Genomic and transcriptomic analysis of the streptomycin-dependent Mycobacterium tuberculosis strain 18b.

The ability of Mycobacterium tuberculosis to establish a latent infection (LTBI) in humans confounds the treatment of tuberculosis. Consequently, there is a need to discover new therapeutic agents that can kill M. tuberculosis both during active disease and LTBI. The streptomycin-dependent strain of M. tuberculosis, 18b, provides a useful tool for this purpose since upon removal of streptomycin (STR) it enters a non-replicating state that mimics latency both in vitro and in animal models. The 4.41 Mb genome sequence of M. tuberculosis 18b was determined and this revealed the strain to belong to clade 3 of the ancient ancestral lineage of the Beijing family. STR-dependence was attributable to insertion of a single cytosine in the 530 loop of the 16S rRNA and to a single amino acid insertion in the N-terminal domain of initiation factor 3. RNA-seq was used to understand the genetic programme activated upon STR-withdrawal and hence to gain insight into LTBI. This revealed reconfiguration of gene expression and metabolic pathways showing strong similarities between non-replicating 18b and M. tuberculosis residing within macrophages, and with the core stationary phase and microaerophilic responses. The findings of this investigation confirm the validity of 18b as a model for LTBI, and provide insight into both the evolution of tubercle bacilli and the functioning of the ribosome.

Trigger and data link system for CMS Resistive Plate Chambers at the LHC accelerator

The purpose of the work was to realize a high-speed digital data transfer system for RPC muon chambers in the CMS experiment on CERN’s new LHC accelerator. This large scale system took many years and many stages of prototyping to develop, and required the participation of tens of people. The system interfaces to Frontend Boards (FEB) at the 200,000-channel detector and to the trigger and readout electronics in the control room of the experiment. The distance between these two is about 80 metres and the speed required for the optic links was pushing the limits of available technology when the project was started. Here, as in many other aspects of the design, it was assumed that the features of readily available commercial components would develop in the course of the design work, just as they did. By choosing a high speed it was possible to multiplex the data from some the chambers into the same fibres to reduce the number of links needed. Further reduction was achieved by employing zero suppression and data compression, and a total of only 660 optical links were needed. Another requirement, which conflicted somewhat with choosing the components a late as possible was that the design needed to be radiation tolerant to an ionizing dose of 100 Gy and to a have a moderate tolerance to Single Event Effects (SEEs). This required some radiation test campaigns, and eventually led to ASICs being chosen for some of the critical parts. The system was made to be as reconfigurable as possible. The reconfiguration needs to be done from a distance as the electronics is not accessible except for some short and rare service breaks once the accelerator starts running. Therefore reconfigurable logic is extensively used, and the firmware development for the FPGAs constituted a sizable part of the work. Some special techniques needed to be used there too, to achieve the required radiation tolerance. The system has been demonstrated to work in several laboratory and beam tests, and now we are waiting to see it in action when the LHC will start running in the autumn 2008.

Ciência como cultura: paradigmas e implicações epistemológicas na educação científica escolar

"Science as culture" is based on the assumption that science is a valuable component of human culture. We therefore have to build the bridge, in cultural terms, from the scientific community to the common citizen. Teaching science as culture requires the co-construction of knowledge and citizenship. Ways of articulating science/technology with society are invoked, pondering on the ethical ambivalence of such connections. The goals of this reflection are to think about: a) epistemological obstacles that, in favouring the logic of monoculture, oppose the implantation of the science as culture; b) epistemological strategies that point towards a diversity of cultural practices and "constellations" of knowledge leading to the reconfiguration of the being through knowledge; c) imperatives that force us to (re)think the epistemological bases suited to the paradigmatic changes and which translate the dynamics and complexity of the evolution of the frameworks that currently sustain science and school scientific education.

