A Macintosh Hypercard compilation of small subunit ribosomal RNA sequences
Molecular biologists, particularly those working with unicellular organisms, are becoming increasingly aware of the importance of understanding the phylogenetic (evolutionary) relationships between their model systems and other organisms. Currently, the best method for determining quantitatively the phylogenetic relationships in a group of organisms is the analysis of small subunit ribosomal RNA (ssu RNA) sequences (Woese, 1984). To assist in this type of analysis, the Ribosomal RNA Database Project (RDP) collects and distributes ssu rRNA sequences and software for phylogenetic analysis (Olsen et al., 1991). The ssu rRNA sequence stack is collection of almost 500 aligned ssu rRNA sequences taken from the first public release of the RDP sequence collection. The ssu rRNA sequence stack consists of a series of 'cards' each containing the ssu rRNA sequence of a single organism , from which the sequence can be copied (either with or without alignment information) or saved as a text file in GenBank format. Navigation in the stack is via a series of linked phylogenetic trees. Starting with a 'universal tree', clicking on the branch of interest takes the user to increasingly more specific and detailed trees. In the most specific trees, clicking on a branch either takes the user directly to the sequence card (if only one sequence is available representing that group) or presents the user with a pop-up menu of available sequences. Alternatively, the user can choose the desired sequence from a list containing the names of all of the available sequences, or choose to search the sequence names for a specific character string. The ssu rRNA sequence stack is written in Hypertalk v. 2.1, and requires v. 2.0 (or greater) of HyperCard, which in turn requires at least a Macintosh Plus, 1 Mbyte of RAM, the Macintosh operating system v 6.0.5 (or greater), and preferably a hard disk drive. The ssu rRNA sequence stack is available by anonymous FTP from ftp.bio.indiana.edu, by E-mail from the author at jwbrown@bio.indiana.edu or brownjw@iubacs.bitnet, or on floppy disk (enclose a single formatted high-density disk) free of charge on written request to the author.

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: On chromatic roots of large subdivisions of graphs
abstract: Given a graph G, we derive an expression for the chromatic polynomials of the graphs resulting from subdividing some (or all) of its edges. For special subfamilies of these, we are able to describe the limits of their chromatic roots. We also prove that for any e >0, all sufficiently large subdivisions of G have their chromatic roots in | z −1| e . A consequence of our work will be a characterization of the graphs having a subdivision whose chromatic polynomial has a root with negative real part.

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: How laminar frontal cortex and basal ganglia circuits interact to control planned and reactive saccades
abstract: How does the brain learn to balance between reactive and planned behaviors? The basal ganglia (BG) and frontal cortex together allow animals to learn planned behaviors that acquire rewards when prepotent reactive behaviors are insufficient. This paper proposes a new model, called TELOS, to explain how laminar circuitry of the frontal cortex, exemplified by the frontal eye fields, interacts with the BG, thalamus, superior colliculus, and inferotemporal and parietal cortices to learn and perform reactive and planned eye movements. The model is formulated as fourteen computational hypotheses. These specify how strategy priming and action planning (in cortical layers III, Va and VI) are dissociated from movement execution (in layer Vb), how the BG help to choose among and gate competing plans, and how a visual stimulus may serve either as a movement target or as a discriminative cue to move elsewhere. The direct, indirect and hyperdirect pathways through the BG are shown to enable complex gating functions, including deferred execution of selected plans, and switching among alternative sensory-motor mappings. Notably, the model can learn and gate the use of a What-to-Where transformation that enables spatially invariant object representations to selectively excite spatially coded movement plans. Model simulations show how dopaminergic reward and non-reward signals guide monkeys to learn and perform saccadic eye movements in the fixation, single saccade, overlap, gap, and delay (memory-guided) saccade tasks. Model cell activation dynamics quantitatively simulate seventeen established types of dynamics exhibited by corresponding real cells during performance of these tasks.

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: Steps Toward Automatic Theory Formation
abstract: This paper describes a theory formation system which can discover a partial axiomization of a data base represented as extensionally defined binary relations.- The system first discovers all possible intensional definitions of each binary relation in terms of the others. It then determines a minimal set of these relations from which the others can be defined. It then attempts to discover all the ways the relations of this minimal set can interact with each other, thus generating a set of inference rules. Although the system was originally designed to explore automatic techniques for theory construction for question-answering systems, it is currently being expanded to function as a symbiotic system to help social scientists explore certain kinds of data bases.