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12,393 results for “materiality”
Supplementary Material
<p>Supplementary material of the article entitled "Hypoxia-inducible factor-2α promotes EMT in esophageal squamous cell carcinoma through the Notch pathway" published on Advances in Clinical and Experimental Medicine.</p>
FIGURES 15–19. Pinnularia hustedtii F in Pinnularia hustedtii (Bacillariophyta): Notes on specimens from Wuling Mountains, China and from type material
FIGURES 15–19. Pinnularia hustedtii F.Meister, scanning electron microscope (SEM) images from Wuling Mountains material. 15–16. Entire valves with girdle attached in Fig. 15. 17–19. Internal detail of striae, raphe, helictoglossae and central nodule. Scale bars: 10 μm (Fig. 15), 20 μm (Fig. 16), 5 μm (Figs 17–19).
FIGURES 20–24. 20 in Pinnularia hustedtii (Bacillariophyta): Notes on specimens from Wuling Mountains, China and from type material
FIGURES 20–24. 20. Internal view of central nodule of raphe. 21–23. External views of striae, raphe, raphe endings at centre. 24. Detail of internal striae. Scale bars: 2 μm (Figs 20–23), 1 μm (Fig. 24).
FIGURES 9–14. Pinnularia hustedtii F in Pinnularia hustedtii (Bacillariophyta): Notes on specimens from Wuling Mountains, China and from type material
FIGURES 9–14. Pinnularia hustedtii F.Meister, light microscope (LM) images from Wuling Mountains material. Scale bar: 50 μm.
FIGURES 1–8. 1. Pinnularia hustedtii F in Pinnularia hustedtii (Bacillariophyta): Notes on specimens from Wuling Mountains, China and from type material
FIGURES 1–8. 1. Pinnularia hustedtii F.Meister, reproduction of Meister 1935: 102, taf. 9, fig. 82. 2, 3, 4, 6. Specimens of Pinnularia hustedtii from 'Z + ZT Meister 3312040'. Fig. 5 is a reproduction of Pinnularia pseudotabellaria H.Kobayasi in H.Kobayasi & Kaz.Ando 1977: 248, pl. 8, figs 60, 61. Fig. 7 is a reproduction of page from Meister's notebook for 'Z + ZT Meister 3312065, lost holotype. Fig. 8 is a reproduction of page from Meister's notebook for 'Z + ZT Meister 3312040', isotype (specimen in Figs 2–6). Scale bars: 50 μm (Figs 2, 3), 10 μm (Figs 4, 6).
Supplementary material for: nQMaker: estimating time non-reversible amino acid substitution models
<p><span>Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly-used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this paper, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time non-reversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the non-reversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of datasets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the dataset. Notably, for the recently published plant and bird trees, these non-reversible models correctly recovered the commonly estimated root placements with very high statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (<a href="http://www.iqtree.org">http://www.iqtree.org</a>), allowing users to estimate non-reversible models and rooted phylogenies from their own protein datasets.</span></p>
Supplemental materials for the study of Stack Overflow
<p>Supplemental materials for the study of Stack Overflow.</p> <p>-Source bib files of the studied papers</p> <p>-Abbreviations and the full names of the selected venues</p> <p>-Correspondences between the authors' abbreviations and full names</p> <p>-Correspondences between the affiliations' abbreviations and full names</p>
Supplementary material 6 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Table S2. Class level identification of OTUs showing the number of OTUs produced with ITS2 and LSU and the proportion of the total OTU set on the rarefied data
Supplementary material 5 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Table S1. Accession numbers corresponding with the reference sequences used to build the phylogenetic trees
Supplementary material 3 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S3. Maximum-likelihood tree constructed in IQ-Tree2 based on three-gene (LSU D1-D2, SSU, ITS2) reference sequence alignments and OTUs for both markers (clustering thresholds: 99% LSU D1-D2 and 98% ITS2)
Supplementary material 2 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S2. Species accumulation curves of the OTUs generated from the ITS (panel right) and LSU (panel left) metabarcodes
Supplementary material 1 from: Di Lorenzo T, Di Marzio W, Piccini L, Messana G, Sáenz M, Galassi D (2018) Survival, metabolic rates and locomotory activities of a groundwater-obligate copepod species under long-term exposures to tetrachloroethylene. ARPHA Conference Abstracts 1: e29966. https://doi.org/10.3897/aca.1.e29966
Survival, metabolic rates and locomotory activities of a groundwater-obligate copepod species under long-term exposures to tetrachloroethylene
Code, data and supplementary material from: Analyzing phylogenetic trees with a tree lattice coordinate system and a graph polynomial
<p>This dataset includes code, used and generated data for the experiments in the paper Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial, and the supplementary material of the paper. The paper introduces representation and comparison methods for rooted unlabelled phylogenetic trees based on a tree lattice that serves as a coordinate system for rooted binary trees with branch lengths and a graph polynomial that fully characterizes tree shapes. The methods provide fast, accurate, likelihood-free, distance-based appraoches to analyzing phylogenetic trees and allow analysis for large trees with more than a thousand taxa. </p> <p>The dataset has three sections. The first section is the implementation of the introduced methods for phylogenetic tree analysis as an R package, inlcuding the source code and the binary of the package. This packege provides basic functions for tree analysis and can be used or edited for related analysis. The secoond section includes all code for analyses performed in the the paper, and all the data used and generated in the analyses. The third section contains the supplementary material for the paper, which includes supplememntary results and figures. For details, please refer to the paper and the README file.</p>
Supplementary material 1 from: lshishka M, Lazarova S, Radoslavov G, Hristov P, Peneva VK (2017) Biogeography and phylogenetic position of Enchodeloides signyensis (Loof, 1975), gen. n., comb. n. from Maritime Antarctic (Nematoda, Nordiidae). ZooKeys 697: 37-58. https://doi.org/10.3897/zookeys.697.13770
18S Parsimoni informative sites TemporaryMEGA17 : Explanation note: 18S rDNA Phylogenetic analysis between tree Genus based on Parsimony informative nucleotide sites.
Supplementary material 1 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Gazetteer : Authors: Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T. R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jesús E. Maldonado
Supplementary material 3 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Supplementary information figure : Authors: Eliécer E. Gutiérrez, Kristofer M. Helgen, Molly M. McDonough, Franziska Bauer, Melissa T. R. Hawkins, Luis A. Escobedo-Morales, Bruce D. Patterson, Jesús E. Maldonado
Supplementary material 1 from: Chen H-y, Talamas EJ, Valerio AA, Masner L, Johnson NF (2018) Revision of the World species of the genus Chromoteleia Ashmead (Hymenoptera, Platygastridae, Scelioninae). ZooKeys 778: 1-95. https://doi.org/10.3897/zookeys.778.25775
Supplementary material 1 from: Chen H-y, Talamas EJ, Valerio AA, Masner L, Johnson NF (2018) Revision of the World species of the genus Chromoteleia Ashmead (Hymenoptera, Platygastridae, Scelioninae). ZooKeys 778: 1-95. https://doi.org/10.3897/zookeys.778.25775
Supplementary material 2 from: lshishka M, Lazarova S, Radoslavov G, Hristov P, Peneva VK (2017) Biogeography and phylogenetic position of Enchodeloides signyensis (Loof, 1975), gen. n., comb. n. from Maritime Antarctic (Nematoda, Nordiidae). ZooKeys 697: 37-58. https://doi.org/10.3897/zookeys.697.13770
28S Parsimoni informative sites TemporaryMEGA15 : Explanation note: 28S rDNA Phylogenetic analysis between tree Genus based on Parsimony informative nucleotide sites.
Supplementary material 2 from: Gutiérrez EE, Helgen KM, McDonough MM, Bauer F, Hawkins MTR, Escobedo-Morales LA, Patterson BD, Maldonado JE (2017) A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling. ZooKeys 697: 87-131. https://doi.org/10.3897/zookeys.697.15124
Name and DNA sequences of pairs of primers used for amplification and sequencing of the CYTB gene : Data type: molecular data
Supplementary material 1 from: {"en": "Salata S, Fisher BL (2020) Pheidole Westwood, 1839 (Hymenoptera, Formicidae) of Madagascar – an introduction and a taxonomic revision of eleven species groups. ZooKeys 905: 1-235. https://doi.org/10.3897/zookeys.905.39592"}
Supplementary material 1 from: {"en": "Salata S, Fisher BL (2020) Pheidole Westwood, 1839 (Hymenoptera, Formicidae) of Madagascar – an introduction and a taxonomic revision of eleven species groups. ZooKeys 905: 1-235. https://doi.org/10.3897/zookeys.905.39592"}
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.