Time-series analysis of Campylobacter incidence in Switzerland

SUMMARY Campylobacteriosis has been the most common food-associated notifiable infectious disease in Switzerland since 1995. Contact with and ingestion of raw or undercooked broilers are considered the dominant risk factors for infection. In this study, we investigated the temporal relationship between the disease incidence in humans and the prevalence of Campylobacter in broilers in Switzerland from 2008 to 2012. We use a time-series approach to describe the pattern of the disease by incorporating seasonal effects and autocorrelation. The analysis shows that prevalence of Campylobacter in broilers, with a 2-week lag, has a significant impact on disease incidence in humans. Therefore Campylobacter cases in humans can be partly explained by contagion through broiler meat. We also found a strong autoregressive effect in human illness, and a significant increase of illness during Christmas and New Year's holidays. In a final analysis, we corrected for the sampling error of prevalence in broilers and the results gave similar conclusions.

Coupling time-stepping numerical methods and standard aerodynamics codes for instability analysis of flows in complex geometries

The development of a global instability analysis code coupling a time-stepping approach, as applied to the solution of BiGlobal and TriGlobal instability analysis 1, 2 and finite-volume-based spatial discretization, as used in standard aerodynamics codes is presented. The key advantage of the time-stepping method over matrix-formulation approaches is that the former provides a solution to the computer-storage issues associated with the latter methodology. To-date both approaches are successfully in use to analyze instability in complex geometries, although their relative advantages have never been quantified. The ultimate goal of the present work is to address this issue in the context of spatial discretization schemes typically used in industry. The time-stepping approach of Chiba 3 has been implemented in conjunction with two direct numerical simulation algorithms, one based on the typically-used in this context high-order method and another based on low-order methods representative of those in common use in industry. The two codes have been validated with solutions of the BiGlobal EVP and it has been showed that small errors in the base flow do not have affect significantly the results. As a result, a three-dimensional compressible unsteady second-order code for global linear stability has been successfully developed based on finite-volume spatial discretization and time-stepping method with the ability to study complex geometries by means of unstructured and hybrid meshes

Matrix-free time-stepping methods for the solution of TriGlobal instability problems

La inmensa mayoría de los flujos de relevancia ingenieril permanecen sin estudiar en el marco de la teoría de estabilidad global. Esto es debido a dos razones fundamentalmente, las dificultades asociadas con el análisis de los flujos turbulentos y los inmensos recursos computacionales requeridos para obtener la solución del problema de autovalores asociado al análisis de inestabilidad de flujos tridimensionales, también conocido como problema TriGlobal. En esta tesis se aborda el problema asociado con la tridimensionalidad. Se ha desarrollado una metodología general para obtener soluciones de problemas de análisis modal de las inestabilidades lineales globales mediante el acoplamiento de métodos de evolución temporal, desarrollados en este trabajo, con códigos de mecánica de fluidos computacional de segundo orden, utilizados de forma general en la industria. Esta metodología consiste en la resolución del problema de autovalores asociado al análisis de inestabilidad mediante métodos de proyección en subespacios de Krylov, con la particularidad de que dichos subespacios son generados por medio de la integración temporal de un vector inicial usando cualquier código de mecánica de fluidos computacional. Se han elegido tres problemas desafiantes en función de la exigencia de recursos computacionales necesarios y de la complejidad física para la demostración de la presente metodología: (i) el flujo en el interior de una cavidad tridimensional impulsada por una de sus tapas, (ii) el flujo alrededor de un cilindro equipado con aletas helicoidales a lo largo su envergadura y (iii) el flujo a través de una cavidad abierta tridimensinal en ausencia de homogeneidades espaciales. Para la validación de la tecnología se ha obtenido la solución del problema TriGlobal asociado al flujo en la cavidad tridimensional, utilizando el método de evolución temporal desarrollado acoplado con los operadores numéricos de flujo incompresible del código CFD OpenFOAM (código libre). Los resultados obtenidos coinciden plentamente con la literatura. La aplicación de esta metodología al estudio de inestabilidades globales de flujos abiertos tridimensionales ha proporcionado por primera vez, información sobre la transición tridimensional de estos flujos. Además, la metodología ha sido adaptada para resolver problemas adjuntos TriGlobales, permitiendo el control de flujo basado en modificaciones de las inestabilidades globales. Finalmente, se ha demostrado que la cantidad moderada de los recursos computacionales requeridos para la solución del problema de valor propio TriGlobal usando este método numérico, junto a su versatilidad al poder acoplarse a cualquier código aerodinámico, permite la realización de análisis de inestabilidad global y control de flujos complejos de relevancia industrial. Abstract Most flows of engineering relevance still remain unexplored in a global instability theory context for two reasons. First, because of the difficulties associated with the analysis of turbulent flows and, second, for the formidable computational resources required for the solution of the eigenvalue problem associated with the instability analysis of three-dimensional base flows, also known as TriGlobal problem. In this thesis, the problem associated with the three-dimensionality is addressed by means of the development of a general approach to the solution of large-scale global linear instability analysis by coupling a time-stepping approach with second order aerodynamic codes employed in industry. Three challenging flows in the terms of required computational resources and physical complexity have been chosen for demonstration of the present methodology; (i) the flow inside a wall-bounded three-dimensional lid-driven cavity, (ii) the flow past a cylinder fitted with helical strakes and (iii) the flow over a inhomogeneous three-dimensional open cavity. Results in excellent agreement with the literature have been obtained for the three-dimensional lid-driven cavity by using this methodology coupled with the incompressible solver of the open-source toolbox OpenFOAM®, which has served as validation. Moreover, significant physical insight of the instability of three-dimensional open flows has been gained through the application of the present time-stepping methodology to the other two cases. In addition, modifications to the present approach have been proposed in order to perform adjoint instability analysis of three-dimensional base flows and flow control; validation and TriGlobal examples are presented. Finally, it has been demonstrated that the moderate amount of computational resources required for the solution of the TriGlobal eigenvalue problem using this method enables the performance of instability analysis and control of flows of industrial relevance.

