Analysis of the immunological and functional features of the Neisserial Heparin Binding Antigen (NHBA)

Neisserial Heparin Binding Antigen (NHBA) is a surface-exposed lipoprotein ubiquitously expressed by genetically diverse Neisseria meningitidis strains and is an antigen of the multicomponent protein-based 4CMenB vaccine, able to induce bactericidal antibodies in humans and to bind heparin-like molecules. The aim of this study is to characterize the immunological and functional properties of NHBA. To evaluate immunogenicity and the contribution of aminoacid sequence variability to vaccine coverage, we constructed recombinant isogenic strains that are susceptible to bactericidal killing only by anti-NHBA antibodies and engineered them to express equal levels of selected NHBA peptides. In these recombinant strains, we observed different titres associated with the different peptide variants. These recombinant strains were then further engineered to express NHBA chimeric proteins to investigate the regions important for immunogenicity. In natural strains, anti-NHBA antibodies were found to be cross-protective against strains expressing different peptides. To investigate the functional properties of this antigen, the recombinant purified NHBA protein was tested in in vitro binding studies and was found to be able to bind epithelial cells. The binding was abolished when cells were treated specifically with heparinase III, suggesting that the interaction with the cells is mediated by heparan sulfate proteoglycans (HSPG). Mutation of the Arg-rich tract of NHBA abrogated the binding, confirming the importance of this region in mediating the binding to heparin-like molecules. In a panel of N. meningitidis strains, the deletion of nhba resulted in a reduction of adhesion with respect to each isogenic wild type strain. Furthermore, the adhesion of the wild-type strain was prevented by using anti-NHBA polyclonal sera, demonstrating the specificity of the interaction. These results suggest that NHBA could be a novel meningococcal adhesin contributing to host-cell interaction. Moreover, we analysed NHBA NalP-mediated cleavage in different NHBA peptides and showed that not all NHBA peptides are cleaved.

Automatic risk evaluation in elderly patients based on Autonomic Nervous System assessment

Dysfunction of Autonomic Nervous System (ANS) is a typical feature of chronic heart failure and other cardiovascular disease. As a simple non-invasive technology, heart rate variability (HRV) analysis provides reliable information on autonomic modulation of heart rate. The aim of this thesis was to research and develop automatic methods based on ANS assessment for evaluation of risk in cardiac patients. Several features selection and machine learning algorithms have been combined to achieve the goals. Automatic assessment of disease severity in Congestive Heart Failure (CHF) patients: a completely automatic method, based on long-term HRV was proposed in order to automatically assess the severity of CHF, achieving a sensitivity rate of 93% and a specificity rate of 64% in discriminating severe versus mild patients. Automatic identification of hypertensive patients at high risk of vascular events: a completely automatic system was proposed in order to identify hypertensive patients at higher risk to develop vascular events in the 12 months following the electrocardiographic recordings, achieving a sensitivity rate of 71% and a specificity rate of 86% in identifying high-risk subjects among hypertensive patients. Automatic identification of hypertensive patients with history of fall: it was explored whether an automatic identification of fallers among hypertensive patients based on HRV was feasible. The results obtained in this thesis could have implications both in clinical practice and in clinical research. The system has been designed and developed in order to be clinically feasible. Moreover, since 5-minute ECG recording is inexpensive, easy to assess, and non-invasive, future research will focus on the clinical applicability of the system as a screening tool in non-specialized ambulatories, in order to identify high-risk patients to be shortlisted for more complex investigations.

