Approximate solution to the speed of spreading viruses

Recently, it has been shown that the speed of virus infections can be explained by time-delayed reactiondiffusion [J. Fort and V. Me´ndez, Phys. Rev. Lett. 89, 178101 (2002)], but no analytical solutions were found. Here we derive formulas for the front speed, valid in appropriate limits. We also integrate numerically the evolution equations of the system. There is good agreement with both numerical and experimental speeds

Programming and analysing measurement experiments using the PicoCricket system

The aim of this project is to get used to another kind of programming. Since now, I used very complex programming languages to develop applications or even to program microcontrollers, but PicoCricket system is the evidence that we don’t need so complex development tools to get functional devices. PicoCricket system is the clear example of simple programming to make devices work the way we programmed it. There’s an easy but effective way to programs mall devices just saying what we want them to do. We cannot do complex algorithms and mathematical operations but we can program them in a short time. Nowadays, the easier and faster we produce, the more we earn. So the tendency is to develop fast, cheap and easy, and PicoCricket system can do it.

Matkustajainformaatiojärjestelmän toteuttaminen junaan

Matkustajainformaatio junassa koostuu vaunujen ulkopuolisilla kylkinäytöillä esitettävistä junan lähtö-, väli- ja määräasematiedoista yhdessä junan ja vaunujen myyntinumeroiden kanssa sekä vaunujen sisäpuolella automaattisista kuulutuksista ja matkustamon näytöillä esitettävästä staattisesta ja vaihtuvasta informaatiosta. Työssä toteutetaan matkustajainformaatiojärjestelmä käytettäväksi matkustajunissa. Järjestelmään syötetään ennen matkan alkua junan tiedot, jonka jälkeen se toimii automaattisesti ilman tarvetta junahenkilökunnan toimenpiteille. Poikkeustilanteissa junahenkilökunta voi estää järjestelmän toiminnan tai valita esiohjelmointuja erikoiskuulutuksia. Toteuttamismenetelmäksi valittiin C-ohjelmointikieli Linux-käyttöjärjestelmällä varustetulla sulautetulla rautatiekäyttöön suunnitellulla laitealustalla.

Comparison Structure Analysis

This study presents an automatic, computer-aided analytical method called Comparison Structure Analysis (CSA), which can be applied to different dimensions of music. The aim of CSA is first and foremost practical: to produce dynamic and understandable representations of musical properties by evaluating the prevalence of a chosen musical data structure through a musical piece. Such a comparison structure may refer to a mathematical vector, a set, a matrix or another type of data structure and even a combination of data structures. CSA depends on an abstract systematic segmentation that allows for a statistical or mathematical survey of the data. To choose a comparison structure is to tune the apparatus to be sensitive to an exclusive set of musical properties. CSA settles somewhere between traditional music analysis and computer aided music information retrieval (MIR). Theoretically defined musical entities, such as pitch-class sets, set-classes and particular rhythm patterns are detected in compositions using pattern extraction and pattern comparison algorithms that are typical within the field of MIR. In principle, the idea of comparison structure analysis can be applied to any time-series type data and, in the music analytical context, to polyphonic as well as homophonic music. Tonal trends, set-class similarities, invertible counterpoints, voice-leading similarities, short-term modulations, rhythmic similarities and multiparametric changes in musical texture were studied. Since CSA allows for a highly accurate classification of compositions, its methods may be applicable to symbolic music information retrieval as well. The strength of CSA relies especially on the possibility to make comparisons between the observations concerning different musical parameters and to combine it with statistical and perhaps other music analytical methods. The results of CSA are dependent on the competence of the similarity measure. New similarity measures for tonal stability, rhythmic and set-class similarity measurements were proposed. The most advanced results were attained by employing the automated function generation – comparable with the so-called genetic programming – to search for an optimal model for set-class similarity measurements. However, the results of CSA seem to agree strongly, independent of the type of similarity function employed in the analysis.

