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1.  Probiotics in the prevention of eczema: a randomised controlled trial 
Archives of Disease in Childhood  2014;99(11):1014-1019.
To evaluate a multistrain, high-dose probiotic in the prevention of eczema.
A randomised, double-blind, placebo-controlled, parallel group trial.
Antenatal clinics, research clinic, children at home.
Pregnant women and their infants.
Women from 36 weeks gestation and their infants to age 6 months received daily either the probiotic (Lactobacillus salivarius CUL61, Lactobacillus paracasei CUL08, Bifidobacterium animalis subspecies lactis CUL34 and Bifidobacterium bifidum CUL20; total of 1010 organisms/day) or matching placebo.
Main outcome measure
Diagnosed eczema at age 2 years. Infants were followed up by questionnaire. Clinical examination and skin prick tests to common allergens were done at 6 months and 2 years.
The cumulative frequency of diagnosed eczema at 2 years was similar in the probiotic (73/214, 34.1%) and placebo arms (72/222, 32.4%; OR 1.07, 95% CI 0.72 to 1.6). Among the secondary outcomes, the cumulative frequency of skin prick sensitivity at 2 years was reduced in the probiotic (18/171; 10.5%) compared with the placebo arm (32/173; 18.5%; OR 0.52, 95% CI 0.28 to 0.98). The statistically significant differences between the arms were mainly in sensitisation to cow's milk and hen's egg proteins at 6 months. Atopic eczema occurred in 9/171 (5.3%) children in the probiotic arm and 21/173 (12.1%) in the placebo arm (OR 0.40, 95% CI 0.18 to 0.91).
The study did not provide evidence that the probiotic either prevented eczema during the study or reduced its severity. However, the probiotic seemed to prevent atopic sensitisation to common food allergens and so reduce the incidence of atopic eczema in early childhood.
Trial registration Number
PMCID: PMC4215350  PMID: 24947281
Allergy; Microbiology; Dermatology
2.  Factors associated with low fitness in adolescents – A mixed methods study 
BMC Public Health  2014;14:764.
Fitness and physical activity are important for cardiovascular and mental health but activity and fitness levels are declining especially in adolescents and among girls. This study examines clustering of factors associated with low fitness in adolescents in order to best target public health interventions for young people.
1147 children were assessed for fitness, had blood samples, anthropometric measures and all data were linked with routine electronic data to examine educational achievement, deprivation and health service usage. Factors associated with fitness were examined using logistic regression, conditional trees and data mining cluster analysis. Focus groups were conducted with children in a deprived school to examine barriers and facilitators to activity for children in a deprived community.
Unfit adolescents are more likely to be deprived, female, have obesity in the family and not achieve in education. There were 3 main clusters for risk of future heart disease/diabetes (high cholesterol/insulin); children at low risk (not obese, fit, achieving in education), children ‘visibly at risk’ (overweight, unfit, many hospital/GP visits) and ‘invisibly at risk’ (unfit but not overweight, failing in academic achievement). Qualitative findings show barriers to physical activity include cost, poor access to activity, lack of core physical literacy skills and limited family support.
Low fitness in the non-obese child can reveal a hidden group who have high risk factors for heart disease and diabetes but may not be identified as they are normal weight. In deprived communities low fitness is associated with non-achievement in education but in non-deprived communities low fitness is associated with female gender. Interventions need to target deprived families and schools in deprived areas with community wide campaigns.
PMCID: PMC4132898  PMID: 25074589
Eduation and health; Risk factors; Diabetes; Heart disease; Physical activity
3.  High activity and Lévy searches: jellyfish can search the water column like fish 
Over-fishing may lead to a decrease in fish abundance and a proliferation of jellyfish. Active movements and prey search might be thought to provide a competitive advantage for fish, but here we use data-loggers to show that the frequently occurring coastal jellyfish (Rhizostoma octopus) does not simply passively drift to encounter prey. Jellyfish (327 days of data from 25 jellyfish with depth collected every 1 min) showed very dynamic vertical movements, with their integrated vertical movement averaging 619.2 m d−1, more than 60 times the water depth where they were tagged. The majority of movement patterns were best approximated by exponential models describing normal random walks. However, jellyfish also showed switching behaviour from exponential patterns to patterns best fitted by a truncated Lévy distribution with exponents (mean μ = 1.96, range 1.2–2.9) close to the theoretical optimum for searching for sparse prey (μopt ≈ 2.0). Complex movements in these ‘simple’ animals may help jellyfish to compete effectively with fish for plankton prey, which may enhance their ability to increase in dominance in perturbed ocean systems.
