In praise of Prais-Winsten: An evaluation of methods used to account for autocorrelation in interrupted time series.

Interrupted time series are increasingly being used to assess the population impact of public health interventions. These data are usually correlated over time (auto correlated) and this must be accounted for in the analysis. Typically, this is done using either the Prais-Winsten method, the Newey-West method, or autoregressive-moving-average (ARMA) modeling. In this paper, we illustrate these methods via a study of pneumococcal vaccine introduction and explore their performance under 20 simulated autocorrelation scenarios with sample sizes ranging between 20 and 300. We show that in terms of mean square error, the Prais-Winsten and ARMA methods perform best, while in terms of coverage the Prais-Winsten method generally performs better than other methods. All three methods are unbiased. As well as having good statistical properties, the Prais-Winsten method is attractive because it is decision-free and produces a single measure of autocorrelation that can be compared between studies and used to guide sample size calculations. We would therefore encourage analysts to consider using this simple method to analyze interrupted time series.

An exploration of the impact of ethanol diluent on breath alcohol concentration in patients receiving paclitaxel chemotherapy.

PURPOSE: This study aimed to provide a better understanding of the impact of paclitaxel chemotherapy on breath alcohol in an Irish population. METHODS: Patients attending the Oncology Day Unit at Beaumont Hospital were invited to participate on the day of their treatment. The brand of paclitaxel used was Actavis Pharma Inc and contained 6 mg/mL paclitaxel in 50% Ethanol/ 50% Cremophor EL. Breath alcohol concentration was measured using the AlcoSense ™ Breathalyser on three separate visits. The primary end-point was the number of patients who were above the legal threshold for drink driving in Ireland. RESULTS: In total, 50 patients were recruited. 36 (68%) were female. The most common diagnosis was breast cancer (56%). Ten (20%) patients had metastatic disease and 4 (8%) had liver metastases. The mean paclitaxel dose administered was 118 mg. The mean amount of ethanol infused was 7.7 g. 27 patients had a detectable breath alcohol level on at least one visit. The mean breath alcohol concentration was 2 mcg/100 mL or 0.02 mg/L of breath. The maximum concentration of ethanol in exhaled breath was 11 mcg/100 mL or 0.11 mg/L which is 50% of the statutory limit for drink driving in Ireland. A weak correlation was observed between ethanol concentration in exhaled breath and the total amount of ethanol administered. Although no patient exceeded the general limit for drink driving in Ireland, three (6%) participants had a breath alcohol concentration above the threshold for professional, learner or novice drivers. CONCLUSION: Although definitive conclusions are limited by relatively small numbers, it seems unlikely that weekly paclitaxel infusions pose any significant risk to patients driving.

Referral pathways between the mental health services and Jigsaw.

OBJECTIVES: To examine similarities and differences in the demographic and clinical profiles of young people (15-25 years of age) referred between the mental health services (MHS) and Jigsaw Galway. METHODS: A retrospective chart review was conducted of clinical files of individuals attending secondary MHS who had been referred to or from Jigsaw Galway over a 5-year period. Differences in demographic and clinical data between individuals referred to or from Jigsaw Galway were compared. RESULTS: A recent act of self-harm was more prevalent in individuals referred from Jigsaw to the adult MHS (p=0.02). No other demographic or clinical differences were detected between individuals attending Jigsaw Galway and the MHS. CONCLUSIONS: Education sessions for clinical staff working in primary care, Jigsaw Galway and the MHS are suggested to support clinicians in choosing the best referral pathway, which may more optimally address young people's mental health difficulties.

Investigating the effects of long-term dornase alfa use on lung function using registry data.

