Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

IRAS 00183-7111: ALMA and X-ray view of an ultra luminous infrared galaxy

The aim of this Thesis work is to study the multi-frequency properties of the Ultra Luminous Infrared Galaxy (ULIRG) IRAS 00183-7111 (I00183) at z = 0.327, connecting ALMA sub-mm/mm observations with those at high energies in order to place constraints on the properties of its central power source and verify whether the gas traced by the CO may be responsible for the obscuration observed in X-rays. I00183 was selected from the so-called Spoon diagnostic diagram (Spoon et al. 2007) for mid-infrared spectra of infrared galaxies based on the equivalent width of the 6.2 μm Polycyclic Aromatic Hydrocarbon (PAH) emission feature versus the 9.7 μm silicate strength. Such features are a powerful tool to investigate the contribution of star formation and AGN activity in this class of objects. I00183 was selected from the top-left region of the plot where the most obscured sources, characterized by a strong Si absorption feature, are located. To link the sub-mm/mm to the X-ray properties of I00183, ALMA archival Cycle 0 data in Band 3 (87 GHz) and Band 6 (270 GHz) have been calibrated and analyzed, using CASA software. ALMA Cycle 0 was the Early Science program for which data reprocessing is strongly suggested. The main work of this Thesis consisted in reprocessing raw data to provide an improvement with respect to the available archival products and results, which were obtained using standard procedures. The high-energy data consists of Chandra, XMM-Newton and NuSTAR observations which provide a broad coverage of the spectrum in the energy range 0.5 − 30 keV. Chandra and XMM archival data were used, with an exposure time of 22 and 22.2 ks, respectively; their reduction was carried out using CIAO and SAS software. The 100 ks NuSTAR are still private and the spectra were obtained by courtesy of the PI (K. Iwasawa). A detailed spectral analysis was done using XSPEC software; the spectral shape was reproduced starting from simple phenomenological models, and then more physical models were introduced to account for the complex mechanisms that involve this source. In Chapter 1, an overview of the scientific background is discussed, with a focus on the target, I00183, and the Spoon diagnostic diagram, from which it was originally selected. In Chapter 2, the basic principles of interferometry are briefly introduced, with a description of the calibration theory applied to interferometric observations. In Chapter 3, ALMA and its capabilities, both current and future, are shown, explaining also the complex structure of the ALMA archive. In Chapter 4, the calibration of ALMA data is presented and discussed, showing also the obtained imaging products. In Chapter 5, the analysis and discussion of the main results obtained from ALMA data is presented. In Chapter 6, the X-ray observations, data reduction and spectral analysis are reported, with a brief introduction to the basic principle of X-ray astronomy and the instruments from which the observations were carried out. Finally, the overall work is summarized, with particular emphasis on the main obtained results and the possible future perspectives.

Architettura cloud per lo sviluppo multi-piattaforma di Sistemi Operativi: Principi generali

Vengono analizzate le strategie di rilascio delle principali Distribuzioni Linux e i metodi per la compilazione automatizzata del software. Si propone quindi una nuova metodologia sia per il rilascio di media installabili e sia per la pacchettizzazione. Sfruttando le tecnologie del campo DevOps, si introduce quindi un alto grado di scalabilità anche in ambienti Cloud, grazie anche alla riproducibilità di ogni componente dell'infrastruttura proposta. Vedremo quindi come questo approccio aumenta l'automatizzazione nei cicli produttivi per la realizzazione della Distribuzione Sabayon Linux e per la definizione di un'infrastruttura automatizzata attualmente in production.

Architettura cloud per lo sviluppo multi-piattaforma di Sistemi Operativi: Applicazioni specifiche

Il mondo dell’Internet of Things e del single board computing sono settori in forte espansione al giorno d’oggi e le architetture ARM sono, al momento, i dominatori in questo ambito. I sistemi operativi e i software si stanno evolvendo per far fronte a questo cambiamento e ai nuovi casi d’uso che queste tecnologie introducono. In questa tesi ci occuperemo del porting della distribuzione Linux Sabayon per queste architetture, la creazione di un infrastruttura per il rilascio delle immagini e la compilazione dei pacchetti software.

