Mapping prior information onto LMI eigenvalue-regions for discrete-time subspace identification

In subspace identification, prior information can be used to constrain the eigenvalues of the estimated state-space model by defining corresponding LMI regions. In this paper, first we argue on what kind of practical information can be extracted from historical data or step-response experiments to possibly improve the dynamical properties of the corresponding model and, also, on how to mitigate the effect of the uncertainty on such information. For instance, prior knowledge regarding the overshoot, the period between damped oscillations and settling time may be useful to constraint the possible locations of the eigenvalues of the discrete-time model. Then, we show how to map the prior information onto LMI regions and, when the obtaining regions are non-convex, to obtain convex approximations.Comment: Under revie

Static detection of anomalies in transactional memory programs

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia InformáticaTransactional Memory (TM) is an approach to concurrent programming based on the transactional semantics borrowed from database systems. In this paradigm, a transaction is a sequence of actions that may execute in a single logical instant, as though it was the only one being executed at that moment. Unlike concurrent systems based in locks, TM does not enforce that a single thread is performing the guarded operations. Instead, like in database systems, transactions execute concurrently, and the effects of a transaction are undone in case of a conflict, as though it never happened. The advantages of TM are an easier and less error-prone programming model, and a potential increase in scalability and performance. In spite of these advantages, TM is still a young and immature technology, and has still to become an established programming model. It still lacks the paraphernalia of tools and standards which we have come to expect from a widely used programming paradigm. Testing and analysis techniques and algorithms for TM programs are also just starting to be addressed by the scientific community, making this a leading research work is many of these aspects. This work is aimed at statically identifying possible runtime anomalies in TMprograms. We addressed both low-level dataraces in TM programs, as well as high-level anomalies resulting from incorrect splitting of transactions. We have defined and implemented an approach to detect low-level dataraces in TM programs by converting all the memory transactions into monitor protected critical regions, synchronized on a newly generated global lock. To validate the approach, we have applied our tool to a set of tests, adapted from the literature, that contain well documented errors. We have also defined and implemented a new approach to static detection of high-level concurrency anomalies in TM programs. This new approach works by conservatively tracing transactions, and matching the interference between each consecutive pair of transactions against a set of defined anomaly patterns. Once again, the approach was validated with well documented tests adapted from the literature

Industry survey in the medical technology industry

Estágio realizado na empresa Simon-Kucher & Partners: Dr. Frank RautenbergTese de mestrado integrado. Engenharia Industrial e Gestão. Faculdade de Engenharia. Universidade do Porto. 201

A comprehensive analysis of Med12 controlled (l)ncRNAs and characterization of a novel Sall1 antisense transcript

