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.
Contributors: Pranav Pandya, Kartikey Hadiya
... This project is one of the academic projects given to us in the Geographic Information System (GIS) Course. Created by: Pranav Pandya (Me) and Kartikey Hadiya We sampled information for pollution emission in Delhi, India. Pollution data was obtained from https://data.gov.in/resources/real-time-air-quality-index-various-locations Pollution index data can be obtained from https://cpcb.nic.in/RealTimeAirQualityData.php Pollution data only had address of Indian Meteorological Department, so each station was located in Google Earth and pin points were added at each station. Then in the sidebar containing those pins on right-click, a new folder was added and all the pins were added in that new folder in google earth. Then that folder was saved as kml file. This kml file was uploaded to Mygeodata: https://mygeodata.cloud/converter/kml-to-csv and was converted into csv. Then the csv file was opened and coordinates were copied in the pollution data file. That file was later saved as CSV and imported in ArcGIS and xy data was displayed. Shapefile was obtained from web search, which is attached as well. That shapefile was imported in ArcGIS and the final view was generated which is shown in the picture.
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: Young-Min Soh, Iain Finley Davidson, Stefano Zamuner, Jerome Basquin, Michael Taschner, Florian Patrick Bock, Jan-Willem Veening, Paolo De Los Rios, Jan-Michael Peters, Stephan Gruber
... Dracala spotting assay, ITC measurements, Malachite Green Assay, in vitro and in vivo crosslinking , DNA loading assay, Sequence alignment used for DCA, Single Molecule Imaging
Contributors: Raúl Roberto poppiel, Marilusa Pinto Coelho Lacerda, José Lucas Safanelli, Rodnei Rizzo, Manuel Pereira de Oliveira junior, Jean Jesus Novais, Jose Alexandre Dematte
... Maps of clay, silt and sand contents (g kg-1) were predicted at 0-20 cm, 20-60 cm and 60-100 cm depths intervals by random forest regression in Google Earth Engine. Gridded soil information covers a part of the Midwest Brazil, from 12° S to 20° S and from 45° W to 54° W, and is available with 250m resolution. The maps were cross-validated and had Coefficient of Determination ranging from 0.64 to 0.85 at all depth intervals.
Contributors: Pradeep Koulgi, Nicholas Clinton, Krithi Karanth
Non-Thermal Atmospheric Pressure Plasma Induces Epigenetic Modifications that Activate the Expression of Various Cytokines and Growth Factors in Human Adipose Tissue-Derived Stem Cells
Contributors: Jeongyeon Park, Kiwon Song
... In this study, by analyzing the whole genome expression profiles of NTAPP-activated ASCs with RNA-seq, we investigated the mechanism by which NTAPP increases the proliferation of ASCs in order to deduce the common mechanism underlying the physiological effects of NTAPP. We demonstrated that NTAPP increases the expression of genes associated with the activity of various cytokines and growth factors, and downregulates the genes involved in the intrinsic apoptotic pathway by inducing epigenetic modifications. We also showed that nitric oxide (NO) generated from NTAPP is a main component of epigenetic modification by NTAPP. The physiological mechanism of NTAPP proven in this study supports the development of NTAPP as an efficient tool for regenerative medicine.
Data for: The WC-Co/Fe-Ni interface: effect of holding time on the microstructure, grain size and grain growth mechanism
Contributors: Peiquan Xu
... The enclosed data provide the X-Ray Diffraction of samples W2, W3, W4, and invar alloy for comparison.
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.