This paper investigated the sensitivity, specificity, accuracy, and precision of laser fluorescence and tactile probing for the detection of subgingival calculus. The gold standard for subgingival calculus detection has always been tactile probing. In this study 27 teeth were collected and 108 surfaces investigated, one tooth was excluded (group #13) where no calculus was observed on any surface, and three surfaces because of subgingival root caries to avoid confounding data, which left a total of 101 surfaces of 26 extracted teeth that meet the investigation criteria. The presence of subgingival calculus was observed on 75 tooth surfaces (74.25%). There was a correlation between tooth surface and the presence of calculus. Subgingival calculus was from most to least frequently observed on the Distal surface (92.0%), Lingual surface (76.9%), Mesial surface (70.8%) and Facial surface (57.7%). The amount of laser fluoresce increased according to the amount of subgingival calculus. There was a correlation between the amount of subgingival calculus and the amount of laser fluorescence. The tactile probing had a similar sensitivity compared to laser fluorescence for the detection of subgingival calculus. The laser fluorescence was more specific compared to tactile probing for the detection of subgingival calculus. The tactile probing had a similar accuracy compared to laser fluorescence for the detection of subgingival calculus. The laser fluorescence had more precision compared to tactile probing for the detection of subgingival calculus. These results show that by using both tactile probing and laser fluorescence the sensitivity, specificity, accuracy, and precision of detecting subgingival calculus can be increased. An increase in the sensitivity, specificity, accuracy, and precision of detecting subgingival calculus could help in the diagnosis and treatment of patients suffering from gingival recession and periodontal disease.

No description available.

Soil-rock probing (Jb-probing) is the most common probing method in Sweden. Due to the penetration capacity of the Jb-probing it can be performed in both soil and rock. However, the capacity also results in inherent limitations and uncertainties, such as the difficulty identifying the soil layer sequences of soft soils. In order to attain a more detailed soil layer sequence it is necessary to perform complementary probing and sampling methods, an inefficient and consequently costly procedure. By instead implementing non-interfering complementary methods performed simultaneously as the Jb-probing the method may be rationalized. The so-called acoustic Jb-probing method may be a potential complement to the Jb-probing. In this thesis a continued study of the acoustic Jb-probing method is performed by means of a case study in Gubbängen with the focus on the potential additional information that the spectrogram (a visual representation of the frequency spectra) may contain compared to the Jb-parameters alone. This was done by obtaining vibration signals during Jb-probing using a triaxle geophone installed four meters from the boreholes. Vibration signals were collected from 13 boreholes. The vibration signals were then analyzed in time- and frequency domain which were compared to corresponding Jb-parameters and classified soil types. The results showed that the clay layers held the most promise for discovering additional information in the spectrogram, however this does not exclude potential in other soil types. Additionally, it was shown that the geophone ought to be fastened in the ground in order to attain satisfactory data. Overall, the acoustic Jb-probing method is a favorable way of collecting and analyzing data, which with continued development of the operational and computational process may be an economical alternative to the conventional method.