Geomorphological and statistical analysis on Ravenna dune fields changes, based on Terrestrial Laser Technology

Coastal sand dunes represent a richness first of all in terms of defense from the sea storms waves and the saltwater ingression; moreover these morphological elements constitute an unique ecosystem of transition between the sea and the land environment. The research about dune system is a strong part of the coastal sciences, since the last century. Nowadays this branch have assumed even more importance for two reasons: on one side the born of brand new technologies, especially related to the Remote Sensing, have increased the researcher possibilities; on the other side the intense urbanization of these days have strongly limited the dune possibilities of development and fragmented what was remaining from the last century. This is particularly true in the Ravenna area, where the industrialization united to the touristic economy and an intense subsidence, have left only few dune ridges residual still active. In this work three different foredune ridges, along the Ravenna coast, have been studied with Laser Scanner technology. This research didn’t limit to analyze volume or spatial difference, but try also to find new ways and new features to monitor this environment. Moreover the author planned a series of test to validate data from Terrestrial Laser Scanner (TLS), with the additional aim of finalize a methodology to test 3D survey accuracy. Data acquired by TLS were then applied on one hand to test some brand new applications, such as Digital Shore Line Analysis System (DSAS) and Computational Fluid Dynamics (CFD), to prove their efficacy in this field; on the other hand the author used TLS data to find any correlation with meteorological indexes (Forcing Factors), linked to sea and wind (Fryberger's method) applying statistical tools, such as the Principal Component Analysis (PCA).

Antarctic cloud spectral emission from ground-based measurements, a focus on far infrared signatures

The present work belongs to the PRANA project, the first extensive field campaign of observation of atmospheric emission spectra covering the Far InfraRed spectral region, for more than two years. The principal deployed instrument is REFIR-PAD, a Fourier transform spectrometer used by us to study Antarctic cloud properties. A dataset covering the whole 2013 has been analyzed and, firstly, a selection of good quality spectra is performed, using, as thresholds, radiance values in few chosen spectral regions. These spectra are described in a synthetic way averaging radiances in selected intervals, converting them into BTs and finally considering the differences between each pair of them. A supervised feature selection algorithm is implemented with the purpose to select the features really informative about the presence, the phase and the type of cloud. Hence, training and test sets are collected, by means of Lidar quick-looks. The supervised classification step of the overall monthly datasets is performed using a SVM. On the base of this classification and with the help of Lidar observations, 29 non-precipitating ice cloud case studies are selected. A single spectrum, or at most an average over two or three spectra, is processed by means of the retrieval algorithm RT-RET, exploiting some main IR window channels, in order to extract cloud properties. Retrieved effective radii and optical depths are analyzed, to compare them with literature studies and to evaluate possible seasonal trends. Finally, retrieval output atmospheric profiles are used as inputs for simulations, assuming two different crystal habits, with the aim to examine our ability to reproduce radiances in the FIR. Substantial mis-estimations are found for FIR micro-windows: a high variability is observed in the spectral pattern of simulation deviations from measured spectra and an effort to link these deviations to cloud parameters has been performed.

