Distribution of hepatitis c virus (hcv) genotypes in patients with chronic infection from Rondônia, Brazil

Abstract Background Hepatitis C virus (HCV) is an important human pathogen affecting around 3% of the human population. In Brazil, it is estimated that there are approximately 2 to 3 million HCV chronic carriers. There are few reports of HCV prevalence in Rondônia State (RO), but it was estimated in 9.7% from 1999 to 2005. The aim of this study was to characterize HCV genotypes in 58 chronic HCV infected patients from Porto Velho, Rondônia (RO), Brazil. Methods A fragment of 380 bp of NS5B region was amplified by nested PCR for genotyping analysis. Viral sequences were characterized by phylogenetic analysis using reference sequences obtained from the GenBank (n = 173). Sequences were aligned using Muscle software and edited in the SE-AL software. Phylogenetic analyses were conducted using Bayesian Markov chain Monte Carlo simulation (MCMC) to obtain the MCC tree using BEAST v.1.5.3. Results From 58 anti-HCV positive samples, 22 were positive to the NS5B fragment and successfully sequenced. Genotype 1b was the most prevalent in this population (50%), followed by 1a (27.2%), 2b (13.6%) and 3a (9.0%). Conclusions This study is the first report of HCV genotypes from Rondônia State and subtype 1b was found to be the most prevalent. This subtype is mostly found among people who have a previous history of blood transfusion but more detailed studies with a larger number of patients are necessary to understand the HCV dynamics in the population of Rondônia State, Brazil.

Reliability of buildings in service limit state for maximum horizontal displacements

Brazilian design code ABNT NBR6118:2003 - Design of Concrete Structures - Procedures - [1] proposes the use of simplified models for the consideration of non-linear material behavior in the evaluation of horizontal displacements in buildings. These models penalize stiffness of columns and beams, representing the effects of concrete cracking and avoiding costly physical non-linear analyses. The objectives of the present paper are to investigate the accuracy and uncertainty of these simplified models, as well as to evaluate the reliabilities of structures designed following ABNT NBR6118:2003[1&] in the service limit state for horizontal displacements. Model error statistics are obtained from 42 representative plane frames. The reliabilities of three typical (4, 8 and 12 floor) buildings are evaluated, using the simplified models and a rigorous, physical and geometrical non-linear analysis. Results show that the 70/70 (column/beam stiffness reduction) model is more accurate and less conservative than the 80/40 model. Results also show that ABNT NBR6118:2003 [1] design criteria for horizontal displacement limit states (masonry damage according to ACI 435.3R-68(1984) [10]) are conservative, and result in reliability indexes which are larger than those recommended in EUROCODE [2] for irreversible service limit states.

Shear force and torsion in reinforced concrete beam elements: theoretical analysis based on Brazilian Standard Code ABNT NBR 6118:2007

Reinforced concrete beam elements are submitted to applicable loads along their life cycle that cause shear and torsion. These elements may be subject to only shear, pure torsion or both, torsion and shear combined. The Brazilian Standard Code ABNT NBR 6118:2007 [1] fixes conditions to calculate the transverse reinforcement area in beam reinforced concrete elements, using two design models, based on the strut and tie analogy model, first studied by Mörsch [2]. The strut angle θ (theta) can be considered constant and equal to 45º (Model I), or varying between 30º and 45º (Model II). In the case of transversal ties (stirrups), the variation of angle α (alpha) is between 45º and 90º. When the equilibrium torsion is required, a resistant model based on space truss with hollow section is considered. The space truss admits an inclination angle θ between 30º and 45º, in accordance with beam elements subjected to shear. This paper presents a theoretical study of models I and II for combined shear and torsion, in which ranges the geometry and intensity of action in reinforced concrete beams, aimed to verify the consumption of transverse reinforcement in accordance with the calculation model adopted As the strut angle on model II ranges from 30º to 45º, transverse reinforcement area (Asw) decreases, and total reinforcement area, which includes longitudinal torsion reinforcement (Asℓ), increases. It appears that, when considering model II with strut angle above 40º, under shear only, transverse reinforcement area increases 22% compared to values obtained using model I.

