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368 results for “consensus”
Data from: The efficacy of consensus tree methods for summarising phylogenetic relationships from a posterior sample of trees estimated from morphological data
Consensus trees are required to summarise trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are co-estimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility contains an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarising diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological datasets contributes to the inability of MCC and MAP trees to present an accurate summary of the posterior distribution. Conversely, majority-rule consensus (MRC) trees report a lower proportion of incorrect nodes when summarising the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarise the results of Bayesian phylogenetic analyses of morphological data.
Data from: ALS drug development guidances and trial guidelines: consensus and opportunities for alignment
The Food and Drug Administration (FDA) developed a draft guidance for drug development in Amyotrophic Lateral Sclerosis (ALS) that was issued in February 2018. The FDA draft guidance considered the recommendations developed by the ALS community which incorporated the views of a large group of clinical investigators, industry representatives, advocacy groups, patients, and caregivers. This external input from the ALS community reviewed the current state of clinical research in ALS and made suggestions over a wide range of drug development topics and served as an educational tool to provide the Agency with additional inputs about ALS, the state of the science and the community's views on key topics. In parallel to this effort, there was an independent effort to revise and update the ALS clinical trial guidelines. We discuss the areas of agreement of these three documents, and the areas that provide opportunities to improve the efficiency of drug development in ALS. It is likely that further research into biomarkers, efficacy endpoints, and predictive algorithms will provide greater alignment among community stakeholders and increase clarity on drug development efforts going forward. Continued patient engagement and inclusion of patient experience data in every aspect of the drug development process will further facilitate the approval of new treatments.
Data from: Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly
A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding frequency signature.
Figure 1. Neighbour-joining consensus tree inferred from the 16S in A new species of Arenallianassa (Decapoda: Axiidea: Callianassidae) from hydrothermal vents with notes on its ecology and a redescription of Arenallianassa arenosa (Poore, 1975)
Figure 1. Neighbour-joining consensus tree inferred from the 16S rRNA gene sequences for eight species of Callianassidae. Genbank Accession numbers are appended. Consensus support (%) based on 1000 bootstrap replicates is shown for each node. Scale indicates patristic distances.
MOOD_Consensus_Landuse_Earthenv_1k_ER
<p>Earthenv consensus land use. </p> <p>Abstract: The Earthenv (<a href="http://www.earthenv.org/" target="_blank" rel="noopener">www.earthenv.org</a>) consensus land cover layers are a combination of a number of public domain land cover datasets, which are considered to be more representative than any of the component datasets. 12 land cover types are provided as proportions, each of which has been extracted for the MOOD extent.</p> <p>File naming scheme:</p> <p>The filenames are given in accompanying file earthenvnames.txt</p> <p>Projection + EPSG code:<br>Latitude-Longitude/WGS84 (EPSG: 4326)</p> <p>Spatial extent:<br>Extent -24.0000000000000000,-38.5000000000000000 : 110.9999999999999432,86.9999999999999432</p> <p>Spatial resolution:<br>0.008333 deg (approx. 1000 m)</p> <p>Accuracy:</p> <p>Based on World Geodetic System 1984 ensemble (EPSG:6326), which has a limited accuracy of at best 2 meters.</p> <p> </p> <p>Source:</p> <p> Earthenv (<a href="http://www.earthenv.org/" target="_blank" rel="noopener">www.earthenv.org</a>) consensus land cover layers</p> <p>Software used:<br>ESRI ArcMap 10.8</p> <p>License: CC-BY-SA 4.0</p> <p>Processed by:<br>ERGO (Environmental Research Group Oxford) <a href="https://ergoonline.co.uk/" target="_blank" rel="noopener">https://ergoonline.co.uk/</a> for the H2020 MOOD Project</p> <p> </p>
Fig. 4. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with ITS2 DNA sequences from 80 in A new genus and three new species of mangrove slugs from the Indo-West Pacific (Mollusca: Gastropoda: Euthyneura: Onchidiidae)
Fig. 4. Maximum parsimony consensus tree within Paromoionchis gen. nov., performed with ITS2 DNA sequences from 80 individuals (including 7 outgroups). Numbers by the branches are the bootstrap values (only numbers>50% are indicated). Numbers for each individual correspond to unique identifiers for DNA extraction. All sequences for specimens of Paromoionchis gen. nov. are new. Information on specimens can be found in the lists of material examined and in Table 1. The letter A corresponds to a clade referred to in the text. The color used for each (mitochondrial) unit is the same as that used in Figs 1–3 and 5–6.
