Showing papers by "Queen's University Belfast published in 2001"

Resolution of the early placental mammal radiation using Bayesian phylogenetics

Abstract: Molecular phylogenetic studies have resolved placental mammals into four major groups, but have not established the full hierarchy of interordinal relationships, including the position of the root. The latter is critical for understanding the early biogeographic history of placentals. We investigated placental phylogeny using Bayesian and maximum-likelihood methods and a 16.4-kilobase molecular data set. Interordinal relationships are almost entirely resolved. The basal split is between Afrotheria and other placentals, at about 103 million years, and may be accounted for by the separation of South America and Africa in the Cretaceous. Crown-group Eutheria may have their most recent common ancestry in the Southern Hemisphere (Gondwana).

Parallel adaptive radiations in two major clades of placental mammals

Abstract: Higher level relationships among placental mammals, as well as the historical biogeography and morphological diversification of this group, remain unclear1,2,3. Here we analyse independent molecular data sets, having aligned lengths of DNA of 5,708 and 2,947 base pairs, respectively, for all orders of placental mammals. Phylogenetic analyses resolve placental orders into four groups: Xenarthra, Afrotheria, Laurasiatheria, and Euarchonta plus Glires. The first three groups are consistently monophyletic with different methods of analysis. Euarchonta plus Glires is monophyletic or paraphyletic depending on the phylogenetic method. A unique nine-base-pair deletion in exon 11 of the BRCA1 gene provides additional support for the monophyly of Afrotheria, which includes proboscideans, sirenians, hyracoids, tubulidentates, macroscelideans, chrysochlorids and tenrecids. Laurasiatheria contains cetartiodactyls, perissodactyls, carnivores, pangolins, bats and eulipotyphlan insectivores. Parallel adaptive radiations have occurred within Laurasiatheria and Afrotheria. In each group, there are aquatic, ungulate and insectivore-like forms.

Chloroplast microsatellites: new tools for studies in plant ecology and evolution

Abstract: The nonrecombinant, uniparentally inherited nature of organelle genomes makes them useful tools for evolutionary studies. However, in plants, detecting useful polymorphism at the population level is often difficult because of the low level of substitutions in the chloroplast genome, and because of the slow substitution rates and intramolecular recombination of mtDNA. Chloroplast microsatellites represent potentially useful markers to circumvent this problem and, to date, studies have demonstrated high levels of intraspecific variability. Here, we discuss the use of these markers in ecological and evolutionary studies of plants, as well as highlighting some of the potential problems associated with such use.

Evolution of an artificial seawater medium: improvements in enriched seawater, artificial water over the last two decades

Abstract: Although most phycologists use natural seawater for culturing marine species, artificial media continue to play important roles in overcoming problems of supply and seasonal variability in the quality of natural seawater and also for experiments involving manipulation of micro- and macronutrients. Several artificial media have been developed over the last 90 years; enriched seawater, artificial water (ESAW) is among the more popular recipes. ESAW has the advantage of an ionic balance that is somewhat closer to that of normal seawater. The original paper compared the growth of 83 strains of microalgae in natural seawater (ESNW) versus ESAW and determined that 23% grew more poorly in the artificial water. Since 1980, however, the composition of ESAW, as used by the original authors, has changed considerably. In particular, the added forms of phosphate, iron, and silicate have been changed and the trace metal mixture has been altered to include nickel, molybdenum, and selenium. We tested whether these changes improved the ability of the artificial medium to grow previously difficult to grow phytoplankton species. To test this, we selected eight species that had been shown to grow better in ESNW than in ESAW and compared their growth again, using the currently used recipe with all the above modifications. For all but one species (Apedinella spinifera), growth rate and final yield was no different between the media but in one case (Emiliania huxleyi) was slightly higher in ESAW. No differences in cell morphology or volume were found in any case. We conclude that changes to the enrichment portion of the recipe have significantly improved this artificial seawater medium and that it can be used to grow an even wider range of coastal and open ocean species.

Benefits and risks of self medication.

Abstract: Self medication is becoming an increasingly important area within healthcare. It moves patients towards greater independence in making decisions about management of minor illnesses, thereby promoting empowerment. Self medication also has advantages for healthcare systems as it facilitates better use of clinical skills, increases access to medication and may contribute to reducing prescribed drug costs associated with publicly funded health programmes. However, self medication is associated with risks such as misdiagnosis, use of excessive drug dosage, prolonged duration of use, drug interactions and polypharmacy. The latter may be particularly problematic in the elderly. Monitoring systems, a partnership between patients, physicians and pharmacists and the provision of education and information to all concerned on safe self medication, are proposed strategies for maximising benefit and minimising risk.

