Nonparametric Evaluation of Quantitative Traits in Population-Based Association Studies when the Genetic Model is Unknown

Statistical association between a single nucleotide polymorphism (SNP) genotype and a quantitative trait in genome-wide association studies is usually assessed using a linear regression model, or, in the case of non-normally distributed trait values, using the Kruskal-Wallis test. While linear regression models assume an additive mode of inheritance via equi-distant genotype scores, Kruskal-Wallis test merely tests global differences in trait values associated with the three genotype groups. Both approaches thus exhibit suboptimal power when the underlying inheritance mode is dominant or recessive. Furthermore, these tests do not perform well in the common situations when only a few trait values are available in a rare genotype category (disbalance), or when the values associated with the three genotype categories exhibit unequal variance (variance heterogeneity). We propose a maximum test based on Marcus-type multiple contrast test for relative effect sizes. This test allows model-specific testing of either dominant, additive or recessive mode of inheritance, and it is robust against variance heterogeneity. We show how to obtain mode-specific simultaneous confidence intervals for the relative effect sizes to aid in interpreting the biological relevance of the results. Further, we discuss the use of a related all-pairwise comparisons contrast test with range preserving confidence intervals as an alternative to Kruskal-Wallis heterogeneity test. We applied the proposed maximum test to the Bogalusa Heart Study dataset, and gained a remarkable increase in the power to detect association, particularly for rare genotypes. Our simulation study also demonstrated that the proposed non-parametric tests control family-wise error rate in the presence of non-normality and variance heterogeneity contrary to the standard parametric approaches. We provide a publicly available R library nparcomp that can be used to estimate simultaneous confidence intervals or compatible multiplicity-adjusted p-values associated with the proposed maximum test.

Statistical modeling of protein lysate array data

The protein lysate array is an emerging technology for quantifying the protein concentration ratios in multiple biological samples. It is gaining popularity, and has the potential to answer questions about post-translational modifications and protein pathway relationships. Statistical inference for a parametric quantification procedure has been inadequately addressed in the literature, mainly due to two challenges: the increasing dimension of the parameter space and the need to account for dependence in the data. Each chapter of this thesis addresses one of these issues. In Chapter 1, an introduction to the protein lysate array quantification is presented, followed by the motivations and goals for this thesis work. In Chapter 2, we develop a multi-step procedure for the Sigmoidal models, ensuring consistent estimation of the concentration level with full asymptotic efficiency. The results obtained in this chapter justify inferential procedures based on large-sample approximations. Simulation studies and real data analysis are used to illustrate the performance of the proposed method in finite-samples. The multi-step procedure is simpler in both theory and computation than the single-step least squares method that has been used in current practice. In Chapter 3, we introduce a new model to account for the dependence structure of the errors by a nonlinear mixed effects model. We consider a method to approximate the maximum likelihood estimator of all the parameters. Using the simulation studies on various error structures, we show that for data with non-i.i.d. errors the proposed method leads to more accurate estimates and better confidence intervals than the existing single-step least squares method.

