Data/Software for "Presynaptic Mitochondria Volume and Abundance Increase During Development of a High-Fidelity Synapse"
Contributors: Connon I. Thomas, Christian Keine, Satoko Okayama, Rachel Satterfield, Morgan Musgrove, Debbie Guerrero-Given, Naomi Kamasawa, Samuel M. Young, Jr.
... Contains data and software from the publication: "Presynaptic Mitochondria Volume and Abundance Increase During Development of a High-Fidelity Synapse" published in the The Journal of Neuroscience (https://doi.org/10.1523/JNEUROSCI.0363-19.2019). The preprint to this data set has been published on bioRxiv (https://doi.org/10.1101/689653). In this study, we created a helper-dependent adenoviral vector (HdAd) to co-express cytoplasmic EGFP and a genetically encoded peroxidase marker (mito-APEX2) at the calyx of Held, an excellent model for deciphering regulatory mechanisms of presynaptic function. ABSTRACT: The calyx of Held, a large glutamatergic presynaptic terminal in the auditory brainstem undergoes developmental changes to support the high action-potential firing rates required for auditory information encoding. In addition, calyx terminals are morphologically diverse which impacts vesicle release properties and synaptic plasticity. Mitochondria influence synaptic plasticity through calcium buffering and are crucial for providing the energy required for synaptic transmission. Therefore, it has been postulated that mitochondrial levels increase during development and contribute to the morphological-functional diversity in the mature calyx. However, the developmental profile of mitochondrial volumes and subsynaptic distribution at the calyx of Held remains unclear. To provide insight on this, we developed a helper-dependent adenoviral vector (HdAd) that expresses the genetically encoded peroxidase marker for mitochondria, mito-APEX2, at the mouse calyx of Held. We developed protocols to detect labeled mitochondria for use with serial block face scanning electron microscopy to carry out semi-automated segmentation of mitochondria, high-throughput whole terminal reconstruction and presynaptic ultrastructure in mice of either sex. Subsequently, we measured mitochondrial volumes and subsynaptic distributions at the immature postnatal day 7 (P7) and the mature (P21) calyx. We found an increase of mitochondria volumes in terminals and axons from P7 to P21 but did not observe differences between stalk and swelling subcompartments in the mature calyx. Based on these findings, we propose that mitochondrial volumes and synaptic localization developmentally increase to support high firing rates required in the initial stages of auditory information processing. Data are sorted by the figures they appear in. Media (movies and 3D models) and custom-written software are located in separate folders.
Contributors: UnaElsLive Natra
... MD-2831 Update Java version in the Docker containers
DATA: Accommodation of manganese into hydroxyapatite and segregation pathway involved in the formation of Mn3O4 nanoparticles
Contributors: Euler Araujo dos Santos
... Raw data and Rietveld refined data used in the article.
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Contributors: Eusebio de la Fuente
... This dataset contain the code, test videos and the results of the developed algorithm. The detection is based on texture analysis using the LBP technique.
Contributors: UnaElsLive Natra, mdgmatest5 live
... RDM - File Type Support 21May2019 ElsCustomer Apart from .u3d all files preview [ .obj / .ply / .vtk / .stl / .ent / .brk / .pdb / .pse / .mol / .mol2 / .cif / .u3d / .dcm / .nii] - .pse is not supported
Contributors: Carlos Palacio
... Raw data for the internal Project 2016210 "Preparation and characterization of magnetic nanoparticles based in ferrites"--> UAN-UdeA.
Contributors: Cian Desmond, Florent Thiebaut, Jimmy Murphy
... An aluminium cross-section approximately 1 m in length was held between 2 flat plates connected to a movable carriage in a wave basin. Under still water conditions, the cross section was moved through the wave basin. Data were collected from an array of load cells in 6 DoF. This process was repeated for four cross sections, each at 4 angles of attack and 7 velocities. These data can be used for all research scientists and engineers working in the fields of fluid mechanics and hydraulics. The data may be used specifically for the validation of numerical models
Contributors: Prashant K. Jha, Robert Lipton
... We share the data used in publishing the article "Numerical convergence of finite difference approximations for state based peridynamic fracture models", see https://doi.org/10.1016/j.cma.2019.03.024. The data set comprises of raw data produced by computational code, post-processed files, and python script files. We consider finite difference approximation of a nonlinear state-based peridynamic model. We run simulation for two problems. In the first problem, we have a square domain with verticle pre-crack originating from the middle of the bottom edge. We apply a constant velocity boundary condition along the horizontal axis on the bottom layer. In response to the boundary conditions, the crack propagates vertically. The data correspond to three different horizons, 2mm, 4mm, and 8mm. For each horizon, we have three results, each corresponding to mesh size horizon/2, horizon/4, and horizon/8. From the approximate displacement fields, we compute the rate of convergence with respect to mesh size, for each fixed horizon. These are post-processed data and can be found in "postprocessing" folder of Example 1. In the second problem, we consider a rectangle domain which is supported at two regions (left and right) near the bottom edge. On the portion of the top edge, we apply a monotonically increasing in time force in the downward direction. We run simulation when the sample has just one vertical pre-crack originating from the middle of the bottom edge and when the sample has two vertical pre-cracks symmetrically located and originating from the bottom edge. We plot the damage at multiple times and show that the crack propagates upwards in response to applied load. All computations are carried out using an in-house developed code. In this data set, we have not shared the computational code. However, we plan on making the code public in the future. If you are interested in our code and if you have some collaborative ideas please feel free to get in touch.
Contributors: Guillermo Reyes
... Characterization of nanocellulose films welded using ionic liquids
Contributors: Robert LeSuer
... Software and hardware files for creating the syringe pump and millifluidic devices described in https://doi.org/10.1016/j.ohx.2018.e00038.