Influence-matrix diagnostic of a data assimilation system

The influence matrix is used in ordinary least-squares applications for monitoring statistical multiple-regression analyses. Concepts related to the influence matrix provide diagnostics on the influence of individual data on the analysis - the analysis change that would occur by leaving one observation out, and the effective information content (degrees of freedom for signal) in any sub-set of the analysed data. In this paper, the corresponding concepts have been derived in the context of linear statistical data assimilation in numerical weather prediction. An approximate method to compute the diagonal elements of the influence matrix (the self-sensitivities) has been developed for a large-dimension variational data assimilation system (the four-dimensional variational system of the European Centre for Medium-Range Weather Forecasts). Results show that, in the boreal spring 2003 operational system, 15% of the global influence is due to the assimilated observations in any one analysis, and the complementary 85% is the influence of the prior (background) information, a short-range forecast containing information from earlier assimilated observations. About 25% of the observational information is currently provided by surface-based observing systems, and 75% by satellite systems. Low-influence data points usually occur in data-rich areas, while high-influence data points are in data-sparse areas or in dynamically active regions. Background-error correlations also play an important role: high correlation diminishes the observation influence and amplifies the importance of the surrounding real and pseudo observations (prior information in observation space). Incorrect specifications of background and observation-error covariance matrices can be identified, interpreted and better understood by the use of influence-matrix diagnostics for the variety of observation types and observed variables used in the data assimilation system. Copyright © 2004 Royal Meteorological Society

Origin and evolution of 3'UTR of flaviviruses: long direct repeats as a basis for the formation of secondary structures and their significance for virus transmission

The 3' untranslated regions (3'UTRs) of flaviviruses are reviewed and analyzed in relation to short sequences conserved as direct repeats (DRs). Previously, alignments of the 3'UTRs have been constructed for three of the four recognized flavivirus groups, namely mosquito-borne, tick-borne, and nonclassified flaviviruses (MBFV, TBFV, and NCFV, respectively). This revealed (1) six long repeat sequences (LRSs) in the 3'UTR and open-reading frame (ORF) of the TBFV, (2) duplication of the 3'UTR of the NCFV by intramolecular recombination, and (3) the possibility of a common origin for all DRs within the MBFV. We have now extended this analysis and review it in the context of all previous published analyses. This has been achieved by constructing a robust alignment between all flaviviruses using the published DRs and secondary RNA structures as "anchors" to reveal additional homologies along the 3'UTR. This approach identified nucleotide regions within the MBFV, NKV (no-known vector viruses), and NCFV 3'UTRs that are homologous to different LRSs in the TBFV 3'UTR and ORF. The analysis revealed that some of the DRs and secondary RNA structures described individually within each flavivirus group share common evolutionary origins. The 3'UTR of flaviviruses, and possibly the ORF, therefore probably evolved through multiple duplication of an RNA domain, homologous to the LRS previously identified only in the TBFV. The short DRs in all virus groups appear to represent the evolutionary remnants of these domains rather than resulting from new duplications. The relevance of these flavivirus DRs to evolution, diversity, 3'UTR enhancer function, and virus transmission is reviewed.

Post-dispersal seed predation of non-target weeds in arable crops

Field experiments were conducted to quantify the natural levels of post-dispersal seed predation of arable weed species in spring barley and to identify the main groups of seed predators. Four arable weed species were investigated that were of high biodiversity value, yet of low to moderate competitive ability with the crop. These were Chenopodium album, Sinapis arvensis, Stellaria media and Polygonum aviculare. Exclusion treatments were used to allow selective access to dishes of seeds by different predator groups. Seed predation was highest early in the season, followed by a gradual decline in predation over the summer for all species. All species were taken by invertebrates. The activity of two phytophagous carabid genera showed significant correlations with seed predation levels. However, in general carabid activity was not related to seed predation and this is discussed in terms of the mainly polyphagous nature of many Carabid species that utilized the seed resource early in the season, but then switched to carnivory as prey populations increased. The potential relevance of post-dispersal seed predation to the development of weed management systems that maximize biological control through conservation and optimize herbicide use, is discussed.

