Using clusters of computers for large QU-GENE simulation experiments

The QU-GENE Computing Cluster (QCC) is a hardware and software solution to the automation and speedup of large QU-GENE (QUantitative GENEtics) simulation experiments that are designed to examine the properties of genetic models, particularly those that involve factorial combinations of treatment levels. QCC automates the management of the distribution of components of the simulation experiments among the networked single-processor computers to achieve the speedup.

A mixture model-based approach to the clustering of microarray expression data

Motivation: This paper introduces the software EMMIX-GENE that has been developed for the specific purpose of a model-based approach to the clustering of microarray expression data, in particular, of tissue samples on a very large number of genes. The latter is a nonstandard problem in parametric cluster analysis because the dimension of the feature space (the number of genes) is typically much greater than the number of tissues. A feasible approach is provided by first selecting a subset of the genes relevant for the clustering of the tissue samples by fitting mixtures of t distributions to rank the genes in order of increasing size of the likelihood ratio statistic for the test of one versus two components in the mixture model. The imposition of a threshold on the likelihood ratio statistic used in conjunction with a threshold on the size of a cluster allows the selection of a relevant set of genes. However, even this reduced set of genes will usually be too large for a normal mixture model to be fitted directly to the tissues, and so the use of mixtures of factor analyzers is exploited to reduce effectively the dimension of the feature space of genes. Results: The usefulness of the EMMIX-GENE approach for the clustering of tissue samples is demonstrated on two well-known data sets on colon and leukaemia tissues. For both data sets, relevant subsets of the genes are able to be selected that reveal interesting clusterings of the tissues that are either consistent with the external classification of the tissues or with background and biological knowledge of these sets.

Evolutionary experiments on mate recognition in the Drosophila serrata species complex

It is becoming increasingly apparent that at least some aspects of the evolution of mate recognition may be amenable to manipulation in evolutionary experiments. Quantitative genetic analyses that focus on the genetic consequences of evolutionary processes that result in mate recognition evolution may eventually provide an understanding of the genetic basis of the process of speciation. We review a series of experiments that have attempted to determine the genetic basis of the response to natural and sexual selection on mate recognition in the Drosophila serrata species complex. The genetic basis of mate recognition has been investigated at three levels: (1) between the species of D. serrata and D. birchii using interspecific hybrids, (2) between populations of D. serrata that are sympatric and allopatric with respect to D. birchii, and (3) within populations of D. serrata. These experiments suggest that it may be possible to use evolutionary experiments to observe important events such as the reinforcement of mate recognition, or the generation of the genetic associations that are central to many sexual selection models.

Patterns of gene expression are altered in the frontal and motor cortices of human alcoholics

Alcoholism is a major health problem in Western countries, yet relatively little is known about the mechanisms by which chronic alcohol abuse causes the pathologic changes associated with the disease. It is likely that chronic alcoholism affects a number of signaling cascades and transcription factors, which in turn result in distinct gene expression patterns. These patterns are difficult to detect by traditional experiments measuring a few mRNAs at a time, but are well suited to microarray analyses. We used cDNA microarrays to analyze expression of approximately 10 000 genes in the frontal and motor cortices of three groups of chronic alcoholic and matched control cases. A functional hierarchy was devised for classification of brain genes and the resulting groups were compared based on differential expression. Comparison of gene expression patterns in these brain regions revealed a selective reprogramming of gene expression in distinct functional groups. The most pronounced differences were found in myelin-related genes and genes involved in protein trafficking. Significant changes in the expression of known alcohol-responsive genes, and genes involved in calcium, cAMP, and thyroid signaling pathways were also identified. These results suggest that multiple pathways may be important for neuropathology and altered neuronal function observed in alcoholism.

Catheter effects in organ perfusion experiments

In a typical isolated organ perfusion experiment, a substance is injected upstream of an organ and then collected at some distance downstream. To reach the organ from the injection site, and then from the organ to the collector, a solute passes through catheters, usually tubes with circular cross-sections. Catheters cause distortion to the concentration-time profile of the perfusion. In this paper, we analyse catheter distribution kinetics from a mathematical point of view, develop the function most suitable for modeling this distribution and successfully apply this function to experimental data. (C) 2002 Academic Press.

Lead stimulus modality change and the attentional modulation of the acoustic and electrical blink reflex

Two experiments investigated the effects of the sensory modality of the lead and of the blink-eliciting stimulus during lead stimulus modality change on blink modulation at lead intervals of 2500 and 3500 ins. Participants were presented with acoustic, visual, or tactile change stimuli after habituation training with lead stimuli from the same or a different sensory modality. In Experiment 1, latency and magnitude of the acoustic blink were facilitated during a change to acoustic or visual lead stimuli, but not during a change to tactile lead stimuli. After habituation to acoustic lead stimuli, blink magnitude was smaller during tactile change stimuli than during habituation stimuli. The latter finding was replicated in Experiment 2 in which blink was elicited by electrical stimulation of the trigeminal nerve. The consistency of the findings across different combinations of lead stimulus and blink-eliciting stimulus modalities does not support a modality-specific account of attentional blink modulation. Rather, blink modulation during generalized orienting reflects modality non-specific processes, although modulation may not always be found during tactile lead stimuli. (C) 2002 Elsevier Science B.V. All rights reserved.