Minimum time control for multiphase buck converter: analysis and application

The combination of minimum time control and multiphase converter is a favorable option for dc-dc converters in applications where output voltage variation is required, such as RF amplifiers and dynamic voltage scaling in microprocessors, due to their advantage of fast dynamic response. In this paper, an improved minimum time control approach for multiphase buck converter that is based on charge balance technique, aiming at fast output voltage transition is presented. Compared with the traditional method, the proposed control takes into account the phase delay and current ripple in each phase. Therefore, by investigating the behavior of multiphase converter during voltage transition, it resolves the problem of current unbalance after the transient, which can lead to long settling time of the output voltage. The restriction of this control is that the output voltage that the converter can provide is related to the number of the phases, because only the duty cycles at which the multiphase converter has total ripple cancellation are used in this approach. The model of the proposed control is introduced, and the design constraints of the buck converters filter for this control are discussed. In order to prove the concept, a four-phase buck converter is implemented and the experimental results that validate the proposed control method are presented. The application of this control to RF envelope tracking is also presented in this paper.

Use of an Inverse Method for Time Series to Estimate the Dynamics of and Management Strategies for the Box Jellyfish Carybdea marsupialis

Frequently, population ecology of marine organisms uses a descriptive approach in which their sizes and densities are plotted over time. This approach has limited usefulness for design strategies in management or modelling different scenarios. Population projection matrix models are among the most widely used tools in ecology. Unfortunately, for the majority of pelagic marine organisms, it is difficult to mark individuals and follow them over time to determine their vital rates and built a population projection matrix model. Nevertheless, it is possible to get time-series data to calculate size structure and densities of each size, in order to determine the matrix parameters. This approach is known as a “demographic inverse problem” and it is based on quadratic programming methods, but it has rarely been used on aquatic organisms. We used unpublished field data of a population of cubomedusae Carybdea marsupialis to construct a population projection matrix model and compare two different management strategies to lower population to values before year 2008 when there was no significant interaction with bathers. Those strategies were by direct removal of medusae and by reducing prey. Our results showed that removal of jellyfish from all size classes was more effective than removing only juveniles or adults. When reducing prey, the highest efficiency to lower the C. marsupialis population occurred when prey depletion affected prey of all medusae sizes. Our model fit well with the field data and may serve to design an efficient management strategy or build hypothetical scenarios such as removal of individuals or reducing prey. TThis This sdfsdshis method is applicable to other marine or terrestrial species, for which density and population structure over time are available.

