Design of experiments for bivariate binary responses modelled by Copula functions

Optimal design for generalized linear models has primarily focused on univariate data. Often experiments are performed that have multiple dependent responses described by regression type models, and it is of interest and of value to design the experiment for all these responses. This requires a multivariate distribution underlying a pre-chosen model for the data. Here, we consider the design of experiments for bivariate binary data which are dependent. We explore Copula functions which provide a rich and flexible class of structures to derive joint distributions for bivariate binary data. We present methods for deriving optimal experimental designs for dependent bivariate binary data using Copulas, and demonstrate that, by including the dependence between responses in the design process, more efficient parameter estimates are obtained than by the usual practice of simply designing for a single variable only. Further, we investigate the robustness of designs with respect to initial parameter estimates and Copula function, and also show the performance of compound criteria within this bivariate binary setting.

Determining the optimal proportion of design in design-build request for proposals (RFPs)

The design-build (DB) system is a popular and effective delivery method of construction projects worldwide. After owners decide to procure their projects through the DB system, they may wish to determine the optimal proportion of design to be provided in the DB request for proposals (RFPs), which serve as solicitations for design-builders and describe the scope of work. However, this presents difficulties to DB owners and there is little, if any, systematic research in this area. This paper reports on an empirical study in the USA entailing both an online questionnaire survey and Delphi survey to identify and evaluate the factors influencing owners’ decisions in determining the proportion of design to include in DB RFPs. Eleven factors are identified, i.e. (1) clarity of project scope; (2) applicability of performance specifications; (3) desire for design innovation; (4) site constraints; (5) availability of competent design-builders; (6) project control requirements; (7) user group involvement level; (8) third party requirements; (9) owner experience with DB; (10) project complexity; and (11) schedule constraints. A statistically significant agreement on the eleven factors was also obtained from the (mainly non-owner) Delphi experts. Although some of the experts hold different opinions on how these factors affect the proportion of design, these findings furnish various stakeholders with a better understanding of the delivery process of DB projects and the appropriate provision of project information in DB RFPs. As the result is mainly industry opinion concerning the optimal proportion of design, in addition and for completeness, future studies should be conducted to obtain a big picture of the optimal proportion of design by means of seeking owners’ inputs.

Comparison of robust criteria for D-optimal design

This study compared the performance of a local and three robust optimality criteria in terms of the standard error for a one-parameter and a two-parameter nonlinear model with uncertainty in the parameter values. The designs were also compared in conditions where there was misspecification in the prior parameter distribution. The impact of different correlation between parameters on the optimal design was examined in the two-parameter model. The designs and standard errors were solved analytically whenever possible and numerically otherwise.

A review of modern computational algorithms for Bayesian optimal design

Bayesian experimental design is a fast growing area of research with many real-world applications. As computational power has increased over the years, so has the development of simulation-based design methods, which involve a number of algorithms, such as Markov chain Monte Carlo, sequential Monte Carlo and approximate Bayes methods, facilitating more complex design problems to be solved. The Bayesian framework provides a unified approach for incorporating prior information and/or uncertainties regarding the statistical model with a utility function which describes the experimental aims. In this paper, we provide a general overview on the concepts involved in Bayesian experimental design, and focus on describing some of the more commonly used Bayesian utility functions and methods for their estimation, as well as a number of algorithms that are used to search over the design space to find the Bayesian optimal design. We also discuss other computational strategies for further research in Bayesian optimal design.

Initial steps in optimal planning of a distribution system

This paper reports the initial steps of research on planning of rural networks for MV and LV. In this paper, two different cases are studied. In the first case, 100 loads are distributed uniformly on a 100 km transmission line in a distribution network and in the second case, the load structure become closer to the rural situation. In case 2, 21 loads are located in a distribution system so that their distance is increasing, distance between load 1 and 2 is 3 km, between 2 and 3 is 6 km, etc). These two models to some extent represent the distribution system in urban and rural areas, respectively. The objective function for the design of the optimal system consists of three main parts: cost of transformers, and MV and LV conductors. The bus voltage is expressed as a constraint and should be maintained within a standard level, rising or falling by no more than 5%.

Biosecurity threats : the design of surveillance systems, based on power and risk

We consider the problem of designing a surveillance system to detect a broad range of invasive species across a heterogeneous sampling frame. We present a model to detect a range of invertebrate invasives whilst addressing the challenges of multiple data sources, stratifying for differential risk, managing labour costs and providing sufficient power of detection.We determine the number of detection devices required and their allocation across the landscape within limiting resource constraints. The resulting plan will lead to reduced financial and ecological costs and an optimal surveillance system.