BACKGROUND: Dornase alfa (DNase) is one of the commonest cystic fibrosis (CF) treatments and is often used for many years. However, studies have not evaluated the effectiveness of its long-term use. We aimed to use UK CF Registry data to investigate the effects of one-, two-, three-, four- and five-years of DNase use on lung function to see if the benefits of short-term treatment use are sustained long term. METHODS: We analysed data from 4,198 people in the UK CF Registry from 2007 to 2015 using g-estimation. By controlling for time-dependent confounding we estimated the effects of long-term DNase use on percent predicted FEV1 (ppFEV1) and investigated whether the effect differed by ppFEV1 at treatment initiation or by age. RESULTS: Considering the population as a whole, there was no significant effect of one-year's use of DNase; change in ppFEV1 over one year was -0.1% in the treated compared to the untreated (p = 0.51) and this did not change with long-term use. However, treatment was estimated to be more beneficial in people with lower lung function (p < 0.001); those with ppFEV1 < 70% at treatment initiation, showed an increase in lung function over one year that was sustained out to five years. The estimated effect of DNase did not depend on age (p = 0.35). CONCLUSIONS: DNase improved lung function in individuals with reduced lung function, bringing a step-change in lung function, but no change in the slope of decline. There was no evidence for a benefit in lung function in those initiating treatment with ppFEV1 > 70%.

Decreased STAT3 in human idiopathic fetal growth restriction contributes to trophoblast dysfunction.

Abnormal trophoblast function is associated with fetal growth restriction (FGR). The JAK-STAT pathway is one of the principal signalling mechanisms by which cytokines and growth factors modulate cell proliferation, differentiation, cell migration and apoptosis. The expression of placental JAK-STAT genes in human idiopathic FGR is unknown. In this study, we propose the hypothesis that JAK-STAT pathway genes are differentially expressed in idiopathic FGR-affected pregnancies and contribute to abnormal feto-placental growth by modulating the expression of the amino acid transporter SNAT2, differentiation marker CGB/human chorionic gonadotrophin beta-subunit (ß-hCG) and apoptosis markers caspases 3 and 8, and TP53. Expression profiling of FGR-affected placentae revealed that mRNA levels of STAT3, STAT2 and STAT5B decreased by 69, 52 and 50%, respectively, compared with gestational-age-matched controls. Further validation by real-time PCR and immunoblotting confirmed significantly lower STAT3 mRNA and STAT3 protein (total and phosphorylated) levels in FGR placentae. STAT3 protein was localised to the syncytiotrophoblast (ST) in both FGR and control placentae. ST differentiation was modelled by in vitro differentiation of primary villous trophoblast cells from first-trimester and term placentae, and by treating choriocarcinoma-derived BeWo cells with forskolin in cell culture. Differentiation in these models was associated with increased STAT3 mRNA and protein levels. In BeWo cells treated with siRNA targeting STAT3, the mRNA and protein levels of CGB/ß-hCG, caspases 3 and 8, and TP53 were significantly increased, while that of SNAT2 was significantly decreased compared with the negative control siRNA. In conclusion, we report that decreased STAT3 expression in placentae may contribute to abnormal trophoblast function in idiopathic FGR-affected pregnancies.

Dietary patterns derived with multiple methods from food diaries and breast cancer risk in the UK Dietary Cohort Consortium.

BACKGROUND/OBJECTIVES: In spite of several studies relating dietary patterns to breast cancer risk, evidence so far remains inconsistent. This study aimed to investigate associations of dietary patterns derived with three different methods with breast cancer risk. SUBJECTS/METHODS: The Mediterranean Diet Score (MDS), principal components analyses (PCA) and reduced rank regression (RRR) were used to derive dietary patterns in a case-control study of 610 breast cancer cases and 1891 matched controls within four UK cohort studies. Dietary intakes were collected prospectively using 4- to 7-day food diaries and resulting food consumption data were grouped into 42 food groups. Conditional logistic regression models were used to estimate odds ratios (ORs) for associations between pattern scores and breast cancer risk adjusting for relevant covariates. A separate model was fitted for post-menopausal women only. RESULTS: The MDS was not associated with breast cancer risk (OR comparing first tertile with third 1.20 (95% CI 0.92; 1.56)), nor the first PCA-derived dietary pattern, explaining 2.7% of variation of diet and characterized by cheese, crisps and savoury snacks, legumes, nuts and seeds (OR 1.18 (95% CI 0.91; 1.53)). The first RRR-derived pattern, a 'high-alcohol' pattern, was associated with a higher risk of breast cancer (OR 1.27; 95% CI 1.00; 1.62), which was most pronounced in post-menopausal women (OR 1.46 (95% CI 1.08; 1.98)). CONCLUSIONS: A 'high-alcohol' dietary pattern derived with RRR was associated with an increased breast cancer risk; no evidence of associations of other dietary patterns with breast cancer risk was observed in this study.

