A descriptive review of variable selection methods in four epidemiologic journals : there is still room for improvement

Background : A review of epidemiological papers conducted in 2009 concluded that several studies employed variable selection methods susceptible to introduce bias and yield inadequate inferences. Many new confounder selection methods have been developed since then. Methods: The goal of the study was to provide an updated descriptive portrait of which variable selection methods are used by epidemiologists for analyzing observational data. Studies published in four major epidemiological journals in 2015 were reviewed. Only articles concerned with a predictive or explicative objective and reporting on the analysis of individual data were included. Method(s) employed for selecting variables were extracted from retained articles. Results : A total of 975 articles were retrieved and 299 met eligibility criteria, 292 of which pursued an explicative objective. Among those, 146 studies (50%) reported using prior knowledge or causal graphs for selecting variables, 34 (12%) used change in effect estimate methods, 26 (9%) used stepwise approaches, 16 (5%) employed univariate analyses, 5 (2%) used various other methods and 107 (37%) did not provide sufficient details to allow classification (more than one method could be employed in a single article). Conclusions : Despite being less frequent than in the previous review, stepwise and univariable analyses, which are susceptible to introduce bias and produce inadequate inferences, were still prevalent. Moreover, 37% studies did not provide sufficient details to assess how variables were selected. We thus believe there is still room for improvement in variable selection methods used by epidemiologists and in their reporting

An investigation of policy makers’ priorities for data and tools and their availability. Deliverable 1.4 of the EC FP7 project DaCoTA

An investigation of policy makers’ priorities for data and tools and their availability. Deliverable 1.4 of the EC FP7 project DaCoT

HPV vaccine knowledge and beliefs among Cambodian American parents and community leaders.

BACKGROUND: The cervical cancer incidence rate among Cambodian American women is 15.0 per 100,000, compared to 7.7 per 100,000 among non-Latina white women. HPV infection has been identified as a universal risk factor for cervical cancer. The HPV vaccine was recently approved in the United States for females aged 9-26 years. There is little information about HPV vaccination knowledge and beliefs in Southeast Asian communities. METHODS: We conducted 13 key informant interviews with Cambodian community leaders, as well as four focus groups with Cambodian parents (37 participants). Two of the focus groups included fathers and two of the focus groups included mothers. Interview and focus group questions addressed HPV vaccine barriers and facilitators. RESULTS: Participants had limited knowledge about HPV infection and the HPV vaccine. Barriers to HPV vaccination included a lack of information about the vaccine, as well as concerns about vaccine safety, effectiveness, and financial costs. The most important facilitators were a health care provider recommendation for vaccination and believing in the importance of disease prevention. DISCUSSION: Future cervical cancer control educational programs for Cambodians should promote use of the HPV vaccine for age-eligible individuals. Health care providers who serve Cambodian communities should be encouraged to recommend HPV vaccination

Hepatitis B knowledge and practices among Cambodian Americans.

Liver cancer occurs more frequently among Americans of Southeast Asian descent than any other group. This health disparity can be attributed to high rates of hepatitis B virus (HBV) infection. We examined HBV awareness, knowledge about HBV transmission, HBV testing levels, and HBV vaccination levels among Cambodian Americans

Factors associated with hepatitis B testing among cambodian american men and women.

Cambodian Americans have an elevated risk of liver cancer. This health disparity is attributable to high rates of hepatitis B virus (HBV) infection. Our study examined factors associated with HBV testing among Cambodian men and women. A population-based survey was conducted in the Seattle area. The Health Behavior Framework guided our survey instrument development. We attempted to interview a man and a woman in each household. The sample included 300 men and 367 women. About one-half of the male (45%) and female (54%) respondents had been tested for HBV. Two factors were independently associated with testing among men and women: a doctor had recommended testing and had asked a doctor for testing. Knowing that someone who looks and feels healthy can spread HBV was independently associated with testing among men. Low levels of HBV testing remain a public health problem among Cambodians. Interventions should improve patient-provider communication by encouraging providers who serve Cambodians to recommend HBV testing, as well as by empowering Cambodians to ask for testing

Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic

Oomycetes are heterotrophic protists that share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a separate and distant region of the eukaryotic tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls. This is a key trait in the pathology of many oomycetes, as the plant cell wall represents a primary barrier to pathogen invasion and a rich source of carbohydrates. Many of the HGT gene families identified have undergone multiple rounds of duplication. Using a combination of phylogenomic analysis and functional assays, we investigate the diversification of a horizontally-transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 genes retained in P. sojae among a complex pattern of gene duplications and losses. Using a phenotype assay, based on heterologous expression in yeast, we show that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional xyloglucanase variants analysed subtend an ancestral node close to the fungi-oomycetes gene transfer, suggesting the horizontally-transferred gene was a bona fide xyloglucanase. Expression of xyloglucanase paralogs in Nicotiana benthamiana triggers distinct patterns of reactive oxygen species (ROS) generation, demonstrating that enzyme variants differentially stimulate pattern-triggered immunity in plants. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze production of variant breakdown profiles, suggesting that secretion of multiple xyloglucanase variants increases efficiency of xyloglucan breakdown, as well as potentially diversifying the range of Damage-Associated Molecular Patterns (DAMPs) released during pathogen attack. We suggest that such patterns of protein neofunctionalization, and variant host responses, represent an aspect of the Red Queen host-pathogen co-evolutionary dynamic

