A brief overview of a biomedical engineering project submitted to the 2019 TDI Fellowship challenge.
Project notebook: MULTISCALE ANALYSES ON ARTERIOVENOUS FISTULA MATURATION
Full data-sets, R scripts, and R notebooks of the project are included in this repository.
DATA-SETS DESCRIPTION & NOTES
GENOMIC DATA-SETS
"Neutrophil.csv", "Monocyte_smaller.csv"
'data.frame': 26831 obs. of 100-150 variables:
$ Gene : Factor w/ 25193 levels "41699","41700",..: 24220 24194 7770 23654 3747 12443 13803 14186 24219 21453 ...
$ X31043.B : num 5.08 5.74 6.42 6.69 5.75 ...
$ X31044.B : num 5.1 5.57 6.44 6.62 5.67 ...
$ X31047.B : num 5.21 5.78 6.53 6.1 5.04 ...
$ X31051.B : num 5 5.66 6.92 6.68 6.01 ...
$ X31059.B : num 5.26 5.93 6.45 6.15 5.56 ...
[...]
- The codes listed in the fist column "Gene" indicate the gene code/name
- The number that follows the "X" in "X31043.B" indicates the patient number (= 31043), following the dot is time of data acquisition (B = baseline, 2W = 2 weeks)
CAUTION: This is a double entry table:
Each row corresponds to a different gene
Each column corresponds to a patient's data recording (there are two data recording times for each patient: baseline and 2 weeks)
Abbreviations:
B = baseline
2W = 2 weeks
HEMODYNAMIC DATA-SETS
"Hemodynamics_Fistula-Artery.csv", "Hemodynamics_Fistula-Vein.csv"
'data.frame': 9001 obs. of 9 variables:
$ Patient: Factor w/ 50 levels "031072 EM","031103 PJ",..: 1 1 1 1 1 1 1 1 1 1 ...
$ Site : Factor w/ 1 level "Florida": 1 1 1 1 1 1 1 1 1 1 ...
$ Scan : int 1 1 1 1 1 1 1 1 1 1 ...
$ d.mm : int 0 1 2 3 4 5 6 7 8 9 ...
$ area : num 15.9 15.9 16.2 16.4 16.6 16.7 16.6 16.5 16.3 16.1 ...
$ WSSave : num 124.1 109.4 92.4 82.6 77.3 ...
$ WSSmax : num 179 154 128 113 106 ...
$ WSSGave: num 637 510 346 296 277 ...
$ OSI : num 0.01 0 0 0 0 0 0 0 0 0 ...
"Patient" indicates the patient number
"Site" indicates the location of the screening hospital
"Scan" indicates the time of CT scan imaging (Scan == 1 #Baseline, Scan == 2 #6 weeks, Scan == 3 #6 months)
"d mm" is distance in millimiters
"area" is the cross sectional area in mm^2
"WSSave" and "WSSmax" are average and maximum wall shrear stress in Pascals
"WSSGave" is the average wall shear stress gradient in 1/Pascals
"OSI" is the oscillatory shear index (no units)
Abbreviations:
WSS = wall shear stress
Ave = average
G = gradient
BRACHIAL ARTERY DILATION DATA-SETS
"FMD_NMD data_N1.xlsx", "FMD_NMD data_M2.xlsx"
Data were collected in two separate files.
Each xlsx file contains two excel sheets (FMD and NMD).
Each sheet is composed by 75-100 rows, one for each patient, and 4 culomns, one for each of the following parameters:
"PID" indicates the patient ID number
"FMD_BRACH_PRE" or "NMD_BRACH_PRE" indicates the FMD/NMD pre-fistula
"FMD_BRACH_POST" or "NMD_BRACH_POST" indicates the FMD/NMD post-fistula
"fmd_brach_per" indicates the percent difference between pre- and post- dilation measurements as [(PRE - POST)/PRE]*100
Abbreviations:
FMD = flow-mediated dilation
NMD = nitroglycerin-mediated dilation