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David Dunn

Publications and source records attributed to David Dunn.

16 recordsLinked to original sources
PubMed2006

Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity.

BACKGROUND: The routine use of drug resistance testing provides an abundant source of HIV-1 sequence data. However, it is not clear how reliable standard genotyping of these sequences is for describing HIV-1 genetic variation and for detecting novel genetic variants and epidemiological trends. OBJECTIVES: To compare assignment of HIV-1 resistance test sequences to reference strains across commonly used genotyping protocols. METHODS: Subtype assignments were compared across three standard genotyping protocols for 10 537 resistance test sequences, representing approximately one-fifth of all reported infections in the United Kingdom. Sequences that were inconsistently genotyped across methods, or that were unassigned by at least one method, were examined for evidence of recombination using sliding-window-based approaches. RESULTS: Although agreement across methods was high for subtypes B, C and H, it was generally much lower (< 50%) for other subtypes. Disagreement between methods typically involved closely related, but epidemiologically distinct, groups or involved a significant proportion ( approximately 12%) of divergent sequences in which analysis revealed widespread evidence of recombination and a remarkable diversity of unusual recombinant forms. CONCLUSIONS: With frequent long-distance transfer of viral strains and widespread recombination between them, genetic and epidemiological relationships within HIV-1 are becoming increasingly complex. Current methods of subtype assignment vary in their ability to identify novel genetic variants and to distinguish epidemiologically distinct strains. Capturing meaningful epidemiological information from resistance test data will require a critical understanding of the methodologies used in order to appreciate the possible sources of error and misclassification.

Databases, Genetic↗
PubMed2006

Ten years of bacterial genome sequencing: comparative-genomics-based discoveries.

It has been more than 10 years since the first bacterial genome sequence was published. Hundreds of bacterial genome sequences are now available for comparative genomics, and searching a given protein against more than a thousand genomes will soon be possible. The subject of this review will address a relatively straightforward question: "What have we learned from this vast amount of new genomic data?" Perhaps one of the most important lessons has been that genetic diversity, at the level of large-scale variation amongst even genomes of the same species, is far greater than was thought. The classical textbook view of evolution relying on the relatively slow accumulation of mutational events at the level of individual bases scattered throughout the genome has changed. One of the most obvious conclusions from examining the sequences from several hundred bacterial genomes is the enormous amount of diversity--even in different genomes from the same bacterial species. This diversity is generated by a variety of mechanisms, including mobile genetic elements and bacteriophages. An examination of the 20 Escherichia coli genomes sequenced so far dramatically illustrates this, with the genome size ranging from 4.6 to 5.5 Mbp; much of the variation appears to be of phage origin. This review also addresses mobile genetic elements, including pathogenicity islands and the structure of transposable elements. There are at least 20 different methods available to compare bacterial genomes. Metagenomics offers the chance to study genomic sequences found in ecosystems, including genomes of species that are difficult to culture. It has become clear that a genome sequence represents more than just a collection of gene sequences for an organism and that information concerning the environment and growth conditions for the organism are important for interpretation of the genomic data. The newly proposed Minimal Information about a Genome Sequence standard has been developed to obtain this information.

Bacterial Vaccines↗
PubMed2006

Outcomes for human immunodeficiency virus-1-infected infants in the United kingdom and Republic of Ireland in the era of effective antiretroviral therapy.

BACKGROUND: There are few data about disease progression and response to antiretroviral therapy (ART) in vertically HIV-infected infants in the era of effective therapy. DESIGN: Cohort study. METHODS: We examined progression to acquired immunodeficiency syndrome (AIDS) and death over calendar time for infants reported to the National Study of HIV in Pregnancy and Childhood in the United Kingdom/Ireland. The use of ART and CD4 and HIV-1 RNA responses were assessed in a subset in the Collaborative HIV Pediatric Study. RESULTS: Among 481 infants, mortality was lower in those born after 1997 (HR 0.30; P < 0.001), with no significant change in progression to AIDS. Of 174 infants born since 1997 in the Collaborative HIV Pediatric Study, 41 (24%) were followed from birth, 77 (44%) presented pre-AIDS and 56 (32%) presented with AIDS. Of 125 (72%) children on 3- or 4-drug ART by the age of 2 years, 59% had HIV-1 RNA <400 at 12 months; median CD4 percentage increased from 24% to 35%. Among 41 infants followed from birth, 12 progressed to AIDS (5 while ART naive) and 3 died; 1 of 10 infants initiating ART before 3 months of age progressed clinically. CONCLUSION: Mortality in HIV-infected infants is significantly lower in the era of effective ART, but symptomatic disease rates remain high. Infrequent clinic attendance and poor compliance with cotrimoxazole prophylaxis and/or ART in infants born to diagnosed HIV-infected women and late presentation of infants identified after birth appear to be major contributors. Poor virologic response to ART during infancy is of concern because of increased likelihood of early development of resistance.

