Showing papers by "University of Reading published in 1999"

Inferring the historical patterns of biological evolution

Abstract: Phylogenetic trees describe the pattern of descent amongst a group of species. With the rapid accumulation of DNA sequence data, more and more phylogenies are being constructed based upon sequence comparisons. The combination of these phylogenies with powerful new statistical approaches for the analysis of biological evolution is challenging widely held beliefs about the history and evolution of life on Earth.

Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut

Abstract: The human intestinal tract harbors a complex microbial ecosystem which plays a key role in nutrition and health. Although this microbiota has been studied in great detail by culture techniques, microscopic counts on human feces suggest that 60 to 80% of the observable bacteria cannot be cultivated. Using comparative analysis of cloned 16S rRNA gene (rDNA) sequences, we have investigated the bacterial diversity (both cultivated and noncultivated bacteria) within an adult-male fecal sample. The 284 clones obtained from 10-cycle PCR were classified into 82 molecular species (at least 98% similarity). Three phylogenetic groups contained 95% of the clones: the Bacteroides group, the Clostridium coccoides group, and the Clostridium leptum subgroup. The remaining clones were distributed among a variety of phylogenetic clusters. Only 24% of the molecular species recovered corresponded to described organisms (those whose sequences were available in public databases), and all of these were established members of the dominant human fecal flora (e.g., Bacteroides thetaiotaomicron, Fusobacterium prausnitzii, and Eubacterium rectale). However, the majority of generated rDNA sequences (76%) did not correspond to known organisms and clearly derived from hitherto unknown species within this human gut microflora.

New Ideas In Optimization

Abstract: Optimization is a pivotal aspect of software design. The techniques treated in this text represent research as elucidated by the leaders in the field. The optimization methods are applied to real problems, such as hilllclimbing, simulated annealing, and tabu search.

The Pareto archived evolution strategy: a new baseline algorithm for Pareto multiobjective optimisation

Abstract: Most popular evolutionary algorithms for multiobjective optimisation maintain a population of solutions from which individuals are selected for reproduction. In this paper, we introduce a simpler evolution scheme for multiobjective problems, called the Pareto archived evolution strategy (PAES). We argue that PAES may represent the simplest possible non-trivial algorithm capable of generating diverse solutions in the Pareto optimal set. The algorithm is identified as being a (1+1) evolution strategy, using local search from a population of one but using a reference archive of previously found solutions in order to identify the approximate dominance ranking of the current and candidate solution vectors. PAES is intended as a good baseline approach, against which more involved methods may be compared, and may also serve well in some real-world applications when local search seems superior to or competitive with population-based methods. The performance of the new algorithm is compared with that of a MOEA based on the niched Pareto GA on a real world application from the telecommunications field. In addition, we include results from experiments carried out on a suite of four test functions, to demonstrate the algorithm's general capability.

Culture specific and cross-culturally generalizable implicit leadership theories: Are attributes of charismatic/transformational leadership universally endorsed?

Abstract: This study focuses on culturally endorsed implicit theories of leadership (CLTs). Although cross-cultural research emphasizes that different cultural groups likely have different conceptions of what leadership should entail, a controversial position is argued here: namely that attributes associated with charismatic/transformational leadership will be universally endorsed as contributing to outstanding leadership. This hypothesis was tested in 62 cultures as part of the Global Leadership and Organizational Behavior Effectiveness (GLOBE) Research Program. Universally endorsed leader attributes, as well as attributes that are universally seen as impediments to outstanding leadership and culturally contingent attributes are presented here. The results support the hypothesis that specific aspects of charismatic/transformational leadership are strongly and universally endorsed across cultures.

