Neural networks for modeling gene-gene interactions in association studies

<p>Abstract</p> <p>Background</p> <p>Our aim is to investigate the ability of neural networks to model different two-locus disease models. We conduct a simulation study to compare neural networks with two standard methods, namely logistic regression models and multifactor dimensionality reduction. One hundred data sets are generated for each of six two-locus disease models, which are considered in a low and in a high risk scenario. Two models represent independence, one is a multiplicative model, and three models are epistatic. For each data set, six neural networks (with up to five hidden neurons) and five logistic regression models (the null model, three main effect models, and the full model) with two different codings for the genotype information are fitted. Additionally, the multifactor dimensionality reduction approach is applied.</p> <p>Results</p> <p>The results show that neural networks are more successful in modeling the structure of the underlying disease model than logistic regression models in most of the investigated situations. In our simulation study, neither logistic regression nor multifactor dimensionality reduction are able to correctly identify biological interaction.</p> <p>Conclusions</p> <p>Neural networks are a promising tool to handle complex data situations. However, further research is necessary concerning the interpretation of their parameters.</p

Growth of nanostructures by cluster deposition : a review

This paper presents a comprehensive analysis of simple models useful to analyze the growth of nanostructures obtained by cluster deposition. After detailing the potential interest of nanostructures, I extensively study the first stages of growth (the submonolayer regime) by kinetic Monte-Carlo simulations. These simulations are performed in a wide variety of experimental situations : complete condensation, growth with reevaporation, nucleation on defects, total or null cluster-cluster coalescence... The main scope of the paper is to help experimentalists analyzing their data to deduce which of those processes are important and to quantify them. A software including all these simulation programs is available at no cost on request to the author. I carefully discuss experiments of growth from cluster beams and show how the mobility of the clusters on the surface can be measured : surprisingly high values are found. An important issue for future technological applications of cluster deposition is the relation between the size of the incident clusters and the size of the islands obtained on the substrate. An approximate formula which gives the ratio of the two sizes as a function of the melting temperature of the material deposited is given. Finally, I study the atomic mechanisms which can explain the diffusion of the clusters on a substrate and the result of their mutual interaction (simple juxtaposition, partial or total coalescence...)Comment: To be published Rev Mod Phys, Oct 99, RevTeX, 37 figure

Association of dietary patterns and type-2 diabetes mellitus in metabolically homogeneous subgroups in the KORA FF4 study.

There is evidence that a change in lifestyle, especially physical activity and diet, can reduce the risk of developing type-2 diabetes mellitus (T2DM). However, the response to dietary changes varies among individuals due to differences in metabolic characteristics. Therefore, we investigated the association between dietary patterns and T2DM while taking into account these differences. For 1287 participants of the population-based KORA FF4 study (Cooperative Health Research in the Region of Augsburg), we identified three metabolically-homogenous subgroups (metabotypes) using 16 clinical markers. Based on usual dietary intake data, two diet quality scores, the Mediterranean Diet Score (MDS) and the Alternate Healthy Eating Index (AHEI), were calculated. We explored the associations between T2DM and diet quality scores. Multi-variable adjusted models, including metabotype subgroup, were fitted. In addition, analyses stratified by metabotype were carried out. We found significant interaction effects between metabotype and both diet quality scores (p&lt; 0.05). In the analysis stratified by metabotype, significant negative associations between T2DM and both diet quality scores were detected only in the metabolically-unfavorable homogenous subgroup (Odds Ratio (OR) = 0.62, 95% confidence interval (CI) = 0.39-0.90 for AHEI and OR = 0.60, 95% CI = 0.40-0.96 for MDS). Prospective studies taking metabotype into account are needed to confirm our results, which allow for the tailoring of dietary recommendations in the prevention of T2DM

Differential associations between diet and prediabetes or diabetes in the KORA FF4 study.

