Random distributions via Sequential Quantile Array

We propose a method to generate random distributions with known quantile distribution, or, more generally, with known distribution for some form of generalized quantile. The method takes inspiration from the random Sequential Barycenter Array distributions (SBA) proposed by Hill and Monticino (1998) which generates a Random Probability Measure (RPM) with known expected value. We define the Sequential Quantile Array (SQA) and show how to generate a random SQA from which we can derive RPMs. The distribution of the generated SQA-RPM can have full support and the RPMs can be both discrete, continuous and differentiable. We face also the problem of the efficient implementation of the procedure that ensures that the approximation of the SQA-RPM by a finite number of steps stays close to the SQA-RPM obtained theoretically by the procedure. Finally, we compare SQA-RPMs with similar approaches as Polya Tree

Recurrence Plot and Recurrence Quantification Analysis Techniques for Detecting a Critical Regime. Examples from Financial Market Indices

Recurrence Plot (RP) and Recurrence Quantification Analysis (RQA) are signal numerical analysis methodologies able to work with non linear dynamical systems and non stationarity. Moreover they well evidence changes in the states of a dynamical system. We recall their features and give practical recipes. It is shown that RP and RQA detect the critical regime in financial indices (in analogy with phase transition) before a bubble bursts, whence allowing to estimate the bubble initial time. The analysis is made on DAX and NASDAQ daily closing price between Jan. 1998 and Nov. 2003. DAX is studied in order to set-up overall considerations, and as a support for deducing technical rules. The NASDAQ bubble initial time has been estimated to be on Oct. 19, 1999.Comment: review paper, submitted to Int.. J. Mod. Phys. C: Comput. Phys.; 32 pages, 22 figures, 5 tables, 43 ref

Energy Barrier Enhancement by Ligand Substitution in Tetrairon(III) Single Molecule Magnets

A dramatic increase of the energy barrier (Ueff) in tetrairon(III) single-mol. magnets can be achieved by simple chem. modification. Site-specific replacement of the six methoxide bridges in [Fe4(OMe)6(dpm)6] (Hdpm = dipivaloylmethane; Ueff/kB = 3.5 K) with two tripodal 1,1,1-tris(hydroxymethyl)ethane (H3thme) ligands affords [Fe4(thme)2(dpm)6] with Ueff/kB = 15.6(2) K and a magnetic relaxation time exceeding 1000 s at T <0.2 K. The prepd. complex is trigonal, space group R-3c, Z = 6, R1 = 0.0370, R2 = 0.1089

The small protein SCO2038 controls Streptomyces coelicolor differentiation by modulating tryptophan biosynthesis

Background In Streptomyces coelicolor amino acid metabolism is an important clue of the morphological and physiological differentiation program and, differently from other bacteria, the expression of amino acid biosynthetic genes is not subjected to endproduct negative regulation. In some amino acid biosynthetic gene clusters, such as tryptophan, histidine and proline, small orfs (about 100-300 nucleotides) were identified. These small orfs, such as sco2038, encode proteins whose cellular role have to be elucidated to highlight possible novel and crucial molecular mechanisms controlling amino acid synthesis and, thus, differentiation program. Objectives The aims of this work are: 1. the understanding of the effects exerted by tryptophan on primary metabolism, morphological differentiation and antibiotic production; 2. the study and characterization of the SCO2038 function as modulator of tryptophan biosynthesis. Methods - Differential proteomic analysis based on 2D-DIGE and MS procedures. - SEM analysis. - Generation and characterization of sco2038 mutants - Identification of potential SCO2038 interaction partners by pull down assay coupled with MS identification and Bacterial Adenylate Cyclase Two Hybrid System. - qRT-PCR analysis. Conclusions The obtained results revealed that tryptophan controls the expression of metabolic and regulatory proteins and promotes aerial mycelium formation, spores production and actinorhodin antibiotic biosynthesis. Moreover, the small orf sco2038, encodes a 7 KDa protein playing a key role in modulating tryptophan biosynthesis and thus, morphological differentiation. In the light of these results we propose to rename sco2038 as trpM, the gene encoding the tryptophan biosynthesis Modulator TrpM

Students' difficulties, conceptions and attitudes towards learning algebra : an intervention study to improve teaching and learning