Application of spatial analysis techniques to adjust for fertility trends and identify interplot competition in early stage sugarcane selection trials

Most sugarcane breeding programs in Australia use large unreplicated trials to evaluate clones in the early stages of selection. Commercial varieties that are replicated provide a method of local control of soil fertility. Although such methods may be useful in detecting broad trends in the field, variation often occurs on a much smaller scale. Methods such as spatial analysis adjust a plot for variability by using information from immediate neighbours. These techniques are routinely used to analyse cereal data in Australia and have resulted in increased accuracy and precision in the estimates of variety effects. In this paper, spatial analyses in which the variability is decomposed into local, natural, and extraneous components are applied to early selection trials in sugarcane. Interplot competition in cane yield and trend in sugar content were substantial in many of the trials and there were often large differences in the selections between the spatial and current method used by the Bureau of Sugar Experiment Stations. A joint modelling approach for tonnes sugar per hectare in response to fertility trends and interplot competition is recommended.

"It's OK if we say it, but you can't": responses to intergroup and intragroup criticism

Three experiments were conducted examining group members' responses to criticism from ingroup and outgroup members. In Experiment I a, Australians read scripts of a person making either negative or positive comments about Australia. The speaker was identified as coming from either Australia (ingroup member) or another country (outgroup member). Responses indicated an intergroup sensitivity effect; that is, while ingroup criticisms were tolerated surprisingly well, outgroup criticisms were met with sensitivity and defensiveness. This pattern was replicated using the identity of,university student' (Experiment 1b). Experiment 2 demonstrated that the intergroup sensitivity effect is driven by perceptions that ingroup criticisms are seen to be more legitimate and more constructive than are outgroup criticisms. The results are discussed in terms of their implications for intragroup and intergroup relations. Copyright (C) 2002 John Wiley Sons, Ltd.

Drawing insight from pictures: The development of concepts of false drawing and false belief in children with deafness, normal hearing, and autism

Theory-of-mind concepts in children with deafness, autism, and normal development (N = 154) were examined in three experiments using a set of standard inferential false-belief tasks and matched sets of tasks involving false drawings. Results of all three experiments replicated previously published findings by showing that primary school children with deafness or autism, aged 6 to 13 years, scored significantly lower than normal-developing 4-year-old preschoolers on standard misleading-container and unseen-change tests of false-belief understanding. Furthermore, deaf and autistic children generally scored higher on drawing-based tests than on corresponding standard tests and, on the most challenging of the false-drawing tests in Experiment 2, they significantly outperformed the normal-developing preschoolers by clearly understanding their own false intentions and another person's false beliefs about an actively misleading drawing. In Experiment 3, preschoolers; outperformed older deaf and autistic children on standard tasks, but did less well on a task that required the drawing of a false belief. Methodological factors could not fully explain the findings, but early social and conversational experiences in the family were deemed likely contributors.

Young children's performance on the balance scale: The influence of relational complexity

Three experiments investigated the effect of complexity on children's understanding of a beam balance. In nonconflict problems, weights or distances varied, while the other was held constant. In conflict items, both weight and distance varied, and items were of three kinds: weight dominant, distance dominant, or balance (in which neither was dominant). In Experiment 1, 2-year-old children succeeded on nonconflict-weight and nonconflict-distance problems. This result was replicated in Experiment 2, but performance on conflict items did not exceed chance. In Experiment 3, 3- and 4-year-olds succeeded on all except conflict balance problems, while 5- and 6-year-olds succeeded on all problem types. The results were interpreted in terms of relational complexity theory. Children aged 2 to 4 years succeeded on problems that entailed binary relations, but 5- and 6-year-olds also succeeded on problems that entailed ternary relations. Ternary relations tasks from other domains-transitivity and class inclusion-accounted for 93% of the age-related variance in balance scale scores. (C) 2002 Elsevier Science (USA).

Relations between high and low power groups: The importance of legitimacy

Using a social identity perspective, two experiments examined the effects of power and the legitimacy of power differentials on intergroup bias. In Experiment 1, 125 math-science students were led to believe that they had high or low representation in a university decision-making body relative to social-science students and that this power position was either legitimate or illegitimate. Power did not have an independent effect on bias; rather, members of both high and low power groups showed more bias when the power hierarchy was illegitimate than when it was legitimate. This effect was replicated in Experiment 2 (N =105). In addition, Experiment 2 showed that groups located within an unfair power hierarchy expected the superordinate power body to be more discriminatory than did those who had legitimately high or low power. The results are discussed in terms of their implications for group relations.

