Fusing Data Mining,Machine Learning and Traditional Statistics to Detect Biomarkers Associated with Depression

Background

Atheoretical large-scale data mining techniques using machine learning algorithms have promise in the analysis of large epidemiological datasets. This study illustrates the use of a hybrid methodology for variable selection that took account of missing data and complex survey design to identify key biomarkers associated with depression from a large epidemiological study.

Methods

The study used a three-step methodology amalgamating multiple imputation, a machine learning boosted regression algorithm and logistic regression, to identify key biomarkers associated with depression in the National Health and Nutrition Examination Study (2009–2010). Depression was measured using the Patient Health Questionnaire-9 and 67 biomarkers were analysed. Covariates in this study included gender, age, race, smoking, food security, Poverty Income Ratio, Body Mass Index, physical activity, alcohol use, medical conditions and medications. The final imputed weighted multiple logistic regression model included possible confounders and moderators.

Results

After the creation of 20 imputation data sets from multiple chained regression sequences, machine learning boosted regression initially identified 21 biomarkers associated with depression. Using traditional logistic regression methods, including controlling for possible confounders and moderators, a final set of three biomarkers were selected. The final three biomarkers from the novel hybrid variable selection methodology were red cell distribution width (OR 1.15; 95% CI 1.01, 1.30), serum glucose (OR 1.01; 95% CI 1.00, 1.01) and total bilirubin (OR 0.12; 95% CI 0.05, 0.28). Significant interactions were found between total bilirubin with Mexican American/Hispanic group (p = 0.016), and current smokers (p<0.001).

Conclusion

The systematic use of a hybrid methodology for variable selection, fusing data mining techniques using a machine learning algorithm with traditional statistical modelling, accounted for missing data and complex survey sampling methodology and was demonstrated to be a useful tool for detecting three biomarkers associated with depression for future hypothesis generation: red cell distribution width, serum glucose and total bilirubin.     

Resource conflicts and the anthropology of the dark and the good in highlands Papua New Guinea

In this article I consider why individuals sacrifice their lives for the collective. In the Porgera Valley of highlands Papua New Guinea, young men who are called ‘Rambos’ engage in sustained tribal conflicts due to increasing social inequalities in an area that is supposedly benefiting from socioeconomic development. The opening of the Porgera Gold Mine in 1990 ushered in an era of anticipated benefits that were hoped to transform the lives of the region's subsistence horticulturalists. Yet, anticipated flows of mining money and social benefits have largely failed to materialise. The abjection experienced by young men eventuated into a series of tribal fights, resulting in deaths, displacements, and the destruction of most infrastructure. I examine the fighting and its aftermath in relation to anthropologies of the dark and the good and argue that these polar opposites can hinder more subtle understandings of value plurality among Porgerans.     

Infectious disease screening of blood specimens collected post-mortem provides comparable results to pre-mortem specimens

Serology assays for standard screening are optimised for use with sera collected from living adults and children. Because of potential changes in the vascular compartments after death, methods used for screening sera from cadaveric organ donors need to be validated before testing these specimens. Serum was separated from blood collected from cadaveric donors within 24?h of death and biochemical parameters measured to detect dilution of protein and haemolysis. In order to demonstrate if any inhibitors that might interfere with the assays were present, pre and post-mortem specimens were spiked with aliquots of human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), human T-cell Lymphotropic Virus (HTLV) and T. pallidum-positive sera. Comparison of serum from living subjects with serum obtained post-mortem showed that while the concentration of total protein decreased, concentrations of albumin, immunoglobulin G (IgG) and immunoglobulin M (IgM) remained unchanged. The degree of haemolysis, as measured by free haemoglobin, was within the limits accepted for the Architect analyser. Spiking of pre- and post-mortem specimens with aliquots of HIV, HCV, HBV, HTLV and T. pallidum-positive sera showed no statistical difference in the signal between pre-mortem and post-mortem results when tested on the Abbott Architect analyser. Positive results were obtained in each of a further nine subjects who had tested positive for HIV (n?=?1), HCV (n?=?8), HBV (n?=?1) on pre-mortem serological testing. These findings suggest that the sensitivity of the Abbott Architect serological screening tests is not significantly affected in specimens collected within 24?h of the cessation of life.     

Dietary Patterns and Depressive Symptoms over Time: Examining the Relationships with Socioeconomic Position,Health Behaviours and Cardiovascular Risk

Introduction

Recent research suggests that diet quality influences depression risk; however, a lack of experimental evidence leaves open the possibility that residual confounding explains the observed relationships. The aim of this study was to document the cross-sectional and longitudinal associations between dietary patterns and symptoms of depression and to undertake a detailed examination of potential explanatory factors, particularly socioeconomic circumstances, in the diet-depression relationship.