A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars

Abstract: Commercial scale fingerprinting of potato cultivars is made difficult by the need for speed, reliability and the ability to distinguish between large numbers of genotypes. There are also problems in extrapolating the results of small experimental studies to predict the performance of techniques or primers for larger applications. The potential of ISSR-PCR for fingerprinting purposes was evaluated using four primers on 34 potato cultivars. The complex band profiles generated were reproducible between repeat PCRs, DNA extractions, electrophoreses and gel scorings. Two primers were each able to distinguish all cultivars. The combined use of any two of the four primers also allowed complete diagnosis. It is concluded that ISSR-PCR provides a quick, reliable and highly informative system for DNA fingerprinting that is amenable for routine applications. Two possible correlates of the ability of primers to distinguish between genotypes were then examined. Marker Index failed to correlate significantly with genotype diagnosis, but a strong and seemingly linear relationship was observed between Resolving Power of a primer and its ability to distinguish genotypes (r2=0.98). Resolving Power of one or a pair of primers was found to provide a moderately accurate estimate of the number of genotypes identified. Possible implications for future studies on DNA fingerprinting are discussed.

The Maximum Likelihood Approach to Reconstructing Ancestral Character States of Discrete Characters on Phylogenies

Abstract: A phylogeny describes the hierarchical pattern of descent of some group of species from a common ancestor. If information is available on the character states of the contemporary species, thepossibility is raised of using that information in combination with the phylogeny to reconstruct the historical events of evolution. These reconstructions can be used to retrieve a picture of theworld as the species evolved alongwhatwould become the branches of the phylogeny. This, in turn, provides a way to test hypotheses about evolution and adaptation. Methods based on the principle of parsimony reconstruct the ancestral character states to minimize the number of historical character changes required to produce the diversity observed among the contemporary species (seeMaddison et al., 1984, for a general account). An alternative to parsimony approaches makes use of the principle of maximum likelihood. Maximum likelihood solutions make the observed data most likely given somemodel of the process under investigation (see Edwards, 1972). In a phylogenetic context this means reconstructing the ancestral character states to make the character states observed among the contemporary species most probable, given some statistical model of the way evolution proceeds. Maximum likelihood solutions may or may not be the mostparsimonious solution. I restrict myself here to using maximum likelihood models to infer ancestral character states for binary discrete characters, that is, for characters that can adopt only two states, although the generalization to more than two states requires no new concepts.My approach to reconstructing ancestral states makes use of a Markov model of binary character evolution on phylogenies (Pagel, 1994). Sanderson (1993) describes a related model for investigating rates of gains and losses of characters for which the ancestral states are assumed to be known. Schluter (1995), Yang et al. (1995), and Koshi and Goldstein (1996) derive methods that are similar to the procedures I will describe here. However, Yang et al. (1995) and Koshi and Goldstein (1996) use what I shall term “global” methods for estimating ancestral characters, I argue for a “local” approach on grounds that the global method does not produce a maximum-likelihood estimate of the hypothesis of interest. Schluter (1995) reported global and local estimators in his investigation of artiodactyl ribonucleases, and Schluter et al. (1997) reported global estimators. In several recent papers, Schluter (1995; Schluter et al., 1997) called attention to the usefulness of reconstructing ancestral character states for testing ideas about adaptation and evolution, and much of what I say here owes its inspiration to these investigations. Mooers and Schluter (1999) now provide important additional examples of how maximum likelihood methods can return both more information about ancestral character states thanparsimony approaches, as well as information that is at odds with parsimony reconstructions. I intend this article to act as a primer to thosewhoare interested in usingmaximumlikelihood methods but who may not be familiar with the mathematics of the approach. Accordingly, I begin with the simplest case of estimating the ancestral state of two species.

Carbon Nanotubes and Related Structures: New Materials for the Twenty-first Century

Abstract: 1 Introduction 2 Synthesis 3 Structure 4 The physics of nanotubes 5 Nano-capsules and nano-test-tubes 6 The ultimate carbon fibre? 7 Curved crystals, inorganic fullerenes and nanorods 8 Carbon onions and spheroidal carbon 9 Future directions Index

On plane-based camera calibration: A general algorithm, singularities, applications

Abstract: We present a general algorithm for plane-based calibration that can deal with arbitrary numbers of views and calibration planes. The algorithm can simultaneously calibrate different views from a camera with variable intrinsic parameters and it is easy to incorporate known values of intrinsic parameters. For some minimal cases, we describe all singularities, naming the parameters that can not be estimated. Experimental results of our method are shown that exhibit the singularities while revealing good performance in non-singular conditions. Several applications of plane-based 3D geometry inference are discussed as well.

Police (canteen) sub-culture. An appreciation

Abstract: Police sub-culture is often portrayed as a pervasive, malign and potent influence on the behaviour of officers. The grounds for this portrayal are, however, insubstantial and appear to rely more upon the condemnatory potential of the concept than its explanatory power. This article reviews the literature on police sub-culture and concludes that what occurs in the canteen is expressive talk designed to give purpose and meaning to inherently problematic occupational experience. The canteen is an arena of action separate from the street, where in contrast to the latter officers act before an audience of their peers.

Anandamide induces overeating: mediation by central cannabinoid (CB1) receptors

Abstract: Rationale: Central cannabinoid systems have been implicated in appetite regulation by the respective hyperphagic actions of exogenous cannabinoids, such as Δ9-THC, and hypophagic effects of selective cannabinoid receptor antagonists. Objective: This study examined whether an endogenous cannabinoid, anandamide, could induce overeating, via a specific action at central (CB1) cannabinoid receptors. Methods: Pre-satiated male rats (n=18), received subcutaneous injections of anandamide (0.5, 1.0, 5.0, 10.0 mg/kg) before 3-h, nocturnal food in- take tests. In a second series of intake tests ( n=8), anand- amide injection (1.0 mg/kg) was preceded by injection of the specific CB1 receptor antagonist, SR141716 (0.1, 0.5, 1.0 mg/kg SC). Results: All doses of anandamide induced significant overeating, with 1.0 mg/kg being most potent. Additionally, hyperphagia induced by 1.0 mg/kg anand- amide was dose-dependently attenuated by SR141716 pretreatment. Conclusion: This first demonstration of an- andamide-induced, CB1-mediated, overeating provides important evidence for the involvement of a central can- nabinoid system in the normal control of eating.

The Socioemotional Development of 5‐year‐old Children of Postnatally Depressed Mothers

Abstract: A community sample of depressed and well mothers, recruited at 2 months postpartum and assessed through to 18 months, was followed up at 5 years. The quality of mother-child interactions was assessed, as was the children's behavioural and social adjustment, using maternal reports and observations of child behaviour during free play at school. Several aspects of child outcome were found to be associated with postnatal depression, even when taking account of current adverse circumstances (maternal depression and parental conflict). These included the child's behaviour with the mother, the presence of behavioural disturbance at home, and the content and social patterning of play at school. These associations with postnatal depression were independent of the child's gender. The child's relationship with the mother appeared to be mediated by the quality of infant attachment at 18 months. The mother's behaviour with her child was more affected by current difficulties, in particular by conflict with the child's father. Together these findings suggest that, while maternal behaviour varies with changing circumstances, exposure to maternal depression in the early postpartum months may have an enduring influence on child psychological adjustment.

Characterization of Hepatitis C Virus E2 Glycoprotein Interaction with a Putative Cellular Receptor, CD81

Abstract: A truncated soluble form of the hepatitis C virus E2 glycoprotein, E2661, binds specifically to the surface of cells expressing human CD81 (hCD81) but not other members of the tetraspanin family (CD9, CD63, and CD151). No differences were noted between the level of E2661 binding to hCD81 expressed on the surface of rat RBL or KM3 cells compared to Daudi and Molt-4 cells, suggesting that additional human-cell-specific factors are not required for the primary interaction of E2 with the cell surface. E2 did not interact with African green monkey (AGM) CD81 on the surface of COS cells, which differs from the hCD81 sequence at four residues within the second extracellular region (EC2) (amino acids [aa] 163, 186, 188, and 196), suggesting that one or more of these residues defines the site of interaction with E2. Various recombinant forms of CD81 EC2 show differences in the ability to bind E2, suggesting that CD81 conformation is important for E2 recognition. Regions of E2 involved in the CD81 interaction were analyzed, and our data suggest that the binding site is of a conformational nature involving aa 480 to 493 and 544 to 551 within the E2 glycoprotein. Finally, we demonstrate that ligation of CD81 by E2661 induced aggregation of lymphoid cells and inhibited B-cell proliferation, demonstrating that E2 interaction with CD81 can modulate cell function.

Post-partum depression and the mother-infant relationship in a South African peri-urban settlement

Abstract: BACKGROUND Post-partum depression in the developing world has received little research attention, and its association with disturbances in the mother-infant relationship is unknown. AIMS To determine the prevalence of post-partum depression and associated disturbances in the mother-infant relationship in Khayelitsha, a South African peri-urban settlement. METHOD The mental state of 147 women who had delivered two months previously was assessed, and the quality of their engagement with their infants was determined. RESULTS The point prevalence of DSM-IV major depression was found to be 34.7%. Maternal depression was associated with poor emotional and practical support from the partner. It was also associated with insensitive engagement with the infants. CONCLUSIONS The rate of post-partum depression in Khayelitsha was around three times that found in British post-partum samples, and these depressions were strongly associated with disturbances in the mother-infant relationship.

Developmental basis of limblessness and axial patterning in snakes

Abstract: The evolution of snakes involved major changes in vertebrate body plan organization, but the developmental basis of those changes is unknown. The python axial skeleton consists of hundreds of similar vertebrae, forelimbs are absent and hindlimbs are severely reduced. Combined limb loss and trunk elongation is found in many vertebrate taxa1, suggesting that these changes may be linked by a common developmental mechanism. Here we show that Hox gene expression domains are expanded along the body axis in python embryos, and that this can account for both the absence of forelimbs and the expansion of thoracic identity in the axial skeleton. Hindlimb buds are initiated, but apical-ridge and polarizing-region signalling pathways that are normally required for limb development are not activated. Leg bud outgrowth and signalling by Sonic hedgehog in pythons can be rescued by application of fibroblast growth factor or by recombination with chick apical ridge. The failure to activate these signalling pathways during normal python development may also stem from changes in Hox gene expression that occurred early in snake evolution.

A broad-scale circulation index for the interannual variability of the Indian summer monsoon

Abstract: A broad-scale circulation index representing the interannual variability of the Indian summer monsoon is proposed and is shown to be well correlated with the interannual variability of precipitation in the Indian monsoon region. Using monthly precipitation analysis based on merging rain-gauge data with satellite estimates of precipitation for the period 1979-96, it is shown that the variability of precipitation on seasonal to interannual time-scales is coherent over a large region covering the Indian continent as well as the north Bay of Bengal and parts of south China. A new index, termed Extended Indian Monsoon Rainfall (EIMR), is defined as the precipitation averaged over the region 70 degrees E-110 degrees E, 10 degrees N-30 degrees N. The EIMR index is expected to represent the convective heating fluctuations associated with the Indian monsoon better than the traditional all India Monsoon Rainfall (IMR) based only on the precipitation over the Indian continent. It is shown that large precipitation over the Bay of Bengal with significant interannual variability cannot be ignored in the definition of Indian summer monsoon and its variability. The June-to-September climatological mean EIMR is found to be larger than that of the LMR even though the former is averaged over a larger area. The dominant mode of interannual variability of the Indian summer monsoon is associated with a dipole between the EIMR region and the north-western Pacific region (110 degrees E-160 degrees E, 10 degrees N-30 degrees N) and a meridional dipole between the EIMR region and the equatorial Indian Ocean (70 degrees E-110 degrees E, 10 degrees S-5 degrees N). It is argued that the interannual variability of the monsoon circulation is primarily driven by gradients of diabatic heating associated with variations of the EIMR, and that the regional monsoon Hadley circulation is a manifestation of this heating. An index of the monsoon Hadley (MH) circulation is defined as the meridional wind-shear anomaly (between 850 hPa and 200 hPa) averaged over the same domain as the EIMR. Using circulation data from two independent reanalysis products, namely the National Centers for Environmental Prediction/National Center for Atmospheric Research reanalysis and the European Centre for Medium-Range Weather Forecasts reanalysis, it is shown that the MH index is significantly correlated with the EIMR. Also it is shown that both the EIMR and MH indices have a dominant quasi-biennial variability, consistent with previous studies of IMR. Teleconnections of IMR, EIMR and MH indices with summer sea surface temperature (SST) have also been investigated. There are indications that the south equatorial Indian Ocean SST has a strong positive correlation with the EIMR. Also it is noted that the correlation of the monsoon indices with the eastern Pacific SST was weak during the period under consideration primarily due to almost a reverse relationship between monsoon and El Nino and Southern Oscillation during the latest eight years.

