Using compression to identify acronyms in text

Text mining is about looking for patterns in natural language text, and may be defined as the process of analyzing text to extract information from it for particular purposes. In previous work, we claimed that compression is a key technology for text mining, and backed this up with a study that showed how particular kinds of lexical tokens---names, dates, locations, etc.---can be identified and located in running text, using compression models to provide the leverage necessary to distinguish different token types (Witten et al., 1999)Comment: 10 pages. A short form published in DCC200

Some experiments in man-machine interaction relevant to computer assisted learning

Various techniques for the communication of instructional material are outlined. Some experiments relevant to the design of multi-media computer assisted learning systems are then described

Optimal Foraging and Population Dynamics: An Archaeological Investigation at the Birch Creek Rockshelters, Idaho

This thesis aims to integrate the study of population change with the expectations of foraging models, and to test whether expectations resulting from integrating these two bodies of theory have greater predictive power than foraging models alone. To compare these models, I monitored prey age, butchery practice, and prey desirability in five prehistoric occupations of the Birch Creek rockshelters of Idaho. I modeled hunting pressure with a human population density estimate based on radiocarbon dates from Idaho archaeological sites, and modeled prey abundance with a model of historic effective moisture. Both models predicted younger prey, lower average prey desirability, and more intensive extraction of nutrients from prey when human hunting pressure is high and when prey are scarce. However, unlike the prey model, the Forager-resource Population Ecology (FPE) model predicts that similarly desirable prey with different reproductive rates should show different degrees of resilience to hunting pressure. Contrary to FPE model predictions, statistical analyses of the Birch Creek faunal materials did not indicate that human hunting pressure disproportionately stressed populations of slowly reproducing prey compared to quicker-reproducing prey. While the faunal specimens from Birch Creek provided a limited and flawed dataset, my results did not support the use of the FPE model

The Bacterial Photosynthetic Reaction Center as a Model for Membrane Proteins

Membrane proteins participate in many fundamental cellular processes. Until recently, an understanding of the function and properties of membrane proteins was hampered by an absence of structural information at the atomic level. A landmark achievement toward understanding the structure of membrane proteins was the crystallization (1) and structure determination (2-5) the photosynthetic reaction center (RC) from the purple bacteria Rhodopseudomonas viridis, followed by that of the RC from Rhodobacter sphaeroides (6-17). The RC is an integral membrane protein-pigment complex, which carries out the initial steps of photosynthesis (reviewed in 18). RCs from the purple bacteria Rps. viridis and Rb. sphaeroides are composed of three membrane-associated protein subunits (designated L, M, and H), and the following cofactors: four bacteriochlorophylls (Bchl or B), two bacteriopheophytins (Bphe or [phi]), two quinones, and a nonheme iron. The cofactors are organized into two symmetrical branches that are approximately related by a twofold rotation axis (2, 8). A central feature of the structural organization of the RC is the presence of 11 hydrophobic [alpha]-helixes, approximately 20-30 residues long, which are believed to represent the membrane-spanning portion of the RC (3, 9). Five membrane-spanning helixes are present in both the L and M subunits, while a single helix is in the H subunit. The folding of the L and M subunits is similar, consistent with significant sequence similarity between the two chains (19-25). The L and M subunits are approximately related by the same twofold rotation axis that relates the two cofactor branches. RCs are the first membrane proteins to be described at atomic resolution; consequently they provide an important model for discussing the folding of membrane proteins. The structure demonstrates that [alpha]-helical structures may be adopted by integral membrane proteins, and provides confirmation of the utility of hydropathy plots in identifying nonpolar membrane-spanning regions from sequence data. An important distinction between the folding environments of water-soluble proteins and membrane proteins is the large difference in water concentration surrounding the proteins. As a result, hydrophobic interactions (26) play very different roles in stabilizing the tertiary structures of these two classes of proteins; this has important structural consequences. There is a striking difference in surface polarity of membrane and water-soluble proteins. However, the characteristic atomic packing and surface area appear quite similar. A computational method is described for defining the position of the RC in the membrane (10). After localization of the RC structure in the membrane, surface residues in contact with the lipid bilayer were identified. As has been found for soluble globular proteins, surface residues are less well conserved in homologous membrane proteins than the buried, interior residues. Methods based on the variability of residues between homologous proteins are described (13); they are useful (a) in defining surface helical regions of membrane and water-soluble proteins and (b) in assigning the side of these helixes that are exposed to the solvent. A unifying view of protein structure suggests that water-soluble proteins may be considered as modified membrane proteins with covalently attached polar groups that solubilize the proteins in aqueous solution

Introduction of Vegetative and Reproductive Characters into Trifolium Repens by Interspecific Hybridisation

Interspecific hybridization between white clover (Trifolium repens L.) and ball clover (T.nigrescens) and Caucasian clover (T.ambiguum) is a means of improving the reproductive growth and persistency of T.repens. F1 hybrids between T.repens and T.nigrescens were produced without ovule culture and confirmed as true hybrids by chromosome counts, isoenzyme analysis and leaf markers. Their growth habit was generally intermediate between the two parents. After backcrossing to T.repens the BC1 and BC2 hybrids had more of the characteristics associated with T.repens though they retained some of the greater reproductive growth of T.nigrescens. Hybrids between T.repens and T.ambiguum were produced using ovule culture. Two F1 seedlings were produced with a morphology intermediate to the two parents. 35 BC1 seedlings were produced with a similar morphology to the F1 but with less of the T.ambiguum growth habit. The BC2 population showed greater variability in the expression of characters from Caucasian clover and contained only 10% of plants with the combined stoloniferous and rhizomatous habit. The implications for improving the growth of T.repens by interspecific hybridization are discussed