Ruthenium-based light harvesting complexes

Polypyridylkomplexe von Ruthenium(II) besitzen eine Vielzahl von Anwendungen, z. B. in Farbstoff-sensibilisierten Solarzellen und als Photokatalysatoren. [Ru(bpy)3]2+ ist einer der prominentesten Ruthenium(II)-Komplexe und besitzt langlebige angeregte 3MLCT-Zustände mit einer Lebensdauer von 1 µs und einer Lumineszenz-Quantenausbeute von 10%. [Ru(bpy)3]2+ ist chiral und kann Stereoisomere bilden, wenn die Liganden unsymmetrisch substituiert sind oder im Falle von oligonuklearen rac/meso-Komplexen. Bis-tridentate Komplexe wie [Ru(tpy)2]2+ sind achiral und umgehen damit unerwünschte Stereoisomere. [Ru(tpy)2]2+ besitzt jedoch enttäuschende photophysikalische Eigenschaften mit einer 3MLCT-Lebensdauer von nur etwa 0.2 ns und einer Quantenausbeute von ≤ 0.0007%. Die Anbringung von Substituenten an [Ru(tpy)2]2+ sowie die Aufweitung der Liganden-Bisswinkel auf 90° bewirken deutlich verbesserte Eigenschaften der emittierenden 3MLCT-Zustände. rnDieser Strategie folgend wurden in der vorliegenden Arbeit neue bis-tridentate Ruthenium(II)-Komplexe entwickelt, synthetisiert und charakterisiert. Durch Anbringen von Ester-Substituenten und Verwenden von Liganden mit erweiterten Bisswinkeln konnten 3MLCT-Lebensdauern von bis zu 841 ns und Quantenausbeuten von bis zu 1.1% erreicht werden. Die neuen bis-tridentaten Komplexe weisen eine deutlich erhöhte Photostabilität im Vergleich zu tris-bidentatem [Ru(bpy)3]2+ auf. rnDie Komplexe wurden als Emitter in Licht-emittierenden elektrochemischen Zellen eingebaut und zeigen Elektrolumineszenz mit einer tiefroten Farbe, die bis ins NIR reicht. Ebenso wurden die Komplexe als Lichtsammler in Farbstoff-sensibilisierten Solarzellen getestet und erreichen Licht-zu-Energie-Effizienzen von bis zu 0.26%. rnDinukleare, stereochemisch einheitliche Ruthenium(II)-Komplexe wurden oxidiert um die Metall-Metall-Wechselwirkung zwischen Ru(II) und Ru(III) in der einfach oxidierten Spezies zu untersuchen. Die unterschiedlichen Redoxeigenschaften der beiden Rutheniumzentren in den verwendeten dinuklearen Verbindungen führt zu einer valenzlokalisierten Situation in der keine Metall-Metall-Wechselwirkung beobachtet wird. Ebenso wurde die Oxidation eines einkernigen Ruthenium(II)-Komplexes sowie dessen spontane Rückreduktion untersucht.rnEnergietransfersysteme wurden mittels Festphasensynthese hergestellt. Dabei ist ein Bis(terpyridin)ruthenium(II)-Komplex als Energie-Akzeptor über eine unterschiedliche Anzahl an Glycineinheiten mit einem Cumarin-Chromophor als Energie-Donor verknüpft. Bei einer kleinen Zahl an Glycineinheiten (0, 1) findet effektiver Energietransfer vom Cumarin- zum Ruthenium-Chromophor statt, wogegen bei zwei Glycineinheiten ein effektiver Energietransfer verhindert ist.rnLicht-induzierte Ladungstrennung wurde erreicht, indem Bis(terpyridin)ruthenium(II)-Komplexe als Chromophore in einem Donor-Chromophor-Akzeptor-Nanokomposit eingesetzt wurden. Dabei wurde ein Triphenylamin-enthaltendes Blockcopolymer als Elektronendonor und ZnO-Nanostäbchen als Elektronenakzeptor verwendet. Bei Bestrahlung des Chromophors werden Elektronen in die ZnO-Nanostäbchen injiziert und die Elektronenlöcher wandern in das Triphenylamin-enthaltende Blockcopolymer. rnrn

Influence of micro-site conditions and environmental gradients on tree-ring based climate reconstructions

Tree-ring chronologies are a powerful natural archive to reconstruct summer temperature variations of the late Holocene with an annual resolution. To develop these long-term proxy records tree-ring series are commonly extended back in time by combining samples from living trees with relict dead material preserved onshore or in lakes. Former studies showed that low frequency variations in such reconstructions can be biased if the relict and recent material is from different origins. A detailed analysis of the influence of various ecological (micro-) habitats representing the recent part is required to estimate potential errors in temperature estimates. The application of collective detrending methods, that comprise absolute growth rates, can produce errors in climate reconstructions and results in an underestimation of past temperatures. The appearance of these kind of micro-site effects is a wide-spread phenomenon that takes place all over Fennoscandia. Future research in this key region for dendroclimatology should take this issue into account. Especially the higher climate response at the lakeshore site is interesting to achieve smaller uncertainties when a tree-ring series is transformed to temperature anomalies. For new composite chronologies the main aim should be to minimize potential biases and this includes also micro-site effects.

