Optimal response-adaptive designs for continuous responses in phase III trials

Optimal response-adaptive designs in phase III clinical trial set up are gaining more interest. Most of the available designs are not based on any optimal consideration. An optimal design for binary responses is given by Rosenberger et al. (2001) and one for continuous responses is provided by Biswas and Mandal (2004). Recently, Zhang and Rosenberger (2006) proposed another design for normal responses. This paper illustrates that the Zhang and Rosenberger (2006) design is not suitable for normally distributed responses, in general. The approach cannot be extended for other continuous response cases, such as exponential or gamma. In this paper, we first describe when the optimal design of Zhang and Rosenberger (2006) fails. We then suggest the appropriate adjustments for designs in different continuous distributions. A unified framework to find optimal response-adaptive designs for two competing treatments is proposed. The proposed methods are illustrated using some real data.     

Application of porous teflon tubing method to automatic fed-batch culture of microorganisms. I. Mass transfer through porous teflon tubing

For the purpose of a rational design for an automatic feedback control system incorporating a porous Teflon tubing sensor in semibatch culture, steady-state mass-transfer characteristics of tubing sensors have been investigated theoretically and experimentally, and also dynamic responses have been studied experimentally. A distributed mathematical model for steady-state diffusion has been solved numerically and its solution has been shown as useful for the sensor design. The overall mass-transfer resistance of radial diffusion has been shown to be the sum of external liquid-film mass-transfer resistance and membrane diffusion resistance. The steady-state experiments using ethanol dissolved in water revealed that its transfer into the tubing was controlled by the molecular diffusion within the tubing-wall membrane. Oxygen transfer from external water into the tubing was shown experimentally to be controlled by the liquid-film resistance outside the tubing. In general, the radial mass transfer of a substance having a small Henry's constant is controlled by the liquid-film resistance. The response of the tubing sensor-detector-recorder system for the stepwise addition of ethanol into the external water could not be represented by a simple combined system of the first-order delay with lag time. The responses depend on the characteristics of the tubing as well as flow rate of the carrier gas, etc., but they were quite excellent in all cases (e.g., 90% in 20 s).     

A comparison of tomato (Lycopersicon esculentum) lectin with its deglycosylated derivative

A regime is proposed for the design of coupled enzyme assays in which auxiliary enzymes are added at concentrations proportional to their Km values. Under these conditions it is possible to calculate the complete time course of the assay including the time required for the system to approach its steady state. The consequence of increasing the number of coupling enzymes is shown to be a considerable decrease in time required to reach the steady state provided that the overall transient time remains the same. The method is extended to the general consideration of pathways and shows that pathways of the same length exhibit identical temporal responses provided that the units of concentration and time used are based on the steady-state concentration of intermediates and the transient time respectively. An unexpected finding is that increasing the number of intermediates in a pathway can decrease the time required to enter a steady state.     

Applications of nonequilibrium response spectroscopy to the study of channel gating. Experimental design and optimization

A novel experimental technique known as non-equilibrium response spectroscopy (NRS) based on ion channel responses to rapidly fluctuating voltage waveforms was recently described (Millonas & Hanck, 1998a). It was demonstrated that such responses can be affected by subtle details of the kinetics that are otherwise invisible when conventional stepped pulses are applied. As a consequence, the kinetics can be probed in a much more sensitive way by supplementing conventional techniques with measurements of the responses to more complex voltage waveforms. In this paper we provide an analysis of the problem of the design and optimization of such waveforms. We introduce some methods for determination of the parametric uncertainty of a class of kinetic models for a particular data set. The parametric uncertainty allows for a characterization of the amount of kinetic information acquired through a set of experiments which can in turn be used to design new experiments that increase this information. We revisit the application of dichotomous noise (Millonas & Hanck, 1998a, b), and further consider applications of a more general class of continuous wavelet -based waveforms. A controlled illustration of these methods is provided by making use of a simplified "toy" model for the potassium channel kinetics.     

