Soil differentiation using fingerprint Fourier transform infrared spectroscopy, chemometrics and genetic algorithm-based feature selection

Elliott, G. N., Worgan, H., Broadhurst, D. I., Draper, J. H., Scullion, J. (2007). Soil differentiation using fingerprint Fourier transform infrared spectroscopy, chemometrics and genetic algorithm-based feature selection. Soil Biology & Biochemistry, 39 (11), 2888-2896. Sponsorship: BBSRC / NERC RAE2008

Evidence in support of a role for plant-mediated proteolysis in the rumens of grazing animals

Kingston-Smith, A. H., Merry, R. J., Leemans, D. K., Thomas, Howard, Theodorou, M. K. (2005). Evidence in support of a role for plant-mediated proteolysis in the rumens of grazing animals. British Journal of Nutrition, 93(1), 73-79. Sponsorship: DEFRA / BBSRC RAE2008

Edward Sapir’s View About International Auxiliary Language

The search for common attributes of all languages is connected with the search for characteristics which differentiate languages. If some attributes cannot be found in every language, what is cause of this situation? Is it linked up with the origin of language or with users of the language?

The extradomain a of fibronectin enhances the efficacy of lipopolysaccharide defective Salmonella bacterins as vaccines in mice

The Extradomain A from fibronectin (EDA) has an immunomodulatory role as fusion protein with viral and tumor antigens, but its effect when administered with bacteria has not been assessed. Here, we investigated the adjuvant effect of EDA in mice immunizations against Salmonella enterica subspecies enterica serovar Enteritidis (Salmonella Enteritidis). Since lipopolysaccharide (LPS) is a major virulence factor and the LPS O-polysaccharide (O-PS) is the immunodominant antigen in serological diagnostic tests, Salmonella mutants lacking O-PS (rough mutants) represent an interesting approach for developing new vaccines and diagnostic tests to differentiate infected and vaccinated animals (DIVA tests). Here, antigenic preparations (hot-saline extracts and formalin-inactivated bacterins) from two Salmonella Enteritidis rough mutants, carrying either intact (SE Delta waaL) or deep-defective (SE Delta gal) LPS-Core, were used in combination with EDA. Biotinylated bacterins, in particular SE Delta waaL bacterin, decorated with EDAvidin (EDA and streptavidin fusion protein) improved the protection conferred by hot-saline or bacterins alone and prevented significantly the virulent infection at least to the levels of live attenuated rough mutants. These findings demonstrate the adjuvant effect of EDAvidin when administered with biotinylated bacterins from Salmonella Enteritidis lacking O-PS and the usefulness of BEDA-SE Delta waaL as non-live vaccine in the mouse model.

Propozycja rozróżnienia teoretycznego kategorii estymy i szacunku

Poniższy tekst odnosi się do debat dotyczących sporów teoretycznych i definicyjnych o znaczenie kategorii szacunku i estymy. Autor porównuje koncepcję prestiżu Henryka Domańskiego i teorie uznania Axela Honnetha zarówno w wymiarze normatywnym, jak i tym dotyczącym badań empirycznych. Autor konkluduje, że założenia normatywne i definicje teoretyczne kategorii estymy i szacunku są bardziej przekonujące i wyszukane pod względem teoretycznym w teorii uznania Axela Honnetha.

Selección de un aislado del nucleopoliedrovirus de Helicoverpa armigera (HearNPV) para su uso como base de un bioinsecticida

