Aggregate Programming in Scala: a Core Library and Actor-Based Platform for Distributed Computational Fields

La programmazione aggregata è un paradigma che supporta la programmazione di sistemi di dispositivi, adattativi ed eventualmente a larga scala, nel loro insieme -- come aggregati. L'approccio prevalente in questo contesto è basato sul field calculus, un calcolo formale che consente di definire programmi aggregati attraverso la composizione funzionale di campi computazionali, creando i presupposti per la specifica di pattern di auto-organizzazione robusti. La programmazione aggregata è attualmente supportata, in modo più o meno parziale e principalmente per la simulazione, da DSL dedicati (cf., Protelis), ma non esistono framework per linguaggi mainstream finalizzati allo sviluppo di applicazioni. Eppure, un simile supporto sarebbe auspicabile per ridurre tempi e sforzi d'adozione e per semplificare l'accesso al paradigma nella costruzione di sistemi reali, nonché per favorire la ricerca stessa nel campo. Il presente lavoro consiste nello sviluppo, a partire da un prototipo della semantica operazionale del field calculus, di un framework per la programmazione aggregata in Scala. La scelta di Scala come linguaggio host nasce da motivi tecnici e pratici. Scala è un linguaggio moderno, interoperabile con Java, che ben integra i paradigmi ad oggetti e funzionale, ha un sistema di tipi espressivo, e fornisce funzionalità avanzate per lo sviluppo di librerie e DSL. Inoltre, la possibilità di appoggiarsi, su Scala, ad un framework ad attori solido come Akka, costituisce un altro fattore trainante, data la necessità di colmare l'abstraction gap inerente allo sviluppo di un middleware distribuito. Nell'elaborato di tesi si presenta un framework che raggiunge il triplice obiettivo: la costruzione di una libreria Scala che realizza la semantica del field calculus in modo corretto e completo, la realizzazione di una piattaforma distribuita Akka-based su cui sviluppare applicazioni, e l'esposizione di un'API generale e flessibile in grado di supportare diversi scenari.

Valutazione del rischio sismico e idrogeologico nelle reti di distribuzione acqua e attuazione dei possibili interventi

L’obbiettivo ultimo di questo elaborato è quello di valutare il rischio per un evento sismico e un evento idrogeologico di tre reti di condotte per la distribuzione dell’acqua, per poter assegnare ai vari gradi di rischio un opportuno intervento. Le condotte delle reti sono identificate con: ID, materiale, pressione nominale, diametro nominale, portata, spessore, tipologia di giunti, rivestimento, protezione catodica, anno di posa, collocazione. Noti i dati, si possono calcolare le classi dei fattori vulnerabilità, esposizione e pericolosità, relativa ad ogni singola condotta e all’intera rete. La vulnerabilità valuta i fattori di suscettibilità e resilienza di una condotta, l’esposizione valuta i costi ad essa associati e la pericolosità valuta la possibilità degli eventi scelti in base alla collocazione fisica della condotta. Le classi sono successivamente combinate per conoscere il rischio della condotta rispetto l’intera rete. Valutato il livello di rischio abbinato al livello di vulnerabilità della condotta, si ottiene l’intervento opportuno per la condotta analizzata.

Confronto simulativo tra architetture per la mobilità: analisi simulatore MIPv6 e confronto con ABPS

