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- Description:
- This dataset is a custom Kraken2 formatted database for the identification of Fungi from shotgun metagenomic data. Kraken2 is a k-mer based read classifier (Wood et al. 2019; https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1891-0). The dataset was built with the default k-mer length (k=35) from all publicly available fungal genomes at JGI Mycocosm ( https://mycocosm.jgi.doe.gov/mycocosm/home), and all archaea, bacteria, viral, plasmid, human, fungi, plant, and protozoa genomes, as well as the UniVec Core and nt reference database at NCBI ( https://www.ncbi.nlm.nih.gov/). The reference genomes and sequences were downloaded from JGI and NCBI in March 2020.
- Keyword:
- protozoa, Kraken2 database, plant, bacteria, genomes, fungi, human, archaea, plasmid, and virus
- Subject:
- Mycology and Genomics
- Creator:
- Dentinger, Bryn T. M.
- Owner:
- Bryn Dentinger
- Language:
- English
- Date Uploaded:
- 06/08/2022
- Date Modified:
- 06/03/2024
- Date Created:
- 2020-03-29
- License:
- CC BY NC - Allows others to use and share your data non-commercially and with attribution.
- Resource Type:
- Software or Program Code and Dataset
- Identifier:
- https://doi.org/10.7278/S50d-154b-fppf
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- Description:
- This dataset accompanies the research article entitled, "Etiology-Specific Remodeling in Ventricular Tissue of Heart Failure Patients and its Implications for Computational Modeling of Electrical Conduction," where we quantified fibrosis and performed electrophysiological simulation to investigate electrical propagation in etiologically varied heart failure tissue samples. Included are raw confocal microscopic images, data for extracting and processing the raw images and script to analyze fibrosis and generate meshes for simulation.
- Keyword:
- human, heart failure, cardiac, confocal microscopic images, simulation, and fibrosis
- Subject:
- cardiology
- Creator:
- Drakos, Stavros G., Sachse, Frank B., Kyriakopoulos, Christos P., Bragard, Jean, Greiner, Joachim, Chakkalakkal Sankarankutty, Aparna, Visker, Joseph R., and Shankar, Thirupura S.
- Owner:
- Aparna Sankarankutty
- Based Near Label Tesim:
- Salt Lake City, Utah, United States
- Language:
- English
- Date Uploaded:
- 06/08/2021
- Date Modified:
- 12/08/2023
- Date Created:
- 2019-01-01 to 2020-11-30
- License:
- CC BY NC - Allows others to use and share your data non-commercially and with attribution.
- Resource Type:
- Dataset
- Identifier:
- https://doi.org/10.7278/S50D-BPS8-R06S
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- Description:
- While several studies have qualitatively investigated age- and region-dependent adhesion between the vitreous and retina, no studies have directly measured the vitreoretinal strength of adhesion. In this study, we developed a rotational peel device and associated methodology to measure the maximum and steady-state peel forces between the vitreous and the retina. Vitreoretinal adhesion in the equator and posterior pole were measured in human eyes from donors ranging 30 to 79 years of age, and in sheep eyes from premature, neonatal, young lamb, and young adult sheep. In human eyes, maximum peel force in the equator (7.24 ± 4.13 mN) was greater than in the posterior pole (4.08 ± 2.03 mN). This trend was especially evident for younger eyes from donors 30 to 39 years of age. After 60 years of age, there was a significant decrease in the maximum equatorial (4.69 ± 2.52 mN, p = 0.016) and posterior pole adhesion (2.95 ± 1.25 mN, p = 0.037). In immature sheep eyes, maximum adhesion was 7.60 ± 3.06 mN, and did not significantly differ between the equator and posterior pole until young adulthood. At this age, the maximum adhesion in the equator nearly doubled (16.67 ± 7.45 mN) that of the posterior pole, similar to the young adult human eyes. Light microscopy images suggest more disruption of the inner limiting membrane (ILM) in immature sheep eyes compared to adult sheep eyes. Interestingly, in human eyes, ILM disruption was significantly greater in the posterior pole (p < 0.05) and in people over 60 years of age (p < 0.02). These findings supplement the current discussion surrounding age-related posterior vitreous detachment, and the risk factors and physiological progressions associated with this condition. In addition, these data further our understanding of the biomechanical mechanisms of vitreoretinal adhesion, and can be used to develop age- appropriate computational models simulating retinal detachment, hemorrhaging, or retinal trauma. See Creveling CJ, Colter J, Coats B. 2018. Changes in vitreoretinal adhesion with age and region in human and sheep eyes. Frontiers in Bioengineering and Biotechnology 6. https://doi.org/10.3389/fbioe.2018.00153.
- Keyword:
- ophthalmology, retina, vitreous, adhesion, ocular, human, eye, peel test, and sheep
- Subject:
- Quantitative measurement and Vitreoretinal adhesion
- Creator:
- Coats, Brittany and Creveling, Christopher
- Contributor:
- Colter, Jourdan
- Owner:
- BRIAN MCBRIDE
- Based Near Label Tesim:
- Salt Lake City, Utah, United States
- Language:
- English
- Date Uploaded:
- 07/10/2019
- Date Modified:
- 06/03/2024
- Date Created:
- Completed 2017-06-01
- License:
- CC BY – Allows others to use and share your data, even commercially, with attribution.
- Resource Type:
- Image, Dataset, and Video
- Identifier:
- https://doi.org/10.7278/S5BK19H3