Data assimilation for state and parameter estimation: application to morphodynamic modelling

Data assimilation is predominantly used for state estimation; combining observational data with model predictions to produce an updated model state that most accurately approximates the true system state whilst keeping the model parameters fixed. This updated model state is then used to initiate the next model forecast. Even with perfect initial data, inaccurate model parameters will lead to the growth of prediction errors. To generate reliable forecasts we need good estimates of both the current system state and the model parameters. This paper presents research into data assimilation methods for morphodynamic model state and parameter estimation. First, we focus on state estimation and describe implementation of a three dimensional variational(3D-Var) data assimilation scheme in a simple 2D morphodynamic model of Morecambe Bay, UK. The assimilation of observations of bathymetry derived from SAR satellite imagery and a ship-borne survey is shown to significantly improve the predictive capability of the model over a 2 year run. Here, the model parameters are set by manual calibration; this is laborious and is found to produce different parameter values depending on the type and coverage of the validation dataset. The second part of this paper considers the problem of model parameter estimation in more detail. We explain how, by employing the technique of state augmentation, it is possible to use data assimilation to estimate uncertain model parameters concurrently with the model state. This approach removes inefficiencies associated with manual calibration and enables more effective use of observational data. We outline the development of a novel hybrid sequential 3D-Var data assimilation algorithm for joint state-parameter estimation and demonstrate its efficacy using an idealised 1D sediment transport model. The results of this study are extremely positive and suggest that there is great potential for the use of data assimilation-based state-parameter estimation in coastal morphodynamic modelling.

Western Chess: Endgame data

This spreadsheet contains key data about that part of the endgame of Western Chess for which Endgame Tables (EGTs) have been generated by computer. It is derived from the EGT work since 1969 of Thomas Ströhlein, Ken Thompson, Christopher Wirth, Eugene Nalimov, Marc Bourzutschky, John Tamplin and Yakov Konoval. The data includes %s of wins, draws and losses (wtm and btm), the maximum and average depths of win under various metrics (DTC = Depth to Conversion, DTM = Depth to Mate, DTZ = Depth to Conversion or Pawn-push), and examples of positions of maximum depth. It is essentially about sub-7-man Chess but is updated as news comes in of 7-man EGT computations.

Western Chess: Zugzwang data

This data is derived from Eugene Nalimov's Depth-to-Mate Endgame Tables for Western Chess. While having the move is normally advantageous, there are positions where the side-to-move would have a better theoretical result if it were the other side to move. These are (Type A) 'zugzwang' positions where the 'obligation to act' is unwelcome. This data provides lists of all zugzwangs in sub-7-man chess, and summary data about those sets of zugzwangs including exemplar zugzwangs of maximum depth.

FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions

The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, utilizing the Matthews Correlation Coefficient (MCC) and Binding-site Distance Test (BDT) metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall’s τ, Spearman’s ρ and Pearson’s r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC) when Receiver Operator Characteristic (ROC) analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%), and one of the top manual groups (FN293) tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site prediction quality, in the absence of experimental data.

Validation of ACE-FTS satellite data in the upper troposphere/lower stratosphere (UTLS) using non-coincident measurements

CO, O3, and H2O data in the upper troposphere/lower stratosphere (UTLS) measured by the Atmospheric Chemistry Experiment Fourier Transform Spectrometer(ACE-FTS) on Canada’s SCISAT-1 satellite are validated using aircraft and ozonesonde measurements. In the UTLS, validation of chemical trace gas measurements is a challenging task due to small-scale variability in the tracer fields, strong gradients of the tracers across the tropopause, and scarcity of measurements suitable for validation purposes. Validation based on coincidences therefore suffers from geophysical noise. Two alternative methods for the validation of satellite data are introduced, which avoid the usual need for coincident measurements: tracer-tracer correlations, and vertical tracer profiles relative to tropopause height. Both are increasingly being used for model validation as they strongly suppress geophysical variability and thereby provide an “instantaneous climatology”. This allows comparison of measurements between non-coincident data sets which yields information about the precision and a statistically meaningful error-assessment of the ACE-FTS satellite data in the UTLS. By defining a trade-off factor, we show that the measurement errors can be reduced by including more measurements obtained over a wider longitude range into the comparison, despite the increased geophysical variability. Applying the methods then yields the following upper bounds to the relative differences in the mean found between the ACE-FTS and SPURT aircraft measurements in the upper troposphere (UT) and lower stratosphere (LS), respectively: for CO ±9% and ±12%, for H2O ±30% and ±18%, and for O3 ±25% and ±19%. The relative differences for O3 can be narrowed down by using a larger dataset obtained from ozonesondes, yielding a high bias in the ACEFTS measurements of 18% in the UT and relative differences of ±8% for measurements in the LS. When taking into account the smearing effect of the vertically limited spacing between measurements of the ACE-FTS instrument, the relative differences decrease by 5–15% around the tropopause, suggesting a vertical resolution of the ACE-FTS in the UTLS of around 1 km. The ACE-FTS hence offers unprecedented precision and vertical resolution for a satellite instrument, which will allow a new global perspective on UTLS tracer distributions.