Il presente elaborato tratta il lavoro di studio, analisi e sperimentazione effettuato dal sottoscritto, Giovanni Sitta, in conclusione al Corso di Laurea Magistrale in Informatica presso l'Università degli Studi di Bologna. Questo ha dapprima previsto un periodo di approfondimento di alcune architetture di supporto alla mobilità dei terminali di rete, in particolare di due protocolli allo stato dell'arte, Mobile IPv6 (MIPv6) e Locator/Identifier Separation Protocol (LISP), e di una terza architettura sperimentale denominata Always Best Packet Switching (ABPS). Sono stati in seguito esaminati tre simulatori, uno per ciascuna architettura di supporto alla mobilità considerata, realizzati come estensioni della libreria INET del framework OMNeT++, assicurandosi che fossero conformi alle specifiche del protocollo implementato (almeno entro i limiti di semplificazione rilevanti ai fini del lavoro), e correggendone eventuali problematiche, mancanze e anomalie in caso questi non le rispettassero. Sono poi stati configurati alcuni scenari simulativi utilizzando le tre librerie, in prima battuta di natura molto semplice, utilizzati per verificare il corretto funzionamento dei simulatori in condizioni ideali, e successivamente più complessi, allestendo un ambiente di esecuzione più verosimile, dotato di un maggior numero di host connessi alla rete e di ostacoli per i segnali radio usati nelle comunicazioni wireless. Tramite i risultati sperimentali ottenuti da queste simulazioni è stato infine possibili realizzare un confronto tra le prestazioni di MIPv6, LISP e ABPS.

Confronto simulativo tra architetture per la mobilità: analisi simulatore LISP e confronto con ABPS

L'utilizzo sempre crescente di dispositivi mobili, lo sviluppo di applicazioni mobile in continuo aumento, e la necessità di una sempre migliore qualità della comunicazione, ha portato grande interesse ad analizzare i protocolli di supporto alla mobilità dei terminali. Questi, tra i quali il più conosciuto è forse Mobile IP, vengono posti in esame utilizzando diverse metriche per valutarne le prestazioni. Si confrontano dunque due protocolli: LISP e ABPS; per ognuno dei quali ne viene presentata e descritta l'architettura e le principali funzionalità; entrambe queste architetture per il supporto alla mobilità, prevedono delle specifiche per fornire continuità nella comunicazione durante il roaming di un nodo multihomed. Vengono presentati poi gli strumenti con i quali verrà effettuata il l'analisi: il simulatore a eventi discreti OMNeT++ e il suo framework INET. Successivamente sono descritte le principali componenti dei simulatori per LISP e ABPS, che modellano le meccaniche dei due protocolli analizzati. Questi sono stati sottoposti a modifiche mirate a correggerne eventuali anomalie di comportamento, e ad introdurre nuove funzionalità, soprattutto per quanto riguarda ABPS, che era solo parzialmente implementato. Sono mostrati gli scenari in cui verranno effettuati i test per il confronto delle prestazioni: uno scenario semplice e uno che cerca di proporre una rete urbana verosimile; di seguito vengono elencati i parametri e le configurazioni utilizzate per ognuno dei due scenari. Infine vengono presentati i risultati mettendo a confronto due aspetti della mobilità dei terminali: durata dell'intervallo di indisponibilità e latenza dei pacchetti.

Determinazione e analisi del rischio sismico e idrogeologico nelle reti di distribuzione acqua

In questo elaborato si è focalizzata l’attenzione sulla determinazione del rischio simico e idrogeologico per una rete di distribuzione acqua. Partendo dalle caratteristiche di ogni singolo elemento si sono valutati la vulnerabilità, l’esposizione e la pericolosità per ogni condotta. In conclusione si è analizzato il rischio al fine di individuare quegli elementi maggiormente compromessi su cui concentrare l’attenzione per possibili interventi futuri.

Coupling biomechanics to a cellular level model: An approach to patient-specific image driven multi-scale and multi-physics tumor simulation

