Design, construction, and analysis of cell line arrays and tissue microarrays for gene expression analysis

Cell line array (CMA) and tissue microarray (TMA) technologies are high-throughput methods for analysing both the abundance and distribution of gene expression in a panel of cell lines or multiple tissue specimens in an efficient and cost-effective manner. The process is based on Kononen's method of extracting a cylindrical core of paraffin-embedded donor tissue and inserting it into a recipient paraffin block. Donor tissue from surgically resected paraffin-embedded tissue blocks, frozen needle biopsies or cell line pellets can all be arrayed in the recipient block. The representative area of interest is identified and circled on a haematoxylin and eosin (H&E)-stained section of the donor block. Using a predesigned map showing a precise spacing pattern, a high density array of up to 1,000 cores of cell pellets and/or donor tissue can be embedded into the recipient block using a tissue arrayer from Beecher Instruments. Depending on the depth of the cell line/tissue removed from the donor block 100-300 consecutive sections can be cut from each CMA/TMA block. Sections can be stained for in situ detection of protein, DNA or RNA targets using immunohistochemistry (IHC), fluorescent in situ hybridisation (FISH) or mRNA in situ hybridisation (RNA-ISH), respectively. This chapter provides detailed methods for CMA/TMA design, construction and analysis with in-depth notes on all technical aspects including tips to deal with common pitfalls the user may encounter. © Springer Science+Business Media, LLC 2011.

Implementing the self-management threshold learning outcome for law : some intentional design strategies from the current curriculum toolbox

There is a growing awareness of the high levels of psychological distress being experienced by law students and the practising profession in Australia. In this context, a Threshold Learning Outcome (TLO) on self-management has been included in the six TLOs recently articulated as minimum learning outcomes for all Australian graduates of the Bachelor of Laws degree (LLB). The TLOs were developed during 2010 as part of the Australian Learning and Teaching Council’s (ALTC’s) project funded by the Australian Government to articulate ‘Learning and Teaching Academic Standards’. The TLOs are the result of a comprehensive national consultation process led by the ALTC’s Discipline Scholars: Law, Professors Sally Kift and Mark Israel.1 The TLOs have been endorsed by the Council of Australian Law Deans (CALD) and have received broad support from members of the judiciary and practising profession, representative bodies of the legal profession, law students and recent graduates, Legal Services Commissioners and the Law Admissions Consultative Committee. At the time of writing, TLOs for the Juris Doctor (JD) are also being developed, utilising the TLOs articulated for the LLB as their starting point but restating the JD requirements as the higher order outcomes expected of graduates of a ‘Masters Degree (Extended)’, this being the award level designation for the JD now set out in the new Australian Qualifications Framework.2 As Australian law schools begin embedding the learning, teaching and assessment of the TLOs in their curricula, and seek to assure graduates’ achievement of them, guidance on the implementation of the self-management TLO is salient and timely.

Incorporating dugong habitats into the marine protected area design for the Great Barrier Reef Marine Park, Queensland, Australia.

Dugong habitats were considered in the design for the new zoning network for the Great Barrier Reef Marine Park as part of the Representative Areas Program. One of the specific design guidelines developed as part of the biophysical operational principles recommended that 50% of all high priority dugong habitats should be incorporated in the network of no-take areas. The high priority dugong habitat incorporated in no-take protection increased from 1396 to 3476 km2 (or 16.9-42.0% of all identified sites). Although this increase in protection fell short of the recommended 50%, overall the level of protection afforded by the Great Barrier Reef Marine Park Zoning Plan 2003 increased for all the locations identified.

Equivalent constitutive model-based design of wave-absorbing material system and controller

A design methodology for wave-absorbing active material system is reported. The design enforces equivalence between an assumed material model having wave-absorbing behavior and a set of target feedback controllers for an array of microelectro-mechanical transducers which are integral part of the active material system. The proposed methodology is applicable to problems involving the control of acoustic waves in passive-active material system with complex constitutive behavior at different length-scales. A stress relaxation type one-dimensional constitutive model involving viscous damping mechanism is considered, which shows asymmetric wave dispersion characteristics about the half-line. The acoustic power flow and asymptotic stability of such material system are studied. A single sensor non-collocated linear feedback control system in a one-dimensional finite waveguide, which is a representative volume element in an active material system, is considered. Equivalence between the exact dynamic equilibrium of these two systems is imposed. It results in the solution space of the design variables, namely the equivalent damping coefficient, the wavelength(s) to be controlled and the location of the sensor. The characteristics of the controller transfer functions and their pole-placement problem are studied. (c) 2005 Elsevier Ltd. All rights reserved.

