A NEW METHOD TO QUANTIFY X-RAY SUBSTRUCTURES IN CLUSTERS OF GALAXIES

We present a new method to quantify substructures in clusters of galaxies, based on the analysis of the intensity of structures. This analysis is done in a residual image that is the result of the subtraction of a surface brightness model, obtained by fitting a two-dimensional analytical model (beta-model or Sersic profile) with elliptical symmetry, from the X-ray image. Our method is applied to 34 clusters observed by the Chandra Space Telescope that are in the redshift range z is an element of [0.02, 0.2] and have a signal-to-noise ratio (S/N) greater than 100. We present the calibration of the method and the relations between the substructure level with physical quantities, such as the mass, X-ray luminosity, temperature, and cluster redshift. We use our method to separate the clusters in two sub-samples of high-and low-substructure levels. We conclude, using Monte Carlo simulations, that the method recuperates very well the true amount of substructure for small angular core radii clusters (with respect to the whole image size) and good S/N observations. We find no evidence of correlation between the substructure level and physical properties of the clusters such as gas temperature, X-ray luminosity, and redshift; however, analysis suggest a trend between the substructure level and cluster mass. The scaling relations for the two sub-samples (high-and low-substructure level clusters) are different (they present an offset, i. e., given a fixed mass or temperature, low-substructure clusters tend to be more X-ray luminous), which is an important result for cosmological tests using the mass-luminosity relation to obtain the cluster mass function, since they rely on the assumption that clusters do not present different scaling relations according to their dynamical state.

Dynamics of the halo gas in disc galaxies

This Thesis studies the dynamics of hot and cold gas outside the plane in galaxies like the Milky-Way (extra-planar gas) and focuses on the interaction between disc and halo material. Stationary models for the cold phase of the extra-planar gas are presented. They show that the kinematics of this phase must be influenced by the interaction with an ambient medium that we identify as the hot cosmological corona that surrounds disc galaxies. To study this interaction a novel hydrodynamical code has been implemented and a series of hydrodynamical simulations has been run to investigate the mass and momentum exchange between the cold extra-planar gas clouds and the hot corona. These simulations show that the coronal gas can condense efficiently in the turbulent wakes that form behind the cold clouds and it can be accreted by the disc to sustain star formation. They also predict that the corona cannot be a static structure but it must rotate and lag by approximately 80-120 km/s with respect to the disc. Implications of the results of this Thesis for the evolution of star-forming galaxies and for the large-scale dynamics of galactic coronae are also briefly discussed.

Development of parallelizable flood inundation models for large scale analysis

Flood disasters are a major cause of fatalities and economic losses, and several studies indicate that global flood risk is currently increasing. In order to reduce and mitigate the impact of river flood disasters, the current trend is to integrate existing structural defences with non structural measures. This calls for a wider application of advanced hydraulic models for flood hazard and risk mapping, engineering design, and flood forecasting systems. Within this framework, two different hydraulic models for large scale analysis of flood events have been developed. The two models, named CA2D and IFD-GGA, adopt an integrated approach based on the diffusive shallow water equations and a simplified finite volume scheme. The models are also designed for massive code parallelization, which has a key importance in reducing run times in large scale and high-detail applications. The two models were first applied to several numerical cases, to test the reliability and accuracy of different model versions. Then, the most effective versions were applied to different real flood events and flood scenarios. The IFD-GGA model showed serious problems that prevented further applications. On the contrary, the CA2D model proved to be fast and robust, and able to reproduce 1D and 2D flow processes in terms of water depth and velocity. In most applications the accuracy of model results was good and adequate to large scale analysis. Where complex flow processes occurred local errors were observed, due to the model approximations. However, they did not compromise the correct representation of overall flow processes. In conclusion, the CA model can be a valuable tool for the simulation of a wide range of flood event types, including lowland and flash flood events.