Methods

Data were drawn from the Personality and Total Health (PATH) Through Life Study, a longitudinal community study following three age cohorts (20+; 40+; 60+yrs) from south-eastern Australia over three assessment periods (n = 3663). Regression analyses evaluated the cross-sectional and longitudinal relationships between dietary patterns, depressive symptoms, age, detailed measures of socioeconomic circumstances, other health behaviours, and cardiovascular risk factors.

Results

The lowest tertile of prudent (healthy) dietary pattern and the highest tertile of western (unhealthy) dietary pattern were associated with an increased likelihood of depressive symptoms. However, these contemporaneous associations were explained by adjustment for detailed measures of socioeconomic circumstances and physical activity. In prospective analyses, lower scores on the healthy dietary pattern and higher scores on the unhealthy dietary pattern independently predicted increased depressive symptoms across time, before and after adjustment for potential confounders and baseline depressive symptoms, but only for those in the oldest cohort. Dietary patterns did not explain the relationship between socioeconomic position and depressive symptoms.

Conclusion

The results of this study confirm that the relationship between habitual dietary intake and depressive symptoms is somewhat explained by socioeconomic circumstances and other health behaviours, but suggest that long term exposure to unhealthy dietary habits independently predisposes to depression over the lifecourse.     

A prospective study of diet quality and mental health in adolescents

Objectives

A number of cross-sectional and prospective studies have now been published demonstrating inverse relationships between diet quality and the common mental disorders in adults. However, there are no existing prospective studies of this association in adolescents, the onset period of most disorders, limiting inferences regarding possible causal relationships.

Methods

In this study, 3040 Australian adolescents, aged 11–18 years at baseline, were measured in 2005–6 and 2007–8. Information on diet and mental health was collected by self-report and anthropometric data by trained researchers.

Results

There were cross-sectional, dose response relationships identified between measures of both healthy (positive) and unhealthy (inverse) diets and scores on the emotional subscale of the Pediatric Quality of Life Inventory (PedsQL), where higher scores mean better mental health, before and after adjustments for age, gender, socio-economic status, dieting behaviours, body mass index and physical activity. Higher healthy diet scores at baseline also predicted higher PedsQL scores at follow-up, while higher unhealthy diet scores at baseline predicted lower PedsQL scores at follow-up. Improvements in diet quality were mirrored by improvements in mental health over the follow-up period, while deteriorating diet quality was associated with poorer psychological functioning. Finally, results did not support the reverse causality hypothesis.

Conclusion

This study highlights the importance of diet in adolescence and its potential role in modifying mental health over the life course. Given that the majority of common mental health problems first manifest in adolescence, intervention studies are now required to test the effectiveness of preventing the common mental disorders through dietary modification.     

Copper salicylate as an anti-inflammatory and analgesic agent in arthritic rats

Recent research indicates that endogenous copper is involved in anti-inflammatory and tissue repair processes. Of interest also is the analgesic efficacy of Cu complexes, since rheumatoid arthritis and similar inflammatory conditions are extremely painful. In pilot experiments, arthritic rats failed to increase voluntarily their rate of drinking a 5 mg/ml solution of copper salicylate (Cu Sal). The data from the experiment reported here showed that a forced oral dose of Cu Sal calculated at 200 mg/kg body weight significantly reduced sensitivity to mechanical pressure in less than 30 minutes but more than 15 minutes. The analgesic effect of the Cu Sal was greater for arthritic than for non-arthritic rats, suggesting that two types of analgesia are involved. First, it produces a direct analgesic effect which works irrespective of the presence of inflammation. Second, it appears to have an indirect analgesic effect due to reduction of inflammatory hyperalgesia. It was also found that Cu Sal administered orally reduces inflammation in rats with adjuvant arthritis. In summary, the results from this experiment demonstrate that Cu Sal has specific and general analgesic properties and anti-inflammatory potential.     

Nutritional psychiatry research: an emerging discipline and its intersection with global urbanization,environmental challenges and the evolutionary mismatch

In 21st-century public health, rapid urbanization and mental health disorders are a growing global concern. The relationship between diet, brain function and the risk of mental disorders has been the subject of intense research in recent years. In this review, we examine some of the potential socioeconomic and environmental challenges detracting from the traditional dietary patterns that might otherwise support positive mental health. In the context of urban expansion, climate change, cultural and technological changes and the global industrialization and ultraprocessing of food, findings related to nutrition and mental health are connected to some of the most pressing issues of our time. The research is also of relevance to matters of biophysiological anthropology. We explore some aspects of a potential evolutionary mismatch between our ancestral past (Paleolithic, Neolithic) and the contemporary nutritional environment. Changes related to dietary acid load, advanced glycation end products and microbiota (via dietary choices and cooking practices) may be of relevance to depression, anxiety and other mental disorders. In particular, the results of emerging studies demonstrate the importance of prenatal and early childhood dietary practices within the developmental origins of health and disease concept. There is still much work to be done before these population studies and their mirrored advances in bench research can provide translation to clinical medicine and public health policy. However, the clear message is that in the midst of a looming global epidemic, we ignore nutrition at our peril.