BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

Numerical combination for nonlinear analysis of structures coupled to layered soils

This paper presents an alternative coupling strategy between the Boundary Element Method (BEM) and the Finite Element Method (FEM) in order to create a computational code for the analysis of geometrical nonlinear 2D frames coupled to layered soils. The soil is modeled via BEM, considering multiple inclusions and internal load lines, through an alternative formulation to eliminate traction variables on subregions interfaces. A total Lagrangean formulation based on positions is adopted for the consideration of the geometric nonlinear behavior of frame structures with exact kinematics. The numerical coupling is performed by an algebraic strategy that extracts and condenses the equivalent soil's stiffness matrix and contact forces to be introduced into the frame structures hessian matrix and internal force vector, respectively. The formulation covers the analysis of shallow foundation structures and piles in any direction. Furthermore, the piles can pass through different layers. Numerical examples are shown in order to illustrate and confirm the accuracy and applicability of the proposed technique.

Safety factors in sheet pile wall design: considerations by using traditional methods and FEM analysis

The purpose of the work is: define and calculate a factor of collapse related to traditional method to design sheet pile walls. Furthermore, we tried to find the parameters that most influence a finite element model representative of this problem. The text is structured in this way: from chapter 1 to 5, we analyzed a series of arguments which are usefull to understanding the problem, while the considerations mainly related to the purpose of the text are reported in the chapters from 6 to 10. In the first part of the document the following arguments are shown: what is a sheet pile wall, what are the codes to be followed for the design of these structures and what they say, how can be formulated a mathematical model of the soil, some fundamentals of finite element analysis, and finally, what are the traditional methods that support the design of sheet pile walls. In the chapter 6 we performed a parametric analysis, giving an answer to the second part of the purpose of the work. Comparing the results from a laboratory test for a cantilever sheet pile wall in a sandy soil, with those provided by a finite element model of the same problem, we concluded that:in modelling a sandy soil we should pay attention to the value of cohesion that we insert in the model (some programs, like Abaqus, don’t accept a null value for this parameter), friction angle and elastic modulus of the soil, they influence significantly the behavior of the system (structure-soil), others parameters, like the dilatancy angle or the Poisson’s ratio, they don’t seem influence it. The logical path that we followed in the second part of the text is reported here. We analyzed two different structures, the first is able to support an excavation of 4 m, while the second an excavation of 7 m. Both structures are first designed by using the traditional method, then these structures are implemented in a finite element program (Abaqus), and they are pushed to collapse by decreasing the friction angle of the soil. The factor of collapse is the ratio between tangents of the initial friction angle and of the friction angle at collapse. At the end, we performed a more detailed analysis of the first structure, observing that, the value of the factor of collapse is influenced by a wide range of parameters including: the value of the coefficients assumed in the traditional method and by the relative stiffness of the structure-soil system. In the majority of cases, we found that the value of the factor of collapse is between and 1.25 and 2. With some considerations, reported in the text, we can compare the values so far found, with the value of the safety factor proposed by the code (linked to the friction angle of the soil).

Pushover analysis of an existing reinforced concrete bridge:Jamboree Road Overcrossing in Irvine, California

