O foco principal do presente trabalho é estender uma metodologia numérica embasada no uso de uma técnica de refinamento adaptativo de malha (AMR - Adaptive Mesh Refinement) e no uso de esquemas temporais multipasso implícitos-explícitos (IMEX) a aplicações envolvendo escoamentos reativos com baixo número de Mach. Originalmente desenvolvida para escoamentos incompressíveis, a formulação euleriana daquela metodologia emprega as equações de Navier-Stokes como modelo matemático para descrever a dinâmica do escoamento e o Método da Projeção, baseado no divergente nulo da velocidade do escoamento, para tratar o acoplamento pressão-velocidade presente na formulação com variáveis primitivas. Tal formulação euleriana original é estendida para acomodar novas equações agregadas ao modelo matemático da fase contínua: conservação de massa, fração de mistura (para representar as concentrações de combustível e oxidante), e energia. Além disso, uma equação termodinâmica de estado é integrada ao modelo matemático estendido e é empregada juntamente com a equação de conservação de massa para produzir uma nova restrição (não nula desta vez) ao divergente do campo de velocidade. Assume-se que o escoamento ocorre a baixo número de Mach (hipótese principal). O Método de Diferença Finita é empregado na discretização espacial das variáveis eulerianas de estado, empregando-se uma malha AMR. As vantagens e dificuldades desta extensão são cuidadosamente investigadas e reportadas. Pela importância, do ponto de vista de aplicações práticas, alguns estudos numéricos preliminares envolvendo escoamentos incompressíveis turbulentos com sprays são realizados (as gotículas compõem a fase dispersa). Num primeiro momento, apenas sprays com gotículas inertes são considerados. Embora ainda apenas iniciais, tais estudos já se mostram importantes pois identificam com clareza, em primeira instância, algumas das dificuldades inerentes a serem enfrentadas ao se tratar dentro desta nova metodologia um conjunto relativamente grande de gotículas lagrangianas. No caso de escoamentos incompressíveis turbulentos com sprays, a integração temporal se dá com métodos IMEX para a fase contínua e com o Método de Euler Modificado para a fase dispersa. A turbulência, em todos os casos que a envolvem, é tratada pelo modelo de Simulação das Grandes Escalas (LES - Large Eddy Simulation). As simulações computacionais se dão em um domínio tridimensional, um parelelepípedo, e empregam uma extensão (resultante do presente trabalho) do código AMR3D, um programa de computador sequencial implementado em Fortran90, oriundo de uma colaboração de longa data entre o IME-USP e o MFLab/FEMEC-UFU (Laboratório de Dinâmica de Fluidos da Universidade Federal de Uberlândia). O processamento foi efetuado no LabMAP (Laboratório da Matemática Aplicada do IME-USP). / It is the main goal of the present work to extend a numerical methodology based on both the use of an adaptive mesh refinement technique (AMR) and the use of a multistep, implicit-explicit time-step strategy (IMEX) to applications involving low Mach number reactive flows. Originally developed for incompressible flows, the Eulerian formulation of that methodology employs the Navier-Stokes equations to model the flow dynamics and the Projection Method, based on the vanishing divergence of the velocity field, to tackle the pressure-velocity coupling present when using primitive variables. That Eulerian formulation is extended by adding a new set of equations to the original mathematical model, describing the various properties of the continuous phase: mass conservation, mixture fraction (to represent concentrations of fuel and oxidizer) and energy. Also, a thermodynamic equation of state is included into the extended mathematical model which is employed, along with the equation for the conservation of mass, to derive a new restriction (this time, different from zero) to the divergence of the velocity field. It is assumed that one is dealing with a low Mach number flow (the main hipothesis). The discretization in space employs the Finite Difference Method for the Eulerian variables on a AMR mesh. Advantages and difficulties of such an extension of the previous methodology are carefully investigated and reported. For its importance in the real-world applications, few preliminary numerical studies involving incompressible turbulent flows with sprays are performed (the droplets form what it is called the dispersed phase). Only sprays formed by inert droplets are considered. Even though initial yet, such studies are most important because they clearly identify, first hand, certain difficulties in handling relatively large sets of Lagrangian droplets in the context of this new AMR methodology. In the context of turbulent incompressible flows with sprays, the overall time-step scheme is given by IMEX methods for the continuous phase and by the Improved Euler Method for the dispersed phase. In all the cases in which it is considered, turbulence is modeled by the Large Eddy Simulation (LES) model. The computational simulations are held in a tridimensional domain given by a paralellepiped and all of them employ the extention (resulting of the present work) of the AMR3D code, a sequencial computer program implemented in Fortran90, whose origin is the collaborative work between IMEUSP and MFLab/FEMEC-UFU (Fluid Dynamics Laboratory, Federal University of Uberlândia). Computations were performed at LabMAP (Applied Mathematics Laboratory at IME-USP).

