DISTING: A web application for fast algorithmic computation of alternative indistinguishable linear compartmental models.

Background And Objectives: We describe and illustrate use of DISTING, a novel web application for computing alternative structurally identifiable linear compartmental models that are input-output indistinguishable from a postulated linear compartmental model. Several computer packages are available for analysing the structural identifiability of such models, but DISTING is the first to be made available for assessing indistinguishability.

Methods: The computational algorithms embedded in DISTING are based on advanced versions of established geometric and algebraic properties of linear compartmental models, embedded in a user-friendly graphic model user interface.

Alternative to Ritt's pseudodivision for finding the input-output equations of multi-output models.

Differential algebra approaches to structural identifiability analysis of a dynamic system model in many instances heavily depend upon Ritt's pseudodivision at an early step in analysis. The pseudodivision algorithm is used to find the characteristic set, of which a subset, the input-output equations, is used for identifiability analysis. A simpler algorithm is proposed for this step, using Gröbner Bases, along with a proof of the method that includes a reduced upper bound on derivative requirements.

Simulation of post-thyroidectomy treatment alternatives for triiodothyronine or thyroxine replacement in pediatric thyroid cancer patients.

Background: As in adults, thyroidectomy in pediatric patients with differentiated thyroid cancer is often followed by (131)I remnant ablation. A standard protocol is to give normalizing oral thyroxine (T(4)) or triiodothyronine (T(3)) after surgery and then withdraw it for 2 to 6 weeks. Thyroid remnants or metastases are treated most effectively when serum thyrotropin (TSH) is high, but prolonged withdrawals should be avoided to minimize hypothyroid morbidity.

Finding identifiable parameter combinations in nonlinear ODE models and the rational reparameterization of their input-output equations.

When examining the structural identifiability properties of dynamic system models, some parameters can take on an infinite number of values and yet yield identical input-output data. These parameters and the model are then said to be unidentifiable. Finding identifiable combinations of parameters with which to reparameterize the model provides a means for quantitatively analyzing the model and computing solutions in terms of the combinations.

TSH regulation dynamics in central and extreme primary hypothyroidism.

Background: Thyrotropin (TSH) changes in extreme primary hypothyroidism include increased secretion, slowed degradation, and diminished or absent TSH circadian rhythms. Diminished rhythms are also observed in central hypothyroid patients and have been speculated to be a cause of central hypothyroidism. We examined whether TSH secretion saturation, previously suggested in extreme primary hypothyroidism, might explain diminished circadian rhythms in both disorders.

Predicting chemical impacts on vertebrate endocrine systems.

Animals have evolved diverse protective mechanisms for responding to toxic chemicals of both natural and anthropogenic origin. From a governmental regulatory perspective, these protective responses complicate efforts to establish acceptable levels of chemical exposure. To explore this issue, we considered vertebrate endocrine systems as potential targets for environmental contaminants.

An algorithm for finding globally identifiable parameter combinations of nonlinear ODE models using Gröbner Bases.

The parameter identifiability problem for dynamic system ODE models has been extensively studied. Nevertheless, except for linear ODE models, the question of establishing identifiable combinations of parameters when the model is unidentifiable has not received as much attention and the problem is not fully resolved for nonlinear ODEs. Identifiable combinations are useful, for example, for the reparameterization of an unidentifiable ODE model into an identifiable one.

TSH-based protocol, tablet instability, and absorption effects on L-T4 bioequivalence.

Background: FDA Guidance for pharmacokinetic (PK) testing of levothyroxine (L-T(4)) for interbrand bioequivalence has evolved recently. Concerns remain about efficacy and safety of the current protocol, based on PK analysis following supraphysiological L-T(4) dosing in euthyroid volunteers, and recent recalls due to intrabrand manufacturing problems also suggest need for further refinement. We examine these interrelated issues quantitatively, using simulated what-if scenarios testing efficacy of a TSH-based protocol and tablet stability and absorption, to enhance precision of L-T(4) bioequivalence methods.

Extensions, validation, and clinical applications of a feedback control system simulator of the hypothalamo-pituitary-thyroid axis.

Background: We upgraded our recent feedback control system (FBCS) simulation model of human thyroid hormone (TH) regulation to include explicit representation of hypothalamic and pituitary dynamics, and updated TH distribution and elimination (D&E) parameters. This new model greatly expands the range of clinical and basic science scenarios explorable by computer simulation.

Methods: We quantified the model from pharmacokinetic (PK) and physiological human data and validated it comparatively against several independent clinical data sets.

L-T4 bioequivalence and hormone replacement studies via feedback control simulations.

