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1,053 results for “MD”
Mesocosm (Marsh Organ) experiment at Blackwater National Wildlife Refuge, MD, 2012
This experiment examines the effects of tidal inundation on the growth of salt marsh vegetation. We measured the response of plants to disturbance across a gradient in inundation times by transplanting tussocks of Schoenoplectus americanus into mesocosms of different elevation. The mesocosms were arranged into structures commonly described as �marsh organs�. Here we utilize two marsh organs each containing 54 mesocosms constructed of 6-inch diameter (0.0182, m2) polyvinyl chloride pipe, arranged into nine rows containing six pipes of identical elevation. We conducted the experiment in a large brackish marsh on the Atlantic Coast of North America. The study site is adjacent to the Blackwater River, a tributary of the Chesapeake Bay (Maryland, USA) (Blackwater, 38.40�N, 76.07�W). Changes in water level are primarily driven by meteorological events, with mean astronomical tides of <0.25 m. Long-term porewater salinities average 10 p.p.t. within the marsh soil, and intertidal vegetation is dominated by Schoenoplectus americanus and Spartina patens.
MD Data for Patterns in protein flexibility: a comparison of NMR "ensembles", MD trajectories and crystallographic B-factors
<p>This data set comprises five zipped directories that contain the scripts and intermediate molecular dynamics (MD) results used in (initially as of April 24, 2017, updated with additional directories on December 15, 2020) a soon to be submitted paper, "Patterns in protein flexibility: a comparison of NMR 'ensembles', MD trajectories and crystallographic B-factors" written by the authors of this entry. An earlier version of this paper is available via BioRxiv, DOI: https://doi.org/10.1101/240655.</p> <p>This paper explores patterns in coordinate variance and coordinate uncertainty in MD trajectories and in protein structures derived from NMR and compares coordinate variances/uncertainties with those crystallographic B-factors. The files, MD_data.zip and MD_data2.zip, each unzip to contain input files and scripts for reproducing the MD trajectories used in this paper (using DESMOND): MD_data.zip contains input files/scripts for the MD trajectories used in the preprint; MD_data2.zip contains input files/scripts for trajectories ran following publication of the preprint. The file btab_analysis_scripts.zip contains key scripts for analyzing those trajectories (following file conversion with VMD and superimposition with THESEUS) in MATLAB (this analysis assumes the presence of the FindCore Toolbox, written by David Snyder and available via the MATLAB Central File Exchange, as well as the MATLAB Statistics and Machine Learning Toolbox). And the files, superimposed_MD_trajectories.zip and superimposed_MD_trajectories2.zip, each unzip to yield the trajectories (superimposed using THESEUS and in PDB multimodel file format) analyzed in the soon to be submitted paper: superimposed_MD_trajectories.zip contains trajectories reported in the preprint and superimposed_MD_trajectories2.zip contains the results of subsequent simulations. </p>
Supplementary Material: Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome?
<p>Supplementary video for <em>Viruses</em> <strong>2015</strong>, <em>7</em>(11), 5962-5986; doi:10.3390/v7112919; http://www.mdpi.com/1999-4915/7/11/2919.</p> <p><strong>Movie S1.</strong> Dynamic interface between 3C and 3D domains revealed by accelerated MD. The 3C and 3D domains are colored cyan and blue, respectively. The active-site residues of the protease (His-40, Glu-71, Cys-147) and the polymerase (Asp-416, Asp-511, Asp-512) domains are represented by red spheres to help identifying the relative orientations of two domains.</p>
Simulation files for POPC lipid membrane with Slipids-VIS force field for Gromacs MD simulation engine
<p>The tar.gz archive contains simulation input files that were used in the publication Transmembrane potential modeling: Comparison between methods of constant electric field and ion imbalance.</p> <p>http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b01202</p> <p>The files are meant to be used with <strong>Gromacs</strong> simulation package (gromacs.org).</p> <p>A modified Slipids force field, <strong>Slipids-VIS</strong>, is introduced. It uses Virtual Interaction sites in order to speed up simulation. The technique is described in the aforementioned work. The archive contains working topology for <strong>POPC</strong> lipid molecules and 6fs timestep without any significant loss of accuracy.</p>
SUPPLEMENTARY (For MD) An integrative pan-genome and subtractive proteomics approach for the identification of potential novel therapeutic drug target against antibiotic resistant honeybee pathogen Paenibacillus larvae
