Bounds on edit metric codes with combinatorial DNA constraints

The design of a large and reliable DNA codeword library is a key problem in DNA based computing. DNA codes, namely sets of fixed length edit metric codewords over the alphabet {A, C, G, T}, satisfy certain combinatorial constraints with respect to biological and chemical restrictions of DNA strands. The primary constraints that we consider are the reverse--complement constraint and the fixed GC--content constraint, as well as the basic edit distance constraint between codewords. We focus on exploring the theory underlying DNA codes and discuss several approaches to searching for optimal DNA codes. We use Conway's lexicode algorithm and an exhaustive search algorithm to produce provably optimal DNA codes for codes with small parameter values. And a genetic algorithm is proposed to search for some sub--optimal DNA codes with relatively large parameter values, where we can consider their sizes as reasonable lower bounds of DNA codes. Furthermore, we provide tables of bounds on sizes of DNA codes with length from 1 to 9 and minimum distance from 1 to 9.

Decoding algorithms using side-effect machines

Bioinformatics applies computers to problems in molecular biology. Previous research has not addressed edit metric decoders. Decoders for quaternary edit metric codes are finding use in bioinformatics problems with applications to DNA. By using side effect machines we hope to be able to provide efficient decoding algorithms for this open problem. Two ideas for decoding algorithms are presented and examined. Both decoders use Side Effect Machines(SEMs) which are generalizations of finite state automata. Single Classifier Machines(SCMs) use a single side effect machine to classify all words within a code. Locking Side Effect Machines(LSEMs) use multiple side effect machines to create a tree structure of subclassification. The goal is to examine these techniques and provide new decoders for existing codes. Presented are ideas for best practices for the creation of these two types of new edit metric decoders.

Investigating the potential of thecamoebians (testate amoebae) as bio-indicators of impact of oil sands mining operations on freshwater environments in Northeastern Alberta, Canada

Thecamoebian (testate amoeba) species diversity and assemblages in reclamation wetlands and lakes in northeastern Alberta respond to chemical and physical parameters associated with oil sands extraction. Ecosystems more impacted by OSPM (oil sands process-affected material) contain sparse, low-diversity populations dominated by centropyxid taxa and Arcella vulgaris. More abundant and diverse thecamoebian populations rich in difflugiid species characterize environments with lower OSPM concentrations. These shelled protists respond quickly to environmental change, allowing year-to-year variations in OSPM impact to be recorded. Their fossil record thus provides corporations with interests in the Athabasca Oil Sands with a potential means of measuring the progression of highlyimpacted aquatic environments to more natural wetlands. Development of this metric required investigation of controls on their fossil assemblage (e.g. seasonal variability, fossilization potential) and their biogeographic distribution, not only in the constructed lakes and wetlands on the oil sands leases, but also in natural environments across Alberta.

Facing Aggression: Cues Differ for Female versus Male Faces

The facial width-to-height ratio (face ratio), is a sexually dimorphic metric associated with actual aggression in men and with observers’ judgements of aggression in male faces. Here, we sought to determine if observers’ judgements of aggression were associated with the face ratio in female faces. In three studies, participants rated photographs of female and male faces on aggression, femininity, masculinity, attractiveness, and nurturing. In Studies 1 and 2, for female and male faces, judgements of aggression were associated with the face ratio even when other cues in the face related to masculinity were controlled statistically. Nevertheless, correlations between the face ratio and judgements of aggression were smaller for female than for male faces (F1,36= 7.43, p= 0.01). In Study 1, there was no significant relationship between judgements of femininity and of aggression in female faces. In Study 2, the association between judgements of masculinity and aggression was weaker in female faces than for male faces in Study 1. The weaker association in female faces may be because aggression and masculinity are stereotypically male traits. Thus, in Study 3, observers rated faces on nurturing (a stereotypically female trait) and on femininity. Judgements of nurturing were associated with femininity (positively) and masculinity (negatively) ratings in both female and male faces. In summary, the perception of aggression differs in female versus male faces. The sex difference was not simply because aggression is a gendered construct; the relationships between masculinity/femininity and nurturing were similar for male and female faces even though nurturing is also a gendered construct. Masculinity and femininity ratings are not associated with aggression ratings nor with the face ratio for female faces. In contrast, all four variables are highly inter-correlated in male faces, likely because these cues in male faces serve as ‘‘honest signals’’.

Age-Related Changes in Visual Spatial Working Memory Cognits: Frontal-Parietal EEG Coherence During Delay

This study explored changes in scalp electrophysiology across two Working Memory (WM) tasks and two age groups. Continuous electroencephalography (EEG) was recorded from 18 healthy adults (18-34 years) and 12 healthy adolescents (14-17) during the performance of two Oculomotor Delayed Response (ODR) WM tasks; (i.e. eye movements were the metric of motor response). Delay-period, EEG data in the alpha frequency was sampled from anterior and parietal scalp sites to achieve a general measure of frontal and parietal activity, respectively. Frontal-parietal, alpha coherence was calculated for each participant for each ODR-WM task. Coherence significantly decreased in adults moving across the two ODR tasks, whereas, coherence significantly increased in adolescents moving across the two ODR tasks. The effects of task in the adolescent and adult groups were large and medium, respectively. Within the limits of this study, the results provide empirical support that WM development during adolescence include complex, qualitative, change.