Modeling of tumor growth has been performed according to various approaches addressing different biocomplexity levels and spatiotemporal scales. Mathematical treatments range from partial differential equation based diffusion models to rule-based cellular level simulators, aiming at both improving our quantitative understanding of the underlying biological processes and, in the mid- and long term, constructing reliable multi-scale predictive platforms to support patient-individualized treatment planning and optimization. The aim of this paper is to establish a multi-scale and multi-physics approach to tumor modeling taking into account both the cellular and the macroscopic mechanical level. Therefore, an already developed biomodel of clinical tumor growth and response to treatment is self-consistently coupled with a biomechanical model. Results are presented for the free growth case of the imageable component of an initially point-like glioblastoma multiforme tumor. The composite model leads to significant tumor shape corrections that are achieved through the utilization of environmental pressure information and the application of biomechanical principles. Using the ratio of smallest to largest moment of inertia of the tumor material to quantify the effect of our coupled approach, we have found a tumor shape correction of 20\% by coupling biomechanics to the cellular simulator as compared to a cellular simulation without preferred growth directions. We conclude that the integration of the two models provides additional morphological insight into realistic tumor growth behavior. Therefore, it might be used for the development of an advanced oncosimulator focusing on tumor types for which morphology plays an important role in surgical and/or radio-therapeutic treatment planning.

Early molecular and cytogenetic response is predictive for long-term progression-free and overall survival in chronic myeloid leukemia (CML)

In the face of competing first-line treatment options for CML, early prediction of prognosis on imatinib is desirable to assure favorable survival or otherwise consider the use of a second-generation tyrosine kinase inhibitor (TKI). A total of 1303 newly diagnosed imatinib-treated patients (pts) were investigated to correlate molecular and cytogenetic response at 3 and 6 months with progression-free and overall survival (PFS, OS). The persistence of BCR-ABL transcript levels >10% according to the international scale (BCR-ABL(IS)) at 3 months separated a high-risk group (28% of pts; 5-year OS: 87%) from a group with >1-10% BCR-ABL(IS) (41% of pts; 5-year OS: 94%; P=0.012) and from a group with 1% BCR-ABL(IS) (31% of pts; 5-year OS: 97%; P=0.004). Cytogenetics identified high-risk pts by >35% Philadelphia chromosome-positive metaphases (Ph+, 27% of pts; 5-year OS: 87%) compared with 35% Ph+ (73% of pts; 5-year OS: 95%; P=0.036). At 6 months, >1% BCR-ABL(IS) (37% of pts; 5-year OS: 89%) was associated with inferior survival compared with 1% (63% of pts; 5-year OS: 97%; P<0.001) and correspondingly >0% Ph+ (34% of pts; 5-year OS: 91%) compared with 0% Ph+ (66% of pts; 5-year OS: 97%; P=0.015). Treatment optimization is recommended for pts missing these landmarks.

Fading pdf of free-space optical communication system with pointing error

A free-space optical (FSO) laser communication system with perfect fast-tracking experiences random power fading due to atmospheric turbulence. For a FSO communication system without fast-tracking or with imperfect fast-tracking, the fading probability density function (pdf) is also affected by the pointing error. In this thesis, the overall fading pdfs of FSO communication system with pointing errors are calculated using an analytical method based on the fast-tracked on-axis and off-axis fading pdfs and the fast-tracked beam profile of a turbulence channel. The overall fading pdf is firstly studied for the FSO communication system with collimated laser beam. Large-scale numerical wave-optics simulations are performed to verify the analytically calculated fading pdf with collimated beam under various turbulence channels and pointing errors. The calculated overall fading pdfs are almost identical to the directly simulated fading pdfs. The calculated overall fading pdfs are also compared with the gamma-gamma (GG) and the log-normal (LN) fading pdf models. They fit better than both the GG and LN fading pdf models under different receiver aperture sizes in all the studied cases. Further, the analytical method is expanded to the FSO communication system with beam diverging angle case. It is shown that the gamma pdf model is still valid for the fast-tracked on-axis and off-axis fading pdfs with point-like receiver aperture when the laser beam is propagated with beam diverging angle. Large-scale numerical wave-optics simulations prove that the analytically calculated fading pdfs perfectly fit the overall fading pdfs for both focused and diverged beam cases. The influence of the fast-tracked on-axis and off-axis fading pdfs, the fast-tracked beam profile, and the pointing error on the overall fading pdf is also discussed. At last, the analytical method is compared with the previous heuristic fading pdf models proposed since 1970s. Although some of previously proposed fading pdf models provide close fit to the experiment and simulation data, these close fits only exist under particular conditions. Only analytical method shows accurate fit to the directly simulated fading pdfs under different turbulence strength, propagation distances, receiver aperture sizes and pointing errors.