Energetics, lifestyle, and reproduction in birds

Theoretical and empirical studies of life history aim to account for resource allocation to the different components of fitness: survival, growth, and reproduction. The pioneering evolutionary ecologist David Lack [(1968) Ecological Adaptations for Breeding in Birds (Methuen and Co.,London)] suggested that reproductive output in birds reflects adaptation to environmental factors such as availability of food and risk of predation, but subsequent studies have not always supported Lack’s interpretation. Here using a dataset for 980 bird species (Dataset S1), a phylogeny, and an explicit measure of reproductive productivity, we test predictions for how mass-specific productivity varies with body size, phylogeny,and lifestyle traits. We find that productivity varies negatively with body size and energetic demands of parental care and positively with extrinsic mortality. Specifically: (i) altricial species are 50% less productive than precocial species; (ii) species with female-only care of offspring are about 20% less productive than species with other methods of parental care; (iii) nonmigrants are 14% less productive than migrants; (iv) frugivores and nectarivores are about 20% less productive than those eating other foods; and (v) pelagic foragers are 40% less productive than those feeding in other habitats. A strong signal of phylogeny suggests that syndromes of similar life-history traits tend to be conservative within clades but also to have evolved independently in different clades. Our results generally support both Lack’s pioneering studies and subsequent research on avian life history.

Price-based demand side management: Assessing the impacts of time-of-use tariffs on residential electricity demand and peak shifting in Northern Italy

One of the most common Demand Side Management programs consists of Time-of-Use (TOU) tariffs, where consumers are charged differently depending on the time of the day when they make use of energy services. This paper assesses the impacts of TOU tariffs on a dataset of residential users from the Province of Trento in Northern Italy in terms of changes in electricity demand, price savings, peak load shifting and peak electricity demand at substation level. Findings highlight that TOU tariffs bring about higher average electricity consumption and lower payments by consumers. A significant level of load shifting takes place for morning peaks. However, issues with evening peaks are not resolved. Finally, TOU tariffs lead to increases in electricity demand for substations at peak time.

Lichens used as monitors of atmospheric pollution around Agadir (Southwestern Morocco) - a case study predating lead-free gasoline

More than 30 epiphytic lichens, collected in Agadir (Morroco) and along a 150-km transect from the Atlantic Ocean eastward, were analyzed for their metal content and lead isotopic composition. This dataset was used to evaluate atmospheric metal contamination and the impact of the city on the surrounding area. The concentrations of Cu, Pb, and Zn (average ± 1 SD) were 20.9 ± 15.2 μg g−1, 13.8 ± 9.0 μg g−1, and 56.6 ± 26.6 μg g−1, respectively, with the highest values observed in lichens collected within the urban area. The 206Pb/207Pb and 208Pb/207Pb ratios in the lichens varied from 1.146 to 1.186 and from 2.423 to 2.460, respectively. Alkyllead-gasoline sold in Morocco by the major petrol companies gave isotopic ratios of 206Pb/207Pb = 1.076–1.081 and 208Pb/207Pb = 2.348–2.360. These new, homogeneous values for gasoline-derived lead improve and update the scarce isotopic database of potential lead sources in Morocco, and may be of great value to future environmental surveys on the presence of lead in natural reservoirs, where it persists over time (e.g., soils and sediments). The interest of normalizing metal concentrations in lichens to concentrations of a lithogenic element is demonstrated by the consistency of the results thus obtained with lead isotopic ratios. Leaded gasoline contributed less than 50% of the total amount of lead accumulated in lichens, even in areas subject to high vehicular traffic. This strongly suggests that the recent banishment of leaded gasoline in Morocco will not trigger a drastic improvement in air quality, at least in Agadir.

