Antimicrobial peptide genes in Bacillus strains from plant environments

The presence of the antimicrobial peptide (AMP) biosynthetic genes srfAA (surfactin), bacA (bacylisin), fenD (fengycin), bmyB (bacyllomicin), spaS (subtilin), and ituC (iturin) was examined in 184 isolates of Bacillus spp. obtained from plant environments (aerial, rhizosphere, soil) in the Mediterranean land area of Spain. Most strains had between two and four AMP genes whereas strains with five genes were seldom detected and none of the strains had six genes. The most frequent AMP gene markers were srfAA, bacA, bmyB, and fenD, and the most frequent genotypes srfAA-bacA-bmyB and srfAAbacA-bmyB-fenD. The dominance of these particular genes in Bacillus strains associated with plants reinforces the competitive role of surfactin, bacyllomicin, fengycin, and bacilysin in the fitness of strains in natural environments. The use of these AMP gene markers may assist in the selection of putative biological control agents of plant pathogens

From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways

Background: Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understanding the differences in drug response. In this regard, it is of particular interest to study the effect of non-synonymous SNPs in the context of biological networks such as cell signalling pathways. UniProt provides curated information about the functional and phenotypic effects of sequence variation, including SNPs, as well as on mutations of protein sequences. However, no strategy has been developed to integrate this information with biological networks, with the ultimate goal of studying the impact of the functional effect of SNPs in the structure and dynamics of biological networks. Results: First, we identified the different challenges posed by the integration of the phenotypic effect of sequence variants and mutations with biological networks. Second, we developed a strategy for the combination of data extracted from public resources, such as UniProt, NCBI dbSNP, Reactome and BioModels. We generated attribute files containing phenotypic and genotypic annotations to the nodes of biological networks, which can be imported into network visualization tools such as Cytoscape. These resources allow the mapping and visualization of mutations and natural variations of human proteins and their phenotypic effect on biological networks (e.g. signalling pathways, protein-protein interaction networks, dynamic models). Finally, an example on the use of the sequence variation data in the dynamics of a network model is presented. Conclusion: In this paper we present a general strategy for the integration of pathway and sequence variation data for visualization, analysis and modelling purposes, including the study of the functional impact of protein sequence variations on the dynamics of signalling pathways. This is of particular interest when the SNP or mutation is known to be associated to disease. We expect that this approach will help in the study of the functional impact of disease-associated SNPs on the behaviour of cell signalling pathways, which ultimately will lead to a better understanding of the mechanisms underlying complex diseases.

Protocol of the COSMIN study: consensus-based standards for the selection of health measurement instruments

Background: Choosing an adequate measurement instrument depends on the proposed use of the instrument, the concept to be measured, the measurement properties (e.g. internal consistency, reproducibility, content and construct validity, responsiveness, and interpretability), the requirements, the burden for subjects, and costs of the available instruments. As far as measurement properties are concerned, there are no sufficiently specific standards for the evaluation of measurement properties of instruments to measure health status, and also no explicit criteria for what constitutes good measurement properties. In this paper we describe the protocol for the COSMIN study, the objective of which is to develop a checklist that contains COnsensus-based Standards for the selection of health Measurement INstruments, including explicit criteria for satisfying these standards. We will focus on evaluative health related patient-reported outcomes (HR-PROs), i.e. patient-reported health measurement instruments used in a longitudinal design as an outcome measure, excluding health care related PROs, such as satisfaction with care or adherence. The COSMIN standards will be made available in the form of an easily applicable checklist.Method: An international Delphi study will be performed to reach consensus on which and how measurement properties should be assessed, and on criteria for good measurement properties. Two sources of input will be used for the Delphi study: (1) a systematic review of properties, standards and criteria of measurement properties found in systematic reviews of measurement instruments, and (2) an additional literature search of methodological articles presenting a comprehensive checklist of standards and criteria. The Delphi study will consist of four (written) Delphi rounds, with approximately 30 expert panel members with different backgrounds in clinical medicine, biostatistics, psychology, and epidemiology. The final checklist will subsequently be field-tested by assessing the inter-rater reproducibility of the checklist.Discussion: Since the study will mainly be anonymous, problems that are commonly encountered in face-to-face group meetings, such as the dominance of certain persons in the communication process, will be avoided. By performing a Delphi study and involving many experts, the likelihood that the checklist will have sufficient credibility to be accepted and implemented will increase.

