INTEGRATION OF INSTRUMENTATION AND PROCESSING SOFTWARE OF A LASER SPECKLE CONTRAST IMAGING SYSTEM

Laser speckle contrast imaging (LSCI) has the potential to be a powerful tool in medicine, but more research in the field is required so it can be used properly. To help in the progression of Michigan Tech's research in the field, a graphical user interface (GUI) was designed in Matlab to control the instrumentation of the experiments as well as process the raw speckle images into contrast images while they are being acquired. The design of the system was successful and is currently being used by Michigan Tech's Biomedical Engineering department. This thesis describes the development of the LSCI GUI as well as offering a full introduction into the history, theory and applications of LSCI.

Advanced 4DT flight guidance and control software system

The work presented in this thesis has been part of a Cranfield University research project. This thesis aims to design a flight control law for large cargo aircraft by using predictive control, which can assure flight motion along the flight path exactly and on time. In particular this work involves the modelling of a Boeing C-17 Globemaster III 6DOF model (used as study case), by using DATCOM and Matlab Simulink software. Then a predictive control algorithm has been developed. The majority of the work is done in a Matlab/Simulink environment. Finally the predictive control algorithm has been applied on the aircraft model and its performances, in tracking given trajectory optimized through a 4DT Research Software, have been evaluated.

Classifying And Predicting Software Security Vulnerabilities based on Reproducibility

Security defects are common in large software systems because of their size and complexity. Although efficient development processes, testing, and maintenance policies are applied to software systems, there are still a large number of vulnerabilities that can remain, despite these measures. Some vulnerabilities stay in a system from one release to the next one because they cannot be easily reproduced through testing. These vulnerabilities endanger the security of the systems. We propose vulnerability classification and prediction frameworks based on vulnerability reproducibility. The frameworks are effective to identify the types and locations of vulnerabilities in the earlier stage, and improve the security of software in the next versions (referred to as releases). We expand an existing concept of software bug classification to vulnerability classification (easily reproducible and hard to reproduce) to develop a classification framework for differentiating between these vulnerabilities based on code fixes and textual reports. We then investigate the potential correlations between the vulnerability categories and the classical software metrics and some other runtime environmental factors of reproducibility to develop a vulnerability prediction framework. The classification and prediction frameworks help developers adopt corresponding mitigation or elimination actions and develop appropriate test cases. Also, the vulnerability prediction framework is of great help for security experts focus their effort on the top-ranked vulnerability-prone files. As a result, the frameworks decrease the number of attacks that exploit security vulnerabilities in the next versions of the software. To build the classification and prediction frameworks, different machine learning techniques (C4.5 Decision Tree, Random Forest, Logistic Regression, and Naive Bayes) are employed. The effectiveness of the proposed frameworks is assessed based on collected software security defects of Mozilla Firefox.

Determinants of the Design and Use of PMS in Portuguese Government Agencies: A Complementary Theoretical Approach

Performance measurement is seen as a main pillar of public management reforms. However, prior research did not mitigate the level of ambiguity on PMS development and use and many questions left unanswered. Our findings provide knowledge on the design and use of PMS in the public sector answer- ing to calls for a complementary approach among institutional and contingency factors. The authors find that the design of PMS and the use of performance information for external purposes are increased to legitimate the organizational’ work and to obtain external support. Moreover, structural variables such as type of agency and management autonomy are also determinants on the organizational responses. Finally, the authors find some coupling between the design of PMS and outcomes. So, both contingent and institutional approaches play an important role on the empirical model.

Abstraction and use of groundwater for heating buildings in a hard rock environment

In order to turn more efficient the heating of class rooms in the lower floor of the old building of the University of Évora (a XVI century building), five drillings were organised inside the area of the university (Figure 1). The purpose was to use the temperature differential of groundwater in relation to air, by means of a heat exchanger, and use this process to heat the rooms using less energy, turning the heating process less expensive. The wells were drilled in fractured rocks (gneisses), and the purpose was to locate them at least around 100 m one from each other, whilst trying to have a hydraulic connection in-between. From the five initial wells, four were successful in terms of productivity, but just two of them (RA1 and RA2) proved to be hydraulically connected. The wells were equipped with screens for all their drilled depth (100 m), except for the first six meters and some two or three pipes of six meters each, to allow space for the installation for submersible pumps. The length of the installed screens guarantees a good efficiency of the system. In the wells with no connection, the heating system can work using each single well for abstraction and injection, but the process is much less efficient than in the cases where interaction between wells is possible through the rock’s fracture network.

Variety, flexibility, and use of abstract concepts. A multiple grounded perspective.

