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1,199 results for “aligners”
Data from: Multiple genotypes of Phelipanche ramosa indicate repeated introductions to the Americas: Sequence alignments and phylogenetic trees
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Data from: Strong selection is poorly aligned with genetic variation in Ipomoea hederacea
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Data from: Properties of Markov chain Monte Carlo performance across many empirical alignments -- part I
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Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments
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Scripts and data sets associated with: On testing homogeneity of the evolutionary process using alignments of homologous sequences
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Do alignment and trimming methods matter for phylogenomic (UCE) analyses?
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RadCases evaluation results: Evaluating acute image ordering for real-world patient cases via language model alignment with radiological guidelines
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Data for: Ocean surface wave slopes and wind-wave alignment observed in Hurricane Idalia
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Aligned DNA sequence matrix for phylogenetic analyses in the article "New species of fossorial salamanders of the genus Oedipina (Plethodontidae) from the northwestern Ecuador"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "New species of fossorial salamanders of the genus Oedipina (Plethodontidae) from the northwestern Ecuador". The matrix is in NEXUS format.</p> <p>Gene partitions are arranged as follows (tRNAs are included as part of larger adjacent genes):</p> <p>16S = 4- 789 1761- 1891 ;<br> ND1-codonPos1 = 790-1759\3;<br> ND1-codonPos2 = 791-1760\3;<br> ND1-codonPos3 = 792-1758\3;<br> CytB-codonPos1 = 1893-2274\3;<br> CytB-codonPos2 = 1894-2275\3;<br> CytB-codonPos3 = 1892-2276\3;</p>
Floristic monitoring of the 1,324 alignment tree bases of 15 streets in the district of Bercy, Paris, France, from 2009 to 2018
<p>Floristic monitoring of the 1,324 alignment tree bases of 15 streets in the district of Bercy, Paris, France, from 2009 to 2018.</p> <p>Nathalie Machon (CESCO, MNHN-CNRS-Sorbonne-Université)</p> <p>Data collectors : Noëlie Maurel, Marion Noualhaguet, Marion Dubois, Sébastien Julliard, Ambre Zéléla Bouvard, Paul Haenel, Florence Devers, Hélène Beaugeard, Gwendoline Chastel, laure Schneider-Maunoury and Mona Omar</p> <p>Centre d’Ecologie et des Sciences de la Conservation, Muséum national d’Histoire naturelle, 61 rue Buffon, 75005 Paris, nathalie.machon@mnhn.fr</p> <p>In cities, trees planted along streets host at their base a high number of spontaneous plants. Thus, they may provide shelters and corridors across the urban matrix.</p> <p>From 2009, we monitor urban tree bases in streets of Paris, France. Our objective is to follow the dynamics of these plant communities (Omar et al. 2018, 2019).</p> <p> </p> <p><strong>Study area and floristic inventories</strong></p> <p>The monitoring was performed in the 12th administrative district of Paris (Postal code: 75012; France; 48°50′26.91″N, 2°23′17.46″E),</p> <p>We monitored the 1,324 tree bases distributed along the 15 streets or avenues which contained at least 30 alignment trees in the district.</p> <p>Tree bases (TB) were for some of them covered by metal grills (grill/soil) to prevent soil compaction to preserve tree roots.</p> <p>The present file gives the list of all wild vascular plant taxa observed in each tree base, in May or June, each year from 2009 to 2018 except in 2013 because of a lack of observers. The taxonomic reference is the French Flora Reference TAXREF v8.0 (Gargominy et al., 2016).</p>
Aligning repository networks to support international sharing of COVID-19 resources and other current issues
<p>Recording of a panel "Aligning repository networks to support international sharing of COVID-19 resources", organized by COAR. This panel presented several national approaches to managing and sharing COVID-19 resources from around the world (Africa, Canada, Europe, Latin America, Asia), followed by a discussion about how we can work more closely across countries and regions to ensure that content can be integrated internationally. Participants: Kathleen Shearer - COAR, Paolo Manghi - OpenAIRE, Europe, Kazuhiro Hayashi, National Institution of Science and Technology Policy, Japan, Ansie Van de Wasthuizen, UNISA, South Africa, Cesar Olivares, CONCYTEC, Peru and LA Referencia, Latin America, Geoff Harder, Canadian Association of Research Libraries<br> <br> Organization Identifiers and Open Repositories: ROR-ing Together – Maria Gould, California Digital Library, University of California Office of the President.<br> <br> Research Data Management: a Stellenbosch University Journey – Samuel Simango, Stellenbosch University Library.<br> <br> Towards Open Data Metrics: enabling data repositories to demonstrate reuse – Kristian Garza, DataCite.</p> <p>DSpace-CRIS 7: What is Coming? – Susanna Mornati, 4Science</p>
Underlying data for "Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms"
<p><strong>Output Files from Structural Alignment of TRP Channels</strong><br> The archive contains the key output files resulting from the structural alignment of members of the TRP channel family described in "Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms", Huffer et al., (2020), eLife.</p> <p><strong>Contents of trp_struct_align_outputs.tar.gz</strong><br> <em>Aligned_structures</em><br> For each alignment where the transmembrane (TM) domain of the mobile structure was aligned to the TM domain of the stationary/reference structure (6co7):<br> 1) mobile_stationary_full_align.pdb: aligned based on Fr-TM-Align output matrix, contains all residues<br> 2) mobile_stationary_tmem_align.pdb: aligned based on Fr-TM-Align output matrix, contains only TM residues used for alignment<br> 3) mobile_stationary_hole.pdb: aligned based on Fr-TM-Align output matrix, contains HOLE profile of mobile structure</p> <p><em>Alignments</em><br> Multiple sequence alignments constructed using the TM domain of each structure as the stationary/reference structure, with all other structures aligned pairwise.<br> 1) stationary_full.ali: Full multiple sequence alignment containing all TM residues from all stationary and mobile structures.<br> 2) stationary_nogap.ali: Multiple sequence alignment containing all TM residues from the stationary structure. Any gaps in the stationary structure removed, which removes any residue in any mobile structure that does not align to the stationary/reference structure.</p> <p><em>Fr-TM-Align_outputs</em><br> - frtmalign_output.csv: contains all information from Fr-TM-Align output files for each pairwise alignment of TM domains, including PDB IDs of mobile and stationary structures, lengths of mobile and stationary structures, length of pairwise alignment sequence, RMSD of alignment, TM-score of alignment, and sequence identity of alignment.<br> - aligned_length.csv, RMSD.csv, sequence_identity.csv, and TM_score.csv: csv files containing the specified values for all pairwise alignments of TM domains, with the mobile structure in rows and stationary structure in columns</p> <p><strong>Reproducibility</strong><br> Code to reproduce this alignment and analysis is available on GitHub at: <a href="https://github.com/kehuffer/TRP_Structural_Alignment">https://github.com/kehuffer/TRP_Structural_Alignment</a></p>
Supplementary Materials for Time-Aligned Edge Plots for Dynamic Graph Visualization
<p><strong>Abstract</strong>: We present <em>time-aligned edge plots</em>: time- and edge-scalable representations of dynamic graphs. Vertices are mapped to two vertical parallel axes. The left axis depicts the source vertices, whereas the right one depicts the destination vertices. The time axis is horizontally embedded in-between the two axes, resulting in a two-dimensional graph layout. Edges are added by drawing straight lines connecting the corresponding source and destination vertices through time, while the pixels along the lines are used to encode the time-varying information. In this way, the depiction of edges at the individual timepoints is reduced to only a few pixels, resulting in a less cluttered representation of dynamic graphs, while the alignment of edges over time reveals the temporal patterns in the data and preserves the users' mental map. We evaluate our approach by comparing it theoretically and empirically against the state-of-the-art using dynamic graphs of varying complexities.</p>
A comparative assessment of the dentoskeletal effects of clear aligners versus miniplate-supported posterior intrusion with fixed appliances in adult anterior open bite patients. A multi-centre, retrospective cohort study.
<p>In this retrospective study, the aim was to evaluate the dentoskeletal effects of clear aligner treatment (Invisalign®) versus miniplate-supported posterior intrusion (MSPI) in adults with anterior open bite.</p>
Alignment free identification of clones in Bcell receptor repertoires
<p>The data sets are used for the analysis of the Alignment free [1] clonal identification approach.</p> <p>[1] "Alignment free identification of clones in B cell receptor repertoires", Ofir Lindenbaum, Nima Nouri, Yuval Kluger, Steven H. Kleinstein .</p> <p>Preprint available at: https://www.biorxiv.org/content/10.1101/2020.03.30.017384v1</p>
Abrupt Indian summer monsoon shifts aligned with Heinrich events and D-O cycles since MIS 3
<p>We present a new high-resolution speleothem-based record of Indian summer monsoon (ISM) variability ranging from ~ 45,000 to 34,000 yr BP combined with a published record up to 5,500 yr BP from Mawmluh cave, NE (North East) India</p>
Dataset for Hyperbolic Optical Metamaterials from Shear-Aligned Block Copolymer Cylinder Arrays
<p>Research Data supporting “Hyperbolic Optical Metamaterials from Shear-Aligned Block Copolymer Cylinder Arrays”</p> <p>Published in Advanced Photonics Research</p> <p>doi: 10.1002/adpr.202000037</p>
Multiple sequence alignment for the native Norwegian vascular plant phylogeny
<p>Methods: We produced a multi-locus Maximum Likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence data to estimate phylogenetic diversity and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple-model inference to identify environmental variables that contributed the most to the patterns of phylogenetic diversity. Finally, we estimated phylogenetic turnover and used this to identify Norwegian plant assemblages in terms of composition and evolutionary history.<br> <br> Results: Our ML phylogeny contained 87% of all currently described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post-glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterised by neo-endemism, while the mild and wet regions were characterised by both paleo- and neo-endemism. Phylogenetic diversity was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway.<br> <br> Main conclusions: Both contemporary ecological factors (climate and habitat heterogeneity), and post-glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.</p>
In-house 3-D printed aligners: effect of in vivo ageing on mechanical properties
<p>Dataset for all analyses in the paper.</p>
1918 influenza A virus alignments
<p>This dataset includes nucleotide alignments for 8 viral segments from five 1918 influenza A virus strains.</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.