The work for the present thesis started in California, during my semester as an exchange student overseas. California is known worldwide for its seismicity and its effort in the earthquake engineering research field. For this reason, I immediately found interesting the Structural Dynamics Professor, Maria Q. Feng's proposal, to work on a pushover analysis of the existing Jamboree Road Overcrossing bridge. Concrete is a popular building material in California, and for the most part, it serves its functions well. However, concrete is inherently brittle and performs poorly during earthquakes if not reinforced properly. The San Fernando Earthquake of 1971 dramatically demonstrated this characteristic. Shortly thereafter, code writers revised the design provisions for new concrete buildings so to provide adequate ductility to resist strong ground shaking. There remain, nonetheless, millions of square feet of non-ductile concrete buildings in California. The purpose of this work is to perform a Pushover Analysis and compare the results with those of a Nonlinear Time-History Analysis of an existing bridge, located in Southern California. The analyses have been executed through the software OpenSees, the Open System for Earthquake Engineering Simulation. The bridge Jamboree Road Overcrossing is classified as a Standard Ordinary Bridge. In fact, the JRO is a typical three-span continuous cast-in-place prestressed post-tension box-girder. The total length of the bridge is 366 ft., and the height of the two bents are respectively 26,41 ft. and 28,41 ft.. Both the Pushover Analysis and the Nonlinear Time-History Analysis require the use of a model that takes into account for the nonlinearities of the system. In fact, in order to execute nonlinear analyses of highway bridges it is essential to incorporate an accurate model of the material behavior. It has been observed that, after the occurrence of destructive earthquakes, one of the most damaged elements on highway bridges is a column. To evaluate the performance of bridge columns during seismic events an adequate model of the column must be incorporated. Part of the work of the present thesis is, in fact, dedicated to the modeling of bents. Different types of nonlinear element have been studied and modeled, with emphasis on the plasticity zone length determination and location. Furthermore, different models for concrete and steel materials have been considered, and the selection of the parameters that define the constitutive laws of the different materials have been accurate. The work is structured into four chapters, to follow a brief overview of the content. The first chapter introduces the concepts related to capacity design, as the actual philosophy of seismic design. Furthermore, nonlinear analyses both static, pushover, and dynamic, time-history, are presented. The final paragraph concludes with a short description on how to determine the seismic demand at a specific site, according to the latest design criteria in California. The second chapter deals with the formulation of force-based finite elements and the issues regarding the objectivity of the response in nonlinear field. Both concentrated and distributed plasticity elements are discussed into detail. The third chapter presents the existing structure, the software used OpenSees, and the modeling assumptions and issues. The creation of the nonlinear model represents a central part in this work. Nonlinear material constitutive laws, for concrete and reinforcing steel, are discussed into detail; as well as the different scenarios employed in the columns modeling. Finally, the results of the pushover analysis are presented in chapter four. Capacity curves are examined for the different model scenarios used, and failure modes of concrete and steel are discussed. Capacity curve is converted into capacity spectrum and intersected with the design spectrum. In the last paragraph, the results of nonlinear time-history analyses are compared to those of pushover analysis.

Fiber beam-columns models with flexure-shear interaction for nonlinear analysis of reinforced concrete structures

The aim of this study was to develop a model capable to capture the different contributions which characterize the nonlinear behaviour of reinforced concrete structures. In particular, especially for non slender structures, the contribution to the nonlinear deformation due to bending may be not sufficient to determine the structural response. Two different models characterized by a fibre beam-column element are here proposed. These models can reproduce the flexure-shear interaction in the nonlinear range, with the purpose to improve the analysis in shear-critical structures. The first element discussed is based on flexibility formulation which is associated with the Modified Compression Field Theory as material constitutive law. The other model described in this thesis is based on a three-field variational formulation which is associated with a 3D generalized plastic-damage model as constitutive relationship. The first model proposed in this thesis was developed trying to combine a fibre beamcolumn element based on the flexibility formulation with the MCFT theory as constitutive relationship. The flexibility formulation, in fact, seems to be particularly effective for analysis in the nonlinear field. Just the coupling between the fibre element to model the structure and the shear panel to model the individual fibres allows to describe the nonlinear response associated to flexure and shear, and especially their interaction in the nonlinear field. The model was implemented in an original matlab® computer code, for describing the response of generic structures. The simulations carried out allowed to verify the field of working of the model. Comparisons with available experimental results related to reinforced concrete shears wall were performed in order to validate the model. These results are characterized by the peculiarity of distinguishing the different contributions due to flexure and shear separately. The presented simulations were carried out, in particular, for monotonic loading. The model was tested also through numerical comparisons with other computer programs. Finally it was applied for performing a numerical study on the influence of the nonlinear shear response for non slender reinforced concrete (RC) members. Another approach to the problem has been studied during a period of research at the University of California Berkeley. The beam formulation follows the assumptions of the Timoshenko shear beam theory for the displacement field, and uses a three-field variational formulation in the derivation of the element response. A generalized plasticity model is implemented for structural steel and a 3D plastic-damage model is used for the simulation of concrete. The transverse normal stress is used to satisfy the transverse equilibrium equations of at each control section, this criterion is also used for the condensation of degrees of freedom from the 3D constitutive material to a beam element. In this thesis is presented the beam formulation and the constitutive relationships, different analysis and comparisons are still carrying out between the two model presented.

