Advantage of single-trial models for response to selection in wheat breeding multi-environment trials

An investigation was conducted to evaluate the impact of experimental designs and spatial analyses (single-trial models) of the response to selection for grain yield in the northern grains region of Australia (Queensland and northern New South Wales). Two sets of multi-environment experiments were considered. One set, based on 33 trials conducted from 1994 to 1996, was used to represent the testing system of the wheat breeding program and is referred to as the multi-environment trial (MET). The second set, based on 47 trials conducted from 1986 to 1993, sampled a more diverse set of years and management regimes and was used to represent the target population of environments (TPE). There were 18 genotypes in common between the MET and TPE sets of trials. From indirect selection theory, the phenotypic correlation coefficient between the MET and TPE single-trial adjusted genotype means [r(p(MT))] was used to determine the effect of the single-trial model on the expected indirect response to selection for grain yield in the TPE based on selection in the MET. Five single-trial models were considered: randomised complete block (RCB), incomplete block (IB), spatial analysis (SS), spatial analysis with a measurement error (SSM) and a combination of spatial analysis and experimental design information to identify the preferred (PF) model. Bootstrap-resampling methodology was used to construct multiple MET data sets, ranging in size from 2 to 20 environments per MET sample. The size and environmental composition of the MET and the single-trial model influenced the r(p(MT)). On average, the PF model resulted in a higher r(p(MT)) than the IB, SS and SSM models, which were in turn superior to the RCB model for MET sizes based on fewer than ten environments. For METs based on ten or more environments, the r(p(MT)) was similar for all single-trial models.

Quantifying effects of soil heterogeneity on groundwater pollution in four sites in the USA

Four sites located in the north-eastern region of the United States of America have been chosen to investigate the impacts of soil heterogeneity in the transport of solutes (bromide and chloride) through the vadose zone (the zone in the soil that lies below the root zone and above the permanent saturated groundwater). A recently proposed mathematical model based on the cumulative beta distribution has been deployed to compare and contrast the regions' heterogeneity from multiple sample percolation experiments. Significant differences in patterns of solute leaching were observed even over a small spatial scale, indicating that traditional sampling methods for solute transport, for example the gravity pan or suction lysimeters, or more recent inventions such as the multiple sample percolation systems may not be effective in estimating solute fluxes in soils when a significant degree of soil heterogeneity is present. Consequently, ignoring soil heterogeneity in solute transport studies will likely result in under- or overprediction of leached fluxes and potentially lead to serious pollution of soils and/or groundwater. The cumulative beta distribution technique is found to be a versatile and simple technique of gaining valuable information regarding soil heterogeneity effects on solute transport. It is also an excellent tool for guiding future decisions of experimental designs particularly in regard to the number of samples within one site and the number of sampling locations between sites required to obtain a representative estimate of field solute or drainage flux.

A Mixture model with random-effects components for clustering correlated gene-expression profiles

Motivation: The clustering of gene profiles across some experimental conditions of interest contributes significantly to the elucidation of unknown gene function, the validation of gene discoveries and the interpretation of biological processes. However, this clustering problem is not straightforward as the profiles of the genes are not all independently distributed and the expression levels may have been obtained from an experimental design involving replicated arrays. Ignoring the dependence between the gene profiles and the structure of the replicated data can result in important sources of variability in the experiments being overlooked in the analysis, with the consequent possibility of misleading inferences being made. We propose a random-effects model that provides a unified approach to the clustering of genes with correlated expression levels measured in a wide variety of experimental situations. Our model is an extension of the normal mixture model to account for the correlations between the gene profiles and to enable covariate information to be incorporated into the clustering process. Hence the model is applicable to longitudinal studies with or without replication, for example, time-course experiments by using time as a covariate, and to cross-sectional experiments by using categorical covariates to represent the different experimental classes. Results: We show that our random-effects model can be fitted by maximum likelihood via the EM algorithm for which the E(expectation) and M(maximization) steps can be implemented in closed form. Hence our model can be fitted deterministically without the need for time-consuming Monte Carlo approximations. The effectiveness of our model-based procedure for the clustering of correlated gene profiles is demonstrated on three real datasets, representing typical microarray experimental designs, covering time-course, repeated-measurement and cross-sectional data. In these examples, relevant clusters of the genes are obtained, which are supported by existing gene-function annotation. A synthetic dataset is considered too.

