Identification of a cis-regulatory element by transient analysis of co-ordinately regulated genes

Background Transcription factors (TFs) co-ordinately regulate target genes that are dispersed throughout the genome. This co-ordinate regulation is achieved, in part, through the interaction of transcription factors with conserved cis-regulatory motifs that are in close proximity to the target genes. While much is known about the families of transcription factors that regulate gene expression in plants, there are few well characterised cis-regulatory motifs. In Arabidopsis, over-expression of the MYB transcription factor PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT 1) leads to transgenic plants with elevated anthocyanin levels due to the co-ordinated up-regulation of genes in the anthocyanin biosynthetic pathway. In addition to the anthocyanin biosynthetic genes, there are a number of un-associated genes that also change in expression level. This may be a direct or indirect consequence of the over-expression of PAP1. Results Oligo array analysis of PAP1 over-expression Arabidopsis plants identified genes co-ordinately up-regulated in response to the elevated expression of this transcription factor. Transient assays on the promoter regions of 33 of these up-regulated genes identified eight promoter fragments that were transactivated by PAP1. Bioinformatic analysis on these promoters revealed a common cis-regulatory motif that we showed is required for PAP1 dependent transactivation. Conclusion Co-ordinated gene regulation by individual transcription factors is a complex collection of both direct and indirect effects. Transient transactivation assays provide a rapid method to identify direct target genes from indirect target genes. Bioinformatic analysis of the promoters of these direct target genes is able to locate motifs that are common to this sub-set of promoters, which is impossible to identify with the larger set of direct and indirect target genes. While this type of analysis does not prove a direct interaction between protein and DNA, it does provide a tool to characterise cis-regulatory sequences that are necessary for transcription activation in a complex list of co-ordinately regulated genes.

Multi-output buck-boost converter with enhanced dynamic response to load and input voltage changes

This paper presents a new multi-output DC/DC converter topology that has step-up and step-down conversion capabilities. In this topology, several output voltages can be generated which can be used in different applications such as multilevel converters with diode-clamped topology or power supplies with several voltage levels. Steady state and dynamic equations of the proposed multi-output converter have been developed, that can be used for steady state and transient analysis. Two control techniques have been proposed for this topology based on constant and dynamic hysteresis band height control to address different applications. Simulations have been performed for different operating modes and load conditions to verify the proposed topology and its control technique. Additionally, a laboratory prototype is designed and implemented to verify the simulation results.

Natural balancing of flying capacitor voltages in multicell inverter under PD carrier-based PWM

The flying capacitor multicell inverter (FCMI) possesses natural balancing property. With the phase-shifted (PS) carrier-based scheme, natural balancing can be achieved in a straightforward manner. However, to achieve natural balancing with the harmonically optimal phase-disposition (PD) carrierbased scheme, the conventional approaches require (n-1) x (n-1) trapezoidal carrier signals for an n-level inverter, which is (n-1) x (n-2) times more than that in the standard PD scheme. This paper proposes two improved natural balancing strategies for FMI under PD scheme, which use the same (n-1) carrier signals as used in the standard PD scheme. In the first scheme, on-line detection is performed of the band in which the modulation signal is located, corresponding period number of the carrier, and rising or falling half cycle of the carrier waveform to generate the switching signals based on certain rules. In the second strategy, the output voltage level selection is first processed and the switching signals are then generated according to a rule based on preferential cell selection algorithm. These methods are easy to use and can be simply implemented as compared to the other available methods. Simulation and experimental results are presented for a five-level inverter to verify these proposed schemes.

