Bioimaging of animal embryogenesis: mathematical methods and computational algorithms

Some fundamental biological processes such as embryonic development have been preserved during evolution and are common to species belonging to different phylogenetic positions, but are nowadays largely unknown. The understanding of cell morphodynamics leading to the formation of organized spatial distribution of cells such as tissues and organs can be achieved through the reconstruction of cells shape and position during the development of a live animal embryo. We design in this work a chain of image processing methods to automatically segment and track cells nuclei and membranes during the development of a zebrafish embryo, which has been largely validates as model organism to understand vertebrate development, gene function and healingrepair mechanisms in vertebrates. The embryo is previously labeled through the ubiquitous expression of fluorescent proteins addressed to cells nuclei and membranes, and temporal sequences of volumetric images are acquired with laser scanning microscopy. Cells position is detected by processing nuclei images either through the generalized form of the Hough transform or identifying nuclei position with local maxima after a smoothing preprocessing step. Membranes and nuclei shapes are reconstructed by using PDEs based variational techniques such as the Subjective Surfaces and the Chan Vese method. Cells tracking is performed by combining informations previously detected on cells shape and position with biological regularization constraints. Our results are manually validated and reconstruct the formation of zebrafish brain at 7-8 somite stage with all the cells tracked starting from late sphere stage with less than 2% error for at least 6 hours. Our reconstruction opens the way to a systematic investigation of cellular behaviors, of clonal origin and clonal complexity of brain organs, as well as the contribution of cell proliferation modes and cell movements to the formation of local patterns and morphogenetic fields.

Elettori e partiti nell'Europa contemporanea: Est ed Ovest a confronto

The research is focused on the origin and the structure of the European party systems in long-standing democracies and in post-communist countries. Considering the differences between the western frozen party systems and the eastern unfrozen party systems, we propose a framework of analysis based on the theoretical and conceptual linkage between genetic approach and spatial theories of competition, identified in the normative component of a cleavage. At first, we propose some operational criteria to distinguish the dimensions of competition from the dimensions of identification through the use of the manifesto project surveys. Then, through the data of an expert survey and of some recent electoral mass surveys, we empirically test a set of propositions concerning, on the one hand, the congruence between party policy positions and party-voters policy positions and, on the other hand, the level of correlation between parties positions on different issue dimensions and their placement on the left-right axis.

Mediterranean brachiopods: morphological, ecological and phylogenetic aspects

The Brachiopoda of the Marine Protected Area “Secche di Tor Paterno”, Central Tyrrhenian Sea, have been investigated in order to give a first glance of the diversity of the brachiopods of this area and provide a new report on the Mediterranean Brachiopod fauna. Four species were reported: Novocrania anomala (Müller, 1776), Megathiris detruncata (Gmelin, 1790), Joania cordata (Risso,1826) and Argyrotheca cuneata (Risso,1826). For all the four species a morphological analysis was carried out. For the two most abundant species, J.cordata and A. cuneata, a morphometric study, based on thickness/width and length/width scattergrams, was carried out, in order to investigate their variability. Size-frequency distributions relative to the three dimensions of the shell were also computed, aimed at a evaluation of population dynamics of these two species. The results showed that, for both species, the parameters which most determine the rise of the shell during the growth of animal are width and length and that frequency distributions are mainly bi- or plurymodal and that they are difficult to interpret, as reported by other studies. Analysis of drill holes found on the shell of some specimens of the two same species revealed a predatory origin and that three different predators are responsible for them. Partial sequences of two different genetic markers, the Internal Transcribed Spacer 1 (ITS1) and the cytochrome oxidase subunit 1 (COI), were used to investigate the phylogenetic relationship between two populations of the eurybathic brachiopod species Gryphus vitreus (Born,1778) across the strait of Gibraltar. This represents the first genetic population study on brachiopods. Results from AMOVA and Bayesian analysis performed on 31 specimens highlighted no genetic differentiation indicating a likely panmixia, dispite the lecitotrophic development of the species.

