Zebrafish as a model for caveolin-associated muscle disease; caveolin-3 is required for myofibril organization and muscle cell patterning

Caveolae are an abundant feature of many animal cells. However, the exact function of caveolae remains unclear. We have used the zebrafish, Danio rerio, as a system to understand caveolae function focusing on the muscle-specific caveolar protein, caveolin-3 (Cav3). We have identified caveolin-1 (alpha and beta), caveolin-2 and Cav3 in the zebrafish. Zebrafish Cav3 has 72% identity to human CAV3, and the amino acids altered in human muscle diseases are conserved in the zebrafish protein. During embryonic development, cav3 expression is apparent by early segmentation stages in the first differentiating muscle precursors, the adaxial cells and slightly later in the notochord. cav3 expression appears in the somites during mid-segmentation stages and then later in the pectoral fins and facial muscles. Cav3 and caveolae are located along the entire sarcolemma of late stage embryonic muscle fibers, whereas beta-dystroglycan is restricted to the muscle fiber ends. Down-regulation of Cav3 expression causes gross muscle abnormalities and uncoordinated movement. Ultrastructural analysis of isolated muscle fibers reveals defects in myoblast fusion and disorganized myofibril and membrane systems. Expression of the zebrafish equivalent to a human muscular dystrophy mutant, CAV3P104L, causes severe disruption of muscle differentiation. In addition, knockdown of Cav3 resulted in a dramatic up-regulation of eng1a expression resulting in an increase in the number of muscle pioneer-like cells adjacent to the notochord. These studies provide new insights into the role of Cav3 in muscle development and demonstrate its requirement for correct intracellular organization and myoblast fusion.

A quasi-chemical viscosity model for fully liquid slags in the Al2O3-CaO-'FeO'-SiO2 system

A structurally based viscosity model for fully liquid silicate slags has been proposed and applied to the Al2O3-CaO-'FeO'-SiO2 system at metallic iron saturation. The model links the slag viscosity to the internal structure of melts through the concentrations of various anion/cation structural units (SUs). The concentrations of structural units are equivalent to the second nearest neighbor bond concentrations calculated by the quasi-chemical thermodynamic model. This viscosity model describes experimental data over the entire temperature and composition range within the Al2O3-CaO-'FeO'-SiO2 system at metallic iron saturation and can be extended to other industrial slag systems.

A geometric approach to quantum circuit lower bounds

What is the minimal size quantum circuit required to exactly implement a specified n-qubit unitary operation, U, without the use of ancilla qubits? We show that a lower bound on the minimal size is provided by the length of the minimal geodesic between U and the identity, I, where length is defined by a suitable Finsler metric on the manifold SU(2(n)). The geodesic curves on these manifolds have the striking property that once an initial position and velocity are set, the remainder of the geodesic is completely determined by a second order differential equation known as the geodesic equation. This is in contrast with the usual case in circuit design, either classical or quantum, where being given part of an optimal circuit does not obviously assist in the design of the rest of the circuit. Geodesic analysis thus offers a potentially powerful approach to the problem of proving quantum circuit lower bounds. In this paper we construct several Finsler metrics whose minimal length geodesics provide lower bounds on quantum circuit size. For each Finsler metric we give a procedure to compute the corresponding geodesic equation. We also construct a large class of solutions to the geodesic equation, which we call Pauli geodesics, since they arise from isometries generated by the Pauli group. For any unitary U diagonal in the computational basis, we show that: (a) provided the minimal length geodesic is unique, it must be a Pauli geodesic; (b) finding the length of the minimal Pauli geodesic passing from I to U is equivalent to solving an exponential size instance of the closest vector in a lattice problem (CVP); and (c) all but a doubly exponentially small fraction of such unitaries have minimal Pauli geodesics of exponential length.

An equivalent distributed magnetic current based FDTD method for the calculation of e-fields induced by gradient coils in MRI

This paper evaluates a low-frequency FDTD method applied to the problem of induced E-fields/eddy currents in the human body resulting from the pulsed magnetic field gradients in MRI. In this algorithm, a distributed equivalent magnetic current (DEMC) is proposed as the electromagnetic source and is obtained by quasistatic calculation of the empty coil's vector potential or measurements therein. This technique circumvents the discretizing of complicated gradient coil geometries into a mesh of Yee cells, and thereby enables any type of gradient coil modeling or other complex low frequency sources. The proposed method has been verified against an example with an analytical solution. Results are presented showing the spatial distribution of gradient-induced electric fields in a multilayered spherical phantom model and a complete body model.

