Molecular characterization of the contribution of autophagy to antigen presentation using quantitative proteomics

L’autophagie est une voie hautement conservée de dégradation lysosomale des constituants cellulaires qui est essentiel à l’homéostasie cellulaire et contribue à l’apprêtement et à la présentation des antigènes. Les rôles relativement récents de l'autophagie dans l'immunité innée et acquise sous-tendent de nouveaux paradigmes immunologiques pouvant faciliter le développement de nouvelles thérapies où la dérégulation de l’autophagie est associée à des maladies auto-immunes. Cependant, l'étude in vivo de la réponse autophagique est difficile en raison du nombre limité de méthodes d'analyse pouvant fournir une définition dynamique des protéines clés impliquées dans cette voie. En conséquence, nous avons développé un programme de recherche en protéomique intégrée afin d’identifier et de quantifier les proteines associées à l'autophagie et de déterminer les mécanismes moléculaires régissant les fonctions de l’autophagosome dans la présentation antigénique en utilisant une approche de biologie des systèmes. Pour étudier comment l'autophagie et la présentation antigénique sont activement régulés dans les macrophages, nous avons d'abord procédé à une étude protéomique à grande échelle sous différentes conditions connues pour stimuler l'autophagie, tels l’activation par les cytokines et l’infection virale. La cytokine tumor necrosis factor-alpha (TNF-alpha) est l'une des principales cytokines pro-inflammatoires qui intervient dans les réactions locales et systémiques afin de développer une réponse immune adaptative. La protéomique quantitative d'extraits membranaires de macrophages contrôles et stimulés avec le TNF-alpha a révélé que l'activation des macrophages a entrainé la dégradation de protéines mitochondriales et des changements d’abondance de plusieurs protéines impliquées dans le trafic vésiculaire et la réponse immunitaire. Nous avons constaté que la dégradation des protéines mitochondriales était sous le contrôle de la voie ATG5, et était spécifique au TNF-alpha. En outre, l’utilisation d’un nouveau système de présentation antigènique, nous a permi de constater que l'induction de la mitophagie par le TNF-alpha a entrainée l’apprêtement et la présentation d’antigènes mitochondriaux par des molécules du CMH de classe I, contribuant ainsi la variation du répertoire immunopeptidomique à la surface cellulaire. Ces résultats mettent en évidence un rôle insoupçonné du TNF-alpha dans la mitophagie et permet une meilleure compréhension des mécanismes responsables de la présentation d’auto-antigènes par les molécules du CMH de classe I. Une interaction complexe existe également entre infection virale et l'autophagie. Récemment, notre laboratoire a fourni une première preuve suggérant que la macroautophagie peut contribuer à la présentation de protéines virales par les molécules du CMH de classe I lors de l’infection virale par l'herpès simplex virus de type 1 (HSV-1). Le virus HSV1 fait parti des virus humains les plus complexes et les plus répandues. Bien que la composition des particules virales a été étudiée précédemment, on connaît moins bien l'expression de l'ensemble du protéome viral lors de l’infection des cellules hôtes. Afin de caractériser les changements dynamiques de l’expression des protéines virales lors de l’infection, nous avons analysé par LC-MS/MS le protéome du HSV1 dans les macrophages infectés. Ces analyses nous ont permis d’identifier un total de 67 protéines virales structurales et non structurales (82% du protéome HSV1) en utilisant le spectromètre de masse LTQ-Orbitrap. Nous avons également identifié 90 nouveaux sites de phosphorylation et de dix nouveaux sites d’ubiquitylation sur différentes protéines virales. Suite à l’ubiquitylation, les protéines virales peuvent se localiser au noyau ou participer à des événements de fusion avec la membrane nucléaire, suggérant ainsi que cette modification pourrait influer le trafic vésiculaire des protéines virales. Le traitement avec des inhibiteurs de la réplication de l'ADN induit des changements sur l'abondance et la modification des protéines virales, mettant en évidence l'interdépendance des protéines virales au cours du cycle de vie du virus. Compte tenu de l'importance de la dynamique d'expression, de l’ubiquitylation et la phosphorylation sur la fonction des proteines virales, ces résultats ouvriront la voie vers de nouvelles études sur la biologie des virus de l'herpès. Fait intéressant, l'infection HSV1 dans les macrophages déclenche une nouvelle forme d'autophagie qui diffère remarquablement de la macroautophagie. Ce processus, appelé autophagie associée à l’enveloppe nucléaire (nuclear envelope derived autophagy, NEDA), conduit à la formation de vésicules membranaires contenant 4 couches lipidiques provenant de l'enveloppe nucléaire où on retrouve une grande proportion de certaines protéines virales, telle la glycoprotéine B. Les mécanismes régissant NEDA et leur importance lors de l’infection virale sont encore méconnus. En utilisant un essai de présentation antigénique, nous avons pu montrer que la voie NEDA est indépendante d’ATG5 et participe à l’apprêtement et la présentation d’antigènes viraux par le CMH de classe I. Pour comprendre l'implication de NEDA dans la présentation des antigènes, il est essentiel de caractériser le protéome des autophagosomes isolés à partir de macrophages infectés par HSV1. Aussi, nous avons développé une nouvelle approche de fractionnement basé sur l’isolation de lysosomes chargés de billes de latex, nous permettant ainsi d’obtenir des extraits cellulaires enrichis en autophagosomes. Le transfert des antigènes HSV1 dans les autophagosomes a été determine par protéomique quantitative. Les protéines provenant de l’enveloppe nucléaire ont été préférentiellement transférées dans les autophagosome lors de l'infection des macrophages par le HSV1. Les analyses protéomiques d’autophagosomes impliquant NEDA ou la macroautophagie ont permis de decouvrir des mécanismes jouant un rôle clé dans l’immunodominance de la glycoprotéine B lors de l'infection HSV1. Ces analyses ont également révélées que diverses voies autophagiques peuvent être induites pour favoriser la capture sélective de protéines virales, façonnant de façon dynamique la nature de la réponse immunitaire lors d'une infection. En conclusion, l'application des méthodes de protéomique quantitative a joué un rôle clé dans l'identification et la quantification des protéines ayant des rôles importants dans la régulation de l'autophagie chez les macrophages, et nous a permis d'identifier les changements qui se produisent lors de la formation des autophagosomes lors de maladies inflammatoires ou d’infection virale. En outre, notre approche de biologie des systèmes, qui combine la protéomique quantitative basée sur la spectrométrie de masse avec des essais fonctionnels tels la présentation antigénique, nous a permis d’acquérir de nouvelles connaissances sur les mécanismes moléculaires régissant les fonctions de l'autophagie lors de la présentation antigénique. Une meilleure compréhension de ces mécanismes permettra de réduire les effets nuisibles de l'immunodominance suite à l'infection virale ou lors du développement du cancer en mettant en place une réponse immunitaire appropriée.