VISUAL-INERTIAL INTEGRATION FOR HUMAN MOTION TRACKING AND NAVIGATION IN FREE-LIVING ENVIRONMENTS

The aging population has become a burning issue for all modern societies around the world recently. There are two important issues existing now to be solved. One is how to continuously monitor the movements of those people having suffered a stroke in natural living environment for providing more valuable feedback to guide clinical interventions. The other one is how to guide those old people effectively when they are at home or inside other buildings and to make their life easier and convenient. Therefore, human motion tracking and navigation have been active research fields with the increasing number of elderly people. However, motion capture has been extremely challenging to go beyond laboratory environments and obtain accurate measurements of human physical activity especially in free-living environments, and navigation in free-living environments also poses some problems such as the denied GPS signal and the moving objects commonly presented in free-living environments. This thesis seeks to develop new technologies to enable accurate motion tracking and positioning in free-living environments. This thesis comprises three specific goals using our developed IMU board and the camera from the imaging source company: (1) to develop a robust and real-time orientation algorithm using only the measurements from IMU; (2) to develop a robust distance estimation in static free-living environments to estimate people’s position and navigate people in static free-living environments and simultaneously the scale ambiguity problem, usually appearing in the monocular camera tracking, is solved by integrating the data from the visual and inertial sensors; (3) in case of moving objects viewed by the camera existing in free-living environments, to firstly design a robust scene segmentation algorithm and then respectively estimate the motion of the vIMU system and moving objects. To achieve real-time orientation tracking, an Adaptive-Gain Orientation Filter (AGOF) is proposed in this thesis based on the basic theory of deterministic approach and frequency-based approach using only measurements from the newly developed MARG (Magnet, Angular Rate, and Gravity) sensors. To further obtain robust positioning, an adaptive frame-rate vision-aided IMU system is proposed to develop and implement fast vIMU ego-motion estimation algorithms, where the orientation is estimated in real time from MARG sensors in the first step and then used to estimate the position based on the data from visual and inertial sensors. In case of the moving objects viewed by the camera existing in free-living environments, a robust scene segmentation algorithm is firstly proposed to obtain position estimation and simultaneously the 3D motion of moving objects. Finally, corresponding simulations and experiments have been carried out.

Changes in species composition in alpine snowbeds with climate change inferred from small-scale spatial patterns

Alpine snowbeds are characterised by a very short growing season. However, the length of the snow-free period is increasingly prolonged due to climate change, so that snowbeds become susceptible to invasions from neighbouring alpine meadow communities. We hypothesised that spatial distribution of species generated by plant interactions may indicate whether snowbed species will coexist with or will be out-competed by invading alpine species – spatial aggregation or segregation will point to coexistence or competitive exclusion, respectively. We tested this hypothesis in snowbeds of the Swiss Alps using the variance ratio statistics. We focused on the relationships between dominant snowbed species, subordinate snowbed species, and potentially invading alpine grassland species. Subordinate snowbed species were generally spatially aggregated with each other, but were segregated from alpine grassland species. Competition between alpine grassland and subordinate snowbed species may have caused this segregation. Segregation between these species groups increased with earlier snowmelt, suggesting an increasing importance of competition with climate change. Further, a dominant snowbed species (Alchemilla pentaphyllea) was spatially aggregated with subordinate snowbed species, while two other dominants (Gnaphalium supinum and Salix herbacea) showed aggregated patterns with alpine grassland species. These dominant species are known to show distinct microhabitat preferences suggesting the existence of hidden microhabitats with different susceptibility to invaders. These results allow us to suggest that alpine snowbed areas are likely to be reduced as a consequence of climate change and that invading species from nearby alpine grasslands could outcompete subordinate snowbed species. On the other hand, microhabitats dominated by Gnaphalium or Salix seem to be particularly prone to invasions by non-snowbed species.

