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2,399 results for “fragmenter”
PanDDA analysis of ligand screen against the NSP3 macrodomain of SARS-CoV-2: ligands from FrankenROCS fragment-linking pipeline and subsequent optimization of AVI-313
<p>This deposition contains the X-ray diffraction data used to run PanDDA in the ligand screen against the NSP3 macrodomain of SARS-CoV-2 described in Correy et al. 2024 (doi: https://doi.org/10.1101/2024.08.25.609621). Compounds were from fragment linking using FrankenROCS and subsequent optimization of AVI-313. </p> <p>frankenROCS_mac1.tar.gz contains structure factor intensities, PanDDA input/output and refined models/maps.</p> <p>frankenROCS_mac1_ligand-bound-states.tar.gz contains the ligand-bound states extracted from the multi-state PDB files.</p>
FIGURE 2. Anthurium caparaoense. A. Forest fragment. B. Terrestrial habit. C-D in Two new species of Anthurium (Araceae) from Caparaó National Park, southeastern Brazil
FIGURE 2. Anthurium caparaoense. A. Forest fragment. B. Terrestrial habit. C-D. Cataphylls, prophylls and petiole. E. Leaf blade green, slightly discolor. F. Spadix greenish at pre-anthesis. G. Spadix at anthesis with yellow pollen grains. H. Spadix at post-anthesis.
FIGURE 5 in A new miniaturized species of leaf chameleon, genus Brookesia, from a littoral forest fragment in eastern Madagascar
FIGURE 5. Morphological comparison of Brookesia nofy sp. nov. and B. ramanantsoai based on preserved specimens. The upper images show (A) the male holotype of B. nofy sp. nov. (ZSM 30/2024) and (B) a comparative male specimen of B. ramamantsoai (ZSM 10/2009; *image mirrored) in lateral view to illustrate the relatively longer tail in B. ramanantsoai. The lower images show (C–D) dorsal views of the heads of the B. nofy sp. nov. holotype and four comparative B. ramanantsoai specimens; in the upper row (C), the specifically distinct parts of the elevated cephalic ridges are indicated by blue respectively purple lines: a U-structure and two central ridges in B. nofy sp. nov. vs. three parallel longitudinal ridges in B. ramanantsoai. Scale bars = 1 mm.
FIGURE 2 in A new miniaturized species of leaf chameleon, genus Brookesia, from a littoral forest fragment in eastern Madagascar
FIGURE 2. Map of Madagascar showing localities of B. nofy sp. nov. and B. ramanantsoai (based on genotyped records and localities in Brygoo & Domergue 1975). The base map on the right shows vegetation across Madagascar from the Madagascar Vegetation Mapping Project (Moat & Smith 2007; available at https://web.archive.org/web/20180419112513/http://www. vegmad.org/). Vegetation is colored as follows: green, humid forest (rainforest); red, western dry deciduous forest; pink, mangroves; orange, spiny forest-thicket; greenish blue, western subhumid forest.
FIGURE 4 in A new miniaturized species of leaf chameleon, genus Brookesia, from a littoral forest fragment in eastern Madagascar
FIGURE 4. Specimens of Brookesia ramanantsoai in life. A, female from Tsinjoarivo, ZSM 285/2010 (FGZC 4557), photographed 2010; B, male from Vohimana, ZSM 132/2016 (FGZC 5042) photographed 2015; C, female probably from the area around Mandraka, photographed 2000 (probably corresponding to ZSM 637/2000 or 638/2000).
FIGURE 1 in A new miniaturized species of leaf chameleon, genus Brookesia, from a littoral forest fragment in eastern Madagascar
FIGURE 1. Maximum Likelihood trees of evolutionary relationships among members of the subgenus Evoluticauda within the genus Brookesia, inferred from the combined mitochondrial gene fragments of 16S and ND2 (1051 bp; upper tree) and the nuclear-encoded c-mos fragment (846 bp; lower tree). Values at nodes are support values in percent from a bootstrap analysis (500 replicates; not shown if <50%). The focal lineage from Ankanin'ny Nofy (B. nofy sp. nov.) and its sister species (B. ramanantsoai) are highlighted with purple and blue color, respectively. Brookesia brygooi was used as the outgroup.