A theoretical study of the characterization and the absorption spectrum of Mg: Tetracycline complexes in aqueous environment.

The complex formed by the tetracycline (TC) molecule with the Mg ion is able to prevent the replication of the genetic material in the bacterial ribosome, making an excellent antibiotic. In general, the absorption and emission spectra of TC are very sensitive to the host ions and the pH of the solvent that the set is immersed. However, the theoretical absorption spectrum available in the literature is scarce and limited to simple models that do not consider the fluctuations of the liquid. Our aim is to obtain the electronic absorption spectrum of TC and the complex Mg:TC in the ratio 1:1 and 2:1. Moreover, we analyze the changes in intensity and shifts of the bands in the systems listed. We performed the simulation using the classical Monte Carlo technique with the Lennard-Jones plus Coulomb potential applied to each atom of the both TC molecule and the Mg:TC complexes in water. The electronic absorption spectrum was obtained from the time-dependent density functional theory using different solvent models. In general, we obtained a good qualitative description of the spectra when compared with the experimental results. The Mg atom shifts the first band by 4 nm in our models, in excellent agreement to the experimental result of 4 nm. The second absorption band is found here to be useful for the characterization of the position where the ion attaches to the TC.

Relationship between body image disturbance and incidence of depression: the SUN prospective cohort

[EN] Background: Body image disturbance is an increasing problem in Western societies and is associated with a number of mental health outcomes including anorexia, bulimia, body dysmorphia, and depression. The aim of this study was to assess the association between body image disturbance and the incidence of depression. Methods: This study included 10,286 participants from a dynamic prospective cohort of Spanish university graduates, who were followed-up for a median period of 4.2 years (Seguimiento Universidad de Navarra – the SUN study). The key characteristic of the study is the permanently open recruitment that started in 1999. The baseline questionnaire included information about body mass index (BMI) and the nine figure schemes that were used to assess body size perception. These variables were grouped according to recommended classifications and the difference between BMI and body size perception was considered as a proxy of body image disturbance. A subject was classified as an incident case of depression if he/she was initially free of depression and reported a physician-made diagnosis of depression and/or the use of antidepressant medication in at least one of the follow-up questionnaires. The association between body image disturbance and the incidence of depression was estimated by calculating the multivariable adjusted Odds Ratio (OR) and its 95% Confidence Interval (95% CI), using logistic regression models. Results: The cumulative incidence of depression during follow-up in the cohort was 4.8%. Men who underestimated their body size had a high percentage of overweight and obesity (50.1% and 12.6%, respectively), whereas women who overestimated their body size had a high percentage of underweight (87.6%). The underestimation exhibited a negative association with the incidence of depression among women (OR: 0.72, 95% CI: 0.54 – 0.95), but this effect disappeared after adjusting for possible confounding variables. The proportion of participants who correctly perceived their body size was high (53.3%) and gross misperception was seldom found, with most cases selecting only one silhouette below (42.7%) or above (2.6%) their actual BMI. Conclusion: We found no association between body image disturbance and subsequent depression in a cohort of university graduates in Spain.

Design and implementation of bioinformatics tools for large scale genome annotation

The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw nucleotide sequences. This is only the first step of the genome annotation process that will deal with the issue of assigning biological information to each sequence. The annotation process is done at each different level of the biological information processing mechanism, from DNA to protein, and cannot be accomplished only by in vitro analysis procedures resulting extremely expensive and time consuming when applied at a this large scale level. Thus, in silico methods need to be used to accomplish the task. The aim of this work was the implementation of predictive computational methods to allow a fast, reliable, and automated annotation of genomes and proteins starting from aminoacidic sequences. The first part of the work was focused on the implementation of a new machine learning based method for the prediction of the subcellular localization of soluble eukaryotic proteins. The method is called BaCelLo, and was developed in 2006. The main peculiarity of the method is to be independent from biases present in the training dataset, which causes the over‐prediction of the most represented examples in all the other available predictors developed so far. This important result was achieved by a modification, made by myself, to the standard Support Vector Machine (SVM) algorithm with the creation of the so called Balanced SVM. BaCelLo is able to predict the most important subcellular localizations in eukaryotic cells and three, kingdom‐specific, predictors were implemented. In two extensive comparisons, carried out in 2006 and 2008, BaCelLo reported to outperform all the currently available state‐of‐the‐art methods for this prediction task. BaCelLo was subsequently used to completely annotate 5 eukaryotic genomes, by integrating it in a pipeline of predictors developed at the Bologna Biocomputing group by Dr. Pier Luigi Martelli and Dr. Piero Fariselli. An online database, called eSLDB, was developed by integrating, for each aminoacidic sequence extracted from the genome, the predicted subcellular localization merged with experimental and similarity‐based annotations. In the second part of the work a new, machine learning based, method was implemented for the prediction of GPI‐anchored proteins. Basically the method is able to efficiently predict from the raw aminoacidic sequence both the presence of the GPI‐anchor (by means of an SVM), and the position in the sequence of the post‐translational modification event, the so called ω‐site (by means of an Hidden Markov Model (HMM)). The method is called GPIPE and reported to greatly enhance the prediction performances of GPI‐anchored proteins over all the previously developed methods. GPIPE was able to predict up to 88% of the experimentally annotated GPI‐anchored proteins by maintaining a rate of false positive prediction as low as 0.1%. GPIPE was used to completely annotate 81 eukaryotic genomes, and more than 15000 putative GPI‐anchored proteins were predicted, 561 of which are found in H. sapiens. In average 1% of a proteome is predicted as GPI‐anchored. A statistical analysis was performed onto the composition of the regions surrounding the ω‐site that allowed the definition of specific aminoacidic abundances in the different considered regions. Furthermore the hypothesis that compositional biases are present among the four major eukaryotic kingdoms, proposed in literature, was tested and rejected. All the developed predictors and databases are freely available at: BaCelLo http://gpcr.biocomp.unibo.it/bacello eSLDB http://gpcr.biocomp.unibo.it/esldb GPIPE http://gpcr.biocomp.unibo.it/gpipe

Population ageing, longevity and migration: an overlapping generations approach

The silent demographic revolution characterizing the main industrialized countries is an unavoidable factor which has major economic, social, cultural and psychological implications. This thesis studies the main consequences of population ageing and the connections with the phenomenon of migration, The theoretical analysis is developed using Overlapping Generations Models (OLG). The thesis is divided in the following four chapters: 1) “A Model for Determining Consumption and Social Assistance Demand in Uncertainty Conditions”, focuses on the relation between demographic impact and social insurance and proposes the institution of a non selfsufficiency fund for the elderly. 2) "Population Ageing, Longevity and Health", analyzes the effects of health investment on intertemporal individual behaviour and capital accumulation. 3) "Population Ageing and the Nursing Flow", studies the consequences of migration in the nursing sector. 4) "Quality of Multiculturalism and Minorities' Assimilation", focuses on the problem of assimilation and integration of minorities.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Informationsgehalt von ERS-1/-2 SAR-Daten zur Erfassung der Arteninventare und des Zustandes landwirtschaftlich genutzter Böden und Vegetation