Helicoverpa armigera (Lepidoptera; Noctuidae), conocida como el taladro del tomate, es una especie polífaga y de amplia distribución, responsable de grandes pérdidas económicas en más de 60 cultivos a lo largo de las regiones tropicales y subtropicales del mundo. Estas plagas se controlan mayoritariamente con plaguicidas químicos, aunque existe un gran interés por desarrollar otros agentes de control biológico. Entre estos, se encuentra el nucleopoliedrovirus de Helicoverpa armigera (HearNPV, Baculoviridae), que por sus características de seguridad y eficacia, sería útil para impulsar los programas de gestión integrada de plagas que se fomentan desde la Directiva 2009/128/CEE. El objetivo de este trabajo fue realizar una caracterización bioquímica y biológica de varios aislados de HearNPV : un aislado silvestre español (Badajoz) HearNPV-SP1, un aislado chino HearSNPV-G4, tres aislados sudafricanos (HearNPV-Whl, HearNPV-Kzn, HearNPV-Alb) y la materia activa de un producto comercial en uso en Europa (HearNPV-Hx). El análisis con las enzimas de restricción determinó que la enzima BglII generaba perfiles similares pero con fragmentos característicos en todos los casos a excepción de los aislados HearNPV-Kzn y HearNPVAlb, que no pudieron ser diferenciados entre sí con ninguna de las enzimas probadas. El análisis filogenético, basado en las secuencias parciales de los genes poliedrina (polh), lef-8 y lef-9, donde se incluyeron las secuencias correspondientes a 18 genomas mostró que el aislado HearNPV-Whl es filogenéticamente próximo a las cepas de origen ibérico, mientras que los aislados HearNPV-Hx y HearNPV-Alb comparten la misma rama que los aislados asiáticos y australiano. La caracterización insecticida de los aislados HearNPV-SP1, HearNPV-Hx y HearNPV-G4 reveló que la virulencia (TMM) del aislado HearNPV-SP1 (104 h) fue significativamente menor que la de los aislados HearNPV-G4 (109 h) y HearNPV-Hx (111 h). En este trabajo, se determinó que el tiempo de acción del HearNPV-SP1 es menor al de otros bioinsecticidas en uso en Europa, por lo que se confirma la posibilidad de mejorar los productos activos en uno de los aspectos más sensibles de cara a su comercialización como es su tiempo de actuación.

Filozofia antyczna wobec problemu interpretacji. Rozwój alegorezy od przedsokratyków do Arystotelesa

