Showing papers by "Royal Holloway, University of London published in 2002"

A systematic review of psychological factors as predictors of chronicity/disability in prospective cohorts of low back pain.

Abstract: Study Design. A systematic review of prospective cohort studies in low back pain. Objectives. To evaluate the evidence implicating psychological factors in the development of chronicity in low back pain. Summary of Background Data. The biopsychosocial model is gaining acceptance in low back pain, and has provided a basis for screening measurements, guidelines and interventions; however, to date, the unique contribution of psychological factors in the transition from an acute presentation to chronicity has not been rigorously assessed. Methods. A systematic literature search was followed by the application of three sets of criteria to each study: methodologic quality, quality of measurement of psychological factors, and quality of statistical analysis. Two reviewers blindly coded each study, followed by independent assessment by a statistician. Studies were divided into three environments: primary care settings, pain clinics, and workplace. Results. Twenty-five publications (18 cohorts) included psychological factors at baseline. Six of these met acceptability criteria for methodology, psychological measurement, and statistical analysis. Increased risk of chronicity (persisting symptoms and/or disability) from psychological distress/depressive mood and, to a lesser extent, somatization emerged as the main findings. Acceptable evidence generally was not found for other psychological factors, although weak support emerged for the role of catastrophizing as a coping strategy. Conclusion. Psychological factors (notably distress, depressive mood, and somatization) are implicated in the transition to chronic low back pain. The development and testing of clinical interventions specifically targeting these factors is indicated. In view of the importance attributed to other psychological factors (particularly coping strategies and fear avoidance) there is a need to clarify their role in back-related disability through rigorous prospective studies

Text classification using string kernels

Abstract: We propose a novel approach for categorizing text documents based on the use of a special kernel. The kernel is an inner product in the feature space generated by all subsequences of length k. A subsequence is any ordered sequence of k characters occurring in the text though not necessarily contiguously. The subsequences are weighted by an exponentially decaying factor of their full length in the text, hence emphasising those occurrences that are close to contiguous. A direct computation of this feature vector would involve a prohibitive amount of computation even for modest values of k, since the dimension of the feature space grows exponentially with k. The paper describes how despite this fact the inner product can be efficiently evaluated by a dynamic programming technique. Experimental comparisons of the performance of the kernel compared with a standard word feature space kernel (Joachims, 1998) show positive results on modestly sized datasets. The case of contiguous subsequences is also considered for comparison with the subsequences kernel with different decay factors. For larger documents and datasets the paper introduces an approximation technique that is shown to deliver good approximations efficiently for large datasets.

Questioning the evidence for Earth's oldest fossils

Abstract: Structures resembling remarkably preserved bacterial and cyanobacterial microfossils from about 3,465-million-year-old Apex cherts of the Warrawoona Group in Western Australia currently provide the oldest morphological evidence for life on Earth and have been taken to support an early beginning for oxygen-producing photosynthesis. Eleven species of filamentous prokaryote, distinguished by shape and geometry, have been put forward as meeting the criteria required of authentic Archaean microfossils, and contrast with other microfossils dismissed as either unreliable or unreproducible. These structures are nearly a billion years older than putative cyanobacterial biomarkers, genomic arguments for cyanobacteria, an oxygenic atmosphere and any comparably diverse suite of microfossils. Here we report new research on the type and re-collected material, involving mapping, optical and electron microscopy, digital image analysis, micro-Raman spectroscopy and other geochemical techniques. We reinterpret the purported microfossil-like structure as secondary artefacts formed from amorphous graphite within multiple generations of metalliferous hydrothermal vein chert and volcanic glass. Although there is no support for primary biological morphology, a Fischer--Tropsch-type synthesis of carbon compounds and carbon isotopic fractionation is inferred for one of the oldest known hydrothermal systems on Earth.

The snowmass Points and slopes: benchmarks for SUSY searches

Abstract: The ”Snowmass Points and Slopes” (SPS) are a set of benchmark points and parameter lines in the MSSM parameter space corresponding to different scenarios in the search for Supersymmetry at present and future experiments. This set of benchmarks was agreed upon at the 2001 ”Snowmass Workshop on the Future of Particle Physics” as a consensus based on different existing proposals.