Learning Robot Motions from Visual Sensing

Learning from demonstration becomes increasingly popular as an efficient way of robot programming. Not only a scientific interest acts as an inspiration in this case but also the possibility of producing the machines that would find application in different areas of life: robots helping with daily routine at home, high performance automata in industries or friendly toys for children. One way to teach a robot to fulfill complex tasks is to start with simple training exercises, combining them to form more difficult behavior. The objective of the Master’s thesis work was to study robot programming with visual input. Dynamic movement primitives (DMPs) were chosen as a tool for motion learning and generation. Assuming a movement to be a spring system influenced by an external force, making this system move, DMPs represent the motion as a set of non-linear differential equations. During the experiments the properties of DMP, such as temporal and spacial invariance, were examined. The effect of the DMP parameters, including spring coefficient, damping factor, temporal scaling, on the trajectory generated were studied.

Thermal behaviour of succinic acid, sodium succinate and its compounds with some bivalent transitions metal ions in dynamic N2 and CO2 atmospheres

Thermal stability and thermal decomposition of succinic acid, sodium succinate and its compounds with Mn(II), Fe(II), Co(II), Ni(II), Cu(II) and Zn(II) were investigated employing simultaneous thermogravimetry and differential thermal analysis (TG-DTA) in nitrogen and carbon dioxide atmospheres and TG-FTIR in nitrogen atmosphere. On heating, in both atmospheres the succinic acid melt and evaporate, while for the sodium succinate the thermal decomposition occurs with the formation of sodium carbonate. For the transition metal succinates the final residue up to 1180 ºC in N2 atmosphere was a mixture of metal and metal oxide in no simple stoichiometric relation, except for Zn compound, where the residue was a small quantity of carbonaceous residue. For the CO2 atmosphere the final residue up to 980 ºC was: MnO, Fe3O4, CoO, ZnO and mixtures of Ni, NiO and Cu, Cu2O.

Promoting Programming Learning. Engagement, Automatic Assessment with Immediate Feedback in Visualizations

The skill of programming is a key asset for every computer science student. Many studies have shown that this is a hard skill to learn and the outcomes of programming courses have often been substandard. Thus, a range of methods and tools have been developed to assist students’ learning processes. One of the biggest fields in computer science education is the use of visualizations as a learning aid and many visualization based tools have been developed to aid the learning process during last few decades. Studies conducted in this thesis focus on two different visualizationbased tools TRAKLA2 and ViLLE. This thesis includes results from multiple empirical studies about what kind of effects the introduction and usage of these tools have on students’ opinions and performance, and what kind of implications there are from a teacher’s point of view. The results from studies in this thesis show that students preferred to do web-based exercises, and felt that those exercises contributed to their learning. The usage of the tool motivated students to work harder during their course, which was shown in overall course performance and drop-out statistics. We have also shown that visualization-based tools can be used to enhance the learning process, and one of the key factors is the higher and active level of engagement (see. Engagement Taxonomy by Naps et al., 2002). The automatic grading accompanied with immediate feedback helps students to overcome obstacles during the learning process, and to grasp the key element in the learning task. These kinds of tools can help us to cope with the fact that many programming courses are overcrowded with limited teaching resources. These tools allows us to tackle this problem by utilizing automatic assessment in exercises that are most suitable to be done in the web (like tracing and simulation) since its supports students’ independent learning regardless of time and place. In summary, we can use our course’s resources more efficiently to increase the quality of the learning experience of the students and the teaching experience of the teacher, and even increase performance of the students. There are also methodological results from this thesis which contribute to developing insight into the conduct of empirical evaluations of new tools or techniques. When we evaluate a new tool, especially one accompanied with visualization, we need to give a proper introduction to it and to the graphical notation used by tool. The standard procedure should also include capturing the screen with audio to confirm that the participants of the experiment are doing what they are supposed to do. By taken such measures in the study of the learning impact of visualization support for learning, we can avoid drawing false conclusion from our experiments. As computer science educators, we face two important challenges. Firstly, we need to start to deliver the message in our own institution and all over the world about the new – scientifically proven – innovations in teaching like TRAKLA2 and ViLLE. Secondly, we have the relevant experience of conducting teaching related experiment, and thus we can support our colleagues to learn essential know-how of the research based improvement of their teaching. This change can transform academic teaching into publications and by utilizing this approach we can significantly increase the adoption of the new tools and techniques, and overall increase the knowledge of best-practices. In future, we need to combine our forces and tackle these universal and common problems together by creating multi-national and multiinstitutional research projects. We need to create a community and a platform in which we can share these best practices and at the same time conduct multi-national research projects easily.