Cross-subtype T-cell immune responses induced by a human immunodeficiency virus type 1 group m consensus env immunogen

The genetic diversity among globally circulating human immunodeficiency virus type 1 (HIV-1) strains is a serious challenge for HIV-1 vaccine design. We have generated a synthetic group M consensus env gene (CON6) for induction of cross-subtype immune responses and report here a comparative study of T-cell responses to this and natural strain env immunogens in a murine model. Three different strains of mice were immunized with CON6 as well as subtype A, B, or C env immunogens, using a DNA prime-recombinant vaccinia virus boost strategy. T-cell epitopes were mapped by gamma interferon enzyme-linked immunospot analysis using five overlapping Env peptide sets from heterologous subtype A, B, and C viruses. The CON6-derived vaccine was immunogenic and induced a greater number of T-cell epitope responses than any single wild-type subtype A, B, and C env immunogen and similar T-cell responses to a polyvalent vaccine. The responses were comparable to within-clade responses but significantly more than between-clade responses. The magnitude of the T-cell responses induced by CON6 (measured by individual epitope peptides) was also greater than the magnitude of responses induced by individual wild-type env immunogens. Though the limited major histocompatibility complex repertoire in inbred mice does not necessarily predict responses in nonhuman primates and humans, these results suggest that synthetic centralized env immunogens represent a promising approach for HIV-1 vaccine design that merits further characterization.     

Hierarchical Bayesian inference for HIV dynamic differential equation models incorporating multiple treatment factors

Studies on HIV dynamics in AIDS research are very important in understanding the pathogenesis of HIV‐1 infection and also in assessing the effectiveness of antiretroviral (ARV) treatment. Viral dynamic models can be formulated through a system of nonlinear ordinary differential equations (ODE), but there has been only limited development of statistical methodologies for inference. This article, motivated by an AIDS clinical study, discusses a hierarchical Bayesian nonlinear mixed‐effects modeling approach to dynamic ODE models without a closed‐form solution. In this model, we fully integrate viral load, medication adherence, drug resistance, pharmacokinetics, baseline covariates and time‐dependent drug efficacy into the data analysis for characterizing long‐term virologic responses. Our method is implemented by a data set from an AIDS clinical study. The results suggest that modeling HIV dynamics and virologic responses with consideration of time‐varying clinical factors as well as baseline characteristics may be important for HIV/AIDS studies in providing quantitative guidance to better understand the virologic responses to ARV treatment and to help the evaluation of clinical trial design in response to existing therapies.     

Regulatory design in a simple system integrating membrane potential generation and metabolic ATP consumption. Robustness and the role of energy dissipating processes

Bacterial physiological responses integrate energy-coupling processes at the membrane level with metabolic energy demand. The regulatory design behind these responses remains largely unexplored. Propionigenium modestum is an adequate organism to study these responses because it presents the simplest scheme known integrating membrane potential generation and metabolic ATP consumption. A hypothetical sodium leak is added to the scheme as the sole regulatory site. Allosteric regulation is assumed to be absent. Information of the rate equations is not available. However, relevant features of the patterns of responses may be obtained using Metabolic Control Analysis (MCA) and Metabolic Control Design (MCD). With these tools, we show that membrane potential disturbances can be compensated by adjusting the leak flux, without significant perturbations of ATP consumption. Perturbations of membrane potential by ATP demand are inevitable and also require compensatory changes in the leak. Numerical simulations were performed with a kinetic model exhibiting the responses for small changes obtained with MCA and MCD. A modest leak (10% of input) was assumed for the reference state. We found that disturbances in membrane potential and ATP consumption, produced by environmental perturbations of the cation concentration, may be reverted to the reference state adjusting the leak. Leak changes can also compensate for undesirable effects on membrane potential produced by changes in nutrient availability or ATP demand, in a wide range of values. The system is highly robust to parameter fluctuations. The regulatory role of energy dissipating processes and the trade-off between energetic efficiency and regulatory capacity are discussed.     

Th1/Th17 cell induction and corresponding reduction in ATP consumption following vaccination with the novel Mycobacterium tuberculosis vaccine MVA85A

Vaccination with Bacille Calmette-Guérin (BCG) has traditionally been used for protection against disease caused by the bacterium Mycobacterium tuberculosis (M.tb). The efficacy of BCG, especially against pulmonary tuberculosis (TB) is variable. The best protection is conferred in temperate climates and there is close to zero protection in many tropical areas with a high prevalence of both tuberculous and non-tuberculous mycobacterial species. Although interferon (IFN)-γ is known to be important in protection against TB disease, data is emerging on a possible role for interleukin (IL)-17 as a key cytokine in both murine and bovine TB vaccine studies, as well as in humans. Modified Vaccinia virus Ankara expressing Antigen 85A (MVA85A) is a novel TB vaccine designed to enhance responses induced by BCG. Antigen-specific IFN-γ production has already been shown to peak one week post-MVA85A vaccination, and an inverse relationship between IL-17-producing cells and regulatory T cells expressing the ectonucleosidease CD39, which metabolises pro-inflammatory extracellular ATP has previously been described. This paper explores this relationship and finds that consumption of extracellular ATP by peripheral blood mononuclear cells from MVA85A-vaccinated subjects drops two weeks post-vaccination, corresponding to a drop in the percentage of a regulatory T cell subset expressing the ectonucleosidase CD39. Also at this time point, we report a peak in co-production of IL-17 and IFN-γ by CD4(+) T cells. These results suggest a relationship between extracellular ATP and effector responses and unveil a possible pathway that could be targeted during vaccine design.     

