Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.

Electrical machine characterisation and analysis for renewable energy applications

There has been an increased use of the Doubly-Fed Induction Machine (DFIM) in ac drive applications in recent times, particularly in the field of renewable energy systems and other high power variable-speed drives. The DFIM is widely regarded as the optimal generation system for both onshore and offshore wind turbines and has also been considered in wave power applications. Wind power generation is the most mature renewable technology. However, wave energy has attracted a large interest recently as the potential for power extraction is very significant. Various wave energy converter (WEC) technologies currently exist with the oscillating water column (OWC) type converter being one of the most advanced. There are fundemental differences in the power profile of the pneumatic power supplied by the OWC WEC and that of a wind turbine and this causes significant challenges in the selection and rating of electrical generators for the OWC devises. The thesis initially aims to provide an accurate per-phase equivalent circuit model of the DFIM by investigating various characterisation testing procedures. Novel testing methodologies based on the series-coupling tests is employed and is found to provide a more accurate representation of the DFIM than the standard IEEE testing methods because the series-coupling tests provide a direct method of determining the equivalent-circuit resistances and inductances of the machine. A second novel method known as the extended short-circuit test is also presented and investigated as an alternative characterisation method. Experimental results on a 1.1 kW DFIM and a 30 kW DFIM utilising the various characterisation procedures are presented in the thesis. The various test methods are analysed and validated through comparison of model predictions and torque-versus-speed curves for each induction machine. Sensitivity analysis is also used as a means of quantifying the effect of experimental error on the results taken from each of the testing procedures and is used to determine the suitability of the test procedures for characterising each of the devices. The series-coupling differential test is demonstrated to be the optimum test. The research then focuses on the OWC WEC and the modelling of this device. A software model is implemented based on data obtained from a scaled prototype device situated at the Irish test site. Test data from the electrical system of the device is analysed and this data is used to develop a performance curve for the air turbine utilised in the WEC. This performance curve was applied in a software model to represent the turbine in the electro-mechanical system and the software results are validated by the measured electrical output data from the prototype test device. Finally, once both the DFIM and OWC WEC power take-off system have been modeled succesfully, an investigation of the application of the DFIM to the OWC WEC model is carried out to determine the electrical machine rating required for the pulsating power derived from OWC WEC device. Thermal analysis of a 30 kW induction machine is carried out using a first-order thermal model. The simulations quantify the limits of operation of the machine and enable thedevelopment of rating requirements for the electrical generation system of the OWC WEC. The thesis can be considered to have three sections. The first section of the thesis contains Chapters 2 and 3 and focuses on the accurate characterisation of the doubly-fed induction machine using various testing procedures. The second section, containing Chapter 4, concentrates on the modelling of the OWC WEC power-takeoff with particular focus on the Wells turbine. Validation of this model is carried out through comparision of simulations and experimental measurements. The third section of the thesis utilises the OWC WEC model from Chapter 4 with a 30 kW induction machine model to determine the optimum device rating for the specified machine. Simulations are carried out to perform thermal analysis of the machine to give a general insight into electrical machine rating for an OWC WEC device.

Electromagnetic tracking and steering for catheter navigation

This thesis explores the use of electromagnetics for both steering and tracking of medical instruments in minimally invasive surgeries. The end application is virtual navigation of the lung for biopsy of early stage cancer nodules. Navigation to the peripheral regions of the lung is difficult due to physical dimensions of the bronchi and current methods have low successes rates for accurate diagnosis. Firstly, the potential use of DC magnetic fields for the actuation of catheter devices with permanently magnetised distal attachments is investigated. Catheter models formed from various materials and magnetic tip formations are used to examine the usefulness of relatively low power and compact electromagnets. The force and torque that can be exerted on a small permanent magnet is shown to be extremely limited. Hence, after this initial investigation we turn our attention to electromagnetic tracking, in the development of a novel, low-cost implementation of a GPS-like system for navigating within a patient. A planar magnetic transmitter, formed on a printed circuit board for a low-profile and low cost manufacture, is used to generate a low frequency magnetic field distribution which is detected by a small induction coil sensor. The field transmitter is controlled by a novel closed-loop system that ensures a highly stable magnetic field with reduced interference from one transmitter coil to another. Efficient demodulation schemes are presented which utilise synchronous detection of each magnetic field component experienced by the sensor. The overall tracking accuracy of the system is shown to be less than 2 mm with an orientation error less than 1°. A novel demodulation implementation using a unique undersampling approach allows the use of reduced sample rates to sample the signals of interest without loss of tracking accuracy. This is advantageous for embedded microcontroller implementations of EM tracking systems. The EM tracking system is demonstrated in the pre-clinical environment of a breathing lung phantom. The airways of the phantom are successfully navigated using the system in combination with a 3D computer model rendered from CT data. Registration is achieved using both a landmark rigid registration method and a hybrid fiducial-free approach. The design of a planar magnetic shield structure for blocking the effects of metallic distortion from below the transmitter is presented which successfully blocks the impact of large ferromagnetic objects such as operating tables. A variety of shielding material are analysed with MuMetal and ferrite both providing excellent shieling performance and an increased signal to noise ratio. Finally, the effect of conductive materials and human tissue on magnetic field measurements is presented. Error due to induced eddy currents and capacitive coupling is shown to severely affect EM tracking accuracy at higher frequencies.

