Surrogate Systems Research Articles

Sequential kriging optimization using multiple-fidelity evaluations

When cost per evaluation on a system of interest is high, surrogate systems can provide cheaper but lower-fidelity information. In the proposed extension of the sequential kriging optimization method, surrogate systems are exploited to reduce the total evaluation cost. The method utilizes data on all systems to build a kriging metamodel that provides a global prediction of the objective function and a measure of prediction uncertainty. The location and fidelity level of the next evaluation are selected by maximizing an augmented expected improvement function, which is connected with the evaluation costs. The proposed method was applied to test functions from the literature and a metal-forming process design problem via finite element simulations. The method manifests sensible search patterns, robust performance, and appreciable reduction in total evaluation cost as compared to the original method.

Partitioning of organic compounds in phases imitating the headgroup and core regions of phospholipid bilayers.

Solvation free energies of drugs, peptides, and other small molecules in the core and headgroup regions of phospholipid bilayers determine their conformations, accumulation, and transport properties. The transfer free energy includes the energy terms for the formation of a cavity for the solute, the interactions of the solute with phospholipids, electrostatic interactions of the solute with the membrane, and dipole potentials and entropy terms. The interaction energies with phospholipids can be estimated by correlating the partitioning in surrogate solvent systems and in the bilayer. As the headgroup surrogate, we use diacetylphosphatidylcholine (DAcPC), the acetylated headgroup of the most abundant mammalian phospholipid, phosphatidylcholine, which forms a homogeneous solution with acceptable viscosity when mixed with water in ratios similar to those in the fully hydrated bilayer. The two-phase system of n-hexadecane (C16) as the core surrogate and hydrated DAcPC was used to monitor partitioning of 16 nonionizable compounds. On the bilogarithmic scale, the C16/DAcPC partition coefficients correlate neither with those in the C16/water and 1-octanol/water systems nor with their difference, which is frequently used as a parameter of hydrogen bonding for prediction of the bilayer location of the solutes. The C16/DAcPC system provides a satisfactory emulation of the solvation properties of the bilayer regions, as reflected in correct predictions of the bilayer location for those of the studied chemicals, for which this information is available.

Phenotyping hepatitis B virus variants: From transfection towards a small animal in vivo infection model

The existence of vaccine escape and drug resistant hepatitis B virus (HBV) variants is now well established, and various of the underlying prototypic mutations have been defined. Genotypic detection of such variants allows to predict their clinical phenotype. However, the relevance of non-predefined mutations occurring during therapy can be assessed only by phenotypic assays. The fundamental properties of a functional virus are the ability to replicate the genome, to form infectious virions, and to cope with the host defense in order to establish and maintain infection; a virus meeting all these criteria is biologically fit. At present, HBV DNA transfection provides a reliable method to address replication-competence and physical formation of complete virus particles. The inherent inter-experiment variability of transient transfection can be overcome by stable cell lines expressing wild-type and prototypic variant HBVs. Such cell lines provide important tools for studying basic aspects of HBV replication as well as for drug discovery. Phenotypic assays measuring HBV infectivity are less advanced but several surrogate systems obviating the need for primary human hepatocyte cultures are being established. The ultimate, and most desirable, phenotypic assay system would be a small, immuno-competent experimental animal in which human HBV can establish chronic infection. Only this would allow to fully address the fitness of HBV variants, and thus to assess the risk of their spreading in the general population. Various ways towards this goal can be envisaged but recent model studies in the duck HBV system indicate that much more has to be learned on the molecular determinants of hepadnaviral host-range to rationally design such experiments.

