> <p> </p> <p><strong>Citation</strong></p> <p>Jagota, M.*, Ye, C.*, Albors, C., Rastogi, R., Koehl, A., Ioannidis, N., and Song, Y.S.†<br> "Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects", bioRxiv (2022)</p> <p>*These authors contributed equally to this work.<br> †To whom correspondence should be addressed: <a href="mailto:yss@berkeley.edu">yss@berkeley.edu</a></p> <p>DOI: <a href="https://doi.org/10.1101/2022.11.15.516532">https://doi.org/10.1101/2022.11.15.516532</a></p>
CPT-1 whole-proteome feature matrices (no-EVE set)
<p><strong>Cross-protein transfer learning for variant effect prediction</strong></p> <p>This repository contains the feature matrices for CPT-1 to make variant effect prediction on 15,557 human proteins NOT in the EVE set (<a href="https://www.nature.com/articles/s41586-021-04043-8">Frazer et al., 2021</a>), initially released with the manuscript "Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects".</p> <p> </p> <p><strong>Citation</strong></p> <p>Jagota, M.*, Ye, C.*, Albors, C., Rastogi, R., Koehl, A., Ioannidis, N., and Song, Y.S.†<br> "Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects", bioRxiv (2022)</p> <p>*These authors contributed equally to this work.<br> †To whom correspondence should be addressed: <a href="mailto:yss@berkeley.edu">yss@berkeley.edu</a></p> <p>DOI: <a href="https://doi.org/10.1101/2022.11.15.516532">https://doi.org/10.1101/2022.11.15.516532</a></p>
Eve et le Serpent
**"Eve tentée par le serpent"** est une oeuvre en bronze du sculpteur belge Albert Desenfans (né à Gemappe en 1845, décédé à Braine Lalleud en 1938). Cette sculpture d'environ 3 m de hauteur, datant de 1913, se situe dans le parc Josaphat à Schaerbeek en Belgique. Source: Objaverse 1.0 / Sketchfab
Eve ou la Tentation
Sculpture en cèdre, de 57 cm de hauteur, réalisée par Yannick Belin au sein de l'Association Basque Topaketak à Arbonne (Pyrénées Atlantiques - France). Exposée à "La Benoiterie" d'Arbonne du 29 au 31 juillet 2022. Source: Objaverse 1.0 / Sketchfab
RAL-eve Study: Raltegravir Substitution Study
ClinicalTrials.gov study NCT00523237. IPD Sharing: Not stated. Countries: 1. Publications: 1.
EVE: Software to identify novel viral insertions in wild-caught arthropod hosts from next-generation short read data
Open the record for dataset details and reuse information.
Data underlying "EVE is an open modular data analysis software for event-based localization microscopy"
<p>Data underlying the manuscript "EVE is an open modular data analysis software for event-based localization microscopy"</p> <p>Contains raw EBS-recorded SMLM (eveSMLM) data of DNA-PAINT nanoruler, E.coli cell, and aTubulin network in Cos-7 cells (3D and high density acquisitions).</p>
Temptation of Eve - Autun Cathedral
[Original model from @auriea](https://sketchfab.com/3d-models/eve-dautun-a8ab38d1422040dd94d95226d341a1dc). An quick exercise for fun doing some remesh and texture baking. [Autun Cathedral](https://en.wikipedia.org/wiki/Autun_Cathedral) Gislebertus' Temptation of Eve (French: La Tentation d'Ève) was originally the lintel of the north door of the cathedral. It is stated that the Temptation of Eve was created around the 1130s at the same time in which the Last Judgment and the narrative capitals were made. This large sculpture is now displayed in the Musée Rolin, Autun, France, restored in recent years. Aspect before restoration:  Source: Objaverse 1.0 / Sketchfab
Ofenkachel mit Eva / Stove tile depicting Eve
***Polychrome Ofenkachel mit einer Darstellung der Eva*** *Wittenberg, Lutherhaus Collegienstraße 54* *1. Hälfte 16. Jh.* *Irdenware, polychrome Glasur* *18,8 × 15,9 × 4,2 cm* >Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt Die Kachel war Teil des Dekors eines prunkvollen Ofens mit verschiedenen Porträts. ________________________ *Wittenberg, Luther House, Collegienstraße 54* *1st-half of the 16th century* *Earthenware, green, blue, white and brown glazing* *18.8 × 15.9 × 4.2 cm* >State Office for Heritage Management and Archaeology Saxony-Anhalt The tile was part of the décor of an ostentatious stove that included portraits. --- Literature: Nebelsick, Louis, 'Polychrome Stove Tile Depicting Eve', in: Harald Meller et al. (eds.), Martin Luther. Treasures of the Reformation. Dresden 2016, No. 262 Source: Objaverse 1.0 / Sketchfab
Dortmund-Eving Berg Apotheke