Developing a hybrid expert system program to aid in the design of plastic injection molding process

Experts in injection molding often refer to previous solutions to find a mold design similar to the current mold and use previous successful molding process parameters with intuitive adjustment and modification as a start for the new molding application. This approach saves a substantial amount of time and cost in experimental based corrective actions which are required in order to reach optimum molding conditions. A Case-Based Reasoning (CBR) System can perform the same task by retrieving a similar case which is applied to the new case from the case library and uses the modification rules to adapt a solution to the new case. Therefore, a CBR System can simulate human e~pertise in injection molding process design. This research is aimed at developing an interactive Hybrid Expert System to reduce expert dependency needed on the production floor. The Hybrid Expert System (HES) is comprised of CBR, flow analysis, post-processor and trouble shooting systems. The HES can provide the first set of operating parameters in order to achieve moldability condition and producing moldings free of stress cracks and warpage. In this work C++ programming language is used to implement the expert system. The Case-Based Reasoning sub-system is constructed to derive the optimum magnitude of process parameters in the cavity. Toward this end the Flow Analysis sub-system is employed to calculate the pressure drop and temperature difference in the feed system to determine the required magnitude of parameters at the nozzle. The Post-Processor is implemented to convert the molding parameters to machine setting parameters. The parameters designed by HES are implemented using the injection molding machine. In the presence of any molding defect, a trouble shooting subsystem can determine which combination of process parameters must be changed iii during the process to deal with possible variations. Constraints in relation to the application of this HES are as follows. - flow length (L) constraint: 40 mm < L < I 00 mm, - flow thickness (Th) constraint: -flow type: - material types: I mm < Th < 4 mm, unidirectional flow, High Impact Polystyrene (HIPS) and Acrylic. In order to test the HES, experiments were conducted and satisfactory results were obtained.

Flexural behaviour and design of hollow flange steel beams

The LiteSteel Beam (LSB) is a new hollow flange channel section developed by OneSteel Australian Tube Mills using a patented Dual Electric Resistance Welding technique. The LSB has a unique geometry consisting of torsionally rigid rectangular hollow flanges and a relatively slender web. It is commonly used as rafters, floor joists and bearers and roof beams in residential, industrial and commercial buildings. It is on average 40% lighter than traditional hot-rolled steel beams of equivalent performance. The LSB flexural members are subjected to a relatively new Lateral Distortional Buckling mode, which reduces the member moment capacity. Unlike the commonly observed lateral torsional buckling of steel beams, lateral distortional buckling of LSBs is characterised by simultaneous lateral deflection, twist and web distortion. Current member moment capacity design rules for lateral distortional buckling in AS/NZS 4600 (SA, 2005) do not include the effect of section geometry of hollow flange beams although its effect is considered to be important. Therefore detailed experimental and finite element analyses (FEA) were carried out to investigate the lateral distortional buckling behaviour of LSBs including the effect of section geometry. The results showed that the current design rules in AS/NZS 4600 (SA, 2005) are over-conservative in the inelastic lateral buckling region. New improved design rules were therefore developed for LSBs based on both FEA and experimental results. A geometrical parameter (K) defined as the ratio of the flange torsional rigidity to the major axis flexural rigidity of the web (GJf/EIxweb) was identified as the critical parameter affecting the lateral distortional buckling of hollow flange beams. The effect of section geometry was then included in the new design rules using the new parameter (K). The new design rule developed by including this parameter was found to be accurate in calculating the member moment capacities of not only LSBs, but also other types of hollow flange steel beams such as Hollow Flange Beams (HFBs), Monosymmetric Hollow Flange Beams (MHFBs) and Rectangular Hollow Flange Beams (RHFBs). The inelastic reserve bending capacity of LSBs has not been investigated yet although the section moment capacity tests of LSBs in the past revealed that inelastic reserve bending capacity is present in LSBs. However, the Australian and American cold-formed steel design codes limit them to the first yield moment. Therefore both experimental and FEA were carried out to investigate the section moment capacity behaviour of LSBs. A comparison of the section moment capacity results from FEA, experiments and current cold-formed steel design codes showed that compact and non-compact LSB sections classified based on AS 4100 (SA, 1998) have some inelastic reserve capacity while slender LSBs do not have any inelastic reserve capacity beyond their first yield moment. It was found that Shifferaw and Schafer’s (2008) proposed equations and Eurocode 3 Part 1.3 (ECS, 2006) design equations can be used to include the inelastic bending capacities of compact and non-compact LSBs in design. As a simple design approach, the section moment capacity of compact LSB sections can be taken as 1.10 times their first yield moment while it is the first yield moment for non-compact sections. For slender LSB sections, current cold-formed steel codes can be used to predict their section moment capacities. It was believed that the use of transverse web stiffeners could improve the lateral distortional buckling moment capacities of LSBs. However, currently there are no design equations to predict the elastic lateral distortional buckling and member moment capacities of LSBs with web stiffeners under uniform moment conditions. Therefore, a detailed study was conducted using FEA to simulate both experimental and ideal conditions of LSB flexural members. It was shown that the use of 3 to 5 mm steel plate stiffeners welded or screwed to the inner faces of the top and bottom flanges of LSBs at third span points and supports provided an optimum web stiffener arrangement. Suitable design rules were developed to calculate the improved elastic buckling and ultimate moment capacities of LSBs with these optimum web stiffeners. A design rule using the geometrical parameter K was also developed to improve the accuracy of ultimate moment capacity predictions. This thesis presents the details and results of the experimental and numerical studies of the section and member moment capacities of LSBs conducted in this research. It includes the recommendations made regarding the accuracy of current design rules as well as the new design rules for lateral distortional buckling. The new design rules include the effects of section geometry of hollow flange steel beams. This thesis also developed a method of using web stiffeners to reduce the lateral distortional buckling effects, and associated design rules to calculate the improved moment capacities.