FIGURE 3 in A new miniaturized species of leaf chameleon, genus Brookesia, from a littoral forest fragment in eastern Madagascar
FIGURE 3. Specimens of Brookesia nofy sp. nov. in life. A–C, male holotype ZSM 30/2024 (ZCMV 13721); D, paratype UADBA-R-70860 (ZCMV 13722), probably a subadult male; E, mating/mate-guarding couple photographed in the wild.
Video Footage for UAV Icing: Impact Testing of Ice Fragments on a Propeller
<p>This dataset contains video material in support of the following publication: <strong><span>Hann, R.</span></strong><span>, Müller, N.C., Wallisch, J. (2024). </span><span><a href="https://folk.ntnu.no/richahan/Publications/2024_Aviation_Hann_Ice%20impact.pdf">UAV Icing: Impact Testing of Ice Fragments on a Propeller</a></span><span>. AIAA 2024-4352. AIAA Aviation Forum and Ascend</span><span>.<em> </em></span><span>doi.org/10.2514/6.2024-4352</span></p> <p> </p> <p><span>https://folk.ntnu.no/richahan/Publications/2024_Aviation_Hann_Ice%20impact.pdf</span></p>
Dataset from the paper: "A new miniaturized species of leaf chameleon, genus Brookesia, from a littoral forest fragment in eastern Madagascar"
<p>Original data from the description of a new species of ground chameleon (Brookesia nofy) from Madagascar. Package includes alignment, sequence files as used for phylogenetic analysis, table with sequence metadata, and screenshots of websites consulted. </p> <p> </p> <p>Rakotoarison, A., A. F. Hasiniaina, F. Glaw & M. Vences (2024): A new miniaturized species of leaf chameleon, genus <em>Brookesia</em>, from a littoral forest fragment in eastern Madagascar. – <em>Zootaxa</em> <strong>5506</strong>: 533-547.</p> <p> </p>
FIGURE 2. Marskea cuspidata leaf structure. A. Leafs and fragments thereof. A in Discovery of isolated leaves of Marskea (Taxaceae) in the Middle Jurassic sediments of Irkutsk Basin (East Siberia, Russia)
FIGURE 2. Marskea cuspidata leaf structure. A. Leafs and fragments thereof. A*. Specimen no. 19-11/7 holotype. B. Upper surface of the epidermis, specimen no. 19-11/7 holotype. C. Cells of the upper epidermis, specimen no. 19-11/4. D. Cells of the upper epidermis, internal view on SEM, specimen no. 19-11/7 holotype. E. Cells of the upper epidermis, specimen no. 19-11/9-1. Flat papillae on periclinal walls are shown by arrows. F, G. Lower surface of the epidermis with two stomatal bands, specimen no. 19-11/7 holotype. H. Cells of lower surface between stomatal band and leaf edge, specimen no. 19-11/7 holotype. I. Fragment of lower surface with stomatal band and central non-stomatal zone. A horizontal row of adjacent stomatal complexes is shown by arrow, specimen no. 19-11/7 holotype.
