The Dirichlet-to-Neumann map for the elliptic sine Gordon

We analyse the Dirichlet problem for the elliptic sine Gordon equation in the upper half plane. We express the solution $q(x,y)$ in terms of a Riemann-Hilbert problem whose jump matrix is uniquely defined by a certain function $b(\la)$, $\la\in\R$, explicitly expressed in terms of the given Dirichlet data $g_0(x)=q(x,0)$ and the unknown Neumann boundary value $g_1(x)=q_y(x,0)$, where $g_0(x)$ and $g_1(x)$ are related via the global relation $\{b(\la)=0$, $\la\geq 0\}$. Furthermore, we show that the latter relation can be used to characterise the Dirichlet to Neumann map, i.e. to express $g_1(x)$ in terms of $g_0(x)$. It appears that this provides the first case that such a map is explicitly characterised for a nonlinear integrable {\em elliptic} PDE, as opposed to an {\em evolution} PDE.

A genetic linkage map of an apple rootstock progeny anchored to the Malus genome sequence

An apple rootstock progeny raised from the cross between the very dwarfing ‘M.27’ and the more vigorous ‘M.116’ (‘M.M.106’ × ‘M.27’) was used for the construction of a linkage map comprising a total of 324 loci: 252 previously mapped SSRs, 71 newly characterised or previously unmapped SSR loci (including 36 amplified by 33 out of the 35 novel markers reported here), and the self-incompatibility locus. The map spanned the 17 linkage groups (LG) expected for apple covering a genetic distance of 1,229.5 cM, an estimated 91% of the Malus genome. Linkage groups were well populated and, although marker density ranged from 2.3 to 6.2 cM/SSR, just 15 gaps of more than 15 cM were observed. Moreover, only 17.5% of markers displayed segregation distortion and, unsurprisingly in a semi-compatible backcross, distortion was particularly pronounced surrounding the self-incompatibility locus (S) at the bottom of LG17. DNA sequences of 273 SSR markers and the S locus, representing a total of 314 loci in this investigation, were used to anchor to the ‘Golden Delicious’ genome sequence. More than 260 of these loci were located on the expected pseudo-chromosome on the ‘Golden Delicious’ genome or on its homeologous pseudo-chromosome. In total, 282.4 Mbp of sequence from 142 genome sequence scaffolds of the Malus genome were anchored to the ‘M.27’ × ‘M.116’ map, providing an interface between the marker data and the underlying genome sequence. This will be exploited for the identification of genes responsible for traits of agronomic importance such as dwarfing and water use efficiency.

A novel bogie design made of glass fibre reinforced plastic

This paper presents a completely new design of a bogie-frame made of glass fibre reinforced composites and its performance under various loading conditions predicted by finite element analysis. The bogie consists of two frames, with one placed on top of the other, and two axle ties connecting the axles. Each frame consists of two side arms and a transom between. The top frame is thinner and more compliant and has a higher curvature compared with the bottom frame. Variable vertical stiffness can be achieved before and after the contact between the two frames at the central section of the bogie to cope with different load levels. Finite element analysis played a very important role in the design of this structure. Stiffness and stress levels of the full scale bogie presented in this paper under various loading conditions have been predicted by using Marc provided by MSC Software. In order to verify the finite element analysis (FEA) models, a fifth scale prototype of the bogie has been made and tested under quasi-static loading conditions. Results of testing on the fifth scale bogie have been used to fine tune details like contact and friction in the fifth scale FEA models. These conditions were then applied to the full scale models. Finite element analysis results show that the stress levels in all directions are low compared with material strengths.

Rapid protein domain assignment from amino acid sequence using predicted secondary structure

The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (±20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed

Contact angle of a hemispherical bubble: an analytical approach

We have calculated the equilibrium shape of the axially symmetric Plateau border along which a spherical bubble contacts a flat wall, by analytically integrating Laplace’s equation in the presence of gravity, in the limit of small Plateau border sizes. This method has the advantage that it provides closed-form expressions for the positions and orientations of the Plateau border surfaces. Results are in very good overall agreement with those obtained from a numerical solution procedure, and are consistent with experimental data. In particular we find that the effect of gravity on Plateau border shape is relatively small for typical bubble sizes, leading to a widening of the Plateau border for sessile bubbles and to a narrowing for pendant bubbles. The contact angle of the bubble is found to depend even more weakly on gravity.