The apoplastic oxidative burst in response to biotic stress in plants: a three‐component system

Abstract: The oxidative burst, the generation of reactive oxygen species (ROS) in response to microbial pathogen attack, is a ubiquitous early part of the resistance mechanisms of plant cells. It has also become apparent from the study of a number of plant-pathogen interactions and those modelled by elicitor treatment of cultured cells that there may be more than one mechanism operating. However, one mechanism may be dominant in any given species. NADPH oxidases have been implicated in a number of systems and have been cloned and characterized. However, the enzyme system which is the major source of ROS in French bean (Phaseolus vulgaris) cells treated with a cell wall elicitor from Colletotrichum lindemuthianum, appears to be dependent on an exocellular peroxidase. The second component, the extracellular alkalinization, occurs as a result of the Ca(2+) and proton influxes and the K(+) efflux common to most elicitation systems as one of the earliest responses. The third component, the actual reductant/substrate, has remained elusive. The low molecular weight compound composition of apoplastic fluid was compared before and after elicitation. The substrate only becomes available some min after elicitation and can be extracted, so that by comparing the profiles by LC-MS it has been possible to identify possible substrates. The mechanism has proved to be complex and may involve a number of low molecular weight components. Stimulation of H(2)O(2) production was observed with saturated fatty acids such as palmitate and stearate without concomitant oxylipin production. This biochemical evidence is supported by immunolocalization studies on papillae forming at bacterial infection sites that show the peroxidase isoform present at sites of H(2)O(2) production revealed by cerium chloride staining together with the cross-linked wall proteins and callose and callose synthase. The peroxidase has been cloned and expressed in Pichia pastoris and has been shown to catalyse the oxidation reaction with the same kinetics as the purified enzyme. Furthermore, Arabidopsis plants transformed heterologously using the French bean peroxidase in antisense orientation have proved to be highly susceptible to bacterial and fungal pathogens. Thus it is possible that Arabidopsis is another species with the potential to mount an apoplastic oxidative burst and these transformed plant lines may be useful to identify the peroxidase that is responsible.

Implementing the Tate Pairing

Abstract: The Tate pairing has found several new applications in cryptography. This paper provides methods to quickly compute the Tate pairing, and hence enables efficient implementation of these cryptosystems. We also give division-free formulae for point tripling on a family of elliptic curves in characteristic three. Examples of the running time for these methods are given.

Predicting depressive symptoms with a new measure of shame: The Experience of Shame Scale

Abstract: Objective. To investigate whether previous findings from interview studies of a prospective relationship between shame and psychopathology (e.g. Andrews, 1995) could be replicated using questionnaires. Design. A total of 163 university students participated in a longitudinal questionnaire study. Method. The Experience of Shame Scale (ESS), a questionnaire based on a previous interview measure, and an established shame scale (TOSCA), were considered in their relation to depressive symptoms assessed at two time points 11 weeks apart. Results. Both scales made significant independent contributions to depressive symptoms at time 1. However, only the ESS predicted additional significant variance in time 2 symptoms when time 1 symptoms were controlled. Conclusions. It was concluded that the reason for the differential performance of the two scales was that the ESS, like the shame interview, assesses specific areas of shame related to self and performance, whereas the TOSCA assesses general shame and may therefore be more prone to mood-state effects.

Chemostratigraphy of the Jurassic System: applications, limitations and implications for palaeoceanography