Adaptive Mesh Refinement (AMR) is a method which dynamically varies the spatio-temporal resolution of localized mesh regions in numerical simulations, based on the strength of the solution features. Due to high resolution discretization of localized regions of interests into rectangular mesh units called patches, AMR provides low cost of computations and high degree of accuracy. General purpose graphics processing units (GPGPUs) with their support for fine-grained parallelism, offer an attractive option for obtaining high performance for AMR applications. The data parallel computations of the finite difference schemes of AMR can be efficiently performed on GPGPUs. This research deals with challenges and develops techniques for efficient executions of AMR applications with uniform and non-uniform patches on GPUs. In the first part of the thesis, we optimize an AMR model with uniform patches. We have developed strategies for continuous online visualization of time evolving data for AMR applications executed on GPUs. In-situ visualization plays an important role for analyzing the time evolving characteristics of the domain structures. Continuous visualization of the output data for various time steps results in better study of the underlying domain and the model used for simulating the domain. We reorder the meshes for computations on the GPU based on the users input related to the subdomain that he wants to visualize. This makes the data available for visualization at a faster rate. We then perform asynchronous executions of the visualization steps and fix-up operations on the coarse meshes on the CPUs while the GPU advances the solution. By performing experiments on Tesla S1070 and Fermi C2070 clusters, we found that our strategies result in up to 60% improvement in response time and 16% improvement in the rate of visualization of frames over the existing strategy of performing fix-ups and visualization at the end of the time steps. The second part of the thesis deals with adaptive strategies for efficient execution of block structured AMR applications with non-uniform patches on GPUs. Most AMR approaches use patches of uniform sizes over regions of interests. Since this leads to over-refinement, some efforts have focused on forming patches of non-uniform dimensions to improve computational efficiency since the dimensions of a patch can be tuned to the geometry of a region of interest. While effective hybrid execution strategies exist for applications with uniform patches, our work considers efficient execution of non-uniform patches with different workloads. Our techniques include a geometric bin-packing method to load balance GPU computations and reduce thread idling, adaptive determination of amount of work to maximize asynchronism between CPU and GPU executions using a knapsack formulation, and scheduling communications for multi-GPU executions. We test our strategies for synthetic inputs as well as for traces from real applications. Our experiments on Tesla S1070 and Fermi C2070 clusters with both single-GPU and multi-GPU executions show that our strategies result in up to 69% improvement in performance over existing strategies. Our bin-packing based load balancing gives performance gains up to 39%, kernel optimizations give an improvement of up to 20%, and our strategies for adaptive asynchronism between CPU-GPU executions give performance improvements of up to 17% over default static asynchronous executions.

