Contributors: Mei-hui Liu
... This set of supplementary data is related to the article “Blended Cross-tier Teacher Development: Designing Online Video-based Pragmatic Assessment.” It contains 1) survey data, 2) data collection methods, and 3) samples of edited video clips retrieved from Youtube links and deigned discourse completion tests. The participants’ interview content and reflection entries cannot be exposed to the public under the ethics guidelines of National Cheng Kung University Human Research Ethics Committee in Taiwan.
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
Top results from Data Repository sources. Show only results like these.
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: 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
Encoding growth factor identity in the temporal dynamics of FoxO3 under the combinatorial control of ERK and AKT Kinases
Contributors: somponnat sampattavanich, Bernhard Steiert, Bernhard Kramer, Benjamin Gyori, john albeck, Peter Sorger
... Sampattavanich et al., Cell Systems (2018) This data repository provides raw datasets for accompanying the paper, "Encoding growth factor identity in the temporal dynamics of FoxO3 under combinatorial regulation by ERK and Akt" by Sampattavanich et al., Cell Systems (2018) Synopsis: Forkhead box O3 transcription factor (FoxO3) functions as an integrative node for diverse upstream signaling networks, and has been implicated in a number of biological processes including cycle arrest, apoptosis, oxidative stress, cell migration and cell metabolism. Regulators of FoxO3, including phosphorylation, energy stress, genotoxic stress, and cytokines, control its abundance, subcellular localization and DNA-binding capacity. In this paper we study how the identities and concentrations of growth factors are encoded in the dynamics of FoxO3 activation. Transcription factors like FoxO3 often switch between on and off states repeatedly over the course of a 12-24 hours period. Immunoblotting and similar methods can obscure this switching behavior due to asynchronicity between cells. In contrast, our use of time-lapse microscopy of fluorescent reporter proteins reveals that FoxO3 exhibits complex low wavelength and pulsatile translocation dynamics responsive to combinatorial control by ERK and Akt with the potential to encode the identities and concentrations of multiple extracellular growth factors. Dataset Content: This dataset includes raw datasets either in .MAT, or .CSV for regenerating all figures in the publication. These folders should be placed inside the /rawdata folder in the git repository folder so that the reader can generate these figures on their own. /parentalVSreporter - This dataset is used to regenerate fig.1B, S1B and S1C. /Workspace - This dataset is important for all fPCA and pulse score analysis in Fig.1-6 /dualsensors - This dataset is used to regenerate Fig.6B /western - This dataset is used to regenerate Fig.1C and S1G /fixedcell - This dataset is used to regenerate Fig.7 /Time-lapse video - This folder gives video files of the main dataset for Fig.1-2, varying different growth factors at various dosing, with different drug pre-treatment. To learn more about this data, please also visit the accompanying HMS LINCS website shown below.
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.