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

Anomalous NMR response of quasicrystalline icosahedral A_{72.4}Pd_{20.5}Mn_{7.1} at low temperatures

We report the observation of an anomalous {27}Al-NMR response of a single grain Al_{72.4}Pd_{20.5}Mn_{7.1} icosahedral quasicrystal at low temperatures. In an external magnetic field of 6 T and upon decreasing temperature, we observe a sharp 100 % increase of the resonance linewidth at 2.5 K. No further changes of the linewidth are observed down to 0.05 K. The linewidth enhancement is accompanied by a small but distinct increase of the spin-lattice relaxation rate T_{1}^{-1} and by a maximum of the spin-spin relaxation time T_{2}(T). All these anomalies are absent in external fields of 2.5 T and below. Our observations indicate unusual variations in the stability of isolated magnetic moments in a quasiperiodic metallic environment.Comment: 5 pages, 5 figures, submitted to Phys. Rev B (Rapid Commun.

Bond Orientational Order, Molecular Motion and Free Energy of High Density DNA Mesophases

By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change between two distinct regions on the liquid crystalline phase digram: a higher-density hexagonally packed region with long-range bond orientational order in the plane perpendicular to the average molecular direction; and a lower-density cholesteric region with fluid-like positional order. X-rays scattering on highly ordered DNA arrays at high density and with the helical axis oriented parallel to the incoming beam showed a six-fold azimuthal modulation of the first order diffraction peak that reflects the macroscopic bond-orientational order. Transition to the less-dense cholesteric phase through osmotically controlled swelling shows the loss of this bond orientational order that had been expected from the change in optical birefringence patterns and that is consistent with a rapid onset of molecular positional disorder. This change in motion was previously inferred from intermolecular force measurements and is now confirmed by $\rm ^{31}P$ NMR. Controlled reversible swelling and compaction under osmotic stress, spanning a range of densities between $\sim 120$ mg/ml to $\sim 600$ mg/ml, allows measurement of the free energy changes throughout each phase and at the phase transition, essential information for theories of liquid-crystalline states.Comment: 14 pages, 3 figures in gif format available at http://abulafia.mgsl.dcrt.nih.gov/pics.html E-mail: [email protected]

Mach Cones and Hydrodynamic Flow: Probing Big Bang Matter in the Laboratory

A critical discussion of the present signals for the phase transition to quark-gluon plasma (QGP) is given. Since hadronic rescattering models predict much larger flow than observed from 1 to 50 A GeV laboratory bombarding energies, this observation is interpreted as potential evidence for a first-order phase transition at high baryon density. A detailed discussion of the collective flow as a barometer for the equation of state (EoS) of hot dense matter at RHIC follows. Here, hadronic rescattering models can explain < 30 % of the observed elliptic flow v_2 for $p_T > 2$ GeV/c. This is interpreted as an evidence for the production of superdense matter at RHIC. The connection of v_2 to jet suppression is examined. A study of Mach shocks generated by fast partonic jets propagating through the QGP is given. The main goal is to take into account different types of collective motion during the formation and evolution of this matter. A significant deformation of Mach shocks in central Au+Au collisions at RHIC and LHC energies as compared to the case of jet propagation in a static medium is predicted. A new hydrodynamical study of jet energy loss is presented.Comment: 18 pages, 12 figures, presented at the IWCF 2006, Nov. 21-24, Hangzhou, Chin

Coulomb Blockade in an Open Quantum Dot

We report the observation of Coulomb blockade in a quantum dot contacted by two quantum point contacts each with a single fully-transmitting mode, a system previously thought to be well described without invoking Coulomb interactions. At temperatures below 50 mK we observe a periodic oscillation in the conductance of the dot with gate voltage that corresponds to a residual quantization of charge. From the temperature and magnetic field dependence, we infer the oscillations are Mesoscopic Coulomb Blockade, a type of Coulomb blockade caused by electron interference in an otherwise open system.Comment: Text and supplementary information. Text: 4 pages, 4 figures. Supplementary information: 4 pages, 4 figure