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Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes
<p>We use computational models based on Direct Coupling Analysis - DCA - trained on PFAM domains of distant distant homologues to accurately predict the polymorphisms segregating in a panel of 61,157 <em>Escherichia coli </em>genomes.</p> <p>We show that the genetic context (<em>i.e. </em>the rest of the protein sequence) strongly constrains the tolerable amino acids in 30% to 50% of amino-acid sites. Our study also suggests the gradual build-up of genetic context over long evolutionary timescales by the accumulation of small epistatic contributions.</p> <p>Please refer to the README file for additional information on the structure of this dataset.</p> <p>Code to analyse this dataset is available at https://github.com/GiancarloCroce/DCA_polymorphism_Ecoli.</p> <p> </p>
Trento 1911 - Building 157
<u>Coordinates</u>: N/A <br><u>Length</u>: 12.92 m<br><u>Width</u>: 10.56 m<br><u>Height</u>: 12.57 m<br><u>Points</u>: 8 <br><u>Vertices</u>: 36 <br><u>Primitives</u>: 12 <br><br><u>Main Files:</u><br><table><tbody><tr><th>Filename</th><th>.glb</th><th>.xml</th><th>.obj</th></tr><tr><td><a href="https://zenodo.org/api/records/12692282/files/building_157.glb/content">building_157.glb</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157.glb/content">Link</a></td><td></td><td></td></tr><tr><td><a href="https://zenodo.org/api/records/12692282/files/building_157.obj/content">building_157.obj</a></td><td></td><td></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157.obj/content">Link</a></td></tr><tr><td><a href="https://zenodo.org/api/records/12692282/files/11568192_metsmods.xml/content">11568192_metsmods.xml</a></td><td></td><td><a href="https://zenodo.org/api/records/12692282/files/11568192_metsmods.xml/content">Link</a></td><td></td></tr><tr><td><a href="https://zenodo.org/api/records/12692282/files/11568192_edm.xml/content">11568192_edm.xml</a></td><td></td><td><a href="https://zenodo.org/api/records/12692282/files/11568192_edm.xml/content">Link</a></td><td></td></tr></tbody></table><br><br><u>Thumbnails:</u><br><table><tbody><tr><th>Perspective</th><th>1000x1000</th><th>512x512</th><th>256x256</th><th>128x128</th></tr><tr><td>Perspective 1</td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_1.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_1_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_1_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_1_128x128.png/content">Link</a></td></tr><tr><td>Perspective 2</td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_2.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_2_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_2_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_2_128x128.png/content">Link</a></td></tr><tr><td>Perspective 3</td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_3.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_3_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_3_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_3_128x128.png/content">Link</a></td></tr><tr><td>Perspective 4</td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_4.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_4_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_4_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_4_128x128.png/content">Link</a></td></tr><tr><td>Perspective Top</td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_top.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_top_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_top_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12692282/files/building_157_perspective_top_128x128.png/content">Link</a></td></tr></tbody></table><br><br><br><u>Changelog</u>: <br> - v<a href="https://doi.org/10.5281/zenodo.12536837">0.0.2</a>: Thumbnails added, Description updated with Link Tables.<br> - v<a href="https://doi.org/10.5281/zenodo.12692282">0.0.3</a>: Added XMLs for Europeana Data Model (EDM) and MetsMods.<br>
Trento 1936 - Building 157
<u>Coordinates</u>: N/A <br><u>Length</u>: 16.93 m<br><u>Width</u>: 15.33 m<br><u>Height</u>: 19.48 m<br><u>Points</u>: 16 <br><u>Vertices</u>: 84 <br><u>Primitives</u>: 28 <br><br><u>Main Files:</u><br><table><tbody><tr><th>Filename</th><th>.glb</th><th>.xml</th><th>.obj</th></tr><tr><td><a href="https://zenodo.org/api/records/12690883/files/building_157.glb/content">building_157.glb</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157.glb/content">Link</a></td><td></td><td></td></tr><tr><td><a href="https://zenodo.org/api/records/12690883/files/building_157.obj/content">building_157.obj</a></td><td></td><td></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157.obj/content">Link</a></td></tr><tr><td><a href="https://zenodo.org/api/records/12690883/files/11572882_metsmods.xml/content">11572882_metsmods.xml</a></td><td></td><td><a href="https://zenodo.org/api/records/12690883/files/11572882_metsmods.xml/content">Link</a></td><td></td></tr><tr><td><a href="https://zenodo.org/api/records/12690883/files/11572882_edm.xml/content">11572882_edm.xml</a></td><td></td><td><a href="https://zenodo.org/api/records/12690883/files/11572882_edm.xml/content">Link</a></td><td></td></tr></tbody></table><br><br><u>Thumbnails:</u><br><table><tbody><tr><th>Perspective</th><th>1000x1000</th><th>512x512</th><th>256x256</th><th>128x128</th></tr><tr><td>Perspective 1</td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_1.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_1_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_1_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_1_128x128.png/content">Link</a></td></tr><tr><td>Perspective 2</td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_2.