Detecting the effects of physical disturbance on benthic assemblages in a subtropical estuary: A Beyond BACI approach

The effects of dredging on the benthic communities in the Noosa River, a subtropical estuary in SE Queensland, Australia, were examined using a 'Beyond BACF experimental design. Changes in the numbers and types of animals and characteristics of the sediments in response to dredging in the coarse sandy sediments near the mouth of the estuary were compared with those occurring naturally in two control regions. Samples were collected twice before and twice after the dredging operations, at multiple spatial scales, ranging from metres to kilometres. Significant effects from the dredging were detected on the abundance of some polychaetes and bivalves and two measures of diversity (numbers of polychaete families and total taxonomic richness). In addition, the dredging caused a significant increase in the diversity of sediment particle sizes found in the dredged region compared with elsewhere. Community composition in the dredged region was more similar to that in the control regions after dredging than before. Changes in the characteristics of the sedimentary environment as a result of the dredging appeared to lead to the benthic communities of the dredged region becoming more similar to those elsewhere in the estuary, so dredging in this system may have led to the loss or reduction in area of a specific type of habitat in the estuary with implications for overall patterns of biodiversity and ecosystem function. (c) 2006 Elsevier B.V. All rights reserved.

Do tinted lenses or filters improve visual performance in low vision? A review of the literature

This is a review of studies that have investigated the proposed rehabilitative benefit of tinted lenses and filters for people with low vision. Currently, eye care practitioners have to rely on marketing literature and anecdotal reports from users when making recommendations for tinted lens or filter use in low vision. Our main aim was to locate a prescribing protocol that was scientifically based and could assist low vision specialists with tinted lens prescribing decisions. We also wanted to determine if previous work had found any tinted lens/task or tinted lens/ocular condition relationships, i.e. were certain tints or filters of use for specific tasks or for specific eye conditions. Another aim was to provide a review of previous research in order to stimulate new work using modern experimental designs. Past studies of tinted lenses and low vision have assessed effects on visual acuity (VA), grating acuity, contrast sensitivity (CS), visual field, adaptation time, glare, photophobia and TV viewing. Objective and subjective outcome measures have been used. However, very little objective evidence has been provided to support anecdotal reports of improvements in visual performance. Many studies are flawed in that they lack controls for investigator bias, and placebo, learning and fatigue effects. Therefore, the use of tinted lenses in low vision remains controversial and eye care practitioners will have to continue to rely on anecdotal evidence to assist them in their prescribing decisions. Suggestions for future research, avoiding some of these experimental shortcomings, are made. © 2002 The College of Optometrists.

Statnote 8: statistical power and sample size

Statistical software is now commonly available to calculate Power (P') and sample size (N) for most experimental designs. In many circumstances, however, sample size is constrained by lack of time, cost, and in research involving human subjects, the problems of recruiting suitable individuals. In addition, the calculation of N is often based on erroneous assumptions about variability and therefore such estimates are often inaccurate. At best, we would suggest that such calculations provide only a very rough guide of how to proceed in an experiment. Nevertheless, calculation of P' is very useful especially in experiments that have failed to detect a difference which the experimenter thought was present. We would recommend that P' should always be calculated in these circumstances to determine whether the experiment was actually too small to test null hypotheses adequately.

Statnote 13: a more complex analysis of variance incorporating a 'repeated measures' factor

Experiments combining different groups or factors and which use ANOVA are a powerful method of investigation in applied microbiology. ANOVA enables not only the effect of individual factors to be estimated but also their interactions; information which cannot be obtained readily when factors are investigated separately. In addition, combining different treatments or factors in a single experiment is more efficient and often reduces the sample size required to estimate treatment effects adequately. Because of the treatment combinations used in a factorial experiment, the degrees of freedom (DF) of the error term in the ANOVA is a more important indicator of the ‘power’ of the experiment than the number of replicates. A good method is to ensure, where possible, that sufficient replication is present to achieve 15 DF for the error term of the ANOVA testing effects of particular interest. Finally, it is important to always consider the design of the experiment because this determines the appropriate ANOVA to use. Hence, it is necessary to be able to identify the different forms of ANOVA appropriate to different experimental designs and to recognise when a design is a split-plot or incorporates a repeated measure. If there is any doubt about which ANOVA to use in a specific circumstance, the researcher should seek advice from a statistician with experience of research in applied microbiology.

