P value and the theory of hypothesis testing: an explanation for new researchers.

In the 1920s, Ronald Fisher developed the theory behind the p value and Jerzy Neyman and Egon Pearson developed the theory of hypothesis testing. These distinct theories have provided researchers important quantitative tools to confirm or refute their hypotheses. The p value is the probability to obtain an effect equal to or more extreme than the one observed presuming the null hypothesis of no effect is true; it gives researchers a measure of the strength of evidence against the null hypothesis. As commonly used, investigators will select a threshold p value below which they will reject the null hypothesis. The theory of hypothesis testing allows researchers to reject a null hypothesis in favor of an alternative hypothesis of some effect. As commonly used, investigators choose Type I error (rejecting the null hypothesis when it is true) and Type II error (accepting the null hypothesis when it is false) levels and determine some critical region. If the test statistic falls into that critical region, the null hypothesis is rejected in favor of the alternative hypothesis. Despite similarities between the two, the p value and the theory of hypothesis testing are different theories that often are misunderstood and confused, leading researchers to improper conclusions. Perhaps the most common misconception is to consider the p value as the probability that the null hypothesis is true rather than the probability of obtaining the difference observed, or one that is more extreme, considering the null is true. Another concern is the risk that an important proportion of statistically significant results are falsely significant. Researchers should have a minimum understanding of these two theories so that they are better able to plan, conduct, interpret, and report scientific experiments.

Direct Effect of Birth Weight on Childhood Blood Pressure: a Causal Mediation Analysis

Background: Numerous studies have shown a negative association between birth weight (BW) and blood pressure (BP) later in life. To estimate the direct effect of BW on BP, it is conventional to condition on current weight (CW). However, such conditioning can induce collider stratification bias in the estimate of the direct effect. Objective: To bound the potential bias due to U, an unmeasured common cause of CW and BP, on the estimate of the (controlled) direct effect of BW on BP. Methods: Data from a school based study in Switzerland were used (N = 4,005; 2,010 B/1,995 G; mean age: 12.3 yr [range: 10.1-14.9]). Measured common causes of BW-BP (SES, smoking, body weight, and hypertension status of the mother) and CW-BP (breastfeeding and child's physical activity and diet) were identified with DAGs. Linear regression models were fitted to estimate the association between BW and BP. Sensitivity analyses were conducted to assess the potential effect of U on the association between BW and BP. U was assumed 1) to be a binary variable that affected BP by the same magnitude in low BWand in normal BW children and 2) to have a different prevalence in low BW children and in normal BW children for a given CW. Results: A small negative association was observed between BW and BP [beta: -0.3 mmHg/kg (95% CI: -0.9 to 0.3)]. The association was strengthened upon conditioning for CW [beta: -1.5 mmHg/kg (95% CI: -2.1 to -0.9)]. Upon further conditioning on common causes of BW-BP and CW-BP, the association did not change substantially [beta: -1.4 mmHg/kg (95% CI: -2.0 to -0.8)]. The negative association could be explained by U only if U was strongly associated with BP and if there was a large difference in the prevalence of U between low BWand normal BW children. Conclusion: The observed negative association between BW and BP upon adjustment for CW was not easily explained by an unmeasured common cause of CWand BP.

Does CRP Play a Causal Role in the Development of Coronary Heart Disease: Results of a Mendelian Randomisation Experiment Involving 128,935 People

Background: C-reactive protein (CRP) is associated with risk of coronary heart disease (CHD). Whether CRP is causally associated with CHD or merely a marker of underlying atherosclerosis is uncertain. Methods: We used a Mendelian randomisation design to investigate the causal relationship of CRP with CHD. We identified three genetic variants in the CRP locus (rs7553007, rs1130864 and rs1205) which influence CRP levels. We tested the three SNPs for association with CHD amongst 28,112 CHD cases and 100,823 controls. We then compared the observed relationship between the SNPs and CHD, with that predicted from the association of SNPs with CRP levels, and of CRP levels with CHD. Results: SNPs in the CRP locus were not associated with CHD: rs7553007, OR 0.98 (95% CI, 0.94-1.01); rs1130864, OR 1.00 (95% CI, 0.86-1.15); rs1205, OR 1.03 (95% CI, 0.99-1.07); combined OR for all three SNPs, 1.00 (95% CI, 0.97-1.02), per 20% lower CRP (figure). In contrast, the predicted OR for CHD from a 20% lower CRP level is 0.94 (95% CI, 0.94- 0.95), based on meta-analysis of observational studies. Conclusions: Though CRP variants are associated with CRP levels, and CRP levels with risk of CHD, we observed that CRP variants are not associated with CHD risk. Our Mendelian randomisation experiment strongly argues against a causal association of CRP with CHD.

