Extracting predictive models from marked-p free-text documents at the Royal Botanic Gardens, Kew, London

In this paper we explore the combination of text-mining, un-supervised and supervised learning to extract predictive models from a corpus of digitised historical floras. These documents deal with the nomenclature, geographical distribution, ecology and comparative morphology of the species of a region. Here we exploit the fact that portions of text in the floras are marked up as different types of trait and habitat. We infer models from these different texts that can predict different habitat-types based upon the traits of plant species. We also integrate plant taxonomy data in order to assist in the validation of our models. We have shown that by clustering text describing the habitat of different floras we can identify a number of important and distinct habitats that are associated with particular families of species along with statistical significance scores. We have also shown that by using these discovered habitat-types as labels for supervised learning we can predict them based upon a subset of traits, identified using wrapper feature selection

Delineation of RAID1, the RACK1 interaction domain located within the unique N-terminal region of the cAMP-specific phosphodiesterase, PDE4D5

Background The cyclic AMP specific phosphodiesterase, PDE4D5 interacts with the β-propeller protein RACK1 to form a signaling scaffold complex in cells. Two-hybrid analysis of truncation and mutant constructs of the unique N-terminal region of the cAMP-specific phosphodiesterase, PDE4D5 were used to define a domain conferring interaction with the signaling scaffold protein, RACK1. Results Truncation and mutagenesis approaches showed that the RACK1-interacting domain on PDE4D5 comprised a cluster of residues provided by Asn-22/Pro-23/Trp-24/Asn-26 together with a series of hydrophobic amino acids, namely Leu-29, Val-30, Leu-33, Leu-37 and Leu-38 in a 'Leu-Xaa-Xaa-Xaa-Leu' repeat. This was done by 2-hybrid analyses and then confirmed in biochemical pull down analyses using GST-RACK1 and mutant PDE4D5 forms expressed in COS cells. Mutation of Arg-34, to alanine, in PDE4D5 attenuated its interaction with RACK1 both in 2-hybrid screens and in pull down analyses. A 38-mer peptide, whose sequence reflected residues 12 through 49 of PDE4D5, bound to RACK1 with similar affinity to native PDE4D5 itself (Ka circa 6 nM). Conclusions The RACK1 Interaction Domain on PDE4D5, that we here call RAID1, is proposed to form an amphipathic helical structure that we suggest may interact with the C-terminal β-propeller blades of RACK1 in a manner akin to the interaction of the helical G-γ signal transducing protein with the β-propeller protein, G-β

Pade-Improved Estimate of Perturbative Contributions to Inclusive Semileptonic b→ub\to u Decays

Pade-approximant methods are used to estimate the three-loop perturbative contributions to the inclusive semileptonic $b \to u$ decay rate. These improved estimates of the decay rate reduce the theoretical uncertainty in the extraction of the CKM matrix element $|V_{ub}|$ from the measured inclusive semileptonic branching ratio.Comment: 3 pages, latex, write-up of talk presented at DPF 200

Pade/renormalization-group improvement of inclusive semileptonic B decay rates

Renormalization Group (RG) and optimized Pade-approximant methods are used to estimate the three-loop perturbative contributions to the inclusive semileptonic b \to u and b \to c decay rates. It is noted that the \bar{MS} scheme works favorably in the b \to u case whereas the pole mass scheme shows better convergence in the b \to c case. Upon the inclusion of the estimated three-loop contribution, we find the full perturbative decay rate to be 192\pi^3\Gamma(b\to u\bar\nu_\ell\ell^-)/(G_F^2| V_{ub}|^2) = 2065 \pm 290{\rm GeV^5} and 192\pi^3\Gamma(b\to c\ell^-\bar\nu_\ell)/(G_F^2|V_{cb}|^2)= 992 \pm 198 {\rm GeV^5}, respectively. The errors are inclusive of theoretical uncertainties and non-perturbative effects. Ultimately, these perturbative contributions reduce the theoretical uncertainty in the extraction of the CKM matrix elements |V_{ub}| and |V_{cb}| from their respective measured inclusive semileptonic branching ratio(s).Comment: 3 pages, latex using espcrc2.sty. Write-up of talk given at BEACH 2002, UBC, Vancouve

The Arabidopsis Mediator complex subunits MED16, MED14 and MED2 regulate Mediator and RNA polymerase II recruitment to CBF-responsive cold-regulated genes

