Natural genetic exchange between Haemophilus and Neisseria: Intergeneric transfer of chromosomal genes between major human pathogens

Members of the bacterial families Haemophilus and Neisseria, important human pathogens that commonly colonize the nasopharynx, are naturally competent for DNA uptake from their environment. In each genus this process is discriminant in favor of its own and against foreign DNA through sequence specificity of DNA receptors. The Haemophilus DNA uptake apparatus binds a 29-bp oligonucleotide domain containing a highly conserved 9-bp core sequence, whereas the neisserial apparatus binds a 10-bp motif. Each motif (“uptake sequence”, US) is highly over-represented in the chromosome of the corresponding genus, particularly concentrated with core sequences in inverted pairs forming gene terminators. Two Haemophilus core USs were unexpectedly found forming the terminator of sodC in Neisseria meningitidis (meningococcus), and sequence analysis strongly suggests that this virulence gene, located next to IS1106, arose through horizontal transfer from Haemophilus. By using USs as search strings in a computer-based analysis of genome sequence, it was established that while USs of the “wrong” genus do not occur commonly in Neisseria or Haemophilus, where they do they are highly likely to flag domains of chromosomal DNA that have been transferred from Haemophilus. Three independent domains of Haemophilus-like DNA were found in the meningococcal chromosome, associated respectively with the virulence gene sodC, the bio gene cluster, and an unidentified orf. This report identifies intergenerically transferred DNA and its source in bacteria, and further identifies transformation with heterologous chromosomal DNA as a way of establishing potentially important chromosomal mosaicism in these pathogenic bacteria.

A genomic approach to gene fusion technology

Gene expression profiling provides powerful analyses of transcriptional responses to cellular perturbation. In contrast to DNA array-based methods, reporter gene technology has been underused for this application. Here we describe a genomewide, genome-registered collection of Escherichia coli bioluminescent reporter gene fusions. DNA sequences from plasmid-borne, random fusions of E. coli chromosomal DNA to a Photorhabdus luminescens luxCDABE reporter allowed precise mapping of each fusion. The utility of this collection covering about 30% of the transcriptional units was tested by analyzing individual fusions representative of heat shock, SOS, OxyR, SoxRS, and cya/crp stress-responsive regulons. Each fusion strain responded as anticipated to environmental conditions known to activate the corresponding regulatory circuit. Thus, the collection mirrors E. coli's transcriptional wiring diagram. This genomewide collection of gene fusions provides an independent test of results from other gene expression analyses. Accordingly, a DNA microarray-based analysis of mitomycin C-treated E. coli indicated elevated expression of expected and unanticipated genes. Selected luxCDABE fusions corresponding to these up-regulated genes were used to confirm or contradict the DNA microarray results. The power of partnering gene fusion and DNA microarray technology to discover promoters and define operons was demonstrated when data from both suggested that a cluster of 20 genes encoding production of type I extracellular polysaccharide in E. coli form a single operon.

Urokinase-type plasminogen activator is effective in fibrin clearance in the absence of its receptor or tissue-type plasminogen activator.

The availability of gene-targeted mice deficient in the urokinase-type plasminogen activator (uPA), urokinase receptor (uPAR), tissue-type plasminogen activator (tPA), and plasminogen permits a critical, genetic-based analysis of the physiological and pathological roles of the two mammalian plasminogen activators. We report a comparative study of animals with individual and combined deficits in uPAR and tPA and show that these proteins are complementary fibrinolytic factors in mice. Sinusoidal fibrin deposits are found within the livers of nearly all adult mice examined with a dual deficiency in uPAR and tPA, whereas fibrin deposits are never found in livers collected from animals lacking uPAR and rarely detected in animals lacking tPA alone. This is the first demonstration that uPAR has a physiological role in fibrinolysis. However, uPAR-/-/tPA-/- mice do not develop the pervasive, multi-organ fibrin deposits, severe tissue damage, reduced fertility, and high morbidity and mortality observed in mice with a combined deficiency in tPA and the uPAR ligand, uPA. Furthermore, uPAR-/-/tPA-/- mice do not exhibit the profound impairment in wound repair seen in uPA-/-/tPA-/- mice when they are challenged with a full-thickness skin incision. These results indicate that plasminogen activation focused at the cell surface by uPAR is important in fibrin surveillance in the liver, but that uPA supplies sufficient fibrinolytic potential to clear fibrin deposits from most tissues and support wound healing without the benefit of either uPAR or tPA.

