Responsible research and innovation: a global perspective

Based on the paper presented at the Doctorate Conference on Technologogy Assessment in July 2013 at the University Nova Lisboa, Caparica campus

Responsible research and innovation: a global perspective

Based on the paper presented at the Doctorate Conference on Technologogy Assessment in July 2013 at the University Nova Lisboa, Caparica campus

An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

Triticales y tricepiros: alternativas para la produccion de pasto y grano. Forage and grain breeding of triticale and tricepiro.

La introducción de nuevos recursos genéticos es esencial en la evolución de la agricultura destinada a la producción de materia prima de alta calidad. La evaluación de nuevo germoplasma, con el objetivo de su difusión comercial o incorporación a programas de mejoramiento, se realiza a través de ensayos comparativos de rendimiento en diferentes ambientes. Las forrajeras anuales de invierno son casi insustituibles para mantener la cadena forrajera en la región pampeana subhúmeda seca y semiárida. En la actualidad tanto triticales como tricepiros son alternativas muy promisorias para su utilización como doble propósito, así como para explorar la posibilidad de producir harinas diferenciadas para uso en la industria de la alimentación humana. En el país, los triticales se han difundido para pastoreo y se requiere de nuevos cultivares. Los tricepiros se trabajan exclusivamente en la Argentina y es necesario desarrollar germoplasma. Se planea identificar germoplasma superior mediante selección en introducciones y cruzamientos propios, ensayos comparativos de pasto y grano, estudiar la estabilidad citológica mediante análisis cromosómicos y genómicos y caracterizar líneas avanzadas por descriptores morfológicos.The introduction of new genetic resources is essential in the agriculture evolution, especially when high quality production is the main objective. New germoplasm must be tested several years in order to be part of breeding programs or to be commercialized due to environmental differences among years. In dry subhumid and semiarid pampeana region, annual winter feed crops are necessary in order to have forage production during winter. Nowadays Triticales and Tricepiros are promising alternatives to be used as double purpose for animal feed and fodder, as well as to obtain differenced flour to human food. In Argentina, Triticale has spread for forage uses and new cultivars are required. Tricepiros are sown only in this country; therefore there is a need to develop Tricepiro germoplasm. The outline includes: identify superior germoplasm in introductions and own crosses through selection; establish comparative forage and grain trials; cytological estability study using chromosomal and genomic analysis and characterize advanced lines through morphological features.

In search of a language textile and text in contemporary women's art

This research uses the textile/text axis concept as a conceptual tool to investigate the role of textile and text in contemporary women’s art practice and theorizing, investigating textile as a largely hitherto unacknowledged element in women’s art practice of the late 20th and early 21st centuries. Textile and text share a common etymological root, from the Latin textere to weave, textus a fabric. The thesis illuminates the pathways whereby textile and text played an important role in women reclaiming a speaking voice as creators of culture and signification during a revolutionary period of renewal in women’s cultural contribution and positioning. The methodological approach used in the research consisted of a comprehensive literature review, the compilation of an inventory of relevant women artists, developing a classificatory system differentiating types of approaches, concerns and concepts underpinning women’s art practice vis a vis the textile/text axis and a series of three in-depth case studies of artists Tracey Emin, Louise Bourgeois and Faith Ringgold. The thesis points to the fact that contemporary women artists and theorists have rounded their art practice and aesthetic discourse in textile as prime visual metaphor and signifier, turning towards the ancient language of textile not merely to reclaim a speaking voice but to occupy a ground breaking locus of signification and representation in contemporary culture. The textile/text axis facilitated women artists in powerfully countering a culturally inscribed status of Lacanian ‘no-woman’ (a position of abjection, absence and lack in the phallocentric symbolic). Turning towards a language of aeons, textile as fertile wellspring, the thesis identifies the methodologies and strategies whereby women artists have inserted their webs of subjectivities and deepest concerns into the records and discourses of contemporary culture. Presenting an anatomy of the textile/text axis, the thesis identifies nine component elements manifesting in contemporary women’s aesthetic practice and discourse. In this cultural renaissance, the textile/text axis, the thesis suggests, served as a complex lexicon, a system of labyrinthine references and signification, a site of layered meanings and ambiguities, a body proxy and a corporeal cartography, facilitating a revolution in women’s aesthetic praxis.

