Read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molec- ular biology, allowing routine clinical sequencing. NGS data consists of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans, with some strains exhibiting antibiotic resistance. Here we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from other pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

See to believe : the Center for Tactical Magic’s sleight of hand

The Bay Area’s Center for Tactical Magic has been performing ‘‘magical’’ art interventions since 2000. The Center’s work augments traditional activist techniques by offering new conceptions of what art and activism can entail in a contemporary urban context. This article explores how Jacques Rancie`re’s reconfigured relationship between art and politics can be applied to the Center’s work, providing new distributions of the sensible for participants.

Sustainable innovation for Queensland’s housing design : a case study

This research provides an assessment tool that assists the selection process of sustainability in detached suburban housing. It investigates the implications of using different design and construction methods including architecturally designed houses, developer housing and prefabricated houses. The study simulates one example of the three types of houses that have been chosen to fulfil a real client brief on a real site on the Sunshine Coast, Queensland Australia. Criteria for sustainability assessment are formulated based on literature reviews, exemplar designs and similar research projects for which the houses can be adequately evaluated. This criterion covers aspects including energy use, materials and thermal performance. The data is collected using computer models and sustainability assessment software to compare and draw conclusions on the success of each house. Our study indicates that architecturally designed housing with prefabricated building techniques are a better alternative to generic developer style housing. Our research provides an insight into the implications of three key elements of sustainability including energy use, materials and thermal performance. Designers, builders, developers and home-buyers are given an insight into some options currently available on the housing market and how the choices made during early design stages can provide a more positive environmental impact.

Who killed fair use? A copyright murder mystery down under

Fair Use Week has been celebrated this week in the United States, with great gusto and enthusiasm. At Harvard Library, Kyle Courtney commented: ‘Fair use is critical and important to innovation, scholarship and research in the United States.’ Kenneth Crews emphasized that ‘the new technological ventures, like other creative pursuits, require fair use and other copyright limitations for experimentation and success.’ Legal director Corynne McSherry of the Electronic Frontier Foundation has highlighted the significance and the importance of the defence of fair use: ‘Fair use provides breathing space in copyright law, making sure that control of the right to copy and distribute doesn’t become control of the right to create and innovate.’ For Techdirt, Mike Masnick has emphasized that fair use is a right – and not an exception or a mere defence. Peter Jaszi and Pat Aufderheide have highlighted the contextual operation of fair use in particular artistic communities. Molly Van Houweling of the Authors Alliance has written about the ecstasy of influence – the role of inspiration and appropriation in all acts of artistic creation. Fair use has been celebrated as a many-splendored legal creation.

School group class portrait including Susan (Susi) Ehrlich; Ulm Portraits; Groups

(l-r): Ruth Altman, Irene Hirsch, Hilde Dannhauser, Suse Barth, Anneliese Hirsch, Suse Saenger, Esther Nathan, Hannelore Baer, Heinz Koerner, Ruth Bauland, Marianne Leiter, Heinz Krippel, Hanna Ullmann, Edith Weil, Otto Eckstein, Susi Ehrlich, Hans Klein, Julie Klappholz, Hanna Chose, Minna Hirsch and Rudolf Loewy

Structure-function analysis of the inverted terminal repeats of the Sleeping Beauty transposon

Translocation of Sleeping Beauty (SB) transposon requires specific binding of SB transposase to inverted terminal repeats (ITRs) of about 230 bp at each end of the transposon, which is followed by a cut-and-paste transfer of the transposon into a target DNA sequence. The ITRs contain two imperfect direct repeats (DRs) of about 32 bp. The outer DRs are at the extreme ends of the transposon whereas the inner DRs are located inside the transposon, 165-166 bp from the outer DRs. Here we investigated the roles of the DR elements in transposition. Although there is a core transposase-binding sequence common to all of the DRs, additional adjacent sequences are required for transposition and these sequences vary in the different DRs. As a result, SB transposase binds less tightly to the outer DRs than to the inner DRs. Two DRs are required in each ITR for transposition but they are not interchangeable for efficient transposition. Each DR appears to have a distinctive role in transposition. The spacing and sequence between the DR elements in an ITR affect transposition rates, suggesting a constrained geometry is involved in the interactions of SB transposase molecules in order to achieve precise mobilization. Transposons are flanked by TA dinucleotide base-pairs that are important for excision; elimination of the TA motif on one side of the transposon significantly reduces transposition while loss of TAs on both flanks of the transposon abolishes transposition. These findings have led to the construction of a more advanced transposon that should be useful in gene transfer and insertional mutagenesis in vertebrates. (C) 2002 Elsevier Science Ltd. All rights reserved.