Dietary modulation of the human gut microflora using the prebiotics oligofructose and inulin.

Abstract: Although largely unproven in humans, better resistance to pathogens, reduction in blood lipids, antitumor properties, hormonal regulation and immune stimulation may all be possible through gut microflora manipulation. One approach advocates the oral intake of live microorganisms (probiotics). Although the probiotic approach has been extensively used and advocated, survivability/viability after ingestion is difficult to guarantee and almost impossible to prove. The prebiotic concept dictates that non viable dietary components fortify certain components of the intestinal flora (e.g., bifidobacteria, lactobacilli). This concept has the advantage that survival of the ingested ingredient through the upper gastrointestinal tract is not a prerequisite because it is indigenous bacterial genera that are targeted. The feeding of oligofructose and inulin to human volunteers alters the gut flora composition in favor of bifidobacteria, a purportedly beneficial genus. Future human studies that exploit the use of modern molecular-based detection methods for bacteria will determine the efficacy of prebiotics. It may be possible to address prophylactically certain gastrointestinal complaints through the selective targeting of gut bacteria.

Stratospheric water vapour changes as a possible contributor to observed stratospheric cooling

Abstract: The observed cooling of the lower stratosphere over the last two decades has been attributed, in previous studies, largely to a combination of stratospheric ozone loss and carbon dioxide increase, and as such it is meant to provide one of the best pieces of evidence for an anthropogenic cause to climate change. This study shows how increases in stratospheric water vapour, inferred from available observations, may be capable of causing as much of the observed cooling as ozone loss does; as the reasons for the stratospheric water vapour increase are neither fully understood nor well characterized, it shows that it remains uncertain whether the cooling of the lower stratosphere can yet be fully attributable to human influences. In addition, the changes in stratospheric water vapour may have contributed, since 1980, a radiative forcing which enhances that due to carbon dioxide alone by 40%.

Lipoprotein-associated phospholipase A2, platelet-activating factor acetylhydrolase, generates two bioactive products during the oxidation of low-density lipoprotein: use of a novel inhibitor.

Abstract: A novel and potent azetidinone inhibitor of the lipoprotein-associated phospholipase A2 (Lp-PLA2), i.e. platelet-activating factor acetylhydrolase, is described for the first time. This inhibitor, SB-222657 (Ki=40+/-3 nM, kobs/[I]=6. 6x10(5) M-1.s-1), is inactive against paraoxonase, is a poor inhibitor of lecithin:cholesterol acyltransferase and has been used to investigate the role of Lp-PLA2 in the oxidative modification of lipoproteins. Although pretreatment with SB-222657 did not affect the kinetics of low-density lipoprotein (LDL) oxidation by Cu2+ or an azo free-radical generator as determined by assay of lipid hydroperoxides (LOOHs), conjugated dienes and thiobarbituric acid-reacting substances, in both cases it inhibited the elevation in lysophosphatidylcholine content. Moreover, the significantly increased monocyte chemoattractant activity found in a non-esterified fatty acid fraction from LDL oxidized by Cu2+ was also prevented by pretreatment with SB-222657, with an IC50 value of 5.0+/-0.4 nM. The less potent diastereoisomer of SB-222657, SB-223777 (Ki=6.3+/-0.5 microM, kobs/[I]=1.6x10(4) M-1.s-1), was found to be significantly less active in both assays. Thus, in addition to generating lysophosphatidylcholine, a known biologically active lipid, these results demonstrate that Lp-PLA2 is capable of generating oxidized non-esterified fatty acid moieties that are also bioactive. These findings are consistent with our proposal that Lp-PLA2 has a predominantly pro-inflammatory role in atherogenesis. Finally, similar studies have demonstrated that a different situation exists during the oxidation of high-density lipoprotein, with enzyme(s) other than Lp-PLA2 apparently being responsible for generating lysophosphatidylcholine.