Simulation of Dynamic Operation of a Single-Cylinder Two-Stroke Engine

Presented is a study that expands the body of knowledge on the effect of in-cycle speed fluctuations on performance of small engines. It uses the engine and drivetrain models developed previously by Callahan, et al. (1) to examine a variety of engines. The predicted performance changes due to drivetrain effects are shown in each case, and conclusions are drawn from those results. The single-cylinder, high performance four-stroke engine showed significant changes in predicted performance compared to the prediction with zero speed fluctuation in the model. Measured speed fluctuations from a firing Yamaha YZ426 engine were applied to the simulation in addition to data from a simple free mass model. Both methods predicted similar changes in performance. The multiple-cylinder, high performance two-stroke engine also showed significant changes in performance depending on the firing configuration. With both engines, the change in performance diminished with increasing mean engine speed. The low output, single-cylinder two-stroke engine simulation showed only a negligible change in performance, even with high amplitude speed fluctuations. Because the torque versus engine speed characteristic for the engine was so flat, this was expected. The cross-charged, multi-cylinder two-stroke engine also showed only a negligible change in performance. In this case, the combination of a relatively high inertia rotating assembly and the multiple cylinder firing events within the revolution smoothing the torque pulsations reduced the speed fluctuation amplitude itself.

Drivetrain Effects on Small Engine Performance

Presented is a study that expands the body of knowledge on the effect of in-cycle speed fluctuations on performance of small engines. It uses the methods developed previously by Callahan, et al. (1) to examine a variety of two-stroke engines and one four-stroke engine. The two-stroke engines were: a high performance single-cylinder, a low performance single-cylinder, a high performance multi-cylinder, and a medium performance multi-cylinder. The four-stroke engine was a high performance single-cylinder unit. Each engine was modeled in Virtual Engines, which is a fully detailed one-dimensional thermodynamic engine simulator. Measured or predicted in-cycle speed data were input into the engine models. Predicted performance changes due to drivetrain effects are shown in each case, and conclusions are drawn from those results. The simulations for the high performance single-cylinder two-stroke engine predicted significant in-cycle crankshaft speed fluctuation amplitudes and significant changes in performance when the fluctuations were input into the engine model. This was validated experimentally on a firing test engine based on a Yamaha YZ250. The four-stroke engine showed significant changes in predicted performance compared to the prediction with zero speed fluctuation assumed in the model. Measured speed fluctuations from a firing Yamaha YZ400F engine were applied to the simulation in addition to data from a simple free mass model. Both methods predicted similar fluctuation profiles and changes in performance. It is shown that the gear reduction between the crankshaft and clutch allowed for this similar behavior. The multi-cylinder, high performance two-stroke engine also showed significant changes in performance, in this case depending on the firing configuration. The low output two-stroke engine simulation showed only a negligible change in performance in spite of high amplitude speed fluctuations. This was due to its flat torque versus speed characteristic. The medium performance multi-cylinder two-stroke engine also showed only a negligible change in performance, in this case due to a relatively high inertia rotating assembly and multiple cylinder firing events within the revolution. These smoothed the net torque pulsations and reduced the amplitude of the speed fluctuation itself.

