XML-structured documents: Retrievable units and inheritance

We consider the retrieval of XML-structured documents, and of passages from such documents, defined as elements of the XML structure. These are considered from the point of view of passage retrieval, as a form of document retrieval. A retrievable unit (an element chosen as defining suitable passages for retrieval) is a textual document in its own right, but may inherit information from the other parts of the same document. Again, this inheritance is defined in terms of the XML structure. All retrievable units are mapped onto a common field structure, and the ranking function is a standard document retrieval function with a suitable field weighting. A small experiment to demonstrate the idea, using INEX data, is described

A Golf Programme for People with Severe and Enduring Mental Health Problems

This article reports a pioneering golf programme for people with severe and enduring mental health problems. Following a discussion of the problems and possibilities of golf as a form of physical activity for this group, we outline the structure, organisation, and ethos of the golf programme. Through an analysis of qualitative case study data collected during the programme, we discuss the response to the programme from service users and mental health professionals. We conclude by highlighting aspects of the programme which were critical to its success and offering suggestions for further initiatives in this area

Non-equilibrium stationary state of a two-temperature spin chain

A kinetic one-dimensional Ising model is coupled to two heat baths, such that spins at even (odd) lattice sites experience a temperature $T_{e}$ ($$). Spin flips occur with Glauber-type rates generalised to the case of two temperatures. Driven by the temperature differential, the spin chain settles into a non-equilibrium steady state which corresponds to the stationary solution of a master equation. We construct a perturbation expansion of this master equation in terms of the temperature difference and compute explicitly the first two corrections to the equilibrium Boltzmann distribution. The key result is the emergence of additional spin operators in the steady state, increasing in spatial range and order of spin products. We comment on the violation of detailed balance and entropy production in the steady state.Comment: 11 pages, 1 figure, Revte

Ensemble prediction for nowcasting with a convection-permitting model—I: description of the system and the impact of radar-derived surface precipitation rates

A key strategy to improve the skill of quantitative predictions of precipitation, as well as hazardous weather such as severe thunderstorms and flash floods is to exploit the use of observations of convective activity (e.g. from radar). In this paper, a convection-permitting ensemble prediction system (EPS) aimed at addressing the problems of forecasting localized weather events with relatively short predictability time scale and based on a 1.5 km grid-length version of the Met Office Unified Model is presented. Particular attention is given to the impact of using predicted observations of radar-derived precipitation intensity in the ensemble transform Kalman filter (ETKF) used within the EPS. Our initial results based on the use of a 24-member ensemble of forecasts for two summer case studies show that the convective-scale EPS produces fairly reliable forecasts of temperature, horizontal winds and relative humidity at 1 h lead time, as evident from the inspection of rank histograms. On the other hand, the rank histograms seem also to show that the EPS generates too much spread for forecasts of (i) surface pressure and (ii) surface precipitation intensity. These may indicate that for (i) the value of surface pressure observation error standard deviation used to generate surface pressure rank histograms is too large and for (ii) may be the result of non-Gaussian precipitation observation errors. However, further investigations are needed to better understand these findings. Finally, the inclusion of predicted observations of precipitation from radar in the 24-member EPS considered in this paper does not seem to improve the 1-h lead time forecast skill

Strong Coupling of Localized Surface Plasmons to Excitons in Light-Harvesting Complexes

Gold nanostructure arrays exhibit surface plasmon resonances that split after attaching light harvesting complexes 1 and 2 (LH1 and LH2) from purple bacteria. The splitting is attributed to strong coupling between the localized surface plasmon resonances and excitons in the light-harvesting complexes. Wild-type and mutant LH1 and LH2 from Rhodobacter sphaeroides containing different carotenoids yield different splitting energies, demonstrating that the coupling mechanism is sensitive to the electronic states in the light harvesting complexes. Plasmon-exciton coupling models reveal different coupling strengths depending on the molecular organization and the protein coverage, consistent with strong coupling. Strong coupling was also observed for self-assembling polypeptide maquettes that contain only chlorins. However, it is not observed for monolayers of bacteriochlorophyll, indicating that strong plasmon-exciton coupling is sensitive to the specific presentation of the pigment molecules

Associative memory storing an extensive number of patterns based on a network of oscillators with distributed natural frequencies in the presence of external white noise

We study associative memory based on temporal coding in which successful retrieval is realized as an entrainment in a network of simple phase oscillators with distributed natural frequencies under the influence of white noise. The memory patterns are assumed to be given by uniformly distributed random numbers on $[0,2\pi)$ so that the patterns encode the phase differences of the oscillators. To derive the macroscopic order parameter equations for the network with an extensive number of stored patterns, we introduce the effective transfer function by assuming the fixed-point equation of the form of the TAP equation, which describes the time-averaged output as a function of the effective time-averaged local field. Properties of the networks associated with synchronization phenomena for a discrete symmetric natural frequency distribution with three frequency components are studied based on the order parameter equations, and are shown to be in good agreement with the results of numerical simulations. Two types of retrieval states are found to occur with respect to the degree of synchronization, when the size of the width of the natural frequency distribution is changed.Comment: published in Phys. Rev.

