parameterize_kramer

This function takes inputs from kramer_eval() and calls parameterize_IVD(). Converts units and sets up variables for kramer_eval().

Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predictions for chemicals
where in vivo data do exist. The models are systems of ordinary
differential equations that are developed in MCSim and solved
using compiled (C-based) code for speed. A Monte Carlo sampler is
included for simulating human biological variability
(Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>)
and propagating parameter uncertainty
(Wambaugh et al., 2019 <doi:10.1093/toxsci/kfz205>).
Empirically calibrated methods are included for predicting
tissue:plasma partition coefficients and volume of distribution
(Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>).
These functions and data provide a set of tools for using IVIVE to
convert concentrations from high-throughput screening experiments
(for example, Tox21, ToxCast) to real-world exposures via reverse
dosimetry (also known as "RTK")
(Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).

John Wambaugh

httk

High-Throughput Toxicokinetics

Sarah Davidson-Fritz

Robert Pearce

Caroline Ring

Greg Honda

Mark Sfeir

Matt Linakis

Dustin Kapraun

Kimberly Truong

Colin Thomson

Meredith Scherer

Annabel Meade

Celia Schacht

Todor Antonijevic

Miyuki Breen

Shannon Bell

Xiaoqing Chang

Jimena Davis

Elaina Kenyon

Gilberto Padilla Mercado

Katie Paul Friedman

Nathan Pollesch

Noelle Sinski

Nisha Sipes

James Sluka

Caroline Stevens

Barbara Wetmore

Lily Whipple

Woodrow Setzer

parameterize_kramer function

<dl><dt>tcdata</dt>
<dd>A data table with well_number corresponding to plate format,
optionally include v_working, sarea, option.bottom, and option.plastic</dd>
<dt>casrn.vector</dt>
<dd>A deprecated argument specifying a single or vector of 
Chemical Abstracts Service Registry 
Number(s) (CAS-RN) of desired chemical(s).</dd>
<dt>this.FBSf</dt>
<dd>Fraction fetal bovine serum</dd>
<dt>this.BSA</dt>
<dd>bovine serum albumin concentration (g/L)</dd>
<dt>this.v_total</dt>
<dd>Total volume per well (uL)</dd>
<dt>this.v_working</dt>
<dd>Working volume per well (uL)</dd>
<dt>this.cell_yield</dt>
<dd>Number of cells/well seeded</dd>
<dt>this.sarea</dt>
<dd>Surface area per well (m^2)</dd>
<dt>this.prot_conc</dt>
<dd>Cell protein concentration (mg protein/million cells)</dd></dl>

Arguments

Author

Parameterize Kramer IVD Model — parameterize_kramer

<dl>

<dt>tcdata</dt>
<dd>A data table with well_number corresponding to plate format,
optionally include v_working, sarea, option.bottom, and option.plastic</dd>


<dt>casrn.vector</dt>
<dd>A deprecated argument specifying a single or vector of 
Chemical Abstracts Service Registry 
Number(s) (CAS-RN) of desired chemical(s).</dd>


<dt>this.FBSf</dt>
<dd>Fraction fetal bovine serum</dd>


<dt>this.BSA</dt>
<dd>bovine serum albumin concentration (g/L)</dd>


<dt>this.v_total</dt>
<dd>Total volume per well (uL)</dd>


<dt>this.v_working</dt>
<dd>Working volume per well (uL)</dd>


<dt>this.cell_yield</dt>
<dd>Number of cells/well seeded</dd>


<dt>this.sarea</dt>
<dd>Surface area per well (m^2)</dd>


<dt>this.prot_conc</dt>
<dd>Cell protein concentration (mg protein/million cells)</dd>

</dl>

Parameterize Kramer IVD Model

Column Name	Description	Units
sarea	surface area	m^2
v_working_m3	working (filled) volume of each well	m^3
v_total_m3	total volume of each well	m^3
v_headspace_m3	volume of headspace per well	m^3
conc_BSA	BSA concentration in media	kg/L
FBSp	Percent fetal bovine serum in media	percent
conc_cell_mg	concentration of cell lipids	mg/m^3
conc_cell	concentration of cell lipids	kg/m^3
conc_plastic	concentration of plastic	m2/m^3

parameterize_kramer: Parameterize Kramer IVD Model

Description

Usage

Value

Arguments

Author

References