The skills necessary to identify and analyse errors and misconceptions made by students are needed by teachers of all levels especially at the lower secondary school level in Malaysia. If students are to be successful in tackling mathematical problems later in their schooling, the one prerequisite is the mastery of basic concepts in algebra. Despite the best efforts of the teachers, students still develop algebra misconceptions. Is it possible to reduce or eliminate these misconceptions? The research involved a survey of 14 year-old students in Form 2 (Grade 8) in the Penampang district of Sabah, East Malaysia. The focus of this study lies in students’ difficulties, conceptions and attitudes towards learning algebra in the framework of conceptual change. A possible way to help students overcome their learning difficulties and misconceptions is by implementing diagnostic teaching involving conflict to foster conceptual change. The study involved evaluating the efficacy of a conceptual change instructional programme involving cognitive conflict in (1) facilitating Form 2 students’ understanding of algebra concepts, and (2) assessing changes in students’ attitudes towards learning mathematics, in a mixed quantitativequalitative research design.A 24-item Algebra Diagnostic Test and a 20-item Test of Mathematics-Related Attitudes (TOMRA) questionnaire were administered as a pretest and a posttest to 39 students in each of a heterogeneous high-achieving class and a below-average achieving class. In addition 9 students were purposefully selected to participate in the interview.The results of the study indicated that students’ difficulties and misconceptions from both classes fell into five broad areas: (1) basic understanding of letters and their place in mathematics, (2) manipulation of these letters or variables, (3) use of rules of manipulation to solve equations, (4) use of knowledge of algebraic structure and syntax to form equations, and (5) generalisation of rule for repetitive patterns or sequences of shapes.The results also showed that there was significant improvement in students’ achievement in mathematics. Further, students’ attitude towards inquiry of mathematics lessons showed significant positive improvement. Enjoyment remained high even though enjoyment of mathematics lesson showed no change. Also, changes in students’ understanding (from unintelligible to intelligible, intelligible to plausible, plausible to fruitful) illustrated the extent of changes in their conceptions.Different pedagogies can affect how conceptual change and challenge of misconceptions occurs. Therefore, knowledge of the origin of different types of misconceptions can be useful in selecting more effective pedagogical techniques for challenging particular misconceptions. Also, for teachers to create an effective learning experience they should be aware of and acknowledge students’ prior knowledge acquired from academic settings and from everyday previous personal experiences. Since all learning involves transfer from prior knowledge and previous experiences, an awareness and understanding of a student’s initial conceptual framework and/or topic can be used to formulate more effective teaching strategies. If this idea is taken a step further, it could be said that, because misconceptions comprise part of a conceptual framework, then understanding origins of misconceptions would further facilitate development of effective teaching strategies.Further research is needed to help teachers to understand how students experience conflict, how students feel when they experience conflict, and how these experiences are related to their final responses because cognitive conflict has both constructive and destructive potential. Thus, by being able to interpret, recognise and manage cognitive conflict, a teacher can then successfully interpret his/her students’ cognitive conflict and be able to make conceptual change more likely or help students to have meaningful learning experiences in secondary school algebra

Observation of a 1750 MeV/c^2 Enhancement in the Diffractive Photoproduction of K^+K^-

Using the FOCUS spectrometer with photon beam energies between 20 and 160 \gev, we confirm the existence of a diffractively photoproduced enhancement in $K^+K^-$ at 1750 \mevcc with nearly 100 times the statistics of previous experiments. Assuming this enhancement to be a single resonance with a Breit-Wigner mass shape, we determine its mass to be $1753.5\pm 1.5\pm 2.3$ \mevcc and its width to be $122.2\pm 6.2\pm 8.0$ \mevcc. We find no corresponding enhancement at 1750 \mevcc in $K^*K$, and again neglecting any possible interference effects we place limits on the ratio $\Gamma (X(1750) \to K^*K)/\Gamma (X(1750) \to K^+K^-)$. Our results are consistent with previous photoproduction experiments, but, because of the much greater statistics, challenge the common interpretation of this enhancement as the $\phi (1680)$ seen in $e^+e^-$ annihilation experiments.Comment: 10 pages, 5 figure