Multilevel converter modulation: implementation and analysis

Multilevel converters provide an attractive solution to bring the benefits of speed-controlled rotational movement to high-power applications. Therefore, multilevel inverters have attracted wide interest in both the academic community and in the industry for the past two decades. In this doctoral thesis, modulation methods suitable especially for series connected H-bridge multilevel inverters are discussed. A concept of duty cycle modulation is presented and its modification is proposed. These methods are compared with other well-known modulation schemes, such as space-vector pulse width modulation and carrier-based modulation schemes. The advantage of the modified duty-cycle modulation is its algorithmic simplicity. A similar mathematical formulation for the original duty cycle modulation is proposed. The modified duty cycle modulation is shown to produce well-formed phase-to-neutral voltages that have lower total harmonic distortion than the space-vector pulse width modulation and the duty cycle modulation. The space-vector-based solution and the duty cycle modulation, on the other hand, result in a better-quality line-to-line voltage and current waveform. The voltage of the DC links in the modules of the series-connected H-bridge inverter are shown to fluctuate while they are under load. The fluctuation causes inaccuracies in the voltage production, which may result in a failure of the flux estimator in the controller. An extension for upper-level modulation schemes, which changes the switching instants of the inverter so that the output voltage meets the reference voltage accurately regardless of the DC link voltages, is proposed. The method is shown to reduce the error to a very low level when a sufficient switching frequency is used. An appropriate way to organize the switching instants of the multilevel inverter is to make only one-level steps at a time. This causes restrictions on the dynamical features of the modulation schemes. The produced voltage vector cannot be rotated several tens of degrees in a single switching period without violating the above-mentioned one-level-step rule. The dynamical capabilities of multilevel inverters are analyzed in this doctoral thesis, and it is shown that the multilevel inverters are capable of operating even in dynamically demanding metal industry applications. In addition to the discussion on modulation schemes, an overvoltage in multilevel converter drives caused by cable reflection is addressed. The voltage reflection phenomenon in drives with long feeder cables causes premature insulation deterioration and also affects the commonmode voltage, which is one of the main reasons for bearing currents. Bearing currents, on the other hand, cause fluting in the bearings, which results in premature bearing failure. The reflection phenomenon is traditionally prevented by filtering, but in this thesis, a modulationbased filterless method to mitigate the overvoltage in multilevel drives is proposed. Moreover, the mitigation method can be implemented as an extension for upper-level modulation schemes. The method exploits the oscillations caused by two consecutive voltage edges so that the sum of the oscillations results in a mitigated peak of the overvoltage. The applicability of the method is verified by simulations together with experiments with a full-scale prototype.

Algorithmic Solutions for Combinatorial Problems in Resource Management of Manufacturing Environments

This thesis studies the use of heuristic algorithms in a number of combinatorial problems that occur in various resource constrained environments. Such problems occur, for example, in manufacturing, where a restricted number of resources (tools, machines, feeder slots) are needed to perform some operations. Many of these problems turn out to be computationally intractable, and heuristic algorithms are used to provide efficient, yet sub-optimal solutions. The main goal of the present study is to build upon existing methods to create new heuristics that provide improved solutions for some of these problems. All of these problems occur in practice, and one of the motivations of our study was the request for improvements from industrial sources. We approach three different resource constrained problems. The first is the tool switching and loading problem, and occurs especially in the assembly of printed circuit boards. This problem has to be solved when an efficient, yet small primary storage is used to access resources (tools) from a less efficient (but unlimited) secondary storage area. We study various forms of the problem and provide improved heuristics for its solution. Second, the nozzle assignment problem is concerned with selecting a suitable set of vacuum nozzles for the arms of a robotic assembly machine. It turns out that this is a specialized formulation of the MINMAX resource allocation formulation of the apportionment problem and it can be solved efficiently and optimally. We construct an exact algorithm specialized for the nozzle selection and provide a proof of its optimality. Third, the problem of feeder assignment and component tape construction occurs when electronic components are inserted and certain component types cause tape movement delays that can significantly impact the efficiency of printed circuit board assembly. Here, careful selection of component slots in the feeder improves the tape movement speed. We provide a formal proof that this problem is of the same complexity as the turnpike problem (a well studied geometric optimization problem), and provide a heuristic algorithm for this problem.

