Maximal information component analysis: a novel non-linear network analysis method.

BackgroundNetwork construction and analysis algorithms provide scientists with the ability to sift through high-throughput biological outputs, such as transcription microarrays, for small groups of genes (modules) that are relevant for further research. Most of these algorithms ignore the important role of non-linear interactions in the data, and the ability for genes to operate in multiple functional groups at once, despite clear evidence for both of these phenomena in observed biological systems.ResultsWe have created a novel co-expression network analysis algorithm that incorporates both of these principles by combining the information-theoretic association measure of the maximal information coefficient (MIC) with an Interaction Component Model. We evaluate the performance of this approach on two datasets collected from a large panel of mice, one from macrophages and the other from liver by comparing the two measures based on a measure of module entropy, Gene Ontology (GO) enrichment, and scale-free topology (SFT) fit. Our algorithm outperforms a widely used co-expression analysis method, weighted gene co-expression network analysis (WGCNA), in the macrophage data, while returning comparable results in the liver dataset when using these criteria. We demonstrate that the macrophage data has more non-linear interactions than the liver dataset, which may explain the increased performance of our method, termed Maximal Information Component Analysis (MICA) in that case.ConclusionsIn making our network algorithm more accurately reflect known biological principles, we are able to generate modules with improved relevance, particularly in networks with confounding factors such as gene by environment interactions

Tuning Interparticle Hydrogen Bonding in Shear-Jamming Suspensions: Kinetic Effects and Consequences for Tribology and Rheology

The shear-jamming of dense suspensions can be strongly affected by molecular-scale interactions between particles, e.g. by chemically controlling their propensity for hydrogen bonding. However, hydrogen bonding not only enhances interparticle friction, a critical parameter for shear jamming, but also introduces (reversible) adhesion, whose interplay with friction in shear-jamming systems has so far remained unclear. Here, we present atomic force microscopy studies to assess interparticle adhesion, its relationship to friction, and how these attributes are influenced by urea, a molecule that interferes with hydrogen bonding. We characterize the kinetics of this process with nuclear magnetic resonance, relating it to the time dependence of the macroscopic flow behavior with rheological measurements. We find that time-dependent urea sorption reduces friction and adhesion, causing a shift in the shear-jamming onset. These results extend our mechanistic understanding of chemical effects on the nature of shear jamming, promising new avenues for fundamental studies and applications alike

Quantification of the Individual Characteristics of the Human Dentition

The considerations for admissibility suggested by the Daubert trilogy challenge forensic experts to provide scientific support for opinion testimony. The defense bar has questioned the reliability of bitemark analysis. Under an award from the U. S. Department of Justice, via the Midwest Forensic Resource Center, a two-year feasibility study was undertaken to quantify six dental characteristics. Using two computer programs, the exemplars of 419 volunteers were digitally scanned, characteristics were measured, and frequency was calculated. The study demonstrates that there were outliers or rare dental characteristics in measurements. An analysis of the intra-observer and inter-observer consistency demonstrated a high degree of agreement. Expansion of the sample size through collaboration with other academic researchers will be necessary to be able to quantify the occurrence of these characteristics in the general population. The automated software application, Tom\u27s Toolbox, developed specifically for this research project, could also provide a template for precisely quantifying other pattern evidence

Manufacture of Regularly Shaped Sol-Gel Pellets

An extrusion batch process for manufacturing regularly shaped sol-gel pellets has been devised as an improved alternative to a spray process that yields irregularly shaped pellets. The aspect ratio of regularly shaped pellets can be controlled more easily, while regularly shaped pellets pack more efficiently. In the extrusion process, a wet gel is pushed out of a mold and chopped repetitively into short, cylindrical pieces as it emerges from the mold. The pieces are collected and can be either (1) dried at ambient pressure to xerogel, (2) solvent exchanged and dried under ambient pressure to ambigels, or (3) supercritically dried to aerogel. Advantageously, the extruded pellets can be dropped directly in a cross-linking bath, where they develop a conformal polymer coating around the skeletal framework of the wet gel via reaction with the cross linker. These pellets can be dried to mechanically robust X-Aerogel

Discrimination of prostate cancer cells and non-malignant cells using secondary ion mass spectrometry

This communication utilises Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) combined with multivariate analysis to obtain spectra from the surfaces of three closely related cell lines allowing their discrimination based upon mass spectral ions

of Airport Landing Slots

Abstract: We investigate the competitive effects of exchanges or sales of airport landing slots. In our model, airlines with potentially asymmetric slot allocations must decide upon which routes to use their landing slots. When all airlines serve the same routes in a slot-constrained Cournot-Nash equilibrium, small changes in slot allocations among airlines do not affect the overall allocation of slots across routes or air fares. In a symmetric equilibrium where slot-holding airlines have the same number of slots, we find that an increase in the number of slot-holding airlines leads to higher social welfare and consumer surplus, although the number of served routes may decline. Under asymmetric slot allocations, larger slot holders serve “thin” demand routes that are not served by smaller slot holders. In this situation, transfers of slots from larger to smaller slot holders increase social welfare and consumer surplus, even though fewer routes may be served. More generally, our results suggest that increases in slot concentration are harmful to consumers and social welfare, although consumers on relatively thin routes may gain air transportation service as a result.