The use of analysis of variance (ANOVA) in applied microbiology

Experiments combining different groups or factors and which use ANOVA are a powerful method of investigation in applied microbiology. ANOVA enables not only the effect of individual factors to be estimated but also their interactions; information which cannot be obtained readily when factors are investigated separately. In addition, combining different treatments or factors in a single experiment is more efficient and often reduces the number of replications required to estimate treatment effects adequately. Because of the treatment combinations used in a factorial experiment, the DF of the error term in the ANOVA is a more important indicator of the ‘power’ of the experiment than the number of replicates. A good method is to ensure, where possible, that sufficient replication is present to achieve 15 DF for each error term of the ANOVA. Finally, it is important to consider the design of the experiment because this determines the appropriate ANOVA to use. Some of the most common experimental designs used in the biosciences and their relevant ANOVAs are discussed by. If there is doubt about which ANOVA to use, the researcher should seek advice from a statistician with experience of research in applied microbiology.

Disentangle contextual and permanent individual motivations:an application to shopping behavior

Past studies resulted in conflicting definitions of consumer motivation. On the one hand, motivations are seen as the consumer’s characteristics that shape her general behavior (motivational trait). On the other hand, they are seen as contextual variables representing the reason why the individual is behaving specific to today’s context (motivational state). The objective of this research is to stress the difference between these two concepts and to understand the impact of each on consumer behavior. We applied our empirical study to shopping motivations; our results show a strong interaction between motivational trait and motivational state. Problem and Hypothesis On the one hand, Westbrook and Black (1985) consider shopping motivations as individual permanent characteristics. This concept is shared by other researchers (Rohm and Swaminathan 2004), which show that some shoppers are functional (they shop for convenience, information seeking, and time saving) while some others are hedonic (they shop for social interaction, bargain hunting and browsing). On the other hand, Kaltcheva and Weitz (2006) define motivations as a contextual orientation changing over time, depending on the situation, and show that contextual shopping motivations have a strong impact on shopping behavior. From our knowledge, no research specifically examined the respective impact of both these shopping motivation types. To deal with this issue, we used the notions of “traits” and “states” that have been largely used in marketing research to designate respectively a permanent characteristic of the individual and a temporary orientation of the consumer (Mowen 2000). The reversal theory (Apter 2001) suggests that two opposite states exist: the telic and the paratelic states. In the telic state, individuals set goals for themselves, must be disciplined to reach these goals, and do not behave in accordance with their personal trait. In the paratelic state, individuals are seeking arousal and enjoyment, do not set rules, and one could postulate that they act in accordance with their natural tendencies. Based on these considerations, we hypothesize the following process: in situations involving paratelic states, hedonic as well as functional individuals should behave according to their natural traits, whereas in situations involving telic states, hedonic people should inhibit their natural propensity to enjoy shopping and behave similarly to functional people. Hence, we postulate the following: Hypothesis: Compared to shoppers with functional motivational trait, shoppers with hedonic motivational trait will a) significantly display more hedonic shopping behavior intentions in a condition of paratelic motivational state, and b) not display more hedonic shopping behavior intentions in a condition a telic motivational state Empirical Research First, 108 participants were asked to fill a multi-items scale about their shopping habits, which actually measured their shopping motivational traits. This questionnaire allowed us to highlight four different dimensions in shopping motivational traits: social interaction, novelty/utility seeking, bargain hunting, and browsing. According to their scores on different items, participants were classified as functional or as hedonic on each of these four dimensions (a single individual may be hedonic on some dimensions and functional on others). Then, participants were then induced to adopt either a telic or a paratelic shopping motivational state while reading an appropriate scenario. Finally, participants were asked for their shopping behavior intentions in response to the shopping context. Four items were developed, corresponding to the four shopping motivational trait dimensions we found with our factor analysis. Results As we found four dimensions in shopping motivational trait, we set up four quasi-experimental designs to capture the entire phenomenon: for each dimension, a 2 (motivational trait) x 2 (motivational state) design was built, where the dependant variable was the shopping behavior element corresponding to the studied dimension. Four 2 x 2 Anovas were performed to assess the interaction between motivational trait and motivational state. Concerning the three dimensions - browsing, novelty/utility seeking, and bargain hunting- , in the paratelic state scenario participants with hedonic motivational trait displayed significantly more hedonic shopping behavior intentions than participants with a functional motivational trait (resp. F = 9.701, p = .003; F = 4.979, p = .03; F = 5.757, p = .02); and in the telic state scenario, there was no significant difference in behavior intentions between participants with hedonic or functional motivation trait. Each time, the interaction effect between motivational state and motivational trait was significant (resp. F = 4.859, p = .03; F = 3.314, p = .07; F = 2.98, p = .08). Concerning the fourth dimension, social interaction, shopping behavior intentions of participants with hedonic and with functional motivational traits were significantly different in the paratelic state scenario (F = 29.898, p <.000) as well as in the telic state scenario (F = 9.559, p = .003). However, the interaction effect showed that this behavioral difference was significantly stronger in the paratelic scenario. All these results support our research hypothesis. Discussion and Implications Our study provides consistent support for our hypotheses saying that there is an interaction effect between shopping motivational states and shopping motivational traits. The generalization of the results is strengthened by the study of four different shopping traits: social interaction, novelty/utility seeking, bargain hunting and browsing. As we proposed, when shopping in a goal-oriented state (telic state), behaviors of hedonic and functional shoppers do not differ significantly. Conversely, when shopping for a recreational reason (paratelic state), hedonic and functional shoppers behave significantly different. These results could explain why some previous studies concluded that shopping motivational traits had no impact on shopping behavior: they did not take into consideration the interaction between motivational trait and motivational state. Moreover, our study shows that marketing surveys performed by store managers to draw the personal profile of their customers must be crossed with contextual motivations in order to accurately forecast shopper behavior. Future Developments Our results can be explained by the self-control process, which pushes hedonic-trait shoppers to behave in a rather functional way in utilitarian situations. However, to be certain that this is the very process that occurs, we plan to add self-control perception scales to our existing measures. This is obviously the next step of this research.

