Optimal control of a Stefan problem with gradient-based methods in FEniCS

Otto-von-Guericke-Universität Magdeburg, Fakultät für Mathematik, Masterarbeit, 2016

The effectiveness of methods of shape analysis / Cliff A. Lemen.

n.s. no.15(1983)

The interference of methods in the collection of teredinids (Mollusca, Bivalvia) in mangrove habitats

In the estuary of the Mamanguape River (Paraíba, Brazil), a new collection technique was developed and applied with virgin poles of mangrove trees Avicennia schaueriana (Verbenaceae), Rhizophora mangle (Rhizophoraceae), and Laguncularia racemosa (Combretaceae), taking into account wood preference, water salinity and depth influence during teredinid larval settlement. Sets of poles were vertically fixed in the riverbed at three sites along a decreasing salinity gradient, where they stayed for four months. The poles were collected and divided into upper, median, and lower segments, in agreement with different immersion regimes. An increase of 239% was obtained in the number of individuals when compared to a previous study in the same area using a different methodology. The species Teredo bartschi (Clapp, 1923), Nausitora fusticula (Jeffreys, 1860) and Bankia fimbriatula Moll & Roch, 1931 were registered in both studies, and the species Psiloteredo healdi (Bartsch, 1931) is here registered for the first time as occurring in that estuary. The species Neoteredo reynei (Bartsch, 1920), previously registered on tree branches of the mangrove habitat, was not found in the present work. Bankia fimbriatula, the most abundant species, did not show preference for any substratum but occurred significantly on the lower segment of the poles. N. fusticula, second in abundance, preferred to settle on poles of A. schaueriana and on any of the three segments. Aiming to assess the habitat variations, a more accurate study on teredinids diversity in mangrove ecosystems should be performed through a concomitant analysis from tree branches of the mangrove habitat, as well as from poles of mangrove trees or panels made of pine wood or mangrove trees wood. These collection devices should be maintained along a decreasing salinity gradient exposed to different tide levels.

The Analysis of interval censoring and double censoring via Markov chain Monte Carlo methods

L'Anàlisi de la supervivència s'utilitza en diferents camps per analitzar el temps transcorregut entre dos esdeveniments. El que distingeix l'anàlisi de la supervivència d'altres àrees de l'estadística és que les dades normalment estan censurades. La censura en un interval apareix quan l'esdeveniment final d'interès no és directament observable i només se sap que el temps de fallada està en un interval concret. Un esquema de censura més complex encara apareix quan tant el temps inicial com el temps final estan censurats en un interval. Aquesta situació s'anomena doble censura. En aquest article donem una descripció formal d'un mètode bayesà paramètric per a l'anàlisi de dades censurades en un interval i dades doblement censurades així com unes indicacions clares de la seva utilització o pràctica. La metodologia proposada s'ilustra amb dades d'una cohort de pacients hemofílics que es varen infectar amb el virus VIH a principis dels anys 1980's.

Eliciting and fostering learners' metacognitive knowledge about language learning in self-directed learning programs: a review of data collection methods and procedures

Són molts els estudis que avui en dia incideixen en la necessitat d’oferir un suport metodològic i psicològic als aprenents que treballen de manera autònoma. L’objectiu d’aquest suport és ajudar-los a desenvolupar les destreses que necessiten per dirigir el seu aprenentatge així com una actitud positiva i una major conscienciació envers aquest aprenentatge. En definitiva, aquests dos tipus de preparació es consideren essencials per ajudar els aprenents a esdevenir més autònoms i més eficients en el seu propi aprenentatge. Malgrat això, si bé és freqüent trobar estudis que exemplifiquen aplicacions del suport metodològic dins els seus programes, principalment en la formació d’estratègies o ajudant els aprenents a desenvolupar un pla de treball, aquest no és el cas quan es tracta de la seva preparació psicològica. Amb rares excepcions, trobem estudis que documentin com s’incideix en les actituds i en les creences dels aprenents, també coneguts com a coneixement metacognitiu (CM), en programes que fomenten l’autonomia en l’aprenentatge. Els objectius d’aquest treball son dos: a) oferir una revisió d’estudis que han utilitzat diferents mitjans per incidir en el CM dels aprenents i b) descriure les febleses i avantatges dels procediments i instruments que utilitzen, tal com han estat valorats en estudis de recerca, ja que ens permetrà establir criteris objectius sobre com i quan utilitzar-los en programes que fomentin l’aprenentatge autodirigit.