To think museology today

In the present text we intend to analyse 5 basic documents that translate the Museological Thinking in our century and that, chiefly, have led professionals of the area to apply this “science” in a less hermetic way and to understand its practice. The option to study and analyse the documents results from the fact that they influence present day museological practice and thinking. It is impossible to speak of museology nowadays without referring to one of these documents, not to mention a few nations that have even modified and/or created specific laws for the management of their preservationist cultural policy. Anyway, we are aware that this text intends only to carry out a preliminary approach to the documents, in the sense that the wealth of its content would allow us to slowx over an infinity of issues that they raise. I specifically refer to the documents produced at UNESCO Regional Seminar on the Role of Museums in Education, which took place in Rio de Janeiro in 1958; at the Santiago Round Table in 1972, in Chile; at the 1rst New Museology International Workshop, in Quebec, Canada, 1984; at the Oaxtepec Meeting, in Mexico 1984; and at the Caracas Meeting in 1992. These are documents elaborated within the ICOM –International Council of Museums. These documents are the result of a joint reflection by professionals who seek the evolution of ideas within their areas of action, recognising that in order to do so it is necessary to leave the cocoon of the museological institutions and try to discuss their conceptual advances with professionals of related areas. It is important to be capacitated to reuse these advances in their areas of action. This is the recognition of the importance of interdisciplinarity for the museological context.

