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Biomedical subjects

D James

Publications and source records attributed to D James.

At least 19 recordsLinked to original sources
PubMed2006

Hearing threshold assessment post grommet insertion. Is it reliable?

We aimed to investigate whether auditory brainstem response (ABR), assessed immediately after grommet insertion, was an accurate measure of hearing threshold. Ten children were recruited (20 ears). Patients underwent transient evoked otoacoustic emission (TEOAE) and ABR tests before and after grommet insertion under general anaesthetic. A third assessment was conducted at a six-week review, without anaesthetic or sedation. The hearing threshold in dB and the presence of TEOAE were recorded by senior audiologists. The results of each investigation were compared. At review, only 15 ABR and 17 TEOAE tests, of a possible 20, were recorded. Transient evoked otoacoustic emissions were recorded in 30 per cent of ears pre-operatively, 20 per cent of ears post-operatively and 82 per cent of ears at six-week review. The average ABR thresholds were 23.75 dB (range 10-45 dB) pre-operatively, 27.25 (range 15-40 dB) post-operatively and 15 dB (range 5-25 dB) at six-week review. Comparing pre- and post-operative assessment, decreased thresholds were seen in six ears and elevated thresholds in 11. Comparing the six-week review ABR with the post-operative ABR, 13 ears had decreased thresholds, by as much as 20 dB. Thresholds of 35 dB or greater were measured in six ears immediately after grommet insertion (maximum 40 dB). Threshold shifts of 15 dB or greater was observed in seven ears. The intra-subject variation was shown to be significant (p<0.001) when repeated measures analysis of variance was applied. We conclude that there is evidence that ABR can be inaccurate after grommet insertion, overestimating hearing thresholds. We believe that the mechanism by which the error is realised is temporary threshold shift.

Audiometry, Evoked Response↗
PubMed2006

The complete genome sequence of an El Amar isolate of plum pox virus (PPV) and its phylogenetic relationship to other PPV strains.

The genomic sequence of an El Amar isolate of plum pox virus (PPV) from Egypt was determined by sequencing overlapping cDNA fragments. This is the first complete sequence of a member of the El Amar (EA) strain of PPV. The genome consists of 9791 nt, excluding a poly(A) tail at the 3' terminus. The complete nt sequence of PPV EA is 79-80%, 80%, 77%, and 77% homologous with isolates of strains D/M, Rec (BOR3), C, and W, respectively. The polyprotein identity ranged from 87-91%. Phylogenetic analysis using the complete genome sequence of PPV EA confirmed its strain status. No significant recombination signals were identified using PhylPro and SimPlot scans of the PPV EA sequence, however an interesting recombination signal was identified in the P1/HC-Pro region of PPV W3174.

Base Sequence↗
PubMed2006

Integrating principles of nitrogen dynamics in a method to estimate leachable nitrogen under agricultural systems.

Surplus nitrogen (N) in ground and surface water is of concern in intensive agricultural regions. Surplus N leaches during lengthy periods where annual crop systems are used in temperate regions. This paper presents a model to estimate the surplus N available for leaching to ground water beneath agricultural systems and applies the model to watersheds in an intensive maize and soybean production system. The model utilizes commonly available georeferenced data on soils, crops, and livestock, making it applicable to watersheds in many regions. The model links stocks of N in soil, crops, livestock, fertilizer and the atmosphere. Nitrogen flow centers on exchange between the soil N stocks. Nitrogen mineralization rates are defined for three soil organic matter pools, crop residue, and manure based on carbon:N ratios. Nitrogen exports from the system are harvested crops, livestock and losses to the atmosphere. Application of the model in 26 Iowa watersheds finds surpluses of 18 to 43 kg-N/ha. Surpluses exceeded measured annual nitrate-N loads in regional streams by amounts equivalent to denitrification rates in groundwater. Deficits in soil N were sufficiently small to suggest that the system is in equilibrium with soils of the region.

Agriculture↗
PubMed2005

Development of activity standard for 90 Y microspheres.

(90)Y microspheres are important therapeutic radiopharmaceuticals used in the treatment of liver cancer through a process known as selective internal radiation therapy. SIR-spheres is a radiopharmaceutical product that is comprised of (90)Y microspheres suspended in sterile, pyrogen-free water for injection into patients. It is necessary to establish for the SIR-spheres production the capability of accurately measuring the activity of this product to a traceable national measurement standard. An activity standard for SIR-spheres was developed from a standard for (90)Y solution, employing a highly quantifiable chemical digestion process. Calibration factors for the manufacturer's ionisation chambers were determined for 1 and 5 ml of the SIR-spheres product placed in Wheaton vials, for both 34% and 44% of (90)Y microsphere concentration.

