Showing papers by "University of Cambridge published in 1997"

An algorithm for suffix stripping

Abstract: The automatic removal of suffixes from words in English is of particular interest in the field of information retrieval. An algorithm for suffix stripping is described, which has been implemented as a short, fast program in BCPL. Although simple, it performs slightly better than a much more elaborate system with which it has been compared. It effectively works by treating complex suffixes as compounds made up of simple suffixes, and removing the simple suffixes in a number of steps. In each step the removal of the suffix is made to depend upon the form of the remaining stem, which usually involves a measure of its syllable length.

Alpha-synuclein in Lewy bodies.

Abstract: Lewy bodies, a defining pathological characteristic of Parkinson's disease and dementia with Lewy bodies (DLB)1,2,3,4, constitute the second most common nerve cell pathology, after the neurofibrillary lesions of Alzheimer's disease. Their formation may cause neurodegeneration, but their biochemical composition is unknown. Neurofilaments and ubiquitin are present5,6,7,8, but it is unclear whether they are major components of the filamentous material of the Lewy body9,10. Here we describe strong staining of Lewy bodies from idiopathic Parkinson's disease with antibodies for α-synuclein, a presynaptic protein of unknown function which is mutated in some familial cases of the disease11. α-Synuclein may be the main component of the Lewy body in Parkinson's disease. We also show staining for α-synuclein of Lewy bodies from DLB, indicating that the Lewy bodies from these two diseases may have identical compositions.

A review of methods for the assessment of prediction errors in conservation presence/absence models

Abstract: Predicting the distribution of endangered species from habitat data is frequently perceived to be a useful technique. Models that predict the presence or absence of a species are normally judged by the number of prediction errors. These may be of two types: false positives and false negatives. Many of the prediction errors can be traced to ecological processes such as unsaturated habitat and species interactions. Consequently, if prediction errors are not placed in an ecological context the results of the model may be misleading. The simplest, and most widely used, measure of prediction accuracy is the number of correctly classified cases. There are other measures of prediction success that may be more appropriate. Strategies for assessing the causes and costs of these errors are discussed. A range of techniques for measuring error in presence/absence models, including some that are seldom used by ecologists (e.g. ROC plots and cost matrices), are described. A new approach to estimating prediction error, which is based on the spatial characteristics of the errors, is proposed. Thirteen recommendations are made to enable the objective selection of an error assessment technique for ecological presence/absence models.

Good error-correcting codes based on very sparse matrices

Abstract: We study two families of error-correcting codes defined in terms of very sparse matrices "MN" (MacKay-Neal (1995)) codes are recently invented, and "Gallager codes" were first investigated in 1962, but appear to have been largely forgotten, in spite of their excellent properties The decoding of both codes can be tackled with a practical sum-product algorithm We prove that these codes are "very good", in that sequences of codes exist which, when optimally decoded, achieve information rates up to the Shannon limit This result holds not only for the binary-symmetric channel but also for any channel with symmetric stationary ergodic noise We give experimental results for binary-symmetric channels and Gaussian channels demonstrating that practical performance substantially better than that of standard convolutional and concatenated codes can be achieved; indeed, the performance of Gallager codes is almost as close to the Shannon limit as that of turbo codes

Charging and rate control for elastic traffic

Abstract: This paper addresses the issues of charging, rate control and routing for a communication network carrying elastic traffic, such as an ATM network offering an available bit rate service. A model is described from which max-min fairness of rates emerges as a limiting special case; more generally, the charges users are prepared to pay influence their allocated rates. In the preferred version of the model, a user chooses the charge per unit time that the user will pay; thereafter the user's rate is determined by the network according to a proportional fairness criterion applied to the rate per unit charge. A system optimum is achieved when users' choices of charges and the network's choice of allocated rates are in equilibrium.

Congenital leptin deficiency is associated with severe early-onset obesity in humans

Abstract: The extreme obesity of the obese (ob/ob) mouse is attributable to mutations in the gene encoding leptin, an adipocyte-specific secreted protein which has profound effects on appetite and energy expenditure We know of no equivalent evidence regarding leptin's role in the control of fat mass in humans We have examined two severely obese children who are members of the same highly consanguineous pedigree Their serum leptin levels were very low despite their markedly elevated fat mass and, in both, a homozygous frame-shift mutation involving the deletion of a single guanine nucleotide in codon 133 of the gene for leptin was found The severe obesity found in these congenitally leptin-deficient subjects provides the first genetic evidence that leptin is an important regulator of energy balance in humans

Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms

Abstract: We describe a global optimization technique using “basin-hopping” in which the potential energy surface is transformed into a collection of interpenetrating staircases. This method has been designed to exploit the features that recent work suggests must be present in an energy landscape for efficient relaxation to the global minimum. The transformation associates any point in configuration space with the local minimum obtained by a geometry optimization started from that point, effectively removing transition state regions from the problem. However, unlike other methods based upon hypersurface deformation, this transformation does not change the global minimum. The lowest known structures are located for all Lennard-Jones clusters up to 110 atoms, including a number that have never been found before in unbiased searches.