A clustering method for robust and reliable large scale functional and structural protein sequence annotation

Bioinformatics, in the last few decades, has played a fundamental role to give sense to the huge amount of data produced. Obtained the complete sequence of a genome, the major problem of knowing as much as possible of its coding regions, is crucial. Protein sequence annotation is challenging and, due to the size of the problem, only computational approaches can provide a feasible solution. As it has been recently pointed out by the Critical Assessment of Function Annotations (CAFA), most accurate methods are those based on the transfer-by-homology approach and the most incisive contribution is given by cross-genome comparisons. In the present thesis it is described a non-hierarchical sequence clustering method for protein automatic large-scale annotation, called “The Bologna Annotation Resource Plus” (BAR+). The method is based on an all-against-all alignment of more than 13 millions protein sequences characterized by a very stringent metric. BAR+ can safely transfer functional features (Gene Ontology and Pfam terms) inside clusters by means of a statistical validation, even in the case of multi-domain proteins. Within BAR+ clusters it is also possible to transfer the three dimensional structure (when a template is available). This is possible by the way of cluster-specific HMM profiles that can be used to calculate reliable template-to-target alignments even in the case of distantly related proteins (sequence identity < 30%). Other BAR+ based applications have been developed during my doctorate including the prediction of Magnesium binding sites in human proteins, the ABC transporters superfamily classification and the functional prediction (GO terms) of the CAFA targets. Remarkably, in the CAFA assessment, BAR+ placed among the ten most accurate methods. At present, as a web server for the functional and structural protein sequence annotation, BAR+ is freely available at http://bar.biocomp.unibo.it/bar2.0.

Spatio-temporal models of the functional architecture of the visual cortex

In this work I tried to explore many aspects of cognitive visual science, each one based on different academic fields, proposing mathematical models capable to reproduce both neuro-physiological and phenomenological results that were described in the recent literature. The structure of my thesis is mainly composed of three chapters, corresponding to the three main areas of research on which I focused my work. The results of each work put the basis for the following, and their ensemble form an homogeneous and large-scale survey on the spatio-temporal properties of the architecture of the visual cortex of mammals.

Validity and reliability of the German version of the short understanding of substance abuse scale

This paper presents the German version of the Short Understanding of Substance Abuse Scale (SUSS) [Humphreys et al.: Psychol Addict Behav 1996;10:38-44], the Verstandnis von Storungen durch Substanzkonsum (VSS), and evaluates its psychometric properties. The VSS assesses clinicians' beliefs about the nature and treatment of substance use disorders, particularly their endorsement of psychosocial and disease orientation. The VSS was administered to 160 treatment staff members at 12 substance use disorder treatment programs in the German-speaking part of Switzerland. Because the confirmatory factor analysis of the VSS did not completely replicate the factorial structure of the SUSS, an exploratory factor analysis was undertaken. This analysis identified two factors: the Psychosocial model factor and a slightly different Disease model factor. The VSS Disease and Psychosocial subscales showed convergent and discriminant validity, as well as sufficient reliability.

Developmental Changes in the Structure and Composition of the Postsynaptic Density

The development of the brain and its underlying circuitry is dependent on the formation of trillions of chemical synapses, which are highly specialized contacts that regulate the flow of information from one neuron to the next. It is through these synaptic connections that neurons wire together into networks capable of performing specific tasks, and activity-dependent changes in their structural and physiological state is one way that the brain is thought to adapt and store information. At the ultrastructural level, developmental and activity-dependent changes in the size and shape of dendritic spines have been well documented, and it is widely believed that structural changes in spines are a hallmark sign of synapse maturation and alteration of synaptic physiology. While changes in spine structure have been studied extensively, changes in one of its most prominent components, the postsynaptic density (PSD), have largely evaded observation. The PSD is a protein-rich organelle on the cytoplasmic side of the postsynaptic membrane, where it sits in direct opposition to the presynaptic terminal. The PSD functions both to cluster neurotransmitter receptors at the cell surface as well as organize the intracellular signaling molecules responsible for transducing extracellular signals to the postsynaptic cell. Much is known about the chemical composition of the PSD, but the structural arrangement of its molecular components is not well documented. Adding to the difficulty of understanding such a complex mass of protein machinery is the fact that its protein composition is known to change in response to synaptic activity, meaning that its structure is plastic and no two PSDs are identical. Here, immuno-gold labeling and electron tomography of PSDs isolated throughout development was used to track changes in both the structure and molecular composition of the PSD. State-of-the-art cryo-electron tomography was used to study the fine structure of the PSD during development, and provides an unprecedented glimpse into its molecular architecture in an un-fixed, unstained and hydrated state. Through this analysis, large structural and compositional changes are apparent and suggest a model by which the PSD is first assembled as a mesh-like lattice of proteins that function as support for the later recruitment of various PSD components. Spatial analysis of the recruitment of proteins into the PSD demonstrated that its assembly has an underlying order.