Australia↗
PubMed2005

Genome segment RNA-1 of a flat apple isolate of Cherry rasp leaf virus: nucleotide sequence analysis and RT-PCR detection.

The sequence of the RNA-1 of a flat apple isolate of Cherry rasp leaf virus (CRLV-FA) was determined using overlapping cDNA fragments. CRLV-FA RNA-1 consists of 6992 nucleotides (nt), excluding a 3' poly (A) tail. A single open reading frame (ORF) consisting of 6705 nt was identified. This ORF encodes a putative polyprotein consisting of 2235 amino acid (aa) residues, approximately 249.6 kDa. When compared to CRLV-pot (potato isolate) RNA-1 ORF, 2 deletions of 5 aa and 10 aa (total 15 aa) were observed at the variable N-terminus of the protease cofactor of CRLV-FA. Non-coding regions were identified at the 5'-(142 nt) and 3'-end (145 nt). CRLV-FA and CRLV-pot are isolates of the same virus with identity levels for the RNA-1 associated nt and deduced aa of 94% and 95%, respectively. RT-PCR targeting CRLV-FA RNA-1 appear to be of similar sensitivity and just as reliable as RT-PCR targeting RNA-2.

Amino Acid Sequence↗
PubMed2005

Nucleotide sequence analysis of Plum pox virus isolate W3174: evidence of a new strain.

The nucleotide sequence of Plum pox virus (PPV) isolate W3174 was determined. The virus genome consists of 9788 nucleotides (nt), excluding the poly(A) tail at the 3'-terminus, with 5'- and 3'-untranslated regions (UTRs) of 146 and 219 nt, respectively. The deduced polyprotein consists of 3141 amino acid (aa) residues, with the coat protein region consisting of 993 nt (331 aa). In comparisons with PPV-D, -M, -EA and -C isolates, nucleotide identity levels ranged from 79 to 80% for the entire genome and from 78 to 79%, 78 to 81%, and 92 to 95% for the NIb, CP, and 3'-UTR regions, respectively. The majority of nucleotide substitutions in the NIb region of W3174 are silent, while substitutions in the CP region are not silent, giving aa identities of 89-91% and 79-81%, respectively. The HC-Pro region contains the KITC and PTK motifs, and the DAG motif is located at positions 12-14 of the deduced CP aa sequence, all associated with aphid transmission. Phylogenetic analysis based on the complete genome sequence, the NIb, CP, and 3'-UTR region were performed. PPV-W3174 consistently formed a distinct clade or group, when compared to members of all four recognized strains of PPV, indicating that it is genetically distinct. These results are consistent with serological and nucleic acid-based strain typing data and justify recognition of this isolate as representative of a new strain identified as PPV-W.

3' Untranslated Regions↗
PubMed2004

Community and hospital spread of Escherichia coli producing CTX-M extended-spectrum beta-lactamases in the UK.

OBJECTIVES: During 2003, the Health Protection Agency's Antibiotic Resistance Monitoring and Reference Laboratory began to receive isolates of Escherichia coli for confirmation of extended-spectrum beta-lactamase production with a phenotype implying a CTX-M-type beta-lactamase, i.e. MICs of cefotaxime > or = 8-fold higher than MICs of ceftazidime. Many were referred as being from community patients. We examined 291 CTX-M-producing isolates from the UK and investigated the genetic basis of their phenotype. METHODS: PCR was used to detect alleles encoding CTX-M enzymes and to assign these to their blaCTX-M phylogenetic groups. Selected alleles were sequenced. Producers were compared by analysis of banding patterns generated by pulsed-field gel electrophoresis of XbaI-digested genomic DNA. MICs were determined by an agar dilution method or by Etest. RESULTS: Of 291 CTX-M-producing E. coli isolates studied from 42 UK centres, 70 (24%) were reportedly from community patients, many of whom had only limited recent hospital contact. Community isolates were referred by 12 centres. Two hundred and seventy-nine (95.9%) producers contained genes encoding group 1 CTX-M enzymes and 12 contained blaCTX-M-9-like alleles. An epidemic CTX-M-15-producing strain was identified, with 110 community and inpatient isolates referred from six centres. Representatives of four other major strains also produced CTX-M-15, as did several sporadic isolates examined. Most producers were multi-resistant to fluoroquinolones, trimethoprim, tetracycline and aminoglycosides as well as to non-carbapenem beta-lactams. CONCLUSIONS: CTX-M-producing E. coli are a rapidly developing problem in the UK, with CTX-M-15 particularly common. The diversity of producers and geographical scatter of referring laboratories indicates wide dissemination of blaCTX-M genes. Because of the public health implications, including for the treatment of community-acquired urinary tract infections, the spread of these strains--and CTX-M-15 beta-lactamase in particular--merits close monitoring.