Design of corona control rings for EHV/UHV line hardwares and substations

The components of EHV/UHV lines and substations can produce significant corona. To limit the consequent Radio Interference and Audible Noise on these systems, suitable corona control rings are employed. The shapes of these rings could vary from circular to rectangular with smooth bends. Many manufacturers seem to adopt trial and error method for arriving at the final design. As such neither the present testing standard nor the final design adopted consider the practical scenario like corona produced by deposition of dirt, bird droppings, etc. The present work aims to make a first step in addressing this practically important problem. This requires an accurate evaluation of the electric field and a reliable method for the evaluation of corona inception. Based on a thorough survey of pertinent literature, the critical avalanche criteria as applicable to large electrodes, has been adopted. Taking the rain drop on the surface as the biggest protrusion, conducting protrusions modeled as semi-ellipsoid is considered as representative for deposition of dust or the boundary of bird droppings etc. Through examples of 4 00 kV and 765 kV class toroidal corona rings, the proposed method is demonstrated. This work is believed to be useful to corona ring manufacturers for EHV/UHV systems.

Membership models and the design of authentication protocols for MANETs

Authentication protocols are very much essential for secure communication in mobile ad hoc networks (MANETs). A number of authentication protocols for MANETs have been proposed in the literature which provide the basic authentication service while trying to optimize their performance and resource consumption parameters. A problem with most of these protocols is that the underlying networking environment on which they are applicable have been left unspecified. As a result, lack of specifications about the networking environments applicable to an authentication protocol for MANETs can mislead about the performance and the applicability of the protocol. In this paper, we first characterize networking environment for a MANET as its 'Membership Model' which is defined as a set of specifications related to the 'Membership Granting Server' (MGS) and the 'Membership Set Pattern' (MSP) of the MANET. We then identify various types of possible membership models for a MANET. In order to illustrate that while designing an authentication protocol for a MANET, it is very much necessary to consider the underlying membership model of the MANET, we study a set of six representative authentication protocols, and analyze their applicability for the membership models as enumerated in this paper. The analysis shows that the same protocol may not perform equally well in all membership models. In addition, there may be membership models which are important from the point of view of users, but for which no authentication protocol is available.

Design of double toggle switching mechanisms

Toggle mechanisms are ubiquitous in electrical switches. However, literature for their mechanical design is scarce. This paper defines and classifies the toggle phenomena observed during switching. The concept of double toggle introduced in this paper enables a systematic screening of kinematic structure for the suitability in high performance switches. Seven structural and three kinematic criteria are identified for this purpose. It is also demonstrated that each such feasible kinematic structure lends itself to multiple physical embodiments. Therefore, the theory and procedure presented in this work can be used for design of numerous kinematically distinct mechanisms. One representative mechanical embodiment for a novel double toggle switch, including mass and geometric shape of links has been included in the paper. The switching behavior of the design is validated using Pro/Mechanism (TM). (C) 2013 Elsevier Ltd. All rights reserved.

Design, specification, and synthesis of aircraft electric power systems control logic

Cyber-physical systems integrate computation, networking, and physical processes. Substantial research challenges exist in the design and verification of such large-scale, distributed sensing, ac- tuation, and control systems. Rapidly improving technology and recent advances in control theory, networked systems, and computer science give us the opportunity to drastically improve our approach to integrated flow of information and cooperative behavior. Current systems rely on text-based spec- ifications and manual design. Using new technology advances, we can create easier, more efficient, and cheaper ways of developing these control systems. This thesis will focus on design considera- tions for system topologies, ways to formally and automatically specify requirements, and methods to synthesize reactive control protocols, all within the context of an aircraft electric power system as a representative application area.

This thesis consists of three complementary parts: synthesis, specification, and design. The first section focuses on the synthesis of central and distributed reactive controllers for an aircraft elec- tric power system. This approach incorporates methodologies from computer science and control. The resulting controllers are correct by construction with respect to system requirements, which are formulated using the specification language of linear temporal logic (LTL). The second section addresses how to formally specify requirements and introduces a domain-specific language for electric power systems. A software tool automatically converts high-level requirements into LTL and synthesizes a controller.

The final sections focus on design space exploration. A design methodology is proposed that uses mixed-integer linear programming to obtain candidate topologies, which are then used to synthesize controllers. The discrete-time control logic is then verified in real-time by two methods: hardware and simulation. Finally, the problem of partial observability and dynamic state estimation is ex- plored. Given a set placement of sensors on an electric power system, measurements from these sensors can be used in conjunction with control logic to infer the state of the system.