The microscope : an introduction to microscopic methods and to histology / by Simon Henry Gage.

11th ed

An illustrated flora of the northern United States, Canada and the British possessions, from Newfoundland to the parallel of the southern boundary of Virginia, and from the Atlantic Ocean westward to the 102d meridian, by Nathaniel Lord Britton and Addison Brown. The descriptive text chiefly prepared by Britton, with the assistance of specialists in several groups; the figures also drawn under his supervision.

2

An illustrated flora of the northern United States, Canada and the British possessions, from Newfoundland to the parallel of the southern boundary of Virginia, and from the Atlantic Ocean westward to the 102d meridian, by Nathaniel Lord Britton and Addison Brown. The descriptive text chiefly prepared by Britton, with the assistance of specialists in several groups; the figures also drawn under his supervision.

3

User-friendly parallel computations with econometric examples

This paper shows how a high level matrix programming language may be used to perform Monte Carlo simulation, bootstrapping, estimation by maximum likelihood and GMM, and kernel regression in parallel on symmetric multiprocessor computers or clusters of workstations. The implementation of parallelization is done in a way such that an investigator may use the programs without any knowledge of parallel programming. A bootable CD that allows rapid creation of a cluster for parallel computing is introduced. Examples show that parallelization can lead to important reductions in computational time. Detailed discussion of how the Monte Carlo problem was parallelized is included as an example for learning to write parallel programs for Octave.

ParallelKnoppix - Rapid deployment of a linux cluster for MPI parallel processing using non-dedicated computers

This note describes ParallelKnoppix, a bootable CD that allows creation of a Linux cluster in very little time. An experienced user can create a cluster ready to execute MPI programs in less than 10 minutes. The computers used may be heterogeneous machines, of the IA-32 architecture. When the cluster is shut down, all machines except one are in their original state, and the last can be returned to its original state by deleting a directory. The system thus provides a means of using non-dedicated computers to create a cluster. An example session is documented.

Encryption methods using formal power series rings

Recently there has been a great deal of work on noncommutative algebraic cryptography. This involves the use of noncommutative algebraic objects as the platforms for encryption systems. Most of this work, such as the Anshel-Anshel-Goldfeld scheme, the Ko-Lee scheme and the Baumslag-Fine-Xu Modular group scheme use nonabelian groups as the basic algebraic object. Some of these encryption methods have been successful and some have been broken. It has been suggested that at this point further pure group theoretic research, with an eye towards cryptographic applications, is necessary.In the present study we attempt to extend the class of noncommutative algebraic objects to be used in cryptography. In particular we explore several different methods to use a formal power series ring R && x1; :::; xn && in noncommuting variables x1; :::; xn as a base to develop cryptosystems. Although R can be any ring we have in mind formal power series rings over the rationals Q. We use in particular a result of Magnus that a finitely generated free group F has a faithful representation in a quotient of the formal power series ring in noncommuting variables.

Development of metabolic labeling strategies to study changes in protein expression

