New methodologies in CT perfusion and MRI analysis to develop cancer imaging biomarkers

Quantitative imaging in oncology aims at developing imaging biomarkers for diagnosis and prediction of cancer aggressiveness and therapy response before any morphological change become visible. This Thesis exploits Computed Tomography perfusion (CTp) and multiparametric Magnetic Resonance Imaging (mpMRI) for investigating diverse cancer features on different organs. I developed a voxel-based image analysis methodology in CTp and extended its use to mpMRI, for performing precise and accurate analyses at single-voxel level. This is expected to improve reproducibility of measurements and cancer mechanisms’ comprehension and clinical interpretability. CTp has not entered the clinical routine yet, although its usefulness in the monitoring of cancer angiogenesis, due to different perfusion computing methods yielding unreproducible results. Instead, machine learning applications in mpMRI, useful to detect imaging features representative of cancer heterogeneity, are mostly limited to clinical research, because of results’ variability and difficult interpretability, which make clinicians not confident in clinical applications. In hepatic CTp, I investigated whether, and under what conditions, two widely adopted perfusion methods, Maximum Slope (MS) and Deconvolution (DV), could yield reproducible parameters. To this end, I developed signal processing methods to model the first pass kinetics and remove any numerical cause hampering the reproducibility. In mpMRI, I proposed a new approach to extract local first-order features, aiming at preserving spatial reference and making their interpretation easier. In CTp, I found out the cause of MS and DV non-reproducibility: MS and DV represent two different states of the system. Transport delays invalidate MS assumptions and, by correcting MS formulation, I have obtained the voxel-based equivalence of the two methods. In mpMRI, the developed predictive models allowed (i) detecting rectal cancers responding to neoadjuvant chemoradiation showing, at pre-therapy, sparse coarse subregions with altered density, and (ii) predicting clinically significant prostate cancers stemming from the disproportion between high- and low- diffusivity gland components.

Gene expression and genome-wide association studies analysis to select heavy pigs for protected designation of origin cured meats production

The high quality of protected designation of origin (PDO) dry-cured pork products depends largely on the chemical and physical parameters of the fresh meat and their variation during the production process of the final product. The discovery of the mechanisms that regulate the variability of these parameters was aided by the reference genome of swine adjuvant to genetic analysis methods. This thesis can contribute to the discovery of genetic mechanisms that regulate the variability of some quality parameters of fresh meat for PDO dry-cured pork production. The first study is of gene expression and showed that between low and high glycolytic potential (GP) samples of Semimembranosus muscle of Italian Large White (ILW) pigs in early postmortem, the differentially expressed genes were all but one over expressed in low GP. These were involved in ATP biosynthesis processes, calcium homeostasis, and lipid metabolism including the potential master regulator gene Peroxisome Proliferator-Activated Receptor Alpha (PPARA). The second is a study in commercial hybrid pigs to evaluate correlations between carcass and fresh ham traits, including carcass and fresh ham lean meat percentages, the former, a potential predictor of the latter. In addition, a genome-wide association study allowed the identification of chromosome-wide associations with phenotypic traits for 19 SNPs, and genome-wide associations for 14 SNPs for ferrochelatase activity. The latter could be a determinant for color variation in nitrite-free dry-cured ham. The third study showed gene expression differences in the Longissimus thoracis muscle of ILW pigs by feeding diets with extruded linseed (source of polyunsaturated fatty acids) and vitamin E and selenium (diet three) or natural (diet four) antioxidants. The diet three promoted a more rapid and massive immune system response possibly determined by improvement in muscle tissue function, while the diet four promoted oxidative stability and increased the anti-inflammatory potential of muscle tissue.

Multivariate analysis to discriminate top quark pair production channels at LHC

Il quark top è una delle particelle fondamentali del Modello Standard, ed è osservato a LHC nelle collisioni a più elevata energia. In particolare, la coppia top-antitop (tt̄) è prodotta tramite interazione forte da eventi gluone-gluone (gg) oppure collisioni di quark e antiquark (qq̄). I diversi meccanismi di produzione portano ad avere coppie con proprietà diverse: un esempio è lo stato di spin di tt̄, che vicino alla soglia di produzione è maggiormente correlato nel caso di un evento gg. Uno studio che voglia misurare l’entità di tali correlazioni risulta quindi essere significativamente facilitato da un metodo di discriminazione delle coppie risultanti sulla base del loro canale di produzione. Il lavoro qui presentato ha quindi lo scopo di ottenere uno strumento per effettuare tale differenziazione, attraverso l’uso di tecniche di analisi multivariata. Tali metodi sono spesso applicati per separare un segnale da un fondo che ostacola l’analisi, in questo caso rispettivamente gli eventi gg e qq̄. Si dice che si ha a che fare con un problema di classificazione. Si è quindi studiata la prestazione di diversi algoritmi di analisi, prendendo in esame le distribuzioni di numerose variabili associate al processo di produzione di coppie tt̄. Si è poi selezionato il migliore in base all’efficienza di riconoscimento degli eventi di segnale e alla reiezione degli eventi di fondo. Per questo elaborato l’algoritmo più performante è il Boosted Decision Trees, che permette di ottenere da un campione con purezza iniziale 0.81 una purezza finale di 0.92, al costo di un’efficienza ridotta a 0.74.

