Kryoelektronenmikroskopie von Proteinen: 3D-Struktur (12 A) des Hämocyanins der Schnecke Haliotis

Zusammenfassung:Die Quartärstruktur des respiratorischen Proteins Hämocyanin (Isoform HtH1) aus der marinen Schnecke Haliotis tuberculata wurde vermittels Kryoelektronen-mikroskopie und 3D-Rekonstruktion untersucht. Das Molekül ist zylinderförmig, hat einen Durchmesser von ca. 35 nm und besteht aus einer Zylinderwand und einem internen Kragenkomplex. Dieser wiederum besteht aus einem Collar und einem Arc.Die kryoelektronenmikroskopischen Aufnahmen von in glasartigem Eis fixierten HtH1-Molekülen brachte eine enorme Verbesserung der Anzahl der zur Verfügung stehenden Ansichtswinkel gegenüber den negativkontrastierten Molekülen, die auf Karbonfilm präpariert waren.Die 3D-Rekonstruktion des HtH1 mittels Aufnahmen bei drei verschiedenen Defo-kuswerten verbesserte die Auflösung noch einmal deutlich gegenüber den Rekon-struktionen, die aus Aufnahmen bei einem festen Defokuswert gemacht wurden, und zwar auf 12 Å. Das Molekül besitzt eine D5-Symmetrie.Aus dieser bisher genausten Rekonstruktion eines Molluskenhämocyanins aus EM-Bildern ließen sich folgende neue Strukturdetails ableiten:· Ein Untereinheitendimer konnte als Repeating Unit im Dekamer des HtH1 beschrieben werden.· Das Untereinheitendimer konnte aus der 3D-Dichtekarte isoliert werden. Es be-steht eindeutig aus 16 Massen, die funktionellen Domänen entsprechen. Zwei dieser Massen bilden den Collar, zwei den Arc und 12 das Wandsegment.· Die gegenläufige Anordnung der beiden Untereinheiten innerhalb dieses Unte-reinheitendimers konnten bestätigt und auf zwei Möglichkeiten eingeschränkt werden.· Die Zahl der alternativen Anordnungen der 16 funktionellen Domänen (HtH1-a bis HtH1-h) im Untereinheitendimer konnten von 80 auf 2 eingeengt werden.· Es konnte über molekulares Modellieren mithilfe einer publizierten Kristallstruk-tur eine 3D-Struktur fastatomarer Auflösung der funktionellen Domäne HtH1-g berechnet werden.· Die funktionelle Domäne HtH1-g konnte als Domänenpaar plausibel in die 3D?Dichtekarte des Untereinheitendimers eingepasst werden, und zwar in die beiden Massen des Arc.Aus der elektronenmikroskopisch gewonnenen Dichtekarte wurde mit Hilfe des

Slope stability analysis by multi-temporal DEMs and 3D modelling: The 2002 and 2007 Stromboli landslide events

Natural hazard related to the volcanic activity represents a potential risk factor, particularly in the vicinity of human settlements. Besides to the risk related to the explosive and effusive activity, the instability of volcanic edifices may develop into large landslides often catastrophically destructive, as shown by the collapse of the northern flank of Mount St. Helens in 1980. A combined approach was applied to analyse slope failures that occurred at Stromboli volcano. SdF slope stability was evaluated by using high-resolution multi-temporal DTMMs and performing limit equilibrium stability analyses. High-resolution topographical data collected with remote sensing techniques and three-dimensional slope stability analysis play a key role in understanding instability mechanism and the related risks. Analyses carried out on the 2002–2003 and 2007 Stromboli eruptions, starting from high-resolution data acquired through airborne remote sensing surveys, permitted the estimation of the lava volumes emplaced on the SdF slope and contributed to the investigation of the link between magma emission and slope instabilities. Limit Equilibrium analyses were performed on the 2001 and 2007 3D models, in order to simulate the slope behavior before 2002-2003 landslide event and after the 2007 eruption. Stability analyses were conducted to understand the mechanisms that controlled the slope deformations which occurred shortly after the 2007 eruption onset, involving the upper part of slope. Limit equilibrium analyses applied to both cases yielded results which are congruent with observations and monitoring data. The results presented in this work undoubtedly indicate that hazard assessment for the island of Stromboli should take into account the fact that a new magma intrusion could lead to further destabilisation of the slope, which may be more significant than the one recently observed because it will affect an already disarranged deposit and fractured and loosened crater area. The two-pronged approach based on the analysis of 3D multi-temporal mapping datasets and on the application of LE methods contributed to better understanding volcano flank behaviour and to be prepared to undertake actions aimed at risk mitigation.

