Automatic lumen segmentation in IVOCT images using binary morphological reconstruction

Abstract Background Atherosclerosis causes millions of deaths, annually yielding billions in expenses round the world. Intravascular Optical Coherence Tomography (IVOCT) is a medical imaging modality, which displays high resolution images of coronary cross-section. Nonetheless, quantitative information can only be obtained with segmentation; consequently, more adequate diagnostics, therapies and interventions can be provided. Since it is a relatively new modality, many different segmentation methods, available in the literature for other modalities, could be successfully applied to IVOCT images, improving accuracies and uses. Method An automatic lumen segmentation approach, based on Wavelet Transform and Mathematical Morphology, is presented. The methodology is divided into three main parts. First, the preprocessing stage attenuates and enhances undesirable and important information, respectively. Second, in the feature extraction block, wavelet is associated with an adapted version of Otsu threshold; hence, tissue information is discriminated and binarized. Finally, binary morphological reconstruction improves the binary information and constructs the binary lumen object. Results The evaluation was carried out by segmenting 290 challenging images from human and pig coronaries, and rabbit iliac arteries; the outcomes were compared with the gold standards made by experts. The resultant accuracy was obtained: True Positive (%) = 99.29 ± 2.96, False Positive (%) = 3.69 ± 2.88, False Negative (%) = 0.71 ± 2.96, Max False Positive Distance (mm) = 0.1 ± 0.07, Max False Negative Distance (mm) = 0.06 ± 0.1. Conclusions In conclusion, by segmenting a number of IVOCT images with various features, the proposed technique showed to be robust and more accurate than published studies; in addition, the method is completely automatic, providing a new tool for IVOCT segmentation.

Theoretical studies of Membrane Proteins : Properties, Prediction Methods and Genome-wide analysis

Membrane proteins are a large and important class of proteins. They are responsible for several of the key functions in a living cell, e.g. transport of nutrients and ions, cell-cell signaling, and cell-cell adhesion. Despite their importance it has not been possible to study their structure and organization in much detail because of the difficulty to obtain 3D structures. In this thesis theoretical studies of membrane protein sequences and structures have been carried out by analyzing existing experimental data. The data comes from several sources including sequence databases, genome sequencing projects, and 3D structures. Prediction of the membrane spanning regions by hydrophobicity analysis is a key technique used in several of the studies. A novel method for this is also presented and compared to other methods. The primary questions addressed in the thesis are: What properties are common to all membrane proteins? What is the overall architecture of a membrane protein? What properties govern the integration into the membrane? How many membrane proteins are there and how are they distributed in different organisms? Several of the findings have now been backed up by experiments. An analysis of the large family of G-protein coupled receptors pinpoints differences in length and amino acid composition of loops between proteins with and without a signal peptide and also differences between extra- and intracellular loops. Known 3D structures of membrane proteins have been studied in terms of hydrophobicity, distribution of secondary structure and amino acid types, position specific residue variability, and differences between loops and membrane spanning regions. An analysis of several fully and partially sequenced genomes from eukaryotes, prokaryotes, and archaea has been carried out. Several differences in the membrane protein content between organisms were found, the most important being the total number of membrane proteins and the distribution of membrane proteins with a given number of transmembrane segments. Of the properties that were found to be similar in all organisms, the most obvious is the bias in the distribution of positive charges between the extra- and intracellular loops. Finally, an analysis of homologues to membrane proteins with known topology uncovered two related, multi-spanning proteins with opposite predicted orientations. The predicted topologies were verified experimentally, providing a first example of "divergent topology evolution".