Development of the response coefficient-root function method for the transient vibration serviceability design of flat concrete floors

The vibration serviceability limit state is an important design consideration for two-way, suspended concrete floors that is not always well understood by many practicing structural engineers. Although the field of floor vibration has been extensively developed, at present there are no convenient design tools that deal with this problem. Results from this research have enabled the development of a much-needed, new method for assessing the vibration serviceability of flat, suspended concrete floors in buildings. This new method has been named, the Response Coefficient-Root Function (RCRF) method. Full-scale, laboratory tests have been conducted on a post-tensioned floor specimen at Queensland University of Technology’s structural laboratory. Special support brackets were fabricated to perform as frictionless, pinned connections at the corners of the specimen. A series of static and dynamic tests were performed in the laboratory to obtain basic material and dynamic properties of the specimen. Finite-element-models have been calibrated against data collected from laboratory experiments. Computational finite-element-analysis has been extended to investigate a variety of floor configurations. Field measurements of floors in existing buildings are in good agreement with computational studies. Results from this parametric investigation have led to the development of new approach for predicting the design frequencies and accelerations of flat, concrete floor structures. The RCRF method is convenient tool to assist structural engineers in the design for the vibration serviceability limit-state of in-situ concrete floor systems.

Rational design of serine protease inhibitors

Proteases regulate a spectrum of diverse physiological processes, and dysregulation of proteolytic activity drives a plethora of pathological conditions. Understanding protease function is essential to appreciating many aspects of normal physiology and progression of disease. Consequently, development of potent and specific inhibitors of proteolytic enzymes is vital to provide tools for the dissection of protease function in biological systems and for the treatment of diseases linked to aberrant proteolytic activity. The studies in this thesis describe the rational design of potent inhibitors of three proteases that are implicated in disease development. Additionally, key features of the interaction of proteases and their cognate inhibitors or substrates are analysed and a series of rational inhibitor design principles are expounded and tested. Rational design of protease inhibitors relies on a comprehensive understanding of protease structure and biochemistry. Analysis of known protease cleavage sites in proteins and peptides is a commonly used source of such information. However, model peptide substrate and protein sequences have widely differing levels of backbone constraint and hence can adopt highly divergent structures when binding to a protease’s active site. This may result in identical sequences in peptides and proteins having different conformations and diverse spatial distribution of amino acid functionalities. Regardless of this, protein and peptide cleavage sites are often regarded as being equivalent. One of the key findings in the following studies is a definitive demonstration of the lack of equivalence between these two classes of substrate and invalidation of the common practice of using the sequences of model peptide substrates to predict cleavage of proteins in vivo. Another important feature for protease substrate recognition is subsite cooperativity. This type of cooperativity is commonly referred to as protease or substrate binding subsite cooperativity and is distinct from allosteric cooperativity, where binding of a molecule distant from the protease active site affects the binding affinity of a substrate. Subsite cooperativity may be intramolecular where neighbouring residues in substrates are interacting, affecting the scissile bond’s susceptibility to protease cleavage. Subsite cooperativity can also be intermolecular where a particular residue’s contribution to binding affinity changes depending on the identity of neighbouring amino acids. Although numerous studies have identified subsite cooperativity effects, these findings are frequently ignored in investigations probing subsite selectivity by screening against diverse combinatorial libraries of peptides (positional scanning synthetic combinatorial library; PS-SCL). This strategy for determining cleavage specificity relies on the averaged rates of hydrolysis for an uncharacterised ensemble of peptide sequences, as opposed to the defined rate of hydrolysis of a known specific substrate. Further, since PS-SCL screens probe the preference of the various protease subsites independently, this method is inherently unable to detect subsite cooperativity. However, mean hydrolysis rates from PS-SCL screens are often interpreted as being comparable to those produced by single peptide cleavages. Before this study no large systematic evaluation had been made to determine the level of correlation between protease