A seven-year follow-up of men following a benign prostate biopsy

Objectives: To determine the incidence and clinical relevance of newly diagnosed cases of prostate cancer in a group of men who had an elevated PSA and benign prostate biopsy 7 years previously. Patients and Method: Patients under the age of 80 years with an elevated PSA who had had a benign prostate biopsy in the 12 months between March 1, 1994 and February 28, 1995 were studied. One hundred and sixty four patients with a mean age of 66.8 years (range 47-79 years) were identified. The mean PSA for this group was 10.3 ng/ml (range 4.1-81 ng/ml). One hundred and fifty nine of the 164 (97%) hospital records were available for review and all but 21 (12.8%) of the General Practitioners were contacted. Results: Eighteen (11%) of the original 164 patients were subsequently diagnosed with prostate cancer, 2 died from their disease. Conclusions: In a population where the follow-up of patients with a benign biopsy was arranged on clinical grounds alone, 11% of the study group were diagnosed with prostate cancer during a seven-year follow-up. Although some of these cancers appear to be slow growing, most of those diagnosed in the initial follow-up period were deemed to be clinically significant and a small proportion progressed rapidly to metastases. All patients who have an elevated PSA, but benign biopsy, should undergo a period of PSA monitoring until it is clear that their PSA is not rising. We propose an initial intensive monitoring period to avoid missing those with clinically aggressive disease. (C) 2003 Elsevier Science B.V. All rights reserved.

Factors controlling the distribution of ozone in the West African lower troposphere during the AMMA (African Monsoon Multidisciplinary Analysis) wet season campaign

Ozone and its precursors were measured on board the Facility for Airborne Atmospheric Measurements (FAAM) BAe 146 Atmospheric Research Aircraft during the monsoon season 2006 as part of the African Monsoon Multidisciplinary Analysis (AMMA) campaign. One of the main features observed in the west African boundary layer is the increase of the ozone mixing ratios from 25 ppbv over the forested area (south of 12 degrees N) up to 40 ppbv over the Sahelian area. We employ a two-dimensional ( latitudinal versus vertical) meteorological model coupled with an O-3-NOx-VOC chemistry scheme to simulate the distribution of trace gases over West Africa during the monsoon season and to analyse the processes involved in the establishment of such a gradient. Including an additional source of NO over the Sahelian region to account for NO emitted by soils we simulate a mean NOx concentration of 0.7 ppbv at 16 degrees N versus 0.3 ppbv over the vegetated region further south in reasonable agreement with the observations. As a consequence, ozone is photochemically produced with a rate of 0.25 ppbv h(-1) over the vegetated region whilst it reaches up to 0.75 ppbv h(-1) at 16 degrees N. We find that the modelled gradient is due to a combination of enhanced deposition to vegetation, which decreases the ozone levels by up to 11 pbbv, and the aforementioned enhanced photochemical production north of 12 degrees N. The peroxy radicals required for this enhanced production in the north come from the oxidation of background CO and CH4 as well as from VOCs. Sensitivity studies reveal that both the background CH4 and partially oxidised VOCs, produced from the oxidation of isoprene emitted from the vegetation in the south, contribute around 5-6 ppbv to the ozone gradient. These results suggest that the northward transport of trace gases by the monsoon flux, especially during nighttime, can have a significant, though secondary, role in determining the ozone gradient in the boundary layer. Convection, anthropogenic emissions and NO produced from lightning do not contribute to the establishment of the discussed ozone gradient.

Comparative costs of the commercial process in different construction procurement methods

The commercial process in construction projects is an expensive and highly variable overhead. Collaborative working practices carry many benefits, which are widely disseminated, but little information is available about their costs. Transaction Cost Economics is a theoretical framework that seeks explanations for why there are firms and how the boundaries of firms are defined through the “make-or-buy” decision. However, it is not a framework that offers explanations for the relative costs of procuring construction projects in different ways. The idea that different methods of procurement will have characteristically different costs is tested by way of a survey. The relevance of transaction cost economics to the study of commercial costs in procurement is doubtful. The survey shows that collaborative working methods cost neither more nor less than traditional methods. But the benefits of collaboration mean that there is a great deal of enthusiasm for collaboration rather than competition.