Use of short-term breath measures to estimate daily methane production by cattle

Methods to measure enteric methane (CH4) emissions from individual ruminants in their production environment are required to validate emission inventories and verify mitigation claims. Estimates of daily methane production (DMP) based on consolidated short-term emission measurements are developing, but method verification is required. Two cattle experiments were undertaken to test the hypothesis that DMP estimated by averaging multiple short-term breath measures of methane emission rate did not differ from DMP measured in respiration chambers (RC). Short-term emission rates were obtained from a GreenFeed Emissions Monitoring (GEM) unit, which measured emission rate while cattle consumed a dispensed supplement. In experiment 1 (Expt. 1), four non-lactating cattle (LW=518 kg) were adapted for 18 days then measured for six consecutive periods. Each period consisted of 2 days of ad libitum intake and GEM emission measurement followed by 1 day in the RC. A prototype GEM unit releasing water as an attractant (GEM water) was also evaluated in Expt. 1. Experiment 2 (Expt. 2) was a larger study based on similar design with 10 cattle (LW=365 kg), adapted for 21 days and GEM measurement was extended to 3 days in each of the six periods. In Expt. 1, there was no difference in DMP estimated by the GEM unit relative to the RC (209.7 v. 215.1 g CH4/day) and no difference between these methods in methane yield (MY, 22.7 v. 23.7 g CH4/kg of dry matter intake, DMI). In Expt. 2, the correlation between GEM and RC measures of DMP and MY were assessed using 95% confidence intervals, with no difference in DMP or MY between methods and high correlations between GEM and RC measures for DMP (r=0.85; 215 v. 198 g CH4/day SEM=3.0) and for MY (r=0.60; 23.8 v. 22.1 g CH4/kg DMI SEM=0.42). When data from both experiments was combined neither DMP nor MY differed between GEM- and RC-based measures (P>0.05). GEM water-based estimates of DMP and MY were lower than RC and GEM (P<0.05). Cattle accessed the GEM water unit with similar frequency to the GEM unit (2.8 v. 3.5 times/day, respectively) but eructation frequency was reduced from 1.31 times/min (GEM) to once every 2.6 min (GEM water). These studies confirm the hypothesis that DMP estimated by averaging multiple short-term breath measures of methane emission rate using GEM does not differ from measures of DMP obtained from RCs. Further, combining many short-term measures of methane production rate during supplement consumption provides an estimate of DMP, which can be usefully applied in estimating MY.

EXCESSO DE PESO DE ADULTOS RESIDENTES EM UM AGLOMERADO URBANO SUBNORMAL

Objetivo: Avaliar a prevalência de excesso de peso e possíveis fatores de risco em adultos residentes em um aglomerado urbano subnormal. Métodos: Estudo observacional do tipo transversal, baseado em uma amostra de 582 adultos, na faixa etária de 20 a 59 anos, residentes no aglomerado urbano subnormal dos Coelhos (Recife). Definiu-se excesso de peso pelo índice de massa corporal (IMC) maior ou igual a 25kg/m2. Foram avaliadas possíveis associações com idade, sexo, raça/cor e fatores socioeconômicos (escolaridade e condição de trabalho). O efeito sobre a ocorrência de excesso de peso foi estimado pelo cálculo do Odds Ratio (OR), mediante o ajuste de modelos de regressão logística simples. A precisão e significância estatística desses ORs foram avaliadas através de intervalos de 95% de confiança e do teste de Wald. Adotou-se nível de significância de 5%. Resultados: A prevalência de excesso de peso foi de 62,5% (n=364), sendo maior nas mulheres (66,1%; n=251) do que nos homens (56,0%; n=113), com um aumento progressivo até a faixa etária de 40 a 49 anos, passando a declinar a partir de então. Nessa faixa, houve um risco de excesso de peso de 2,6 vezes. Além da idade, pertencer ao sexo feminino e não trabalhar também representaram condições de risco. Conclusão: A elevada prevalência do excesso de peso na população adulta residente no aglomerado urbano subnormal dos Coelhos se mostrou associada ao sexo, faixa etária e condição de trabalho, constituindo-se, assim, como possíveis fatores de risco do problema.

Psychosocial, musculoskeletal and somatoform comorbidity in patients with chronic low back pain: original results from the Dutch Transition Project

International audience

Association of type of birth attendant and place of delivery on infant mortality in sub-Saharan Africa.

Objective: To examine the association between type of birth attendant and place of delivery, and infant mortality (IM). Methods: This cross-sectional study used self-reported data from the Demographic Health Surveys for women in Ghana, Kenya, and Sierra Leone. Logistic regression estimated odds ratios (ORs) and95% confidence intervals. Results: In Ghana and Sierra Leone, odds of IM were higher for women who delivered at a health facility versus women who delivered at a household residence (OR=3.18, 95% confidence interval, CI: 1.29-7.83, p=0.01 and OR=1.62, 95% CI: 1.15-2.28, p=0.01, respectively). Compared to the use of health professionals, the use of birth attendants for assistance with delivery was not significantly associated with IM for women in Ghana or Sierra Leone (OR=2.17, 95% CI: 0.83-5.69, p=0.12 and OR=1.25, 95% CI: 0.92-1.70, p=0.15, respectively). In Kenya, odds of IM, though nonsignificant, were lower for women who used birth attendants than those who used health professionals to assist with delivery (OR=0.85, 95% CI: 0.51-1.41, p=0.46), and higher with delivery at a health facility versus a household residence (OR=1.29, 95% CI: 0.81-2.03, p=0.28). Conclusions: Women in Ghana and Sierra Leone who delivered at a health facility had statistically significant increased odds of IM. Birth attendant type-IM associations were not statistically significant.Future research should consider culturally-sensitive interventions to improve maternal health and help reduce IM.