Water lubricated bearings

The increasing ecological awareness and stringent requirements for environmental protection have led to the development of water lubricated bearings in many applications where oil was used as the lubricant. The chapter details the theoretical analysis to determine both the static and dynamic characteristics,including the stability (using both the linearised perturbation method and the nonlinear transient analysis) of multiple axial groove water lubricated bearings. Experimental measurements and computational fluid dynamics (CFD) simulations by the Tribology research group at Queensland University of Technology,Australia and Manipal Institute of Technology, India, have highlighted a significant gap in the understanding of the flow phenomena and pressure conditions within the lubricating fluid. An attempt has been made to present a CFD approach to model fluid flow in the bearing with three equi-spaced axial grooves and supplied with water from one end of the bearing. Details of the experimental method used to measure the film pressure in the bearing are outlined. The lubricant is subjected to a velocity induced flow (as the shaft rotates) and a pressure induced flow (as the water is forced from one end of the bearing to the other). Results are presented for the circumferential and axial pressure distribution in the bearing clearance for different loads, speeds and supply pressures. The axial pressure profile along the axial groove located in the loaded part of the bearing is measured. The theoretical analysis shows that smaller the groove angle better will be the load-carrying capacity and stability of these bearings. Results are compared with experimentally measured pressure distributions.

Electrical imaging and fluid modeling of convective fingering in a shallow water-table aquifer

Unstable density-driven flow can lead to enhanced solute transport in groundwater. Only recently has the complex fingering pattern associated with free convection been documented in field settings. Electrical resistivity (ER) tomography has been used to capture a snapshot of convective instabilities at a single point in time, but a thorough transient analysis is still lacking in the literature. We present the results of a 2 year experimental study at a shallow aquifer in the United Arab Emirates that was designed to specifically explore the transient nature of free convection. ER tomography data documented the presence of convective fingers following a significant rainfall event. We demonstrate that the complex fingering pattern had completely disappeared a year after the rainfall event. The observation is supported by an analysis of the aquifer halite budget and hydrodynamic modeling of the transient character of the fingering instabilities. Modeling results show that the transient dynamics of the gravitational instabilities (their initial development, infiltration into the underlying lower-density groundwater, and subsequent decay) are in agreement with the timing observed in the time-lapse ER measurements. All experimental observations and modeling results are consistent with the hypothesis that a dense brine that infiltrated into the aquifer from a surficial source was the cause of free convection at this site, and that the finite nature of the dense brine source and dispersive mixing led to the decay of instabilities with time. This study highlights the importance of the transience of free convection phenomena and suggests that these processes are more rapid than was previously understood.

Mode switching DFIG for low voltage ride through

With the rapid development of world-wide wind energy generation using doubly fed induction generations (DFIGs), low voltage ride through (LVRT) has become a great concern. This paper focuses on a unique topology of DFIG called IG connection mode to help the DFIG ride through grid faults smoothly. Transient analysis of IG connection mode is carried out to derive the generator currents. With this analysis, the control strategy for IG connection mode DFIG was developed. From the simulation results, it is clearly visible that IG mode could work in both normal and low grid voltage conditions. Simulation results clearly show that the DFIG with the proposed mode switching control could smoothly ride through low voltage grid faults while satisfying grid code requirements.

Applications of wavelet transform for analysis of freeway traffic : bottlenecks, transient traffic, and traffic oscillations

This paper demonstrates the capabilities of wavelet transform (WT) for analyzing important features related to bottleneck activations and traffic oscillations in congested traffic in a systematic manner. In particular, the analysis of loop detector data from a freeway shows that the use of wavelet-based energy can effectively identify the location of an active bottleneck, the arrival time of the resulting queue at each upstream sensor location, and the start and end of a transition during the onset of a queue. Vehicle trajectories were also analyzed using WT and our analysis shows that the wavelet-based energies of individual vehicles can effectively detect the origins of deceleration waves and shed light on possible triggers (e.g., lane-changing). The spatiotemporal propagations of oscillations identified by tracing wavelet-based energy peaks from vehicle to vehicle enable analysis of oscillation amplitude, duration and intensity.

Stress analysis of carotid atheroma in transient ischemic attack patients: Evidence for extreme stress-induced plaque rupture

