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182 results for “molecular collections”
Fig. 3. Plectanocotyle jeanloujustinei n in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden
Fig. 3. Plectanocotyle jeanloujustinei n. sp. ex Chelidonichthys lastoviza from the western Mediterranean (Algeria), hologenophores. A-E, Body lacking only the haptor. F. Body lacking a lateral part posterior part. G-H, anterior end of the body including the male copulatory organ. The missing parts were excised and used for DNA extraction. A, (HEL1729). B, (HEL1730). C, (HEL1732). D, (HEL1733). E, (HEL1734). F, (HEL1731). G, (HEL1727). H, (HEL17287).
Fig. 2 in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden
Fig. 2. Plectanocotyle gurnardi (Van Beneden and Hesse, 1863) sensu stricto ex Eutrigla gurnardus from the North Sea, Sweden, hologenophores, body lacking only a lateral part; excised used for DNA extraction A, (SMNH 216644). B, (SMNH 216645). C, (SMNH 216646).
Fig. 1 in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden
Fig. 1. One of the unstudied specimens of Plectanocotyle gurnardi (Van Beneden and Hesse, 1863) from the type-host Eutrigla gurnardus available for study before this paper, and that hinted the presence of Plectanocotyle gurnardi in Swedish waters of the North Sea. The slide containing two specimens of Plectanocotyle gurnardi labeled as "Phyllocotyle gurnardi": unstudied specimens collected by Theodor Odhner from the gills of Eutrigla gurnardus from Kristineberg, Sweden, Northeast Atlantic.
Fig. 6 in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden
Fig. 6. Plectanocotyle gurnardi (Van Beneden and Hesse, 1863) sensu stricto ex Eutrigla gurnardus from the North Sea, Sweden. A, Body, ventral view (SMNH 216639). B, Clamp, ventral view (SMNH 216593). C, Anterior end showing male copulatory organ, ventral view (SMNH 216586). D, Egg, (SMNH 216594).
Fig. 7 in "Something old, something new, something borrowed, and the oioxeny is true": description of Plectanocotyle jeanloujustinei n. sp. (Polyopisthocotylea, Plectanocotylidae) from the MNHN Helminthology collection with novel molecular and morphological data for P. gurnardi (Van Beneden & Hesse, 1863) (sensu stricto) from Sweden
Fig. 7. Plectanocotyle gurnardi (Van Beneden and Hesse, 1863) sensu stricto ex Eutrigla gurnardus from the North Sea, Sweden, disposition of clamps sclerites. A, Dorsal jaw. B, Ventral jaw. C, Clamp, ventral view (SMNH 216593). 3.2. Morphology
Collection: Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes Confined Between Electrodes
<p>Metadata record collecting related data sets that contain molecular dynamics simulations of PEO-LiTFSI polymer electrolytes confined between model electrodes.</p> <p>Related data sets:</p> <ul> <li>Uncharged electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13164944">https://doi.org/10.5281/zenodo.13164944</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13165450">https://doi.org/10.5281/zenodo.13165450</a>:<br>Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13165725">https://doi.org/10.5281/zenodo.13165725</a>:<br>Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> <li><a href="https://doi.org/10.5281/zenodo.13166024">https://doi.org/10.5281/zenodo.13166024</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Uncharged Electrodes</li> </ul> </li> <li>Charged electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13166152">https://doi.org/10.5281/zenodo.13166152</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167128">https://doi.org/10.5281/zenodo.13167128</a>:<br>Molecular Dynamics Simulations of Monoglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167338">https://doi.org/10.5281/zenodo.13167338</a>:<br>Molecular Dynamics Simulations of Tetraglyme-LiTFSI Liquid Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167551">https://doi.org/10.5281/zenodo.13167551</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Salt Concentrations Confined Between Charged Electrodes (+/- 1.00 e/nm²)</li> <li><a href="https://doi.org/10.5281/zenodo.13167614">https://doi.org/10.5281/zenodo.13167614</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths Confined Between Charged Electrodes With Various Surface Charges</li> </ul> </li> <li>Plots: <ul> <li><a href="https://doi.org/10.5281/zenodo.13168242">https://doi.org/10.5281/zenodo.13168242</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths and Salt Concentrations Confined Between Charged Electrodes With Various Surface Charges: Plots</li> </ul> </li> </ul>
Collection: Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes in the Bulk and Confined Between Electrodes
<p>Metadata record collecting related data sets that contain molecular dynamics simulations of PEO-LiTFSI polymer electrolytes in the bulk and confined between model electrodes.</p> <p>Related data sets:</p> <ul> <li>In the Bulk: <ul> <li><a href="https://doi.org/10.5281/zenodo.13144737">https://doi.org/10.5281/zenodo.13144737</a>:<br>Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes With Various Chain Lengths and Salt Concentrations in the Bulk</li> </ul> </li> <li>Confined Between Electrodes: <ul> <li><a href="https://doi.org/10.5281/zenodo.13169120">https://doi.org/10.5281/zenodo.13169120</a>:<br>Collection: Molecular Dynamics Simulations of PEO-LiTFSI Polymer Electrolytes Confined Between Electrodes</li> </ul> </li> </ul>
Figure 2 in Molecular identification of Haemaphysalis sulcata (Acari: Ixodidae) larval stages collected using the Berlese funnel in Northern Iran
Figure 2. Phylogenetic tree generated based on ITS2 sequence data of the Haemaphysalis species of this study and sequences retrieved from GenBank database constructed using Bayesian Inference method. The main clade of tree separated by a yellow rectangular box. The taxa were defined with a name and GenBank accession number and taxa of the present study is bold. Posterior probability values inserted in the place of nodes. Branch lengths are proportional to the evolutionary changes.