Early nutritional determinants in cardio-metabolic programming – A prospective randomized controlled dietary intervention study

Western societies have been faced with the fact that overweight, impaired glucose regulation and elevated blood pressure are already prevalent in pediatric populations. This will inevitably mean an increase in later manifestations of cardio-metabolic diseases. The dilemma has been suggested to stem from fetal life and it is surmised that the early nutritional environment plays an important role in the process called programming. The aim of the present study was to characterize early nutritional determinants associating with cardio-metabolic risk factors in fetuses, infants and children. Further, the study was designated to establish whether dietary counseling initiated in early pregnancy can modify this cascade. Healthy mother-child pairs (n=256) participating in a dietary intervention study were followed from early pregnancy to childhood. The intervention included detailed dietary counseling by a nutritionist targeting saturated fat intake in excess of recommendations and fiber consumption below recommendations. Cardio-metabolic programming was studied by characterizing the offspring’s cardio-metabolic risk factors such as over-activation of the autonomic nervous system, elevated blood pressure and adverse metabolic status (e.g. serum high split proinsulin concentration). Fetal cardiac sympathovagal activation was measured during labor. Postnatally, children’s blood pressure was measured at six-month and four-year follow-up visits. Further, infants’ metabolic status was assessed by means of growth and serum biomarkers (32-33 split proinsulin, leptin and adiponectin) at the age of six months. This study proved that fetal cardiac sympathovagal activity was positively associated with maternal pre-pregnancy body mass index indicating adverse cardio-metabolic programming in the offspring. Further, a reduced risk of high split proinsulin in infancy and lower blood pressure in childhood were found in those offspring whose mothers’ weight gain and amount and type of fats in the diet during pregnancy were as recommended. Of note, maternal dietary counseling from early pregnancy onwards could ameliorate the offspring’s metabolic status by reducing the risk of high split proinsulin concentration, although it had no effect on the other cardio-metabolic markers in the offspring. At postnatal period breastfeeding proved to entail benefits in cardio-metabolic programming. Finally, the recommended dietary protein and total fat content in the child’s diet were important nutritional determinants reducing blood pressure at the age of four years. The intrauterine and immediate postnatal period comprise a window of opportunity for interventions aiming to reduce the risk of cardio-metabolic disorders and brings the prospect of achieving health benefits over one generation.

Tool-supported invariant-based programming

The development of correct programs is a core problem in computer science. Although formal verification methods for establishing correctness with mathematical rigor are available, programmers often find these difficult to put into practice. One hurdle is deriving the loop invariants and proving that the code maintains them. So called correct-by-construction methods aim to alleviate this issue by integrating verification into the programming workflow. Invariant-based programming is a practical correct-by-construction method in which the programmer first establishes the invariant structure, and then incrementally extends the program in steps of adding code and proving after each addition that the code is consistent with the invariants. In this way, the program is kept internally consistent throughout its development, and the construction of the correctness arguments (proofs) becomes an integral part of the programming workflow. A characteristic of the approach is that programs are described as invariant diagrams, a graphical notation similar to the state charts familiar to programmers. Invariant-based programming is a new method that has not been evaluated in large scale studies yet. The most important prerequisite for feasibility on a larger scale is a high degree of automation. The goal of the Socos project has been to build tools to assist the construction and verification of programs using the method. This thesis describes the implementation and evaluation of a prototype tool in the context of the Socos project. The tool supports the drawing of the diagrams, automatic derivation and discharging of verification conditions, and interactive proofs. It is used to develop programs that are correct by construction. The tool consists of a diagrammatic environment connected to a verification condition generator and an existing state-of-the-art theorem prover. Its core is a semantics for translating diagrams into verification conditions, which are sent to the underlying theorem prover. We describe a concrete method for 1) deriving sufficient conditions for total correctness of an invariant diagram; 2) sending the conditions to the theorem prover for simplification; and 3) reporting the results of the simplification to the programmer in a way that is consistent with the invariantbased programming workflow and that allows errors in the program specification to be efficiently detected. The tool uses an efficient automatic proof strategy to prove as many conditions as possible automatically and lets the remaining conditions be proved interactively. The tool is based on the verification system PVS and i uses the SMT (Satisfiability Modulo Theories) solver Yices as a catch-all decision procedure. Conditions that were not discharged automatically may be proved interactively using the PVS proof assistant. The programming workflow is very similar to the process by which a mathematical theory is developed inside a computer supported theorem prover environment such as PVS. The programmer reduces a large verification problem with the aid of the tool into a set of smaller problems (lemmas), and he can substantially improve the degree of proof automation by developing specialized background theories and proof strategies to support the specification and verification of a specific class of programs. We demonstrate this workflow by describing in detail the construction of a verified sorting algorithm. Tool-supported verification often has little to no presence in computer science (CS) curricula. Furthermore, program verification is frequently introduced as an advanced and purely theoretical topic that is not connected to the workflow taught in the early and practically oriented programming courses. Our hypothesis is that verification could be introduced early in the CS education, and that verification tools could be used in the classroom to support the teaching of formal methods. A prototype of Socos has been used in a course at Åbo Akademi University targeted at first and second year undergraduate students. We evaluate the use of Socos in the course as part of a case study carried out in 2007.