Performance characterization of megavoltage computed tomography imaging on a helical tomotherapy unit

Helical tomotherapy is an innovative means of delivering IGRT and IMRT using a device that combines features of a linear accelerator and a helical computed tomography (CT) scanner. The HI-ART II can generate CT images from the same megavoltage x-ray beam it uses for treatment. These megavoltage CT (MVCT) images offer verification of the patient position prior to and potentially during radiation therapy. Since the unit uses the actual treatment beam as the x-ray source for image acquisition, no surrogate telemetry systems are required to register image space to treatment space. The disadvantage to using the treatment beam for imaging, however, is that the physics of radiation interactions in the megavoltage energy range may force compromises between the dose delivered and the image quality in comparison to diagnostic CT scanners. The performance of the system is therefore characterized in terms of objective measures of noise, uniformity, contrast, and spatial resolution as a function of the dose delivered by the MVCT beam. The uniformity and spatial resolutions of MVCT images generated by the HI-ART II are comparable to that of diagnostic CT images. Furthermore, the MVCT scan contrast is linear with respect to the electron density of material imaged. MVCT images do not have the same performance characteristics as state-of-the art diagnostic CT scanners when one objectively examines noise and low-contrast resolution. These inferior results may be explained, at least partially, by the low doses delivered by our unit; the dose is 1.1 cGy in a 20 cm diameter cylindrical phantom. In spite of the poorer low-contrast resolution, these relatively low-dose MVCT scans provide sufficient contrast to delineate many soft-tissue structures. Hence, these images are useful not only for verifying the patient's position at the time of therapy, but they are also sufficient for delineating many anatomic structures. In conjunction with the ability to recalculate radiotherapy doses on these images, this enables dose guidance as well as image guidance of radiotherapy treatments.

Low-dose ionizing radiation: induction of differential intracellular signalling possibly affecting intercellular communication

Given the complexity of the carcinogenic process and the lack of any mechanistic understanding of how ionizing radiation at low-level exposures affects the multistage, multimechanism processes of carcinogenesis, it is imperative that concepts and paradigms be reexamined when extrapolating from high dose to low dose. Any health effect directly linked to low-dose radiation exposure must have molecular/biochemical and biological bases. On the other hand, demonstrating some molecular/biochemical or cellular effect, using surrogate systems for the human being, does not necessarily imply a corresponding health effect. Given the general acceptance of an extrapolated LNT model, our current understanding of carcinogenesis cries out for a resolution of a real problem. How can a low-level acute, or even a chronic, exposure of ionizing radiation bring about all the different mechanisms (mutagenic, cytotoxic, and epigenetic) and genotypic/phenotypic changes needed to convert normal cells to an invasive, malignant cell, given all the protective, repair, and suppressive systems known to exist in the human body? Until recently, the prevailing paradigm that ionizing radiation brings about cancer primarily by DNA damage and its conversion to gene and chromosomal mutations, drove our interpretation of radiation carcinogenesis. Today, our knowledge includes the facts both that epigenetic events play a major role in carcinogenesis and that low-dose radiation can also induce epigenetic events in and between cells in tissues. This challenges any simple extrapolation of the LNT model. Although a recent delineation of "hallmarks" of the cancer process has helped to focus on how ionizing radiation might contribute to the induction of cancers, several other hallmarks, previously ignored--namely, the stem cells in tissues as targets for carcinogenesis and the role of cell-cell communication processes in modulating the radiation effects on the target cell--must be considered, particularly for the adaptive response, bystander effects, and genomic instability phenomena.

Surrogate in-vehicle information systems and driver behaviour in an urban environment: A field study on the effects of visual and cognitive load

Abstract This field study was designed to investigate and compare the potential or sensitivity of the selected HASTE assessment methods to reflect the effects of different surrogate in-vehicle information systems (S-IVIS) on driver behaviour in an urban environment. Two types of S-IVIS were used, an auditory one representing cognitive tasks and a visual one. The interaction with other vehicles in yielding situations changed somewhat when conducting the secondary task compared to normal driving. Both S-IVIS tasks tended to decrease the proportion of proper yielding of the right-of-way to other vehicles at urban intersections. In addition, the interaction with vulnerable road users was affected by secondary task performance as well. The S-IVIS tasks tended to produce increases in speed before the intersection in cases when there were vulnerable road users present at the urban intersection compared to driving without the secondary task. However, the cognitive task seemed more frequently to cause observed inappropriate behaviour towards vulnerable road users at urban intersections than the visual task. For both S-IVIS tasks, the percentage of correct responses was highest for the static situation and lowest when conducted in urban environment and the percentage of correct responses decreased with increasing task difficulty. In general, the results suggest that driving with a secondary task in an urban environment caused some changes in driving behaviour. In particular, proper interaction with other road users suffered when the driver had a secondary task.