Uittonippujen sidelangan valinta ja sitomiskonstruktion suunnittelu

Työssä suunniteltiin uittonippujen sidonnan koneellistamiseksi tarvittavan sidontalangan käsittelylaitteisto. Sen toiminnalliset pääkomponentit ovat langan ohjauskouru, syöttölaite sekä solminta- ja katkaisulaitteet. Lisäksi työssä tehtiin koneelliseen sidontaan sopivan sidontalangan määrityksiä.

Liikkuvan kivimurskaimen syötinosan rakenneanalyysi osarakennetekniikan avulla

Työn tarkoituksena oli selvittää, miten osarakennetekniikkaa voidaan soveltaa siirrettävän kivimurskaimen syötinosan simuloinnissa. Tätä tutkittiin luomalla kahdella eri ohjelmistolla simulaatiomalli syötinosasta ja mallintamalla syötinosan runko joustavaksi kappaleeksi osarakennetekniikan avulla. Luotujen simulointimallien tarkkuutta selvitettiin vertaamalla niistä saatuja rungon jännityksiä tutkittavan rakenteen rungosta mitattuihin jännityksiin. Työn tarkoituksena oli myös tutkia, miten hyvin simulaatiomallit soveltuvat käytettäväksi syötinosan tuotekehityksessä. Tässä työssä käytettiin syötinosan simulaatiomallin luomiseen ANSYS-ohjelmistoa ja ADAMS-ohjelmistoa. Simulaatiomalleihin lisättiin tutkittavasta järjestelmästä mitattu ohjaussignaali sekä syötinosan jousien arvot. Järjestelmän rakenneominaisuudet saatiin suoraan valmistajan luovuttamista tiedoista. ADAMS-ohjelmistolla mallinnetussa simulaatiomallissa runko mallinnettiin joustavaksi ANSYS-ohjelmistossa, josta se siirrettiin ADAMS-ohjelmistoon. Saaduista tuloksista kävi ilmi, että osarakennetekniikkaa voidaan hyödyntää syötinosan joustavan rungon simuloinnissa. Tutkittavasta järjestelmästä mitatuissa jännityksissä ja simulaatiomalleista saaduissa jännityksissä oli eroja, mutta jännityshistorian muodot ja suuruusluokat vastasivat pääosin toisiaan. Tulosten parantamiseksi tulee selvittää lisää alkuarvoja tutkittavasta järjestelmästä ja varmistua nyt saatujen jousiparametrien oikeellisuudesta.

Diagnosis and clinic-pathological findings of influenza virus infection in Brazilian pigs

Influenza A virus (IAV) is a respiratory pathogen of pigs and is associated with the porcine respiratory disease complex (PRDC), along with other respiratory infectious agents. The aim of this study was to diagnose and to perform a clinic-pathological characterization of influenza virus infection in Brazilian pigs. Lung samples from 86 pigs in 37 farrow-to-finish and two farrow-to-feeder operations located in the States of Minas Gerais, São Paulo, Paraná, Rio Grande do Sul, Santa Catarina, and Mato Grosso were studied. Virus detection was performed by virus isolation and quantitative real time reverse-transcription PCR (qRT-PCR). Pathologic examination and immunohistochemistry (IHC) were performed in 60 lung formalin-fixed paraffin-embedded tissue fragments. Affected animals showed coughing, sneezing, nasal discharge, hyperthermia, inactivity, apathy, anorexia, weight loss and growth delay, which lasted for five to 10 days. Influenza virus was isolated from 31 (36.0%) lung samples and 36 (41.9%) were positive for qRT-PCR. Thirty-eight (63.3%) lung samples were positive by IHC and the most frequent microscopic lesion observed was inflammatory infiltrate in the alveoli, bronchiole, or bronchi wall or lumen (76.7%). These results indicate that influenza virus is circulating and causing disease in pigs in several Brazilian states.

