Solutions to common issues in widefield microscopy: vignetting, mosaicing and depth of focus

In this thesis we have developed solutions to common issues regarding widefield microscopes, facing the problem of the intensity inhomogeneity of an image and dealing with two strong limitations: the impossibility of acquiring either high detailed images representative of whole samples or deep 3D objects. First, we cope with the problem of the non-uniform distribution of the light signal inside a single image, named vignetting. In particular we proposed, for both light and fluorescent microscopy, non-parametric multi-image based methods, where the vignetting function is estimated directly from the sample without requiring any prior information. After getting flat-field corrected images, we studied how to fix the problem related to the limitation of the field of view of the camera, so to be able to acquire large areas at high magnification. To this purpose, we developed mosaicing techniques capable to work on-line. Starting from a set of overlapping images manually acquired, we validated a fast registration approach to accurately stitch together the images. Finally, we worked to virtually extend the field of view of the camera in the third dimension, with the purpose of reconstructing a single image completely in focus, stemming from objects having a relevant depth or being displaced in different focus planes. After studying the existing approaches for extending the depth of focus of the microscope, we proposed a general method that does not require any prior information. In order to compare the outcome of existing methods, different standard metrics are commonly used in literature. However, no metric is available to compare different methods in real cases. First, we validated a metric able to rank the methods as the Universal Quality Index does, but without needing any reference ground truth. Second, we proved that the approach we developed performs better in both synthetic and real cases.

Key issues in diagnosing and treating acute aortic syndromes: results from the metropolitan area of Bologna network

Background: Survival of patients with Acute Aortic Syndrome (AAS) may relate to the speed of diagnosis. Diagnostic delay is exacerbated by non classical presentations such as myocardial ischemia or acute heart failure (AHF). However little is known about clinical implications and pathophysiological mechanisms of Troponin T elevation and AHF in AAS. Methods and Results: Data were collected from a prospective metropolitan AAS registry (398 patients diagnosed between 2000 and 2013). Troponin T values (either standard or high sensitivity assay, HS) were available in 248 patients (60%) of the registry population; the overall frequency of troponin positivity was 28% (ranging from 16% to 54%, using standard or HS assay respectively, p = 0.001). Troponin positivity was associated with a twofold increased risk of long in-hospital diagnostic time (OR 1.92, 95% CI 1.05-3.52, p = 0.03), but not with in-hospital mortality. The combination of positive troponin and ACS-like ECG abnormalities resulted in a significantly increased risk of inappropriate therapy due to a misdiagnosis of ACS (OR 2.48, 95% CI 1.12-5.54, p = 0.02). Patients with AHF were identified by the presence of dyspnea as presentation symptom or radiological signs of pulmonary congestion or cardiogenic shock. The overall frequency of AHF was 28 % (32% type A vs. 20% type B AAS, p = 0.01). AHF was due to a variety of pathophysiological mechanisms including cardiac tamponade (26%), aortic regurgitation (25%), myocardial ischemia (17%), hypertensive crisis (10%). AHF was associated with increased surgical delay and with increased risk of in-hospital death (adjusted OR 1.97 95% CI1.13-3.37,p=0.01). Conclusions: Troponin positivity (particularly HS) was a frequent finding in AAS. Abnormal troponin values were strongly associated with ACS-like ECG findings, in-hospital diagnostic delay, and inappropriate therapy. AHF was associated with increased surgical delay and was an independent predictor of in-hospital mortality.

Stability issues in racing motorcycles: an in-depth analysis of the chatter vibration

Racing motorcycles are prone to an unstable oscillatory motion of the swingarm and rear wheel, commonly known as ���chatter���. This vibration mode typically has a frequency of 17 Hz to 22 Hz and typically occurs during heavy braking manoeuvres. The appearance of chatter can cause reduced rider confidence, and therefore lead to longer lap times during races and the increased risk of crashing. This thesis looks to further the understanding of this mode. It includes the development of a simplified model to explore the effects roll angle and lateral dynamics have on the chatter mode using linear analysis. The mechanisms of instability and parameter sensitivities are also examined. The effects of the nonlinearities present in the minimal model equations of motion are examined, including the identification of limit cycles and their stability, inspecting individual nonlinear terms and their effects, and introducing tyre relaxation and determining the effect it has on the dynamics. Finally, an exploratory study of the mid-corner region of a typical racing manoeuvre is performed in hopes to better understand if any high frequency tyre induced instabilities like chatter can occur.

