Longitudinal study on the colonisation and transmission of methicillin-resistant Staphylococcus aureus in pig farms.

Knowledge about the dynamics of methicillin-resistant Staphylococcus aureus (MRSA) in pigs lacks detail at the level of individual animal. The aim of our study was therefore to determine the colonisation status of MRSA in individual pigs from birth to slaughter in order to gain a better understanding of substantial factors involved in transmission. Two farrow-to-finish and two grow-to-finish herds were included in the study. A total of 1728 nasal swabs from 390 pigs and 592 environmental wipes were collected at 11 different time points. Intermittent colonisation throughout the entire production cycle was conspicuous in the tracking of MRSA in individual pigs. Almost all pigs from a MRSA-positive herd changed MRSA status several times, which implies that pigs are transiently rather than permanently colonised. We highly recommend the definition of MRSA status at herd level rather that at the level of the individual pig when considering prevention measures against MRSA. Therefore, to avoid the further spread of MRSA in countries with moderate prevalence, such as in Switzerland, defining farms as MRSA positive or MRSA negative and allowing the trade of pigs only within herds of the same status seems feasible. This will also be important for combating the further dissemination of livestock-associated (LA)-MRSA into healthcare facilities and the community via humans who have close contact with animals.

Co-simulation Methodologies for Hybrid and Electric Vehicle Dynamics

In recent decades, full electric and hybrid electric vehicles have emerged as an alternative to conventional cars due to a range of factors, including environmental and economic aspects. These vehicles are the result of considerable efforts to seek ways of reducing the use of fossil fuel for vehicle propulsion. Sophisticated technologies such as hybrid and electric powertrains require careful study and optimization. Mathematical models play a key role at this point. Currently, many advanced mathematical analysis tools, as well as computer applications have been built for vehicle simulation purposes. Given the great interest of hybrid and electric powertrains, along with the increasing importance of reliable computer-based models, the author decided to integrate both aspects in the research purpose of this work. Furthermore, this is one of the first final degree projects held at the ETSII (Higher Technical School of Industrial Engineers) that covers the study of hybrid and electric propulsion systems. The present project is based on MBS3D 2.0, a specialized software for the dynamic simulation of multibody systems developed at the UPM Institute of Automobile Research (INSIA). Automobiles are a clear example of complex multibody systems, which are present in nearly every field of engineering. The work presented here benefits from the availability of MBS3D software. This program has proven to be a very efficient tool, with a highly developed underlying mathematical formulation. On this basis, the focus of this project is the extension of MBS3D features in order to be able to perform dynamic simulations of hybrid and electric vehicle models. This requires the joint simulation of the mechanical model of the vehicle, together with the model of the hybrid or electric powertrain. These sub-models belong to completely different physical domains. In fact the powertrain consists of energy storage systems, electrical machines and power electronics, connected to purely mechanical components (wheels, suspension, transmission, clutch…). The challenge today is to create a global vehicle model that is valid for computer simulation. Therefore, the main goal of this project is to apply co-simulation methodologies to a comprehensive model of an electric vehicle, where sub-models from different areas of engineering are coupled. The created electric vehicle (EV) model consists of a separately excited DC electric motor, a Li-ion battery pack, a DC/DC chopper converter and a multibody vehicle model. Co-simulation techniques allow car designers to simulate complex vehicle architectures and behaviors, which are usually difficult to implement in a real environment due to safety and/or economic reasons. In addition, multi-domain computational models help to detect the effects of different driving patterns and parameters and improve the models in a fast and effective way. Automotive designers can greatly benefit from a multidisciplinary approach of new hybrid and electric vehicles. In this case, the global electric vehicle model includes an electrical subsystem and a mechanical subsystem. The electrical subsystem consists of three basic components: electric motor, battery pack and power converter. A modular representation is used for building the dynamic model of the vehicle drivetrain. This means that every component of the drivetrain (submodule) is modeled separately and has its own general dynamic model, with clearly defined inputs and outputs. Then, all the particular submodules are assembled according to the drivetrain configuration and, in this way, the power flow across the components is completely determined. Dynamic models of electrical components are often based on equivalent circuits, where Kirchhoff’s voltage and current laws are applied to draw the algebraic and differential equations. Here, Randles circuit is used for dynamic modeling of the battery and the electric motor is modeled through the analysis of the equivalent circuit of a separately excited DC motor, where the power converter is included. The mechanical subsystem is defined by MBS3D equations. These equations consider the position, velocity and acceleration of all the bodies comprising the vehicle multibody system. MBS3D 2.0 is entirely written in MATLAB and the structure of the program has been thoroughly studied and understood by the author. MBS3D software is adapted according to the requirements of the applied co-simulation method. Some of the core functions are modified, such as integrator and graphics, and several auxiliary functions are added in order to compute the mathematical model of