Naturally Occurring Resistance-Associated Variants of Hepatitis C Virus Protease Inhibitors in Poor Responders to Pegylated Interferon-Ribavirin

International audience

SEMIPARAMETRIC METHODS IN THE ESTIMATION OF TAIL PROBABILITIES AND EXTREME QUANTILES

In quantitative risk analysis, the problem of estimating small threshold exceedance probabilities and extreme quantiles arise ubiquitously in bio-surveillance, economics, natural disaster insurance actuary, quality control schemes, etc. A useful way to make an assessment of extreme events is to estimate the probabilities of exceeding large threshold values and extreme quantiles judged by interested authorities. Such information regarding extremes serves as essential guidance to interested authorities in decision making processes. However, in such a context, data are usually skewed in nature, and the rarity of exceedance of large threshold implies large fluctuations in the distribution's upper tail, precisely where the accuracy is desired mostly. Extreme Value Theory (EVT) is a branch of statistics that characterizes the behavior of upper or lower tails of probability distributions. However, existing methods in EVT for the estimation of small threshold exceedance probabilities and extreme quantiles often lead to poor predictive performance in cases where the underlying sample is not large enough or does not contain values in the distribution's tail. In this dissertation, we shall be concerned with an out of sample semiparametric (SP) method for the estimation of small threshold probabilities and extreme quantiles. The proposed SP method for interval estimation calls for the fusion or integration of a given data sample with external computer generated independent samples. Since more data are used, real as well as artificial, under certain conditions the method produces relatively short yet reliable confidence intervals for small exceedance probabilities and extreme quantiles.

Méthodes de Bootstrap pour les modèles à facteurs

Cette thèse développe des méthodes bootstrap pour les modèles à facteurs qui sont couram- ment utilisés pour générer des prévisions depuis l'article pionnier de Stock et Watson (2002) sur les indices de diffusion. Ces modèles tolèrent l'inclusion d'un grand nombre de variables macroéconomiques et financières comme prédicteurs, une caractéristique utile pour inclure di- verses informations disponibles aux agents économiques. Ma thèse propose donc des outils éco- nométriques qui améliorent l'inférence dans les modèles à facteurs utilisant des facteurs latents extraits d'un large panel de prédicteurs observés. Il est subdivisé en trois chapitres complémen- taires dont les deux premiers en collaboration avec Sílvia Gonçalves et Benoit Perron. Dans le premier article, nous étudions comment les méthodes bootstrap peuvent être utilisées pour faire de l'inférence dans les modèles de prévision pour un horizon de h périodes dans le futur. Pour ce faire, il examine l'inférence bootstrap dans un contexte de régression augmentée de facteurs où les erreurs pourraient être autocorrélées. Il généralise les résultats de Gonçalves et Perron (2014) et propose puis justifie deux approches basées sur les résidus : le block wild bootstrap et le dependent wild bootstrap. Nos simulations montrent une amélioration des taux de couverture des intervalles de confiance des coefficients estimés en utilisant ces approches comparativement à la théorie asymptotique et au wild bootstrap en présence de corrélation sérielle dans les erreurs de régression. Le deuxième chapitre propose des méthodes bootstrap pour la construction des intervalles de prévision permettant de relâcher l'hypothèse de normalité des innovations. Nous y propo- sons des intervalles de prédiction bootstrap pour une observation h périodes dans le futur et sa moyenne conditionnelle. Nous supposons que ces prévisions sont faites en utilisant un ensemble de facteurs extraits d'un large panel de variables. Parce que nous traitons ces facteurs comme latents, nos prévisions dépendent à la fois des facteurs estimés et les coefficients de régres- sion estimés. Sous des conditions de régularité, Bai et Ng (2006) ont proposé la construction d'intervalles asymptotiques sous l'hypothèse de Gaussianité des innovations. Le bootstrap nous permet de relâcher cette hypothèse et de construire des intervalles de prédiction valides sous des hypothèses plus générales. En outre, même en supposant la Gaussianité, le bootstrap conduit à des intervalles plus précis dans les cas où la dimension transversale est relativement faible car il prend en considération le biais de l'estimateur des moindres carrés ordinaires comme le montre une étude récente de Gonçalves et Perron (2014). Dans le troisième chapitre, nous suggérons des procédures de sélection convergentes pour les regressions augmentées de facteurs en échantillons finis. Nous démontrons premièrement que la méthode de validation croisée usuelle est non-convergente mais que sa généralisation, la validation croisée «leave-d-out» sélectionne le plus petit ensemble de facteurs estimés pour l'espace généré par les vraies facteurs. Le deuxième critère dont nous montrons également la validité généralise l'approximation bootstrap de Shao (1996) pour les regressions augmentées de facteurs. Les simulations montrent une amélioration de la probabilité de sélectionner par- cimonieusement les facteurs estimés comparativement aux méthodes de sélection disponibles. L'application empirique revisite la relation entre les facteurs macroéconomiques et financiers, et l'excès de rendement sur le marché boursier américain. Parmi les facteurs estimés à partir d'un large panel de données macroéconomiques et financières des États Unis, les facteurs fortement correlés aux écarts de taux d'intérêt et les facteurs de Fama-French ont un bon pouvoir prédictif pour les excès de rendement.

