Contributors: Gaetan Montero, Cécile Tannier
... Contributors: Gaëtan Montero, Cécile Tannier, Isabelle Thomas Date:2019-16-10 Description: This data set can be used to reproduce the analyses made by the authors in their paper “Morphological delineation of cities based on scaling properties of urban patterns: a comparison of three methods”. It contains 12 shapefiles that represent theoretical urban patterns and 4 shapefiles that can be used to delineate the morphological agglomeration of Brussels (Belgium). It also contains a R script to calculate the carrying capacity of a logistic percolation function. Description of each file 2_Figure_1: theoretical street network for testing the Natural Cities method 3_Figure_2: theoretical street network for the comparison of two variants of the Natural Cities method 4_Figure_3: theoretical street network to evaluate the effects of the spatial extent of the study area on the delineation of Natural Cities 5_Figure_5a: theoretical pattern for testing MorphoLim (building footprints) – dense urban core 6_Figure_5b: theoretical pattern for testing MorphoLim (building footprints) – less dense urban core 7_Figure_6: theoretical pattern (building footprints) to evaluate the effects of the geographic extent of the study area on the delineation with MorphoLim 8_Percolation_C_Calculation: R code to calculate the carrying capacity of a logistic function (Hierarchical Percolation) 9_Figure_7: theoretical street network for testing Hierarchical Percolation 10_Figure_8: theoretical polycentric street network for testing Hierarchical Percolation 11_Figure_9ac: theoretical urban pattern crossed by a large non built area (road intersections) 12_Figure_9b: theoretical urban pattern crossed by a large non built area (building footprints) 13_Figure_10ac: theoretical pattern where a built ribbon links two urban centres (roads intersections ) 14_Figure_10b: theoretical pattern where a built ribbon links two urban centres (building footprints) 15_Belgium_buildings: cadastral data of buildings (2D) for Belgium (© 2009 Administration Générale de la Documentation Patrimoniale) 16_Brabant_buildings: cadastral data of buildings (2D) for the province of Brabant (© 2009 Administration Générale de la Documentation Patrimoniale) 17_Belgium_roads: road network data come from the platform Geofabrik of OpenStreetMap (http://download.geofabrik.de, accessed 08/21/2018) for Belgium 18_Brabant_roads: Road network data come from the platform Geofabrik of OpenStreetMap (http://download.geofabrik.de, accessed 08/21/2018) for the province of Brabant.
A Novel Optimization-Based Tool to Automate Infeasible Cycle-Free Gapfilling of Genome-Scale Metabolic Models, Schroeder and Saha
Contributors: Wheaton Schroeder, Rajib Saha
... Dataset related to the paper of the same title submitted for publication in the journal iScience. The abstract is as follows.
Contributors: Danilo Silva Lisboa
... This repository contains all model components (plotted as animated maps), files and Matlab codes used to construct, train and validate the Bayesian Networks model for coral bleaching forecast in the North Atlantic Ocean. In addition, we provide geographic locations maps of reef observations used by the model, broken down by the model's ability to predict them.
Top results from Data Repository sources. Show only results like these.
Contributors: Tetsuji Okada
... DSA files of human (N to Z, by gene name) : UniProt ID is used for a protein to which no gene name is assigned.
Contributors: Carolina Granados Mendoza
... Supplementary material of: Carolina Granados Mendoza, Matthias Jost, Eric Hágsater, Susana Magallón, Cassio van den Berg, Emily Moriarty Lemmon, Alan R. Lemmon, Gerardo A. Salazar, Stefan Wanke. In review. Target nuclear and off-target plastid hybrid enrichment data inform a range of evolutionary depths in the orchid genus Epidendrum. Frontiers in Plant Science.
Reshaping commensal gut microbiota in early life with amoxicillin presents with lower blood pressure
Contributors: Saroj Chakraborty
... Pediatric hypertension is recognized as an emerging global health concern. While new guidelines are developed for facilitating clinical management, the reasons for the prevalence of hypertension in children remain unknown. Genetics and environmental factors do not fully account for the growing incidence of pediatric hypertension. Because stable bacterial flora in early life are linked with health outcomes later in life, we hypothesized that reshaping of gut microbiota in early developmental stages of life affects blood pressure (BP) of pediatric subjects. To test this hypothesis, we administered amoxicillin, the most commonly prescribed pediatric antibiotic, to alter gut microbiota of young, genetically hypertensive rats (study 1) and dams during gestation and lactation to reshape microbiota of offspring (study 2). Reshaping of microbiota, with reductions in Firmicutes/Bacteriodetes ratio observed in Amoxicillin treated young rats and in dams. Amoxicillin treated rats also had lower blood pressure compared to the untreated rats. In the young rats treated with amoxicillin, the lowering effect on blood pressure persisted even after the antibiotics were discontinued. Similarly, the offspring from the dams treated with amoxicillin also showed lower systolic blood pressure compared to the control rats. Remarkably, in all cases, a decrease in BP was associated with lowering of Veillonellaceae, which are succinate-producing bacteria. Elevated plasma succinate is reported in hypertension. Accordingly, serum succinate was measured and found lower in animals treated with amoxicillin. Our results demonstrate a direct correlation between succinate-producing gut microbiota and early development of hypertension, and indicate that reshaping gut microbiota, especially by depleting succinate-producing microbiota early in life may have long-term benefits for hypertension-prone individuals.
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".
Contributors: Solam Lee
... AloNet Author: Solam Lee (firstname.lastname@example.org) 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.
Contributors: Sergio Valadez-Godínez, Juan Humberto Sossa Azuela, Raúl Santiago-Montero
... This data contains the Supplementary material for the paper "On the Accuracy and Computational Cost of Spiking Neuron Implementation." This is divided into five folders: 1) Source code, 2) Raw data, 3) Calculations, 4) Tables, and 5) Figures. The Source code folder has the script files written in Python 3.7.3. There are two sub-folders inside this folder separating the scripts into constant and random input current tests, respectively. Each sub-folder has a separate Python script that performs a benchmark test for each Spiking Neuron (SN) model. The Raw data folder collects the data generated by executing the scripts in the Source code folder and by following the instructions in the Testing procedure section of the paper. This stores the raw data for several SNs, firing frequencies, and input currents. This folder has a sub-folder with several files recording the random input currents used in the benchmark tests. The Raw data folder also has two sub-folders with the benchmark test results, each for a specific stimulation current type. The Benchmark test sub-folders give the CPU execution time, the SCF (Spike Coincidence Factor), the VCF (Voltage Coincidence Factor), the last spike displacement, and the firing frequency for each Numerical Method (NM) and time step. Other four sub-folders are containing the spike-timing and voltage time course data. These data are separated into constant and random input currents and NM and time step. The Calculations folder gives two files in .xlsx format with several estimates used in the paper. These files collect the CPU time, SCF, VCF, last spike displacement, and firing frequency from Raw data folder and compute the CCF (Computational Cost Factor) and GPF (Global Performance Factor) for several SNs and firing frequencies. Also, these files calculate the average and increment/decrement percent in FLOPS, CPU time, CCF, SCF, VCF, last spike displacement, and GPF among several SNs and NMs. Furthermore, these files examine the balanced, lower limit, upper limit, Skocik-Long, and Izhikevich configurations mentioned in the paper. Fourth and fifth folders contain the supplementary tables and figures, respectively, referenced in the article.