Eulerian superpath approach to correct sequencing error in shotgun assembly

This work describes an error correction method based on the Euler Superpath problem. Sequence data is mapped to an Euler Superpath dynamically by Merging Transformation. With restriction and guiding rules, data consistency is maintained and error paths are separated from correct data: Error edges are mapped to the correct ones and after substitution (of error edges with right paths), corresponding errors in the sequencing data are eliminated.

Narcotics Anonymous participation and changes in substance use and social support

In Victoria (a southern Australian state) in 1995, Narcotics Anonymous had a small but growing membership providing an opportunity to study the early experience of new self-help members. Ninety-one new members were interviewed and 62 (68%) were reinterviewed after 12 months. Three measures of self-help participation were examined: service role involvement, step work, and stable meeting attendance. Lower prior involvement in treatment services and greater participation in self-help predicted subsequent self-help participation. Higher levels of secondary school education predicted service role involvement and longer periods in stable meeting attendance. Higher self-help participation through the 12 months prior to follow-up was associated with lower levels of hazardous alcohol use and higher emotional support at reinterview. Multivariate regression analysis suggested stable self-help meeting attendance and step work continued to predict reductions in hazardous alcohol use and improvements in social support, after controlling for a range of alternative predictors.

Where did we go wrong? An examination of students treatment of experimental error in engineering mechanics laboratories

The ability of engineers and applied scientists to undertake experimental measurements is a fundamental requirement of the profession. However, it is not simply good enough to be able to perform experiments if we are not able to interpret the results. In this study, reports prepared by mechanical engineering students were examined to determine how students dealt with the disparity between experimental measurements and theoretical results in their Engineering Mechanics laboratories. Analysis of the reports, and discussions with students in their laboratory classes, revealed a superficial understanding or regard for experimental error. This superficial treatment of experimental error is, most likely, due to a number of factors that are discussed. Some possible strategies for addressing the issue are also examined.

Exploring the role and patterns of developmental trauma in substance using offenders

 The thesis explored the relationship between developmental trauma, substance use and offending behaviour. While a lack of sufficient power did not allow patterns and trajectories to emerge, it was demonstrated that developmental trauma was experienced disproportionally more in offender and substance using populations. Further, the study proposed the utility of the Good Lives Model in developing holistic treatment plans that encompass primary goods identified by these individuals.

Prevalence of substance use and delinquent behavior in adolescents from Victoria, Australia and Washington State, United States

This article compares prevalence estimates of substance use and  delinquent behavior in Washington State, United States and Victoria, Australia, two states chosen for their different policy environments around problem behavior. Few comparisons of international differences on rates of multiple problem behavior exist, and most are based on methods that are not matched, raising the question of whether findings are based on  methodological differences rather than actual rate differences. The  International Youth Development Study used standardized methods to recruit and administer an adaptation of the Communities That Care Youth Survey to representative state samples of fifth-, seventh-, and ninth-grade students in each state. Rates of delinquent behavior were generally comparable.  However, striking differences in substance use were noted, with Victoria students reporting higher rates of alcohol use, alcohol misuse, smoking, and inhalant use, whereas Washington State students reported higher rates of marijuana use. Implications for conducting international comparisons are discussed.

Effects of N-acetylcysteine on substance use in bipolar disorder : a randomized placebo controlled clinical trial

Objective: To evaluate the effect of N-acetylcysteine (NAC) on substance use in a double-blind, placebo-controlled trial of NAC in bipolar disorder. It is hypothesised that NAC will be superior to placebo for reducing scores on the Clinical Global Impressions scale for Substance Use (CGI-SU).

Methods: Participants were randomised to 6-months of treatment with 2 g/day NAC (n = 38) or placebo (n = 37). Substance use was assessed at baseline using the Habits instrument. Change in substance use was assessed at regular study visits using the CGI-SU.

Results: Amongst the 75 participants 78.7% drank alcohol (any frequency), 45.3% smoked tobacco and 92% consumer caffeine. Other substances were used by fewer than six participants. Caffeine use was significantly lower for NAC-treated participants compared with placebo at week 2 of treatment but not at other study visits.

Conclusion: NAC appeared to have little effect on substance use in this population. A larger study on a substance using population will be necessary to determine if NAC may be a useful treatment for substance use.

Risk and protective factors for adolescent substance use in Washington State, the United States and Victoria, Australia : a longitudinal study

Purpose
To compare the levels of risk and protective factors and the predictive influence of these factors on alcohol, tobacco, and cannabis use over a 12-month follow-up period in Washington State in the United States and in Victoria, Australia.

Method
The study involved a longitudinal school-based survey of students drawn as a two-stage cluster sample recruited through schools, and administered in the years 2002 and 2003 in both states. The study used statewide representative samples of students in the seventh and ninth grades (n = 3,876) in Washington State and Victoria.

Results
Washington State students, relative to Victorian students, had higher rates of cannabis use but lower rates of alcohol and tobacco use at time 1. Levels of risk and protective factors showed few but important differences that contribute to the explanation of differences in substance use; Washington State students, relative to Victorian students, reported higher religiosity (odds ratio, .96 vs. .79) and availability of handguns (odds ratio, 1.23 vs. 1.18), but less favorable peer, community, and parental attitudes to substance use. The associations with substance use at follow-up are generally comparable, but in many instances were weaker in Washington State.

Conclusions
Levels of risk and protective factors and their associations with substance use at follow-up were mostly similar in the two states. Further high-quality longitudinal studies to establish invariance in the relations between risk and protective factors and substance use in adolescence across diverse countries are warranted.

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.