Is perception of upper body orientation based on the inertia tensor? Normogravity versus microgravity conditions

During lateral leg raising, a synergistic inclination of the supporting leg and trunk in the opposite direction to the leg movement is performed in order to preserve equilibrium. As first hypothesized by Pagano and Turvey (J Exp Psychol Hum Percept Perform, 1995, 21:1070-1087), the perception of limb orientation could be based on the orientation of the limb's inertia tensor. The purpose of this study was thus to explore whether the final upper body orientation (trunk inclination relative to vertical) depends on changes in the trunk inertia tensor. We imposed a loading condition, with total mass of 4 kg added to the subject's trunk in either a symmetrical or asymmetrical configuration. This changed the orientation of the trunk inertia tensor while keeping the total trunk mass constant. In order to separate any effects of the inertia tensor from the effects of gravitational torque, the experiment was carried out in normo- and microgravity. The results indicated that in normogravity the same final upper body orientation was maintained irrespective of the loading condition. In microgravity, regardless of loading conditions the same (but different from the normogravity) orientation of the upper body was achieved through different joint organizations: two joints (the hip and ankle joints of the supporting leg) in the asymmetrical loading condition, and one (hip) in the symmetrical loading condition. In order to determine whether the different orientations of the inertia tensor were perceived during the movement, the interjoint coordination was quantified by performing a principal components analysis (PCA) on the supporting and moving hips and on the supporting ankle joints. It was expected that different loading conditions would modify the principal component of the PCA. In normogravity, asymmetrical loading decreased the coupling between joints, while in microgravity a strong coupling was preserved whatever the loading condition. It was concluded that the trunk inertia tensor did not play a role during the lateral leg raising task because in spite of the absence of gravitational torque the final upper body orientation and the interjoint coupling were not influenced.

Functional and Physiological Determinants of Perceived Disability in Individuals Diagnosed with Osteoarthritis of the Hip

Objectives: The main objective of this pilot study was to investigate which standardized functional and physiological test best predicted perceived disability in a single group of 21 individuals diagnosed with osteoarthritis of the hip. Design: Men and women between 60 and 70 years old with osteoarthritis of the hip were selected. If participants passed study criteria, the Western Ontario McMaster University questionnaire (WOMAC), 6 Minute Walk Test (6MWT) and Timed up and Go (TUG), strength testing and aerobic testing were obtained in one single assessment. Results: Regression analysis revealed that wait time, hip abduction strength of the affected side, Aerobic Capacity (VO2 Peak), hip Extension Peak Torque, hip Flexion Peak Torque, TUG and 6MWT were significantly correlated with the WOMAC. Yet, the 6MWT had the highest significant correlation (r = -0.86, p ≤ 0.0001); R2 = 0.75 or 75% with the WOMAC total scores, (r = -0.82, p ≤ 0.0001); R2 = 0.67 or 67% with the WOMAC function and (r = -0.60, p = .002); R2 = 0.36 or 36% with the WOMAC stiffness. While the VO2 Peak revealed the highest significant correlation (r = 0.76, p ≤ .0001); R2 = 0.57 or 57% with the WOMAC pain. Conclusions: The 6MWT and the VO2 Peak seem to be essential functional and physiological assessment tools to determine perceived disability in individuals with hip OA. The perceived disability may provide new or comprehensive knowledge of the disability problems experienced by individuals with osteoarthritis of the hip, and the association of patient perception with objective measures of functional and physiological capacity might strengthen the clinical value of this knowledge.

The interference effects of non-rotated versus counter-rotated trials in visuomotor adaptation

An isometric torque-production task was used to investigate interference and retention in adaptation to multiple visuomotor environments. Subjects produced isometric flexion-extension and pronation-supination elbow torques to move a cursor to acquire targets as quickly as possible. Adaptation to a 30 degrees counter-clockwise (CCW) rotation (task A), was followed by a period of rest (control), trials with no rotation (task B0), or trials with a 60 degrees clockwise (CW) rotation (task B60). For all groups, retention of task A was assessed 5 h later. With initial training, all groups reduced the angular deviation of cursor paths early in the movements, indicating feedforward adaptation. For the control group, performance at commencement of the retest was significantly better than that at the beginning of the initial learning. For the B0 group, performance in the retest of task A was not dissimilar to that at the start of the initial learning, while for the B60 group retest performance in task A was markedly worse than initially observed. Our results indicate that close juxtaposition of two visuomotor environments precludes improved retest performance in the initial environment. Data for the B60 group, specifically larger angular errors upon retest compared with initial exposures, are consistent with the presence of anterograde interference. Furthermore, full interference occurred even when the visuomotor environment encountered in the second task was not rotated (B0). This latter novel result differs from those obtained for force field learning, where interference does not occur when task B does not impose perturbing forces, i.e., when B consists of a null field (Brashers-Krug et al., Nature 382:252-255, 1996). The results are consistent with recent proposals suggesting different interference mechanisms for visuomotor (kinematic) compared to force field (dynamic) adaptations, and have implications for the use of washout trials when studying interference between multiple visuomotor environments.