Effect of naloxone on food competition aggression in food-restricted high and low aggression pigeons (Columba livia)

We determined the effect of the opiate receptor antagonist naloxone on aggression, emotion, feeder control, and eating behavior in high and low aggression female pigeons maintained at 80% of their normal weight and exposed to food competition interactions. Pigeons were divided into pairs by previously ranked high aggression (total time spent in offensive aggression exceeding 60 s/5 min; N = 6 pairs) and low aggression females (time spent in offensive aggression less than 10 s/5 min; N = 6 pairs). A pigeon in each pair received an sc dose of naloxone (1 mg kg-1 ml saline-1) and the other animal received the vehicle. Trials (10 min) were performed 30 min after the naloxone/vehicle administration. The naloxone group of high aggression pigeons showed lower scores of total time spent in offensive aggression (control: 98.6 ± 12.0; naloxone: 46.8 ± 6.6 s; P < 0.05) and higher scores of time spent in emotional responses (control: 3.5 ± 0.6; naloxone: 10.8 ± 2.4 s; P < 0.05) than controls. The other behaviors scored, feeder control and eating behavior, were not affected in this group. The naloxone group of low aggression pigeons, however, showed higher scores of offensive aggression than their controls (5.3 ± 1.3; naloxone: 28.7 ± 8.0 s; P < 0.05). The present results suggest that opiate receptor mechanisms are implicated in offensive aggression responses in high and low aggression pigeons. However, as reported for brain 5-hydroxytryptamine manipulation and GABA-A-benzodiazepine receptor manipulation, the effect of the opiate receptor antagonist on food competition aggression in pigeons was related to their pretreatment level of aggression.

Agent-based management systems for many-core platforms : rigorous design and efficient implementation

Due to various advantages such as flexibility, scalability and updatability, software intensive systems are increasingly embedded in everyday life. The constantly growing number of functions executed by these systems requires a high level of performance from the underlying platform. The main approach to incrementing performance has been the increase of operating frequency of a chip. However, this has led to the problem of power dissipation, which has shifted the focus of research to parallel and distributed computing. Parallel many-core platforms can provide the required level of computational power along with low power consumption. On the one hand, this enables parallel execution of highly intensive applications. With their computational power, these platforms are likely to be used in various application domains: from home use electronics (e.g., video processing) to complex critical control systems. On the other hand, the utilization of the resources has to be efficient in terms of performance and power consumption. However, the high level of on-chip integration results in the increase of the probability of various faults and creation of hotspots leading to thermal problems. Additionally, radiation, which is frequent in space but becomes an issue also at the ground level, can cause transient faults. This can eventually induce a faulty execution of applications. Therefore, it is crucial to develop methods that enable efficient as well as resilient execution of applications. The main objective of the thesis is to propose an approach to design agentbased systems for many-core platforms in a rigorous manner. When designing such a system, we explore and integrate various dynamic reconfiguration mechanisms into agents functionality. The use of these mechanisms enhances resilience of the underlying platform whilst maintaining performance at an acceptable level. The design of the system proceeds according to a formal refinement approach which allows us to ensure correct behaviour of the system with respect to postulated properties. To enable analysis of the proposed system in terms of area overhead as well as performance, we explore an approach, where the developed rigorous models are transformed into a high-level implementation language. Specifically, we investigate methods for deriving fault-free implementations from these models into, e.g., a hardware description language, namely VHDL.