New markov chain based methods for single and cross-domain sentiment classification

Nowadays communication is switching from a centralized scenario, where communication media like newspapers, radio, TV programs produce information and people are just consumers, to a completely different decentralized scenario, where everyone is potentially an information producer through the use of social networks, blogs, forums that allow a real-time worldwide information exchange. These new instruments, as a result of their widespread diffusion, have started playing an important socio-economic role. They are the most used communication media and, as a consequence, they constitute the main source of information enterprises, political parties and other organizations can rely on. Analyzing data stored in servers all over the world is feasible by means of Text Mining techniques like Sentiment Analysis, which aims to extract opinions from huge amount of unstructured texts. This could lead to determine, for instance, the user satisfaction degree about products, services, politicians and so on. In this context, this dissertation presents new Document Sentiment Classification methods based on the mathematical theory of Markov Chains. All these approaches bank on a Markov Chain based model, which is language independent and whose killing features are simplicity and generality, which make it interesting with respect to previous sophisticated techniques. Every discussed technique has been tested in both Single-Domain and Cross-Domain Sentiment Classification areas, comparing performance with those of other two previous works. The performed analysis shows that some of the examined algorithms produce results comparable with the best methods in literature, with reference to both single-domain and cross-domain tasks, in $2$-classes (i.e. positive and negative) Document Sentiment Classification. However, there is still room for improvement, because this work also shows the way to walk in order to enhance performance, that is, a good novel feature selection process would be enough to outperform the state of the art. Furthermore, since some of the proposed approaches show promising results in $2$-classes Single-Domain Sentiment Classification, another future work will regard validating these results also in tasks with more than $2$ classes.

Sistema Bluetooth-based di remarketing pervasivo

Il progetto si propone di dotare la realta fisica di un estensione digitale. Sensori, attuatori e tecnologie embedded hanno cambiato il nostro modo di lavorare, allenarci e seguire i nostri interessi. Il mondo del commercio non e rimasto a guardare ed ha dovuto adattarsi alla metamorfosi high-tech del settore dei servizi. Il sistema proposto costituisce un promotore per acquisti ed un raccoglitore intelligente di abitudini sullo shopping e si compone di applicazione mobile, microcontroller e web server. Caratteristica prima e principale del progetto e sicuramente la pervasivita. All'utente ed utilizzatore dell'app dello shopping center deve essere certamente resa nota la collaborazione al fine di raccogliere dati statistici sulle sue abitudini, tuttavia sono le modalita di tale operazione a dover rimanere velate, in modo da non appesantire il cliente con tediose operazioni di invio di feedback e valutazioni ed allo stesso tempo permettere una raccolta capillare delle informazioni. Parallelamente alla raccolta di dati funzionali al producer, sono state implementate features per il consumatore, come notifiche promozionali place-triggered e pubblicita mirata. Tra tutte le tecnologie adibite allo scambio di informazioni, si e scelto l'utilizzo del Bluetooth e del piu recente Bluetooth Low Energy (BLE) per permettere ai dispositivi di comunicare tra loro.

Numerical model of the human cornea based on stromal microstructure: identification of mechanical properties for two age groups

The optical quality of the human eye mainly depends on the refractive performance of the cornea. The shape of the cornea is a mechanical balance between intraocular pressure and tissue intrinsic stiffness. Several surgical procedures in ophthalmology alter the biomechanics of the cornea to provoke local or global curvature changes for vision correction. Legitimated by the large number of surgical interventions performed every day, the demand for a deeper understanding of corneal biomechanics is rising to improve the safety of procedures and medical devices. The aim of our work is to propose a numerical model of corneal biomechanics, based on the stromal microstructure. Our novel anisotropic constitutive material law features a probabilistic weighting approach to model collagen fiber distribution as observed on human cornea by Xray scattering analysis (Aghamohammadzadeh et. al., Structure, February 2004). Furthermore, collagen cross-linking was explicitly included in the strain energy function. Results showed that the proposed model is able to successfully reproduce both inflation and extensiometry experimental data (Elsheikh et. al., Curr Eye Res, 2007; Elsheikh et. al., Exp Eye Res, May 2008). In addition, the mechanical properties calculated for patients of different age groups (Group A: 65-79 years; Group B: 80-95 years) demonstrate an increased collagen cross-linking, and a decrease in collagen fiber elasticity from younger to older specimen. These findings correspond to what is known about maturing fibrous biological tissue. Since the presented model can handle different loading situations and includes the anisotropic distribution of collagen fibers, it has the potential to simulate clinical procedures involving nonsymmetrical tissue interventions. In the future, such mechanical model can be used to improve surgical planning and the design of next generation ophthalmic devices.