The nature of concepts is a matter of intense debate in cognitive sciences. While traditional views claim that conceptual knowledge is represented in a unitary symbolic system, recent Embodied and Grounded Cognition theories (EGC) submit the idea that conceptual system is couched in our body and influenced by the environment (Barsalou, 2008). One of the major challenges for EGC is constituted by abstract concepts (ACs), like fantasy. Recently, some EGC proposals addressed this criticism, arguing that the ACs comprise multifaced exemplars that rely on different grounding sources beyond sensorimotor one, including interoception, emotions, language, and sociality (Borghi et al., 2018). However, little is known about how ACs representation varies as a function of life experiences and their use in communication. The theoretical arguments and empirical studies comprised in this dissertation aim to provide evidence on multiple grounding of ACs taking into account their varieties and flexibility. Study I analyzed multiple ratings on a large sample of ACs and identified four distinct subclusters. Study II validated this classification with an interference paradigm involving motor/manual, interoceptive, and linguistic systems during a difficulty rating task. Results confirm that different grounding sources are activated depending on ACs kind. Study III-IV investigate the variability of institutional concepts, showing that the higher the law expertise level, the stronger the concrete/emotional determinants in their representation. Study V introduced a novel interactive task in which abstract and concrete sentences serve as cues to simulate conversation. Analysis of language production revealed that the uncertainty and interactive exchanges increase with abstractness, leading to generating more questions/requests for clarifications with abstract than concrete sentences. Overall, results confirm that ACs are multidimensional, heterogeneous, and flexible constructs and that social and linguistic interactions are crucial to shaping their meanings. Investigating ACs in real-time dialogues may be a promising direction for future research.

Fluorogenic hyaluronan-based probe: characterization and use in advanced microscopy

Among all, the application of nanomaterials in biomedical research and most recently in the environmental one has opened the fields of nanomedicine and nanoremediation. Sensing methods based on fluorescence optical probe are generally requested for their selectivity, sensitivity. However, most imaging methods in literature rely on a fluorescent covalent labelling of the system. Therefore, the main aim of this project was to synthetise a biocompatible fluorogenic hyaluronan probe (HA) polymer functionalised with a rhomadine B (RB) moieties and study its behaviour as an optical probe with different materials with microscopy techniques. A derivatization of HA with RB (HA-RB) was successfully obtained providing a photophysical characterization showing a particular fluorescence mechanism of the probe. Firstly, we tested the interaction with different lab-grade micro and nanoplastics in water. Thanks to the peculiar photophysical behaviour of the probe nanoplastics can be detected with confocal microscopy and more interestingly their nature can be discriminated based on the fluorescence lifetime decay with FLIM microscopy. After, the interaction of a model plant derived metabolic enzyme GAPC1 undergoing oxidative-triggered aggregation was explored with the HA-RB. We highlighted the probe interaction with the protein even at early stage of the kinetic. Moreover, nanoparticle tracking analysis (NTA) experiment demonstrates that the probe is in fact able to interact with the small pre-aggregates in the early stage of the aggregation kinetic. Ultimately, we focused on the possibility to apply the probe in a super resolution microscopy technique, PALM, exploiting its aspecific interaction to characterize the surface topography of PTFE polydisperse microplastics. Optimal conditions were reached at high concentration of the probe (70 nM) where 0.5-5 nM is always advisable for this technique. Thanks to the polymeric nature and fluorescence mechanism of the probe, this technique was able to reveal features of PTFE surface under the diffraction limit (< 250 nm).

Free Open Source Software and Dual-Use: Loophole or Dissent?

The Free Open Source Software (FOSS) seem far from the military field but in some cases, some technologies normally used for civilian purposes may have military applications. These products and technologies are called dual-use. Can we manage to combine FOSS and dual-use products? On one hand, we have to admit that this kind of association exists - dual-use software can be FOSS and many examples demonstrate this duality - but on the other hand, dual-use software available under free licenses lead us to ask many questions. For example, the dual-use export control laws aimed at stemming the proliferation of weapons of mass destruction. Dual-use export in United States (ITAR) and Europe (regulation 428/2009) implies as a consequence the prohibition or regulation of software exportation, involving the closing of source code. Therefore, the issues of exported softwares released under free licenses arises. If software are dual-use goods and serve for military purposes, they may represent a danger. By the rights granted to licenses to run, study, redistribute and distribute modified versions of the software, anyone can access the free dual-use software. So, the licenses themselves are not at the origin of the risk, it is actually linked to the facilitated access to source codes. Seen from this point of view, it goes against the dual-use regulation which allows states to control these technologies exportation. For this analysis, we will discuss about various legal questions and draft answers from either licenses or public policies in this respect.