Theory and data for area summation of contrast with and without uncertainty:evidence for a noisy energy model

Contrast sensitivity improves with the area of a sine-wave grating, but why? Here we assess this phenomenon against contemporary models involving spatial summation, probability summation, uncertainty, and stochastic noise. Using a two-interval forced-choice procedure we measured contrast sensitivity for circular patches of sine-wave gratings with various diameters that were blocked or interleaved across trials to produce low and high extrinsic uncertainty, respectively. Summation curves were steep initially, becoming shallower thereafter. For the smaller stimuli, sensitivity was slightly worse for the interleaved design than for the blocked design. Neither area nor blocking affected the slope of the psychometric function. We derived model predictions for noisy mechanisms and extrinsic uncertainty that was either low or high. The contrast transducer was either linear (c1.0) or nonlinear (c2.0), and pooling was either linear or a MAX operation. There was either no intrinsic uncertainty, or it was fixed or proportional to stimulus size. Of these 10 canonical models, only the nonlinear transducer with linear pooling (the noisy energy model) described the main forms of the data for both experimental designs. We also show how a cross-correlator can be modified to fit our results and provide a contemporary presentation of the relation between summation and the slope of the psychometric function.

The antecedents and consequences of anticipatory identification

The aim of this thesis was to investigate anticipatory identification: newcomers’ identification with an organisation prior to entry; in particular by exploring the antecedents and consequences of the construct. Although organisational identification has been frequently investigated over the past 25 years, surprisingly little is known about what causes an individual to identify with a new organisation before entry and whether this has an impact on their relationship with the organisation after formally taking up membership. Drawing on a Social Identity approach to organisational identification, it was hypothesised that newcomers would more closely identify with an organisation prior to entry when the organisation was seen as a source of positive social identity and was situationally relevant and meaningful to the newcomer, i.e. salient, during the pre-entry period. It was also hypothesised that anticipatory identification would have post-entry consequences and would predict newcomers’ post-entry identification, turnover intentions and job satisfaction. An indirect relationship between anticipatory identification and post-entry identification through post-entry social identity judgements (termed a “feedback loop” mechanism) was additionally proposed. Finally anticipatory identification was also predicted to moderate the relationship between post-entry social identity judgements and post-entry identification (termed a “buffering” mechanism). Four studies were conducted to test these hypotheses. Study One served as a pilot study, using a retrospective self-report design with s sample of 124 university students to initially test the proposed conceptual model. Studies Two and Three adopted experimental designs. Each used a unique sample of 72 staff and students from Aston University to respectively test the hypothesised positive social identity motive and salience antecedents of anticipatory identification. Study Four explored the relationship between anticipatory identification, its antecedents and consequences longitudinally, using an organisational sample of 45 employees. Overall, these studies found support for a social identity motive antecedent of anticipatory identification, as well as more limited evidence that anticipatory identification was associated with the salience of an organisation prior to entry. Support was inconsistent for a direct relationship between anticipatory identification and post-entry identification and there was no evidence that anticipatory identification was a significant direct predictor of turnover intention and job satisfaction. Anticipatory identification was however found to act as a buffer in the relationship between post-entry social identity judgements and post-entry identification in all but one of the four samples measured. A feedback loop mechanism was observed within the experimental designs of Studies Two and Three, but not within the organisational samples of Studies One and Four. Overall the findings of these four studies highlight key ways through which anticipatory identification can develop prior to entry into an organisation. Moreover, the research observed several important post-entry consequences of anticipatory identification, indicating that an understanding of post-entry identification may be enriched by attending more closely to the extent to which newcomers identify with an organisation prior to entry.