<p>Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a <br>German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. <br>gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): <br>https://kalliope-verbund.info/DE-611-BF-70963<br>[Funktion: Im Findbuch anzeigen]<br>Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot <br>be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf <br>Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht <br>veröffentlicht werden dürfen).</p>
The eVe reference polarisation lidar system for Cal/Val of Aeolus L2A product
<p>eVe lidar data used in publication:</p> <p>Paschou, P., Siomos, N., Tsekeri, A., Louridas, A., Georgoussis, G., Freudenthaler, V., Binietoglou, I., Tsaknakis, G., Tavernarakis, A., Evangelatos, C., von Bismarck, J., Kanitz, T., Meleti, C., Marinou, E., and Amiridis, V.: The eVe reference polarisation lidar system for Cal/Val of Aeolus L2A product, Atmos. Meas. Tech. Discuss. [preprint], https://doi.org/10.5194/amt-2021-268, in review, 2021.</p>
Quantitative data on expression of eve, gt and hb in early Drosophila embryo
<p>This dataset is supplementary to the following manuscript:</p> <p>Svetlana Surkova, Alena Sokolkova, Konstantin Kozlov, Sergey V. Nuzhdin and Maria Samsonova (2019). Quantitative analysis reveals genotype- and domain- specific differences between mRNA and protein expression of segmentation genes in <em>Drosophila</em>. <strong><em>Developmental Biology</em></strong>, doi: 10.1016/j.ydbio.2019.01.006.</p> <p>The archive contains recently obtained quantitative data on expression of <em>eve, gt</em> and <em>hb</em> in <em>Drosophila</em> early embryo at the level of mRNA and protein. It also includes integrated expression profiles of these genes, combined with the prior datasets (Surkova et al., 2008, Surkova et al., 2013).</p> <p>Embryos are classified into 8 time classes within cleavage cycle 14A. Genotype is specified as “wt” (wild type), “het” (<em>Kr+/Kr-</em> heterozygotes) and "mut" (<em>Kr</em> null mutants).</p> <p>Stained channels: EHG (<em>eve</em> mRNA, <em>hb</em> mRNA, <em>gt</em> mRNA); GGE (<em>gt</em> mRNA, Gt protein, <em>eve</em> mRNA); GE (<em>gt </em>mRNA, <em>eve</em> mRNA); ghe (<em>gt</em> mRNA, Hb protein, <em>eve</em> mRNA); HHE (Hb protein, <em>hb</em> mRNA, <em>eve</em> mRNA); GHH (<em>gt</em> mRNA, Hb protein, <em>hb</em> mRNA).</p> <p><strong>The data are arranged in three folders:</strong></p> <p><strong>1. QData_norm</strong></p> <p>Includes coordinates and fluorescence intensities of segmented nuclei for each individual embryo after subtraction of non-specific background signal.</p> <p><em>Files are arranged according to time class (T1-T8) and named according to the following scheme:</em></p> <p><stained channel><number>_norm.txt</p> <p><em>Structure of data file:</em></p> <p><strong>A-P-coord | D-V-coord | channel 1 | channel 2 | channel 3 </strong></p> <p><strong>2. QData_registered</strong></p> <p>Registered one-dimensional gene expression profiles.</p> <p><em>Files are arranged according to time class (T1-T8) and named according to the following scheme:</em></p> <p><stained channel><number>_reg.txt</p> <p><em>Structure of data file:</em></p> <p><strong>Number | A-P-coord | channel 3 | channel 2 | channel 1</strong></p> <p><strong>3. Integrated_data</strong></p> <p>Integrated one-dimensional profiles of <em>eve, hb</em> and <em>gt</em> expression at mRNA and protein levels for wild type embryos, <em>Kr</em> mutants and <em>Kr+/Kr</em>- heterozygotes.</p> <p><em>eve </em>and <em>gt</em> profiles were normalized on stripe 1 and second anterior domain respectively (see "Materials and Methods)".</p> <p><em>Files are named according to the following scheme:</em></p> <p><strong><gene><genotype><gene product><time class>_100</strong></p> <p><em>Structure of data file:</em></p> <p><strong>Number | A-P<em> </em>coord of an averaged nucleus | averaged intensity</strong></p> <p><em>hb profiles are named according to the following scheme:</em></p> <p><strong><gene><genotype><gene product><time class></strong></p> <p><em>Structure of data file:</em></p> <p><strong>Number | A-P<em> </em>coord of an averaged nucleus | averaged intensity | standard deviation</strong></p> <p><strong>References</strong></p> <ol> <li>Surkova S., Kosman D., Kozlov K., Myasnikova E., Samsonova A.A., Spirov A., Vanario-Alonso C.E., Samsonova M., Reinitz J. (2008). Characterization of the <em>Drosophila</em> segment determination morphome. Developmental biology 313(2):844-862.</li> <li>Surkova S., Golubkova E., Manu, Panok L., Mamon L., Reinitz J., Samsonova M. (2013) Quantitative dynamics and increased variability of segmentation gene expression in the <em>Drosophila Kruppel</em> and <em>knirps</em> mutants (2013). Dev Biol. 376: 99-112. doi: 10.1016/j.ydbio.2013.01.008.</li> </ol> <p> </p>
BPASS-EvE database
<p><strong>NOTE 2023-01-23: Not compatible with Python 3.7</strong>. A user reported that the dataframes are pickled with protocol 5 only available from python 3.8 (thanks Beth!).</p> <p><strong>EDIT 2022-12-19: Added an extended jupyter notebook with the tutorial presented at the MIAPbP workshop</strong></p> <p>EvE contains a number of tables summarising the BPASSv2.2.1 stellar library to facilitate identifying progenitor systems.</p> <p><strong>If you are a user you only need EvE.hdf5.</strong> The rest is the code used to make this version of eve. The code is versioned on github (closed repo as of the publication date) but this acts as a "frozen" version of the code made to create this particular file. </p> <p>This database was created with BPASSv2.2.1 and <a href="http://github.com/HeloiseS/hoki">hoki</a></p> <p><strong>References</strong></p> <p><strong>BPASSv2.2.1:</strong> <a href="https://ui.adsabs.harvard.edu/abs/2017PASA...34...58E/abstract">Eldridge et al. 2017</a> and <a href="https://ui.adsabs.harvard.edu/abs/2018MNRAS.479...75S/abstract">Stanway et al. 2018</a> | <strong>hoki: </strong><a href="https://ui.adsabs.harvard.edu/abs/2020JOSS....5.1987S/abstract">Stevance et al. 2022</a></p> <p><strong>Contact: </strong>hfstevance@gmail.com</p>
Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence
<p>Abstract Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.</p>
Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence
Open the record for dataset details and reuse information.
Supplementary material 2 from: Veltjen E, Asselman P, Baert W, Baeyen S, Beirinckx L, Breyne L, Brosens D, Claerhout T, Cogneau S, Cox K, Cuypers L, Delgat L, Desmeth P, de Raad J, Esselens L, Eves Down M-R, Helsen P, Leliaert F, Meganck K, Pereboom Z, Smitz N, Sonet G, Trekels M, Vanden Broeck A, Van Driessche C, De Wever A (2024) The key to bringing DNA collections to the next level. Research Ideas and Outcomes 10: e135978. https://doi.org/10.3897/rio.10.e135978
Interactive format of the Key including the guidance documentation
Supplementary material 1 from: Veltjen E, Asselman P, Baert W, Baeyen S, Beirinckx L, Breyne L, Brosens D, Claerhout T, Cogneau S, Cox K, Cuypers L, Delgat L, Desmeth P, de Raad J, Esselens L, Eves Down M-R, Helsen P, Leliaert F, Meganck K, Pereboom Z, Smitz N, Sonet G, Trekels M, Vanden Broeck A, Van Driessche C, De Wever A (2024) The key to bringing DNA collections to the next level. Research Ideas and Outcomes 10: e135978. https://doi.org/10.3897/rio.10.e135978
Definitions
Profiling of Islet, Lim3, Hb9 and Eve genomic binding in Drosophila with DamID
GEO Series GSE53446. Drosophila melanogaster. 11 samples. Type: Genome binding/occupancy profiling by genome tiling array.
modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[eve] from E1-6h on Illumina Genome Analyzer.
GEO Series GSE24139. Drosophila melanogaster. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[eve] from E8-16h on Illumina Genome Analyzer.
GEO Series GSE24143. Drosophila melanogaster. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
ScienceDex guides
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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.