Towards the on-farm conservation of the assassin bug Pristhesancus plagipennis (Walker) (Hemiptera : Reduviidae) during winter using crop plants as refuges

Habitat instability associated with seasonal crop succession in broad-acre farming systems presents a problem for the conservation and utilisation of beneficial insects in annual field crops. The present paper describes two experiments used to measure the potential of seven plant species to be utilised as winter refuges to support and conserve the predatory bug Pristhesancus plagipennis (Walker). In the first experiment, replicated plots of canola (Brassica napus ), red salvia (Salvia coccinea ), niger (Guizotia abyssinica ), linseed (Linum usitatissimum ), lupins (Lupinus angustifolius ), and lucerne (Medicago falcata ) were planted in a randomized experiment during Autumn 1998. Upon crop establishment, adults and nymphs of P. plagipennis were released into treatment plots and their numbers were assessed, along with those of their potential prey, throughout the ensuing winter months. Post-release sampling suggested that canola and niger retained a proportion of adult P. plagipennis , while niger, lucerne and canola retained some nymphs. The other plant species failed to support P. plagipennis nymphs and adults postrelease. In the second experiment, niger was compared with two lines of sunflower (Helianthus annus ). Both sunflower lines harboured significantly higher (P < 0.05) densities of P. plagipennis nymphs than did niger. The more successful refuge treatments (sunflower, niger and canola) had an abundance of yellow flowers that were attractive to pollinating insects, which served as supplementary prey on which P. plagipennis were observed to feed. Sunflower and niger also supported high densities of the prey insect Creontiades dilutus (Stal) and provided protective leafy canopies which supplied shelter during the winter months. The potential and limitations for using each plant species as a winter refuge to retain P. plagipennis during winter are discussed.

Water table waves in an unconfined aquifer: Experiments and modeling

[1] Comprehensive measurements are presented of the piezometric head in an unconfined aquifer during steady, simple harmonic oscillations driven by a hydrostatic clear water reservoir through a vertical interface. The results are analyzed and used to test existing hydrostatic and nonhydrostatic, small-amplitude theories along with capillary fringe effects. As expected, the amplitude of the water table wave decays exponentially. However, the decay rates and phase lags indicate the influence of both vertical flow and capillary effects. The capillary effects are reconciled with observations of water table oscillations in a sand column with the same sand. The effects of vertical flows and the corresponding nonhydrostatic pressure are reasonably well described by small-amplitude theory for water table waves in finite depth aquifers. That includes the oscillation amplitudes being greater at the bottom than at the top and the phase lead of the bottom compared with the top. The main problems with respect to interpreting the measurements through existing theory relate to the complicated boundary condition at the interface between the driving head reservoir and the aquifer. That is, the small-amplitude, finite depth expansion solution, which matches a hydrostatic boundary condition between the bottom and the mean driving head level, is unrealistic with respect to the pressure variation above this level. Hence it cannot describe the finer details of the multiple mode behavior close to the driving head boundary. The mean water table height initially increases with distance from the forcing boundary but then decreases again, and its asymptotic value is considerably smaller than that previously predicted for finite depth aquifers without capillary effects. Just as the mean water table over-height is smaller than predicted by capillarity-free shallow aquifer models, so is the amplitude of the second harmonic. In fact, there is no indication of extra second harmonics ( in addition to that contained in the driving head) being generated at the interface or in the interior.

Surface stickiness of drops of carbohydrate and organic acid solutions during convective drying: Experiments and modeling

Drying kinetics of low molecular weight sugars such as fructose, glucose, sucrose and organic acid such as citric acid and high molecular weight carbohydrate such as maltodextrin (DE 6) were determined experimentally using single drop drying experiments as well as predicted numerically by solving the mass and heat transfer equations. The predicted moisture and temperature histories agreed with the experimental ones within 6% average relative (absolute) error and average difference of +/- 1degreesC, respectively. The stickiness histories of these drops were determined experimentally and predicted numerically based on the glass transition temperature (T-g) of surface layer. The model predicted the experimental observations with good accuracy. A nonsticky regime for these materials during spray drying is proposed by simulating a drop, initially 120 mum in diameter, in a spray drying environment.

Optical experiments beyond the quantum limit: Squeezing entanglement and teleportation

Results of experiments recently performed are reported, in which two optical parametric amplifiers were set up to generate two independently quadrature squeezed continuous wave laser beams. The transformation of quadrature squeezed states into polarization squeezed states and into states with spatial quantum correlations is demonstrated. By utilizing two squeezed laser beams, a polarization squeezed state exhibiting three simultaneously squeezed Stokes operator variances was generated. Continuous variable polarization entanglement was generated and the Einstein-Podolsky-Rosen paradox was observed. A pair of Stokes operators satisfied both the inseparability criterion and the conditional variance criterion. Values of 0.49 and 0.77, respectively, were observed, with entanglement requiring values below unity. The inseparability measure of the observed quadrature entanglement was 0.44. This value is sufficient for a demonstration of quantum teleportation, which is the next experimental goal of the authors.