Identification of design motifs with pattern matching algorithms

Design patterns are important in software maintenance because they help in understanding and re-engineering systems. They propose design motifs, solutions to recurring design problems. The identification of occurrences of design motifs in large systems consists of identifying classes whose structure and organization match exactly or approximately the structure and organization of classes as suggested by the motif. We adapt two classical approximate string matching algorithms based on automata simulation and bit-vector processing to efficiently identify exact and approximate occurrences of motifs. We then carry out two case studies to show the performance, precision, and recall of our algorithms. In the first case study, we assess the performance of our algorithms on seven medium-to-large systems. In the second case study, we compare our approach with three existing approaches (an explanation-based constraint approach, a metric-enhanced explanation-based constraint approach, and a similarity scoring approach) by applying the algorithms on three small-to-medium size systems, JHotDraw, Juzzle, and QuickUML. Our studies show that approximate string matching based on bit-vector processing provides efficient algorithms to identify design motifs.     

Effect of the incorporation of a low amount of carbohydrate-containing monomer on the swelling properties of polyacrylamide hydrogels

In this work, the influence of the incorporation of a small amount of carbohydrate-containing monomer N-acryloyllactosylamine (LAM) on the swelling behavior of covalently-crosslinked polyacrylamide hydrogels in water has been reported. The incorporation of LAM into the copolymer was assessed by ATR–FTIR and thermogravimetric experiments. The main result is that the equilibrium water uptake was significantly decreased as soon as the hydrogel contained LAM considering a constant amount of crosslinking agent. The greatest difference of water uptakes between carbohydrate-free hydrogel and carbohydrate-containing hydrogel occurred for the lowest crosslinker amount of 1 mol%. In that case, the value of the water uptake reached 56-fold for the carbohydrate-free hydrogel and decreased down to 41-fold for the 10 mol% LAM hydrogel. Additional NMR experiments were used to measure the amount of non-crystallizable water which was higher for carbohydrate-free hydrogel than that for lactose-containing hydrogel confirming the water uptake results.     

Net N immobilisation during the biodegradation of mucilage in soil as affected by repeated mineral and organic fertilisation

Repeated fertilisation of crops with manure commonly increases both the amount and the quality of soil organic matter, the mineralisation of which strongly determines the availability of N to plants. In the rhizosphere, the microbial mineralisation/immobilisation of N is enhanced due to rhizodeposition (release of organic compounds from roots). In this work, we studied N transformations during incubation of maize root mucilage in soils that had been previously fertilized with composted pig manure or with ammonium nitrate for 7 years. Our work revealed mucilage was rapidly mineralised (average half-life of 3 days), inducing a rapid N immobilisation of 94 mg N g⁻¹ of mucilage C, followed by a slow remineralisation. Fertilisation with manure induced a persistent stimulation of the soil organic matter mineralisation, leading to an enhanced content of soil inorganic N (+23% in 58 days of incubation). Due to this stimulation of microbial activity in the soil fertilized with manure, the decrease in inorganic N during the biodegradation of mucilage lasted a shorter time as compared to the mineral fertilisation. However, the type of fertilisation did not significantly change the amount of N immobilised.     

BRIDGING CAPITAL GAPS TO PROMOTE INNOVATION IN FRANCE

With the withdrawal of state ascendancy over the financial sector, the national system of financing has taken a new turn in France. This paper deals with the capacity of this new system to promote innovation and argues that the capacity of French banks to finance innovation is now limited. In this context the supply of equity to firms is a critical factor. For small firms, however, there was a critical shortage in equity supply right up to the mid-1990s. Since then new policies and institutional reforms have been launched to cope with French financial gaps and to financially promote innovation. Amongst these institutional innovations the paper mentions the Nouveau Marché; the Development Bank for SMEs; and the impetus given the venture capital industry by earmarking a proportion of funds from the privatization of France Telecom to support innovative small enterprises.     

The invasion of a large lake by the Eurasian genotype of common reed: The influence of roads and residential construction

The Eurasian genotype of common reed (Phragmites australis) is one of the most aggressive plant invading North American wetlands. There is, however, little published evidence on establishment patterns of populations along lakes of the St. Lawrence River–Great Lakes watershed. We tested the hypothesis that the recent invasion of Great Lake Saint-François (Québec, Canada) by common reed was facilitated by a dense road system and by an intense residence construction activity along lakeshores. A total of 345 and 2914 reed stands were mapped along lakeshores, and along the road system of the study area, respectively. The probability of finding a reed stand on a lakeshore increases with the proximity of the lake's outlet, and of a paved road, but decreases with the proximity of a residence built since 1990. It is likely that common reed first spread along the road system, and that wind dispersal of seeds then favored the establishment of populations on lakeshores. Our model does not support the hypothesis that residential construction facilitated the establishment of reed stands, probably because the recent residential construction boom occurred essentially in the southern part of the lake, where the number of roadside reed populations is much lower than in the northern part (lower seed rain). The invasion of Great Lake Saint-François shows that the spread of the plant is not restricted to major river or road systems. Large or small lakes, if submitted to intense diaspore pressure, can also be at risk.     