Radiolabeled bicyclic somatostatin-based analogs: a novel class of potential radiotracers for SPECT/PET of neuroendocrine tumors

A variety of radiolabeled somatostatin analogs have been developed for targeting of somatostatin receptor (sst)-positive tumors. Bicyclic somatostatin-based radiopeptides have not been studied yet. Hypothesizing that the introduction of conformational constraints may lead to receptor subtype selectivity or may help to delineate structural features determining pansomatostatin potency, we developed and evaluated first examples of this new class of potential radiotracers for imaging or therapy of neuroendocrine tumors.

Influence of Smoothing on Voxel-Based Mesh Accuracy in Micro-Finite Element

The interest in automatic volume meshing for finite element analysis (FEA) has grown more since the appearance of microfocus CT (μCT), due to its high resolution, which allows for the assessment of mechanical behaviour at a high precision. Nevertheless, the basic meshing approach of generating one hexahedron per voxel produces jagged edges. To prevent this effect, smoothing algorithms have been introduced to enhance the topology of the mesh. However, whether smoothing also improves the accuracy of voxel-based meshes in clinical applications is still under question. There is a trade-off between smoothing and quality of elements in the mesh. Distorted elements may be produced by excessive smoothing and reduce accuracy of the mesh. In the present work, influence of smoothing on the accuracy of voxel-based meshes in micro-FE was assessed. An accurate 3D model of a trabecular structure with known apparent mechanical properties was used as a reference model. Virtual CT scans of this reference model (with resolutions of 16, 32 and 64 μm) were then created and used to build voxel-based meshes of the microarchitecture. Effects of smoothing on the apparent mechanical properties of the voxel-based meshes as compared to the reference model were evaluated. Apparent Young’s moduli of the smooth voxel-based mesh were significantly closer to those of the reference model for the 16 and 32 μm resolutions. Improvements were not significant for the 64 μm, due to loss of trabecular connectivity in the model. This study shows that smoothing offers a real benefit to voxel-based meshes used in micro-FE. It might also broaden voxel-based meshing to other biomechanical domains where it was not used previously due to lack of accuracy. As an example, this work will be used in the framework of the European project ContraCancrum, which aims at providing a patient-specific simulation of tumour development in brain and lungs for oncologists. For this type of clinical application, such a fast, automatic, and accurate generation of the mesh is of great benefit.

Personalized X-Ray Reconstruction of the Proximal Femur via Intensity-Based Non-rigid 2D-3D Registration

This paper presents a new approach for reconstructing a patient-specific shape model and internal relative intensity distribution of the proximal femur from a limited number (e.g., 2) of calibrated C-arm images or X-ray radiographs. Our approach uses independent shape and appearance models that are learned from a set of training data to encode the a priori information about the proximal femur. An intensity-based non-rigid 2D-3D registration algorithm is then proposed to deformably fit the learned models to the input images. The fitting is conducted iteratively by minimizing the dissimilarity between the input images and the associated digitally reconstructed radiographs of the learned models together with regularization terms encoding the strain energy of the forward deformation and the smoothness of the inverse deformation. Comprehensive experiments conducted on images of cadaveric femurs and on clinical datasets demonstrate the efficacy of the present approach.

Modeling Features at Runtime

A feature represents a functional requirement fulfilled by a system. Since many maintenance tasks are expressed in terms of features, it is important to establish the correspondence between a feature and its implementation in source code. Traditional approaches to establish this correspondence exercise features to generate a trace of runtime events, which is then processed by post-mortem analysis. These approaches typically generate large amounts of data to analyze. Due to their static nature, these approaches do not support incremental and interactive analysis of features. We propose a radically different approach called live feature analysis, which provides a model at runtime of features. Our approach analyzes features on a running system and also makes it possible to grow feature representations by exercising different scenarios of the same feature, and identifies execution elements even to the sub-method level. We describe how live feature analysis is implemented effectively by annotating structural representations of code based on abstract syntax trees. We illustrate our live analysis with a case study where we achieve a more complete feature representation by exercising and merging variants of feature behavior and demonstrate the efficiency or our technique with benchmarks.