CHIANTI - an atomic database for emission lines - I. Wavelengths greater than 50 Å

Abstract: CHIANTI consists of a critically evaluated set of atomic data and transition probabilities necessary to calculate the emission line spectrum of astrophysical plasmas. The data consist of atomic energy levels, atomic radiative data such as wavelengths, weighted oscillator strengths and A values, and electron collisional excitation rates. A set of programs that use these data to calculate the spectrum in a desired wavelength range as a function of temperature and density is also provided. A suite of programs has been developed to carry out plasma diagnostics of astrophysical plasmas. The state-of-the-art contents of the CHIANTI database will be described and some of the most important results obtained from the use of the CHIANTI database will be reviewed.

Cellular energy utilization and molecular origin of standard metabolic rate in mammals

Abstract: The molecular origin of standard metabolic rate and thermogenesis in mammals is examined. It is pointed out that there are important differences and distinctions between the cellular reactions that 1) couple to oxygen consumption, 2) uncouple metabolism, 3) hydrolyze ATP, 4) control metabolic rate, 5) regulate metabolic rate, 6) produce heat, and 7) dissipate free energy. The quantitative contribution of different cellular reactions to these processes is assessed in mammals. We estimate that approximately 90% of mammalian oxygen consumption in the standard state is mitochondrial, of which approximately 20% is uncoupled by the mitochondrial proton leak and 80% is coupled to ATP synthesis. The consequences of the significant contribution of proton leak to standard metabolic rate for tissue P-to-O ratio, heat production, and free energy dissipation by oxidative phosphorylation and the estimated contribution of ATP-consuming processes to tissue oxygen consumption rate are discussed. Of the 80% of oxygen consumption coupled to ATP synthesis, approximately 25-30% is used by protein synthesis, 19-28% by the Na(+)-K(+)-ATPase, 4-8% by the Ca2(+)-ATPase, 2-8% by the actinomyosin ATPase, 7-10% by gluconeogenesis, and 3% by ureagenesis, with mRNA synthesis and substrate cycling also making significant contributions. The main cellular reactions that uncouple standard energy metabolism are the Na+, K+, H+, and Ca2+ channels and leaks of cell membranes and protein breakdown. Cellular metabolic rate is controlled by a number of processes including metabolic demand and substrate supply. The differences in standard metabolic rate between animals of different body mass and phylogeny appear to be due to proportionate changes in the whole of energy metabolism. Heat is produced by some reactions and taken up by others but is mainly produced by the reactions of mitochondrial respiration, oxidative phosphorylation, and proton leak on the inner mitochondrial membrane. Free energy is dissipated by all cellular reactions, but the major contributions are by the ATP-utilizing reactions and the uncoupling reactions. The functions and evolutionary significance of standard metabolic rate are discussed.

Another advanced test of theory of mind: evidence from very high functioning adults with autism or asperger syndrome.

Abstract: Previous studies have found a subgroup of people with autism or Asperger Syndrome who pass second-order tests of theory of mind. However, such tests have a ceiling in developmental terms corresponding to a mental age of about 6 years. It is therefore impossible to say if such individuals are intact or impaired in their theory of mind skills. We report the performance of very high functioning adults with autism or Asperger Syndrome on an adult test of theory of mind ability. The task involved inferring the mental state of a person just from the information in photographs of a person's eyes. Relative to age-matched normal controls and a clinical control group (adults with Tourette Syndrome), the group with autism and Asperger Syndrome were significantly impaired on this task. The autism and Asperger Syndrome sample was also impaired on Happe's strange stories tasks. In contrast, they were unimpaired on two control tasks: recognising gender from the eye region of the face, and recognising basic emotions from the whole face. This provides evidence for subtle mindreading deficits in very high functioning individuals on the autistic continuum.

A new location technique for the active office

Abstract: Configuration of the computing and communications systems found at home and in the workplace is a complex task that currently requires the attention of the user. Researchers have begun to examine computers that would autonomously change their functionality based on observations of who or what was around them. By determining their context, using input from sensor systems distributed throughout the environment, computing devices could personalize themselves to their current user, adapt their behaviour according to their location, or react to their surroundings. The authors present a novel sensor system, suitable for large-scale deployment in indoor environments, which allows the locations of people and equipment to be accurately determined. We also describe some of the context-aware applications that might make use of this fine-grained location information.

A specific neural substrate for perceiving facial expressions of disgust

Abstract: Recognition of facial expressions is critical to our appreciation of the social and physical environment, with separate emotions having distinct facial expressions. Perception of fearful facial expressions has been extensively studied, appearing to depend upon the amygdala. Disgust-literally 'bad taste'-is another important emotion, with a distinct evolutionary history, and is conveyed by a characteristic facial expression. We have used functional magnetic resonance imaging (fMRI) to examine the neural substrate for perceiving disgust expressions. Normal volunteers were presented with faces showing mild or strong disgust or fear. Cerebral activation in response to these stimuli was contrasted with that for neutral faces. Results for fear generally confirmed previous positron emission tomography findings of amygdala involvement. Both strong and mild expressions of disgust activated anterior insular cortex but not the amygdala; strong disgust also activated structures linked to a limbic cortico-striatal-thalamic circuit. The anterior insula is known to be involved in responses to offensive tastes. The neural response to facial expressions of disgust in others is thus closely related to appraisal of distasteful stimuli.

A calculus for cryptographic protocols: the spi calculus

Abstract: We introduce the spi calculus, an extension of the pi calculus designed for describing and analyzing cryptographic protocols. We show how to use the spi calculus, particularly for studying authentication protocols. The pi calculus (without extension) suffices for some abstract protocols; the spi calculus enables us to consider cryptographic issues in more detail. We represent protocols as processes in the spi calculus and state their security properties in terms of coarse-grained notions of protocol equivalence. ] 1999 Academic Press

Biochemical and Cellular Effects of Roscovitine, a Potent and Selective Inhibitor of the Cyclin‐Dependent Kinases cdc2, cdk2 and cdk5

Abstract: Cyclin-dependent kinases (cdk) play an essential role in the intracellular control of the cell division cycle (cdc). These kinases and their regulators are frequently deregulated in human tumours. Enzymatic screening has recently led to the discovery of specific inhibitors of cyclin-dependent kinases, such as butyrolactone I, flavopiridol and the purine olomoucine. Among a series of C2, N6, N9-substituted adenines tested on purified cdc2/cyclin B, 2-(1-ethyl-2-hydroxyethylamino)-6-benzylamino-9-isopropylpurine (roscovitine) displays high efficiency and high selectivity towards some cyclin-dependent kinases. The kinase specificity of roscovitine was investigated with 25 highly purified kinases (including protein kinase A, G and C isoforms, myosin light-chain kinase, casein kinase 2, insulin receptor tyrosine kinase, c-src, v-abl). Most kinases are not significantly inhibited by roscovitine. cdc2/cyclin B, cdk2/cyclin A, cdk2/cyclin E and cdk5/p35 only are substantially inhibited (IC50 values of 0.65, 0.7, 0.7 and 0.2 microM, respectively). cdk4/cyclin D1 and cdk6/cyclin D2 are very poorly inhibited by roscovitine (IC50 > 100 microM). Extracellular regulated kinases erk1 and erk2 are inhibited with an IC50 of 34 microM and 14 microM, respectively. Roscovitine reversibly arrests starfish oocytes and sea urchin embryos in late prophase. Roscovitine inhibits in vitro M-phase-promoting factor activity and in vitro DNA synthesis in Xenopus egg extracts. It blocks progesterone-induced oocyte maturation of Xenopus oocytes and in vivo phosphorylation of the elongation factor eEF-1. Roscovitine inhibits the proliferation of mammalian cell lines with an average IC50 of 16 microM. In the presence of roscovitine L1210 cells arrest in G1 and accumulate in G2. In vivo phosphorylation of vimentin on Ser55 by cdc2/cyclin B is inhibited by roscovitine. Through its unique selectivity for some cyclin-dependent kinases, roscovitine provides a useful antimitotic reagent for cell cycle studies and may prove interesting to control cells with deregulated cdc2, cdk2 or cdk5 kinase activities.