<p> Tissue plasminogen activator (tPA), is commonly used as thrombolytic agent for the treatment of various cardiovascular diseases. This thesis constitutes the first report on cloning and expression of tPA in the methylotrphic yeast Pichia pastoris. </p> <p> The tPA gene was first cloned into an E. coli/Pichia shuttle plasmid and then integrated into the Pichia genome. The recombinant Pichia was able to express tPA intracellularly, under methanol induction. The tPA produced by the Pichia had a similar molecular weight as native tPA and it had serine protease activity. At the shake flask scale, the recombinant Pichia strain was able to produce twice as much tPA as reported for E. coli. </p> <p> Elastin-like polypeptides (ELP) are proteins that have a peculiar characteristic: they are able to undergo a reversible inverse phase transition temperature within a very narrow temperature range. On a second aspect of heterologous protein, a construct composed of thioredoxin-intein-ELP was used to provide direct evidence, for the first time, that protein folding and activity, in this case the intein, was maintained when the tripartite fusion was present in the aggregated state. These results are important, since they provide the necessary degree of confidence to stimulate future work directed towards expression and maintenance of proper folding of aggregation-prone proteins when expressed in-vivo E. Coli as ELP directed inclusion bodies. It is also shown that the intein-ELP system may be a very interesting system to be used as a drug delivery vehicle. </p> / Thesis / Master of Applied Science (MASc)

Probing methods for trace estimation of large, sparse matrices has been studied for several decades. In recent years, there has been some work to extend these techniques to instead estimate the diagonal entries of these systems directly. We extend some analysis of trace estimators to their corresponding diagonal estimators, propose a new class of deterministic diagonal estimators which are well-suited to parallel architectures along with heuristic arguments for the design choices in their construction, and conclude with numerical results on diagonal estimation and ordering problems, demonstrating the strengths of our newly-developed methods alongside existing methods. / Master of Science / In the past several decades, as computational resources increase, a recurring problem is that of estimating certain properties very large linear systems (matrices containing real or complex entries). One particularly important quantity is the trace of a matrix, defined as the sum of the entries along its diagonal. In this thesis, we explore a problem that has only recently been studied, in estimating the diagonal entries of a particular matrix explicitly. For these methods to be computationally more efficient than existing methods, and with favorable convergence properties, we require the matrix in question to have a majority of its entries be zero (the matrix is sparse), with the largest-magnitude entries clustered near and on its diagonal, and very large in size. In fact, this thesis focuses on a class of methods called probing methods, which are of particular efficiency when the matrix is not known explicitly, but rather can only be accessed through matrix vector multiplications with arbitrary vectors. Our contribution is new analysis of these diagonal probing methods which extends the heavily-studied trace estimation problem, new applications for which probing methods are a natural choice for diagonal estimation, and a new class of deterministic probing methods which have favorable properties for large parallel computing architectures which are becoming ever-more-necessary as problem sizes continue to increase beyond the scope of single processor architectures.

Les travaux de recherche présentés dans ce manuscrit de thèse ont pour principal objectif d’aider à comprendre les différents mécanismes et phénomènes qui interviennent lors de l’interaction d’un laser avec un semiconducteur dans une analyse de circuits intégrés submicroniques. Le but étant de maitriser et améliorer les techniques d’analyse par laser en mode sonde. La miniaturisation et la densification des composants électroniques fait que les techniques d’analyse par laser atteignent leurs limites. Connaitre l’impact des différents paramètres physiques, optiques et électriques sur une analyse sonde est un facteur clé pour pouvoir améliorer la compréhension des signaux sonde mesuré. Ces travaux montrent également l’effet non négligeable de la température sur les techniques d’analyse par laser en mode sonde. / The main objective of the presented research work in this PhD thesis is to help to understand the different mechanisms and phenomena involved in the interaction of a laser with a semiconductor in the analysis of a submicron integrated circuit. The aim is to master and improve the Electro Optical Probing techniques. Miniaturization and densification of electronic components lead the failure analysis techniques using Laser to their limits. Knowing the impact of different physical, optical and electrical parameters on a probing analysis is a key to improve the understanding the measured EOP signals. These studies also show the significant effect of temperature on the EOP techniques.