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_2_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_2_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_2_128x128.png/content">Link</a></td></tr><tr><td>Perspective 3</td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_3.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_3_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_3_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_3_128x128.png/content">Link</a></td></tr><tr><td>Perspective 4</td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_4.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_4_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_4_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_4_128x128.png/content">Link</a></td></tr><tr><td>Perspective Top</td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_top.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_top_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_top_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12690883/files/building_157_perspective_top_128x128.png/content">Link</a></td></tr></tbody></table><br><br><br><u>Changelog</u>: <br> - v<a href="https://doi.org/10.5281/zenodo.12540801">0.0.2</a>: Thumbnails added, Description updated with Link Tables.<br> - v<a href="https://doi.org/10.5281/zenodo.12690883">0.0.3</a>: Added XMLs for Europeana Data Model (EDM) and MetsMods.<br>
Sion 1640 - Building 157 (LoD-1)
<u>Coordinates</u>: N/A <br><u>Length</u>: 13.73 m<br><u>Width</u>: 12.03 m<br><u>Height</u>: 8.71 m<br><u>Vertices</u>: 42 <br><u>Primitives</u>: 24 <br><br> The Length, Width, Height, Vertices and Primitives listed above have been derived directly from the OBJ file.<br><br><u>Main Files:</u><br><table><tbody><tr><th>Filename</th><th>.glb</th><th>.obj</th><th>.mtl</th><th>.xml</th></tr><tr><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157.obj/content">0___LoD1__id-157.obj</a></td><td></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157.obj/content">Link</a></td><td></td><td></td></tr><tr><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157.glb/content">0___LoD1__id-157.glb</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157.glb/content">Link</a></td><td></td><td></td><td></td></tr><tr><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157.mtl/content">0___LoD1__id-157.mtl</a></td><td></td><td></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157.mtl/content">Link</a></td><td></td></tr><tr><td><a href="https://zenodo.org/api/records/12686359/files/11249914_edm.xml/content">11249914_edm.xml</a></td><td></td><td></td><td></td><td><a href="https://zenodo.org/api/records/12686359/files/11249914_edm.xml/content">Link</a></td></tr><tr><td><a href="https://zenodo.org/api/records/12686359/files/11249914_metsmods.xml/content">11249914_metsmods.xml</a></td><td></td><td></td><td></td><td><a href="https://zenodo.org/api/records/12686359/files/11249914_metsmods.xml/content">Link</a></td></tr></tbody></table><br><br><u>Thumbnails:</u><br><table><tbody><tr><th>Perspective</th><th>1000x1000</th><th>512x512</th><th>256x256</th><th>128x128</th></tr><tr><td>Perspective 1</td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_1.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_1_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_1_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_1_128x128.png/content">Link</a></td></tr><tr><td>Perspective 2</td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_2.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_2_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_2_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_2_128x128.png/content">Link</a></td></tr><tr><td>Perspective 3</td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_3.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_3_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_3_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_3_128x128.png/content">Link</a></td></tr><tr><td>Perspective 4</td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_4.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_4_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_4_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_4_128x128.png/content">Link</a></td></tr><tr><td>Perspective Top</td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_top.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_top_512x512.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_top_256x256.png/content">Link</a></td><td><a href="https://zenodo.org/api/records/12686359/files/0___LoD1__id-157_perspective_top_128x128.png/content">Link</a></td></tr></tbody></table><br><br><br><u>Changelog</u>: <br> - v<a href="https://doi.org/10.5281/zenodo.11487834">0.0.2</a>: Thumbnails added, Description updated with Link Tables.<br> - v<a href="https://doi.org/10.5281/zenodo.12686359">0.0.3</a>: Added XMLs for Europeana Data Model (EDM) and MetsMods.<br>
Figs 143–157 in A revision of the spider genus Anemesia (Araneae, Cyrtaucheniidae)
Figs 143–157. Anemesia spp., ♀♀ (143–146, 151–157) and ƋƋ (147–150), distal edge of chelicerae (143–146), palpal organ (147, 149), tip of embolus (148, 150), palpal claw (151), tarsal claws of leg I (152–154, 156) and leg IV (155, 157); apical (143–146, 151, 156–157), retrolateral (147–148, 154–155), ventral (149–150) and ventroapical (152–153) views. 143–144. A. pococki sp. nov. 145– 146. A. karatauvi (Andreeva, 1966). 147–150, 156–157. A. incana Zonstein, 2001. 151–153. A. oxiana sp. nov. 154–155. A. sogdiana sp. nov.