Not the right job but a secure one : over-education and temporary employment in France, Italy and Spain

Resorting to four waves of the European Community Household Panel, this research explores the association between temporary employment and the likelihood of being over-educated. Such an association has been largely ignored by the literature explaining over-education, more inclined to attribute such a mismatch to the system of education. Selecting three similarly standarised and stratified systems of education (France, Italy and Spain) and controlling for many other variables likely to affect over-education, like gender, age, tenure, job change, firm size or sector, the paper demonstrates that such an association between temporary employment and over-education exists. Being a stepping stone towards a more stable and adjusted position in the labour market, holding a temporary employment may be associated to a higher likelihood of being over-educated. Such an association is more likely in Italy and France. Yet, the opposite sign prevails where permanent employment becomes such a valuable asset as to make individuals trade human capital by employment security. This is the case of Spain.

Emotion and reason in everyday risk perception

Although research has documented the importance of emotion in risk perception, little is knownabout its prevalence in everyday life. Using the Experience Sampling Method, 94 part-timestudents were prompted at random via cellular telephones to report on mood state and threeemotions and to assess risk on thirty occasions during their working hours. The emotions valence, arousal, and dominance were measured using self-assessment manikins (Bradley &Lang, 1994). Hierarchical linear models (HLM) revealed that mood state and emotions explainedsignificant variance in risk perception. In addition, valence and arousal accounted for varianceover and above reason (measured by severity and possibility of risks). Six risks were reassessedin a post-experimental session and found to be lower than their real-time counterparts.The study demonstrates the feasibility and value of collecting representative samples of data withsimple technology. Evidence for the statistical consistency of the HLM estimates is provided inan Appendix.

Regions of rationality: Maps for bounded agents

An important problem in descriptive and prescriptive research in decision making is to identify regions of rationality, i.e., the areas for which heuristics are and are not effective. To map the contours of such regions, we derive probabilities that heuristics identify the best of m alternatives (m > 2) characterized by k attributes or cues (k > 1). The heuristics include a single variable (lexicographic), variations of elimination-by-aspects, equal weighting, hybrids of the preceding, and models exploiting dominance. We use twenty simulated and four empirical datasets for illustration. We further provide an overview by regressing heuristic performance on factors characterizing environments. Overall, sensible heuristics generally yield similar choices in many environments. However, selection of the appropriate heuristic can be important in some regions (e.g., if there is low inter-correlation among attributes/cues). Since our work assumes a hit or miss decision criterion, we conclude by outlining extensions for exploring the effects of different loss functions.

Pre-play communication and credibility: A test of Aumann's conjecture

The effectiveness of pre-play communication in achieving efficientoutcomes has long been a subject of controversy. In some environments,cheap talk may help to achieve coordination. However, Aumannconjectures that, in a variant of the Stag Hunt game, a signal forefficient play is not self-enforcing and concludes that an "agreementto play [the efficient outcome] conveys no information about what theplayers will do." Harsanyi and Selten (1988) cite this example as anillustration of risk-dominance vs. payoff-dominance. Farrell and Rabin(1996) agree with the logic, but suspect that cheap talk willnonetheless achieve efficiency. The conjecture is tested with one-waycommunication. When the sender first chooses a signal and then anaction, there is impressive coordination: a 94% probability for thepotentially efficient (but risky) play, given a signal for efficientplay. Without communication, efforts to achieve efficiency wereunsuccessful, as the proportion of B moves is only 35%. I also test ahypothesis that the order of the action and the signal affects theresults, finding that the decision order is indeed important. WhileAumann s conjecture is behaviorally disconfirmed when the signal isdetermined initially, the signal s credibility seems to be much moresuspect when the sender is known to have first chosen an action, andthe results are not statistically distinguishable from those whenthere is no signal. Some applications and issues in communication andcoordination are discussed.

