Cost733cat: a database of weather and circulation type classifications

A new database of weather and circulation type catalogs is presented comprising 17 automated classification methods and five subjective classifications. It was compiled within COST Action 733 "Harmonisation and Applications of Weather Type Classifications for European regions" in order to evaluate different methods for weather and circulation type classification. This paper gives a technical description of the included methods using a new conceptual categorization for classification methods reflecting the strategy for the definition of types. Methods using predefined types include manual and threshold based classifications while methods producing types derived from the input data include those based on eigenvector techniques, leader algorithms and optimization algorithms. In order to allow direct comparisons between the methods, the circulation input data and the methods' configuration were harmonized for producing a subset of standard catalogs of the automated methods. The harmonization includes the data source, the climatic parameters used, the classification period as well as the spatial domain and the number of types. Frequency based characteristics of the resulting catalogs are presented, including variation of class sizes, persistence, seasonal and inter-annual variability as well as trends of the annual frequency time series. The methodological concept of the classifications is partly reflected by these properties of the resulting catalogs. It is shown that the types of subjective classifications compared to automated methods show higher persistence, inter-annual variation and long-term trends. Among the automated classifications optimization methods show a tendency for longer persistence and higher seasonal variation. However, it is also concluded that the distance metric used and the data preprocessing play at least an equally important role for the properties of the resulting classification compared to the algorithm used for type definition and assignment.

Long run relationships between City office rents and the economy in the UK: creating a database for research

This paper sets out progress during the first eighteen months of doctoral research into the City of London office market. The overall aim of the research is to explore relationships between office rents and the economy in the UK over the last 150 years. To do this, a database of lettings has been created from which a long run index of City office rents can be constructed. With this index, it should then be possible to analyse trends in rents and relationships with their long run determinants. The focus of this paper is on the creation of the rent database. First, it considers the existing secondary sources of long run rental data for the UK. This highlights a lack of information for years prior to 1970 and the need for primary data collection if earlier periods are to be studied. The paper then discusses the selection of the City of London and of the time period chosen for research. After this, it describes how a dataset covering the period 1860-1960 has been assembled using the records of property companies active in the City office market. It is hoped that, if successful, this research will contribute to existing knowledge on the long run characteristics of commercial real estate. In particular, it should add a price dimension (rents) to the existing long run information on stock/supply and investment. Hence, it should enable a more complete picture of the development and performance of commercial real estate through time to be gained.

The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms

Currently, the Genomic Threading Database (GTD) contains structural assignments for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes. Structural annotations are carried out using a modified version of GenTHREADER, a reliable fold recognition method. The Gen THREADER annotation jobs are distributed across multiple clusters of processors using grid technology and the predictions are deposited in a relational database accessible via a web interface at http://bioinf.cs.ucl.ac.uk/GTD. Using this system, up to 84% of proteins encoded within a genome can be confidently assigned to known folds with 72% of the residues aligned. On average in the GTD, 64% of proteins encoded within a genome are confidently assigned to known folds and 58% of the residues are aligned to structures.

The Genomic Threading Database

The Genomic Threading Database currently contains structural annotations for the genomes of over 100 recently sequenced organisms. Annotations are carried out by using our modified GenTHREADER software and through implementing grid technology.

The role of the international cocoa germplasm database and the international cocoa quarantine centre in information management and distribution of cocoa genetic resources

A range of physiological parameters (canopy light transmission, canopy shape, leaf size, flowering and flushing intensity) were measured from the International Clone Trial, typically over the course of two years. Data were collected from six locations, these being: Brazil, Ecuador, Trinidad, Venezuela, Côte d’Ivoire and Ghana. Canopy shape varied significantly between clones, although it showed little variation between locations. Genotypic variation in leaf size was differentially affected by the growth location; such differences appeared to underlie a genotype by environment interaction in relation to canopy light transmission. Flushing data were recorded at monthly intervals over the course of a year. Within each location, a significant interaction was observed between genotype and time of year, suggesting that some genotypes respond to a greater extent than others to environmental stimuli. A similar interaction was observed for flowering data, where significant correlations were found between flowering intensity and temperature in Brazil and flowering intensity and rainfall in Côte d’Ivoire. The results demonstrate the need for local evaluation of cocoa clones and also suggest that the management practices for particular planting material may need to be fine-tuned to the location in which they are cultivated.

Breast, colorectal, and prostate cancer risk in the European Prospective Investigation into Cancer and Nutrition–Norfolk in relation to phytoestrogen intake derived from an improved database

