Showing papers by "Peter Simmonds published in 2002"
TL;DR: In this article, the authors examined the transatlantic transport of anthropogenic ozone and its impact on surface ozone in Europe and North America by using a 5-year simulation with the GEOS-CHEM global three-dimensional model of tropospheric chemistry.
Abstract: [1] We examine the transatlantic transport of anthropogenic ozone and its impact on surface ozone in Europe and North America by using a 5-year (1993–1997) simulation with the GEOS-CHEM global three-dimensional model of tropospheric chemistry. Long-term time series of ozone and CO at Mace Head (Ireland) and Sable Island (Canada) are used to evaluate transatlantic transport in the model. North American anthropogenic emissions contribute on average 5 ppbv to surface ozone at Mace Head, and up to 10–20 ppbv during transatlantic transport events, which are forerunners of broader events in Europe. These events are associated with low-level westerly flow driven by an intense Icelandic low between Iceland and the British Isles. North American influence on ozone at Mace Head is strongly correlated with the North Atlantic Oscillation (NAO), implying that the NAO index can be used to forecast transatlantic transport of North American pollution to Europe. European anthropogenic emissions contribute on average less than 2 ppbv to surface ozone at Sable Island but up to 5–10 ppbv during transatlantic transport events. These events are associated with low-level easterly flow established by anomalous low pressure at 45°N over the North Atlantic. North American anthropogenic emissions enhance surface ozone in continental Europe by 2–4 ppbv on average in summer and by 5–10 ppbv during transatlantic transport events; transport in the boundary layer and subsidence from the free troposphere are both important mechanisms. We find in the model that 20% of the violations of the European Council ozone standard (55 ppbv, 8-hour average) in the summer of 1997 over Europe would not have occurred in the absence of anthropogenic emissions from North America. North American influence on surface ozone in Europe is particularly strong at the thresholds used for the European standards (55–65 ppbv).
295 citations
TL;DR: In this article, the authors used a two-dimensional (2-D), 12-box model with transport constrained by the GAGE/AGAGE chlorofluorocarbon measurements, and calculated that the proportion of the emissions coming from the Northern Hemisphere is between 73 and 81%.
Abstract: [1] Continuous measurements of methane since 1986 at the Global Atmospherics Gases Experiment/Advanced Global Atmospherics Gases Experiment (GAGE/AGAGE) surface sites are described. The precisions range from approximately 10 ppb at Mace Head, Ireland, during GAGE to better than 2 ppb at Cape Grim, Tasmania, during AGAGE (i.e., since 1993). The measurements exhibit good agreement with coincident measurements of air samples from the same locations analyzed by Climate Monitoring and Diagnostics Laboratory (CMDL) except for differences of approximately 5 ppb before 1989 (GAGE lower) and about 4 ppb from 1991 to 1995 (GAGE higher). These results are obtained before applying a factor of 1.0119 to the GAGE/AGAGE values to place them on the Tohoku University scale. The measurements combined with a 12-box atmospheric model and an assumed atmospheric lifetime of 9.1 years indicates net annual emissions (emissions minus soil sinks) of 545 Tg CH4 with a variability of only ±20 Tg from 1985 to 1997 but an increase in the emissions in 1998 of 37 ± 10 Tg. The effect of OH changes inferred by Prinn et al. [2001] is to increase the estimated methane emissions by approximately 20 Tg in the mid-1980s and to reduce them by 20 Tg in 1997 and by more thereafter. Using a two-dimensional (2-D), 12-box model with transport constrained by the GAGE/AGAGE chlorofluorocarbon measurements, we calculate that the proportion of the emissions coming from the Northern Hemisphere is between 73 and 81%, depending on the OH distribution used. However, this result includes an adjustment of 5% derived from a simulation of the 2-D estimation procedure using the 3-D MOZART model. This adjustment is needed because of the very different spatial emission distributions of the chlorofluorocarbons and methane which makes chlorofluorocarbons derived transport rates inaccurate for the 2-D simulation of methane. The 2-D model combined with the annual cycle in OH from Spivakovsky et al. [2000] provide an acceptable fit to the observed 12-month cycles in methane. The trend in the amplitude of the annual cycle of methane at Cape Grim is used to infer a trend in OH in 30°–90°S of 0 ± 5% per decade from 1985 to 2000, in qualitative agreement with Prinn et al. [2001] for the Southern Hemisphere.