Bycatch and discard issues in the Adriatic demersal fisheries

Commercial fisheries exploiting the demersal resources of Western Adriatic Sea produce high bycatch and discard rates; the most important are bottom trawls, hydraulic dredges and passive nets. The five papers here published assess these fisheries��� impacts and investigate the potential of specific solutions to promote more sustainable exploitation. Papers I, II, III focused on bottom trawl fishery. Paper I compared the catch performance of the two legal codends by accounting for the entire species community in trawl catches. 50% of the catch in weight and 80% in count numbers consisted of discarded species, highlighting the severe impact of this fishery. Paper II estimated the selectivity of experimental codend having meshes turned 90�� (T90) and of traditional diamond mesh codend with same mesh size. The T90 codend improved the size selection for all the target species. Paper III investigated the use of T90 meshes in the extension piece together with a reduction in mesh number at extension circumference. Results revealed that both these changes applied in the extension piece did not improve the selectivity of the main target species. Paper IV focused on hydraulic dredge fishery targeting the striped venus clam by assessing the clams��� size selection process operated by the dredge. 25% of the clams caught were not size selected due to clogging phenomenon in the dredge. The clam length with 50% retention probability was 18.9 mm, highlighting that the additional size selection process of sorting sieve is necessary to land only the legal clams >22 mm. Paper V compared the catch performance of innovative fish pots and of traditional trammel net. A similar catch efficiency between the two gears for the commercial portion was observed, while the trammel net produced significantly more discards in terms of species number and weight. All the results are discussed in fisheries management perspective.

Characterization and modeling of low-frequency noise in MOSFETs

For many years, RF and analog integrated circuits have been mainly developed using bipolar and compound semiconductor technologies due to their better performance. In the last years, the advance made in CMOS technology allowed analog and RF circuits to be built with such a technology, but the use of CMOS technology in RF application instead of bipolar technology has brought more issues in terms of noise. The noise cannot be completely eliminated and will therefore ultimately limit the accuracy of measurements and set a lower limit on how small signals can be detected and processed in an electronic circuit. One kind of noise which affects MOS transistors much more than bipolar ones is the low-frequency noise. In MOSFETs, low-frequency noise is mainly of two kinds: flicker or 1/f noise and random telegraph signal noise (RTS). The objective of this thesis is to characterize and to model the low-frequency noise by studying RTS and flicker noise under both constant and switched bias conditions. The effect of different biasing schemes on both RTS and flicker noise in time and frequency domain has been investigated.

X-ray and lensing mass estimates in galaxy clusters

In this Thesis we have presented our work on the analysis of galaxy clusters through their X-ray emission and the gravitational lensing effect that they induce. Our research work was mainly finalised to verify and possibly explain the observed mismatch between the galaxy cluster mass distributions estimated through two of the most promising techniques, i.e. the X-ray and the gravitational lensing analyses. Moreover, it is an established evidence that combined, multi-wavelength analyses are extremely effective in addressing and explaining the open issues in astronomy: however, in order to follow this approach, it is crucial to test the reliability and the limitations of the individual analysis techniques. In this Thesis we also assessed the impact of some factors that could affect both the X-ray and the strong lensing analyses.

Valorizzazione di cartografia storica attraverso moderne tecniche geomatiche: recupero metrico, elaborazione e consultazione in ambiente digitale