A Multilevel Model with Time Series Components for the Analysis of Tribal Art Prices

In the present work we perform an econometric analysis of the Tribal art market. To this aim, we use a unique and original database that includes information on Tribal art market auctions worldwide from 1998 to 2011. In Literature, art prices are modelled through the hedonic regression model, a classic fixed-effect model. The main drawback of the hedonic approach is the large number of parameters, since, in general, art data include many categorical variables. In this work, we propose a multilevel model for the analysis of Tribal art prices that takes into account the influence of time on artwork prices. In fact, it is natural to assume that time exerts an influence over the price dynamics in various ways. Nevertheless, since the set of objects change at every auction date, we do not have repeated measurements of the same items over time. Hence, the dataset does not constitute a proper panel; rather, it has a two-level structure in that items, level-1 units, are grouped in time points, level-2 units. The main theoretical contribution is the extension of classical multilevel models to cope with the case described above. In particular, we introduce a model with time dependent random effects at the second level. We propose a novel specification of the model, derive the maximum likelihood estimators and implement them through the E-M algorithm. We test the finite sample properties of the estimators and the validity of the own-written R-code by means of a simulation study. Finally, we show that the new model improves considerably the fit of the Tribal art data with respect to both the hedonic regression model and the classic multilevel model.

Numerical analysis of Dielectric Barrier Discharge

A numerical investigation of dielectric barrier discharge aimed to simulate the electro hydro dynamic interaction is presented. A discharge drift diffusive model according to the Townsend avalanche is described and used to duplicate the plasma kinetics of a DBD actuator. The discharge characteristics dependence upon dielectric material and applied voltage are simulated and the EHD force field according to a simplified approach is presented and discussed. The coupling of DBD results with a fluid dynamic code is also shown. Finally, a new non invasive diagnostic technique for EHD interaction based on Schlieren imaging is computationally validated.

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.

Experimental analysis and FE Modeling of Aluminium alloys Microstructural Evolution in Extrusion

Extrusion is a process used to form long products of constant cross section, from simple billets, with a high variety of shapes. Aluminum alloys are the materials most processed in the extrusion industry due to their deformability and the wide field of applications that range from buildings to aerospace and from design to automotive industries. The diverse applications imply different requirements that can be fulfilled by the wide range of alloys and treatments, that is from critical structural application to high quality surface and aesthetical aspect. Whether one or the other is the critical aspect, they both depend directly from microstructure. The extrusion process is moreover marked by high deformations and complex strain gradients making difficult the control of microstructure evolution that is at present not yet fully achieved. Nevertheless the evolution of Finite Element modeling has reached a maturity and can therefore start to be used as a tool for investigation and prediction of microstructure evolution. This thesis will analyze and model the evolution of microstructure throughout the entire extrusion process for 6XXX series aluminum alloys. Core phase of the work was the development of specific tests to investigate the microstructure evolution and validate the model implemented in a commercial FE code. Along with it two essential activities were carried out for a correct calibration of the model beyond the simple research of contour parameters, thus leading to the understanding and control of both code and process. In this direction activities were also conducted on building critical knowhow on the interpretation of microstructure and extrusion phenomena. It is believed, in fact, that the sole analysis of the microstructure evolution regardless of its relevance in the technological aspects of the process would be of little use for the industry as well as ineffective for the interpretation of the results.

