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695 results for “topologies”
Simulation codes and data from: Efficient Flocking: metric versus topological interactions
<p>Flocking is a fascinating phenomenon observed across a wide range of living organisms. We investigate, based on a simple theoretical particle model, how the emergence of ordered motion in a collectively moving group is influenced by the local rules of interactions among the individuals, namely, metric versus topological interactions as debated over in the current literature.</p>
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
Dynamical topological phase realized in a trapped-ion quantum simulator
<p>Experimental and simulation data as presented.</p>
Supporting data for Kealhofer et al., "Controlling and visualizing Dirac physics in topological semimetal heterostructures" (2022)
<p>This repository contains data supporting Kealhofer et al., "Controlling and visualizing Dirac physics in topological semimetal heterostructures" (2022). Please see the corresponding publication for the corresponding author's contact information.</p>
TLA: Topological landscape analysis
<p>Python "pickled" topological features used for single-objective COCO problem classification. </p>
Topological phonon transport in an optomechanical system
<p>This file contains the data and code for the paper "Topological phonon transport in an optomechanical system" (https://www.nature.com/articles/s41467-022-30941-0).</p>
DomainMapper: Accurate Domain Structure Annotation Including Those with Non-contiguous Topologies
<p>List of Uniprot proteomes used in the study "DomainMapper: Accurate Domain Structure Annotation Including Those with Non-contiguous Topologies"</p> <p>Contains the following proteomes:</p> <p>Aug 9 2021 H. spaiens - uniprot-proteome_UP000005640.fasta</p> <p>Aug 9 2021 D. melanogaster - uniprot-proteome_UP000000803.fasta</p> <p>Aug 9 2021 E. coli - uniprot-proteome_UP000000625.fasta</p> <p>Aug 9 2021 M. musculus - uniprot-proteome_UP000000589.fasta</p> <p>Aug 9 2021 S. cerevisiae - uniprot-proteome_UP000002311.fasta</p> <p>Nov 1 2021 S. aureus - uniprot-proteome_UP000008816.fasta</p> <p>Nov 1 2021 Z. mays - uniprot-proteome_UP000007305.fasta</p> <p>Jul 28 2022 M. jannaschii - uniprot-proteome_UP000000805.fasta</p>
Observation of non-Hermitian topology in a multi-terminal quantum Hall device
<p>This repository contains our measurements and the codes used to produce the figures of the manuscript/supplementary information.</p>
Source Data for Xiao et al., Topological Superfluid Defects with Discrete Point Group Symmetries , Nature Communications 13, 4635 (2022).
<p>Source data for Figures 2-5. Source data for Supplementary Figures S2-S5 available upon request to David Hall (dshall@amherst.edu).</p>
Data for "Transparent Josephson Junctions in Higher-Order Topological Insulator WTe2 via Pd Diffusion"
<p>Data for the publication "Transparent Josephson Junctions in Higher-Order Topological Insulator WTe<sub>2</sub> via Pd Diffusion".</p> <p>Updated version as accepted by Physical Review Materials. </p>
Figure 1 in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 1. Maximum-likelihood (ML) tree showing the phylogenetic relationships among 41 newly sequenced specimens of pilidiophorans (indicated with solid blue circles). Numbers near nodes are support values, ML bootstrap/Bayesian inference (BI) posterior probability. Nodes with yellow triangles are fully supported, with 100% ML bootstrap and 1.00 BI posterior probability. New species names are indicated in bold. Some nodes were polytomous in the BI tree (indicated by hyphens in place of posterior probability values).
Figure 7. A in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 7. A, Baseodiscus narusei sp. nov., holotype, ICHUM 6310, entire body, showing characteristic lateral edges; B, Baseodiscus paracelensis sp. nov., holotype, MIMB 33132, entire body; C, Baseodiscus aff. marmoratus (Bürger, 1890), anterior end of body, ventral view, head to the left; D, E, Baseodiscus ohtsukai sp. nov., holotype, ICHUM, 6327, drawings of anterior end of body viewed dorsally (D) and ventrally (E); F, G, Baseodiscus urgorrii sp. nov., holotype, MCZ IZ-135319, anterior end of body viewed dorsally (F) and ventrolaterally (G). Photos by T. Naruse (A), A. V. Chernyshev (B, C), and G. Giribet (F, G).
Figure 5. Cephalomastax brevis Iwata, 1957, ICHUM 6267. A in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 5. Cephalomastax brevis Iwata, 1957, ICHUM 6267. A, anterior fragment in contracted state, lateral view; B, anterior end of body, ventral view; C, transverse section showing proboscis; D, magnification of anterior proboscis musculature (arrowhead, radial muscle fibre); E, transverse section showing rhynchocoel musculature. Photos by H. Kajihara.
