NASAmouseHG

Data and script for analyzing ionizing radiation tumorigenesis outside low-earth orbit. The results are presented in Huang et al., (2019).

Repository Contents

NASAmouseHG

The main directory. Houses our primary R scripts for analysis, licensing information, git integration, and important subfolders. The primary scripts, in order of development, are: dataAndInfo.R, synergyTheory.R, monteCarlo.R, plots.R, and supplementPlots.R.

data

Data files, strictly in CSV format.

paper

Paper drafts, supplementary materials, and writing materials.

exploration

Scripts for indirectly related analyses, ideas, and experiments.

misc_materials

Meeting minutes, example scripts for various procedures, past agendas, and past papers.

Attribution

# Copyright:    (C) 2017-2018 Sachs Undergraduate Research Apprentice Program
#               This program and its accompanying materials are distributed 
#               under the terms of the GNU General Public License v3.
# Project:      NASAmouseHG
# Purpose:      Data and script concerning synergy theory for murine Harderian
#               gland tumorigenesis after irradiation by mixtures of ionized, 
#               high-energy, atomic nuclei. 
# Contact:      Rainer K. Sachs 
# Website:      https://github.com/sachsURAP/NASAmouseHG
# Mod history:  22 Jun 2018
# Attribution:  These R scripts and related files were developed at 
#               UC Berkeley 2017-18. An early version was written by 
#               Dae Woong Ham Summer 2017. Additions, corrections, changes, 
#               quality control, and major reorganization by Edward G. Huang, 
#               Yimin Lin, Mark Ebert, Yunzhi Zhang and Ray Sachs, 
#               UCB Fall 2017 - Summer 2018.

License Notice

#  NASAmouseHG is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
# 
#  NASAmouseHG is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
# 
#  You should have received a copy of the GNU General Public License
#  along with NASAmouseHG. If not, see <http://www.gnu.org/licenses/>.

Relevant References and Abbreviations:

#   ".93Alp" = Alpen et al. "Tumorigenic potential of high-Z, high-LET charged-
#                           particle radiations." Rad Res 136:382-391 (1993)
#
#   ".94Alp" = Alpen et al. "Fluence-based relative biological effectiveness for
#                           charged particle carcinogenesis in mouse Harderian 
#                           gland." Adv Space Res 14(10): 573-581. (1994).  
#
#   "16Chang" = Chang et al. "Harderian Gland Tumorigenesis: Low-Dose and LET 
#                            Response." Radiat Res 185(5): 449-460. (2016). 
#
#   "16Srn" = Siranart et al. "Mixed Beam Murine Harderian Gland Tumorigenesis: 
#                             Predicted Dose-Effect Relationships if neither 
#                             Synergism nor Antagonism Occurs." 
#                             Radiat Res 186(6): 577-591 (2016).  
#
#   "17Cuc" = Cucinotta & Cacao. "Non-Targeted Effects Models Predict 
#                                Significantly Higher Mars Mission Cancer Risk 
#                                than Targeted Effects Models." 
#                                Sci Rep 7(1): 1832. (2017). PMC5431989
#
#   "HZE"    = High atomic number and energy
#   "LET"    = Linear energy transfer
#   "NTE"    = Non-targeted effects
#   "TE"     = Targeted effects
#   "DER"    = Dose-effect Relation(ship) 
#   "SEA"    = Simple Effect Additivity
#   "IEA"    = Incremental Effect Additivity
#   "cGy"    = Centigray