Definition, realization and evaluation of a software reference architecture for use in space applications

A recent initiative of the European Space Agency (ESA) aims at the definition and adoption of a software reference architecture for use in on-board software of future space missions. Our PhD project placed in the context of that effort. At the outset of our work we gathered all the industrial needs relevant to ESA and all the main European space stakeholders and we were able to consolidate a set of technical high-level requirements for the fulfillment of them. The conclusion we reached from that phase confirmed that the adoption of a software reference architecture was indeed the best solution for the fulfillment of the high-level requirements. The software reference architecture we set on building rests on four constituents: (i) a component model, to design the software as a composition of individually verifiable and reusable software units; (ii) a computational model, to ensure that the architectural description of the software is statically analyzable; (iii) a programming model, to ensure that the implementation of the design entities conforms with the semantics, the assumptions and the constraints of the computational model; (iv) a conforming execution platform, to actively preserve at run time the properties asserted by static analysis. The nature, feasibility and fitness of constituents (ii), (iii) and (iv), were already proved by the author in an international project that preceded the commencement of the PhD work. The core of the PhD project was therefore centered on the design and prototype implementation of constituent (i), a component model. Our proposed component model is centered on: (i) rigorous separation of concerns, achieved with the support for design views and by careful allocation of concerns to the dedicated software entities; (ii) the support for specification and model-based analysis of extra-functional properties; (iii) the inclusion space-specific concerns.

On the hardware and software architecture of the robuter mobile platform: a hands-on approach

The Robuter is a robotic mobile platform that is located in the “Hands-On” Laboratory of the IPP-Hurray! Research Group, at the School of Engineering of the Polytechnic Institute of Porto. Recently, the Robuter was subject of an upgrading process addressing two essential areas: the Hardware Architecture and the Software Architecture. This upgrade in process was triggered due to technical problems on-board of the robot and also to the fact that the hardware/software architecture has become obsolete. This Technical Report overviews the most important aspects of the new Hardware and Software Architectures of the Robuter. This document also presents a first approach on the first steps towards the use of the Robuter platform, and provides some hints on future work that may be carried out using this mobile platform.

Non-preemptive and SRP-based fullypreemptive scheduling of real-time Software Transactional Memory

Recent embedded processor architectures containing multiple heterogeneous cores and non-coherent caches renewed attention to the use of Software Transactional Memory (STM) as a building block for developing parallel applications. STM promises to ease concurrent and parallel software development, but relies on the possibility of abort conflicting transactions to maintain data consistency, which in turns affects the execution time of tasks carrying transactions. Because of this fact the timing behaviour of the task set may not be predictable, thus it is crucial to limit the execution time overheads resulting from aborts. In this paper we formalise a FIFO-based algorithm to order the sequence of commits of concurrent transactions. Then, we propose and evaluate two non-preemptive and one SRP-based fully-preemptive scheduling strategies, in order to avoid transaction starvation.

Biana: a software framework for compiling biological interactions and analyzing networks

Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.Results: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.Conclusions: BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

Software and Code Finder: making research outputs visible

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Software development methods and quality assurance: Special focus on South Korea

The purpose of this study was to explore software development methods and quality assurance practices used by South Korean software industry. Empirical data was collected by conducting a survey that focused on three main parts: software life cycle models and methods, software quality assurance including quality standards, the strengths and weaknesses of South Korean software industry. The results of the completed survey showed that the use of agile methods is slightly surpassing the use of traditional software development methods. The survey also revealed an interesting result that almost half of the South Korean companies do not use any software quality assurance plan in their projects. For the state of South Korean software industry large number of the respondents thought that despite of the weakness, the status of software development in South Korea will improve in the future.

Comparative analysis of vitamin A and iron content in food according to different food composition tables and nutritional evaluation software programs

The objective of this study was to analyze retinol equivalent and iron content in different food composition tables and nutritional evaluation software programs. A literature search was conduct to identify tables and software available in Brazil containing information about retinol equivalent and iron content that are currently used by nutritionists. Ten tables and five software programs were selected for this study. The methodology used to present the retinol equivalent and iron content was evaluated and no pattern to obtain such content was found in the tables and software programs analyzed. Only one of the tables had enough information for the calculation of retinol equivalents; this table is recommended to all Latin America As for the iron content, three of the tables analyzed stand out and therefore should be used; two of them are based on national foods and the other is recommended for use in all Latin America countries. None of the software programs evaluated use the conversion factors suggested by IVACG to assess the vitamin A content in foods. Special attention should be given to the content of iron provided in the software programs since they use tables as international sources and fortified foods.