Contributors: Miguel Angel Gonzales Calle
... This dataset contains information related to the experimental miniature reproduction of a raking test of a ship bottom structure in 1:30 reduced scale using a thin walled 316L steel model made by additive manufacturing (powder bed fusion process). The dataset contains: STL geometry files of miniature structure and tensile test samples, force-displacement data of raking test from large-scale ship bottom structure test and miniature model test, some test images and video extracted from miniature test.
Contributors: Solam Lee
... AloNet Author: Solam Lee (email@example.com) AloNet is a convolutional neural network based on U-Net that can identify the hair loss and the scalp area by analying clinical photograph. This model was developed for the automated calculation of the Severity of Alopecia Tools (SALT) score in assessment of patients with alopecia areata. This repository posts the Mendeley Supplementary Materials, the program code, and the relevant data used in the paper titled "Clinically Applicable Deep Learning Framework for Measurement of the Severity of Alopecia Tool Score in Patients with Alopecia Areata". Along with the programs in the "/Program/" directory, a total of 2716 pixelwise annotations used for train the hair loss identifier (mask) and the hair loss identifier (target) could be find in the "/Data/" directory. However, please note that the clinical photograph of the patients could not be made publicly available because of strict privacy regulation. Before using AloNet program with your dataset, you should convert your dataset into numpy files. One clinical photograph (saved in .jpg with RGB format) need each annotation for the scalp area (saved in .gif with black&white color) and the hair loss (saved in .gif with black&white color), respectively. Please make sure that they have same image size each other, or the conversion will fail. We are now currently working on several postprocessing algorithms for AloNet to be available for general use. The Flask web application and its code will be made available publicly when the program is ready to use.
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.
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Structural Composite Supercapacitor using Carbon Nanotube Mat Electrodes with Interspersed Metallic Iron Nanoparticles: Additional Data
Contributors: Benjamin Mapleback, Tristan Simons, Youssof Shekibi, Kamran Ghorbani, Andrew Rider
... This additional data for the article, “Structural Composite Supercapacitor using Carbon Nanotube Mat Electrodes with Interspersed Metallic Iron Nanoparticles”  presents supplementary methods, microscopy, spectroscopy, electrochemical and structural data for the use of a carbon nanotube (CNT) mat interspersed with metallic iron nanoparticles as a structural supercapacitor electrode material that could be incorporated into fiber-reinforced composites. Advanced transmission electron microscopy and is presented as a full tilt series and then processed using electron tomography and presented as selected slices and models. Composite structural supercapacitor manufacturing method is detailed, and initial results presented.
Contributors: Ling-Ling Chen
... Detailed description of this data can be accessed in Yang et al. Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems.
Contributors: Pablo Ferrada
... -Folder MATLAB files contains *mat files, which is data to start the described code in the data in brief manuscript. -Folder Photographs, Flasks 1-4 contains pictures of rising bubbles in a flask. -Folder Videos, Flasks 1-4 contains videos of the rising bubbles in a flask.
Contributors: Massimo Salvi
... This repository contains the FAST algorithm graphical user interface and some sample image used in the following work: - Salvi M., Cerrato V., Buffo A., and Molinari F., "Automated Segmentation of Brain Cells for Clonal Analyses in Fluorescence Microscopy Images", J Neurosci Methods 2019 (DOI: 10.1016/j.jneumeth.2019.108348) ABSTRACT The understanding of how cell diversity within and across distinct brain regions is ontogenetically achieved is a pivotal topic in neuroscience. Clonal analyses based on multicolor cell labeling represent a powerful tool to tackle this issue and disclose lineage relationships, but produce enormous sets of fluorescence images, leading to time consuming analyses that may be biased by the operator’s subjectivity. Thus, time-efficient automated software are needed to analyze images easily, accurately and without subjective bias. In this paper, we present a fully automated method, named FAST (‘Fluorescent cell Analysis Segmentation Tool’), for the segmentation of neural cells labeled by multicolor combinations of fluorophores and for their classification into clones. The proposed method was tested on 77 high-magnification fluorescence images of adult mouse cerebellar tissues acquired using a confocal microscope. Automatic results were compared with manual annotations and two open-source software designed for cell detection in microscopic imaging. The algorithm showed very good performance in the cellular detection and in the assignment of the clonal identity. To the best of our knowledge, FAST is the first fully automated technique for the analysis of cellular clones based on combinatorial expression of fluorescent proteins. The proposed approach allows to perform clonal analyses easily, accurately and objectively, overcoming those biases and errors that may result from manual annotations. Moreover, it can be broadly applied to the quantification and colocalization within cells of fluorescent markers, therefore representing a versatile and powerful tool for automated quantitative analyses in fluorescence microscopy.