Teaching mathematics and programming : new approaches with empirical evaluation

Programming and mathematics are core areas of computer science (CS) and consequently also important parts of CS education. Introductory instruction in these two topics is, however, not without problems. Studies show that CS students find programming difficult to learn and that teaching mathematical topics to CS novices is challenging. One reason for the latter is the disconnection between mathematics and programming found in many CS curricula, which results in students not seeing the relevance of the subject for their studies. In addition, reports indicate that students' mathematical capability and maturity levels are dropping. The challenges faced when teaching mathematics and programming at CS departments can also be traced back to gaps in students' prior education. In Finland the high school curriculum does not include CS as a subject; instead, focus is on learning to use the computer and its applications as tools. Similarly, many of the mathematics courses emphasize application of formulas, while logic, formalisms and proofs, which are important in CS, are avoided. Consequently, high school graduates are not well prepared for studies in CS. Motivated by these challenges, the goal of the present work is to describe new approaches to teaching mathematics and programming aimed at addressing these issues: Structured derivations is a logic-based approach to teaching mathematics, where formalisms and justifications are made explicit. The aim is to help students become better at communicating their reasoning using mathematical language and logical notation at the same time as they become more confident with formalisms. The Python programming language was originally designed with education in mind, and has a simple syntax compared to many other popular languages. The aim of using it in instruction is to address algorithms and their implementation in a way that allows focus to be put on learning algorithmic thinking and programming instead of on learning a complex syntax. Invariant based programming is a diagrammatic approach to developing programs that are correct by construction. The approach is based on elementary propositional and predicate logic, and makes explicit the underlying mathematical foundations of programming. The aim is also to show how mathematics in general, and logic in particular, can be used to create better programs.

Dynamic interplay between the intermediate filament protein nestin and Cyclin-dependent kinase 5