Dynamic perceptual mapping

Perceptual maps have been used for decades by market researchers to illuminatethem about the similarity between brands in terms of a set of attributes, to position consumersrelative to brands in terms of their preferences, or to study how demographic and psychometricvariables relate to consumer choice. Invariably these maps are two-dimensional and static. Aswe enter the era of electronic publishing, the possibilities for dynamic graphics are opening up.We demonstrate the usefulness of introducing motion into perceptual maps through fourexamples. The first example shows how a perceptual map can be viewed in three dimensions,and the second one moves between two analyses of the data that were collected according todifferent protocols. In a third example we move from the best view of the data at the individuallevel to one which focuses on between-group differences in aggregated data. A final exampleconsiders the case when several demographic variables or market segments are available foreach respondent, showing an animation with increasingly detailed demographic comparisons.These examples of dynamic maps use several data sets from marketing and social scienceresearch.

Endogenous price leadership

We consider a linear price setting duopoly game with di®erentiatedproducts and determine endogenously which of the players will lead andwhich will follow. While the follower role is most attractive for each firm, we show that waiting is more risky for the low cost firm so that,consequently, risk dominance considerations, as in Harsanyi and Selten(1988), allow the conclusion that only the high cost firm will choose towait. Hence, the low cost firm will emerge as the endogenous price leader.

The changing relationship between tax and financial reporting in Spain

The degree of connection between tax and financial reporting is regarded as a key factor in the study of international accounting differences. The position for Spain is briefly outlined in previous research but without examination of any specific accounting issues except, in outline only, depreciation and the tax-free revaluation of assets from 1977 to 1983. The absence of a detailed study of the major tax/accounting linkages for Spain is of particular importance because the relationship is regarded as having changed dramatically in the early 1990s, from a position of tax dominance. In order to measure the links between tax and financial reporting, we adopt the methodology of Lamb et al. (1998) by assessing major accounting topics using a five-case classification shown as Table 1. We refute the proposition that suggests that the link between tax/accounting has been reduced substantially.

On some geometry and equivalence classes of normal form games

Equivalence classes of normal form games are defined using the geometryof correspondences of standard equilibiurm concepts like correlated, Nash,and robust equilibrium or risk dominance and rationalizability. Resultingequivalence classes are fully characterized and compared across differentequilibrium concepts for 2 x 2 games. It is argued that the procedure canlead to broad and game-theoretically meaningful distinctions of games aswell as to alternative ways of viewing and testing equilibrium concepts.Larger games are also briefly considered.

Take-the-best and other simple strategies: Why and when they work 'well' in binary choice

The effectiveness of decision rules depends on characteristics of bothrules and environments. A theoretical analysis of environments specifiesthe relative predictive accuracies of the lexicographic rule 'take-the-best'(TTB) and other simple strategies for binary choice. We identify threefactors: how the environment weights variables; characteristics of choicesets; and error. For cases involving from three to five binary cues, TTBis effective across many environments. However, hybrids of equal weights(EW) and TTB models are more effective as environments become morecompensatory. In the presence of error, TTB and similar models do not predictmuch better than a naïve model that exploits dominance. We emphasizepsychological implications and the need for more complete theories of theenvironment that include the role of error.

Endogenous price leadership

We consider a linear price setting duopoly game with differentiated products and determine endogenously which of the players will lead and which will follow. While the follower role is most attractive for each firm, we show that waiting is more risky for the low cost firm so that, consequently, risk dominance considerations, as in Harsanyi and Selten (1988), allow the conclusion that only the highcost firm will choose to wait. Hence, the low cost firm will emerge as the endogenous price leader.

Endogenous Stackelberg leadership

We consider a linear quantity setting duopoly game and analyzewhich of the players will commit when both players have the possibility todo so. To that end, we study a 2-stage game in which each player caneither commit to a quantity in stage 1 or wait till stage 2. We show thatcommitting is more risky for the high cost firm and that, consequently,risk dominance considerations, as in Harsanyi and Selten (1988), allowthe conclusion that only the low cost firm will choose to commit.Hence, the low cost firm will emerge as the endogenous Stackelberg leader.

Salience and consumer choice

We present a theory of context-dependent choice in which a consumer's attention is drawnto salient attributes of goods, such as quality or price. An attribute is salient for a good when itstands out among the good's attributes, relative to that attribute's average level in the choice set (orgenerally, the evoked set). Consumers attach disproportionately high weight to salient attributesand their choices are tilted toward goods with higher quality/price ratios. The model accounts fora variety of disparate evidence, including decoy effects, context-dependent willingness to pay, andlarge shifts in demand in response to price shocks.