PMCID: PMC3234559  PMID: 21752825
plankton thin layers; Lasker's stable ocean hypothesis; zooplankton; superdiffusion; biologging
4.  A multicentre randomised controlled trial evaluating lactobacilli and bifidobacteria in the prevention of antibiotic-associated diarrhoea in older people admitted to hospital: the PLACIDE study protocol 
BMC Infectious Diseases  2012;12:108.
Antibiotic associated diarrhoea complicates 5–39% of courses of antibiotic treatment. Major risk factors are increased age and admission to hospital. Of particular importance is C. difficile associated diarrhoea which occurs in about 4% of antibiotic courses and may result in severe illness, death and high healthcare costs. The emergence of the more virulent 027 strain of C. difficile has further heightened concerns. Probiotics may prevent antibiotic associated diarrhoea by several mechanisms including colonization resistance through maintaining a healthy gut flora.
This study aims to test the hypothesis that administration of a probiotic comprising two strains of lactobacilli and two strains of bifidobacteria alongside antibiotic treatment prevents antibiotic associated diarrhoea. We have designed a prospective, parallel group trial where people aged 65 years or more admitted to hospital and receiving one or more antibiotics are randomly allocated to receive either one capsule of the probiotic or a matching placebo daily for 21 days. The primary outcomes are the frequency of antibiotic associated and C. difficile diarrhoea during 8–12 weeks follow-up. To directly inform routine clinical practice, we will recruit a sufficient number of patients to demonstrate a 50% reduction in the frequency of C. difficile diarrhoea with a power of 80%. To maximize the generalizability of our findings and in view of the well-established safety record of probiotics, we will recruit a broad range of medical and surgical in-patients from two different health regions within the UK.
Antibiotic associated diarrhoea constitutes a significant health burden. In particular, current measures to prevent and control C. difficile diarrhoea are expensive and disrupt clinical care. This trial may have considerable significance for the prevention of antibiotic associated diarrhoea in hospitals.
Trial registration
International Standard Randomised Controlled Trial Number Register ISRCTN70017204.
PMCID: PMC3447682  PMID: 22559011
Probiotic; Lactobacilli; Bifidobacteria; Antibiotic; Antibiotic associated diarrhoea; Clostridium difficile diarrhoea; Elderly; Hospital in-patient
5.  Evolutionary Fingerprinting of Genes 
Molecular Biology and Evolution  2009;27(3):520-536.
Over time, natural selection molds every gene into a unique mosaic of sites evolving rapidly or resisting change—an “evolutionary fingerprint” of the gene. Aspects of this evolutionary fingerprint, such as the site-specific ratio of nonsynonymous to synonymous substitution rates (dN/dS), are commonly used to identify genetic features of potential biological interest; however, no framework exists for comparing evolutionary fingerprints between genes. We hypothesize that protein-coding genes with similar protein structure and/or function tend to have similar evolutionary fingerprints and that comparing evolutionary fingerprints can be useful for discovering similarities between genes in a way that is analogous to, but independent of, discovery of similarity via sequence-based comparison tools such as Blast.
To test this hypothesis, we develop a novel model of coding sequence evolution that uses a general bivariate discrete parameterization of the evolutionary rates. We show that this approach provides a better fit to the data using a smaller number of parameters than existing models. Next, we use the model to represent evolutionary fingerprints as probability distributions and present a methodology for comparing these distributions in a way that is robust against variations in data set size and divergence. Finally, using sequences of three rapidly evolving RNA viruses (HIV-1, hepatitis C virus, and influenza A virus), we demonstrate that genes within the same functional group tend to have similar evolutionary fingerprints. Our framework provides a sound statistical foundation for efficient inference and comparison of evolutionary rate patterns in arbitrary collections of gene alignments, clustering homologous and nonhomologous genes, and investigation of biological and functional correlates of evolutionary rates.
PMCID: PMC2877558  PMID: 19864470
adaptive evolution; codon models; evolutionary distance; machine classification
6.  Parental factors associated with walking to school and participation in organised activities at age 5: Analysis of the Millennium Cohort Study 
BMC Public Health  2011;11:14.
Physical activity is associated with better health. Two sources of activity for children are walking to school and taking part in organised sports and activities. This study uses a large national cohort to examine factors associated with participation in these activities.
The Millennium Cohort study contains 5 year follow-up of 17,561 singleton children recruited between 2000-2002 in the UK. All participants were interviewed in their own homes at 9 months, 3 years and 5 years follow-up and all measures were self reports. Logistic regression and likelihood ratio tests were used.