Abstract: Current chemostratigraphical studies of the Jurassic System primarily involve the use of one sedimentary component (marine organic carbon), one divalent transition metal substituted in carbonate (manganese), and two isotopic tracers: strontium-isotope ratios ( 87 Sr/ 86 Sr) and carbon-isotope ratios (δ 13 C carb and δ 13 C org ) in carbonate and in organic matter. Other parameters such as Mg/Ca and Sr/Ca ratios in calcite, oxygen-isotope ratios (δ 18 O) in carbonate, sulphur-isotope ratios (δ 34 S) in carbonate-hosted sulphate, nitrogen-isotope ratios (δ 15 N org ) in organic matter, osmium-isotope ratios ( 187 Os/ 188 Os) in black shales and neodymium-isotope ratios ( 143 Nd/ 144 Nd) in various mineral phases are also useful but at present give poor resolution because the database is incomplete or compromised by various factors. Stratigraphical patterns in total organic carbon (TOC) can be of either local or regional significance, depending on the lateral extent of the former nutrient-rich and productive water mass. Divalent manganese follows a similar pattern, being concentrated, most probably as a very early diagenetic phase, only in oxygen-depleted waters that typically underlie zones of elevated organic productivity. Shifts in Mg/Ca and Sr/Ca ratios on the time scale of ammonite subzones seem largely to reflect temperature changes. Strontium-isotope ratios from pristine skeletal calcite provide a global signal; δ 13 C values from carbonates with minimal diagenetic overprint potentially do the same, although small spatial differences in palaeo-water-mass composition may have been locally significant. Oxygen-isotope determinations on carbonate rocks and fossils generally yield values that are too scattered to be stratigraphically useful, because they reflect palaeotemperature, the evaporation–precipitation balance in sea water and the impact of any diagenesis involving an aqueous phase. Nitrogen-isotope ratios in organic matter reflect the chemistry of ancient water masses as affected by nitrate utilization and denitrification, and the stratigraphical pattern of this parameter is more likely to correlate only on a regional basis. Neodymium-isotope ratios in sea water are also water mass dependent and greatly affected by regional sources and oceanic current systems. Preliminary data on sulphur-isotope ratios in carbonates and osmium-isotope ratios in organic-rich shales, both potentially offering global correlation, indicate that these tracers may be valuable, although the records at present are not sufficiently well established to allow high-resolution regional correlation. In all cases, biostratigraphically well-dated reference sections, against which the relevant geochemical data have been calibrated, are required in the first instance. To date, studies on the stratigraphical distribution of organic carbon have been principally carried out in both northern (Boreal) and southern (Tethyan) Europe; carbon-isotope stratigraphy has been undertaken primarily, but not exclusively, on bulk pelagic sediments from the Alpine–Mediterranean or Tethyan domain; and strontium-isotope stratigraphy has been undertaken largely on calcitic skeletal material (belemnites and oysters) from northern and southern Europe. In many sections, including those containing ammonites, multi-parameter chemostratigraphy can give resolution that exceeds that attainable by classic biostratigraphical means. Strontium-isotope ratios in skeletal calcite are a particularly powerful tool for illustrating changes in sedimentary rate and revealing gaps in the stratigraphical record.

Stacked 2.6‐Ma grain size record from the Chinese loess based on five sections and correlation with the deep‐sea δ18O record

Abstract: [1] This study aims to establish a stacked climate record of the Quaternary period from the Chinese loess sequence and to address the forcing mechanisms for the regional climate history of the Loess Plateau by correlating the stacked record with a composite δ18O record in deep-sea sediments. A total of 18,352 samples were obtained from five loess sections, located at Baoji, Lingtai, Jingchuan, Puxian, and Pingliang in the southern and middle Loess Plateau. These yielded high-resolution grain size records. Between-section correlation of these shows that although small depositional hiatuses are present in places within a single section, most parts of the sections display near-continuous dust deposition throughout the Quaternary. The grain size records were tuned simultaneously to the theoretical variations in obliquity and precession of the Earth’s orbit. The grain size records plotted on their orbital timescales were then averaged to form a stacked loess grain size time series, termed the “Chiloparts” record. This resolves most of the orbital timescale paleoclimate events buried in the loess-soil sequences of the southern and middle Loess Plateau and can be used as a regional archive of the Pleistocene climate history in the Loess Plateau. Comparison of the “Chiloparts” record with a composite marine δ18O record shows that for the past 1.8 Ma, the loess-paleosol record can be correlated almost cycle by cycle with the marine record. Several discrepancies in the climatic events between the two records have also been identified, implying that regional forcing mechanisms may have played a part in the climatic evolution of the Chinese Loess Plateau.

Spatial price competition: A semiparametric approach

Abstract: We investigate the nature of price competition among firms that produce differentiated products and compete in markets that are limited in extent. We propose an instrumental variables series estimator for the matrix of cross price response coefficients, demonstrate that our estimator is consistent, and derive its asymptotic distribution. Our semiparametric approach allows us to discriminate among models of global competition, in which all products compete with all others, and local competition, in which products compete only with their neighbors. We apply our semiparametric estimator to data from U.S. wholesale gasoline markets and find that, in this market, competition is highly localized.