Nanoscale-electrical and optical properties of iii-nitrides

III-nitrides are wide-band gap materials that have applications in both electronics and optoelectronic devices. Because to their inherent strong polarization properties, thermal stability and higher breakdown voltage in Al(Ga,In)N/GaN heterostructures, they have emerged as strong candidates for high power high frequency transistors. Nonetheless, the use of (Al,In)GaN/GaN in solid state lighting has already proved its success by the commercialization of light-emitting diodes and lasers in blue to UV-range. However, devices based on these heterostructures suffer problems associated to structural defects. This thesis primarily focuses on the nanoscale electrical characterization and the identification of these defects, their physical origin and their effect on the electrical and optical properties of the material. Since, these defects are nano-sized, the thesis deals with the understanding of the results obtained by nano and micro-characterization techniques such as atomic force microscopy(AFM), current-AFM, scanning kelvin probe microscopy (SKPM), electron beam induced current (EBIC) and scanning tunneling microscopy (STM). This allowed us to probe individual defects (dislocations and cracks) and unveil their electrical properties. Taking further advantage of these techniques,conduction mechanism in two-dimensional electron gas heterostructures was well understood and modeled. Secondarily, origin of photoluminescence was deeply investigated. Radiative transition related to confined electrons and photoexcited holes in 2DEG heterostructures was identified and many body effects in nitrides under strong optical excitations were comprehended.

Who can (not) be Greek? Citizenship, Identity and Belonging among youth of sub-Saharan African background in Athens

‘Who can be Greek?’ This was the question posed to the Greek society for the first time before the implementation of the Act 3838 in March 2010 which gave the right to access the Greek citizenship -under specific preconditions- to all children of legal migrants born or schooled in Greece. This change of the Nationality Code in order to include all those children was coincided by the economic crisis resulting into the rise of xenophobia, racism and extreme-right rhetoric. The outcome was the cancellation of the Act 3838 by the State Council in February 2013. Under this particular framework, the notions of identity and belonging formed among the youth of African background in Athens are explored. The ways those youngsters perceive not only themselves but also their peers, their countries of origin and the country they live in, are crucial elements of their self-identification. Researches have shown that the integration of the second generation is highly connected to their legal and social status. However, integration is a rather complex process, influenced and shaped by many variables and multiple factors. It is not linear; therefore, its outcomes are difficult to be predicted. Yet, I argue that citizenship acquisition facilitates the process as it transforms those children from ‘aliens’ to ‘citizens’. How these youngsters are perceived by the majority society and the State is one of the core questions of the research, focusing on the imposed dual ‘otherness’ they are subject to. On the one hand, they have to deal with the ‘otherness’ originating from the migrant status inherited to them by their parents, and on the other with the ‘otherness’ deriving from their different phenotypic characteristics. Race matters and becomes a means of discrimination against youth of African background who are perceived as inassimilable and ‘forever others’.

Identification and genetic diversity in phytoplasmas associated with diseases of cassava and other agronomic relevant crops in south-east Asia and Latin America

Identification and genetic diversity of phytoplasmas infecting tropical plant species, selected among those most agronomically relevant in South-east Asia and Latin America were studied. Correlation between evolutionary divergence of relevant phytoplasma strains and their geographic distribution by comparison on homologous genes of phytoplasma strains detected in the same or related plant species in other geographical areas worldwide was achieved. Molecular diversity was studied on genes coding ribosomal proteins, groEL, tuf and amp besides phytoplasma 16S rRNA. Selected samples infected by phytoplasmas belonging to diverse ribosomal groups were also studied by in silico RFLP followed by phylogenetic analyses. Moreover a partial genome annotation of a ‘Ca. P. brasiliense’ strain was done towards future application for epidemiological studies. Phytoplasma presence in cassava showing frog skin (CFSD) and witches’ broom (CWB) diseases in Costa Rica - Paraguay and in Vietnam – Thailand, respectively, was evaluated. In both cases, the diseases were associated with phytoplasmas related to aster yellows, apple proliferation and “stolbur” groups, while only phytoplasma related to X-disease group in CFSD, and to hibiscus witches’ broom, elm yellows and clover proliferation groups in CWB. Variability was found among strains belonging to the same ribosomal group but having different geographic origin and associated with different disease. Additionally, a dodder transmission assay to elucidate the role of phytoplasmas in CWB disease was carried out, and resulted in typical phytoplasma symptoms in periwinkle plants associated with the presence of aster yellows-related strains. Lethal wilt disease, a severe disease of oil palm in Colombia that is spreading throughout South America was also studied. Phytoplasmas were detected in symptomatic oil palm and identified as ‘Ca. P. asteris’, ribosomal subgroup 16SrI-B, and were distinguished from other aster yellows phytoplasmas used as reference strains; in particular, from an aster yellows strain infecting corn in the same country.