Altaica from Harrassowitz

Kirjallisuusarvostelu

Numerical study of ultrasound induced non-linear shape and size bubble oscillations in viscoelastic media

The theoretical study of forced bubble oscillations is motivated by the importance of cavitation bubbles and oscillating encapsulated microbubbles (i.e. contrast agents) in medical sciences. In more details,theoretical studies on bubble dynamics addressing the sound-bubble interaction phenomenon provide the basis for understanding the dynamics of contrast agent microbubbles used in medical diagnosis and of non-linearly oscillating cavitation bubbles in the case of high-intensity ultrasound therapy. Moreover, the inclusion of viscoelasticity is of vital importance for an accurate theoretical analysis since most biological tissues and fluids exhibit non-Newtonian behavior.

Statistical modeling of bowing control applied to violin sound synthesis

Excitation-continuous music instrument control patterns are often not explicitly represented in current sound synthesis techniques when applied to automatic performance. Both physical model-based and sample-based synthesis paradigmswould benefit from a flexible and accurate instrument control model, enabling the improvement of naturalness and realism. Wepresent a framework for modeling bowing control parameters inviolin performance. Nearly non-intrusive sensing techniques allow for accurate acquisition of relevant timbre-related bowing control parameter signals.We model the temporal contour of bow velocity, bow pressing force, and bow-bridge distance as sequences of short Bézier cubic curve segments. Considering different articulations, dynamics, and performance contexts, a number of note classes are defined. Contours of bowing parameters in a performance database are analyzed at note-level by following a predefined grammar that dictates characteristics of curve segment sequences for each of the classes in consideration. As a result, contour analysis of bowing parameters of each note yields an optimal representation vector that is sufficient for reconstructing original contours with significant fidelity. From the resulting representation vectors, we construct a statistical model based on Gaussian mixtures suitable for both the analysis and synthesis of bowing parameter contours. By using the estimated models, synthetic contours can be generated through a bow planning algorithm able to reproduce possible constraints caused by the finite length of the bow. Rendered contours are successfully used in two preliminary synthesis frameworks: digital waveguide-based bowed stringphysical modeling and sample-based spectral-domain synthesis.

Emotional well-being and adjustment to vision loss in later life: a meta-synthesis of qualitative studies.

Purpose: To review perceived emotional well-being in older people with visual impairment and perceived factors that inhibit/facilitate psychosocial adjustment to vision loss. Method: The databases of MEDLINE, EMBASE, PsycINFO and CINAHL were searched for studies published from January 1980 to December 2010, which recruited older people with irreversible vision loss, and used qualitative methods for both data collection and analysis. Results sections of the papers were synthesised using a thematic-style analysis to identify the emergent and dominant themes. Results: Seventeen qualitative papers were included in the review, and five main themes emerged from the synthesis: 1) the trauma of an ophthalmic diagnosis, 2) impact of vision loss on daily life, 3) negative impact of visual impairment on psychosocial well-being, 4) factors that inhibit social well-being, and 5) factors that facilitate psychological well-being. We found the response shift model useful for explaining our synthesis. Conclusions: Acquired visual impairment can have a significant impact on older people's well-being and make psychosocial adjustment to the condition a major challenge. Acceptance of the condition and a positive attitude facilitate successful psychosocial adjustment to vision loss as well as social support from family, friends and peers who have successfully adjusted to the condition. [Box: see text].

A flexible (C)LP-based approach to the analysis of object-oriented programs

Static analyses of object-oriented programs usually rely on intermediate representations that respect the original semantics while having a more uniform and basic syntax. Most of the work involving object-oriented languages and abstract interpretation usually omits the description of that language or just refers to the Control Flow Graph(CFG) it represents. However, this lack of formalization on one hand results in an absence of assurances regarding the correctness of the transformation and on the other it typically strongly couples the analysis to the source language. In this work we present a framework for analysis of object-oriented languages in which in a first phase we transform the input program into a representation based on Horn clauses. This allows on one hand proving the transformation correct attending to a simple condition and on the other being able to apply an existing analyzer for (constraint) logic programming to automatically derive a safe approximation of the semantics of the original program. The approach is flexible in the sense that the first phase decouples the analyzer from most languagedependent features, and correct because the set of Horn clauses returned by the transformation phase safely approximates the standard semantics of the input program. The resulting analysis is also reasonably scalable due to the use of mature, modular (C)LP-based analyzers. The overall approach allows us to report results for medium-sized programs.

