U.K. HiGEM: The New U.K. High-Resolution Global Environment Model—Model Description and Basic Evaluation

This article describes the development and evaluation of the U.K.’s new High-Resolution Global Environmental Model (HiGEM), which is based on the latest climate configuration of the Met Office Unified Model, known as the Hadley Centre Global Environmental Model, version 1 (HadGEM1). In HiGEM, the horizontal resolution has been increased to 0.83° latitude × 1.25° longitude for the atmosphere, and 1/3° × 1/3° globally for the ocean. Multidecadal integrations of HiGEM, and the lower-resolution HadGEM, are used to explore the impact of resolution on the fidelity of climate simulations. Generally, SST errors are reduced in HiGEM. Cold SST errors associated with the path of the North Atlantic drift improve, and warm SST errors are reduced in upwelling stratocumulus regions where the simulation of low-level cloud is better at higher resolution. The ocean model in HiGEM allows ocean eddies to be partially resolved, which dramatically improves the representation of sea surface height variability. In the Southern Ocean, most of the heat transports in HiGEM is achieved by resolved eddy motions, which replaces the parameterized eddy heat transport in the lower-resolution model. HiGEM is also able to more realistically simulate small-scale features in the wind stress curl around islands and oceanic SST fronts, which may have implications for oceanic upwelling and ocean biology. Higher resolution in both the atmosphere and the ocean allows coupling to occur on small spatial scales. In particular, the small-scale interaction recently seen in satellite imagery between the atmosphere and tropical instability waves in the tropical Pacific Ocean is realistically captured in HiGEM. Tropical instability waves play a role in improving the simulation of the mean state of the tropical Pacific, which has important implications for climate variability. In particular, all aspects of the simulation of ENSO (spatial patterns, the time scales at which ENSO occurs, and global teleconnections) are much improved in HiGEM.

Microbial perchlorate reduction: A precise laboratory determination of the chlorine isotope fractionation and its possible biochemical basis

Perchlorate-reducing bacteria fractionate chlorine stable isotopes giving a powerful approach to monitor the extent of microbial consumption of perchlorate in contaminated sites undergoing remediation or natural perchlorate containing sites. This study reports the full experimental data and methodology used to re-evaluate the chlorine isotope fractionation of perchlorate reduction in duplicate culture experiments of Azospira suillum strain PS at 37 degrees C (Delta Cl-37(Cr)--ClO4-) previously reported, without a supporting data set by Coleman et al. [Coleman, M.L., Ader, M., Chaudhuri, S., Coates,J.D., 2003. Microbial Isotopic Fractionation of Perchlorate Chlorine. Appl. Environ. Microbiol. 69, 4997-5000] in a reconnaissance study, with the goal of increasing the accuracy and precision of the isotopic fractionation determination. The method fully described here for the first time, allows the determination of a higher precision Delta Cl-37(Cl)--ClO4- value, either from accumulated chloride content and isotopic composition or from the residual perchlorate content and isotopic composition. The result sets agree perfectly, within error, giving average Delta Cl-37(Cl)--ClO4- = -14.94 +/- 0.15%omicron. Complementary use of chloride and perchlorate data allowed the identification and rejection of poor quality data by applying mass and isotopic balance checks. This precise Delta Cl-37(Cl)--ClO4-, value can serve as a reference point for comparison with future in situ or microcosm studies but we also note its similarity to the theoretical equilibrium isotopic fractionation between a hypothetical chlorine species of redox state +6 and perchlorate at 37 degrees C and suggest that the first electron transfer during perchlorate reduction may occur at isotopic equilibrium between art enzyme-bound chlorine and perchlorate. (C) 2008 Elsevier B.V. All rights reserved.

A simple model for predicting soil temperature in snow-covered and seasonally frozen soil: model description and testing

Microbial processes in soil are moisture, nutrient and temperature dependent and, consequently, accurate calculation of soil temperature is important for modelling nitrogen processes. Microbial activity in soil occurs even at sub-zero temperatures so that, in northern latitudes, a method to calculate soil temperature under snow cover and in frozen soils is required. This paper describes a new and simple model to calculate daily values for soil temperature at various depths in both frozen and unfrozen soils. The model requires four parameters average soil thermal conductivity, specific beat capacity of soil, specific heat capacity due to freezing and thawing and an empirical snow parameter. Precipitation, air temperature and snow depth (measured or calculated) are needed as input variables. The proposed model was applied to five sites in different parts of Finland representing different climates and soil types. Observed soil temperatures at depths of 20 and 50 cm (September 1981-August 1990) were used for model calibration. The calibrated model was then tested using observed soil temperatures from September 1990 to August 2001. R-2-values of the calibration period varied between 0.87 and 0.96 at a depth of 20 cm and between 0.78 and 0.97 at 50 cm. R-2 -values of the testing period were between 0.87 and 0.94 at a depth of 20cm. and between 0.80 and 0.98 at 50cm. Thus, despite the simplifications made, the model was able to simulate soil temperature at these study sites. This simple model simulates soil temperature well in the uppermost soil layers where most of the nitrogen processes occur. The small number of parameters required means, that the model is suitable for addition to catchment scale models.