The diffusion of innovations within a UKCI context: An explanatory framework

The UK Construction Industry has been criticized for being slow to change and adopt innovations. The idiosyncrasies of participants, their roles in a social system and the contextual differences between sections of the UK Construction Industry are viewed as being paramount to explaining innovation diffusion within this context. Three innovation diffusion theories from outside construction management literature are introduced, Cohesion, Structural Equivalence and Thresholds. The relevance of each theory, in relation to the UK Construction Industry, is critically reviewed using literature and empirical data. Analysis of the data results in an explanatory framework being proposed. The framework introduces a Personal Awareness Threshold concept, highlights the dominant role of Cohesion through the main stages of diffusion, together with the use of Structural Equivalence during the later stages of diffusion and the importance of Adoption Threshold levels.

Assessing reading at Key Stage 2: SATs as measures of children's inferential abilities

This article describes two studies. The first study was designed to investigate the ways in which the statutory assessments of reading for 11-year-old children in England assess inferential abilities. The second study was designed to investigate the levels of performance achieved in these tests in 2001 and 2002 by 11-year-old children attending state-funded local authority schools in one London borough. In the first study, content and questions used in the reading papers for the Standard Assessment Tasks (SATs) in the years 2001 and 2002 were analysed to see what types of inference were being assessed. This analysis suggested that the complexity involved in inference making and the variety of inference types that are made during the reading process are not adequately sampled in the SATs. Similar inadequacies are evident in the ways in which the programmes of study for literacy recommended by central government deal with inference. In the second study, scripts of completed SATs reading papers for 2001 and 2002 were analysed to investigate the levels of inferential ability evident in scripts of children achieving different SATs levels. The analysis in this article suggests that children who only just achieve the 'target' Level 4 do so with minimal use of inference skills. They are particularly weak in making inferences that require the application of background knowledge. Thus, many children who achieve the reading level (Level 4) expected of 11-year-olds are entering secondary education with insecure inference-making skills that have not been recognised.

Glucosinolates in brassica vegetables: the influence of the food supply chain on intake, bioavailability and human health

Glucosinolates (GLSs) are found in Brassica vegetables. Examples of these sources include cabbage, Brussels sprouts, broccoli, cauliflower and various root vegetables (e.g. radish and turnip). A number of epidemiological studies have identified an inverse association between consumption of these vegetables and the risk of colon and rectal cancer. Animal studies have shown changes in enzyme activities and DNA damage resulting from consumption of Brassica vegetables or isothiocyanates, the breakdown products (BDP) of GLSs in the body. Mechanistic studies have begun to identify the ways in which the compounds may exert their protective action but the relevance of these studies to protective effects in the human alimentary tract is as yet unproven. In vitro studies with a number of specific isothiocyanates have suggested mechanisms that might be the basis of their chemoprotective effects. The concentration and composition of the GLSs in different plants, but also within a plant (e.g. in the seeds, roots or leaves), can vary greatly and also changes during plant development. Furthermore, the effects of various factors in the supply chain of Brassica vegetables including breeding, cultivation, storage and processing on intake and bioavailability of GLSs are extensively discussed in this paper.

Evaluation of a Lagrangian box model using field measurements from EASE (Eastern Atlantic Summer Experiment) 1996

