Interpretation of pooling experiments using the Markov chain Monte Carlo method

This paper describes an effective method for extracting as much information as possible from pooling experiments for library screening. Pools are collections of clones, and screening a pool with a probe determines whether any of these clones are positive for the probe. The results of the pool screenings are interpreted, or decoded, to infer which clones are candidates to be positive. These candidate positives are subjected to confirmatory testing. Decoding the pool screening results is complicated by the presence of errors, which typically lead to ambiguities in the inference of positive clones. However, in many applications there are reasonable models for the prior distributions for positives and for errors, and Bayes inference is the preferred method for ranking candidate positives. Because of the combinatoric complexity of the Bayes formulation, we implemented a decoding algorithm using a Markov chain Monte Carlo method. The algorithm was used in screening a library with 1298 clones using 47 pools. We corroborated the posterior probabilities for positives with results from confirmatory screening. We also simulated the screening of a 10-fold coverage library of 33,000 clones using 253 pools. The use of our algorithm, effective under conditions where combinatorial decoding techniques are imprudent, allows the use of fewer pools and also introduces needed robustness.     

On DNA Codes

We develop and study the concept of similarity functions for q-ary sequences. For the case q = 4, these functions can be used for a mathematical model of the DNA duplex energy [1,2], which has a number of applications in molecular biology. Based on these similarity functions, we define a concept of DNA codes [1]. We give brief proofs for some of our unpublished results [3] connected with the well-known deletion similarity function [4–6]. This function is the length of the longest common subsequence; it is used in the theory of codes that correct insertions and deletions [5]. Principal results of the present paper concern another function, called the similarity of blocks. The difference between this function and the deletion similarity is that the common subsequences under consideration should satisfy an additional biologically motivated [2] block condition, so that not all common subsequences are admissible. We prove some lower bounds on the size of an optimal DNA code for the block similarity function. We also consider a construction of close-to-optimal DNA codes which are subcodes of the parity-check one-error-detecting code in the Hamming metric [7].     

The effect of intermittent punishment-partial reward training on resistance to continuous punishment.

Investigated the effect of adding a partial reinforcement procedure to an intermittent punishment procedure on subsequent resistance to continuous punishment. 36 naive male albino Wistar rats served as Ss. Results indicate that the addition of partial reinforcement training increases the resistance to continuous punishment. This superior resistance cannot be seen as being equal to a simple sum of resistance due to intermittent punishment alone or partial reward alone. Results are discussed in terms of theories of resistance to fear and frustration. (French summary) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Social information use and the evolution of unresponsiveness in collective systems

Animal groups in nature often display an enhanced collective information-processing capacity. It has been speculated that natural selection will tune this response to be optimal, ensuring that the group is reactive while also being robust to noise. Here, we show that this is unlikely to be the case. By using a simple model of decision-making in a dynamic environment, we find that when individuals behave rationally and are subject to selection based on their accuracy, optimality of collective decision-making is not attained. Instead, individuals overly rely on social information and evolve to be too readily influenced by their neighbours. This is due to a classic evolutionary conflict between individual and collective interest. The result is a sub-optimal system that is poised on the cusp of total unresponsiveness. Individuals in the evolved group exhibit delayed reactions to changes in the environment, before responding with rapid, socially reinforced transitions, reminiscent of familiar human and animal social systems (markets, stampedes, fashions, etc.). Our results demonstrate that behaviour of this type may not be pathological, but instead could represent an evolutionary attractor for such collective systems.     

Influence of children's stories on dependency, a sex-typed behavior.

Examined the influence of models in stories on the dependent behavior (help seeking) and independent behavior (the withholding of help-seeking responses) of 80 5-yr-olds. Before hearing 1 of 4 stories, each S was told that he/she would be asked questions to see how much was remembered from it. In 2 stories, the behavior of a child model was dependent: the model sought help in and was verbally reinforced for solving a puzzle. Results suggest a somewhat more complex model for the process of sex role development than is frequently proposed. That females who were not exposed to any verbally presented models did not differ significantly from males in help seeking is in accord with previous findings (R. M. Oetzel, 1966) that sex differences in dependent behavior are not very strong in young children. Following exposure to either a dependent or an independent child model, females showed a significantly greater willingness to seek help than did males exposed to the same models. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A note on legislation affecting Canadian psychology: The Ontario model.

New legislation affecting Psychology has been proposed recently in Ontario. If enacted, this legislation would set up a College of Psychology with wide discretionary powers and broad duties. Other legislation is proposed to govern such Colleges (Health Disciplines Act) and to create a College to credential competence rather than profession (the College of Mental Health Practitioners). These developments and their implications are discussed with respect to their impact on psychology across Canada. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Generalization of persistence: The transfer of approach behaviour to differing aversive stimuli.

In 3 experiments it was found that intermittent punishment with electric shock increased persistence to quantitatively and qualitatively different punishers but failed to increase resistance to extinction. Male albino Wistar rats (N=16, 26, and 17, respectively) served as Ss. It is suggested that while approach tendencies acquired to 1 fear state may be elicited by quite different fear states, generalization between fear and frustration may be limited by fairly narrow boundary conditions. (French summary) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Radiation detection with distributed sensor networks

In any assessment of potential terrorist attacks, the nuclear threat takes center stage. Although weapons-grade nuclear materials arc heavily guarded, a plausible scenario involves terrorists detonating a simple radiological dispersion device (ROD) capable of broadcasting nonfissile but highly radioactive particles over a densely populated area. In most cases, a motor vehicle has to transport the device and its payload commonly known as a "dirty bomb" - to the target destination. As a final defense against such a weapon, select traffic choke points in the US have large portal monitoring systems to help detect illicit isotopes. The distributed sensor network project at Los Alamos National Laboratory, in cooperation with the University of New Mexico, is developing a network of radiation detectors that, coupled with other sensors that collect supportive data, is suitable for ROD interdiction in either urban or rural environments. Compared to a portal monitor, a DSN is much less visible, uses less power per detector, is hand carried and thus more rapidly deployable, and simplifies coverage of multiple transport avenues. Also, to function effectively, portal monitoring systems typically require slow or halted traffic, whereas our DSN can be tailored for any moderate traffic speed.