A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies

Phylogenetic comparative methods are increasingly used to give new insights into the dynamics of trait evolution in deep time. For continuous traits the core of these methods is a suite of models that attempt to capture evolutionary patterns by extending the Brownian constant variance model. However, the properties of these models are often poorly understood, which can lead to the misinterpretation of results. Here we focus on one of these models – the Ornstein Uhlenbeck (OU) model. We show that the OU model is frequently incorrectly favoured over simpler models when using Likelihood ratio tests, and that many studies fitting this model use datasets that are small and prone to this problem. We also show that very small amounts of error in datasets can have profound effects on the inferences derived from OU models. Our results suggest that simulating fitted models and comparing with empirical results is critical when fitting OU and other extensions of the Brownian model. We conclude by making recommendations for best practice in fitting OU models in phylogenetic comparative analyses, and for interpreting the parameters of the OU model.

Underreporting of Energy Intake in Brazilian Women Varies According to Dietary Assessment: A Cross-Sectional Study Using Doubly Labeled Water

Objective Underreporting of energy intake is prevalent in food surveys, but there is controversy about which dietary assessment method provides greater underreporting rates. Our objective is to compare validity of self-reported energy intake obtained by three dietary assessment methods with total energy expenditure (TEE) obtained by doubly labeled water (DLW) among Brazilian women. Design We used a cross-sectional study. Subjects/setting Sixty-five females aged 18 to 57 years (28 normal-weight, 10 over-weight, and 27 obese) were recruited from two universities to participate. Main outcome measures TEE determined by DLW, energy intake estimated by three 24-hour recalls, 3-day food record, and a food frequency questionnaire (FFQ). Statistical analyses performed Regression and analysis of variance with repeated measures compared TEE and energy intake values, and energy intake-to-TEE ratios and energy intake-TEE values between dietary assessment methods. Bland and Altman plots were provided for each method. chi(2) test compared proportion of underreporters between the methods. Results Mean TEE was 2,622 kcal (standard deviation [SD] =490 kcal), while mean energy intake was 2,078 kcal (SD=430 kcal) for the diet recalls; 2,044 kcal (SD=479 kcal) for the food record and 1,984 kcal (SD=832 kcal) for the FFQ (all energy intake values significantly differed from TEE; P<0.0001). Bland and Altman plots indicated great dispersion, negative mean differences between measurements, and wide limits of agreement. Obese subjects underreported more than normal-weight subjects in the diet recalls and in the food records, but not in the FFQ. Years of education, income and ethnicity were associated with reporting accuracy. Conclusions The FFQ produced greater under- and overestimation of energy intake. Underreporting of energy intake is a serious and prevalent error in dietary self-reports provided by Brazilian women, as has been described in studies conducted in developed countries.

Bayesian analysis for a skew extension of the multivariate null intercept measurement error model

Skew-normal distribution is a class of distributions that includes the normal distributions as a special case. In this paper, we explore the use of Markov Chain Monte Carlo (MCMC) methods to develop a Bayesian analysis in a multivariate, null intercept, measurement error model [R. Aoki, H. Bolfarine, J.A. Achcar, and D. Leao Pinto Jr, Bayesian analysis of a multivariate null intercept error-in -variables regression model, J. Biopharm. Stat. 13(4) (2003b), pp. 763-771] where the unobserved value of the covariate (latent variable) follows a skew-normal distribution. The results and methods are applied to a real dental clinical trial presented in [A. Hadgu and G. Koch, Application of generalized estimating equations to a dental randomized clinical trial, J. Biopharm. Stat. 9 (1999), pp. 161-178].

Do logbooks influence recall of physical activity in validation studies?

