Sterically controlled recognition of macromolecular sequence information by molecular tweezers

Sequence-specific binding is demonstrated between pyrene-based tweezer molecules and soluble, high molar mass copolyimides. The binding involves complementary pi - pi stacking interactions, polymer chain-folding, and hydrogen bonding and is extremely sensitive to the steric environment around the pyromellitimide binding-site. A detailed picture of the intermolecular interactions involved has been obtained through single-crystal X-ray studies of tweezer complexes with model diimides. Ring-current magnetic shielding of polyimide protons by the pyrene '' arms '' of the tweezer molecule induces large complexation shifts of the corresponding H-1 NMR resonances, enabling specific triplet sequences to be identified by their complexation shifts. Extended comonomer sequences (triplets of triplets in which the monomer residues differ only by the presence or absence of a methyl group) can be '' read '' by a mechanism which involves multiple binding of tweezer molecules to adjacent diimide residues within the copolymer chain. The adjacent-binding model for sequence recognition has been validated by two conceptually different sets of tweezer binding experiments. One approach compares sequence-recognition events for copolyimides having either restricted or unrestricted triple-triplet sequences, and the other makes use of copolymers containing both strongly binding and completely nonbinding diimide residues. In all cases the nature and relative proportions of triple-triplet sequences predicted by the adjacent-binding model are fully consistent with the observed H-1 NMR data.

Identifying problematic classes in text classification

Real-world text classification tasks often suffer from poor class structure with many overlapping classes and blurred boundaries. Training data pooled from multiple sources tend to be inconsistent and contain erroneous labelling, leading to poor performance of standard text classifiers. The classification of health service products to specialized procurement classes is used to examine and quantify the extent of these problems. A novel method is presented to analyze the labelled data by selectively merging classes where there is not enough information for the classifier to distinguish them. Initial results show the method can identify the most problematic classes, which can be used either as a focus to improve the training data or to merge classes to increase confidence in the predicted results of the classifier.

Surveillance camera calibration from observations of a pedestrian

Calibrated cameras are an extremely useful resource for computer vision scenarios. Typically, cameras are calibrated through calibration targets, measurements of the observed scene, or self-calibrated through features matched between cameras with overlapping fields of view. This paper considers an approach to camera calibration based on observations of a pedestrian and compares the resulting calibration to a commonly used approach requiring that measurements be made of the scene.

High frequency scattering by convex curvilinear polygons

We consider the scattering of a time-harmonic acoustic incident plane wave by a sound soft convex curvilinear polygon with Lipschitz boundary. For standard boundary or finite element methods, with a piecewise polynomial approximation space, the number of degrees of freedom required to achieve a prescribed level of accuracy grows at least linearly with respect to the frequency of the incident wave. Here we propose a novel Galerkin boundary element method with a hybrid approximation space, consisting of the products of plane wave basis functions with piecewise polynomials supported on several overlapping meshes; a uniform mesh on illuminated sides, and graded meshes refined towards the corners of the polygon on illuminated and shadow sides. Numerical experiments suggest that the number of degrees of freedom required to achieve a prescribed level of accuracy need only grow logarithmically as the frequency of the incident wave increases.

Non-word repetition in adolescents with Specific Language Impairment and Autism plus Language Impairments: a qualitative analysis

Non-word repetition (NWR) was investigated in adolescents with typical development, Specific Language Impairment (SLI) and Autism Plus language Impairment (ALI) (n = 17, 13, 16, and mean age 14;4, 15;4, 14;8 respectively). The study evaluated the hypothesis that poor NWR performance in both groups indicates an overlapping language phenotype (Kjelgaard & Tager-Flusberg, 2001). Performance was investigated both quantitatively, e.g. overall error rates, and qualitatively, e.g. effect of length on repetition, proportion of errors affecting phonological structure, and proportion of consonant substitutions involving manner changes. Findings were consistent with previous research (Whitehouse, Barry, & Bishop, 2008) demonstrating a greater effect of length in the SLI group than the ALI group, which may be due to greater short-term memory limitations. In addition, an automated count of phoneme errors identified poorer performance in the SLI group than the ALI group. These findings indicate differences in the language profiles of individuals with SLI and ALI, but do not rule out a partial overlap. Errors affecting phonological structure were relatively frequent, accounting for around 40% of phonemic errors, but less frequent than straight Consonant-for-Consonant or vowel-for-vowel substitutions. It is proposed that these two different types of errors may reflect separate contributory mechanisms. Around 50% of consonant substitutions in the clinical groups involved manner changes, suggesting poor auditory-perceptual encoding. From a clinical perspective algorithms which automatically count phoneme errors may enhance sensitivity of NWR as a diagnostic marker of language impairment. Learning outcomes: Readers will be able to (1) describe and evaluate the hypothesis that there is a phenotypic overlap between SLI and Autism Spectrum Disorders (2) describe differences in the NWR performance of adolescents with SLI and ALI, and discuss whether these differences support or refute the phenotypic overlap hypothesis, and (3) understand how computational algorithms such as the Levenshtein Distance may be used to analyse NWR data.