Biological and environmental time series obtained from Point B, Bay of Villefranche

Ecological succession provides a widely accepted description of seasonal changes in phytoplankton and mesozooplankton assemblages in the natural environment, but concurrent changes in smaller (i.e. microbes) and larger (i.e. macroplankton) organisms are not included in the model because plankton ranging from bacteria to jellies are seldom sampled and analyzed simultaneously. Here we studied, for the first time in the aquatic literature, the succession of marine plankton in the whole-plankton assemblage that spanned 5 orders of magnitude in size from microbes to macroplankton predators (not including fish or fish larvae, for which no consistent data were available). Samples were collected in the northwestern Mediterranean Sea (Bay of Villefranche) weekly during 10 months. Simultaneously collected samples were analyzed by flow cytometry, inverse microscopy, FlowCam, and ZooScan. The whole-plankton assemblage underwent sharp reorganizations that corresponded to bottom-up events of vertical mixing in the water-column, and its development was top-down controlled by large gelatinous filter feeders and predators. Based on the results provided by our novel whole-plankton assemblage approach, we propose a new comprehensive conceptual model of the annual plankton succession (i.e. whole plankton model) characterized by both stepwise stacking of four broad trophic communities from early spring through summer, which is a new concept, and progressive replacement of ecological plankton categories within the different trophic communities, as recognised traditionally.

Design and implementation of generalized topologies of time-interleaved variable bandpass Σ−Δ modulators

In this thesis, novel analog-to-digital and digital-to-analog generalized time-interleaved variable bandpass sigma-delta modulators are designed, analysed, evaluated and implemented that are suitable for high performance data conversion for a broad-spectrum of applications. These generalized time-interleaved variable bandpass sigma-delta modulators can perform noise-shaping for any centre frequency from DC to Nyquist. The proposed topologies are well-suited for Butterworth, Chebyshev, inverse-Chebyshev and elliptical filters, where designers have the flexibility of specifying the centre frequency, bandwidth as well as the passband and stopband attenuation parameters. The application of the time-interleaving approach, in combination with these bandpass loop-filters, not only overcomes the limitations that are associated with conventional and mid-band resonator-based bandpass sigma-delta modulators, but also offers an elegant means to increase the conversion bandwidth, thereby relaxing the need to use faster or higher-order sigma-delta modulators. A step-by-step design technique has been developed for the design of time-interleaved variable bandpass sigma-delta modulators. Using this technique, an assortment of lower- and higher-order single- and multi-path generalized A/D variable bandpass sigma-delta modulators were designed, evaluated and compared in terms of their signal-to-noise ratios, hardware complexity, stability, tonality and sensitivity for ideal and non-ideal topologies. Extensive behavioural-level simulations verified that one of the proposed topologies not only used fewer coefficients but also exhibited greater robustness to non-idealties. Furthermore, second-, fourth- and sixth-order single- and multi-path digital variable bandpass digital sigma-delta modulators are designed using this technique. The mathematical modelling and evaluation of tones caused by the finite wordlengths of these digital multi-path sigmadelta modulators, when excited by sinusoidal input signals, are also derived from first principles and verified using simulation and experimental results. The fourth-order digital variable-band sigma-delta modulator topologies are implemented in VHDL and synthesized on Xilinx® SpartanTM-3 Development Kit using fixed-point arithmetic. Circuit outputs were taken via RS232 connection provided on the FPGA board and evaluated using MATLAB routines developed by the author. These routines included the decimation process as well. The experiments undertaken by the author further validated the design methodology presented in the work. In addition, a novel tunable and reconfigurable second-order variable bandpass sigma-delta modulator has been designed and evaluated at the behavioural-level. This topology offers a flexible set of choices for designers and can operate either in single- or dual-mode enabling multi-band implementations on a single digital variable bandpass sigma-delta modulator. This work is also supported by a novel user-friendly design and evaluation tool that has been developed in MATLAB/Simulink that can speed-up the design, evaluation and comparison of analog and digital single-stage and time-interleaved variable bandpass sigma-delta modulators. This tool enables the user to specify the conversion type, topology, loop-filter type, path number and oversampling ratio.

Incomplete DJH rearrangements as a novel tumor target for minimal residual disease quantitation in multiple myeloma using real-time PCR.