Purpose: To examine whether physical activity logbooks influence estimates of validity of 7-d recall physical activity questionnaires. Methods: A  convenience sample of 551 adults aged 18–75 yr wore an MTI  accelerometer for seven consecutive days and were then randomly administered two of four 7-d recall physical activity questionnaires that varied in length and format (Active Australia Survey (AAS), long and short  International Physical Activity Questionnaires (IPAQ-L and IPAQ-S), and Behavioral Risk Factor Surveillance System (BRFSS)). A subsample of 75% concurrently completed a physical activity logbook. Results: Correlations (rho) between self-reported and measured duration of moderate- and vigorous-intensity activity and total activity were similar among participants who received a logbook and those who did not for each of the four instruments. There was also no interaction between assessment method (survey, accelerometer) and the assignment of a logbook. For the IPAQ-L, however, variability in the difference between accelerometer data and responses to the vigorous items was smaller among those assigned a logbook (F = 4.128, df = 260, P = 0.043). Overall, there were no differences in percent agreement or kappa for participation in sufficient levels of physical activity according to receipt of a logbook for any of the surveys. Conclusion: The process of self-monitoring through completion of a logbook does not appear to influence estimates of validity for brief or long questionnaires with global questions. Whereas the magnitude of error in accuracy of recall of particular types of activity may be reduced by completion of a logbook that is similar in structure to the survey being validated, this does not appear to influence overall estimates of validity.

Early impact of the BEST intervention for parents stressed by adolescent substance abuse.

Youth involvement in substance abuse can be a source of considerable distress for their parents. Unilateral family interventions have been advocated as one means by which concerned family members can be supported to assist substance-abusing family members. To date there has been little research examining the impact of unilateral family interventions on the directly participating family members. In this study the early impact of an 8-week parent-group programme known as Behavioural Exchange Systems Training (BEST) was evaluated using a quasi-experimental, waiting list control design. The professionally led programme had been developed to support and assist parents in their efforts to cope with adolescent substance abuse. Subjects were 66 parents (48 families) accepted for entry into the programme between 1997 and 1998. Comparison was made between 46 parents offered immediate entry into the programme and 20 parents whose entry to the programme was delayed by an 8-week waiting list. At the first assessment 87% of parents showed elevated mental health symptoms on the General Health Questionnaire. Evidence suggested exposure to the intervention had a positive impact on parents. Compared to parents on the waiting list, parents entered immediately into the intervention demonstrated greater reductions in mental health symptoms, increased parental satisfaction, and increased use of assertive parenting behaviours.

Single-point isotope measurements in blood cells and plasma to estimate the time since diet switches

1. Understanding ecological phenomena often requires an accurate assessment of the timing of events. To estimate the time since a diet shift in animals without knowledge on the isotope ratios of either the old or the new diet, isotope ratio measurements in two different tissues (e.g. blood plasma and blood cells) at a single point in time can be used. For this ‘isotopic-clock’ principle, we present here a mathematical model that yields an analytical and easily calculated outcome.

2. Compared with a previously published model, our model assumes the isotopic difference between the old and new diets to be constant if multiple measurements are taken on the same subject at different points in time. Furthermore, to estimate the time since diet switch, no knowledge of the isotopic signature of tissues under the old diet, but only under the new diet is required.

3. The two models are compared using three calibration data sets including a novel one based on a diet shift experiment in a shorebird (red knot Calidris canutus); sensitivity analyses were conducted. The two models behaved differently and each may prove rather unsatisfactory depending on the system under investigation. A single-tissue model, requiring knowledge of both the old and new diets, generally behaved quite reliably.

4. As blood (cells) and plasma are particularly useful tissues for isotopic-clock research, we trawled the literature on turnover rates in whole blood, cells and plasma. Unfortunately, turnover rate predictions using allometric relations are too unreliable to be used directly in isotopic-clock calculations.

5. We advocate that before applying the isotopic-clock methodology, the propagation of error in the ‘time-since-diet-shift’ estimation is carefully assessed for the system under scrutiny using a sensitivity analysis as proposed here.

The effects of topological inaccuracy in evolutionary trees on the phylogenetic comparative method of independent contrasts

Computer simulations were used to test the effect of increasing phylogenetic topological inaccuracy on the results obtained from correlation tests of independent contrasts. Predictably, increasing the number of disruptions in the tree increases the likelihood of significant error in the r values produced and in the statistical conclusions drawn from the analysis. However, the position of the disruption in the tree is important: Disruptions closer to the tips of the tree have a greater effect than do disruptions that are close to the root of the tree. Independent contrasts derived from inaccurate topologies are more likely to lead to erroneous conclusions when there is a true significant relationship between the variables being tested (i.e., they tend to be conservative). The results also suggest that random phylogenies perform no better than nonphylogenetic analyses and, under certain conditions, may perform even worse than analyses using raw species data. Therefore, the use of random phylogenies is not beneficial in the absence of knowledge of the true phylogeny.

Variation in the gene coding for the M5 muscarinic receptor (CHRM5) influences cigarette dose but is not associated with dependence to drugs of addiction : evidence from a prospective population based cohort study of young adults

Background: The mesolimbic structures of the brain are important in the anticipation and perception of reward. Moreover, many drugs of addiction elicit their response in these structures. The M5 muscarinic receptor (M5R) is expressed in dopamine-containing neurones of the substantia nigra pars compacta and ventral tegmental area, and regulates the release of mesolimbic dopamine. Mice lacking M5R show a substantial reduction in both reward and withdrawal responses to morphine and cocaine. The CHRM5, the gene that codes for the M5R, is a strong biological candidate for a role in human addiction. We screened the coding and core promoter sequences of CHRM5 using denaturing high performance liquid chromatography to identify common polymorphisms. Additional polymorphisms within the coding and core promoter regions that were identified through dbSNP were validated in the test population. We investigated whether these polymorphisms influence substance dependence and dose in a cohort of 1947 young Australians.

Results: Analysis was performed on 815 participants of European ancestry who were interviewed at wave 8 of the cohort study and provided DNA. We observed a 26.8% increase in cigarette consumption in carriers of the rs7162140 T-allele, equating to 20.1 cigarettes per week (p=0.01). Carriers of the rs7162140 T-allele were also found to have nearly a 3-fold increased risk of developing cannabis dependence (OR=2.9 (95%CI 1.1-7.4); p=0.03).

Conclusion: Our data suggest that variation within the CHRM5 locus may play an important role in tobacco and cannabis but not alcohol addiction in European ancestry populations. This is the first study to show an association between CHRM5 and substance use in humans. These data support the further investigation of this gene as a risk factor in substance use and dependence.

Recruitment into diabetes prevention programs : what is the impact of errors in self-reported measures of obesity?

Background
Error in self-reported measures of obesity has been frequently described, but the effect of self-reported error on recruitment into diabetes prevention programs is not well established. The aim of this study was to examine the effect of using self-reported obesity data from the Finnish diabetes risk score (FINDRISC) on recruitment into the Greater Green Triangle Diabetes Prevention Project (GGT DPP).

Methods
The GGT DPP was a structured group-based lifestyle modification program delivered in primary health care settings in South-Eastern Australia. Between 2004–05, 850 FINDRISC forms were collected during recruitment for the GGT DPP. Eligible individuals, at moderate to high risk of developing diabetes, were invited to undertake baseline tests, including anthropometric measurements performed by specially trained nurses. In addition to errors in calculating total risk scores, accuracy of self-reported data (height, weight, waist circumference (WC) and Body Mass Index (BMI)) from FINDRISCs was compared with baseline data, with impact on participation eligibility presented.

Results
Overall, calculation errors impacted on eligibility in 18 cases (2.1%). Of n&thinsp;=&thinsp;279 GGT DPP participants with measured data, errors (total score calculation, BMI or WC) in self-report were found in n&thinsp;=&thinsp;90 (32.3%). These errors were equally likely to result in under- or over-reported risk. Under-reporting was more common in those reporting lower risk scores (Spearman-rho&thinsp;=&thinsp;&minus;0.226, p-value&thinsp;<&thinsp;0.001). However, underestimation resulted in only 6% of individuals at high risk of diabetes being incorrectly categorised as moderate or low risk of diabetes.

Conclusions
Overall FINDRISC was found to be an effective tool to screen and recruit participants at moderate to high risk of diabetes, accurately categorising levels of overweight and obesity using self-report data. The results could be generalisable to other diabetes prevention programs using screening tools which include self-reported levels of obesity.

The influence of protective and risk factors in individual, peer and school domains on Thai adolescents' alcohol and illicit drug use: a survey

This study investigates risk and protective factors for substance abuse in a sample of 1778 students attending technical colleges in Bangkok and Nakhon Ratchasima provinces of Thailand using a self-report questionnaire modified from the Communities That Care youth survey. Low school commitment was strongly associated with illicit drug use, with adjusted odds ratios ranging from 2.84 (glue sniffing) to 10.06 (ecstasy). Having friends using drugs, and friends with delinquent behaviors increased the risk of using alcohol and illegal drugs, with adjusted odds ratios of 6.84 and 6.72 respectively for marijuana use. For protective factors, approximately 40-60% of students with high levels of moral belief, participation in religious activities, and social skills were less likely to use alcohol. It is concluded that peer influence is a significant contributor to Thai adolescents' participation in substance abuse and that engaging in religiosity may assist adolescents to internalize negative aspects of harmful drugs into positive perceptions and encourage them to avoid alcohol and illegal drugs.

The relationship between labour market conditions and welfare receipt in Australia: A stock-flow analysis

Understanding the determinants of changes in welfare caseloads is an important, but little studied, topic in Australia. This paper evaluates the role of labour market conditions in explaining the changes in the Australian welfare caseload since the late 1990s. The paper employs a stock-flow approach to better control for persistence in welfare receipt and includes different specifications to deal with measurement error in labour market data. The results suggest that the labour market is an important determinant of movements on and off welfare, accounting for the majority of the caseload decline during 1997-2005. The results also highlight the importance of robustness checks when data are measured with error.

Quantification of spatial and thematic uncertainty in the application of underwater video for benthic habitat mapping

This study presents an analysis of the application of underwater video data collected for training and validating benthic habitat distribution models. Specifically, we quantify the two major sources of error pertaining to collection of this type of reference data. A theoretical spatial error budget is developed for a positioning system used to co-register video frames to their corresponding locations at the seafloor. Second, we compare interpretation variability among trained operators assessing the same video frames between times over three hierarchical levels of a benthic classification scheme. Propagated error in the positioning system described was found to be highly correlated with depth of operation and varies from 1.5m near the surface to 5.7m in 100m of water. In order of decreasing classification hierarchy, mean overall observer agreement was found to be 98% (range 6%), 82% (range 12%) and 75% (range 17%) for the 2, 4, and 6 class levels of the scheme, respectively. Patterns in between-observer variation are related to the level of detail imposed by each hierarchical level of the classification scheme, the feature of interest, and to the amount of observer experience. © 2014 Copyright © Taylor & Francis Group, LLC.

An alternative (partial) justification for the holding in Kirk

In Kirk v Industrial Court (NSW), the High Court determined that, based on“accepted doctrine at the time of Federation”, s 73 of the Constitutionentrenched the jurisdiction of the State Supreme Courts to review thedecisions of State decision-makers on the grounds of jurisdictional error. In anearlier article, the author argued that this reasoning was seriously flawed. Thisarticle propounds an alternative, partial justification for the holding in Kirk,based on features inherent in the text and structure of Ch III of the Constitutionat Federation and the preservation of those features in the face of thepost-Federation dismantling of the imperial legal system. It argues that animplication can be inserted into s 73 which entrenches the jurisdiction of theState Supreme Courts to review the decisions of “Lower State Courts”, but not“State Administrators”.

Application of ionospheric corrections in the equatorial region for L1 GPS users

In the absence of the selective availability, which was turned off on May 1, 2000, the ionosphere can be the largest source of error in GPS positioning and navigation. Its effects on GPS observable cause a code delays and phase advances. The magnitude of this error is affected by the local time of the day, season, solar cycle, geographical location of the receiver and Earth's magnetic field. As it is well known, the ionosphere is the main drawback for high accuracy positioning, when using single frequency receivers, either for point positioning or relative positioning of medium and long baselines. The ionosphere effects were investigated in the determination of point positioning and relative positioning using single frequency data. A model represented by a Fourier series type was implemented and the parameters were estimated from data collected at the active stations of RBMC (Brazilian Network for Continuous Monitoring of GPS satellites). The data input were the pseudorange observables filtered by the carrier phase. Quality control was implemented in order to analyse the adjustment and to validate the significance of the estimated parameters. Experiments were carried out in the equatorial region, using data collected from dual frequency receivers. In order to validate the model, the estimated values were compared with ground truth. For point and relative positioning of baselines of approximately 100 km, the values of the discrepancies indicated an error reduction better than 80% and 50% respectively, compared to the processing without the ionospheric model. These results give an indication that more research has to be done in order to provide support to the L1 GPS users in the Equatorial region.

Prevalence of Refractive Errors in a Brazilian Population: The Botucatu Eye Study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)