Auf einer drei Anbauperioden umfassenden Ground Truth Datenbasis wird der Informationsgehalt multitemporaler ERS-1/-2 Synthetic Aperture Radar (SAR) Daten zur Erfassung der Arteninventare und des Zustandes landwirtschaftlich genutzter Böden und Vegetation in Agrarregionen Bayerns evaluiert.Dazu wird ein für Radardaten angepaßtes, multitemporales, auf landwirtschaftlichen Schlägen beruhendes Klassifizierungsverfahren ausgearbeitet, das auf bildstatistischen Parametern der ERS-Zeitreihen beruht. Als überwachte Klassifizierungsverfahren wird vergleichend der Maximum-Likelihood-Klassifikator und ein Neuronales-Backpropagation-Netz eingesetzt. Die auf Radarbildkanälen beruhenden Gesamtgenauigkeiten variieren zwischen 75 und 85%. Darüber hinaus wird gezeigt, daß die interferometrische Kohärenz und die Kombination mit Bildkanälen optischer Sensoren (Landsat-TM, SPOT-PAN und IRS-1C-PAN) zur Verbesserung der Klassifizierung beitragen. Gleichermaßen können die Klassifizierungsergebnisse durch eine vorgeschaltete Grobsegmentierung des Untersuchungsgebietes in naturräumlich homogene Raumeinheiten verbessert werden. Über die Landnutzungsklassifizierung hinaus, werden weitere bio- und bodenphysikalische Parameter aus den SAR-Daten anhand von Regressionsmodellen abgeleitet. Im Mittelpunkt stehen die Paramter oberflächennahen Bodenfeuchte vegetationsfreier/-armer Flächen sowie die Biomasse landwirtschaftlicher Kulturen. Die Ergebnisse zeigen, daß mit ERS-1/-2 SAR-Daten eine Messung der Bodenfeuchte möglich ist, wenn Informationen zur Bodenrauhigkeit vorliegen. Hinsichtlich der biophysikalischen Parameter sind signifikante Zusammenhänge zwischen der Frisch- bzw. Trockenmasse des Vegetationsbestandes verschiedener Getreide und dem Radarsignal nachweisbar. Die Biomasse-Informationen können zur Korrektur von Wachstumsmodellen genutzt werden und dazu beitragen, die Genauigkeit von Ertragsschätzungen zu steigern.

Effetti idrodinamici prodotti dal costume tecnico sul nuotatore

L’introduzione dei costumi tecnici nel nuoto ha portato miglioramenti senza precedenti sulla prestazione. I miglioramenti nella velocità di nuoto sono stati attribuiti dalla letteratura a riduzioni nelle resistenze idrodinamiche sul nuotatore. Tuttavia, gli effetti specifici dovuti all’utilizzo di questo tipo di costume non sono ancora completamente chiariti. Questa tesi aveva l’obiettivo di indagare gli effetti del costume tecnico sul galleggiamento statico, sulla posizione del corpo e sulla resistenza idrodinamica in avanzamento passivo. Nello studio preliminare sono stati misurati la spinta idrostatica, i volumi polmonari dinamici e la circonferenza toracica di 9 nuotatori che indossavano un costume tradizionale o un costume tecnico in gomma sintetica. Indossare il costume tecnico ha determinato una riduzione significativa del galleggiamento statico, e la compressione toracica causata da questo tipo di costume potrebbe avere una relazione con la significativa riduzione dei volumi polmonari misurati quando il nuotatore indossa questo tipo di costume. Un successiva analisi prevedeva il traino passivo di 14 nuotatori che mantenevano la miglior posizione idrodinamica di scivolamento indossando un costume tradizionale, tecnico in tessuto e tecnico in gomma. La posizione del corpo in avanzamento è stata misurata con un’analisi cinematica. La resistenza passiva indossando i costumi tecnici è risultata significativamente minore per entrambi i costumi tecnici rispetto alla prova con costume tradizionale. L’analisi condotta attraverso modelli di regressione lineari ha mostrato che una parte della riduzione della resistenza passiva era legata a proprietà intrinseche dei costumi tecnici. Tuttavia, anche l’area di impatto frontale determinata dall’inclinazione del tronco del soggetto in scivolamento e l’inclinazione degli arti inferiori hanno mostrato una marcata influenza sulla resistenza idrodinamica passiva. Pertanto, la riduzione di resistenza idrodinamica durante lo scivolamento passivo effettuato con costume tecnico da nuoto è attribuibile, oltre all’effetto del materiale di composizione del costume, ad una variazione della posizione del corpo del nuotatore.