Trends in the incidence of childhood-onset diabetes in Europe 1989-1998.

Abstract: Aims/hypothesis: To study the epidemiology of childhood-onset (Type I) insulin-dependent diabetes mellitus in Europe, the EURODIAB collaborative group in 1988 established prospective, geographically-defined registers of all children diagnosed with Type I diabetes under 15 years of age. This report is based on 24 423 children, registered by 36 centres, with complete participation during the period 1989–1998 and representing most European countries with a population coverage of approximately 20 million children.

Intermolecular potentials for simulations of liquid imidazolium salts

Abstract: Intermolecular potentials suitable for molecular dynamics or Monte Carlo simulations have been developed for dimethyl imidazolium and methyl ethyl imidazolium ions. The predicted crystal structures were compared with experimental crystal structures for chloride and PF− 6 salts and found to be satisfactory when the dominant electrostatic interactions were modelled by either an accurate distributed multipole description or a simplified atomic point charge model. A further simplification of using united atoms in place of methyl or methylene groups on the side chains gave a much less satisfactory reproduction of the crystal structures. Liquid dimethyl imidazolium chloride and dimethyl imidazolium PF− 6 were simulated using the explicit atom and united atom potentials. The local structure showed a strong preference for the chloride ions to be located in certain regions around the cation, and a similar, but less strong localization of the larger PF− 6. Significant differences in density and diffusion rates were...

Attractive intramolecular edge-to-face aromatic interactions in flexible organic molecules.

Abstract: Recent X-ray crystallographic and NMR evidence indicates that relatively weak intramolecular edge-to-face interactions between aromatic rings can affect or determine the conformation of organic molecules in the solid state and in solution. Experimental estimates indicate that these interactions are energetically attractive by ca. 1.5 kcal mol-1 but disfavored in solution by entropic factors due to the restricted internal mobility. Hence, these interactions are more manifest at low temperature in solution or in crystal structures where conformational entropy effects are negligible.

Catalytic water formation on platinum: a first-principles study.

Abstract: The study of catalytic behavior begins with one seemingly simple process, namely the hydrogenation of O to H2O on platinum. Despite the apparent simplicity its mechanism has been much debated. We have used density functional theory with gradient corrections to examine microscopic reaction pathways for several elementary steps implicated in this fundamental catalytic process. We find that H2O formation from chemisorbed O and H atoms is a highly activated process. The largest barrier along this route, with a value of approximately 1 eV, is the addition of the first H to O to produce OH. Once formed, however, OH groups are easily hydrogenated to H2O with a barrier of approximately 0.2 eV. Disproportionation reactions with 1:1 and 2:1 stoichiometries of H2O and O have been examined as alternative routes for OH formation. Both stoichiometries of reaction produce OH groups with barriers that are much lower than that associated with the O + H reaction. H2O, therefore, acts as an autocatalyst in the overall H2O formation process. Disproportionation with a 2:1 stoichiometry is thermodynamically and kinetically favored over disproportionation with a 1:1 stoichiometry. This highlights an additional (promotional) role of the second H2O molecule in this process. In support of our previous suggestion that the key intermediate in the low-temperature H2O formation reaction is a mixed OH and H2O overlayer we find that there is a very large barrier for the dissociation of the second H2O molecule in the 2:1 disproportionation process. We suggest that the proposed intermediate is then hydrogenated to H2O through a very facile proton-transfer mechanism.

Near-Field Distribution of Optical Transmission of Periodic Subwavelength Holes in a Metal Film

Abstract: Recent experimental discovery of the enhanced optical transmission through metal films with periodic subwavelength holes has given rise to a considerable interest in the optical properties of such structures due to their possible numerous applications in optics and optoelectronics as well as rich physics behind the phenomenon of the transmission enhancement [1–4]. The transmission of a subwavelength aperture is very low and proportional to the fourth power of the ratio of its diameter and light wavelength. However, if a metal film is perforated with a periodic array of such holes, the optical transmission can be significantly enhanced [1]. Being normalized to the total area of the illuminated holes, the transmission coefficient corresponds to an enhancement up to 3 orders of magnitude compared to the transmission of the same number of individual holes. This enhancement depends on the array geometry (hole diameter and periodicity), light wavelength, angle of incidence, as well as material of a film.

Advanced glycation: an important pathological event in diabetic and age related ocular disease.