The Cambridge Tropospheric Trajectory model of Chemistry and Transport (CiTTyCAT), a Lagrangian chemistry model, has been evaluated using atmospheric chemical measurements collected during the East Atlantic Summer Experiment 1996 (EASE '96). This field campaign was part of the UK Natural Environment Research Council's (NERC) Atmospheric Chemistry Studies in the Oceanic Environment (ACSOE) programme, conducted at Mace Head, Republic of Ireland, during July and August 1996. The model includes a description of gas-phase tropospheric chemistry, and simple parameterisations for surface deposition, mixing from the free troposphere and emissions. The model generally compares well with the measurements and is used to study the production and loss of O3 under a variety of conditions. The mean difference between the hourly O3 concentrations calculated by the model and those measured is 0.6 ppbv with a standard deviation of 8.7 ppbv. Three specific air-flow regimes were identified during the campaign – westerly, anticyclonic (easterly) and south westerly. The westerly flow is typical of background conditions for Mace Head. However, on some occasions there was evidence of long-range transport of pollutants from North America. In periods of anticyclonic flow, air parcels had collected emissions of NOx and VOCs immediately before arriving at Mace Head, leading to O3 production. The level of calculated O3 depends critically on the precise details of the trajectory, and hence on the emissions into the air parcel. In several periods of south westerly flow, low concentrations of O3 were measured which were consistent with deposition and photochemical destruction inside the tropical marine boundary layer.

Sting jets in simulations of a real cyclone by two mesoscale models

The existence of sting jets as a potential source of damaging surface winds during the passage of extratropical cyclones has recently been recognized However, there are still very few published studies on the subject Furthermore, although ills known that other models are capable of reproducing sting jets, in the published literature only one numerical model [the Met Office Unified Model (MetUM)] has been used to numerically analyze these phenomena This article alms to improve our understanding of the processes that contribute to the development of sting jets and show that model differences affect the evolution of modeled sting jets A sting jet event during the passage of a cyclone over the United Kingdom on 26 February 2002 has been simulated using two mesoscale models namely the MetUM and the Consortium for Small Scale Modeling (COSMO) model to compare their performance Given the known critical importance of vertical resolution in the simulation of sting jets the vertical resolution of both models has been enhanced with respect to their operational versions Both simulations have been verified against surface measurements of maximum gusts, satellite imagery and Met Office operational synoptic analyses, as well as operational analyses from the ECMWF It is shown that both models are capable of reproducing sting jets with similar, though not identical. features Through the comparison of the results from these two models, the relevance of physical mechanisms, such as evaporative cooling and the release of conditional symmetric instability, in the generation and evolution of sting jets is also discussed

N-nitroso compound exposure-associated transcriptomic profiles are indicative of an increased risk for colorectal cancer

Endogenous formation of N-nitroso compounds (NOCs), which are known animal carcinogens, could contribute to human carcinogenesis but definitive evidence is still lacking. To investigate the relevance of NOCs in human colorectal cancer (CRC) development, we analyzed whole genome gene expression modifications in human colon biopsies in relation to fecal NOC exposure. We had a particular interest in patients suffering from intestinal inflammation as this may stimulate endogenous NOC formation, and consequently predispose to CRC risk. Inflammatory bowel disease (IBD) patients diagnosed with ulcerative colitis and irritable bowel syndrome patients without inflammation, serving as controls, were therefore recruited. Fecal NOC were demonstrated in the majority of subjects. By associating gene expression levels of all subjects to fecal NOC levels, we identified a NOC exposure-associated transcriptomic response that suggests that physiological NOC concentrations may potentially induce genotoxic responses and chromatin modifications in human colon tissue, both of which are linked to carcinogenicity. In a network analysis, chromatin modifications were linked to 11 significantly modulated histone genes, pointing towards a possible epigenetic mechanism that may be relevant in comprehending NOC-induced carcinogenesis. In addition, pro-inflammatory transcriptomic modifications were identified in visually non-inflamed regions of the IBD colon. However, fecal NOC levels were slightly but not significantly increased in IBD patients, suggesting that inflammation did not strongly stimulate NOC formation. We conclude that NOC exposure is associated with gene expression modifications in the human colon that may suggest a potential role of these compounds in CRC development.