<p><strong>Parameters</strong></p><p>Force field: AMBER ff19SB</p><p>Water type: TIP3P</p><p>Ions: NaCl </p><p>Ligand topology force field: GAFF2</p><p>Temperature: 298k</p><p>Pressure: 1 bar</p><p>minimization step: 20000 on 5 nanoseconds</p><p>initial velocity is changed by changing "ntx" and "ig"</p><p>C2: ntx = 5 , ig = 8</p><p>C3: ntx = 2 , ig = 5</p><p> </p><p><strong>Uploads</strong>- </p><p>1. Zip file of all 3 main files</p><p>2. Unzip file of C1 (Trajectory, PDB complex after each 10 ns run, and Mp4 video of Complex)</p><p>3. Zip file of C1</p><p>4. Unzip file of C2 (Trajectory, PDB complex after each 10 ns run, and Mp4 video of Complex)</p><p>5. Zip file of C2</p><p>6. Unzip file of C3 (Trajectory, PDB complex after each 10 ns run, and Mp4 video of Complex)</p><p>7. Zip file of C3</p><p>8. Zip and unzip file of <strong>Initial</strong> PDB of complex prior to MD simulation with <strong>Post</strong> MD PDB (C1, C2, C3)</p><p>9. Zip file of <strong>topology</strong> files for C1, C2, and C3</p>
Sample MD trajectory
<p>MD trajectory used for training graph convolutional neural networks as coarse grained force fields as described in the following publications:</p> <ul> <li>E. Ricci, G. Giannakopoulos, V. Karkaletsis, D. N. Theodorou, N. Vergadou. 2022. "<em>Developing Machine-Learned Potentials for Coarse-Grained Molecular Simulations: Challenges and Pitfalls</em>". In Proceedings of 12th Conference on Artificial Intelligence (SETN). ACM, New York, NY, USA, 7 pages. <a href="https://doi.org/10.1145/3549737.3549793">https://doi.org/10.1145/3549737.3549793</a>. <strong>Open access</strong> <a href="../record/7078577">https://zenodo.org/record/7078577</a></li> <li>Gerakinis, D.-P., Ricci, E., Giannakopoulos, G., Karkaletsis, V., Theodorou, D. N., & Vergadou, N. (2024). <em>Machine Learning-Based Coarse Grained Interaction Potentials for Molecular Systems</em>. Zenodo. <a href="https://doi.org/10.5281/zenodo.10501037">https://doi.org/10.5281/zenodo.10501037</a></li> </ul> <p>The compressed archive contains input and output files for a NVT molecular dynamics simulation of a system containing 500 molecules of liquid benzene at 300 K, performed using LAMMPS.</p> <p>The reference code used to train the model, with detailed usage instructions, is available at: <a href="https://github.com/ml-multimem/schnetpack-for-bulk-systems">https://github.com/ml-multimem/schnetpack-for-bulk-systems</a></p>
Water will find its way: transport through narrow tunnels in hydrolases (Hal protein with different MD simulation settings)
<h1>Hal_2fs.zip</h1> <h2><em>"Water will find a way: transport through narrow tunnels in hydrolases (Hal_2fs protein variant)"</em></h2> <p>The input files and results used for the paper <em>"Water will find a way: transport through narrow tunnels in hydrolases"</em> are separated in the different folders depending the stage they belong to.</p> <h3>Folders</h3> <p>1. <em>01_Simulations.tar.gz</em>: All the files used to get the data employing Molecular Dynamics simulations. <br>2. <em>02_Caver.tar.gz</em>: Caver config used together with the <em>"Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations"</em> method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.<br> 3. <em>03_Aquaduct.tar.gz</em>: Aquaduct results for all the MD trajectories.<br> 4. <em>04_TransportTools.tar.gz</em>: TransportTools results (https://doi.org/10.1093/bioinformatics/btab872).<br> 5. <em>05_WaterAnalysis.tar.gz</em>: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the <em>minimum sphere event</em> is present. Also the txt files with the results from the H-bond analysis are here.</p> <h3>Files</h3> <p> 1. <em>01_build_database.py</em>: Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.<br> 2. <em>Hal_2fs.dat</em>: Parsed database of transport events for Hal system. Command used: <br><em>python3 01_build_database.py -c 04_TransportTools/Hal_2fs.ini -o Hal_2fs.dat</em></p> <p> </p> <h1>Hal_300K.zip</h1> <h2><em>"Water will find a way: transport through narrow tunnels in hydrolases (Hal_300K protein variant)"</em></h2> <p>The input files and results used for the paper <em>"Water will find a way: transport through narrow tunnels in hydrolases"</em> are separated in the different folders depending the stage they belong to.</p> <h3>Folders</h3> <p>1. <em>01_Simulations.tar.gz</em>: All the files used to get the data employing Molecular Dynamics simulations. <br>2. <em>02_Caver.tar.gz</em>: Caver config used together with the <em>"Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations"</em> method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.<br> 3. <em>03_Aquaduct.tar.gz</em>: Aquaduct results for all the MD trajectories.