JKSimFloat V6: Improving flotation circuit performance and understanding

Methods of analysing and optimising flotation circuits have improved significantly over the last 15 years. Mineral flotation is now generally better understood through major advances in measuring and modelling the sub-processes within the flotation system. JKSimFloat V6 is a user-friendly Windows-based software package incorporating simulation, mass balancing, and, currently under development, liberation data viewing and model fitting. This paper presents an overview of the development of the program up to its current status, and the plans established for the future. The application of the simulator, in particular, at various operations is also discussed with emphasis on the use of the program in improving flotation circuit performance.

S. cerevisiae as a model for studying mutations in the human gene OPA1 associated with dominant optic atrophy and for drug discovery

L’atrofia ottica dominante (ADOA) è una malattia mitocondriale caratterizzata da difetti visivi, che si manifestano durante l’infanzia, causati da progressiva degenerazione delle cellule gangliari della retina (RGC). ADOA è una malattia genetica associata, nella maggior parte dei casi, a mutazioni nel gene OPA1 che codifica per la GTPasi mitocondriale OPA1, appartenente alla famiglia delle dinamine, principalmente coinvolta nel processo di fusione mitocondriale e nel mantenimento del mtDNA. Finora sono state identificate più di 300 mutazioni patologiche nel gene OPA1. Circa il 50% di queste sono mutazioni missenso, localizzate nel dominio GTPasico, che si pensa agiscano come dominanti negative. Questa classe di mutazioni è associata ad una sindrome più grave nota come “ADOA-plus”. Nel lievito Saccharomyces cerevisiae MGM1 è l’ortologo del gene OPA1: nonostante i due geni abbiano domini funzionali identici le sequenze amminoacidiche sono scarsamente conservate. Questo costituisce una limitazione all’uso del lievito per lo studio e la validazione di mutazioni patologiche nel gene OPA1, infatti solo poche sostituzioni possono essere introdotte e studiate nelle corrispettive posizioni del gene di lievito. Per superare questo ostacolo è stato pertanto costruito un nuovo modello di S. cerevisiae, contenente il gene chimerico MGM1/OPA1, in grado di complementare i difetti OXPHOS del mutante mgm1Δ. Questo gene di fusione contiene una larga parte di sequenza corrispondente al gene OPA1, nella quale è stato inserito un set di nuove mutazioni trovate in pazienti affetti da ADOA e ADOA-plus. La patogenicità di queste mutazioni è stata validata sia caratterizzando i difetti fenotipici associati agli alleli mutati, sia la loro dominanza/recessività nel modello di lievito. A tutt’oggi non è stato identificato alcun trattamento farmacologico per la cura di ADOA e ADOA-plus. Per questa ragione abbiamo utilizzato il nostro modello di lievito per la ricerca di molecole che agiscono come soppressori chimici, ossia composti in grado di ripristinare i difetti fenotipici indotti da mutazioni nel gene OPA1. Attraverso uno screening fenotipico high throughput sono state testate due differenti librerie di composti chimici. Questo approccio, noto con il nome di drug discovery, ha permesso l’identificazione di 23 potenziali molecole attive.

Modelling and control of a hybrid stepping motor

The integration of a microprocessor and a medium power stepper motor in one control system brings together two quite different disciplines. Various methods of interfacing are examined and the problems involved in both hardware and software manipulation are investigated. Microprocessor open-loop control of the stepper motor is considered. The possible advantages of microprocessor closed-loop control are examined and the development of a system is detailed. The system uses position feedback to initiate each motor step. Results of the dynamic response of the system are presented and its performance discussed. Applications of the static torque characteristic of the stepper motor are considered followed by a review of methods of predicting the characteristic. This shows that accurate results are possible only when the effects of magnetic saturation are avoided or when the machine is available for magnetic circuit tests to be carried out. A new method of predicting the static torque characteristic is explained in detail. The method described uses the machine geometry and the magnetic characteristics of the iron types used in the machine. From this information the permeance of each iron component of the machine is calculated and by using the equivalent magnetic circuit of the machine, the total torque produced is predicted. It is shown how this new method is implemented on a digital computer and how the model may be used to investigate further aspects of the stepper motor in addition to the static torque.

