A text-mining system for extracting metabolic reactions from full-text articles

Background: Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway—metabolic pathways—has been largely neglected. Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein–protein interactions. Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task. Conclusions: We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein–protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed

Range imager performance comparison in homodyne and heterodyne operating modes

Range imaging cameras measure depth simultaneously for every pixel in a given field of view. In most implementations the basic operating principles are the same. A scene is illuminated with an intensity modulated light source and the reflected signal is sampled using a gain-modulated imager. Previously we presented a unique heterodyne range imaging system that employed a bulky and power hungry image intensifier as the high speed gain-modulation mechanism. In this paper we present a new range imager using an internally modulated image sensor that is designed to operate in heterodyne mode, but can also operate in homodyne mode. We discuss homodyne and heterodyne range imaging, and the merits of the various types of hardware used to implement these systems. Following this we describe in detail the hardware and firmware components of our new ranger. We experimentally compare the two operating modes and demonstrate that heterodyne operation is less sensitive to some of the limitations suffered in homodyne mode, resulting in better linearity and ranging precision characteristics. We conclude by showing various qualitative examples that demonstrate the system’s three-dimensional measurement performance

Accelerating vaccine development and deployment: report of a Royal Society satellite meeting.

The Royal Society convened a meeting on the 17th and 18th November 2010 to review the current ways in which vaccines are developed and deployed, and to make recommendations as to how each of these processes might be accelerated. The meeting brought together academics, industry representatives, research sponsors, regulators, government advisors and representatives of international public health agencies from a broad geographical background. Discussions were held under Chatham House rules. High-throughput screening of new vaccine antigens and candidates was seen as a driving force for vaccine discovery. Multi-stakeholder, small-scale manufacturing facilities capable of rapid production of clinical grade vaccines are currently too few and need to be expanded. In both the human and veterinary areas, there is a need for tiered regulatory standards, differentially tailored for experimental and commercial vaccines, to allow accelerated vaccine efficacy testing. Improved cross-fertilization of knowledge between industry and academia, and between human and veterinary vaccine developers, could lead to more rapid application of promising approaches and technologies to new product development. Identification of best-practices and development of checklists for product development plans and implementation programmes were seen as low-cost opportunities to shorten the timeline for vaccine progression from the laboratory bench to the people who need it

Alternative Buffer-Layers for the Growth of SrBi2Ta2O9 on Silicon

In this work we investigate the influence of the use of YSZ and CeO2/YSZ as insulators for Metal- Ferroelectric-Insulator-Semiconductor (MFIS) structures made with SrBi2Ta2O9 (SBT). We show that by using YSZ only the a-axis oriented Pyrochlore phase could be obtained. On the other hand the use of a CeO2/YSZ double-buffer layer gave a c-axis oriented SBT with no amorphous SiO2 inter- diffusion layer. The characteristics of MFIS diodes were greatly improved by the use of the double buffer. Using the same deposition conditions the memory window could be increased from 0.3 V to 0.9 V. From the piezoelectric response, nano-meter scale ferroelectric domains could be clearly identified in SBT thin films.Comment: 5 pages, 9 figures, 13 refernece

Mechanisms of burst release from pH-responsive polymeric microparticles.

Microencapsulation of drugs into preformed polymers is commonly achieved through solvent evaporation techniques or spray drying. We compared these encapsulation methods in terms of controlled drug release properties of the prepared microparticles and investigated the underlying mechanisms responsible for the “burst release” effect. Using two different pH-responsive polymers with a dissolution threshold of pH 6 (Eudragit L100 and AQOAT AS-MG), hydrocortisone, a model hydrophobic drug, was incorporated into microparticles below and above its solubility within the polymer matrix. Although, spray drying is an attractive approach due to rapid particle production and relatively low solvent waste, the oil-in-oil microencapsulation method is superior in terms of controlled drug release properties from the microparticles. Slow solvent evaporation during the oil-in-oil emulsification process allows adequate time for drug and polymer redistribution in the microparticles and reduces uncontrolled drug burst release. Electron microscopy showed that this slower manufacturing procedure generated non-porous particles whereas thermal analysis and X-ray diffractometry showed that drug loading above the solubility limit of the drug in the polymer generated excess crystalline drug on the surface of the particles. Raman spectral mapping illustrated that drug was homogeneously distributed as a solid solution in the particles when loaded below saturation in the polymer with consequently minimal burst release

Simulated Versus Observed Cluster Eccentricity Evolution

The rate of galaxy cluster eccentricity evolution is useful in understanding large scale structure. Rapid evolution for $z <$ 0.13 has been found in two different observed cluster samples. We present an analysis of projections of 41 clusters produced in hydrodynamic simulations augmented with radiative cooling and 43 clusters from adiabatic simulations. This new, larger set of simulated clusters strengthens the claims of previous eccentricity studies. We find very slow evolution in simulated clusters, significantly different from the reported rates of observational eccentricity evolution. We estimate the rate of change of eccentricity with redshift and compare the rates between simulated and observed clusters. We also use a variable aperture radius to compute the eccentricity, r$_{200}$. This method is much more robust than the fixed aperture radius used in previous studies. Apparently radiative cooling does not change cluster morphology on scales large enough to alter eccentricity. The discrepancy between simulated and observed cluster eccentricity remains. Observational bias or incomplete physics in simulations must be present to produce halos that evolve so differently.Comment: ApJ, in press, minor revision