Alleles↗
PubMed2004

parkin mutation analysis in clinic patients with early-onset Parkinson [corrected] disease.

parkin Mutations are the most common identified cause of Parkinson's disease (PD). It has been suggested that patients with young-onset PD be screened for parkin mutations as a part of their clinical work-up. The aim of this study was to assess parkin mutation frequency in a clinical setting, correlate genotype with phenotype, and evaluate the current justification for clinical parkin testing. Patients were selected from a movement disorder clinic based on diagnosis of PD and onset age </=40 years. parkin was genotyped by sequence and dosage analysis for all 12 exons. Key relatives and controls were screened for identified mutations. Mutations were found in 7/39 patients. Two patients were compound heterozygous; five were heterozygous. Mutations included deletions in exons 2, 3, and 8, duplications in exons 2-4, and 9, and P437L substitution. Seventy-eight percent of mutations were deletions/multiplications. A novel substitution (R402W) was found in one patient and in one control. None of the point mutations found in patients were detected in 96 controls. parkin phenotypes were consistent with idiopathic PD. In conclusion, parkin mutations are common in the clinic setting: 10% of PD patients had early-onset and 18% of them had parkin mutations. However, if parkin is recessive, only 5% of early-onset cases who had compound mutations could be attributed to this locus. Mutation frequency was 0.12 (95% CI 0.04-0.19). parkin cases can present as typical idiopathic PD, distinguishable only by molecular testing. Seventy percent of parkin cases were heterozygous. It is unclear whether heterozygous mutations are pathogenic. parkin-based diagnosis and counseling require a better understanding of the mode of inheritance, penetrance, and carrier frequencies.

Adolescent↗
PubMed2004

Reliability of routine disc susceptibility testing by the British Society for Antimicrobial Chemotherapy (BSAC) method.

OBJECTIVES: To ascertain the agreement between MICs determined at a central laboratory, and susceptible, intermediate and resistant categorizations based on zone diameters recorded at diagnostic laboratories using the BSAC standardized method. METHODS: Standardized disc susceptibility tests were performed at sentinel laboratories in three surveys, with MIC tests performed on the collected isolates at a reference laboratory. The organisms comprised over 3300 Enterobacteriaceae, Acinetobacter spp., pseudomonads, staphylococci and enterococci, with over 29 000 antibiotic/organism tests in total. RESULTS: More than 90% of the antibiotic/organism combinations classed as susceptible by disc tests in the sentinel laboratories were confirmed by MIC testing. Disagreements were more frequent where disc tests indicated resistance, with half of the piperacillin/tazobactam resistance and one-third of the cephalosporin resistance found in Enterobacteriaceae by disc tests not being confirmed, and with three-quarters of teicoplanin resistance in enterococci not confirmed. None of the few apparent cases of meropenem resistance in Enterobacteriaceae or linezolid, quinupristin/dalfopristin or vancomycin resistance in staphylococci were confirmed by MIC testing. When disagreements were found between disc- and MIC-based categorization, MICs were commonly, although not invariably, one to three doubling dilutions above or below the breakpoint. However, many of the disagreements where MICs were three or more dilutions from the breakpoint were not seen when disc tests were repeated in the central laboratory. CONCLUSIONS: The BSAC disc method seems adequate for confirming susceptibility to guide therapy and to monitor resistance trends. Nevertheless, there must be concern about the over-estimation of many resistances, and frequent zone:MIC disagreements for isolates with borderline susceptibility.

Bacteria↗
PubMed2004

Orthopaedic intervention in early rheumatoid arthritis. Occurrence and predictive factors in an inception cohort of 1064 patients followed for 5 years.