Chercher pour or chercher après: arguing the case for contact-induced linguistic innovation in different varieties of French

This paper provides evidence for the claim made in Baetens Beardsmore (1971) that the grammatical collocation "chercher après" «to look for», which is very frequent in Brussels French, is the result of transfer from the contact language, Brussels Dutch. A detailed quantitative analysis of this construction in different varieties of French which have more or less contact with a Germanic language was made to investigate the likelihood of influence from the Germanic substrate. The differences between the meaning of "chercher" and "chercher après" are also analysed in some depth, to find out whether or not the particle is redundant. According to Trudgill (2004) redundant constructions are more often found in contact situations involving long-term, stable contact and child bilingualism. The particle "après" was found to add a particular shade of meaning to "chercher", and is thus not redundant. Therefore no evidence could be obtained from the current data for Trudgill’s (2004) claim.

Borrowing and shift-induced interference: contrasting patterns in French-Germanic contact in Brussels and Strasbourg

The main aim of the present article is to test hypotheses derived from the model for contact- induced language change as formulated in Thomason and Kaufman (1988 et seq.). As the model correctly predicts the asymmetries between the mutual influences of the Germanic and the Romance varieties in Brussels and Strasbourg it is a very powerful tool for describing the contact patterns in these cities. The analysis shows that the contact patterns are very similar, both from a quantitative and from a qualitative point of view, despite important differences in the sociolinguistic situation of both cities. The striking similarities in the outcome of language contact seem to find a plausible explanation in the fact that the language contact situations in both cities are similar from a typological point of view: in each city a variety of French is in contact with a Germanic variety (Alsatian and Brussels Dutch). Thus, the claim of the present article is that the structure of the languages plays a more prominent role in the outcome of language contact than the sociolinguistic history of the speakers.

The role of transfer in language variation and change: Evidence from contact varieties of French

In this Special Issue, the focus is on contact-induced language variation and change in situations of societal bilingualism that involve long-term contact between French and another language. As is well known, when two or more languages are spoken by groups of speakers in the same geographical area, over time, features from one language can be transferred to the other language, especially when the languages in question are unequal in terms of prestige, institutional support and demographic factors. The process that leads to the adoption of such features in the contact languages is generally known as INTERFERENCE or TRANSFER, and these terms are also used to describe the features in question (i.e. the end product of the process of transfer). In this issue we prefer to use the term TRANSFER over the use of the notion INTERFERENCE, as the former has fewer negative connotations than the latter.

Effect of pH, temperature and surface contact on the elaboration of fimbriae and flagella by Salmonella serotype Enteritidis

Survival of enteric pathogens exposed to various environmental stresses depends upon a number of protective responses, some of which are associated with induction of virulence determinants. Flagella and fimbriae are putative virulence determinants of Salmonella spp, and ELISAs specific for the detection of flagella and SEF21, SEF14 and SEF17 fimbriae were used to assess the effect of temperature and pH upon their elaboration by isolates of Salmonella serotype Enteritidis in planktonic growth and on the surface of two-dimensional gradient agar plates, For three phage type 4 isolates of Enteritidis of comparative clinical provenance, similar phenotypes for the elaboration of these surface antigens were observed. SEF14 fimbriae were elaborated in planktonic growth at 37 degrees C, but not 20 degrees C, at pH 4.77 and above but not at pH 4.04; whereas on agar gradient plates SEF14 fimbriae were elaborated poorly but with best yields at pH 4.04, SEF17 fimbriae were elaborated in planktonic growth at 20 degrees C, but not at 37 degrees C, at pH 6.18 and above but not at pH 5.09 or below; whereas on agar gradient plates SEF17 fimbriae were elaborated well even at pH 4.65, SEF21 fimbriae were expressed very poorly under all conditions tested, Planktonic growth at 37 degrees C induced least flagella whereas growth at 20 degrees C, and particularly surface growth at lower pH values, induced a 'hyper-flagellate' phenotype, Single colonies allowed to form on gradient agar plates were shown to generate different colonial morphologies which were dependent on initial pH. These results demonstrate that the physicochemical environment is an important determinant of bacterial response, especially the induction of putative virulence factors.