Fig. 4. Bootstrap consensus tree inferred from 1000 replicates, using the Maximum Likelihood method. The analysis involved 20 in Severe coenurosis caused by larvae of Taenia serialis in an olive baboon (Papio anubis) in Benin
Fig. 4. Bootstrap consensus tree inferred from 1000 replicates, using the Maximum Likelihood method. The analysis involved 20 sequences of 12S rDNA gene of cestodes having coenurus type larvae (Taenia serialis and T. multiceps) and one sequence of Echinococcus granulosus, as outgroup. For each sequence, the GenBank Accession number, species, developmental stage, host and geographic origin are provided. A total of 320 positions were included in the dataset. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches.
SpatialCVGAE: Spatial Domain Identification via Consensus Clustering Integrated Variational Graph Autoencoder
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Phenotypically active ORF and CRISPR consensus profiles
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Figures 315–316. Vatellini species, consensus cladograms. 315 in Revision of the New World and south-east Asian Vatellini (Coleoptera: Dytiscidae: Hydroporinae) and phylogenetic analysis of the tribe
Figures 315–316. Vatellini species, consensus cladograms. 315, Consensus cladogram of 72 most parsimonious cladograms (length = 78, CI = 67, RI = 92) resulting from cladistic analysis of Vatellini including Calicovatellus petrodytes. 316, Consensus cladogram of five most parsimonious cladograms (length = 74, CI = 70, RI = 93) resulting from cladistic analysis of Vatellini not including Calicovatellus petrodytes. Numbers above branches are Bremer support values.
Construction of an Ultra-High-Density Consensus Linkage Map in Sorghum bicolor
<p>A consensus genetic map were created by merging linkage maps from four published studies (Ji et al. 2017; Lopez et al. 2017; Kong et al. 2018; Phuong et al. 2019) using package LPmerge of R software.</p>
Fig. 11. Strict consensus tree resulting from 42 in Born from rock: eight new species of Itauara Müller, 1888 (Trichoptera: Glossosomatidae) from southeastern Brazil, including phylogenetic and distributional comments on the genus
Fig. 11. Strict consensus tree resulting from 42 most parsimonious trees (length = 242 steps; consistency index = 0.4291; retention index = 0.6602) from an equally weighted parsimony analysis of Itauara Müller, 1888 based on 93 morphological characters (6 constant, 19 variable and parsimony uninformative) modified from the matrix of Robertson & Holzenthal (2013). Apomorphies for the clades are indicated by the characters, with its states between parentheses. Bootstrap values (> 50%) are indicated under branches within the Itauara clade.
A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction
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Consensus-based Algorithms to Address Opioid Misuse Behaviors Among Individuals Prescribed Long-term Opioid Therapy
ClinicalTrials.gov study NCT05182606. IPD Sharing: NO. Countries: 1. Publications: 0.
The Nordic Consensus Study
ClinicalTrials.gov study NCT04763863. IPD Sharing: NO. Countries: 1. Publications: 0.
The Dissemination of Consensus Recommendations on Upper Gastrointestinal Bleeding
ClinicalTrials.gov study NCT00840008. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Registry to Improve the Adoption of Consensus Treatment Guidelines (IMPROVE Brady)
ClinicalTrials.gov study NCT01643707. IPD Sharing: Not stated. Countries: 7. Publications: 0.
Data from: Revised Airlie House consensus guidelines for design and implementation of ALS clinical trials
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Data from: ALS drug development guidances and trial guidelines: consensus and opportunities for alignment
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Data from: The efficacy of consensus tree methods for summarising phylogenetic relationships from a posterior sample of trees estimated from morphological data
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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.