En bioinformatique structurale, la prédiction de la (des) structure(s) secondaire(s) des acides ribonucléiques (ARNs) constitue une direction de recherche majeure pour comprendre les mécanismes cellulaires. Une approche classique pour la prédiction de la structure postule qu'à l'équilibre thermodynamique, l'ARN adopte plusieurs conformations, caractérisées par leur énergie libre, dans l’ensemble de Boltzmann. Les approches modernes privilégient donc une considération des conformations dominantes. Ces approches voient leur précision limitées par l'imprécision des modèles d'énergie et les restrictions topologiques pesant sur les espaces de conformations.Les données expérimentales peuvent être utilisées pour pallier aux lacunes des méthodes de prédiction. Différents protocoles permettent ainsi la révélation d'informations structurales partielles via une exposition à un réactif chimique/enzymatique, dont l'effet dépend, et est donc révélateur, de la (les) structure(s) adoptée(s). Les données de sondage mono-réactif sont utilisées pour valider et complémenter les modèles d’énergie libre, permettant ainsi d’améliorer la précision des prédictions. En pratique, cependant, les praticiens basent leur modélisation sur des données de sondage produites dans diverses conditions expérimentales, utilisant différents réactifs ou associées à une collection de séquences mutées. Une telle approche intégrative est répandue mais reste manuelle, onéreuse et subjective. Au cours de cette thèse, nous avons développé des méthodes in silico pour une modélisation automatisée de la structure à partir de plusieurs sources de données de sondage.En premier lieu, nous avons établi des pipelines d’analyse automatisés pour l'acquisition de profils de réactivité à partir de données brutes produites à travers une série de protocoles. Nous avons ensuite conçu et implémenté une nouvelle méthode qui permet l'intégration simultanée de plusieurs profils de sondage. Basée sur une combinaison d'échantillonnage de l'ensemble de Boltzmann et de clustering structurel, notre méthode produit des conformations dominantes, stables et compatible avec les données de sondage. En favorisant les structures récurrentes, notre méthode permet d’exploiter la complémentarité entre plusieurs données de sondage. Ses performances dans le cas mono-sondage sont comparables ou meilleures que celles des méthodes prédictives de pointe.Cette méthode a permis de proposer des modèles pour les régions structurées des virus. En collaboration avec des expérimentalistes, nous avons suggéré une structure raffinée de l'IRES du VIH-1 Gag, compatible avec les données de sondage chimiques et enzymatiques, qui nous a permis d’identifier des sites d'interactions putatifs avec le ribosome. Nous avons également modélisé la structure des régions non traduites d'Ebola. Cohérents avec les données de sondage SHAPE et les données de covariation, nos modèles montrent l’existence d'une tige-boucle conservée et stable à l'extrémité 5', une structure typiquement présente dans les génomes viraux pour protéger l'ARN de la dégradation par les nucléases.L’extension de notre méthode pour l’analyse simultanée de variants, appliquée dans un premier temps sur des mutants produits par le protocole Mutate-and-Map et sondés par le DMS, a permis d'enregistrer une amélioration en précision de prédiction. Pour éviter la production systématique de mutants ponctuels et exploiter le protocole récent SHAPEMap, nous avons conçu un protocole expérimental basé sur une mutagenèse non dirigé et le séquençage, où plusieurs ARN mutés sont produits et simultanément sondés. Nous avons traité l’affectation des reads aux mutants de références à l'aide d'une instance de l'algorithme "Expectation-Maximization" dont les résultats préliminaires, sur un échantillon de reads réduit/simulé, ont montré un faible taux d’erreurs d'assignation par rapport à une affectation classique des reads aux séquences d'ARN de référence. / In structural bioinformatics, predicting the secondary structure(s) of ribonucleic acids (RNAs) represents a major direction of research to understand cellular mechanisms. A classic approach for structure postulates that, at the thermodynamic equilibrium, RNA adopts its various conformations according to a Boltzmann distribution based on its free energy. Modern approaches, therefore, favor the consideration of the dominant conformations. Such approaches are limited in accuracy due to the imprecision of the energy model and the structure topology restrictions.Experimental data can be used to circumvent the shortcomings of predictive computational methods. RNA probing encompasses a wide array of experimental protocols dedicated to revealing partial structural information through exposure to a chemical or enzymatic reagent, whose effect depends on, and thus reveals, features of its adopted structure(s). Accordingly, single-reagent