Anyone for non-scalarity?

This paper examines the status of scalarity in the analysis of the meaning of the English determiner any. The latter’s position as a prime exemplar of the category of polarity-sensitive items has led it to be generally assumed to have scalar meaning. Scalar effects are absent however from a number of common uses of this word. This suggests that any does not involve scales as part of its core meaning, but produces them as a derived interpretative property. The role of three factors in the derivation of the expressive effect of scalarity is explored: grammatical number, stress and the presence of gradable concepts in the NP. The general conclusions point to the importance of developing a causal semantic analysis in which the contributions of each of the various meaningful components of an utterance to the overall message expressed are carefully distinguished.

Identifying and correcting non-Markov states in peptide conformational dynamics

Conformational transitions in proteins define their biological activity and can be investigated in detail using the Markov state model. The fundamental assumption on the transitions between the states, their Markov property, is critical in this framework. We test this assumption by analyzing the transitions obtained directly from the dynamics of a molecular dynamics simulated peptide valine-proline-alanine-leucine and states defined phenomenologically using clustering in dihedral space. We find that the transitions are Markovian at the time scale of ˜ 50 ps and longer. However, at the time scale of 30–40 ps the dynamics loses its Markov property. Our methodology reveals the mechanism that leads to non-Markov behavior. It also provides a way of regrouping the conformations into new states that now possess the required Markov property of their dynamics.

Discriminating antigen and non-antigen using proteome dissimilarity III:tumour and parasite antigens

Computational genome analysis enables systematic identification of potential immunogenic proteins within a pathogen. Immunogenicity is a system property that arises through the interaction of host and pathogen as mediated through the medium of a immunogenic protein. The overt dissimilarity of pathogenic proteins when compared to the host proteome is conjectured by some to be the determining principal of immunogenicity. Previously, we explored this idea in the context of Bacterial, Viral, and Fungal antigen. In this paper, we broaden and extend our analysis to include complex antigens of eukaryotic origin, arising from tumours and from parasite pathogens. For both types of antigen, known antigenic and non-antigenic protein sequences were compared to human and mouse proteomes. In contrast to our previous results, both visual inspection and statistical evaluation indicate a much wider range of homologues and a significant level of discrimination; but, as before, we could not determine a viable threshold capable of properly separating non-antigen from antigen. In concert with our previous work, we conclude that global proteome dissimilarity is not a useful metric for immunogenicity for presently available antigens arising from Bacteria, viruses, fungi, parasites, and tumours. While we see some signal for certain antigen types, using dissimilarity is not a useful approach to identifying antigenic molecules within pathogen genomes.

Case Comment : Challenging the validity of leasehold guarantees:undue influence, non-est factum and formality issues

Case: Beardsley Theobalds Retirement Benefit Scheme Trustees v Yardley [2011] EWHC 1380 (QB) (QBD). The recent case of Beardsley Theobalds Retirement Benefit Scheme Trustees v Yardley, nicely illustrates, inter alia, the impact of the contractual defences of undue influence and the plea of non est factum in the context of avoiding liability under leasehold guarantees, within the setting of the landlord and tenant relationship. Additionally, the case also gives us an insight into the possible application of other technical defences relating to the law of formalities for leases. Judgment in this case was handed down on September 30, 2011.