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

Imagining the future of cell therapies: clinical trials, innovation and the intersection of clinical-academic and commercial visions

This paper examines the role of clinical trials in regenerative medicine innovation, exploring how trials have contributed to translational challenges in the field. Using data from an ethnographic study of UK cell therapy trials I interrogate the institutional framework for clinical trials and the identity-making of trialists. This analysis uncovers a disconnect between a commercially-aligned regulatory framework and a clinical-academic identity apparent in the majority of current trialling activity. These different pathways appear to represent two distinct sociotechnical imaginaries for cell therapies; one which reflects the assumptions of commercial innovation and prioritises economic success, and another which embodies the cultural expectations of academia and emphasises the importance of clinical care. These two imaginaries operate in synergy to some extent but there are significant tensions between them. How and to what extent these tensions are reconciled is likely to determine both the long-term success and the future shape of the field

Do free schools create “competitive threats”? The perceptions of neighbouring schools

A central policy claim for opening free schools in England was that these new schools would create competitive threats that incentivise nearby schools to improve. Where comparable policies have been pursued, notably charter schools in America, research has often measured competitive effects quantitatively. The perceptions of local actors assumed to experience competition can be overlooked. Responding, this article develops the first qualitative analysis of a sample of 28 schools neighbouring 14 free schools. The analysis evidences the importance of market contexts, with perceived competition mediated by supply and demand for places, choice geographies and school status hierarchies. Resulting diversity does not support simplistic assumptions nearby schools perceive competition or respond by seeking to improve. Just under half the schools studied perceived free schools created few competitive threats. Where competition was perceived, headteachers reported taking actions on promotion and national performance indicators, but rarely classroom practices. Where competition was strongest, headteachers reported intensive social selection, with free schools perceived to increase inequalities. The influence of school status on competitive logics of action was also revealed. Unequal material and symbolic resources afforded by status positioning informed headteachers’ perceptions of their relative capacity for effective action. Nine ideal types of logics of action are outlined, identifying how the context of competition and a school’s status influenced orientations to action. These logics are shown to be important in how intensive competition increased socio-economic inequalities by concentrating the negative effects of opening free schools, where these existed, in lower status schools serving more disadvantaged students

Developing responsible leadership through a 'pedagogy of challenge': An investigation into the impact of leadership education on teenagers

This paper proposes a new model for understanding education through ‘responsible leadership’ – a term which draws on the models of distributed and authentic leadership and on a dialogic understanding of responsible action. It defines ‘dispositions for learning’ as different forms of the single quality of ‘openness to learning’. A ‘pedagogy of challenge’ is proposed as a way of developing these dispositions. The model is tested through a small-scale investigation into the effect of a two-day leadership education course on five 14-year-old students which conforms to the proposed model. This suggests a link between the students' participation and their dispositions for learning; in addition, it suggests change in their attitude towards, and perceived performance in, their academic subjects over a four-month period. It also highlights potential conflicts between promoting responsible leadership and curricular, assessment-focused learning. Larger-scale studies are recommended

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

Dense packing crystal structures of physical tetrahedra

We present a method for discovering dense packings of general convex hard particles and apply it to study the dense packing behavior of a one-parameter family of particles with tetrahedral symmetry representing a deformation of the ideal mathematical tetrahedron into a less ideal, physical, tetrahedron and all the way to the sphere. Thus, we also connect the two well studied problems of sphere packing and tetrahedron packing on a single axis. Our numerical results uncover a rich optimal-packing behavior, compared to that of other continuous families of particles previously studied. We present four structures as candidates for the optimal packing at different values of the parameter, providing an atlas of crystal structures which might be observed in systems of nano-particles with tetrahedral symmetry

Early agriculture at the crossroads of China and Southeast Asia: Archaeobotanical evidence and radiocarbon dates from Baiyangcun, Yunnan

We report archaeobotanical results from systematic flotation at what is presently the earliest Neolithic site with hard evidence for crop cultivation in the Southwestern Chinese province of Yunnan, at the site of Baiyangcun. Direct AMS dates on rice and millet seeds, included together in a Bayesian model, suggests that sedentary agricultural occupation began ca. 2650 BCE, with cultivation of already domesticated rice (Oryza sativa), broomcorn millet (Panicum miliaceum), and foxtail millet (Setaria italica). Soybean (Glycine cf. max) was also present and presumably cultivated, although it still resembles its wild progenitor in terms of seed size. Additional possible cultivars include melon (Cucumis melo) and an unknown Vigna pulse, while wild gathered resources include fruits and nuts, including hawthorn (Crateagus) and aquatic foxnut (Euryale ferox). Weed flora suggests at least some rice was cultivated in wet (flooded or irrigated fields), while dryland weeds may derive from millet fields. This subsistence system persisted throughout the site's occupation, up to ca. 2050 BCE. These data provide secure evidence for the spread of Chinese Neolithic crops to Yunnan, and provide new evidence for reconstructing possible sources of cereal agriculture in mainland Southeast Asia

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