Cellen har ett s.k. cytoskelett som bl.a. ger stadga åt cellen och deltar i dess form- och rörelsefunktioner. Intermediärfilamenten är en viktig del av cytoskelettet och de har länge varit kända för sina väsentliga roller i att upprätthålla den cellulära organisationen och vävnadernas integritet. På senare år har man insett att intermediärfilamenten har en större funktionell mångsidighet än man tidigare tänkts sig, i och med att en rad olika studier har visat betydelsen av intermediärfilamenten vid olika signaleringprocesser. Dessa proteinnätverk samverkar nämligen med kinaser och andra viktiga signalfaktorer och deltar därmed i cellens signaleringmaskineri. Intermediärfilamentproteinet nestin används ofta som en markör för stamceller men dess fysiologiska funktioner är i stort sett okända. Interaktion mellan nestin och ett signalkomplex bestående av cyklin-beroende kinas 5 (eng. Cyclin-dependent kinase, Cdk5) och dess aktivatorprotein p35 upptäcktes i vårt laboratorium före denna avhandling påbörjades. Därför var syftet med min avhandling att undersöka den funktionella betydelsen av nestin i regleringen av Cdk5/p35 komplexet. Cdk5 är ett multifunktionellt kinas som reglerar både utvecklingen och stressreaktioner i nerver och muskler. Vi visade att nestin skyddar neuronala stamceller under oxidativ stress genom dess förmåga att hämma Cdk5s skadliga aktivitet. Genom att förankra Cdk5/p35 komplexet, reglerar nestin den subcellulära lokaliseringen av Cdk5/p35 och minskar klyvningen av p35 till den mer stabila aktivatorn p25. Vi demonstrerade också aktiveringsmekanismen för Cdk5 under differentiering av muskelceller. Proteinkinas C zeta (PKCzeta) avslöjades ha en förmåga att accelera klyvningen av p35 till p25, och därmed öka aktiviteten hos Cdk5. Nestin kunde genom sin förmåga att reglera Cdk5 signalkomplexet styra muskelcellernas differentiering. Denna doktorsavhandling har på ett avgörande vis ökat förståelsen av de reglerande mekanismer som styr Cdk5 aktivering. Avhandling presenterar nestin och PKCzeta som kritiska faktorer i denna reglering. Vidare innehåller avhandlingen ny information om de cellulära funktionerna hos nestin som vi har visat vara en viktig reglerare av cellernas överlevnad och differentiering.

Methods and Models for Accelerating Dynamic Simulation of Fluid Power Circuits

The objective of this dissertation is to improve the dynamic simulation of fluid power circuits. A fluid power circuit is a typical way to implement power transmission in mobile working machines, e.g. cranes, excavators etc. Dynamic simulation is an essential tool in developing controllability and energy-efficient solutions for mobile machines. Efficient dynamic simulation is the basic requirement for the real-time simulation. In the real-time simulation of fluid power circuits there exist numerical problems due to the software and methods used for modelling and integration. A simulation model of a fluid power circuit is typically created using differential and algebraic equations. Efficient numerical methods are required since differential equations must be solved in real time. Unfortunately, simulation software packages offer only a limited selection of numerical solvers. Numerical problems cause noise to the results, which in many cases leads the simulation run to fail. Mathematically the fluid power circuit models are stiff systems of ordinary differential equations. Numerical solution of the stiff systems can be improved by two alternative approaches. The first is to develop numerical solvers suitable for solving stiff systems. The second is to decrease the model stiffness itself by introducing models and algorithms that either decrease the highest eigenvalues or neglect them by introducing steady-state solutions of the stiff parts of the models. The thesis proposes novel methods using the latter approach. The study aims to develop practical methods usable in dynamic simulation of fluid power circuits using explicit fixed-step integration algorithms. In this thesis, twomechanisms whichmake the systemstiff are studied. These are the pressure drop approaching zero in the turbulent orifice model and the volume approaching zero in the equation of pressure build-up. These are the critical areas to which alternative methods for modelling and numerical simulation are proposed. Generally, in hydraulic power transmission systems the orifice flow is clearly in the turbulent area. The flow becomes laminar as the pressure drop over the orifice approaches zero only in rare situations. These are e.g. when a valve is closed, or an actuator is driven against an end stopper, or external force makes actuator to switch its direction during operation. This means that in terms of accuracy, the description of laminar flow is not necessary. But, unfortunately, when a purely turbulent description of the orifice is used, numerical problems occur when the pressure drop comes close to zero since the first derivative of flow with respect to the pressure drop approaches infinity when the pressure drop approaches zero. Furthermore, the second derivative becomes discontinuous, which causes numerical noise and an infinitely small integration step when a variable step integrator is used. A numerically efficient model for the orifice flow is proposed using a cubic spline function to describe the flow in the laminar and transition areas. Parameters for the cubic spline function are selected such that its first derivative is equal to the first derivative of the pure turbulent orifice flow model in the boundary condition. In the dynamic simulation of fluid power circuits, a tradeoff exists between accuracy and calculation speed. This investigation is made for the two-regime flow orifice model. Especially inside of many types of valves, as well as between them, there exist very small volumes. The integration of pressures in small fluid volumes causes numerical problems in fluid power circuit simulation. Particularly in realtime simulation, these numerical problems are a great weakness. The system stiffness approaches infinity as the fluid volume approaches zero. If fixed step explicit algorithms for solving ordinary differential equations (ODE) are used, the system stability would easily be lost when integrating pressures in small volumes. To solve the problem caused by small fluid volumes, a pseudo-dynamic solver is proposed. Instead of integration of the pressure in a small volume, the pressure is solved as a steady-state pressure created in a separate cascade loop by numerical integration. The hydraulic capacitance V/Be of the parts of the circuit whose pressures are solved by the pseudo-dynamic method should be orders of magnitude smaller than that of those partswhose pressures are integrated. The key advantage of this novel method is that the numerical problems caused by the small volumes are completely avoided. Also, the method is freely applicable regardless of the integration routine applied. The superiority of both above-mentioned methods is that they are suited for use together with the semi-empirical modelling method which necessarily does not require any geometrical data of the valves and actuators to be modelled. In this modelling method, most of the needed component information can be taken from the manufacturer’s nominal graphs. This thesis introduces the methods and shows several numerical examples to demonstrate how the proposed methods improve the dynamic simulation of various hydraulic circuits.