The hypervariable regions of immunoglobulin heavy-chain (IgH) rearrangements provide a specific tumor marker in multiple myeloma (MM). Recently, real-time PCR assays have been developed in order to quantify the number of tumor cells after treatment. However, these strategies are hampered by the presence of somatic hypermutation (SH) in VDJH rearrangements from multiple myeloma (MM) patients, which causes mismatches between primers and/or probes and the target, leading to a nonaccurate quantification of tumor cells. Our group has recently described a 60% incidence of incomplete DJH rearrangements in MM patients, with no or very low rates of SH. In this study, we compare the efficiency of a real-time PCR approach for the analysis of both complete and incomplete IgH rearrangements in eight MM patients using only three JH consensus probes. We were able to design an allele-specific oligonucleotide for both the complete and incomplete rearrangement in all patients. DJH rearrangements fulfilled the criteria of effectiveness for real-time PCR in all samples (ie no unspecific amplification, detection of less than 10 tumor cells within 10(5) polyclonal background and correlation coefficients of standard curves higher than 0.98). By contrast, only three out of eight VDJH rearrangements fulfilled these criteria. Further analyses showed that the remaining five VDJH rearrangements carried three or more somatic mutations in the probe and primer sites, leading to a dramatic decrease in the melting temperature. These results support the use of incomplete DJH rearrangements instead of complete somatically mutated VDJH rearrangements for investigation of minimal residual disease in multiple myeloma.

Residential schools in a first-year undergraduate engineering programme

BACKGROUND OR CONTEXT: For over 20 years, Deakin University has delivered an accredited undergraduate engineering course by means of distance education. Prior to 2004, off-campus students were not required to attend classes in person on campus. The course was designed so that the off campus students were able to undertake all study and assessment tasks remotely from the university campus. Offering accredited domestic undergraduate engineering courses via distance education has been seen as an important strategy for helping to provide graduate domestically educated engineers to meet Australia’s current and future needs. From 2000 the Australian accreditation management system for professional engineers, as managed by Engineers Australia, has increased its scrutiny of accredited domestic undergraduate engineering courses that were provided in distance-education mode. This led to a series of policies and recommendations for Australian universities that offer accredited engineering courses in distance-education mode: one of the recommendations was that off campus
enrolled engineering students should periodically attend some campus-based activities throughout the course. During the 2004 accreditation review of engineering courses at Deakin University, the
accreditation panel requested that mandatory campus-based activities be incorporated into the accredited undergraduate engineering course. Specifically the request was that Deakin mandate that all off-campus students enrolled in an accredited undergraduate engineering course provided by university attend in person a residential school at least once during every year of equivalent full-time study load. The accreditation panel suggested a program model for the residential school component of the course as developed by the University of Southern Queensland.
PURPOSE OR GOAL: This paper describes the development of the mandatory residential school component of accredited distance education undergraduate engineering courses at Deakin University with
a particular focus on how the residential school program is implemented at level 1 (first-year full-time equivalent level) of the courses.
APPROACH: To be compliant with accreditation requirements, since 2005 Deakin has conducted residential schools for off-campus students at its Geelong Waurn Ponds Campus. Initially the schools were conducted annually over two-weeks during the first semester, and have transitioned to the current mode where the residential school is conducted as a one week programme in each of the trimesters. During these schools, activities are organised around the respective engineering-course units undertaken by students during the trimester.
DISCUSSION: The minimum requirements for the on-campus components of distance-education-mode accredited engineering courses were developed by Engineers Australia in consultation with members of the Washington Accord (International Education Alliance) and at the time of development, generated considerable debate (Palmer, 2005, 2008). The intended purpose of residential schools was for off-campus enrolled students to have reasonable exposure to a typical “on-the-campus” student experience periodically throughout the course. Elements considered suitable and worthwhile for inclusion in residential school programs included:
• in person engagement with their academic lecturers,
• presentations and interaction with guest speakers from industry,
• industry-based site visits,
• engagement in sole and group-based learning and assessment activities on campus, and
• social interaction with other students.
RECOMMENDATIONS/IMPLICATIONS/CONCLUSION: We have found that advantages to the students who attends a residential school include completing real practical work without the need to assemble their own materials at home, and social engagement with staff and students. Off-campus students leave the residential school with a sense of belonging to a “community”, “one of many doing the same and not the only one”. They have the opportunity to share their often significant professional experience with the generally younger and less experienced on-campus student colleagues. Through this interaction between on-campus and off-campus students, the on-campus students benefit as much as the off-campus students. The disadvantages to the off-campus students is the requirement to travel to Geelong for an extended time, which costs the students both money and time away from work and family. From our experience, we recommend to other institutions starting residential schools of their own that they exploit the mandatory on-campus-presence requirement to enhance learning outcomes, well publicised timetables be available to students before trimester begins (certainly before census date), a standardised academic week during trimester be set for all residential schools, encourage student feedback on the program, and apply a practice of uniformity and consistency in how the programme is managed, especially mandated student attendance. Our residential schools for off-campus-mode students have been running for over 10 years. We have found that the educational and social advantages to the student outweigh the disadvantages.