The present work examines the beginnings of ancient hermeneutics. More specifically, it discusses the connection between the rise of the practice of allegoresis, on the one hand, and the emergence of the first theory of figurative language, on the other. Thus, this book investigates the specific historical and cultural circumstances that enabled the ancient Greeks not only to discover the possibility of allegorical interpretation, but also to treat figurative language as a philosophical problem. By posing difficulties in understanding the enigmatic sense of various esoteric doctrines, poems, oracles and riddles, figurative language created the context for theoretical reflection on the meaning of these “messages”. Hence, ancient interpreters began to ponder over the nature and functions of figurative (“enigmatic”) language as well as over the techniques of its proper use and interpretation. Although the practice of allegorical interpretation was closely linked to the development of the whole of ancient philosophy, the present work covers only the period from the 6th to the 4th century B.C. It concentrates, then, on the philosophical and cultural consequences of allegoresis in the classical age. The main thesis advocated here has it that the ancient Greeks were in-clined to regard allegory as a cognitive problem rather than merely as a stylistic or a literary one. When searching for the hidden meanings of various esoteric doc-trines, poems, oracles and riddles, ancient interpreters of these “messages” assumed allegory to be the only tool suitable for articulating certain matters. In other words, it was their belief that the use of figurative language resulted from the necessity of expressing things that were otherwise inexpressible. The present work has been organized in the following manner. The first part contains historical and philological discussions that provide the point of departure for more philosophical considerations. This part consists of two introductory chapters. Chapter one situates the practice of allegorical interpretation at the borderline of two different traditions: the rhetorical-grammatical and the hermeneutical. In order to clearly differentiate between the two, chapter one distinguishes between allegory and allegoresis, on the one hand, and allegoresis and exegesis, on the other. While pointing to the conventionality (and even arbitrariness) of such distinctions, the chapter argues, nevertheless, for their heuristic usefulness. The remaining part of chapter one focuses on a historical and philological reconstruction of the most important conceptual tools of ancient hermeneutics. Discussing the semantics of such terms as allēgoría, hypónoia, ainigma and symbolon proves important for at least two crucial reasons. Firstly, it reveals the mutual affinity between allegoresis and divination, i.e., practices that are inherently connected with the need to discover the latent meaning of the “message” in question (whether poem or oracle). Secondly, these philological analyses bring to light the specificity of the ancient understanding of such concepts as allegory or symbol. It goes without saying that antiquity employed these terms in a manner quite disparate from modernity. Chapter one concludes with a discussion of ancient views on the cognitive value of figurative (“enigmatic”) language. Chapter two focuses on the role that allegoresis played in the process of transforming mythos into logos. It is suggested here that it was the practice of allegorical interpretation that made it possible to preserve the traditional myths as an important point of reference for the whole of ancient philosophy. Thus, chapter two argues that the existence of a clear opposition between mythos into logos in Preplatonic philosophy is highly questionable in light of the indisputable fact that the Presocratics, Sophists and Cynics were profoundly convinced about the cognitive value of mythos (this conviction was also shared by Plato and Aristotle, but their attitude towards myth was more complex). Consequently, chapter two argues that in Preplatonic philosophy, myth played a function analogous to the concepts discussed in chapter one (i.e., hidden meanings, enigmas and symbols), for in all these cases, ancient interpreters found tools for conveying issues that were otherwise difficult to convey. Chapter two concludes with a classification of various types of allegoresis. Whilst chapters one and two serve as a historical and philological introduction, the second part of this book concentrates on the close relationship between the development of allegoresis, on the one hand, and the flowering of philosophy, on the other. Thus, chapter three discusses the crucial role that allegorical interpretation came to play in Preplatonic philosophy, chapter four deals with Plato’s highly complex and ambivalent attitude to allegoresis, and chapter five has been devoted to Aristotle’s original approach to the practice of allegorical interpretation. It is evident that allegoresis was of paramount importance for the ancient thinkers, irrespective of whether they would value it positively (Preplatonic philosophers and Aristotle) or negatively (Plato). Beginning with the 6th century B.C., the ancient practice of allegorical interpretation is motivated by two distinct interests. On the one hand, the practice of allegorical interpretation reflects the more or less “conservative” attachment to the authority of the poet (whether Homer, Hesiod or Orpheus). The purpose of this apologetic allegoresis is to exonerate poetry from the charges leveled at it by the first philosophers and, though to a lesser degree, historians. Generally, these allegorists seek to save the traditional paideia that builds on the works of the poets. On the other hand, the practice of allegorical interpretation reflects also the more or less “progressive” desire to make original use of the authority of the poet (whether Homer, Hesiod or Orpheus) so as to promote a given philosophical doctrine. The objective of this instrumental allegoresis is to exculpate philosophy from the accusations brought against it by the more conservative circles. Needless to say, these allegorists significantly contribute to the process of the gradual replacing of the mythical view of the world with its more philosophical explanation. The present book suggests that it is the philosophy of Aristotle that should be regarded as a sort of acme in the development of ancient hermeneutics. The reasons for this are twofold. On the one hand, the Stagirite positively values the practice of allegoresis, rehabilitating, thus, the tradition of Preplatonic philosophy against Plato. And, on the other hand, Aristotle initiates the theoretical reflection on figurative (“enigmatic”) language. Hence, in Aristotle we encounter not only the practice of allegoresis, but also the theory of allegory (although the philosopher does not use the term allēgoría). With the situation being as it is, the significance of Aristotle’s work cannot be overestimated. First of all, the Stagirite introduces the concept of metaphor into the then philosophical considerations. From that moment onwards, the phenomenon of figurative language becomes an important philosophical issue. After Aristo-tle, the preponderance of thinkers would feel obliged to specify the rules for the appropriate use of figurative language and the techniques of its correct interpretation. Furthermore, Aristotle ascribes to metaphor (and to various other “excellent” sayings) the function of increasing and enhancing our knowledge. Thus, according to the Stagirite, figurative language is not only an ornamental device, but it can also have a significant explanatory power. Finally, Aristotle observes that figurative expressions cause words to become ambiguous. In this context, the philosopher notices that ambiguity can enrich the language of a poet, but it can also hinder a dialectical discussion. Accordingly, Aristotle is inclined to value polysemy either positively or negatively. Importantly, however, the Stagirite is perfectly aware of the fact that in natural languages ambiguity is unavoidable. This is why Aristotle initiates a syste-matic reflection on the phenomenon of ambiguity and distinguishes its various kinds. In Aristotle, ambiguity is, then, both a problem that needs to be identified and a tool that can help in elucidating intricate philosophical issues. This unique approach to ambiguity and figurative (“enigmatic”) language enabled Aristotle to formulate invaluable intuitions that still await appropriate recognition.