MsnLib multi-stage fragmentation mass spectral libraries - raw negative
<p>The data for <a href="https://doi.org/10.26434/chemrxiv-2024-l1tqh-v2">MSnLib</a> are divided into several Zenodo records due to size constraints. </p> <p>raw positive: <a href="https://doi.org/10.5281/zenodo.10966404">10966404</a><br>raw negative: <a href="https://doi.org/10.5281/zenodo.10967081">10967081</a><br>mzml positive and negative: <a href="https://doi.org/10.5281/zenodo.10966280">10966280</a><br>spectral libraries: <a href="https://doi.org/10.5281/zenodo.11163380">11163380</a></p> <p>This record includes zipped files containing the raw negative data, acquired using a flow injection method on an Orbitrap ID-X instrument, for all compound libraries.</p> <p>7 Compound Libraries:</p> <ul> <li>Short Name: Full name, Provider (Catalog number), total compounds (not all detected during library building)</li> <li>mce_bioactive: Bioactive Compound Library, MedChemExpress (HY-L001), 10,315 compounds</li> <li>mce_scaffold: 5k Scaffold Library, MedChemExpress, (HY-L902), 4998 compounds</li> <li>nih: NIH NPAC ACONN collection of NP, NIH/NCATS, 3988 compounds</li> <li>otavapep: Alpha-helix Peptiomimetic Library, OTAVAchemicals (a-helix-Peptido), 1298 compounds</li> <li>enamdisc: Discovery Diversity Set -10, Enamine (DDS-10), 10,240 compounds</li> <li>enammol: Carboxylic Acid Fragment Library + Random, Enamine and Molport, 4378 compounds</li> <li>mcedrug: FDA-Approved Drug Library, MedChemExpress (HY-L022), 2610 compounds</li> </ul>
MsnLib multi-stage fragmentation mass spectral libraries - raw positive
<p>The data for <a href="https://doi.org/10.26434/chemrxiv-2024-l1tqh-v2">MSnLib</a> are divided into several Zenodo records due to size constraints. </p> <p>raw positive: <a href="https://doi.org/10.5281/zenodo.10966404">10966404</a><br>raw negative: <a href="https://doi.org/10.5281/zenodo.10967081">10967081</a><br>mzml positive and negative: <a href="https://doi.org/10.5281/zenodo.10966280">10966280</a><br>spectral libraries: <a href="https://doi.org/10.5281/zenodo.11163380">11163380</a></p> <p>This record includes zipped files containing the raw positive data, acquired using a flow injection method on an Orbitrap ID-X instrument, for all compound libraries.</p> <p>7 Compound Libraries:</p> <ul> <li>Short Name: Full name, Provider (Catalog number), total compounds (not all detected during library building)</li> <li>mce_bioactive: Bioactive Compound Library, MedChemExpress (HY-L001), 10,315 compounds</li> <li>mce_scaffold: 5k Scaffold Library, MedChemExpress, (HY-L902), 4998 compounds</li> <li>nih: NIH NPAC ACONN collection of NP, NIH/NCATS, 3988 compounds</li> <li>otavapep: Alpha-helix Peptiomimetic Library, OTAVAchemicals (a-helix-Peptido), 1298 compounds</li> <li>enamdisc: Discovery Diversity Set -10, Enamine (DDS-10), 10,240 compounds</li> <li>enammol: Carboxylic Acid Fragment Library + Random, Enamine and Molport, 4378 compounds</li> <li>mcedrug: FDA-Approved Drug Library, MedChemExpress (HY-L022), 2610 compounds</li> </ul>
Figure 3 in Importance of riparian vegetation and wood-pastures in the maintenance of bat assemblages in a highly fragmented landscape in Veracruz, Mexico
Figure 3: Rank abundance curves of bats captured in wood-pastures (A) and riparian vegetation (B) in Jamapa, Veracruz, Mexico. Numbers indicate species, 1: Artibeus jamaicensis, 2: Sturnira parvidens, 3: A. lituratus, 4: S. hondurensis, 5: Glossophaga soricina, 6: G. commissarissi, 7: Rhogeesa tumida, 8: Desmodus rotundus, 9: Phyllostomus discolor, 10: Eptesicus furinalis, 11: Carollia sowelli, 12: A. phaeotis, 13: Uroderma bilobatum, 14: Molossus rufus, 15: C. perspicillata, 16: Chiroderma salvini, 17: A. watsoni, 18: C. villosum, 19: Pteronotus parnelli, 20: Platyrrhinus helleri, 21: Micronycteris microtis, 22: A. toltecus, 23: Centurio senex, 24: P. davyi, 25: Mormoops megallophylla, 26: Eumops bonariensis, 27: Promops centralis, 28: Myotis californicus, 29: M. keaysi.