probing data is used to supplement free-energy models within computational methods, leading to significant gains in prediction accuracy. In practice, however, structural biologists integrate probing data produced in various experimental conditions, using different reagents or over a collection of mutated sequences, to model RNA structure(s). This integrative approach remains manual, time-consuming and arguably subjective in its modeling principles. In this Ph.D., we contributed in silico methods for an automated modeling of RNA structure(s) from multiple sources of probing data.We have first established automated pipelines for the acquisition of reactivity profiles from primary data produced through a variety of protocols (SHAPE, DMS using Capillary Electrophoresis, SHAPE-Map/Ion Torrent). We have designed and implemented a new, versatile, method that simultaneously integrates multiple probing profiles. Based on a combination of Boltzmann sampling and structural clustering, it produces alternative stable conformations jointly supported by a set of probing experiments. As it favors recurrent structures, our method allows exploiting the complementarity of several probing assays. The quality of predictions produced using our method compared favorably against state-of-the-art computational predictive methods on single-probing assays.Our method was used to identify models for structured regions in RNA viruses. In collaboration with experimental partners, we suggested a refined structure of the HIV-1 Gag IRES, showing a good compatibility with chemical and enzymatic probing data. The predicted structure allowed us to build hypotheses on binding sites that are functionally relevant to the translation. We also proposed conserved structures in Ebola Untranslated regions, showing a high consistency with both SHAPE probing and evolutionary data. Our modeling allows us to detect conserved and stable stem-loop at the 5’end of each UTR, a typical structure found in viral genomes to protect the RNA from being degraded by nucleases.Our method was extended to the analysis of sequence variants. We analyzed a collection of DMS probed mutants, produced by the Mutate-and-Map protocol, leading to better structural models for the GIR1 lariat-capping ribozyme than from the sole wild-type sequence. To avoid systematic production of point-wise mutants, and exploit the recent SHAPEMap protocol, we designed an experimental protocol based on undirected mutagenesis and sequencing, where several mutated RNAs are produced and simultaneously probed. Produced reads must then be re-assigned to mutants to establish their reactivity profiles used later for structure modeling. The assignment problem was modeled as a likelihood maximization joint inference of mutational profiles and assignments, and solved using an instance of the "Expectation-Maximization" algorithm. Preliminary results on a reduced/simulated sample of reads showed a remarkable decrease of the reads assignment errors compared to a classic algorithm.

Geotekniska undersökningar används för att få en uppfattning om markförhållanden. Ett exempel på en geoteknisk undersökningsmetod är standard penetration test (SPT). Denna metod kombinerar dynamisk sondering med provtagning och används för att kunna härleda bärförmåga i en jord. Metoden uppstod i början av 1900-talet och utrustningen korrigerades fram till 1930-talet. Sedan dess har utvecklingen av metoden i princip stått still. Det finns ingen internationell standard för SPT idag och metoden kan därför skilja sig i olika delar av världen. Sonderingen utförs i botten av ett förborrat borrhål med en öppen provtagare. Serier om maximalt 450 millimeter kan tas samtidigt och intervallet mellan serierna rekommenderas till 0,75–1,5 meter. SPT är en välanvänd metod internationellt sett, medan användandet i Sverige är begränsat. En av de mer frekvent använda dynamiska sonderingsmetoderna som används i Sverige är hejarsondering med frifallshejare och fast dyna (HfA). Metoden utvecklades från den traditionella hejarsonderingsmetoden under 1960-talet och sedan HfA standardiserades på 1970-talet har metoden knappt utvecklats. Idag finns metoden i den europeiska standarden under namnet DPSH-A med tillägg i en svensk bilaga. HfA använder sig av en konspets som slås ned av en fallande hammare. HfA kan användas om fasta jordlager söks men även för att härleda jordparametrar som friktionsvinkel och elasticitetsmodul. Syftet med rapporten är att se om metoderna SPT och HfA relaterar till varandra. Undersökningar med respektive metod har genomförts i fyra områden, Luleå hamn, Gammelstad, Aitik respektive Kristineberg. Avståndet mellan sonderingspunkterna för de två metoderna i Luleå hamn, Gammelstad och Kristineberg är ungefär en meter, medan avståndet i Aitik varierar mellan 10–30 meter. För att avgöra vilken jordart sonderingarna utförts i har okulär