OBJECTIVES: To assess the occurrence of and predictive factors for orthopaedic surgery in an inception cohort of rheumatoid arthritis (RA) patients recruited and followed prospectively for 5 yr in nine regions in England. METHODS: Standard clinical, laboratory and radiological assessments and all interventions were recorded at baseline and yearly in RA patients (less than 2 yrs symptoms) prior to the use of disease-modifying drugs. RESULTS: One thousand and sixty-four patients completed 5 yr of follow-up. Two hundred and sixty-four orthopaedic procedures for RA were performed in 181 (17%) patients at a median of 36.5 months from baseline. Seventy-five (7%) had replacements of major joints. Risk factors at baseline for large joint replacement surgery were a low haemoglobin concentration [odds ratio scores (OR) 3.4, 95% confidence interval (CI) 2.1-5.8] and high scores for erythrocyte sedimentation rate (ESR) (OR 3.2, CI 1.8-5.3), disease activity (DAS) (OR 2.1, CI 1.2-3.5) and Larsen X-rays (OR 2.6, CI 1.4-4.8). For hand or foot joint surgery (4%), risk factors included female gender (OR 3.2, CI 1.3-7.6), joint score (OR 2.3, CI 1.2-4.3), erosions (OR 2.3, CI 1.1-4.8), DAS (OR 2.4, 1.3-4.5) and Health Assessment Questionnaire score (OR 1.9, CI 1.0-3.6). No significant associations were seen for tendon, soft tissue or other minor procedures (6%). The HLA-DRB1 RA shared epitope was associated with any type of orthopaedic surgery (OR 1.7, CI 1.1-2.7). CONCLUSIONS: Eleven per cent of RA patients treated with conventional drug therapy for 5 yr underwent large- or small-joint surgery, an outcome which could be compared against that for new disease-modifying drugs. Risk factors varied according to type of surgery, but included standard clinical and laboratory measures. In order to reduce the eventual need for surgery, a therapeutic target in the first year of RA is the suppression of disease activity, as measured by haemoglobin and ESR. These are useful details for clinicians, health professionals and patients.

Adult↗
PubMed2004

Recognition of nonpeptide antigens by human V gamma 9V delta 2 T cells requires contact with cells of human origin.

SUMMARY It is becoming apparent that gamma delta T cells form an important part of the adaptive immune response. However, the ligands recognized by gamma delta T cell receptors (TCRs) and the exact biological function of the cells that express this receptor remain unclear. Numerous studies have shown that the dominant human peripheral blood subset of gamma delta T cells, which express a V gamma 9V delta 2 TCR, can activate in response to low molecular weight nonpeptidic molecules. Some of these components have been purified from bacteria or parasites. We examined the activation of polyclonal gamma delta T cell lines, clones with V gamma 9V delta 2 and V gamma 9V delta 1 TCRs, and gamma delta T cells directly ex vivo in response to multiple phosphate, alkylamine and aminobisphosphonate (nBP) antigens and purified protein derivative from Mycobacterium tuberculosis (PPD). V gamma 9V delta 2 T cells were able to respond to multiple small organic molecules of highly variable structure whereas cells expressing a similar V gamma 9 chain paired with a V delta 1 chain failed to recognize these antigens. Thus, the TCR delta chain appears to make an important contribution to the recognition of these antigens. The kinetics of responses to alkylphosphate and alkylamine antigens differ from those of responses to the nBP pamidronate. These different classes of antigen are believed to have differed mechanisms of action. Such differences explain why nBPs can be pulsed onto antigen presenting cells (APCs) and still retain their ability to activate gamma delta T cells while alkylphosphate and alkylamine antigens cannot. We also demonstrate that a substantial proportion of the cells that produce IFN gamma directly ex vivo in response to PPD are gamma delta T cells and that gamma delta T cell activation requires contact with cells of human origin.

Antigen-Antibody Reactions↗
PubMed2003

Successful outcome of advanced abdominal pregnancy with exclusive omental insertion.

We report the case of an advanced abdominal pregnancy with exclusive omental insertion whose extrauterine location was not established until delivery by Cesarean section at 35 weeks' gestation. It is hard to believe that omental placentation alone would be sufficient to sustain a pregnancy beyond a gestation where the fetus is viable. However, this report challenges such myths and opens the debate as to what represents the minimal placental maternal viscus contact necessary to achieve fetal viability. The case also demonstrates the continuing difficulty in diagnosing this rare but serious condition despite advances in obstetric imaging, and advocates methods to avoid missing the diagnosis, which could be easily incorporated at booking and mid-trimester scans. Apart from this case, few reports describe normal umbilical artery Doppler velocimetry in advanced abdominal pregnancy. There is a paucity of research on suitable clinical investigations prognostic for abdominal pregnancy, although this case provides further evidence for the use of Doppler as a useful surveillance tool in such cases. Finally, this case propagates the ethical and clinical controversy that exists in managing abdominal pregnancy, particularly when diagnosed late after attaining fetal viability. Expectant management may represent a feasible alternative to surgical termination provided the woman is fully informed of the attendant risks and close surveillance of the pregnancy is undertaken.

Adult↗
PubMed2003

Susceptibility of Gram-positive bacteria from ICU patients in UK hospitals to antimicrobial agents.