Societal development and the traditional museum: Applying New Museology to a different context

The Dapperstreet[1] ...Anything is a lot, when you expect so little Life keeps its wonders hidden To suddenly reveal them in a divine state. I thought about all t Soaking wet, one drizzly morning, Simply happy in the Dapperstreet. The Dapperstreet is part of a neighbourhood often referred to as “East”, situated in the eastern part of Amsterdam. It is a lively and vibrant multi-cultural part of the city. It has a daily market with food from around the world, but is also known worldwide because of the murder on Theo van Gogh, the Dutch film director who was killed there in 2001 because of his critical and provocative statements on the Islam. Thus it can be concluded that it is certainly a neighbourhood with its own problems but, as can be read in Bloem’s poem, a place to call home and long for. [1] Poem by J.C. Bloem, The Dapperstreet (Het Verlangen, 1921). Translation by Davida de Hond.

Reproduction recovery of the crustacean Daphnia magna after chronic exposure to ibuprofen

In mammals, the pharmaceutical ibuprofen (IB), a non-steroidal anti-inflammatory drug, primarily functions by reversibly inhibiting the cyclooxygenase (COX) pathway in the synthesis of eicosanoids (e.g. prostaglandins). Previous studies suggest that IB may act in a similar manner to interrupt production of eicosanoids reducing reproduction in the model crustacean Daphnia magna. On this basis withdrawal of IB should lead to the recovery of D. magna reproduction. Here we test whether the effect of IB is reversible in D. magna, as it is in mammals, by observing reproduction recovery following chronic exposure. D. magna (5-days old) were exposed to a range of IB concentrations (0, 20, 40 and 80 mg l(-1)) for 10 days followed by a 10 day recovery period in uncontaminated water. During the exposure period, individuals exposed to higher concentrations produced significantly fewer offspring. Thereafter, IB-stressed individuals produced offspring faster during recovery, having similar average population growth rates (PGR) (1.15-1.28) to controls by the end of the test. It appears that maternal daphnids are susceptible to IB during egg maturation. This is the first recorded recovery of reproduction in aquatic invertebrates that suffered reproductive inhibition during chronic exposure to a chemical stressor. Our results suggest a possible theory behind the compensatory fecundity that we referred to as 'catch-up reproduction'.

The return due to diversification of real estate to the US mixed-asset portfolio

Booth and Fama (1992) observe that the compound return and so the terminal wealth of a portfolio is greater than the weighted average of the compound returns of the individual investments, a difference referred to as the return due to diversification (RDD). Thus assets that offer high RDD should be particularly attractive investments. This paper test the proposition that US direct real estate is such an asset class using annual data over the period 1951-2001. The results show that adding real estate to an existing mixed-asset portfolio increases the compound return and so the terminal wealth of the fund. However, the results are dependent on the percentage allocation to real estate and the asset class replaced.

CPD records for revalidation: assessing fitness-to-practise using ‘revalidation standards’ and an Outcomes Framework

