Calibrating flood inundation models: methods for assessing model performance

Satellite observed data for flood events have been used to calibrate and validate flood inundation models, providing valuable information on the spatial extent of the flood. Improvements in the resolution of this satellite imagery have enabled indirect remote sensing of water levels by using an underlying LiDAR DEM to extract the water surface elevation at the flood margin. Further to comparison of the spatial extent, this now allows for direct comparison between modelled and observed water surface elevations. Using a 12.5m ERS-1 image of a flood event in 2006 on the River Dee, North Wales, UK, both of these data types are extracted and each assessed for their value in the calibration of flood inundation models. A LiDAR guided snake algorithm is used to extract an outline of the flood from the satellite image. From the extracted outline a binary grid of wet / dry cells is created at the same resolution as the model, using this the spatial extent of the modelled and observed flood can be compared using a measure of fit between the two binary patterns of flooding. Water heights are extracted using points at intervals of approximately 100m along the extracted outline, and the students T-test is used to compare modelled and observed water surface elevations. A LISFLOOD-FP model of the catchment is set up using LiDAR topographic data resampled to the 12.5m resolution of the satellite image, and calibration of the friction parameter in the model is undertaken using each of the two approaches. Comparison between the two approaches highlights the sensitivity of the spatial measure of fit to uncertainty in the observed data and the potential drawbacks of using the spatial extent when parts of the flood are contained by the topography.

Data assimilation for marine monitoring and prediction: The MERCATOR operational assimilation systems and the MERSEA developments

During the past 15 years, a number of initiatives have been undertaken at national level to develop ocean forecasting systems operating at regional and/or global scales. The co-ordination between these efforts has been organized internationally through the Global Ocean Data Assimilation Experiment (GODAE). The French MERCATOR project is one of the leading participants in GODAE. The MERCATOR systems routinely assimilate a variety of observations such as multi-satellite altimeter data, sea-surface temperature and in situ temperature and salinity profiles, focusing on high-resolution scales of the ocean dynamics. The assimilation strategy in MERCATOR is based on a hierarchy of methods of increasing sophistication including optimal interpolation, Kalman filtering and variational methods, which are progressively deployed through the Syst`eme d’Assimilation MERCATOR (SAM) series. SAM-1 is based on a reduced-order optimal interpolation which can be operated using ‘altimetry-only’ or ‘multi-data’ set-ups; it relies on the concept of separability, assuming that the correlations can be separated into a product of horizontal and vertical contributions. The second release, SAM-2, is being developed to include new features from the singular evolutive extended Kalman (SEEK) filter, such as three-dimensional, multivariate error modes and adaptivity schemes. The third one, SAM-3, considers variational methods such as the incremental four-dimensional variational algorithm. Most operational forecasting systems evaluated during GODAE are based on least-squares statistical estimation assuming Gaussian errors. In the framework of the EU MERSEA (Marine EnviRonment and Security for the European Area) project, research is being conducted to prepare the next-generation operational ocean monitoring and forecasting systems. The research effort will explore nonlinear assimilation formulations to overcome limitations of the current systems. This paper provides an overview of the developments conducted in MERSEA with the SEEK filter, the Ensemble Kalman filter and the sequential importance re-sampling filter.

High resolution photoacoustic overtone spectroscopy of monofluoroacetylene, HCCF, with a titanium:sapphire ring laser

Intracavity photoacoustic overtone spectrum of monofluoroacetylene, HCCF, has been recorded in the wave number region 10 750–14 500 cm−1 with a titanium:sapphire ring laser. The spectrum contains many dense vibration–rotation band systems which can be resolved with Doppler limited resolution. Altogether 58 individual overtone bands have been analyzed rotationally. Many of the observed bands show perturbations of which some have been attributed to anharmonic resonance interactions. A Fermi resonance model based on conventional rectilinear normal coordinate theory has been used to assign vibrationally bands from this work and from earlier studies. Many of the observed vibrational term values and rotational constants can be reproduced well with this model. The results show the importance of the Fermi resonance interactions at the high overtone excitations.