Identyfikacja domen WG/GW zaangażowanych w wiązanie białek Argonaute oraz analiza mechanizmów molekularnych odpowiedzialnych za ich zmienność

Wydział Biologii: Instytut Biologii Molekularnej i Biotechnologii

Síndrome Dolorosa Miofascial no contexto da Medicina Dentária

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Medicina Dentária

Branqueamento Dentário

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Medicina Dentária

On the Marginal Utility of Deploying Measurement Infrastructure

The cost and complexity of deploying measurement infrastructure in the Internet for the purpose of analyzing its structure and behavior is considerable. Basic questions about the utility of increasing the number of measurements and/or measurement sites have not yet been addressed which has lead to a "more is better" approach to wide-area measurements. In this paper, we quantify the marginal utility of performing wide-area measurements in the context of Internet topology discovery. We characterize topology in terms of nodes, links, node degree distribution, and end-to-end flows using statistical and information-theoretic techniques. We classify nodes discovered on the routes between a set of 8 sources and 1277 destinations to differentiate nodes which make up the so called "backbone" from those which border the backbone and those on links between the border nodes and destination nodes. This process includes reducing nodes that advertise multiple interfaces to single IP addresses. We show that the utility of adding sources goes down significantly after 2 from the perspective of interface, node, link and node degree discovery. We show that the utility of adding destinations is constant for interfaces, nodes, links and node degree indicating that it is more important to add destinations than sources. Finally, we analyze paths through the backbone and show that shared link distributions approximate a power law indicating that a small number of backbone links in our study are very heavily utilized.

Web Mediators for Accessible Browsing

We present a highly accurate method for classifying web pages based on link percentage, which is the percentage of text characters that are parts of links normalized by the number of all text characters on a web page. K-means clustering is used to create unique thresholds to differentiate index pages and article pages on individual web sites. Index pages contain mostly links to articles and other indices, while article pages contain mostly text. We also present a novel link grouping algorithm using agglomerative hierarchical clustering that groups links in the same spatial neighborhood together while preserving link structure. Grouping allows users with severe disabilities to use a scan-based mechanism to tab through a web page and select items. In experiments, we saw up to a 40-fold reduction in the number of commands needed to click on a link with a scan-based interface, which shows that we can vastly improve the rate of communication for users with disabilities. We used web page classification and link grouping to alter web page display on an accessible web browser that we developed to make a usable browsing interface for users with disabilities. Our classification method consistently outperformed a baseline classifier even when using minimal data to generate article and index clusters, and achieved classification accuracy of 94.0% on web sites with well-formed or slightly malformed HTML, compared with 80.1% accuracy for the baseline classifier.

A Neural Network Architecture for Autonomous Learning, Recognition, and Prediction in a Nonstationary World

In a constantly changing world, humans are adapted to alternate routinely between attending to familiar objects and testing hypotheses about novel ones. We can rapidly learn to recognize and narne novel objects without unselectively disrupting our memories of familiar ones. We can notice fine details that differentiate nearly identical objects and generalize across broad classes of dissimilar objects. This chapter describes a class of self-organizing neural network architectures--called ARTMAP-- that are capable of fast, yet stable, on-line recognition learning, hypothesis testing, and naming in response to an arbitrary stream of input patterns (Carpenter, Grossberg, Markuzon, Reynolds, and Rosen, 1992; Carpenter, Grossberg, and Reynolds, 1991). The intrinsic stability of ARTMAP allows the system to learn incrementally for an unlimited period of time. System stability properties can be traced to the structure of its learned memories, which encode clusters of attended features into its recognition categories, rather than slow averages of category inputs. The level of detail in the learned attentional focus is determined moment-by-moment, depending on predictive success: an error due to over-generalization automatically focuses attention on additional input details enough of which are learned in a new recognition category so that the predictive error will not be repeated. An ARTMAP system creates an evolving map between a variable number of learned categories that compress one feature space (e.g., visual features) to learned categories of another feature space (e.g., auditory features). Input vectors can be either binary or analog. Computational properties of the networks enable them to perform significantly better in benchmark studies than alternative machine learning, genetic algorithm, or neural network models. Some of the critical problems that challenge and constrain any such autonomous learning system will next be illustrated. Design principles that work together to solve these problems are then outlined. These principles are realized in the ARTMAP architecture, which is specified as an algorithm. Finally, ARTMAP dynamics are illustrated by means of a series of benchmark simulations.