Background: Currently, all pharmacists and technicians registered with the Royal Pharmaceutical Society of Great Britain must complete a minimum of nine Continuing Professional Development (CPD) record (entries) each year. From September 2010 a new regulatory body, the General Pharmaceutical Council, will oversee the regulation (including revalidation) of all pharmacy registrants in Great Britain. CPD may provide part of the supporting evidence that a practitioner submits to the regulator as part of the revalidation process. Gaps in knowledge necessitated further research to examine the usefulness of CPD in a pharmacy revalidation Project aims: The overall aims of this project were to summarise pharmacy professionals’ past involvement in CPD, examine the usability of current CPD entries for the purpose of revalidation, and to examine the impact of ‘revalidation standards’ and a bespoke Outcomes Framework on the conduct and construction of CPD entries for future revalidation of pharmacy professionals. We completed a comprehensive review of the literature, devised, validated and tested the impact of a new CPD Outcomes Framework and related training material in an empirical investigation involving volunteer pharmacy professionals and also spoke with our participants to bring meaning and understanding to the process of CPD conduct and recording and to gain feedback on the study itself. Key findings: The comprehensive literature review identified perceived barriers to CPD and resulted in recommendations that could potentially rectify pharmacy professionals’ perceptions and facilitate participation in CPD. The CPD Outcomes Framework can be used to score CPD entries Compared to a control (CPD and ‘revalidation standards’ only), we found that training participants to apply the CPD Outcomes Framework resulted in entries that scored significantly higher in the context of a quantitative method of CPD assessment. Feedback from participants who had received the CPD Outcomes Framework was positive and a number of useful suggestions were made about improvements to the Framework and related training. Entries scored higher because participants had consciously applied concepts linked to the CPD Outcomes Framework whereas entries scored low where participants had been unable to apply the concepts of the Framework for a variety of reasons including limitations posed by the ‘Plan & Record’ template. Feedback about the nature of the ‘revalidation standards’ and their application to CPD was not positive and participants had not in the main sought to apply the standards to their CPD entries – but those in the intervention group were more likely to have referred to the revalidation standards for their CPD. As assessors, we too found the process of selecting and assigning ‘revalidation standards’ to individual CPD entries burdensome and somewhat unspecific. We believe that addressing the perceived barriers and drawing on the facilitators will help deal with the apparent lack of engagement with the revalidation standards and have been able to make a set of relevant recommendations. We devised a model to explain and tell the story of CPD behaviour. Based on the concepts of purpose, action and results, the model centres on explaining two types of CPD behaviour, one following the traditional CE pathway and the other a more genuine CPD pathway. Entries which scored higher when we applied the CPD Outcomes Framework were more likely to follow the CPD pathway in the model above. Significant to our finding is that while participants following both models of practice took part in this study, the CPD Outcomes Framework was able to change people’s CPD behaviour to make it more inline with the CPD pathway. The CPD Outcomes Framework in defining the CPD criteria, the training pack in teaching the basis and use of the Framework and the process of assessment in using the CPD Outcomes Framework, would have interacted to improve participants’ CPD through a collective process. Participants were keen to receive a curriculum against which certainly CE-type activities could be conducted and another important observation relates to whether CE has any role to play in pharmacy professionals’ revalidation. We would recommend that the CPD Outcomes Framework is used in the revalidation of pharmacy professionals in the future provided the requirement to submit 9 CPD entries per annum is re-examined and expressed more clearly in relation to what specifically participants are being asked to submit – i.e. the ratio of CE to CPD entries. We can foresee a benefit in setting more regular intervals which would act as deadlines for CPD submission in the future. On the whole, there is value in using CPD for the purpose of pharmacy professionals’ revalidation in the future.

Mutation of toxB and a truncated version of the efa-1 gene in Escherichia coli O157 : H7 influences the expression and secretion of locus of enterocyte effacement-encoded proteins but not intestinal colonization in calves or sheep

Enterohemorrhagic Escherichia coli (EHEC) strains comprise a broad group of bacteria, some of which cause attaching and effacing (AE) lesions and enteritis in humans and animals. Non-O157:H7 EHEC strains contain the gene efa-1 (referred to in previous publications as efa1), which influences adherence to cultured epithelial cells. An almost identical gene in enteropathogenic E. coli (lifA) mediates the inhibition of lymphocyte proliferation and proinflammatory cytokine synthesis. We have shown previously that significantly lower numbers of EHEC 05 and 0111 efa-1 mutants are shed in feces following experimental infection in calves and that these mutants exhibit reduced adherence to intestinal epithelia compared with isogenic wild-type strains. E. coli O157:H7 strains lack efa-1 but encode a homolog on the pO157 plasmid (toxB/l7095) and contain a truncated version of the efa-1 gene (efa-1'/z4332 in O island 122 of the EDL933 chromosome). Here we report that E. coli O157:H7 toxB and efa-1' single and double mutants exhibit reduced adherence to cultured epithelial cells and show reduced expression and secretion of proteins encoded by the locus of enterocyte effacement (LEE), which plays a key role in the host-cell interactions of EHEC. The activity of LEE1, LEE4, and LEE5 promoters was not significantly altered in E. coli O157:H7 strains harboring toxB or efa-1' mutations, indicating that the effect on the expression of LEE-encoded secreted proteins occurs at a posttranscriptional level. Despite affecting type III secretion, mutation of toxB and efa-1' did not significantly affect the course of fecal shedding of E. coli O157:H7 following experimental inoculation of 10- to 14-day-old calves or 6-week-old sheep. Mutation of tir caused a significant reduction in fecal shedding of E. coli O157:H7 in calves, indicating that the formation of AE lesions is important for colonization of the bovine intestine.