Speeding stroke recovery? A systematic review of amphetamine after stroke

Introduction: The use of drugs to enhance recovery (“rehabilitation pharmacology”) has been assessed. Amphetamine can improve outcome in experimental models of stroke, and several small clinical trials have assessed its use in stroke. Methods: Electronic searches were performed to identify randomised controlled trials of amphetamine in stroke (ischaemic or haemorrhagic). Outcomes included functional outcome (assessed as combined death or disability/dependency), safety (death) and haemodynamic measures. Data were analysed as dichotomous or continuous outcomes, using odds ratios (OR), weighted or standardised mean difference, (WMD or SMD) using random-effects models with 95% confidence intervals (95% CI); statistical heterogeneity was assessed. Results: Eleven completed trials (n=329) were identified. Treatment with amphetamine was associated with non-significant trends to increased death (OR 2.78 (95% CI, 0.75– 10.23), n=329, 11 trials) and improved motor scores (WMD 3.28 (95% CI −0.48–7.04) n=257, 9 trials) but had no effect on the combined outcome of death and dependency (OR 1.15 (95% CI 0.65–2.06, n=206, 5 trials). Amphetamine increased systolic blood pressure (WMD 9.3 mmHg, 95% CI 3.3–15.3, n=106, 3 trials) and heart rate (WMD 7.6 beats per minute (bpm), 95% CI 1.8–13.4, n=106, 3 trials). Despite variations in treatment regimes, outcomes and follow-up duration there was no evidence of significant heterogeneity or publication bias. Conclusion: No evidence exists at present to support the use of amphetamine after stroke. Despite a trend to improved motor function, doubts remain over

Relationship between therapeutic changes in blood pressure and outcomes in acute stroke: a metaregression

Both low and high blood pressure (BP) during the acute phase of stroke are associated independently with a poor outcome. Several small clinical trials have involved the alteration of BP and this study assessed the relationship between change in BP and functional outcome. Randomised controlled trials of interventions that would be expected, on pharmacological grounds, to alter BP in patients within one week of the onset of acute ischaemic or haemorrhagic stroke were sought using electronic searches. Data were collected on BP and clinical outcome. The relationship between the difference in on-treatment BP and odds ratios (OR) for outcomes was assessed using meta-regression. Thirty-seven trials involving 9,008 patients were included. A ‘U’ or ‘J’ shaped relationship were found between on-treatment BP difference and early death, death at the end of 90 day follow up, and combined death or dependency at the end of follow up. Although outcomes were not significantly reduced at any level of change in BP, the lowest odds occurred at: early death (OR 0.87, 95% confidence interval, CI 0.54 to 1.23) - 8.1 mmHg; death at end of follow up (OR 0.96, 95% CI 0.31 to 1.65) - 14.4 mmHg; and combined death or dependency at end of follow up (OR 0.95, 95% CI 0.11 to 1.72) - 14.6 mmHg. Although large falls or increases in BP are associated with a worse outcome, modest reductions may reduce death, and combined death or dependency, although the confidence intervals are wide and compatible with overall benefit or hazard.