A Response-Additive Model for Analyzing Mixtures of Two Chemicals in the Salmonella Reversion Assay

A statistical model is proposed for analyzing the mutagenic responses produced by mixtures of two chemicals in the Salmonella reversion assay. This model is based on the simplex-lattice design for mixtures with the total concentration fixed. The dose-response relationship is expressed as a function of both the proportions of the two chemicals and the total concentration of the chemicals in the mixture. If the joint action of two chemicals can be predicted by response-additivity, then the response of the mixture at the total concentration T can be represented by the weighted average of the responses produced by the individual chemicals at the same concentration T with the weights for individual responses being equal to the proportions of the chemicals in the mixture. Two non-additive models, synergism and antagonism, are discussed. An example is illustrated by analyzing the joint mutagenic effects of 1-nitrobenzo(a)pyrene (1-NBP), and 3-NBP in the Salmonella reversion assay.     

Soft sensor based on 2D‐fluorescence and process data enabling real‐time estimation of biomass in Escherichia coli cultivations

In bioprocesses, specific process responses such as the biomass cannot typically be measured directly on‐line, since analytical sampling is associated with unavoidable time delays. Accessing those responses in real‐time is essential for Quality by Design and process analytical technology concepts. Soft sensors overcome these limitations by indirectly measuring the variables of interest using a previously derived model and actual process data in real time. In this study, a biomass soft sensor based on 2D‐fluorescence data and process data, was developed for a comprehensive study with a 20‐L experimental design, for Escherichia coli fed‐batch cultivations. A multivariate adaptive regression splines algorithm was applied to 2D‐fluorescence spectra and process data, to estimate the biomass concentration at any time during the process. Prediction errors of 4.9% (0.99 g/L) for validation and 3.8% (0.69 g/L) for new data (external validation), were obtained. Using principal component and parallel factor analyses on the 2D‐fluorescence data, two potential chemical compounds were identified and directly linked to cell metabolism. The same wavelength pairs were also important predictors for the regression‐model performance. Overall, the proposed soft sensor is a valuable tool for monitoring the process performance on‐line, enabling Quality by Design.     

Design a questionnaire.

The design of questionnaires is a craft which has been badly neglected by the medical profession. A questionnaire should be appropriate, intelligible, unambiguous, unbiased, capable of coping with all possible responses, satisfactorily coded, piloted, and ethical. The key steps in designing a questionnaire are to: decide what data you need, select items for inclusion, design the individual questions, compose the wording, design the layout and presentation, think about coding, prepare the first draft and pretest, pilot, and evaluate the form, and perform the survey. Despite the apparently complicated nature of the task, theoretical knowledge is no substitute for practical experience.     

Time-locked and phase-locked features of P300 event-related potentials (ERPs) for brain–computer interface speller

The brain–computer interface P300 speller is aimed to help those patients unable to activate muscles to spell words by utilizing their brain activity. However, a problem associated with the use of this brain–computer interface paradigm is the generation mechanics of P300 related to responses to visual stimuli. Herein, we investigated the event-related potential (ERP) response for the P300-based brain–computer interface speller. A signal preprocessing method integrated coherent average, principal component analysis (PCA) and independent component analysis (ICA) to reduce the dimensions and noise in the raw data. The time–frequency analysis was based on wavelet and two characteristic parameters of event-related spectral perturbation (ERSP) and inter-trial coherence (ITC) were computed to indicate the evoked response (time-locked) and phase reset (phase-locked) activity, respectively. Results demonstrated that the proposed method was valid for the time-locked and phase-locked feature extraction and both the evoked response and phase reset contributed to the genesis of the P300 signal. These electrophysiological responses characteristics of ERPs would be used for BCI P300 speller design and its signal processing strategies.     