Fig. 157 in Epimeria of the Southern Ocean with notes on their relatives (Crustacea, Amphipoda, Eusiroidea)
Fig. 157. Epimeria (Hoplepimeria) georgiana subgen. nov. (Schellenberg, 1931), ♀, lectotype, South Georgia, Swedish South Polar Expedition 1901–1903, stn 34, SMNH - type 673. A. Gnathopod 1. B. Gnathopod 2.
Figs 157–164 in On Venezuelan pholcid spiders (Araneae, Pholcidae)
Figs 157–164. Coryssocnemis guacharo Huber sp. nov.; from Monagas, near Cueva del Guácharo (type locality; ZFMK Ar 21853). 157–159. Left palpal tarsus and procursus, prolateral, dorsal, and retrolateral views (arrow: ventral femur apophysis). 160–162. Left genital bulb, prolateral, dorsal, and retrolateral views. 163. Male chelicerae, frontal view. 164. Cleared female genitalia, dorsal view. Scale lines: 0.3 mm.
Figs 155–164. Tituboea atriceps Pic, 1924. 155–157 in Identity of species-group taxa of the Western Palaearctic Clytrini (Coleoptera: Chrysomelidae) described by Maurice Pic and Louis Kocher
Figs 155–164. Tituboea atriceps Pic, 1924. 155–157 – Invalid type of T. minor var. atriceps (female, 5.2 mm): 155 habitus; 156 – head; 157 – labels. 158–160 – Holotype of T. minor var. decemmaculata Pic, 1937 (female, 3.9 mm): 158 – habitus; 159 – head; 160 – labels. 161 – male (4.4 mm); 162 – head of male. 163–164 – Holotype of Antipa israelita Medvedev, 1992 (male, Romantsov orig.): 163 – habitus; 164 – labels.
FIGURES 149 157 in An illustrated key to Neotropical termite genera (Insecta: Isoptera) based primarily on soldiers
FIGURES 149 157. Termitidae: Termitinae, soldiers. 149 150. Amitermes amifer; 151 152. Onkotermes brevicorniger; 153 154. Cylindrotermes parvignathus; 155 156. Microcerotermes strunckii; 157. Gnathamitermes tubiformans. (scale bars = 0.5 mm)
FIGURES 154 – 163. Oskoron crawfordi. Fig. 54, female palpus. Fig. 155, male palpus. Figs. 156, penis. Fig. 157, glans penis. Fig. 158 in The harvestman genus Taracus Simon 1879, and the new genus Oskoron (Opiliones: Ischyropsalidoidea: Taracidae)
FIGURES 154 – 163. Oskoron crawfordi. Fig. 54, female palpus. Fig. 155, male palpus. Figs. 156, penis. Fig. 157, glans penis. Fig. 158, female, dorsal view. Fig. 159, female, lateral view. Fig. 160, male, lateral view. Fig. 161, female chelicerae, lateral view. Fig. 162, male palpus. Fig. 163, setae of glandular area of male palpal patella.
Figs. 157–166 in The Andean Goblin Spiders Of The New Genera Niarchos And Scaphios (Araneae, Oonopidae)
Figs. 157–166. Niarchos tapiai, new species, female. 157. Habitus, dorsal view. 158. Same, ventral view. 159. Carapace, dorsal view. 160. Sternum and mouthparts, ventral view. 161. Habitus, lateral view. 162. Same, anterior view. 163. Carapace, lateral view. 164. Epigastric region, ventral view. 165. Genitalia, ventral view. 166. Same, dorsal view.