A study of the effect of harmonics in the system on the performance of residual current-operated circuit-breakers and electromechanical overcurrent relays

Residual current-operated circuit-breakers (RCCBs) have proved useful devices for the protection of both human beings against ventricular fibrillation and installations against fire. Although they work well with sinusoidal waveforms, there is little published information on their characteristics. Due to shunt connected non-linear devices, not the least of which is the use of power electronic equipment, the supply is distorted. Consequently, RCCBs as well as other protection relays are subject to non-sinusoidal current waveforms. Recent studies showed that RCCBs are greatly affected by harmonics, however the reasons for this are not clear. A literature search has also shown that there are inconsistencies in the analysis of the effect of harmonics on protection relays. In this work, the way RCCBs operate is examined, then a model is built with the aim of assessing the effect of non-sinusoidal current on RCCBs. Tests are then carried out on a number of RCCBs and these, when compared with the results from the model showed good correlation. In addition, the model also enables us to explain the RCCBs characteristics for pure sinusoidal current. In the model developed, various parameters are evaluated but special attention is paid to the instantaneous value of the current and the tripping mechanism movement. A similar assessment method is then used to assess the effect of harmonics on two types of protection relay, the electromechanical instantaneous relay and time overcurrent relay. A model is built for each of them which is then simulated on the computer. Tests results compare well with the simulation results, and thus the model developed can be used to explain the relays behaviour in a harmonics environment. The author's models, analysis and tests show that RCCBs and protection relays are affected by harmonics in a way determined by the waveform and the relay constants. The method developed provides a useful tool and the basic methodology to analyse the behaviour of RCCBs and protection relays in a harmonics environment. These results have many implications, especially the way RCCBs and relays should be tested if harmonics are taken into account.

Chemical studies of plasma etchants used in integrated circuit manufacture

Plasma or "dry" etching is an essential process for the production of modern microelectronic circuits. However, despite intensive research, many aspects of the etch process are not fully understood. The results of studies of the plasma etching of Si and Si02 in fluorine-containing discharges, and the complementary technique of plasma polymerisation are presented in this thesis. Optical emission spectroscopy with argon actinometry was used as the principle plasma diagnostic. Statistical experimental design was used to model and compare Si and Si02 etch rates in CF4 and SF6 discharges as a function of flow, pressure and power. Etch mechanisms m both systems, including the potential reduction of Si etch rates in CF4 due to fluorocarbon polymer formation, are discussed. Si etch rates in CF4 /SF6 mixtures were successfully accounted for by the models produced. Si etch rates in CF4/C2F6 and CHF3 as a function of the addition of oxygen-containing additives (02, N20 and CO2) are shown to be consistent with a simple competition between F, 0 and CFx species for Si surface sites. For the range of conditions studied, Si02 etch rates were not dependent on F-atom concentration, but the presence of fluorine was essential in order to achieve significant etch rates. The influence of a wide range of electrode materials on the etch rate of Si and Si02 in CF4 and CF4 /02 plasmas was studied. It was found that the Si etch rate in a CF4 plasma was considerably enhanced, relative to an anodised aluminium electrode, in the presence of soda glass or sodium or potassium "doped" quartz. The effect was even more pronounced in a CF4 /02 discharge. In the latter system lead and copper electrodes also enhanced the Si etch rate. These results could not be accounted for by a corresponding rise in atomic fluorine concentration. Three possible etch enhancement mechanisms are discussed. Fluorocarbon polymer deposition was studied, both because of its relevance to etch mechanisms and its intrinsic interest, as a function of fluorocarbon source gas (CF4, C2F6, C3F8 and CHF3), process time, RF power and percentage hydrogen addition. Gas phase concentrations of F, H and CF2 were measured by optical emission spectroscopy, and the resultant polymer structure determined by X-ray photoelectron spectroscopy and infrared spectroscopy. Thermal and electrical properties were measured also. Hydrogen additions are shown to have a dominant role in determining deposition rate and polymer composition. A qualitative description of the polymer growth mechanism is presented which accounts for both changes in growth rate and structure, and leads to an empirical deposition rate model.