Anti-HIV Agents↗
PubMed2005

Time trends in primary resistance to HIV drugs in the United Kingdom: multicentre observational study.

OBJECTIVE: To examine whether the level of primary resistance to HIV drugs is increasing in the United Kingdom. DESIGN: Multicentre observational study. SETTING: All virology laboratories in the United Kingdom carrying out tests for HIV resistance as part of routine clinical care. PARTICIPANTS: 2357 people infected with HIV who were tested for resistance before receiving antiretroviral therapy. MAIN OUTCOME MEASURE: Prevalence of drug resistance on basis of the Stanford genotypic interpretation system. RESULTS: Over the study period (February 1996 to May 2003), 335 (14.2%, 95% confidence interval 12.8% to 15.7%) samples had mutations that conferred resistance to one or more antiretroviral drugs (9.3% high level resistance, 5.9% medium level resistance). The prevalence of primary resistance has increased markedly over time, although patterns are specific to drug class; the largest increase was for non-nucleoside reverse transcriptase inhibitors. In 2002-3, the prevalence of resistance to any antiretroviral drug to nucleoside or nucleotide reverse transcriptase inhibitors, to non-nucleoside reverse transcriptase inhibitors, or to protease inhibitors was 19.2% (15.7% to 23.2%), 12.4% (9.5% to 15.9%), 8.1% (5.8% to 11.1%), and 6.6% (4.4% to 9.3%), respectively. The risk of primary resistance was only weakly related to most demographic and clinical factors, including ethnicity and viral subtype. CONCLUSIONS: The United Kingdom has one of the highest reported rates of primary resistance to HIV drugs worldwide. Prevalence seems still to be increasing and is high in all demographic subgroups.

Adolescent↗
PubMed2005

Estimating HIV-1 drug resistance in antiretroviral-treated individuals in the United Kingdom.

Good estimates of the prevalence of human immunodeficiency virus drug resistance are important for assessing requirements for new drug classes and modeling the spread of resistance. However, little consensus exists on optimal methodologies to generate such data. To compare methodologies, we used the national data set of resistance tests from >4000 patients in the United Kingdom performed between 1998 and 2002. When single-time-point analysis (method 1) was used, the proportion of tests with any form of resistance was approximately 80%, with little time trend. When a cumulative model of resistance (method 2) was used and placed in the context of all treated patients, the prevalence of any resistance increased by year, reaching 17% of treated patients in 2002. Method 2 also nearly doubles estimates of numbers of individuals infected with multiclass drug-resistant virus. Our results identify an urgent need for new drugs within existing classes and new classes of antiretroviral therapy.

Anti-HIV Agents↗
PubMed2005

Long term probability of detection of HIV-1 drug resistance after starting antiretroviral therapy in routine clinical practice.

BACKGROUND: Little is known about the long term risk of development of HIV-1 drug resistance for patients starting antiretroviral therapy (ART) with three or four drug regimens in routine clinical practice. METHODS: We analysed a large cohort study of patients seen in one of six large HIV clinics in and around London, UK. The focus of this analysis was on patients who started ART with two nucleosides plus either a single protease inhibitor (PI), a PI with ritonavir, abacavir or a non-nucleoside reverse transcriptase inhibitor (NNRTI). RESULTS: 4306 patients were followed; 1436 (33%) started with a single PI, 279 (6%) with a PI plus ritonavir, 156 (4%) with triple nucleosides and 2435 (57%) with an NNRTI. The overall cumulative risk of viral load failure was 38% by 6 years. Risk of > or =1 major IAS-USA mutation was 27% by 6 years; risk of mutations from at least two of the three main drug classes was 20% over the same period. These are lower limit estimates as test results were not available for many with viral load failure. Risk of PI mutations being detected in people who started ART with regimens containing a PI with ritonavir was significantly lower than the risk of NNRTI mutations being detected in those starting with NNRTI-containing regimens (relative hazard 0.3195% CI 0.15-0.61; p = 0.0008). CONCLUSION: In routine practice, rates of viral load failure and of resistance detection in patients who started ART with three or four drugs are appreciable.

Adult↗
PubMed2005

A randomized, placebo-controlled study of once-daily atomoxetine in the school setting in children with ADHD.

