Semantic integration of gene expression analysis tools and data sources using software connectors

Abstract Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

Evidence-based clinical use of insulin premixtures

Brazil is expected to have 19.6 million patients with diabetes by the year 2030. A key concept in the treatment of type 2 diabetes mellitus (T2DM) is establishing individualized glycemic goals based on each patient’s clinical characteristics, which impact the choice of antihyperglycemic therapy. Targets for glycemic control, including fasting blood glucose, postprandial blood glucose, and glycated hemoglobin (A1C), are often not reached solely with antihyperglycemic therapy, and insulin therapy is often required. Basal insulin is considered an initial strategy; however, premixed insulins are convenient and are equally or more effective, especially for patients who require both basal and prandial control but desire a more simplified strategy involving fewer daily injections than a basal-bolus regimen. Most physicians are reluctant to transition patients to insulin treatment due to inappropriate assumptions and insufficient information. We conducted a nonsystematic review in PubMed and identified the most relevant and recently published articles that compared the use of premixed insulin versus basal insulin analogues used alone or in combination with rapid-acting insulin analogues before meals in patients with T2DM. These studies suggest that premixed insulin analogues are equally or more effective in reducing A1C compared to basal insulin analogues alone in spite of the small increase in the risk of nonsevere hypoglycemic events and nonclinically significant weight gain. Premixed insulin analogues can be used in insulin-naïve patients, in patients already on basal insulin therapy, and those using basal-bolus therapy who are noncompliant with blood glucose self-monitoring and titration of multiple insulin doses. We additionally provide practical aspects related to titration for the specific premixed insulin analogue formulations commercially available in Brazil.

Semantic-based middleware solutions to support context-aware service provisioning in pervasive environments

The dynamicity and heterogeneity that characterize pervasive environments raise new challenges in the design of mobile middleware. Pervasive environments are characterized by a significant degree of heterogeneity, variability, and dynamicity that conventional middleware solutions are not able to adequately manage. Originally designed for use in a relatively static context, such middleware systems tend to hide low-level details to provide applications with a transparent view on the underlying execution platform. In mobile environments, however, the context is extremely dynamic and cannot be managed by a priori assumptions. Novel middleware should therefore support mobile computing applications in the task of adapting their behavior to frequent changes in the execution context, that is, it should become context-aware. In particular, this thesis has identified the following key requirements for novel context-aware middleware that existing solutions do not fulfil yet. (i) Middleware solutions should support interoperability between possibly unknown entities by providing expressive representation models that allow to describe interacting entities, their operating conditions and the surrounding world, i.e., their context, according to an unambiguous semantics. (ii) Middleware solutions should support distributed applications in the task of reconfiguring and adapting their behavior/results to ongoing context changes. (iii) Context-aware middleware support should be deployed on heterogeneous devices under variable operating conditions, such as different user needs, application requirements, available connectivity and device computational capabilities, as well as changing environmental conditions. Our main claim is that the adoption of semantic metadata to represent context information and context-dependent adaptation strategies allows to build context-aware middleware suitable for all dynamically available portable devices. Semantic metadata provide powerful knowledge representation means to model even complex context information, and allow to perform automated reasoning to infer additional and/or more complex knowledge from available context data. In addition, we suggest that, by adopting proper configuration and deployment strategies, semantic support features can be provided to differentiated users and devices according to their specific needs and current context. This thesis has investigated novel design guidelines and implementation options for semantic-based context-aware middleware solutions targeted to pervasive environments. These guidelines have been applied to different application areas within pervasive computing that would particularly benefit from the exploitation of context. Common to all applications is the key role of context in enabling mobile users to personalize applications based on their needs and current situation. The main contributions of this thesis are (i) the definition of a metadata model to represent and reason about context, (ii) the definition of a model for the design and development of context-aware middleware based on semantic metadata, (iii) the design of three novel middleware architectures and the development of a prototypal implementation for each of these architectures, and (iv) the proposal of a viable approach to portability issues raised by the adoption of semantic support services in pervasive applications.