Abstract: The formation of advanced glycation end products (AGEs) is a key pathophysiological event with links to a range of important human diseases. It is now clear that AGEs may act as mediators, not only of diabetic complications 12 but also of widespread age related pathology such as Alzheimer’s disease, 3 decreased skin elasticity, 45 male erectile dysfunction, 67 pulmonary fibrosis, 8 and atherosclerosis. 91 0 Since many cells and tissues of the eye are profoundly influenced by both diabetes and ageing, it is fitting that advanced glycation is now receiving considerable attention as a possible modulator in important visual disorders. An increasing number of reports confirm widespread AGE accumulation at sites of known ocular pathology and demonstrate how these products mediate crosslinking of long lived molecules in the eye. Such studies also underscore the putative pathophysiological role of advanced glycation in ocular cell dysfunction in vitro and in vivo. This article reviews some of the important eVects that advanced glycation has on ocular tissues and the role that AGEs, and their specific receptors, have in the initiation and progression of sight threatening disorders such as diabetic retinopathy, glaucoma, cataract formation, and age related macular degeneration (AMD). This review also considers pharmacological strategies to prevent or neutralise the eVects of AGEs and the recent development of potential therapies for AGE induced disease processes.

Approaches for determining phytoplankton nutrient limitation

Abstract: Aquatic primary productivity is frequently limited by the availability of nutrients. The ability to identify factors limiting algal growth is of considerable importance to our understanding of the ecology of aquatic plants and to water management practices. Methods used to identify limiting resources in the past have included a) analysis of nutrient availability, b) elemental composition and cell quotas for various nutrients, c) bio-assays monitoring growth of test species or of natural populations following nutrient enrichment and d) measurements of various physiological parameters, such as enhancement of respiration and dark carbon fixation rates and perturbation of photosynthetic rate following re-supply of nutrients.¶In this paper we briefly review the merits and methodological limitations of these approaches for the assessment of the nutrient status of algal populations. We discuss how an understanding of biochemical and metabolic changes induced by nutrient limitation has led to the development of rapid and simple tools to monitor the nutrient status of aquatic plants and algae. In particular, we describe the use of transient changes in chlorophyll a fluorescence as a potential tool for rapid assessment of algal nutrient status and the development of molecular probes specific to nutrient limited cells, such as flavodoxin as a diagnostic tool for Fe-limitation.

Quantum-information processing for a coherent superposition state via a mixedentangled coherent channel

Abstract: An entangled two-mode coherent state is studied within the framework of 2\ifmmode\times\else\texttimes\fi{}2-dimensional Hilbert space. An entanglement concentration scheme based on joint Bell-state measurements is worked out. When the entangled coherent state is embedded in vacuum environment, its entanglement is degraded but not totally lost. It is found that the larger the initial coherent amplitude, the faster entanglement decreases. We investigate a scheme to teleport a coherent superposition state while considering a mixed quantum channel. We find that the decohered entangled coherent state may be useless for quantum teleportation as it gives the optimal fidelity of teleportation less than the classical limit 2/3.

Assessment of DNA integrity and morphology of ejaculated spermatozoa from fertile and infertile men before and after cryopreservation

Abstract: Cryopreservation of human spermatozoa is extensively used in artificial insemination and IVF programmes Despite various advances in cryopreservation methodology, the recovery rate of functional post-thaw spermatozoa remains mediocre, with sperm motility being significantly decreased after freezing This aim of this study was to investigate the effects of cryopreservation on both DNA integrity and morphology of spermatozoa from fertile and infertile men Semen samples were obtained from 17 fertile and 40 infertile men All samples were prepared by discontinuous Percoll density centrifugation (950:475) Samples were divided into aliquots to allow direct comparison of fresh and frozen spermatozoa from the same ejaculate Aliquots for cryopreservation were mixed with a commercial cryoprotectant and frozen by static phase vapour cooling before plunging into liquid nitrogen Thawing was carried out slowly at room temperature Sperm DNA integrity was determined using a modified alkaline single cell gel electrophoresis (comet) assay and sperm morphology analysed using the Tygerberg criteria DNA of semen and prepared spermatozoa from fertile men was found to be unaffected by cryopreservation In marked contrast, spermatozoa from infertile men were significantly damaged by freeze-thawing Cryopreservation had a detrimental effect on morphology of semen and prepared samples from fertile and infertile men

Effect of Plasma Scale Length on Multi-MeV Proton Production by Intense Laser Pulses