Stereotype threat and the standardized testing experiences of African American children at an urban elementary school

Stereotype threat (Steele & Aronson, 1995) refers to the risk of confirming a negative stereotype about one’s group in a particular performance domain. The theory assumes that performance in the stereotyped domain is most negatively affected when individuals are more highly identified with the domain in question. As federal law has increased the importance of standardized testing at the elementary level, it can be reasonably hypothesized that the standardized test performance of African American children will be depressed when they are aware of negative societal stereotypes about the academic competence of African Americans. This sequential mixed-methods study investigated whether the standardized testing experiences of African American children in an urban elementary school are related to their level of stereotype awareness. The quantitative phase utilized data from 198 African American children at an urban elementary school. Both ex-post facto and experimental designs were employed. Experimental conditions were diagnostic and non-diagnostic testing experiences. The qualitative phase utilized data from a series of six focus group interviews conducted with a purposefully selected group of 4 African American children. The interview data were supplemented with data from 30 hours of classroom observations. Quantitative findings indicated that the stereotype threat condition evoked by diagnostic testing depresses the reading test performance of stereotype-aware African American children (F[1, 194] = 2.21, p < .01). This was particularly true of students who are most highly domain-identified with reading (F[1, 91] = 19.18, p < .01). Moreover, findings indicated that only stereotype-aware African American children who were highly domain-identified were more likely to experience anxiety in the diagnostic condition (F[1, 91] = 5.97, p < .025). Qualitative findings revealed 4 themes regarding how African American children perceive and experience the factors related to stereotype threat: (1) a narrow perception of education as strictly test preparation, (2) feelings of stress and anxiety related to the state test, (3) concern with what “others” think (racial salience), and (4) stereotypes. A new conceptual model for stereotype threat is presented, and future directions including implications for practice and policy are discussed.

Social and seasonal plasticity of the electric fish, Brachyhypopomus gauderio

The South American electric knifefish, Brachyhypopomus gauderio, uses weakly electric fields to see and communicate in the dark. Only one study to date has investigated natural behavior in this species during the breeding season; this study proposed that B. guarerio has an exploded lek polygyny breeding system. To test this hypothesis, artificial marshes simulating the native vegetation, temperature, and water conductivities of the South American subtropics were created to study seasonal variation in associative behavior of B. gauderio during the breeding and non-breeding seasons. Mark/recapture methods were used to keep track of individual fish and their dispersion inside the experimental designs. The experimental design proved to be extremely successful at eliciting reproduction. Differences were found in seasonal variations of social behaviors between adult and juvenile populations. Although no apparent sex. differences in movement patterns were found during the breeding season; a trend for male-male aversion was found, suggesting male-male avoidance as a possible strategy guiding aspects of social behaviors in this species. Further, movement may be a tactic for mate seeking as the individuals who moved the most during the breeding season obtained the most opposite sex interactions. These findings support the exploded lek polygyny model. Social interactions are subject to complex regulation by social, physiologic and ecological factors; the extent to which these associations are repeatable may provide novel insights on the evolution of sociality as it has been shaped by natural selection.