Lateral boundary contributions to wave-activity invariants and nonlinear stability theorems for balanced dynamics

The slow advective-timescale dynamics of the atmosphere and oceans is referred to as balanced dynamics. An extensive body of theory for disturbances to basic flows exists for the quasi-geostrophic (QG) model of balanced dynamics, based on wave-activity invariants and nonlinear stability theorems associated with exact symmetry-based conservation laws. In attempting to extend this theory to the semi-geostrophic (SG) model of balanced dynamics, Kushner & Shepherd discovered lateral boundary contributions to the SG wave-activity invariants which are not present in the QG theory, and which affect the stability theorems. However, because of technical difficulties associated with the SG model, the analysis of Kushner & Shepherd was not fully nonlinear. This paper examines the issue of lateral boundary contributions to wave-activity invariants for balanced dynamics in the context of Salmon's nearly geostrophic model of rotating shallow-water flow. Salmon's model has certain similarities with the SG model, but also has important differences that allow the present analysis to be carried to finite amplitude. In the process, the way in which constraints produce boundary contributions to wave-activity invariants, and additional conditions in the associated stability theorems, is clarified. It is shown that Salmon's model possesses two kinds of stability theorems: an analogue of Ripa's small-amplitude stability theorem for shallow-water flow, and a finite-amplitude analogue of Kushner & Shepherd's SG stability theorem in which the ‘subsonic’ condition of Ripa's theorem is replaced by a condition that the flow be cyclonic along lateral boundaries. As with the SG theorem, this last condition has a simple physical interpretation involving the coastal Kelvin waves that exist in both models. Salmon's model has recently emerged as an important prototype for constrained Hamiltonian balanced models. The extent to which the present analysis applies to this general class of models is discussed.

Children and adolescents referred for treatment of anxiety disorders: differences in clinical characteristics

Background: Reports of the clinical characteristics of children and adolescents with anxiety disorders are typically based on community populations or from clinical samples with exclusion criterion applied. Little is known about the clinical characteristics of children and adolescents routinely referred for treatment for anxiety disorders. Furthermore, children and adolescents are typically treated as one homogeneous group although they may differ in ways that are clinically meaningful. Methods: A consecutive series of children (n = 100, aged 6-12 years) and adolescents (n = 100, aged 13-18 years), referred to a routine clinical service, were assessed for anxiety and comorbid disorders, school refusal and parental symptoms of psychopathology. Results: Children were significantly more likely to be diagnosed with separation anxiety disorder than adolescents. Adolescents with a primary anxiety disorder had significantly higher self and clinician rated anxiety symptoms and had more frequent primary diagnoses of social anxiety disorder, diagnoses and symptoms of mood disorders, and irregular school attendance. Limitations: Childhood and adolescence were considered categorically as distinct, developmental periods; in reality changes would be unlikely to occur in such a discrete manner. Conclusions: The finding that children and adolescents with anxiety disorders have distinct clinical characteristics has clear implications for treatment. Simply adapting treatments designed for children to make the materials more ‘adolescent-friendly’ is unlikely to sufficiently meet the needs of adolescents.