Assimilation of RAPID array observations into an ocean model

Experiments assimilating the RAPID dataset of deep temperature and salinity profiles at 26.5°N on the western and eastern Atlantic boundaries into a 1° global NEMO ocean model have been performed. The meridional overturning circulation (MOC) is then assessed against the transports calculated directly from observations. The best initialization found for this short period was obtained by assimilating the EN3 upper-ocean hydrography database prior to 2004, after which different methods of assimilating 5-day average RAPID profiles at the western boundary were tested. The model MOC is strengthened by ∼ 2 Sv giving closer agreement with the RAPID array transports, when the western boundary profiles are assimilated only below 900 m (the approximate depth of the Florida Straits, which are not well resolved) and when the T,S observations are spread meridionally from 10 to 35°N along the deep western boundary. The use of boundary-focused covariances has the largest impact on the assimilation results, otherwise using more conventional Gaussian covariances has a very local impact on the MOC at 26°N with strong adverse impacts on the MOC stream function at higher and lower latitudes. Even using boundary-focused covariances only enables the MOC to be strengthened for ∼ 2 years, after which the increased transport of warm waters leads to a negative feedback on water formation in the subpolar gyre which then reduces the MOC. This negative feedback can be mitigated if EN3 hydrography data continue to be assimilated along with the RAPID array boundary data. Copyright © 2012 Royal Meteorological Society and Crown in the right of Canada.

What people study when they study Twitter: classifying Twitter related academic papers

PURPOSE: Since its introduction in 2006, messages posted to the microblogging system Twitter have provided a rich dataset for researchers, leading to the publication of over a thousand academic papers. This paper aims to identify this published work and to classify it in order to understand Twitter based research. DESIGN/METHODOLOGY/APPROACH: Firstly the papers on Twitter were identified. Secondly, following a review of the literature, a classification of the dimensions of microblogging research was established. Thirdly, papers were qualitatively classified using open coded content analysis, based on the paper’s title and abstract, in order to analyze method, subject, and approach. FINDINGS: The majority of published work relating to Twitter concentrates on aspects of the messages sent and details of the users. A variety of methodological approaches are used across a range of identified domains. RESEARCH LIMITATIONS/IMPLICATIONS: This work reviewed the abstracts of all papers available via database search on the term “Twitter” and this has two major implications: 1) the full papers are not considered and so works may be misclassified if their abstract is not clear, 2) publications not indexed by the databases, such as book chapters, are not included. ORIGINALITY/VALUE: To date there has not been an overarching study to look at the methods and purpose of those using Twitter as a research subject. Our major contribution is to scope out papers published on Twitter until the close of 2011. The classification derived here will provide a framework within which researchers studying Twitter related topics will be able to position and ground their work

Acidity controls on dissolved organic carbon mobility in organic soils

Dissolved organic carbon (DOC) concentrations in surface waters have increased across much of Europe and North America, with implications for the terrestrial carbon balance, aquatic ecosystem functioning, water treatment costs and human health. Over the past decade, many hypotheses have been put forward to explain this phenomenon, from changing climate and land-management to eutrophication and acid deposition. Resolution of this debate has been hindered by a reliance on correlative analyses of time-series data, and a lack of robust experimental testing of proposed mechanisms. In a four-year, four-site replicated field experiment involving both acidifying and de-acidifying treatments, we tested the hypothesis that DOC leaching was previously suppressed by high levels of soil acidity in peat and organo-mineral soils, and therefore that observed DOC increases a consequence of decreasing soil acidity. We observed a consistent, positive relationship between DOC and acidity change at all sites. Responses were described by similar hyperbolic relationships between standardised changes in DOC and hydrogen ion concentrations at all sites, suggesting potentially general applicability. These relationships explained a substantial proportion of observed changes in peak DOC concentrations in nearby monitoring streams, and application to a UK-wide upland soil pH dataset suggests that recovery from acidification alone could have led to soil solution DOC increases in the range 46-126% by habitat type since 1978. Our findings raise the possibility that changing soil acidity may have wider impacts on ecosystem carbon balances. Decreasing sulphur deposition may be accelerating terrestrial carbon loss, and returning surface waters to a natural, high-DOC condition.