Många förändringar sker idag inom industrin och särskilt med tanke på omställning till industri 4.0. Dana Incorporated har genom Högskolan Väst efterfrågat en studie om automatiserade transporter i deras planerade fabrik i Åmål. Fabriken ska ligga i yttersta framkant gällande automation och effektivitet med industri 4.0 som mål. För att hitta rätt system behandlar denna rapport flera viktiga aspekter som behöver tas i beaktning vid övergång eller nyetablering av AGV/AMR truckar och robotar. Studier, intervjuer och fakta används i rapporten för att hitta rätt system i en föränderlig miljö där flexibilitet efterfrågas. Förstudierna om godsets förpackning, AGV/AMR-systemets modell och flexibilitet visar sig vara ytterst viktiga faktorer i studien. Det är stor skillnad mellan olika AGV/AMR-system i både pris och utförande, vilket gör att stora kostnader går att spara vid grundlig undersökning. Ju mer arbete och tid som läggs i förstudierna desto mer underlättar implementering och sparar på investeringskostnaden. Studien visar att ju längre tid det tar att implementera, blir kostnaden högre på grund av att företaget samtidigt belastas med operatörskostnader. Längre implementeringstid ger högre kostnad men innebär ett lägre risktagande. Att hitta den perfekta balansen mellan dessa två faktorer är svårt och tidskrävande. Det är ändå viktigt att ha vetskap om att både en för djärv och en för långsam satsning resulterar i onödiga kostnader. Strukturen och flexibilitet är andra delar som påverkar val av system. Inget AGV/AMR-system kan idag ha samma flexibilitet som en mänsklig truckförare. Organisationen måste därför struktureras till den flexibilitetsgrad som det tänkta systemet kan hantera. Vilken grad av vinst och resultat som ges genom det tänkta AGV/AMR-systemet grundas mycket genom kunskap om AGV/AMR-systemen som skulle passa företaget innan val av produkt. / Many changes are taking place today in the industry and especially with a view to conversion to industry 4.0. Through University West, Dana Incorporated has requested a study on automated transports in their planned factory in Åmål. The factory will be at the forefront of automation and efficiency with industry 4.0 as its goal. To find the right system, this report addresses several important aspects that need to be taken into account when transitioning or establishing new AGV / AMR trucks and robots. Studies, interviews and facts are used in the report to find the right system in a changing environment where flexibility is required. The feasibility studies on the packaging of the goods, the model and flexibility of the AGV / AMR system prove to be extremely important factors in the study. There is a big difference between different AGV / AMR systems in both price and design, which means that large costs can be saved during a thorough examination. The more work and time that is put into the feasibility studies, the easier it is to implement and save on the investment cost. The study shows that the longer the time implementation requires, the higher the cost due to contemporary operator costs. Longer implementation time results in higher costs but means lower risk-taking. Finding the perfect balance between these two factors is hard and time consuming. It´s still a good knowledge to know that both a too bold and a too slow investment results in unnecessary costs. The structure and flexibility are other parts that influence the choice of system. No AGV / AMR system today can have the same flexibility as a human truck driver. The organization must therefore be structured to the flexibility that is possible to handle for the selected system. The degree of profit and results given through the intended AGV / AMR system is largely based on knowledge before choosing a product.

Automation is a key enabler of modern manufacturing. It can result in increased flexibility, safety, and reduced costs. Internal logistics processes have thus far been automated to a lower level compared to other processes in a manufacturing system. Autonomous Mobile Robots (AMRs) are an emerging technology with potential to automate internal logistics processes, but there exists limited literature on their integration and implementation. In a literature study, no papers were identified that directly studied the mechanical challenges that arise in the implementation of AMRs, and none suggested solutions to overcome those challenges. The industry has shown interest in exploring the benefits of employing mixed AMR fleets where different types of AMRs, with different mechanical specifications, can work together and share tasks.  This thesis aims to contribute to the flexible integration of AMRs into manufacturing lines, especially in the context of mixed AMR fleets. A self-adjusting logistic cart is the outcome of a systematic systems engineering concept development and design process. The advantage of flexible logistic infrastructure, regardless of the type of fleet employed (i.e., mixed or homogenous), is that it can provide the industry with freedom and time to learn which AMRs and fleets best fit their needs. The novel concept provides the industry with flexibility to optimise their line feeding processes without the added problem-solving and time required to adapt and/or update logistic infrastructure such as carts. In addition to the concept development, a generalised guide for the design of carts used with AMRs is contributed to facilitate future design for AMRs studies. The concept and prototype design are evaluated and discussed. Further iterations of the design process are needed for the concept to reach maturity. Future studies into the benefits and shortcomings of the concept are encouraged. / Automation är en viktig faktor för modern tillverkning. Den kan resultera i ökad flexibilitet, säkerhet och minskade kostnader. Interna logistikprocesser har hitintills automatiserats till en lägre nivå jämfört med andra processer i tillverkningssystemen. Autonoma Mobila Robotar (AMR) är en framväxande teknik med potential att automatisera interna logistikprocesser, men det finns begränsad litteratur som beskriver deras integration och implementering. I en litteraturstudie identifierades inga artiklar som direkt studerade de mekaniska utmaningar som uppstår vid en implementering av AMR, och inga förslag till lösningar för att övervinna dessa utmaningar. Branschen har visat intresse för att utforska fördelarna med att använda blandade AMR-flottor där olika typer av AMR med olika mekaniska specifikationer arbetar tillsammans och delar uppgifter.  Denna avhandling syftar till att bidra med kunskap om flexibel integration av AMR i tillverkningslinjer, särskilt i system med blandade flottor. En självjusterande logistikvagn är resultatet av systematisk konceptutveckling och konstruktionsprocess. Fördelen med en flexibel logistikinfrastruktur, oavsett vilken typ av flotta som används (dvs. blandad eller homogen), är att den kan ge industriell frihet och tid att lära sig vilka typer av AMR och flottor som bäst passar varje företags behov. Konceptet ger branschen flexibilitet att optimera sina linjematningsprocesser utan den extra problemlösning och den tid som krävs för att anpassa och/eller uppdatera logistikinfrastruktur med vagnar. Förutom konceptutvecklingen bidrar en generell guide för konstruktion av vagnar, som används med AMR, till att underlätta framtida AMR-studier. Konceptet och prototypkonstruktionen utvärderas och diskuteras. Ytterligare iterationer av utvecklings- och konstruktionsprocessen behövs för att konceptet ska bli moget. Framtida studier av fördelarna och bristerna hos det föreslagna konceptet uppmuntras.