Flow-R, a model for susceptibility mapping of debris flows and other gravitational hazards at a regional scale

The development of susceptibility maps for debris flows is of primary importance due to population pressure in hazardous zones. However, hazard assessment by process-based modelling at a regional scale is difficult due to the complex nature of the phenomenon, the variability of local controlling factors, and the uncertainty in modelling parameters. A regional assessment must consider a simplified approach that is not highly parameter dependant and that can provide zonation with minimum data requirements. A distributed empirical model has thus been developed for regional susceptibility assessments using essentially a digital elevation model (DEM). The model is called Flow-R for Flow path assessment of gravitational hazards at a Regional scale (available free of charge under http://www.flow-r.org) and has been successfully applied to different case studies in various countries with variable data quality. It provides a substantial basis for a preliminary susceptibility assessment at a regional scale. The model was also found relevant to assess other natural hazards such as rockfall, snow avalanches and floods. The model allows for automatic source area delineation, given user criteria, and for the assessment of the propagation extent based on various spreading algorithms and simple frictional laws. We developed a new spreading algorithm, an improved version of Holmgren's direction algorithm, that is less sensitive to small variations of the DEM and that is avoiding over-channelization, and so produces more realistic extents. The choices of the datasets and the algorithms are open to the user, which makes it compliant for various applications and dataset availability. Amongst the possible datasets, the DEM is the only one that is really needed for both the source area delineation and the propagation assessment; its quality is of major importance for the results accuracy. We consider a 10 m DEM resolution as a good compromise between processing time and quality of results. However, valuable results have still been obtained on the basis of lower quality DEMs with 25 m resolution.

Reduced bone breakage and increased bone strength in free range laying hens fed omega-3 polyunsaturated fatty acid supplemented diets

INTRODUCTION The omega-3 and omega-6 polyunsaturated fatty acids (PUFAs) are the immediate precursors to a number of important mediators of immunity, inflammation and bone function, with products of omega-6 generally thought to promote inflammation and favour bone resorption. Western diets generally provide a 10 to 20-fold deficit in omega-3 PUFAs compared with omega-6, and this is thought to have contributed to the marked rise in incidence of disorders of modern human societies, such as heart disease, colitis and perhaps osteoporosis. Many of our food production animals, fed on grains rich in omega-6, are also exposed to a dietary deficit in omega-3, with perhaps similar health consequences. Bone fragility due to osteoporotic changes in laying hens is a major economic and welfare problem, with our recent estimates of breakage rates indicating up to 95% of free range hens suffer breaks during lay. METHODS Free range hens housed in full scale commercial systems were provided diets supplemented with omega-3 alpha linolenic acid, and the skeletal benefits were investigated by comparison to standard diets rich in omega-6. RESULTS There was a significant 40-60% reduction in keel bone breakage rate, and a corresponding reduction in breakage severity in the omega-3 supplemented hens. There was significantly greater bone density and bone mineral content, alongside increases in total bone and trabecular volumes. The mechanical properties of the omega-3 supplemented hens were improved, with strength, energy to break and stiffness demonstrating significant increases. Alkaline phosphatase (an osteoblast marker) and tartrate-resistant acid phosphatase (an osteoclast marker) both showed significant increases with the omega-3 diets, indicating enhanced bone turnover. This was corroborated by the significantly lower levels of the mature collagen crosslinks, hydroxylysyl pyridinoline, lysyl pyridinoline and histidinohydroxy-lysinonorleucine, with a corresponding significant shift in the mature:immature crosslink ratio. CONCLUSIONS The improved skeletal health in laying hens corresponds to as many as 68million fewer hens suffering keel fractures in the EU each year. The biomechanical and biochemical evidence suggests that increased bone turnover has enhanced the bone mechanical properties, and that this may suggest potential benefits for human osteoporosis.

Neural correlates of free T3 alteration after catecholamine depletion in subjects with remitted major depressive disorder and in controls.