Evaluation of transgenic tomato plants expressing an additional phytoene synthase in a fruit-specific manner.

Abstract: Phytoene synthase from the bacterium Erwinia uredovora (crtB) has been overexpressed in tomato (Lycopersicon esculentum Mill. cv. Ailsa Craig). Fruit-specific expression was achieved by using the tomato polygalacturonase promoter, and the CRTB protein was targeted to the chromoplast by the tomato phytoene synthase-1 transit sequence. Total fruit carotenoids of primary transformants (T0) were 2–4-fold higher than the controls, whereas phytoene, lycopene, β-carotene, and lutein levels were increased 2.4-, 1.8-, and 2.2-fold, respectively. The biosynthetically related isoprenoids, tocopherols plastoquinone and ubiquinone, were unaffected by changes in carotenoid levels. The progeny (T1 and T2 generations) inherited both the transgene and phenotype. Determination of enzyme activity and Western blot analysis revealed that the CRTB protein was plastid-located and catalytically active, with 5–10-fold elevations in total phytoene synthase activity. Metabolic control analysis suggests that the presence of an additional phytoene synthase reduces the regulatory effect of this step over the carotenoid pathway. The activities of other enzymes in the pathway (isopentenyl diphosphate isomerase, geranylgeranyl diphosphate synthase, and incorporation of isopentenyl diphosphate into phytoene) were not significantly altered by the presence of the bacterial phytoene synthase.

Linear Programming Boosting via Column Generation

Abstract: We examine linear program (LP) approaches to boosting and demonstrate their efficient solution using LPBoost, a column generation based simplex method. We formulate the problem as if all possible weak hypotheses had already been generated. The labels produced by the weak hypotheses become the new feature space of the problem. The boosting task becomes to construct a learning function in the label space that minimizes misclassification error and maximizes the soft margin. We prove that for classification, minimizing the 1-norm soft margin error function directly optimizes a generalization error bound. The equivalent linear program can be efficiently solved using column generation techniques developed for large-scale optimization problems. The resulting LPBoost algorithm can be used to solve any LP boosting formulation by iteratively optimizing the dual misclassification costs in a restricted LP and dynamically generating weak hypotheses to make new LP columns. We provide algorithms for soft margin classification, confidence-rated, and regression boosting problems. Unlike gradient boosting algorithms, which may converge in the limit only, LPBoost converges in a finite number of iterations to a global solution satisfying mathematically well-defined optimality conditions. The optimal solutions of LPBoost are very sparse in contrast with gradient based methods. Computationally, LPBoost is competitive in quality and computational cost to AdaBoost.

Brief screening instrument for post-traumatic stress disorder

Abstract: Background Brief screening instruments appear to be a viable way of detecting post-traumatic stress disorder (PTSD) but none has yet been adequately validated. Aims To test and cross-validate a brief instrument that is simple to administer and score. Method Forty-one survivors of a rail crash were administered a questionnaire, followed by a structured clinical interview 1 week later. Results Excellent prediction of a PTSD diagnosis was provided by respondents endorsing at least six re-experiencing or arousal symptoms, in any combination. The findings were replicated on data from a previous study of 157 crime victims. Conclusions Performance of the new measure was equivalent to agreement achieved between two full clinical interviews.

Quantum probabilities as Bayesian probabilities

Abstract: In the Bayesian approach to probability theory, probability quantifies a degree of belief for a single trial, without any a priori connection to limiting frequencies. In this paper, we show that, despite being prescribed by a fundamental law, probabilities for individual quantum systems can be understood within the Bayesian approach. We argue that the distinction between classical and quantum probabilities lies not in their definition, but in the nature of the information they encode. In the classical world, maximal information about a physical system is complete in the sense of providing definite answers for all possible questions that can be asked of the system. In the quantum world, maximal information is not complete and cannot be completed. Using this distinction, we show that any Bayesian probability assignment in quantum mechanics must have the form of the quantum probability rule, that maximal information about a quantum system leads to a unique quantum-state assignment, and that quantum theory provides a stronger connection between probability and measured frequency than can be justified classically. Finally, we give a Bayesian formulation of quantum-state tomography.