The environment is increasingly recognised as a key player in the emergence and mobilisation of antibiotic resistance, which negatively impacts human health, healthcare systems, and farming practices worldwide. Recent work has demonstrated concentrations of antibiotics in the natural environment may select for resistance in situ, but a scarcity of meaningful data has prevented rigorous environmental risk assessment of antibiotics. Without such data, mitigation strategies, such as improved antibiotic stewardship or environmental discharge limits, cannot be effectively designed or implemented. This thesis designed and developed two methods for determining effect concentrations of antibiotics in complex microbial communities, thereby generating a significant amount of data to address this knowledge gap. Minimal selective concentrations (MSCs) were determined in long term selection experiments for four classes of antibiotic at concentrations as low as 0.4 μg/L, which is below many measured environmental concentrations. Lowest observed effect concentrations were determined using a short term, growth based assay which were highly predictive of MSCs. A novel finding was significant selection for cefotaxime resistance occurred at a wide range of antibiotic concentrations, from 125 μg/L - 64 mg/L, which has important clinical implications. Determination of MSC in single species assays was also shown to be a poor predictor of MSC in a complex microbial community. Co-selection for antimicrobial resistance was demonstrated in selection experiments and through improved understanding of class 1 integron evolution, assessing selective effects on resistance gene acquisition using a novel PCR method and next-generation sequencing. In the final study, a novel resistance determinant (UDP-galactose 4-epimerase) conferring cross-resistance to biocides and antibiotics was discovered, providing a target for further study. These findings indicate selection and co-selection for antimicrobial resistance is likely to occur in the environment, and provides the means to rapidly generate further data to aid in the development of appropriate mitigation strategies.

Aim: This thesis aims to explore and investigate the level and process of adoption of Antimicrobial Stewardship Programmes (ASPs) and factors influencing their implementation in Saudi Ministry of Health (MOH) hospitals. The findings of this study will provide hospitals and policy makers with evidence-based recommendations on how barriers to ASPs adoption can be overcome, which will ultimately improve antimicrobial use and reduce antimicrobial resistance (AMR). Method: A mixed method approach was carried out using both qualitative and quantitative research methods. Semi-structured interviews were conducted with healthcare professionals in three Saudi hospitals to explore the enablers and barriers to their adoption of ASPs. A survey was then developed based on these findings to investigate the level of hospitals' adoption of ASPs and factors influencing their implementation at a national level. Further, a case study using in-depth interviews was utilised to understand the process of ASP adoption in a Saudi hospital, and how adoption challenges were addressed. Finally, a self-administered questionnaire was used to examine patients' knowledge and perceptions of antimicrobial use and resistance, and to evaluate the institutional role of patient education on antimicrobial use in two Saudi hospitals. The overall methodology of the research is summarised in Figure I. Results: Despite the introduction of a national ASP strategy, adoption of ASPs in Saudi MOH hospitals remains low. Organisational barriers such as the lack of senior management support, lack of supportive IT infrastructure and the shortage of ASP team members hinder hospitals' efforts to adopt ASPs. Further barriers relate to the lack of formal enforcement by MOH and the physicians fears of patients' complications and clinical liability. Patients admitted to Saudi hospitals lack knowledge and perceptions of AMR, and the adoption of ASPs may improve hospitals' role in patients' education. Conclusions: Despite the established benefits of ASPs, their adoption in Saudi MOH hospitals remains low. Urgent action is needed to address the strategies priorities associated with AMR, including access to antimicrobials, antimicrobial stewardship and education and research. Policy makers are urged to consider making ASPs adoption in hospitals a regulatory requirement supported by national guidelines and surveillance programmes. It is essential to increase the provision of ID and infection control residency and training programmes to meet the extreme shortage of ID physicians, pharmacists, microbiologists and infection control practitioners. Higher education institutions and teaching hospitals are required to introduce antimicrobial prescribing and stewardship competencies into undergraduate Medical, Pharmacy, Dental, Nursing and Veterinary curriculum, as well as introduction of AMR topics in order to increase knowledge and awareness of ASPs and AMR. Collaboration between ASPs adopting and non-adopting hospitals is essential to share implementation experience, strategies and solutions to overcome barriers. Healthcare specialised associations are needed to be part of AMR conversation and guide healthcare professionals' training and accreditation. Multiple stakeholders should be actively part of the conversations around tacking AMR. Primary care, secondary care, community pharmacies and policy makers should strive to create a shared culture of responsibility among all healthcare partners to improve antimicrobial therapy and reduce risks of AMR.