Gene expression profiling of human hibernating myocardium: Increased expression of B-type natriuretic peptide and proenkephalin in hypocontractile vs normally-contracting regions of the heart

A greater understanding of the molecular basis of hibernating myocardium may assist in identifying those patients who would most benefit from revascularization. Paired heart biopsies were taken from hypocontractile and normally-contracting myocardium (identified by cardiovascular magnetic resonance) from 6 patients with chronic stable angina scheduled for bypass grafting. Gene expression profiles of hypocontractile and normally-contracting samples were compared using Affymetrix microarrays. The data for patients with confirmed hibernating myocardium were analysed separately and a different, though overlapping, set (up to 380) of genes was identified which may constitute a molecular fingerprint for hibernating myocardium. The expression of B-type natriuretic peptide (BNP) was increased in hypocontractile relative to normally-contracting myocardium. The expression of BNP correlated most closely with the expression of proenkephalin and follistatin 3, which may constitute additional heart failure markers. Our data illustrate differential gene expression in hypocontractile and/hibernating myocardium relative to normally-contracting myocardium within individual human hearts. Changes in expression of these genes, including increased relative expression of natriuretic and other factors, may constitute a molecular signature for hypocontractile and/or hibernating myocardium.

Innovation in facilities management: from trajectories to ownership

Purpose – Innovation in facilities management (FM) is a complex process as FM is a diverse discipline. This paper aims to use innovation trajectories to explore this complex process through the introduction of a technology innovation in two FM services of security and workspace management. It also aims to consider the discourse of individuals within their trajectory to understand their positions toward the innovation. Design/methodology/approach – A two-year case study was conducted and it was based in an in-house FM department that was part of a financial institution. The specific methods used for the paper were semi-structured interviews with key participants of the project. Critical discourse analysis was used to examine the data. Findings – Individuals who were involved in introducing the technology to the FM department were both internal and external to FM as innovation in FM does not happen in isolation to the organisation. Innovation trajectories were often intertwined or occurred simultaneously during the process of a project which sometimes resulted in conflict. Tensions within the discourse of ownership of the project were particularly apparent as this discourse had a power dimension in driving the project through to implementation. Research limitations/implications – The research is limited by being a single case study so it is not possible to generalise findings but the findings may have resonances with other organisations. Originality/value – The paper presents an original idea about how to understand innovation processes in FM services.

A specific group of genes respond to cold dehydration stress in cut Alstroemeria flowers whereas ambient dehydration stress accelerates developmental senescence expression patterns

Petal development and senescence entails a normally irreversible process. It starts with petal expansion and pigment production, and ends with nutrient remobilization and ultimately cell death. In many species this is accompanied by petal abscission. Post-harvest stress is an important factor in limiting petal longevity in cut flowers and accelerates some of the processes of senescence such as petal wilting and abscission. However, some of the effects of moderate stress in young flowers are reversible with appropriate treatments. Transcriptomic studies have shown that distinct gene sets are expressed during petal development and senescence. Despite this, the overlap in gene expression between developmental and stress-induced senescence in petals has not been fully investigated in any species. Here a custom-made cDNA microarray from Alstroemeria petals was used to investigate the overlap in gene expression between developmental changes (bud to first sign of senescence) and typical post-harvest stress treatments. Young flowers were stressed by cold or ambient temperatures without water followed by a recovery and rehydration period. Stressed flowers were still at the bud stage after stress treatments. Microarray analysis showed that ambient dehydration stress accelerates many of the changes in gene expression patterns that would normally occur during developmental senescence. However, a higher proportion of gene expression changes in response to cold stress were specific to this stimulus and not senescence related. The expression of 21 transcription factors was characterized, showing that overlapping sets of regulatory genes are activated during developmental senescence and by different stresses.

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution.

