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title: A Qualitative Physics Based on Confluences
abstract: A qualitative physics predicts and explains the behavior of mechanisms in qualitative terms. The goals for the qualitative physics are (1) to be far simpler than the classical physics and yet retain all the important distinctions (e.g., state, oscillation, gain, momentum) without invoking the mathematics of continuously varying quantities and differential equations, (2) to produce causal accounts of physical mechanisms that are easy to understand, and (3) to provide the foundations for commonsense models for the next generation of expert systems. This paper presents a fairly encompassing account of qualitative physics. First, we discuss the general subject of naive physics and some of its methodological considerations. Second, we present a framework for modeling the generic behavior of individual components of a device based on the notions of qualitative differential equations (confluences) and qualitative state. This requires developing a qualitative version of the calculus. The modeling primitives induce two kinds of behavior, intrastate and interstate, which are governed by different laws. Third, we present algorithms for determining the behavior of a composite device from the generic behavior of its components. Fourth, we examine a theory of explanation for these predictions based on logical proof. Fifth, we introduce causality as an ontological commitment for explaining how devices behave.

title: The Ribonuclease P Database
abstract: Ribonuclease P is responsible for the removal of leader sequences from tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria the RNA subunit alone is catalytically active in vitro, i.e. it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information, available via the World Wide Web.

title: Handling long-latency loads in a simultaneous multithreading processor
abstract: Simultaneous multithreading architectures have been defined previously with fully shared execution resources. When one thread in such an architecture experiences a very long-latency operation, such as a load miss, the thread will eventually stall, potentially holding resources which other threads could be using to make forward progress.This paper shows that in many cases it is better to free the resources associated with a stalled thread rather than keep that thread ready to immediately begin execution upon return of the loaded data. Several possible architectures are examined, and some simple solutions are shown to be very effective, achieving speedups close to 6.0 in some cases, and averaging 15% speedup with four threads and over 100% speedup with two threads running. Response times are cut in half for several workloads in open system experiments.

title: Plant snoRNA database
abstract: The Plant snoRNA database (http://www.scri.sari.ac.uk/plant_snoRNA/) provides information on small nucleolar RNAs from Arabidopsis and eighteen other plant species. Information includes sequences, expression data, methylation and pseudouridylation target modification sites, initial gene organization (polycistronic, single gene and intronic) and the number of gene variants. The Arabidopsis information is divided into box C/D and box H/ACA snoRNAs, and within each of these groups, by target sites in rRNA, snRNA or unknown. Alignments of orthologous genes and gene variants from different plant species are available for many snoRNA genes. Plant snoRNA genes have been given a standard nomenclature, designed wherever possible, to provide a consistent identity with yeast and human orthologues.

title: Computational and neural mechanisms of task switching
abstract: Switching between tasks that overlap in perceptual and response characteristics is assumed to rely upon the maintenance of task representations in prefrontal cortex (PFC). However, task-switching studies demonstrate ''switch costs,'' even when there is sufficient time to prepare for a new task. These costs suggest that task-switching performance reflects a complex interplay between priming and the updating and maintenance of task representations. We describe a computational model in which this interaction is made explicit and linked to the dynamics of PFC. Simulation results account for a variety of empirical phenomena and predict a double dissociation in lateral PFC that was subsequently identified.

title: The Ultimate Categorical Independence Ratio of a Graph
abstract: Let $\beta(G)$ denote the independence number of a graph $G$. We introduce $A(G) = \lim_{k \rightarrow \infty}\beta(G^{k})/|V(G)|^{k}$, where the categorical graph product is used. This limit, surprisingly, lies in the range $(0,1/2]\cup\{1\}$. We can show that this limit can take any such rational number, but is there any $G$ for which $A(G)$ is irrational? A useful technique for bounding $A(G)$ is to consider special spanning subgraphs. These bounds allow us to efficiently compute $A(G)$ for many $G$. We give a condition which if true for $G$ shows that $A(G)>\beta(G)/|V(G)|$. This brings up the question: for which $G$ does $A(G)=\beta(G)/|V(G)|$? This happens if $G$ is a Cayley graph of an Abelian group or if $G$ is a connected graph that has an automorphism which has a single orbit.