Plaque rupture has been considered to be the result of its structural failure. The aim of this study is to suggest a possible link between higher stresses and rupture sites observed from in vivo magnetic resonance imaging (MRI) of transient ischemic attack (TIA) patients, by using stress analysis methods. Three patients, who had recently suffered a TIA, underwent in vivo multi-spectral MR imaging. Based on plaque geometries reconstructed from the post-rupture status, six pre-rupture plaque models were generated for each patient dataset with different reconstructions of rupture sites to bridge the gap of fibrous cap from original MRI images. Stress analysis by fluid structure interaction simulation was performed on the models, followed by analysis of local stress concentration distribution and plaque rupture sites. Furthermore, the sensitivity of stress analysis to the pre-rupture plaque geometry reconstruction was examined. Local stress concentrations were found to be located at the plaque rupture sites for the three subjects studied. In the total of 18 models created, the locations of the stress concentration regions were similar in 17 models in which rupture sites were always associated with high stresses. The local stress concentration region moved from circumferential center to the shoulder region (slightly away from the rupture site) for a case with a thick fibrous cap. Plaque wall stress level in the rupture locations was found to be much higher than the value in non-rupture locations. The good correlation between local stress concentrations and plaque rupture sites, and generally higher plaque wall stress level in rupture locations in the subjects studied could provide indirect evidence for the extreme stress-induced plaque rupture hypothesis. Local stress concentration in the plaque region could be one of the factors contributing to plaque rupture.

Stress analysis of carotid atheroma in a transient ischaemic attack patient using the MRI-based fluid-structure interaction method

Rupture of atherosclerotic plaque is a major cause of mortality. Plaque stress analysis, based on patient-specific multisequence in vivo MRI, can provide critical information for the understanding of plaque rupture and could eventually lead to plaque rupture prediction. However, the direct link between stress and plaque rupture is not fully understood. In the present study, the plaque from a patient who recently experienced a transient ischaemic attack (TIA) was studied using a fluid-structure interaction method to quantify stress distribution in the plaque region based on in vivo MR images. The results showed that wall shear stress is generally low in the artery with a slight increase at the plaque throat owing to minor luminal narrowing. The oscillatory shear index is much higher in the proximal part of the plaque. Both local wall stress concentrations and the relative stress variation distribution during a cardiac cycle indicate that the actual plaque rupture site is collocated with the highest rupture risk region in the studied patient.

