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

Modelling the cAMP pathway using BioNessie, and the use of BVP techniques for solving ODEs (Poster Presentation)

Copyright @ 2007 Gu et al; licensee BioMed Central LtdBiochemists often conduct experiments in-vivo in order to explore observable behaviours and understand the dynamics of many intercellular and intracellular processes. However an intuitive understanding of their dynamics is hard to obtain because most pathways of interest involve components connected via interlocking loops. Formal methods for modelling and analysis of biochemical pathways are therefore indispensable. To this end, ODEs (ordinary differential equations) have been widely adopted as a method to model biochemical pathways because they have an unambiguous mathematical format and are amenable to rigorous quantitative analysis. BioNessie http://www.bionessie.com webcite is a workbench for the composition, simulation and analysis of biochemical networks which is being developed in by the Systems Biology team at the Bioinformatics Research Centre as a part of a large DTI funded project 'BPS: A Software Tool for the Simulation and Analysis of Biochemical Networks' http://www.brc.dcs.gla.ac.uk/projects/dti_beacon webcite. BioNessie is written in Java using NetBeans Platform libraries that makes it platform independent. The software employs specialised differential equations solvers for stiff and non-stiff systems to produce model simulation traces. BioNessie provides a user-friendly interfact that comes up with an intuitive tree-based graphical layout, an edition function to SBML-compatible models and feature of data output

Radiocarbon dates from the Oxford AMS system: archaeometry datelist 35

This is the 35th list of AMS radiocarbon determinations measured at the Oxford Radiocarbon Accelerator Unit (ORAU). Amongst some of the sites included here are the latest series of determinations from the key sites of Abydos, El Mirón, Ban Chiang, Grotte de Pigeons (Taforalt), Alepotrypa and Oberkassel, as well as others dating to the Palaeolithic, Mesolithic and later periods. Comments on the significance of the results are provided by the submitters of the material

Ranking the importance of nuclear reactions for activation and transmutation events

Pathways-reduced analysis is one of the techniques used by the Fispact-II nuclear activation and transmutation software to study the sensitivity of the computed inventories to uncertainties in reaction cross-sections. Although deciding which pathways are most important is very helpful in for example determining which nuclear data would benefit from further refinement, pathways-reduced analysis need not necessarily define the most critical reaction, since one reaction may contribute to several different pathways. This work examines three different techniques for ranking reactions in their order of importance in determining the final inventory, comparing the pathways based metric (PBM), the direct method and one based on the Pearson correlation coefficient. Reasons why the PBM is to be preferred are presented.Comment: 30 pages, 10 figure

Information mobility in complex networks

The concept of information mobility in complex networks is introduced on the basis of a stochastic process taking place in the network. The transition matrix for this process represents the probability that the information arising at a given node is transferred to a target one. We use the fractional powers of this transition matrix to investigate the stochastic process at fractional time intervals. The mobility coefficient is then introduced on the basis of the trace of these fractional powers of the stochastic matrix. The fractional time at which a network diffuses 50% of the information contained in its nodes (1/ k50 ) is also introduced. We then show that the scale-free random networks display better spread of information than the non scale-free ones. We study 38 real-world networks and analyze their performance in spreading information from their nodes. We find that some real-world networks perform even better than the scale-free networks with the same average degree and we point out some of the structural parameters that make this possible

Assessment of oxygen plasma ashing as a pre-treatment for radiocarbon dating

This study investigates the potential of low-temperature oxygen plasma ashing as a technique for decontaminating charcoal and wood samples prior to radiocarbon dating. Plasma ashing is demonstrated to be rapid, controllable and surface-specific, and clear differences are identified in the rate of ashing in different organic materials. However, the ability of plasma ashing to selectively remove these different components is limited in heterogeneous sample matrices. This is because oxidation is confined to the immediate sample surface. Comparison of radiocarbon dates obtained from identical aliquots of contaminated ancient charcoal pre-treated by acid-base-acid (ABA), acid-base-oxidation-stepped combustion (ABOx-SC) and plasma ashing suggests that the technique performs as well as the ABA pre-treatment but does not remove as much contamination as the ABOx-SC technique. Plasma-ashing may be particularly useful in cases where sample size is limiting