A Predictive Reinforcement Model of Dopamine Neurons for Learning Approach Behavior

A neural network model of how dopamine and prefrontal cortex activity guides short- and long-term information processing within the cortico-striatal circuits during reward-related learning of approach behavior is proposed. The model predicts two types of reward-related neuronal responses generated during learning: (1) cell activity signaling errors in the prediction of the expected time of reward delivery and (2) neural activations coding for errors in the prediction of the amount and type of reward or stimulus expectancies. The former type of signal is consistent with the responses of dopaminergic neurons, while the latter signal is consistent with reward expectancy responses reported in the prefrontal cortex. It is shown that a neural network architecture that satisfies the design principles of the adaptive resonance theory of Carpenter and Grossberg (1987) can account for the dopamine responses to novelty, generalization, and discrimination of appetitive and aversive stimuli. These hypotheses are scrutinized via simulations of the model in relation to the delivery of free food outside a task, the timed contingent delivery of appetitive and aversive stimuli, and an asymmetric, instructed delay response task.     

Moth hearing in response to bat echolocation calls manipulated independently in time and frequency

We measured the auditory responses of the noctuid moth Noctua pronuba to bat echolocation calls which were manipulated independently in time and frequency. Such manipulations are important in understanding how insect hearing influences the evolution of echolocation call characteristics. We manipulated the calls of three bat species (Rhinolophus hipposideros, Myotis nattereri and Pipistrellus pipistrellus) that use different echolocation call features by doubling their duration or reducing their frequency, and measured the auditory thresholds from the A1 cells of the moths. Knowing the auditory responses of the moth we tested three predictions. (i) The ranking of the audibility of unmanipulated calls to the moths should be predictable from their temporal and/or frequency structure. This was supported. (ii) Doubling the duration of the calls should increase their audibility by ca. 3 dB for all species. Their audibility did indeed increase by 2.1-3.5 dB. (iii) Reducing the frequency of the calls would increase their audibility for all species. Reducing the frequency had small effects for the two bat species which used short duration (2.7-3.6 ms) calls. However, the relatively long-duration (50 ms), largely constant-frequency calls of R. hipposideros increased in audibility by 21.6 dB when their frequency was halved. Time and frequency changes influence the audibility of calls to tympanate moths in different ways according to call design. Large changes in frequency and time had relatively small changes on the audibility of calls for short, largely broadband calls. Channelling energy into the second harmonic of the call substantially decreased the audibility of calls for bats which use long-duration, constant-frequency components in echolocation calls. We discuss our findings in the contexts of the evolution of both bat echolocation call design and the potential responses of insects which hear ultrasound.     

Development and validation of a capillary zone electrophoresis method for the determination of ephedrine and related compounds in urine without extraction

A capillary zone electrophoresis (CZE) method, with UV detection and in the presence of dimethyl-beta-CD, was optimized by means of an experimental design for the separation and the simultaneous quantitation of ephedrine, pseudoephedrine, norephedrine (phenylpropanolamine) and norpseudoephedrine (cathine) in urine without any extraction. In this application, the optimization of the analytical conditions with an experimental design was preferred to a univariate study. Therefore, a central composite design was used and the following factors were investigated and varied simultaneously: buffer concentration, buffer pH and dimethyl-beta-CD concentration. In order to evaluate the influence of each experimental parameter on the analytical separation, the resolutions between the four compounds, as well as the separation time and generated current were observed and established as responses of the experimental design. A model was obtained for each response by linear multiple regression of a second-degree mathematical expression. After acceptance of the mathematical models, the most favorable conditions were determined by maximizing the resolutions between the four compounds and by setting the other responses at threshold values. Successful results were obtained with a 260 mM Tris-phosphate buffer at pH 3.5 in the presence of 13.3 mM dimethyl-beta-CD at 25 degrees C and with an applied voltage of 30 kV. Under these optimized conditions, a baseline separation of the four compounds was achieved in less than 6 min. The method was validated in terms of precision, linearity, accuracy and successfully applied for the determination of these compounds in urine samples without any extraction as well as in nutritional supplements.     