A cluster randomized controlled trial to reduce office workers' sitting time: impact on activity outcomes

PURPOSE: To evaluate, compared to usual practice, the initial and long-term effectiveness of a workplace intervention targeting reducing sitting on activity outcomes.

METHODS: Office worksites (≥1km apart) from a single organization in Victoria, Australia were cluster randomized to intervention (n=7) or control (n=7). Participants were 231 desk-based office workers (5 to 39 participants per worksite) working at least 0.6 full time equivalent. The workplace-delivered intervention addressed organizational, physical environment, and individual behavioural change to reduce sitting time. Assessments occurred at baseline, three-, and 12-months, with the primary outcome participants' objectively measured (activPAL3 device) workplace sitting time (mins/8-h workday). Secondary activity outcomes were: workplace time spent standing, stepping (light, moderate-vigorous and total) and in prolonged (≥30min) sitting bouts (h/8-h workday); usual duration of workplace sitting bouts; and, overall sitting, standing and stepping time (mins/16-h day). Analysis was by linear mixed models, accounting for repeated measures and clustering and adjusting for baseline values and potential confounders.

RESULTS: At baseline, on average, participants (68% women; mean±SD age = 45.6±9.4 years) sat, stood and stepped for 78.8±9.5%, 14.3±8.2%, and 6.9±2.9% of work hours respectively. Workplace sitting time was significantly reduced in the intervention group compared to the controls at three months (-99.1 [95% CI -116.3 to -81.8] min/8-h workday) and 12 months (-45.4 [-64.6 to -26.2] min/8-h workday). Significant intervention effects (all favoring intervention) were observed for standing, prolonged sitting, and usual sitting bout duration at work, as well as overall sitting and standing time, with no significant nor meaningful effects observed for stepping.

CONCLUSIONS: This workplace-delivered multicomponent intervention was successful at reducing workplace and overall daily sitting time in both the short- and long- term.

Assessment of lifetime cumulative sun exposure using a self-administered questionnaire : reliability of two approaches

Few studies have evaluated the reliability of lifetime sun exposure estimated from inquiring about the number of hours people spent outdoors in a given period on a typical weekday or weekend day (the time-based approach). Some investigations have suggested that women have a particularly difficult task in estimating time outdoors in adulthood due to their family and occupational roles. We hypothesized that people might gain additional memory cues and estimate lifetime hours spent outdoors more reliably if asked about time spent outdoors according to specific activities (an activity-based approach). Using self-administered, mailed questionnaires, test-retest responses to time-based and to activity-based approaches were evaluated in 124 volunteer radiologic technologist participants from the United States: 64 females and 60 males 48 to 80 years of age. Intraclass correlation coefficients (ICC) were used to evaluate the test-retest reliability of average number of hours spent outdoors in the summer estimated for each approach. We tested the differences between the two ICCs, corresponding to each approach, using a t test with the variance of the difference estimated by the jackknife method. During childhood and adolescence, the two approaches gave similar ICCs for average numbers of hours spent outdoors in the summer. By contrast, compared with the time-based approach, the activity-based approach showed significantly higher ICCs during adult ages (0.69 versus 0.43, P = 0.003) and over the lifetime (0.69 versus 0.52, P = 0.05); the higher ICCs for the activity-based questionnaire were primarily derived from the results for females. Research is needed to further improve the activity-based questionnaire approach for long-term sun exposure assessment. (Cancer Epidemiol Biomarkers Prev 2009;18(2):464–71)