Surrogate in-vehicle information systems and driver behaviour: Effects of visual and cognitive load in simulated rural driving

The underlying aim of HASTE, an EU FP5 project, is the development of a valid, cost-effective and reliable assessment protocol to evaluate the potential distraction of an in-vehicle information system on driving performance. As part of this development, the current study was performed to examine the systematic relationship between primary and secondary task complexity for a specific task modality in a particular driving environment. Two fundamentally distinct secondary tasks (or surrogate in-vehicle information systems, sIVIS) were developed: a visual search task, designed such that it only required visual processing/demand and an auditory continuous memory task, intended to cognitively load drivers without any visual stimulus. A high fidelity, fixed-base driving simulator was used to test 48 participants on a car following task. Virtual traffic scenarios varied in driving demand. Drivers compensated for both types of sIVIS by reducing their speed (this result was more prominent during interaction with the visual task). However, they seemed incapable of fully prioritising the primary driving task over either the visual or cognitive secondary tasks as an increase in sIVIS demand was associated with a reduction in driving performance: drivers showed reduced anticipation of braking requirements and shorter time-to-collision. These results are of potential interest to designers of in-vehicle systems.

Comparing the driving performance of average and older drivers: The effect of surrogate in-vehicle information systems

Two Surrogate In-Vehicle Information Systems (S-IVIS) were developed for this study: a visual S-IVIS was designed to investigate the effect of increasing visual information on driving performance, whilst the effect of increasing cognitive demand was studied using a auditory memory task. The interaction between each of these tasks and driving was observed in a field study using Finnish drivers, and in the Leeds advanced driving simulator, using British participants. For each site, drivers were selected from one of two age groups: (i) average drivers aged between 25 and 50, with at least five years’ driving experience and (ii) older participants over the age of 60. Each secondary task was performed in isolation, and in combination with driving. Compared to the older drivers, average drivers were more successful at performing the two S-IVIS tasks, both in isolation, and with driving. In the field, the effect of the two S-IVIS tasks was found to be more profound on older drivers, resulting in closer car following, more speed variation and less lane keeping compared to average drivers. The effect of the two secondary tasks on simulated driving was found to be slightly different to that of the field drives, with older drivers keeping longer distance headways and reducing their speed in the presence of the S-IVIS tasks. The implications of these findings are discussed.

Design and Analysis of Variable Fidelity Experimentation Applied to Engine Valve Heat Treatment Process Design

Summary When experimentation on a real system is expensive, data are often collected by using cheaper, lower fidelity surrogate systems. The paper concerns response surface methods in the context of variable fidelity experimentation. We propose the use of generalized least squares to generate the predictions. We also present perhaps the first optimal designs for variable fidelity experimentation, using an extension of the expected integrated mean-squared error criterion. Numerical tests are used to compare the performance of the method with alternatives and to investigate the robustness to incorporated assumptions. The method is applied to automotive engine valve heat treatment process design in which real world data were mixed with data from two types of computer simulation.

The role of stem cells and cell–cell communication in radiation carcinogenesis: ignored concepts

Given the complexity of the carcinogenic process and the relative lack of mechanistic understanding about how ionising radiation at low level exposures affects the multistage, multimechanism processes of carcinogenesis, it is imperative that major concepts and paradigms be re-examined when extrapolating from high level to low level results. Clearly, any health effect directly linked to low level radiation exposure must have molecular/biochemical and biological bases. On the other hand, demonstrating some molecular/biochemical or cellular effect, using surrogate systems for the whole human being, may not have a corresponding health effect. Given the general acceptance of an extrapolated linear no-threshold (LNT) model, our current understanding of the multistage, multimechanism process of carcinogenesis cries out for a resolution of a real problem. How can a low level acute, or even chronic, exposure of ionising radiation bring about all the different mechanisms (mutagenic, cytotoxic and epigenetic) and ge...