Context detection and abstraction in smart environments

Context-aware computing is currently considered the most promising approach to overcome information overload and to speed up access to relevant information and services. Context-awareness may be derived from many sources, including user profile and preferences, network information, sensor analysis; usually context-awareness relies on the ability of computing devices to interact with the physical world, i.e. with the natural and artificial objects hosted within the "environment”. Ideally, context-aware applications should not be intrusive and should be able to react according to user’s context, with minimum user effort. Context is an application dependent multidimensional space and the location is an important part of it since the very beginning. Location can be used to guide applications, in providing information or functions that are most appropriate for a specific position. Hence location systems play a crucial role. There are several technologies and systems for computing location to a vary degree of accuracy and tailored for specific space model, i.e. indoors or outdoors, structured spaces or unstructured spaces. The research challenge faced by this thesis is related to pedestrian positioning in heterogeneous environments. Particularly, the focus will be on pedestrian identification, localization, orientation and activity recognition. This research was mainly carried out within the “mobile and ambient systems” workgroup of EPOCH, a 6FP NoE on the application of ICT to Cultural Heritage. Therefore applications in Cultural Heritage sites were the main target of the context-aware services discussed. Cultural Heritage sites are considered significant test-beds in Context-aware computing for many reasons. For example building a smart environment in museums or in protected sites is a challenging task, because localization and tracking are usually based on technologies that are difficult to hide or harmonize within the environment. Therefore it is expected that the experience made with this research may be useful also in domains other than Cultural Heritage. This work presents three different approaches to the pedestrian identification, positioning and tracking: Pedestrian navigation by means of a wearable inertial sensing platform assisted by the vision based tracking system for initial settings an real-time calibration; Pedestrian navigation by means of a wearable inertial sensing platform augmented with GPS measurements; Pedestrian identification and tracking, combining the vision based tracking system with WiFi localization. The proposed localization systems have been mainly used to enhance Cultural Heritage applications in providing information and services depending on the user’s actual context, in particular depending on the user’s location.

Self-Organizing Mechanisms for Task Allocation in a Knowledge-Based Economy

A prevalent claim is that we are in knowledge economy. When we talk about knowledge economy, we generally mean the concept of “Knowledge-based economy” indicating the use of knowledge and technologies to produce economic benefits. Hence knowledge is both tool and raw material (people’s skill) for producing some kind of product or service. In this kind of environment economic organization is undergoing several changes. For example authority relations are less important, legal and ownership-based definitions of the boundaries of the firm are becoming irrelevant and there are only few constraints on the set of coordination mechanisms. Hence what characterises a knowledge economy is the growing importance of human capital in productive processes (Foss, 2005) and the increasing knowledge intensity of jobs (Hodgson, 1999). Economic processes are also highly intertwined with social processes: they are likely to be informal and reciprocal rather than formal and negotiated. Another important point is also the problem of the division of labor: as economic activity becomes mainly intellectual and requires the integration of specific and idiosyncratic skills, the task of dividing the job and assigning it to the most appropriate individuals becomes arduous, a “supervisory problem” (Hogdson, 1999) emerges and traditional hierarchical control may result increasingly ineffective. Not only specificity of know how makes it awkward to monitor the execution of tasks, more importantly, top-down integration of skills may be difficult because ‘the nominal supervisors will not know the best way of doing the job – or even the precise purpose of the specialist job itself – and the worker will know better’ (Hogdson,1999). We, therefore, expect that the organization of the economic activity of specialists should be, at least partially, self-organized. The aim of this thesis is to bridge studies from computer science and in particular from Peer-to-Peer Networks (P2P) to organization theories. We think that the P2P paradigm well fits with organization problems related to all those situation in which a central authority is not possible. We believe that P2P Networks show a number of characteristics similar to firms working in a knowledge-based economy and hence that the methodology used for studying P2P Networks can be applied to organization studies. Three are the main characteristics we think P2P have in common with firms involved in knowledge economy: - Decentralization: in a pure P2P system every peer is an equal participant, there is no central authority governing the actions of the single peers; - Cost of ownership: P2P computing implies shared ownership reducing the cost of owing the systems and the content, and the cost of maintaining them; - Self-Organization: it refers to the process in a system leading to the emergence of global order within the system without the presence of another system dictating this order. These characteristics are present also in the kind of firm that we try to address and that’ why we have shifted the techniques we adopted for studies in computer science (Marcozzi et al., 2005; Hales et al., 2007 [39]) to management science.

