5,960 research outputs found

    PASQUAL: Parallel Techniques for Next Generation Genome Sequence Assembly

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    Understanding sorting algorithms using music and spatial distribution

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    This thesis is concerned with the communication of information using auditory techniques. In particular, a music-based interface has been used to communicate the operation of a number of sorting algorithms to users. This auditory interface has been further enhanced by the creation of an auditory scene including a sound wall, which enables the auditory interface to utilise music parameters in conjunction with 2D/3D spatial distribution to communicate the essential processes in the algorithms. The sound wall has been constructed from a grid of measurements using a human head to create a spatial distribution. The algorithm designer can therefore communicate events using pitch, rhythm and timbre and associate these with particular positions in space. A number of experiments have been carried out to investigate the usefulness of music and the sound wall in communicating information relevant to the algorithms. Further, user understanding of the six algorithms has been tested. In all experiments the effects of previous musical experience has been allowed for. The results show that users can utilise musical parameters in understanding algorithms and that in all cases improvements have been observed using the sound wall. Different user performance was observed with different algorithms and it is concluded that certain types of information lend themselves more readily to communication through auditory interfaces than others. As a result of the experimental analysis, recommendations are given on how to improve the sound wall and user understanding by improved choice of the musical mappings

    The Role of Preconceived Ideas in Macroeconomic Policy: Japan's Experiences in Two Deflationary Periods

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    This paper examines the role of misleading economic ideas that most likely promoted the economic disasters of the two deflationary periods in Japanese economic history. Misleading ideas deepened the depression during the interwar years, and erroneous thinking has prolonged the stagnation of the Japanese economy since the 1990s. While the current framework of political economy is based on the self-interest of political agents as well as of voters, we highlight the role of ideas in policy making, in particular, in the field of macro-economy where the incidence of a particular policy is not clear to the public. Using two significant examples, this paper illustrates the role of preconceived ideas, in contrast to economic interests, as dominant forces influencing economic policy making.

    How Not to Attack an Economist (and an Economy): Getting the Numbers Right

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    This paper continues a debate over the extent of economic and social progress in Venezuela that began with an article in the March/April 2008 issue of Foreign Affairs. This article argued that “a close look at the evidence reveals just how much Chávez's 'revolution' has hurt Venezuela's economy -- and that the poor are hurting most of all.” CEPR responded with “An Empty Research Agenda: The Creation of Myths About Contemporary Venezuela,” showing that the main allegations of the article were wrong. The author of the Foreign Affairs article, economist Francisco Rodriguez, then responded with an Economics Working Paper at Wesleyan University, which defended his original analysis. The current paper demonstrates that Rodriguez's assertions in his response are almost all without merit. His argument that inequality has increased during the Chávez years is contradicted by the best available data (in fact these data show a reduction in inequality). His claim that the amount of poverty reduction in Venezuela during the last four years, relative to its economic growth, compares unfavorably to other countries is clearly wrong; in fact, Venezuela's poverty reduction has been much better than the vast majority of countries for the amount of growth that it has had. His argument that the Chávez government did not demonstrate any change of priorities with regard to public spending is wrong and misleading and his assertion that Venezuela's literacy program has not had any distinguishable effect on literacy cannot be demonstrated from the data that he uses.Chavez, Venezuela, poverty

    Large Genomes Assembly Using MAPREDUCE Framework

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    Knowing the genome sequence of an organism is the essential step toward understanding its genomic and genetic characteristics. Currently, whole genome shotgun (WGS) sequencing is the most widely used genome sequencing technique to determine the entire DNA sequence of an organism. Recent advances in next-generation sequencing (NGS) techniques have enabled biologists to generate large DNA sequences in a high-throughput and low-cost way. However, the assembly of NGS reads faces significant challenges due to short reads and an enormously high volume of data. Despite recent progress in genome assembly, current NGS assemblers cannot generate high-quality results or efficiently handle large genomes with billions of reads. In this research, we proposed a new Genome Assembler based on MapReduce (GAMR), which tackles both limitations. GAMR is based on a bi-directed de Bruijn graph and implemented using the MapReduce framework. We designed a distributed algorithm for each step in GAMR, making it scalable in assembling large-scale genomes. We also proposed novel gap-filling algorithms to improve assembly results to achieve higher accuracy and more extended continuity. We evaluated the assembly performance of GAMR using benchmark data and compared it against other NGS assemblers. We also demonstrated the scalability of GAMR by using it to assemble loblolly pine (~22Gbp). The results showed that GAMR finished the assembly much faster and with a much lower requirement of computing resources