Microbiologists in 25 sentinel laboratories were each asked to refer up to 100 clinically-significant Gram-positive bacteria isolated from consecutive intensive care unit (ICU) patients. A total of 1595 isolates were collected from patients in 23 hospitals; these included Staphylococcus aureus (47.6%), coagulase-negative staphylococci (CNS) (30.6%), enterococci (14.3%), pneumococci (2.8%) and other streptococci (3.5%). A few coryneforms, other bacilli and a Nocardia sp. were also collected. Rates of oxacillin resistance among S. aureus and CNS isolates were 59.3 and 78.5%, respectively. Vancomycin-resistant S. aureus were not detected, although two isolates (0.3%) were resistant to teicoplanin [minimum inhibitory concentrations (MICs) 8 mg/L]. In contrast, 13.7% of CNS were teicoplanin resistant (MICs 8-32 mg/L) and 1.2% were resistant to vancomycin. Among the enterococci, 72.5% were Enterococcus faecalis and 24.5% were Enterococcus faecium, the remainder including isolates of Enterococcus casseliflavus or Enterococcus gallinarum. Eighteen percent of E. faecium isolates were vancomycin-resistant, compared with only 3% of E. faecalis isolates. Rates of high-level gentamicin resistance in E. faecalis and E. faecium were 40 and 25%, respectively. Nine percent of pneumococci and streptococci were resistant to penicillin, with 7 and 11%, respectively, resistant to erythromycin. None of the isolates showed resistance to linezolid, with the MICs for the entire study population falling in the range of 0.5-4 mg/L.

Coagulase↗
PubMed2003

In vitro activity of piperacillin/tazobactam and other broad-spectrum antibiotics against bacteria from hospitalised patients in the British Isles.

Piperacillin/tazobactam is used for empirical therapy of severe and complex infections. We assessed its activity, 9 years after launch, against consecutive, clinically significant isolates from in-patients in UK and Ireland. Standardised disc susceptibility tests were performed on 5031 isolates at 28 hospitals. For quality assurance purposes, 5% of these isolates were collected centrally for MIC tests, as were those with exceptional resistances. Compared with a similar pre-launch survey in 1991, there were major increases in the proportions of Staphylococcus aureus, Pseudomonas aeruginosa, beta-haemolytic streptococci and Enterococcus faecium isolates collected, balanced by decreases in Escherichia coli, Proteus mirabilis and coagulase-negative staphylococci. These changes in species prevalence mostly favoured organisms with inherent resistance(s) or-in the case of S. aureus-reflected the massive increase of MRSA, up from 0.7% of all isolates in 1991 to 14.8% in 2001. Based on the disc tests, piperacillin/tazobactam retained activity against 87% of Enterobacteriaceae isolates, 95% of P. aeruginosa, 99% of streptococci and 96% of Enterococcus faecalis. Resistance nevertheless had increased since 1991 in E. coli from 4 to 10%, Klebsiella spp. (5 to 21%) and in AmpC-inducible Enterobacteriaceae (17 to 23%), though not in P. mirabilis or P. aeruginosa. MIC tests confirmed most of the piperacillin/tazobactam resistance found by disc tests in Enterobacter spp., but indicated susceptibility for about half of the E. coli isolates recorded as resistant in disc tests. This situation might be remedied by reducing the zone breakpoint, but this would increase the "false susceptible" rate unacceptably. Thus, if disc tests suggest that an isolate is marginally resistant to piperacillin/tazobactam and the drug is sought as therapy, it is recommended that MIC be determined with, e.g., an Etest.

Bacteria↗
PubMed2003

Principal mutation hotspot for central core disease and related myopathies in the C-terminal transmembrane region of the RYR1 gene.

The congenital myopathies are a group of disorders characterised by the predominance of specific histological features observed in biopsied muscle. Central core disease and nemaline myopathy are examples of congenital myopathies that have specific histological characteristics but significantly overlapping clinical pictures. Central core disease is an autosomal dominant disorder with variable penetrance which has been linked principally to the gene for the skeletal muscle calcium release channel (RYR1). Two recent reports have identified the 3' transmembrane domain of this gene as a common site for mutations. Two other studies have reported single families that have features of both central core disease and nemaline myopathy (core/rod disease) caused by mutations in RYR1. Screening of the 3' region (exons 93-105) of the RYR1 gene for mutations in 27 apparently unrelated patients with either central core disease or core/rod disease by single strand conformation polymorphism analysis and DNA sequencing identified three described and nine novel mutations in 15 patients.

DNA Mutational Analysis↗