Evaluate the updated Armitage model
Evaluate the Armitage model for chemical distributon in vitro. Takes input as data table or vectors of values. Outputs a data table. Updates over the model published in Armitage et al. 2014 include binding to plastic walls and lipid and protein compartments in cells.
armitage_eval( casrn.vector = NA_character_, nomconc.vector = 1, this.well_number = 384, this.FBSf = NA_real_, tcdata = NA, this.sarea = NA_real_, this.v_total = NA_real_, this.v_working = NA_real_, this.cell_yield = NA_real_, this.Tsys = 37, this.Tref = 298.15, this.option.kbsa2 = F, this.option.swat2 = F, this.pseudooct = 0.01, this.memblip = 0.04, this.nlom = 0.2, this.P_nlom = 0.035, this.P_dom = 0.05, this.P_cells = 1, this.csalt = 0.15, this.celldensity = 1, this.cellmass = 3, this.f_oc = 1 )
casrn.vector |
For vector or single value, CAS number |
nomconc.vector |
For vector or single value, micromolar nominal concentration (e.g. AC50 value) |
this.well_number |
For single value, plate format default is 384, used if is.na(tcdata)==TRUE |
this.FBSf |
Fraction fetal bovine serum, must be entered by user. |
tcdata |
A data.table with casrn, nomconc, MP, gkow, gkaw, gswat, sarea, v_total, v_working. Otherwise supply single values to this.params. |
this.sarea |
Surface area per well (m^2) |
this.v_total |
Total volume per well (m^3) |
this.v_working |
Working volume per well (m^3) |
this.cell_yield |
Number of cells per well |
this.Tsys |
System temperature (degrees C) |
this.Tref |
Reference temperature (degrees K) |
this.option.kbsa2 |
Use alternative bovine-serum-albumin partitioning model |
this.option.swat2 |
Use alternative water solubility correction |
this.pseudooct |
Pseudo-octanol cell storage lipid content |
this.memblip |
Membrane lipid content of cells |
this.nlom |
Structural protein conent of cells |
this.P_nlom |
Proportionality constant to octanol structural protein |
this.P_dom |
Proportionality constant to dissolve organic material |
this.P_cells |
Proportionality constant to octanol storage lipid |
this.csalt |
Ionic strength of buffer, mol/L |
this.celldensity |
Cell density kg/L, g/mL |
this.cellmass |
Mass per cell, ng/cell |
this.f_oc |
1, everything assumed to be like proteins |
| Column | Description | units |
| casrn | Chemical Abstracts Service Registry Number | |
| nomconc | Nominal Concentration | mol/L |
| well_number | Number of wells in plate | unitless |
| sarea | Surface area of well | m^2 |
| v_total | Total volume of well | m^3 |
| v_working | Filled volume of well | m^3 |
| cell_yield | Number of cells | cells |
| gkow | log10 octanol to water partition coefficient (PC) | log10 |
| logHenry | log10 Henry's law constant ' | log10 atm-m3/mol |
| gswat | log10 Water solubility | log10 mol/L |
| MP | Melting Point | degrees Celsius |
| MW | Molecular Weight | g/mol |
| gkaw | air to water PC | (mol/m3)/(mol/m3) |
| dsm | ||
| duow | ||
| duaw | ||
| dumw | ||
| gkmw | ||
| gkcw | ||
| gkbsa | ||
| gkpl | ||
| ksalt | ||
| Tsys | ||
| Tref | ||
| option.kbsa2 | ||
| option.swat2 | ||
| FBSf | ||
| pseudooct | ||
| memblip | ||
| nlom | ||
| P_nlom | ||
| P_dom | dissolved organic matter to water PC | Dimensionless |
| P_cells | ||
| csalt | ||
| celldensity | ||
| cellmass | ||
| f_oc | ||
| cellwat | ||
| Tcor | ||
| Vm | Volume of media | L |
| Vwell | volume of medium (aqueous phase only) | L |
| Vair | volume of head space | L |
| Vcells | volume of cells/tissue | |
| Valb | volume of serum albumin | |
| Vslip | volume of serum lipids | |
| Vdom | volume of dissolved organic matter | |
| F_ratio | ||
| gs1.GSE | ||
| s1.GSE | ||
| gss.GSE | ||
| ss.GSE | ||
| kmw | ||
| kow | octanol to water PC | |
| kaw | the air towater PC | dimensionless |
| swat | ||
| kpl | ||
| kcw | cell/tissue to water PC | dimensionless |
| kbsa | ||
| swat_L | ||
| oct_L | ||
| scell_L | ||
| cinit | Initial concentration | mol |
| mtot | Total moles | mol |
| cwat | Total concentration in water | mol/L |
| cwat_s | Dissolved concentration in water | mol/L |
| csat | Is the solution saturated (1/0) | Boolean |
| activity | ||
| cair | mol/L | |
| calb | mol/L | |
| cslip | mol/L | |
| cdom | concentration of/in dissolved organic matter | mol/L |
| ccells | mol/L | |
| cplastic | mol/L | |
| mwat_s | Mass dissolved in water | mols |
| mair | Mass in air | mols |
| mbsa | Mass bound to bovine serum albumin | mols |
| mslip | Mass bound to serum lipids | mols |
| mdom | Mass bound to dissolved organic matter | mols |
| mcells | Mass in cells | mols |
| mplastic | Mass bond to plastic | mols |
| mprecip | Mass precipitated out of solution | |
| xwat_s | Fraction dissolved in water | fraction |
| xair | Fraction in the air | fraction |
| xbsa | Fraction bound to bovine serum albumin | fraction |
| xslip | Fraction bound to serum lipids | fraction |
| xdom | Fraction bound to dissolved organic matter | fraction |
| xcells | Fraction within cells | fraction |
| xplastic | Fraction bound to plastic | fraction |
| xprecip | Fraction precipitated out of solution | fraction |
| eta_free | effective availability ratio | fraction |
| cfree.invitro | Free concentration in the in vitro media (use for Honda1 and Honda2) | micromolar |
Greg Honda
Armitage, J. M.; Wania, F.; Arnot, J. A. Environ. Sci. Technol. 2014, 48, 9770-9779. https://doi.org/10.1021/es501955g
Honda et al. PloS one 14.5 (2019): e0217564. https://doi.org/10.1371/journal.pone.0217564
library(httk)
# Check to see if we have info on the chemical:
"80-05-7" %in% get_cheminfo()
#We do:
temp <- armitage_eval(casrn.vector = c("80-05-7", "81-81-2"), this.FBSf = 0.1,
this.well_number = 384, nomconc = 10)
print(temp$cfree.invitro)
# Check to see if we have info on the chemical:
"793-24-8" %in% get_cheminfo()
# Since we don't look up phys-chem from dashboard:
cheminfo <- data.frame(
Compound="6-PPD",
CASRN="793-24-8",
DTXSID="DTXSID9025114",
logP=4.27,
logHenry=log10(7.69e-8),
logWSol=log10(1.58e-4),
MP= 99.4,
MW=268.404
)
# Add the information to HTTK's database:
chem.physical_and_invitro.data <- add_chemtable(
cheminfo,
current.table=chem.physical_and_invitro.data,
data.list=list(
Compound="Compound",
CAS="CASRN",
DTXSID="DTXSID",
MW="MW",
logP="logP",
logHenry="logHenry",
logWSol="logWSol",
MP="MP"),
species="Human",
reference="CompTox Dashboard 31921")
# Run the Armitage et al. (2014) model:
out <- armitage_eval(
casrn.vector = "793-24-8",
this.FBSf = 0.1,
this.well_number = 384,
nomconc = 10)
print(out)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.