the electrical components. By coupling and co-simulating both subsystems, it is possible to evaluate the dynamic interaction among all the components of the drivetrain. ‘Tight-coupling’ method is used to cosimulate the sub-models. This approach integrates all subsystems simultaneously and the results of the integration are exchanged by function-call. This means that the integration is done jointly for the mechanical and the electrical subsystem, under a single integrator and then, the speed of integration is determined by the slower subsystem. Simulations are then used to show the performance of the developed EV model. However, this project focuses more on the validation of the computational and mathematical tool for electric and hybrid vehicle simulation. For this purpose, a detailed study and comparison of different integrators within the MATLAB environment is done. Consequently, the main efforts are directed towards the implementation of co-simulation techniques in MBS3D software. In this regard, it is not intended to create an extremely precise EV model in terms of real vehicle performance, although an acceptable level of accuracy is achieved. The gap between the EV model and the real system is filled, in a way, by introducing the gas and brake pedals input, which reflects the actual driver behavior. This input is included directly in the differential equations of the model, and determines the amount of current provided to the electric motor. For a separately excited DC motor, the rotor current is proportional to the traction torque delivered to the car wheels. Therefore, as it occurs in the case of real vehicle models, the propulsion torque in the mathematical model is controlled through acceleration and brake pedal commands. The designed transmission system also includes a reduction gear that adapts the torque coming for the motor drive and transfers it. The main contribution of this project is, therefore, the implementation of a new calculation path for the wheel torques, based on performance characteristics and outputs of the electric powertrain model. Originally, the wheel traction and braking torques were input to MBS3D through a vector directly computed by the user in a MATLAB script. Now, they are calculated as a function of the motor current which, in turn, depends on the current provided by the battery pack across the DC/DC chopper converter. The motor and battery currents and voltages are the solutions of the electrical ODE (Ordinary Differential Equation) system coupled to the multibody system. Simultaneously, the outputs of MBS3D model are the position, velocity and acceleration of the vehicle at all times. The motor shaft speed is computed from the output vehicle speed considering the wheel radius, the gear reduction ratio and the transmission efficiency. This motor shaft speed, somehow available from MBS3D model, is then introduced in the differential equations corresponding to the electrical subsystem. In this way, MBS3D and the electrical powertrain model are interconnected and both subsystems exchange values resulting as expected with tight-coupling approach.When programming mathematical models of complex systems, code optimization is a key step in the process. A way to improve the overall performance of the integration, making use of C/C++ as an alternative programming language, is described and implemented. Although this entails a higher computational burden, it leads to important advantages regarding cosimulation speed and stability. In order to do this, it is necessary to integrate MATLAB with another integrated development environment (IDE), where C/C++ code can be generated and executed. In this project, C/C++ files are programmed in Microsoft Visual Studio and the interface between both IDEs is created by building C/C++ MEX file functions. These programs contain functions or subroutines that can be dynamically linked and executed from MATLAB. This process achieves reductions in simulation time up to two orders of magnitude. The tests performed with different integrators, also reveal the stiff character of the differential equations corresponding to the electrical subsystem, and allow the improvement of the cosimulation process. When varying the parameters of the integration and/or the initial conditions of the problem, the solutions of the system of equations show better dynamic response and stability, depending on the integrator used. Several integrators, with variable and non-variable step-size, and for stiff and non-stiff problems are applied to the coupled ODE system. Then, the results are analyzed, compared and discussed. From all the above, the project can be divided into four main parts: 1. Creation of the equation-based electric vehicle model; 2. Programming, simulation and adjustment of the electric vehicle model; 3. Application of co-simulation methodologies to MBS3D and the electric powertrain subsystem; and 4. Code optimization and study of different integrators. Additionally, in order to deeply understand the context of the project, the first chapters include an introduction to basic vehicle dynamics, current classification of hybrid and electric vehicles and an explanation of the involved technologies such as brake energy regeneration, electric and non-electric propulsion systems for EVs and HEVs (hybrid electric vehicles) and their control strategies. Later, the problem of dynamic modeling of hybrid and electric vehicles is discussed. The integrated development environment and the simulation tool are also briefly described. The core chapters include an explanation of the major co-simulation methodologies and how they have been programmed and applied to the electric powertrain model together with the multibody system dynamic model. Finally, the last chapters summarize the main results and conclusions of the project and propose further research topics. In conclusion, co-simulation methodologies are applicable within the integrated development environments MATLAB and Visual Studio, and the simulation tool MBS3D 2.0, where equation-based models of multidisciplinary subsystems, consisting of mechanical and electrical components, are coupled and integrated in a very efficient way.