Sequence and phylogenetic analysis of viper venom serine proteases

Snakebites are a major neglected tropical disease responsible for as many as 95000 deaths every year worldwide. Viper venom serine proteases disrupt haemostasis of prey and victims by affecting various stages of the blood coagulation system. A better understanding of their sequence, structure, function and phylogenetic relationships will improve the knowledge on the pathological conditions and aid in the development of novel therapeutics for treating snakebites. A large dataset for all available viper venom serine proteases was developed and analysed to study various features of these enzymes. Despite the large number of venom serine protease sequences available, only a small proportion of these have been functionally characterised. Although, they share some of the common features such as a C-terminal extension, GWG motif and disulphide linkages, they vary widely between each other in features such as isoelectric points, potential N-glycosylation sites and functional characteristics. Some of the serine proteases contain substitutions for one or more of the critical residues in catalytic triad or primary specificity pockets. Phylogenetic analysis clustered all the sequences in three major groups. The sequences with substitutions in catalytic triad or specificity pocket clustered together in separate groups. Our study provides the most complete information on viper venom serine proteases to date and improves the current knowledge on the sequence, structure, function and phylogenetic relationships of these enzymes. This collective analysis of venom serine proteases will help in understanding the complexity of envenomation and potential therapeutic avenues.

Performance drivers of UK unlisted property funds

An unlisted property fund is a private investment vehicle which aims to provide direct property total returns and may also employ financial leverage which will accentuate performance. They have become a far more prevalent institutional property investment conduit since the early 2000’s. Investors have been primarily attracted to them due to the ease of executing a property exposure, both domestically and internationally, and for their diversification benefits given the capital intensive nature of constructing a well diversified commercial property investment portfolio. However, despite their greater prominence there has been little academic research conducted on the performance and risks of unlisted property fund investments. This can be attributed to a paucity of available data and limited time series where it exists. In this study we have made use of a unique dataset of institutional UK unlisted non-listed property funds over the period 2003Q4 to 2011Q4, using a panel modelling framework in order to determine the key factors which impact on fund performance. The sample provided a rich set of unlisted property fund factors including market exposures, direct property characteristics and the level of financial leverage employed. The findings from the panel regression analysis show that a small number of variables are able to account for the performance of unlisted property funds. These variables should be considered by investors when assessing the risk and return of these vehicles. The impact of financial leverage upon the performance of these vehicles through the recent global financial crisis and subsequent UK commercial property market downturn was also studied. The findings indicate a significant asymmetric effect of employing debt finance within unlisted property funds.

Trends in office rents in the City of London: 1867-1959

This paper details the construction and analysis of a dataset of office lettings, which is used to produce a rent index for the City of London spanning the late nineteenth and early twentieth centuries. It advances prior research through application of a modern version of the repeat measures technique and in coverage of years where office rents have not been previously measured. Results show that there has been no real growth in rents over the period as a whole. However, there have been distinct phases of rental growth and decline that correspond with the wider economic fortunes of the City.

Risk reduction and diversification in UK commercial property portfolios

The issue of diversification in direct real estate investment portfolios has been widely studied in academic and practitioner literature. Most work, however, has been done using either partially aggregated data or data for small samples of individual properties. This paper reports results from tests of both risk reduction and diversification that use the records of 10,000+ UK properties tracked by Investment Property Databank. It provides, for the first time, robust estimates of the diversification gains attainable given the returns, risks and cross‐correlations across the individual properties available to fund managers. The results quantify the number of assets and amount of money needed to construct both ‘balanced’ and ‘specialist’ property portfolios by direct investment. Target numbers will vary according to the objectives of investors and the degree to which tracking error is tolerated. The top‐level results are consistent with previous work, showing that a large measure of risk reduction can be achieved with portfolios of 30–50 properties, but full diversification of specific risk can only be achieved in very large portfolios. However, the paper extends previous work by demonstrating on a single, large dataset the implications of different methods of calculating risk reduction, and also by showing more disaggregated results relevant to the construction of specialist, sector‐focussed funds.