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Figure 2 in Histology of ganoid scales from the early Late Cretaceous of the Kem Kem beds , SE Morocco : systematic and evolutionary implications
Figure 2. - Scales of Bawitius (SEM). Upper surface. A: A ridged scale. The circles and the arrowheads localize respectively the areas of the observation of ganoine microreliefs and vascular apertures; B: Detail of the posterior extremity of a ganoine ridge. The contact between the ganoine and the dentine looks regular. Vascular apertures on the ganoine surface are visible (arrowheads); C: Detail of a ganoine ridge showing its contact with dentine (black arrowheads). The white arrowheads and arrows point to holes indicating vascular canal apertures respectively at the surface of ganoine and at the surface of dentine; D: Detail of ganoine near the dentine layer showing some microtubercles on the right and elongate hollows on the left; E: Detail of ganoine at the surface of a ridge showing the thin elongate hollows. (d = dentine; g = ganoine). Scale bars: A = 500 µm; B = 25 µm; C = 100 µm; D, E = 10 µm.
Figure 1 in Histology of ganoid scales from the early Late Cretaceous of the Kem Kem beds , SE Morocco : systematic and evolutionary implications
Figure 1. - Isolated scales of the Kem Kem beds. A, C-H: Scales studied by Tabaste (1963). A: Adrianaichthys sp. (fig. 9, Pl X); B: Adrianaichthys sp., scale sampled by one of us D.D.; C-E: Obaichthys sp. (figs 6, 7, 9, Pl XI); F,H: Bawitius sp. (figs 4, 5, Pl XI); G, I: Palaeonisciformes (figs 1, 2, Pl XI). Scale bars: A, B, F-I = 1 cm; C-E = 5 mm.
Fig. 4. Clidastes propython Cope, 1869 in The first record of the mosasaur Clidastes from Europe and its palaeogeographical implications
Fig. 4. Clidastes propython Cope, 1869, marginal tooth−crowns, Belemnellocamax mammillatus zone, Åsen, Kristianstad Basin, southern Sweden; all × 3.5. A. LO 8231t, a tooth−crown from a small juvenile; lingual (A1), anterior (A2), posterior (A3), and buccal (A4) views. B. LO 8232t, a crown from the mid−portion of the jaw; buccal (B1), occlusal (B2), and lingual (B3) views. C. RM PZ R1799, a large tooth−crown from the anterior part of the mid−portion of the jaw; lingual (C1), occlusal (C2), and buccal (C3) views. D. RM PZ R1798, a large crown from the mid−portion of the jaw; buccal (D1), occlusal (D2), and lingual (D3) views. E. RM PZ R1801, a crown from the posterior portion of the jaw; buccal (E1), occlusal (E2), and lingual (E3) views. F. RM PZ R1800, a juvenile crown from the anterior part of the mid−portion of the jaw; lingual (F1, stereo pair) and buccal (F2, stereo pair) views. G. RM PZ R1803, a crown from the posterior portion of the jaw; buccal (G1),occlusal (G2), and lingual (G3) views.
Fig. 5. Clidastes propython Cope, 1869 in The first record of the mosasaur Clidastes from Europe and its palaeogeographical implications
Fig. 5. Clidastes propython Cope, 1869. Pterygoid tooth−crowns, Belemnellocamax mammillatus zone, Åsen, Kristianstad Basin, southern Sweden; all × 3.5. A. RM PZ R1804, buccal (A1), posterior (A2), anterior (A3), and lingual (A4) views. B. RM PZ R1805, buccal (B1, stereo pair) and lingual (B2, stereo pair) views.
Fig. 2. Clidastes propython Cope, 1869 in The first record of the mosasaur Clidastes from Europe and its palaeogeographical implications
Fig. 2. Clidastes propython Cope, 1869, anteriorly situated marginal toothcrowns of juvenile individuals, Belemnellocamax mammillatus zone, Åsen, Kristianstad Basin, southern Sweden; All × 3.5. A. RM PZ R1794, first premaxillary or first dentary tooth−crown; buccal (A1, stereo pair), posterior (A2), and lingual (A3) views. Note the absence of a posterior cutting edge. B. RM PZ R1795, second premaxillary or second dentary tooth−crown; lingual (B1), anterior (B2), and buccal (B3) views. C. RM PZ R1796, first premaxillary or first dentary tooth−crown; lingual (C1), occlusal (C2), and buccal (C3) views.