Figure 2 in Importance of riparian vegetation and wood-pastures in the maintenance of bat assemblages in a highly fragmented landscape in Veracruz, Mexico
Figure 2: Species accumulation curves for wood-pastures and riparian vegetation in the locality of Jamapa, Veracruz, Mexico. Hill's numbers (effective numbers of species) are in brackets. According to non-overlapping confidence intervals only q1 ("typical" species) and q2 (dominant species) were significantly higher in riparian vegetation compared to pastures.
Figure 4 in Morphological symmetry of Rhipidomys mastacalis (Mammalia, Rodentia, Cricetidae) in fragmented habitats of the Atlantic Forest in Northeastern Brazil: a study on the influence of the environment on an endemic species
Figure 4: Scatter diagrams based on a simple linear model (fluctuating asymmetry vs. vegetation cover), for four anatomical structures of Rhipidomys mastacalis three vegetation classes in Northeastern Brazil. The trend line is shown in black; the gray area represents the 95 % of confidence intervals.
Figure 1 in Morphological symmetry of Rhipidomys mastacalis (Mammalia, Rodentia, Cricetidae) in fragmented habitats of the Atlantic Forest in Northeastern Brazil: a study on the influence of the environment on an endemic species
Figure 1: Map of Northeastern Brazil, showing the geographical location of the Rhipidomys mastacalis samples selected for this study.
Figure 3 in Morphological symmetry of Rhipidomys mastacalis (Mammalia, Rodentia, Cricetidae) in fragmented habitats of the Atlantic Forest in Northeastern Brazil: a study on the influence of the environment on an endemic species
Figure 3: Box plot comparing the fluctuating asymmetry (FA) in Rhipidomys mastacalis from three vegetation classes in Northeastern Brazil. (A) Skulls, (B) mandibles, (C) scapulae,and (D) pelvis. The horizontal lines outside the boxes represent the smallest and largest variance for each population, and the horizontal line inside each box represents the mean value.
Figure 2 in Morphological symmetry of Rhipidomys mastacalis (Mammalia, Rodentia, Cricetidae) in fragmented habitats of the Atlantic Forest in Northeastern Brazil: a study on the influence of the environment on an endemic species
Figure 2: Anatomical structures (left and right), showing the location of morphological landmarks in a specimen of Rhipidomys mastacalis (CMARF–1701) from Brazil. (A) Occlusal view of skulls, (B) mandibles, (C) scapulae, and (D) pelvis.
Molecular Dynamics Trajectories of Membrane-bound Influenza Hemagglutinin (A/duck/Alberta/35/76) in Complex with 0-3 Copies of FISW84 Fab Fragments
<p>MD simulation trajectories of influenza hemagglutinin (A/duck/Alberta/35/76) in a bilayer mimicking the viral membrane, with 0-3 copies of FISW84 antibody's Fab domains bound.</p> <p>Files are named as (copy number of Fab).(simulation replica ID).(file type extension). The systems were constructed in CHARMM format PSF files and the trajectories were recorded in DCD format.</p> <p>Simulations were performed with NAMD3. The trajectories were re-centered and re-wrapped about the periodic boundary from the raw trajectories, in order to keep the HA-Fab complex and the lipid bilayer appearing as a single continuous entity instead of isolated molecules at the opposite side of the periodic boundary. Water molecules in the simulation were removed in these trajectories due to file size limitations.</p>
Refitting and Matching Neolithic Pottery Fragments from the Taï site, France
<p>Refitting and matching Neolithic pottery fragments from the Taï site, France. </p> <p>This record includes three CSV files:</p> <ul> <li><strong>20210211_tai-cr-na.csv</strong>: connection relationships between fragments (physical refits)</li> <li><strong>20210411_tai-sherds-na.csv</strong>: similarity relationships between fragments</li> <li><strong>20210510_similarites-PD1_nm.csv</strong>: information about fragments</li> </ul>
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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.
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DANDI Archive for NWB datasets
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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.