Use of a Mendelian randomization approach to assess the causal relation of gamma-Glutamyltransferase with blood pressure and serum insulin levels.

Elevated levels of γ-glutamyltransferase (GGT) have been associated with elevated blood pressure (BP) and diabetes. However, the causality of these relations has not been addressed. The authors performed a cross-sectional analysis (2003-2006) among 4,360 participants from the population-based Cohorte Lausannoise (CoLaus) Study (Lausanne, Switzerland). The rs2017869 variant of the γ-glutamyltransferase 1 (GGT1) gene, which explained 1.6% of the variance in GGT levels, was used as an instrument for Mendelian randomization (MR). Sex-specific GGT quartiles were strongly associated with both systolic and diastolic BP (all P's < 0.0001). After multivariable adjustment, these relations were attenuated but remained significant. Using MR, the authors observed no positive association of GGT with BP (systolic: β -5.68, 95% confidence interval (CI): -11.51, 0.16 (P = 0.06); diastolic: β = -2.24, 95% CI: -5.98, 1.49 (P = 0.24)). The association of GGT with insulin was also attenuated after multivariable adjustment but persisted in the fully adjusted model (β = 0.07, 95% CI: 0.04, 0.09; P < 0.0001). Using MR, the authors also observed a positive association of GGT with insulin (β = 0.19, 95% CI: 0.01, 0.37; P = 0.04). In conclusion, the authors found evidence for a direct causal relation of GGT with fasting insulin but not with BP.

Fastidious intracellular bacteria as causal agents of community-acquired pneumonia.

Intracellular bacteria are common causes of community-acquired pneumonia that grow poorly or not at all on standard culture media and do not respond to beta-lactam antibiotic therapy. Apart from well-established agents of pneumonia such as Legionella pneumophila, Mycoplasma pneumoniae, Chlamydia pneumoniae, Chlamydia psittaci and Coxiella burnetii, some new emerging pathogens have recently been recognized, mainly Parachlamydia acanthamoebae and Simkania negevensis, two Chlamydia-related bacteria. Most of them are causes of benign and self-limited infections. However, they may cause severe pneumonia in some cases (i.e., Legionnaires' disease) and they may cause outbreaks representing a public health problem deserving prompt recognition and appropriate therapy. Although extrapulmonary manifestations are often present, no clinical features allow them to be distinguished from classical bacterial agents of pneumonia such as Streptococcus pneumoniae. Thus, specific molecular diagnostic tools are very helpful for early recognition of the offending bacteria, whereas serology often only allows retrospective or late diagnosis. Macrolides remain the best empirical treatment of intracellular respiratory pathogens, although some observational studies suggest that quinolones may be superior for the treatment of legionellosis.

Etude des niveaux de concentration d'hydrocarbures aromatiques polycycliques (HAPs) dans la poussière de bois et des marqueurs biologiques d'effets génotoxiques chez les travailleurs du bois