���Cartographic heritage��� is different from ���cartographic history���. The second term refers to the study of the development of surveying and drawing techniques related to maps, through time, i.e. through different types of cultural environment which were background for the creation of maps. The first term concerns the whole amount of ancient maps, together with these different types of cultural environment, which the history has brought us and which we perceive as cultural values to be preserved and made available to many users (public, institutions, experts). Unfortunately, ancient maps often suffer preservation problems of their analog support, mostly due to aging. Today, metric recovery in digital form and digital processing of historical cartography allow preserving map heritage. Moreover, modern geomatic techniques give us new chances of using historical information, which would be unachievable on analog supports. In this PhD thesis, the whole digital processing of recovery and elaboration of ancient cartography is reported, with a special emphasis on the use of digital tools in preservation and elaboration of cartographic heritage. It is possible to divide the workflow into three main steps, that reflect the chapter structure of the thesis itself: ��� map acquisition: conversion of the ancient map support from analog to digital, by means of high resolution scanning or 3D surveying (digital photogrammetry or laser scanning techniques); this process must be performed carefully, with special instruments, in order to reduce deformation as much as possible; ��� map georeferencing: reproducing in the digital image the native metric content of the map, or even improving it by selecting a large number of still existing ground control points; this way it is possible to understand the projection features of the historical map, as well as to evaluate and represent the degree of deformation induced by the old type of cartographic transformation (that can be unknown to us), by surveying errors or by support deformation, usually all errors of too high value with respect to our standards; ��� data elaboration and management in a digital environment, by means of modern software tools: vectorization, giving the map a new and more attractive graphic view (for instance, by creating a 3D model), superimposing it on current base maps, comparing it to other maps, and finally inserting it in GIS or WebGIS environment as a specific layer. The study is supported by some case histories, each of them interesting from the point of view of one digital cartographic elaboration step at least. The ancient maps taken into account are the following ones: ��� three maps of the Po river delta, made at the end of the XVI century by a famous land-surveyor, Ottavio Fabri (he is single author in the first map, co-author with Gerolamo Pontara in the second map, co-author with Bonajuto Lorini and others in the third map), who wrote a methodological textbook where he explains a new topographical instrument, the squadra mobile (mobile square) invented and used by himself; today all maps are preserved in the State Archive of Venice; ��� the Ichnoscenografia of Bologna by Filippo de��� Gnudi, made in the 1702 and today preserved in the Archiginnasio Library of Bologna; it is a scenographic view of the city, captured in a bird���s eye flight, but also with an icnographic value, as the author himself declares; ��� the map of Bologna by the periti Gregorio Monari and Antonio Laghi, the first map of the city derived from a systematic survey, even though it was made only ten years later (1711���1712) than the map by de��� Gnudi; in this map the scenographic view was abandoned, in favor of a more correct representation by means of orthogonal projection; today the map is preserved in the State Archive of Bologna; ��� the Gregorian Cadastre of Bologna, made in 1831 and updated until 1927, now preserved in the State Archive of Bologna; it is composed by 140 maps and 12 brogliardi (register volumes). In particular, the three maps of the Po river delta and the Cadastre were studied with respect to their acquisition procedure. Moreover, the first maps were analyzed from the georeferencing point of view, and the Cadastre was analyzed with respect to a possible GIS insertion. Finally, the Ichnoscenografia was used to illustrate a possible application of digital elaboration, such as 3D modeling. Last but not least, we must not forget that the study of an ancient map should start, whenever possible, from the consultation of the precious original analogical document; analysis by means of current digital techniques allow us new research opportunities in a rich and modern multidisciplinary context.

Geografie in rete e in biblioteca: la ricerca bibliografica in ambito geografico, turistico e ambientale

The purpose of this work is to provide a methodological tool for literature searching in geography, tourism and environmental conservation. Knowledge of bibliographic and documentary resources and learning research strategies form an essential part of training for students and researchers. Literature searching is also a critical element of communication and scientific output. This work aims to analyze the characteristics, and critical issues in geography literature searching in order to provide a critical mass of useful information to correctly prepare a search. Having addressed the issue of information literacy for the study of geography and related disciplines, including a comparison of various approaches, this work describes the physical locations of the research: libraries and archives. It outlines the issues related to the cataloging and digitization of cartographic materials. The particular characteristics of scientific communication and its primary means of dissemination, the scientific journal, are then outlined. This is followed by a description of information sources and types of documents used within the realm of geography. Tools, strategies and resources are then illustrated for conducting an effective literature search both on the web and in the library.

La nutrizione-idratazione artificiale �� terapia? All'interfaccia tra scienza, diritto e bioetica, il fine vita in Italia, secondo una prospettiva di comunicazione della scienza post-accademica e Science&Technologies Studies (STS)

The question ���artificial nutrition and hydration (ANH) is therapy or not?��� is one of the key point of end-of-life issues in Italy, since it was (and it is also nowadays) a strategic and crucial point of the Italian Bioethics discussion about the last phases of human life: determining if ANH is therapy implies the possibility of being included in the list of treatments that could be mentioned for refusal within the living will document. But who is entitled to decide and judge if ANH is a therapy or not? Scientists? The Legislator? Judges? Patients? This issue at first sight seems just a matter of science, but at stake there is more than a scientific definition. According to several scholars, we are in the era of post-academic Science, in which Science broaden discussion, production, negotation and decision to other social groups that are not just the scientific communities. In this process, called co-production, on one hand scientific knowledge derives from the interaction between scientists and society at large. On the other hand, science is functional to co-production of social order. The continuous negotation on which science has to be used in social decisions is just the evidence of the mirroring negotation for different way to structure and interpret society. Thus, in the interaction between Science and Law, deciding what kind of Science could be suitable for a specific kind of Law, envisages a well defined idea of society behind this choice. I have analysed both the legislative path (still in progress) in the living will act production in Italy and Eluana Englaro���s judicial case (that somehow collapsed in the living will act negotiation), using official documents (hearings, texts of the official conference, committees comments and ruling texts) and interviewing key actors in the two processes from the science communication point of view (who talks in the name of science? Who defines what is a therapy? And how do they do?), finding support on the theoretical framework of the Science&Technologies Studies (S&TS).