Résumé : Les progrès techniques de la spectrométrie de masse (MS) ont contribué au récent développement de la protéomique. Cette technique peut actuellement détecter, identifier et quantifier des milliers de protéines. Toutefois, elle n'est pas encore assez puissante pour fournir une analyse complète des modifications du protéome corrélées à des phénomènes biologiques. Notre objectif était le développement d'une nouvelle stratégie pour la détection spécifique et la quantification des variations du protéome, basée sur la mesure de la synthèse des protéines plutôt que sur celle de la quantité de protéines totale. Pour cela, nous volions associer le marquage pulsé des protéines par des isotopes stables avec une méthode d'acquisition MS basée sur le balayage des ions précurseurs (precursor ion scan, ou PIS), afin de détecter spécifiquement les protéines ayant intégré les isotopes et d'estimer leur abondance par rapport aux protéines non marquées. Une telle approche peut identifier les protéines avec les plus hauts taux de synthèse dans une période de temps donnée, y compris les protéines dont l'expression augmente spécifiquement suite à un événement précis. Nous avons tout d'abord testé différents acides aminés marqués en combinaison avec des méthodes PIS spécifiques. Ces essais ont permis la détection spécifique des protéines marquées. Cependant, en raison des limitations instrumentales du spectromètre de masse utilisé pour les méthodes PIS, la sensibilité de cette approche s'est révélée être inférieure à une analyse non ciblée réalisée sur un instrument plus récent (Chapitre 2.1). Toutefois, pour l'analyse différentielle de deux milieux de culture conditionnés par des cellules cancéreuses humaines, nous avons utilisé le marquage métabolique pour distinguer les protéines d'origine cellulaire des protéines non marquées du sérum présentes dans les milieux de culture (Chapitre 2.2). Parallèlement, nous avons développé une nouvelle méthode de quantification nommée IBIS, qui utilise des paires d'isotopes stables d'acides aminés capables de produire des ions spécifiques qui peuvent être utilisés pour la quantification relative. La méthode IBIS a été appliquée à l'analyse de deux lignées cellulaires cancéreuses complètement marquées, mais de manière différenciée, par des paires d'acides aminés (Chapitre 2.3). Ensuite, conformément à l'objectif initial de cette thèse, nous avons utilisé une variante pulsée de l'IBIS pour détecter des modifications du protéome dans des cellules HeLa infectée par le virus humain Herpes Simplex-1 (Chapitre 2.4). Ce virus réprime la synthèse des protéines des cellules hôtes afin d'exploiter leur mécanisme de traduction pour la production massive de virions. Comme prévu, de hauts taux de synthèse ont été mesurés pour les protéines virales détectées, attestant de leur haut niveau d'expression. Nous avons de plus identifié un certain nombre de protéines humaines dont le rapport de synthèse et de dégradation (S/D) a été modifié par l'infection virale, ce qui peut donner des indications sur les stratégies utilisées par les virus pour détourner la machinerie cellulaire. En conclusion, nous avons montré dans ce travail que le marquage métabolique peut être employé de façon non conventionnelle pour étudier des dimensions peu explorées en protéomique. Summary : In recent years major technical advancements greatly supported the development of mass spectrometry (MS)-based proteomics. Currently, this technique can efficiently detect, identify and quantify thousands of proteins. However, it is not yet sufficiently powerful to provide a comprehensive analysis of the proteome changes correlated with biological phenomena. The aim of our project was the development of ~a new strategy for the specific detection and quantification of proteomé variations based on measurements of protein synthesis rather than total protein amounts. The rationale for this approach was that changes in protein synthesis more closely reflect dynamic cellular responses than changes in total protein concentrations. Our starting idea was to couple "pulsed" stable-isotope labeling of proteins with a specific MS acquisition method based on precursor ion scan (PIS), to specifically detect proteins that incorporated the label and to simultaneously estimate their abundance, relative to the unlabeled protein isoform. Such approach could highlight proteins with the highest synthesis rate in a given time frame, including proteins specifically up-regulated by a given biological stimulus. As a first step, we tested different isotope-labeled amino acids in combination with dedicated PIS methods and showed that this leads to specific detection of labeled proteins. Sensitivity, however, turned out to be lower than an untargeted analysis run on a more recent instrument, due to MS hardware limitations (Chapter 2.1). We next used metabolic labeling to distinguish the proteins of cellular origin from a high background of unlabeled (serum) proteins, for the differential analysis of two serum-containing culture media conditioned by labeled human cancer cells (Chapter 2.2). As a parallel project we developed a new quantification method (named ISIS), which uses pairs of stable-isotope labeled amino acids able to produce specific reporter ions, which can be used for relative quantification. The ISIS method was applied to the analysis of two fully, yet differentially labeled cancer cell lines, as described in Chapter 2.3. Next, in line with the original purpose of this thesis, we used a "pulsed" variant of ISIS to detect proteome changes in HeLa cells after the infection with human Herpes Simplex Virus-1 (Chapter 2.4). This virus is known to repress the synthesis of host cell proteins to exploit the translation machinery for the massive production of virions. As expected, high synthesis rates were measured for the detected viral proteins, confirming their up-regulation. Moreover, we identified a number of human proteins whose synthesis/degradation ratio (S/D) was affected by the viral infection and which could provide clues on the strategies used by the virus to hijack the cellular machinery. Overall, in this work, we showed that metabolic labeling can be employed in alternative ways to investigate poorly explored dimensions in proteomics.

Exploration of the visual system : Part 2. In vivo analysis methods : virtual-reality optomotor system, fundus examination and fluorescent angiography

The mouse has emerged as an animal model for many diseases. At IRO, we have used this animal to understand the development of many eye diseases and treatment of some of them. Precise evaluation of vision is a prerequisite for both these approaches. In this unit we describe three ways to measure vision: testing the optokinetic response, and evaluating the fundus by direct observation and by fluorescent angiography.