A question-answering system using argumentation

This paper presents a novel approach to question answering: the use of argumentation techniques. Our question answering system deals with argumentation in student essays: it sees an essay as an answer to a question and gauges its quality on the basis of the argumentation found in it. Thus, the system looks for expected types of argumentation in essays (i.e. the expectation is that the kind of argumentation in an essay is correlated to the type of question). Another key feature of our work is our proposed categorisation for argumentation in student essays, as opposed to categorisation of argumentation in research papers, where - unlike the case of student essays - it is relatively well-known which kind of argumentation can be found in specific sections

On-shelf transport of slope water lenses within the seasonal pycnocline

We show that discrete lenses of anomalously high-salinity water, originating from the shelf edge and trapped within the seasonal pycnocline, are advected 100 km or more onto the Celtic Sea continental shelf. We propose that the lenses are created by increased diapycnal mixing at the shelf edge associated with breaking high-frequency internal wave packets. Quasi-synoptic hydrography sections show the lenses to be 3–5 km wide, their temporal persistence confirmed by moored instrumentation and a series of CTD casts. Estimates of the propagation speed of these features (∼0.020 m s−1) compare favorably with the magnitude of observed residual currents. Residual current variability within the pycnocline is dominated by vertical structures most consistent with the second baroclinic mode. The residual flow is therefore thought to be predominantly driven by non-linear second mode internal tidal waves. These are observations of a shelf edge exchange process not previously identified

Changes in turbulent mixing shift competition for light between phytoplankton species

The intriguing impact of physical mixing processes on species interactions has always fascinated ecologists. Here, we exploit recent advances in plankton models to develop competition theory that predicts how changes in turbulent mixing affect competition for light between buoyant and sinking phytoplankton species. We compared the model predictions with a lake experiment, in which the turbulence structure of the entire lake was manipulated using artificial mixing. Vertical eddy diffusivities were calculated from the measured temperature microstructure in the lake. Changes in turbulent mixing of the lake caused a dramatic shift in phytoplankton species composition, consistent with the predictions of the competition model. The buoyant and potentially toxic cyanobacterium Microcystis dominated at low turbulent diffusivity, whereas sinking diatoms and green algae dominated at high turbulent diffusivity. These findings warn that changes in the turbulence structure of natural waters, for instance driven by climate change, may induce major shifts in the species composition of phytoplankton communities

The C-terminus of the phage λ Orf recombinase is involved in DNA binding

Phage λ Orf substitutes for the activities of the Escherichia coli RecFOR proteins in vivo and is therefore implicated as a recombination mediator, encouraging the assembly of bacterial RecA onto single-stranded DNA (ssDNA) coated with SSB. Orf exists as a dimer in solution, associates with E. coli SSB and binds preferentially to ssDNA. To help identify interacting domains we analysed Orf and SSB proteins carrying mutations or truncations in the C-terminal region. A cluster of acidic residues at the carboxy-terminus of SSB is known to attract multiple protein partners to assist in DNA replication and repair. In this case an alternative domain must be utilized since Orf association with SSB was unaffected by an SSB113 point mutant (P176S) or removal of the last ten residues (ΔC10). Structurally the Orf C-terminus consists of a helix with a flexible tail that protrudes from each side of the dimer and could serve as a binding site for either SSB or DNA. Eliminating the six residue flexible tail (ΔC6) or the entire helix (ΔC19) had no significant impact on the Orf–SSB interaction. However, the OrfΔC6 protein exhibited reduced DNA binding, a feature shared by single amino acid substitutions within (W141F) or adjacent (R140A) to this region. The OrfΔC19 mutant bound poorly to DNA and secondary structure analysis in solution revealed that this truncation induces protein misfolding and aggregation. The results show that the carboxy-terminus of Orf is involved in nucleic acid recognition and also plays an unexpected role in maintaining structural integrity

The ring of the rhodopsin chromophore in a hydrophobic activation switch within the binding pocket.

Contains fulltext : 57945.pdf (publisher's version ) (Closed access)The current view that the beta-ionone ring of the rhodopsin chromophore vacates its binding pocket within the protein early in the photocascade has been adopted in efforts to provide structural models of photoreceptor activation. This event casts doubt on the ability of this covalently bonded ligand to participate directly in later stages involving activation of the photoreceptor and it is difficult to translate into predictions for the activation of related G protein-coupled receptors by diffusable ligands (e.g. neurotransmitters). The binding pocket fixes the formally equivalent pair of ring methyl groups (C16/C17) in different orientations that can be distinguished easily by (13)C NMR. Solid-state NMR observations on C16 and C17 are reported here that show instead that the ring is retained with strong selective interactions within the binding site into the activated state. We further show how increased steric interactions for this segment in the activated receptor can be explained by adjustment in the protein structure around the ring whilst it remains in its original location. This describes a plausible role for the ring in operating a hydrophobic switch from within the aromatic cluster of helix 6 of rhodopsin, which is coupled to electronic changes within the receptor through water-mediated, hydrogen-bonded networks between the conserved residues in G protein-coupled receptors

Phage Orf family recombinases: conservation of activities and involvement of the central channel in DNA binding

Genetic and biochemical evidence suggests that λ Orf is a recombination mediator, promoting nucleation of either bacterial RecA or phage Redβ recombinases onto single-stranded DNA (ssDNA) bound by SSB protein. We have identified a diverse family of Orf proteins that includes representatives implicated in DNA base flipping and those fused to an HNH endonuclease domain. To confirm a functional relationship with the Orf family, a distantly-related homolog, YbcN, from Escherichia coli cryptic prophage DLP12 was purified and characterized. As with its λ relative, YbcN showed a preference for binding ssDNA over duplex. Neither Orf nor YbcN displayed a significant preference for duplex DNA containing mismatches or 1-3 nucleotide bulges. YbcN also bound E. coli SSB, although unlike Orf, it failed to associate with an SSB mutant lacking the flexible C-terminal tail involved in coordinating heterologous protein-protein interactions. Residues conserved in the Orf family that flank the central cavity in the λ Orf crystal structure were targeted for mutagenesis to help determine the mode of DNA binding. Several of these mutant proteins showed significant defects in DNA binding consistent with the central aperture being important for substrate recognition. The widespread conservation of Orf-like proteins highlights the importance of targeting SSB coated ssDNA during lambdoid phage recombination