Boundary-layer suction system design for laminar-flying-wing aircraft

The present study aims to provide insight into the parameters affecting practical laminar-flow-control suction power requirements for a commercial laminar-flying-wing transport aircraft. It is shown that there is a minimum power requirement independent of the suction system design, associated with the stagnation pressure loss in the boundary layer. This requirement increases with aerofoil section thickness, but depends only weakly on Mach number and (for a thick, lightly loaded laminar flying wing) lift coefficient. Deviation from the optimal suction distribution, due to a practical chamber-based architecture, is found to have very little effect on the overall suction coefficient; hence, to a good approximation, the power penalty is given by the product of the optimal suction flow rate coefficient and the average skin pressure drop. In the spanwise direction, through suitable choice of chamber depth, the pressure drop due to frictional and inertial effects may be rendered negligible. Finally, if there are fewer pumps than chambers, the average pressure drop from the aerofoil surface to the pump collector ducts, rather than to the chambers, determines the power penalty. For the representative laminar-flying-wing aircraft parameters considered here, the minimum power associated with boundary-layer losses alone contributes some 80-90% of the total power requirement. © 2011 by the American Institute of Aeronautics and Astronautics, Inc.

Improvements in interface design through implicit modeling

Touchscreen devices are often limited by the complexity of their user interface design. In the past, iterative design processes using representative user groups to test prototypes were the standard method for increasing the inclusivity of a given design, but cognitive modeling has potential to be an alternative to rigorous user testing. However, these modeling approaches currently have many limitations, some of which are based on the assumptions made in translating a User Interface (UI) into a definition file that cognitive modeling frameworks can process. This paper discusses these issues and postulates potential approaches to improvements to the translation procedure. © 2013 Springer-Verlag Berlin Heidelberg.

Parametrically excited MEMS vibration energy harvesters with design approaches to overcome the initiation threshold amplitude

Resonant-based vibration harvesters have conventionally relied upon accessing the fundamental mode of directly excited resonance to maximize the conversion efficiency of mechanical-to-electrical power transduction. This paper explores the use of parametric resonance, which unlike the former, the resonant-induced amplitude growth, is not limited by linear damping and wherein can potentially offer higher and broader nonlinear peaks. A numerical model has been constructed to demonstrate the potential improvements over the convention. Despite the promising potential, a damping-dependent initiation threshold amplitude has to be attained prior to accessing this alternative resonant phenomenon. Design approaches have been explored to passively reduce this initiation threshold. Furthermore, three representative MEMS designs were fabricated with both 25 and 10 μm thick device silicon. The devices include electrostatic cantilever-based harvesters, with and without the additional design modification to overcome initiation threshold amplitude. The optimum performance was recorded for the 25 μm thick threshold-aided MEMS prototype with device volume ∼0.147 mm3. When driven at 4.2 ms -2, this prototype demonstrated a peak power output of 10.7 nW at the fundamental mode of resonance and 156 nW at the principal parametric resonance, as well as a 23-fold decrease in initiation threshold over the purely parametric prototype. An approximate doubling of the half-power bandwidth was also observed for the parametrically excited scenario. © 2013 IOP Publishing Ltd.

Design and modeling of an integrated device for acoustic resonance spectroscopy

This paper investigates the design and modelling of an integrated device for acoustic resonance spectroscopy (ARS). Miniaturisation of such platforms can be achieved using MEMS technology thereby enabling scaling of device dimensions to investigate smaller specimens while simultaneously operating at higher frequencies. We propose an integrated device where the transducers are mounted in close proximity with the specimen to be analysed (e.g. by integrating ultrasound transducers within a microfluidic channel). A finite element (FE) model and a simplified analytical model have been constructed to predict the acoustic response of a sample embedded in such a device configuration. A FE simulation is performed in COMSOL by embedding the piezoelectric transducers in representative fluid media. Resonant frequencies associated with the measurement can be extracted from this data. The response of various media modelled through FEA matches with analytical predictions for a range of biological media. A variety of biological media may be identified by using the measured resonant frequencies as a signature of relevant physical characteristics. The paper establishes the modelling basis of an integrated acoustic resonant spectrometer that is then applied to examine the impact of geometrical scaling on system resolution. © 2013 IEEE.

Generating Representative ISP Technologies From First-Principles

Understanding and modeling the factors that underlie the growth and evolution of network topologies are basic questions that impact capacity planning, forecasting, and protocol research. Early topology generation work focused on generating network-wide connectivity maps, either at the AS-level or the router-level, typically with an eye towards reproducing abstract properties of observed topologies. But recently, advocates of an alternative "first-principles" approach question the feasibility of realizing representative topologies with simple generative models that do not explicitly incorporate real-world constraints, such as the relative costs of router configurations, into the model. Our work synthesizes these two lines by designing a topology generation mechanism that incorporates first-principles constraints. Our goal is more modest than that of constructing an Internet-wide topology: we aim to generate representative topologies for single ISPs. However, our methods also go well beyond previous work, as we annotate these topologies with representative capacity and latency information. Taking only demand for network services over a given region as input, we propose a natural cost model for building and interconnecting PoPs and formulate the resulting optimization problem faced by an ISP. We devise hill-climbing heuristics for this problem and demonstrate that the solutions we obtain are quantitatively similar to those in measured router-level ISP topologies, with respect to both topological properties and fault-tolerance.

Design, synthesis and development of novel indolocarbazole derivatives as potential anti-cancer agents

This thesis describes work carried out on the design of new routes to a range of bisindolylmaleimide and indolo[2,3-a]carbazole analogs, and investigation of their potential as successful anti-cancer agents. Following initial investigation of classical routes to indolo[2,3-a]pyrrolo[3,4-c]carbazole aglycons, a new strategy employing base-mediated condensation of thiourea and guanidine with a bisindolyl β-ketoester intermediate afforded novel 5,6-bisindolylpyrimidin-4(3H)-ones in moderate yields. Chemical diversity within this H-bonding scaffold was then studied by substitution with a panel of biologically relevant electrophiles, and by reductive desulfurisation. Optimisation of difficult heterogeneous literature conditions for oxidative desulfurisation of thiouracils was also accomplished, enabling a mild route to a novel 5,6-bisindolyluracil pharmacophore to be developed within this work. The oxidative cyclisation of selected acyclic bisindolyl systems to form a new planar class of indolo[2,3-a]pyrimido[5,4-c]carbazoles was also investigated. Successful conditions for this transformation, as well as the limitations currently prevailing for this approach are discussed. Synthesis of 3,4-bisindolyl-5-aminopyrazole as a potential isostere of bisindolylmaleimide agents was encountered, along with a comprehensive derivatisation study, in order to probe the chemical space for potential protein backbone H-bonding interactions. Synthesis of a related 3,4-arylindolyl-5-aminopyrazole series was also undertaken, based on identification of potent kinase inhibition within a closely related heterocyclic template. Following synthesis of approximately 50 novel compounds with a diversity of H-bonding enzyme-interacting potential within these classes, biological studies confirmed that significant topo II inhibition was present for 9 lead compounds, in previously unseen pyrazolo[1,5-a]pyrimidine, indolo[2,3-c]carbazole and branched S,N-disubstituted thiouracil derivative series. NCI-60 cancer cell line growth inhibition data for 6 representative compounds also revealed interesting selectivity differences between each compound class, while a new pyrimido[5,4-c]carbazole agent strongly inhibited cancer cell division at 10 µM, with appreciable cytotoxic activity observed across several tumour types.

Effect of the crown design and interface lute parameters on the stress-state of a machined crown-tooth system: A finite element analysis

The effect of preparation design and the physical properties of the interface lute on the restored machined ceramic crown-tooth complex are poorly understood. The aim of this work was to determine, by means of three-dimensional finite element analysis (3D FEA) the effect of the tooth preparation design and the elastic modulus of the cement on the stress state of the cemented machined ceramic crown-tooth complex. The three-dimensional structure of human premolar teeth, restored with adhesively cemented machined ceramic crowns, was digitized with a micro-CT scanner. An accurate, high resolution, digital replica model of a restored tooth was created. Two preparation designs, with different occlusal morphologies, were modeled with cements of 3 different elastic moduli. Interactive medical image processing software (mimics and professional CAD modeling software) was used to create sophisticated digital models that included the supporting structures; periodontal ligament and alveolar bone. The generated models were imported into an FEA software program (hypermesh version 10.0, Altair Engineering Inc.) with all degrees of freedom constrained at the outer surface of the supporting cortical bone of the crown-tooth complex. Five different elastic moduli values were given to the adhesive cement interface 1.8 GPa, 4 GPa, 8 GPa, 18.3 GPa and 40 GPa; the four lower values are representative of currently used cementing lutes and 40 GPa is set as an extreme high value. The stress distribution under simulated applied loads was determined. The preparation design demonstrated an effect on the stress state of the restored tooth system. The cement elastic modulus affected the stress state in the cement and dentin structures but not in the crown, the pulp, the periodontal ligament or the cancellous and cortical bone. The results of this study suggest that both the choice of the preparation design and the cement elastic modulus can affect the stress state within the restored crown-tooth complex.