Increasing frequency of extreme El Niño events due to greenhouse warming

El Niño events are a prominent feature of climate variability with global climatic impacts. The 1997/98 episode, often referred to as ‘the climate event of the twentieth century’1, 2, and the 1982/83 extreme El Niño3, featured a pronounced eastward extension of the west Pacific warm pool and development of atmospheric convection, and hence a huge rainfall increase, in the usually cold and dry equatorial eastern Pacific. Such a massive reorganization of atmospheric convection, which we define as an extreme El Niño, severely disrupted global weather patterns, affecting ecosystems4, 5, agriculture6, tropical cyclones, drought, bushfires, floods and other extreme weather events worldwide3, 7, 8, 9. Potential future changes in such extreme El Niño occurrences could have profound socio-economic consequences. Here we present climate modelling evidence for a doubling in the occurrences in the future in response to greenhouse warming. We estimate the change by aggregating results from climate models in the Coupled Model Intercomparison Project phases 3 (CMIP3; ref. 10) and 5 (CMIP5; ref. 11) multi-model databases, and a perturbed physics ensemble12. The increased frequency arises from a projected surface warming over the eastern equatorial Pacific that occurs faster than in the surrounding ocean waters13, 14, facilitating more occurrences of atmospheric convection in the eastern equatorial region.

Climate change projections using the IPSL-CM5 Earth System Model: from CMIP3 to CMIP5

We present the global general circulation model IPSL-CM5 developed to study the long-term response of the climate system to natural and anthropogenic forcings as part of the 5th Phase of the Coupled Model Intercomparison Project (CMIP5). This model includes an interactive carbon cycle, a representation of tropospheric and stratospheric chemistry, and a comprehensive representation of aerosols. As it represents the principal dynamical, physical, and bio-geochemical processes relevant to the climate system, it may be referred to as an Earth System Model. However, the IPSL-CM5 model may be used in a multitude of configurations associated with different boundary conditions and with a range of complexities in terms of processes and interactions. This paper presents an overview of the different model components and explains how they were coupled and used to simulate historical climate changes over the past 150 years and different scenarios of future climate change. A single version of the IPSL-CM5 model (IPSL-CM5A-LR) was used to provide climate projections associated with different socio-economic scenarios, including the different Representative Concentration Pathways considered by CMIP5 and several scenarios from the Special Report on Emission Scenarios considered by CMIP3. Results suggest that the magnitude of global warming projections primarily depends on the socio-economic scenario considered, that there is potential for an aggressive mitigation policy to limit global warming to about two degrees, and that the behavior of some components of the climate system such as the Arctic sea ice and the Atlantic Meridional Overturning Circulation may change drastically by the end of the twenty-first century in the case of a no climate policy scenario. Although the magnitude of regional temperature and precipitation changes depends fairly linearly on the magnitude of the projected global warming (and thus on the scenario considered), the geographical pattern of these changes is strikingly similar for the different scenarios. The representation of atmospheric physical processes in the model is shown to strongly influence the simulated climate variability and both the magnitude and pattern of the projected climate changes.

PCA Tomography: how to extract information from data cubes

Astronomy has evolved almost exclusively by the use of spectroscopic and imaging techniques, operated separately. With the development of modern technologies, it is possible to obtain data cubes in which one combines both techniques simultaneously, producing images with spectral resolution. To extract information from them can be quite complex, and hence the development of new methods of data analysis is desirable. We present a method of analysis of data cube (data from single field observations, containing two spatial and one spectral dimension) that uses Principal Component Analysis (PCA) to express the data in the form of reduced dimensionality, facilitating efficient information extraction from very large data sets. PCA transforms the system of correlated coordinates into a system of uncorrelated coordinates ordered by principal components of decreasing variance. The new coordinates are referred to as eigenvectors, and the projections of the data on to these coordinates produce images we will call tomograms. The association of the tomograms (images) to eigenvectors (spectra) is important for the interpretation of both. The eigenvectors are mutually orthogonal, and this information is fundamental for their handling and interpretation. When the data cube shows objects that present uncorrelated physical phenomena, the eigenvector`s orthogonality may be instrumental in separating and identifying them. By handling eigenvectors and tomograms, one can enhance features, extract noise, compress data, extract spectra, etc. We applied the method, for illustration purpose only, to the central region of the low ionization nuclear emission region (LINER) galaxy NGC 4736, and demonstrate that it has a type 1 active nucleus, not known before. Furthermore, we show that it is displaced from the centre of its stellar bulge.