Implications of finding synergic in vitro drug-drug interactions between interferon- and ribavirin for the treatment of hepatitis C virus

Hepatitis C virus (HCV) infections are currently treated using a combination of interferon-alpha (IFN-alpha) and ribavirin (RBV). If IFN-alpha is utilized alone, the sustained virological response (SVR) rate is approximately 20%, whereas when RBV is used alone it does not lead to an SVR. However, when IFN-alpha and RBV are used together, the combination leads to an SVR rate of approximately 40%. This clinical synergy is thought to be due to the direct antiviral effects of RBV, or to indirect effects of RBV that stimulate the immune response. Evidence for either hypothesis is limited. Recently, we undertook an in vitro drug-drug combination analysis using surrogate model systems of HCV replication and found a reproducible synergy of antiviral effects between the two drugs at physiologically relevant drug concentrations. Our findings provide experimental support for the contention that the direct effects of these drugs' antiviral activity are responsible for the clinical synergy observed in patients.

The 3rd Cabo Gene Therapy Focus Panel: On the Offensive for Biodefense

The 3rd Cabo Gene Therapy Focus Panel: On the Offensive for Biodefense

Toxicogenomics: Impact on human health

Toxicology is the science of adverse effects of chemicals, drugs, environmental agents, and stressors. Genomics defines the structure, sequence (code), and function of the entire DNA complement of organisms. The interface of these diverse disciplines is called toxicogenomics and is based upon the application of genomic technologies to define globally the changes in gene expression (both mRNA and proteins) as a consequence of exposures. DNA microarray technology enables the simultaneous measurement of transcription of thousands of genes using microchips containing thousands of probes of complementary DNA (cDNA) immobilized in a predetermined array. The ultimate application of this technology to toxicology holds great promise but faces several formidable problems. With the solution to these problems, it will be possible to develop a substantial database of Chemical Effects in Biological Systems (CEBS). Such a database will provide the capacity to relate specific changes in gene expression to specific adverse effects and to look for similar pathways in different organisms. Such data will provide an objective way of assessing surrogate systems for reporting or predicting potential adverse effects in humans. While the potential for toxicogenomics is thus very high for studying active substances, the task must be approached in a deliberate, incremental manner to insure that only high-quality data are compiled and analyzed. This workshop will present the latest results of research conducted in leading international laboratories studying endocrine-mediated toxicity.

Hepatitis C virus cell culture replication systems: their potential use for the development of antiviral therapies.

Hepatitis C virus is a significant public health problem. Current drug regimens have low efficacy against some hepatitis C virus genotypes, while no vaccine is available. The absence of an efficient cell culture system and an accessible small animal model to study hepatitis C virus replication and pathogenesis are major obstacles to the development of effective antiviral therapies. Studies of surrogate model systems, either related viruses or chimeric viruses containing part of the hepatitis C virus genome, have given insight into hepatitis C virus replication, in addition to being a powerful tool for drug discovery. The recent development of an efficient system for the initiation of replication in cell culture provides a viable screen for inhibitors of hepatitis C virus replication. It also brings us much closer to the ultimate goal of an infectious cell culture system for hepatitis C virus.

New animal models of hepatitis B and C.

The narrow host range of infection and lack of suitable tissue culture systems for the propagation of hepatitis B and C viruses are limitations that have prevented a more thorough understanding of persistent infection and the pathogenesis of chronic liver disease. With hepatitis B virus (HBV), this lack of knowledge has been partially overcome by the discovery and characterization of HBV-like viruses in wild animals. With hepatitis C virus (HCV), related flaviviruses have been used as surrogate systems for such studies. Other laboratories have developed transgenic mice that express virus gene products and/or support virus replication. Some HBV transgenic mouse models develop fulminant hepatitis, acute hepatitis, or chronic liver disease after adoptive transfer, and others spontaneously develop hepatocellular carcinoma (HCC), as in human infections. Among HCV transgenic mice, most develop no disease, but acute hepatitis has been observed in one model, and HCC in another. Although mice are not susceptible to HBV and HCV, their ability to replicate these viruses and to develop liver diseases characteristic of human infections provides new opportunities to study pathogenesis and develop novel therapeutics.

