Handling misclassified stratification variables in the analysis of randomised trials with continuous outcomes

Many trials use stratified randomisation, where participants are randomised within strata defined by one or more baseline covariates. While it is important to adjust for stratification variables in the analysis, the appropriate method of adjustment is unclear when stratification variables are affected by misclassification and hence some participants are randomised in the incorrect stratum. We conducted a simulation study to compare methods of adjusting for stratification variables affected by misclassification in the analysis of continuous outcomes when all or only some stratification errors are discovered, and when the treatment effect or treatment-by-covariate interaction effect is of interest. The data were analysed using linear regression with no adjustment, adjustment for the strata used to perform the randomisation (randomisation strata), adjustment for the strata if all errors are corrected (true strata), and adjustment for the strata after some errors are discovered and corrected (updated strata). The unadjusted model performed poorly in all settings. Adjusting for the true strata was optimal, while the relative performance of adjusting for the randomisation strata or the updated strata varied depending on the setting. As the true strata are unlikely to be known with certainty in practice, we recommend using the updated strata for adjustment and performing subgroup analyses, provided the discovery of errors is unlikely to depend on treatment group, as expected in blinded trials. Greater transparency is needed in the reporting of stratification errors and how they were addressed in the analysis.Lisa N. Yelland, Jennie Louise, Brennan C. Kahan, Tim P. Morris, Katherine J. Lee, Thomas R. Sulliva

Adjusting for treatment switching in oncology trials: A systematic review and recommendations for reporting

Objectives To systematically review the quality of reporting on the application of switching adjustment approaches in published oncology trials and industry submissions to the National Institute for Health and Care Excellence Although methods such as the rank preserving structural failure time model (RPSFTM) and inverse probability of censoring weights (IPCW) have been developed to address treatment switching, the approaches are not widely accepted within health technology assessment. This limited acceptance may partly be a consequence of poor reporting on their application. Methods Published trials and industry submissions were obtained from searches of PubMed and nice.org.uk, respectively. The quality of reporting in these studies was judged against a checklist of reporting recommendations, which was developed by the authors based on detailed considerations of the methods. Results Thirteen published trials and 8 submissions to nice.org.uk satisfied inclusion criteria. The quality of reporting around the implementation of the RPSFTM and IPCW methods was generally poor. Few studies stated whether the adjustment approach was prespecified, more than a third failed to provide any justification for the chosen method, and nearly half neglected to perform sensitivity analyses. Further, it was often unclear how the RPSFTM and IPCW methods were implemented. Conclusions Inadequate reporting on the application of switching adjustment methods increases uncertainty around results, which may contribute to the limited acceptance of these methods by decision makers. The proposed reporting recommendations aim to support the improved interpretation of analyses undertaken to adjust for treatment switching

Variable preterm oral microbiome stabilizes and reflects a full-term infant profile within three months.

OnlinePublBACKGROUND: Preterm infants suffer higher morbidity and mortality rates compared to full-term infants, but little is known about how changes to oral and respiratory tract microbiota may impact disease development. METHODS: Here, very preterm neonates (n = 50) were selected to study oral and respiratory microbiota development during the first few months post-birth, where 26 individuals were diagnosed with BPD and/or sepsis. These infants were compared to 14 healthy full-term infants and 16 adults. Microbiota diversity, composition, and species abundances were calculated from 16S ribosomal RNA gene sequences in buccal swabs and tracheal aspirates at two time points (within a week and 1-3 months post-birth). RESULTS: Collection time point was the biggest factor to significantly influence the preterm oral microbial diversity and composition. In addition, BPD and sepsis were linked to distinct preterm oral microbiota diversity and composition, and opportunistic pathogens previously associated with these diseases were identified in the initial sample for both healthy preterm neonates and those with the disease. Compared to the full-term infant and adult dataset, preterm infant diversity and composition was initially significantly different, but resembled full-term infant diversity and composition over time. CONCLUSION: Overall, consequences of microbiota development need further examination in preterm infant infections and later development. IMPACT: Non-gut microbiota research on preterm infants is limited. At one week post-birth, preterm infants harbor distinct oral microbiota that are not shared with full-term children or adults, eventually becoming similar to full-term infants at 36 weeks postmenstrual age. DNA from potential opportunistic pathogens was observed in the mouth and lungs of preterm infants within a week of birth, and microbes associated with BPD were identified in the lungs. Oral microbiota in preterm infants over the first 2-3 months is unique and may be connected to short- and long-term health outcomes in these children.Caitlin A. Selway, Carmel T. Collins, Maria Makrides, Thomas R. Sullivan, N3RO Steering Committee, and Laura S. Weyric

Prenatal omega-3 LCPUFA and symptoms of allergic disease and sensitization throughout early childhood - a longitudinal analysis of long-term follow-up of a randomized controlled trial

Background: Randomized controlled trials of prenatal omega (ω-3) long chain polyunsaturated fatty acid (LCPUFA) supplementation are suggestive of some protective effects on allergic sensitization and symptoms of allergic disease in childhood. Due to the nature of the atopic march, investigation of any effects of this prenatal intervention may be most informative when consistently assessed longitudinally during childhood. Methods: Follow-up of children (n = 706) with familial risk of allergy from the Docosahexaenoic Acid to Optimize Mother Infant Outcome (DOMInO) trial. The intervention group received fish oil capsules (900 mg of ω-3 LCPUFA) daily from <21 weeks’ gestation until birth; the control group received vegetable oil capsules without ω-3 LCPUFA. This new longitudinal analysis reports previously unpublished data collected at 1 and 3 years of age. The allergic disease symptom data at 1, 3 and 6 years of age were consistently reported by parents using the "International Study of Asthma and Allergies in Childhood" (ISAAC) questionnaire. Sensitization was determined by skin prick test to age specific, common allergen extracts. Results: Changes over time in symptoms of allergic disease with sensitization (IgE-mediated) and sensitization did not differ between the groups; interaction p = 0.49, p = 0.10, respectively. Averaged across the 1, 3 and 6-year assessments, there were no significant effects of prenatal ω-3 LCPUFA supplementation on IgE-mediated allergic disease symptoms (adjusted relative risk 0.88 (95% CI 0.69, 1.12), p = 0.29) or sensitization (adjusted relative risk 0.97 (95% CI 0.82, 1.15), p = 0.76). Sensitization patterns to common allergens were consistent with the atopic march, with egg sensitization at 1 year strongly associated with house dust mite sensitization at 6 years, (p < 0.0001). Discussion: Although there is some evidence to suggest that maternal supplementation with 900mg ω-3 LCPUFA has a protective effect on early symptoms of allergic disease and sensitization in the offspring, we did not observe any differences in the progression of disease over time in this longitudinal analysis. Further investigation into the dose and timing of ω-3 LCPUFA supplementation, including long-term follow up of children using consistent outcome reporting, is essential to determine whether this intervention may be of benefit as a primary prevention strategy for allergic disease. Conclusion: Maternal supplementation with 900 mg of ω-3 LCPUFA did not change the progression of IgE-mediated allergic disease symptoms or sensitization throughout childhood from 1 to 6 years.K. P. Best, T. R. Sullivan, D. J. Palmer, M. Gold, J. Martin, D. Kennedy and M. Makride

The efficacy and safety of peripheral intravenous parenteral nutrition vs 10% glucose in preterm infants born 30 to 33 weeks' gestation: a randomised controlled trial

Background: Preterm infants born 30 to 33 weeks' gestation often require early support with intravenous fluids because of respiratory distress, hypoglycemia or feed intolerance. When full feeds are anticipated to be reached within the first week, risks associated with intravenous delivery mode and type must be carefully considered. Recommendations are for parenteral nutrition to be infused via central venous lines (because of the high osmolarity), however, given the risks associated with central lines, clinicians may opt for 10% glucose via peripheral venous catheter when the need is short-term. We therefore compare a low osmolarity peripheral intravenous parenteral nutrition (P-PN) solution with peripheral intravenous 10% glucose on growth rate in preterm infants born 30 to 33 weeks' gestation. Methods: In this parallel group, single centre, superiority, non-blinded, randomised controlled trial, 92 (P-PN 42, control 50) infants born 30⁺⁰ to 33⁺⁶ weeks' gestation, were randomised within 24 h of age, to receive either P-PN (8% glucose, 30 g/L amino acids, 500 IU/L heparin and SMOFlipid®) or a control of peripheral intravenous 10% glucose. Both groups received enteral feeds according to hospital protocol. The primary outcome was rate of weight gain from birth to 21 days of age. Results: The rate of weight gain was significantly increased in P-PN infants compared with control (P-PN, n = 42, 18.7, SD 6.6 g/d vs control, n = 50, 14.8, SD 6.0 g/d; adjusted mean difference 3.9 g/d, 95% CI 1.3 to 6.6; P = 0.004), with the effect maintained to discharge home. Days to regain birthweight were significantly reduced and length gain significantly increased in P-PN infants. One infant in the P-PN group had a stage 3 extravasation which rapidly resolved. Blood urea nitrogen and triglyceride levels were significantly higher in the P-PN group in the first week of life, but there were no instances of abnormally high levels. There were no significant differences in any other clinical or biochemical outcomes. Conclusion: P-PN improves the rate of weight gain to discharge home in preterm infants born 30 to 33 weeks gestation compared with peripheral intravenous 10% glucose.Hiroki Suganuma, Dennis Bonney, Chad C. Andersen, Andrew J. McPhee, Thomas R. Sullivan, Robert A. Gibson and Carmel T. Collin