Statistical problems related to excitation threshold and reset value of membrane potentials

Die vorliegende Arbeit ist motiviert durch biologische Fragestellungen bezüglich des Verhaltens von Membranpotentialen in Neuronen. Ein vielfach betrachtetes Modell für spikende Neuronen ist das Folgende. Zwischen den Spikes verhält sich das Membranpotential wie ein Diffusionsprozess X der durch die SDGL dX_t= beta(X_t) dt+ sigma(X_t) dB_t gegeben ist, wobei (B_t) eine Standard-Brown'sche Bewegung bezeichnet. Spikes erklärt man wie folgt. Sobald das Potential X eine gewisse Exzitationsschwelle S überschreitet entsteht ein Spike. Danach wird das Potential wieder auf einen bestimmten Wert x_0 zurückgesetzt. In Anwendungen ist es manchmal möglich, einen Diffusionsprozess X zwischen den Spikes zu beobachten und die Koeffizienten der SDGL beta() und sigma() zu schätzen. Dennoch ist es nötig, die Schwellen x_0 und S zu bestimmen um das Modell festzulegen. Eine Möglichkeit, dieses Problem anzugehen, ist x_0 und S als Parameter eines statistischen Modells aufzufassen und diese zu schätzen. In der vorliegenden Arbeit werden vier verschiedene Fälle diskutiert, in denen wir jeweils annehmen, dass das Membranpotential X zwischen den Spikes eine Brown'sche Bewegung mit Drift, eine geometrische Brown'sche Bewegung, ein Ornstein-Uhlenbeck Prozess oder ein Cox-Ingersoll-Ross Prozess ist. Darüber hinaus beobachten wir die Zeiten zwischen aufeinander folgenden Spikes, die wir als iid Treffzeiten der Schwelle S von X gestartet in x_0 auffassen. Die ersten beiden Fälle ähneln sich sehr und man kann jeweils den Maximum-Likelihood-Schätzer explizit angeben. Darüber hinaus wird, unter Verwendung der LAN-Theorie, die Optimalität dieser Schätzer gezeigt. In den Fällen OU- und CIR-Prozess wählen wir eine Minimum-Distanz-Methode, die auf dem Vergleich von empirischer und wahrer Laplace-Transformation bezüglich einer Hilbertraumnorm beruht. Wir werden beweisen, dass alle Schätzer stark konsistent und asymptotisch normalverteilt sind. Im letzten Kapitel werden wir die Effizienz der Minimum-Distanz-Schätzer anhand simulierter Daten überprüfen. Ferner, werden Anwendungen auf reale Datensätze und deren Resultate ausführlich diskutiert.

Implications of regional fault distribution and kinematics for the uplift of rift flanks around the Rwenzori Mountains, Southwestern Uganda