<br> 4. <em>04_TransportTools.tar.gz</em>: TransportTools results (https://doi.org/10.1093/bioinformatics/btab872).<br> 5. <em>05_WaterAnalysis.tar.gz</em>: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the <em>minimum sphere event</em> is present. Also the txt files with the results from the H-bond analysis are here.</p> <h3>Files</h3> <p> 1. <em>01_build_database.py</em>: Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.<br> 2. <em>Hal_300K.dat:</em> Parsed database of transport events for Hal system. Command used:<br><em>python3 01_build_database.py -c 04_TransportTools/Hal_300K.ini -o Hal_300K.dat</em></p> <p> </p> <h1>Hal_TIP3P.zip</h1> <h2><em>"Water will find a way: transport through narrow tunnels in hydrolases (TIP3P protein variant)"</em></h2> <p>The input files and results used for the paper <em>"Water will find a way: transport through narrow tunnels in hydrolases"</em> are separated in the different folders depending the stage they belong to.</p> <h3>Folders</h3> <p>1. <em>01_Simulations.tar.gz</em>: All the files used to get the data employing Molecular Dynamics simulations. <br>2. <em>02_Caver.tar.gz</em>: Caver config used together with the <em>"Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations"</em> method (https://doi.org/10.1016/j.mex.2022.101968), and after re-clustering as described in the methods section of the paper.<br> 3. <em>03_Aquaduct.tar.gz</em>: Aquaduct results for all the MD trajectories.<br> 4. <em>04_TransportTools.tar.gz</em>: TransportTools results (https://doi.org/10.1093/bioinformatics/btab872).<br> 5. <em>05_WaterAnalysis.tar.gz</em>: The results from the exact matching analysis were parsed to perform H-bond analysis. Here are the PDBs where the <em>minimum sphere event</em> is present. Also the txt files with the results from the H-bond analysis are here.</p> <h3>Files</h3> <p> 1. <em>01_build_database.py</em>: Python3 script to parse the results from the exact matching analysis from TransportTools into a dictionary of transport events. For more detailed information read the script documentation.</p> <p> 2. <em>Hal_TIP3P.dat</em>: Parsed database of transport events for Hal system. Command used:<br><em>python3 01_build_database.py -c 04_TransportTools/Hal_TIP3P.ini -o Hal_TIP3P.dat</em></p>
Supplementary data frames, AlphaFold models, Normal Mode Analysis (NMA) Data, and NMA of Corresponding NMR Ensembles in the S2RCI, MD, and S2 Datasets for "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics"
<h1><strong>Changes applied to V2</strong></h1> <p>In addition to the supplementary dataframes and AlphaFold models from each dataset in V1, V2 includes the additional data outlined below.</p> <p>The <strong>S2RCI</strong> and <strong>MD</strong> datasets include comprehensive analyses of AlphaFold2 models (both before and after truncation). These datasets feature: </p> <ul> <li><strong>AlphaFold2 Models</strong>: Both original and truncated structures. </li> <li><strong>WEBnma Modes</strong>: `modes.txt` files generated from WEBnma analysis, available for both non-truncated and truncated AF2 models. </li> <li><strong>Root-Mean-Square-Fluctuations (RMSF)</strong>: Profiles calculated before and after truncation of AF2 models. </li> <li><strong>NMR Data: Normal Mode Analysis (NMA)</strong>: Performed on corresponding NMR ensembles (see below). </li> </ul> <p> </p> <p>The <strong>NMR Data</strong> of NMA in these datasets includes: </p> <ul> <li>NMR ensembles </li> <li>Individual NMR models extracted from each ensemble </li> <li>STRIDE secondary structure calculations per-individual NMR models</li> <li>RMSF profiles per-individual NMR models</li> </ul> <p>For detailed information, please refer to the `Readme.txt` file within each corresponding folder. </p> <p>The <strong>S2 dataset</strong> includes all the features listed above, except for the NMR analysis.</p>
MD Simulation of AtALMT9 TMD Using Martini3 and charmm36 Force Field
<p>This dataset contains the MD simulation data associated with the article:</p> <p>"Structural basis for malate-driven, pore lipid-regulated activation of the Arabidopsis vacuolar anion channel ALMT9"</p> <p><em>(Not published yet)</em></p> <p> </p> <p>Folder</p> <p>AA : All-atom simulation files.</p> <p>CG : Coarse-grained simulation files.</p> <p>toppar : parameter files.</p> <p> </p> <p>File Description</p> <p>conf.pdb : Initial structure of the simulation.</p> <p>all.fit.10ns.now.zen.xtc : trajectory file without water. </p> <p>now.pdb : coordinate file of corresponding trajectory.</p> <p>topol.top : GROMACS topology file.</p> <p> </p> <p> </p>
Ion permeation through a narrow cavity constriction in KCNQ1 channels, scours files of MD simulations and analysis of electrophysiological experiments.
