Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach

Motivation: Finding genes that are preferentially expressed in a particular tissue or condition is a problem that cannot be solved by standard statistical testing procedures. A relatively unknown procedure that can be used is the intersection–union test (IUT). However, two disadvantages of the IUT are that it is conservative and it conveys only the information of the least differing target tissue–other tissue pair.

Results: We propose a Bayesian procedure that quantifies how much evidence there is in the overall expression profile for selective over-expression. In a small simulation study, it is shown that the proposed method outperforms the IUT when it comes to finding selectively expressed genes. An application to publicly available data consisting of 22 tissues shows that the Bayesian method indeed selects genes with functions that reflect the specific tissue functions. The proposed method can also be used to find genes that are underexpressed in a particular tissue.

Availability: Both MATLAB and R code that implement the IUT and the Bayesian procedure in an efficient way, can be downloaded at http://ppw.kuleuven.be/okp/software/BayesianIUT/.

Contact:katrijn.vandeun@psy.kuleuven.be

The usefulness of experience sampling in understanding the urge to move in anorexia nervosa

BACKGROUND

Physical hyperactivity has often been described in anorexia nervosa (AN) patients but up until now in-depth research has been scarce. Experience sampling methodology (ESM), a structured diary technique assessing momentary mental state at random times during the day, may be useful in studying hyperactivity in AN.

METHODS

In two single case reports, ESM was used to investigate the variation across time of the urge to move in relation to potentially relevant eliciting conditions such as positive and negative emotions, weight preoccupation and attractiveness.

RESULTS

Frequency distribution of the involved variables indicated substantial individual differences between patients. While both patients' tendency to be hyperactive was positively related to their weight preoccupation and negative emotions, in only one patient, the urge to move turned out to be significantly related to (the absence of) positive emotions.

CONCLUSIONS

ESM can be useful to test whether general theories of psychopathology apply to specific patients, and it may be conceived as an individually tailored approach to self-monitoring. As such, it may guide the clinician to devise therapeutic interventions in particular patients.

Three-way component analysis: principles and illustrative application

Three-way component analysis techniques are designed for descriptive analysis of 3-way data, for example, when data are collected on individuals, in different settings, and on different measures. Such techniques summarize all information in a 3-way data set by summarizing, for each way of the 3-way data set, the associated entities through a few components and describing the relations between these components. In this article, 3-mode principal components analysis is described at an elementary level. Guidance is given concerning the choices to be made in each step of the process of analyzing 3-way data by this technique. The complete process is illustrated with a detailed description of the analysis of an empirical 3-way data set.

Predicting conjunction typicalities by component typicalities

In two studies, we investigated to what extent typicalities in conjunctive concepts phrased as relative clauses--such as pets that are also birds--can be predicted from simple functions of constituent typicalities and from extensions of such functions. In a first study, analyses of a large aggregated data set, based on seven different experiments, showed that a calibrated minimum rule model and some extensions of this model accounted for a very large part of the variance in the conjunction typicalities. The same models can also account for the so-called guppy effect. A psychological explanation is presented, which states that typicalities in contrast categories, like pets that are not birds and birds that are not pets, further improve the prediction of conjunction typicalities. This hypothesis is tested in a second study.

Not guppies, nor goldfish, but tumble dryers, Noriega, Jesse Jackson, panties, car crashes, bird books, and Stevie Wonder

This paper focuses on the guppy effect (Osherson & Smith, 1981), that is, on the existence of examples of conjunctive concepts that are more typical of the conjunction than of both constituents. The most frequently given examples of this effect, guppy and goldfish, are shown not to be more typical of the conjunction pet fish than of fish in two between-subjects and one within-subjects experiment. The frequency of the effect in a large empirical study is investigated, and better examples of the effect are suggested.

Dominance and noncommutativity effects in concept conjunctions: extensional or intensional basis?

Dominance and noncommutativity effects are investigated in relative clause descriptions of five conjunctive concepts (birds and pets, sports and games, vehicles and machines, office equipment and writing implements, and shoes and sports equipment). Both asymmetry phenomena are studied at the extensional level (using membership ratings) and at the intensional level (using feature-importance ratings). A clear dominance effect was found for both the membership ratings and the feature-importance ratings, whereas the noncommutativity effect emerged only occasionally in the membership ratings and almost never in the feature-importance ratings. The data suggested that the dominance effect and the much weaker noncommutativity effect have an extensional basis.

Part-instance association in the categorization of acts

Rips and Conrad (1989) found a kind-part reciprocal effect in models of the mind, in that one mental activity is part of another if the second is a kind of the first, and vice versa. In the present paper, we hypothesize that a formally analogous effect occurs at the level of activity instances. In particular, we hypothesize that an act is judged to be an instance of an act category referred to by an activity verb if the activity is judged to be an important part of the act, and vice versa. Empirical support for this hypothesis is found in three studies with activity verbs. The converse part-instance relation is further noted to parallel the part-instance association for a specific type of metonymically defined categories. Rips and Conrad's kind-part reciprocal effect is shown to be a logical consequence of the converse part-instance relation.