Role of mprF1 and mprF2 in the Pathogenicity of Enterococcus faecalis

Aujourd hui, Enterococcus faecalis est considéré comme l un des plus importants agents pathogènes causant des maladies nosocomiales. En raison de sa résistance innée et acquise aux antibiotiques, l identification de nouvelles cibles pour le traitement de cette bactérie est une grande priorité. Le facteur Multiple Peptide Résistance (MprF), qui a été décrit en premier chez Staphylococcus aureus, modifie le phosphatidylglycérol avec de la lysine et réduit ainsi la charge négative de l enveloppe cellulaire. Ceci a comme conséquence d augmenter la résistance aux peptides antimicrobiens cationiques (PAC). Deux gènes paralogues putatifs (mprF1 et mprF2) ont été identifiés chez E. faecalis par recherche BLAST en utilisant le gène décrit chez S. aureus. Une caractérisation de ces deux gènes d E. faecalis ainsi que des mécanismes conduisant à une résistance aux PAC, pourrait aider à développer des nouvelles stratégies thérapeutiques contre ce pathogène. Deux mutants de délétion et un double mutant ont été construits par recombinaison homologue chez E. faecalis. L analyse des phospholipides des membranes cytoplasmiques des deux mutants mprF1 et mprF2 par chromatographie sur couche mince a montré que seule l inactivation de mprF2 inhibe la synthèse de trois amino-phosphatidlyglycérol distincts (comme la Lysine-PG, l Alanine-PG et l Arginine-PG). De plus, le mutant mprF2 est également plus sensible aux PAC que la souche sauvage. La capacité de formation d un biofilm est généralement considérée comme un facteur important de virulence, ce qui est également le cas pour les entérocoques. Le mutant mprF2 montre une capacité accrue dans ce phénomène. Ceci semble être du à une augmentation de la concentration d ADN extracellulaire dans le biofilm formé par ce mutant. Curieusement, cette augmentation est indépendante d une autolyse. Le mutant mprF2 est également plus résistant à l opsonophagocytose. Cependant, le gène mprF2 ne joue aucun rôle dans les bactériémies de souris et les endocardites de rats.En revanche, aucun phénotype n a été trouvé pour un mutant mprF1 jusqu à présent. Cette mutation ne modifie ni la synthèse de l aminoacyl-PG en condition de laboratoire ni la résistance aux PAC et à l opsonophagocytose. Par conséquent, il semble que mprF2 soit le seul gène mprF fonctionnel chez E. faecalis. Néanmoins, contrairement à d autres bactéries, mprF2 ne semble pas être un facteur de virulence majeur pour cette espèce.Enterococcus faecalis is regarded nowadays as one of the most important nosocomial pathogens. Due to its innate and acquired resistance to antibiotics, identification of new targets for antimicrobial treatment of E. faecalis is a high priority. The multiple peptides resistance factor (MprF), which was first described in Staphylococcus aureus, modifies phosphatidylglycerol with lysine and reduces the negative charge of the membrane, thus increasing resistance to cationic antimicrobial peptides (CAMPs). Two putative mprF paralogs (mprF1 and mprF2) were identified in E. faecalis by Blast search using the well-described S. aureus gene as a lead. A better understanding of these two genes and mechanisms leads to enterococcal resistance to CAMPs might help designing therapeutic strategies against this bacteria. Two single deletion mutants and double mutant in E. faecalis were created by homologues recombination. Analysis of cell membrane phospholipids from both mutants by thin-layer chromatography showed that inactivation of mprF2 abolished the synthesis of three distinct amino-phosphatidylglycerol (mostly likely Lysin-PG, Alanine-PG and Argine-PG). The CAMPs testing assay demonstrated that the deletion mutant of mprF2 was more susceptible to CAMPs than the wild type. Biofilm formation is usually regarded as a virulence factor which provides an important way for enterococci to cause infections. Inactivation of mprF2 led to increase the biofilm formation which we showed that it was due to the accumulation of eDNA in the biofilm, but the release of eDNA is independent from autolysis. The mprF2 mutant was resistance to killing by opsonophagocytosis more than wild type. However, the mprF2 gene plays no role in bacteremia in mice and rat endocarditis. Our results showed that non polar effect mprF1 mutant does not affect in the synthesis of aminoacyl-PG in the laboratory condition. It also has no effect on susceptible to CAMPs, opsonic killing and autolysis. Therefore, it seems that mprF2 is the only functional mprF gene in E. faecalis in the laboratory condition. Unlike mprF found in other bacteria, mprF does not seem to be a major virulence factor in enterococci.CAEN-BU Sciences et STAPS (141182103) / SudocSudocFranceF