<p>Source files of Molecular Dynamic (MD) simulations and analysis files of electrophysiology data in Igor pro software format. KCNQ1 channel pore region (G245-K354) was embedded in a lipid bilayer consisting of phosphatidylcholine phospholipids (POPC) and ion permission mechanism was analized by MD simulations using the computational electrophysiology (compEL) method implemented in GROMACS v2022.4. Ion imbalance between compartments of double-membrane system created a membrane potential of abour 300 mV which drives ion movment.</p>
MD simulations on MnmE
<p>Unbiased and biased MD simulations of MnmE that were generated in the context of the research presented in the following publication:</p> <blockquote> <p>INSERT PUBLICATION</p> </blockquote>
A Subset of HTP-MD dataset used for training different generative models
Open the record for dataset details and reuse information.
6MSM_CFTR_MD_EQUILIBRATED_MISSING_R_DOMAIN_FRAGMENT_MODELLED
<p>A protein structure based on PDB ID 6MSM with the unidentified fragment filled in based on results from molecular dynamics investigations and comparisons with alphafold.</p> <p>In addition to the molecular dynamics workflow used to simulate it.</p>
CH3CH2OCH3 conformer molecule 200 ps MD trajectory with energies and forces
<p>Forces and Energies for 200 ps MD trajectory of OCH2C2H6 molecule by xTB/GFN-2, NVE ensemble</p> <p>--------------------------------------------------</p> <p>MD params:</p> <p>temp = 300.0 K / 500.0 K<br> time = 200.0 ps<br> dump time = 10.0 fs<br> step = 0.4 fs</p> <p> </p> <p>SOAP params:</p> <p>species=["H", "C", "O"],</p> <p>periodic=False,</p> <p>rcut=5.0,</p> <p>sigma=0.5,</p> <p>nmax=5,</p> <p>lmax=5,</p> <p>average="outer" / "inner",</p> <p>crossover=True,</p> <p>dtype="float64",</p> <p>------------------------------------------------</p> <p>SOAP invariants were calculated with DScribe library (https://pypi.org/project/dscribe/1.2.1/)</p> <p> </p> <p>Energies and forces are in eV and eV/Angstrom</p> <p>Filenames are intended to be self-explanatory</p> <p>Dataset is intended to be used for machine learning algorithms tests.</p>
MD simulation of the crystal unit cell of the second PDZ domain of LNX2 protein
<p>This molecular dynamics simulation data is provided as part of the manuscript "<strong>LAWS: Local Alignment for Water Sites - a method to analyze crystallographic water in simulations</strong>". The code for the algorithm is provided: <a href="https://github.com/rauscher-lab/LAWS">on github</a><br> <br> The system contains one unit cell of the crystal (PDB ID: 5E11) with 4 symmetrically related protein chains. The total simulation length is 1 microsecond. </p> <p><strong>Force field + water model</strong>: CHARMM36m + CHARMM-modified TIP3P<br> <strong>Number of atoms</strong>: 9650<br> <strong>Number of time frames:</strong> 100,000 with 10-ps stride<br> <em>The details of the simulations are provided in the manuscript.</em></p>
Fig.ç3.D isasterina akajimaensis sp. nov., holotype (NSMT E-6758). A, Anal pore and a patch; B, madreporite; C, proximal part of arm, abactinal view; D, oral plate pair and interradial uncalci ed area, some oral spines have been lost (see also Fig. 6 for oral plate pair and interradial uncalci ed area at another interradius); E, proximal part of ambulacral furrow (oral plates seen at the lower-le corner are drawn in Fig. 6); F, inferomarginal spinelets, abactinal view. Abbreviations: als, actinolateral spine; apo, anal pore; fs, furrow spine; imp, inferomarginal plate; ims, inferomarginal spine; ir, interradial; iua, interradial uncalci ed area; md, madreporite; op, oral plate; os, oral spine; r, radial; rp, rigid patch; sas, subambulacral spine. in A New Asterinid Sea Star, Disasterina akajimaensis (Echinodermata: Asteroidea) from the Ryukyu Islands, Japan, with Notes on the Genus Disasterina
Fig.ç3.D isasterina akajimaensis sp. nov., holotype (NSMT E-6758). A, Anal pore and a patch; B, madreporite; C, proximal part of arm, abactinal view; D, oral plate pair and interradial uncalci ed area, some oral spines have been lost (see also Fig. 6 for oral plate pair and interradial uncalci ed area at another interradius); E, proximal part of ambulacral furrow (oral plates seen at the lower-le corner are drawn in Fig. 6); F, inferomarginal spinelets, abactinal view. Abbreviations: als, actinolateral spine; apo, anal pore; fs, furrow spine; imp, inferomarginal plate; ims, inferomarginal spine; ir, interradial; iua, interradial uncalci ed area; md, madreporite; op, oral plate; os, oral spine; r, radial; rp, rigid patch; sas, subambulacral spine.
