Syntactic generation of practice novice programs in Python

Abstract: In the present day, computer programs are written in high level languages and parsed syntactically as part of a compilation process. These parsers are defined with context-free grammars (CFGs), a language recogniser for the respective programming language. Formal grammars in general are used for language recognition or generation. In this paper, we present the automatic generation of procedural programs in Python using a CFG. We have defined CFG rules to model program templates and implemented these rules to produce infinitely many distinct practice programs in Python. Each generated program is designed to test a novice programmer’s knowledge of functions, expressions, loops, and/or conditional statements. The CFG rules are highly generic and can be extended to generate programs in other procedural languages. The resulting programs can be used as practice, test or examination problems in introductory programming courses. 500,000 iterations of generated programs can be found at: https://tinyurl.com/ pythonprogramgenerator. A survey of 103 students’ perception showed that 93.1% strongly agreed that these programs can help them in practice and improve their programming skills

If players are sparse social dilemmas are too: Importance of percolation for evolution of cooperation

Spatial reciprocity is a well known tour de force of cooperation promotion. A thorough understanding of the effects of different population densities is therefore crucial. Here we study the evolution of cooperation in social dilemmas on different interaction graphs with a certain fraction of vacant nodes. We find that sparsity may favor the resolution of social dilemmas, especially if the population density is close to the percolation threshold of the underlying graph. Regardless of the type of the governing social dilemma as well as particularities of the interaction graph, we show that under pairwise imitation the percolation threshold is a universal indicator of how dense the occupancy ought to be for cooperation to be optimally promoted. We also demonstrate that myopic updating, due to the lack of efficient spread of information via imitation, renders the reported mechanism dysfunctional, which in turn further strengthens its foundations.Comment: 6 two-column pages, 5 figures; accepted for publication in Scientific Reports [related work available at http://arxiv.org/abs/1205.0541

Stability of oligosaccharides derived from lactulose during the processing of milk and apple juice

The scientific evidence on the bioactivity of oligosaccharides from lactulose has encouraged us to study their physicochemical modifications during the processing of milk and apple juice. The carbohydrate fraction with a degree of polymerization ≥3 was stable in milk heated at temperatures up to 100°C for 30 min and in apple juice heated up to 90°C for 15 min. An assessment of the Maillard reaction in heated milk pointed out a higher formation of furosine in milk with oligosaccharides from lactulose as compared to its counterpart without this ingredient, due to a higher presence of galactose. The organoleptic properties of juice with oligosaccharides from lactulose were acceptable and similar to those of apple juice with commercial galactooligosaccharides. The results presented herein demonstrate that oligosaccharides from lactulose can be used as prebiotic ingredients in a wide range of functional foods, including those intended for diabetics and lactose intolerant individuals.This work has been supported by project AGL2011-27884 from Spanish Ministerio de Economía y Competitividad.Peer Reviewe

N-Terminal 1–54 Amino Acid Sequence and Armadillo Repeat Domain Are Indispensable for P120-Catenin Isoform 1A in Regulating E-Cadherin

P120-catenin (p120ctn) exerts important roles in regulating E-cadherin and invasiveness in cancer cells. However, the mechanisms by which p120ctn isoforms 1 and 3 modulate E-cadherin expression are poorly understood. In the current study, HBE, H460, SPC and LTE cell lines were used to examine the effects of p120ctn isoforms 1A and 3A on E-cadherin expression and cell invasiveness. E-cadherin was localized on the cell membrane of HBE and H460 cells, while it was confined to the cytoplasm in SPC and LTE cells. Depletion of endogenous p120ctn resulted in reduced E-cadherin expression; however, p120ctn ablation showed opposite effects on invasiveness in the cell lines by decreasing invasiveness in SPC and LTE cells and increasing it in HBE and H460 cells. Restitution of 120ctn isoform 1A restored E-cadherin on the cell membrane and blocked cell invasiveness in H460 and HBE cells, while it restored cytoplasmic E-cadherin and enhanced cell invasiveness in SPC and LTE cells. P120ctn isoform 3A increased the invasiveness in all four cell lines despite the lack of effect on E-cadherin expression, suggesting a regulatory pathway independent of E-cadherin. Moreover, five p120ctn isoform 1A deletion mutants were constructed and expressed in H460 and SPC cells. The results showed that only the M4 mutant, which contains N-terminal 1–54 amino acids and the Armadillo repeat domain, was functional in regulating E-cadherin and cell invasiveness, as observed in p120ctn isoform 1A. In conclusion, the N-terminal 1–54 amino acid sequence and Armadillo repeat domain of p120ctn isoform 1A are indispensable for regulating E-cadherin protein. P120ctn isoform 1A exerts opposing effects on cell invasiveness, corresponding to the subcellular localization of E-cadherin