Das Ziel dieser Arbeit bestand in der Untersuchung der Störungsverteilung und der Störungskinematik im Zusammenhang mit der Hebung der Riftschultern des Rwenzori Gebirges.rnDas Rwenzori Gebirge befindet sich im NNE-SSWbis N-S verlaufenden Albertine Rift, des nördlichsten Segments des westlichen Armes des Ostafrikanischen Grabensystems. Das Albertine Rift besteht aus Becken unterschiedlicher Höhe, die den Lake Albert, Lake Edward, Lake George und Lake Kivu enthalten. Der Rwenzori horst trennt die Becken des Lake Albert und des Lake Edward. Es erstreckt sich 120km in N-S Richtung, sowie 40-50km in E-W Richtung, der h¨ochste Punkt befindet sich 5111 ü. NN. Diese Studie untersucht einen Abschnitt des Rifts zwischen etwa 1°N und 0°30'S Breite sowie 29°30' und 30°30' östlicher Länge ersteckt. Auch die Feldarbeit konzentrierte sich auf dieses Gebiet.rnrnHauptzweck dieser Studie bestand darin, die folgende These auf ihre Richtigkeit zu überprüfen: ’Wenn es im Verlauf der Zeit tatsächlich zu wesentlichen Änderungen in der Störungskinematik kam, dann ist die starke Hebung der Riftflanken im Bereich der Rwenzoris nicht einfach durch Bewegung entlang der Graben-Hauptst¨orungen zu erklären. Vielmehr ist sie ein Resultat des Zusammenspiels mehrerer tektonische Prozesse, die das Spannungsfeld beeinflussen und dadurch Änderungen in der Kinematik hervorrufen.’ Dadurch konzentrierte sich die Studie in erster Linie auf die Störungsanalyse.rnrnDie Kenntnis regionaler Änderungen der Extensionsrichtung ist entscheidend für das Verständnis komplexer Riftsysteme wie dem Ostafrikanischen Graben. Daher bestand der Kern der Untersuchung in der Kartierung von Störungen und der Untersuchung der Störungskinematik. Die Aufnahme strukturgeologischer Daten konzentrierte sich auf die Ugandische Seite des Rifts, und Pal¨aospannungen wurden mit Hilfe von St¨orungsdaten durch Spannungsinversion rekonstruiert.rnDie unterschiedliche Orientierung spr¨oder Strukturen im Gelände, die geometrische Analyse der geologischen Strukturen sowie die Ergebnisse von Mikrostrukturen im Dünnschliff (Kapitel 4) weisen auf verschiedene Spannungsfelder hin, die auf mögliche Änderungen der Extensionsrichtung hinweisen. Die Resultate der Spannungsinversion sprechen für Ab-, Über- und Blattverschiebungen sowie für Schrägüberschiebungen (Kapitel 5). Aus der Orientierung der Abschiebungen gehen zwei verschiedene Extensionsrichtungen hervor: im Wesentlichen NW-SE Extension in fast allen Gebieten, sowie NNE-SSW Extension im östlichen Zentralbereich.rnAus der Analyse von Blattverschiebungen ergaben sich drei unterschiedliche Spannungszustände. Zum Einen NNW-SSE bis N-S Kompression in Verbindung mit ENE-WSW bzw E-W Extension wurde für die nördlichen und die zentralen Ruwenzoris ausgemacht. Ein zweiter Spannungszustand mit WNW-ESE Kompression/NNE-SSW Extension betraf die Zentralen Rwenzoris. Ein dritter Spannungszustand mit NNW-SSE Extension betraf den östlichen Zentralteil der Rwenzoris. Schrägüberschiebungen sind durch dazu schräge Achsen charakterisiert, die für N-S bis NNW-SSE Kompression sprechen und ausschließlich im östlichen Zentralabschnitt auftreten. Überschiebungen, die hauptsächlich in den zentralen und den östlichen Rwenzoris auftreten, sprechen für NE-SW orientierten σ2-Achsen und NW-SE Extension.rnrnEs konnten drei unterschiedliche Spannungseinflüsse identifiziert werden: auf die kollisionsbedingte Bildung eines Überschiebungssystem folgte intra-kratonische Kompression und schließlich extensionskontrollierte Riftbildung. Der Übergang zwischen den beiden letztgenannten Spannungszuständen erfolgte Schrittweise und erzeugte vermutlich lokal begrenzte Transpression und Transtension. Gegenw¨artig wird die Störungskinematik der Region durch ein tensiles Spannungsregime in NW-SE bis N-S Richtung bestimmt.rnrnLokale Spannungsvariationen werden dabei hauptsächlich durch die Interferenzrndes regionalen Spannungsfeldes mit lokalen Hauptst¨orungen verursacht. Weitere Faktoren die zu lokalen Veränderungen des Spannungsfeldes führen können sind unterschiedliche Hebungsgeschwindigkeiten, Blockrotation oder die Interaktion von Riftsegmenten. Um den Einfluß präexistenter Strukturen und anderer Bedingungen auf die Hebung der Rwenzoris zu ermitteln, wurde der Riftprozeß mit Hilfe eines analogen ’Sandbox’-Modells rekonstruiert (Kapitel 6). Da sich die Moho-Diskontinuität im Bereich des Arbeitsgebietes in einer Tiefe von 25 km befindet, aktive Störungen aber nur bis zu einer Tiefe von etwa 20 km beobachtet werden können (Koehn et al. 2008), wurden nur die oberen 25 km im Modell nachbebildet. Untersucht und mit Geländebeobachtungen verglichen wurden sowohl die Reihenfolge, in der Riftsegmente entstehen, als auch die Muster, die sich im Verlauf der Nukleierung und des Wachstums dieser Riftsegmente ausbilden. Das Hauptaugenmerk wurde auf die Entwicklung der beiden Subsegmente gelegt auf denen sich der Lake Albert bzw. der Lake Edward und der Lake George befinden, sowie auf das dazwischenliegende Rwenzori Gebirge. Das Ziel der Untersuchung bestand darin herauszufinden, in welcher Weise das südwärts propagierende Lake Albert-Subsegment mit dem sinistral versetzten nordwärts propagierenden Lake Edward/Lake George-Subsegment interagiert.rnrnVon besonderem Interesse war es, in welcherWeise die Strukturen innerhalb und außerhalb der Rwenzoris durch die Interaktion dieser Riftsegmente beeinflußt wurden. rnrnDrei verschiedene Versuchsreihen mit unterschiedlichen Randbedingungen wurden miteinander verglichen. Abhängig vom vorherrschenden Deformationstyp der Transferzone wurden die Reihen als ’Scherungs-dominiert’, ’Extensions-dominiert’ und als ’Rotations-dominiert’ charakterisiert. Die Beobachtung der 3-dimensionalen strukturellen Entwicklung der Riftsegmente wurde durch die Kombination von Modell-Aufsichten mit Profilschnitten ermöglicht. Von den drei genannten Versuchsreihen entwickelte die ’Rotationsdominierten’ Reihe einen rautenförmiger Block im Tranferbereich der beiden Riftsegmente, der sich um 5−20° im Uhrzeigersinn drehte. DieserWinkel liegt im Bereich des vermuteten Rotationswinkel des Rwenzori-Blocks (5°). Zusammengefasst untersuchen die Sandbox-Versuche den Einfluss präexistenter Strukturen und der Überlappung bzw. Überschneidung zweier interagierender Riftsegmente auf die Entwicklung des Riftsystems. Sie befassen sich darüber hinaus mit der Frage, welchen Einfluss Blockbildung und -rotation auf das lokale Stressfeld haben.