Increased decidual mRNA expression levels of candidate maternal pre-eclampsia susceptibility genes are associated with clinical severity.

INTRODUCTION: Pre-eclampsia (PE) has a familial association, with daughters of women who had PE during pregnancy having more than twice the risk of developing PE themselves. Through genome-wide linkage and genetic association studies in PE-affected families and large population samples, we previously identified the following as positional candidate maternal susceptibility genes for PE; ACVR1, INHA, INHBB, ERAP1, ERAP2, LNPEP, COL4A1 and COL4A2. The aims of this study were to determine mRNA expression levels of previously identified candidate maternal pre-eclampsia susceptibility genes from normotensive and severe PE (SPE) pregnancies and correlate mRNA expression levels with the clinical severity of SPE. METHODS: Third trimester decidual tissues were collected from both normotensive (n = 21) and SPE pregnancies (n = 24) and mRNA expression levels were determined by real-time PCR. Gene expression was then correlated with several parameters of clinical severity in SPE. Statistical significance was determined by Mann-Whitney U test and Spearman's Correlation. RESULTS: The data demonstrate significantly increased decidual mRNA expression levels of ACVR1, INHBB, ERAP1, ERAP2, LNPEP, COL4A1 and COL4A2 in SPE (p < 0.05). Increased mRNA expression levels of several genes - INHA, INHBB, COL4A1 and COL4A2 were correlated with earlier onset of PE and earlier delivery of the fetus (p < 0.05). CONCLUSION: These results suggest altered expression of maternal susceptibility genes may play roles in PE development and the course of disease severity.

Homeobox genes and down-stream transcription factor PPARγ in normal and pathological human placental development.

The placenta provides critical transport functions between the maternal and fetal circulations during intrauterine development. Formation of this interface is controlled by nuclear transcription factors including homeobox genes. Here we summarize current knowledge regarding the expression and function of homeobox genes in the placenta. We also describe the identification of target transcription factors including PPARγ, biological pathways regulated by homeobox genes and their role in placental development. The role of the nuclear receptor PPARγ, ligands and target genes in human placental development is also discussed. A better understanding of these pathways will improve our knowledge of placental cell biology and has the potential to reveal new molecular targets for the early detection and diagnosis of pregnancy complications including human fetal growth restriction.

Indigenous Health: ACTION on Prevention - 50th annual Australian Society for Medical Research National Scientific Conference.

The 50th annual National Scientific Conference of the Australian Society for Medical Research was held in Cairns, Queensland, 13-16 November 2011. The theme, 'Indigenous Health: ACTION on Prevention' highlighted the direct action being undertaken by health and medical researchers, as well as allied health professionals, to improve long-term health outcomes for Indigenous Australians.

Vitamin C intake from diary recordings and risk of breast cancer in the UK Dietary Cohort Consortium.

BACKGROUND/OBJECTIVES: Vitamin C intake has been inversely associated with breast cancer risk in case-control studies, but not in meta-analyses of cohort studies using Food Frequency Questionnaires, which can over-report fruit and vegetable intake, the main source of vitamin C. This is the first study to investigate associations between vitamin C intake and breast cancer risk using food diaries. SUBJECTS/METHODS: Estimated dietary vitamin C intake was derived from 4-7 day food diaries pooled from five prospective studies in the UK Dietary Cohort Consortium. This nested case-control study of 707 incident breast cancer cases and 2144 matched controls examined breast cancer risk in relation to dietary vitamin C intake using conditional logistic regression adjusting for relevant covariates. Additionally, total vitamin C intake from supplements and diet was analysed in three cohorts. RESULTS: No evidence of associations was observed between breast cancer risk and vitamin C intake analysed for dietary vitamin C intake (odds ratios (OR)=0.98 per 60 mg/day, 95% confidence interval (CI): 0.88-1.09, P (trend)=0.7), dietary vitamin C density (OR=0.97 per 60 mg/day, 95% CI: 0.87-1.07, P (trend)=0.5 ) or total vitamin C intake (OR=1.01 per 60 mg/day, 95% CI: 0.99-1.03, P (trend)=0.3). Additionally, there was no significant association for post-menopausal women (OR=1.02 per 60 mg/day, 95% CI: 0.99-1.05, P (trend)=0.3). CONCLUSIONS: This pooled analysis of individual UK women found no evidence of significant associations between breast cancer incidence and dietary or total vitamin C intake derived uniquely from detailed diary recordings.

Fibre intake in relation to serum total cholesterol levels and CHD risk: a comparison of dietary assessment methods.

BACKGROUND/OBJECTIVES: Prospective diet diaries may be more accurate than retrospective food frequency questionnaires (FFQ). The objective of this study was to compare FFQ and 7-day diet diary (7DD) measurements of fibre intake with the incidence of coronary heart disease (CHD). SUBJECTS/METHODS: We compared 7DD and FFQ fibre intake in a nested case-control study in a population of 25639 men and women aged 40-79 years, surveyed in 1993-97 and followed up until 2007. Among 2151 CHD cases and 5354 controls, FFQ and 7DD fibre intake (6 g/day) was examined in relation to serum total cholesterol and CHD using linear and logistic regression adjusted for age and additionally for body mass index, physical activity, smoking status, family history of CHD, social class, diabetes, alcohol, energy, saturated fat and use of lipid lowering medication, antihypertensive medication or aspirin. RESULTS: Age-adjusted serum total cholesterol was inversely associated with 7DD fibre among men and women, but with FFQ fibre among men only. In the multivariate analysis, associations with 7DD fibre were attenuated among men (regression coefficient -0.036 mmol/l, s.e. 0.021, P-value 0.087) and women (regression coefficient -0.069 mmol/l, s.e. 0.036, P-value 0.053), and were non-significant for FFQ fibre. Among men, age-adjusted CHD risk was inversely associated with 7DD fibre (odds ratio (OR) 0.84, 95% confidence interval (CI) 0.79-0.90), but not with FFQ fibre (OR 0.96, 95% CI 0.90-1.12). Among women, age-adjusted CHD risk was inversely associated with 7DD fibre (OR 0.83, 95% CI 0.75-0.93), and had a weaker inverse borderline-significant association with FFQ fibre (OR 0.93, 95% CI 0.87-1.01). Multivariate models yielded similar results. CONCLUSIONS: Inconsistencies in diet-CHD relationships in population studies may be associated with the use of different dietary assessment methods.

Self-reported and measured anthropometric data and risk of colorectal cancer in the EPIC-Norfolk study.

BACKGROUND: Epidemiological studies have shown inconsistent results for the association between body size and colorectal cancer (CRC) risk. Inconsistencies may be because of the reliance on self-reported measures of body size. OBJECTIVE: We examined the association of self-reported and directly assessed anthropometric data (body height, weight, body mass index (BMI), waist, hip, waist-to-hip ratio (WHR) and chest circumference) with CRC risk in the EPIC-Norfolk study. DESIGN: A total of 20,608 participants with complete self-reported and measured height and weight and without any history of cancer were followed up an average of 11 years, during which 357 incident CRC cases were recorded. Hazard Ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards models. RESULTS: After adjustment for confounders, HRs among women in the highest quintile of the body size measure relative to the lowest quintile showed that measured height (HR=1.98, 95% CI=1.19-3.28, P (trend)=0.009), measured waist circumference (HR=1.65, 95% CI=0.97-2.86, P (trend)=0.009) and measured WHR (HR=2.07, 95% CI=1.17-3.67, P (trend)=0.001) were associated with increased CRC risk. Associations using corresponding self-reported measures were attenuated and not statistically significant. Conversely, the association of BMI with CRC risk in women was weaker using measured BMI (HR=1.57, 95% CI=0.91-2.73, P (trend)=0.05) compared with self-reported BMI (HR=1.97, 95% CI=1.18-3.30, P (trend)=0.02). In men no significantly increased CRC risk was observed with any of the anthropometric measures. CONCLUSIONS: Measured height, waist circumference and WHR were associated with CRC risk in women, whereas any significant associations with those measures were attenuated when self-reported data were used.

Effects of body size and sociodemographic characteristics on differences between self-reported and measured anthropometric data in middle-aged men and women: the EPIC-Norfolk study.

BACKGROUND/OBJECTIVES: To investigate the effects of body size and sociodemographic characteristics on differences between self-reported (SR) and measured anthropometric data in men and women. SUBJECTS/METHODS: This study comprises 9933 men and 11,856 women aged 39-79 years at baseline survey (1993-1997) in the EPIC-Norfolk study (Norfolk arm of the European Investigation into Cancer and Nutrition Study). The effects of sex, measured height, weight, age group, educational level and social class on differences between SR and measured weight, height, body mass index (BMI), waist, hip and waist-to-hip ratio (WHR) were examined. RESULTS: There were systematic differences between SR and measured anthropometric measurements by sex, measured height, weight and sociodemographic characteristics. Height was overestimated in both sexes while weight, waist, hip, and consequently, BMI and WHR were underestimated. Being male, shorter, heavier, older, and having no educational qualifications and manual occupation were independently associated with overreporting of height, and underreporting of weight was associated independently with being female, shorter, heavier, younger age, and higher education level and social class. Underreporting of waist circumference was strongly associated with being female and higher measured waist circumference, while underreporting of hip circumference was associated with being male and higher measured hip circumference. Furthermore, there was substantial degree of misclassification of BMI and waist circumference categories for both general and central obesity associated with SR data. CONCLUSIONS: These findings suggest that errors in SR anthropometric data, especially waist and hip circumference are influenced by actual body size as well as sociodemographic characteristics. These systematic differences may influence associations between SR anthropometric measures and health outcomes in epidemiological studies.

Alcohol intake and risk of colorectal cancer: results from the UK Dietary Cohort Consortium.

BACKGROUND: Epidemiological studies have suggested that excessive alcohol intake increases colorectal cancer (CRC) risk. However, findings regarding tumour subsites and sex differences have been inconsistent. METHODS: We investigated the prospective associations between alcohol intake on overall and site- and sex-specific CRC risk. Analyses were conducted on 579 CRC cases and 1996 matched controls nested within the UK Dietary Cohort Consortium using standardised data obtained from food diaries as a main nutritional method and repeated using data from food frequency questionnaire (FFQ). RESULTS: Compared with individuals in the lightest category of drinkers (>0-<5 g per day), the multivariable odds ratios of CRC were 1.16 (95% confidence interval (95% CI): 0.88, 1.53) for non-drinkers, 0.91 (95% CI: 0.67, 1.24) for drinkers with 5-<15 g per day, 0.90 (95% CI: 0.65, 1.25) for drinkers with 15-<30 g per day, 1.02 (95% CI: 0.66, 1.58) for drinkers with 30-<45 g per day and 1.19 (95% CI: 0.75, 1.91) for drinkers with >or=45 g per day. No clear associations were observed between site-specific CRC risk and alcohol intake in either sex. Analyses using FFQ showed similar results. CONCLUSION: We found no significantly increased risk of CRC up to 30 g per day of alcohol intake within the UK Dietary Cohort Consortium.

New technology for investigating trophoblast function.

Measuring trophoblast function involves performing end-point assays that represent the response at a single time point. New technology from Roche Applied Science enables continuous monitoring of cells in real-time using specialized culture dishes containing micro-electrodes. The xCELLigence System allows continuous measurement and quantification of cell adhesion, proliferation, migration and invasion, thus creating a true picture of trophoblast function. Lag and log growth phases can be determined thus pinpointing optimal times to treat and harvest cells. Use of this system will provide valuable insights into trophoblast functions as well as the behaviour of other cell types found at the maternal-fetal interface.

Live cell image analysis of cell-cell interactions reveals the specific targeting of vascular smooth muscle cells by fetal trophoblasts.

In early pregnancy, fetal trophoblasts selectively invade and remodel maternal spiral arteries. A healthy pregnancy is dependent on this adaptation to allow sufficient maternal blood to reach the placenta and the developing fetus. However, little is known of the role played by trophoblasts in this adaptation process. In this study, the interactions between trophoblast cells (TC) and vascular smooth muscle cells (VSMC) were examined using novel live cell image analysis methods which allow quantitative assessment of the behaviour of these two cell types in co-culture. TC and VSMC were simultaneously tracked in co-culture and, for each cell type, directionality, speed and the cell-cell interaction were assessed. The overall migratory behaviour of TC was markedly different in the presence of VSMC with co-cultured TC migrating further with directional movement while mono-cultured TC moved more randomly. Furthermore, TC were shown to specifically target VSMC, suggesting that invading TC may initiate targeted vascular remodelling. Analysis of movement behaviour and cell-cell attraction will be useful in other co-culture systems in addition to answering important questions in the reproductive field.

Inverse sampling of controls in a matched case control study.

A method of inverse sampling of controls in a matched case-control study is described in which, for each case, controls are sampled until a discordant set is achieved. For a binary exposure, inverse sampling is used to determine the number of controls for each case. When most individuals in a population have the same exposure, standard case-control sampling may result in many case-control sets being concordant with respect to exposure and thus uninformative in the conditional logistic analysis. The method using inverse control sampling is proposed as a solution to this problem in situations when it is practically feasible. In many circumstances, inverse control sampling is found to offer improved statistical efficiency relative to a comparable study with a fixed number of controls per case.

BeWo cells stimulate smooth muscle cell apoptosis and elastin breakdown in a model of spiral artery transformation.

BACKGROUND: During pregnancy, extravillous trophoblast invades the uterine wall and enters the spiral arteries. Remodelling ensues, with loss of vascular smooth muscle cells (SMCs) to create high flow, low resistance vessels. Pregnancies complicated by pre-eclampsia are characterized by incomplete arterial remodelling. Endovascular trophoblast is not easily accessible for studies to establish the pathogenesis of pre-eclampsia, so we have developed a model appropriate to carry out mechanistic studies of vessel wall transformation. METHODS AND RESULTS: Segments of human spiral artery were perfused with the choriocarcinoma cell line, BeWo; cells invaded the vessel wall and induced apoptosis of vascular SMC. Perfusion of vessels with BeWo-conditioned medium also induced SMC apoptosis, indicating the presence of a soluble apoptotic factor. BeWo express Fas ligand (FasL) and tumour necrosis factor-related apoptosis-inducing ligand (TRAIL). Treatment of BeWo-conditioned medium with antibodies against FasL inhibited vascular SMC apoptosis in vitro. Antibodies that blocked TRAIL receptor function had no effect. Extracellular matrix degradation is also a prerequisite for vascular remodelling; BeWo express matrix metalloproteinase-12 (MMP-12) and BeWo-conditioned medium increased MMP-12 expression in spiral artery SMC. CONCLUSIONS: BeWo induce arterial remodelling via FasL- and MMP-12-dependent mechanisms. BeWo-derived factors up-regulate protease expression in spiral artery SMC to facilitate matrix breakdown.

Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi.

The extent to which the order of genes along chromosomes is conserved between Saccharomyces cerevisiae and related species was studied by analysing data from DNA sequence database. As expected, the extent of gene order conservation decreases with increasing evolutionary distance. About 59% of adjacent gene pairs in Kluyveromyces lactis or K. marxianus are also adjacent in S. cerevisiae, and a further 16% of Kluyveromyces neighbours can be explained in terms of the inferred ancestral gene order in Saccharomyces prior to the occurrence of an ancient whole-genome duplication. Only 13% of Candida albicans linkages, and no Schizosaccharomyces pombe linkages, are conserved. Analysis of gene order arrangements, chromosome numbers, and ribosomal RNA sequences suggests that genome duplication occurred before the divergence of the four species in Saccharomyces sensu stricto (all of which have 16 chromosomes), but after this lineage had diverged from Saccharomyces kluyveri and the Kluyveromyces lactislmarxianus species assemblage.