An extensible benchmark and tooling for comparing reverse engineering approaches

Various tools exist to reverse engineer software source code and generate design information, such as UML projections. Each has specific strengths and weaknesses, however no standardised benchmark exists that can be used to evaluate and compare their performance and effectiveness in a systematic manner. To facilitate such comparison in this paper we introduce the Reverse Engineering to Design Benchmark (RED-BM), which consists of a comprehensive set of Java-based targets for reverse engineering and a formal set of performance measures with which tools and approaches can be analysed and ranked. When used to evaluate 12 industry standard tools performance figures range from 8.82\% to 100\% demonstrating the ability of the benchmark to differentiate between tools. To aid the comparison, analysis and further use of reverse engineering XMI output we have developed a parser which can interpret the XMI output format of the most commonly used reverse engineering applications, and is used in a number of tools

Coordinated Reuse and Deployment for Scientific Software Prototypes with D-UEA-ST

D-UEA-ST (pronounced due east) is a plugin architecture that enables easy development of scientific software prototypes aimed at supporting software developers. Prototypes are developed as D-UEA-ST plugins that make use of knowledge representation models, reasoners and optimisers, and visualisation APIs. D-UEA-ST also defines a clear workflow that allows for continuous integration and deployment. This makes it easy for target users to try the tools and for researchers to get rapid feedback

Bacterial Growth Kinetics under a Novel Flexible Methacrylate Dressing Serving as a Drug Delivery Vehicle for Antiseptics

A flexible methacrylate powder dressing (Altrazeal®) transforms into a wound contour conforming matrix once in contact with wound exudate. We hypothesised that it may also serve as a drug delivery vehicle for antiseptics. The antimicrobial efficacy and influence on bacterial growth kinetics in combination with three antiseptics was investigated in an in vitro porcine wound model. Standardized in vitro wounds were contaminated with Staphylococcus aureus (MRSA; ATCC 33591) and divided into six groups: no dressing (negative control), methacrylate dressing alone, and combinations with application of 0.02% Polyhexamethylene Biguanide (PHMB), 0.4% PHMB, 0.1% PHMB + 0.1% betaine, 7.7 mg/mL Povidone-iodine (PVP-iodine), and 0.1% Octenidine-dihydrochloride (OCT) + 2% phenoxyethanol. Bacterial load per gram tissue was measured over five days. The highest reduction was observed with PVP-iodine at 24 h to log10 1.43 cfu/g, followed by OCT at 48 h to log10 2.41 cfu/g. Whilst 0.02% PHMB resulted in a stable bacterial load over 120 h to log10 4.00 cfu/g over 120 h, 0.1% PHMB + 0.1% betaine inhibited growth during the first 48 h, with slightly increasing bacterial numbers up to log10 5.38 cfu/g at 120 h. These results indicate that this flexible methacrylate dressing can be loaded with various antiseptics serving as drug delivery system. Depending on the selected combination, an individually shaped and controlled antibacterial effect may be achieved using the same type of wound dressing

East Bay Coalition for the Homeless: Branding Study and Marketing Strategy

There are a number of potential positioning strategies. The two which make the most sense for the EBCH are to “position the EBCH away from others in the category” and to “position the EBCH as unique.” These strategies have the advantage of setting the EBCH apart from the other organizations that address homelessness. Occupying its own “position” in the minds of potential and current donors is not only an effective communications/marketing strategy but also a less costly one because it avoids head-to-head competition and comparisons

Vorticity, Kinetic Energy, and Suppressed Gravitational-Wave Production in Strong First-Order Phase Transitions

We have performed the first three-dimensional simulations of strong first-order thermal phase transitions in the early universe. For deflagrations, we find that the rotational component of the fluid velocity increases as the transition strength is increased. For detonations, however, the rotational velocity component remains constant and small. We also find that the efficiency with which kinetic energy is transferred to the fluid falls below theoretical expectations as we increase the transition strength. The probable origin of the kinetic energy deficit is the formation of reheated droplets of the metastable phase during the collision, slowing the bubble walls. The rate of increase in the gravitational wave energy density for deflagrations in strong transitions is suppressed compared to that predicted in earlier work. This is largely accounted for by the reduction in kinetic energy. Current modeling therefore substantially overestimates the gravitational wave signal for strong transitions with deflagrations, in the most extreme case by a factor of 10(3). Detonations are less affected.Peer reviewe

