Empirical studies in reverse engineering: state of the art and future trends

Starting with the aim of modernizing legacy systems, often written in old programming languages, reverse engineering has extended its applicability to virtually every kind of software system. Moreover, the methods originally designed to recover a diagrammatic, high-level view of the target system have been extended to address several other problems faced by programmers when they need to understand and modify existing software. The authors’ position is that the next stage of development for this discipline will necessarily be based on empirical evaluation of methods. In fact, this evaluation is required to gain knowledge about the actual effects of applying a given approach, as well as to convince the end users of the positive cost–benefit trade offs. The contribution of this paper to the state of the art is a roadmap for the future research in the field, which includes: clarifying the scope of investigation, defining a reference taxonomy, and adopting a common framework for the execution of the experiments.     

Community research activities in secure and trustworthy ICT infrastructures

Secure and trusted Information and Communication Technology (ICT) infrastructures are key enablers for the development of a trustworthy Information Society. The European Union, recognising this, has launched over the last few years a number of research initiatives aiming at designing and building secure and dependable ICT systems and networks, which respect citizens’ rights and protect their privacy and personal data. The European Commission is already funding more than 37 R&D projects in this area under the IST programme, which is part of the 6th Framework Programme (2002 to 2006). The paper first presents the main research challenges in the development of secure, dependable and trusted ICT infrastructures. It then describes a representative set of these IST projects dealing with advanced research in network and service security. The paper also presents upcoming opportunities for research funding in this area under the newly launched ICT programme, part of the 7th Framework Programme that extends from 2007 to 2013.     

DNA double-strand break repair: a theoretical framework and its application

DNA double-strand breaks (DSBs) are formed as a result of genotoxic insults, such as exogenous ionizing radiation, and are among the most serious types of DNA damage. One of the earliest molecular responses following DSB formation is the phosphorylation of the histone H2AX, giving rise to γH2AX. Many copies of γH2AX are generated at DSBs and can be detected in vitro as foci using well-established immuno-histochemical methods. It has previously been shown that anti-γH2AX antibodies, modified by the addition of the cell-penetrating peptide TAT and a fluorescent or radionuclide label, can be used to visualize and quantify DSBs in vivo. Moreover, when labelled with a high amount of the short-range, Auger electron-emitting radioisotope, ¹¹¹In, the amount of DNA damage within a cell can be increased, leading to cell death. In this report, we develop a mathematical model that describes how molecular processes at individual sites of DNA damage give rise to quantifiable foci. Equations that describe stochastic mean behaviours at individual DSB sites are derived and parametrized using population-scale, time-series measurements from two different cancer cell lines. The model is used to examine two case studies in which the introduction of an antibody (anti-γH2AX-TAT) that targets a key component in the DSB repair pathway influences system behaviour. We investigate: (i) how the interaction between anti-γH2AX-TAT and γH2AX effects the kinetics of H2AX phosphorylation and DSB repair and (ii) model behaviour when the anti-γH2AX antibody is labelled with Auger electron-emitting ¹¹¹In and can thus instigate additional DNA damage. This work supports the conclusion that DSB kinetics are largely unaffected by the introduction of the anti-γH2AX antibody, a result that has been validated experimentally, and hence the hypothesis that the use of anti-γH2AX antibody to quantify DSBs does not violate the image tracer principle. Moreover, it provides a novel model of DNA damage accumulation in the presence of Auger electron-emitting ¹¹¹In that is supported qualitatively by the available experimental data.     

Impact of the Nanoscale Gap Morphology on the Plasmon Coupling in Asymmetric Nanoparticle Dimer Antennas

Coupling of plasmon resonances in metallic gap antennas is of interest for a wide range of applications due to the highly localized strong electric fields supported by these structures, and their high sensitivity to alterations of their structure, geometry, and environment. Morphological alterations of asymmetric nanoparticle dimer antennas with (sub)‐nanometer size gaps are assigned to changes of their optical response in correlative dark‐field spectroscopy and high‐resolution transmission electron microscopy (HR‐TEM) investigations. This multimodal approach to investigate individual dimer structures clearly demonstrates that the coupling of the plasmon modes, in addition to well‐known parameters such as the particle geometry and the gap size, is also affected by the relative alignment of both nanoparticles. The investigations corroborate that the alignment of the gap forming facets, and with that the gap area, is crucial for their scattering properties. The impact of a flat versus a rounded gap structure on the optical properties of equivalent dimers becomes stronger with decreasing gap size. These results hint at a higher confinement of the electric field in the gap and possibly a different onset of quantum transport effects for flat and rounded gap antennas in corresponding structures for very narrow gaps.     