Discursive constructions of social and environmental accounting in Brazil: the case of Petrobras.

In the 29 years following \"Our Common Future\" by the United Nations, there is considerable debate among governments, civil society, interest groups and business organisations about what constitutes sustainable development, which constitutes evidence for a contested discourse concerning sustainability. The purpose of this study is to understand this debate in the developing economic context of Brazil, and in particular, to understand and critique the social and environmental accounting [SEA] discursive constructions relating to the State-owned, Petrobras as well as to understand the Brazilian literature on SEA. The discourse theory [DT]-based analysis employs rhetorical redescription to analyse twenty-two reports from Petrobras from 2004-2013. I investigate the political notions by employing the methodological framework of the Logics of Critical Explanation [LCE]. LCE engenders five methodological steps: problematisation, retroduction, logics (social, political and fantasmatic), articulation and critique. The empirical discussion suggests that the hegemony of economic development operates to obfuscate, rhetorically, the development of sustainability, so as to maintain the core business of Petrobras conceived as capital accumulation. Equally, these articulations also illustrate how the constructions of SEA operate to serve the company\'s purpose with few (none) profound changes in integration of sustainability. The Brazilian literature on SEA sustains the status quo of neo-liberal market policies that operate to protect the dominant business case approach to maintain an agenda of wealth-creation in relation to social and environmental needs. The articulations of the case manifested in policies regarding, for example, corruption, which involved over-payments for contracts and unsustainable practices relating to the use of fossil fuels and demonstrated that there was antagonism between action and disclosure. The corruption scandal that emerged after SEA disclosures highlighted the rhetorical nature of disclosure when financial resources were subtracted from the company for political parties and engineering contractors hid facts through incomplete disclosures. The articulations of SEA misrepresent a broader context of the meanings associated with sustainability, which restricted the constructions of SEA to principally serve and represent the intention of the most powerful groups. The significance of SEA, then is narrowed to represent particular interests. The study argues for more critical studies as limited Brazilian literature concerning SEA kept a \'safe distance\' from substantively critiquing the constructions of SEA and its articulations in the Brazilian context. The literature review and the Petrobras\' case illustrate a variety of naming, instituting and articulatory practices that endeavour to maintain the current hegemony of development in an emerging economy, which allows Petrobras to continue to exercise significant profit at the expense of the social and environmental. The constructed idea of development in Petrobras\' discourses emphasises a rhetoric of wider development, but, in reality, these discourses were the antithesis of political, social and ethical developmental issues. These constructions aim to hide struggles between social inequalities and exploitation of natural resources and constitute excuses about a fanciful notion of rhetorical and hegemonic neo-liberal development. In summary, this thesis contributes to the prior literature in five ways: (i) the addition of DT to the analysis of SEA enhances the discussion of political elements such as hegemony, antagonism, logic of equivalence/difference, ideology and articulation; (ii) the analysis of an emerging economy such as Brazil incorporates a new perspective of the discussion of the discourses of SEA and development; (iii) this thesis includes a focus on rhetoric to discuss the maintenance of the status quo; (iv) the holistic structure of the LCE approach enlarges the understanding of the social, political and fantasmatic logics of SEA studies and; (v) this thesis combines an analysis of the literature and the case of Petrobras to characterise and critique the state of the Brazilian academy and its impacts and reflections on the significance of SEA. This thesis, therefore, argues for more critical studies in the Brazilian academy due to the persistence of idea of SEA and development that takes-for-granted deep exclusions and contradictions and provide little space for critiques.