An analysis of the use of photogrammetric sorting to audit construction and demolition waste production on site

This study analyses the area of construction and demolition waste (C & D W) auditing. The production of C&DW has grown year after year since the Environmental Protection Agency (EPA) first published a report in 1996 which provided data for C&D W quantities for 1995 (EPA, 1996a). The most recent report produced by the EPA is based on data for 2005 (EPA, 2006). This report estimated that the quantity of C&DW produced for that period to be 14 931 486 tonnes. However, this is a ‘data update’ report containing an update on certain waste statistics so any total provided would not be a true reflection of the waste produced for that period. This illustrates that a more construction site-specific form of data is required. The Department of Building and Civil Engineering in the Galway-Mayo Institute of Technology have carried out two recent research projects (Grimes, 2005; Kelly, 2006) in this area, which have produced waste production indicators based on site-specific data. This involved the design and testing of an original auditing tool based on visual characterisation and the application of conversion factors. One of the main recommendations of these studies was to compare this visual characterisation approach with a photogrammetric sorting methodology. This study investigates the application of photogrammetric sorting on a residential construction site in the Galway region. A visual characterisation study is also carried out on the same project to compare the two methodologies and assess the practical application in a construction site environment. Data collected from the waste management contractor on site was also used to provide further evaluation. From this, a set of waste production indicators for new residential construction was produced: □ 50.8 kg/m2 for new residential construction using data provided by the visual characterisation method and the Landfill Levy conversion factors. □ 43 kg/m2 for new residential construction using data provided by the photogrammetric sorting method and the Landfill Levy conversion factors. □ 23.8 kg/m2 for new residential construction using data provided by Waste Management Contractor (WMC). The acquisition of the data from the waste management contractor was a key element for testing of the information produced by the visual characterisation and photogrammetric sorting methods. The actual weight provided by the waste management contractor shows a significant difference between the quantities provided.

Skull morphometrics of adult male Antartic fur seal, Arctocephalus gazella, and South American fur seal A. australis

The skull morphometrics of adult male Antarctic fur seal, Arctocephalus gazella (Peters, 1875) and South American fur seal, A. australis (Zimmermann, 1783) were investigated using a collection of 45 and 38 skulls, respectively. Eighteen measurements were taken for each specimen. Comparative univariate and multivariate statistical analyses included standard statistics, one-way analysis of variance, principal component analysis and discriminant analysis. Individual variation was relatively high for some variables, as expressed by the coefficient of variation. Skulls of A. gazella were larger than those of A. australis for all but two variables: squamosal jugal suture and rostral length. Both species differed significantly as shown by both univariate and multivariate analyses. The discriminant function correctly classified all specimens. The standardized canonical coefficients showed that the variables which most contribute to the differentiation between species were, in decreasing order, the rostral length, palatal length, palatal width at postcanine 5 and braincase width. The present study corroborates that A. gazella and A. australis are phenotipically distinct species.