Structure learning of graphical models for task-oriented robot grasping

In the collective imaginaries a robot is a human like machine as any androids in science fiction. However the type of robots that you will encounter most frequently are machinery that do work that is too dangerous, boring or onerous. Most of the robots in the world are of this type. They can be found in auto, medical, manufacturing and space industries. Therefore a robot is a system that contains sensors, control systems, manipulators, power supplies and software all working together to perform a task. The development and use of such a system is an active area of research and one of the main problems is the development of interaction skills with the surrounding environment, which include the ability to grasp objects. To perform this task the robot needs to sense the environment and acquire the object informations, physical attributes that may influence a grasp. Humans can solve this grasping problem easily due to their past experiences, that is why many researchers are approaching it from a machine learning perspective finding grasp of an object using information of already known objects. But humans can select the best grasp amongst a vast repertoire not only considering the physical attributes of the object to grasp but even to obtain a certain effect. This is why in our case the study in the area of robot manipulation is focused on grasping and integrating symbolic tasks with data gained through sensors. The learning model is based on Bayesian Network to encode the statistical dependencies between the data collected by the sensors and the symbolic task. This data representation has several advantages. It allows to take into account the uncertainty of the real world, allowing to deal with sensor noise, encodes notion of causality and provides an unified network for learning. Since the network is actually implemented and based on the human expert knowledge, it is very interesting to implement an automated method to learn the structure as in the future more tasks and object features can be introduced and a complex network design based only on human expert knowledge can become unreliable. Since structure learning algorithms presents some weaknesses, the goal of this thesis is to analyze real data used in the network modeled by the human expert, implement a feasible structure learning approach and compare the results with the network designed by the expert in order to possibly enhance it.

Design of alternative energy storage systems for hybrid vehicles based on statistical processing of driving cycles information

Hybrid vehicles represent the future for automakers, since they allow to improve the fuel economy and to reduce the pollutant emissions. A key component of the hybrid powertrain is the Energy Storage System, that determines the ability of the vehicle to store and reuse energy. Though electrified Energy Storage Systems (ESS), based on batteries and ultracapacitors, are a proven technology, Alternative Energy Storage Systems (AESS), based on mechanical, hydraulic and pneumatic devices, are gaining interest because they give the possibility of realizing low-cost mild-hybrid vehicles. Currently, most literature of design methodologies focuses on electric ESS, which are not suitable for AESS design. In this contest, The Ohio State University has developed an Alternative Energy Storage System design methodology. This work focuses on the development of driving cycle analysis methodology that is a key component of Alternative Energy Storage System design procedure. The proposed methodology is based on a statistical approach to analyzing driving schedules that represent the vehicle typical use. Driving data are broken up into power events sequence, namely traction and braking events, and for each of them, energy-related and dynamic metrics are calculated. By means of a clustering process and statistical synthesis methods, statistically-relevant metrics are determined. These metrics define cycle representative braking events. By using these events as inputs for the Alternative Energy Storage System design methodology, different system designs are obtained. Each of them is characterized by attributes, namely system volume and weight. In the last part the work, the designs are evaluated in simulation by introducing and calculating a metric related to the energy conversion efficiency. Finally, the designs are compared accounting for attributes and efficiency values. In order to automate the driving data extraction and synthesis process, a specific script Matlab based has been developed. Results show that the driving cycle analysis methodology, based on the statistical approach, allows to extract and synthesize cycle representative data. The designs based on cycle statistically-relevant metrics are properly sized and have satisfying efficiency values with respect to the expectations. An exception is the design based on the cycle worst-case scenario, corresponding to same approach adopted by the conventional electric ESS design methodologies. In this case, a heavy system with poor efficiency is produced. The proposed new methodology seems to be a valid and consistent support for Alternative Energy Storage System design.