Work relationships in telephone call centres: understanding emotional exhaustion and employee withdrawal

Abstract: This paper examines the nature of employment and the conditions of work in five telephone call centres in the telecommunications industry in Australia. Call centre work typically requires high levels of sustained interpersonal interaction with customers which can lead to burnout and employee withdrawal. Customer service staff can also become targets of customer hostility and abuse. In addition, this form of work tends to involve extensive employee monitoring and surveillance with little job discretion or variety of tasks. The paper draws upon survey data from 480 telephone service operators to identify the factors that are associated with emotional exhaustion and the frequency of absence amongst the employees. A modelling of the data using LISREL VIII revealed that a number of job and work-setting variables affected the level of emotional exhaustion of employees. These included interactions with the customer, a high workload and a lack of variety of work tasks. Moreover, higher rates of absence were associated with emotional exhaustion.

Regulation of carotenoid formation during tomato fruit ripening and development

Abstract: Carotenoid biosynthesis and its regulation during tomato fruit development and ripening is a complex process that occurs alongside the differentiation of chloroplasts into chromoplasts and changes to the organoleptic properties of the fruit. Unusually for plants, the ripe tomato fruit accumulates large amounts of lycopene, as the pattern of gene expression found in green fruit changes during fruit ripening. Although the control of gene expression is thought to be the main regulatory mechanism for these alterations in carotenoids, post-transcriptional regulation has also been reported, including feedback inhibition. The use of genetic manipulation of carotenogenesis in tomato has been used primarily for biotechnological reasons, but it has also facilitated investigations into these regulatory mechanisms, as well as into the effects of such perturbations on other isoprenoids such as gibberellins, tocopherols and sterols.

Adult attachment style. I: Its relationship to clinical depression.

Abstract: Background Although there are an increasing number of studies showing an association of adult attachment style to depressive disorder, such studies have rarely utilised epidemiological approaches with large community-based series and have relied heavily on brief self-report measurement of both attachment style and symptoms. The result is a wide inconsistency in the type of insecure style shown to relate to disorder. The present study examined adult attachment style in a high-risk community sample of women in relation to clinical depression. It utilised an interview measure of adult attachment which allowed for an assessment of both type of attachment style and the degree of insecurity of attachment. A companion paper examines its relationship with other depressive-vulnerability (Bifulco et al. 2002). Method Two hundred and twenty-two high-risk and 80 comparison women were selected from questionnaire screenings of London GP patient lists and intensively interviewed. A global scale of attachment style based on supportive relationships (with partner and very close others) together with attitudes to support-seeking, derived the four styles paralleling those from self-report attachment assessments (Secure, Enmeshed, Fearful, Avoidant). In order to additionally reflect hostility in the scheme, the Avoidant category was subdivided into “Angry-dismissive” and “Withdrawn”. The degree to which attitudes and behaviour within such styles were dysfunctional (“non-standard”) was also assessed. Attachment style was examined in relation to clinical depression in a 12-month period. For a third of the series this was examined prospectively to new onset of disorder. Results The presence of any insecure style was significantly related to 12-month depression. However, when controls were made for depressive symptomatology at interview, only the “non-standard” levels of Enmeshed, Fearful or Angry-dismissive styles related to disorder. Withdrawn-avoidance was not significantly related to disorder. Conclusion The relationship of attachment style to clinical depression is increased by differentiating the degree of insecurity of style and differentiating hostile and non-hostile avoidance.

Patient perceptions of diabetes and diabetes therapy: assessing quality of life.

