RESRES: The story behind the paper “Research in software engineering: An analysis of the literature”

This article is a background report describing a comprehensive study of research in the three computing disciplines Computer Science, Software Engineering, and Information Systems. Findings relate to research topics, approaches, methods, reference disciplines, and levels of analysis. The article informally describes the process used and the research products produced.     

Long term assessment of a hybrid electrochemical treatment

Monitoring the performance of systems installed to protect against/halt the corrosion of reinforcing steel in concrete is essential in ensuring that the reinforcing bar (rebar) is adequately protected and remains in a non‐corroding state. A chloride contaminated concrete test block containing a hybrid anode system has been periodically monitored over the past 4.5 years to assess the anode current output and thus, the protection offered to the steel. De‐polarisation and impedance analysis data have been acquired to calculate steel corrosion rates. Both tests indicated that the steel was passive in the concrete environment and that the anode was able to protect all of the embedded steel despite the difficult geometry of the sample. It was also found that after 2 years it was still possible to drive a high current from the installed anode.     

Combining hygrothermal and corrosion models to predict corrosion of metal fasteners embedded in wood

A combined heat, moisture, and corrosion model is presented and used to simulate the corrosion of metal fasteners embedded in solid wood exposed to the exterior environment. First, the moisture content and temperature at the wood/fastener interface is determined at each time step. Then, the amount of corrosion is determined spatially using an empirical corrosion rate model and the inputs of the first step. The result is a corrosion profile along the length of the fastener generated by summing the corrosion depths determined at each time step. We apply the combined model to predict the annual corrosion depth along a metal fastener in wood decks situated in nine different US cities. Corrosion profiles are found to exhibit the same general shape independently of climatic load, with the largest amount of corrosion occurring at 1–5 mm from the wood surface with corrosion depths ranging from 5 μm in Phoenix, Arizona to 45 μm in Hilo, Hawaii. Corrosion is confined to the first 7–20 mm of the fastener below the wood surface. By varying the climatic loads, we find that although there is a definite relation between total annual rain and total annual corrosion, under the same rain loads corrosion is higher for a climate with more evenly distributed rain events. The proposed combined model is able to capture corrosion behavior under varying loading. A sensitivity analysis gives guidelines for future corrosion modeling work for fasteners in wood.     

Identification of microglial signal transduction pathways mediating a neurotoxic response to amyloidogenic fragments of beta-amyloid and prion proteins

Microglial interaction with amyloid fibrils in the brains of Alzheimer's and prion disease patients results in the inflammatory activation of these cells. We observed that primary microglial cultures and the THP-1 monocytic cell line are stimulated by fibrillar beta-amyloid and prion peptides to activate identical tyrosine kinase-dependent inflammatory signal transduction cascades. The tyrosine kinases Lyn and Syk are activated by the fibrillar peptides and initiate a signaling cascade resulting in a transient release of intracellular calcium that results in the activation of classical PKC and the recently described calcium-sensitive tyrosine kinase PYK2. Activation of the MAP kinases ERK1 and ERK2 follows as a subsequent downstream signaling event. We demonstrate that PYK2 is positioned downstream of Lyn, Syk, and PKC. PKC is a necessary intermediate required for ERK activation. Importantly, the signaling response elicited by beta-amyloid and prion fibrils leads to the production of neurotoxic products. We have demonstrated in a tissue culture model that conditioned media from beta-amyloid- and prion-stimulated microglia or from THP-1 monocytes are neurotoxic to mouse cortical neurons. This toxicity can be ameliorated by treating THP-1 cells with specific enzyme inhibitors that target various components of the signal transduction pathway linked to the inflammatory responses.     

Coherence measures and their relation to fuzzy similarity and inconsistency in knowledge bases

Intuitively it seems that the coherence of information received from heterogeneous sources should be one factor in determining the reliability or truthfulness of the information, yet the concept of coherence is extremely difficult to define. This paper draws on recent work on probabilistic measures of coherence by investigating two measures with contrasting properties and then explores how this work relates to similarity of fuzzy sets and comparison of knowledge bases in cases where inconsistency is present. In each area contrasting measures are proposed analogous to the probabilistic case. In particular, concepts of fuzzy and logical independence are proposed and in each area it is found that sensitivity to the relevant concept of independence is a distinguishing feature between the contrasting measures. In the case of inconsistent knowledge bases, it is argued that it is important to take agreeing information and not just conflicting and total information into account when comparing two knowledge bases. One of the measures proposed achieves this and is shown to have a number of properties which enable it to overcome some problems encountered by other approaches.     