Different population dynamics of human T cell lymphotropic virus type II in intravenous drug users compared with endemically infected tribes

The phylogeny of human T cell lymphotropic virus type II (HTLV-II) was investigated by using strains isolated from Amerindian and Pygmy tribes, in which the virus is maintained primarily through mother-to-child transmission via breast-feeding, and strains from intravenous drug users (IDUs), in which spread is mainly blood-borne via needle sharing. Molecular clock analysis showed that HTLV-II has two different evolutionary rates with the molecular clock for the virus in IDUs ticking 150–350 times faster than the one in endemically infected tribes: 2.7 × 10−4 compared with 1.71/7.31 × 10−7 nucleotide substitutions per site per year in the long terminal repeat region. This dramatic acceleration of the evolutionary rate seems to be related with the mode of transmission. Mathematical models showed the correlation of these two molecular clocks with an endemic spread of HTLV-II in infected tribes compared with the epidemic spread in IDUs. We also noted a sharp increase in the population size of the virus among IDUs during the last decades probably caused by the worldwide increase in intravenous drug use.

Interplay Between Structure, Stoichiometry, and Electron Transfer Dynamics in SILAR-based Quantum Dot-Sensitized Oxides

We quantify the rate and efficiency of picosecond electron transfer (ET) from PbS nanocrystals, grown by successive ionic layer adsorption and reaction (SILAR), into a mesoporous SnO2 support. Successive SILAR deposition steps allow for stoichiometry- and size-variation of the QDs, characterized using transmission electron microscopy. Whereas for sulfur-rich (p-type) QD surfaces substantial electron trapping at the QD surface occurs, for lead-rich (n-type) QD surfaces, the QD trapping channel is suppressed and the ET efficiency is boosted. The ET efficiency increase achieved by lead-rich QD surfaces is found to be QD-size dependent, increasing linearly with QD surface area. On the other hand, ET rates are found to be independent of both QD size and surface stoichiometry, suggesting that the donor–acceptor energetics (constituting the driving force for ET) are fixed due to Fermi level pinning at the QD/oxide interface. Implications of our results for QD-sensitized solar cell design are discussed.

Interpersonal Emotion Dynamics in Mother-Daughter Dyads during Adolescence

Thesis (Ph.D, Psychology) -- Queen's University, 2016-05-16 14:38:20.622

An investigation of contact transmission of methicillin resistant-Staphylococcus aureus

Hand hygiene is critical in the healthcare setting and it is believed that methicillin-resistant Staphylococcus aureus (MRSA), for example, is transmitted from patient to patient largely via the hands of health professionals. A study has been carried out at a large teaching hospital to estimate how often the gloves of a healthcare worker are contaminated with MRSA after contact with a colonized patient. The effectiveness of handwashing procedures to decontaminate the health professionals' hands was also investigated, together with how well different healthcare professional groups complied with handwashing procedures. The study showed that about 17% (9-25%) of contacts between a healthcare worker and a MRSA-colonized patient results in transmission of MRSA from a patient to the gloves of a healthcare worker. Different health professional groups have different rates of compliance with infection control procedures. Non-contact staff (cleaners, food services) had the shortest handwashing times. In this study, glove use compliance rates were 75% or above in all healthcare worker groups except doctors whose compliance was only 27%. (C) 2004 The Hospital Infection Society. Published by Elsevier Ltd. All rights reserved.

Evolutionary dynamics of wAu-Like Wolbachia variants in neotropical Drosophila spp.

Wolbachia bacteria are common intracellular symbionts of arthropods and have been extensively studied in Drosophila. Most research focuses on two Old Word hosts, Drosophila melanogaster and Drosophila simulans, and does not take into account that some of the Wolbachia associations in these species may have evolved only after their fast global expansion and after the exposure to Wolbachia of previously isolated habitats. Here we looked at Wolbachia of Neotropical Drosophila species. Seventy-one lines of 16 Neotropical Drosophild species sampled in different regions and at different time points were analyzed. Wolbachia is absent in lines of Drosophild willistoni collected before the 1970s, but more recent samples are infected with a strain designated wWiL Wolbachia is absent in all other species of the willistoni group. Polymorphic wWil-related strains were detected in some saltans group species, with D. septentriosaltans being coinfected with at least four variants. Based on wsp and ftsZ sequence data, wWil of D. willistoni is identical to wAu, a strain isolated from D. simulans, but can be discriminated when using a polymorphic minisatellite marker. In contrast to wAu, which infects both germ line and somatic tissues of D. simulans, wWil is found exclusively in the primordial germ line cells of D. willistoni embryos. We report on a pool of closely related Wolbachia strains in Neotropical Drosophila species as a potential source for the wAu strain in D. simulans. Possible evolutionary scenarios reconstructing the infection history of wAu-like Wolbachia in Neotropical Drosophild species and the Old World species D. simulans are discussed.