OBJECTIVE: Five studies have demonstrated the effectiveness of atomoxetine compared with placebo in reducing symptoms of attention-deficit/hyperactivity disorder (ADHD) based on parent reports. The primary objective of this clinical trial was to assess the efficacy of once-daily atomoxetine compared with placebo using teacher reports. METHOD: One hundred fifty-three patients aged 8-12 years were randomly assigned to receive once-daily atomoxetine or placebo in a 2:1 ratio for 7 weeks. ADHD symptoms at school were primarily assessed by baseline-to-endpoint change on the Attention-Deficit/Hyperactivity Disorder Rating Scale-IV-Teacher Version: Investigator administered and scored (ADHDRS-IV-Teacher:Inv) as rated by investigators using teacher reports. RESULTS: ADHDRS-IV-Teacher:Inv total scores were significantly lower for children treated with atomoxetine compared with those treated with placebo (p = .001). Similar results were observed for the inattentive (p = .016) and hyperactive/impulsive (p < .001) ADHDRS-IV-Teacher:Inv subscales, the clinician-rated Clinical Global Impressions severity scale (p = .001), the Conners Global Index-Teacher scale (p = .008), and the Conners Parent Rating Scale-Revised: Short Form ADHD Index T-Score (p < .001). Discontinuations due to adverse events were low in both groups (atomoxetine 5.9%, placebo 0%, p = .096). CONCLUSIONS: This study extends previous results based on parent reports showing that once-daily administration of atomoxetine is safe and effective in improving ADHD symptoms in children and demonstrates that outcomes at school are similar when symptoms are reported by teachers.

Atomoxetine Hydrochloride↗
PubMed2005

Adolescents with disruptive behavior disorder investigated using an optimized MR diffusion tensor imaging protocol.

Adolescents with disruptive behavior disorder (DBD) and controls were investigated using an optimized MR diffusion tensor imaging (DTI) protocol in order to assess any possible structural abnormalities associated with DBD. Thirty-six patients and 40 normal subjects were examined. The extracted diffusion fractional anisotropy (FA) results demonstrate that for the DBD patients there is significantly reduced FA in both the frontal and left temporal regions. The largest brain area with significantly reduced FA is located within the arcuate fasciculus, which has projections extending from the temporal lobe to the frontal lobe along the lateral ventricle, lateral to the tapetum. The reduced FA reflects directly a lower extent of myelination and less coherent fiber track structures in the fasciculus, which in turn may indicate communication weakness among the associated cortical areas. The detected white matter microstructural abnormality, therefore, may be related to the developmental deficits observed in the patient group.

Adolescent↗
PubMed2004

Outcome at 3 years with a prednisone-free maintenance regimen: a single-center experience with 349 kidney transplant recipients.

Historically, late steroid withdrawal after kidney transplants has been associated with an increased rejection rate. Recently, low rejection rates have been reported for recipients treated with complete avoidance or rapid elimination of steroids. However, follow-up has been short. We herein report on 3-year outcome in recipients whose prednisone was rapidly eliminated and who were maintained on a steroid-free regimen. From 10/1/1999 through 5/1/2003, 349 recipients (254 LD, 95 CAD; 319 in first 30 s) were immunosuppressed with polyclonal antibody (Thymoglobulin), a calcineurin inhibitor, either mycophenolate mofetil or sirolimus, and rapid discontinuation of prednisone. Actuarial 3-year patient survival was 95%; graft survival, 93%. Acute rejection-free graft survival at 1 year was 94%; at 3 years, 92%. There was no difference between LD and CAD. At 2 years, the mean (+/- SE) serum creatinine level for LDs was 1.6 +/- 0.5 mg/dL; for CAD, 1.6 +/- 0.4 mg/dL. We have no new cases of PTLD or avascular necrosis; 22 recipients (6%) developed CMV. Currently, 84% of recipients remain prednisone-free. We conclude that excellent 3-year patient and graft survival can be achieved without maintenance prednisone. With such a protocol, steroid-related side-effects are minimal.

Antilymphocyte Serum↗
PubMed2004

Strengthening the nursing curriculum: an interdisciplinary course addressing agricultural health and safety.

1.) Agricultural work is a dangerous occupation and incorporating content on agricultural health and safety issues into the nursing curriculum presents a challenge. 2.) The traditional strategy for dealing with these issues has been a single discipline approach. 3.) An interdisciplinary course bringing together faculty and students from the disciplines of agriculture, nursing, and public health proved successful in addressing this content in the curricula of the disciplines involved. 4.) When teaching agricultural health and safety content, it is essential to emphasize an interdisciplinary approach and frame the course in the context of rurality.

