Exotic B-c-like molecules in QCD sum rules

We use the QCD sum rules to study possible B-c-like molecular states. We consider isoscalar J(P) = 0(+) and J(P) = 1(+) D(*) B(*) molecular currents. We consider the contributions of condensates up to dimension eight and we work at leading order in alpha(s). We obtain for these states masses around 7 GeV. (C) 2012 Elsevier B.V. All rights reserved.

Contributions to underwater glider path planning

[ES] La Planificación de Rutas o Caminos es un disciplina de Robótica que trata la búsqueda de caminos factibles u óptimos. Para la mayoría de vehículos y entornos, no es un problema trivial y por tanto nos encontramos con un gran diversidad de algoritmos para resolverlo, no sólo en Robótica e Inteligencia Artificial, sino también como parte de la literatura de Optimización, con Métodos Numéricos y Algoritmos Bio-inspirados, como Algoritmos Genéticos y el Algoritmo de la Colonia de Hormigas. El caso particular de escenarios de costes variables es considerablemente difícil de abordar porque el entorno en el que se mueve el vehículo cambia con el tiempo. El presente trabajo de tesis estudia este problema y propone varias soluciones prácticas para aplicaciones de Robótica Submarina.

Heregulin -beta 1 directly associates with RhoA via the immunoglobulin -like domain thereby modulating breast cancer metastasis-related properties

Heregulins constitute a family of growth factors belonging to the epidermal growth factor (EGF) family. Breast cancers that overexpress specific members of the EGF receptor family (EGFR, ErbB2, ErbB3, ErbB4) have increased metastatic potential, and Heregulin-β1 (HRGβ1), a ligand for ErbB3 and ErbB4, has also been shown to induce metastasis-related properties in breast cancer cells in vitro. The secreted form of the HRGβ1 is composed of five distinct structural domains, including the N-terminal domain, an immunoglobulin-like domain (IgG-like), a glycosylation domain, an EGF-like domain, and a β1-specific domain. Of these, the EGF-like domain is well characterized for its function in metastasis-related properties as well as its structure. However, the contributions of the other HRGβ1 domains in breast cancer metastasis remains unclear. ^ To investigate this, HRGβ1 proteins with targeted domain deletions were purified and subjected to assays for metastasis-related properties, including aggregation, invasion, activation of EGFR family members, and motility of breast cancer cells. These assays showed that retaining the EGF-like domain of HRGβ1 is important for activation of EGFRs. Interestingly, the HRGβ1 protein lacking the IgG-like domain (NGEB) led to a decrease in breast cancer cell motility, indicating the IgG-like domain modulates cell motility, an important step in cancer metastasis. ^ To understand the underlying mechanisms, I performed protein sequence and structural analysis of HRGβ1 and identified that the IgG-like domain of HRGβ1 shares sequence homology and three-dimensional structural similarity with the IgG-like domain of TRIO. TRIO is a cytoplasmic protein that directly associates with RhoA, a GTPase involved in cell reorganization and cell motility. Therefore, I hypothesized that HRGβ1 may translocate inside the breast cancer cells through receptor mediated endocytosis and bind to RhoA via its IgG-like domain. I show wild type HRGβ1 but not NGEB binds RhoA in vitro and in vivo, leading to RhoA activation. Inhibition of HRG-β1 internalization via endocytosis disrupted HRGβ1 binding to RhoA. Additionally, breast cancer cell motility induced by HRG-β1 is reduced after treatment with inhibitors to both endocytosis and RhoA function, similar to levels seen with NGEB treatment. ^ Thus, in addition to the well-known role of HRGβ1 as an extracellular stimulator of the EGFR family members, HRGβ1 also functions within the cell as a binding partner and activator of RhoA to modulate cancer cell motility. ^

Evaluating the reinforcement of inorganic fullerene-like nanoparticles in thermoplastic matrices by depth-sensing indentation