Creazione e sviluppo di corpora multimediali. Nuove metodologie di ricerca nella traduzione audiovisiva

The construction and use of multimedia corpora has been advocated for a while in the literature as one of the expected future application fields of Corpus Linguistics. This research project represents a pioneering experience aimed at applying a data-driven methodology to the study of the field of AVT, similarly to what has been done in the last few decades in the macro-field of Translation Studies. This research was based on the experience of Forlixt 1, the Forlì Corpus of Screen Translation, developed at the University of Bologna’s Department of Interdisciplinary Studies in Translation, Languages and Culture. As a matter of fact, in order to quantify strategies of linguistic transfer of an AV product, we need to take into consideration not only the linguistic aspect of such a product but all the meaning-making resources deployed in the filmic text. Provided that one major benefit of Forlixt 1 is the combination of audiovisual and textual data, this corpus allows the user to access primary data for scientific investigation, and thus no longer rely on pre-processed material such as traditional annotated transcriptions. Based on this rationale, the first chapter of the thesis sets out to illustrate the state of the art of research in the disciplinary fields involved. The primary objective was to underline the main repercussions on multimedia texts resulting from the interaction of a double support, audio and video, and, accordingly, on procedures, means, and methods adopted in their translation. By drawing on previous research in semiotics and film studies, the relevant codes at work in visual and acoustic channels were outlined. Subsequently, we concentrated on the analysis of the verbal component and on the peculiar characteristics of filmic orality as opposed to spontaneous dialogic production. In the second part, an overview of the main AVT modalities was presented (dubbing, voice-over, interlinguistic and intra-linguistic subtitling, audio-description, etc.) in order to define the different technologies, processes and professional qualifications that this umbrella term presently includes. The second chapter focuses diachronically on various theories’ contribution to the application of Corpus Linguistics’ methods and tools to the field of Translation Studies (i.e. Descriptive Translation Studies, Polysystem Theory). In particular, we discussed how the use of corpora can favourably help reduce the gap existing between qualitative and quantitative approaches. Subsequently, we reviewed the tools traditionally employed by Corpus Linguistics in regard to the construction of traditional “written language” corpora, to assess whether and how they can be adapted to meet the needs of multimedia corpora. In particular, we reviewed existing speech and spoken corpora, as well as multimedia corpora specifically designed to investigate Translation. The third chapter reviews Forlixt 1's main developing steps, from a technical (IT design principles, data query functions) and methodological point of view, by laying down extensive scientific foundations for the annotation methods adopted, which presently encompass categories of pragmatic, sociolinguistic, linguacultural and semiotic nature. Finally, we described the main query tools (free search, guided search, advanced search and combined search) and the main intended uses of the database in a pedagogical perspective. The fourth chapter lists specific compilation criteria retained, as well as statistics of the two sub-corpora, by presenting data broken down by language pair (French-Italian and German-Italian) and genre (cinema’s comedies, television’s soapoperas and crime series). Next, we concentrated on the discussion of the results obtained from the analysis of summary tables reporting the frequency of categories applied to the French-Italian sub-corpus. The detailed observation of the distribution of categories identified in the original and dubbed corpus allowed us to empirically confirm some of the theories put forward in the literature and notably concerning the nature of the filmic text, the dubbing process and Italian dubbed language’s features. This was possible by looking into some of the most problematic aspects, like the rendering of socio-linguistic variation. The corpus equally allowed us to consider so far neglected aspects, such as pragmatic, prosodic, kinetic, facial, and semiotic elements, and their combination. At the end of this first exploration, some specific observations concerning possible macrotranslation trends were made for each type of sub-genre considered (cinematic and TV genre). On the grounds of this first quantitative investigation, the fifth chapter intended to further examine data, by applying ad hoc models of analysis. Given the virtually infinite number of combinations of categories adopted, and of the latter with searchable textual units, three possible qualitative and quantitative methods were designed, each of which was to concentrate on a particular translation dimension of the filmic text. The first one was the cultural dimension, which specifically focused on the rendering of selected cultural references and on the investigation of recurrent translation choices and strategies justified on the basis of the occurrence of specific clusters of categories. The second analysis was conducted on the linguistic dimension by exploring the occurrence of phrasal verbs in the Italian dubbed corpus and by ascertaining the influence on the adoption of related translation strategies of possible semiotic traits, such as gestures and facial expressions. Finally, the main aim of the third study was to verify whether, under which circumstances, and through which modality, graphic and iconic elements were translated into Italian from an original corpus of both German and French films. After having reviewed the main translation techniques at work, an exhaustive account of possible causes for their non-translation was equally provided. By way of conclusion, the discussion of results obtained from the distribution of annotation categories on the French-Italian corpus, as well as the application of specific models of analysis allowed us to underline possible advantages and drawbacks related to the adoption of a corpus-based approach to AVT studies. Even though possible updating and improvement were proposed in order to help solve some of the problems identified, it is argued that the added value of Forlixt 1 lies ultimately in having created a valuable instrument, allowing to carry out empirically-sound contrastive studies that may be usefully replicated on different language pairs and several types of multimedia texts. Furthermore, multimedia corpora can also play a crucial role in L2 and translation teaching, two disciplines in which their use still lacks systematic investigation.