A pattern language for goals

Previous work has established the value of goal-oriented approaches to requirements engineering. Achieving clarity and agreement about stakeholders’ goals and assumptions is critical for building successful software systems and managing their subsequent evolution. In general, this decision-making process requires stakeholders to understand the implications of decisions outside the domains of their own expertise. Hence it is important to support goal negotiation and decision making with description languages that are both precise and expressive, yet easy to grasp. This paper presents work in progress to develop a pattern language for describing goal refinement graphs. The language has a simple graphical notation, which is supported by a prototype editor tool, and a symbolic notation based on modal logic.

Vibration–rotation variational calculations: precise results on HCN up to 25 000 cm−1

Variation calculations of the vibration–rotation energy levels of many isotopomers of HCN are reported, for J=0, 1, and 2, extending up to approximately 8 quanta of each of the stretching vibrations and 14 quanta of the bending mode. The force field, which is represented as a polynomial expansion in Morse coordinates for the bond stretches and even powers of the angle bend, has been refined by least squares to fit simultaneously all observed data on the Σ and Π state vibrational energies, and the Σ state rotational constants, for both HCN and DCN. The observed vibrational energies are fitted to roughly ±0.5 cm−1, and the rotational constants to roughly ±0.0001 cm−1. The force field has been used to predict the vibration rotation spectra of many isotopomers of HCN up to 25 000 cm−1. The results are consistent with the axis‐switching assignments of some weak overtone bands reported recently by Jonas, Yang, and Wodtke, and they also fit and provide the assignment for recent observations by Romanini and Lehmann of very weak absorption bands above 20 000 cm−1.

Variational calculations of rovibrational states: a precise high-energy potential surface for HCN [and discussion]

We report the results of variational calculations of the rovibrational energy levels of HCN for J = 0, 1 and 2, where we reproduce all the ca. 100 observed vibrational states for all observed isotopic species, with energies up to 18000 cm$^{-1}$, to about $\pm $1 cm$^{-1}$, and the corresponding rotational constants to about $\pm $0.001 cm$^{-1}$. We use a hamiltonian expressed in internal coordinates r$_{1}$, r$_{2}$ and $\theta $, using the exact expression for the kinetic energy operator T obtained by direct transformation from the cartesian representation. The potential energy V is expressed as a polynomial expansion in the Morse coordinates y$_{i}$ for the bond stretches and the interbond angle $\theta $. The basis functions are built as products of appropriately scaled Morse functions in the bond-stretches and Legendre or associated Legendre polynomials of cos $\theta $ in the angle bend, and we evaluate matrix elements by Gauss quadrature. The hamiltonian matripx is factorized using the full rovibrational symmetry, and the basis is contracted to an optimized form; the dimensions of the final hamiltonian matrix vary from 240 $\times $ 240 to 1000 $\times $ 1000.We believe that our calculation is converged to better than 1 cm$^{-1}$ at 18 000 cm$^{-1}$. Our potential surface is expressed in terms of 31 parameters, about half of which have been refined by least squares to optimize the fit to the experimental data. The advantages and disadvantages and the future potential of calculations of this type are discussed.

Evaluation of NRC, UC Davis and ADAS approaches to estimate the metabolizable energy values of feeds at maintenance energy intake from equations utilizing chemical assays and in vitro determinations

Feed samples received by commercial analytical laboratories are often undefined or mixed varieties of forages, originate from various agronomic or geographical areas of the world, are mixtures (e.g., total mixed rations) and are often described incompletely or not at all. Six unified single equation approaches to predict the metabolizable energy (ME) value of feeds determined in sheep fed at maintenance ME intake were evaluated utilizing 78 individual feeds representing 17 different forages, grains, protein meals and by-product feedstuffs. The predictive approaches evaluated were two each from National Research Council [National Research Council (NRC), Nutrient Requirements of Dairy Cattle, seventh revised ed. National Academy Press, Washington, DC, USA, 2001], University of California at Davis (UC Davis) and ADAS (Stratford, UK). Slopes and intercepts for the two ADAS approaches that utilized in vitro digestibility of organic matter and either measured gross energy (GE), or a prediction of GE from component assays, and one UC Davis approach, based upon in vitro gas production and some component assays, differed from both unity and zero, respectively, while this was not the case for the two NRC and one UC Davis approach. However, within these latter three approaches, the goodness of fit (r(2)) increased from the NRC approach utilizing lignin (0.61) to the NRC approach utilizing 48 h in vitro digestion of neutral detergent fibre (NDF:0.72) and to the UC Davis approach utilizing a 30 h in vitro digestion of NDF (0.84). The reason for the difference between the precision of the NRC procedures was the failure of assayed lignin values to accurately predict 48 h in vitro digestion of NDF. However, differences among the six predictive approaches in the number of supporting assays, and their costs, as well as that the NRC approach is actually three related equations requiring categorical description of feeds (making them unsuitable for mixed feeds) while the ADAS and UC Davis approaches are single equations, suggests that the procedure of choice will vary dependent Upon local conditions, specific objectives and the feedstuffs to be evaluated. In contrast to the evaluation of the procedures among feedstuffs, no procedure was able to consistently discriminate the ME values of individual feeds within feedstuffs determined in vivo, suggesting that the quest for an accurate and precise ME predictive approach among and within feeds, may remain to be identified. (C) 2004 Elsevier B.V. All rights reserved.

