GeneRank: Using search engine technology for the analysis of microarray experiments

Copyright @ 2005 Morrison et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method – based on the PageRank algorithm employed by the popular search engine Google – that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information. Results: GeneRank is an intuitive modification of PageRank that maintains many of its mathematical properties. It combines gene expression information with a network structure derived from gene annotations (gene ontologies) or expression profile correlations. Using both simulated and real data we find that the algorithm offers an improved ranking of genes compared to pure expression change rankings. Conclusion: Our modification of the PageRank algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about the underlying network. GeneRank offers an improvement compared to assessing the importance of a gene based on its experimentally observed fold-change alone and may be used as a basis for further analytical developments

Delta method, an empirical drag buildup technique

An empirical drag correlation technique was developed from analysis of 19 subsonic and supersonic military aircraft and 15 advanced or supercritical airfoil configurations which can be applied in conceptual and advanced aircraft design activities. The Delta Method may be used for estimating the clean wing drag polar for cruise and maneuver conditions up to buffet onset, and to approximately Mach 2.0. This technique incorporates a unique capability of predicting the off-design performance of advanced or supercritical airfoil sections. The buffet onset limit may also be estimated. The method is applicable to wind tunnel models as well as to full scale configurations. This technique has been converted into a computer code for use on the IBM 360 and CDC 7600 computer facilities at NASA AMES. Results obtained using this method to predict known aircraft characteristics are good and agreement can be obtained within a degree of accuracy judged to be sufficient for the initial processes of preliminary design

Generalized poisson brackets and nonlinear Liapunov stability application to reduces mhd

A method is presented for obtaining Liapunov functionals (LF) and proving nonlinear stability. The method uses the generalized Poisson bracket (GPB) formulation of Hamiltonian dynamics. As an illustration, certain stationary solutions of ideal reduced MHD (RMHD) are shown to be nonlinearly stable. This includes Grad-Shafranov and Alfven solutions

Linguistic Reflection in Java

Reflective systems allow their own structures to be altered from within. Here we are concerned with a style of reflection, called linguistic reflection, which is the ability of a running program to generate new program fragments and to integrate these into its own execution. In particular we describe how this kind of reflection may be provided in the compiler-based, strongly typed object-oriented programming language Java. The advantages of the programming technique include attaining high levels of genericity and accommodating system evolution. These advantages are illustrated by an example taken from persistent programming which shows how linguistic reflection allows functionality (program code) to be generated on demand (Just-In-Time) from a generic specification and integrated into the evolving running program. The technique is evaluated against alternative implementation approaches with respect to efficiency, safety and ease of use.Comment: 25 pages. Source code for examples at http://www-ppg.dcs.st-and.ac.uk/Java/ReflectionExample/ Dynamic compilation package at http://www-ppg.dcs.st-and.ac.uk/Java/DynamicCompilation

Migration, ethnicity and solidarity: 'multinational workers' in the former Soviet Union

We investigate migrant construction workers’ experiences in the Former Soviet Union, examining their attitudes to other ethno-national groups, unions and collective action. Industrial relations and migration studies view migrant workers’ hypermobility and diversity, under conditions of low union coverage and rising nationalism, as potentially obstructing consciousness-raising and mobilizing. Workers in our study faced union indifference, ethno-national segregation and discrimination. However, managerial abuses, informality and contestation from below led to spontaneous mobilisation. Lack of institutional channels to solve these disputes drove workers’ further mobility. Complex mobility trajectories and collective action translated into increased awareness of collective interests and rejection of nationalist ideologies. The outcome is ‘multinational workers’ potentially resistant to nation-state politics and capital’s logics but also aware of the value and usefulness of collective solidarities. Thus, previous arguments solely associating exit with individualistic attitudes, and post-socialist legacies with workers’ quiescence present only partial pictures

Effective transport barriers in nontwist systems

In fluids and plasmas with zonal flow reversed shear, a peculiar kind of transport barrier appears in the shearless region, one that is associated with a proper route of transition to chaos. These barriers have been identified in symplectic nontwist maps that model such zonal flows. We use the so-called standard nontwist map, a paradigmatic example of nontwist systems, to analyze the parameter dependence of the transport through a broken shearless barrier. On varying a proper control parameter, we identify the onset of structures with high stickiness that give rise to an effective barrier near the broken shearless curve. Moreover, we show how these stickiness structures, and the concomitant transport reduction in the shearless region, are determined by a homoclinic tangle of the remaining dominant twin island chains. We use the finite-time rotation number, a recently proposed diagnostic, to identify transport barriers that separate different regions of stickiness. The identified barriers are comparable to those obtained by using finite-time Lyapunov exponents.FAPESPCNPqCAPESMCT/CNEN (Rede Nacional de Fusao)Fundacao AraucariaUS Department of Energy DE-FG05-80ET-53088Physic

Hamiltonian approach to hybrid plasma models

The Hamiltonian structures of several hybrid kinetic-fluid models are identified explicitly, upon considering collisionless Vlasov dynamics for the hot particles interacting with a bulk fluid. After presenting different pressure-coupling schemes for an ordinary fluid interacting with a hot gas, the paper extends the treatment to account for a fluid plasma interacting with an energetic ion species. Both current-coupling and pressure-coupling MHD schemes are treated extensively. In particular, pressure-coupling schemes are shown to require a transport-like term in the Vlasov kinetic equation, in order for the Hamiltonian structure to be preserved. The last part of the paper is devoted to studying the more general case of an energetic ion species interacting with a neutralizing electron background (hybrid Hall-MHD). Circulation laws and Casimir functionals are presented explicitly in each case.Comment: 27 pages, no figures. To appear in J. Phys.