Social aspects of organic agriculture and other multifunctional benefits - Successful EU models compared with possibilities for organic developments in Croatia

Main objective of the dissertation is to illustrate how social and educational aspects (in close interaction with other multifunctional aspects in organic agriculture) which are developed on different multifunctional organic farms in Italy and Netherlands, as well as established agricultural policy frameworks in these countries, can be compared with the situation in Croatian organics and can contribute to further developent of organic issues in the Repubic of Croatia. So, through different chapters, the dissertation describes the performance of organic agriculture sectors in Italy, Netherlands and Croatia within the national agricultural policy frameworks, it analyzes the role of national institutions and policy in Croatia in connection with Croatia's status of candidate country for enterance into EU and harmonization of legislation with the CAP, as well as analyzes what is the role of national authorities, universities, research centres, but also of private initiatives, NGOs and cooperatives in organic agriculture in Netherlands, Italy and Croatia. Its main part describes how social and educational aspects are interacting with other multifunctional aspects in organic agriculture and analyzes the benefits and contribution of multifunctional activites performed on organic farms to education, healthy nourishment, environment protection and health care. It also assess the strengths and weaknesses of organic agriculture in all researched countries. The dissertation concludes with development opportunities for multifunctional organic agriculture in Croatia, as well as giving perspectives and recommendations for different approaches on the basis of experiences learned from successful EU models accompanied with some personal ideas and proposals.

L'accertamento dei reati di guida in stato di ebbrezza e alterazione da droghe

La tesi affronta le questioni processuali connesse alla verifica dei reati di guida in stato di ebbrezza e di alterazione da droghe. La ricerca si sviluppa in tre direzioni. La prima parte studia la disciplina tedesca. L���analisi parte dalle norme sostanziali che definiscono le fattispecie incriminatrici contemplate dall���ordinamento osservato; s���interessa, poi, degli equilibri tra gli strumenti di captazione della prova utili ai reati in discorso ed il principio nemo tenetur se detegere (l��� estensione del diritto di difesa tedesco copre anche le prove reali e non prevede obblighi di collaborazione all���alcoltest). Prosegue, infine, con l���esame delle metodologie di acquisizione della prova, dall���etilometro agli screening per le droghe, sino al prelievo ematico coattivo, indispensabile per l���accertamento penale. La seconda sezione esamina gli artt. 186 e 187 del codice della strada italiano, alla luce del principio di libert�� personale e del diritto a non autoincriminarsi. Particolarmente delicati gli equilibri rispetto a quest���ultimo: l���obbligatoriet�� di un atto potenzialmente autoaccusatorio �� evitabile solo a pena di una severa sanzione. Occorre definire se il diritto di difesa copra anche il mero facere o garantisca il solo silenzio. Se si ammette, infatti, che il nemo tenetur sia applicabile anche alle prove reali, la collaborazione obbligatoria imposta al conducente �� scelta incompatibile con il diritto di difesa: la disciplina italiana presenta, dunque, profili d���illegittimit�� costituzionale. La terza parte riguarda le problematiche processuali poste dai controlli stradali che emergono dall���analisi della giurisprudenza. Si affrontano, cos��, le diverse vicende della formazione della prova: ci si interroga sull���istituto processuale cui ricondurre gli accertamenti, sulle garanzie di cui goda il guidatore durante e dopo l���espletamento dell���atto, sulle eventuali sanzioni processuali derivanti da una violazione delle predette garanzie. Si esaminano, infine, le regole di apprezzamento della prova che guidano il giudice nella delicata fase valutativa.

Aspetti di sostenibilit�� in agricoltura a diverse scale spaziali e temporali. Valutazioni ambientali, economiche ed energetiche.

