Computational Properties of SNAFU

Sensor applications in Sensoria [1] are expressed using STEP (Sensorium Task Execution Plan). SNAFU (Sensor-Net Applications as Functional Units) serves as a high-level sensor-programming language, which is compiled into STEP. In SNAFU’s current form, its differences with STEP are relatively minor, as they are limited to shorthands and macros not available in STEP. We show that, however restrictive it may seem, SNAFU has in fact universal power; technically, it is a Turing-complete language, i.e., any Turing program can be written in SNAFU (though not always conveniently). Although STEP may be allowed to have universal power, as a low-level language not directly available to Sensorium users, SNAFU programmers may use this power for malicious purposes or inadvertently introduce errors with destructive consequences. In future developments of SNAFU, we plan to introduce restrictions and highlevel features with safety guards, such as those provided by a type system, which will make SNAFU programming safer.

Safe Compositional Specification of Network Systems With Polymorphic, Constrained Types

In the framework of iBench research project, our previous work created a domain specific language TRAFFIC [6] that facilitates specification, programming, and maintenance of distributed applications over a network. It allows safety property to be formalized in terms of types and subtyping relations. Extending upon our previous work, we add Hindley-Milner style polymorphism [8] with constraints [9] to the type system of TRAFFIC. This allows a programmer to use for-all quantifier to describe types of network components, escalating power and expressiveness of types to a new level that was not possible before with propositional subtyping relations. Furthermore, we design our type system with a pluggable constraint system, so it can adapt to different application needs while maintaining soundness. In this paper, we show the soundness of the type system, which is not syntax-directed but is easier to do typing derivation. We show that there is an equivalent syntax-directed type system, which is what a type checker program would implement to verify the safety of a network flow. This is followed by discussion on several constraint systems: polymorphism with subtyping constraints, Linear Programming, and Constraint Handling Rules (CHR) [3]. Finally, we provide some examples to illustrate workings of these constraint systems.

Programming multicores safely : handling barrier deadlocks

Tese de doutoramento, Informática (Ciências da Computação), Universidade de Lisboa, Faculdade de Ciências, 2015

Memory Usage Inference for Object-Oriented Programs

We present a type-based approach to statically derive symbolic closed-form formulae that characterize the bounds of heap memory usages of programs written in object-oriented languages. Given a program with size and alias annotations, our inference system will compute the amount of memory required by the methods to execute successfully as well as the amount of memory released when methods return. The obtained analysis results are useful for networked devices with limited computational resources as well as embedded software.

Rehabilitation with ear prosthesis linked to osseointegrated implants

Background: The absence of an ear, which can be the result of a congenital malformation, surgical tumour resection or traumatic injury, is a significant aesthetic problem. Attachment of ear prostheses with adhesives can cause local irritation for the wearer and affect the colour of the prostheses. Use of implants in craniofacial reconstruction can improve the retention and stability of prostheses giving to patient greater comfort and security relative to adhesive attachment.Objective: The aim of this report was to present a clinical case of a mutilated patient who was rehabilitated by means of installing an ear prosthesis fixed through osseointegrated implants.Materials and methods: The patient had two implants installed in the mastoid region that were linked by a bar, and a clip-type system was used. The ear prosthesis was constructed from medical-use silicone, pigmented to match the patient's skin colour and linked to the retention system.Conclusion: The patient's rehabilitation was satisfactory from both a functional and an aesthetic point of view, making it possible for the patient to return to a normal social life and regain lost self-esteem.

Comunicação científica: agregação, compartilhamento e reuso de elementos informacionais

Pós-graduação em Ciência da Informação - FFC

Visão contemporânea do uso de implantes de conexão interna tipo cone morse

The Morse Taper implant system, developed from its introduction in engineering, has become increasingly effective for use in dentistry. However, other systems, main external hexagon type, have been used more frequently today. Current studies have been reported the positive features of the Morse taper system and even emphasized as ideal within the systems used in implantology. Unfortunately, some professional duty by not knowing this system, or even prefer hexagon type system by decreased cost of components, have refused to use it. Thus, this study was aimed to perform a brief review of the Morse taper system, emphasizing its main points of interest in dentistry, in an attempt to familiarize the professionals to at least learn more about this system that has the prospect to become the leading system implants used in dentistry in the coming years. It is concluded that this system of dental implants is favorable showing predictability and success.