Improve the interfacial adhesion, corrosion resistance and combustion properties of aluminum powder by modification of nickel and dopamine
Contributors: Li Liang, Xiaode Guo, Xin Liao, Zhipeng Chang
... To improve the interface incompatibility, poor corrosion resistance, and limited combustion efficiency of aluminum powder for propellant applications. The surface of the naked aluminum was coated with a layer of dense nickel of about 100 nm by replacement method. A polydopamine film was then deposited by self-polymerization. The double-layer structure and chemical composition were investigated. The polydopamine content of composite particles was 2.3% by thermal analysis. And its heat release around 1050 C reached 4137 J g-1, which was much higher than that of aluminum of 1644 J g-1. The surface energies was used to calculate the theoretical adhesion work of aluminum and composite particles to propellant binder. The adhesion work after modification was increased from 62.33 mN m-1 to 74.89 mN m-1. No matter in the weak acid/alkaline or neutral environment, the composite particles exhibited excellent stability at 50 C. In addition, the combustion test revealed that the composite particles had higher combustion efficiency, smaller condensed phase product size, and stronger ignition ability. All the conclusions indicate after modification by nickel and dopamine, the comprehensive performance of aluminum is improved, and it may be used as an energy component in propellants or other energetic fields.
Contributors: UnaElsLive Natra
... MD-2831 Update Java version in the Docker containers
Supplementary Information for: "Simulation of convective moistening of extratropical lower stratosphere using a numerical weather prediction model"
Contributors: Zhipeng Qu
... Video SI.1: the animation of 1 km simulation on a chosen cross-section during the convection event from 18:40 to 20:40 UTC, 25 Aug 2013. 1st panel: temperature (colour) and isentropic lines (thin white lines); 2nd panel: ice water content in logarithm scale; 3rd panel: water vapor content in ppmv (colour saturated at 20 ppmv); 4th panel: vertical wind speed (m s-1). Video SI.2: water vapor content in ppmv at the altitude of 16.5 km from 18:00 to 23:00 UTC (5 hours) within the evaluation Domain A. Figure SI.1: the transported water vapor in the simulation domain of 0.25 km (green box in Fig. 1) from 1800 to 19:00 UTC 25 Aug. The vertical advection of 10 km simulation is decomposed into two parts: grid scale advection (light blue bar) and sub-grid scale advection from KFC parameterization (darker blue bar). For the results presented in Fig. SI.1, the evaluation is performed for the simulated domain of 0.25 km grid-spacing (green box in Fig. 1) for the first hour of the evaluation time window (from 18:00 to 19:00 UTC 25 Aug for the three high resolution models, from 21:30 to 22:30 UTC 25 Aug for 10 km simulation). The tropopause levels are defined using the mean laps rate <2˚C km-1. The use of limited time window is due to the fact that the storm moves quickly to the outside of the simulation domain. Figure SI.1 shows the mass transport budget for the 4 simulations with different horizontal resolutions, we found that the direct transport of water vapor of 0.25 km simulation is higher than all the other simulations. Although the contributions from ice sublimation and turbulent mixing of 0.25 km simulation are the lowest. The contribution from ice sublimation is negative which suggests that vapor deposition rate is very high in the convection updrafts and exceeds that of ice sublimation. Although the results presented here should be viewed with caution due to the short evaluation period (1 hour), it corroborates the finding that higher resolution model tends to have a stronger direct vertical transport of water vapor and a weaker contribution from the ice sublimation.