A depth camera-based system for estimating cyclist-bike projected frontal area

A major component of total resistive force in cycling is aerodynamic drag. For speeds greater than ~14 m/s aerodynamic drag accounts for approximately 90% of total resistive force (Debraux et al., 2009: International Journal of Sports Medicine, 30, 266-272). Together with the air density, the coefficient of drag and the velocity of the cyclist-bike, an important determinant of aerodynamic drag is projected frontal area. Several techniques have been used to estimate the projected frontal area of a cyclist-bike, including the weighing of photographs and image digitising (Debraux et al., 2009). These techniques are similar as they involve extracting the cyclist-bike from a two-dimensional (2D) image and using scaling information from a plane of known dimensions. With the weighing photographs method this is done physically using sensitive weighing scales whereas image processing software is used for the image digitising technique. Both techniques require the collection of a calibration plane, involve considerable post-processing and cannot be performed in real time. We have developed a depth camera-based system for estimating cyclist-bike projected frontal area which addresses these issues. The depth camera algorithm works by creating a metrically scaled, three-dimensional point cloud of the cyclist-bike. The point cloud is projected on to a 2D representation of the scene and the area of the point cloud is calculated using a technique similar to ‘voxelization’; points in the cloud occupy spaces in a fine grid – the sum of the occupied grid spaces gives total area. The aim of this study was to investigate the agreement between our new method and the image digitising technique.After institutional ethics approval, eight regular cyclists volunteered to participate and provided written informed consent. Participants wore their normal cycling clothing and their bicycle was mounted on a stationary indoor trainer. The bicycle was positioned against a white background to help with the image digitising method. Participants placed their feet on the pedals and held the cranks parallel to the floor. A digital camera (Canon EOS 400D, 10.1 megapixel) and Kinect depth camera (Microsoft, Redmond, WA, USA) were mounted on tripods at a height of 1.1 m and positioned 5 m and 2.2 m in front of the participant, respectively. Similar to Debraux et al. (2009), participants adopted two positions on the bike: 1. Upright – upright torso with hands close to the stem and 2. Drops Position – hands on the drops. Three repeat captures were performed in each position, with the participant relaxing between each capture. The digitising method was performed as described by Debraux et al. (2009). Agreement between methods was assessed using limits of agreement (LOA - Bland and Altman, 1986: Lancet, 1, 307-310). A two-way repeated measures analysis of variance (method by position) was used to assess the effect of cyclist position on the systematic difference between measurement methods.There was no interaction between cyclist position and measurement method (p = 0.201) indicating that the same effect of cyclist position was observed using both measurement techniques. A significant main effect for cyclist position (p = 0.017) indicated that projected frontal area was smaller with hands on the drops (upright: 0.485 m2, drops: 0.434 m2). There was also a significant main effect for measurement method (p < 0.001) indicating a significantly smaller estimation of projected frontal area using the Kinect (Kinect: 0.416 m2, Image: 0.503 m2). A predominantly systematic difference between methods was also suggested by the LOA analysis (upright: 0.086 ± 0.029 m2, drops: 0.090 ± 0.033 m2).The aim of this study was to assess the agreement between a common method of estimating cyclist-bike frontal area and a new depth camera-based technique. The new technique estimated systematically smaller projected frontal area than the image digitisation method but there was relatively little random variation and the same effect of cyclist position was observed with both techniques. Which technique gives the most accurate estimate of projected frontal area is not clear as the image digitisation technique - to which the new technique was compared - has associated errors e.g. identification of the cyclist-bike outline and out-of-plane errors. However, it was apparent during testing that the depth camera-based system often failed to identify parts of the bike and this is most likely the cause of the difference between techniques. Regardless, the results of this study suggest that the new technique can be used to assess changes in projected frontal area – as the cyclist changes position, for example. Further, the new technique offers the possibility of analysing changes in projected frontal area in real time – there is no requirement for calibration or post-processing

Eyes wide shut? UK consumer perceptions on aviation climate impacts and travel decisions to New Zealand

The purview of climate change concern has implicated air travel, as evidenced in a growing body of academic literature concerned with aviation CO2 emissions. This article assesses the relevance of climate change to long haul air travel decisions to New Zealand for United Kingdom consumers. Based on 15 semi-structured open-ended interviews conducted in Bournemouth, UK during June 2009, it was found that participants were unlikely to forgo potential travel decisions to New Zealand because of concern over air travel emissions. Underpinning the interviewees’ understandings and responses to air travel’s climate impact was a spectrum of awareness and attitudes to air travel and climate change. This spectrum ranged from individuals who were unaware of air travel’s climate impact to those who were beginning to consume air travel with a ‘carbon conscience’. Within this spectrum were some who were aware of the impact but not willing to change their travel behaviours at all. Rather than implicating long haul air travel, the empirical evidence instead exemplifies changing perceptions towards frequent short haul air travel and voices calls for both government and media in the UK to deliver more concrete messages on air travel’s climate impact