Application of Submerged Grouted Anchors in Sheet Pile Quay Walls

Sheet pile walls are one of the oldest earth retention systems utilized in civil engineering projects. They are used for various purposes; such as excavation support system, cofferdams, cut-off walls under dams, slope stabilization, waterfront structures, and flood walls. Sheet pile walls are one of the most common types of quay walls used in port construction. The worldwide increases in utilization of large ships for transportation have created an urgent need of deepening the seabed within port areas and consequently the rehabilitation of its wharfs. Several methods can be used to increase the load-carrying capacity of sheet-piling walls. The use of additional anchored tie rods grouted into the backfill soil and arranged along the exposed wall height is one of the most practical and appropriate solutions adopted for stabilization and rehabilitation of the existing quay wall. The Ravenna Port Authority initiated a project to deepen the harbor bottom at selected wharves. An extensive parametric study through the finite element program, PLAXIS 2D, version 2012 was carried out to investigate the enhancement of using submerged grouted anchors technique on the load response of sheet-piling quay wall. The influence of grout-ties area, length of grouted body, anchor inclination and anchor location were considered and evaluated due to the effect of different system parameters. Also a comparative study was conducted by Plaxis 2D and 3D program to investigate the behavior of these sheet pile quay walls in terms of horizontal displacements induced along the sheet pile wall and ground surface settlements as well as the anchor force and calculated factor of safety. Finally, a comprehensive study was carried out by using different constitutive models to simulate the mechanical behavior of the soil to investigate the effect of these two models (Mohr-Coulomb and Hardening Soil) on the behavior of these sheet pile quay walls.

