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  5. Data from: STRAINS: A Big Data Method for Classifying Cellular Response to Stimuli at the Tissue Scale

Data from: STRAINS: A Big Data Method for Classifying Cellular Response to Stimuli at the Tissue Scale

File(s)
ZHENG_STRAINS_DATA_README.txt (9.74 KB)
Zheng_STRAINS_19_09_26_Example_Outputs.tar (94.59 MB)
ZHENG_STRAINS_Supplementary_Materials.pdf (423.62 KB)
Zheng_STRAINS_Python_Classification_Data.tar (66.3 MB)
Zheng_STRAINS_19_09_26_impact.tar (2.31 GB)
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Permanent Link(s)
https://doi.org/10.7298/3kwt-pm43
https://hdl.handle.net/1813/111415
Collections
Physics Research
Author
Zheng, Jingyang
Jackson, Thomas Wyse
Fortier, Lisa
Bonassar, Lawrence
Delco, Michelle
Cohen, Itai
Abstract

These files contain data supporting all results reported in Zheng et. al., STRAINS: A Big Data Method for Classifying Cellular Response to Stimuli at the Tissue Scale. Cellular response to stimulation governs tissue scale processes ranging from growth and development to maintaining tissue health and initiating disease. To determine how cells coordinate their response to such stimuli, it is necessary to simultaneously track and measure the spatiotemporal distribution of their behaviors throughout the tissue. Here, we report on a novel SpatioTemporal Response Analysis IN Situ (STRAINS) tool that uses fluorescent micrographs, cell tracking, and machine learning to measure such behavioral distributions. STRAINS is broadly applicable to any tissue where fluorescence can be used to indicate changes in cell behavior. For illustration, we use STRAINS to simultaneously analyze the mechanotransduction response of 5000 chondrocytes---over 20 million data points---in cartilage during the 50 ms to 4 hours after the tissue was subjected to local mechanical injury, known to initiate osteoarthritis. We find that chondrocytes exhibit a range of mechanobiological responses indicating activation of distinct biochemical pathways with clear spatial patterns related to the induced local strains during impact. These results illustrate the power of this approach.

Description
Please cite as: Zheng, Jingyang, Thomas Wyse Jackson, Lisa Fortier, Lawrence Bonassar, Michelle Delco, and Itai Cohen (2022). Data from: STRAINS: A Big Data Method for Classifying Cellular Response to Stimuli at the Tissue Scale [Dataset] Cornell University Library eCommons Digital Repository. https://doi.org/10.7298/3kwt-pm43
Sponsorship
The work was supported by the NIH National Institute of Arthritis and Musculoskeletal and Skin Diseases, Contract: 5R01AR071394-04, K08AR068470, R03AR075929, and The Harry M. Zweig Fund for Equine Research. Additionally, this work was supported by the National Science Foundation grants DMR-1807602, DMR-1808026, CBET-1604712, CMMI 1927197, and BMMB-1536463. Lastly, this work made use of the Cornell Center for Materials Research Shared Facilities which are supported through the NSF MRSEC program (DMR-1719875).
Date Issued
2022
Keywords
Mechanotransduction
•
machine learning
•
time series classification
•
cartilage injury
Related To
Zheng, Jingyang, Thomas Wyse Jackson, Lisa Fortier, Lawrence Bonassar, Michelle Delco, and Itai Cohen (2022). Code from: STRAINS: A Big Data Method for Classifying Cellular Response to Stimuli at the Tissue Scale [Source Code] Cornell University Library eCommons Digital Repository. https://doi.org/10.7298/ds7s-nc16
Related To
https://doi.org/10.7298/ds7s-nc16
Related Publication(s)
Zheng, J., Wyse Jackson, T., Fortier, L. A., Bonassar, L. J., Delco, M. L., & Cohen, I. (2022). STRAINS: A big data method for classifying cellular response to stimuli at the tissue scale. PLOS ONE, 17(12), e0278626. https://doi.org/10.1371/journal.pone.0278626
Link(s) to Related Publication(s)
https://doi.org/10.1371/journal.pone.0278626
Rights
CC0 1.0 Universal
Rights URI
http://creativecommons.org/publicdomain/zero/1.0/
Type
dataset
Accessibility Hazard
none

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