Abstract: Efforts to prevent complications of diabetes often overlook the impact of the condition and its treatment on current quality of life (QoL). The Diabetes Treatment Satisfaction Questionnaire (DTSQ) has proved valuable for understanding and measuring patients' treatment satisfaction in assessments of new treatments and strategies. For example, the DTSQ has demonstrated improved patient satisfaction with fast-acting insulin lispro versus standard soluble insulin and with long-acting insulin glargine versus NPH insulin. However, improvements in treatment satisfaction are often inferred to be improvements in overall QoL without recognizing the limited scope of the satisfaction measure. It is necessary to evaluate not only satisfaction with treatment per se but also the impact of diabetes and its treatment on a broad range of life domains in order to assess the impact on QoL. The Audit of Diabetes-Dependent Quality of Life (ADDQoL) measure is a diabetes-specific instrument that assesses the impact of diabetes on 18 life domains. Use of the ADDQoL with people with type 1 or type 2 diabetes has shown, on average, almost universally negative impact of diabetes on all domains. Significant differences have also been shown in the magnitude of effect between insulin-treated and non-insulin-treated patients and patients with and without complications. The negative impact of diabetes on QoL has been observed despite high levels of treatment satisfaction (as measured by the DTSQ). The greatest negative impact was observed for the domain 'Freedom to eat as I wish', indicating the strong influence of dietary restrictions on QoL. Studies to assess the outcomes of treatment approaches designed to improve dietary flexibility are under way.

Bacillus probiotics: spore germination in the gastrointestinal tract

Abstract: Spores of Bacillus species are being used commercially as probiotics and competitive exclusion agents. Unlike the more commonly used Lactobacillus-type probiotics, spores are dormant life forms. To address how spore probiotics might function we have investigated whether spores can germinate in the gastrointestinal tract by using a murine model. Using a genetically engineered chimeric gene, ftsH-lacZ, which is strongly expressed only in vegetative cells, we have developed a sensitive competitive reverse transcription-PCR assay which has enabled detection of as few as 10(2) vegetative bacteria in the mouse gut. Using this method we have administered doses of ftsH-lacZ spores to groups of mice and shown that spores can germinate in significant numbers in the jejunum and ileum. The levels of detection we obtained suggest that spores may colonize the small intestine, albeit briefly.

Impacts of Soil Faunal Community Composition on Model Grassland Ecosystems

Abstract: Human impacts, including global change, may alter the composition of soil faunal communities, but consequences for ecosystem functioning are poorly understood. We constructed model grassland systems in the Ecotron controlled environment facility and manipulated soil community composition through assemblages of different animal body sizes. Plant community composition, microbial and root biomass, decomposition rate, and mycorrhizal colonization were all markedly affected. However, two key ecosystem processes, aboveground net primary productivity and net ecosystem productivity, were surprisingly resistant to these changes. We hypothesize that positive and negative faunal-mediated effects in soil communities cancel each other out, causing no net ecosystem effects.

Inferring a Semantic Representation of Text via Cross-Language Correlation Analysis

Abstract: The problem of learning a semantic representation of a text document from data is addressed, in the situation where a corpus of unlabeled paired documents is available, each pair being formed by a short English document and its French translation. This representation can then be used for any retrieval, categorization or clustering task, both in a standard and in a cross-lingual setting. By using kernel functions, in this case simple bag-of-words inner products, each part of the corpus is mapped to a high-dimensional space. The correlations between the two spaces are then learnt by using kernel Canonical Correlation Analysis. A set of directions is found in the first and in the second space that are maximally correlated. Since we assume the two representations are completely independent apart from the semantic content, any correlation between them should reflect some semantic similarity. Certain patterns of English words that relate to a specific meaning should correlate with certain patterns of French words corresponding to the same meaning, across the corpus. Using the semantic representation obtained in this way we first demonstrate that the correlations detected between the two versions of the corpus are significantly higher than random, and hence that a representation based on such features does capture statistical patterns that should reflect semantic information. Then we use such representation both in cross-language and in single-language retrieval tasks, observing performance that is consistently and significantly superior to LSI on the same data.

What are the Effects of Fiscal Policy Shocks

Abstract: We propose and apply a new approach for analyzing the effects of fiscal policy using vector autoregressions Specifically, we use sign restrictions to identify a government revenue shock as well as a government spending shock, while controlling for a generic business cycle shock and a monetary policy shock We explicitly allow for the possibility of announcement effects, ie, that a current fiscal policy shock changes fiscal policy variables in the future, but not at present We construct the impulse responses to three linear combinations of these fiscal shocks, corresponding to the three scenarios of deficit-spending, deficit-financed tax cuts and a balanced budget spending expansion We apply the method to US quarterly data from 1955-2000 We find that deficit-financed tax cuts work best among these three scenarios to improve GDP, with a maximal present value multiplier of five dollars of total additional GDP per each dollar of the total cut in government revenue five years after the shock