Development of a robust canopy height model derived from ALS point clouds for predicting individual crown attributes at the species level

ABSTRACT

Tree crown attributes are important parameters during the assessment and monitoring of forest ecosystems. Canopy height models (CHMs) derived from airborne laser scanning (ALS) data have proved to be a reliable source for extracting different biophysical characteristics of single trees and at stand level. However, ALS-derived tree measurements (e.g., mean crown diameter) can be negatively affected by pits that appear in the CHMs. Thus, we propose a novel method for generating pit-free CHMs from ALS point clouds for estimating crown attributes (i.e., area and mean diameter) at the species level. The method automatically calculates a threshold for a pixel based on the range of height values within neighbouring pixels; if the pixel falls below the threshold then it is recognized as a pitted pixel. The pit is then filled with the median of the values of the neighbouring pixels. Manually delineated individual tree crowns (ITC) of four deciduous and two coniferous species on Colour Infrared (CIR) stereo images were used as a reference in the analysis. In addition, a variety of different algorithms for constructing CHMs were compared to investigate the performance of different CHMs in similar forest conditions. Comparisons between the estimated and observed crown area (R² = 0.95, RMSE% = 19.12% for all individuals) and mean diameter (R² = 0.92, RMSE% = 12.16% for all individuals) revealed that ITC attributes were correctly estimated by segmentation of the pit-free CHM proposed in this study. The goodness of matching and geometry revealed that the delineated crowns correctly matched up to the reference data and had identical geometry in approximately 70% of cases. The results showed that the proposed method produced a CHM that estimates crown attributes more accurately than the other investigated CHMs. Furthermore, the findings suggest that the proposed algorithm used to fill pits with the median of height observed in surrounding pixels significantly improve the accuracy of the results the species level due to a higher correlation between the estimated and observed crown attributes. Based on these results, we concluded that the proposed pit filling method is capable of providing an automatic and objective solution for constructing pit-free CHMs for assessing individual crown attributes of mixed forest stands.     

Flood regulation using nonlinear model predictive control

In this paper the flood problem of the river Demer, a river located in Belgium, is discussed. First a simplified model of the Demer basin is derived based on the conceptual reservoir modeling concept. This model was calibrated to simulations results with a more detailed full hydrodynamic model. Afterwards, the focus is shifted to a nonlinear model predictive controller (NMPC) which is based on a new semi-condensed optimization procedure combined with a line search approach. Finally, simulations are performed based on historical data in which the NMPC is compared with the current control strategy used by the local water administration. Uncertainties are added to the rainfall predictions in order to assess the robustness of the NMPC.     

Ionic Modifiers in Phase Transition Extraction

The influence of the addition of NaCl on the temperature‐induced phase separation of 3‐methoxypropionitrile and water was investigated experimentally and theoretically. Experiments performed under direct microscopic observation revealed an enhanced domain growth speed and an improved clarifying behavior. It was found that the relevant physical properties changed dramatically with the addition of NaCl, which induced a shift of the equilibrium curve and a change of the operational temperature. Dissipative particle dynamics simulations have also predicted this shift, although electrostatic interactions were not taken into account explicitly in the current study.     

Counting with Fuzzy Sets

The notion of fuzzy set cardinality is examined. Zadeh's suggested measure of fuzzy cardinality, the sigma-count, is adopted and shown to generalize classical counting measure. This allows many combinatorial structures and counting techniques to be fuzzified, and hence used in knowledge representation and pattern recognition models. A fuzzy set review is found in the Appendix.     

Apoptosis in the morphology of Lyme borreliosis

BACKGROUND: Morphological, mainly ultrastructural changes in borreliosis has been the matter of contemporary interest indeed and it seems to be more and more clear that they are the product of an immunologic reaction. The aim of this study is to find out the epidermal changes of erythema migrans and acrodermatitis chronica on the ultrastructural level. METHODS AND RESULTS: There were 14 cases of erythema migrans and 5 acrodermatitis examined and many apoptotic keratinocytes, but also Langerhans cells and melanocytes were the dominant findings. Considering the very short time needed for apoptosis there is a good reason to take our findings as an important component of the borreliosis pathogenesis. CONCLUSIONS: The presence of many apoptotic cells in Lyme disease epidermis emphasises the importance of the immunology in the borreliosis pathogenesis. The striking number of apoptotic melanocytes suggests the higher affinity of the borrelia to the neuroectodermal tissue.