A mathematical modelling technique for the analysis of the dynamics of a simple continuous EDA

This paper presents some initial attempts to mathematically model the dynamics of a continuous estimation of distribution algorithm (EDA) based on a Gaussian distribution and truncation selection. Case studies are conducted on both unimodal and multimodal problems to highlight the effectiveness of the proposed technique and explore some important properties of the EDA. With some general assumptions, we show that, for ID unimodal problems and with the (mu, lambda) scheme: (1). The behaviour of the EDA is dependent only on the general shape of the test function, rather than its specific form; (2). When initialized far from the global optimum, the EDA has a tendency to converge prematurely; (3). Given a certain selection pressure, there is a unique value for the proposed amplification parameter that could help the EDA achieve desirable performance; for ID multimodal problems: (1). The EDA could get stuck with the (mu, lambda) scheme; (2). The EDA will never get stuck with the (mu, lambda) scheme.

Jobs, Unemployment, and Macroeconomic Transmission

Measuring Job Openings: Evidence from Swedish Plant Level Data. In modern macroeconomic models “job openings'' are a key component. Thus, when taking these models to the data we need an empirical counterpart to the theoretical concept of job openings. To achieve this, the literature relies on job vacancies measured either in survey or register data. Insofar as this concept captures the concept of job openings well we should see a tight relationship between vacancies and subsequent hires on the micro level. To investigate this, I analyze a new data set of Swedish hires and job vacancies on the plant level covering the period 2001-2012. I find that vacancies contain little power in predicting hires over and above (i) whether the number of vacancies is positive and (ii) plant size. Building on this, I propose an alternative measure of job openings in the economy. This measure (i) better predicts hiring at the plant level and (ii) provides a better fitting aggregate matching function vis-à-vis the traditional vacancy measure. Firm Level Evidence from Two Vacancy Measures. Using firm level survey and register data for both Sweden and Denmark we show systematic mis-measurement in both vacancy measures. While the register-based measure on the aggregate constitutes a quarter of the survey-based measure, the latter is not a super-set of the former. To obtain the full set of unique vacancies in these two databases, the number of survey vacancies should be multiplied by approximately 1.2. Importantly, this adjustment factor varies over time and across firm characteristics. Our findings have implications for both the search-matching literature and policy analysis based on vacancy measures: observed changes in vacancies can be an outcome of changes in mis-measurement, and are not necessarily changes in the actual number of vacancies. Swedish Unemployment Dynamics. We study the contribution of different labor market flows to business cycle variations in unemployment in the context of a dual labor market. To this end, we develop a decomposition method that allows for a distinction between permanent and temporary employment. We also allow for slow convergence to steady state which is characteristic of European labor markets. We apply the method to a new Swedish data set covering the period 1987-2012 and show that the relative contributions of inflows and outflows to/from unemployment are roughly 60/30. The remaining 10\% are due to flows not involving unemployment. Even though temporary contracts only cover 9-11\% of the working age population, variations in flows involving temporary contracts account for 44\% of the variation in unemployment. We also show that the importance of flows involving temporary contracts is likely to be understated if one does not account for non-steady state dynamics. The New Keynesian Transmission Mechanism: A Heterogeneous-Agent Perspective. We argue that a 2-agent version of the standard New Keynesian model---where a ``worker'' receives only labor income and a “capitalist'' only profit income---offers insights about how income inequality affects the monetary transmission mechanism. Under rigid prices, monetary policy affects the distribution of consumption, but it has no effect on output as workers choose not to change their hours worked in response to wage movements. In the corresponding representative-agent model, in contrast, hours do rise after a monetary policy loosening due to a wealth effect on labor supply: profits fall, thus reducing the representative worker's income. If wages are rigid too, however, the monetary transmission mechanism is active and resembles that in the corresponding representative-agent model. Here, workers are not on their labor supply curve and hence respond passively to demand, and profits are procyclical.

Unequal OTDM channels in a 2R regenerated, dispersion managed transmission system

The dynamics of switching and transmission of an optical signal comprising individual OTDM channels of unequal amplitudes in a dispersion-managed link with in-line non-linear fibre loop mirrors is investigated for the first time.

WDM of solitons in dispersion managed transmission systems

This thesis investigates the physical behaviour of solitons in wavelength division multiplexed (WDM) systems with dispersion management in a wide range of dispersion regimes. Background material is presented to show how solitons propagate in optical fibres, and key problems associated with real systems are outlined. Problems due to collision induced frequency shifts are calculated using numerical simulation, and these results compared with analytical techniques where possible. Different two-step dispersion regimes, as well as the special cases of uniform and exponentially profiled systems, are identified and investigated. In shallow profile, the constituent second-order dispersions in the system are always close to the average soliton value. It is shown that collision-induced frequency shifts in WDM soliton transmission systems are reduced with increasing dispersion management. New resonances in the collision dynamics are illustrated, due to the relative motion induced by the dispersion map. Consideration of third-order dispersion is shown to modify the effects of collision-induced timing jitter and third-order compensation investigated. In all cases pseudo-phase-matched four-wave mixing was found to be insignificant compared to collision induced frequency shift in causing deterioration of data. It is also demonstrated that all these effects are additive with that of Gordon-Haus jitter.

Nonlinearly regenerated long haul data transmission

This thesis experimentally examines the use of different techniques for optical fibre transmission over ultra long haul distances. Its format firstly examines the use of dispersion management as a means of achieving long haul communications. Secondly, examining the use concatenated NOLMs for DM autosoliton ultra long haul propagation, by comparing their performance with a generic system without NOLMs. Thirdly, timing jitter in concatenated NOLM system is examined and compared to the generic system and lastly issues of OTDM amplitude non-uniformity from channel to channel in a saturable absorber, specifically a NOLM, are raised. Transmission at a rate of 40Gbit/s is studied in an all-Raman amplified standard fibre link with amplifier spacing of the order of 80km. We demonstrate in this thesis that the detrimental effects associated with high power Raman amplification can be minimized by dispersion map optimization. As a result, a transmission distance of 1600 km (2000km including dispersion compensating fibre) has been achieved in standard single mode fibre. The use of concatenated NOLMs to provide a stable propagation regime has been proposed theoretically. In this thesis, the observation experimentally of autosoliton propagation is shown for the first time in a dispersion managed optical transmission system. The system is based on a strong dispersion map with large amplifier spacing. Operation at transmission rates of 10, 40 and 80Gbit/s is demonstrated. With an insertion of a stabilizing element to the NOLM, the transmission of a 10 and 20Gbit/s data stream was extended and demonstrated experimentally. Error-free propagation over 100 and 20 thousand kilometres has been achieved at 10 and 20Gbit/s respectively, with terrestrial amplifier spacing. The monitor of timing jitter is of importance to all optical systems. Evolution of timing jitter in a DM autosoliton system has been studied in this thesis and analyzed at bit ranges from 10Gbit/s to 80Gbit/s. Non-linear guiding by in-line regenerators considerably changes the dynamics of jitter accumulation. As transmission systems require higher data rates, the use of OTDM will become more prolific. The dynamics of switching and transmission of an optical signal comprising individual OTDM channels of unequal amplitudes in a dispersion-managed link with in-line non-linear fibre loop mirrors is investigated.

True soliton transmission through ultra-long laser links

We present the first experimental demonstration of true (not loss managed) soliton pulse transmission in conventional optical fibre. Experimental FROG spectrograms and numerical simulations confirm the soliton pulse evolution dynamics.

Long-distance soliton transmission through ultralong fiber lasers

We present the first experimental demonstration (to our knowledge) of long-distance unperturbed fundamental optical soliton transmission in conventional single-mode optical fiber. The virtual transparency in the fiber required for soliton transmission, over 15 complete periods, was achieved by using an ultralong Raman fiber laser amplification scheme. Optical soliton pulse duration, pulse bandwidth, and peak intensity are shown to remain constant along the transmission length. Frequency-resolved optical gating spectrograms and numerical simulations confirm the observed optical soliton dynamics.

Optimal packing for cascaded regenerative transmission based on phase sensitive amplifiers

We investigate the transmission performance of advanced modulation formats in nonlinear regenerative channels based on cascaded phase sensitive amplifiers. We identify the impact of amplitude and phase noise dynamics along the transmission line and show that after a cascade of regenerators, densely packed single ring PSK constellations outperform multi-ring constellations. The results of this study will greatly simplify the design of future nonlinear regenerative channels for ultra-high capacity transmission