Eigenschaftskorrelationen in kolloidalen Festkörpern und Fluiden aus optischen Experimenten

Die Arbeit beschäftigt sich mit ein- und zweikomponentigen, geladenen Kolloidsystemen, die in vollentsalzten wässrigen und organischen Dispersionen kristalline Strukturen ausbilden. Im ersten Teil der Arbeit wird die Wechselwirkung der Kolloide mit verschiedenen Methoden charakterisiert. Dabei zeigten sich quantitative Übereinstimmungen zwischen den Resultaten aus Zellenmodellrechnungen und aus elektrokinetischen Messungen einerseits und Messungen des Phasenverhaltens und der Elastizität andererseits. Diese nunmehr gut gesicherten Diskrepanzen und Korrelationen bedürfen des theoretischen Verständnisses. Im zweiten Teil der Arbeit wurde das Erstarrungsverhalten kolloidaler Scherschmelzen in den kristallinen Zustand mit (zeitaufgelöster) statischer Lichtstreuung und mikroskopischen Methoden untersucht. Dies erlaubte zunächst die kritische Überprüfung klassischer Modelle zur Kristallisationskinetik (Wilson- Frenkel- Gesetz, klassische Nukleationstheorie, Kolmogorov- Johnson- Mehl- Avrami (KJMA)- Modell). Es zeigte sich, dass diese Modelle gut geeignet sind die Verfestigung auch geladener kolloidaler Schmelzen zu beschreiben, wenn die diffusive Einteilchendynamik korrekt berücksichtigt wird. Erstmals wurden Oberflächenspannungen zwischen Kristallkeim und Schmelze für geladene Systeme bestimmt, die im Gegensatz zu Hartkugel- Systemen eine lineare Zunahme mit der Partikelkonzentration aufweisen. Der Methodenpark und die Auswerteverfahren wurden sodann auf binäre kolloidale Mischungen übertragen. Entsprechend den Einzelkomponenten kristallisieren alle Mischungen in einer kubischen Struktur. Leitfähigkeitsmessungen und Elastizität stehen meist im Einklang mit der Nukleation zufallsgeordneter Substitutionskristalle. Für mehrere Proben mit unterschiedlichen Größenverhältnissen wurde mit statischer Lichtstreuung der Einfluss der Komposition und der Partikelkonzentration auf das Nukleationsverhalten untersucht. Im Allgemeinen wurde das Nukleationsszenario einkomponentiger Systeme mit einigen unerwarteten, quantitativen Unterschieden reproduziert. Für eine Probe, die eine Kompositionsordnung andeutet, wurden interessante Korrelationen zwischen der Nukleationskinetik und den Eigenschaften des resultierenden Festkörpers gefunden.

Comparison between analytical and numerical methods for the assessment of masonry arch bridges: Case study of Clemente Bridge on Savio river

This research has focused on the study of the behavior and of the collapse of masonry arch bridges. The latest decades have seen an increasing interest in this structural type, that is still present and in use, despite the passage of time and the variation of the transport means. Several strategies have been developed during the time to simulate the response of this type of structures, although even today there is no generally accepted standard one for assessment of masonry arch bridges. The aim of this thesis is to compare the principal analytical and numerical methods existing in literature on case studies, trying to highlight values and weaknesses. The methods taken in exam are mainly three: i) the Thrust Line Analysis Method; ii) the Mechanism Method; iii) the Finite Element Methods. The Thrust Line Analysis Method and the Mechanism Method are analytical methods and derived from two of the fundamental theorems of the Plastic Analysis, while the Finite Element Method is a numerical method, that uses different strategies of discretization to analyze the structure. Every method is applied to the case study through computer-based representations, that allow a friendly-use application of the principles explained. A particular closed-form approach based on an elasto-plastic material model and developed by some Belgian researchers is also studied. To compare the three methods, two different case study have been analyzed: i) a generic masonry arch bridge with a single span; ii) a real masonry arch bridge, the Clemente Bridge, built on Savio River in Cesena. In the analyses performed, all the models are two-dimensional in order to have results comparable between the different methods taken in exam. The different methods have been compared with each other in terms of collapse load and of hinge positions.