General method for plasmid construction using homologous recombination

We describe a general method for plasmid assembly that uses yeast and extends beyond yeast-specific research applications. This technology exploits the homologous recombination, double-stranded break repair pathway in Saccharomyces cerevisiae to join DNA fragments. Synthetic, double-stranded "recombination linkers" were used to "subclone" a DNA fragment into a plasmid with > 80% efficiency. Quantitative data on the influence of DNA concentration and overlap length on the efficiency of recombination are presented. Using a simple procedure, plasmids were shuttled from yeast into E. coli for subsequent screening and large-scale plasmid preps. This simple method for plasmid construction has several advantages. (i) It bypasses the need for extensive PCR amplification and for purification, modification and/or ligation techniques routinely used for plasmid constructions. (ii) The method does not rely on available restriction sites, thus fragment and vector DNA can be joined within any DNA sequence. This enables the use of multifunctional cloning vectors for protein expression in mammalian cells, other yeast species, E. coli and other expression systems as discussed. (iii) Finally, the technology exploits yeast strains, plasmids and microbial techniques that are inexpensive and readily available.     

Decentralized adaptive control of electrically-driven manipulators

This paper presents two new decentralized strategies for motion control of uncertain electrically-driven manipulators. The first controller is an adaptive position regulation scheme which ensures semiglobal asymptotic convergence of the position error if no external disturbances are present and semiglobal convergence of the error to an arbitrarily small neighborhood of zero in the presence of bounded disturbances. It is shown that the regulation scheme can be modified to provide accurate trajectory tracking control through the introduction of adaptive feedforward elements in the control law; this second control strategy retains the simple decentralized structure of the first controller and ensures arbitrarily accurate tracking in the presence of bounded disturbances. Each of the adaptive schemes is very efficient computationally and requires virtually no information concerning either the manipulator or actuator models. The results of computer simulations and laboratory experiments with both terrestrial and space manipulators demonstrate that accurate and robust motion control can be achieved by using the proposed approach.     

Finite element modeling of three-dimensional pulsatile flow in the abdominal aorta: relevance to atherosclerosis

The infrarenal abdominal aorta is particularly prone to atherosclerotic plaque formation while the thoracic aorta is relatively resistant. Localized differences in hemodynamic conditions, including differences in velocity profiles, wall shear stress, and recirculation zones have been implicated in the differential localization of disease in the infrarenal aorta. A comprehensive computational framework was developed, utilizing a stabilized, time accurate, finite element method, to solve the equations governing blood flow in a model of a normal human abdominal aorta under simulated rest, pulsatile, flow conditions. Flow patterns and wall shear stress were computed. A recirculation zone was observed to form along the posterior wall of the infrarenal aorta. Low time-averaged wall shear stress and high shear stress temporal oscillations, as measured by an oscillatory shear index, were present in this location, along the posterior wall opposite the superior mesenteric artery and along the anterior wall between the superior and inferior mesenteric arteries. These regions were noted to coincide with a high probability-of-occurrence of sudanophilic lesions as reported by Cornhill et al. (Monogr. Atheroscler. 15:13-19, 1990). This numerical investigation provides detailed quantitative data on hemodynamic conditions in the abdominal aorta heretofore lacking in the study of the localization of atherosclerotic disease.     

Experimental infection of domestic sheep with culture-derived Leishmania donovani promastigotes

Domestic sheep were intradermally inoculated with culture-derived stationary phase Leishmania donovani promastigotes. Sampling of site of inoculation, liver and spleen for 244 days showed that this parasite can stay alive in the skin for up to 28 days post-inoculation. Apart from pyrexia that was evident in all the animals for 42 days, no other symptoms of kala-azar were seen. No parasites were recovered from the visceral organs throughout the sampling period, suggesting that sheep are not susceptible to infection with L. donovani. It is therefore unlikely that sheep can be synanthropic reservoirs for this parasite.