Background: The characterization of phytoestrogen intake and cancer risk has been hindered by the absence of accurate dietary phytoestrogen values. Objective: We examined the risk of breast, colorectal, and prostate cancers relative to phytoestrogen intake on the basis of a comprehensive database. Design: Demographic and anthropometric characteristics, a medical history, and 7-d records of diet were collected prospectively from participants (aged 40–79 y) in the European Prospective Investigation into Cancer and Nutrition–Norfolk (EPIC-Norfolk). Five hundred nine food items were analyzed by liquid chromatography–mass spectrometry/mass spectrometry, and 13C3-labeled internal standards were analyzed for isoflavones (genistein, daidzein, glycitein, biochanin A, and formononetin), lignans (secoisolariciresinol and matairesinol), and enterolignans from gut microbial metabolism in animal food sources (equol and enterolactone). From the direct analysis, values for 10,708 foods were calculated. Odds ratios (ORs) for breast (244 cases, 941 controls), colorectal (221 cases, 886 controls), and prostate (204 cases, 812 controls) cancers were calculated relative to phytoestrogen intake. Results: Phytoestrogen intake was not associated with breast cancer among women or colorectal cancer among men. Among women, colorectal cancer risk was inversely associated with enterolactone (OR: 0.33; 95% CI: 0.14, 0.74) and total enterolignans (OR: 0.32; 95% CI: 0.13, 0.79), with a positive trend detected for secoisolariciresinol (OR: 1.60; 95% CI: 0.96, 2.69). A positive trend between enterolignan intake and prostate cancer risk (OR: 1.27; 95% CI: 0.97, 1.66) was attenuated after adjustment for dairy intake (OR: 1.19; 95% CI: 0.77, 1.82). Conclusion: Dietary phytoestrogens may contribute to the risk of colorectal cancer among women and prostate cancer among men.

Intakes and sources of isoflavones, lignans, enterolignans, coumestrol and soya-containing foods in the Norfolk arm of the European Prospective Investigation into Cancer and Nutrition (EPIC-Norfolk), from 7-day food diaries, using a newly updated database

Objective: A phytoestrogen-rich diet has been suggested to protect against a variety of common diseases but UK intake data on phytoestrogens or their food sources is sparse. This study aims to estimate the average intake of isoflavones, lignans, enterolignans and coumestrol from 7-day food diaries (7dFD), and to provide data on total isoflavone, lignan and phytoestrogen consumption by food group. Design: Development of a food composition database for twelve phytoestrogens and analysis of soya food and phytoestrogen consumption in a population-based study. Setting: Men and women, aged 40-79 years from the general population participating in EPIC-Norfolk between 1993 and 1997, with nutrient and food data from 7dFD. Subjects: A subset of 20 437 participants. Results: The median daily phytoestrogen intake for men was 1.20mg (interquartile range (IQR) 0.93-1.54 mg; mean 1.50 mg, SD 1.50 mg) and 0.89 mg for women (IQR 0.71-1.14 mg; mean 1.20 mg, SD 1.70 mg). In soya-consumers (SC), median daily intakes were higher: 2.86 mg in men (IQR – 1.30-7.27mg; mean 5.05 mg, SD 5.03 mg) and 3.14 mg in women (IQR – 1.09-7.33mg; mean 5.40 mg, SD 6.09 mg). In both men and women, bread made the greatest contribution to phytoestrogen intake – 40.7% and 35.7% respectively. In SC men and women, vegetable dishes and soya/goat’s/sheep’s milks were the main contributors – 42.6% and 18.9% in men and 38.8% and 29.1% in women, respectively. Conclusions: The ability to estimate phytoestrogen intake in Western populations more accurately will aid investigations into their suggested effects on health.

An extratropical cyclone database: A tool for illustrating cyclone structure and evolution characteristics

Extratropical cyclone lifecycles have been studied extensively with the aim of understanding the dynamical mechanisms involved in their development. Previous work has often been based on subjective analysis of individual case studies. Such case studies have contributed heavily to the generation of conceptual models of extratropical cyclones that provide a framework for understanding the dynamical evolution of cyclones. These conceptual models are widely used in educational meteorology courses throughout the world to illustrate the basic structure and evolution of extratropical cyclones. This article presents a database of extratropical cyclone composites which highlight the average structure and evolution of 20 years of extratropical cyclones, as opposed to individual case studies. The composite fields are achieved by combining a database containing cyclone tracks from the ERA-Interim reanalysis (1989-2009, 6 hourly) with the full 3D ERA-Interim reanalysis fields. Vertical and horizontal composites of cyclone structure for cyclones generated in the Atlantic and Pacific regions identifying features such as the relative positions of cold, warm and occluded fronts and their associated wind and cloud patterns are shown. In addition the evolution of cyclonic flows such as the warm and cold conveyor belts and dry intrusion are illustrated. A webpage containing an archive of the composited data is freely available for educational purposes.

The data-mining of studies database 'HHdbIV'

This article clarifies what was done with the sub-7-man positions in data-mining Harold van der Heijden's 'HHdbIV' database of chess studies prior to its publication. It emphasises that only positions in the main lines of studies were examined and that the information about uniqueness of move was not incorporated in HHdbIV. There is some reflection on the separate technical and artistic dimensions of study evaluation.