Interaction of quinolone antibiotics with the human intestinal CACO-2 cell model

The transport of a group of quinolone antibiotics across the human intestinal model, Caco-2 cells, was investigated. It was found that the transport of the quinolones generally correlated with the lipophilicity of the compounds, indicating the passive diffusional transcellular processes were involved. However, it was observed that the transport in both directions apical-to-basolateral and basolateral-to-apical was not equivalent, and polarised transport occurred. For all the quinolones studied except, BMS-284756-01, it was found that the basolateral-to-apical transport was significantly greater than the apical-to-basolateral transport. This finding suggested that the quinolones underwent a process of active secretion. The pKas and logPs for the quinolones were determined using potentiometric titrations. The measured logP values were compared with those determined using theoretical methods. The theoretical methods for calculating logP including the Moriguchi method correlated poorly with the measured logP values. Further investigations revealed that there may be an active transporter involved in the apical-to-basolateral transport of quinolones as well. This mechanism was sensitive to competing quinolones, but, it was unaffected by the metabolic inhibitor combination of sodium azide (15mM) with 2-deoxy-D-glucose (50mM). The basolateral-to-apical transport of quinolones was found to be sensitive to inhibition by a number of different inhibitors. The metabolic inhibitors, sodium azide (15mM) with 2-deoxy-D-glucose (50mM) and 2,4-dinitrophenol (1mM), were able to reduce the basolateral-to-apical transport of quinolones. A reduction in temperature from 37°C to 2°C caused an 80-fold decrease in the transport of gatifloxacin in both directions, however, this effect was not sufficient to abolish the greater basolateral-to-apical secretion. As with apical-to-basolateral transport, it was found that quinolones competed with gatifloxacin for basolateral-to-apical transport, both ofloxacin (100μM) and norfloxacin (100μM) significantly (P<0.003) decreased the basolateral-to-apical transport of gatifloxacin; however, ciprofloxacin (100μM and 300μM) had no effect. A number of inhibitors of various transport systems were also investigated. It was found that the anion transport inhibitor, probenecid (100 μM) had a significant inhibitory effect on the basolateral-to-apical transport of ciprofloxacin (P=0.039), while the cation transport inhibitor cimetidine (100μM and 500μM) had no effect. The organic anion exchange inhibitor 4,4'diisothiocyanostilbene-2-2' -disulphonic acid DIDS (400μM) also had a significant inhibitory effect (P=O.O 13). The PgP inhibitor and anion exchange inhibitor verapamil (400Mμ) was able to completely abolish the basolateral-to-apical secretion of gatifloxacin and bring it into line with the apical-to-basolateral flux. In conclusion, the apical-to-basolateral and basolateral-toapical transport of quinolones involved an active component. The basolateral-to-apical secretion was abolished by a verapamil (400μM), a bisubstrate for PgP and the anion transporter.

Vibration analysis of a printed circuit board

The reliability of the printed circuit board assembly under dynamic environments, such as those found onboard airplanes, ships and land vehicles is receiving more attention. This research analyses the dynamic characteristics of the printed circuit board (PCB) supported by edge retainers and plug-in connectors. By modelling the wedge retainer and connector as providing simply supported boundary condition with appropriate rotational spring stiffnesses along their respective edges with the aid of finite element codes, accurate natural frequencies for the board against experimental natural frequencies are obtained. For a PCB supported by two opposite wedge retainers and a plug-in connector and with its remaining edge free of any restraint, it is found that these real supports behave somewhere between the simply supported and clamped boundary conditions and provide a percentage fixity of 39.5% more than the classical simply supported case. By using an eigensensitivity method, the rotational stiffnesses representing the boundary supports of the PCB can be updated effectively and is capable of representing the dynamics of the PCB accurately. The result shows that the percentage error in the fundamental frequency of the PCB finite element model is substantially reduced from 22.3% to 1.3%. The procedure demonstrated the effectiveness of using only the vibration test frequencies as reference data when the mode shapes of the original untuned model are almost identical to the referenced modes/experimental data. When using only modal frequencies in model improvement, the analysis is very much simplified. Furthermore, the time taken to obtain the experimental data will be substantially reduced as the experimental mode shapes are not required.In addition, this thesis advocates a relatively simple method in determining the support locations for maximising the fundamental frequency of vibrating structures. The technique is simple and does not require any optimisation or sequential search algorithm in the analysis. The key to the procedure is to position the necessary supports at positions so as to eliminate the lower modes from the original configuration. This is accomplished by introducing point supports along the nodal lines of the highest possible mode from the original configuration, so that all the other lower modes are eliminated by the introduction of the new or extra supports to the structure. It also proposes inspecting the average driving point residues along the nodal lines of vibrating plates to find the optimal locations of the supports. Numerical examples are provided to demonstrate its validity. By applying to the PCB supported on its three sides by two wedge retainers and a connector, it is found that a single point constraint that would yield maximum fundamental frequency is located at the mid-point of the nodal line, namely, node 39. This point support has the effect of increasing the structure's fundamental frequency from 68.4 Hz to 146.9 Hz, or 115% higher.