Effect of Docosahexaenoic Acid (DHA) Supplementation of Preterm Infants on Growth, Body Composition, and Blood Pressure at 7-Years Corrected Age: Follow-Up of a Randomized Controlled Trial

Aim: To determine if supplementation of infants born 0.1). High-DHA group infants were more likely to be classified as obese (relative risk 1.6 (95% CI 1.0, 2.6); p = 0.05). Conclusions: DHA supplementation of premature infants did not affect growth, body composition, or blood pressure at 7-year CA overall by sex and birthweight strata. The finding of a higher risk of obesity in children who receive high-DHA needs to be interpreted with caution due to the small number of children classified as obese.Karen P. Best, Thomas R. Sullivan, Anoja W. Gunaratne, Jacqueline F. Gould, Robert A. Gibson, Carmel T. Collins, Maria Makrides, and Tim J. Gree

Predictors of compliance with higher dose omega-3 fatty acid supplementation during pregnancy and implications for the risk of prematurity: exploratory analysis of the ORIP randomised trial

Background: Intention-to-treat analyses of the Omega‐3 to Reduce the Incidence of Prematurity (ORIP) trial found that omega-3 (n-3) fatty acid supplementation reduces the risk of prematurity in the subgroup of women with a singleton pregnancy and low n-3 status early in pregnancy, but not overall. However, results may have been influenced by less-than-optimal compliance. Objectives: To identify predictors of compliance with n-3 supplementation and determine treatment effects among compliers. Design: Exploratory analyses of a multicentre-blinded randomised trial. Setting: 6 tertiary care centres in Australia. Participants: 5328 singleton pregnancies. Interventions: Daily capsules containing 900 mg n-3 long-chain polyunsaturated fatty acids or vegetable oil, consumed from before 20 weeks gestation until 34 weeks gestation. Outcome measures: Early preterm (<34 weeks gestation) and preterm birth (<37 weeks gestation). Women were considered compliant if they reported missing less than a third of their allocated capsules in the previous week during a mid-pregnancy appointment. Results: Among 2654 singleton pregnancies in the n-3 intervention group, 1727 (65%) were deemed compliant with supplementation. Maternal characteristics associated with compliance included age, years of full-time education, consuming alcohol but not smoking in the 3 months leading up to pregnancy, fewer previous births and taking dietary supplements at enrolment. Based on complier average causal effects, n-3 supplementation reduced the risk of preterm birth in compliers (relative risk=0.76; 95% CI 0.60 to 0.97), but not early preterm birth (relative risk=0.80; 95% CI 0.44 to 1.46). Consistent with intention-to-treat analyses, the lack of an overall effect on early preterm birth in compliers appeared to be due to beneficial effects in women with low n-3 status at enrolment but not women with replete status. Conclusions: Results in compliers were similar to those from intention-to-treat analyses, suggesting that non-compliance was not a major factor in explaining outcomes from the ORIP trial. Trial registration number: ACTRN12613001142729.Thomas R Sullivan, Lisa N Yelland, Robert A Gibson, Sagar K Thakkar, Fang Huang, Karen P Best, Surabhi Devaraj, Irma Silva Zolezzi, Maria Makride

Identifying women who may benefit from higher dose omega-3 supplementation during pregnancy to reduce their risk of prematurity: exploratory analyses from the ORIP trial.

OBJECTIVES: The risk factors for prematurity are multifactorial and include low omega-3 status. Omega-3 supplementation in pregnancy has been found to reduce prematurity risk, particularly among women with low omega-3 levels. This study aimed to identify maternal characteristics that predict whether women with a singleton pregnancy will benefit from omega-3 supplementation to reduce their risk of prematurity. DESIGN: Exploratory analyses of a multicentre, double-blind randomised trial. SETTING: 6 tertiary care centres in four states in Australia. PARTICIPANTS: 5328 singleton pregnancies in 5305 women recruited before 20 weeks of gestation. INTERVENTIONS: Fish oil capsules containing 900 mg omega-3 long-chain polyunsaturated fatty acids per day versus vegetable oil capsules consumed from enrolment until 34 weeks' gestation. OUTCOME MEASURES: Early preterm birth (EPTB, <34 weeks' gestation) and preterm birth (PTB, <37 weeks' gestation) analysed using logistic regression models with interactions between treatment group and a range of maternal biological, clinical and demographic characteristics. RESULTS: Omega-3 supplementation reduced the odds of EPTB for women with low total omega-3 status in early pregnancy (OR=0.30, 95% CI 0.10-0.93). No additional maternal characteristics influenced whether omega-3 supplementation reduced the odds of EPTB. For PTB, women were more likely to benefit from omega-3 supplementation if they were multiparous (OR=0.65, 95% CI 0.49-0.87) or avoided alcohol in the lead up to pregnancy (OR=0.62, 95% CI 0.45-0.86). CONCLUSIONS: Our results support previous findings that women with low total omega-3 levels in early pregnancy are most likely to benefit from taking omega-3 supplements to reduce their risk of EPTB. Understanding how other maternal characteristics influence the effectiveness of omega-3 supplementation on reducing PTB requires further investigation. TRIAL REGISTRATION NUMBER: ACTRN12613001142729.Lisa N Yelland, Thomas R Sullivan, Robert A Gibson, Lucy A Simmonds, Sagar K Thakkar, Fang Huang, Surabhi Devaraj, Karen P Best, Irma Silva Zolezzi, Maria Makride

A Review of the fossil record of turtles of the clade Baenidae

The fossil record of the turtle clade Baenidae ranges from the Early Cretaceous (Aptian—Albian) to the Eocene. The group is present throughout North America during the Early Cretaceous, but is restricted to the western portions of the continents in the Late Cretaceous and Paleogene. No credible remains of the clade have been reported outside of North America to date. Baenids were warmadapted freshwater aquatic turtles that supported high levels of diversity at times through niche partitioning, particularly by adapting to a broad range of dietary preferences ranging from omnivorous to molluscivorous. Current phylogenies place Baenidae near the split of crown-group Testudines. Within Baenidae three more inclusive, named clades are recognized: Baenodda, Palatobaeninae and Eubaeninae. A taxonomic review of the group concludes that of 49 named taxa, 30 are nomina valida, 12 are nomina invalida and 7 are nomina dubia

LD Hub:a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis

Motivation: LD score regression is a reliable and efficient method of using genome-wide association study (GWAS) summary-level results data to estimate the SNP heritability of complex traits and diseases, partition this heritability into functional categories, and estimate the genetic correlation between different phenotypes. Because the method relies on summary level results data, LD score regression is computationally tractable even for very large sample sizes. However, publicly available GWAS summary-level data are typically stored in different databases and have different formats, making it difficult to apply LD score regression to estimate genetic correlations across many different traits simultaneously. Results: In this manuscript, we describe LD Hub - a centralized database of summary-level GWAS results for 173 diseases/traits from different publicly available resources/consortia and a web interface that automates the LD score regression analysis pipeline. To demonstrate functionality and validate our software, we replicated previously reported LD score regression analyses of 49 traits/diseases using LD Hub; and estimated SNP heritability and the genetic correlation across the different phenotypes. We also present new results obtained by uploading a recent atopic dermatitis GWAS meta-analysis to examine the genetic correlation between the condition and other potentially related traits. In response to the growing availability of publicly accessible GWAS summary-level results data, our database and the accompanying web interface will ensure maximal uptake of the LD score regression methodology, provide a useful database for the public dissemination of GWAS results, and provide a method for easily screening hundreds of traits for overlapping genetic aetiologies