Country-of-Origin Labeling for Processed Foods

The country-of-origin is the “nationality” of a food when it goes through customs in a foreign country, and is a “brand” when the food is for sale in a foreign market. My research on country-of-origin labeling (COOL) started from a case study on the extra virgin olive oil exported from Italy to China; the result shows that asymmetric and imperfect origin information may lead to market inefficiency, even market failure in emerging countries. Then, I used the Delphi method to conduct qualitative and systematic research on COOL; the panel of experts in food labeling and food policy was composed of 19 members in 13 countries; the most important consensus is that multiple countries of origin marking can provide accurate information about the origin of a food produced by two or more countries, avoiding misinformation for consumers. Moreover, I enhanced the research on COOL by analyzing the rules of origin and drafting a guideline for the standardization of origin marking. Finally, from the perspective of information economics I estimated the potential effect of the multiple countries of origin labeling on the business models of international trade, and analyzed the regulatory options for mandatory or voluntary COOL of main ingredients. This research provides valuable insights for the formulation of COOL policy.

X-ray properties and evolution of high-redshift AGN, and the gas content of host galaxies

In this thesis, I have investigated the evolution of the high-redshift (z > 3) AGN population by collecting data from some of the major Chandra and XMM-Newton surveys. The final sample (141 sources) is one of the largest selected at z> 3 in the X- rays and it is characterised by a very high redshift completeness (98%). I derived the spectral slopes and obscurations through a spectral anaysis and I assessed the high-z evolution by deriving the luminosity function and the number counts of the sample. The best representation of the AGN evolution is a pure density evolution (PDE) model: the AGN space density is found to decrease by a factor of 10 from z=3 to z=5. I also found that about 50% of AGN are obscured by large column densities (logNH > 23). By comparing these data with those in the Local Universe, I found a positive evolution of the obscured AGN fraction with redshift, especially for luminous (logLx > 44) AGN. I also studied the gas content of z < 1 AGN-hosting galaxies and compared it with that of inactive galaxies. For the first time, I applied to AGN a method to derive the gas mass previously used for inactive galaxies only. AGN are found to live preferentially in gas-rich galaxies. This result on the one hand can help us in understanding the AGN triggering mechanisms, on the other hand explains why AGN are preferentially hosted by star-forming galaxies.

Origin of the spin Seebeck effect

Der Spin Seebeck Effekt repräsentiert einen neuartigen Spin kalorischen Effekt mit vorteilhaften und aussichtsreichen Eigenschaften für Anwendungen in den Gebieten der Spintronik und Thermoelektrik.rnIn dieser Arbeit präsentieren wir eine umfangreiche Untersuchung des Spin Seebeck Effekts in isolierenden, magnetischen Granaten und geben Antworten zum kontrovers diskutierten Ursprung des Effekts. Um dieses Ziel zu erreichen, haben wir die Abhängigkeit des Spin Seebeck Effekts von der Dicke des Ferromagneten, der Temperatur, der Stärke des magnetisches Feldes, der Grenzflächen und des Detektormaterials, sowie Kombinationen dieser Parameter gemessen. Im Zuge dessen haben wir das Wachstum der untersuchten magnetischen Granate optimiert und eine umfassende Analyse der strukturellen und magnetischen Parameter durchgeführt, um Einflüsse der Probenqualität auszuschließen. Des Weiteren zeigte eine Untersuchung des magnetoresistiven Effekts, welcher als mögliche Ursache des Effekts galt, in Kombination mit einer Studie des Messaufbaus, dass parasitäre Einflüsse auf das Messergebnis ausgeschlossen werden können. Unsere Ergebnisse zeigen, dass der Spin Seebeck Effekt mit zunehmender Dicke des Ferromagneten eine Sättigung des Signals aufweist. Diese hängt zudem von der Temperatur ab, da mit abnehmender Temperatur die Sättigung erst bei dickeren Filmen auftritt. Außerdem fanden unsere Messungen ein Maximum des Spin Seebeck Effekts für Temperaturen unterhalb der Raumtemperatur, welcher sowohl von der Dicke des Materials als auch der Magnetfeldstärke und dem Detektormaterial beeinflusst wird. In Messungen bei hohen magnetischen Feldstärken beobachteten wir eine Unterdrückung des Messsignals, dessen Ursache mithilfe von Simulationen auf den magnonischen Ursprung des Spin Seebeck Effekts zurückgeführt werden kann. Dies unterstreicht, dass der Effekt auf vom Ferromagneten emittierten Magnonen basiert. Im letzten Abschnitt dieser Arbeit präsentieren wir Messungen in einem bislang nicht untersuchten ferrimagnetischen Material, welche zwei Vorzeichenwechsel des Spin Seebeck Effekts als Funktion der Temperatur aufzeigen. Dieses bisher unbekannte Signalverhalten betont, dass der Effekt aus einem komplexen Zusammenspiel der magnonischen Moden resultiert und zusätzlich vom Detektormaterial abhängt.rnSomit tragen unsere Ergebnisse und Beobachtungen im hohen Maße zur Beantwortung der Frage nach dem Ursprungs des Spin Seebeck Effekts bei und zeigen neuartige bisher nicht beobachtete Effekte, welche ein neues Kapitel für das Gebiet der Spin Kaloritronik eröffnen.