<p>The interest for various multimedia services accessed via the Internet has been growing immensely along with the bandwidth available. A similar development has emerged in the 3G mobile network. The focus of this master thesis is on the speech/audio part of a 3G multimedia application. The purpose has been to implement a traffic generating tool that can measure QoS (Quality of Service) in 3G networks. The application is compliant to the 3G standards, i.e. it uses AMR (Adaptive Multi Rate), SIP (Session Initiation Protocol) and RTP (Real Time Transport Protocol). AMR is a speech compression algorithm with the special feature that it can compress speech into several different bitrates. SIP signalling is used so that different applications can agree on how to communicate. RTP carries the speech frames over the network, in order to provide features that are necessary for media/multimedia applications. Issues like perception of audio and QoS related parameters is also discussed, from the perspective of users and developers.</p>

A block-based adaptive mesh refinement (AMR) finite-volume scheme is developed for solution of hyperbolic conservation laws on two-dimensional hybrid multi-block meshes. A Godunov-type upwind finite-volume spatial-discretization scheme, with piecewise limited linear reconstruction and Riemann-solver based flux functions, is applied to the quadrilateral cells of a hybrid multi-block mesh and these computational cells are embedded in either body-fitted structured or general unstructured grid partitions of the hybrid grid. A hierarchical quadtree data structure is used to allow local refinement of the individual subdomains based on heuristic physics-based refinement criteria. An efficient and scalable parallel implementation of the proposed algorithm is achieved via domain decomposition. The performance of the proposed scheme is demonstrated through application to solution of the compressible Euler equations for a number of flow configurations and regimes in two space dimensions. The efficiency of the AMR procedure and accuracy, robustness, and scalability of the hybrid mesh scheme are assessed.

A block-based adaptive mesh refinement (AMR) finite-volume scheme is developed for solution of hyperbolic conservation laws on two-dimensional hybrid multi-block meshes. A Godunov-type upwind finite-volume spatial-discretization scheme, with piecewise limited linear reconstruction and Riemann-solver based flux functions, is applied to the quadrilateral cells of a hybrid multi-block mesh and these computational cells are embedded in either body-fitted structured or general unstructured grid partitions of the hybrid grid. A hierarchical quadtree data structure is used to allow local refinement of the individual subdomains based on heuristic physics-based refinement criteria. An efficient and scalable parallel implementation of the proposed algorithm is achieved via domain decomposition. The performance of the proposed scheme is demonstrated through application to solution of the compressible Euler equations for a number of flow configurations and regimes in two space dimensions. The efficiency of the AMR procedure and accuracy, robustness, and scalability of the hybrid mesh scheme are assessed.

The interest for various multimedia services accessed via the Internet has been growing immensely along with the bandwidth available. A similar development has emerged in the 3G mobile network. The focus of this master thesis is on the speech/audio part of a 3G multimedia application. The purpose has been to implement a traffic generating tool that can measure QoS (Quality of Service) in 3G networks. The application is compliant to the 3G standards, i.e. it uses AMR (Adaptive Multi Rate), SIP (Session Initiation Protocol) and RTP (Real Time Transport Protocol). AMR is a speech compression algorithm with the special feature that it can compress speech into several different bitrates. SIP signalling is used so that different applications can agree on how to communicate. RTP carries the speech frames over the network, in order to provide features that are necessary for media/multimedia applications. Issues like perception of audio and QoS related parameters is also discussed, from the perspective of users and developers.