L-histidine enhances learning in stressed zebrafish

The aim of the present study was to determine the effect of the histaminergic precursor L-histidine and the H3 receptor antagonist thioperamide on the learning process of zebrafish submitted or not to confinement stress. On each of the 5 consecutive days of experiment (D1, D2, D3, D4, D5), animals had to associate an interruption of the aquarium air supply with food offering. Non-stressed zebrafish received an intraperitoneal injection of 100 mg/kg L-histidine, 10 mg/kg thioperamide or saline after training. Stressed animals received drug treatment and then were submitted to confinement stress for 1 h before the learning procedure. Time to approach the feeder was measured (in seconds) and was considered to be indicative of learning. A decrease in time to approach the feeder was observed in the saline-treated group (D1 = 141.92 ± 13.57; D3 = 55 ± 13.54), indicating learning. A delay in learning of stressed animals treated with saline was observed (D1 = 217.5 ± 25.66). L-histidine facilitated learning in stressed (D1 = 118.68 ± 13.9; D2 = 45.88 ± 8.2) and non-stressed (D1 = 151.11 ± 19.20; D5 = 62 ± 14.68) animals. Thioperamide inhibited learning in non-stressed (D1 = 110.38 ± 9.49; D4 = 58.79 ± 16.83) and stressed animals (D1 = 167.3 ± 26.39; D5 = 172.15 ± 27.35). L-histidine prevented the increase in blood glucose after one session of confinement (L-histidine = 65.88 ± 4.50; control = 53 ± 3.50 mg/dL). These results suggest that the histaminergic system enhances learning and modulates stress responses in zebrafish.

Successful scale-up of human embryonic stem cell production in a stirred microcarrier culture system

Future clinical applications of human embryonic stem (hES) cells will require high-yield culture protocols. Currently, hES cells are mainly cultured in static tissue plates, which offer a limited surface and require repeated sub-culturing. Here we describe a stirred system with commercial dextran-based microcarriers coated with denatured collagen to scale-up hES cell production. Maintenance of pluripotency in the microcarrier-based stirred system was shown by immunocytochemical and flow cytometry analyses for pluripotency-associated markers. The formation of cavitated embryoid bodies expressing markers of endoderm, ectoderm and mesoderm was further evidence of maintenance of differentiation capability. Cell yield per volume of medium spent was more than 2-fold higher than in static plates, resulting in a significant decrease in cultivation costs. A total of 10(8) karyotypically stable hES cells were obtained from a unitary small vessel that needed virtually no manipulation during cell proliferation, decreasing risks of contamination. Spinner flasks are available up to working volumes in the range of several liters. If desired, samples from the homogenous suspension can be withdrawn to allow process validation needed in the last expansion steps prior to transplantation. Especially when thinking about clinical trials involving from dozens to hundreds of patients, the use of a small number of larger spinners instead of hundreds of plates or flasks will be beneficial. To our knowledge, this is the first description of successful scale-up of feeder- and Matrigel™-free production of undifferentiated hES cells under continuous agitation, which makes this system a promising alternative for both therapy and research needs.

Improving oral healthcare in Scotland with special reference to sustainability and caries prevention

Brett Duane Improving oral healthcare in Scotland with special reference to sustainability and caries prevention University of Turku, Faculty of Medicine, Institute of Dentistry, Community Dentistry, Finnish Doctoral Program in Oral Sciences (FINDOS-Turku), Turku, Finland Annales Universitatis Turkuensis, Sarja- Ser. D, Medica-Odontologica. Painosalama Oy, Turku, Finland, 2015. Dentistry must provide sustainable, evidence-based, and prevention-focused care. In Scotland oral health prevention is delivered through the Childsmile programme, with an increasing use of high concentration fluoride toothpaste (HCFT). Compared with other countries there is little knowledge of xylitol prevention. The UK government has set strict carbon emission limits with which all national health services (NHS) must comply. The purpose of these studies was firstly to describe the Scottish national oral health prevention programme Childsmile (CS), to determine if the additional maternal use of xylitol (CS+X) was more effective at affecting the early colonisation of mutans streptococci (MS) than this programme alone; secondly to analyse trends in the prescribing and management of HCFT by dentists; and thirdly to analyse data from a dental service in order to improve its sustainability. In all, 182 mother/child pairs were selected on the basis of high maternal MS levels. Motherswere randomly allocated to a CS or CS+X group, with both groups receiving Childsmile. Theintervention group consumed xylitol three times a day, from when the child was 3 months until 24 months. Children were examined at age two to assess MS levels. In order to understand patterns of HCFT prescribing, a retrospective secondary data analysis of routine prescribing data for the years 2006-2012 was performed. To understand the sustainability of dental services, carbon accounting combined a top-down approach and a process analysis approach, followed by the use of Pollard’s decision model (used in other healthcare areas) to analyse and support sustainable service reconfiguration. Of the CS children, 17% were colonised with MS, compared with 5% of the CS+X group. This difference was not statistically significant (P=0.1744). The cost of HCFT prescribing increased fourteen-fold over five years, with 4% of dentists prescribing 70% of the total product. Travel (45%), procurement (36%) and building energy (18%) all contributed to the 1800 tonnes of carbon emissions produced by the service, around 4% of total NHS emissions. Using the analytical model, clinic utilisation rates improved by 56% and patient travel halved significantly reducing carbon emissions. It can be concluded that the Childsmile programme was effective in reducing the risk for MS transmission. HCFT is increasing in Scotland and needs to be managed. Dentistry has similar carbon emissions proportionally as the overall NHS, and the use of an analytic tool can be useful in helping identify these emissions. Key words: Sustainability, carbon emissions, xylitol, mutans streptococci, fluoride toothpaste, caries prevention.