Tor network forensics and hidden service deanonymization

The cybernetics revolution of the last years improved a lot our lives, having an immediate access to services and a huge amount of information over the Internet. Nowadays the user is increasingly asked to insert his sensitive information on the Internet, leaving its traces everywhere. But there are some categories of people that cannot risk to reveal their identities on the Internet. Even if born to protect U.S. intelligence communications online, nowadays Tor is the most famous low-latency network, that guarantees both anonymity and privacy of its users. The aim of this thesis project is to well understand how the Tor protocol works, not only studying its theory, but also implementing those concepts in practice, having a particular attention for security topics. In order to run a Tor private network, that emulates the real one, a virtual testing environment has been configured. This behavior allows to conduct experiments without putting at risk anonymity and privacy of real users. We used a Tor patch, that stores TLS and circuit keys, to be given as inputs to a Tor dissector for Wireshark, in order to obtain decrypted and decoded traffic. Observing clear traffic allowed us to well check the protocol outline and to have a proof of the format of each cell. Besides, these tools allowed to identify a traffic pattern, used to conduct a traffic correlation attack to passively deanonymize hidden service clients. The attacker, controlling two nodes of the Tor network, is able to link a request for a given hidden server to the client who did it, deanonymizing him. The robustness of the traffic pattern and the statistics, such as the true positive rate, and the false positive rate, of the attack are object of a potential future work.

Interplay between yawning and vigilance: a review of the experimental evidence

Yawning is a phylogenetically old behavior of ubiquitous occurrence. The origin and function of this conspicuous phenomenon have been subject to speculation for centuries. A widely held hypothesis posits that yawning increases the arousal level during sleepiness; thus, providing a homeostatic regulation of vigilance.

Core networks for visual-concrete and abstract thought content: a brain electric microstate analysis

Commonality of activation of spontaneously forming and stimulus-induced mental representations is an often made but rarely tested assumption in neuroscience. In a conjunction analysis of two earlier studies, brain electric activity during visual-concrete and abstract thoughts was studied. The conditions were: in study 1, spontaneous stimulus-independent thinking (post-hoc, visual imagery or abstract thought were identified); in study 2, reading of single nouns ranking high or low on a visual imagery scale. In both studies, subjects' tasks were similar: when prompted, they had to recall the last thought (study 1) or the last word (study 2). In both studies, subjects had no instruction to classify or to visually imagine their thoughts, and accordingly were not aware of the studies' aim. Brain electric data were analyzed into functional topographic brain images (using LORETA) of the last microstate before the prompt (study 1) and of the word-type discriminating event-related microstate after word onset (study 2). Conjunction analysis across the two studies yielded commonality of activation of core networks for abstract thought content in left anterior superior regions, and for visual-concrete thought content in right temporal-posterior inferior regions. The results suggest that two different core networks are automatedly activated when abstract or visual-concrete information, respectively, enters working memory, without a subject task or instruction about the two classes of information, and regardless of internal or external origin, and of input modality. These core machineries of working memory thus are invariant to source or modality of input when treating the two types of information.