El Programa de Educación en Alimentación y Nutrición (1961-1982) y la capacitación de las amas de casa como responsables del bienestar familiar

El objetivo de este trabajo es analizar desde una perspectiva de género, a través del ejemplo del Programa de Educación en Alimentación y Nutrición (EDALNU) que se desarrolló en España en las décadas finales del siglo XX, los mensajes y estrategias de educación alimentaria nutricional que iban dirigidos a mejorar la capacitación de las amas de casa como garantes del bienestar familiar y como expertas en la gestión de los diversos aspectos del hogar. Su acción específica sobre las amas de casa y los argumentos sobre los que se sostenía dicha intervención afianzaron el modelo social de género en el que los hombres eran los únicos responsables de los recursos económicos del hogar y las mujeres las proveedoras de cuidados familiares y en concreto los relacionados con la alimentación y la nutrición.

Defying the Treaty: The Influence of the Polish and Lithuanian Council Presidencies on the Development of the Eastern Partnership. EU Diplomacy Paper No. 6, October 2014

Many scholars now argue that the Treaty of Lisbon has removed the role and influence of the rotating Council Presidency in the domain of the European Union’s foreign affairs. This paper will, however, go beyond a superficial, treaty-based analysis of the influence of the post-Lisbon rotating Council Presidency and instead look at two primary, residual, informal Presidential roles, namely agenda-shaping and brokering. It will examine the extent to which these informal roles allowed the Polish and Lithuanian Council Presidencies of July to December 2011 and 2013 respectively to influence the development of the bilateral, multilateral and internal tracks of the Eastern Partnership. The paper will argue that the considerable influence of these rotating Presidencies defied the logic of the Lisbon Treaty, suggesting that the ‘golden age’ of this six-month position, whereby individual Member States pursue foreign policy issues of significant domestic interest at the European level, has not yet passed.

Banks and the political economy of the sovereign debt crisis in Italy and Spain. CES Papers - Open Forum #18, 2013-2014

This paper sets out to explain why Spain experienced a full-fledged sovereign debt crisis and had to resort to euroarea financial assistance for its banks, whereas Italy did not. It undertakes a structured comparison, dissecting the sovereign debt crisis into a banking crisis and a balance of payments crisis. It argues that the distinctive features of bank business models and of national banking systems in Italy and Spain have considerable analytical leverage in explaining the different scenarios of the crises in each country. This ‘bank-based’ analysis contributes to the flourishing literature that examines changes in banking with a view to account for the differentiated impact of the global banking crisis first and the sovereign debt crisis in the euroarea later.

Modelled spatial and seasonal distribution of Blue Whiting (Micromesistius poutassou) larvae in the North-East Atlantic (1951 to 2005)

Blue whiting (Micromesistius poutassou, http://www.marinespecies.org/aphia.php?p=taxdetails&id=126439) is a small mesopelagic planktivorous gadoid found throughout the North-East Atlantic. This data contains the results of a model-based analysis of larvae captured by the Continuous Plankton Recorder (CPR) during the period 1951-2005. The observations are analysed using Generalised Additive Models (GAMs) of the the spatial, seasonal and interannual variation in the occurrence of larvae. The best fitting model is chosen using the Aikaike Information Criteria (AIC). The probability of occurrence in the continous plankton recorder is then normalised and converted to a probability distribution function in space (UTM projection Zone 28) and season (day of year). The best fitting model splits the distribution into two separate spawning grounds north and south of a dividing line at 53 N. The probability distribution is therefore normalised in these two regions (ie the space-time integral over each of the two regions is 1). The modelled outputs are on a UTM Zone 28 grid: however, for convenience, the latitude ("lat") and longitude ("lon") of each of these grid points are also included as a variable in the NetCDF file. The assignment of each grid point to either the Northern or Southern component (defined here as north/south of 53 N), is also included as a further variable ("component"). Finally, the day of year ("doy") is stored as the number of days elapsed from and included January 1 (ie doy=1 on January 1) - the year is thereafter divided into 180 grid points.