147 citations
TL;DR: The structure predictions in this study could provide the starting point for functional investigations using recently developed self-replicating clones of HCV, although predictions of secondary structures were limited by the absence of comparative sequence data for this virus.
Abstract: The existence and functional importance of RNA secondary structure in the replication of positive-stranded RNA viruses is increasingly recognized. We applied several computational methods to detect RNA secondary structure in the coding region of hepatitis C virus (HCV), including thermodynamic prediction, calculation of free energy on folding, and a newly developed method to scan sequences for covariant sites and associated secondary structures using a parsimony-based algorithm. Each of the prediction methods provided evidence for complex RNA folding in the core- and NS5B-encoding regions of the genome. The positioning of covariant sites and associated predicted stem-loop structures coincided with thermodynamic predictions of RNA base pairing, and localized precisely in parts of the genome with marked suppression of variability at synonymous sites. Combined, there was evidence for a total of six evolutionarily conserved stem-loop structures in the NS5B-encoding region and two in the core gene. The virus most closely related to HCV, GB virus-B (GBV-B) also showed evidence for similar internal base pairing in its coding region, although predictions of secondary structures were limited by the absence of comparative sequence data for this virus. While the role(s) of stem-loops in the coding region of HCV and GBV-B are currently unknown, the structure predictions in this study could provide the starting point for functional investigations using recently developed self-replicating clones of HCV.
144 citations
TL;DR: The degree of city-specific segregation of HCV subtype 1a sequences was linearly related to that of subtype 3a, indicating that these subtypes have spread through similar transmission networks.
Abstract: Hepatitis C virus (HCV) genotype 1a and 3a partial NS5B gene segment sequences obtained from 154 HCV-infected injection drug users were studied to determine the extent to which HCV transmission occurs between injection drug user communities in London, Edinburgh, Glasgow (United Kingdom), Marseilles (France), and Melbourne. Phylogenetic relationships between sequences were analyzed by conventional methods and by a recently developed method that numerically scores the extent of sequence segregation between groups through calculation of association indices. The association indices revealed that none of the cities sampled support an HCV population that is completely isolated from that circulating in the other cities. Sequences from Melbourne were most isolated, whereas those from London were most dispersed. This suggests that HCV transmission between these cities occurs, with London playing a pivotal role. The degree of city-specific segregation of HCV subtype 1a sequences was linearly related to that of subtype 3a, indicating that these subtypes have spread through similar transmission networks.
75 citations
TL;DR: A combination of atmospheric transport modelling using the Lagrangian dispersion model and satellite imagery and observational data from Mace Head has shown that the most likely origin of the episode was long range transport of dust from the Sahara region of North Africa.
73 citations
TL;DR: Collection of clinically well‐characterized HIV‐infected tissues such as those in the Edinburgh Brain Bank are a vital resource to support ongoing studies of viral pathogenesis in the CNS and interactions with drug abuse.
Abstract: The Edinburgh cohort of intravenous drug users (IVDUs) became infected with HIV between 1983 and 1984. Before the era of effective therapy, many of these infected IVDUs displayed cognitive impairments on progressing to AIDS and were found to have HIV encephalitis (HIVE). Full autopsies were conducted on these patients, providing an opportunity to study the intersecting pathology of pure HIVE and drug use. High proviral load in the brain correlated well with the presence of giant cells and HIV p24 positivity. In presymptomatic HIV infection, IVDUs were found to have a lymphocytic infiltrate in the central nervous system (CNS). Apart from the expected microglial activation in the presence of HIV infection of the CNS, drug use in its own right was found to be associated with microglial activation. Examination of HIV-negative IVDUs revealed a number of neuropathologic features, including microglial activation, which may underpin HIV-related pathology in the CNS. HIV isolated from different regions of the brain was exclusively of R5-tropic type throughout the course of infection. Detailed studies of p17 and V3 sequences suggest that viral sequestration occurs in the CNS before the onset of AIDS and that increasing diversity of HIV variants within the brain is associated with increasing severity of HIVE. Because brain isolates have proved to be different from those in lymphoid tissue (and blood), it is likely that selective neuroadaptive pressures operate before HIVE supervenes. Drug abuse may be synergistic in this process through activation of microglia, breakdown of the blood-brain barrier, and direct neurotoxicity. Collections of clinically well-characterized HIV-infected tissues such as those in the Edinburgh Brain Bank are a vital resource to support ongoing studies of viral pathogenesis in the CNS and interactions with drug abuse.
69 citations
TL;DR: In this article, the authors used radon-222 ( 222 Rn) as a reference compound to estimate unknown sources of other species, such as CO 2, CH 4, N 2 O and CHCl 3, over Ireland.
Abstract: Flux estimates of CO 2 , CH 4 , N 2 O and CHCl 3 over Ireland are inferred from continuous atmospheric records of these species. We use radon-222 ( 222 Rn) as a reference compound to estimate unknown sources of other species. The correlation between each species and 222 Rn is calculated for a suite of diurnal events that have been selected in the Mace Head record over the period 1995–1997 to represent air masses exposed to sources over Ireland. We established data selection criteria based on 222 Rn and 212 Pb concentrations. We estimated flux densities of 12×10 3 kg CH 4 km −2 yr −1, 680 kg N 2 O km −2 yr −1 and 20 kg CHCl 3 km −2 yr −1 for CH 4 , N 2 O and CHCl 3 , respectively. We also inferred flux densities of 250×10 3 kg C km −2 yr −1 for CO 2 during wintertime, and of 760×10 3 kg C km −2 yr −1 for CO 2 during summer night-time. Our CH 4 inferred flux compare well with the CORINAIR90 and CORNAIR94 inventories for Ireland. The N 2 O emission flux we inferred is close to the inventory value by CORINAIR90, but twice the inventory value by CORINAIR94 and EDGAR 2.0. This discrepancy may have been caused by the use of the revised 1996 IPCC guidelines for national greenhouse gas inventories in 1994, which include a new methodology for N 2 O emissions from agriculture. We carried out the first estimation of CHCl 3 emission fluxes over Ireland. This estimation is 4 times larger than the CHCl 3 emission fluxes measured close to the Mace Head station over peatlands. Our CHCl 3 emission fluxes estimate is consistent with the interpretation of the same data by Ryall (personal communication, 2000), who obtained, using a Lagrangian atmospheric transport model, CHCl 3 fluxes of 24±7 kg CHCl 3 km −2 yr −1 . Our estimates of CO 2 emission fluxes during summer night-time and wintertime are close to those estimated from inventories and to one biogeochemical model of heterotrophic respiration. DOI: 10.1034/j.1600-0889.2002.00228.x
51 citations
TL;DR: The background atmospheric mixing ratios for cyclic perfluorocarbons (cyclic-PFCs) have been measured by gas chromatography-mass spectrometry in negative ion-chemical ionization mode as discussed by the authors.
39 citations
TL;DR: In this paper, a 5-yr record of continuous high-frequency carbon dioxide CO2 observations over the 1995-1999 period for the Mace Head Atmospheric Research Station has been examined to reveal a complex interplay between local and regional-scale sources and sinks.
35 citations
34 citations
TL;DR: A new phylogenetic clade of HIV-1 is described, spreading at a slower pace than the other subtypes found in the DRC region, and is not yet named as a subtype as per the recommendation of the nomenclature committee.
Abstract: The high genetic heterogeneity of HIV-1 in the Democratic Republic of Congo (DRC) constitutes a real challenge for the development of vaccines to counter the spread of the HIV-1 epidemic. It is important to continue to monitor the epidemic by studying the circulating strains and their impact on the overall spread. As part of the ongoing effort to study the global distribution of HIV-1 subtypes and circulating recombinant forms (CRFs), here we describe a new phylogenetic clade of HIV-1 by the analysis of two full-length sequences (83CD003 and 90CD121E12) collected from two individuals at a 7-year interval (1983 and 1990, respectively). One of the two sequences (90CD121E12) was obtained from a vertically infected, 12-month-old baby in Kimpese, rural DRC, an area with low and stable seroprevalence of HIV-1 in women attending antenatal clinics. The two sequences are genetically similar by 95% of their full genome and topologically form a distinct cluster that is equidistant from the existing subtypes (A through K) by the analysis of both the full genome and subgenomic regions. Furthermore, they share several other genetic features, including an additional pair of cysteine residues, predictive of an extra disulfide bridge, in the V4 loop of gp120. This new clade is currently rare, spreading at a slower pace than the other subtypes found in the DRC region. Pending the identification of at least one partial length sequence of the same lineage from another patient who is epidemiologically unlinked to those described here, this clade is not yet named as a subtype as per the recommendation of the nomenclature committee.
TL;DR: Hepatitis C virus, discovered as the cause of non-A non-B hepatitis in 1989, is estimated to infect 3% Of the world population and has become established as the major infectious cause of chronic liver disease in Western countries.
Abstract: Hepatitis C virus, discovered as the cause of non-A non-B hepatitis in 1989, is estimated to infect 3% Of the world population and has become established as the major infectious cause of chronic liver disease in Western countries. HCY is primarily spread by blood contact, and therefore has particularly targeted risk groups such as injecting drug users (IDDs), and recip ients of blood products or unsafe medical interventions. In industrialised nations, infection from blood products has been effectively halted by screening (Schreiber et al., 1996), and injecting drug use is the major risk activity. Current seroprevalence rates within IOU populations range from 30 to 90% (Hope et al., 2001; Macdonald et al., 2000; Taylor et al., 2000; Trepo and Pradat, 1999) and although attempts to control transmission between IDUs through behavioural intervention have had some encouraging results (Goldberg et al., 2001), the rate of spread remains unacceptably high. In nonindustrialised nations the correlates of transmission are less well understood, but unsafe medical injections are thought to playa major role (Sanchez et al., 2000).
TL;DR: The physical processes governing flow and pollutantdispersion at the neighbourhood scale, a spatial scale intermediate between the street scale and the city scale, is notwell understood as discussed by the authors.
Abstract: The physical processes governing flow and pollutantdispersion at the neighbourhood scale, a spatial scaleintermediate between the street scale and the city scale, is notwell understood. Furthermore, it is not clear whether a traditional approach using averaged characteristics such as theaerodynamic roughness length is sufficient to predict the concentration field at this scale. To investigate pollutant dispersion in a real urban area, three field experiments were designed within the UK-URGENT programme sponsored by NERC. Theexperiments were performed in the City of Birmingham using a finite duration release of inert, non-toxic and non-depositingtracers, vis. perfluoromethylcyclohexane (PMCH) and perfluoromethylcyclopentane (PMCP). Measurements were taken using air bag samplers placedin an arc at 3.5 km (first experiment) and 1 km (second andthird experiments) from the source; some trap samplers wereplaced outside the main arc in the outskirts of the city. Measurements were analysed in the laboratory using anovel gas-chromatography technique. Data so obtained werecompared with predictions from a simple steady-state modeland a time-dependent model. The concentration-time serieswere very asymmetrical with a sharp rise, a plateau followedby a relatively slow decrease and finally a long-livedplateau above (or possibly very slow decrease to) thebackground level.
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Abstract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
01 Jan 2002
TL;DR: Genotype results of the first group and donor-recipient couples, and sequence analysis of genotype 1b and 1a isolates showed that the source of infection was not a unique strain and there were multiple breaks in universal precautions while managing these patients.
01 Jan 2002