Fig. 2. The two Gerarda prevostiana specimens collected 1 in Further specimens of the mud snake, Gerarda prevostiana (Homalopsidae) from Sri Lanka with insights from molecular phylogenetics
Fig. 2. The two Gerarda prevostiana specimens collected 1 km offshore from Vankale, Mannar, Sri Lanka. 2013.18.01.NH: A, C, E, G, I, K; 2013.19.01.NH: B, D, F, H, J, L. Scale bar is 3 mm. Dorsal (A, B), lateral (C, D) and ventral (E, F) aspect of the heads. Dorsal (G, H), lateral (I, J) and ventral (K, L) aspect of mid-body.
Dataset for "Species diversity and molecular characterization of Alternaria section Alternaria isolates collected mainly from cereal crops in Canada" by Jeremy R. Dettman, Quinn Eggertson, and Natalie E. Kim
<p>Dataset consists of three files, each containing aligned nucleotide sequences from 559 Alternaria strains. The three sequenced loci are ASA-10, ASA-19, and rpb2. Strain names are stated in the header of each sequence.</p>
Data from: Integrating deep learning derived morphological traits and molecular data for total-evidence phylogenetics: lessons from digitized collections
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BioExcel Use Case 1: collection of output data from molecular dynamics simulation
<p>The Use Case aims to address all the challenges related to antibody design through an integrative approach combining the core BioExcel software comprising of GROMACS, HADDOCK and PMX.</p> <p>The folder contains the GROMACS output files (xtc and pdb file). Molecular Dynamics simulations have been performed with GROMACS version 2020 and CHARMM36 force field. The input files and scripts of the final protocol are publicly available on BioExcel GitHub https://github.com/bioexcel/BioExcel-UseCase1.</p> <p>The Use Case 1 protocol was presented at the BioExcel Summer School on Biomolecular Simulation in 2021 (see <a href="https://doi.org/10.5281/zenodo.7009238">https://doi.org/10.5281/zenodo.7009238</a> or <a href="https://youtu.be/_TDKfKX4kwM">https://youtu.be/_TDKfKX4kwM</a>)</p> <p> </p>
Collection data and molecular datasets for: Defining species-specific seed sourcing strategies for restoration: An example of how to use genetic data to inform seed collections for multiple co-occurring species
<p>Two files for each dataset are provided:</p> <p>Metadata files contain colelcting information for the samples in each molecular dataset as well as the group assignments (species, genetic neighbourhood and sites) used in analyses, saved as an excel spreadsheet.</p> <p>Molecular datasets containing samples and SNPs used in analyses. The data is formatted as a genlight object saved as an RData file that can be read into the R statisical environment and analysed using the 'dartR' package (Gruber et al. 2018).</p>
Figure 1 in Molecular identification of Haemaphysalis sulcata (Acari: Ixodidae) larval stages collected using the Berlese funnel in Northern Iran
Figure 1. Dorsal aspect of a tick larvae sample collected in this study.