Enabling constructive alignment in programming instruction

In this thesis, simple methods have been sought to lower the teacher’s threshold to start to apply constructive alignment in instruction. From the phases of the instructional process, aspects that can be improved with little effort by the teacher have been identified. Teachers have been interviewed in order to find out what students actually learn in computer science courses. A quantitative analysis of the structured interviews showed that in addition to subject specific skills and knowledge, students learn many other skills that should be mentioned in the learning outcomes of the course. The students’ background, such as their prior knowledge, learning style and culture, affects how they learn in a course. A survey was conducted to map the learning styles of computer science students and to see if their cultural background affected their learning style. A statistical analysis of the data indicated that computer science students are different learners than engineering students in general and that there is a connection between the student’s culture and learning style. In this thesis, a simple self-assessment scale that is based on Bloom’s revised taxonomy has been developed. A statistical analysis of the test results indicates that in general the scale is quite reliable, but single students still slightly overestimate or under-estimate their knowledge levels. For students, being able to follow their own progress is motivating, and for a teacher, self-assessment results give information about how the class is proceeding and what the level of the students’ knowledge is.

The effectiveness of short-term literacy skills intervention on children at risk of reading and writing difficulties in Tanzania : a study of grade one children with dynamic assessment approach

The aim of the study was to create and evaluate an intervention programme for Tanzanian children from a low-income area who are at risk of reading and writing difficulties. The learning difficulties, including reading and writing difficulties, are likely to be behind many of the common school problems in Tanzania, but they are not well understood, and research is needed. The design of the study included an identification and intervention phase with follow-up. A group based dynamic assessment approach was used in identifying children at risk of difficulties in reading and writing. The same approach was used in the intervention. The study was a randomized experiment with one experimental and two control groups. For the experimental and the control groups, a total of 96 (46 girls and 50 boys) children from grade one were screened out of 301 children from two schools in a low income urban area of Dar-es-Salaam. One third of the children, the experimental group, participated in an intensive training programme in literacy skills for five weeks, six hours per week, aimed at promoting reading and writing ability, while the children in the control groups had a mathematics and art programme. Follow-up was performed five months after the intervention. The intervention programme and the tests were based on the Zambian BASAT (Basic Skill Assessment Tool, Ketonen & Mulenga, 2003), but the content was drawn from the Kiswahili school curriculum in Tanzania. The main components of the training and testing programme were the same, only differing in content. The training process was different from traditional training in Tanzanian schools in that principles of teaching and training in dynamic assessment were followed. Feedback was the cornerstone of the training and the focus was on supporting the children in exploring knowledge and strategies in performing the tasks. The experimental group improved significantly more (p = .000) than the control groups during the intervention from pre-test to follow-up (repeated measures ANOVA). No differences between the control groups were noticed. The effect was significant on all the measures: phonological awareness, reading skills, writing skills and overall literacy skills. A transfer effect on school marks in Kiswahili and English was found. Following a discussion of the results, suggestions for further research and adaptation of the programme are presented.