A Jaworskian analysis of four senior class primary teachers endeavouring to teach mathematics from a constructivist-compatible perspective

A constructivist philosophy underlies the Irish primary mathematics curriculum. As constructivism is a theory of learning its implications for teaching need to be addressed. This study explores the experiences of four senior class primary teachers as they endeavour to teach mathematics from a constructivist-compatible perspective with primary school children in Ireland over a school-year period. Such a perspective implies that children should take ownership of their learning while working in groups on tasks which challenge them at their zone of proximal development. The key question on which the research is based is: to what extent will an exposure to constructivism and its implications for the classroom impact on teaching practices within the senior primary mathematics classroom in both the short and longer term? Although several perspectives on constructivism have evolved (von Glaserfeld (1995), Cobb and Yackel (1996), Ernest (1991,1998)), it is the synthesis of the emergent perspective which becomes pivotal to the Irish primary mathematics curriculum. Tracking the development of four primary teachers in a professional learning initiative involving constructivist-compatible approaches necessitated the use of Borko’s (2004) Phase 1 research methodology to account for the evolution in teachers’ understanding of constructivism. Teachers’ and pupils’ viewpoints were recorded using both audio and video technology. Teachers were interviewed at the beginning and end of the project and also one year on to ascertain how their views had evolved. Pupils were interviewed at the end of the project only. The data were analysed from a Jaworskian perspective i.e. using the categories of her Teaching Triad of management of learning, mathematical challenge and sensitivity to students. Management of learning concerns how the teacher organises her classroom to maximise learning opportunities for pupils. Mathematical challenge is reminiscent of the Vygotskian (1978) construct of the zone of proximal development. Sensitivity to students involves a consciousness on the part of the teacher as to how pupils are progressing with a mathematical task and whether or not to intervene to scaffold their learning. Through this analysis a synthesis of the teachers’ interpretations of constructivist philosophy with concomitant implications for theory, policy and practice emerges. The study identifies strategies for teachers wishing to adopt a constructivist-compatible approach to their work. Like O’Shea (2009) it also highlights the likely difficulties to be experienced by such teachers as they move from utilising teacher-dominated methods of teaching mathematics to ones in which pupils have more ownership over their learning.

Learning processes and the neural analysis of conditioning

Classical and operant conditioning principles, such as the behavioral discrepancy-derived assumption that reinforcement always selects antecedent stimulus and response relations, have been studied at the neural level, mainly by observing the strengthening of neuronal responses or synaptic connections. A review of the literature on the neural basis of behavior provided extensive scientific data that indicate a synthesis between the two conditioning processes based mainly on stimulus control in learning tasks. The resulting analysis revealed the following aspects. Dopamine acts as a behavioral discrepancy signal in the midbrain pathway of positive reinforcement, leading toward the nucleus accumbens. Dopamine modulates both types of conditioning in the Aplysia mollusk and in mammals. In vivo and in vitro mollusk preparations show convergence of both types of conditioning in the same motor neuron. Frontal cortical neurons are involved in behavioral discrimination in reversal and extinction procedures, and these neurons preferentially deliver glutamate through conditioned stimulus or discriminative stimulus pathways. Discriminative neural responses can reliably precede operant movements and can also be common to stimuli that share complex symbolic relations. The present article discusses convergent and divergent points between conditioning paradigms at the neural level of analysis to advance our knowledge on reinforcement.

Performance of different immobilized lipases in palm oil biodiesel synthesis

Performance of different immobilized lipases in palm oil biodiesel synthesis. Optimized conditions for palm oil and ethanol enzymatic biodiesel synthesis were determined with different immobilized lipases SiO(2)-PVA-immobilized lipase from Pseudomonas fluorescens and acrylic resin-immobilized lipase, Novozym (R) 435, from Candida antartica, in solvent-free medium. A full factorial design assessed the influence of temperature (42 - 58 degrees C) and ethanol: palm oil (6:1 - 18:1) molar ratio on the transesterification yield. Main effects were adjusted by multiple regression analysis to linear models and the maximum transesterification yield was obtained at 42 degrees C and 18:1 ethanol: palm oil molar ratio. Mathematical models featuring total yield for each immobilized lipase were suitable to describe the experimental results.