Structural, metamorphic and geochronological relations between the Zanskar Shear Zone and the Miyar Shear Zone (NW Indian Himalaya): Evidence for two distinct tectonic structures and implications for the evolution of the High Himalayan Crystalline of Zanskar

The geologic structures and metamorphic zonation of the northwestern Indian Himalaya contrast significantly with those in the central and eastern parts of the range, where the high-grade metamorphic rocks of the High Himalayan Crystalline (HHC) thrust southward over the weakly metamorphosed sediments of the Lesser Himalaya along the Main Central Thrust (MCT). Indeed, the hanging wall of the MCT in the NW Himalaya mainly consists of the greenschist facies metasediments of the Chamba zone, whereas HHC high-grade rocks are exposed more internally in the range as a large-scale dome called the Gianbul dome. This Gianbul dome is bounded by two oppositely directed shear zones, the NE-dipping Zanskar Shear Zone (ZSZ) on the northern flank and the SW-dipping Miyar Shear Zone (MSZ) on the southern limb. Current models for the emplacement of the HHC in NW India as a dome structure differ mainly in terms of the roles played by both the ZSZ and the MSZ during the tectonothermal evolution of the HHC. In both the channel flow model and wedge extrusion model, the ZSZ acts as a backstop normal fault along which the high-grade metamorphic rocks of the HHC of Zanskar are exhumed. In contrast, the recently proposed tectonic wedging model argues that the ZSZ and the MSZ correspond to one single detachment system that operates as a subhorizontal backthrust off of the MCT. Thus, the kinematic evolution of the two shear zones, the ZSZ and the MSZ, and their structural, metamorphic and chronological relations appear to be diagnostic features for discriminating the different models. In this paper, structural, metamorphic and geochronological data demonstrate that the MSZ and the ZSZ experienced two distinct kinematic evolutions. As such, the data presented in this paper rule out the hypothesis that the MSZ and the ZSZ constitute one single detachment system, as postulated by the tectonic wedging model. Structural, metamorphic and geochronological data are used to present an alternative tectonic model for the large-scale doming in the NW Indian Himalaya involving early NE-directed tectonics, weakness in the upper crust, reduced erosion at the orogenic front and rapid exhumation along both the ZSZ and the MSZ.

Dynamics of a local Alpine flooding event in October 2011: moisture source and large-scale circulation

Alpine heavy precipitation events often affect small catchments, although the circulation pattern leading to the event extends over the entire North Atlantic. The various scale interactions involved are particularly challenging for the numerical weather prediction of such events. Unlike previous studies focusing on the southern Alps, here a comprehensive study of a heavy precipitation event in the northern Alps in October 2011 is presented with particular focus on the role of the large-scale circulation in the North Atlantic/European region. During the event exceptionally high amounts of total precipitable water occurred in and north of the Alps. This moisture was initially transported along the flanks of a blocking ridge over the North Atlantic. Subsequently, strong and persistent northerly flow established at the upstream flank of a trough over Europe and steered the moisture towards the northern Alps. Lagrangian diagnostics reveal that a large fraction of the moisture emerged from the West African coast where a subtropical upper-level cut-off low served as an important moisture collector. Wave activity flux diagnostics show that the ridge was initiated as part of a low-frequency, large-scale Rossby wave train while convergence of fast transients helped to amplify it locally in the North Atlantic. A novel diagnostic for advective potential vorticity tendencies sheds more light on this amplification and further emphasizes the role of the ridge in amplifying the trough over Europe. Operational forecasts misrepresented the amplitude and orientation of this trough. For the first time, this study documents an important pathway for northern Alpine flooding, in which the interaction of synoptic-scale to large-scale weather systems and of long-range moisture transport from the Tropics are dominant. Moreover, the trapping of moisture in a subtropical cut-off near the West African coast is found to be a crucial precursor to the observed European high-impact weather.