OGRE: analisi di un motore grafico 3D

In questa tesi descriveremo e analizzeremo il motore grafico OGRE, acronimo di Object-Oriented Graphics Rendering Engine. La scelta di analizzare proprio questo motore grafico è legata a diverse considerazioni. Innanzitutto, OGRE è rilasciato con licenza open source e quindi rende disponibile il suo codice sorgente. Questo è molto importante, in un contesto di studio e sperimentazione come quello universitario, perché permette di comprendere e analizzare anche il funzionamento interno del motore grafico. Inoltre, OGRE è un progetto maturo e stabile con una vasta comunità di sviluppatori e utilizzatori alle spalle. Esiste molta documentazione a riguardo, tra wiki, libri e manuali, e un forum molto attivo per la richiesta di aiuto e consigli. A conferma, sia della bontà del progetto che delle ottime prestazioni del motore grafico, basta dire che OGRE è utilizzato anche da applicazioni commerciali, come videogame, editor 3D e simulatori. Infine, la caratteristica che contraddistingue OGRE da tutti gli altri motori grafici è il fatto di essere "solamente" un motore di rendering puro. Ciò significa che qualsiasi funzionalità non direttamente legata al rendering, come ad esempio la gestione degli input dell'utente, non è supportata da OGRE. Anche se questo può sembrare un difetto, in realtà ciò permetterà di concentrarci solamente sugli aspetti legati al rendering che, in un motore grafico, costituiscono la parte fondamentale.

Realisierung einer 3D-Kreuzkorrelationsanlage zur Untersuchung von Struktur und Dynamik hochkonzentrierter Kolloide

Realisierung einer 3D-Kreuzkorrelationsanlage zur Untersuchung von Struktur und Dynamik hochkonzentrierter Kolloide Im Rahmen dieser Arbeit wird eine neuartige 3D-Kreuzkorrelationsanlage zur mehrfachstreufreien Untersuchung des diffusiven Verhaltens hochkonzentrierter kolloidaler Suspensionen vorgestellt. Hierzu werden zwei Lichtstreuexperimente gleichzeitig am gleichen Streuvolumen und mit dem gleichen Streuvektor durchgeführt. Aus der so gewonnenen Kreuzkorrelationsfunktion kann das dynamische Verhalten der Kolloide bestimmt werden. Für die Diffusion der Partikel spielen neben der direkten Wechselwirkung elektroviskoser Effekt und die hydrodynamische Wechselwirkung eine entscheidende Rolle. Insbesondere bei hohen Konzentrationen kann keiner der drei Effekte vernachlässigt werden. Die zu messenden Unterschiede in den Diffusionskoeffizienten sind sehr klein. Daher wurde der experimentelle Aufbau detailliert charakterisiert. Hierbei konnten theoretische Überlegungen hinsichtlich des Nachpulsens und der Totzeit der verwendeten Si-Avalanche-Photodioden überprüft werden. Der Kurzzeitselbstdiffusionskoeffizient hochkonzentrierter geladener kolloidaler Suspensionen wurde gemessen. Um die Daten bei hohen Konzentrationen korrekt zu normieren, wurde der elektroviskose Effekt bei geringen Konzentrationen ausführlich untersucht. Hierbei zeigte sich, dass der elektroviskose Einzelteilcheneffekt zu einer monotonen Abnahme des Diffusionskoeffizienten bei abnehmender Ionenstärke führt. Anhand der volumenbruchabhängigen Daten des Kurzzeitselbstdiffusionskoeffizienten konnte zum ersten Mal gezeigt werden, dass die hydrodynamische Wechselwirkung einen geringeren Einfluss auf die Diffusion hat, falls das direkte Wechselwirkungspotential ein Coulomb-Potential anstelle eines Harte-Kugel-Potentials ist.