FDA Guidance for testing bioequivalence of levothyroxine (L-T(4)) preparations has been challenged by several groups, based on multiple issues. The efficacy of single versus combined hormone therapy also is receiving additional scrutiny. To examine these concerns, we developed a new nonlinear feedback system simulation model of whole-body regulation mechanisms involving dynamics of T(3), T(4), TSH, plasma protein binding, extravascular regulatory enzyme systems, and the hypothalamic-pituitary-thyroid axis, all quantified from human data.

A two-tiered physiologically based model for dually labeled single-chain Fv-Fc antibody fragments.

Monoclonal antibodies (mAb) are being used at an increasing rate in the treatment of cancer, with current efforts focused on developing engineered antibodies that exhibit optimal biodistribution profiles for imaging and/or radioimmunotherapy. We recently developed the single-chain Fv-Fc (scFv-Fc) mAb, which consists of a single-chain antibody Fv fragment (light-chain and heavy-chain variable domains) coupled to the IgG1 Fc region. Point mutations that attenuate binding affinity to FcRn were introduced into the Fc region of the wild-type scFv-Fc mAb, resulting in several new antibodies, each with a different half-life.

W3MAMCAT: a world wide web based tool for mammillary and catenary compartmental modeling and expert system distinguishability.

W(3)MAMCAT is a new web-based and interactive system for building and quantifying the parameters or parameter ranges of n-compartment mammillary and catenary model structures, with input and output in the first compartment, from unstructured multiexponential (sum-of-n-exponentials) models. It handles unidentifiable as well as identifiable models and, as such, provides finite parameter interval solutions for unidentifiable models, whereas direct parameter search programs typically do not. It also tutorially develops the theory of model distinguishability for same order mammillary versus catenary models, as did its desktop application predecessor MAMCAT+.

Role of endosomal trafficking dynamics on the regulation of hepatic insulin receptor activity: models for Fao cells.

Evidence indicates that endosomal insulin receptor (IR) trafficking plays a role in regulating insulin signal transduction. To evaluate its importance, we developed a series of biokinetic models for quantifying activated surface and endosomal IR dynamics from published experimental data. Starting with a published two-compartment Fao hepatoma model, a four-pool model was formulated that depicts IR autophosphorylation after receptor binding, IR endosomal internalization/trafficking, insulin dissociation from and dephosphorylation of internalized IR, and recycling of unliganded, dephosphorylated IR to the plasma membrane.

A predictive model of therapeutic monoclonal antibody dynamics and regulation by the neonatal Fc receptor (FcRn).

We constructed a novel physiologically-based pharmacokinetic (PBPK) model for predicting interactions between the neonatal Fc receptor (FcRn) and anti-carcinoembryonic antigen (CEA) monoclonal antibodies (mAbs) with varying affinity for FcRn. Our new model, an integration and extension of several previously published models, includes aspects of mAb-FcRn dynamics within intracellular compartments not represented in previous PBPK models. We added mechanistic structure that details internalization of class G immunoglobulins by endothelial cells, subsequent FcRn binding, recycling into plasma of FcRn-bound IgG and degradation of free endosomal IgG.

Automated expert multiexponential biomodeling interactively over the Internet.

DIMSUM, an acronym for DIMension of a SUM of exponentials, is a highly automated expert system for fitting multiexponential models of increasing dimension to time series data. Up to now, a researcher has needed an individual copy of DIMSUM on his or her own computer as well as support to learn how to use it. W3DIMSUM, a new implementation of DIMSUM, is web-based, new territory for interactive biomodeling, allowing interactive multiexponential model building and model discrimination over the Internet.

W3MCSim: an online and reconfigurable Monte Carlo simulator for interactive probabilistic/statistical modeling.

We have implemented a Monte Carlo simulator (W3MCSim) as an Internet software tool, primarily for interactive use by students, educators, life and other physical scientists, as well as other practitioners of probabilistic and statistical modeling. Interested users download, install and run W3MCSim by visiting the application website. This application incorporates three freely available Microsoft web technologies, namely the Internet Explorer web browser, the Component Object Model software framework and the JScript web page script interpreter.

Thyroid hormone production rates in rat liver and intestine in vivo: a novel graph theory and experimental solution.

We develop a novel method for finding sufficient experimental conditions for discriminating and quantifying individual biomolecule production sources in distributed, inhomogeneous multisource systems in vivo, and we apply it experimentally to a complex, unsolved problem in endocrinology. The majority of hormonal triiodothyronine (T3) is produced from prohormone thyroxine (T4) in numerous nonthyroidal organs and, with one exception, the T3 production rate has not been fully resolved in any single extrathyroidal organ of any species. Using a readily generalized graphic method called cut-set analysis, we show here that measured steady-state responses in several organs to three independent tracer infusions, two into blood and one directly into the organ(s) of interest, are sufficient to resolve this problem for organs fully accessible to direct infusion in vivo.