Synthesis of a systolic array genetic algorithm

The paper presents a design for a hardware genetic algorithm which uses a pipeline of systolic arrays. These arrays have been designed using systolic synthesis techniques which involve expressing the algorithm as a set of uniform recurrence relations. The final design divorces the fitness function evaluation from the hardware and can process chromosomes of different lengths, giving the design a generic quality. The paper demonstrates the design methodology by progressively re-writing a simple genetic algorithm, expressed in C code, into a form from which systolic structures can be deduced. This paper extends previous work by introducing a simplification to a previous systolic design for the genetic algorithm. The simplification results in the removal of 2N 2 + 4N cells and reduces the time complexity by 3N + 1 cycles.

The systolic array genetic algorithm, an example of systolic arrays as a reconfigurable design methodology

We advocate the use of systolic design techniques to create custom hardware for Custom Computing Machines. We have developed a hardware genetic algorithm based on systolic arrays to illustrate the feasibility of the approach. The architecture is independent of the lengths of chromosomes used and can be scaled in size to accommodate different population sizes. An FPGA prototype design can process 16 million genes per second.

The high-resolution infrared spectrum of HOF near 2700 cm-1: the ground and 2v2 states

The a/b hybrid-type ν1 fundamental and 2ν2 overtone bands of HOF were investigated by FTIR spectroscopy with a resolution close to 0.008 cm−1. Improved ground state parameters of HOF were determined from a merge of more than 3000 ground state combination differences formed from ν1 and previously measured ν2 transitions with the reported pure rotational lines. Excited state parameters of the v2 = 2 state, ν0 = 2686.924 6(1) and χ22 = −9.942 4(1) cm−1, were determined employing Watson's A-reduced Hamiltonian up to sixth order in I′ representation. The 2ν2 state was found to be unperturbed, the excited state parameters being closely related to those of ν2.

The seventh colloquium on high resolution molecular spectroscopy

This conference, held 14-18 September 1981, addressed many aspects of high resolution molecular spectroscopy. Measurement techniques for remotely identifying trace gases in the atmosphere were discussed. Instrumentation for highly accurate and precise measurement of molecular emissions were described. The objective of the colloquium was to bring together molecular spectroscopists working in different regions of the electromagnetic spectrum from the ultraviolet to radio frequencies. These scientists shared a common interest in high resolution gas phase spectra and their analyses. The objective was met through the presentation of about 20 invited papers and many more contributed papers.

Time patterns in UK demand for alcohol and tobacco: an application of the EM algorithm

Capturing the pattern of structural change is a relevant task in applied demand analysis, as consumer preferences may vary significantly over time. Filtering and smoothing techniques have recently played an increasingly relevant role. A dynamic Almost Ideal Demand System with random walk parameters is estimated in order to detect modifications in consumer habits and preferences, as well as changes in the behavioural response to prices and income. Systemwise estimation, consistent with the underlying constraints from economic theory, is achieved through the EM algorithm. The proposed model is applied to UK aggregate consumption of alcohol and tobacco, using quarterly data from 1963 to 2003. Increased alcohol consumption is explained by a preference shift, addictive behaviour and a lower price elasticity. The dynamic and time-varying specification is consistent with the theoretical requirements imposed at each sample point. (c) 2005 Elsevier B.V. All rights reserved.

Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.

High throughput, high resolution selection of polymorphic microsatellite loci for multiplex analysis

Background Large-scale genetic profiling, mapping and genetic association studies require access to a series of well-characterised and polymorphic microsatellite markers with distinct and broad allele ranges. Selection of complementary microsatellite markers with non-overlapping allele ranges has historically proved to be a bottleneck in the development of multiplex microsatellite assays. The characterisation process for each microsatellite locus can be laborious and costly given the need for numerous, locus-specific fluorescent primers. Results Here, we describe a simple and inexpensive approach to select useful microsatellite markers. The system is based on the pooling of multiple unlabelled PCR amplicons and their subsequent ligation into a standard cloning vector. A second round of amplification utilising generic labelled primers targeting the vector and unlabelled locus-specific primers targeting the microsatellite flanking region yield allelic profiles that are representative of all individuals contained within the pool. Suitability of various DNA pool sizes was then tested for this purpose. DNA template pools containing between 8 and 96 individuals were assessed for the determination of allele ranges of individual microsatellite markers across a broad population. This helped resolve the balance between using pools that are large enough to allow the detection of many alleles against the risk of including too many individuals in a pool such that rare alleles are over-diluted and so do not appear in the pooled microsatellite profile. Pools of DNA from 12 individuals allowed the reliable detection of all alleles present in the pool. Conclusion The use of generic vector-specific fluorescent primers and unlabelled locus-specific primers provides a high resolution, rapid and inexpensive approach for the selection of highly polymorphic microsatellite loci that possess non-overlapping allele ranges for use in large-scale multiplex assays.