Environmental risk factors for oesophageal cancer in Malawi: A case-control study

Aim There is a high burden of oesophageal cancer in Malawi with dismal outcomes. It is not known whether environmental factors are associated with oesophageal cancer. Without knowing this critical information, prevention interventions are not possible. The purpose of this analysis was to explore environmental factors associated with oesophageal cancer in the Malawian context. Methods A hospital-based case-control study of the association between environmental risk factors and oesophageal cancer was conducted at Kamuzu Central Hospital in Lilongwe, Malawi and Queen Elizabeth Central Hospital in Blantyre, Malawi. Ninety-six persons with squamous cell carcinoma and 180 controls were enrolled and analyzed. These two groups were compared for a range of environmental risk factors, using logistic regression models. Unadjusted and adjusted odds ratios and 95% confidence intervals (CI) were calculated. Results Firewood cooking, cigarette smoking, and use of white maize flour all had strong associations with squamous cell carcinoma of the oesophagus, with adjusted odds ratios of 12.6 (95% CI: 4.2-37.7), 5.4 (95% CI: 2.0-15.2) and 6.6 (95% CI: 2.3-19.3), respectively. Conclusions Several modifiable risk factors were found to be strongly associated with squamous cell carcinoma. Research is needed to confirm these associations and then determine how to intervene on these modifiable risk factors in the Malawian context.

Comparative toxicity of antifouling compounds on the development of sea urchin

In the present study, embryotoxicity experiments using the sea urchin Lytechinus variegatus were carried out to better clarify the ecotoxicological effects of tributyltin (TBT) and triphenyltin (TPT) (the recently banned antifouling agents), and Irgarol and Diuron (two of the new commonly used booster biocides). Organisms were individually examined to evaluate the intensity and type of effects on embryo-larval development, this procedure has not been commonly used, however it showed to be a potentially suitable approach for toxicity assessment. NOEC and LOEC were similar for compounds of same chemical class, and IC10 values were very close and showed overlapping of confidence intervals between TBT and TPT, and between Diuron and Irgarol. In addition, IC10 were similar to NOEC values. Regardless of this, the observed effects were different. Embryo development was interrupted at the gastrula and blastula stages at 1.25 and 2.5 mu g l(-1) of TBT, respectively, whereas pluteus stage was reached with the corresponding concentrations of TPT. Furthermore, embryos reached the prism and morula stages at 5 mu g l(-1) of TPT and TBT, respectively. The effects induced by Irgarol were also more pronounced than those caused by Diuron. Pluteus stage was always reached at any tested Diuron concentration, while embryogenesis was interrupted at blastula/gastrula stages at the highest concentrations of Irgarol. Therefore, this study proposes a complementary approach for interpreting embryo-larval responses that may be employed together with the traditional way of analysis. Consequently, this application leads to a more powerful ecotoxicological assessment tool focused on embryotoxicity.

Does therapeutic writing help people with long-term conditions? Systematic review, realist synthesis and economic considerations