Preparation and study of magnetic thin film based sub-micron structures

Due to its high Curie temperature of 420K and band structure calculations predicting 100% spin polarisation, Sr2FeMoO6 is a potential candidate for spintronic devices. However, the preparation of good quality thin films has proven to be a non-trivial task. Epitaxial Sr2FeMoO6 thin films were prepared by pulsed laser deposition on different substrates. Differing from previous reports a post-deposition annealing step at low oxygen partial pressure (10-5 mbar) was introduced and enabled the fabrication of reproducible, high quality samples. According to the structural properties of the substrates the crystal structure and morphology of the thin films are modified. The close interrelation between the structural, magnetic and electronic properties of Sr2FeMoO6 was studied. A detailed evaluation of the results allowed to extract valuable information on the microscopic nature of magnetism and charge transport. Smooth films with a mean roughness of about 2 nm have been achieved, which is a pre-requisite for a possible inclusion of this material in future devices. In order to establish device-oriented sub-micron patterning as a standard technique, electron beam lithography and focussed ion beam etching facilities have been put into operation. A detailed characterisation of these systems has been performed. To determine the technological prospects of new spintronics materials, the verification of a high spin polarisation is of vital interest. A popular technique for this task is point contact Andreev reflection (PCAR). Commonly, the charge transport in a transparent metal-superconductor contact of nanometer dimensions is attributed solely to coherent transport. If this condition is not fulfilled, inelastic processes in the constriction have to be considered. PCAR has been applied to Sr2FeMoO6 and the Heusler compound Co2Cr0.6Fe0.4Al. Systematic deviations between measured spectra and the standard models of PCAR have been observed. Therefore existing approaches have been generalised, in order to include the influence of heating. With the extended model the measured data was successfully reproduced but the analysis has revealed grave implications for the determination of spin polarisation, which was found to break down completely in certain cases.

Spectrum Sensing Algorithms for Cognitive Radio Applications

Future wireless communications systems are expected to be extremely dynamic, smart and capable to interact with the surrounding radio environment. To implement such advanced devices, cognitive radio (CR) is a promising paradigm, focusing on strategies for acquiring information and learning. The first task of a cognitive systems is spectrum sensing, that has been mainly studied in the context of opportunistic spectrum access, in which cognitive nodes must implement signal detection techniques to identify unused bands for transmission. In the present work, we study different spectrum sensing algorithms, focusing on their statistical description and evaluation of the detection performance. Moving from traditional sensing approaches we consider the presence of practical impairments, and analyze algorithm design. Far from the ambition of cover the broad spectrum of spectrum sensing, we aim at providing contributions to the main classes of sensing techniques. In particular, in the context of energy detection we studied the practical design of the test, considering the case in which the noise power is estimated at the receiver. This analysis allows to deepen the phenomenon of the SNR wall, providing the conditions for its existence and showing that presence of the SNR wall is determined by the accuracy of the noise power estimation process. In the context of the eigenvalue based detectors, that can be adopted by multiple sensors systems, we studied the practical situation in presence of unbalances in the noise power at the receivers. Then, we shift the focus from single band detectors to wideband sensing, proposing a new approach based on information theoretic criteria. This technique is blind and, requiring no threshold setting, can be adopted even if the statistical distribution of the observed data in not known exactly. In the last part of the thesis we analyze some simple cooperative localization techniques based on weighted centroid strategies.