Ozone database in support of CMIP5 simulations: results and corresponding radiative forcing

A continuous tropospheric and stratospheric vertically resolved ozone time series, from 1850 to 2099, has been generated to be used as forcing in global climate models that do not include interactive chemistry. A multiple linear regression analysis of SAGE I+II satellite observations and polar ozonesonde measurements is used for the stratospheric zonal mean dataset during the well-observed period from 1979 to 2009. In addition to terms describing the mean annual cycle, the regression includes terms representing equivalent effective stratospheric chlorine (EESC) and the 11-yr solar cycle variability. The EESC regression fit coefficients, together with pre-1979 EESC values, are used to extrapolate the stratospheric ozone time series backward to 1850. While a similar procedure could be used to extrapolate into the future, coupled chemistry climate model (CCM) simulations indicate that future stratospheric ozone abundances are likely to be significantly affected by climate change, and capturing such effects through a regression model approach is not feasible. Therefore, the stratospheric ozone dataset is extended into the future (merged in 2009) with multimodel mean projections from 13 CCMs that performed a simulation until 2099 under the SRES (Special Report on Emission Scenarios) A1B greenhouse gas scenario and the A1 adjusted halogen scenario in the second round of the Chemistry-Climate Model Validation (CCMVal-2) Activity. The stratospheric zonal mean ozone time series is merged with a three-dimensional tropospheric data set extracted from simulations of the past by two CCMs (CAM3.5 and GISSPUCCINI)and of the future by one CCM (CAM3.5). The future tropospheric ozone time series continues the historical CAM3.5 simulation until 2099 following the four different Representative Concentration Pathways (RCPs). Generally good agreement is found between the historical segment of the ozone database and satellite observations, although it should be noted that total column ozone is overestimated in the southern polar latitudes during spring and tropospheric column ozone is slightly underestimated. Vertical profiles of tropospheric ozone are broadly consistent with ozonesondes and in-situ measurements, with some deviations in regions of biomass burning. The tropospheric ozone radiative forcing (RF) from the 1850s to the 2000s is 0.23Wm−2, lower than previous results. The lower value is mainly due to (i) a smaller increase in biomass burning emissions; (ii) a larger influence of stratospheric ozone depletion on upper tropospheric ozone at high southern latitudes; and possibly (iii) a larger influence of clouds (which act to reduce the net forcing) compared to previous radiative forcing calculations. Over the same period, decreases in stratospheric ozone, mainly at high latitudes, produce a RF of −0.08Wm−2, which is more negative than the central Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) value of −0.05Wm−2, but which is within the stated range of −0.15 to +0.05Wm−2. The more negative value is explained by the fact that the regression model simulates significant ozone depletion prior to 1979, in line with the increase in EESC and as confirmed by CCMs, while the AR4 assumed no change in stratospheric RF prior to 1979. A negative RF of similar magnitude persists into the future, although its location shifts from high latitudes to the tropics. This shift is due to increases in polar stratospheric ozone, but decreases in tropical lower stratospheric ozone, related to a strengthening of the Brewer-Dobson circulation, particularly through the latter half of the 21st century. Differences in trends in tropospheric ozone among the four RCPs are mainly driven by different methane concentrations, resulting in a range of tropospheric ozone RFs between 0.4 and 0.1Wm−2 by 2100. The ozone dataset described here has been released for the Coupled Model Intercomparison Project (CMIP5) model simulations in netCDF Climate and Forecast (CF) Metadata Convention at the PCMDI website (http://cmip-pcmdi.llnl.gov/).

TRY: a global database of plant traits

Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

Coupling ensemble weather predictions based on TIGGE database with Grid-Xinanjiang model for flood forecast

The incorporation of numerical weather predictions (NWP) into a flood forecasting system can increase forecast lead times from a few hours to a few days. A single NWP forecast from a single forecast centre, however, is insufficient as it involves considerable non-predictable uncertainties and lead to a high number of false alarms. The availability of global ensemble numerical weather prediction systems through the THORPEX Interactive Grand Global Ensemble' (TIGGE) offers a new opportunity for flood forecast. The Grid-Xinanjiang distributed hydrological model, which is based on the Xinanjiang model theory and the topographical information of each grid cell extracted from the Digital Elevation Model (DEM), is coupled with ensemble weather predictions based on the TIGGE database (CMC, CMA, ECWMF, UKMO, NCEP) for flood forecast. This paper presents a case study using the coupled flood forecasting model on the Xixian catchment (a drainage area of 8826 km2) located in Henan province, China. A probabilistic discharge is provided as the end product of flood forecast. Results show that the association of the Grid-Xinanjiang model and the TIGGE database gives a promising tool for an early warning of flood events several days ahead.

Fire history and the Global Charcoal Database: a new tool for hypothesis testing and data exploration

Version 1 of the Global Charcoal Database is now available for regional fire history reconstructions, data exploration, hypothesis testing, and evaluation of coupled climate–vegetation–fire model simulations. The charcoal database contains over 400 radiocarbon-dated records that document changes in charcoal abundance during the Late Quaternary. The aim of this public database is to stimulate cross-disciplinary research in fire sciences targeted at an increased understanding of the controls and impacts of natural and anthropogenic fire regimes on centennial-to-orbital timescales. We describe here the data standardization techniques for comparing multiple types of sedimentary charcoal records. Version 1 of the Global Charcoal Database has been used to characterize global and regional patterns in fire activity since the last glacial maximum. Recent studies using the charcoal database have explored the relation between climate and fire during periods of rapid climate change, including evidence of fire activity during the Younger Dryas Chronozone, and during the past two millennia.