La Tesi analizza le relazioni tra i processi di sviluppo agricolo e l���uso delle risorse naturali, in particolare di quelle energetiche, a livello internazionale (paesi in via di sviluppo e sviluppati), nazionale (Italia), regionale (Emilia Romagna) e aziendale, con lo scopo di valutare l���eco-efficienza dei processi di sviluppo agricolo, la sua evoluzione nel tempo e le principali dinamiche in relazione anche ai problemi di dipendenza dalle risorse fossili, della sicurezza alimentare, della sostituzione tra superfici agricole dedicate all���alimentazione umana ed animale. Per i due casi studio a livello macroeconomico �� stata adottata la metodologia denominata ���SUMMA��� SUstainability Multi-method, multi-scale Assessment (Ulgiati et al., 2006), che integra una serie di categorie d���impatto dell���analisi del ciclo di vita, LCA, valutazioni costi-benefici e la prospettiva di analisi globale della contabilit�� emergetica. L���analisi su larga scala �� stata ulteriormente arricchita da un caso studio sulla scala locale, di una fattoria produttrice di latte e di energia elettrica rinnovabile (fotovoltaico e biogas). Lo studio condotto mediante LCA e valutazione contingente ha valutato gli effetti ambientali, economici e sociali di scenari di riduzione della dipendenza dalle fonti fossili. I casi studio a livello macroeconomico dimostrano che, nonostante le politiche di supporto all���aumento di efficienza e a forme di produzione ���verdi���, l���agricoltura a livello globale continua ad evolvere con un aumento della sua dipendenza dalle fonti energetiche fossili. I primi effetti delle politiche agricole comunitarie verso una maggiore sostenibilit�� sembrano tuttavia intravedersi per i Paesi Europei. Nel complesso la energy footprint si mantiene alta poich�� la meccanizzazione continua dei processi agricoli deve necessariamente attingere da fonti energetiche sostitutive al lavoro umano. Le terre agricole diminuiscono nei paesi europei analizzati e in Italia aumentando i rischi d���insicurezza alimentare giacch�� la popolazione nazionale sta invece aumentando.

A threshold hypothesis of institutional change: collective action in the Italian Alps during the 13th - 19th centuries.

This dissertation is about collective action issues in common property resources. Its focus is the ���threshold hypothesis,��� which posits the existence of a threshold in group size that drives the process of institutional change. This hypothesis is tested using a six-century dataset concerning the management of the commons by hundreds of communities in the Italian Alps. The analysis seeks to determine the group size threshold and the institutional changes that occur when groups cross this threshold. There are five main findings. First, the number of individuals in villages remained stable for six centuries, despite the population in the region tripling in the same period. Second, the longitudinal analysis of face-to-face assemblies and community size led to the empirical identification of a threshold size that triggered the transition from informal to more formal regimes to manage common property resources. Third, when groups increased in size, gradual organizational changes took place: large groups split into independent subgroups or structured interactions into multiple layers while maintaining a single formal organization. Fourth, resource heterogeneity seemed to have had no significant impact on various institutional characteristics. Fifth, social heterogeneity showed statistically significant impacts, especially on institutional complexity, consensus, and the relative importance of governance rules versus resource management rules. Overall, the empirical evidence from this research supports the ���threshold hypothesis.��� These findings shed light on the rationale of institutional change in common property regimes, and clarify the mechanisms of collective action in traditional societies. Further research may generalize these conclusions to other domains of collective action and to present-day applications.

The Application of European Competition Law in Arbitration Proceedings

This work provides several policy proposals capable to strengthen the private enforcement of EU competition law in arbitration. It focuses on the procedural law aspects that are permeated by legal uncertainty and that have not yet fallen under the scrutiny of the law and economics debate. The policy proposals described herein are based on the functional approach to law and economics and aim to promote a more qualified decision making process by: adjudicators, private parties and lawmakers. The resulting framework of procedural rules would be a cost-effective policy tool that could sustain the European Commission���s effort to guarantee a workable level of competition in the EU internal market. This project aims to answer the following broad research question: which procedural rules can improve the efficiency of antitrust arbitration by decreasing litigation costs for private parties on the one hand, and by increasing private parties��� compliance with competition law on the other hand?Throughout this research project, such broad question has been developed into research sub-questions revolving around several key legal issues. The chosen sub-research questions result from a vacuum in the European enforcement system that leaves several key legal issues in antitrust arbitration unresolved. The legal framework proposed in this research project could prevent such a blurry scenario from impairing the EU private enforcement of competition law in arbitration. Therefore, our attention was triggered by those legal issues whose proposed solutions lead to relevant uncertainties and that are most suitable for a law and economics analysis.