Fig. 6. Clidastes propython Cope, 1869. A in The first record of the mosasaur Clidastes from Europe and its palaeogeographical implications
Fig. 6. Clidastes propython Cope, 1869. A. RM PZ R1778, the third? cervical vertebra from a juvenile individual, Belemnellocamax mammillatus zone, Åsen, Kristianstad Basin, southern Sweden, × 2.0; ventral (A1, stereo pair), posterior (A2, stereo pair), and lateral (A3, stereo pair) views. B. Clidastes propython Cope, 1869, the third? cervical vertebra of YPM 1123, late Santonian part of the Smoky Hill Chalk Member of the Niobrara Formation in western Kansas, USA, × 2.0; ventral (B1), posterior (B2), and lateral (B3) views. C. RM PZ R1752, two fragments (R1752a, C1, C3, C4 and R1752b, C2) of an axis vertebra from a very large individual, Belemnellocamax mammillatus zone, Axeltorp, Kristianstad Basin, southern Sweden, × 1.0; lateral (C1), anterior (C2), posterior (C3), and dorsal (C4) views.
Therapeutic Potential of the Laminin-1-Derived Peptide C16 in Interactions with αvβ3 and α5β1 Integrins: In Silico Analysis and Implications for Angiogenesis, Cancer, and Tissue Regeneration
<p>Molecular Dynamics<br><br>Molecular Docking there has also been performed molecular dynamics simulation studies by GROMACS 2023 to study the relationship between structure and function and properties by the analysis of molecular conformation sampling (cluster analysis, dominant conformation identification), interaction analysis (hydrogen bonding network, Contact-Map, Binding free energy calculations (MM-PBSA), backbone fluctuation analysis (RMSD, RMSF), Conformational transition analysis (simple normal mode analysis, dominant conformation identification), and physicochemical property analysis (energy, volume, pressure, temperature, density monitoring) (Luzik et al., 2019; Zhang et al., 2003).</p> <p>For simulation purposes, a simulation system was set up for the protein-ligand complex with solvent using GPU-enabled GROMACS 2024.2 package (Abraham et al., 2024). The αvβ3 and α5β1 in water simulation were performed with GROMACS standard protocols also, αvβ3_S1@C16, αvβ3_S2@C16, α5β1@C16 complex, and αvβ3, αvβ3 proteins MD simulation was carried out in triplicate. All necessary topology files were generated using CHARMM-GUI (Lee et al., 2016; Park et al., 2023). <br>CHARMM-GUI was used to build the simulation system (Allouche, 2012). And provided scripts compatible with GROMACS (Lee et al., 2016), provideding TIP3P water model to solvate the system.</p> <p>The dimensions of the box were defined by ensuring at least a 10 Å distance between the protein and the box edges to avoid boundary effects. Proper neutralization of the system was achieved by adding counterions (Na+ and Cl−) based on the protein’s charge automatically calculated by CHARMM-GUI. CHARMM36 force field was chosen, which provides parameters for proteins and peptides. Before the production MD simulation, energy minimization was performed to remove any unfavorable contacts or steric clashes in the system. CHARMM-GUI The system was equilibrated in two stages. First, the system was equilibrated under an NVT ensemble (constant number of particles, volume, and temperature) with restraints applied to the heavy atoms of the protein to allow the water and ions to relax around the solute. This phase runs for 100 ps. Second, the restraints were removed, and the system was equilibrated under an NPT ensemble (constant number of particles, pressure, and temperature) for an additional 1 ns to stabilize the density of the system (Galmozzi et al., 2014; K. W. Wang et al., 2022).</p> <p>The minimization, equilibration, and production steps were performed using the GROMACS 2024.2 The steepest-descent energy minimization was used, and the maximum force was set to 100 kJ/(mol∙nm) on any atom. The solvated system was equilibrated with two steps. First, the system was equilibrated for 1 ns under a constant volume ensemble (NVT) without restraints applied. Second, the system was equilibrated for another 1 ns under a constant pressure ensemble (NPT) without any restraint. Production simulation was conducted for 100 ns under the NPT ensemble. All bonds containing hydrogen atoms were constrained using the default LINCS constraint algorithm. The coupling algorithm of Nose-Hoover was used to maintain temperature (310 K) and Parrinello-Rahman algorithm to maintain temperature pressure (1 atm, 101 325 Pa) with a constant of 1.0 ps. The electrostatic interactions were treated with the particle mesh-Ewald (PME) method. The integration time step was set to 2 fs and periodic boundary conditions were applied in all directions (Bansal et al., 2021; H. Yu et al., 2015). </p> <p>2.4.1. MMPBSA analyses <br>GROMACS modules gmx rms for root mean square deviation (RMSD), gmx rmsf for root mean square fluctuation (RMSF), gmx hbond for numbers of hydrogen-bond (Hbond), gmx gyrate for the radius of gyration (Rg), gmx sasa for solvent accessible surface area (SASA) were used to analyze each complex system. The xmgrace module was employed to generate plots and graphs to represent binding energies, interaction frequencies, and structural changes. The Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) binding free energies like van der Waals and electrostatic interactions, potential energy, polar, and non-polar solvation energies were calculated by gmx_MMPBSA a tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files (Valdés-Tresanco et al., 2021). It has employed the visualization tools VMD and PyMOL to examine the trajectory and interaction details.