The function of the Mediator subunit Med12 on gene regulation has been widely studied and its interaction and regulation of protein coding genes broadly documented. However, only recently has its interaction with non-coding genes been verified. Analysis of transcriptome data from Med12 deficient embryonic stem cells (ESCs) revealed hundreds of misregulated protein coding genes, including multiple Wnt targets and genes involved in the developmental processes that were found affected in embryos previously generated with these cells. In addition to the protein coding genes, multiple misregulated non-coding genes were found during the analysis of transcriptome data generated from Med12 mutant cells, including several putative novel transcripts. Among these, an uncharacterized long non-coding (lnc)RNA was found to be differentially expressed cells, tissues and mouse embryos. This gene, designated as LN-BP18, encodes for antisense transcripts of Sall1, a gene also misregulated in the analysed cells. In humans, mutations in this gene are associated with Townes-Brocks syndrome (TBS), which shows several overlapping characteristics with MED12-associated X-linked intellectual disability syndromes. These features led to the deeper characterization of LN-BP18. Detailed gene and transcript analyses of this novel lncRNA led to the identification of two distinct transcription start sites (TSSs), termed TSS1 and TSS2. While TSS1 was active in all analysed tissues, TSS2 was found active only in ESCs. In vitro differentiation of ESCs confirmed this observation, with expression of transcripts originating from TSS1 increasing throughout the differentiation protocol, while the opposite dynamic occurring for TSS2 transcripts. Characterization of the gene structure revealed a complex splicing pattern, with its 7 exons spliced into 9 different isoforms, including spliced variants for three of the exons. Multiple analyses confirmed the lack of coding potential of all identified isoforms. BLAST searches revealed no homologous transcripts in other species, however, a non-conserved predicted lncRNA was described in human, which was also present in a divergent configuration relative to SALL1, suggesting a potential functional similarity to LN-BP18 despite the low sequence similarity. Expression analyses of the different mutant ESCs generated revealed a dynamic expression of LN-BP18. TSS2 transcripts, which were only detected in ESCs and not in embryonic tissues, showed a positive correlation with different pluripotency markers. This correlation, together with the ESC-specific activation of this TSS, suggested a potential role in the pluripotency network for isoforms originating from TSS2. Sall1 and LN-BP18 TSS1 transcripts were downregulated in Med12 depleted ESCs. Additionally, in Sall1-depleted cells, LN-BP18 was downregulated, with a strong effect observed for the TSS1 transcripts compared to TSS2. These observations, together with the co-expression of these two genes in embryonic tissues, suggested LN-BP18, specifically the TSS1, as a target of Sall1 activation. This activation is potentially Med12-dependent, since the effect on LN-BP18 expression was stronger upon Med12 depletion than in Sall1 deplete cells. A heterozygous LN-BP18-β-galactosidase reporter mutant ESC line was generated to detect expression of LN-BP18 in a more sensitive way. Expression of the reporter gene identified in addition to embryonal limb and caudal end expression seen by whole mount in situ hybridization (WISH), a clear expression in the pronephros, somites, neural tube, forebrain/midbrain- and midbrain/hindbrain-boundaries, demonstrating the importance of this reporter line for studying LN-BP18 expression and function during development. Finally, RNA-seq data from Med12 depleted ESC mutant cells was analysed together with public Med12 chromatin immunoprecipitation sequencing (ChIP-seq) data from ESCs. This analysis allowed identifying 12 lncRNAs, both annotated as well as new predictions, representing candidate lncRNAs whose expression is mediated by Med12. Compiled information for these genes presented here, offer insight into possible systems to analyse these genes in future studies as well as putative targets. Data from this thesis describe the genetic structure and expression of a previously uncharacterized lncRNA. These data, together with the different mutants generated of this gene establish the ground work for future studies clarifying the functions of LN-BP18 in ESCs, but also during embryonic development

Shaper-GA: automatic shape generation for modular housing

This work presents an automatic system that, from the specification of an architectural language of design, generates several alternative floor plants for the construction of modular homes. The system uses Genetic Algorithms and is capable of efficiently producing various plant solutions. The rules of architecture are implemented in the fitness function translating the rules of a Shape Grammar created by the architect. Different solutions of feasible plants are generated, that is, solutions that obey the rules of Shape Grammar and do not have overlays between the rooms. The system can be integrated with a user-friendly interface in the future, to allow for the house owners customization of their own house. Such a tool can also be delivered to construction companies for them to manage the design of modular houses that meet specific clients requirements.Este trabalho apresenta um sistema automático que, a partir da especificação de uma linguagem arquitetural de design, gera plantas alternativas para residências de construção modular. O sistema usa Algoritmos Genéticos e é capaz de produzir várias soluções de plantas de modo eficiente. As regras de arquitetura são implementadas na função de fitness a partir de uma Gramática de Forma criada pelo arquiteto. São geradas diferentes soluções de plantas exequíveis, isto é, soluções que obedecem à Gramática de Forma e não têm sobreposições entre as suas divisões. Pode ser futuramente integrado com uma interface amigável para o utilizador de forma a que este personalize e crie a sua futura casa. Tal ferramenta pode também ser entregue às companhias de construção de forma a que estas gerem uma planta para uma casa modular personalizada