Central cholinergic systems and cognition

Abstract: The organization and possible functions of basal forebrain and pontine cholinergic systems are reviewed. Whereas the basal forebrain cholinergic neuronal projections likely subserve a common electrophysiological function, e.g. to boost signal-to-noise ratios in cortical target areas, this function has different effects on psychological processes dependent upon the neural network operations within these various cortical domains. Evidence is presented that (a) the nucleus basalis-neocortical cholinergic system contributes greatly to visual attentional function, but not to mnemonic processes per se; (b) the septohippocampal projection is involved in the modulation of short-term spatial (working) memory processes, perhaps by prolonging the neural representation of external stimuli within the hippocampus; and (c) the diagonal band-cingulate cortex cholinergic projection impacts on the ability to utilize response rules through conditional discrimination. We also suggest that nucleus basalis-amygdala cholinergic projections have a role in the retention of affective conditioning while brainstem cholinergic projections to the thalamus and midbrain dopamine neurons affect basic arousal processes (e.g. sleep-wake cycle) and behavioral activation, respectively. The possibilities and limitations of therapeutic interventions with procholinergic drugs in patients with Alzheimer's disease and other neurodegenerative disorders in which basal forebrain cholinergic neurons degenerate are also discussed.

Unit Cell Refinement from Powder Diffraction Data: The Use of Regression Diagnostics

Abstract: We discuss the use of regression diagnostics combined with nonlinear least-squares to refine cell parameters from powder diffraction data, presenting a method which minimizes residuals in the experimentallydetermined quantity (usually 20hkt or energy, Ehkt). Regression diagnostics, particularly deletion diagnostics, are invaluable in detection of outliers and influential data which could be deleterious to the regressed results. The usual practice of simple inspection of calculated residuals alone often fails to detect the seriously deleterious outliers in a dataset, because bare residuals provide no information on the leverage (sensitivity) of the datum concerned. The regression diagnostics which predict the change expected in each cell constant upon deletion of each observation (hkl reflection) are particularly valuable in assessing the sensitivity of the calculated results to individual reflections. A new computer program, implementing nonlinear regression methods and providing the diagnostic output, is described. I~YWORDS: powder diffraction, regression diagnostics, lattice parameters, computer program.

Optical and long wavelength afterglow from gamma-ray bursts

Abstract: We discuss the evolution of cosmological gamma-ray burst remnants, consisting of the cooling and expanding fireball ejecta together with any swept-up external matter, after the gamma-ray event. We show that significant optical emission is predicted, which should be measurable for timescales of hours after the event, and in some cases radio emission may be expected days to weeks after the event. The flux at optical, X-ray, and other long wavelengths decays as a power of time, and the initial value of the flux or magnitude, as well as the value of the time-decay exponent, should help to distinguish between possible types of dissipative fireball models.

Strategic Choice in the Analysis of Action, Structure, Organizations and Environment: Retrospect and Prospect

Abstract: This paper examines the place of the strategic choice perspective in the study of organizations and considers its contemporary contribution. The main fea tures of the original analysis are summarized, followed by a review of the key issues which arise from it. The paper discusses the integrative potential of strategic choice theory within organization studies and examines its contribu tion to an evolutionary perspective on the subject.

Better jet clustering algorithms

Abstract: We investigate modifications to the k⊥-clustering jet algorithm which preserve the advantages of the original Durham algorithm while reducing non-perturbative corrections and providing better resolution of jet substructure. We find that a simple change in the sequence of clustering (combining smaller-angle pairs first), together with the `freezing' of soft resolved jets, has beneficial effects.

Obesity and impaired prohormone processing associated with mutations in the human prohormone convertase 1 gene

Abstract: Human obesity has an inherited component, but in contrast to rodent obesity, precise genetic defects have yet to be defined. A mutation of carboxypeptidase E (CPE), an enzyme active in the processing and sorting of prohormones, causes obesity in the fat/fat mouse. We have previously described a women with extreme childhood obesity (Fig. 1), abnormal glucose homeostasis, hypogonadotrophic hypogonadism, hypocortisolism and elevated plasma proinsulin and pro-opiomelanocortin (POMC) concentrations but a very low insulin level, suggestive of a defective prohormone processing by the endopeptidase, prohormone convertase 1 (PC1; ref. 4). We now report this proband to be a compound heterozygote for mutations in PC1. Gly-->Arg483 prevents processing of proPC1 and leads to its retention in the endoplasmic reticulum (ER). A-->C+4 of the intro-5 donor splice site causes skipping of exon 5 leading to loss of 26 residues, a frameshift and creation of a premature stop codon within the catalytic domain. PC1 acts proximally to CPE in the pathway of post-translational processing of prohormones and neuropeptides. In view of the similarity between the proband and the fat/fat mouse phenotype, we infer that molecular defects in prohormone conversion may represent a generic mechanism for obesity, common to humans and rodents.