</p> <p>References:</p> <p>Allouche, A. (2012). Software News and Updates Gabedit — A Graphical User Interface for Computational Chemistry Softwares. Journal of Computational Chemistry, 32, 174–182. https://doi.org/10.1002/jcc.</p> <p>Galmozzi, A., Dominguez, E., Cravatt, B. F., & Saez, E. (2014). CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. Methods Enzymol., 538(1), 151–169.</p> <p>Bansal, R., Mohagaonkar, S., Sen, A., Khanam, U., & Rathi, B. (2021). In-silico study of peptide-protein interaction of antimicrobial peptides potentially targeting SARS and SARS-CoV-2 nucleocapsid protein. In Silico Pharmacology, 9(1), 1–14. https://doi.org/10.1007/s40203-021-00103-z.</p> <p>Park, S. J., Kern, N., Brown, T., Lee, J., & Im, W. (2023). CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation. Journal of Molecular Biology, 435(14), 167995. https://doi.org/10.1016/j.jmb.2023.167995.</p> <p>Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., Wei, S., Buckner, J., Jeong, J. C., Qi, Y., Jo, S., Pande, V. S., Case, D. A., Brooks, C. L., MacKerell, A. D., Klauda, J. B., & Im, W. (2016). CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation, 12(1), 405–413. https://doi.org/10.1021/acs.jctc.5b00935. </p> <p>Luzik, D. A., Rogacheva, O. N., Izmailov, S. A., Indeykina, M. I., Kononikhin, A. S., & Skrynnikov, N. R. (2019). Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2. Scientific Reports, 9(1), 1–18. https://doi.org/10.1038/s41598-019-56078-7.</p> <p>Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx\_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645.</p> <p>Wang, K. W., Lee, J., Zhang, H., Suh, D., & Im, W. (2022). CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs. Journal of Physical Chemistry B, 126(38), 7354–7364. https://doi.org/10.1021/acs.jpcb.2c05294. </p> <p>Yu, H., Wang, M. jun, Xuan, N. xia, Shang, Z. cai, & Wu, J. (2015). Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides. Journal of Zhejiang University: Science B, 16(10), 883–896. https://doi.org/10.1631/jzus.B1500106. </p> <p>Zhang, Z., Shi, Y., & Liu, H. (2003). Molecular dynamics simulations of peptides and proteins with amplified collective motions. Biophysical Journal, 84(6), 3583–3593. https://doi.org/10.1016/S0006-3495(03)75090-5. </p>
Analgesics in the Pre-hospital Setting: Implications on Hemorrhage Tolerance - Morphine
ClinicalTrials.gov study NCT04138615. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Therapeutic Termination of Pregnancy and Psychiatric Implications
ClinicalTrials.gov study NCT04080141. IPD Sharing: UNDECIDED. Countries: 0. Publications: 27.
Adherence to HIV Treatment Postpartum: The Implications of Transitions Among Women Living With HIV in South Africa
ClinicalTrials.gov study NCT04846569. IPD Sharing: YES. Countries: 1. Publications: 0.
Clinical and Economic Implications of Genetic Testing for Warfarin Management
ClinicalTrials.gov study NCT00964353. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Central Sodium Sensing: Implications for Blood Pressure Regulation
ClinicalTrials.gov study NCT05480722. IPD Sharing: YES. Countries: 1. Publications: 0.
PrOgnostic Implications of PRe-stent Pullback Pressure GradIent and Post-stent Quantitative Flow Ratio in Patients UnderGoing Percutaneous Coronary INtervention
ClinicalTrials.gov study NCT05104580. IPD Sharing: UNDECIDED. Countries: 0. Publications: 4.
Analgesics in the Pre-hospital Setting: Implications on Hemorrhage Tolerance - Sufentanil
ClinicalTrials.gov study NCT04959812. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Gut Microbiota Dysbiosis in Opioid Use Disorders: Implications for Clinical Symptoms and Relapse Rate.
ClinicalTrials.gov study NCT06231849. IPD Sharing: UNDECIDED. Countries: 0. Publications: 3.
Radiation Therapy in Uterine Cancer: Dosimetry Analysis, Clinical Implication, and Survival Analysis
ClinicalTrials.gov study NCT04251676. IPD Sharing: NO. Countries: 0. Publications: 1.
Implications of Anesthetics on Sleep Consolidation
ClinicalTrials.gov study NCT04329091. IPD Sharing: NO. Countries: 1. Publications: 0.
Effect of Seminal Fluid on the Colon Wall; Implications for HIV Transmission
ClinicalTrials.gov study NCT01053741. IPD Sharing: NO. Countries: 1. Publications: 0.
Pharmacogenetics of Alcohol: Treatment Implications
ClinicalTrials.gov study NCT00734656. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Prognostic Implication of Angiography-Derived IMR in STEMI Patients
ClinicalTrials.gov study NCT04628377. IPD Sharing: UNDECIDED. Countries: 0. Publications: 1.
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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.