Co-ordinate single-cell expression of LEE4- and LEE5-encoded proteins of Escherichia coli O157:H7

Escherichia coli O157:H7 is a zoonotic pathogen that can express a type III secretion system (TTSS) considered important for colonization and persistence in ruminants. E. coli O157:H7 strains have been shown to vary markedly in levels of protein secreted using the TTSS and this study has confirmed that a high secretion phenotype is more prevalent among isolates associated with human disease than isolates shed by healthy cattle. The variation in secretion levels is a consequence of heterogeneous expression, being dependent on the proportion of bacteria in a population that are actively engaged in protein secretion. This was demonstrated by indirect immunofluorescence and eGFP fusions that examined the expression of locus of enterocyte effacement (LEE)-encoded factors in individual bacteria. In liquid media, the expression of EspA, tir::egfp, intimin, but not map::egfp were co-ordinated in a subpopulation of bacteria. In contrast to E. coli O157:H7, expression of tir::egfp in EPEC E2348/69 was equivalent in all bacteria although the same fusion exhibited variable expression when transformed into an E. coli O157:H7 background. An E. coli O157:H7 strain deleted for the LEE demonstrated weak but variable expression of tir::egfp indicating that the elements controlling the heterogeneous expression lie outside the LEE. The research also demonstrated the rapid induction of tir::egfp and map::egfp on contact with bovine epithelial cells. This control in E. coli O157:H7 may be required to limit exposure of key surface antigens, EspA, Tir and intimin during colonization of cattle but allow their rapid production on contact with bovine gastrointestinal epithelium at the terminal rectum.

The integration of proteomics and systems approaches to map regulatory mechanisms underpinning platelet function.

Platelets in the circulation are triggered by vascular damage to activate, aggregate and form a thrombus that prevents excessive blood loss. Platelet activation is stringently regulated by intracellular signalling cascades, which when activated inappropriately lead to myocardial infarction and stroke. Strategies to address platelet dysfunction have included proteomics approaches which have lead to the discovery of a number of novel regulatory proteins of potential therapeutic value. Global analysis of platelet proteomes may enhance the outcome of these studies by arranging this information in a contextual manner that recapitulates established signalling complexes and predicts novel regulatory processes. Platelet signalling networks have already begun to be exploited with interrogation of protein datasets using in silico methodologies that locate functionally feasible protein clusters for subsequent biochemical validation. Characterization of these biological systems through analysis of spatial and temporal organization of component proteins is developing alongside advances in the proteomics field. This focused review highlights advances in platelet proteomics data mining approaches that complement the emerging systems biology field. We have also highlighted nucleated cell types as key examples that can inform platelet research. Therapeutic translation of these modern approaches to understanding platelet regulatory mechanisms will enable the development of novel anti-thrombotic strategies.

Estimating root–soil contact from 3D X-ray microtomographs

Adequate contact with the soil is essential for water and nutrient adsorption by plant roots, but the determination of root–soil contact is a challenging task because it is difficult to visualize roots in situ and quantify their interactions with the soil at the scale of micrometres. A method to determine root–soil contact using X-ray microtomography was developed. Contact areas were determined from 3D volumetric images using segmentation and iso-surface determination tools. The accuracy of the method was tested with physical model systems of contact between two objects (phantoms). Volumes, surface areas and contact areas calculated from the measured phantoms were compared with those estimated from image analysis. The volume was accurate to within 0.3%, the surface area to within 2–4%, and the contact area to within 2.5%. Maize and lupin roots were grown in soil (<2 mm) and vermiculite at matric potentials of −0.03 and −1.6 MPa and in aggregate fractions of 4–2, 2–1, 1–0.5 and < 0.5 mm at a matric potential of −0.03 MPa. The contact of the roots with their growth medium was determined from 3D volumetric images. Macroporosity (>70 µm) of the soil sieved to different aggregate fractions was calculated from binarized data. Root-soil contact was greater in soil than in vermiculite and increased with decreasing aggregate or particle size. The differences in root–soil contact could not be explained solely by the decrease in porosity with decreasing aggregate size but may also result from changes in particle and aggregate packing around the root.