Molecular-scale substrate anisotropy, crowding, and division drive collective behaviors in cell monolayers
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Individual molecular motors use low forces to bypass roadblocks during collective cargo transport
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Data from: Multi-objective optimization for plant germplasm collection conservation of genetic resources based on molecular variability
Germplasm collections play a significant role among strategies for conservation of diversity. It is common to select a core collection to represent the genetic diversity of a germplasm collection, in order to minimize the cost of conservation, while ensuring the maximization of genetic variation. We aimed to solve two main problems: (1) to select a set of individuals, from an in situ data set, that is genetically complementary to an existing germplasm collection, and (2) to define a core collection for a germplasm collection. We proposed a new multi-objective optimization (MOO) approach based on principles of systematic conservation planning (SCP) incorporating heterozygosity information; therefore, optimization takes genotypic diversity and variability patterns into account as well. As a case study, we used Dipteryx alata microsatellite loci information from two sources, an ex situ germplasm collection located at the Agronomy School of the Federal University of Goiás (UFG-AS), and an in situ data set composed of 642 sampled individual trees. We were able to identify within a population of several individuals, the exact accessions/samples that should be chosen in order to preserve the species diversity. We found that material from nine in situ individual trees are enough to complement the UFG-AS germplasm collection as it is, and that it is possible to define a core collection of 20 individual trees representing all studied genetic diversity. Moreover, we defined a method (a protocol) to deal with large amounts of accessions in the context of MOO. The proposed approach can be used to help constructing collections with maximal allelic richness and can also be extended to the in situ conservation. As far as we know, this is the first time that principles of SCP and the MOO approach are applied to the problem of complementing a germplasm collection and of finding a core collection for a germplasm collection.
Data from: Morphological and molecular diagnostic species characters of Staurozoa (Cnidaria) collected on the coast of Helgoland (German Bight, North Sea)
Scientific knowledge and records on staurozoans are limited probably because of their inconspicuous life habit and the small number of specialists for this taxon. To increase the awareness for Staurozoa, we identified morphological and molecular features of the three staurozoan species Haliclystus tenuis Kishinouye, 1910, Haliclystus auricula Clark, 1863, and Craterolophus convolvulus (Johnston, 1835) collected on the coast of the island Helgoland to evaluate their suitability as diagnostic characters. Useful macromorphological diagnostic features were the patterns of white spots of nematocysts and internal arm structures, whereas tentacle and gonad follicle numbers showed high intraspecific variations. Morphometric measurements on photographs of living specimens provided reliable data for interspecific comparisons. Comprehensive nematocyst analyses revealed interspecific shape differences of isorhizas and three types of rhopaloids, indicating that the staurozoan cnidome is more diverse than previously assumed. However, the taxonomic value of nematocyst analyses in Staurozoa remains unclear because comprehensive data is still lacking for most species. Comparative molecular genetic sequence analyses of mitochondrial 16S and COI and nuclear 18S ribosomal DNA identified the three species and confirmed their morphological identification. In comparison to published data, our analyses indicate similarities between H. auricula and Haliclystus antarcticus Pfeffer, 1889. Proteomic fingerprinting by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) differentiated all three species, suggesting that this technique could provide an alternative rapid identification method for staurozoans.
FIGURES 35–43 in Notes on the diatom collection of the Natural History Museum, London (BM) IX: Campylodiscus hardmanianus, with a discussion on synapomorphy and the poverty of molecular monophyly
FIGURES 35–43. Reproductions of original illustrations for species of Coronia. Figures 35: Coronia echenëis Ehrenb., Wismar, Germany Figures 36: Coronia limbatus Bréb., Cherbourg (after Brébisson 1854: pl. 1, fig. 1) Figures 37: Coronia decorus Bréb., Cherbourg (after Brébisson 1854: pl. 1, fig. 2) Figures 38: Coronia ambiguus Grev., Jamaica (after Greville 1860: pl. 1, fig. 5) Figures 39: Coronia undulatus Grev., Bermuda (after Greville 1863: pl. 9, fig. 4) Figures 40: Coronia daemelianus Grunow, Australia (?) (after Grunow in A.W.F.Schmidt et al. 1877: pl. 54, fig. 1) Figures 41: Coronia samoensis Grunow, Samoa (after Grunow in A.W.F.Schmidt et al. 1875: pl. 15, fig. 20) Figures 42: Coronia impressus Grunow, Balearic Islands (after Grunow in A.W.F.Schmidt et al. 1877: pl. 51, fig. 10) Figures 43: Coronia hardmanianus, Hong Kong (Unpublished drawing, BM)
FIGURES 30–34 in Notes on the diatom collection of the Natural History Museum, London (BM) IX: Campylodiscus hardmanianus, with a discussion on synapomorphy and the poverty of molecular monophyly
FIGURES 30–34. SEM images of Coronia echeneis, specimeNs from BeLize; scaLe bar = 50.0μm (FigUres 30, 31), scaLe bar = 6.0μm (FigUres 32, 34), scaLe bar = 7.5μm (FigUre 33)
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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.