Dynamic Niche Clustering: a fuzzy variable radius niching technique for multimodal optimisation in GAs

This paper describes the recent developments and improvements made to the variable radius niching technique called Dynamic Niche Clustering (DNC). DNC is fitness sharing based technique that employs a separate population of overlapping fuzzy niches with independent radii which operate in the decoded parameter space, and are maintained alongside the normal GA population. We describe a speedup process that can be applied to the initial generation which greatly reduces the complexity of the initial stages. A split operator is also introduced that is designed to counteract the excessive growth of niches, and it is shown that this improves the overall robustness of the technique. Finally, the effect of local elitism is documented and compared to the performance of the basic DNC technique on a selection of 2D test functions. The paper is concluded with a view to future work to be undertaken on the technique.

A variable radius niching technique for speciation in genetic algorithms

In this paper, a continuation of a variable radius niche technique called Dynamic Niche Clustering developed by (Gan & Warwick, 1999) is presented. The technique employs a separate dynamic population of overlapping niches that coexists alongside the normal population. An empirical analysis of the updated methodology on a large group of standard optimisation test-bed functions is also given. The technique is shown to perform almost as well as standard fitness sharing with regards to stability and the accuracy of peak identification, but it outperforms standard fitness sharing with regards to time complexity. It is also shown that the technique is capable of forming niches of varying size depending on the characteristics of the underlying peak that the niche is populating.

Plutarch's 'Lives' and the critical reader

This paper analyses the kind of reader constructed in the Lives and the response expected of that reader. It begins by attempting a typology of moralising in the Lives. Plutarch does sometimes make general 'gnomic' statements about right and wrong, and occasionally passes explicit judgement on a subject's behaviour. In addition, the language with which Plutarch describes character is inherently moralistic; and even when he does not pass explicit judgment, Plutarch can rely on a common set of notions about what makes behaviour virtuous or vicious. However, the application of any moral lessons is left to the reader's own judgement. Furthermore, Plutarch's use of multiple focalisations means that the reader is sometimes presented with varying ways of looking at the same individual or the same historical situation. In addition, many incidents or anecdotes are marked by 'multivalence': that is, they resist reduction to a single moral message or lesson. In such cases, the reader is encouraged to exercise his or her own critical faculties. Indeed, the prologues which precede many pairs of Lives and the synkriseis which follow them sometimes explicitly invite the reader's participation in the work of judging. The syncritic structure of the Parallel Lives also invites the reader's participation, as do the varying perspectives provided by a corpus of overlapping Lives. In fact, the presence of a critical, engaged reader is presupposed by the agonistic nature of much of Greek literature, and of several texts in the Moralia which stage opposing viewpoints or arguments. Plutarch himself argues for such a reader in his How the young man should listen to poems.

The interaction of flexural-gravity waves with periodic geometries

A periodic structure of finite extent is embedded within an otherwise uniform two-dimensional system consisting of finite-depth fluid covered by a thin elastic plate. An incident harmonic flexural-gravity wave is scattered by the structure. By using an approximation to the corresponding linearised boundary value problem that is based on a slowly varying structure in conjunction with a transfer matrix formulation, a method is developed that generates the whole solution from that for just one cycle of the structure, providing both computational savings and insight into the scattering process. Numerical results show that variations in the plate produce strong resonances about the ‘Bragg frequencies’ for relatively few periods. We find that certain geometrical variations in the plate generate these resonances above the Bragg value, whereas other geometries produce the resonance below the Bragg value. The familiar resonances due to periodic bed undulations tend to be damped by the plate.

Construction management strategies : a theory of construction management

The construction industry has become a truly global network of interconnected stakeholders making demands which require the involvement of skilled workforces from all over the world. Construction Management Strategies sets the foundations for understanding and managing construction’s inherent complexity and uniqueness. It establishes clear definitions of commonly accepted terms like built environment, construction, civil engineering, etc. which are often given confusing and conflicting interpretations. It cuts through the plethora of overlapping role titles currently used in the construction sector that make it difficult to establish how projects are actually managed.

Provincialism and the modern diaspora: T.S. Eliot and David Jones

This article considers how T. S. Eliot's promotion of the work of the Anglo-Welsh poet David Jones after the Second World War further involved him in a process of considering the resonances of the local and familiar as operative within the displacements of modernity. This promotion therefore retrospectively prioritized an aspect of Eliot's poetics which had been present, but occluded, all along. Conversely, the article considers how similar resonances in Jones's own work were enhanced by his encounter with Eliot's translation of the Francophone Caribbean poet St-John Perse's Anabase, an encounter which enabled Jones to establish an idiom responsive to the divergent cultural affinities inherent in ‘our situation’.