Approximation of photonic crystal fibres with large air holes by the step index fibre model

An equivalent step index fibre with a silica core and air cladding is used to model photonic crystal fibres with large air holes. We model this fibre for linear polarisation (we focus on the lowest few transverse modes of the electromagnetic field). The equivalent step index radius is obtained by equating the lowest two eigenvalues of the model to those calculated numerically for the photonic crystal fibres. The step index parameters thus obtained can then be used to calculate nonlinear parameters like the nonlinear effective area of a photonic crystal fibre or to model nonlinear few-mode interactions using an existing model.

Investigation of EDFA power transients in circuit-switched and packet-switched optical networks

Erbium-doped fibre amplifiers (EDFA’s) are a key technology for the design of all optical communication systems and networks. The superiority of EDFAs lies in their negligible intermodulation distortion across high speed multichannel signals, low intrinsic losses, slow gain dynamics, and gain in a wide range of optical wavelengths. Due to long lifetime in excited states, EDFAs do not oppose the effect of cross-gain saturation. The time characteristics of the gain saturation and recovery effects are between a few hundred microseconds and 10 milliseconds. However, in wavelength division multiplexed (WDM) optical networks with EDFAs, the number of channels traversing an EDFA can change due to the faulty link of the network or the system reconfiguration. It has been found that, due to the variation in channel number in the EDFAs chain, the output system powers of surviving channels can change in a very short time. Thus, the power transient is one of the problems deteriorating system performance. In this thesis, the transient phenomenon in wavelength routed WDM optical networks with EDFA chains was investigated. The task was performed using different input signal powers for circuit switched networks. A simulator for the EDFA gain dynamicmodel was developed to compute the magnitude and speed of the power transients in the non-self-saturated EDFA both single and chained. The dynamic model of the self-saturated EDFAs chain and its simulator were also developed to compute the magnitude and speed of the power transients and the Optical signal-to-noise ratio (OSNR). We found that the OSNR transient magnitude and speed are a function of both the output power transient and the number of EDFAs in the chain. The OSNR value predicts the level of the quality of service in the related network. It was found that the power transients for both self-saturated and non-self-saturated EDFAs are close in magnitude in the case of gain saturated EDFAs networks. Moreover, the cross-gain saturation also degrades the performance of the packet switching networks due to varying traffic characteristics. The magnitude and the speed of output power transients increase along the EDFAs chain. An investigation was done on the asynchronous transfer mode (ATM) or the WDM Internet protocol (WDM-IP) traffic networks using different traffic patterns based on the Pareto and Poisson distribution. The simulator is used to examine the amount and speed of the power transients in Pareto and Poisson distributed traffic at different bit rates, with specific focus on 2.5 Gb/s. It was found from numerical and statistical analysis that the power swing increases if the time interval of theburst-ON/burst-OFF is long in the packet bursts. This is because the gain dynamics is fast during strong signal pulse or with long duration pulses, which is due to the stimulatedemission avalanche depletion of the excited ions. Thus, an increase in output power levelcould lead to error burst which affects the system performance.

Development of a probabilistic graphical structure from a model of mental health clinical expertise

This thesis explores the process of developing a principled approach for translating a model of mental-health risk expertise into a probabilistic graphical structure. Probabilistic graphical structures can be a combination of graph and probability theory that provide numerous advantages when it comes to the representation of domains involving uncertainty, domains such as the mental health domain. In this thesis the advantages that probabilistic graphical structures offer in representing such domains is built on. The Galatean Risk Screening Tool (GRiST) is a psychological model for mental health risk assessment based on fuzzy sets. In this thesis the knowledge encapsulated in the psychological model was used to develop the structure of the probability graph by exploiting the semantics of the clinical expertise. This thesis describes how a chain graph can be developed from the psychological model to provide a probabilistic evaluation of risk that complements the one generated by GRiST’s clinical expertise by the decomposing of the GRiST knowledge structure in component parts, which were in turned mapped into equivalent probabilistic graphical structures such as Bayesian Belief Nets and Markov Random Fields to produce a composite chain graph that provides a probabilistic classification of risk expertise to complement the expert clinical judgements

Anisotropic model of kinetic roughening:he strong-coupling regime

We study the strong coupling (SC) limit of the anisotropic Kardar-Parisi-Zhang (KPZ) model. A systematic mapping of the continuum model to its lattice equivalent shows that in the SC limit, anisotropic perturbations destroy all spatial correlations but retain a temporal scaling which shows a remarkable crossover along one of the two spatial directions, the choice of direction depending on the relative strength of anisotropicity. The results agree with exact numerics and are expected to settle the long-standing SC problem of a KPZ model in the infinite range limit. © 2007 The American Physical Society.