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".
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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.
Contributors: Alon Poleg-Polsky
... Simulation of neuronal processing of noise-corrupted inputs NEURON simulation (http://neuron.yale.edu/neuron)
Contributors: M. Sana Ullah Sahar
... This archive contains firmware of the nerve stretcher as well as necessary files to develop PCB for the device. This project is actively being maintained at GitHub. The updated versions of these scripts can be downloaded any time from our GitHub repository (https://github.com/msanaullahsahar/nestv2). If you find any issue/problem/error in these scripts please do not hesitate to report at (https://github.com/msanaullahsahar/nestv2/issues).
Contributors: Qiankun Liu, Jingang Jiang, Changwei Jing, Zhong Liu, Jiaguo Qi
... In this paper, a new, alternative, multi-scale, multi-pollution source waste load allocation (WLA) system was developed, with a goal to produce optimal, fair quota allocations at multiple scales. The new WLA system integrates multi-constrained environmental Gini coefficients (EGCs) and Delphi-analytic hierarchy process (Delphi-AHP) optimization models to achieve the stated goal. This dataset consists of the raw data and the source code of models (The multi-constrained environmental Gini coefficients and Delphi-analytic hierarchy process optimization models). The source code of the multi-constrained EGCs and Delphi-AHP models was used to run the program in MATLAB environment to allocate waste load reduction quotas at both the regional scale and the site-specific scale with multiple pollution sources. The raw data mainly consists of the following two parts: (1) The shp files of various geographic information data, which was used to depicture the administrative divisions, pollution source distribution, geographical characteristics and patterns of Xian-jiang watershed; (2) The basic data includes the statistical yearbook data of villages and towns in Ningbo city, the various indicator data using to calculate the weights at criteria level and decision-making level, the contribution coefficients, and the EGC values of the three pollutants. On the basis of these data, a new, alternative, multi-scale, multi-sector optimal WLA framework was developed. The new scheme provides decision-makers critical information (i.e., the best compromise solutions of WLA) and practical guidance as they address the related water pollution control. The results, in comparison with existing practices by the local governments, suggested that the pollution discharge quota at regional scale is much fairer than the existing WLA and, even have some environmental economic benefits at pollutant source scale after optimal WLA. Some important conclusions had been found: 1) Reductions and proportions of pollutants at regional scale are significantly associated with the region’s actual socioeconomic development modes. 2）There are certain characteristics that high-reduced pollution sources tend to share (which are listed in the article). The sources with the above features should be the top priorities in the reduction of removals. 3）Most previous studies reported primarily on the WLA of removals among point sources pollution. Conversely, we found that the industrial pollution source should be the last option for reduction from an environmental-economic benefit perspective. Instead, the often overlooked types, such as agricultural non-point source and domestic sources, deserve more attention, especially in extensive rural areas.
Contributors: Ryan Watkins
... Version 1.0, September 9, 2019 Purpose: Created as part of a project funded by NASA’S Lunar Data Analysis Program (LDAP), the purpose of this dataset is to provide locations and diameters of boulders around small, young impact craters on the Moon. These boulder counts were conducted as part of a study aimed at determining regolith production rates and assessing landing site hazards, as discussed in the associated publications. Researchers are encouraged to read the publications and data description document to understand how the data was acquired and used. This database contains boulder distributions around small (< 1 km), young (< 200 Ma) lunar impact craters located near spacecraft landing sites. The most up-to-date database contains boulder diameters and coordinates for counts around Surveyor (Apollo 12), Cone (Apollo 14), North Ray (Apollo 16), South Ray (Apollo 16), Camelot (Apollo 17), and Zi Wei (Chang’e-3) craters. Boulders were manually identified and measured on Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) images (Robinson et al., 2010) at scales of ~0.5-2 m/pixel. LROC NAC images allow for boulders ~1-2m in size and larger to be identified and measured. The tools for measuring boulders were CraterTools (Kneissl et al., 2011) and Crater Helper Tools (Nava, 2011), both developed for the ArcMap GIS platform. These boulder distributions are being used to understand boulder degradation rates on the lunar surface, and to assess landing site hazards for future surface missions to the Moon. This dataset is being archived in Mendeley Data and at the Planetary Data System (PDS) Cartography and Imaging Node for use in future boulder distribution and landing hazard studies. Future boulder counts and any refinements to existing measurements will be uploaded into subsequent versions of this dataset here and at the PDS IMG Annex: https://astrogeology.usgs.gov/search/map/Moon/Research/Regolith/lunar_boulder_data_bundle