jordartsbedömning gjorts på provtagning från SPT för områdena Luleå hamn, Aitik och Kristineberg. För proverna från Gammelstad har siktningslaboration utförts. Rekommendationer för att korrigera uppmätt antal slag för SPT tar hänsyn till olika faktorer beroende på vart metoden geografiskt sett används. Enligt den europeiska standarden ska metoden korrigeras för energiförhållandet i testutrustningen, längden på borrstål samt vertikalspänning orsakat av överbelastning av jord. Housing and Building Research Institute rekommenderar att uppmätt antal slag även korrigeras för borrhålets diameter och provtagartyp. Enligt U.S. Department of Transportation ska antalet slag endast korrigeras för energiförhållandet i testutrustningen och för vertikalspänning orsakat av överbelastning av jord. För att beräkna friktionsvinkel utifrån SPT-resultat kan åtta ekvationer användas. Elastisitetsmodul kan beräknas med två ekvationer. För HfA rekommenderas en ekvation för korrigering, en för beräkning av friktionsvinkel och en för beräkning av elasticitetsmodul. Tidigare gjorda jämförelser tyder på att det kan finnas ett samband mellan metoderna. Även resultatet från denna rapport tyder på att det kan vara möjligt att hitta ett samband, även om metoderna skiljer sig i vissa lägen. Elasticitetsmodulen skiljer sig kraftigt mellan HfA och SPT, men även för de två ekvationerna som presenterats för SPT. Friktionsvinkeln för SPT ger en stor spridning och den beräknade friktionsvinkeln för HfA hamnar kring medelvärdet för SPT. / Geotechnical investigations are mainly used to get an idea the condition of the subsurface. An example of a geotechnical investigation method is the standard penetration test (SPT). This method combines dynamic sounding with sampling and can be used to deduce the bearing capacity of a soil. SPT was invented in the beginning of the 20:th century and corrections of the method was done until the 1930s. Since then, the development of the method has been at a standstill. Today there is no international standard for SPT, and the execution does therefore vary across the globe. SPT is performed with an open sampler at the bottom of a predrilled borehole. Series of a maximum of 450 millimeters can be taken at the same time and the interval between the series is recommended to 0,75-1,5 meters. SPT is commonly used internationally, but the usage of the method in Sweden is limited. A commonly used dynamic sounding method is the Swedish dynamic probing (HfA). This method was developed in the 1960s. The development of the method has been on a standstill since it was standardized in the 1970. Today, the method goes by the category DPSH-A supplemented by a Swedish appendix in the European standard. HfA uses a conical tip which is blown down by a falling hammer. HfA is used in the search for solid soil layers but can also be used to deduce soil parameters such as angle of friction and elasticity modulus. The aim with this master thesis is to determine if SPT and HfA relates to one another. Investigations has been performed in four areas, Luleå harbour, Gammelstad, Aitik and Kristineberg. The distance between the probing points for SPT and HfA at Luleå harbour, Gammelstad and Kristineberg is about one meter. The distance in Aitik varies between 10 to 30 meters. Ocular soil type assessment was performed for the soil samples in Luleå harbour, Aitik and Kristineberg and sieving was performed for the samples taken in Gammelstad. Recommendations for correction of the number of blows for SPT takes different factors into consideration depending on where the test is performed. According to the European standard, the energy efficiency of the equipment, length of the rods and the overburden pressure should be corrected for. Housing and Building Research Institute recommends adding on corrections for the borehole diameter and the type of sampler. Correction should only be done for the energy efficiency of the equipment and the overburden pressure according to U.S. Department of Transportation. There is a total of ten equations available to determine the angle of friction based on results from SPT, while there are two equations available to determine the elasticity modulus. On the other hand, there is only one equation for correction, one to determine angle of friction and one to determine the elasticity modulus for HfA. Previous comparisons of these two methods shows that there is a possibility to find a relation between the methods. The result from this report also indicates that there may be possible to find a relation between the methods, even if they do differ in some cases. The elasticity modulus does vary a lot between the two methods, but also between the two equations found for SPT. The angle of friction for SPT shows a large variation but the calculated angle of friction for HfA ends up around the mean value for the equations for SPT.