Land use policies and practices for reducing vulnerability in rural Tajikistan

Tajikistan, with 93% of its surface area taken up by mountains and 65% of its labor force employed in agriculture, is judged to be highly vulnerable to risks, including climate change risks and food insecurity risks. The article examines a set of land use policies and practices that can be used to mitigate the vulnerability of Tajikistan’s large rural population, primarily by increasing family incomes. Empirical evidence from Tajikistan and other CIS countries suggests that families with more land and higher commercialization earn higher incomes and achieve higher well-being. The recommended policy measures that are likely to increase rural family incomes accordingly advocate expansion of smallholder farms, improvement of livestock productivity, increase of farm commercialization through improvement of farm services, and greater diversification of both income sources and the product mix. The analysis relies for supporting evidence on official statistics and recent farm surveys. Examples from local initiatives promoting sustainable land management practices and demonstrating the implementation of the proposed policy measures are presented.

Epidemiology and predictors of spinal injury in adult major trauma patients: European cohort study

This is a European cohort study on predictors of spinal injury in adult (≥16 years) major trauma patients, using prospectively collected data of the Trauma Audit and Research Network from 1988 to 2009. Predictors for spinal fractures/dislocations or spinal cord injury were determined using univariate and multivariate logistic regression analysis. 250,584 patients were analysed. 24,000 patients (9.6%) sustained spinal fractures/dislocations alone and 4,489 (1.8%) sustained spinal cord injury with or without fractures/dislocations. Spinal injury patients had a median age of 44.5 years (IQR = 28.8-64.0) and Injury Severity Score of 9 (IQR = 4-17). 64.9% were male. 45% of patients suffered associated injuries to other body regions. Age <45 years (≥45 years OR 0.83-0.94), Glasgow Coma Score (GCS) 3-8 (OR 1.10, 95% CI 1.02-1.19), falls >2 m (OR 4.17, 95% CI 3.98-4.37), sports injuries (OR 2.79, 95% CI 2.41-3.23) and road traffic collisions (RTCs) (OR 1.91, 95% CI 1.83-2.00) were predictors for spinal fractures/dislocations. Age <45 years (≥45 years OR 0.78-0.90), male gender (female OR 0.78, 95% CI 0.72-0.85), GCS <15 (OR 1.36-1.93), associated chest injury (OR 1.10, 95% CI 1.01-1.20), sports injuries (OR 3.98, 95% CI 3.04-5.21), falls >2 m (OR 3.60, 95% CI 3.21-4.04), RTCs (OR 2.20, 95% CI 1.96-2.46) and shooting (OR 1.91, 95% CI 1.21-3.00) were predictors for spinal cord injury. Multilevel injury was found in 10.4% of fractures/dislocations and in 1.3% of cord injury patients. As spinal trauma occurred in >10% of major trauma patients, aggressive evaluation of the spine is warranted, especially, in males, patients <45 years, with a GCS <15, concomitant chest injury and/or dangerous injury mechanisms (falls >2 m, sports injuries, RTCs and shooting). Diagnostic imaging of the whole spine and a diligent search for associated injuries are substantial.

Aberrant E-cadherin, beta-catenin, and glial fibrillary acidic protein (GFAP) expression in canine choroid plexus tumors

Expression of E-cadherin and beta-catenin has been widely studied in various human and canine epithelial tumors and has been correlated with dedifferentiation, invasiveness, and metastasis. Choroid plexus tumors (CPTs) are of epithelial origin, and the most important prognostic factor in human medicine is the tumor grade. Limited information is available regarding E-cadherin and beta-catenin expression in human CPTs, and no information is found in the veterinary literature. In the current study, 42 canine CPTs (19 choroid plexus papillomas and 23 choroid plexus carcinomas) were retrospectively reviewed, and the intensity and cellular staining pattern of E-cadherin and beta-catenin were correlated with histological features, paying special attention to grade, invasion, and metastasis. In addition, cytokeratin and glial fibrillary acidic protein (GFAP) antibodies were evaluated as markers for canine CPTs. It was found that loss of E-cadherin and beta-catenin expression was uncommon in canine CPTs. Rather, membranous expression of both molecules was increased in CPTs compared to normal choroid plexus (NCP), regardless of tumor grade. Additionally, aberrant cytoplasmic or nuclear expression of both E-cadherin and beta-catenin was often observed in CPTs. GFAP was frequently expressed in CPTs in contrast to NCP. None of these parameters were correlated with malignancy, and therefore, do not appear to be useful for prognostic information. Nevertheless, a panel of antibodies including E-cadherin and GFAP might be useful to support the diagnosis of CPTs and help to differentiate them from other tumors, such as ependymomas and metastatic epithelial tumors.