The genus Borassus (Arecaceae) in West Africa, with a description of a new species from Burkina Faso

Borassus akeassii Bayton, Ouedraogo & Guinko sp. nov. (Arecaceae) is described as a new species from western Burkina Faso in West Africa. It has been confused with the widely distributed African species B. aethiopum and more recently with the Asian B. flabellifer. However, it is distinguished by its glaucous, green leaves with weakly armed petioles and a characteristic pattern of lamina venation. The fruits have a pointed apex and are greenish when ripe, and the flowers of the pistillate inflorescence are arranged in three spirals. The pollen has a reticulate tectum and distinctive ornamentation. The distribution of B. akeassii is discussed and the status of the varieties of Borassus aethiopum (var. bagamojensis and var. senegalensis) is examined. (c) 2006 The Linnean Society of London.

Synthesis, spectroscopic and redox properties of some ruthenium(II) thiosemicarbazone complexes: structural description of four of these complexes

Sixteen neutral mixed ligand thiosemicarbazone complexes of ruthenium having general formula [Ru(PPh3)(2)L-2], where LH = 1-(arylidine)4-aryl thiosemicarbazones, have been synthesized and characterized. All complexes are diamagnetic and hence ruthenium is in the +2 oxidation state (low-spin d(6), S = 0). The complexes show several intense peaks in the visible region due to allowed metal to ligand charge transfer transitions. The structures of four of the complexes have been determined by single-crystal X-ray diffraction and they show that thiosemicarbazone ligands coordinate to the ruthenium center through the hydrazinic nitrogen and sulfur forming four-membered chelate rings with ruthenium in N2S2P2 coordination environment. In dichloromethane solution, the complexes show two quasi-reversible oxidative responses corresponding to loss of electron from HOMO and HOMO - 1. The E-0 values of the above two oxidations shows good linear relationship with Hammett substituents constant (sigma) as well as with the HOMO energy of the molecules calculated by the EHMO method. A DFT calculation on one representative complex suggests that there is appreciable contribution of the sulfur p-orbitals to the HOMO and HOMO - 1. Thus, assignment of the oxidation state of the metal in such complexes must be made with caution. (c) 2005 Elsevier B.V. All rights reserved.

Formate-dependent growth and homoacetogenic fermentation by a bacterium from human feces: Description of Bryantella formatexigens gen. nov., sp nov.

Formate stimulates growth of a new bacterium from human feces. With high formate, it ferments glucose to acetate via the Wood-Ljungdahl pathway. The original isolate fermented vegetable cellulose and carboxymethylcellulose, but it lost this ability after storage at -76degreesC. 16S rRNA gene sequencing identifies it as a distinct line within the Clostridium coccoides supra-generic rRNA grouping. We propose naming it Bryantella formatexigens gen. nov., sp. nov.

Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a New Genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp nov., from human sources

During studies on the bacteriology of appendicitis in children, we often isolated from inflamed and non-inflamed tissue samples, an unusual bile-resistant pigment-producing strictly anaerobic gram-negative rod. Phenotypically this organism resembles members of Bacteroides fragilis group of species, as it is resistant to bile and exhibits a special-potency-disk pattern (resistance to vancomycin, kanamycin and colistin) typical for the B. fragilis group. However, the production of brown pigment on media containing haemolysed blood and a cellular fatty acid composition dominated by iso-C15:0, suggests that the organism most closely resembles species of the genus Porphyromonas. However, the unidentified organism differs from porphyromonads by being bile-resistant and by not producing butyrate as a metabolic end-product. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism represents a distinct sub-line, associated with but distinct from, the miss-classified species Bacteroides putredinis. The clustering of the unidentified bacterium with Bacteroides putredinis was statistically significant, but they displayed >4% sequence divergence with each other. Chromosomal DNA-DNA pairing studies further confirmed the separateness of the unidentified bacterium and Bacteroides putredinis. Based on phenotypic and phylogenetic considerations, it is proposed that Bacteroides putredinis and the unidentified bacterium from human sources be classified in a new genus Alistipes, as Alistipes putredinis comb. nov. and Alistipes finegoldii sp. nov., respectively. The type strain of Alistipes finegoldii is CCUG 46020(T) (= AHN2437(T)).