MD setup data for ansamer amanitin derivatives and precursors for atroposelective synthesis
<p>Setup files to reproduce the MD simulations for the amanitin derivatives <strong>4a </strong>and <strong>4b</strong> as well as the precursors <strong>3b</strong> and <strong>3c. </strong>The MD simulations were part of the study:</p> <p>G. Yao, S. Kosol, M. T. Wenz, E. Irran, B. G. Keller, O. Trapp, R. D. Süssmuth, <em>ChemRxiv</em> 2022, DOI 10.26434/chemrxiv-2022-ll8lq.</p> <p>For further instructions on the files, please refer to '0_README'.</p>
Text-fig. 9. Paramblypterus cf. rohani. Scale bars 5 mm. a, b: drawing and photograph of the skull in lateral view, locality Otovice "Stěnava", DP 4529; c, d: photograph and drawing of the skull in lateral view, locality Otovice "Chmelnice", P 64673; e: bones of the skull roof in dorsal view, locality Otovice "Chmelnice", P 64656; f: bones of the skull roof in dorsal view, locality Otovice "Chmelnice", P 30945; g, h: drawing and photograph (whitened) of the bones of the skull roof in dorsal view, locality Otovice "Chmelnice", P 64658. Abbreviations: ap – anterior pit line, Cl – cleithrum, Cor – coronoid, Dhy – dermohyal, Dpt – dermopterotic, Dsph – dermosphenotic, Extl – extrascapular lateral, Extm – extrascapular medial, Fr – frontal, Gul – lateral gular, Gum – medial gular, ioc – infraorbital canal, Ios – infraorbital superior, Ju – jugal, mc – mandibular canal, Md – mandible, Mx – maxila, mp – medial pit line, Na – nasal, Op – operculum, Pa – parietal, Pop – preoperculum, pp – posterior pit line, Psp – postspiracular, Pt – posttemporal, Ptr – postrostral, Qu – quadratum, Rbr – branchiostegaly rays, Sbo – suborbital, soc – supraorbital canal, Sop – suboperculum, Spi – spiracular. in Actinopterygians Of The Broumov Formation (Permian) In The Czech Part Of The Intra-Sudetic Basin (The Czech Republic)
Text-fig. 9. Paramblypterus cf. rohani. Scale bars 5 mm. a, b: drawing and photograph of the skull in lateral view, locality Otovice "Stěnava", DP 4529; c, d: photograph and drawing of the skull in lateral view, locality Otovice "Chmelnice", P 64673; e: bones of the skull roof in dorsal view, locality Otovice "Chmelnice", P 64656; f: bones of the skull roof in dorsal view, locality Otovice "Chmelnice", P 30945; g, h: drawing and photograph (whitened) of the bones of the skull roof in dorsal view, locality Otovice "Chmelnice", P 64658. Abbreviations: ap – anterior pit line, Cl – cleithrum, Cor – coronoid, Dhy – dermohyal, Dpt – dermopterotic, Dsph – dermosphenotic, Extl – extrascapular lateral, Extm – extrascapular medial, Fr – frontal, Gul – lateral gular, Gum – medial gular, ioc – infraorbital canal, Ios – infraorbital superior, Ju – jugal, mc – mandibular canal, Md – mandible, Mx – maxila, mp – medial pit line, Na – nasal, Op – operculum, Pa – parietal, Pop – preoperculum, pp – posterior pit line, Psp – postspiracular, Pt – posttemporal, Ptr – postrostral, Qu – quadratum, Rbr – branchiostegaly rays, Sbo – suborbital, soc – supraorbital canal, Sop – suboperculum, Spi – spiracular.
