Contributors: marco mendoza, Maria B. Goncalves, Jonathan Corcoran
... Differential gene expression analysis (RNA-sequencing) assessed in the SC from L5-SNL rats and non-injured rats, treated with vehicle or C286. Raw counts per gene (Raw counts.zip file) were normalized (quantile normalization; Normaliez counts.zip), then used for a differential gene expression analysis relative to the sample non-injured + vehicle (Diff_expression_DESeq2.zip). In addition, we have included herein a supplementary Table containing Gene Ontology (GO) terms per gene co-expression paths issued from the differential expression analysis. Notice that GO terms are described by their confidence of enrichment, expressend on "-10*log10(p-value).
Contributors: Willem Roux, Imtiaz Gandikota, Guilian Yi
... These are the computer models used for structural topology optimization from the paper "A spatial kernel approach for topology optimization" by Roux, Yi, and Gandikota.
A Mathematical Model for the Berth Allocation Problem with Variable Service Time and Continuous Time Horizon
Contributors: Bruno Luís Hönigmann Cereser
... Tests, Results and Codes of the paper "A Mathematical Model for the Berth Allocation Problem with Variable Service Time and Continuous Time Horizon".
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A Mathematical Model for the Berth Allocation Problem with Machine Patterns and Continuous Time Horizon
Contributors: Bruno Luís Hönigmann Cereser
... Intances, codes and results.
A new method for analyzing sustainability performance of global supply chains and its application to material resources
Contributors: Livia Cabernard, Stephan Pfister, Stefanie Hellweg
... VERSION 2 Compared to version 1, version 2 runs without matlab. The file “Instructions.pdf” attached below explains how to install and use this application. The file “Explanation_method_examples.pptx” attached below illustrates the principle of the method and how to use the application with several examples. OVERALL DESCRIPTION (same as for version 1): We share here the data compiled to calculate the results presented in the study «A new method for analyzing sustainability performance of global supply chains and its application to material resources». In order to allow for the compilation of all results of interest, we provide an application. This application is based on the multi-regional-input output database EXIOBASE3 (version 3.4) and data to assess the potential environmental impacts of emissions and resource use. While the data for assessing the environmental impacts is provided here, the user must download the Exiobase data from the Exiobase website (due to copyright issues). The provided application allows to assess the cumulated upstream impacts of any sector or region on the globe without double-counting and to track these impacts upstream and downstream the global value chain. The application covers a broad set of environmental and socio-economic indicators and the timespan from 1995 to 2011. The methodology of this application is comprehensively explained in the study: «A new method for analyzing sustainability performance of global supply chains and its application to material resources» (e.g Section 2.1 gives a broad overview of the principle of the method). Link to the study: https://doi.org/10.1016/j.scitotenv.2019.04.434
Contributors: Denis Mikryukov
... Here we store the coefficients of the planetary disturbing function in computer-readable form. These were obtained by Maxima computer algebra system. The method is described by Laskar and Robutel (CMDA, 62, 193-217, 1995). We should note that our coefficients of secular Hamiltonian up to degree 4 coincide with those presented by Laskar and Robutel (see Section 7, CMDA, 62, 193-217, 1995). Therefore we hope that our expansions are error free. We plan to provide more thorough and complete comments on all of these data in the near future.
Data/Software for "Presynaptic Mitochondria Volumes and Complexity of Subsynaptic Distribution Increase During Development at 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 Volumes and Complexity of Subsynaptic Distribution Increase During Development at a High-fidelity Synapse" currently under review. 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-APEX, at the mouse calyx of Held. We developed protocols to detect labeled mitochondria for use serial block face SEM (SBF-SEM) 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 developmentally increase to support high firing rates but have limited contribution to morphological-functional diversity at the calyx. Data are sorted by the figures they appear in. Media (movies and 3D models) and custom-written software are located in separate folders.
Contributors: Marsel Rabaev, Handy Pratama, Ka Ching Chan
... This data set was generated using Arena Simulation
Contributors: Damian Matuszewski, Carolina Wählby, Jordi Carreras-Puigvert, Ida-Maria Sintorn
... PopulationProfiler – is light-weight cross-platform open-source tool for data analysis in image-based screening experiments. The main idea is to reduce per-cell measurements to per-well distributions, each represented by a histogram. These can be optionally further reduced to sub-type counts based on gating (setting bin ranges) of known control distributions and local adjustments to histogram shape. Such analysis is necessary in a wide variety of applications, e.g. DNA damage assessment using foci intensity distributions, assessment of cell type specific markers, and cell cycle analysis. The software imports measurements from a simple text file, visualizes population distributions in a compact and comprehensive way, and can create gates for subpopulation classes based on control samples. The simple graphical user interface (GUI) allows selection of multiple csv files with image-based screening data. Each file is treated as a separate plate (i.e. independent experiment) with rows representing cell measurements. One measurement is processed at a time and cells are grouped based on well labels. The measurement is selected by the user from a drop-down list created from the csv file header (first row). The GUI also allows selection of control wells based on the treatment labels. If such labels are not available, the user can select control wells manually. The corresponding data is pooled and stored as a separate record in the output csv file. PopulationProfiler thereafter calculates and displays the distribution of the selected measurement as a histogram for each well. A vector representation of each well’s histogram is saved in the output file, and can be used as input for e.g., cluster analysis, elsewhere. The cell count for each well is also saved as a measure of statistical relevance of population effects. Cite this software as: Matuszewski, D.J., Wählby, C., Puigvert, J.C., Sintorn, I.-M. (2016) PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data. PloS one, 11(3), e0151554. The Python source code, sample data and user manual are available free of charge.
Data for: An approach to fabricate high performance cooler with nearly ideal emissive spectrum for above ambient radiative cooling
Contributors: YuXiang Zheng
... These are the research data files of "An approach to fabricate high performance cooler with nearly ideal emissive spectrum for above ambient radiative cooling".