Darstellung der Grenze zwischen dem rechten und linken Leberlappen mit 3D-Rekonstruktionen von Spiral-Computertomographien

Zusammenfassung:Hintergrund/Ziel: Die Beschreibung der funktionellen Einteilung der Leber basiert auf dem Schema von Claude de Couinaud. Die Grenze zwischen der rechten und linken Leberhälfte scheint leicht durch die Lage der mittleren Lebervene lokalisierbar. Nach der gängigen Meinung wird diese Grenze nicht durch die Trias aus Pfortader, Arterie und Gallengang überschritten. Es soll untersucht werden, ob die Lage dieser gefäßarmen Zone zwischen den Pfortaderästen benachbarter Segmente von der Lage der Grenzebene durch die mittlere Lebervene abweicht.Methode: Bei 73 Patienten wurden im Rahmen der normalen präoperativen Diagnostik dreiphasige Spiral-CT Untersuchungen durchgeführt. Aus diesen Daten wurden dreidimensionale Rekonstruktionen erzeugt und ausgewertet. Ergebnisse: In der vorliegenden Untersuchung konnte gezeigt werden, dass die mittlere Sektorengrenze unterschiedliche Positionen einnimmt, je nach welchem Gefäßsystem sie bestimmt wird. Die mittlere Sektorengrenze zeigt hierbei einen Unterschied in ihrer Lage von 14,2° im Median. An der ventralen Leberoberfläche liegt die Grenzebene nach der mittleren Lebervene damit rechts lateral der gefäßarmen Zone zwischen den Pfortaderästen.Schlussfolgerung: Der Unterschied der Grenzebenen ist in dreidimensionalen Rekonstruktionen demonstrierbar und findet Anwendung bei der Segmentzuordnung von Läsionen. Diese Rekonstruktionen erleichtern die interdisziplinäre Kommunikation und erlauben eine vereinfachte und möglicherweise präzisere Operationsplanung.

Magnetic properties of selected 3d- and 4f-systems on alpha-Al 2 O 3 substrates

In this work the growth and the magnetic properties of the transition metals molybdenum, niobium, and iron and of the highly-magnetostrictive C15 Laves phases of the RFe2 compounds (R: Rare earth metals: here Tb, Dy, and Tb{0.3}Dy{0.7} deposited on alpha-Al2O3 (sapphire) substrates are analyzed. Next to (11-20) (a-plane) oriented sapphire substrates mainly (10-10) (m-plane) oriented substrates were used. These show a pronounced facetting after high temperature annealing in air. Atomic force microscopy (AFM) measurements reveal a dependence of the height, width, and angle of the facets with the annealing temperature. The observed deviations of the facet angles with respect to the theoretical values of the sapphire (10-1-2) and (10-11) surfaces are explained by cross section high resolution transmission electron microscopy (HR-TEM) measurements. These show the plain formation of the (10-11) surface while the second, energy reduced (10-1-2) facet has a curved shape given by atomic steps of (10-1-2) layers and is formed completely solely at the facet ridges and valleys. Thin films of Mo and Nb, respectively, deposited by means of molecular beam epitaxy (MBE) reveal a non-twinned, (211)-oriented epitaxial growth as well on non-faceted as on faceted sapphire m-plane, as was shown by X-Ray and TEM evaluations. In the case of faceted sapphire the two bcc crystals overgrow the facets homogeneously. Here, the bcc (111) surface is nearly parallel to the sapphire (10-11) facet and the Mo/Nb (100) surface is nearly parallel to the sapphire (10-1-2) surface. (211)-oriented Nb templates on sapphire m-plane can be used for the non-twinned, (211)-oriented growth of RFe2 films by means of MBE. Again, the quality of the RFe2 films grown on faceted sapphire is almost equal to films on the non-faceted substrate. For comparison thin RFe2 films of the established (110) and (111) orientation were prepared. Magnetic and magnetoelastic measurements performed in a self designed setup reveal a high quality of the samples. No difference between samples with undulated and flat morphology can be observed. In addition to the preparation of covering, undulating thin films on faceted sapphire m-plane nanoscopic structures of Nb and Fe were prepared by shallow incidence MBE. The formation of the nanostructures can be explained by a shadowing of the atomic beam due to the facets in addition to de-wetting effects of the metals on the heated sapphire surface. Accordingly, the nanostructures form at the facet ridges and overgrow them. The morphology of the structures can be varied by deposition conditions as was shown for Fe. The shape of the structures vary from pearl-necklet strung spherical nanodots with a diameter of a few 10 nm to oval nanodots of a few 100 nm length to continuous nanowires. Magnetization measurements reveal uniaxial magnetic anisotropy with the easy axis of magnetization parallel to the facet ridges. The shape of the hysteresis is depending on the morphology of the structures. The magnetization reversal processes of the spherical and oval nanodots were simulated by micromagnetic modelling and can be explained by the formation of magnetic vortices.