Landscape ecology and genetics of the wolf in Italy

This PhD Thesis includes five main parts on diverse topics. The first two parts deal with the trophic ecology of wolves in Italy consequently to a recent increase of wild ungulates abundance. Data on wolf diet across time highlighted how wild ungulates are important food resource for wolves in Italy. Increasing wolf population, increasing numbers of wild ungulates and decreasing livestock consume are mitigating wolf-man conflicts in Italy in the near future. In the third part, non-invasive genetic sampling techniques were used to obtain genotypes and genders of about 400 wolves. Thus, wolf packs were genetically reconstructed using diverse population genetic and parentage software. Combining the results on pack structure and genetic relatedness with sampling locations, home ranges of wolf packs and dispersal patterns were identified. These results, particularly important for the conservation management of wolves in Italy, illustrated detailed information that can be retrieved from genetic identification of individuals. In the fourth part, wolf locations were combined with environmental information obtained as GIS-layers. Modern species distribution models (niche models) were applied to infer potential wolf distribution and predation risk. From the resulting distribution maps, information pastures with the highest risk of depredation were derived. This is particularly relevant as it allows identifying those areas under danger of carnivore attack on livestock. Finally, in the fifth part, habitat suitability models were combined with landscape genetic analysis. On one side landscape genetic analyses on the Italian wolves provided new information on the dynamics and connectivity of the population and, on the other side, a profound analysis of the effects that habitat suitability methods had on the parameterization of landscape genetic analyses was carried out to contributed significantly to landscape genetic theory.

High sensitivity analysis of BRAF mutations in neoplastic and non-neoplastic thyroid lesions

The clonal distribution of BRAFV600E in papillary thyroid carcinoma (PTC) has been recently debated. No information is currently available about precursor lesions of PTCs. My first aim was to establish whether the BRAFV600E mutation occurs as a subclonal event in PTCs. My second aim was to screen BRAF mutations in histologically benign tissue of cases with BRAFV600E or BRAFwt PTCs in order to identify putative precursor lesions of PTCs. Highly sensitive semi-quantitative methods were used: Allele Specific LNA quantitative PCR (ASLNAqPCR) and 454 Next-Generation Sequencing (NGS). For the first aim 155 consecutive formalin-fixed and paraffin-embedded (FFPE) specimens of PTCs were analyzed. The percentage of mutated cells obtained was normalized to the estimated number of neoplastic cells. Three groups of tumors were identified: a first had a percentage of BRAF mutated neoplastic cells > 80%; a second group showed a number of BRAF mutated neoplastic cells < 30%; a third group had a distribution of BRAFV600E between 30-80%. The large presence of BRAFV600E mutated neoplastic cell sub-populations suggests that BRAFV600E may be acquired early during tumorigenesis: therefore, BRAFV600E can be heterogeneously distributed in PTC. For the second aim, two groups were studied: one consisted of 20 cases with BRAFV600E mutated PTC, the other of 9 BRAFwt PTCs. Seventy-five and 23 histologically benign FFPE thyroid specimens were analyzed from the BRAFV600E mutated and BRAFwt PTC groups, respectively. The screening of BRAF mutations identified BRAFV600E in “atypical” cell foci from both groups of patients. “Unusual” BRAF substitutions were observed in histologically benign thyroid associated with BRAFV600E PTCs. These mutations were very uncommon in the group with BRAFwt PTCs and in BRAFV600E PTCs. Therefore, lesions carrying BRAF mutations may represent “abortive” attempts at cancer development: only BRAFV600E boosts neoplastic transformation to PTC. BRAFV600E mutated “atypical foci” may represent precursor lesions of BRAFV600E mutated PTCs.