Health-effects related structure–toxicity relationships: a paradigm for the first decade of the new millennium

Prediction of the effects of industrial chemicals to humans will be an area of increasing concern in the next century. The role of quantitative structure–activity relationships (QSARs) is to aid in the prediction of effects by determination of the limits of variation in structure that are consistent with the production of a specific toxic effect and define the ways in which alterations in structure influences toxicity. The paradigm followed in the development of QSARs for ecotoxic-endpoints has been successful as a direct result of the availability of in vivo toxicity data in which to build initial QSARs and validate surrogate test systems. However, the lack of quantitative in vivo toxicity data means this paradigm cannot be used in the prediction of human health-effect endpoints. Therefore, a new paradigm, which provides guidance in the use of predictive QSARs for health-effects that serves to circumvent the problems associated with the lack of whole-mammal toxicity data must be established. A scenario is given that provides for the development, standardization, and validation of health-effects related QSARs in the first decade of the 21st century. Due to the structural diversity and sheer number of industrial organic chemicals, assays used to garner health-effects data must be based on quantifiable, rapid, reliable, and inexpensive surrogate endpoints. New ‘biotools’ developed using modern molecular techniques will aid in the circumvention of in vivo health-effects data and provide measurable endpoints, which can be used as surrogates for health-effects endpoints. This has particular application in receptor-mediated toxicity and gene expression. The lack of whole-mammal health-effects data means that the standardization and validation, of these endpoints will be accomplished in novel ways. Databases garnered using modern biotools will allow the derivation of QSARs developed for validated surrogate health-effect endpoints. If QSARs are to be useful in bridging gaps in health-effects data, they must be based on accurate, reproducible data for a robust series of non-congeneric chemicals. The latter applies to both toxicity and descriptor values. Because health-effects are often the result of metabolic activation, if these new QSARs are to be meaningful, validated software for predicting metabolite formation must be incorporated. Lastly, once QSARs and software are developed and validated, they will need to be linked into some type of expert system.

Chromatographic methods for the determination of the logL16 solute descriptor.

A squalane packed column and two open-tubular columns coated with an immobilized stationary phase film of poly(dimethylsiloxane) or poly(methyloctylsiloxane) are evaluated as surrogate chromatographic systems for the determination of the logL16 solute descriptor by gas chromatography. Retention on the squalane column is dominated by gas-liquid partitioning with a significant temperature-dependent contribution from interfacial adsorption at the liquid-solid interface. Using the gas-liquid partition coefficient as the dependent model variable allows logL16 to be estimated to +/- 0.026 log units over the temperature range 60-120 degrees C. Without correction for interfacial adsorption a single column estimation of logL16 with phase loadings of 8 to 20% (m/m) over the temperature range 80-120 degrees C is possible for compounds with moderate hydrogen-bond basicity. The poly(dimethylsiloxane) stationary phase is both dipolar and hydrogen-bond basic and less suitable than the poly(methyloctylsiloxane) stationary phase, which is less cohesive and has similar dipolarity but no hydrogen-bond basicity. The determination of logL16 on the poly(methyloctylsiloxane) column requires prior knowledge of the solute dipolarity/polarizability descriptor to avoid significant errors in the measurement of logL16 for polar compounds. In such circumstances a single column estimation of logL16 over the temperature range 60-140 degrees C with an error of +/- 0.05-0.09 log units is possible.

EDDS, an Escherichia coli-based system with a variety applications amenable to miniaturization