selectivity as predicted by screening against a library of combinatorial peptides and cleavage of individual peptides. This subject is specifically explored in the studies described here. In order to establish whether PS-SCL screens could accurately determine the substrate preferences of proteases, a systematic comparison of data from PS-SCLs with libraries containing individually synthesised peptides (sparse matrix library; SML) was carried out. These SML libraries were designed to include all possible sequence combinations of the residues that were suggested to be preferred by a protease using the PS-SCL method. SML screening against the three serine proteases kallikrein 4 (KLK4), kallikrein 14 (KLK14) and plasmin revealed highly preferred peptide substrates that could not have been deduced by PS-SCL screening alone. Comparing protease subsite preference profiles from screens of the two types of peptide libraries showed that the most preferred substrates were not detected by PS SCL screening as a consequence of intermolecular cooperativity being negated by the very nature of PS SCL screening. Sequences that are highly favoured as result of intermolecular cooperativity achieve optimal protease subsite occupancy, and thereby interact with very specific determinants of the protease. Identifying these substrate sequences is important since they may be used to produce potent and selective inhibitors of protolytic enzymes. This study found that highly favoured substrate sequences that relied on intermolecular cooperativity allowed for the production of potent inhibitors of KLK4, KLK14 and plasmin. Peptide aldehydes based on preferred plasmin sequences produced high affinity transition state analogue inhibitors for this protease. The most potent of these maintained specificity over plasma kallikrein (known to have a very similar substrate preference to plasmin). Furthermore, the efficiency of this inhibitor in blocking fibrinolysis in vitro was comparable to aprotinin, which previously saw clinical use to reduce perioperative bleeding. One substrate sequence particularly favoured by KLK4 was substituted into the 14 amino acid, circular sunflower trypsin inhibitor (SFTI). This resulted in a highly potent and selective inhibitor (SFTI-FCQR) which attenuated protease activated receptor signalling by KLK4 in vitro. Moreover, SFTI-FCQR and paclitaxel synergistically reduced growth of ovarian cancer cells in vitro, making this inhibitor a lead compound for further therapeutic development. Similar incorporation of a preferred KLK14 amino acid sequence into the SFTI scaffold produced a potent inhibitor for this protease. However, the conformationally constrained SFTI backbone enforced a different intramolecular cooperativity, which masked a KLK14 specific determinant. As a consequence, the level of selectivity achievable was lower than that found for the KLK4 inhibitor. Standard mechanism inhibitors such as SFTI rely on a stable acyl-enzyme intermediate for high affinity binding. This is achieved by a conformationally constrained canonical binding loop that allows for reformation of the scissile peptide bond after cleavage. Amino acid substitutions within the inhibitor to target a particular protease may compromise structural determinants that support the rigidity of the binding loop and thereby prevent the engineered inhibitor reaching its full potential. An in silico analysis was carried out to examine the potential for further improvements to the potency and selectivity of the SFTI-based KLK4 and KLK14 inhibitors. Molecular dynamics simulations suggested that the substitutions within SFTI required to target KLK4 and KLK14 had compromised the intramolecular hydrogen bond network of the inhibitor and caused a concomitant loss of binding loop stability. Furthermore in silico amino acid substitution revealed a consistent correlation between a higher frequency of formation and the number of internal hydrogen bonds of SFTI-variants and lower inhibition constants. These predictions allowed for the production of second generation inhibitors with enhanced binding affinity toward both targets and highlight the importance of considering intramolecular cooperativity effects when engineering proteins or circular peptides to target proteases. The findings from this study show that although PS-SCLs are a useful tool for high throughput screening of approximate protease preference, later refinement by SML screening is needed to reveal optimal subsite occupancy due to cooperativity in substrate recognition. This investigation has also demonstrated the importance of maintaining structural determinants of backbone constraint and conformation when engineering standard mechanism inhibitors for new targets. Combined these results show that backbone conformation and amino acid cooperativity have more prominent roles than previously appreciated in determining substrate/inhibitor specificity and binding affinity. The three key inhibitors designed during this investigation are now being developed as lead compounds for cancer chemotherapy, control of fibrinolysis and cosmeceutical applications. These compounds form the basis of a portfolio of intellectual property which will be further developed in the coming years.