Boron determination in biological samples - Intercomparison of three analytical methods to assist development of a treatment protocol for neoplastic diseases of the liver with Boron Neutron Capture Therapy

Die Bor-Neuroneneinfang-Therapie (engl.: Boron Neutron Capture Therapy, BNCT) ist eine indirekte Strahlentherapie, welche durch die gezielte Freisetzung von dicht ionisierender Strahlung Tumorzellen zerstört. Die freigesetzten Ionen sind Spaltfragmente einer Kernreaktion, bei welcher das Isotop 10B ein niederenergetisches (thermisches) Neutron einfängt. Das 10B wird durch ein spezielles Borpräparat in den Tumorzellen angereichert, welches selbst nicht radioaktiv ist. rnAn der Johannes Gutenberg-Universität Mainz wurde die Forschung für die Anwendung eines klinischen Behandlungsprotokolls durch zwei Heilversuche bei Patienten mit kolorektalen Lebermetastasen an der Universität Pavia, Italien, angeregt, bei denen die Leber außerhalb des Körpers in einem Forschungsreaktor bestrahlt wurde. Als erster Schritt wurde in Kooperation verschiedener universitärer Institute eine klinische Studie zur Bestimmung klinisch relevanter Parameter wie der Borverteilung in verschiedenen Geweben und dem pharmakokinetischen Aufnahmeverhalten des Borpräparates initiiert.rnDie Borkonzentration in den Gewebeproben wurde hinsichtlich ihrer räumlichen Verteilung in verschiedenen Zellarealen bestimmt, um mehr über das Aufnahmeverhalten der Zellen für das BPA im Hinblick auf ihre biologischen Charakteristika zu erfahren. Die Borbestimung wurde per Quantitative Neutron Capture Radiography, Prompt Gamma Activation Analysis und Inductively Coupled Plasma Mass Spectroscopy parallel zur histologischen Analyse des Gewebes durchgeführt. Es war möglich zu zeigen, dass in Proben aus Tumorgewebe und aus tumorfreiem Gewebe mit unterschiedlichen morphologischen Eigenschaften eine sehr heterogene Borverteilung vorliegt. Die Ergebnisse der Blutproben werden für die Erstellung eines pharmakokinetischen Modells verwendet und sind in Übereinstimmung mit existierenden pharmakokinetische Modellen. Zusätzlich wurden die Methoden zur Borbestimmung über speziell hergestellte Referenzstandards untereinander verglichen. Dabei wurde eine gute Übereinstimmung der Ergebnisse festgestellt, ferner wurde für alle biologischen Proben Standardanalyseprotokolle erstellt.rnDie bisher erhaltenen Ergebnisse der klinischen Studie sind vielversprechend, lassen aber noch keine endgültigen Schlussfolgerungen hinsichtlich der Wirksamkeit von BNCT für maligne Lebererkrankungen zu. rn

Die Debatte über die Ziele des Vierten Kreuzzugs : ein Beitrag zur Lösung geschichtswissenschaftlich umstrittener Fragen mit Hilfe sozialwissenschaftlicher Instrumente