Effect of the polyunsaturated fatty acid composition of beef muscle on the profile of aroma volatiles.

Abstract: The effect of n-3 polyunsaturated fatty acids (PUFAs) in beef muscle on the composition of the aroma volatiles produced during cooking was measured. The meat was obtained from groups of steers fed different supplementary fats: (i) a palm-oil-based control; (ii) bruised whole linseed, which increased muscle levels of alpha-linolenic (C18:3 n-3) and eicosapentaenoic acid (EPA, C20:5 n-3); (iii) fish oil, which increased EPA and docosahexaenoic acid (C22:6 n-3); (iv) equal quantities of linseed and fish oil. Higher levels of lipid oxidation products were found in the aroma extracts of all of the steaks with increased PUFA content, after cooking. In particular, n-alkanals, 2-alkenals, 1-alkanols, and alkylfurans were increased up to 4-fold. Most of these compounds were derived from the autoxidation of the more abundant mono- and di-unsaturated fatty acids during cooking, and such autoxidation appeared to be promoted by increased levels of PUFAs.

Adaptive Constraints for Feature Tracking

Abstract: In this paper extensions to an existing tracking algorithm are described. These extensions implement adaptive tracking constraints in the form of regional upper-bound displacements and an adaptive track smoothness constraint. Together, these constraints make the tracking algorithm more flexible than the original algorithm (which used fixed tracking parameters) and provide greater confidence in the tracking results. The result of applying the new algorithm to high-resolution ECMWF reanalysis data is shown as an example of its effectiveness.

A review of methods to calculate extreme wind speeds

Abstract: Methods to calculate extreme wind speeds are described and reviewed, including ‘classical’ methods based on the generalized extreme value (GEV) distribution and the generalized Pareto distribution (GPD), and approaches designed specifically to deal with short data sets. The emphasis is very much on the needs of users who seek an accurate method to derive extreme wind speeds but are not fully conversant with up-to-date developments in this complex subject area. First, ‘standard’ methods are reviewed: annual maxima, independent storms, r-largest extremes with the GEV distribution, and peak-over-threshold extremes with the GPD. Techniques for calculating the distribution parameters and quantiles are described. There follows a discussion of the factors which must be considered in order to fulfil the criterion that the data should be independent and identically distributed, and in order to minimize standard errors. It is commonplace in studies of extreme wind speeds that the time series available for analysis are very short. Finally, therefore, the paper deals with techniques applicable to data sets as short as two years, including simulation modelling and methods based on the parameters of the parent distribution.

Maintenance of the African easterly jet

Abstract: The maintenance of the African easterly jet (AEJ) has been examined using a zonally symmetric general circulation model with simple parametrizations. It is shown that the AEJ is maintained in association with two diabatically forced meridional circulations: one associated with surface fluxes and dry convection in the Saharan heat-low region and one associated with deep moist convection in the intertropical convergence zone equatorward of this. the heat-low heating, which reaches the height of the AEJ around 700 mb, is particularly important in maintaining the AEJ and its associated meridional gradients in potential vorticity. It is concluded that the mean observed AEJ results from a combination of the diabatically forced meridional circulations which maintain it and easterly waves which weaken it.