Figs 152–157. Closterocerus spp. C in Eulophidae Of Costa Rica (Hymenoptera: Chalcidoidea), 4 The Genus Closterocerus Westwood S.Str.
Figs 152–157. Closterocerus spp. C. scitulus, paratype ♀ – (152) habitus dorsal view; (153) habitus lateral view. C. setosus, holotype ♀ – (154) habitus dorsal view; (155) head frontal view. C. arenalensis, holotype ♀ – (156) habitus dorsal view; (157) head frontal view.
Figs. 152–157 in The Andean Goblin Spiders Of The New Genera Paradysderina And Semidysderina (Araneae, Oonopidae)
Figs. 152–157. Paradysderina asymmetrica, new species, female. 152. Carapace, dorsal view. 153. Abdomen, lateral view. 154. Same, ventral view. 155, 156. Epigastric region, ventral view. 157. Same, dorsal view.
Figures 157–162 in Revision of the genus Olivierus in Xinjiang, China, with comments on Mesobuthus thersites (Scorpiones: Buthidae)
Figures 157–162: Exemplar specimens of Olivierus martensii (Karsch, 1879) in vivo habitus. Figures 157–158. Adult male (157) and female (158) of typical phenotype from Luoyang City, Henan Province, China. Figures 159–160. Hypomelanistic (159; adult male) and piebaldistic (160; immature males) phenotypes. Figures 161–162. Leucistic (161; immature male) and albino (162; adult female) phenotypes.
Figures 157–162 in A survey of proximal sensilla associated with denticle subrows on scorpion pedipalp fingers (Arachnida: Scorpiones), with observations on scorpion fluorescence
Figures 157–162. Dentate margins of pedipalp movable fingers. Buthidae: 'Ananteris-Isometrus' group. Figures 157–159. Ananteris terueli ♂. Right finger (157), distal finger (158), and subrow 2 (159). Figures 160–162. Babycurus centrurimorphus ♂. Right finger (160), distal finger (161), and subrow 4 (162). Denticle subrow numbering and arrow conventions as described under Figs. 5–10. Scale bars: 400 μm (157), 50 μm (158), 50 μm (159), 1 mm (160), and 100 μm (161–162). UV fluorescence (157, 160–162) and transmitted white light (158–159).
Figures 157–162 in Revision of the genus Olivierus in Xinjiang, China, with comments on Mesobuthus thersites (Scorpiones: Buthidae)
Figures 157–162: Exemplar specimens of Olivierus martensii (Karsch, 1879) in vivo habitus. Figures 157–158. Adult male (157) and female (158) of typical phenotype from Luoyang City, Henan Province, China. Figures 159–160. Hypomelanistic (159; adult male) and piebaldistic (160; immature males) phenotypes. Figures 161–162. Leucistic (161; immature male) and albino (162; adult female) phenotypes.
FIGURE 157 in Taxonomic Revision of the Spider Genus Actinopus Perty, 1833 (Araneae, Mygalomorphae, Actinopodidae)
FIGURE 157. Actinopus pindapoy sp. nov., male: A–F MACN-Ar 19824: A. Abdomen, dorsal; B. Carapace, dorsal; C. Sternum, ventral; D. Cheliceral teeth, ventral; E. Rastellum, dorsal; F. Rastellum, ventral.
Figures 156–157 in Notes on Compsobuthus: redescription of C. arabicus Levy et al., 1973 from Arabia, and description of two new species from North Africa (Scorpiones: Buthidae)
Figures 156–157. Compsobuthus turieli sp. n. Figure 156. Locality, Morocco, North of Zag. Figure 157. Female paratype from this locality with newborns.
FIGURE 157 in Grenadiers (Teleostei: Gadiformes: Macrouridae) of Japan and adjacent waters, a taxonomic monograph
FIGURE 157. Fresh specimen of Lucigadus nigromarginatus. FAKU 204468, 31.0 mm HL, 156+ mm TL, Dong-gang fish market, southwestern Taiwan, South China Sea. (A) Lateral view; (B) dorsal and (C) ventral views of the head and trunk. [Photos: N. Nakayama]
Figures 156–157 in Scorpions of Sri Lanka (Scorpiones Buthidae, Chaerilidae, Scorpionidae) with description of four new species of the genera Charmus Karsch, 1879 and Reddyanus Vachon, 1972, stat n
Figures 156–157: Lychas srilankensis, male from locality 15CO in dorsal (156) and ventral (157) views.
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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.