L'exposition aux poussières de bois est associé à un risque accru d'adénocarcinomes des fosses nasales et des sinus paranasaux (SNC, 'Sinonasal cancer') chez les travailleurs du bois. Les poussières de bois sont ainsi reconnues comme cancérogènes avérés pour l'homme par le Centre international de Recherche sur le Cancer (CIRC). Toutefois, l'agent causal spécifique et le mécanisme sous-jacent relatifs au cancer lié aux poussières de bois demeurent inconnus. Une possible explication est une co-exposition aux poussières de bois et aux Hydrocarbures Aromatiques Polycycliques (HAP), ces derniers étant potentiellement cancérogènes. Dans les faits, les travailleurs du bois sont non seulement exposés aux poussières de bois naturel, mais également à celles générées lors d'opérations effectuées à l'aide de machines (ponceuses, scies électriques, etc.) sur des finitions de bois (bois traités) ou sur des bois composites, tels que le mélaminé et les panneaux de fibres à densité moyenne (MDF, 'Medium Density Fiberboard'). Des HAP peuvent en effet être générés par la chaleur produite par l'utilisation de ces machines sur la surface du bois. Les principaux objectifs de cette thèse sont les suivants: (1) quantifier HAP qui sont présents dans les poussières générées lors de diverses opérations courantes effectuées sur différents bois (2) quantifier l'exposition individuelle aux poussières de bois et aux HAP chez les travailleurs, et (3) évaluer les effets génotoxiques (dommages au niveau de l'ADN et des chromosomes) due à l'exposition aux poussières de bois et aux HAP. Cette thèse est composée par une étude en laboratoire (objectif 1) et par une étude de terrain (objectifs 2 et 3). Pour l'étude en laboratoire, nous avons collecté des poussières de différents type de bois (sapin, MDF, hêtre, sipo, chêne, bois mélaminé) générées au cours de différentes opérations (comme le ponçage et le sciage), et ceci dans une chambre expérimentale et dans des conditions contrôlées. Ensuite, pour l'étude de terrain, nous avons suivi, dans le cadre de leur activité professionnelle, 31 travailleurs de sexe masculin (travailleurs du bois et ébenistes) exposés aux poussières de bois pendant deux jours de travail consécutifs. Nous avons également recruté, comme groupe de contrôle, 19 travailleurs non exposés. Pour effectuer une biosurveillance, nous avons collecté des échantillons de sang et des échantillons de cellules nasales et buccales pour chacun des participants. Ces derniers ont également rempli un questionnaire comprenant des données démographiques, ainsi que sur leur style de vie et sur leur exposition professionnelle. Pour les travailleurs du bois, un échantillonnage individuel de poussière a été effectué sur chaque sujet à l'aide d'une cassette fermée, puis nous avons évalué leur exposition à la poussière de bois et aux HAP, respectivement par mesure gravimétrique et par Chromatographie en phase gazeuse combinée à la spectrométrie de masse. L'évaluation des dommages induits à l'ADN et aux chromosomes (génotoxicité) a été, elle, effectuée à l'aide du test des micronoyaux (MN) sur les cellules nasales et buccales et à l'aide du test des comètes sur les échantillons de sang. Nos résultats montrent dans la poussière de la totalité des 6 types de bois étudiés la présence de HAP (dont certains sont cancérogènes). Des différences notoires dans les concentrations ont été néanmoins constatées en fonction du matériau étudié : les concentrations allant de 0,24 ppm pour la poussière de MDF à 7.95 ppm pour le mélaminé. Nos résultats montrent également que les travailleurs ont été exposés individuellement à de faibles concentrations de HAP (de 37,5 à 119,8 ng m-3) durant les opérations de travail du bois, alors que les concentrations de poussières inhalables étaient relativement élevés (moyenne géométrique de 2,8 mg m-3). En ce qui concerne la génotoxicité, les travailleurs exposés à la poussière de bois présentent une fréquence significativement plus élevée en MN dans les cellules nasales et buccales que les travailleurs du groupe témoin : un odds ratio de 3.1 a été obtenu pour les cellules nasales (IC 95% : de 1.8 à 5.1) et un odds ratio de 1,8 pour les cellules buccales (IC 95% : de 1.3 à 2.4). En outre, le test des comètes a montré que les travailleurs qui ont déclaré être exposés aux poussières de MDF et/ou de mélaminé avaient des dommages à l'ADN significativement plus élevés que les deux travailleurs exposés à la poussière de bois naturel (sapin, épicéa, hêtre, chêne) et que les travailleurs du groupe témoin (p <.01). Enfin, la fréquence des MN dans les cellules nasales et buccales augmentent avec les années d'exposition aux poussières de bois. Par contre, il n'y a pas de relation dose-réponse concernant la génotoxicité due à l'exposition journalière à la poussière et aux HAP. Cette étude montre qu'une exposition aux HAP eu bien lieu lors des opérations de travail du bois. Les travailleurs exposés aux