    The Unbearable Lightness of the Economics-Made-Fun Genre

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    Several commentators have argued that the Economics-Made-Fun (“EMF”) genre contains very little actual economics. As such, it would seem that criticisms of EMF do not apply economics more broadly. In this paper I take a contrary view, arguing that, in fact, at a deep conceptual level, the engine of EMF analyses is precisely the engine of mainstream economics. Specifically, I argue that both EMF and mainstream economics rest on a conceptual foundation known as the Principal of the Substitution of Similars (“PSS”). Understanding how PSS leads EMF practitioners to make claims well beyond what is warranted by their analysis also offers insight into how PSS leaves mainstream economists in danger of overestimating the power and scope of their analyses. I explore the consequences of such problems through an example of economic analysis of the U.S. housing market in the lead-up to the recent financial crisis.Methodology, Popular Economics, William Stanley Jevons, Ontology, Anthropology of Finance

    Fidelity versus Vanguard: Comparing the Performance of the Two Largest Mutual Fund Families

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    This paper compares the risk and return of investing in equity mutual funds provided by the world's two largest mutual fund families: Fidelity and Vanguard over a long horizon. We believe this will help guide investors; this study is an example of the calculations that mutual fund companies should facilitate by being required to provide accurate, accessible and free data. Over the entire period 1977 through 2003 both Fidelity's (no load) and Vanguard's diversified U.S. funds out returned the Wilshire 5000 index; Fidelity's portfolio out returned Vanguard's portfolio by 0.62 % per year but under returned it by 0.39 % when risk adjusted.

    Financialisation and Capitalist Accumulation : Structural Accounts of the Crisis of 2007-9

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    The crisis of 2007-9 resulted from a financial bubble marked by weak production, expanding bank assets, and growing household indebtedness. For these reasons the crisis casts light on the financialisation of capitalist economies. The literature on financialisation generally links weak production with booming finance; according to some, causation runs from weak production to booming finance, while for others it runs in the opposite direction. This article argues that there is no direct causation between booming finance and weak production. Rather, financialisation represents systemic transformation of capitalist production and finance, which ultimately accounts for the crisis of 2007-9, and has three main features. First, less reliance of large corporations on banks; second, banks shifting their activities toward mediating in open markets and transacting with individuals; third, increasing implication of individuals in the operations of finance.

    A new algorithm for de novo genome assembly

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    The enormous amount of short reads produced by next generation sequencing (NGS) techniques such as Roche/454, Illumina/Solexa and SOLiD sequencing opened the possibility of de novo genome assembly. Some of the de novo genome assemblers (e.g., Edena, SGA) use an overlap graph approach to assemble a genome, while others (e.g., ABySS and SOAPdenovo) use a de Bruijn graph approach. Currently, the approaches based on the de Bruijn graph are the most successful, yet their performance is far from being able to assemble entire genomic sequences. We developed a new overlap graph based genome assembler called Paired-End Genome ASsembly Using Short-sequences (PEGASUS) for paired-end short reads produced by NGS techniques. PEGASUS uses a minimum cost network flow approach to predict the copy count of the input reads more precisely than other algorithms. With the help of accurate copy count and mate pair support, PEGASUS can accurately unscramble the paths in the overlap graph that correspond to DNA sequences. PEGASUS exhibits comparable and in many cases better performance than the leading genome assemblers

    The Case for an Intermediate Exchange Rate Regime with Endogenizing Market Structures and Capital Mobility

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    Set in the context of the recent theoretical and policy debates on appropriate exchange rate regimes for emerging market economies in a world of free capital mobility, the paper attempts to present the case for an intermediate exchange rate regime, drawing on recent theoretical and empirical literatures on behavioural finance and currency market structures; and to examine empirically the experiences and evolution of Brazil.s foreign exchange market under different exchange rate regimes.exchange rate management, emerging markets, Brazil
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