Neuromuscular adaptation during skill acquisition on a two degree-of-freedom target-acquisition task: Dynamic movement

In this experiment, we examined the extent to which the spatiotemporal reorganization of muscle synergies mediates skill acquisition on a two degree-of-freedom (df) target-acquisition task. Eight participants completed five practice sessions on consecutive days. During each session they practiced movements to eight target positions presented by a visual display. The movements required combinations of flexion/extension and pronation/supination of the elbow joint complex. During practice sessions, eight targets displaced 5.4 cm from the start position ( representing joint excursions of 54) were presented 16 times. During pre- and posttests, participants acquired the targets at two distances (3.6 cm [36 degrees] and 7.2 cm [72 degrees]). EMG data were recorded from eight muscles contributing to the movements during the pre- and posttests. Most targets were acquired more rapidly after the practice period. Performance improvements were, in most target directions, accompanied by increases in the smoothness of the movement trajectories. When target acquisition required movement in both dfs, there were also practice-related decreases in the extent to which the trajectories deviated from a direct path to the target. The contribution of monofunctional muscles ( those producing torque in a single df) increased with practice during movements in which they acted as agonists. The activity in bifunctional muscles ( those contributing torque in both dfs) remained at pretest levels in most movements. The results suggest that performance gains were mediated primarily by changes in the spatial organization of muscles synergies. These changes were expressed most prominently in terms of the magnitude of activation of the monofunctional muscles.

Effector dynamics of rhythmic wrist activity and its implications for (modeling) bimanual coordination

To examine the role of the effector dynamics of the wrist in the production of rhythmic motor activity, we estimated the phase shifts between the EMG and the task-related output for a rhythmic isometric torque production task and an oscillatory movement, and found a substantial difference (45-52degrees) between the two. For both tasks, the relation between EMG and task-related output (torque or displacement) was adequately reproduced with a physiologically motivated musculoskeletal model. The model simulations demonstrated the importance of the contribution of passive structures to the overall dynamics and provided an account for the observed phase shifts in the dynamic task. Additional simulations of the musculoskeletal model with added load suggested that particular changes in the phase relation between EMG and movement may follow largely from the intrinsic muscle dynamics, rather than being the result of adaptations in the neural control of joint stiffness. The implications of these results are discussed in relation to (models of) interlimb coordination in rhythmic tasks. (C) 2004 Elsevier B.V. All rights reserved.

Transfer of resistance training to enhance rapid coordinated force production by older adults

The purpose of this study was to examine the capacity of resistance training to enhance the rapid and coordinated production of force by older people. Thirty adults (greater than or equal to 60 years) completed a visually guided aiming task that required the generation of isometric torque in 2 df about the elbow prior to and following a 4-week training period. Groups of six participants were allocated to two progressive ( 40 - 100% maximal voluntary contraction (MVC)) resistance-training (PRT) groups, to two constant low-load (10% MVC) training groups (CLO) and to one no-training control group. Training movements required the generation of either combined flexion and supination (FLESUP), or combined extension and supination (EXTSUP). In response to training, target acquisition times in the aiming task decreased for all groups; however, both the nature of the training load and the training movement influenced the pattern and magnitude of improvements (EXTSUP_ CLO: 36%, FLESUP_ PRT 26%, EXTSUP_ PRT 22%, FLESUP_ CLO 20%, CONTROL 15%). For one group that trained with progressively increasing loads, there arose a subsequent decrease in performance in one condition of the transfer task. For each group, these adaptations were accompanied by systematic changes in the coordination of muscles about the elbow joint, particularly the biceps brachii.

The sites of neural adaptation induced by resistance training in humans

Although it has long been supposed that resistance training causes adaptive changes in the CNS, the sites and nature of these adaptations have not previously been identified. In order to determine whether the neural adaptations to resistance training occur to a greater extent at cortical or subcortical sites in the CNS, we compared the effects of resistance training on the electromyographic (EMG) responses to transcranial magnetic (TMS) and electrical (TES) stimulation. Motor evoked potentials (MEPs) were recorded from the first dorsal interosseous muscle of 16 individuals before and after 4 weeks of resistance training for the index finger abductors (n=8), or training involving finger abduction-adduction without external resistance (n=8). TMS was delivered at rest at intensities from 5% below the passive threshold to the maximal output of the stimulator. TMS and TES were also delivered at the active threshold intensity while the participants exerted torques ranging from 5 to 60% of their maximum voluntary contraction (MVC) torque. The average latency of MEPs elicited by TES was significantly shorter than that of TMS MEPs (TES latency=21.5+/-1.4 ms; TMS latency=23.4+/-1.4 ms; P