Text-fig. 4. Paramblypterus vratislaviensis (AGASSIZ, 1833). Locality Olivětín. Scale bars 5 mm. a, b: photograph and drawing of the skull. Photograph immersed in ethyl alcohol, NM-M 2461; c, d: photograph and drawing of the skull. Photograph immersed in ethyl alcohol, NM-M 900. Abbreviations: Dhy – dermohyal, Dpt – dermopterotic, Dsph – dermosphenotic, Ext – extrascapular, Fr – frontal, Ios – infraorbital superior, Ju – jugal, La – lacrymal, Md – mandible, Mx – maxilla, Na – nasal, Na+So – nasal coalesces with the supraorbital anterior, Op – operculum, Otol – otolith, Pa – parietal, Pop – preoperculum, Pt – posttemporal, Ptr – postrostral, Scl – supracleithrum, soc – supraorbital canal, sr – sclerotic ring. in Actinopterygians Of The Broumov Formation (Permian) In The Czech Part Of The Intra-Sudetic Basin (The Czech Republic)
Text-fig. 4. Paramblypterus vratislaviensis (AGASSIZ, 1833). Locality Olivětín. Scale bars 5 mm. a, b: photograph and drawing of the skull. Photograph immersed in ethyl alcohol, NM-M 2461; c, d: photograph and drawing of the skull. Photograph immersed in ethyl alcohol, NM-M 900. Abbreviations: Dhy – dermohyal, Dpt – dermopterotic, Dsph – dermosphenotic, Ext – extrascapular, Fr – frontal, Ios – infraorbital superior, Ju – jugal, La – lacrymal, Md – mandible, Mx – maxilla, Na – nasal, Na+So – nasal coalesces with the supraorbital anterior, Op – operculum, Otol – otolith, Pa – parietal, Pop – preoperculum, Pt – posttemporal, Ptr – postrostral, Scl – supracleithrum, soc – supraorbital canal, sr – sclerotic ring.
Text-fig. 6. Paramblypterus vratislaviensis (AGASSIZ, 1833). a: restoration of the body in lateral view, scale bar 10 mm; b: restoration of the skull in lateral view (bones that are not clearly retained on the skull are marked with dashed lines), scale bar 10 mm; c: restoration of the skull in dorsal view, scale bar 10 mm. Abbreviations: Cl – cleithrum, Dhy – dermohyal, Dpt – dermopterotic, Dsph – dermosphenotic, Ext – extrascapular, Fr – frontal, Gul – lateral gular, Ios – infraorbital superior, Ju – jugal, La – lacrymal, Md – mandible, Mx – maxilla, Na – nasal, Op – operculum, Orb – orbit, Pa – parietal, Pmx – premaxilla, Pop – preoperculum, Pt – posttemporal, Ptr – postrostral, Rbr- branchiostegal rays, Scl – supracleithrum, Soant – supraorbital anterior, Sop – suboperculum, Spi – spiracular, sr – sclerotic ring. in Actinopterygians Of The Broumov Formation (Permian) In The Czech Part Of The Intra-Sudetic Basin (The Czech Republic)
Text-fig. 6. Paramblypterus vratislaviensis (AGASSIZ, 1833). a: restoration of the body in lateral view, scale bar 10 mm; b: restoration of the skull in lateral view (bones that are not clearly retained on the skull are marked with dashed lines), scale bar 10 mm; c: restoration of the skull in dorsal view, scale bar 10 mm. Abbreviations: Cl – cleithrum, Dhy – dermohyal, Dpt – dermopterotic, Dsph – dermosphenotic, Ext – extrascapular, Fr – frontal, Gul – lateral gular, Ios – infraorbital superior, Ju – jugal, La – lacrymal, Md – mandible, Mx – maxilla, Na – nasal, Op – operculum, Orb – orbit, Pa – parietal, Pmx – premaxilla, Pop – preoperculum, Pt – posttemporal, Ptr – postrostral, Rbr- branchiostegal rays, Scl – supracleithrum, Soant – supraorbital anterior, Sop – suboperculum, Spi – spiracular, sr – sclerotic ring.
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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
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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
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