Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments. In previous work, we presented a novel algorithm that allows the BWT of human genome scale data to be computed on very moderate hardware, thus enabling us to investigate the BWT as a tool for the compression of such datasets. Results We first used simulated reads to explore the relationship between the level of compression and the error rate, the length of the reads and the level of sampling of the underlying genome and compare choices of second-stage compression algorithm. We demonstrate that compression may be greatly improved by a particular reordering of the sequences in the collection and give a novel `implicit sorting' strategy that enables these benefits to be realised without the overhead of sorting the reads. With these techniques, a 45x coverage of real human genome sequence data compresses losslessly to under 0.5 bits per base, allowing the 135.3Gbp of sequence to fit into only 8.2Gbytes of space (trimming a small proportion of low-quality bases from the reads improves the compression still further). This is more than 4 times smaller than the size achieved by a standard BWT-based compressor (bzip2) on the untrimmed reads, but an important further advantage of our approach is that it facilitates the building of compressed full text indexes such as the FM-index on large-scale DNA sequence collections.Comment: Version here is as submitted to Bioinformatics and is same as the previously archived version. This submission registers the fact that the advanced access version is now available at http://bioinformatics.oxfordjournals.org/content/early/2012/05/02/bioinformatics.bts173.abstract . Bioinformatics should be considered as the original place of publication of this article, please cite accordingl

Precision determination of absolute neutron flux

A technique for establishing the total neutron rate of a highly-collimated monochromatic cold neutron beam was demonstrated using a method of an alpha-gamma counter. The method involves only the counting of measured rates and is independent of neutron cross sections, decay chain branching ratios, and neutron beam energy. For the measurement, a target of 10B-enriched boron carbide totally absorbed the neutrons in a monochromatic beam, and the rate of absorbed neutrons was determined by counting 478keV gamma rays from neutron capture on 10B with calibrated high-purity germanium detectors. A second measurement based on Bragg diffraction from a perfect silicon crystal was performed to determine the mean de Broglie wavelength of the beam to a precision of 0.024 %. With these measurements, the detection efficiency of a neutron monitor based on neutron absorption on 6Li was determined to an overall uncertainty of 0.058 %. We discuss the principle of the alpha-gamma method and present details of how the measurement was performed including the systematic effects. We also describe how this method may be used for applications in neutron dosimetry and metrology, fundamental neutron physics, and neutron cross section measurements.Comment: 44 page

Scapegoat: John Dewey and the character education crisis

Many conservatives, including some conservative scholars, blame the ideas and influence of John Dewey for what has frequently been called a crisis of character, a catastrophic decline in moral behavior in the schools and society of North America. Dewey’s critics claim that he is responsible for the undermining of the kinds of instruction that could lead to the development of character and the strengthening of the will, and that his educational philosophy and example exert a ubiquitous and disastrous influence on students’ conceptions of moral behavior. This article sets forth the views of some of these critics and juxtaposes them with what Dewey actually believed and wrote regarding character education. The juxtaposition demonstrates that Dewey neither called for nor exemplified the kinds of character-eroding pedagogy his critics accuse him of championing; in addition, this paper highlights the ways in which Dewey argued consistently and convincingly that the pedagogical approaches advocated by his critics are the real culprits in the decline of character and moral education

Deweyan tools for inquiry and the epistemological context of critical pedagogy

This article develops the notion of resistance as articulated in the literature of critical pedagogy as being both culturally sponsored and cognitively manifested. To do so, the authors draw upon John Dewey\u27s conception of tools for inquiry. Dewey provides a way to conceptualize student resistance not as a form of willful disputation, but instead as a function of socialization into cultural models of thought that actively truncate inquiry. In other words, resistance can be construed as the cognitive and emotive dimensions of the ongoing failure of institutions to provide ideas that help individuals both recognize social problems and imagine possible solutions. Focusing on Dewey\u27s epistemological framework, specifically tools for inquiry, provides a way to grasp this problem. It also affords some innovative solutions; for instance, it helps conceive of possible links between the regular curriculum and the study of specific social justice issues, a relationship that is often under-examined. The aims of critical pedagogy depend upon students developing dexterity with the conceptual tools they use to make meaning of the evidence they confront; these are background skills that the regular curriculum can be made to serve even outside social justice-focused curricula. Furthermore, the article concludes that because such inquiry involves the exploration and potential revision of students\u27 world-ordering beliefs, developing flexibility in how one thinks may be better achieved within academic subjects and topics that are not so intimately connected to students\u27 current social lives, especially where students may be directly implicated

Future Research Directions for Innovating Pedagogy

A series of reports on Innovating Pedagogy were launched in 2012 to look at the trends that show how practitioners may engage in innovation in pedagogy. This paper looks at the latest set of trends, and highlights four 2015 trends that seem particularly rich for researchers to explore in the next five years

Decentring emotion regulation: from emotion regulation to relational emotion

YesThis article takes a critical approach to emotion regulation suggesting that the concept needs supplementing with a relational position on the generation and restraint of emotion. I chart the relational approach to emotion, challenging the ‘two-step’ model of emotion regulation. From this, a more interdisciplinary approach to emotion is developed using concepts from social science to show the limits of instrumental, individualistic and cognitivist orientations in the psychology of emotion regulation, centred on appraisal theory. Using a social interactionist approach I develop an ontological position in which social relations form the fundamental contexts in which emotions are generated, toned, and restrained, so that regulation is decentred and seen as just one moment or aspect in the relational patterning of emotion

Social presence in the 21st Century: an adjustment to the Community of Inquiry framework

The Community of Inquiry framework, originally proposed by Garrison, Anderson and Archer (2000) identifies teaching, social and cognitive presences as central to a successful online educational experience. This article presents the findings of a study conducted in Uruguay between 2007 and 2010. The research aimed to establish the role of cognitive, social and teaching presences in the professional development of 40 English language teachers on Continuous Professional Development (CPD) programmes delivered in blended learning settings. The findings suggest that teaching presence and cognitive presence have themselves 'become social'. The research points to social presence as a major lever for engagement, sense-making and peer support. Based on the patterns identified in the study, this article puts forward an adjustment to the Community of Inquiry framework, which shows social presence as more prominent within the teaching and cognitive constructs than the original version of the framework suggests