Type 2 diabetes mellitus (T2DM) is a global public health epidemic. Diet and lifestyle changes have been demonstrated as effective measures in managing T2DM and preventing or delaying the progression from prediabetes to diabetes, yet the relationship between diet, prediabetes and diabetes is still not entirely clear. The present study aimed to further elucidate the relationship between diet, diabetes and especially prediabetes. A total of 1542 participants of the cross-sectional, population-based Cooperative Health Research in the Region of Augsburg (KORA) FF4 study (2013/2014) were included in this analysis. Dietary intake was derived using a method combining information from a FFQ and repeated 24-h food lists. Glucose tolerance status was assessed via oral glucose tolerance tests in all participants without a previous physician-confirmed diagnosis of T2DM, and was classified according to the 2003 American Diabetes Association criteria. Crude and fully adjusted multinomial logistic regression models were fitted to examine associations between diet and prediabetes, undetected diabetes mellitus (UDM) and prevalent T2DM. After adjusting for major covariates, fruit was significantly inversely and total meat, processed meat, sugar-sweetened beverages and moderate alcohol significantly associated with UDM and/or prevalent diabetes. Sex-specific analyses showed that in men, coffee was significantly inversely (OR 0&middot;80; 95&nbsp;% CI 0&middot;67, 0&middot;96) and heavy alcohol significantly (OR 1&middot;84; 95&nbsp;% CI 1&middot;14, 2&middot;95) associated with prediabetes. Our findings on diet and T2DM are consistent with current literature, while our results regarding coffee, heavy alcohol consumption and prediabetes highlight new possible targets for primary prevention of the derangement of glucose homeostasis

Evaluation of the metabotype concept identified in an Irish population in the German KORA cohort study.

Scope: Previous work identified three metabolically homogeneous subgroups of individuals (“metabotypes”) using k-means cluster analysis based on fasting serum levels of triacylglycerol, total cholesterol, HDL cholesterol, and glucose. The aim is to reproduce these findings and describe metabotype groups by dietary habits and by incident disease occurrence. Methods and results: 1744 participants from the KORA F4 study and 2221 participants from the KORA FF4 study are assigned to the three metabotype clusters previously identified by minimizing the Euclidean distances. In both KORA studies, the assignment of participants results in three metabolically distinct clusters, with cluster 3 representing the group of participants with the most unfavorable metabolic characteristics. Individuals of cluster 3 are further characterized by the highest incident disease occurrence during follow-up; they also reveal the most unfavorable diet with significantly lowest intakes of vegetables, dairy products, and fibers, and highest intakes of total, red, and processed meat. Conclusion: The three metabotypes originally identified in an Irish population are successfully reproduced. In addition to this validation approach, the observed differences in disease incidence across metabotypes represent an important new finding that strongly supports the metabotyping approach as a tool for risk stratification

Plasma concentrations of anserine, carnosine and pi-methylhistidine as biomarkers of habitual meat consumption

BACKGROUND/OBJECTIVES Dietary intake of red and processed meat has been associated with disease risk. Since dietary intake assessment methods are prone to measurement errors, identifying biomarkers of meat intake in bio-samples could provide more valid intake estimates. We examined associations of habitual red and processed meat, poultry, fish, and dairy products consumption with plasma concentrations of anserine, carnosine, pi-methylhistidine (Π-MH), tau-methylhistidine (T-MH), and the ratio of T-MH to Π-MH in a cross-sectional study. SUBJECTS/METHODS Plasma anserine, carnosine, Π-MH, and T-MH concentrations were measured using ion-pair LC-MS/MS in 294 participants in the second Bavarian Food Consumption Survey (BVS II). Habitual food consumption was assessed using three 24-h dietary recalls. Associations between plasma metabolites concentrations and meat, fish, eggs, and dairy products consumption were assessed by fitting generalized linear model, adjusted for age, sex, and BMI. RESULTS Total meat intake was associated with plasma concentrations of anserine, carnosine, Π-MH and, the ratio of T-MH to Π-MH. Red meat intake was related to carnosine (p-trend = 0.0028) and Π-MH plasma levels (p-trend = 0.0493). Poultry (p-trend = 0.0006) and chicken (p-trend = 0.0003) intake were associated with Π-MH. The highest anserine concentrations were observed in individuals consuming processed meat or turkey. For T-MH we did not observe any association with meat intake. CONCLUSIONS Our results indicate an association between habitual meat consumption and plasma concentrations of anserine, carnosine, Π-MH and the ratio of T-MH to Π-MH. Intervention studies should clarify whether the analyzed plasma metabolites are indicative for a specific type of meat before proposing them as biomarkers of habitual meat intake in epidemiologic studies