Uterine EHG Processing for Obstetrical Monitorng

The temporal and spectral properties of the human uterine electromyogram are first described, related to two different situations: pregnancy and parturition. Thus, a parameter set is selected, and a discriminant analysis is performed, in order to obtain the best discriminant vector for these two situations. A dynamic control of the efficiency of the contractions during labor is described. The good results of this dynamic control permit us to propose a monitoring device providing information on contraction rate and efficiency.     

Application of the HeapSim model to the heap bioleaching of the Pueblo Viejo ore deposit

The HeapSim computer model can simulate column, crib, and heap leach processes for a variety of sulfide ores. In this work, the model was used to evaluate the feasibility of heap biooxidizing the high-grade pyrite ore from the Pueblo Viejo deposit in the Dominican Republic. Simulations have revealed few but critical conditions for the success of a full-scale heap.The heap should be inoculated with mesophiles and moderate thermophiles bacteria, as well as extreme thermophilic archaea at the start-up of the biooxidation pretreatment. These microorganisms were isolated from two slurry cultures collected at site and grown in the laboratory at different temperatures. All cell types may be indigenous to the site, but inoculation of the ore and leach solution with all cell types is necessary for the transition into different temperature regimes for best sulfide oxidation performance.To ensure that all parts of the heap achieve at least 65% sulfide oxidation in the planned 400 days of treatment, the heap height should be less than 8 m if aerated at 2 m³/m²/h and irrigated at 8 L/m²/h. These conditions would preclude the formation of “hot spots” that could inhibit even the extreme thermophiles. By increasing the aeration rate to 4 m³/m²/h and the irrigation rate to 11 L/m²/h, the heap could be stacked to 8 m. Large aeration and irrigation rates would lower the temperatures at the top and bottom of the heap. Under these conditions, all parts of the heap could be expected to achieve 65% sulfide oxidation in only 250 days, as indicated by the model.     

Phase structure and mechanical properties of PP/EPR/CaCO3 nanocomposites: Effect of particle's size and treatment

Calcium carbonate (CaCO₃) reinforced polypropylene/ethylene propylene rubber (PP/EPR) copolymer composites for automotive use were developed by means of extrusion and injection molding process. Three kinds of CaCO₃ (stearic acid treated and untreated) nanoparticles and microparticles were used as fillers. The influence of stearic acid, particle size, and filler content on the state distribution and morphology were investigated by SEM and rheological measurements. Two different morphologies were observed: EPR and CaCO₃ dispersed in the PP matrix and a core shell structure, depending on the interactions between EPR and CaCO₃. Toughening mechanisms and mechanical properties of the different systems were investigated. Significant improvement in tensile modulus is observed in all composites, depending on filler content. Elongation and notched impact strength were drastically decreased, especially for composites with nano CaCO₃. Better impact properties were obtained with low content of treated particles, showing the importance of filler treatment. POLYM. ENG. SCI., 55:2859–2868, 2015. © 2015 Society of Plastics Engineers     

Enzymatic Evidence for a Revised Congocidine Biosynthetic Pathway

Naturally produced pyrrolamides, such as congocidine, are nonribosomal peptides that bind to the minor groove of DNA. Efforts to delineate the biosynthetic machinery responsible for their assembly have mainly employed genetic methods, and the enzymes responsible for their biosynthesis remain largely uncharacterized. We report the biochemical characterization of four proteins involved in congocidine formation: the adenylation‐thiolation (A–T) di‐domain Cgc18(1–610), its MbtH‐like partner SAMR0548, the AMP‐binding enzyme Cgc3*, and the T domain Cgc19. We assayed the ATP‐dependent activation of various commercially available and chemically synthesized compounds with Cgc18(1–610) and Cgc3*. We report the revised substrate specificities of Cgc18(1–610) and Cgc3*, and loading of 4‐acetamidopyrrole‐2‐carboxylic acid onto Cgc19. Based on these biochemical studies, we suggest a revised congocidine biosynthetic pathway.     

Thioether Analogues of Disulfide‐Bridged Cyclic Peptides Targeting Death Receptor 5: Conformational Analysis,Dimerisation and Consequences for Receptor Activation

Cyclic peptides containing redox‐stable thioether bridges might provide a useful alternative to disulfide‐bridged bioactive peptides. We report the effect of replacing the disulfide bridge with a lanthionine linkage in a 16‐mer cyclic peptide that binds to death receptor 5 (DR5, TRAIL‐R2). Upon covalent oligomerisation, the disulfide‐bridged peptide has previously shown similar behaviour to that of TNF‐related apoptosis inducing ligand (TRAIL), by selectively triggering the DR5 cell death pathway. The structural and biological properties of the DR5‐binding peptide and its desulfurised analogue were compared. Surface plasmon resonance (SPR) data suggest that these peptides bind DR5 with comparable affinities. The same holds true for dimeric versions of these peptides: the thioether is able to induce DR5‐mediated apoptosis of BJAB lymphoma and tumorigenic BJELR cells, albeit to a slightly lower extent compared to its disulfide homologue. NMR analysis revealed subtle variation in the conformations of the two peptides and suggests that the thioether peptide is slightly less folded than its disulfide homologue. These observations could account for the different capability of the two dimers to cluster DR5 receptors on the cell surface and to trigger apoptosis. Nevertheless, our results suggest that the thioether peptide is a potential candidate for evaluation in animal models.