A kinetics and mechanistic study of the atmospherically relevant reaction between molecular chlorine and dimethyl sulfide (DMS)

A gas-phase kinetics study of the atmospherically important reaction between Cl2 and dimethyl sulfide (DMS)Cl2 + CH3SCH3 → productshas been made using a flow-tube interfaced to a photoelectron spectrometer. The rate constant for this reaction has been measured at 1.6 and 3.0 torr at T = (294 ± 2) K as (3.4 ± 0.7) × 10−14 cm3 molecule−1 s−1. Reaction (1) has been found to proceed via an intermediate, (CH3)2SCl2, to give CH3SCH2Cl and HCl as the products. The mechanism of this reaction and the structure of the intermediate were investigated using electronic structure calculations. A comparison of the mechanisms of the reactions between Cl atoms and DMS, and Cl2 and DMS has been made and the relevance of the results to atmospheric chemistry is discussed.

Two-photon excitation with pico-second fluorescence lifetime imaging to detect nuclear association of flavanols

Two-photon excitation enabled for the first time the observation and measurement of excited state fluorescence lifetimes from three flavanols in solution, which were ∼1.0 ns for catechin and epicatechin, but <45 ps for epigallocatechin gallate (EGCG). The shorter lifetime for EGCG is in line with a lower fluorescence quantum yield of 0.003 compared to catechin (0.015) and epicatechin (0.018). In vivo experiments with onion cells demonstrated that tryptophan and quercetin, which tend to be major contributors of background fluorescence in plant cells, have sufficiently low cross sections for two-photon excitation at 630 nm and therefore do not interfere with detection of externally added or endogenous flavanols in Allium cepa or Taxus baccata cells. Applying two-photon excitation to flavanols enabled 3-D fluorescence lifetime imaging microscopy and showed that added EGCG penetrated the whole nucleus of onion cells. Interestingly, EGCG and catechin showed different lifetime behaviour when bound to the nucleus: EGCG lifetime increased from <45 to 200 ps, whilst catechin lifetime decreased from 1.0 ns to 500 ps. Semi-quantitative measurements revealed that the relative ratios of EGCG concentrations in nucleoli associated vesicles: nucleus: cytoplasm were ca. 100:10:1. Solution experiments with catechin, epicatechin and histone proteins provided preliminary evidence, via the appearance of a second lifetime (τ2 = 1.9–3.1 ns), that both flavanols may be interacting with histone proteins. We conclude that there is significant nuclear absorption of flavanols. This advanced imaging using two-photon excitation and biophysical techniques described here will prove valuable for probing the intracellular trafficking and functions of flavanols, such as EGCG, which is the major flavanol of green tea.

Seasonality and interannual variability of the westerly jet in the Tibetan Plateau region

In this study, 40-yr ECMWF Re-Analysis (ERA-40) data are used for the description of the seasonal cycle and the interannual variability of the westerly jet in the Tibetan Plateau region. To complement results based on the analysis of monthly mean horizontal wind speeds, an occurrence-based jet climatology is constructed by identifying the locations of the jet axes at 6-hourly intervals throughout 1958–2001. Thus, a dataset describing the highly transient and localized features of jet variability is obtained. During winter and summer the westerly jet is located, respectively, to the south and north of the Tibetan Plateau. During the spring and autumn seasons there are jet transitions from south to north and vice versa. The median dates for these transitions are 28 April and 12 October. The spring transition is associated with large interannual variations, while the fall transition occurs more reliably within a 3-week period. The strength of the jet exhibits a peculiar seasonal cycle. During northward migration in April/May, the jet intensity weakens and its latitudinal position varies largely. In some springs, there are several transitions and split configurations occur before the jet settles in its northern summer position. In June, a well-defined and unusually strong jet reappears at the northern flanks of the Tibetan Plateau. In autumn, the jet gradually but reliably recedes to the south and is typically more intense than in spring. The jet transitions between the two preferred locations follow the seasonal latitudinal migration of the jet in the Northern Hemisphere. An analysis of interannual variations shows the statistical relationship between the strength of the summer jet, the tropospheric meridional temperature gradient, and the all-India rainfall series. Both this analysis and results from previous studies point to the particular dynamical relevance of the onsetting Indian summer monsoon precipitation and the associated diabatic heating for the formation of the strong summer jet. Finally, an example is provided that illustrates the climatological significance of the jet in terms of the covariation between the jet location and the spatial precipitation distribution in central Asia.