Integrazione sistemi a eventi e multi-agente: Kafka, TuCSoN e JADE

La tesi esplora le problematiche relative all'integrazione di tecnologie per lo sviluppo di sistemi multi-agente e tecnologie per lo sviluppo di sistemi di comunicazione ad eventi. In particolare è stata posta l'attenzione sui concetti condivisi da entrambe le tecnologie e su come sia possibile realizzare l'integrazione preservando i principi fondamentali delle due tipologie di sistemi, tramite l'implementazione di un'astrazione di coordinazione oggettiva. Inoltre viene mostrato un esempio di integrazione tra JADE, TuCSoN e Kafka, tramite un caso di studio che permette di utilizzare i tre modelli di coordinazione offerti da questi framework in un unico sistema multi-agente.

Deterministic and probabilistic verification of multi-model meteorological forecasts on the subseasonal timescale

In questo studio, un multi-model ensemble è stato implementato e verificato, seguendo una delle priorità di ricerca del Subseasonal to Seasonal Prediction Project (S2S). Una regressione lineare è stata applicata ad un insieme di previsioni di ensemble su date passate, prodotte dai centri di previsione mensile del CNR-ISAC e ECMWF-IFS. Ognuna di queste contiene un membro di controllo e quattro elementi perturbati. Le variabili scelte per l'analisi sono l'altezza geopotenziale a 500 hPa, la temperatura a 850 hPa e la temperatura a 2 metri, la griglia spaziale ha risoluzione 1 ◦ × 1 ◦ lat-lon e sono stati utilizzati gli inverni dal 1990 al 2010. Le rianalisi di ERA-Interim sono utilizzate sia per realizzare la regressione, sia nella validazione dei risultati, mediante stimatori nonprobabilistici come lo scarto quadratico medio (RMSE) e la correlazione delle anomalie. Successivamente, tecniche di Model Output Statistics (MOS) e Direct Model Output (DMO) sono applicate al multi-model ensemble per ottenere previsioni probabilistiche per la media settimanale delle anomalie di temperatura a 2 metri. I metodi MOS utilizzati sono la regressione logistica e la regressione Gaussiana non-omogenea, mentre quelli DMO sono il democratic voting e il Tukey plotting position. Queste tecniche sono applicate anche ai singoli modelli in modo da effettuare confronti basati su stimatori probabilistici, come il ranked probability skill score, il discrete ranked probability skill score e il reliability diagram. Entrambe le tipologie di stimatori mostrano come il multi-model abbia migliori performance rispetto ai singoli modelli. Inoltre, i valori più alti di stimatori probabilistici sono ottenuti usando una regressione logistica sulla sola media di ensemble. Applicando la regressione a dataset di dimensione ridotta, abbiamo realizzato una curva di apprendimento che mostra come un aumento del numero di date nella fase di addestramento non produrrebbe ulteriori miglioramenti.

Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations

The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.

Studio multi-banda dal sub-parsec al kilo-parsec dell'emissione del getto nella radio galassia IC 1531

In questo lavoro di tesi si presenta il primo studio multi-scala e multi-frequenza focalizzato sul getto della radiogalassia IC1531 (z=0.026) con i satelliti Chandra, XMM-Newton e Fermi con l’obiettivo di tracciarne l’emissione alle alte energie; definire i processi radiativi responsabili dell’emissione osservata e stimare i principali parametri fisici del getto; stimare l’energetica del getto alle diverse scale. La sorgente è stata selezionata per la presenza di un getto esteso (≈5’’) osservato in radio e ai raggi X, inoltre, era riportata come possibile controparte della sorgente gamma 3FGLJ0009.6-3211 presente nel terzo catalogo Fermi (3FGL). La presenza di emissione ai raggi γ, confermata dal nostro studio, è importante per la modellizzazione della SED della regione nucleare. L’emissione X del nucleo è dominata da una componente ben riprodotta da una legge di potenza con indice spettrale Γ=2.2. L’analisi dell’emissione in banda gamma ha evidenziato una variabilità su scale di 5 giorni, dalla quale è stato possibile stimare le dimensioni delle regione emittente. Inoltre viene presentato lo studio della distribuzione spettrale dell’energia della regione nucleare di IC 1531 dalla banda radio ai raggi γ. I modelli ci permettono di determinare la natura dell’emissione gamma e stimare la potenza cinetica del getto a scale del su-pc. Gli osservabili sono stati utilizzati per ottenere le stime sui parametri del modello. La modellizzazione così ottenuta ha permesso di stimare i parametri fisici del getto e la potenza trasportata del getto a scale del sub-pc. Le stime a 151MHz suggerisco che il getto abbia basse velocita' (Γ≤7) e angolo di inclinazione rispetto alla linea di vista 10°<ϑ<20°; nel complesso, il trasporto di energia da parte del getto risulta efficiente. L’origine dell’emissione X del getto a grandi scale è consistente con un’emissione di sincrotrone, che conferma la classificazione di IC1531 come sorgente di bassa potenza MAGN.

