Does replication groups scoring reduce false positive rate in SNP interaction discovery?

BACKGROUNG. Computational methods that infer single nucleotide polymorphism (SNP) interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousands of SNPs but record only hundreds of samples. Candidate SNP pairs inferred by interaction analysis may include a high proportion of false positives. Recently, Gayan et al. (2008) proposed to reduce the number of false positives by combining results of interaction analysis performed on subsets of data (replication groups), rather than analyzing the entire data set directly. If performing as hypothesized, replication groups scoring could improve interaction analysis and also any type of feature ranking and selection procedure in systems biology. Because Gayan et al. do not compare their approach to the standard interaction analysis techniques, we here investigate if replication groups indeed reduce the number of reported false positive interactions. RESULTS. A set of simulated and false interaction-imputed experimental SNP data sets were used to compare the inference of SNP-SNP interactions by means of replication groups to the standard approach where the entire data set was directly used to score all candidate SNP pairs. In all our experiments, the inference of interactions from the entire data set (e.g. without using the replication groups) reported fewer false positives. CONCLUSIONS. With respect to the direct scoring approach the utility of replication groups does not reduce false positive rates, and may, depending on the data set, often perform worse

Nanoparticle ordering in sandwiched polymer brushes

The organization of nano-particles inside grafted polymer layers is governed by the interplay of polymer-induced entropic interactions and the action of externally applied fields. Earlier work had shown that strong external forces can drive the formation of colloidal structures in polymer brushes. Here we show that external fields are not essential to obtain such colloidal patterns: we report Monte Carlo and Molecular dynamics simulations that demonstrate that ordered structures can be achieved by compressing a `sandwich' of two grafted polymer layers, or by squeezing a coated nanotube, with nano-particles in between. We show that the pattern formation can be efficiently controlled by the applied pressure, while the characteristic length--scale, i.e. the typical width of the patterns, is sensitive to the length of the polymers. Based on the results of the simulations, we derive an approximate equation of state for nano-sandwiches.Comment: 18 pages, 4 figure

Groundwater Protection Legislation in Slovenia: Theory and Practice

As an EU member, Slovenia implemented the Water Framework Directive (WFD) guidelines into national legislation quite successfully, but in many parts of the country, groundwater is still under threat, mainly from nitrate. The problematic areas, as is the case in many other EU countries, are mostly shallow-soiled alluvial plains. Their groundwater is the country’s biggest source of drinking water, but at the same time, the fertile soil on their flat surface is considered to be the most suitable for agricultural activities. We are aiming to provide an overview of groundwater protection practices in Slovenia. To evaluate the “theory,” we will take a close look at the national legislation concerning the subject. From the “practical” perspective, we will research what guidelines and solutions were drawn from legislation to comply with WFD objectives. Furthermore, we will also discuss the current activities aimed at improving Slovenia’s groundwater status

Bonding interactions between ligand-decorated colloidal particles

<p>We study the interactions between particles that form reversible bonds. Theoretically, we find that the mean association constant between a pair of such particles can be well approximated by a double exponential function of the individual bond free energy when at least one of the following conditions holds: (i) when the individual bond strength is sufficiently weak and (ii) when the bond-forming ligands are randomly (Poisson) distributed among the particles in the system. In experiments with ligand-grafted colloidal particles, randomness in both the number of the ligands per colloid and the spatial distribution on the colloid is inherent to common fabrication techniques. We theoretically investigate the effect of quenched disordered ligand positions on interaction heterogeneity. Furthermore, we perform Monte Carlo simulations of colloidal particles decorated with mobile, quenched disordered, or uniformly distributed ligands to investigate the extent to which the mean association constant is a good approximation for the magnitude of the effective interactions in such systems, and to define the limits of applicability of the double exponential expression. We find that for large enough particles (100 nm–1 µm in diameter) at usual experimental parameters, the simple analytical expression provides a good description of the inter-particle interactions. The theory is finally extended beyond dimeric bonds to general multimeric complexes.</p