Novos materiais multifuncionais para aplicação em fotocatálise

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Costrutti ed Applicazioni di Programmazione Generica in Linguaggi Object-Oriented

Generic programming is likely to become a new challenge for a critical mass of developers. Therefore, it is crucial to refine the support for generic programming in mainstream Object-Oriented languages — both at the design and at the implementation level — as well as to suggest novel ways to exploit the additional degree of expressiveness made available by genericity. This study is meant to provide a contribution towards bringing Java genericity to a more mature stage with respect to mainstream programming practice, by increasing the effectiveness of its implementation, and by revealing its full expressive power in real world scenario. With respect to the current research setting, the main contribution of the thesis is twofold. First, we propose a revised implementation for Java generics that greatly increases the expressiveness of the Java platform by adding reification support for generic types. Secondly, we show how Java genericity can be leveraged in a real world case-study in the context of the multi-paradigm language integration. Several approaches have been proposed in order to overcome the lack of reification of generic types in the Java programming language. Existing approaches tackle the problem of reification of generic types by defining new translation techniques which would allow for a runtime representation of generics and wildcards. Unfortunately most approaches suffer from several problems: heterogeneous translations are known to be problematic when considering reification of generic methods and wildcards. On the other hand, more sophisticated techniques requiring changes in the Java runtime, supports reified generics through a true language extension (where clauses) so that backward compatibility is compromised. In this thesis we develop a sophisticated type-passing technique for addressing the problem of reification of generic types in the Java programming language; this approach — first pioneered by the so called EGO translator — is here turned into a full-blown solution which reifies generic types inside the Java Virtual Machine (JVM) itself, thus overcoming both performance penalties and compatibility issues of the original EGO translator. Java-Prolog integration Integrating Object-Oriented and declarative programming has been the subject of several researches and corresponding technologies. Such proposals come in two flavours, either attempting at joining the two paradigms, or simply providing an interface library for accessing Prolog declarative features from a mainstream Object-Oriented languages such as Java. Both solutions have however drawbacks: in the case of hybrid languages featuring both Object-Oriented and logic traits, such resulting language is typically too complex, thus making mainstream application development an harder task; in the case of library-based integration approaches there is no true language integration, and some “boilerplate code” has to be implemented to fix the paradigm mismatch. In this thesis we develop a framework called PatJ which promotes seamless exploitation of Prolog programming in Java. A sophisticated usage of generics/wildcards allows to define a precise mapping between Object-Oriented and declarative features. PatJ defines a hierarchy of classes where the bidirectional semantics of Prolog terms is modelled directly at the level of the Java generic type-system.

Expression profiling und rationale Expressionsoptimierung am Beispiel eines prokaryontischen Wirt-,Vektor-Systems

