This readme file was created 2021-12-06 By Thomas Wyse Jackson
This readme file describes the dataset titled: Data from: Structural Origins of Cartilage Shear Mechanics


Corresponding author information:
Email: tsw64@cornell.edu (Thomas Wyse Jackson); ic64@cornell.edu (Itai Cohen)


This dataset is shared under a Creative Commons Attribution 4.0 International license (CC BY 4.0); the data will be openly available to share and adapt, but appropriate credit to the original data creators is required upon reuse.


When using this dataset, please cite:

The dataset:
Thomas Wyse Jackson, Michel Jonathan, Lwin Pancy, Fortier Lisa A., Das Moumita, Bonassar Lawrence J., and Cohen Itai. (2022) Data from: Structural Origins of Cartilage Shear Mechanics [dataset]. Cornell University eCommons Repository. https://doi.org/10.7298/fz4d-cy87.

AND the paper: 
Thomas Wyse Jackson, Michel Jonathan, Lwin Pancy, Fortier Lisa A., Das Moumita, Bonassar Lawrence J., and Cohen Itai. “Structural Origins of Cartilage Shear Mechanics.” Science Advances 8(6): eabk2805. https://doi.org/10.1126/sciadv.abk2805.


This work was supported by the National Science Foundation grants DMR-1807602, DMR-1808026, CBET-1604712, CMMI 1927197, and BMMB-1536463. This work was also supported by the NIH National Institute of Arthritis and Musculoskeletal and Skin Diseases, Contract: 5R01AR071394-04. Last, this work made use of the Cornell Center for Materials Research Facilities supported by the National Science Foundation under Award Number DMR-1719875.
 

Hello! Thanks for enjoying my paper.


____________Complete_Dataset____________
To load into matlab: >> load('Complete_Dataset.mat')

Complete_Dataset is a structure containing two structures:
Degradation - the individual results of individual samples
Results - the compiled results of all the individual samples combined, for the healthy and degraded datasets.


____________Results____________
Results has two individual structures with identical formatting, with one for the healthy samples, and one for the degraded samples.

The numbering of the samples comes from the batches of experiments over a few weeks they were taken in, with 0XX being the first set, 1XX being the second, and 2XX being the third. Even numbered samples are all healthy, undegraded samples, and odd numbered samples are degraded samples. Missing numbers are due to samples which were not appropriate, either due to failed experiments, or did not fall into typical behavior of composition or mechanics.

All contains all of the data for the sample type, whereas Filter has had data removed which was not relevant to the final result (eg, aggrecan concentration was too high/trimming data down to same length).

Going into filter, because this is where the data processing occurred, there are further structures:
indv, which contains every individual datapoint from each depth of the sample 
Average is the averaged results by depth (Properties), or by collagen concentration (SvC).

In SvC you'll find the properties based on collagen concentration (CollBins) such as shear modulus, aggrecan, the phase, the strain, the storage modulus (elastic) and the loss modulus (viscous).


____________Degradation____________
Contains the individual results from each sample.

Each sample contains Input, Properties, and Output.

Properties just contains some of the details of the tissue such as area, volume, and length.

Input has all of the details such as the raw mechanical inputs from our line tracking code (See Buckley 2010), data of the FTIR measurements, biochemistry measurements, whether the sample is degraded or not (0 - not degraded, 1 - degraded), and where the FTIR measurements should be taken from (process).

Output contains the outputted properties with depth, such as the aggrecan and collagen data, and the shear modulus (full, storage, loss).


____________Other Files____________
Bio_Data contains the aggrecan and hydroxyproline measurements in units of mg.
FTIR_Data contains the absorption spectrum from every depth for each value of wave number.
FTIR_Standards contain the used FTIR standards taken from Camacho 2001.
FTIR_Start_End contains the start and end points of the samples in the FTIR measurements (as some empty space was measured).
Simulation data contains the 3D surface as described in the paper, with column 1 the collagen concentration, column 2 the aggrecan concentration, and column 3 as the log10(Shear Modulus).