Relation of the work of the artist Antonio Lopez with the photography. Methods of a teacher rejected as a professor

In 1966 the artist Antonio Lopez was rejected for the chair in “Preparatorio de colorido” (Preparatory Colouring) by the San Fernando School of Fine Arts where he himself presented his work Nevera de hielo (Ice Box). After 5 years as a “stand in” for this post he left the Institution. This article analyzes the circumstances and proof of a decade where there appears to be evidence of a definite change in his work, more toward Realism, uncomfortable in a system that maintained with difficulty the traditional academic model copy, and incompatible with, in those years was imposed by Spain. At the same time his relation with photography conditioned by the theoretical thoughts of the artist, and his work methods also are analyzed in this article.

Influence of the type of coarse lightweight aggregate on properties of Semi-Lightweight Self-Consolidating Concrete

This paper presents studies on the properties of fresh and hardened semilightweight self-consolidating concrete (SLWSCC) mixtures, produced with two types of manufactured coarse lightweight aggregates (LWA) and normal weight sand. The first type, a sintered pulverized fuel ash, was made from an industrial by-product, fly ash, whereas the second one, an expanded clay, was produced from a naturally sourced clay. For all mixtures, normal weight sand was used as a fine fraction of aggregates, and the portland cement was partially replaced with a limestone powder. The SLWSCC was produced with different water presaturation regimes of the LWAs. The desired initial slump-flow spread was set between 700 and 800 mm. The effect of three superplasticizers was evaluated by testing properties of SLWSCC, normal weight SCC, and paste mixtures. Three SCC fresh properties were measured: the slump-flow, the V-funnel flow time, and the J-ring blocking step. Moreover, the slump-flow loss was evaluated. The degree of segregation was assessed in both fresh and hardened states. Additionally, the hardened density and the compressive strengths were tested. All SLWSCC mixtures were produced with a desired range of slump-flow spread and with satisfactory passing ability assessed with the J-ring test. SLWSCCs prepared with the expanded clay LWA were less sensitive to the variation of water presaturation levels and showed lower viscosity than those made with the sintered pulverized fuel ash LWA. Only mixtures containing SP-3 superplasticizer showed acceptable workability loss resistance. The saturated surface-dry density of all of the mixtures varied in a range of 2,025–2,125??kg/m 3 . Mixtures containing 29% of coarse LWAs and 71% of sand (by mass) had 24-h and 28-day compressive strengths above 20 and 40 MPa, respectively, but the mixtures made with the expanded clay were slightly weaker.

Variabilidade dos limites de estabilidade na posição ortostática em utentes com Acidente Vascular Encefálico

Introdução: O controlo postural (CP), intimamente ligado aos limites de estabilidade, é fundamental nas atividades da vida diária e encontra-se comprometido após Acidente Vascular Encefálico (AVE). Objectivo: Descrever as alterações nos limites de estabilidade, na posição ortostática, em utentes com AVE, face à aplicação de um programa de intervenção baseado num processo de raciocínio clínico. Métodos: Estudo de série de casos, de três indivíduos com alterações do CP do tronco e/ou das grandes articulações, decorrentes de AVE, mas capazes de assumir e manter a posição ortostática. Para avaliar os limites de estabilidade foram utilizados a plataforma de pressões Emed (coordenadas do centro de pressão, COPx e COPy) e o MultidirectionalReachTest (MDRT). Foram também aplicadas, a Fugl-Meyer Assessmentof Sensoriomotor Recovery After Stroke (FMA) e a Berg Balance Scale (BBS). Os instrumentos de avaliação foram aplicados antes e após a intervenção (M0 e M1), de 8 semanas, baseada nos princípios do conceito de Bobath. Resultados: Os valores dos testes de alcance no MDRT aumentaram em todos os utentes. Os limites e os deslocamentos médio-lateral (COPx) e, ântero-posterior (COPy) dos valores do CPr aumentaram, entre M0 e M1. No que se refere à FMA e a BBS, verificou-se que todos apresentaram um aumento dos scores. Conclusão: Os utentes modificaram os seus limites de estabilidade no sentido do aumento, assim como, da função motora e do equilíbrio. Deste modo, a intervenção de acordo com os princípios do conceito de Bobath aparenta introduzir os estímulos necessários à reorganização funcional do sistema nervoso central lesado.

Dependência entre a performance de baterias VRLA e as características físico-químicas da matéria activa positiva

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Química e Biológica

Remistura de vídeo: um estudo exploratório de diferentes estilos

Dissertação apresentada à Escola Superior de Comunicação Social como parte dos requisitos para obtenção de grau de mestre em Audiovisual e Multimédia.