Analysis of the stakeholder survey: perceived priority and availability of data and tools and relation to the stakeholders' characteristics. Deliverable 1.5 (Vol. 1) of the EC FP7 project DaCoTA

Analysis of the stakeholder survey: perceived priority and availability of data and tools and relation to the stakeholders' characteristics. Deliverable 1.5 (Vol. 1) of the EC FP7 project DaCoT

Evidence on the extent of harms experienced by children as a result of online risks: Implications for policy and research

This is an Accepted Manuscript of an article published by Taylor & Francis in Information, Communication and Society on 8/7/2014, available online: http://wwww.tandfonline.com/10.1080/1369118X.2014.934387Intense media and policy focus on issues of online child protection have prompted a resurgence of moral panics about children and adolescents' Internet use, with frequent confounding of different types of risk and harm and little reference to empirical evidence of actual harm. Meanwhile, within the academic literature, the quantity and quality of studies detailing the risks and opportunities of online activity for children and young people has risen substantially in the past 10 years, but this is also largely focused on risk rather than evidence of harm. Whilst this is understandable given the methodological and ethical challenges of studying Internet-related harms to minors, the very concept of risk is dependent on some prior understanding of harm, meaning that without efforts to study what harms are connected with children's online experiences, discussions of risk lack a strong foundation. This article makes a key contribution to the field by reviewing available evidence about the scale and scope of online harms from across a range of disciplines and identifying key obstacles in this research area as well as the major policy implications. The findings are based on a review of 148 empirical studies. Results were found in relation to main types of harms: health-related harms as a result of using pro-eating disorder, self-harm or pro-suicide websites; sex-related harms such as Internet-initiated sexual abuse of minors and cyber-bullying

Assessment of the healthy worker survivor effect in the relationship between psychosocial work-related factors and hypertension.

OBJECTIVES: The healthy worker survivor effect (HWSE) usually leads to underestimation of the effects of harmful occupational exposures. HWSE is characterised by the concomitance of three associations: (1) job status-subsequent exposure, (2) job status-disease and (3) previous exposure-job status. No study has reported the coexistence of these associations in the relationship between psychosocial work-related factors and health. We assessed if HWSE is present when measuring the effects of cumulative exposure to psychosocial work-related factors on the prevalence of hypertension in white-collar workers. METHODS: Data were obtained from two timepoints (1991-1993 at baseline and 1999-2001 at follow-up) of a prospective cohort study. At baseline, the population was composed of 9188 white-collar employees (women: 49.9%) in Quebec City. Job strain as psychosocial work-related factor and blood pressure were measured using validated methods. Job status (retirees vs employees) at follow-up was self-reported. Multiple multilevel robust Poisson regressions were used to estimate prevalence ratios of hypertension and risk ratios of retirement separately by gender. We performed multiple imputations to control selection bias due to missing values. RESULTS: Retirement eliminated the subsequent exposure to job strain de facto and was associated with the reduction in the prevalence of hypertension in younger (-33%) and older (-11%) men and in older women (-39%). Job strain was associated with job status in younger men and in women of any age. CONCLUSION: Data showed the presence of HWSE in younger men and older women given the coexistence of the three structural associations

Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic

Oomycete protists share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a distant region of the tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to- oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls, a barrier to pathogen invasion and a rich source of carbohydrates. Using a combination of phylogenomics and functional assays, we investigate the diversification of a horizontally transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 xyloglucanase paralogs retained in P. sojae. Using heterologous expression in yeast, we show consistent evidence that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional variants analyzed subtend a phylogenetic node close to the fungi-to- oomycete transfer, suggesting the horizontally transferred gene was a bona fide xyloglucanase. Expression of three xyloglucanase paralogs in Nicotiana benthamiana triggers high-reactive oxygen species (ROS) generation, while others inhibit ROS responses to bacterial immunogens, demonstrating that the paralogs differentially stimulate pattern-triggered immunity. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze the production of variant breakdown profiles, suggesting that secretion of variant xyloglucanases increases efficiency of xyloglucan breakdown as well as diversifying the damage-associated molecular patterns released. We suggest that this pattern of neofunctionalization and the variant host responses represent an aspect of the Red Queen host pathogen coevolutionary dynamic