Biological wastes as plant growth substrate amendments

Globally, agriculture is being intensified with mechanization and increased use of synthetic fertilizers and pesticides. There has been a scaling up of production to satisfy the demands of supermarket distribution. Problems associated with intensification of production, trade globalisation and a larger market demand for greater volumes of fresh produce, include consumers' concern about pesticide residues and leaching of nutrients and pesticides into the environment, as well as increases in the transmission of human food-poisoning pathogens on raw vegetables and in fruit juices. The first part of this research was concerned with the evaluation of a biological control strategy for soil-borne pathogens, these are difficult to eliminate and the chemicals of which the most effective fumigants e.g. methyl bromide, are being withdrawn form use. Chitin-containing crustaceans shellfish waste was investigated as a selective growth substrate amendment in the field, in glasshouse and in storage trials against Sclerotinia disease of Helianthus tuberosus, Phytophthora fragariae disease of Fragaria vesca and Fusarium disease of Dianthus. Results showed that addition to shellfish waste stimulated substrate microbial populations and lytic activity and induced plant defense proteins, namely chitinases and cellulases. Protective effects were seen in all crop models but the results indicate that further trials are required to confirm long-term efficacy. The second part of the research investigated the persistence of enteric bacteria in raw salad vegetables using model food poisoning isolates. In clinical investigations plants are sampled for bacterial contamination but no attempt is made to differentiate between epiphytes and endophytes. Results here indicate that the mode isolates persist endophytically thereby escaping conventional chlorine washes and they may also induce host defenses, which results in their suppression and in negative results in conventional plate count screening. Finally a discussion of criteria that should be considered for a HACCP plan for safe raw salad vegetable production is presented.

The role of metabolism in the pathogenesis of adherent invasive Escherichia coli (AIEC)

Crohn’s disease (CD) is a chronic, relapsing inflammatory condition affecting the gastrointestinal tract of humans, of which there is currently no cure. The precise etiology of CD is unknown, although it has become widely accepted that it is a multifactorial disease which occurs as a result of an abnormal immune response to commensal enteric bacteria in a genetically susceptible host. Recent studies have shown that a new group of Escherichia coli, called Adherent Invasive Escherichia coli (AIEC) are present in the guts of CD patients at a higher frequency than in healthy subjects, suggesting that they may play a role in the initiation and/or maintenance of the inflammation associated with CD. Two phenotypes define an AIEC and differentiate them from other groups of E. coli. Firstly, AIEC can adhere to and invade epithelial cells; and secondly, they can replicate in macrophages. In this study, we use a strain of AIEC which has been isolated from the colonic mucosa of a CD patient, called HM605, to examine the relationship between AIEC and the macrophage. We show, using a systematic mutational approach, that while the Tricarboxylic acid (TCA) cycle, the glyoxylate pathway, the Entner-Doudoroff (ED) pathway, the Pentose Phosphate (PP) pathway and gluconeogenesis are dispensable for the intramacrophagic growth of HM605, glycolysis is an absolute requirement for the ability of this organism to replicate intracellularly. We also show that HM605 activates the inflammasome, a major driver of inflammation in mammals. Specifically, we show that macrophages infected with HM605 produce significantly higher levels of the pro-inflammatory cytokine IL-1β than macrophages infected with a non-AIEC strain, and we show by immunoblotting that this is due to cleavage of caspase-1. We also show that macrophages infected with HM605 exhibit significantly higher levels of pyroptosis, a form of inflammatory cell death, than macrophages infected with a non-AIEC strain. Therefore, AIEC strains are more pro-inflammatory than non-AIEC strains and this may have important consequences in terms of CD pathology. Moreover, we show that while inflammasome activation by HM605 is independent of intracellular bacterial replication, it is dependent on an active bacterial metabolism. Through the establishment of a genetic screen aimed at identifying mutants which activate the inflammasome to lower levels than the wild-type, we confirm our observation that bacterial metabolism is essential for successful inflammasome activation by HM605 and we also uncover new systems/structures that may be important for inflammasome activation, such as the BasS/BasR two-component system, a type VI secretion system and a K1 capsule. Finally, in this study, we also identify a putative small RNA in AIEC strain LF82, which may be involved in modulating the motility of this strain. Overall this works shows that, in the absence of specialised virulence factors, the ability of AIEC to metabolise within the host cell may be a key determinant of its pathogenesis.