Enhancements in reservoir flood risk mapping: example application for Ulley

In July 2007, at Ulley Reservoir, South Yorkshire, a catastrophic dam failure was narrowly avoided due to emergency preventative actions. During the event, a number of homes were evacuated and roads were closed for precautionary measures. Within very close proximity of the reservoir lies the town of Rotherham, the busy M1 motorway and a trunk freight railway line. The incident highlights the need for detailed flood risk and hazard modelling to improve management of the risk and better incident planning.Hazards and population vary in both time and space, but when traditionally modelling flood risk, the population are invariably located within the residential housing stock. This paper innovatively combines flood inundation and spatio-temporal population modelling for better estimates of the population potentially at risk. This is demonstrated though application to Ulley for the most probable worst case failure scenario should the preventative measures not have been undertaken and the dam have failed.This paper proposes an enhanced flood risk assessment in three stages: (i) probabilistic modelling of a failure scenario using embankment breach models; (ii) hydrodynamic inundation modelling for assessment of flood water spreading, depths and velocities; (iii) spatio-temporal population modelling to assess the risk to the population likely to be present. The combination with spatio-temporal population outputs aims to demonstrate the enhancements achievable in reservoir flood risk mapping when vulnerable populations are concerned

Alginate hydrogel has a negative impact on in vitro collagen 1 deposition by fibroblasts

Hydrogels have been widely investigated as 3D culture substrates because of their reported structural similarity to the extracellular matrix (ECM). Limited ECM deposition, however, occurs within these materials, so the resulting “tissues” bear little resemblance to those found in the body. Here matrix deposition by fibroblasts encapsulated within a calcium alginate (Ca-alg) hydrogel was investigated. Although the cells transcribed mRNA for coll Iα over a period of 3 weeks, very little collagen protein deposition was observed within the gel by histology or immunohistochemistry (IHC). Although molecular diffusion demonstrated charge dependency, this did not prevent the flux of both positively and negative charged amino acids through the gel, suggesting that the absence of ECM could not be attributed to substrate limitation. The flux of protein, however, was charge-dependent as proteins with a net negative charge passed quickly through the Ca-alg into the medium. The minimal collagen deposition within the Ca-alg was attributed to a combination of rapid movement of negatively charged procollagen through the gel and steric hindrance of fibril formation

Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes

Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured bacteria are known to degrade crystalline cellulose, little is known of the polysaccharide hydrolases expressed by cellulose-degrading microbial communities, particularly in the marine environment. Next generation 454 Pyrosequencing was applied to analyze the microbial community that colonizes and degrades insoluble polysaccharides in situ in the Irish Sea. The bioinformatics tool MG-RAST was used to examine the randomly sampled data for taxonomic markers and functional genes, and showed that the community was dominated by members of the Gammaproteobacteria and Bacteroidetes. Furthermore, the identification of 211 gene sequences matched to a custom-made database comprising the members of nine glycoside hydrolase families revealed an extensive repertoire of functional genes predicted to be involved in cellulose utilization. This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. The research reported here is the first designed to specifically address the bacterial communities that colonize and degrade cellulose in the marine environment and to evaluate the glycoside hydrolase (cellulase and chitinase) gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques

Ontology and the Future of Dental Research Informatics.

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR)

Infrared Lightcurves of Near Earth Objects

We present lightcurves and derive periods and amplitudes for a subset of 38 near earth objects (NEOs) observed at 4.5 microns with the IRAC camera on the the Spitzer Space Telescope, many of them having no previously reported rotation periods. This subset was chosen from about 1800 IRAC NEO observations as having obvious periodicity and significant amplitude. For objects where the period observed did not sample the full rotational period, we derived lower limits to these parameters based on sinusoidal fits. Lightcurve durations ranged from 42 to 544 minutes, with derived periods from 16 to 400 minutes. We discuss the effects of lightcurve variations on the thermal modeling used to derive diameters and albedos from Spitzer photometry. We find that both diameters and albedos derived from the lightcurve maxima and minima agree with our previously published results, even for extreme objects, showing the conservative nature of the thermal model uncertainties. We also evaluate the NEO rotation rates, sizes, and their cohesive strengths.Comment: 16 pages, 4 figures, 3 tables, to appear in the Astrophysical Journal Supplement Serie

A domain ontology for the non-coding RNA field

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology

The Discovery of Cometary Activity in Near-Earth Asteroid (3552) Don Quixote

The near-Earth object (NEO) population, which mainly consists of fragments from collisions between asteroids in the main asteroid belt, is thought to include contributions from short-period comets as well. One of the most promising NEO candidates for a cometary origin is near-Earth asteroid (3552) Don Quixote, which has never been reported to show activity. Here we present the discovery of cometary activity in Don Quixote based on thermal-infrared observations made with the Spitzer Space Telescope in its 3.6 and 4.5 {\mu}m bands. Our observations clearly show the presence of a coma and a tail in the 4.5 {\mu}m but not in the 3.6 {\mu}m band, which is consistent with molecular band emission from CO2. Thermal modeling of the combined photometric data on Don Quixote reveals a diameter of 18.4 (-0.4/+0.3) km and an albedo of 0.03 (-0.01/+0.02), which confirms Don Quixote to be the third-largest known NEO. We derive an upper limit on the dust production rate of 1.9 kg s^-1 and derive a CO2 gas production rate of (1.1+-0.1)10^26 molecules s^-1. Spitzer IRS spectroscopic observations indicate the presence of fine-grained silicates, perhaps pyroxene rich, on the surface of Don Quixote. Our discovery suggests that CO2 can be present in near-Earth space over a long time. The presence of CO2 might also explain that Don Quixote's cometary nature remained hidden for nearly three decades.Comment: 40 pages, 8 figures, accepted by Ap

The Non-Coding RNA Ontology : a comprehensive resource for the unification of non-coding RNA biology

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users