Der Rational-Choice-Ansatz (RCA) hat in den letzten Jahrzehnten eine weite Ver-rnbreitung in vielen sozialwissenschaftlichen Disziplinen erfahren. Insbesondere in den letzten zwei Jahrzehnten gab es wiederholte Bemühungen, den RCA auchrnauf geschichtswissenschaftliche Fragestellungen und Themen anzuwenden. Ein interssanter Ansatz dafür ist eine integrative Methodik, die unter der Bezeichnung „Analytic Narrative“ bekannt wurde. Damit wird versucht, die klassische narrative Form der Erklärung historischer Phänomene mit spieltheoretischen Modellierungen zu verbinden. Inspiriert durch diesen Ansatz geht die vorliegende Untersuchung der Frage nach, in welcher Form und unter welchen Umständen der RCA als analytische Grundlage für historische Themenfelder und Fragestellungen geeignet sein mag. Dies wird nicht nur theoretisch, sondern an einem historischen Beispiel untersucht. Konkreter Betrachtungsgegenstand der Arbeit ist der Vierte Kreuzzug. Vor über 800 Jahren endete dieser mit der Eroberung und Plünderung Konstantinopels sowie der Zerschlagung des Byzantinischen Reichs. Seit mehr als 150 Jahren streiten Historiker über die Ursachen für diese Ereignisse. Die theoretischenrnGrundpositionen, die innerhalb dieser Debatte durch einzelne Historiker einge-rnnommen wurden, dienen als Ausgangspunkt für die hier verfolgte Untersuchung.rnEs wird gezeigt, dass die Daten, die uns über den Vierten Kreuzzug vorliegen,rndie Möglichkeit eröffnen, verschiedene auf dem RCA basierende Analyseverfah-rnren zur Anwendung zu bringen. Das zentrale Ziel der Analyse besteht darin, ausrnden vorhandenen Quellen neue Einsichten in die strategischen Handlungsoptionen der für den Verlauf des Kreuzzugs relevanten Akteure zu generieren undrnüberdies ein Höchstmaß an Überprüfbarkeit zu gewährleisten.

Gamification

Nowadays games are so popular that they have become an important part of our lives. Inspired by the motivational properties of games, some scholars made the proposal of applying game mechanics and elements into other fields thus emerged the concept of “Gamification”, along with various other popular concepts for the realization of the application. The effectiveness of gamification in improving user engagement and changing behaviors is demonstrated not only in theory but also in practice. This thesis aims to introduce the related concepts of gamification and the gamification design framework. In addition, this thesis introduces also the concept of MOOCs and the challenges faced by MOOCs platforms. Some of those challenges such as high dropout rate and low participation rate could be solved by gamification. Through creating a more interesting game experience and consequently fostering user motivation, high engagement will be ensured. Following this logic, this thesis explores how to use gamification on MOOCs platform to improve user engagement and the corresponding impacts. Despite of the lack of a quantitative analysis of the effects of gamification on MOOCs platform, the facts found and observed in this thesis support the effectiveness of gamification in improving user engagement on MOOCs platforms.

Bundling Strategies When Products Are Vertically Differentiated and Capacities Are Limited

We consider a seller who owns two capacity-constrained resources and markets two products (components) corresponding to these resources as well as a bundle comprising the two components. In an environment where all customers agree that one of the two components is of higher quality than the other and that the bundle is of the highest quality, we derive the seller's optimal bundling strategy. We demonstrate that the optimal solution depends on the absolute and relative availabilities of the two resources as well as upon the extent of subadditivity of the quality of the products. The possible strategies that can arise as equilibrium behavior include a pure components strategy, a partial- or full-spectrum mixed bundling strategy, and a pure bundling strategy, where the latter strategy is optimal when capacities are unconstrained. These conclusions are contrary to findings in the prior literature on bundling that demonstrated the unambiguous dominance of the full-spectrum mixed bundling strategy. Thus, our work expands the frontier of bundling to an environment with vertically differentiated components and limited resources. We also explore how the bundling strategies change as we introduce an element of horizontal differentiation wherein different types of customers value the available components differently.

Some Investigations on Quantitative Measurement of Amalgamation

Amalgamation is a process in which precious metals are collected by mercury. The exact way in which the mercury holds the other metals is not positively known. It is proba­ble that a series of intermetallic compounds form. Very little work has been done so far on the theory of amalgama­tion.

Oil and Gas Production Methods in Montana

Montana's oil and gas industries aggregate a gross income of over 12,000,000 annually to the state. Oil and gas fields have been thoroughly discussed in liter­ature as to geology, location, production and future possibilities. The specific object of this report has been to compile a comprehensive study of the production methods as they occur.

The Theory of Alloy Deposition and The Effect of a Rotating Cathode Upon Such Deposition, with Special Attention to the Possibility of Depositing Sterling Silver

In the past few years a great deal of atten­tion has been given to the electrodeposition of alloys. For the main part, this investigation has been of scien­tific interest only; but in a few instances, such work has attained commercial importance.