Stereotype Threat and the Standardized Testing Experiences of African American Children at an Urban Elementary School

Stereotype threat (Steele & Aronson, 1995) refers to the risk of confirming a negative stereotype about one’s group in a particular performance domain. The theory assumes that performance in the stereotyped domain is most negatively affected when individuals are more highly identified with the domain in question. As federal law has increased the importance of standardized testing at the elementary level, it can be reasonably hypothesized that the standardized test performance of African American children will be depressed when they are aware of negative societal stereotypes about the academic competence of African Americans. This sequential mixed-methods study investigated whether the standardized testing experiences of African American children in an urban elementary school are related to their level of stereotype awareness. The quantitative phase utilized data from 198 African American children at an urban elementary school. Both ex-post facto and experimental designs were employed. Experimental conditions were diagnostic and non-diagnostic testing experiences. The qualitative phase utilized data from a series of six focus group interviews conducted with a purposefully selected group of 4 African American children. The interview data were supplemented with data from 30 hours of classroom observations. Quantitative findings indicated that the stereotype threat condition evoked by diagnostic testing depresses the reading test performance of stereotype-aware African American children (F[1, 194] = 2.21, p < .01). This was particularly true of students who are most highly domain-identified with reading (F[1, 91] = 19.18, p < .01). Moreover, findings indicated that only stereotype-aware African American children who were highly domain-identified were more likely to experience anxiety in the diagnostic condition (F[1, 91] = 5.97, p < .025). Qualitative findings revealed 4 themes regarding how African American children perceive and experience the factors related to stereotype threat: (1) a narrow perception of education as strictly test preparation, (2) feelings of stress and anxiety related to the state test, (3) concern with what “others” think (racial salience), and (4) stereotypes. A new conceptual model for stereotype threat is presented, and future directions including implications for practice and policy are discussed.

Recuperação e purificação do antígeno 503 de Leishmania i. chagasi expresso em E. coli e remoção de endotoxina utilizando adsorção em leito expandido

The growing interest and applications of biotechnology products have increased the development of new processes for recovery and purification of proteins. The expanded bed adsorption (EBA) has emerged as a promising technique for this purpose. It combines into one operation the steps of clarification, concentration and purification of the target molecule. Hence, the method reduces the time and the cost of operation. In this context, this thesis aim was to evaluate the recovery and purification of 503 antigen of Leishmania i. chagasi expressed in E. coli M15 and endotoxin removal by EBA. In the first step of this study, batch experiments were carried out using two experimental designs to define the optimal adsorption and elution conditions of 503 antigen onto Streamline chelating resin. For adsorption assays, using expanded bed, it was used a column of 2.6 cm in diameter by 30.0 cm in height coupled to a peristaltic pump. In the second step of study, the removal of endotoxin during antigen recovery process was evaluated employing the non-ionic surfactant Triton X-114 in the washing step ALE. In the third step, we sought developing a mathematical model able to predict the 503 antigen breakthrough curves in expanded mode. The experimental design results to adsorption showed the pH 8.0 and the NaCl concentration of 2.4 M as the optimum adsorption condition. In the second design, the only significant factor for elution was the concentration of imidazole, which was taken at 600 mM. The adsorption isotherm of the 503 antigen showed a good fit to the Langmuir model (R = 0.98) and values for qmax (maximum adsorption capacity) and Kd (equilibrium constant) estimated were 1.95 mg/g and 0.34 mg/mL, respectively. Purification tests directly from unclarified feedstock showed a recovery of 59.2% of the target protein and a purification factor of 6.0. The addition of the non-ionic surfactant Triton X-114 to the washing step of EBA led to high levels (> 99%) of LPS removal initially present in the samples for all conditions tested. The mathematical model obtained to describe the 503 antigen breakthrough curves in Streamline Chelanting resin in expanded mode showed a good fit for both parameter estimation and validation steps. The validated model was used to optimize the efficiencies, achieving maximum values of the process and of the column efficiencies of 89.2% and 75.9%, respectively. Therefore, EBA is an efficient alternative for the recovery of the target protein and removal of endotoxin from an E. coli unclarified feedstock in just one step.