Document re-ranking by generality in bio-medical information retrieval

Document ranking is an important process in information retrieval (IR). It presents retrieved documents in an order of their estimated degrees of relevance to query. Traditional document ranking methods are mostly based on the similarity computations between documents and query. In this paper we argue that the similarity-based document ranking is insufficient in some cases. There are two reasons. Firstly it is about the increased information variety. There are far too many different types documents available now for user to search. The second is about the users variety. In many cases user may want to retrieve documents that are not only similar but also general or broad regarding a certain topic. This is particularly the case in some domains such as bio-medical IR. In this paper we propose a novel approach to re-rank the retrieved documents by incorporating the similarity with their generality. By an ontology-based analysis on the semantic cohesion of text, document generality can be quantified. The retrieved documents are then re-ranked by their combined scores of similarity and the closeness of documents’ generality to the query’s. Our experiments have shown an encouraging performance on a large bio-medical document collection, OHSUMED, containing 348,566 medical journal references and 101 test queries.

CRÍTICOS & CRITICADOS A CRÍTICA CINEMATOGRÁFICA E SUA RELAÇÃO COM OS CINEASTAS DA RETOMADA

O objetivo deste estudo é analisar a crítica cinematográfica durante o período chamado de Retomada do cinema nacional. Foram escolhidos os maiores veículos de circulação da região Sudeste do País, os jornais O Globo (Rio de Janeiro), Folha de S.Paulo e O Estado de S.Paulo (São Paulo) e a revista Veja para fazer uma análise de conteúdo das críticas das seis maiores bilheterias da Retomada para, em seguida, conferir a recepção das mesmas pelos diretores desses filmes, por meio de entrevistas semi-estruturadas. A intenção é analisar quais conflitos permeiam a relação entre os críticos de cinema e os cineastas, a fim de contribuir para o melhor entendimento do trabalho de dois elementos dos mais importantes da área de cinema. O confronto do material da análise com as entrevistas confirmou a hipótese da existência de conflitos de valores e opiniões entre os dois lados e permitiu identificar pré-julgamentos, simpatias e antipatias, análises emotivas e não-fundamentadas de alguns críticos e cineastas, mas também opiniões e valores fundamentados de outros, demonstrando uma rica diversidade que não se encaixa em uma única definição.(AU)

Bayesian retrieval of scatterometer wind fields

The retrieval of wind fields from scatterometer observations has traditionally been separated into two phases; local wind vector retrieval and ambiguity removal. Operationally, a forward model relating wind vector to backscatter is inverted, typically using look up tables, to retrieve up to four local wind vector solutions. A heuristic procedure, using numerical weather prediction forecast wind vectors and, often, some neighbourhood comparison is then used to select the correct solution. In this paper we develop a Bayesian method for wind field retrieval, and show how a direct local inverse model, relating backscatter to wind vector, improves the wind vector retrieval accuracy. We compare these results with the operational U.K. Meteorological Office retrievals, our own CMOD4 retrievals and a neural network based local forward model retrieval. We suggest that the neural network based inverse model, which is extremely fast to use, improves upon current forward models when used in a variational data assimilation scheme.

Statistical mechanics of low-density parity-check codes

We review recent theoretical progress on the statistical mechanics of error correcting codes, focusing on low-density parity-check (LDPC) codes in general, and on Gallager and MacKay-Neal codes in particular. By exploiting the relation between LDPC codes and Ising spin systems with multispin interactions, one can carry out a statistical mechanics based analysis that determines the practical and theoretical limitations of various code constructions, corresponding to dynamical and thermodynamical transitions, respectively, as well as the behaviour of error-exponents averaged over the corresponding code ensemble as a function of channel noise. We also contrast the results obtained using methods of statistical mechanics with those derived in the information theory literature, and show how these methods can be generalized to include other channel types and related communication problems.