The miniaturization of molecular biology technologies into formats reminiscent of electronic 'chips' has proceeded rapidly, with nucleic acids allowing high-throughput DNA and RNA analysis. This has ushered in new eras in both biology and commerce with potentials yet to be fully appreciated and realized. Similar developments will be possible in other biological areas, as appropriate tools are adapted to formats amenable to miniaturization. Microchips with fluid-handling capabilities will allow for the growth of organisms in micro-formats. Whole-cell-based approaches will permit complex biological endpoints to be assayed. Escherichia coli provides a robust platform for a variety of assays that cover a diverse collection of biological endpoints, and we have developed a number of E. coli-based assays. Our most advanced platform is EDDS (E. coli dimer detection system). EDDS is a protein-protein interaction system (in some ways analogous to the yeast two-hybrid system) that is uniquely able to address membrane protein interactions. This presentation describes the principles behind EDDS and several of its implementations. We have developed applications of EDDS that include small molecule drug discovery, receptor-ligand interactions and matching, and proteomic applications that generate reagents useful in the description of gene function. EDDS and other microbial models that express mammalian genes provide surrogate systems for the development of many assays with diverse biological endpoints. Microbes are more robust and economical than mammalian cells and with their simple growth requirements will be amenable to the development of chip-based assays. A nanoliter of culture media can contain over 103 bacterium that can be engineered to provide signals that could be based on a wide range of complex biological endpoints.

Technological advances in high-throughput screening

A variety of assay technologies continue to be developed for high-throughput screening. These include cell-based assays, surrogate systems using microbial cells such as yeast and bacterial two-hybrid and three-hybrid systems, and systems to measure nucleic acid-protein and receptor-ligand interactions. Modifications have been developed for cell-free, homogeneous assay systems, such as time-resolved fluorescence, fluorescence polarization and the scintillation proximity assay. Innovations in engineering and chemistry have led to delivery systems for nanoliter volumes and sensitive biosensors for ultra-high-throughout screening conducted in nanoliter and picoliter volumes. Spectroscopic methods have been extended to read single molecule fluorescence. Technologies are being developed to identify new targets from genomic information in order to design the next generation of screens.

Expression cloning and receptor pharmacology of human calcitonin receptors from MCF-7 cells and their relationship to amylin receptors.

Human breast cell carcinoma MCF-7 cells were found to bind 125I-labeled rat amylin (rAmylin) and the peptide amylin antagonist radioligand 125I-AC512 with high affinity. This high affinity binding possessed characteristics unique to the already defined high affinity binding site for amylin in the rat nucleus accumbens [Mol. Pharmacol. 44:493-497 (1993); J. Pharmacol. Exp. Ther. 270:779-787 (1994); Eur. J. Pharmacol. 262:133-141 (1994)]. To further define this receptor, we report results of expression cloning studies from an MCF-7 cell library. We isolated two variants of a seven-transmembrane receptor that were identical to two previously described human calcitonin receptors (hCTR1 and hCTR2). These receptors were characterized by expression in different surrogate host cell systems. Transient expression of hCTR1 in COS cells yielded membranes that bound 125I-AC512 and 125I-salmon calcitonin with high affinity, but no high affinity binding was observed with 125I-human calcitonin (hCAL) or 125I-rAmylin. Stable expression of hCTR1 in HEK 293 cells produced similar data. In contrast, expression of hCTR2 in COS cells yielded membranes that bound 125I-AC512, 125I-hCAL, and 125I-rAmylin with high affinity. The agonists 125I-hCAL and 125I-rAmylin bound 65% and 1.5%, respectively, of the sites bound by the antagonist radioligand 125I-AC512 in this expression system. This pattern of binding was repeated in HEK 293 cells stably transfected with hCTR2 (125I-hCAL = 24.8% Bmax, 125I-rAmylin = 8% Bmax). In both expression systems, the agonists hCAL and rAmylin were much more potent in displacing their radioligand counterparts than was the antagonist radioligand 125I-AC512. For example, the pKi value for displacement of 125I-AC512 by rAmylin was 7.2 in HEK 293 cells but rose to 9.1 when displacing 125I-rAmylin. Finally, hCTR2 was expressed in baculovirus-infected Ti ni cells. In this system, only specific binding to the antagonist 125I-AC512 and agonist 125I-hCAL was observed; no binding to 125I-rAmylin could be detected. These data are discussed in terms of two working hypotheses. The first is that amylin is a weak agonist for hCTR2 and that this receptor is unrelated to the amylin receptor found in this cell line. The second is that hCTR2 couples to different G proteins for calcitonin and amylin function in different cells. At present, these data cannot be used to disprove conclusively either hypothesis.