Theoretical investigation of mechanisms of formation and interaction of nanoparticles

In this thesis an investigation into theoretical models for formation and interaction of nanoparticles is presented. The work presented includes a literature review of current models followed by a series of five chapters of original research. This thesis has been submitted in partial fulfilment of the requirements for the degree of doctor of philosophy by publication and therefore each of the five chapters consist of a peer-reviewed journal article. The thesis is then concluded with a discussion of what has been achieved during the PhD candidature, the potential applications for this research and ways in which the research could be extended in the future. In this thesis we explore stochastic models pertaining to the interaction and evolution mechanisms of nanoparticles. In particular, we explore in depth the stochastic evaporation of molecules due to thermal activation and its ultimate effect on nanoparticles sizes and concentrations. Secondly, we analyse the thermal vibrations of nanoparticles suspended in a fluid and subject to standing oscillating drag forces (as would occur in a standing sound wave) and finally on lattice surfaces in the presence of high heat gradients. We have described in this thesis a number of new models for the description of multicompartment networks joined by a multiple, stochastically evaporating, links. The primary motivation for this work is in the description of thermal fragmentation in which multiple molecules holding parts of a carbonaceous nanoparticle may evaporate. Ultimately, these models predict the rate at which the network or aggregate fragments into smaller networks/aggregates and with what aggregate size distribution. The models are highly analytic and describe the fragmentation of a link holding multiple bonds using Markov processes that best describe different physical situations and these processes have been analysed using a number of mathematical methods. The fragmentation of the network/aggregate is then predicted using combinatorial arguments. Whilst there is some scepticism in the scientific community pertaining to the proposed mechanism of thermal fragmentation,we have presented compelling evidence in this thesis supporting the currently proposed mechanism and shown that our models can accurately match experimental results. This was achieved using a realistic simulation of the fragmentation of the fractal carbonaceous aggregate structure using our models. Furthermore, in this thesis a method of manipulation using acoustic standing waves is investigated. In our investigation we analysed the effect of frequency and particle size on the ability for the particle to be manipulated by means of a standing acoustic wave. In our results, we report the existence of a critical frequency for a particular particle size. This frequency is inversely proportional to the Stokes time of the particle in the fluid. We also find that for large frequencies the subtle Brownian motion of even larger particles plays a significant role in the efficacy of the manipulation. This is due to the decreasing size of the boundary layer between acoustic nodes. Our model utilises a multiple time scale approach to calculating the long term effects of the standing acoustic field on the particles that are interacting with the sound. These effects are then combined with the effects of Brownian motion in order to obtain a complete mathematical description of the particle dynamics in such acoustic fields. Finally, in this thesis, we develop a numerical routine for the description of "thermal tweezers". Currently, the technique of thermal tweezers is predominantly theoretical however there has been a handful of successful experiments which demonstrate the effect it practise. Thermal tweezers is the name given to the way in which particles can be easily manipulated on a lattice surface by careful selection of a heat distribution over the surface. Typically, the theoretical simulations of the effect can be rather time consuming with supercomputer facilities processing data over days or even weeks. Our alternative numerical method for the simulation of particle distributions pertaining to the thermal tweezers effect use the Fokker-Planck equation to derive a quick numerical method for the calculation of the effective diffusion constant as a result of the lattice and the temperature. We then use this diffusion constant and solve the diffusion equation numerically using the finite volume method. This saves the algorithm from calculating many individual particle trajectories since it is describes the flow of the probability distribution of particles in a continuous manner. The alternative method that is outlined in this thesis can produce a larger quantity of accurate results on a household PC in a matter of hours which is much better than was previously achieveable.

A geometrical analysis of trajectory design for underwater vehicles

Designing trajectories for a submerged rigid body motivates this paper. Two approaches are addressed: the time optimal approach and the motion planning ap- proach using concatenation of kinematic motions. We focus on the structure of singular extremals and their relation to the existence of rank-one kinematic reduc- tions; thereby linking the optimization problem to the inherent geometric frame- work. Using these kinematic reductions, we provide a solution to the motion plan- ning problem in the under-actuated scenario, or equivalently, in the case of actuator failures. We finish the paper comparing a time optimal trajectory to one formed by concatenation of pure motions.