Setar Modelling of Traffic Count Data.

As part of a SERC funded project investigating outlier detection and replacement with transport data, univariate Box-Jenkins (1976) models have already been successfully applied to traffic count series (see Redfern et al, 1992). However, the underlying assumption of normality for ARIMA models implies they are not ideally suited for time series exhibiting certain behavioural characteristics. The limitations of ARIMA models are discussed in some detail by Tong (1983), including problems with time irreversibility, non-normality, cyclicity and asymmetry. Data with irregularly spaced extreme values are unlikely to be modelled well by ARIMA models, which are better suited to data where the probability of a very high value is small. Tong (1983) argues that one way of modelling such non-normal behaviour might be to retain the general ARIMA framework and allow the white noise element to be non-gaussian. As an alternative he proposes abandoning the linearity assumption and defines a group of non linear structures, one of which is the Self-Exciting Threshold Autoregressive (SETAR) model. The model form is described in more detail below but basically consists of two (or more) piecewise linear models, with the time series "tripping" between each model according to its value with respect to a threshold point. The model is called "Self-Exciting" because the indicator variable determining the appropriate linear model for each piece of data is itself a function of the data series. Intuitively this means the mechanism driving the alternation between each model form is not an external input such as a related time series (other models can be defined where this exists), but is actually contained within the series itself. The series is thus Self-Exciting. The three concepts embedded within the SETAR model structure are those of the threshold, limit cycle and time delay, each of which can be illustrated by the diverse applications such models can take. The threshold can be defined as some point beyond which, if the data falls, the series structure changes inherently and so an alternative linear model form would be appropriate. In hydrology this is seen as the non-linearity of soil infiltration, where at the soil saturation point (threshold) a new model for infiltration would become appropriate. Limit cycles describe the stable cyclical phenomena which we sometimes observe within time series. The cyclical behaviour is stationary, ie consists of regular, sustained oscillations and is an intrinsic property of the data. The limit cycle phenomena is physically observable in the field of radio-engineering where a triode valve is used to generate oscillations (see Tong, 1983 for a full description). Essentially the triode value produces self-sustaining oscillations between emitting and collecting electrons, according to the voltage value of a grid placed between the anode and cathode (thereby acting as the threshold indicator). The third essential concept within the SETAR structure is that of the time delay and is perhaps intuitively the easiest to grasp. It can be seen within the field of population biology where many types of non-linear model may apply. For example within the cyclical oscillations of blowfly population data there is an inbuilt "feedback" mechanism given by the hatching period for eggs, which would give rise to a time delay parameter within the model. For some processes this inherent delay may be so small as to be virtually instantaneous and so the delay parameter could be omitted. In general time series Tong (1983) found the SETAR model well suited to the cyclical nature of the Canadian Lynx trapping series and for modelling riverflow systems (Tong, Thanoon & Gudmundsson, 1984). Here we investigate their applicability with time series traffic counts, some of which have exhibited the type of non-linear and cyclical characteristics which could undermine a straightforward linear modelling process

Synchrotron X-ray microscopy of marine calcifiers: how plankton record past climate change

We have used STXM and PEEM to reveal the underpinning chemistry and nanoscale structure behind palaeo-climate geochemical signatures, such as trace Mg in shells- proposed proxies for palaeo-ocean temperature. This has allowed us to test the chemical assumptions and mechanisms underpinning the use of such empirical proxies. We have determined the control on driving chemical variations in biogenic carbonates using STXM at the absorption edge of Mg, B, and Na in the shells of modern plankton. The power of these observations lies in their ability to link changes in chemistry, microstructure, and growth process in biogenic carbonate to environmental influences. We have seen that such changes occur at length scales of tens of nanometres and demonstrated that STXM provides an invaluable route to understanding chemical environment and key heterogeneity at the appropriate length scale. This new understanding provides new routes for future measurements of past climate variation in the sea floor fossil record

Using Administrative Data to Count Local Populations

There is growing evidence that official population statistics based on the decennial census are inaccurate at the local authority level—the fundamental administrative unit of the UK. This paper investigates the use of locally available administrative data sets for counting populations. The method uses truth tables for combining different data sources with different population coverage according to a defined and therefore replicable set of rules. The result is timelier and geographically more flexible data which is more cost-effective to produce than a survey-based census. Associated techniques for linking diverse data sources at individual and household level are briefly discussed. The methodology is then applied to administrative data from a London borough with about 170,000 people. The results are evaluated and compared with other population sources. The paper concludes by discussing potential improvements including scaling up the work to cover multiple local authorities. The practicalities of using alternative central government data sets are briefly considered. A sequel paper in this journal provides examples of key applications of this approach at local level

H2O and the dehydroxylation of phyllosilicates: an infrared spectroscopic study

As shown by in situ infrared spectroscopy and analysis of quenched samples, phyllosilicates (muscovite, sericite, pyrophyllite, and talc) under dehydroxylation conditions lack the characteristic bands near 1600 cm–1 (bending) and 5200 cm–1 (combination) of H2O, and they contain virtually no H2O but an abundance of OH. This observation appears to be at variance with the formal description of dehydroxylation in bulk samples as 2(OH) -> H2O + O, whereas it is suggested that hydrogen diffuses in the form of (OH) – or/and H+ in dehydroxylation. The upper limit of H2O in the dehydroxlated bulk is likely to be at the parts per million level in phyllosilicates that contain structural OH ions equivalent to 4–5 wt% H2O. The observations suggest that H2O molecules are probably formed near the surface of the sample

Unpulsed UBV Optical Emission from the Crab Pulsar

Based on observations of the Crab pulsar using the TRIFFID high speed imaging photometer in the UBV bands using the Special Astrophysical Observatory's 6m telescope in the Russian Caucasus, we report the detection of pronounced emission during the so-called `off' phase of emission. Following de-extinction, this unpulsed component of emission is shown to be consistent with a power law with an exponent of alpha = -0.60 +/- 0.37, the uncertainty being dominated by the error associated with the independent CCD photometry used to reference the TRIFFID data. This suggests a steeper power law form than that reported elsewhere in the literature for the total integrated spectrum, which is essentially flat with alpha ~ 0.1, although the difference in this case is only significant at the ~ 2 sigma level. Deeper reference integrated and TRIFFID phase-resolved photometry in these bands in conjunction with further observations in the UV and R region would constrain this fit further.Comment: 26 pages, 2 figures, uses aasms4.sty, accepted for publication in the Astrophysical Journa

The protozoan parasite Trichomonas gallinae causes adult and nestling mortality in a declining population of European Turtle Doves, Streptopelia turtur

Studies incorporating the ecology of clinical and sub-clinical disease in wild populations of conservation concern are rare. Here we examine sub-clinical infection by Trichomonas gallinae in a declining population of free-living European Turtle Doves and suggest caseous lesions cause mortality in adults and nestlings through subsequent starvation and/or suffocation. We found a 100% infection rate by T. gallinae in adult and nestling Turtle Doves (n = 25) and observed clinical signs in three adults and four nestlings (28%). Adults with clinical signs displayed no differences in any skeletal measures of size but had a mean 3·7% reduction in wing length, with no overlap compared to those without clinical signs. We also identified T. gallinae as the suggested cause of mortality in one Red-legged Partridge although disease presentation was different. A minimum of four strains of T. gallinae, characterized at the ITS/5·8S/ITS2 ribosomal region, were isolated from Turtle Doves. However, all birds with clinical signs (Turtle Doves and the Red-legged Partridge) carried a single strain of T. gallinae, suggesting that parasite spill over between Columbidae and Galliformes is a possibility that should be further investigated. Overall, we highlight the importance of monitoring populations for sub-clinical infection rather than just clinical disease

FLORA: a novel method to predict protein function from structure in diverse superfamilies

Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA) that automatically generates structural motifs associated with different functional sub-families (FSGs) within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2–3 fold increase in coverage at low error rates) popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (α, β, αβ) and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues

A comparison of the ability of the National Early Warning Score and the National Early Warning Score 2 to identify patients at risk of in-hospital mortality: a multi-centre database study

AIMS:To compare the ability of the National Early Warning Score (NEWS) and the National Early Warning Score 2 (NEWS2) to identify patients at risk of in-hospital mortality and other adverse outcomes. METHODS:We undertook a multi-centre retrospective observational study at five acute hospitals from two UK NHS Trusts. Data were obtained from completed adult admissions who were not fit enough to be discharged alive on the day of admission. Diagnostic coding and oxygen prescriptions were used to identify patients with type II respiratory failure (T2RF). The primary outcome was in-hospital mortality within 24 h of a vital signs observation. Secondary outcomes included unanticipated intensive care unit admission or cardiac arrest within 24 h of a vital signs observation. Discrimination was assessed using the c-statistic. RESULTS:Among 251,266 adult admissions, 48,898 were identified to be at risk of T2RF by diagnostic coding. In this group, NEWS2 showed statistically significant lower discrimination (c-statistic, 95% CI) for identifying in-hospital mortality within 24 h (0.860, 0.857-0.864) than NEWS (0.881, 0.878-0.884). For 1394 admissions with documented T2RF, discrimination was similar for both systems: NEWS2 (0.841, 0.827-0.855), NEWS (0.862, 0.848-0.875). For all secondary endpoints, NEWS2 showed no improvements in discrimination. CONCLUSIONS:NEWS2 modifications to NEWS do not improve discrimination of adverse outcomes in patients with documented T2RF and decrease discrimination in patients at risk of T2RF. Further evaluation of the relationship between SpO2 values, oxygen therapy and risk should be investigated further before wide-scale adoption of NEWS2.Marco A.F. Pimentel, Oliver C. Redfern, Stephen Gerry, Gary S. Collins, James Malycha, David Prytherch ... et al

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure