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Biomedical subjects

J Banks

Publications and source records attributed to J Banks.

At least 19 recordsLinked to original sources
PubMed2007

Turbulence modeling in three-dimensional stenosed arterial bifurcations.

Under normal healthy conditions, blood flow in the carotid artery bifurcation is laminar. However, in the presence of a stenosis, the flow can become turbulent at the higher Reynolds numbers during systole. There is growing consensus that the transitional k-omega model is the best suited Reynolds averaged turbulence model for such flows. Further confirmation of this opinion is presented here by a comparison with the RNG k-epsilon model for the flow through a straight, nonbifurcating tube. Unlike similar validation studies elsewhere, no assumptions are made about the inlet profile since the full length of the experimental tube is simulated. Additionally, variations in the inflow turbulence quantities are shown to have no noticeable affect on downstream turbulence intensity, turbulent viscosity, or velocity in the k-epsilon model, whereas the velocity profiles in the transitional k-omega model show some differences due to large variations in the downstream turbulence quantities. Following this validation study, the transitional k-omega model is applied in a three-dimensional parametrically defined computer model of the carotid artery bifurcation in which the sinus bulb is manipulated to produce mild, moderate, and severe stenosis. The parametric geometry definition facilitates a powerful means for investigating the effect of local shape variation while keeping the global shape fixed. While turbulence levels are generally low in all cases considered, the mild stenosis model produces higher levels of turbulent viscosity and this is linked to relatively high values of turbulent kinetic energy and low values of the specific dissipation rate. The severe stenosis model displays stronger recirculation in the flow field with higher values of vorticity, helicity, and negative wall shear stress. The mild and moderate stenosis configurations produce similar lower levels of vorticity and helicity.

Animals↗
PubMed2006

Recent epidemiology and ecology of influenza A viruses in avian species in Europe and the Middle East.

There have been at least ten distinct outbreaks of LPAI or HPAI in poultry caused by H5 or H7 viruses in the last eight years in Europe and the Middle East. There appears to be an increased occurrence of such episodes consistent with global trends. As a result, surveillance systems have been enhanced to facilitate early detection of infection in poultry, together with active surveillance of wild bird populations. These complementary activities have resulted in the detection of a number of viruses in wild bird populations, including some with high genetic similarity to newly detected viruses in poultry, for example, H7N3 in Italy and H7N7 in the Netherlands. Furthermore, there is evidence for continued circulation of H5 and H7 viruses in wild Anseriformes, thereby presenting a real and current threat for the introduction of viruses to domestic poultry, especially those reared in outdoor production systems. Viruses of H9N2 subtype continue to circulate widely in the Middle East and are associated with significant disease problems in poultry. The epidemiology has the potential to be complicated further by introduction of novel viruses through illegal importation of captive birds, such as was detected with H5N1 in Belgium in 2004. Continual genetic exchange in the avian virus gene pool and independent evolution of all gene segments either within an individual host species or among wild bird hosts suggests that these viruses are not in evolutionary stasis in the natural reservoir.

Animals↗
PubMed2004

Retrospective characterization of Newcastle Disease Virus Antrim '73 in relation to other epidemics, past and present.

In November 1973 Newcastle disease suddenly appeared in Northern Ireland, where the viscerotropic disease had not been seen in 3 1/2 years and the two Irelands had been regarded as largely disease free for 30 years. It was successfully controlled with only 36 confirmed affected layer flocks, plus 10 more slaughtered as 'dangerous contacts'. Contemporary investigations failed to reveal the source of the Irish epidemic. Using archival virus samples from most of the affected flocks, RT PCR was conducted with primers selected for all six NDV genes. Phylogenetic analyses of three genes, HN, M and F, confirmed vaccine as the cause of one of the outbreaks. The other six samples were identical and closely related to previous outbreaks in the United States and western Europe initiated by infected imported Latin American parrots. The probable cause of the epidemic followed from the importation from The Netherlands of bulk feed grains contaminated with infected pigeon faeces.

HN Protein↗
PubMed2004

SERF: a new antigen in the Cromer blood group system.

The Cromer blood group system consists of eight high incidence and three low incidence antigens carried on decay-accelerating factor (DAF). This report describes the identification and characterization of a new Cromer high incidence antigen, named SERF. Sequence analyses of DNA from a Thai female whose serum contained the alloantibody to a high incidence antigen in the Cromer blood group system (anti-SERF) and from her two children were performed. Reverse transcriptase-polymerase chain reaction (RT-PCR) and sequence analysis on cDNA from the proband and PCR-restriction fragment length polymorphism analysis on DNA from Thais were also performed. To map the epitope, DAF deletion mutants were tested by immunoblotting with anti-SERF. Sequence analysis revealed a substitution of 647C>T in exon 5 DAF in the proband. The proband's two children and two of 100 Thais were heterozygotes 647C/T. Analysis using DAF deletion mutants revealed the antigenic determinant to be within short consensus repeat 3 (SCR3), which is encoded by exon 5. This study describes a novel high incidence antigen (SERF) in the Cromer blood group system characterized by the amino acid proline at position 182 in SCR3 of DAF. The SERF-negative proband has a substitution mutation that predicts for leucine at this position. SERF has been provisionally assigned the International Society of Blood Transfusion number 021.012 (CROM 12).

Base Sequence↗
PubMed2004

LU21: a new high-frequency antigen in the Lutheran blood group system.

BACKGROUND AND OBJECTIVES: The Lutheran blood group system comprises 18 antigens numbered LU1 to LU20, with two numbers obsolete. Thirteen antigens are of high frequency. MATERIALS AND METHODS: Serological tests were performed by conventional methods. The monoclonal antibody-specific immobilization of erythrocyte antigens (MAIEA) assay was carried out with monoclonal antibodies to Lutheran glycoprotein. All exons of the LU gene were amplified by the polymerase chain reaction (PCR) and directly sequenced from genomic DNA. RESULTS: A patient was found to have an antibody to a high-frequency red cell antigen during her second pregnancy. The antibody was shown to be Lutheran-related and was distinguished from all reported Lutheran antibodies. MAIEA suggested the antibody was defining a novel epitope in domain 1 of the Lu-glycoprotein. Sequencing of the LU gene revealed a new homozygous single-point mutation, C282G, in exon 3, encoding an Asp94Glu change in the first domain of the Lu-glycoprotein. CONCLUSIONS: The antibody detected a new high-frequency Lutheran antigen, numbered LU21, that appears to result from an Asp94Glu substitution in the first, N-terminal domain of the Lu-glycoprotein.

Antibodies, Monoclonal↗
PubMed2003

Genotypic and phenotypic characterization of the dynamics of the lactic acid bacterial population of adjunct-containing Cheddar cheese manufactured from raw and microfiltered pasteurised milk.

AIMS: This study investigates the dynamics of the microflora, particularly the lactobacilli, in Cheddar cheese manufactured from raw and microfiltered milk containing different adjunct cultures. METHODS AND RESULTS: Sixteen cheeses - raw milk, adjunct and control cheeses - were manufactured in four trials. Lactobacilli were identified by PCR methods in one trial, and by phenotypic typing for all trials. Numbers of lactobacilli were significantly different at day 1 and 3 months in the control and adjunct-containing cheeses. In the raw milk cheeses, Lactobacillus paracasei was detected throughout ripening, Lact. curvatus at the end, and Lact. plantarum at day 1 only. Lactobacillus strain diversity decreased from raw, control to adjunct cheeses. Enteroccoci and coliform numbers further differentiated raw cheeses from the others. Lactococcal starter numbers also differed in the three cheese types and differences were observed within adjunct cheeses. Although adjunct lactobacilli dominated in the cheese to which they were added, strains with similar phenotypic profiles were also detected on occasions in some of the control cheeses. CONCLUSIONS: The addition of adjunct lactobacilli modified the growth kinetics of both adventitious lactobacilli and starter lactococci during ripening. Appropriate strain tracking is necessary to monitor changes in the population profiles of control and experimental cheeses in trials utilizing adjunct cultures. SIGNIFICANCE AND IMPACT OF THE STUDY: Investigations of the role of adjunct strain(s) in cheeses may be complicated by the interactions between the adjunct and the other cheese strains, and effective strain monitoring by genotypic or phenotypic methods is essential if valid comparisons are to be made.

Animals↗
PubMed2003

Fate of ochratoxin A in the processing of whole wheat grains during milling and bread production.

Batches of whole wheat contaminated with ochratoxin A were produced by inoculation with Penicillium verrucosum under controlled conditions in the laboratory. The fate of ochratoxin was followed through initial cleaning, abrasive scouring of the outer grain coat, milling into wholemeal wheat or into 10 milled fractions. Bread was baked from both wholemeal flour and straight-run white flour. Concentrations of ochratoxin A in the cleanings, scourings, and the bran and offal fractions were increased, but reduced in the white flour. Scouring removed up to 44% of the ochratoxin A present, but only a small further loss occurred in the bread-making process. An overall reduction of about 75% could be achieved in white bread using a combination of cleaning scouring and removal of the bran and offal fractions. Maximum overall reduction in producing wholemeal bread was about 40%. The reduction in ochratoxin A that can be achieved must be considered in relation to economic constraints concerning the disposal of wasted grain. Appropriate strategies for the use or disposal of potentially highly contaminated cleanings, scourings, bran or offal must be established.

Bread↗
PubMed2003

A molecular epidemiological study of avian paramyxovirus type 1 (Newcastle disease virus) isolates by phylogenetic analysis of a partial nucleotide sequence of the fusion protein gene.

A sequence 375 nucleotides in length, which included the region encoding the cleavage activation site and signal peptide of the fusion protein gene, was determined for 174 isolates of Newcastle disease virus (avian paramyxovirus type 1). These were compared with the sequences of 164 isolates published on GenBank, and the resulting alignment was analysed phylogenetically using maximum likelihood. The results are presented as unrooted phylogenetic trees. Briefly, the isolates divided into six broadly distinct groups (lineages 1 to 6). Lineages 3 and 4 were further subdivided into four sublineages (a to d) and lineage 5 into five lineages (a to e). Considerable genetic heterogeneity was detected within avian paramyxoviruses type 1, which appears to be influenced by host, time and geographical origin. It is concluded that by using this dataset it will be possible to type future virus isolates rapidly on the basis of their nucleotide sequence and make inferences about their origins.

Animals↗
PubMed2003

Additional glycosylation at the receptor binding site of the hemagglutinin (HA) for H5 and H7 viruses may be an adaptation to poultry hosts, but does it influence pathogenicity?

Sequence analysis of the hemagglutinin (HA) gene of H5 and H7 viruses was used to determine phylogenetic relationships between high-pathogenicity avian influenza (HPAI) and low-pathogenicity avian influenza (LPAI) viruses from avian influenza (AI) outbreaks in Norfolk in 1979 and 1991 and Italy in 1999-2000. A common feature within these groups of viruses was the acquisition of additional glycosylation sites near the receptor binding site of the HA. Passage of H5 viruses through 14-day-old embryonated fowls' eggs readily selected viruses with additional glycosylation of HA1. Although additional glycosylation may not correlate with increased pathogenicity for fowl, it may predispose viruses to become highly pathogenic.

Animals↗
PubMed2001

Long term variation in water colour from Yorkshire catchments.

Water colour is a problem in the upland water-gathering grounds of the UK. It has shown considerable variation over recent years and this needs to be put into the longer-term context. In order to do this, factors to convert water colour measured in absorbance units per metre (Au/m) to Hazen units are presented for ten sites in the Yorkshire region using data from August 1997 to June 1998. The conversion factors are site-specific and there is some evidence that they may show seasonal variation. There is also a short-term upward trend in the conversion factor for a number of catchments, which may be related to their recovery following the 1995 drought. Time series of water colour in Hazen from 1980 to 1998 are shown for selected sites. The seasonal variation in colour levels is disrupted at all sites during and following drought periods, notably 1990-1992 and 1995-1998 and, in the case of two sites with long-term colour measurements, the 1975-1976 drought. These periods are followed by enhanced levels of colour and, since the end of the 1995 drought, unprecedented high values have been recorded at some catchments.

Environmental Monitoring↗
PubMed2001

Membrane inlet mass spectrometric measurement of O2 and CO2 gradients in cultures of Lactobacillus paracasei and a developing Cheddar cheese ecosystem.

Membrane inlet mass spectrometry was used to measure O2 and CO2 as depth profiles in stab cultures of 0.1% agar Man Rogosa Sharpe medium inoculated with Lactobacillus paracasei CI3. Diffusion of CO2 from the central column of growth into the medium was observed to show lower concentrations where bacteria were absent. CO2 profiles developed in a manner similar to those in Cheddar cheese and O2 was undetectable at similar depths. Gases were analysed in Cheddar cheese over a maturation period of 200 d. O2 was detectable to depths of 13, 6 and 2.5 mm on days 2, 9 and 15, respectively, but then became undetectable at depths of 2.5-3 mm. CO2 concentrations measured within the cheese increased 10-fold from day 2 to day 200 to reach a value of around 15 mM. The progress of measured CO2 concentration over time at a given depth in cheese shows a hyperbolic type increase. Coefficient of regression values increase with depth to a maximum value of R2 = 0.93. In both systems, reductions and increases in CO2 were due to the absence or presence of bacterial growth, respectively. Confocal scanning laser and scanning electron microscopy was used to show spatial heterogeneity of microcolonies within the cheese ecosystem. This information can potentially be used as a non-sensory evaluation of cheese maturity status. Measurement of gases in a cheese ecosystem provides the first description of mass spectrometry being used to monitor the processes of microbial gaseous exchange with respect to O2 and CO2 in a cheese ecosystem.

Carbon Dioxide↗
PubMed2001

Changes in the haemagglutinin and the neuraminidase genes prior to the emergence of highly pathogenic H7N1 avian influenza viruses in Italy.

Outbreaks of avian influenza due to an H7N1 virus of low pathogenicity occurred in domestic poultry in northern Italy from March 1999 until December 1999 when a highly pathogenic avian influenza (HPAI) virus emerged. Nucleotide sequences were determined for the HA1 and the stalk region of the neuraminidase (NA) for viruses from the outbreaks. The HPAI viruses have an unusual multibasic haemagglutinin (HA) cleavage site motif, PEIPKGSRVRRGLF. Phylogenetic analysis showed that the HPAI viruses arose from low pathogenicity viruses and that they are most closely related to a wild bird isolate, A/teal/Taiwan/98. Additional glycosylation sites were present at amino acid position 149 of the HA for two separate lineages, and at position 123 for all HPAI and some low pathogenicity viruses. Other viruses had no additional glycosylation sites. All viruses examined from the Italian outbreaks had a 22 amino acid deletion in the NA stalk that is not present in the N1 genes of the wild bird viruses examined. We conclude that the Italian HPAI viruses arose from low pathogenicity strains, and that a deletion in the NA stalk followed by the acquisition of additional glycosylation near the receptor binding site of HA1 may be an adaptation of H7 viruses to a new host species i.e. domestic poultry.

Amino Acid Motifs↗
PubMed2001

Analytical approaches to measuring cospeciation of host and parasites: through a glass, darkly.

Studies of cophylogenetic associations between hosts and parasites have become increasingly common. Historically, congruence between host and parasite phylogenies has been seen as evidence for cospeciation. Analyses of such coevolutionary relationships, however, are made extremely difficult by the complex interplay of cospeciation, host switching, sorting (extinction), duplication (intrahost speciation) and inertia (lack of parasite speciation) events, all of which may produce incongruence between host and parasite phylogenies. Here we review several methods of analysing cospeciation. We illustrate these methods with an example from a Procellariiformes (seabird) and chewing louse (Halipeurus) association.

Animals↗
PubMed2001

Doing things with illness. The micro politics of the CFS clinic.

This paper focuses on lay and professional ideas about the nature of chronic fatigue syndrome (CFS), and in particular, the ways in which understandings of the disorder are developed in a clinical setting. Our data are drawn from observations of consultations between sufferers and physicians in a UK medical out-patients clinic. We treat the clinic as a political field. That is to say, as an arena in which 'problems' (about the management of illness) are constituted, and alternative approaches and solutions to such problems are pressed. We note that in the realms of symptoms, aetiology and treatment evaluation, lay people in the CFS clinic have quite distinct ideas about what their problems are and how they might be analysed and managed--ideas that are often in conflict with those of medical professionals. Thus, lay sufferers, for example, operate within a different conceptual terrain from that of many professional experts. They are more likely to refer to a disease (myalgic encephalomyelitis or ME), rather than a syndrome. They call upon different kinds of hypotheses to explain their symptoms. They hold to conflicting ideas about the order of causal sequences, and they give emphasis to different kinds of phenomena in their accounts of illness. As a consequence, clinical consultations can often take on the form of a political contest between physician and patient to define the true and real nature of the patient's disorder--a micro political struggle in which neurological symptoms can be re-framed as psychiatric symptoms, and psychiatric symptoms as neurological. In short, a contest in which the demarcation lines between mind and body are continually assessed and re-defined, and the tenets of 'biomedicine' are constantly challenged.

Anecdotes as Topic↗
PubMed2000

H9N2 subtype influenza A viruses in poultry in pakistan are closely related to the H9N2 viruses responsible for human infection in Hong Kong.

Following the outbreak of H5N1 "bird flu" in Hong Kong in 1997, the isolation of H9N2 subtype viruses from patients in southern China and Hong Kong SAR once again raised the spectre of a possible influenza pandemic. H9N2 viruses have recently been responsible for disease in poultry in various parts of the world and preliminary studies of the H9 haemagglutinin (HA) genes of viruses isolated during 1998 and 1999 in Germany, Iran, Pakistan, and Saudi Arabia showed a close relationship to the HA genes of the viruses that infected two children in Hong Kong SAR. Analysis of the complete genome of a Pakistan isolate, A/chicken/Pakistan/2/99, showed that it is closely related in all eight genes (97-99% homology) to the human H9N2 isolates and furthermore that the six genes encoding internal components of the virus are similar to the corresponding genes of the H5N1 viruses that caused 6 (out of 18) fatal cases of human infection. Thus H9N2 viruses similar to those that caused human infections in Hong Kong are circulating more widely in other parts of the world. Whether or not these H9N2 viruses also have features that facilitate avian-to-human transmission is not known. Since avian H9N2 viruses are currently perceived to represent a significant threat to human health it is important to determine whether or not viruses of this subtype circulating in poultry in various parts of the world have the potential to infect people.

Animals↗
PubMed2000

Complement-resistant Moraxella catarrhalis forms a genetically distinct lineage within the species.

Moraxella catarrhalis is a bacterial species that has been implicated in 15-20% of all cases of otitis media in the USA and the complement-resistant variant of M. catarrhalis has been considered particularly pathogenic. A collection of geographically diverse, complement-sensitive (n=28) and -resistant strains (n=47) of M. catarrhalis was assembled in order to analyse the bacterial population structure. All strains were identified as M. catarrhalis by conventional microbiological and biochemical methods. Amplification of the small subunit (ssu) ribosomal RNA gene followed by restriction fragment length polymorphism (RFLP) analysis did not reveal consistent differences between serum-susceptible and -resistant M. catarrhalis isolates. Interestingly, upon automated ribotyping using the Qualicon RiboPrinter(R) microbial characterisation system, the complement-sensitive and -resistant strains segregated into two groups. This suggested the existence of two clearly distinguishable lineages within the species M. catarrhalis. This observation was corroborated by pulsed field gel electrophoresis (PFGE) of DNA macro-restriction fragments, a non-ribosomal PCR RFLP procedure and random amplification of polymorphic DNA (RAPD) analysis. All procedures grouped the two variants similarly. Redefinition of the taxonomic status of complement-resistant M. catarrhalis or even the definition of a new species may be opportune.

Bacterial Typing Techniques↗