Mobilization of xanthine oxidase from the gastrointestinal tract in acute pancreatitis

BACKGROUND: Xanthine oxidoreductase has been proposed to play a role in the development of local and systemic effects of acute pancreatitis. Under physiologic conditions, the enzyme exists mainly as xanthine dehydrogenase (XDH) but can be converted by proteolytic cleavage to its superoxide-generating form xanthine oxidase (XOD). In addition to its intracellular location XDH/XOD is also associated to the polysaccharide chains of proteoglycans on the external endothelial cell membrane. In the early stages of acute pancreatitis, this enzyme seems to be arising from its mobilization from the gastrointestinal endothelial cell surface. Taking into account the ability of α-amylase to hydrolyze the internal α-1,4 linkages of polysaccharides, we wanted to elucidate the involvement of α-amylase in XDH/XOD mobilization from the gastrointestinal endothelial cell surface and the relevance of the ascitic fluid (AF) as the source of α-amylase in experimental acute pancreatitis. METHODS: Acute pancreatitis was induced in male Wistar rats by intraductal administration of 5% sodium taurocholate. In another experimental group 3000 U/Kg α-amylase was i.v. administered. The concentrations of XDH, XOD and α-amylase in plasma and AF and myeloperoxidase (MPO) in lung have been evaluated. In additional experiments, the effect of peritoneal lavage and the absorption of α-amylase present in the AF by an isolated intestine have been determined. RESULTS: Similar increase in XDH+XOD activity in plasma was observed after induction of acute pancreatitis and after i.v. administration of α-amylase. Nevertheless, the conversion from XDH to XOD was only observed in the pancreatitis group. Lung inflammation measured as MPO activity was observed only in the pancreatitis group. In addition peritoneal lavage prevented the increase in α-amylase and XDH+XOD in plasma after induction of pancreatitis. Finally, it was observed that α-amylase is absorbed from the AF by the intestine. CONCLUSIONS: During the early stages of acute pancreatitis, α-amylase absorbed from AF through the gastrointestinal tract could interfere with the binding of XDH/XOD attached to glycoproteins of the endothelial cells. Proteolytic enzymes convert XDH into its oxidase form promoting an increase in circulating XOD that has been reported to be one of the mechanisms involved in the triggering of the systemic inflammatory process

Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data

Inferring regulatory and metabolic network models from quantitative genetic interaction data remains a major challenge in systems biology. Here, we present a novel quantitative model for interpreting epistasis within pathways responding to an external signal. The model provides the basis of an experimental method to determine the architecture of such pathways, and establishes a new set of rules to infer the order of genes within them. The method also allows the extraction of quantitative parameters enabling a new level of information to be added to genetic network models. It is applicable to any system where the impact of combinatorial loss-of-function mutations can be quantified with sufficient accuracy. We test the method by conducting a systematic analysis of a thoroughly characterized eukaryotic gene network, the galactose utilization pathway in Saccharomyces cerevisiae. For this purpose, we quantify the effects of single and double gene deletions on two phenotypic traits, fitness and reporter gene expression. We show that applying our method to fitness traits reveals the order of metabolic enzymes and the effects of accumulating metabolic intermediates. Conversely, the analysis of expression traits reveals the order of transcriptional regulatory genes, secondary regulatory signals and their relative strength. Strikingly, when the analyses of the two traits are combined, the method correctly infers ∼80% of the known relationships without any false positives

Optical gain in 1.3-μm electrically driven dilute nitride VCSOAs

We report the observation of room-temperature optical gain at 1.3 μm in electrically driven dilute nitride vertical cavity semiconductor optical amplifiers. The gain is calculated with respect to injected power for samples with and without a confinement aperture. At lower injected powers, a gain of almost 10 dB is observed in both samples. At injection powers over 5 nW, the gain is observed to decrease. For nearly all investigated power levels, the sample with confinement aperture gives slightly higher gain