Team Member’s Centrality, Cohesion, Conflict, and Performance in Multi-University Geographically Distributed Project Teams

This study examined team processes and outcomes among 12 multi-university distributed project teams from 11 universities during its early and late development stages over a 14-month project period. A longitudinal model of team interaction is presented and tested at the individual level to consider the extent to which both formal and informal network connections—measured as degree centrality—relate to changes in team members’ individual perceptions of cohesion and conflict in their teams, and their individual performance as a team member over time. The study showed a negative network centrality-cohesion relationship with significant temporal patterns, indicating that as team members perceive less degree centrality in distributed project teams, they report more team cohesion during the last four months of the project. We also found that changes in team cohesion from the first three months (i.e., early development stage) to the last four months (i.e., late development stage) of the project relate positively to changes in team member performance. Although degree centrality did not relate significantly to changes in team conflict over time, a strong inverse relationship was found between changes in team conflict and cohesion, suggesting that team conflict emphasizes a different but related aspect of how individuals view their experience with the team process. Changes in team conflict, however, did not relate to changes in team member performance. Ultimately, we showed that individuals, who are less central in the network and report higher levels of team cohesion, performed better in distributed teams over time.

Elaborazione di un modello di simulazione per una rete di trasporto multi-modale

Questo lavoro di tesi si prefigge l’obiettivo di simulare il trasporto di organi destinati a trapianto sul territorio nazionale italiano. Lo scopo della simulazione è mettere in luce le criticità e le eventuali soluzioni alternative in modo da raggiungere un duplice obiettivo: la certezza di portare a compimento il trasporto da un ospedale ad un altro entro i tempi clinici necessari affinché l’organo sia ancora utilizzabile e la riduzione dei costi del trasporto, che negli ultimi anni si sono rivelati elevati a causa del ricorso frequente a voli di Stato. Nella prima parte del lavoro viene delineato il problema e le necessità di ottimizzazione della rete, dopodiché si illustra il modello creato per simulare la situazione di as-is ed infine si espone il modello da utilizzare in futuro, dove si prevedono i tempi futuri di percorrenza. Per la modellazione della situazione attuale sono stati utilizzati due livelli di dettaglio diversi, uno che si basa sulla suddivisione dei trapianti in ingresso e uscita da una regione specifica e uno che approfondisce ulteriormente la rete modellando gli spostamenti di città in città. I modelli predittivi presentati sono due, uno che considera tempi predittivi deterministici e uno che considera tempi stocastici. Dopo ciascuna modellazione vengono esposti i risultati e le statistiche più significative; vengono infine messi in evidenza gli aspetti critici e gli sviluppi futuri della simulazione. Il software scelto per creare e simulare il trasporto degli organi sulla rete è Arena.