Riconoscimento di gesti: estensione a più punti del corpo e ad attori multipli

Negli ultimi anni si è assistito ad una radicale rivoluzione nell’ambito dei dispositivi di interazione uomo-macchina. Da dispositivi tradizionali come il mouse o la tastiera si è passati allo sviluppo di nuovi sistemi capaci di riconoscere i movimenti compiuti dall’utente (interfacce basate sulla visione o sull’uso di accelerometri) o rilevare il contatto (interfacce di tipo touch). Questi sistemi sono nati con lo scopo di fornire maggiore naturalezza alla comunicazione uomo-macchina. Le nuove interfacce sono molto più espressive di quelle tradizionali poiché sfruttano le capacità di comunicazione naturali degli utenti, su tutte il linguaggio gestuale. Essere in grado di riconoscere gli esseri umani, in termini delle azioni che stanno svolgendo o delle posture che stanno assumendo, apre le porte a una serie vastissima di interessanti applicazioni. Ad oggi sistemi di riconoscimento delle parti del corpo umano e dei gesti sono ampiamente utilizzati in diversi ambiti, come l’interpretazione del linguaggio dei segni, in robotica per l’assistenza sociale, per indica- re direzioni attraverso il puntamento, nel riconoscimento di gesti facciali [1], interfacce naturali per computer (valida alternativa a mouse e tastiera), ampliare e rendere unica l’esperienza dei videogiochi (ad esempio Microsoft 1 Introduzione Kinect© e Nintendo Wii©), nell’affective computing1 . Mostre pubbliche e musei non fanno eccezione, assumendo un ruolo cen- trale nel coadiuvare una tecnologia prettamente volta all’intrattenimento con la cultura (e l’istruzione). In questo scenario, un sistema HCI deve cercare di coinvolgere un pubblico molto eterogeneo, composto, anche, da chi non ha a che fare ogni giorno con interfacce di questo tipo (o semplicemente con un computer), ma curioso e desideroso di beneficiare del sistema. Inoltre, si deve tenere conto che un ambiente museale presenta dei requisiti e alcune caratteristiche distintive che non possono essere ignorati. La tecnologia immersa in un contesto tale deve rispettare determinati vincoli, come: - non può essere invasiva; - deve essere coinvolgente, senza mettere in secondo piano gli artefatti; - deve essere flessibile; - richiedere il minor uso (o meglio, la totale assenza) di dispositivi hardware. In questa tesi, considerando le premesse sopracitate, si presenta una sistema che può essere utilizzato efficacemente in un contesto museale, o in un ambiente che richieda soluzioni non invasive. Il metodo proposto, utilizzando solo una webcam e nessun altro dispositivo personalizzato o specifico, permette di implementare i servizi di: (a) rilevamento e (b) monitoraggio dei visitatori, (c) riconoscimento delle azioni.