Background Writing therapy to improve physical or mental health can take many forms. The most researched model of therapeutic writing (TW) is unfacilitated, individual expressive writing (written emotional disclosure). Facilitated writing activities are less widely researched. Data sources Databases including: MEDLINE, EMBASE, PsychINFO, Linguistics and Language Behavior Abstracts, AMED, and CINHAL were searched from inception to March 2013. Review methods Four TW practitioners provided expert advice. Study procedures were conducted by one reviewer and checked by a second. Randomised controlled trials (RCTs) and non-randomised comparative studies were included. Quality was appraised using the Cochrane risk of bias tool. Unfacilitated and facilitated TW studies were analysed separately under ICD-10 chapter headings. Meta-analyses were performed where possible using Revman 5.2. Costs were estimated from an NHS perspective and three cost-consequence case studies were prepared. Realist synthesis followed RAMESES guidelines. Objectives To review the clinical and cost-effectiveness of TW for people with long-term health conditions (LTCs) compared to no writing, or other controls, reporting any relevant clinical outcomes. To conduct a realist synthesis to understand how TW might work, and for whom. Results From 14,658 unique citations, 284 full text papers were reviewed and 64 studies (58 RCTs) were included in the final effectiveness reviews. Five studies examined facilitated TW, these were extremely heterogeneous with unclear or high risk of bias, but suggested that facilitated TW interventions may be beneficial in individual LTCs. Unfacilitated expressive writing was examined in 59 studies of variable, or unreported, quality. Overall there was very little or no evidence of any benefit reported in the following conditions (number of studies): HIV (six); breast cancer (eight); gynaecological and genitourinary cancers (five); mental health (five); asthma (four); psoriasis (three); chronic pain (four). In inflammatory arthropathies (six) there was a reduction in disease severity (n= 191, standardised mean difference (SMD) - 0.61 [95% confidence intervals (95% CI) -0.96, -0.26]) in the short term on meta-analysis of four studies. For all other LTCs there was either no, or sparse, data with no, or inconsistent, evidence of benefit. Meta-analyses conducted across all the LTCs provided no evidence that unfacilitated EW had any effect on depression at short term (n= 1,563, SMD -0.06, 95% CI -0.29 to 0.17, substantial heterogeneity), or long term (n= 778, SMD-0.04 95% CI -0.18 to 0.10, little heterogeneity) follow up, or on anxiety, physiological or biomarker-based outcomes. One study reported costs, none reported cost-effectiveness, twelve reported resource use; meta-analysis suggested reduced medication use but no impact on health centre visits. Estimated costs of intervention were low, but there was insufficient evidence to judge cost-effectiveness. Realist review findings suggested that facilitated TW is a complex intervention and group interaction contributes to the perception of benefit. It was unclear from the available data who might benefit most from facilitated TW. Limitations Difficulties with developing realist review programme theory meant that mechanisms operating during TW remain obscure. Conclusions Overall there is little evidence to support the effectiveness or cost-effectiveness of unfacilitated expressive writing interventions in people with LTCs. Further research focussed on facilitated TW in people with LTCs could be informative.

Early consumption of liquids different to breast milk in Mexican infants under 1 year: results of the probabilistic National Health and Nutrition Survey 2012

Introduction: Studies on infant dietary intake do not generally focus on the types of liquids consumed. Objective: To document by age and breastfeeding status, the types of liquids present in the diet of Mexican children under 1 year of age (< 1 y) who participated in the National Health and Nutrition Survey 2012 (ENSANUT-2012). Methods: Analysis of the infant < 1 y feeding practices from the ENSANUT-2012 survey in non-breastfed (non-BF) and breastfed (BF) infants by status quo for the consumption of liquids grouped in: water, formula, fortified LICONSA milk, nutritive liquids (NL; thin cereal-based gruel with water or milk and coffee with milk) and non-nutritive liquids (non-NL) as sugared water, water-based drinks, tea, beans or chicken broth, aguamiel and coffee. In this infants < 1 y we analyzed the not grouped consumption of liquids in the first three days of life (newborns) from the mother's recall. Percentage and confidence intervals (95% CI) were calculated adjusting for survey design. Statistical differences were analyzed by Z test. Results: We observed a high consumption of human milk followed by formula (56.7%) and water (51.1%) in infants under 6 months of age (< 6 mo). The proportion of non-BF infants consuming non-NL was higher than for BF infants (p < 0.05). More than 60% of older infants (6 mo and < 1 y) consumed formula and were non-BF. In newborns formula consumption was predominant, followed by tea or infusion and water. Conclusions: Non-breast milk liquids are present undesirably in Mexican infants' diet and non-NL are consumed earlier than NL, revealing inadequate early dietary practices.