Associativity-Based Routing for Ad Hoc Mobile Networks

Abstract: This paper presents a new, simple and bandwidth-efficient distributed routing protocol to support mobile computing in a conference size ad-hoc mobile network environment. Unlike the conventional approaches such as link-state and distance-vector distributed routing algorithms, our protocol does not attempt to consistently maintain routing information in every node. In an ad-hoc mobile network where mobile hosts (MHs) are acting as routers and where routes are made inconsistent by MHs‘ movement, we employ an associativity-based routing scheme where a route is selected based on nodes having associativity states that imply periods of stability. In this manner, the routes selected are likely to be long-lived and hence there is no need to restart frequently, resulting in higher attainable throughput. Route requests are broadcast on a per need basis. The association property also allows the integration of ad-hoc routing into a BS-oriented Wireless LAN (WLAN) environment, providing the fault tolerance in times of base stations (BSs) failures. To discover shorter routes and to shorten the route recovery time when the association property is violated, the localised-query and quick-abort mechanisms are respectively incorporated into the protocol. To further increase cell capacity and lower transmission power requirements, a dynamic cell size adjustment scheme is introduced. The protocol is free from loops, deadlock and packet duplicates and has scalable memory requirements. Simulation results obtained reveal that shorter and better routes can be discovered during route re-constructions.

Transient optical emission from the error box of the gamma-ray burst of 28 February 1997

Abstract: For almost a quarter of a century1, the origin of γ-ray bursts— brief, energetic bursts of high-energy photons—has remained unknown. The detection of a counterpart at another wavelength has long been thought to be a key to understanding the nature of these bursts (see, for example, ref. 2), but intensive searches have not revealed such a counterpart. The distribution and properties of the bursts3 are explained naturally if they lie at cosmological distances (a few Gpc)4, but there is a countervailing view that they are relatively local objects5, perhaps distributed in a very large halo around our Galaxy. Here we report the detection of a transient and fading optical source in the error box associated with the burst GRB970228, less than 21 hours after the burst6,7. The optical transient appears to be associated with a faint galaxy7,8, suggesting that the burst occurred in that galaxy and thus that γ-ray bursts in general lie at cosmological distance.

Is There a "Language of the Eyes"? Evidence from Normal Adults, and Adults with Autism or Asperger Syndrome

Abstract: Previous work suggests that a range of mental states can be read from facial expressions, beyond the “basic emotions”. Experiment 1 tested this in more detail, by using a standardized method, and by testing the role of face parts (eyes vs. mouth vs. the whole face). Adult subjects were shown photographs of an actress posing 10 basic emotions (happy, sad, angry, afraid, etc.) and 10 complex mental states (scheme, admire, interest, thoughtfulness, etc.). For each mental state, each subject was shown the whole face, the eyes alone, or the mouth alone, and were given a forced choice of two mental state terms. Results indicated that: (1) Subjects show remarkable agreement in ascribing a wide range of mental states to facial expressions, (2) for the basic emotions, the whole face is more informative than either the eyes or the mouth, (3) for the complex mental states, seeing the eyes alone produced significantly better performance than seeing the mouth alone, and was as informative as the whole face. In Experim...

Readings in information retrieval

Abstract: Chapter 1 Overall Introduction Chapter 2 History Chapter 3 Key Concepts Chapter 4 Evaluation Chapter 5 Models Chapter 6 Techniques Chapter 7 Systems Chapter 8 Extensions Chapter 9 Envoi

Organic Fluorine Hardly Ever Accepts Hydrogen Bonds

Abstract: Statistical analysis of structural data and detailed inspection of individual crystal structures culled from the Cambridge Structural Database and the Brookhaven Protein Data Bank show that covalently bound fluorine (in contrast to anionic fluoride) hardly ever acts as a hydrogen-bond acceptor. The weakness of covalently bound fluorine as hydrogen-bond acceptor is backed by results of new molecular orbital calculations on model systems using ab initio intermolecular perturbation theory (IMPT), and is in accord with results of other physicochemical studies and with the physical properties of fluorinated organic compounds. Factors influencing the strength of hydrogen bonding in extended systems are discussed.