httk (version 2.1.0)

armitage_eval: Evaluate the updated Armitage model

Description

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.

Usage

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 = FALSE,
  this.option.swat2 = FALSE,
  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,
  this.conc_ser_alb = 24,
  this.conc_ser_lip = 1.9,
  this.Vdom = 0
)

Value

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-water partition coefficient	(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

Arguments

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

this.conc_ser_alb

24 g/L, mass concentration of albumin in serum.

this.conc_ser_lip

1.9 g/L, mass concentration of lipids in serum.

this.Vdom

0 ml, the volume of dissolved organic matter (DOM)

Author

Greg Honda

References

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

Examples

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 have any info, let's 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)