Figure 3. A in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 3. A, Baseodiscus aff. marmoratus (Bürger, 1890) (voucher DNA, ICHUM 6322); B, Baseodiscus aff. maculosus (Bürger, 1895a) (voucher DNA, ICHUM 6324); C–E, Baseodiscus delineatus (Delle Chiaje, 1822-1829), ICHUM 6326; F, Baseodiscus cf. curtus (Hubrecht, 1879), ICHUM 6328; G, H, Baseodiscus urgorrii sp. nov., holotype, MCZ IZ-135319, entire body (G) and protruding proboscis (indicated by an arrowhead, H); I, Baseodiscus punnetti (Coe, 1904), specimen different from any voucher specimens in this study; J, K, Baseodiscus kakuii sp. nov., holotype, ICHUM 6334, anterior body (J) and
Figure 4. A–C in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 4. A–C, Eopilidion misakiense gen. et sp. nov., holotype, ICHUM 6303, anterior end of body, ventral view, head to the right (A), frontal view (B), squeezed-slide preparation (C); D, Valencinura jambio sp. nov., holotype, ICHUM 6305, anterior end of body, ventral view. Photos by H. Kajihara.
Figure 6. A–E in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 6. A–E, Baseodiscus takakurai Gibson, 1995, ICHUM 6308, A, anterior end of body, ventral view; B, middle body region, showing appearance of body markings in differently contracted states; C, juvenile, showing dorsal mottling; D, juvenile, with head viewed ventrolaterally, showing two ocelli; E, transverse section of proboscis; F, Baseodiscus komatsui sp. nov., holotype, NSNM NMNS-Ne 1, entire body. Photos by H. Kajihara (A–E) and H. Komatsu (F).
Figure 2. A in Exploring the basal topology of the heteronemertean tree of life: establishment of a new family, along with turbotaxonomy of Valenciniidae (Nemertea: Pilidiophora: Heteronemertea)
Figure 2. A, Eopilidion misakiense gen. et sp. nov., holotype, ICHUM 6303, lateral view, head to the right; B, Oxypolella hiebertae sp. nov., holotype, MIMB 42256; C, Cephalomastax brevis Iwata, 1957, ICHUM 6304; D, E, Valencinura jambio sp. nov., holotype, ICHUM 6305, anterior body fragment (D) and enlargement of intestinal region (E) showing yellowish proboscis (indicated by arrowheads); F, Baseodiscus takakurai Gibson, 1995, ICHUM 6306; G, Baseodiscus profundus sp. nov., holotype, MIMB 42257; H, I, Baseodiscus narusei sp. nov., holotype, ICHUM 6310, anterior end of body, dorsal (H) and ventral (I) views; J, Baseodiscus paracelensis sp. nov., holotype, MIMB 33132; K, Baseodiscus komatsui sp. nov., holotype, NMNS-Ne 1; L, Baseodiscus unicolor Stiasny-Wijnhoff, 1925; M, Baseodiscus giribeti sp. nov., holotype, MCZ IZ-135324; N, Baseodiscus cf. amboinensis (Staub, 1900); O, Baseodiscus hemprichii (Ehrenberg, 1828-1831), specimen from Okinawa, different from any voucher specimens in this study; P, Baseodiscus zebra sp. nov., holotype, RUMF-ZN-00001; Q, Baseodiscus quinquelineatus (Quoy & Gaimard, 1833), ICHUM 6319. Photographs by H. Kajihara (A, C, D, E, F, O), A. V. Chernyshev (B, G, J), T. Naruse (H, I), H. Komatsu (K), G. Giribet (L, M), D. Uyeno (P), and R. Yoshida (Q).
case60nordic random topology power grid dataset
<p>Dataset of randomly generated power grids derived from the case60nordic (also known as nordic32).</p> <p>Random object disconnections.</p> <p>Data generation script available at : <a href="https://github.com/bdonon/powerdatagen">https://github.com/bdonon/powerdatagen</a></p>
Two type I topoisomerases maintain DNA topology in human mitochondria
<p>Raw image data from the article "Two type I topoisomerases maintain DNA topology in human mitochondria" by Katja E. Menger et al.</p>
Simulation input files and analysis scripts for "Optimal bond-constraint topology for molecular dynamics simulations of cholesterol"
<p>Simulation input files and analysis scripts for "Optimal bond-constraint topology for molecular dynamics simulations of cholesterol".</p> <p>See ... for details.</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.