HER2 testing in breast cancer: Opportunities and challenges

Human epidermal growth factor receptor 2 (HER2) is overexpressed in 15-25% of breast cancers, usually as a result of HER2 gene amplification. Positive HER2 status is considered to be an adverse prognostic factor. Recognition of the role of HER2 in breast cancer growth has led to the development of anti-HER2 directed therapy, with the humanized monoclonal antibody trastuzumab (Herceptin (R)) having been approved for the therapy of HER2-positive metastatic breast cancer. Clinical studies have further suggested that HER2 status can provide important information regarding success or failure of certain hormonal therapies or chemotherapies. As a result of these developments, there has been increasing demand to perform HER2 testing on current and archived breast cancer specimens. This article reviews the molecular background of HER2 function, activation and inhibition as well as current opinions concerning its role in chemosensitivity and interaction with estrogen receptor biology. The different tissue-based assays used to detect HER2 amplification and overexpression are discussed with respect to their advantages and disadvantages, when to test (at initial diagnosis or pre-treatment), where to test (locally or centralized) and the need for quality assurance to ensure accurate and valid testing results

Crystal nucleation and growth of spherulites demonstrated by coral skeletons and phase-field simulations

Spherulites are radial distributions of acicular crystals, common in biogenic, geologic, and synthetic systems, yet exactly how spherulitic crystals nucleate and grow is still poorly understood. To investigate these processes in more detail, we chose scleractinian corals as a model system, because they are well known to form their skeletons from aragonite (CaCO3) spherulites, and because a comparative study of crystal structures across coral species has not been performed previously. We observed that all 12 diverse coral species analyzed here exhibit plumose spherulites in their skeletons, with well-defined centers of calcification (CoCs), and crystalline fibers radiating from them. In 7 of the 12 species, we observed a skeletal structural motif not observed previously: randomly oriented, equant crystals, which we termed “sprinkles”. In Acropora pharaonis, these sprinkles are localized at the CoCs, while in 6 other species, sprinkles are either layered at the growth front (GF) of the spherulites, or randomly distributed. At the nano- and micro-scale, coral skeletons fill space as much as single crystals of aragonite. Based on these observations, we tentatively propose a spherulite formation mechanism in which growth front nucleation (GFN) of randomly oriented sprinkles, competition for space, and coarsening produce spherulites, rather than the previously assumed slightly misoriented nucleations termed “non-crystallographic branching”. Phase-field simulations support this mechanism, and, using a minimal set of thermodynamic parameters, are able to reproduce all of the microstructural variation observed experimentally in all of the investigated coral skeletons. Beyond coral skeletons, other spherulitic systems, from aspirin to semicrystalline polymers and chocolate, may also form according to the mechanism for spherulite formation proposed here. Statement of Significance: Understanding the fundamental mechanisms of spherulite nucleation and growth has broad ranging applications in the fields of metallurgy, polymers, food science, and pharmaceutical production. Using the skeletons of reef-building corals as a model system for investigating these processes, we propose a new spherulite growth mechanism that can not only explain the micro-structural diversity observed in distantly related coral species, but may point to a universal growth mechanism in a wide range of biologically and technologically relevant spherulitic materials systems

Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization

Citation: Benoit, I., Zhou, M. M., Duarte, A. V., Downes, D. J., Todd, R. B., Kloezen, W., . . . de Vries, R. P. (2015). Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization. Scientific Reports, 5(1), 1-13. https://doi.org/10.1038/srep13592Degradation of plant biomass to fermentable sugars is of critical importance for the use of plant materials for biofuels. Filamentous fungi are ubiquitous organisms and major plant biomass degraders. Single colonies of some fungal species can colonize massive areas as large as five soccer stadia. During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a major determinant of spatial gene expression in colonies of Aspergillus niger. We analyzed whole-genome gene expression in five concentric zones of 5-day-old colonies utilizing sugar beet pulp as a complex carbon source. Growth, protein production and secretion occurred throughout the colony. Genes involved in carbon catabolism were expressed uniformly from the centre to the periphery whereas genes encoding plant biomass degrading enzymes and nitrate utilization were expressed differentially across the colony. A combined adaptive response of carbon-catabolism and enzyme production to locally available monosaccharides was observed. Finally, our results demonstrate that A. niger employs different enzymatic tools to adapt its metabolism as it colonizes complex environments