Agriculture↗
PubMed2003

Short-term risk of disease progression in HIV-1-infected children receiving no antiretroviral therapy or zidovudine monotherapy: a meta-analysis.

BACKGROUND: Data on the short-term risk of disease progression in HIV-1-infected children are needed to address the question of when to begin combination antiretroviral therapy. We estimated 12-month risks of progression to AIDS and death, by age and most recent measurement of CD4 T-cell percentage (CD4%) or viral load, in children receiving no antiretroviral therapy or zidovudine monotherapy only. METHODS: We undertook a meta-analysis of individual longitudinal data for 3941 children from eight cohort studies and nine randomised trials in Europe and the USA. Estimates of risk were derived from parametric survival models. FINDINGS: 997 AIDS-defining events were recorded over 7297 person-years of follow-up in the analysis of CD4%, and 284 events over 2282 person-years in the viral load analysis, corresponding to 568 deaths (9087 person-years) and 129 deaths (2816 person-years), respectively. In children older than 2 years, risk of death increased sharply when CD4% was less than about 10%, or 15% for risk of AIDS, with a low and fairly stable risk at greater CD4%. Children younger than 2 years had worse outlook than older children with the same CD4%. Risk of progression increased when viral load exceeded about 10(5) copies per mL, although this association was more gradual compared with CD4%. Both markers had independent predictive value for disease progression; CD4% was the stronger predictor. INTERPRETATION: This information is important for paediatricians making decisions, and for researchers designing trials, about when to initiate or restart antiretroviral therapy.

Acquired Immunodeficiency Syndrome↗
PubMed2002

The dangers of inferring treatment effects from observational data: a case study in HIV infection.

Several recent articles have implicitly questioned the need for randomized controlled trials, based on a comparison of treatment effects from observational studies and related randomized controlled trials. We present here a counterexample of a comparison of two antiretroviral drugs used in the treatment of HIV infection, in which the observational analysis gave a potentially misleading result. Examples such as this emphasize the need to regard randomized controlled trials as the primary mechanism for assessing therapeutic efficacy.

Adult↗
PubMed2002

Once-daily atomoxetine treatment for children and adolescents with attention deficit hyperactivity disorder: a randomized, placebo-controlled study.

OBJECTIVE: The authors assessed the efficacy of once-daily atomoxetine administration in the treatment of children and adolescents with attention deficit hyperactivity disorder (ADHD). METHOD: In a double-blind study, children and adolescents with ADHD (N=171, age range=6-16 years) were randomly assigned to receive 6 weeks of treatment with either atomoxetine (administered once daily) or placebo. RESULTS: Outcomes among atomoxetine-treated patients were superior to those of the placebo treatment group as assessed by investigator, parent, and teacher ratings. The treatment effect size (0.71) was similar to those observed in previous atomoxetine studies that used twice-daily dosing. Parent diary ratings suggested that drug-specific effects were sustained late in the day. Discontinuations due to adverse events were low (less than 3%) for both treatment groups, and no serious safety concerns were observed. CONCLUSIONS: Once-daily administration of atomoxetine is an effective treatment for children and adolescents with ADHD.

Adolescent↗
PubMedDate not supplied

Fly ash as a liming material for cotton.

A field experiment was conducted to determine the effect of fly ash from a coal combustion electric power facility on soil acidity in a cotton (Gossypium hirsutum L.) field. Fresh fly ash was applied to a Bosket fine sandy loam (fine-loamy, mixed, thermic Mollic Hapludalf) soil with an initial soil pH(salt) of 4.8. The fly ash was equivalent to 42 g kg(-1) calcium carbonate with 97% passing through a 60 mesh (U.S. standard) sieve. Fly ash was applied one day before cotton planting in 1999 at 0, 3.4, 6.7, and 10.1 Mg ha(-1). No fly ash was applied in 2000. Within 60 d of fly ash application in 1999, all rates of fly ash significantly increased soil pH above 6.0. Manganese levels in cotton petioles were reduced significantly by 6.7 and 10.1 Mg ha(-1) of fly ash. Soil boron (B) and sodium (Na) concentrations were significantly increased with fly ash. In 1999, B in cotton leaves ranged from 72 to 84 mg kg(-1) in plots with fly ash applications. However, no visual symptoms of B toxicity in plants were observed. In 1999, cotton lint yield decreased on average 12 kg ha(-1) for each Mg of fly ash applied. In 2000, cotton yields were significantly greater for the residual 3.4 and 6.7 Mg fly ash ha(-1) plots than the untreated check. Due to the adverse yield effects measured in the first year following application, fly ash would not be a suitable soil amendment for cotton on this soil at this time.

Boron↗