Consequential Life Cycle Assessment With Market‐Driven Design

This article describes the development of a consequential life cycle assessment (cLCA) with endogenous market‐driven design (MDD). Incorporation of MDD within cLCA (cLCA‐MDD) is beneficial because design decisions, influenced by market forces, are a major source of environmental emissions and resource consumption in many life cycle systems. cLCA‐MDD captures the environmental impact of these design responses resulting from industrial and policy decisions. We begin by developing the concept of cLCA‐MDD, then present a case study that demonstrates how design responses can be endogenously captured in a cLCA analysis. The case study is in two parts: First, we incorporate endogenous design responses into a cLCA of a mid‐size vehicle and, second, we conduct a policy analysis using a cLCA‐MDD approach. The case study illustrates that cLCA‐MDD can capture multiple “ripple effects” resulting from an industrial decision (e.g., downsizing a vehicle's engine) or a policy decision (e.g., raising gasoline taxes) and that these effects significantly influence results. A key challenge of the approach is appropriately managing and communicating uncertainties associated with the choice of economic parameters or models. We discuss sources of uncertainty in cLCA‐MDD and demonstrate a presentation scheme to facilitate communication of result sensitivity to uncertainties from input parameters, models, and model structure.     

Parvovirus-like particles as vaccine vectors.

A wide array of systems have been developed to improve "classic" vaccines. The use of small polypeptides able to elicit potent antibody and cytotoxic responses seems to have enormous potential in the design of safer vaccines. While peptide coupling to large soluble proteins such as keyhole limpet hemocyanin is the current method of choice for eliciting antibody responses and insertion in live viruses for cytotoxic T-lymphocyte responses, alternative cheaper and/or safer methods will clearly be required in the future. Virus-like particles constitute very immunogenic molecules that allow for covalent coupling of the epitopes of interest in a simple way. In this article, we detail the methodology employed for the preparation of efficient virus vectors as delivery systems. We used parvovirus as the model for the design of new vaccine vectors. Recently parvovirus-like particles have been engineered to express foreign polypeptides in certain positions, resulting in the production of large quantities of highly immunogenic peptides, and to induce strong antibody, helper-T-cell, and cytotoxic T-lymphocyte responses. We discuss the different alternatives and the necessary steps to carry out this process, placing special emphasis on the flow of decisions that need to be made during the project.     

Quantifying latitudinal clines to light responses in natural populations of Arabidopsis thaliana (Brassicaceae)

Evidence of adaptation in Arabidopsis thaliana (Brassicaceae) phenotypic traits has rarely been shown. We demonstrate latitudinal clines in two A. thaliana traits: hypocotyl responses to red and far-red light. Natural populations of A. thaliana were sampled along a latitudinal gradient from southern to northern Norway. Seeds from maternal families within each population were subjected to 1 wk of constant red, far-red, blue, white, and dark treatments. Hypocotyl lengths were measured for each maternal family within each population. Significant variability within and among populations in hypocotyl responses for the various treatments was found. There was a significant latitudinal cline in hypocotyl responses for red and far-red treatments, with northern populations being more de-etiolated than southern populations. These results suggest that northern populations are more responsive to red and far-red light than southern populations. Thus, differentiation of seedling traits in natural populations of A. thaliana seems in part to be mediated by the phytochrome pathway. There was no correlation between hypocotyl responses and flowering time for any treatment. This suggests that flowering time variability and variability in hypocotyl responses may not be governed by genes shared between the pathways, such as those involved in photoreception or the circadian clock.     

The use of historical environmental monitoring data to test predictions on cross-scale ecological responses to alterations in river flows

Determination of ecological responses to river flows is fundamental to understanding how flow-dependent ecosystems have been altered by regulation, water diversions and climate change, and how to effect river restoration. Knowledge of ecohydrological relationships can support water management and policy, but this is not always the case. Management rules have tended to be developed ahead of scientific knowledge. The lag between practice and knowledge could be addressed by using historical monitoring data on ecological responses to changes in flows to determine significant empirical ecohydrological relationships, as an adjunct to investigating responses prospectively. This possibility was explored in the Murray–Darling Basin, Australia. We assessed 359 data sets collected during monitoring programs across the basin. Of these, only 32 (9%) were considered useful, based on a match between the scale at which sampling was done and ecological responses are likely to occur, and used to test flow–ecology predictions for phytoplankton, macroinvertebrates, fishes, waterbirds, floodplain trees, basin-scale vegetation and estuarine biota. We found relationships between flow and ecological responses were likely to be more strongly supported for large, long-lived, widespread biota (waterbirds, basin-scale vegetation, native fishes), than for more narrowly distributed (e.g. estuarine fishes) or smaller, short-lived organisms (e.g. phytoplankton, macroinvertebrates). This pattern is attributed to a mismatch between the design of monitoring programs and the response time frames of individual biota and processes, and to the use of local river discharge as a primary predictor variable when, for many biotic groups, other predictors need to be considered.