Time-lapse microscopy and classification of 2D human mesenchymal stem cells based on cell shape picks up myogenic from osteogenic and adipogenic differentiation

Current methods to characterize mesenchymal stem cells (MSCs) are limited to CD marker expression, plastic adherence and their ability to differentiate into adipogenic, osteogenic and chondrogenic precursors. It seems evident that stem cells undergoing differentiation should differ in many aspects, such as morphology and possibly also behaviour; however, such a correlation has not yet been exploited for fate prediction of MSCs. Primary human MSCs from bone marrow were expanded and pelleted to form high-density cultures and were then randomly divided into four groups to differentiate into adipogenic, osteogenic chondrogenic and myogenic progenitor cells. The cells were expanded as heterogeneous and tracked with time-lapse microscopy to record cell shape, using phase-contrast microscopy. The cells were segmented using a custom-made image-processing pipeline. Seven morphological features were extracted for each of the segmented cells. Statistical analysis was performed on the seven-dimensional feature vectors, using a tree-like classification method. Differentiation of cells was monitored with key marker genes and histology. Cells in differentiation media were expressing the key genes for each of the three pathways after 21 days, i.e. adipogenic, osteogenic and chondrogenic, which was also confirmed by histological staining. Time-lapse microscopy data were obtained and contained new evidence that two cell shape features, eccentricity and filopodia (= 'fingers') are highly informative to classify myogenic differentiation from all others. However, no robust classifiers could be identified for the other cell differentiation paths. The results suggest that non-invasive automated time-lapse microscopy could potentially be used to predict the stem cell fate of hMSCs for clinical application, based on morphology for earlier time-points. The classification is challenged by cell density, proliferation and possible unknown donor-specific factors, which affect the performance of morphology-based approaches. Copyright © 2012 John Wiley & Sons, Ltd.

Tumor budding score based on 10 high-power fields is a promising basis for a standardized prognostic scoring system in stage II colorectal cancer

Tumor budding is recognized by the World Health Organization as an additional prognostic factor in colorectal cancer but remains unreported in diagnostic work due to the absence of a standardized scoring method. This study aims to assess the most prognostic and reproducible scoring systems for tumor budding in colorectal cancer. Tumor budding on pancytokeratin-stained whole tissue sections from 105 well-characterized stage II patients was scored by 3 observers using 7 methods: Hase, Nakamura, Ueno, Wang (conventional and rapid method), densest high-power field, and 10 densest high-power fields. The predictive value for clinicopathologic features, the prognostic significance, and interobserver variability of each scoring method was analyzed. Pancytokeratin staining allowed accurate evaluation of tumor buds. Interobserver agreement for 3 observers was excellent for densest high-power field (intraclass correlation coefficient, 0.83) and 10 densest high-power fields (intraclass correlation coefficient, 0.91). Agreement was moderate to substantial for the conventional Wang method (κ = 0.46-0.62) and moderate for the rapid method (κ = 0.46-0.58). For Nakamura, moderate agreement (κ = 0.41-0.52) was reached, whereas concordance was fair to moderate for Ueno (κ = 0.39-0.56) and Hase (κ = 0.29-0.51). The Hase, Ueno, densest high-power field, and 10 densest high-power field methods identified a significant association of tumor budding with tumor border configuration. In multivariate analysis, only tumor budding as evaluated in densest high-power field and 10 densest high-power fields had significant prognostic effects on patient survival (P < .01), with high prognostic accuracy over the full 10-year follow-up. Scoring tumor buds in 10 densest high-power fields is a promising method to identify stage II patients at high risk for recurrence in daily diagnostics; it is highly reproducible, accounts for heterogeneity, and has a strong predictive value for adverse outcome.