The Mediator16 (MED16; formerly termed SENSITIVE TO FREEZING6 [SFR6]) subunit of the plant Mediator transcriptional coactivator complex regulates cold-responsive gene expression in Arabidopsis thaliana, acting downstream of the C-repeat binding factor (CBF) transcription factors to recruit the core Mediator complex to cold-regulated genes. Here, we use loss-of-function mutants to show that RNA polymerase II recruitment to CBF-responsive cold-regulated genes requires MED16, MED2, and MED14 subunits. Transcription of genes known to be regulated via CBFs binding to the C-repeat motif/drought-responsive element promoter motif requires all three Mediator subunits, as does cold acclimation–induced freezing tolerance. In addition, these three subunits are required for low temperature–induced expression of some other, but not all, cold-responsive genes, including genes that are not known targets of CBFs. Genes inducible by darkness also required MED16 but required a different combination of Mediator subunits for their expression than the genes induced by cold. Together, our data illustrate that plants control transcription of specific genes through the action of subsets of Mediator subunits; the specific combination defined by the nature of the stimulus but also by the identity of the gene induced

Gearlike rolling motion mediated by commensurate contact: Carbon nanotubes on HOPG

We report on experiments in which multiwall carbon nanotubes (CNT's) are manipulated with atomic force microscopy (AFM) on a graphite highly oriented pyrolytic graphite (HOPG) substrate. We find certain discrete orientations in which the lateral force of manipulation dramatically increases as we rotate the CNT in the plane of the HOPG surface with the AFM tip. The threefold symmetry of these discrete orientations indicates commensurate contact of the hexagonal graphene surfaces of the HOPG and CNT. As the CNT moves into commensurate contact, we observe the motion change from sliding/rotating in-plane to stick-roll motion

Renormalization-Group Improvement of Effective Actions Beyond Summation of Leading Logarithms

Invariance of the effective action under changes of the renormalization scale $\mu$ leads to relations between those (presumably calculated) terms independent of $\mu$ at a given order of perturbation theory and those higher order terms dependent on logarithms of $\mu$. This relationship leads to differential equations for a sequence of functions, the solutions of which give closed form expressions for the sum of all leading logs, next to leading logs and subsequent subleading logarithmic contributions to the effective action. The renormalization group is thus shown to provide information about a model beyond the scale dependence of the model's couplings and masses. This procedure is illustrated using the $\phi_6^3$ model and Yang-Mills theory. In the latter instance, it is also shown by using a modified summation procedure that the $\mu$ dependence of the effective action resides solely in a multiplicative factor of $g^2 (\mu)$ (the running coupling). This approach is also shown to lead to a novel expansion for the running coupling in terms of the one-loop coupling that does not require an order-by-order redefinition of the scale factor $\Lambda_{QCD}$. Finally, logarithmic contributions of the instanton size to the effective action of an SU(2) gauge theory are summed, allowing a determination of the asymptotic dependence on the instanton size $\rho$ as $\rho$ goes to infinity to all orders in the SU(2) coupling constant.Comment: latex2e, 30 pages, 2 eps figures embedded in mansucript. v2 corrects several minor errors in equation

Incidence and risk factors for injury in non-elite netball.

This paper identifies the risk and protective factors for injury in non-elite netball. Three hundred and sixty eight non-elite netballers completed a baseline questionnaire at the commencement of the 1997 preseason. Participants were telephoned each month during the 1997 and 1998 playing seasons to provide details of their exposure at training and games and any injury experiences in the previous four weeks. The incidence of injury in this study was 14 injuries per 1000 player hours. The risk factors for injury were identified as: not warming up before a game (IRR 1.11, 95% CI 1.00 - 1.23) and not being open to new ideas (IRR 1.04, 95% CI 1.00 - 1.07). Training for four or more hours per week (IRR 0.66, 95% CI 0.45 - 0.98) and not sustaining an injury in the previous 12 months (IRR 0.58, 95% CI 0.43 - 0.79) were found to be protective against injury. The risk and protective factors for injury identified in this study can be used as the basis for the development of evidence-based injury prevention strategies that seek to reduce the risk of injury in sport. Injury prevention strategies should focus on the development of effective training programs that include netball-specific skills, activities and movements. Further investigation into the mechanisms associated with the risk and protective factors identified would provide further understanding of why these factors increase or decrease the risk of injury

On the selection of AGN neutrino source candidates for a source stacking analysis with neutrino telescopes

The sensitivity of a search for sources of TeV neutrinos can be improved by grouping potential sources together into generic classes in a procedure that is known as source stacking. In this paper, we define catalogs of Active Galactic Nuclei (AGN) and use them to perform a source stacking analysis. The grouping of AGN into classes is done in two steps: first, AGN classes are defined, then, sources to be stacked are selected assuming that a potential neutrino flux is linearly correlated with the photon luminosity in a certain energy band (radio, IR, optical, keV, GeV, TeV). Lacking any secure detailed knowledge on neutrino production in AGN, this correlation is motivated by hadronic AGN models, as briefly reviewed in this paper. The source stacking search for neutrinos from generic AGN classes is illustrated using the data collected by the AMANDA-II high energy neutrino detector during the year 2000. No significant excess for any of the suggested groups was found.Comment: 43 pages, 12 figures, accepted by Astroparticle Physic

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte