Beware the F-test (or, how to compare variances)

This is the author accepted manuscript. The final version is available from Elsevier Masson via the DOI in this record.Biologists commonly compare variances among samples, to test whether underlying populations have equal spread. However, despite warnings from statisticians, incorrect testing is rife. Here we show that one of the most commonly employed of these tests, the F-test, is extremely sensitive to deviations from Normality. The F-test suffers greatly elevated false-positive errors when the underlying distributions are heavy-tailed, a distribution feature which is very hard to detect using standard Normality tests. We highlight and assess a selection of parametric, jackknife and permutation tests, consider their performance in terms of false positives, and power to detect signal when it exists, then show correct methods to compare measures of variation among samples. Based on these assessments, we recommend using Levene’s Test, Box-Anderson Test, Jackknifing or Permutation Tests to compare variances when Normality is in doubt. Levene’s and Box-Anderson tests are the most powerful at small sample sizes, but the Box-Anderson test may not control Type I error for extremely heavy-tailed distributions. As noted previously, do not use F-tests to compare variances.DHod is supported by NERC standard grant NE/L007770/1 and by NERC International Opportunities Fund NE/N006798/1 and DHos by the Leverhulme Trust (RF-2015-001)

Phytoestrogens

Collectively, plants contain several different families of natural products among which are compounds with weak estrogenic or antiestrogenic activity toward mammals. These compounds, termed phytoestrogens, include certain isoflavonoids, flavonoids, stilbenes, and lignans. The best-studied dietary phytoestrogens are the soy isoflavones and the flaxseed lignans. Their perceived health beneficial properties extend beyond hormone-dependent breast and prostate cancers and osteoporosis to include cognitive function, cardiovascular disease, immunity and inflammation, and reproduction and fertility. In the future, metabolic engineering of plants could generate novel and exquisitely controlled dietary sources with which to better assess the potential health beneficial effects of phytoestrogens

Income differences in food consumption in the 1995 Australian national nutrition survey

Objective: To assess the relationships between an index of per capita income and the intake of a variety of individual foods as well as groups of food for men and women in different age groups. Design: Cross-sectional national survey of free-living men and women. Subjects: A sample of 5053 males and 5701 females aged 18 y and over who completed the Australian National Nutrition Survey 1995. Methods: Information about the frequency of consumption of 88 food items was obtained. On the basis of scores on the Food Frequency Questionnaire, regular and irregular consumers of single foods were identified. The relationships between regularity of consumption of individual foods and per capita income were analysed via contingency tables. Food variety scores were derived by assigning individual foods to conventional food group taxonomies, and then summing up the dichotomised intake scores for individual foods within each food group. Two-way ANOVA (income age group) were performed on the food variety scores for males and females, respectively. Results: Per capita income was extensively related to the reported consumption of individual foods and to total and food group variety indices. Generally, both men and women in low income households had less varied diets than those in higher-income households. However, several traditional foods were consumed less often by young high-income respondents, especially young women. Conclusions: Major income differentials in food variety occur in Australia but they are moderated by age and gender. Younger high-income women, in particular, appear to have rejected a number of traditional foods, possibly on the basis of health beliefs. The findings also suggest that data aggregation has marked effects on income and food consumption relationships.<br /

Exploring local knowledge and perceptions on zoonoses among pastoralists in northern and eastern Tanzania

Background: Zoonoses account for the most commonly reported emerging and re-emerging infectious diseases in Sub-Saharan Africa. However, there is limited knowledge on how pastoral communities perceive zoonoses in relation to their livelihoods, culture and their wider ecology. This study was carried out to explore local knowledge and perceptions on zoonoses among pastoralists in Tanzania. Methodology and principal findings: This study involved pastoralists in Ngorongoro district in northern Tanzania and Kibaha and Bagamoyo districts in eastern Tanzania. Qualitative methods of focus group discussions, participatory epidemiology and interviews were used. A total of 223 people were involved in the study. Among the pastoralists, there was no specific term in their local language that describes zoonosis. Pastoralists from northern Tanzania possessed a higher understanding on the existence of a number of zoonoses than their eastern districts' counterparts. Understanding of zoonoses could be categorized into two broad groups: a local syndromic framework, whereby specific symptoms of a particular illness in humans concurred with symptoms in animals, and the biomedical framework, where a case definition is supported by diagnostic tests. Some pastoralists understand the possibility of some infections that could cross over to humans from animals but harm from these are generally tolerated and are not considered as threats. A number of social and cultural practices aimed at maintaining specific cultural functions including social cohesion and rites of passage involve animal products, which present zoonotic risk. Conclusions: These findings show how zoonoses are locally understood, and how epidemiology and biomedicine are shaping pastoralists perceptions to zoonoses. Evidence is needed to understand better the true burden and impact of zoonoses in these communities. More studies are needed that seek to clarify the common understanding of zoonoses that could be used to guide effective and locally relevant interventions. Such studies should consider in their approaches the pastoralists' wider social, cultural and economic set up

Search for direct pair production of the top squark in all-hadronic final states in proton-proton collisions at s√=8 TeV with the ATLAS detector

The results of a search for direct pair production of the scalar partner to the top quark using an integrated luminosity of 20.1fb−1 of proton–proton collision data at √s = 8 TeV recorded with the ATLAS detector at the LHC are reported. The top squark is assumed to decay via t˜→tχ˜01 or t˜→ bχ˜±1 →bW(∗)χ˜01 , where χ˜01 (χ˜±1 ) denotes the lightest neutralino (chargino) in supersymmetric models. The search targets a fully-hadronic final state in events with four or more jets and large missing transverse momentum. No significant excess over the Standard Model background prediction is observed, and exclusion limits are reported in terms of the top squark and neutralino masses and as a function of the branching fraction of t˜ → tχ˜01 . For a branching fraction of 100%, top squark masses in the range 270–645 GeV are excluded for χ˜01 masses below 30 GeV. For a branching fraction of 50% to either t˜ → tχ˜01 or t˜ → bχ˜±1 , and assuming the χ˜±1 mass to be twice the χ˜01 mass, top squark masses in the range 250–550 GeV are excluded for χ˜01 masses below 60 GeV

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT

Factors influencing the experience of sexual and reproductive healthcare for female adolescents with perinatally-acquired HIV: a qualitative case study

Background: Young people living with perinatally-acquired HIV require age-appropriate support regarding sex and relationships as they progress towards adulthood. HIV affects both genders but evidence suggests that young women are particularly vulnerable to sexual abuse and more prone to engaging in sexual behaviours to meet their daily survival needs. This can result in poor sexual and reproductive health (SRH) outcomes. HIV services in Malawi provide support for young women’s HIV-related clinical needs, but it is unclear whether there is sufficient provision for their SRH needs as they become adults. This paper explores the sex and relationship experiences of young women growing up with perinatally-acquired HIV in order to understand how to improve SRH care and associated outcomes. Methods: A qualitative case study approach was adopted in which each ‘case’ comprised a young woman (15–19 years) with perinatally acquired HIV, a nominated caregiver and service provider. Participants were purposively selected from three multidisciplinary centres providing specialised paediatric/adolescent HIV care in Malawi. Data was collected for 14 cases through in-depth interviews (i.e. a total of 42 participants) and analysed using within-case and cross-case approaches. The interviews with adolescents were based on an innovative visual method known as ‘my story book’ which encouraged open discussion on sensitive topics. Results: Young women reported becoming sexually active at an early age for different reasons. Some sought a sense of intimacy, love, acceptance and belonging in these relationships, noting that they lacked this at home and/or within their peer groups. For others, their sexual activity was more functional – related to meeting survival needs. Young women reported having little control over negotiating safer sex or contraception. Their priority was preventing unwanted pregnancies yet several of the sample already had babies, and transfer to antenatal services created major disruptions in their HIV care. In contrast, caregivers and nurses regarded sexual activity from a clinical perspective, fearing onward transmission of HIV and advocating abstinence or condoms where possible. In addition, a cultural silence rooted in dominant religious and traditional norms closed down possibilities for discussion about sexual matters and prevented young women from accessing contraception. Conclusion: The study has shown how young women, caregivers and service providers have contrasting perspectives and priorities around SRH care. Illumination of these differences highlights a need for service improvement. It is suggested that young women themselves are involved in future service improvement initiatives to encourage the development of culturally and socially acceptable pathways of care

DIgital Alcohol Management ON Demand (DIAMOND) feasibility randomised controlled trial of a web-based intervention to reduce alcohol consumption in people with hazardous and harmful use versus a face-to-face intervention: protocol.

BACKGROUND: "Hazardous and harmful" drinkers make up approximately 23 % of the adult population in England. However, only around 10 % of these people access specialist care, such as face-to-face extended brief treatment in community alcohol services. This may be due to stigma, difficulty accessing services during working hours, a shortage of trained counsellors and limited provision of services in many places. Web-based alcohol treatment programmes may overcome these barriers and may better suit people who are reluctant or unable to attend face-to-face services, but there is a gap in the evidence base for the acceptability, effectiveness and cost-effectiveness of these programmes compared with treatment as usual (TAU) in community alcohol services. This study aims investigate the feasibility of all parts of a randomised controlled trial (RCT) of a psychologically informed web-based alcohol treatment programme called Healthy Living for People who use Alcohol (HeLP-Alcohol) versus TAU in community alcohol services, e.g. recruitment and retention, online data collection methods, and the use and acceptability of the intervention to participants. METHODS: A feasibility RCT delivered in north London community alcohol services, comparing HeLP-Alcohol with TAU. Potential participants are aged ≥18 years referred or self-referred for hazardous and harmful use of alcohol, without co-morbidities or other complex problems. The main purpose of this study is to demonstrate the feasibility of recruiting participants to the study and will test online methods for collecting baseline demographic and outcome questionnaire data, randomising participants and collecting 3-month follow-up data. The acceptability of this intervention will be measured by recruitment and retention rates, automated log-in data collection and an online service satisfaction questionnaire. The feasibility of using tailored text message, email or phone prompt to maintain engagement with the intervention will also be explored. Results of the study will inform a definitive Phase 3 RCT. RESULTS: Recruitment started on 26 September 2014 and will run for 1 year. CONCLUSION: The proposed trial will provide data to inform a fully powered non-inferiority effectiveness and cost-effectiveness RCT comparing HeLP-Alcohol with TAU. TRIAL REGISTRATION: ISRCTN31789096

Towards the clinical implementation of pharmacogenetics in bipolar disorder.

BackgroundBipolar disorder (BD) is a psychiatric illness defined by pathological alterations between the mood states of mania and depression, causing disability, imposing healthcare costs and elevating the risk of suicide. Although effective treatments for BD exist, variability in outcomes leads to a large number of treatment failures, typically followed by a trial and error process of medication switches that can take years. Pharmacogenetic testing (PGT), by tailoring drug choice to an individual, may personalize and expedite treatment so as to identify more rapidly medications well suited to individual BD patients.DiscussionA number of associations have been made in BD between medication response phenotypes and specific genetic markers. However, to date clinical adoption of PGT has been limited, often citing questions that must be answered before it can be widely utilized. These include: What are the requirements of supporting evidence? How large is a clinically relevant effect? What degree of specificity and sensitivity are required? Does a given marker influence decision making and have clinical utility? In many cases, the answers to these questions remain unknown, and ultimately, the question of whether PGT is valid and useful must be determined empirically. Towards this aim, we have reviewed the literature and selected drug-genotype associations with the strongest evidence for utility in BD.SummaryBased upon these findings, we propose a preliminary panel for use in PGT, and a method by which the results of a PGT panel can be integrated for clinical interpretation. Finally, we argue that based on the sufficiency of accumulated evidence, PGT implementation studies are now warranted. We propose and discuss the design for a randomized clinical trial to test the use of PGT in the treatment of BD