Europeiska Unionen står inför en komplex uppgift med att införa Digitala Produktpass (DPP) – en digital mekanism som strävar efter att förbättra hur information om produkters livslängd, tillförlitlighet och återanvändbarhet samlas och delas. Detta arbete utförs med syfte att utveckla och förbättra användbarheten i ett användargränssnitt som är tänkt att integreras i samband med onlineköp för att effektivisera och förenkla processen för skapandet av DPP. Genom att omfamna metoden Design Thinking, har arbetet utvecklat och utvärderat en prototyp. Detta genom att identifiera och analysera problem med användbarhet i en utvärdering beståendes av intervju, användartest i form av Retrospective Probing och en enkät. Resultaten från utvärderingen visade brister i användarnas förståelse för användargränssnittet och DPP. Detta har specifikt lett till förbättringar av designen för initieringsknappen i användargränssnittet. I initieringsknappens beskrivande text har det lagts till mer informtion om Digitala Produktpass, vilket syftar till att öka interaktionens tydlighet och användarnas nöjdhet. Slutsatserna av arbetet belyser både framgångar och identifierade begränsningar. Det framhäver inte bara de förbättringar som redan har genomförts med initieringsknappen, utan också de områden där ytterligare insatser krävs för att optimera användbarheten, som flera iterationer av Design Thinking. Arbetet ger även vägledning för kommande studier och implementeringar inom området genom att föreslå riktningar för framtida forskning för utvecklandet av användbarhet i användargränssnitt för DPP. Genom att skapa en smidig och intuitiv interaktion mellan användare och DPP kan det öka engagemanget och uppmuntra till ökad användning av DPP. Vilket slutligen hjälper Europeiska Unionen införa DPP. / The European Union faces a complex task in introducing the Digital Product Passport (DPP) – a digital mechanism that aims to improve the way information about product lifespan, reliability and reusability is collected and shared. This work is carried out with the aim of developing and improving the usability of a user interface that is intended to be integrated in connection with online purchases, in order to streamline and simplify the process of creating DPP. By embracing the Design Thinking method, the work has developed and evaluated a prototype. This was made by identifying and analysing usability issues in an evaluation consisting of interview, user tests in the form of Retrospective Probing Probing and surveys. The results from the evaluation, showed deficiencies in users’ understanding of the user interface and DPPs. This has specifically led to improvements in the design of the initiation button in the user interface. In the initiation button’s describing text, more information about Digital Product Passports has been added, which aims to increase the clarity of the interaction and the satisfaction of the users. The conclusions of the work highlights both successes and identified limitations. It not only highlights the improvements that have already been made with the initiation button, but also the areas where efforts are required to optimize usability, such as further iterations of Design Thinking. The work also provides guidance for future studies and implementations in the field, by suggesting directions for future research for the development of usability in user interfaces for DPP. By creating a smooth and intuitive interaction between users and DPP, it can increase engagement and encourage increased use of DPP. Which ultimately helps the European Union introduce the DPP.

Data mining can be defined as the extraction of implicit, previously un-known, and potentially useful information from data. Numerous re-searchers have been developing security technology and exploring new methods to detect cyber-attacks with the DARPA 1998 dataset for Intrusion Detection and the modified versions of this dataset KDDCup99 and NSL-KDD, but until now no one have examined the performance of the Top 10 data mining algorithms selected by experts in data mining. The compared classification learning algorithms in this thesis are: C4.5, CART, k-NN and Naïve Bayes. The performance of these algorithms are compared with accuracy, error rate and average cost on modified versions of NSL-KDD train and test dataset where the instances are classified into normal and four cyber-attack categories: DoS, Probing, R2L and U2R. Additionally the most important features to detect cyber-attacks in all categories and in each category are evaluated with Weka’s Attribute Evaluator and ranked according to Information Gain. The results show that the classification algorithm with best performance on the dataset is the k-NN algorithm. The most important features to detect cyber-attacks are basic features such as the number of seconds of a network connection, the protocol used for the connection, the network service used, normal or error status of the connection and the number of data bytes sent. The most important features to detect DoS, Probing and R2L attacks are basic features and the least important features are content features. Unlike U2R attacks, where the content features are the most important features to detect attacks.