Gene sequences of the lichen Cetraria aculeata

Lichens are symbioses between fungi (mycobionts) and photoautotrophic green algae or cyanobacteria (photobionts). Many lichens occupy large distributional ranges covering several climatic zones. So far, little is known about the large-scale phylogeography of lichen photobionts and their role in shaping the distributional ranges of lichens. We studied south polar, temperate and north polar populations of the widely distributed fruticose lichen Cetraria aculeata. Based on the DNA sequences from three loci for each symbiont, we compared the genetic structure of mycobionts and photobionts. Phylogenetic reconstructions and Bayesian clustering methods divided the mycobiont and photobiont data sets into three groups. An AMOVA shows that the genetic variance of the photobiont is best explained by differentiation between temperate and polar regions and that of the mycobiont by an interaction of climatic and geographical factors. By partialling out the relative contribution of climate, geography and codispersal, we found that the most relevant factors shaping the genetic structure of the photobiont are climate and a history of codispersal. Mycobionts in the temperate region are consistently associated with a specific photobiont lineage. We therefore conclude that a photobiont switch in the past enabled C. aculeata to colonize temperate as well as polar habitats. Rare photobiont switches may increase the geographical range and ecological niche of lichen mycobionts by associating them with locally adapted photobionts in climatically different regions and, together with isolation by distance, may lead to genetic isolation between populations and thus drive the evolution of lichens.

Strontium isotope ratios of planktonic foraminifera from sediment samples acroos the K/T boundary

Seawater 87Sr/86Sr values increase abruptly by 28 * 10**-6 across the Cretaceous/Tertiary boundary (KTB). This small, but rapid shift is superimposed on the larger scale structure of the seawater Sr isotope curve. The time scale of radiogenic Sr addition appears to be too rapid to reconcile with sources associated with volcanism, and we show that the amount of Sr required to produce even this small increase is too large to be derived from: (1) a KT bolide of the size constrained by the Ir anomaly, (2) continental crust ejecta from the impact of such a bolide, (3) soot from global wildfires initiated by an impact, or (4) any combination of these sources. The probable source of the radiogenic Sr is enhanced continental weathering, but the high rate of increase appears to rule out processes such as sea level regression, glaciation or tectonism. A plausible mechanism for rapid addition of radiogenic Sr to the oceans is enhanced weathering associated with globally distributed acid rain (pH c. 1) which is a proposed by-product of a bolide impact (Prinn and Fegley, 1987, doi:10.1016/0012-821X(87)90046-X).

(Table 1) Magnetic susceptibility readings in the western part of the Sør Rondane Montains

The Sør Rondane Mountains (SRM) in eastern Dronning Maud Land (DML) are located in an area, where two apparent Pan-African (650-520 Ma) orogenic mobile belts appear to intersect, the East African-Antarctic Orogen and the Kuunga Orogen. Hence, a better understanding of the tectonic structure of the Sør Rondane region is an important key for unravelling the complex geodynamic evolution of the eastern DML and adjacent regions of East Antarctica during the Late Neoproterozoic/Early Palaeozoic amalgamation of Gondwana. The SRM were recently (2011-2012) aerogeophysically investigated with a 5 km flight line spacing, covering a total area of ~140,000 km². The aeromagnetic data are correlated with ground-based magnetic susceptibility measurements and geological field data and allow to project tectonic terranes and individual structures into ice-covered areas. Magnetic anomalies and basement foliation trends are collinear in areas dominated by simple shear deformation, whereas an area of large-scale refolding correlates with a subdued small-scale broken magnetic anomaly pattern. The latter area can be regarded as a distinct tectonic domain, the central Sør Rondane corridor. It magnetically separates the SRM into an eastern, a central, and a western portion. This subdivision is presumably related to late Pan-African extensional tectonics and suggests that such a tectonic regime may play a larger role than previously assumed. Voluminous late Pan-African granitoids, which are mainly undeformed, correlate with positive magnetic anomalies between +30 and +80 nT, while a strong magnetic high (+680 nT) near the granitic intrusion at Dufekfjellet is caused by a highly magnetised enigmatic body. The recently discovered prominent magnetic anomaly province of southeastern DML continues into the southern part of the Sør Rondane region, where only a few outcrops are exposed. Findings at these westernmost nunataks of the SRM indicate that the subdued magnetic anomaly pattern of this southeastern DML province is most likely caused by the predominance of metasedimentary rocks of yet unknown age.