The induction of mental and contact contamination

Background: Extreme fear of contamination within Obsessive Compulsive Disorder is traditionally conceptualised as a physical phenomenon. More recent research has supported the notion of ‘mental’ contamination, in which people feel contaminated in the absence of physical contact. The current research sought to determine whether feelings of contact and mental contamination could be induced within a non-clinical sample, whether the impact of mental and contact contamination was comparable in terms of associated feelings and behaviour and whether related psychopathology related to the impact of the tasks. Methods: Undergraduate students (n=60) completed OCD relevant measures and were randomly assigned to either a contact contamination condition (CC: moving a bucket of fake vomit) or a mental contamination condition (MC: thinking about a bucket of vomit). Results: Both manipulations induced feelings of contamination. Participants in the contact condition had significantly greater urges to wash than those in the mental condition. Neutralising behaviour did not differ across conditions. Conclusions: Feelings of contamination can be induced in the absence of physical contact and for those in the MC group, some aspects of OCD-relevant psychopathology were related to the impact of the manipulation. These findings have implications for the understanding and treatment of contamination-related fears in OCD.

A Web Map Service implementation for the visualization of multidimensional gridded environmental data

We describe ncWMS, an implementation of the Open Geospatial Consortium’s Web Map Service (WMS) specification for multidimensional gridded environmental data. ncWMS can read data in a large number of common scientific data formats – notably the NetCDF format with the Climate and Forecast conventions – then efficiently generate map imagery in thousands of different coordinate reference systems. It is designed to require minimal configuration from the system administrator and, when used in conjunction with a suitable client tool, provides end users with an interactive means for visualizing data without the need to download large files or interpret complex metadata. It is also used as a “bridging” tool providing interoperability between the environmental science community and users of geographic information systems. ncWMS implements a number of extensions to the WMS standard in order to fulfil some common scientific requirements, including the ability to generate plots representing timeseries and vertical sections. We discuss these extensions and their impact upon present and future interoperability. We discuss the conceptual mapping between the WMS data model and the data models used by gridded data formats, highlighting areas in which the mapping is incomplete or ambiguous. We discuss the architecture of the system and particular technical innovations of note, including the algorithms used for fast data reading and image generation. ncWMS has been widely adopted within the environmental data community and we discuss some of the ways in which the software is integrated within data infrastructures and portals.

Contributions of roots and rootstocks to sustainable, intensified crop production

Sustainable intensification is seen as the main route for meeting the world’s increasing demands for food and fibre. As demands mount for greater efficiency in the use of resources to achieve this goal, so the focus on roots and rootstocks and their role in acquiring water and nutrients, and overcoming pests and pathogens, is increasing. The purpose of this review is to explore some of the ways in which understanding root systems and their interactions with soils could contribute to the development of more sustainable systems of intensive production. Physical interactions with soil particles limit root growth if soils are dense, but root–soil contact is essential for optimal growth and uptake of water and nutrients. X-ray microtomography demonstrated that maize roots elongated more rapidly with increasing root–soil contact, as long as mechanical impedance was not limiting root elongation, while lupin was less sensitive to changes in root–soil contact. In addition to selecting for root architecture and rhizosphere properties, the growth of many plants in cultivated systems is profoundly affected by selection of an appropriate rootstock. Several mechanisms for scion control by rootstocks have been suggested, but the causal signals are still uncertain and may differ between crop species. Linkage map locations for quantitative trait loci for disease resistance and other traits of interest in rootstock breeding are becoming available. Designing root systems and rootstocks for specific environments is becoming a feasible target.