Un sistema location-based per la mappatura degli access point

Trattasi di un sistema basato sulla mappatura degli access point utilizzabile su un'applicazione per smartphone con piattaforma Android. Sono stati usati ambienti di lavoro come Eclipse, affiancato da Lamp e API, utili per visualizzare le mappe da Google Maps. E' stato creato un database online, in modo tale che gli utenti possano condividere le proprie registrazioni (solo quelle che non richiedono una password e quindi utilizzabili da tutti). Il tutto testato tramite un emulatore Android

A Semantic-based Framework for Digital Survey of Architectural Heritage

The research aims at developing a framework for semantic-based digital survey of architectural heritage. Rooted in knowledge-based modeling which extracts mathematical constraints of geometry from architectural treatises, as-built information of architecture obtained from image-based modeling is integrated with the ideal model in BIM platform. The knowledge-based modeling transforms the geometry and parametric relation of architectural components from 2D printings to 3D digital models, and create large amount variations based on shape grammar in real time thanks to parametric modeling. It also provides prior knowledge for semantically segmenting unorganized survey data. The emergence of SfM (Structure from Motion) provides access to reconstruct large complex architectural scenes with high flexibility, low cost and full automation, but low reliability of metric accuracy. We solve this problem by combing photogrammetric approaches which consists of camera configuration, image enhancement, and bundle adjustment, etc. Experiments show the accuracy of image-based modeling following our workflow is comparable to that from range-based modeling. We also demonstrate positive results of our optimized approach in digital reconstruction of portico where low-texture-vault and dramatical transition of illumination bring huge difficulties in the workflow without optimization. Once the as-built model is obtained, it is integrated with the ideal model in BIM platform which allows multiple data enrichment. In spite of its promising prospect in AEC industry, BIM is developed with limited consideration of reverse-engineering from survey data. Besides representing the architectural heritage in parallel ways (ideal model and as-built model) and comparing their difference, we concern how to create as-built model in BIM software which is still an open area to be addressed. The research is supposed to be fundamental for research of architectural history, documentation and conservation of architectural heritage, and renovation of existing buildings.

Searching and retrieving in content-based repositories of formal mathematical knowledge

In this thesis, the author presents a query language for an RDF (Resource Description Framework) database and discusses its applications in the context of the HELM project (the Hypertextual Electronic Library of Mathematics). This language aims at meeting the main requirements coming from the RDF community. in particular it includes: a human readable textual syntax and a machine-processable XML (Extensible Markup Language) syntax both for queries and for query results, a rigorously exposed formal semantics, a graph-oriented RDF data access model capable of exploring an entire RDF graph (including both RDF Models and RDF Schemata), a full set of Boolean operators to compose the query constraints, fully customizable and highly structured query results having a 4-dimensional geometry, some constructions taken from ordinary programming languages that simplify the formulation of complex queries. The HELM project aims at integrating the modern tools for the automation of formal reasoning with the most recent electronic publishing technologies, in order create and maintain a hypertextual, distributed virtual library of formal mathematical knowledge. In the spirit of the Semantic Web, the documents of this library include RDF metadata describing their structure and content in a machine-understandable form. Using the author's query engine, HELM exploits this information to implement some functionalities allowing the interactive and automatic retrieval of documents on the basis of content-aware requests that take into account the mathematical nature of these documents.

Un sistema location-based per la mappatura degli Access Point su Android

un' applicazione in grado di memorizzare e mappare tutti i punti dove è possibile collegarsi, in modo gratuito, ad internet usando il nostro Smartphone. Per tenere traccia di questi punti si utilizza un meccanismo in grado di determinare la posizione geografica del dispositivo mediante il quale l’utente si connette alla rete. Inoltre è possibile la condivisione di tutti i punti registrati su un database online per rendere pubbliche le proprie registrazioni.