Abundance and biomass of in- and epibenthic invertebrate macrofauna in the German Bight from 1969 to 2000

In order to examine the long-term development of offshore macrozoobenthic soft-bottom communities of the German Bight, four representative permanent stations (MZB-SSd, -FSd, -Slt, -WB) have been sampled continuously since 1969. Inter-annual variability and possible long-term trends were analysed based on spring-time samples from 1969 until 2000. This is part of the ecological long-term series of the AWI and is supplemented by periodic large-scale mapping of the benthos. The main factors influencing the development of the benthic communities are biological interactions, climate, food supply (eutrophication) and the disturbance regime. The most frequent disturbances are sediment relocations during strong storms or by bottom trawling, while occasional oxygen deficiencies and extremely cold winters are important disturbance events working on a much larger scale. Benthic communities at the sampling stations show a large inter-annual variability combined with a variation on a roughly decadal scale. In accordance with large-scale system shifts reported for the North Sea, benthic community transitions occurred between roughly the 1970ies, 80ies and 90ies. The transitions between periods are not distinctly marked by strong changes but rather reflected in gradual changes of the species composition and dominance structure.

Background heat flow values in the region of the Sea of Okhotsk

Particular features of tectonic structure and anomalous distribution of geothermal, geomagnetic, and gravity fields in the region of the Sea of Okhotsk are considered. On the basis of heat flow data, ages of large-scale structures in the Sea of Okhotsk are estimated at 65 Ma for the Central Okhotsk Rise and 36 Ma for the South Okhotsk Basin. Age of the South Okhotsk Basin is confirmed by data on kinematics and corresponds to 50 km thickness of the lithosphere. This is in accordance with thickness value obtained by magnetotelluric soundings. Comparative analysis of model geothermal background and measured heat flow values on the Akademii Nauk Rise is performed. Analysis points to abnormally high (~20%) measured heat flow agrees with high negative gradient of gravity anomalies. Estimates of deep heat flow and basement age of riftogenic basins in the Sea of Okhotsk were carried out in the following areas: Deryugin Basin (18 Ma, Early Miocene), TINRO Basin (12 Ma, Middle Miocene), and West Kamchatka Basin (23 Ma, Late Oligocene). Temperatures at boundaries of the main lithological complexes of the sedimentary cover are calculated and zones of oil and gas generation are defined. On the basis of geothermal, magnetic, structural, and other geological-geophysical data a kinematic model of the region of the Sea of Okhotsk for period of 36 Ma was calculated and constructed.

Parameterization of the atmospheric boundary layer for offshore wind resource assessment with a limited length-scale k-ε model

The structure of the atmospheric boundary layer (ABL) is modelled with the limited- length-scale k-ε model of Apsley and Castro. Contrary to the standard k-ε model, the limited-length-scale k-ε model imposes a maximum mixing length which is derived from the boundary layer height, for neutral and unstable atmospheric situations, or by Monin-Obukhov length when the atmosphere is stably stratified. The model is first verified reproducing the famous Leipzig wind profile. Then the performance of the model is tested with measurements from FINO-1 platform using sonic anemometers to derive the appropriate maximum mixing length.