Individuazione di punti salienti in dati 3D mediante rappresentazioni strutturate

Questa tesi si inserisce nel filone di ricerca dell'elaborazione di dati 3D, e in particolare nella 3D Object Recognition, e delinea in primo luogo una panoramica sulle principali rappresentazioni strutturate di dati 3D, le quali rappresentano una prerogativa necessaria per implementare in modo efficiente algoritmi di processing di dati 3D, per poi presentare un nuovo algoritmo di 3D Keypoint Detection che è stato sviluppato e proposto dal Computer Vision Laboratory dell'Università di Bologna presso il quale ho effettuato la mia attività di tesi.

Methodological improvement of 3D fluoroscopic analysis for the robust quantification of 3D kinematics of human joints

3D video-fluoroscopy is an accurate but cumbersome technique to estimate natural or prosthetic human joint kinematics. This dissertation proposes innovative methodologies to improve the 3D fluoroscopic analysis reliability and usability. Being based on direct radiographic imaging of the joint, and avoiding soft tissue artefact that limits the accuracy of skin marker based techniques, the fluoroscopic analysis has a potential accuracy of the order of mm/deg or better. It can provide fundamental informations for clinical and methodological applications, but, notwithstanding the number of methodological protocols proposed in the literature, time consuming user interaction is exploited to obtain consistent results. The user-dependency prevented a reliable quantification of the actual accuracy and precision of the methods, and, consequently, slowed down the translation to the clinical practice. The objective of the present work was to speed up this process introducing methodological improvements in the analysis. In the thesis, the fluoroscopic analysis was characterized in depth, in order to evaluate its pros and cons, and to provide reliable solutions to overcome its limitations. To this aim, an analytical approach was followed. The major sources of error were isolated with in-silico preliminary studies as: (a) geometric distortion and calibration errors, (b) 2D images and 3D models resolutions, (c) incorrect contour extraction, (d) bone model symmetries, (e) optimization algorithm limitations, (f) user errors. The effect of each criticality was quantified, and verified with an in-vivo preliminary study on the elbow joint. The dominant source of error was identified in the limited extent of the convergence domain for the local optimization algorithms, which forced the user to manually specify the starting pose for the estimating process. To solve this problem, two different approaches were followed: to increase the optimal pose convergence basin, the local approach used sequential alignments of the 6 degrees of freedom in order of sensitivity, or a geometrical feature-based estimation of the initial conditions for the optimization; the global approach used an unsupervised memetic algorithm to optimally explore the search domain. The performances of the technique were evaluated with a series of in-silico studies and validated in-vitro with a phantom based comparison with a radiostereometric gold-standard. The accuracy of the method is joint-dependent, and for the intact knee joint, the new unsupervised algorithm guaranteed a maximum error lower than 0.5 mm for in-plane translations, 10 mm for out-of-plane translation, and of 3 deg for rotations in a mono-planar setup; and lower than 0.5 mm for translations and 1 deg for rotations in a bi-planar setups. The bi-planar setup is best suited when accurate results are needed, such as for methodological research studies. The mono-planar analysis may be enough for clinical application when the analysis time and cost may be an issue. A further reduction of the user interaction was obtained for prosthetic joints kinematics. A mixed region-growing and level-set segmentation method was proposed and halved the analysis time, delegating the computational burden to the machine. In-silico and in-vivo studies demonstrated that the reliability of the new semiautomatic method was comparable to a user defined manual gold-standard. The improved fluoroscopic analysis was finally applied to a first in-vivo methodological study on the foot kinematics. Preliminary evaluations showed that the presented methodology represents a feasible gold-standard for the validation of skin marker based foot kinematics protocols.