Salmonella enterica Serovar Typhimurium Vaccine Strains Expressing a Nontoxic Shiga-Like Toxin 2 Derivative Induce Partial Protective Immunity to the Toxin Expressed by Enterohemorrhagic Escherichia coli

Shiga-like toxin 2 (Stx2)-producing enterohemorrhagic Escherichia coli (referred to as EHEC or STEC) strains are the primary etiologic agents of hemolytic-uremic syndrome (HUS), which leads to renal failure and high mortality rates. Expression of Stx2 is the most relevant virulence-associated factor of EHEC strains, and toxin neutralization by antigen-specific serum antibodies represents the main target for both preventive and therapeutic anti-HUS approaches. In the present report, we describe two Salmonella enterica serovar Typhimurium aroA vaccine strains expressing a nontoxic plasmid-encoded derivative of Stx2 (Stx2 Delta AB) containing the complete nontoxic A2 subunit and the receptor binding B subunit. The two S. Typhimurium strains differ in the expression of flagellin, the structural subunit of the flagellar shaft, which exerts strong adjuvant effects. The vaccine strains expressed Stx2 Delta AB, either cell bound or secreted into the extracellular environment, and showed enhanced mouse gut colonization and high plasmid stability under both in vitro and in vivo conditions. Oral immunization of mice with three doses of the S. Typhimurium vaccine strains elicited serum anti-Stx2B (IgG) antibodies that neutralized the toxic effects of the native toxin under in vitro conditions (Vero cells) and conferred partial protection under in vivo conditions. No significant differences with respect to gut colonization or the induction of antigen-specific antibody responses were detected in mice vaccinated with flagellated versus nonflagellated bacterial strains. The present results indicate that expression of Stx2 Delta AB by attenuated S. Typhimurium strains is an alternative vaccine approach for HUS control, but additional improvements in the immunogenicity of Stx2 toxoids are still required.

On comparing two sequences of numbers and its applications to clustering analysis

A conceptual problem that appears in different contexts of clustering analysis is that of measuring the degree of compatibility between two sequences of numbers. This problem is usually addressed by means of numerical indexes referred to as sequence correlation indexes. This paper elaborates on why some specific sequence correlation indexes may not be good choices depending on the application scenario in hand. A variant of the Product-Moment correlation coefficient and a weighted formulation for the Goodman-Kruskal and Kendall`s indexes are derived that may be more appropriate for some particular application scenarios. The proposed and existing indexes are analyzed from different perspectives, such as their sensitivity to the ranks and magnitudes of the sequences under evaluation, among other relevant aspects of the problem. The results help suggesting scenarios within the context of clustering analysis that are possibly more appropriate for the application of each index. (C) 2008 Elsevier Inc. All rights reserved.

A complex network approach to text summarization

Automatic summarization of texts is now crucial for several information retrieval tasks owing to the huge amount of information available in digital media, which has increased the demand for simple, language-independent extractive summarization strategies. In this paper, we employ concepts and metrics of complex networks to select sentences for an extractive summary. The graph or network representing one piece of text consists of nodes corresponding to sentences, while edges connect sentences that share common meaningful nouns. Because various metrics could be used, we developed a set of 14 summarizers, generically referred to as CN-Summ, employing network concepts such as node degree, length of shortest paths, d-rings and k-cores. An additional summarizer was created which selects the highest ranked sentences in the 14 systems, as in a voting system. When applied to a corpus of Brazilian Portuguese texts, some CN-Summ versions performed better than summarizers that do not employ deep linguistic knowledge, with results comparable to state-of-the-art summarizers based on expensive linguistic resources. The use of complex networks to represent texts appears therefore as suitable for automatic summarization, consistent with the belief that the metrics of such networks may capture important text features. (c) 2008 Elsevier Inc. All rights reserved.