A morphological, isoenzymatic and behavioural study of ten populations of Anopheles(Nyssorhynchus) albitarsis Lynch-Arribalzaga, 1878 (Diptera: culicidae) including from the type-locality - Baradero, Argentina

Anopheles (Nyssorhynchus) albitarsis Lynch-Arribalzaga, 1878 shows morphological and behavioural variations which results in it being sometimes considered as a major malaria vector and at other times as playing no important role in epidemiology. With the aim of clarifying the taxonomy of the species, comparative morphological and isoenzymatic studies were made in populations from the type-locality, Baradero, Argentina and from 9 different localities inBrazil. Morphological studies consisted of the observation of eggs in scanning electron microscopy, of complete chaetotaxy of larvae and pupae and of the detailed drawing of male and female adults. Only Guajara-Mirim and Rio Branco populations, described previously as Anopheles deaneorum sp.n., showed morphological differences. Isoenzymes were studied using 4th instar larvae homogenate and agarosegel electrophoresis. Eleven enzymatic loci were analyzed. By calculation of Nei's Genetic Distance (D), the populations could be separated into 5 groups: i)Baradero, ii)Marajo, iii)Boa Vista, iv)Angra, Itaguai and Paraipaba and v)Guajara-Mirim and Rio Branco. These groups belong to 2 major clusters called I and II, separated by D = 0.345. In the I cluster are groups i, ii and iii and in II clusteriv and v. In I, D=0.246 separates i and ii from iii, while i is separated by D =0.181 from ii. In II, D = 0.223 between iv and v. Only the population of group vcould be distinguished morphologically from the others, leading to the description of an independent species An. deaneorum.

Rapid bacterial genome sequencing: methods and applications in clinical microbiology.

The recent advances in sequencing technologies have given all microbiology laboratories access to whole genome sequencing. Providing that tools for the automated analysis of sequence data and databases for associated meta-data are developed, whole genome sequencing will become a routine tool for large clinical microbiology laboratories. Indeed, the continuing reduction in sequencing costs and the shortening of the 'time to result' makes it an attractive strategy in both research and diagnostics. Here, we review how high-throughput sequencing is revolutionizing clinical microbiology and the promise that it still holds. We discuss major applications, which include: (i) identification of target DNA sequences and antigens to rapidly develop diagnostic tools; (ii) precise strain identification for epidemiological typing and pathogen monitoring during outbreaks; and (iii) investigation of strain properties, such as the presence of antibiotic resistance or virulence factors. In addition, recent developments in comparative metagenomics and single-cell sequencing offer the prospect of a better understanding of complex microbial communities at the global and individual levels, providing a new perspective for understanding host-pathogen interactions. Being a high-resolution tool, high-throughput sequencing will increasingly influence diagnostics, epidemiology, risk management, and patient care.

Aspects of immunity for the AMA-1 family of molecules in humans and non-human primates malarias

The apical membrane antigen (AMA-1) family of malaria merozoite proteins is characterised by a high degree of inter-species conservation. Evidence that the protein (PK66/AMA-1) from the simian parasite Plasmodium knowlesi was protective in rhesus monkeys suggested that the 83kDa P. falciparum equivalent (PF83/AMA-1) should be investigated for protective effects in humans. Here we briefly review pertinent comparative data, and describe the use of an eukaryotic full length recombinant PF83/AMA-1 molecule to develop a sensitive ELISA for the determination of serological responses in endemic populations. The assay has revealed surprisingly high levels of humoral response to this quantitatively minor antigen. We also show that PK66/AMA-1 inhibitory mAb's are active against merozoites subsequent to release from schizont-infected red cells, further implicating AMA-1 molecules in red cell invasion.