Analysis of distrubances in large interconnected power systems

World economies increasingly demand reliable and economical power supply and distribution. To achieve this aim the majority of power systems are becoming interconnected, with several power utilities supplying the one large network. One problem that occurs in a large interconnected power system is the regular occurrence of system disturbances which can result in the creation of intra-area oscillating modes. These modes can be regarded as the transient responses of the power system to excitation, which are generally characterised as decaying sinusoids. For a power system operating ideally these transient responses would ideally would have a “ring-down” time of 10-15 seconds. Sometimes equipment failures disturb the ideal operation of power systems and oscillating modes with ring-down times greater than 15 seconds arise. The larger settling times associated with such “poorly damped” modes cause substantial power flows between generation nodes, resulting in significant physical stresses on the power distribution system. If these modes are not just poorly damped but “negatively damped”, catastrophic failures of the system can occur. To ensure system stability and security of large power systems, the potentially dangerous oscillating modes generated from disturbances (such as equipment failure) must be quickly identified. The power utility must then apply appropriate damping control strategies. In power system monitoring there exist two facets of critical interest. The first is the estimation of modal parameters for a power system in normal, stable, operation. The second is the rapid detection of any substantial changes to this normal, stable operation (because of equipment breakdown for example). Most work to date has concentrated on the first of these two facets, i.e. on modal parameter estimation. Numerous modal parameter estimation techniques have been proposed and implemented, but all have limitations [1-13]. One of the key limitations of all existing parameter estimation methods is the fact that they require very long data records to provide accurate parameter estimates. This is a particularly significant problem after a sudden detrimental change in damping. One simply cannot afford to wait long enough to collect the large amounts of data required for existing parameter estimators. Motivated by this gap in the current body of knowledge and practice, the research reported in this thesis focuses heavily on rapid detection of changes (i.e. on the second facet mentioned above). This thesis reports on a number of new algorithms which can rapidly flag whether or not there has been a detrimental change to a stable operating system. It will be seen that the new algorithms enable sudden modal changes to be detected within quite short time frames (typically about 1 minute), using data from power systems in normal operation. The new methods reported in this thesis are summarised below. The Energy Based Detector (EBD): The rationale for this method is that the modal disturbance energy is greater for lightly damped modes than it is for heavily damped modes (because the latter decay more rapidly). Sudden changes in modal energy, then, imply sudden changes in modal damping. Because the method relies on data from power systems in normal operation, the modal disturbances are random. Accordingly, the disturbance energy is modelled as a random process (with the parameters of the model being determined from the power system under consideration). A threshold is then set based on the statistical model. The energy method is very simple to implement and is computationally efficient. It is, however, only able to determine whether or not a sudden modal deterioration has occurred; it cannot identify which mode has deteriorated. For this reason the method is particularly well suited to smaller interconnected power systems that involve only a single mode. Optimal Individual Mode Detector (OIMD): As discussed in the previous paragraph, the energy detector can only determine whether or not a change has occurred; it cannot flag which mode is responsible for the deterioration. The OIMD seeks to address this shortcoming. It uses optimal detection theory to test for sudden changes in individual modes. In practice, one can have an OIMD operating for all modes within a system, so that changes in any of the modes can be detected. Like the energy detector, the OIMD is based on a statistical model and a subsequently derived threshold test. The Kalman Innovation Detector (KID): This detector is an alternative to the OIMD. Unlike the OIMD, however, it does not explicitly monitor individual modes. Rather it relies on a key property of a Kalman filter, namely that the Kalman innovation (the difference between the estimated and observed outputs) is white as long as the Kalman filter model is valid. A Kalman filter model is set to represent a particular power system. If some event in the power system (such as equipment failure) causes a sudden change to the power system, the Kalman model will no longer be valid and the innovation will no longer be white. Furthermore, if there is a detrimental system change, the innovation spectrum will display strong peaks in the spectrum at frequency locations associated with changes. Hence the innovation spectrum can be monitored to both set-off an “alarm” when a change occurs and to identify which modal frequency has given rise to the change. The threshold for alarming is based on the simple Chi-Squared PDF for a normalised white noise spectrum [14, 15]. While the method can identify the mode which has deteriorated, it does not necessarily indicate whether there has been a frequency or damping change. The PPM discussed next can monitor frequency changes and so can provide some discrimination in this regard. The Polynomial Phase Method (PPM): In [16] the cubic phase (CP) function was introduced as a tool for revealing frequency related spectral changes. This thesis extends the cubic phase function to a generalised class of polynomial phase functions which can reveal frequency related spectral changes in power systems. A statistical analysis of the technique is performed. When applied to power system analysis, the PPM can provide knowledge of sudden shifts in frequency through both the new frequency estimate and the polynomial phase coefficient information. This knowledge can be then cross-referenced with other detection methods to provide improved detection benchmarks.

TCSC control design for transient stability improvement of a multi-machine power system using trajectory sensitivity

This paper discusses the effects of thyristor controlled series compensator (TCSC), a series FACTS controller, on the transient stability of a power system. Trajectory sensitivity analysis (TSA) has been used to measure the transient stability condition of the system. The TCSC is modeled by a variable capacitor, the value of which changes with the firing angle. It is shown that TSA can be used in the design of the controller. The optimal locations of the TCSC-controller for different fault conditions can also be identified with the help of TSA. The paper depicts the advantage of the use of TCSC with a suitable controller over fixed capacitor operation.

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.

Stability boundary analysis of the dynamic voltage restorer in weak systems with dynamic loads

In this contribution, a stability analysis for a dynamic voltage restorer (DVR) connected to a weak ac system containing a dynamic load is presented using continuation techniques and bifurcation theory. The system dynamics are explored through the continuation of periodic solutions of the associated dynamic equations. The switching process in the DVR converter is taken into account to trace the stability regions through a suitable mathematical representation of the DVR converter. The stability regions in the Thevenin equivalent plane are computed. In addition, the stability regions in the control gains space, as well as the contour lines for different Floquet multipliers, are computed. Besides, the DVR converter model employed in this contribution avoids the necessity of developing very complicated iterative map approaches as in the conventional bifurcation analysis of converters. The continuation method and the DVR model can take into account dynamics and nonlinear loads and any network topology since the analysis is carried out directly from the state space equations. The bifurcation approach is shown to be both computationally efficient and robust, since it eliminates the need for numerically critical and long-lasting transient simulations.