Role of peripheral afference during acquisition of a complex coordination task

It has long been supposed that the interference observed in certain patterns of coordination is mediated, at least in part, by peripheral afference from the moving limbs. We manipulated the level of afferent input, arising from movement of the opposite limb, during the acquisition of a complex coordination task. Participants learned to generate flexion and extension movements of the right wrist, of 75degrees amplitude, that were a quarter cycle out of phase with a 1-Hz sinusoidal visual reference signal. On separate trials, the left wrist either was at rest, or was moved passively by a torque motor through 50degrees, 75degrees or 100degrees, in synchrony with the reference signal. Five acquisition sessions were conducted on successive days. A retention session was conducted I week later. Performance was initially superior when the opposite limb was moved passively than when it was static. The amplitude and frequency of active movement were lower in the static condition than in the driven conditions and the variation in the relative phase relation across trials was greater than in the driven conditions. In addition, the variability of amplitude, frequency and the relative phase relation during each trial was greater when the opposite limb was static than when driven. Similar effects were expressed in electromyograms. The most marked and consistent differences in the accuracy and consistency of performance (defined in terms of relative phase) were between the static condition and the condition in which the left wrist was moved through 50degrees. These outcomes were exhibited most prominently during initial exposure to the task. Increases in task performance during the acquisition period, as assessed by a number of kinematic variables, were generally well described by power functions. In addition, the recruitment of extensor carpi radialis (ECR), and the degree of co-contraction of flexor carpi radialis and ECR, decreased during acquisition. Our results indicate that, in an appropriate task context, afferent feedback from the opposite limb, even when out of phase with the focal movement, may have a positive influence upon the stability of coordination.

The Synergistic Organization of Muscle Recruitment Constrains Visuomotor Adaptation

Reaching to visual targets engages the nervous system in a series of transformations between sensory information and motor commands. That which remains to be determined is the extent to which the processes that mediate sensorimotor adaptation to novel environments engage neural circuits that represent the required movement in joint-based or muscle-based coordinate systems. We sought to establish the contribution of these alternative representations to the process of visuomotor adaptation. To do so we applied a visuomotor rotation during a center-out isometric torque production task that involved flexion/extension and supination/pronation at the elbow-joint complex. In separate sessions, distinct half-quadrant rotations (i.e., 45°) were applied such that adaptation could be achieved either by only rescaling the individual joint torques (i.e., the visual target and torque target remained in the same quadrant) or by additionally requiring torque reversal at a contributing joint (i.e., the visual target and torque target were in different quadrants). Analysis of the time course of directional errors revealed that the degree of adaptation was lower (by ~20%) when reversals in the direction of joint torques were required. It has been established previously that in this task space, a transition between supination and pronation requires the engagement of a different set of muscle synergists, whereas in a transition between flexion and extension no such change is required. The additional observation that the initial level of adaptation was lower and the subsequent aftereffects were smaller, for trials that involved a pronation–supination transition than for those that involved a flexion–extension transition, supports the conclusion that the process of adaptation engaged, at least in part, neural circuits that represent the required motor output in a muscle-based coordinate system.

Coordinated control of DFIG’s rotor and grid side converters during network unbalance

This paper proposes a coordinated control of the rotor and grid side converters (RSC & GSC) of doubly-fed induction generator (DFIG) based wind generation systems under unbalanced voltage conditions. System behaviors and operations of the RSC and GSC under unbalanced voltage are illustrated. To provide enhanced operation, the RSC is controlled to eliminate the torque oscillations at double supply frequency under unbalanced stator supply. The oscillation of the stator output active power is then cancelled by the active power output from the GSC, to ensure constant active power output from the overall DFIG generation system. To provide the required positive and negative sequence currents control for the RSC and GSC, a current control strategy containing a main controller and an auxiliary controller is analyzed. The main controller is implemented in the positive (dq)+ frame without involving positive/negative sequence decomposition whereas the auxiliary controller is implemented in the negative sequence (dq)? frame with negative sequence current extracted. Simulation results using EMTDC/PSCAD are presented for a 2MW DFIG wind generation system to validate the proposed control scheme and to show the enhanced system operation during unbalanced voltage supply.