Durch globale Expressionsprofil-Analysen auf Transkriptom-, Proteom- oder Metabolom-Ebene können biotechnologische Produktionsprozesse besser verstanden und die Erkenntnisse für die zielgerichtete, rationale Optimierung von Expressionssystemen genutzt werden. In der vorliegenden Arbeit wurde die Überexpression einer Glukose-Dehydrogenase (EC 1.1.5.2), die von der Roche Diagnostics GmbH für die diagnostische Anwendung optimiert worden war, in Escherichia coli untersucht. Die Enzymvariante unterscheidet sich in sieben ihrer 455 Aminosäuren vom Wildtyp-Enzym und wird im sonst isogenen Wirt-/Vektor-System in signifikant geringeren Mengen (Faktor 5) gebildet. Das prokaryontische Expressionssystem wurde auf Proteom-Ebene charakterisiert. Die 2-dimensionale differenzielle Gelelektrophorese (DIGE) wurde zuvor unter statistischen Aspekten untersucht. Unter Berücksichtigung von technischen und biologischen Variationen, falsch-positiven (α-) und falsch-negativen (β-) Fehlern sowie einem daraus abgeleiteten Versuchsdesign konnten Expressionsunterschiede als signifikant quantifiziert werden, wenn sie um den Faktor ≥ 1,4 differierten. Durch eine Hauptkomponenten-Analyse wurde gezeigt, dass die DIGE-Technologie für die Expressionsprofil-Analyse des Modellsystems geeignet ist. Der Expressionsstamm für die Enzymvariante zeichnete sich durch eine höhere Variabilität an Enzymen für den Zuckerabbau und die Nukleinsäure-Synthese aus. Im Expressionssystem für das Wildtyp-Enzym wurde eine unerwartet erhöhte Plasmidkopienzahl nachgewiesen. Als potenzieller Engpass in der Expression der rekombinanten Glukose-Dehydrogenase wurde die Löslichkeitsvermittlung identifiziert. Im Expressionsstamm für das Wildtyp-Enzym wurden viele Proteine für die Biogenese der äußeren Membran verstärkt exprimiert. Als Folge dessen wurde ein sog. envelope stress ausgelöst und die Zellen gingen in die stationäre Wuchsphase über. Die Ergebnisse der Proteomanalyse wurden weiterführend dazu genutzt, die Produktionsleistung für die Enzymvariante zu verbessern. Durch den Austausch des Replikationsursprungs im Expressionsvektor wurde die Plasmidkopienzahl erhöht und die zelluläre Expressionsleistung für die diagnostisch interessantere Enzymvariante um Faktor 7 - 9 gesteigert. Um die Löslichkeitsvermittlung während der Expression zu verbessern, wurde die Plasmidkopienzahl gesenkt und die Coexpression von Chaperonen initiiert. Die Ausbeuten aktiver Glukose-Dehydrogenase wurden durch die Renaturierung inaktiven Produkts aus dem optimierten Expressionssystem insgesamt um einen Faktor von 4,5 erhöht. Somit führte im Rahmen dieser Arbeit eine proteombasierte Expressionsprofil-Analyse zur zielgerichteten, rationalen Expressionsoptimierung eines prokaryontischen Modellsystems.

A study of two Languages for Active Objects with Futures

In computer systems, specifically in multithread, parallel and distributed systems, a deadlock is both a very subtle problem - because difficult to pre- vent during the system coding - and a very dangerous one: a deadlocked system is easily completely stuck, with consequences ranging from simple annoyances to life-threatening circumstances, being also in between the not negligible scenario of economical losses. Then, how to avoid this problem? A lot of possible solutions has been studied, proposed and implemented. In this thesis we focus on detection of deadlocks with a static program analysis technique, i.e. an analysis per- formed without actually executing the program. To begin, we briefly present the static Deadlock Analysis Model devel- oped for coreABS−− in chapter 1, then we proceed by detailing the Class- based coreABS−− language in chapter 2. Then, in Chapter 3 we lay the foundation for further discussions by ana- lyzing the differences between coreABS−− and ASP, an untyped Object-based calculi, so as to show how it can be possible to extend the Deadlock Analysis to Object-based languages in general. In this regard, we explicit some hypotheses in chapter 4 first by present- ing a possible, unproven type system for ASP, modeled after the Deadlock Analysis Model developed for coreABS−−. Then, we conclude our discussion by presenting a simpler hypothesis, which may allow to circumvent the difficulties that arises from the definition of the ”ad-hoc” type system discussed in the aforegoing chapter.

Deadlock analysis of asynchronous sequential processes

In this thesis we present ad study an object-oriented language, characterized by two different types of objects, passive and active objects, of which we define the operational syntax and semantics. For this language we also define the type system, that will be used for the type checking and for the extraction of behavioral types, which are an abstract description of the behavior of the methods, used in deadlock analysis. Programs can manifest deadlock due to the errors of the programmer. To statically identify possible unintended behaviors we studied and implemented a technique for the analysis of deadlock based on behavioral types.