A comparison of segmental and wrist-to-ankle methodologies of bioimpedance analysis

The common approach of bioelectrical impedance analysis to estimate body water uses a wrist-to-ankle methodology which, although not indicated by theory, has the advantage of ease of application particularly for clinical studies involving patients with debilitating diseases. A number of authors have suggested the use of a segmental protocol in which the impedances of the trunk and limbs are measured separately to provide a methodology more in keeping with basic theory. The segmental protocol hits not, however, been generally adopted, partly because of the increased complexity involved in its application, and partly because studies comparing the two methodologies have not clearly demonstrated a significant improvement from the segmental methodology. We have conducted a small pilot study involving ten subjects to investigate the efficacy of the two methodologies in a group of normal subjects. The study did not require the independent measure of body water, by for example isotope dilution, as the subjects were maintained in a state of constant hydration with only the distribution between limbs and trunk changing as a result of change in posture. The results demonstrate a significant difference between the two methodologies in predicting the expected constancy of body water in this study, with the segmental methodology indicating a mean percentage change in extracellular water of -2.2%; which was not significantly different from the expected null result, whereas the wrist-to-ankle methodology indicated a mean percentage change in extracellular water of -6.6%. This is significantly different from the null result, and from the value obtained from the segmental methodology (p = 0.006). Similar results were obtained using estimates of total body water from the two methodologies. (C) 1998 Elsevier Science Ltd. All rights reserved.

Enamel matrix derivative induces matrix synthesis by cultured human periodontal fibroblast cells

Background: Periodontal wound healing and regeneration require that new matrix be synthesized, creating an environment into which cells can migrate. One agent which has been described as promoting periodontal regeneration is an enamel matrix protein derivative (EMD). Since no specific growth factors have been identified in EMD preparations, it is postulated that EMD acts as a matrix enhancement factor. This study was designed to investigate the effect of EMD in vitro on matrix synthesis by cultured periodontal fibroblasts. Methods: The matrix response of the cells was evaluated by determination of the total proteoglycan synthesis, glycosaminoglycan profile, and hyaluronan synthesis by the uptake of radiolabeled precursors. The response of the individual proteoglycans, versican, decorin, and biglycan were examined at the mRNA level by Northern blot analysis. Hyaluronan synthesis was probed by identifying the isotypes of hyaluronan synthase (HAS) expressed in periodontal fibroblasts as HAS-2 and HAS-3 and the effect of EMD on the levels of mRNA for each enzyme was monitored by reverse transcription polymerase chain reaction (RTPCR). Comparisons were made between gingival fibroblast (GF) cells and periodontal ligament (PDLF) cells. Results: EMD was found to significantly affect the synthesis of the mRNAs for the matrix proteoglycans versican, biglycan, and decorin, producing a response similar to, but potentially greater than, mitogenic cytokines. EMD also stimulated hyaluronan synthesis in both GF and PDLF cells. Although mRNA for HAS-2 was elevated in GF after exposure to EMD, the PDLF did not show a similar response. Therefore, the point at which the stimulation of hyaluronan becomes effective may not be at the level of stimulation of the mRNA for hyaluronan synthase, but, rather, at a later point in the pathway of regulation of hyaluronan synthesis. In all cases, GF cells appeared to be more responsive to EMD than PDLF cells in vitro. Conclusions: EMD has the potential to significantly modulate matrix synthesis in a manner consistent with early regenerative events.

A Model-to-model analysis of the repeated Prisoners' Dilemma: genetic algorithms vs. evolutionary dynamics

We study the properties of the well known Replicator Dynamics when applied to a finitely repeated version of the Prisoners' Dilemma game. We characterize the behavior of such dynamics under strongly simplifying assumptions (i.e. only 3 strategies are available) and show that the basin of attraction of defection shrinks as the number of repetitions increases. After discussing the difficulties involved in trying to relax the 'strongly simplifying assumptions' above, we approach the same model by means of simulations based on genetic algorithms. The resulting simulations describe a behavior of the system very close to the one predicted by the replicator dynamics without imposing any of the assumptions of the analytical model. Our main conclusion is that analytical and computational models are good complements for research in social sciences. Indeed, while on the one hand computational models are extremely useful to extend the scope of the analysis to complex scenar

Schooling in the Network Society : Internet in Primary and Secondary Education. Research report (synthesis document)

Aquest projecte té la intenció d'identificar i analitzar els efectes de la introducció d'Internet a les escoles catalanes (educació primària i secundària). L'objectiu és posar de manifest la manera com s'utilitza la xarxa en aquest àmbit i en quina mesura contribueix a l'aparició, en els centres educatius, d'una nova cultura adaptada a les necessitats de la societat xarxa. Amb aquest propòsit, aquest projecte desplega les seves línies d'anàlisi per a fer atenció al procés d'incorporació d'Internet, principalment, en tres direccions: la pràctica pedagògica, les formes d'organització i gestió dels centres educatius i la seva vinculació amb la comunitat i el territori. Aquesta investigació ha estat desenvolupada pel grup de recerca ENS (Education and Network Society). Amb una perspectiva comparativa, el treball d'aquest grup vol contribuir, sobre la base de dades empíriques, a interpretar la transformació de l'àmbit educatiu no universitari en els paràmetres que estableix, avui dia, la nostra societat.