poussières de bois, et donc aux HAP, courent un risque plus élevé (génotoxicité) par rapport au groupe témoin. Étant donné que certains des HAP détectés sont reconnus potentiellement cancérogènes, il est envisageable que les HAP générés au cours du travail sur les matériaux de bois sont un des agents responsables de la génotoxicité de la poussière de bois et du risque élevé de SNC observé chez les travailleurs du secteur. Etant donné la corrélation entre augmentation de la fréquence des MN, le test des micronoyaux dans les cellules nasales et buccales constitue sans conteste un futur outil pour la biosurveillance et pour la détection précoce du risque de SNC chez les travailleurs. - Exposures to wood dust have been associated with an elevated risk of adenocarcinomas of the Dasal cavity and the paranasal sinuses (sinonasal cancer or SNC) among wood workers. Wood dust is recognized as a human carcinogen by the International Agency for Research on Cancer. However, the specific cancer causative agent(s) and the mechanism(s) behind wood dust related carcinogenesis remains unknown. One possible explanation is a co-exposure to wood dust and polycyclic aromatic hydrocarbons (PAH), the latter being carcinogenic. In addition, wood workers are not only exposed to natural wood but also to wood finishes and composite woods such as wood melamine and medium density fiber (MDF) boards during the manipulation with power tools. The heat produced by the use of power tools can cause the generation of PAH from wood materials. The main objectives of the present thesis are to: (1) quantify possible PAH concentrations in wood dust generated during various common woodworking operations using different wood materials; (2) quantify personal wood dust concentrations and PAH exposures among wood workers; and (3) assess genotoxic effects (i.e., DNA and chromosomal damage) of wood dust and PAH exposure in wood workers. This thesis is composed by a laboratory study (objective 1) and a field study (objectives 2 and 3). In the laboratory study we collected wood dust from different wood materials (fir, MDF, beech, mahagany, oak, and wood melamine) generated during different wood operations (e.g., sanding and sawing) in an experimental chamber under controlled conditions. In the following field study, we monitored 31 male wood workers (furniture and construction workers) exposed to wood dust during their professional activity for two consecutive work shifts. Additionally, we recruited 19 non exposed workers as a control group. We collected from each participant blood samples, and nasal and buccal cell samples. They answered a questionnaire including demographic and life-style data and occupational exposure (current and past). Personal wood dust samples were collected using a closed-face cassette. We used gravimetrie analysis to determine the personal wood dust concentrations and capillary gas chromatography - mass spectrometry analysis to determine PAH concentrations. Genotoxicity was assessed with the micronucleus (MN) assay for nasal and buccal cells and with the comet assay for blood samples. Our results show that PAH (some of them carcinogenic) were present in dust from all six wood materials tested, yet at different concentrations depending on the material. The highest concentration was found in dust from wood melamine (7.95 ppm) and the lowest in MDF (0.24 ppm). Our results also show that workers were individually exposed to low concentrations of PAHs (37.5-119.8 ng m"3) during wood working operations, whereas the concentrations of inhalable dust were relatively high (geometric mean 2.8 mg m"3). Concerning the genotoxicity, wood workers had a significantly higher MN frequency in nasal and buccal cells than the workers in the control group (odds ratio for nasal cells 3.1 (95%CI 1.8-5.1) and buccal cells 1.8 (95%CI 1.3-2.4)). Furthermore, the comet assay showed that workers who reported to be exposed to dust from wooden boards (MDF and wood melamine) had significantly higher DNA damage than both the workers exposed to natural woods (fir, spruce, beech, oak) and the workers in the control group (p < 0.01). Finally, MN frequency in nasal and buccal cells increased with increasing years of exposure to wood dust. However, there was no genotoxic dose-response relationship with the per present day wood dust and PAH exposure. This study shows that PAH exposure occurred during wood working operations. Workers exposed to wood dust, and thus to PAH, had a higher risk for genotoxicity compared to the control group. Since some of the detected PAH are potentially carcinogenic, PAH generated from operations on wood materials may be one of the causative agents for the observed increased genotoxicity in wood workers. Since increased genotoxicity is manifested in an increased MN frequency, the MN assay in nasal and buccal cells may become a relevant biomonitoring tool in the future for early detection of SNC risk.