Enhancing legacy software system analysis by combining behavioural and semantic information sources

Computer software is, by its very nature highly complex and invisible yet subject to a near-continual pressure to change. Over time the development process has become more mature and less risky. This is in large part due to the concept of software traceability; the ability to relate software components back to their initial requirements and between each other. Such traceability aids tasks such as maintenance by facilitating the prediction of “ripple effects” that may result, and aiding comprehension of software structures in general. Many organisations, however, have large amounts of software for which little or no documentation exists; the original developers are no longer available and yet this software still underpins critical functions. Such “legacy software” can therefore represent a high risk when changes are required. Consequently, large amounts of effort go into attempting to comprehend and understand legacy software. The most common way to accomplish this, given that reading the code directly is hugely time consuming and near-impossible, is to reverse engineer the code, usually to a form of representative projection such as a UML class diagram. Although a wide number of tools and approaches exist, there is no empirical way to compare them or validate new developments. Consequently there was an identified need to define and create the Reverse Engineering to Design Benchmark (RED-BM). This was then applied to a number of industrial tools. The measured performance of these tools varies from 8.8% to 100%, demonstrating both the effectiveness of the benchmark and the questionable performance of several tools. In addition to the structural relationships detectable through static reverse engineering, other sources of information are available with the potential to reveal other types of relationships such as semantic links. One such source is the mining of source code repositories which can be analysed to find components within a software system that have, historically, commonly been changed together during the evolution of the system and from the strength of that infer a semantic link. An approach was implemented to mine such semantic relationships from repositories and relationships were found beyond those expressed by static reverse engineering. These included groups of relationships potentially suitable for clustering. To allow for the general use of multiple information sources to build traceability links between software components a uniform approach was defined and illustrated. This includes rules and formulas to allow combination of sources. The uniform approach was implemented in the field of predictive change impact analysis using reverse engineering and repository mining as information sources. This implementation, the Java Code Relationship Anlaysis (jcRA) package, was then evaluated against an industry standard tool, JRipples. Depending on the target, the combined approach is able to outperform JRipples in detecting potential impacts with the risk of over-matching (a high number of false-positives and overall class coverage on some targets)

From CFTR biology toward combinatorial pharmacotherapy:expanded classification of cystic fibrosis mutations

More than 2000 mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) have been described that confer a range of molecular cell biological and functional phenotypes. Most of these mutations lead to compromised anion conductance at the apical plasma membrane of secretory epithelia and cause cystic fibrosis (CF) with variable disease severity. Based on the molecular phenotypic complexity of CFTR mutants and their susceptibility to pharmacotherapy, it has been recognized that mutations may impose combinatorial defects in CFTR channel biology. This notion led to the conclusion that the combination of pharmacotherapies addressing single defects (e.g., transcription, translation, folding, and/or gating) may show improved clinical benefit over available low-efficacy monotherapies. Indeed, recent phase 3 clinical trials combining ivacaftor (a gating potentiator) and lumacaftor (a folding corrector) have proven efficacious in CF patients harboring the most common mutation (deletion of residue F508, ΔF508, or Phe508del). This drug combination was recently approved by the U.S. Food and Drug Administration for patients homozygous for ΔF508. Emerging studies of the structural, cell biological, and functional defects caused by rare mutations provide a new framework that reveals a mixture of deficiencies in different CFTR alleles. Establishment of a set of combinatorial categories of the previously defined basic defects in CF alleles will aid the design of even more efficacious therapeutic interventions for CF patients

Magnetic Attraction of Gaze: Further Evidence of Hemispheric Imbalance in Schizophrenia?

A case is reported of a young man with a clinical diagnosis of schizophrenia and unusual oculo-motor abnormalities. The relationship between oculo-motor dysfunction and hemispheric balance in schizophrenia is discussed