Practical, Pluggable Types for a Dynamic Language

Most languages fall into one of two camps: either they adopt a unique, static type system, or they abandon static type-checks for run-time checks. Pluggable types blur this division by (i) making static type systems optional, and (ii) supporting a choice of type systems for reasoning about different kinds of static properties. Dynamic languages can then benefit from static-checking without sacrificing dynamic features or committing to a unique, static type system. But the overhead of adopting pluggable types can be very high, especially if all existing code must be decorated with type annotations before any type-checking can be performed. We propose a practical and pragmatic approach to introduce pluggable type systems to dynamic languages. First of all, only annotated code is type-checked. Second, limited type inference is performed on unannotated code to reduce the number of reported errors. Finally, external annotations can be used to type third-party code. We present Typeplug, a Smalltalk implementation of our framework, and report on experience applying the framework to three different pluggable type systems.

Study of Basic Wood Decay Mechanisms and Their Biotechnological Applications

The overall objective of this thesis was to gain further understanding of the non-enzymatic mechanisms involved in brown-rot wood decay, especially the role of pH, oxalic acid, and low molecular catecholate compounds on the dissolution and reduction of iron, and the formation of reactive oxygen species. Another focus of this study will be the potential application of a biomimetic free radical generating system inspired from fungi wood decay process, especially the non-enzymatic mechanism. The possible pathways of iron uptake and iron redox cycling in non-enzymatic brown-rot decay were investigated in this study. UV-Vis spectroscopy and HPLC were employed to study the kinetics and pathways of the interaction between iron and model catecholate compounds under different pH and chelator/iron molar ratio conditions. Iron chelation and reduction during early non-enzymatic wood decay processes have been studied in this thesis. The results indicate that the effects of the chelator/iron ratio, the pH, and other reaction parameters on the hydroxyl radical generation in a Fenton type system can be determined using ESR spin-trapping techniques. Data also support the hypothesis that superoxide radicals are involved in chelator-mediated Fenton processes. The mechanisms involved in free radical activation of Thermal Mechanical Pulp fibers were investigated. The activation of TMP fibers was evaluated by ESR measurement of free phenoxy radical generation on solid fibers. The results indicate that low molecular weight chelators can improve Fenton reactions, thus in turn stimulating the free radical activation of TMP fibers. A mediated Fenton system was evaluated for decolorization of several types of dyes. The result shows that the Fenton system mediated by a catecholate-type chelator effectively reduced the color of a diluted solution of synthetic dyes after 90 minutes of treatment at room temperature. The results show that compared to a neat Fenton process, the mediated Fenton decolorization process increased the production, and therefore the effective longevity, of hydroxyl radical species to increase the decolorization efficiency.

The little-studied cluster Berkeley 90 I. LS III +46 11: a very massive O3.5 If* + O3.5 If* binary

Context. It appears that most (if not all) massive stars are born in multiple systems. At the same time, the most massive binaries are hard to find owing to their low numbers throughout the Galaxy and the implied large distances and extinctions. Aims. We want to study LS III +46 11, identified in this paper as a very massive binary; another nearby massive system, LS III +46 12; and the surrounding stellar cluster, Berkeley 90. Methods. Most of the data used in this paper are multi-epoch high S/N optical spectra, although we also use Lucky Imaging and archival photometry. The spectra are reduced with dedicated pipelines and processed with our own software, such as a spectroscopic-orbit code, CHORIZOS, and MGB. Results. LS III +46 11 is identified as a new very early O-type spectroscopic binary [O3.5 If* + O3.5 If*] and LS III +46 12 as another early O-type system [O4.5 V((f))]. We measure a 97.2-day period for LS III +46 11 and derive minimum masses of 38.80 ± 0.83 M⊙ and 35.60 ± 0.77 M⊙ for its two stars. We measure the extinction to both stars, estimate the distance, search for optical companions, and study the surrounding cluster. In doing so, a variable extinction is found as well as discrepant results for the distance. We discuss possible explanations and suggest that LS III +46 12 may be a hidden binary system where the companion is currently undetected.