Validation of the CFD code NEPTUNE for a full scale simulator for decay heat removal systems with in-pool heat exchangers

In the present work, a multi physics simulation of an innovative safety system for light water nuclear reactor is performed, with the aim to increase the reliability of its main decay heat removal system. The system studied, denoted by the acronym PERSEO (in Pool Energy Removal System for Emergency Operation) is able to remove the decay power from the primary side of the light water nuclear reactor through a heat suppression pool. The experimental facility, located at SIET laboratories (PIACENZA), is an evolution of the Thermal Valve concept where the triggering valve is installed liquid side, on a line connecting two pools at the bottom. During the normal operation, the valve is closed, while in emergency conditions it opens, the heat exchanger is flooded with consequent heat transfer from the primary side to the pool side. In order to verify the correct system behavior during long term accidental transient, two main experimental PERSEO tests are analyzed. For this purpose, a coupling between the mono dimensional system code CATHARE, which reproduces the system scale behavior, with a three-dimensional CFD code NEPTUNE CFD, allowing a full investigation of the pools and the injector, is implemented. The coupling between the two codes is realized through the boundary conditions. In a first analysis, the facility is simulated by the system code CATHARE V2.5 to validate the results with the experimental data. The comparison of the numerical results obtained shows a different void distribution during the boiling conditions inside the heat suppression pool for the two cases of single nodalization and three volume nodalization scheme of the pool. Finaly, to improve the investigation capability of the void distribution inside the pool and the temperature stratification phenomena below the injector, a two and three dimensional CFD models with a simplified geometry of the system are adopted.

Development of new tools and devices for CMB and foreground data analysis and future experiments

The discovery of the Cosmic Microwave Background (CMB) radiation in 1965 is one of the fundamental milestones supporting the Big Bang theory. The CMB is one of the most important source of information in cosmology. The excellent accuracy of the recent CMB data of WMAP and Planck satellites confirmed the validity of the standard cosmological model and set a new challenge for the data analysis processes and their interpretation. In this thesis we deal with several aspects and useful tools of the data analysis. We focus on their optimization in order to have a complete exploitation of the Planck data and contribute to the final published results. The issues investigated are: the change of coordinates of CMB maps using the HEALPix package, the problem of the aliasing effect in the generation of low resolution maps, the comparison of the Angular Power Spectrum (APS) extraction performances of the optimal QML method, implemented in the code called BolPol, and the pseudo-Cl method, implemented in Cromaster. The QML method has been then applied to the Planck data at large angular scales to extract the CMB APS. The same method has been applied also to analyze the TT parity and the Low Variance anomalies in the Planck maps, showing a consistent deviation from the standard cosmological model, the possible origins for this results have been discussed. The Cromaster code instead has been applied to the 408 MHz and 1.42 GHz surveys focusing on the analysis of the APS of selected regions of the synchrotron emission. The new generation of CMB experiments will be dedicated to polarization measurements, for which are necessary high accuracy devices for separating the polarizations. Here a new technology, called Photonic Crystals, is exploited to develop a new polarization splitter device and its performances are compared to the devices used nowadays.

Experimental Analysis and Numerical Simulation of Quench in Superconducting HTS Tapes and Coils

The quench characteristics of second generation (2 G) YBCO Coated Conductor (CC) tapes are of fundamental importance for the design and safe operation of superconducting cables and magnets based on this material. Their ability to transport high current densities at high temperature, up to 77 K, and at very high fields, over 20 T, together with the increasing knowledge in their manufacturing, which is reducing their cost, are pushing the use of this innovative material in numerous system applications, from high field magnets for research to motors and generators as well as for cables. The aim of this Ph. D. thesis is the experimental analysis and numerical simulations of quench in superconducting HTS tapes and coils. A measurements facility for the characterization of superconducting tapes and coils was designed, assembled and tested. The facility consist of a cryostat, a cryocooler, a vacuum system, resistive and superconducting current leads and signal feedthrough. Moreover, the data acquisition system and the software for critical current and quench measurements were developed. A 2D model was developed using the finite element code COMSOL Multiphysics R . The problem of modeling the high aspect ratio of the tape is tackled by multiplying the tape thickness by a constant factor, compensating the heat and electrical balance equations by introducing a material anisotropy. The model was then validated both with the results of a 1D quench model based on a non-linear electric circuit coupled to a thermal model of the tape, to literature measurements and to critical current and quench measurements made in the cryogenic facility. Finally the model was extended to the study of coils and windings with the definition of the tape and stack homogenized properties. The procedure allows the definition of a multi-scale hierarchical model, able to simulate the windings with different degrees of detail.

Code synchronization and interference management techniques for satellite navigation and communications

This thesis collects the outcomes of a Ph.D. course in Telecommunications engineering and it is focused on enabling techniques for Spread Spectrum (SS) navigation and communication satellite systems. It provides innovations for both interference management and code synchronization techniques. These two aspects are critical for modern navigation and communication systems and constitute the common denominator of the work. The thesis is organized in two parts: the former deals with interference management. We have proposed a novel technique for the enhancement of the sensitivity level of an advanced interference detection and localization system operating in the Global Navigation Satellite System (GNSS) bands, which allows the identification of interfering signals received with power even lower than the GNSS signals. Moreover, we have introduced an effective cancellation technique for signals transmitted by jammers, exploiting their repetitive characteristics, which strongly reduces the interference level at the receiver. The second part, deals with code synchronization. More in detail, we have designed the code synchronization circuit for a Telemetry, Tracking and Control system operating during the Launch and Early Orbit Phase; the proposed solution allows to cope with the very large frequency uncertainty and dynamics characterizing this scenario, and performs the estimation of the code epoch, of the carrier frequency and of the carrier frequency variation rate. Furthermore, considering a generic pair of circuits performing code acquisition, we have proposed a comprehensive framework for the design and the analysis of the optimal cooperation procedure, which minimizes the time required to accomplish synchronization. The study results particularly interesting since it enables the reduction of the code acquisition time without increasing the computational complexity. Finally, considering a network of collaborating navigation receivers, we have proposed an innovative cooperative code acquisition scheme, which allows exploit the shared code epoch information between neighbor nodes, according to the Peer-to-Peer paradigm.

Analysis and mathematical modeling of wave-structure interaction

The aim of this thesis, included within the THESEUS project, is the development of a mathematical model 2DV two-phase, based on the existing code IH-2VOF developed by the University of Cantabria, able to represent together the overtopping phenomenon and the sediment transport. Several numerical simulations were carried out in order to analyze the flow characteristics on a dike crest. The results show that the seaward/landward slope does not affect the evolution of the flow depth and velocity over the dike crest whereas the most important parameter is the relative submergence. Wave heights decrease and flow velocities increase while waves travel over the crest. In particular, by increasing the submergence, the wave height decay and the increase of the velocity are less marked. Besides, an appropriate curve able to fit the variation of the wave height/velocity over the dike crest were found. Both for the wave height and for the wave velocity different fitting coefficients were determined on the basis of the submergence and of the significant wave height. An equation describing the trend of the dimensionless coefficient c_h for the wave height was derived. These conclusions could be taken into consideration for the design criteria and the upgrade of the structures. In the second part of the thesis, new equations for the representation of the sediment transport in the IH-2VOF model were introduced in order to represent beach erosion while waves run-up and overtop the sea banks during storms. The new model allows to calculate sediment fluxes in the water column together with the sediment concentration. Moreover it is possible to model the bed profile evolution. Different tests were performed under low-intensity regular waves with an homogeneous layer of sand on the bottom of a channel in order to analyze the erosion-deposition patterns and verify the model results.