Utilidad de los conceptos y estrategias comunitarias en el marketing online para la prevención de la copia ilegal en el mercado musical

Esta investigación se dirige a determinar cuál es la utilidad de los conceptos y estrategias comunitarias en el marketing online para la prevención de la copia ilegal en el mercado musical. Con este proyecto se desea que por medio de una nueva disquera enfocada en el comercio online, y usando los conceptos del mercadeo comunitario y el mercadeo relacional, se pueda desarrollar nuevas estrategias de mercadeo en donde se logre incentivar y promover la compra de música original por medio de la creación de una relación más estrecha entre la compañía y el cliente, en la cual pueda afectar de forma positiva a la comunidad a la que este pertenece. El objetivo general es determinar cuál es la utilidad de los conceptos y estrategias comunitarias en el marketing online para la prevención de la copia ilegal en el mercado musical. Los objetivos específicos son: 1. Mostrar la utilidad de los conceptos y estrategias del marketing comunitario en la prevención de la copia ilegal del mercado musical y 2. Implementar las estrategias logradas en la investigación en un plan de creación de empresa. Se utilizará el método de investigación y análisis de caso, utilizando el plan de empresa en la creación de una empresa del mercado musical, tomando la relación estratégica comunitaria y el marketing dentro del plan de mercadeo como estrategia para la prevención de la copia ilegal. Mediante este proyecto se desea que por medio del marketing relacional y de los conceptos del mercadeo hacia comunidades, enfocado en une- marketing sepuedanestablecerestrategiasparalaprevencióndelacopiailegalydelacomprade estos productos Además, se busca implementar dichos resultados en la empresa que se pretende crear en el sector de la industria musical, puesto que la seguridad que tendrán los productos a la venta, serán la ventaja competitiva de la empresa.

A maize bacterial artificial chromosome (BAC) library from the European flint inbred line F2

We report here the construction and characterisation of a BAC library from the maize flint inbred line F2, widely used in European maize breeding programs. The library contains 86,858 clones with an average insert size of approximately 90 kb, giving approximately 3.2-times genome coverage. High-efficiency BAC cloning was achieved through the use of a single size selection for the high-molecular-weight genomic DNA, and co-transformation of the ligation with yeast tRNA to optimise transformation efficiency. Characterisation of the library showed that less than 0.5% of the clones contained no inserts, while 5.52% of clones consisted of chloroplast DNA. The library was gridded onto 29 nylon filters in a double-spotted 8 × 8 array, and screened by hybridisation with a number of single-copy and gene-family probes. A 3-dimensional DNA pooling scheme was used to allow rapid PCR screening of the library based on primer pairs from simple sequence repeat (SSR) and expressed sequence tag (EST) markers. Positive clones were obtained in all hybridisation and PCR screens carried out so far. Six BAC clones, which hybridised to a portion of the cloned Rp1-D rust resistance gene, were further characterised and found to form contigs covering most of this complex resistance locus.

Layout och typografi i vetenskapliga artiklar : En kartläggning av konventioner gällande grafisk formgivning inom matematik, medicin och utbildningsvetenskap

En deskriptiv visuell innehållsanalys genomfördes med en korpus bestående av vetenskapliga artiklar från 30 topprankade tidskrifter jämnt fördelade på de tre disciplinerna matematik, medicin och utbildningsvetenskap, med syfte att undersöka om det fanns ett samband mellan tidskrifternas disciplintillhörighet och den grafiska formgivningen. Kartläggningen omfattade layout (bl.a. sidformat, spalter, marginalstorlek, användning av grafiska element, placering av tabeller, figurer och pagina) och typografiskt utseende hos titel, rubriker, brödtext och abstrakt (t.ex. teckenstorlek, textjustering, teckengrovlek, typsnitt, färg och radavstånd). Resultaten visar att disciplinerna använde olika men även gemensamma konventioner i sitt grafiska utseende. Matematik uppvisade enkelspaltig layout med liten typografisk variation, genomgående användning av typsnitt från familjen Transitional eller Transitional/Didone för hela dokumentet, avsaknad av kulört färg och sällan användning av grafiska element. Medicin uppvisade större variation med användning av kulört färg, icke-centrerad typografi med både sansseriff- och seriff-typsnitt, grafiska element och ramar som förstärker det ofta använda dubbelspaltiga gridsystemet. Utbildningsvetenskap uppvisade en grafisk design som återfanns i båda disciplinerna, men påminde mest om matematik till utseendet. Kodbok ingår i sin helhet som bilaga. Uppsatsen i sig är delvis formgiven med utgångspunkt i de erhållna resultaten.