RATIONALE: Thyroid hormones and their interactions with catecholamines play a potentially important role in alterations of mood and cognition. OBJECTIVES: This study aimed to examine the neurobiological effects of catecholamine depletion on thyroid hormones by measuring endocrine and cerebral metabolic function in unmedicated subjects with remitted major depressive disorder (RMDD) and in healthy controls. METHODS: This was a randomized, placebo-controlled, and double-blind crossover trial that included 15 unmedicated RMDD subjects and 13 healthy control subjects. The participants underwent two 3-day-long sessions at 1-week intervals; each participant was randomly administered oral α-methyl-para-tyrosine in one session (catecholamine depletion) and an identical capsule containing hydrous lactose (sham depletion) in the other session prior to a [(18)F]-fluorodeoxyglucose positron emission tomography scan. RESULTS: Serum concentrations of free T3 (FT3), free T4 (FT4), and TSH were obtained and assessed with respect to their relationship to regional cerebral glucose metabolism. Both serum FT3 (P = 0.002) and FT4 (P = 0.0009) levels were less suppressed after catecholamine depletion compared with placebo treatment in the entire study sample. There was a positive association between both FT3 (P = 0.0005) and FT4 (P = 0.002) and depressive symptoms measured using the Montgomery-Åsberg Depression Rating Scale. The relative elevation in FT3 level was correlated with a decrease in regional glucose metabolism in the right dorsolateral prefrontal cortex (rDLPFC; P < 0.05, corrected). CONCLUSIONS: This study provided evidence of an association between a thyroid-catecholamine interaction and mood regulation in the rDLPFC.

Frost-Free Record Reconstruction for Eastern Massachusetts, 1733-1980

A reconstruction methodology utilizing such varied documents as diaries, agricultural journals, U.S. Weather Bureau killing frost records and instrumental records is discussed. A resultant 248-year frost record for eastern Massachusetts exhibits marked variations in the length of the growing season, that occur on a time scale of approximately 70 years. There is an apparent systematic long-term relationship between the timing of spring and fall killing frosts and the last 100 years of record reveals a decline in year-to-year variability.

Geophysical and Hydrological Evaluation of Two Bog Complexes in a Northern Peatland: Implications for the Distribution of Biogenic Gases at the Basin Scale

Ground penetrating radar (GPR) was used to determine peat basin geometry and the spatial distribution of free-phase biogenic gasses in two separate units of a northern peatland (Central and Southern Unit of Caribou Bog, Maine). The Central Unit is characterized by a deep basin structure (15 m maximum depth) and a raised (eccentric) bog topographic profile (up to 2 m topographic variation). Here numerous regions of electromagnetic (EM) wave scattering are considered diagnostic of the presence of extensive free-phase biogenic gas. In contrast, the Southern Unit is shallower (8 m maximum depth) and has a slightly convex upwards bog profile (less than 1 m topographic variation), and areas of EM wave scattering are notably absent. The biogenic gas zones interpreted from GPR in the Central Unit are associated with: (1) wooded heath vegetation at the surface, (2) open pools at the surface, (3) high water table elevations near the center of the basin, and (4) a region of overpressure (at approximately 5 m depth) immediately below the zone of free-phase gas accumulation. The latter suggests (1) a transient pressure head associated with low hydraulic conductivity resulting from the biogenic gasses themselves or confining layers in the peat that restrict both gas release and groundwater flow and/or (2) overpressure in the peat column as a result of the gas buildup itself. In contrast, the Southern Unit, where zones of EM scattering are absent, is characterized by: (1) predominantly shrub vegetation, (2) a lack of open pools, (3) only minor variations (less than 1 m) in water table elevation throughout the entire unit; and (4) generally upward groundwater flow throughout the basin. The results illustrate the nonuniformity of free-phase biogenic gas distribution at the peat basin scale and provide insights into the processes and controls associated with CH4 and CO2 accumulation in peatlands.