Commentary : beyond vague causal effect estimation of obesity on health outcomes

In the current issue of epidemiology, Danaei and colleagues elegantly estimated both the direct effect and the indirect effect-that is, the effect mediated by blood pressure, cholesterol, glucose, fibrinogen, and high-sensitivity C-reactive protein-of body mass index (BMI) on the risk of coronary heart disease (CHD). they analyzed data from 9 cohort studies including 58,322 patients and 9459 CHD events, with baseline measurements between 1954 and 2001. Using sophisticated and cutting-edge methods for direct and indirect effect estimations, the authors estimated that half of the risk of overweight and obesity would be mediated by blood pressure, cholesterol, and glucose. Few additional percentage points of the risk would be mediated by fibrinogen and hs-CRP. How should we understand these estimates? Can we say that if obese persons reduce their body weight and reach a normal body weight, their excess risk of CHD would be reduced by half through an improvement in these mediators and by half through the reduction in BmI itself? Is that also true if these individuals are prevented from becoming obese in the first place? Can we also conclude that if these mediators are well controlled in obese individuals through other means than a body weight reduction, their excess risk of CHD would be reduced by half? Let us confront these estimates with observations from studies evaluating 2 interventions to reduce body weight, that is, bariatric surgery in patients with severe obesity and intensive lifestyle intervention in overweight patients with diabetes

Amoebal pathogens as emerging causal agents of pneumonia.

Despite using modern microbiological diagnostic approaches, the aetiological agents of pneumonia remain unidentified in about 50% of cases. Some bacteria that grow poorly or not at all in axenic media used in routine clinical bacteriology laboratory but which can develop inside amoebae may be the agents of these lower respiratory tract infections (RTIs) of unexplained aetiology. Such amoebae-resisting bacteria, which coevolved with amoebae to resist their microbicidal machinery, may have developed virulence traits that help them survive within human macrophages, i.e. the first line of innate immune defence in the lung. We review here the current evidence for the emerging pathogenic role of various amoebae-resisting microorganisms as agents of RTIs in humans. Specifically, we discuss the emerging pathogenic roles of Legionella-like amoebal pathogens, novel Chlamydiae (Parachlamydia acanthamoebae, Simkania negevensis), waterborne mycobacteria and Bradyrhizobiaceae (Bosea and Afipia spp.).

Heavier smoking may lead to a relative increase in waist circumference: evidence for a causal relationship from a Mendelian randomisation meta-analysis. The CARTA consortium.

OBJECTIVES: To investigate, using a Mendelian randomisation approach, whether heavier smoking is associated with a range of regional adiposity phenotypes, in particular those related to abdominal adiposity. DESIGN: Mendelian randomisation meta-analyses using a genetic variant (rs16969968/rs1051730 in the CHRNA5-CHRNA3-CHRNB4 gene region) as a proxy for smoking heaviness, of the associations of smoking heaviness with a range of adiposity phenotypes. PARTICIPANTS: 148 731 current, former and never-smokers of European ancestry aged ≥16 years from 29 studies in the consortium for Causal Analysis Research in Tobacco and Alcohol (CARTA). PRIMARY OUTCOME MEASURES: Waist and hip circumferences, and waist-hip ratio. RESULTS: The data included up to 66 809 never-smokers, 43 009 former smokers and 38 913 current daily cigarette smokers. Among current smokers, for each extra minor allele, the geometric mean was lower for waist circumference by -0.40% (95% CI -0.57% to -0.22%), with effects on hip circumference, waist-hip ratio and body mass index (BMI) being -0.31% (95% CI -0.42% to -0.19), -0.08% (-0.19% to 0.03%) and -0.74% (-0.96% to -0.51%), respectively. In contrast, among never-smokers, these effects were higher by 0.23% (0.09% to 0.36%), 0.17% (0.08% to 0.26%), 0.07% (-0.01% to 0.15%) and 0.35% (0.18% to 0.52%), respectively. When adjusting the three central adiposity measures for BMI, the effects among current smokers changed direction and were higher by 0.14% (0.05% to 0.22%) for waist circumference, 0.02% (-0.05% to 0.08%) for hip circumference and 0.10% (0.02% to 0.19%) for waist-hip ratio, for each extra minor allele. CONCLUSIONS: For a given BMI, a gene variant associated with increased cigarette consumption was associated with increased waist circumference. Smoking in an effort to control weight may lead to accumulation of central adiposity.