Use of a novel Hill-climbing genetic algorithm in protein folding simulations

We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide's backbone. The dihedral angles determining the chain's configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain's configuration is determined by its radius of gyration. A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 Angstrom with an optimised hydrophobic term in the fitness function. (C) 2003 Elsevier Ltd. All rights reserved.

Asymmetric synthesis of (1R,2S,3R)-3-methylcispentacin and (1S,2S,3R)-3-methyltranspentacin by kinetic resolution of tert-butyl (+/-)-3-methylcyclopentene-1-carboxylate

Conjugate addition of lithium dibenzylamide to tert-butyl (+/-)-3-methylcyclopentene-1-carboxylate occurs with high levels of stereocontrol, with preferential addition of lithium dibenzylamide to the face of the cyclic alpha,beta-unsaturated acceptor anti- to the 3-methyl substituent. High levels of enantiorecognition are observed between tert-butyl (+/-)-3-methylcyclopentene-1-carboxylate and an excess of lithium (+/-)-N-benzyl-N-alpha-methylbenzylamide (10 eq.) (E > 140) in their mutual kinetic resolution, while the kinetic resolution of tert-butyl (+/-)-3-methylcyclopentene-1-carboxylate with lithium (S)-N-benzyl-N-alpha-methylbenzylamide proceeds to give, at 51% conversion, tert-butyl (1R, 2S, 3R,alphaS)-3-methyl-2-N-benzyl-N-alpha-methylbenzylaminocyclopentane-1-c arboxylate consistent with E > 130, and in 39% yield and 99 +/- 0.5% de after purification. Subsequent deprotection by hydrogenolysis and ester hydrolysis gives (1R, 2S, 3R)-3-methylcispentacin in > 98% de and 98 +/- 1% ee. Selective epimerisation of tert-butyl (1R, 2S, 3R, alphaS)-3-methyl-2-N- benzyl-N-alpha-methylbenzylaminocyclopentane-1-carboxylate by treatment with (KOBu)-Bu-t in (BuOH)-Bu-t gives tert-butyl (1S, 2S, 3R, alphaS)-3-methyl-2-N-benzyl-N-alpha-methylbenzylaminocyclopentane-1-carb oxylate in quantitative yield and in > 98% de, with subsequent deprotection by hydrogenolysis and ester hydrolysis giving (1S, 2S, 3R)-3-methyltranspentacin hydrochloride in > 98% de and 97 +/- 1% ee.

High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications

A high-resolution crystal structure is reported for d(TpA)*, the intramolecular thymine-adenine photoadduct that is produced by direct ultraviolet excitation of the dinucleoside monophosphate d(TpA). It confirms the presence of a central 1,3-diazacyclooctatriene ring linking the remnants of the T and A bases, as previously deduced from heteronuclear NMR measurements by Zhao et al. (The structure of d(TpA)*, the major photoproduct of thymidylyl-(3'-5')-deoxyadenosine. Nucleic Acids Res., 1996, 24, 1554-1560). Within the crystal, the d(TpA)* molecules exist as zwitterions with a protonated amidine fragment of the eight-membered ring neutralizing the charge of the internucleotide phosphate monoanion. The absolute configuration at the original thymine C5 and C6 atoms is determined as 5S,6R. This is consistent with d(TpA)* arising by valence isomerization of a precursor cyclobutane photoproduct with cis-syn stereochemistry that is generated by [2 + 2] photoaddition of the thymine 5,6-double bond across the C6 and C5 positions of adenine. This mode of photoaddition should be favoured by the stacked conformation of adjacent T and A bases in B-form DNA. It is probable that the primary photoreaction is mechanistically analogous to pyrimidine dimerization despite having a much lower quantum yield.