Formal development of resilient distributed systems

Resilience is the property of a system to remain trustworthy despite changes. Changes of a different nature, whether due to failures of system components or varying operational conditions, significantly increase the complexity of system development. Therefore, advanced development technologies are required to build robust and flexible system architectures capable of adapting to such changes. Moreover, powerful quantitative techniques are needed to assess the impact of these changes on various system characteristics. Architectural flexibility is achieved by embedding into the system design the mechanisms for identifying changes and reacting on them. Hence a resilient system should have both advanced monitoring and error detection capabilities to recognise changes as well as sophisticated reconfiguration mechanisms to adapt to them. The aim of such reconfiguration is to ensure that the system stays operational, i.e., remains capable of achieving its goals. Design, verification and assessment of the system reconfiguration mechanisms is a challenging and error prone engineering task. In this thesis, we propose and validate a formal framework for development and assessment of resilient systems. Such a framework provides us with the means to specify and verify complex component interactions, model their cooperative behaviour in achieving system goals, and analyse the chosen reconfiguration strategies. Due to the variety of properties to be analysed, such a framework should have an integrated nature. To ensure the system functional correctness, it should rely on formal modelling and verification, while, to assess the impact of changes on such properties as performance and reliability, it should be combined with quantitative analysis. To ensure scalability of the proposed framework, we choose Event-B as the basis for reasoning about functional correctness. Event-B is a statebased formal approach that promotes the correct-by-construction development paradigm and formal verification by theorem proving. Event-B has a mature industrial-strength tool support { the Rodin platform. Proof-based verification as well as the reliance on abstraction and decomposition adopted in Event-B provides the designers with a powerful support for the development of complex systems. Moreover, the top-down system development by refinement allows the developers to explicitly express and verify critical system-level properties. Besides ensuring functional correctness, to achieve resilience we also need to analyse a number of non-functional characteristics, such as reliability and performance. Therefore, in this thesis we also demonstrate how formal development in Event-B can be combined with quantitative analysis. Namely, we experiment with integration of such techniques as probabilistic model checking in PRISM and discrete-event simulation in SimPy with formal development in Event-B. Such an integration allows us to assess how changes and di erent recon guration strategies a ect the overall system resilience. The approach proposed in this thesis is validated by a number of case studies from such areas as robotics, space, healthcare and cloud domain.

La reconfiguración economica internacional

The international economic reconfiguration. The developed and developing countries have adjusted with varying degrees of success to the new international order. The world's evolution has not stopped: Europe and the emerging Asian economies, are struggling to create a multipolar World. In the periphery, some countries (Asia) are modernizing at a fast rate, while others (Latin America) are lagging behind and in need to revise their growth strategies. The decentralization of production and trade driven by transnational firms are shifting the geographic distribution of investment and employment. As a result, the industrialized countries have ceased to provide the bulk of the world's savings, changing somehow the foundations of the international financial system.