A Practical, Accurate, Information Criterion for Nth Order Markov Processes

The recent increase in the breath of computational methodologies has been matched with a corresponding increase in the difficulty of comparing the relative explanatory power of models from different methodological lineages. In order to help address this problem a Markovian information criterion (MIC) is developed that is analogous to the Akaike information criterion (AIC) in its theoretical derivation and yet can be applied to any model able to generate simulated or predicted data, regardless of its methodology. Both the AIC and proposed MIC rely on the Kullback–Leibler (KL) distance between model predictions and real data as a measure of prediction accuracy. Instead of using the maximum likelihood approach like the AIC, the proposed MIC relies instead on the literal interpretation of the KL distance as the inefficiency of compressing real data using modelled probabilities, and therefore uses the output of a universal compression algorithm to obtain an estimate of the KL distance. Several Monte Carlo tests are carried out in order to (a) confirm the performance of the algorithm and (b) evaluate the ability of the MIC to identify the true data-generating process from a set of alternative models

In Vitro Evaluation of Enterococcus faecalis Adhesion on Various Endodontic Medicaments

E. faecalis in endodontic infection represents a biofilm type of disease, which explains the bacteria’s resistance to various antimicrobial compounds and the subsequent failure after endodontic treatment. The purpose of this study was to compare antimicrobial activities and bacteria kinetic adhesion in vitro for three endodontic medicaments with a clinical isolate of E. faecalis. We devised a shake culture which contained the following intracanalar preparations: CPD, Endoidrox (EIX), PulpCanalSealer (PCS); these were immersed in a liquid culture medium inoculated with the microorganism. The shake system velocity was able to prevent non-specific bacteria adhesion and simulated the salivary flow. Specimens were collected daily (from both the medium and medicaments) for 10 days; the viable cells were counted by plate count, while the adhesion index AI° [E. faecalis fg DNA] /mm2 was evaluated in the pastes after DNA extraction, by quantitative real time PCR for the 16S rRNA gene. A partial growth inhibition, during the first 24 hours, was observed in the liquid medium and on the medicaments for EIX and subsequently for CPD (six logs). EIX showed the lowest adhesion coefficient (5*102 [fg DNA]/mm2) for nine days and was similar to the control. PCS showed no antimicrobial/antibiofilm properties. This showed that “calcium oxide” base compounds could be active against biofilm progression and at least in the short term (2-4 days) on E. faecalis cells growing in planktonic cultures

Identification of surface proteins in Enterococcus faecalis V583

<p>Abstract</p> <p>Background</p> <p>Surface proteins are a key to a deeper understanding of the behaviour of Gram-positive bacteria interacting with the human gastro-intestinal tract. Such proteins contribute to cell wall synthesis and maintenance and are important for interactions between the bacterial cell and the human host. Since they are exposed and may play roles in pathogenicity, surface proteins are interesting targets for drug design.</p> <p>Results</p> <p>Using methods based on proteolytic "shaving" of bacterial cells and subsequent mass spectrometry-based protein identification, we have identified surface-located proteins in <it>Enterococcus faecalis </it>V583. In total 69 unique proteins were identified, few of which have been identified and characterized previously. 33 of these proteins are predicted to be cytoplasmic, whereas the other 36 are predicted to have surface locations (31) or to be secreted (5). Lipid-anchored proteins were the most dominant among the identified surface proteins. The seemingly most abundant surface proteins included a membrane protein with a potentially shedded extracellular sulfatase domain that could act on the sulfate groups in mucin and a lipid-anchored fumarate reductase that could contribute to generation of reactive oxygen species.</p> <p>Conclusions</p> <p>The present proteome analysis gives an experimental impression of the protein landscape on the cell surface of the pathogenic bacterium <it>E. faecalis</it>. The 36 identified secreted (5) and surface (31) proteins included several proteins involved in cell wall synthesis, pheromone-regulated processes, and transport of solutes, as well as proteins with unknown function. These proteins stand out as interesting targets for further investigation of the interaction between <it>E. faecalis </it>and its environment.</p