Children are less likely to walk to school as income and parental education increase [Adjusted odds: 0.7 (95%CI: 0.6-0.8) for higher income/education compared to low income/no qualifications]. However, if the parent plays with the child in high income families the child is more likely to walk to school [Adjusted odds: 1.67 (95%CI: 1.3-2.1)]. Children taking part in organised activities are from higher income, higher education families, with a car, in a "good" area with non-working mothers. However, in low socio-economic families where the parent plays with the child the child is more likely to take part in organised activities [Adjusted odds: 2.0 (95% CI: 1.5-2.7)].
Income is an important determinant of the type of activity available to children. Families that report good health behaviours (non-smoking, low TV viewing) and play with their children show higher levels of physical activity. Thus, parenting practice appears to have a strong impact on their child's physical activity.
PMCID: PMC3027134  PMID: 21210998
7.  Population based absolute and relative survival to 1 year of people with diabetes following a myocardial infarction: A cohort study using hospital admissions data 
BMC Public Health  2010;10:338.
People with diabetes who experience an acute myocardial infarction (AMI) have a higher risk of death and recurrence of AMI. This study was commissioned by the Department for Transport to develop survival tables for people with diabetes following an AMI in order to inform vehicle licensing.
A cohort study using data obtained from national hospital admission datasets for England and Wales was carried out selecting all patients attending hospital with an MI for 2003-2006 (inclusion criteria: aged 30+ years, hospital admission for MI (defined using ICD 10 code I21-I22). STATA was used to create survival tables and factors associated with survival were examined using Cox regression.
Of 157,142 people with an MI in England and Wales between 2003-2006, the relative risk of death or recurrence of MI for those with diabetes (n = 30,407) in the first 90 days was 1.3 (95%CI: 1.26-1.33) crude rates and 1.16 (95%CI: 1.1-1.2) when controlling for age, gender, heart failure and surgery for MI) compared with those without diabetes (n = 129,960). At 91-365 days post AMI the risk was 1.7 (95% CI 1.6-1.8) crude and 1.50 (95%CI: 1.4-1.6) adjusted. The relative risk of death or re-infarction was higher at younger ages for those with diabetes and directly after the AMI (Relative risk; RR: 62.1 for those with diabetes and 28.2 for those without diabetes aged 40-49 [compared with population risk]).
This is the first study to provide population based tables of age stratified risk of re-infarction or death for people with diabetes compared with those without diabetes. These tables can be used for giving advice to patients, developing a baseline to compare intervention studies or developing license or health insurance guidelines.
PMCID: PMC2894776  PMID: 20546579
8.  Risk factors for childhood obesity at age 5: Analysis of the Millennium Cohort Study 
BMC Public Health  2009;9:467.
Weight at age 5 is a predictor for future health of the individual. This study examines risk factors for childhood obesity with a focus on ethnicity.
Data from the Millennium Cohort study were used. 17,561 singleton children of White/European (n = 15,062), Asian (n = 1,845) or African (n = 654) background were selected. Logistic regression and likelihood ratio tests were used to examine factors associated with obesity at age 5. All participants were interviewed in their own homes. The main exposures examined included; Birth weight, sedentary lifestyle, family health behaviours, ethnicity, education and income.
Children with a sedentary lifestyle, large at birth, with high risk family health behaviours (overweight mothers, smoking near the child, missing breakfast) and from a family with low income or low educational attainment, were more likely to be obese regardless of ethnicity. Feeding solid food before 3 months was associated with obesity in higher income White/European families. Even when controlling for socioeconomic status, ethnic background is an important independent risk factor for childhood obesity [Odds ratio of obesity; was 1.7 (95%CI: 1.2-2.3) for Asian and 2.7 (95%CI: 1.9-3.9) for African children, compared to White/European]. The final adjusted model suggests that increasing income does not have a great impact on lowering obesity levels, but that higher academic qualifications are associated with lower obesity levels [Odds of obesity: 0.63 (95%CI: 0.52-0.77) if primary carer leaves school after age 16 compared at age 16].
Education of the primary carer is an important modifiable factor which can be targeted to address rising obesity levels in children. Interventions should be family centred supporting and showing people how they can implement lifestyle changes in their family.
PMCID: PMC2803190  PMID: 20015353
9.  Internet-based randomised controlled trials for the evaluation of complementary and alternative medicines: probiotics in spondyloarthropathy 
The clinical effectiveness of complementary and alternative medicines (CAMs) is widely debated because of a lack of clinical trials. The internet may provide an effective and economical approach for undertaking randomised controlled trials (RCTs) of low-risk interventions. We investigated whether the internet could be used to perform an internet-based RCT of a CAM fulfilling the revised CONSORT (Consolidated Standards of Reporting Trials) statement quality checklist for reporting of RCTs. A secondary aim was to examine the effect of probiotics compared to placebo in terms of well-being over 12 weeks.
People aged ≥18 years with confirmed spondyloarthropathy living in the United Kingdom with internet access were invited to participate in an internet-based RCT of probiotic compared to placebo for improving well-being and bowel symptoms. The intervention was a probiotic containing 4 strains of live bacteria or identical placebo taken by mouth daily for 3 months. The primary outcome measure was the performance of the trial according to the revised CONSORT statement.
147 people were randomised into the trial. The internet-based trial of the CAM fulfilled the revised CONSORT statement such as efficient blinding, allocation concealment, intention to treat analysis and flow of participants through the trial. Recruitment of the required number of participants was completed in 19 months. Sixty-five percent (96/147) completed the entire 3 months of the trial. The trial was low cost and demonstrated that in an intention to treat analysis, probiotics did not improve well-being or bowel symptoms.
The internet-based RCT proved to be a successful and economical method for examining this CAM intervention. Recruitment, adherence and completion rate were all similar to those reported with conventional RCTs but at a fraction of the cost. Internet-based RCTs can fulfil all the criteria of the revised CONSORT statement and are an appropriate method for studying low-risk interventions.
Trial registration
PMCID: PMC2241591  PMID: 18190710
10.  Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses 
PLoS Computational Biology  2006;2(6):e62.
Several codon-based methods are available for detecting adaptive evolution in protein-coding sequences, but to date none specifically identify sites that are selected differentially in two populations, although such comparisons between populations have been historically useful in identifying the action of natural selection. We have developed two fixed effects maximum likelihood methods: one for identifying codon positions showing selection patterns that persist in a population and another for detecting whether selection is operating differentially on individual codons of a gene sampled from two different populations. Applying these methods to two HIV populations infecting genetically distinct human hosts, we have found that few of the positively selected amino acid sites persist in the population; the other changes are detected only at the tips of the phylogenetic tree and appear deleterious in the long term. Additionally, we have identified seven amino acid sites in protease and reverse transcriptase that are selected differentially in the two samples, demonstrating specific population-level adaptation of HIV to human populations.
Despite the efforts devoted to surveying HIV genetic diversity and the development of an effective vaccine, there is still no consensus on the extent to which the former prejudices the latter. Experimental studies show that escape from cell-mediated immunity is selected for in HIV and SIV, and sometimes very quickly. Conversely, escape mutants may be selected against at transmission, so how much does this selection within individuals influence the genotype of the circulating HIV population overall? Kosakovsky Pond, Leigh Brown, and colleagues have developed a new statistical approach to address this question. Using sequences from the globally most abundant HIV subtype (subtype C), the authors directly compared virus of the same subtype infecting genetically different human populations. They show at least half of the amino acid sites selected within individuals are not selected at a population level, and they identify six amino acid sites in the RT gene that are selected differentially between populations. We can now partition molecular adaptation between individual and population components for whatever genes may be included in candidate vaccines, in the target populations themselves. The methods are also important beyond the HIV world, where analogous issues arise in the more general question of the evolution of virulence in pathogens.
PMCID: PMC1480537  PMID: 16789820
11.  Induction of T Helper Type 1 and 2 Responses to 19-Kilodalton Merozoite Surface Protein 1 in Vaccinated Healthy Volunteers and Adults Naturally Exposed to Malaria 
Infection and Immunity  2002;70(3):1417-1421.
Plasmodium falciparum malaria is a major cause of death in the tropics. The 19-kDa subunit of P. falciparum merozoite surface protein 1 (MSP-119), a major blood stage vaccine candidate, is the target of cellular and humoral immune responses in animals and humans. In this phase I trial of MSP-119, immunization of nonexposed human volunteers with either of the two allelic forms of recombinant MSP-119 induced high levels of antigen-specific Th1 (gamma interferon) and Th2 (interleukin 4 [IL-4] and IL-10) type lymphokines. The adjustment of the antigen dose and number of immunizations regulated the level of specificity of immune responses and Th1/Th2 bias of responses induced by vaccination. Novel conserved and allelic T-cell epitopes which induced cross-strain immune responses were identified. Importantly, responses to many of these novel epitopes were also present in adults exposed to malaria, both in east (Kenya) and west Africa (The Gambia). These data suggest that epitope-specific naturally acquired MSP-119 immune responses in endemic populations can be boosted by vaccination.
PMCID: PMC127736  PMID: 11854228

Results 1-11 (11)