Design Without Borders: A Multi-Everything Masters

Design is increasingly a global activity: addressing issues that challenge and affect people and populations other than our own, involving stakeholders from many cultures, realized through borderless networks of knowledge, services, materials, manufacturing and distribution. There is an appetite among graduates, especially in design and engineering, to broaden horizons and raise ambitions, to tackle big issues through innovation to bring about life-changing or world-changing impact. Employers demand such thinkers and doers: culturally attuned, multidisciplinary and T-shaped, unafraid to shake things up. In 2013, twelve postgraduates embarked on a new joint Masters course in London; students from eight different nations, studying together in three capital cities over two years. This programme is a collaboration between four centres of academic excellence in UK, USA and Japan; these students soon become its first graduating cohort, having experienced differing teaching styles, perspectives and specialisms around design, technology and innovation from four world-class institutions; immersion in three very different cultures; collaboration with students and faculty from many diverse disciplines and cultures; forming friendships and networks spanning the globe. This paper outlines the rationale and philosophy of the course, the challenges in its realisation and development so far, and its likely future evolution.

Analysis and modelling of immune cell behaviour in lymph nodes based on multi-photon imaging

This thesis presents quantitative studies of T cell and dendritic cell (DC) behaviour in mouse lymph nodes (LNs) in the naive state and following immunisation. These processes are of importance and interest in basic immunology, and better understanding could improve both diagnostic capacity and therapeutic manipulations, potentially helping in producing more effective vaccines or developing treatments for autoimmune diseases. The problem is also interesting conceptually as it is relevant to other fields where 3D movement of objects is tracked with a discrete scanning interval. A general immunology introduction is presented in chapter 1. In chapter 2, I apply quantitative methods to multi-photon imaging data to measure how T cells and DCs are spatially arranged in LNs. This has been previously studied to describe differences between the naive and immunised state and as an indicator of the magnitude of the immune response in LNs, but previous analyses have been generally descriptive. The quantitative analysis shows that some of the previous conclusions may have been premature. In chapter 3, I use Bayesian state-space models to test some hypotheses about the mode of T cell search for DCs. A two-state mode of movement where T cells can be classified as either interacting to a DC or freely migrating is supported over a model where T cells would home in on DCs at distance through for example the action of chemokines. In chapter 4, I study whether T cell migration is linked to the geometric structure of the fibroblast reticular network (FRC). I find support for the hypothesis that the movement is constrained to the fibroblast reticular cell (FRC) network over an alternative 'random walk with persistence time' model where cells would move randomly, with a short-term persistence driven by a hypothetical T cell intrinsic 'clock'. I also present unexpected results on the FRC network geometry. Finally, a quantitative method is presented for addressing some measurement biases inherent to multi-photon imaging. In all three chapters, novel findings are made, and the methods developed have the potential for further use to address important problems in the field. In chapter 5, I present a summary and synthesis of results from chapters 3-4 and a more speculative discussion of these results and potential future directions.

Information and Communication Technologies (ICT) to Improve Prescription Appropriateness and Therapy Adherence in the Multi-morbid Elderly

Multimorbidity patients pose severe challenges to which information and communication technology (ICT) can help patients and doctors to answer with effective and efficient care.

Acute Q Fever Presenting with Multi-Organ Failure: Re-Evaluation of the Initial Diagnosis

We present the case of a 48-year-old man admitted to the critical care unit with atrial fibrillation, and acute heart and kidney failure accompanied by coagulopathy and an abnormal liver test. Initially diagnosed as a non-ST elevation myocardial infarction, re-evaluation of the case led to the consideration of severe sepsis. Q fever and leptospirosis were the most probable causes and empiric treatment was initiated. A complete recovery was achieved following treatment.

Ventricular Fibrillation in Patient with Multi-vessel Coronary Spasm Four Days after the Initiation of Oral Beta-blocker

We describe a case of ventricular fibrillation occurring in a patient with multi-vessel coronary spasm after the initiation of an oral beta-blocker. A 56-year-old man began to experience chest discomfort and his computed tomography revealed intermediate coronary stenoses. He was administered medications including an oral beta-blocker but suddenly collapsed while walking 4 days later. An automated external defibrillator detected ventricular fibrillation and delivered successful electrical cardioversion. An acetylcholine provocation test after stabilization of the status revealed triple-vessel coronary spasm. Beta-blockers may provoke exacerbation of coronary spasm and result in lethal arrhythmia.