Law and the practise of principle in diverse societies

Projecte de recerca elaborat a partir d’una estada a la London School of Economics and Political Science, United Kingdom, entre 2007 i 2009. L’objecte principal del projecte ha estat analitzar les implicacions jurídico-polítiques i institucionals d’una teoria de la justícia i la igualtat liberals aplicada a societats multiculturals amb un marcat predomini de la diversitat cultural. L’anàlisi desenvolupa una línia d'investigació interdisciplinar - entre el dret i la teoria política - iniciada en una tesis doctoral sobre multiculturalisme i drets de les minories culturals (UPF, 2000) que va culminar en la publicació de Group Rights as Human Rights (Springer, 2006). La recerca adopta com a punt de partida les conclusions de l'esmentada obra, en especial, la rellevància del reconeixement de drets col•lectius; tanmateix, el tipus de qüestions plantejades, l’enfoc i la metodologia emprades són substancialment diferents. En concret, s'adrecen preguntes específiques sobre el model i aspiracions del constitucionalisme democràtic i el paper del dret en contextos multiculturals. També s’atorga un pes central a la dimensió institucional dels models de gestió de la diversitat que s’analitzen, prioritzant un enfocament comparatiu a partir de l’estudi de controvèrsies concretes. L’objectiu és superar algunes limitacions importants de la literatura actual, com ara la tendència a examinar en abstracte la compatibilitat de determinades demandes amb el constitucionalisme democràtic, sense abordar el funcionament d'estratègies de gestió de la diversitat cultural emprades en contextos concrets. Els treballs producte d'aquest projecte articulen les línies bàsiques d’un model pluralista, basat en principis més que en regles, que desafia els plantejaments dominants actualment. Aquest model es caracteritza pel compromís amb la legitimitat i igualtat comparatives, rebutjant el paternalisme i les visions liberals típiques sobre el paper de la regulació. La presumpció de l’“standing” moral dels grups identitaris és fonamental per tal de considerar-los interlocutors vàlids amb interessos genuïns. També s’argumenta que la integració social en contextos multiculturals no depèn tant de l’eliminació del conflicte sinó, sobre tot, d’una gestió eficient que eviti abusos de poder sistemàtics. El model defensa el rol del dret en la institucionalització del diàleg intercultural, però admet que el diàleg no necessàriament condueix a l’acord o a una estructura reguladora coherent i uniforme. Les aspiracions del ordre jurídic pluralista són més modestes: afavorir la negociació i resolució en cada conflicte, malgrat la persistència de la fragmentació i la provisionalitat dels acords. La manca d'un marc regulador comú esdevé una virtut en la mesura que permet la interacció de diferents subordres; una interacció governada per una multiplicitat de regles no necessàriament harmòniques. Els avantatges i problemes d’aquest model s'analitzen a partir de l'anàlisi de l’estructura fragmentària de l'ordre jurídic internacional i del règim Europeu de drets humans.

Susceptibility of Colombian Plasmodium falciparum isolates to 4-aminoquinolines and the definition of amodiaquine resistance in vitro

There are wide variations in the threshold used to define in vitro resistance of Plasmodium falciparum to amodiaquine (AQ), probably due to differences in methodology and interpretation. In vitro susceptibility data of Colombian P. falciparum strains to AQ and N-desethylamodiaquine is used to illustrate the need to standardized methodologies and compare inhibitory concentrations, instead of resistant/susceptible phenotypes, when studying the mechanisms of resistance to AQ and monitoring drug susceptibility trends in the field.

Religious identity and intercultural dialogue

(Résumé de l'ouvrage) In a world society ruled by economic globalisation, by political interests and theories such as Huntington's «clash of civilisations» that widen the gap between the North and the South, the question should be asked of the role of the religion. To what extent religion and politics can work together? Can faith still be thought as a means of saving the world? Considering that Christianity, Islam and Judaism have much in common, this collection of miscellanies wonders if these religions can join their forces for public benefit. Senior and junior scholars from all over the world, gathered for an interdisciplinary seminar, analyse the contemporary international relationships and geopolitics through the prism of religion, discussing whether it can provide practical solutions to solve conflicts and increase the respect of human rights.

Free Technology Academy : a Joint Venture of Free Software and OER

The decision to publish educational materials openly and under free licenses brings up the challenge of doing it in a sustainable way. Some lessons can be learned from the business models for production, maintenance and distribution of Free and Open Source Software. The Free Technology Academy (FTA) has taken on these challenges and has implemented some of these models. We briefly review the FTA educational programme, methodologies and organisation, and see to which extent these models are proving successful in the case of the FTA.