Abstract: The influence of the plasma density scale length on the production of MeV protons from thin foil targets irradiated at $I{\ensuremath{\lambda}}^{2}\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}5\ifmmode\times\else\texttimes\fi{}{10}^{19}\phantom{\rule{0ex}{0ex}}\mathrm{W}\mathrm{cm}{}^{\ensuremath{-}2}$ has been studied. With an unperturbed foil, protons with energy $g20\phantom{\rule{0ex}{0ex}}\mathrm{MeV}$ were formed in an exponential energy spectrum with a temperature of $2.5\ifmmode\pm\else\textpm\fi{}0.3\mathrm{MeV}$. When a plasma with a scale length of $100\ensuremath{\mu}\mathrm{m}$ was preformed on the back of the foil, the maximum proton energy was reduced to $l5\phantom{\rule{0ex}{0ex}}\mathrm{MeV}$ and the beam was essentially destroyed. The experimental results are consistent with an electrostatic accelerating mechanism that requires an ultrashort scale length at the back of the target.

A Bangladesh soap opera: privatisation, accounting, and regimes of control in a less developed country

Abstract: This paper reports an intensive case study of a soap manufacturing company in Bangladesh that was nationalised upon Bangladesh's independence in 1971 and privatised in 1993. Theoretically it is informed by Burawoy's contributions to labour process theory, especially how the consent of labour is manufactured through internal states, internal labour markets and games, and how regimes of control in less developed ex-colonial countries are transformed by state and production politics. How the role of accounting systems may shape and be shaped by these processes is traced. Nationalisation brought state attempts to manufacture consent by the methods described in Burawoy's depiction of hegemonic regimes. However, idealistic attempts to secure accountability, rational planning and control, and consent through bureaucratic means were subverted and transformed into a regime of political hegemony. Here control was secured by political interventions, often at the behest of trade unions, for party political rather than commercial ends. Detailed systems of accounting for control and accountability were maintained but became marginal, ritualistic, and de-coupled from operations. Privatisation brought changes consistent with Burawoy's prediction of coercive controls within a new despotic regime. New owners destroyed the internal state and internal labour markets and, following widespread redundancies, most workers were hired through internal subcontracting. The changes heightened worker divisions and rendered workers powerless to resist. Gaming was observed but this relieved the pressures of work intensification and proved functional to management. Significant changes to accounting controls were made. External reporting ceased in violation of legal requirements — financial accounting became the preserve of the owning family and was beset with irregularities. Budgets became more market oriented and were transmitted downwards in a physical form to reinforce coercive pressures upon managers and thence the shop floor. The paper concludes by relating the findings to a revised model of transformation of control regimes in Bangladesh

Increased oxidative stress in Alzheimer's disease as assessed with 4-hydroxynonenal but not malondialdehyde.

Abstract: Oxidative stress is thought to play a major role in the pathogenesis of Alzheimer's disease (AD). Although there is strong post-mortem and experimental evidence of oxidative damage occurring in AD brains, the use of markers in the peripheral circulation to show oxidative stress is less convincing. We examined plasma from AD patients for markers of increased oxidative stress. We report elevated levels of 4-hydroxy-nonenal (4-HNE) in AD patients compared to controls (median 20.6, IQR 6.0-25.2 vs. 7.8, 3.3-14.5 micomol/l, respectively; p=0.001) but not malondialdehyde (MDA), and lower levels of ascorbate in AD plasma when compared to age-matched controls (9.9, 6.0-33.7 vs. 24.2, 13.9-48.6 micromol/l; p<0.05). Levels of 4-HNE in AD patients were inversely related to ascorbate (r=-0.337; p=0.07) and Folstein Mini-Mental State Examination (MMSE) (r=-0.474; p=0.015). The concentration of protein sulphydryls, free-radical scavengers, was directly related to the MMSE result (r=0.427; p=0.03). Increased production of 4-HNE indicates increased oxidative stress (lipid peroxidation), which is not evident using the more common marker MDA. This elevation of 4-HNE was related to the degree of cognitive impairment (MMSE).

Objective Psychomotor Skills Assessment of Experienced, Junior,and Novice Laparoscopists with Virtual Reality

Abstract: Objective assessment of psychomotor skills in surgery is now a priority; however, this assessment is difficult to achieve because of measurement difficulties associated with the reliability and validity of assessing surgical skills in vivo and in the laboratory. In this study virtual reality (VR) was used to overcome these problems in the objective psychomotor assessment of senior, junior, and novice laparoscopists. Twelve experienced laparoscopic surgeons (performed >50 Minimal Access Surgery (MAS) procedures), 12 inexperienced laparoscopic surgeons (<10 MAS procedures), and 12 laparoscopic novices (no MAS procedures) participated in the study. Each subject completed all six tasks of the Minimally Invasive Surgical Trainer; Virtual Reality (MIST VR). In comparison to the other groups, experienced laparoscopic surgeons performed the tasks significantly (p < 0.01) faster, had a lower error rate, were more economic in their movement of surgical instruments and in the use of diathermy. As a group they also showed greater consistency in their performance. MIST VR distinguished between the three groups of laparoscopists. VR provides a useful objective assessment tool for evaluating psychomotor skills for laparoscopic surgery.

