Providing Self-Aware Systems with Reflexivity

We propose a new type of self-aware systems inspired by ideas from higher-order theories of consciousness. First, we discussed the crucial distinction between introspection and reflexion. Then, we focus on computational reflexion as a mechanism by which a computer program can inspect its own code at every stage of the computation. Finally, we provide a formal definition and a proof-of-concept implementation of computational reflexion, viewed as an enriched form of program interpretation and a way to dynamically "augment" a computational process.Comment: 12 pages plus bibliography, appendices with code description, code of the proof-of-concept implementation, and examples of executio

Capsular profiling of the Cronobacter genus and the association of specific Cronobacter sakazakii and C. malonaticus capsule types with neonatal meningitis and necrotizing enterocolitis

Background: Cronobacter sakazakii and C. malonaticus can cause serious diseases especially in infants where they are associated with rare but fatal neonatal infections such as meningitis and necrotising enterocolitis. Methods: This study used 104 whole genome sequenced strains, covering all seven species in the genus, to analyse capsule associated clusters of genes involved in the biosynthesis of the O-antigen, colanic acid, bacterial cellulose, enterobacterial common antigen (ECA), and a previously uncharacterised K-antigen. Results: Phylogeny of the gnd and galF genes flanking the O-antigen region enabled the defining of 38 subgroups which are potential serotypes. Two variants of the colanic acid synthesis gene cluster (CA1 and CA2) were found which differed with the absence of galE in CA2. Cellulose (bcs genes) were present in all species, but were absent in C. sakazakii sequence type (ST) 13 and clonal complex (CC) 100 strains. The ECA locus was found in all strains. The K-antigen capsular polysaccharide Region 1 (kpsEDCS) and Region 3 (kpsMT) genes were found in all Cronobacter strains. The highly variable Region 2 genes were assigned to 2 homology groups (K1 and K2). C. sakazakii and C. malonaticus isolates with capsular type [K2:CA2:Cell+] were associated with neonatal meningitis and necrotizing enterocolitis. Other capsular types were less associated with clinical infections. Conclusion: This study proposes a new capsular typing scheme which identifies a possible important virulence trait associated with severe neonatal infections. The various capsular polysaccharide structures warrant further investigation as they could be relevant to macrophage survival, desiccation resistance, environmental survival, and biofilm formation in the hospital environment, including neonatal enteral feeding tubes

Biochemical systems identification by a random drift particle swarm optimization approach

BACKGROUND: Finding an efficient method to solve the parameter estimation problem (inverse problem) for nonlinear biochemical dynamical systems could help promote the functional understanding at the system level for signalling pathways. The problem is stated as a data-driven nonlinear regression problem, which is converted into a nonlinear programming problem with many nonlinear differential and algebraic constraints. Due to the typical ill conditioning and multimodality nature of the problem, it is in general difficult for gradient-based local optimization methods to obtain satisfactory solutions. To surmount this limitation, many stochastic optimization methods have been employed to find the global solution of the problem. RESULTS: This paper presents an effective search strategy for a particle swarm optimization (PSO) algorithm that enhances the ability of the algorithm for estimating the parameters of complex dynamic biochemical pathways. The proposed algorithm is a new variant of random drift particle swarm optimization (RDPSO), which is used to solve the above mentioned inverse problem and compared with other well known stochastic optimization methods. Two case studies on estimating the parameters of two nonlinear biochemical dynamic models have been taken as benchmarks, under both the noise-free and noisy simulation data scenarios. CONCLUSIONS: The experimental results show that the novel variant of RDPSO algorithm is able to successfully solve the problem and obtain solutions of better quality than other global optimization methods used for finding the solution to the inverse problems in this study

QCD-like theories at nonzero temperature and density

We investigate the properties of hot and/or dense matter in QCD-like theories with quarks in a (pseudo)real representation of the gauge group using the Nambu-Jona-Lasinio model. The gauge dynamics is modeled using a simple lattice spin model with nearest-neighbor interactions. We first keep our discussion as general as possible, and only later focus on theories with adjoint quarks of two or three colors. Calculating the phase diagram in the plane of temperature and quark chemical potential, it is qualitatively confirmed that the critical temperature of the chiral phase transition is much higher than the deconfinement transition temperature. At a chemical potential equal to half of the diquark mass in the vacuum, a diquark Bose-Einstein condensation (BEC) phase transition occurs. In the two-color case, a Ginzburg-Landau expansion is used to study the tetracritical behavior around the intersection point of the deconfinement and BEC transition lines, which are both of second order. We obtain a compact expression for the expectation value of the Polyakov loop in an arbitrary representation of the gauge group (for any number of colors), which allows us to study Casimir scaling at both nonzero temperature and chemical potential.Comment: JHEP class, 31 pages, 7 eps figures; v2: error in Eq. (3.11) fixed, two references added; matches published versio

Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites

Peer reviewedPublisher PD

Quasi-Normal Modes of Stars and Black Holes

Perturbations of stars and black holes have been one of the main topics of relativistic astrophysics for the last few decades. They are of particular importance today, because of their relevance to gravitational wave astronomy. In this review we present the theory of quasi-normal modes of compact objects from both the mathematical and astrophysical points of view. The discussion includes perturbations of black holes (Schwarzschild, Reissner-Nordstr\"om, Kerr and Kerr-Newman) and relativistic stars (non-rotating and slowly-rotating). The properties of the various families of quasi-normal modes are described, and numerical techniques for calculating quasi-normal modes reviewed. The successes, as well as the limits, of perturbation theory are presented, and its role in the emerging era of numerical relativity and supercomputers is discussed.Comment: 74 pages, 7 figures, Review article for "Living Reviews in Relativity

Mapping and pyramiding of two major genes for resistance to the brown planthopper (Nilaparvata lugens [Stål]) in the rice cultivar ADR52

The brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most serious and destructive pests of rice, and can be found throughout the rice-growing areas of Asia. To date, more than 24 major BPH-resistance genes have been reported in several Oryza sativa ssp. indica cultivars and wild relatives. Here, we report the genetic basis of the high level of BPH resistance derived from an Indian rice cultivar, ADR52, which was previously identified as resistant to the whitebacked planthopper (Sogatella furcifera [Horváth]). An F2 population derived from a cross between ADR52 and a susceptible cultivar, Taichung 65 (T65), was used for quantitative trait locus (QTL) analysis. Antibiosis testing showed that multiple loci controlled the high level of BPH resistance in this F2 population. Further linkage analysis using backcross populations resulted in the identification of BPH-resistance (antibiosis) gene loci from ADR52. BPH25 co-segregated with marker S00310 on the distal end of the short arm of chromosome 6, and BPH26 co-segregated with marker RM5479 on the long arm of chromosome 12. To characterize the virulence of the most recently migrated BPH strain in Japan, preliminary near-isogenic lines (pre-NILs) and a preliminary pyramided line (pre-PYL) carrying BPH25 and BPH26 were evaluated. Although both pre-NILs were susceptible to the virulent BPH strain, the pre-PYL exhibited a high level of resistance. The pyramiding of resistance genes is therefore likely to be effective for increasing the durability of resistance against the new virulent BPH strain in Japan

The effect of the electric field on lag phase, β-galactosidase production and plasmid stability of a recombinant Saccharomyces cerevisiae strain growing on lactose

Ethanol and β-galactosidase production from cheese whey may significantly contribute to minimise environmental problems while producing value from lowcost raw materials. In this work, the recombinant Saccharomyces cerevisiae NCYC869-A3/pVK1.1 flocculent strain expressing the lacA gene (coding for β-galactosidase) of Aspergillus niger under ADHI promoter and terminator was used. This strain shows high ethanol and β-galactosidase productivities when grown on lactose. Batch cultures were performed using SSlactose medium with 50 gL−1 lactose in a 2-L bioreactor under aerobic and microaerophilic conditions. Temperature was maintained at 30 °C and pH 4.0. In order to determine the effect of an electric field in the fermentation profile, titanium electrodes were placed inside the bioreactor and different electric field values (from 0.5 to 2 Vcm−1) were applied. For all experiments, β-galactosidase activity, biomass, protein, lactose, glucose, galactose and ethanol concentrations were measured. Finally, lag phase duration and specific growth rate were calculated. Significant changes in lag phase duration and biomass yield were found when using 2 Vcm−1. Results show that the electric field enhances the early stages of fermentation kinetics, thus indicating that its application may improve industrial fermentations’ productivity. The increase in electric field intensity led to plasmid instability thus decreasing β-galactosidase production.The authors gratefully acknowledge Fundacao para a Ciencia e a Tecnologia (Portugal) for the scholarships SFRH/BD/11230/2002 and SFRH/BDP/63831/2009 granted to authors I. Castro and C. Oliveira, respectively

Comparison of two normative paediatric gait databases

The availability of age-matched normative data is an essential component of clinical gait analyses. Comparison of normative gait databases is difficult due to the high-dimensionality and temporal nature of the various gait waveforms. The purpose of this study was to provide a method of comparing the sagittal joint angle data between two normative databases. We compared a modern gait database to the historical San Diego database using statistical classifiers developed by Tingley et al. (2002). Gait data were recorded from 60 children aged 1–13 years. A six-camera Vicon 512 motion analysis system and two force plates were utilized to obtain temporal-spatial, kinematic, and kinetic parameters during walking. Differences between the two normative data sets were explored using the classifier index scores, and the mean and covariance structure of the joint angle data from each lab. Significant differences in sagittal angle data between the two databases were identified and attributed to technological advances and data processing techniques (data smoothing, sampling, and joint angle approximations). This work provides a simple method of database comparison using trainable statistical classifiers