Statistical methods for the analysis of DNA sequences: application to dinucleotide distribution in the human genome

Questa tesi si inserisce nell'ambito delle analisi statistiche e dei metodi stocastici applicati all'analisi delle sequenze di DNA. Nello specifico il nostro lavoro è incentrato sullo studio del dinucleotide CG (CpG) all'interno del genoma umano, che si trova raggruppato in zone specifiche denominate CpG islands. Queste sono legate alla metilazione del DNA, un processo che riveste un ruolo fondamentale nella regolazione genica. La prima parte dello studio è dedicata a una caratterizzazione globale del contenuto e della distribuzione dei 16 diversi dinucleotidi all'interno del genoma umano: in particolare viene studiata la distribuzione delle distanze tra occorrenze successive dello stesso dinucleotide lungo la sequenza. I risultati vengono confrontati con diversi modelli nulli: sequenze random generate con catene di Markov di ordine zero (basate sulle frequenze relative dei nucleotidi) e uno (basate sulle probabilità di transizione tra diversi nucleotidi) e la distribuzione geometrica per le distanze. Da questa analisi le proprietà caratteristiche del dinucleotide CpG emergono chiaramente, sia dal confronto con gli altri dinucleotidi che con i modelli random. A seguito di questa prima parte abbiamo scelto di concentrare le successive analisi in zone di interesse biologico, studiando l’abbondanza e la distribuzione di CpG al loro interno (CpG islands, promotori e Lamina Associated Domains). Nei primi due casi si osserva un forte arricchimento nel contenuto di CpG, e la distribuzione delle distanze è spostata verso valori inferiori, indicando che questo dinucleotide è clusterizzato. All’interno delle LADs si trovano mediamente meno CpG e questi presentano distanze maggiori. Infine abbiamo adottato una rappresentazione a random walk del DNA, costruita in base al posizionamento dei dinucleotidi: il walk ottenuto presenta caratteristiche drasticamente diverse all’interno e all’esterno di zone annotate come CpG island. Riteniamo pertanto che metodi basati su questo approccio potrebbero essere sfruttati per migliorare l’individuazione di queste aree di interesse nel genoma umano e di altri organismi.

Habitat use of migrating dwarf minke whales (Balaenoptera acutorostrata subspecies) in Tasmanian waters

The Great Barrier Reef hosts the only known reliable aggregation of dwarf minke whale (Balaenoptera acutorostrata subspecies) in Australian waters. While this short seasonal aggregation is quite predictable, the distribution and movements of the whales during the rest of their annual cycle are poorly understood. In particular, feeding and resting areas on their southward migration which are likely to be important have not been described. Using satellite telemetry data, I modelled the habitat use of seven whales during their southward migration through waters surrounding Tasmania. The whales were tagged with LIMPET satellite tags in the GBR in July 2013 (2 individuals) and 2014 (5 individuals). The study area around Tasmania was divided into 10km² cells and the time spent by each individual in each cell was calculated and averaged based on the number of animals using the cell. Two areas of high residency time were highlighted: south-western Bass Strait and Storm Bay (SE Tasmania). Remotely sensed ocean data were extracted for each cell and averaged temporally during the entire period of residency. Using Generalised Additive Models I explored the influence of key environmental characteristics. Nine predictors (bathymetry, distance from coast, distance from shore, gradient of sea surface temperature, sea surface height (absolute and variance), gradient of current speed, wind speed and chlorophyll-a concentration) were retained in the final model which explained 68% of the total variance. Regions of higher time-spent values were characterised by shallow waters, proximity to the coast (but not to the shelf break), high winds and sea surface height but low gradient of sea surface temperature. Given that the two high residency areas corresponded with regions where other marine predators also forage in Bass Strait and Storm Bay, I suggest the whales were probably feeding, rather than resting in these areas.