‘Europeanizing’ Civil Society: NGOs as Agents of Political Socialization

Abstract: As a strategy for tackling the ‘democratic deficit’, attention is increasingly shifting towards the ‘Europeanization’ of civil society, the latter being traditionally viewed as a means both to limit state power and to promote intra-citizenry solidarity. However, this attempted change requires in turn actors who are both able and willing to act as agents of political socialization in the context of EU policy-making. This article examines the emphasis placed by both EU actors and the current academic literature on NGOs as such agents. Drawing on an analysis of similar claims made in development policy, I isolate the main indicators of NGOs' ability to foster the Europeanization of civil society via political socialization and put forward seven key tests of their ability to carry out this function in the EU context. These are then evaluated against the results of original empirical investigations. I argue that NGOs are currently unsuited to the task of Europeanizing civil society thanks to their inability to promote the political socialization of their supporters. As a consequence that task requires EU-level institutional reform informed by iterated public dialogue, as well as change in the working practices of NGOs.

Tyrosine-phosphorylated SOCS-3 inhibits STAT activation but binds to p120 RasGAP and activates Ras.

Abstract: Suppressors of cytokine signalling (SOCS, also known as CIS and SSI) are encoded by immediate early genes that act in a feedback loop to inhibit cytokine responses and activation of 'signal transducer and activator of transcription' (STAT). Here we show that SOCS-3 is strongly tyrosine-phosphorylated in response to many growth factors, including interleukin-2 (IL-2), erythropoietin (EPO), epidermal growth factor (EGF) and platelet-derived growth factor (PDGF). The principal phosphorylation sites on SOCS-3 are residues 204 and 221 at the carboxy terminus, and upon phosphorylation tyrosine 221 interacts with the Ras inhibitor p120 RasGAP. After IL-2 stimulation, phosphorylated SOCS-3 strongly inhibits STAT5 activation but, by binding to RasGAP, maintains activation of extracellular-signal-regulated kinase (ERK). A tyrosine mutant of SOCS-3 still blocks STAT phosphorylation, but also strongly inhibits IL-2-dependent activation of ERK and cell proliferation. Moreover, it also inhibits EPO- and PDGF-induced proliferation and ERK activation. Therefore, although SOCS proteins inhibit growth-factor responses, tyrosine phosphorylation of SOCS-3 can ensure cell survival and proliferation through the Ras pathway.

Geographical variation of presentation at diagnosis of Type I diabetes in children: the EURODIAB Study

Abstract: Aims/hypothesis: We aimed to describe the frequency and degree of diabetic ketoacidosis in children across Europe at the time of diagnosis of Type I (insulin-dependent) diabetes mellitus and to determine if factors such as age and geographical region contribute to the risk of diabetic ketoacidosis.

Postoperative residual block after intermediate-acting neuromuscular blocking drugs

Abstract: The frequency and duration of postoperative residual neuromuscular block on arrival of 150 patients in the recovery ward following the use of vecuronium (n = 50), atracurium (n = 50) and rocuronium (n = 50) were recorded. Residual block was defined as a train-of-four ratio of <0.8. An additional group of 10 patients received no neuromuscular blocking drugs during anaesthesia. The incidence of postoperative residual neuromuscular block was 64%, 52% and 39% after the use of vecuronium, atracurium and rocuronium, respectively. Similar numbers of patients were not able to maintain a sustained head or leg lift for 5 s on arrival in the recovery ward. The mean [range] times to attaining a train-of-four ratio of ≥0.8 after arrival in the recovery ward were 9.2 [1–61], 6.9 [1–24] and 14.7 [1.5–83] min for vecuronium, atracurium and rocuronium, respectively. None of the 10 patients who did not receive neuromuscular blocking drugs had train-of-four ratios <0.8 on arrival in the recovery ward. It is concluded that a large proportion of patients arrive in the recovery ward with a train-of-four ratio <0.8, even with the use of intermediate-acting neuromuscular blocking drugs. Although the residual block is relatively short lasting, it may occasionally be prolonged, requiring close observation and monitoring of such patients in the recovery ward.