Inventory parameter management and focused continuous improvement for repetitive batch manufacturers

What this thesis proposes is a methodology to assist repetitive batch manufacturers in the adoption of certain aspects of the Lean Production principles. The methodology concentrates on the reduction of inventory through the setting of appropriate batch sizes, taking account of the effect of sequence dependent set-ups and the identification and elimination of bottlenecks. It uses a simple Pareto and modified EBQ based analysis technique to allocate items to period order day classes based on a combination of each item's annual usage value and set-up cost. The period order day classes the items are allocated to are determined by the constraints limits in the three measured dimensions, capacity, administration and finance. The methodology overcomes the limitations associated with MRP in the area of sequence dependent set-ups, and provides a simple way of setting planning parameters taking this effect into account by concentrating on the reduction of inventory through the systematic identification and elimination of bottlenecks through set-up reduction processes, so allowing batch sizes to reduce. It aims to help traditional repetitive batch manufacturers in a route to continual improvement by: Highlighting those areas where change would bring the greatest benefits. Modelling the effect of proposed changes. Quantifying the benefits that could be gained through implementing the proposed changes. Simplifying the effort required to perform the modelling process. It concentrates on increasing flexibility through managed inventory reduction through rationally decreasing batch sizes, taking account of sequence dependent set-ups and the identification and elimination of bottlenecks. This was achieved through the development of a software modelling tool, and validated through a case study approach.

Three-factor models versus time series models:quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data

Signal integration determines cell fate on the cellular level, affects cognitive processes and affective responses on the behavioural level, and is likely to be involved in psychoneurobiological processes underlying mood disorders. Interactions between stimuli may subjected to time effects. Time-dependencies of interactions between stimuli typically lead to complex cell responses and complex responses on the behavioural level. We show that both three-factor models and time series models can be used to uncover such time-dependencies. However, we argue that for short longitudinal data the three factor modelling approach is more suitable. In order to illustrate both approaches, we re-analysed previously published short longitudinal data sets. We found that in human embryonic kidney 293 cells cells the interaction effect in the regulation of extracellular signal-regulated kinase (ERK) 1 signalling activation by insulin and epidermal growth factor is subjected to a time effect and dramatically decays at peak values of ERK activation. In contrast, we found that the interaction effect induced by hypoxia and tumour necrosis factor-alpha for the transcriptional activity of the human cyclo-oxygenase-2 promoter in HEK293 cells is time invariant at least in the first 12-h time window after stimulation. Furthermore, we applied the three-factor model to previously reported animal studies. In these studies, memory storage was found to be subjected to an interaction effect of the beta-adrenoceptor agonist clenbuterol and certain antagonists acting on the alpha-1-adrenoceptor / glucocorticoid-receptor system. Our model-based analysis suggests that only if the antagonist drug is administer in a critical time window, then the interaction effect is relevant.

Do many hands make light work? How to overcome social loafing and gain motivation in work teams

Purpose – The purpose of this paper is to challenge the assumption that process losses of individuals working in teams are unavoidable. The paper aims to challenge this assumption on the basis of social identity theory and recent research. Design/methodology/approach – The approach adopted in this paper is to review the mainstream literature providing strong evidence for motivation problems of individuals working in groups. Based on more recent literature, innovative ways to overcome these problems are discussed. Findings – A social identity-based analysis and recent findings summarized in this paper show that social loafing can be overcome and that even motivation gains in group work can be expected when groups are important for the individual group members' self-concepts. Practical implications – The paper provides human resource professionals and front-line managers with suggestions as to how individual motivation and performance might be increased when working in teams. Originality/value – The paper contributes to the literature by challenging the existing approach to reducing social loafing, i.e. individualizing workers as much as possible, and proposes a team-based approach instead to overcome motivation problems.