The reinforcing effect of inorganic fullerene-like tungsten disulfide (IF-WS2) nanoparticles in two different polymer matrices, isotactic polypropylene (iPP) and polyphenylene sulfide (PPS), has been investigated by means of dynamic depth-sensing indentation. The hardness and elastic modulus enhancement upon filler addition is analyzed in terms of two main contributions: changes in the polymer matrix nanostructure and intrinsic properties of the filler including matrix-particle load transfer. It is found that the latter mainly determines the overall mechanical improvement, whereas the nanostructural changes induced in the polymer matrix only contribute to a minor extent. Important differences are suggested between the mechanisms of deformation in the two nanocomposites, resulting in a moderate mechanical enhancement in case of iPP (20% for a filler loading of 1%), and a remarkable hardness increase in case of PPS (60% for the same filler content). The nature of the polymer amorphous phase, whether in the glassy or rubbery state, seems to play here an important role. Finally, nanoindentation and dynamic mechanical analysis measurements are compared and discussed in terms of the different directionality of the stresses applied.

Is water structure around hydrophobic groups clathrate-like?

The term "clathrate structure" is quantified for solvation of nonpolar groups by enumerating hydrogen-bonded ring sizes both in the solvation shell and through the shell-bulk interface and comparing it to a bulk control using the ST4 water model. For clathrate-like structure to be evident, the distributions along the hydrophobic surface are expected to be dominated by pentagons, with significant depletion of hexagons and larger polygons. While the distribution in this region is indeed distinguished by a large number of pentagons, there are significant contributions from hexagons and larger rings as well. Calculated polygon distributions through the shell-bulk interface indicate that when water structure is highly cooperative along the hydrophobic surface, hydrogen-bonded pathways leading back into bulk are then reduced. These results are qualitatively consistent with the observation that hydrophobicity is proportional to the nonpolar solute surface area.

Photo-dissolution of flocculent, detrital material in aquatic environments: Contributions to the dissolved organic matter pool

This study shows that light exposure of flocculent material (floc) from the Florida Coastal Everglades (FCE) results in significant dissolved organic matter (DOM) generation through photo-dissolution processes. Floc was collected at two sites along the Shark River Slough (SRS) and irradiated with artificial sunlight. The DOM generated was characterized using elemental analysis and excitation emission matrix fluorescence coupled with parallel factor analysis. To investigate the seasonal variations of DOM photo-generation from floc, this experiment was performed in typical dry (April) and wet (October) seasons for the FCE. Our results show that the dissolved organic carbon (DOC) for samples incubated under dark conditions displayed a relatively small increase, suggesting that microbial processes and/or leaching might be minor processes in comparison to photo-dissolution for the generation of DOM from floc. On the other hand, DOC increased substantially (as much as 259 mgC gC−1) for samples exposed to artificial sunlight, indicating the release of DOM through photo-induced alterations of floc. The fluorescence intensity of both humic-like and protein-like components also increased with light exposure. Terrestrial humic-like components were found to be the main contributors (up to 70%) to the chromophoric DOM (CDOM) pool, while protein-like components comprised a relatively small percentage (up to 16%) of the total CDOM. Simultaneously to the generation of DOC, both total dissolved nitrogen and soluble reactive phosphorus also increased substantially during the photo-incubation period. Thus, the photo-dissolution of floc can be an important source of DOM to the FCE environment, with the potential to influence nutrient dynamics in this system.

Addressing deficits and injustices : the potential epistemic contributions of patients to research

Acknowledgments The research for this paper was primarily funded by an Australian Research Council (ARC) grant (DP120101092), How do we know what works? Ethics and evidence in surgical research. Katrina Hutchison’s research was also partly funded by the ARC Centre of Excellence for Electromaterials Science, where she has worked since June 2015. Discussions about the paper were facilitated by Macquarie University funding of a visit by Vikki A. Entwistle to participate in a Centre for Agency, Values and Ethics (CAVE) seminar on Capabilities Approaches to Justice. The authors would like to thank the anonymous reviewers for a number of helpful comments.

Relative Contributions of Prenylation and Postprenylation Processing in Cryptococcus neoformans Pathogenesis.

Prenyltransferase enzymes promote the membrane localization of their target proteins by directing the attachment of a hydrophobic lipid group at a conserved C-terminal CAAX motif. Subsequently, the prenylated protein is further modified by postprenylation processing enzymes that cleave the terminal 3 amino acids and carboxymethylate the prenylated cysteine residue. Many prenylated proteins, including Ras1 and Ras-like proteins, require this multistep membrane localization process in order to function properly. In the human fungal pathogen Cryptococcus neoformans, previous studies have demonstrated that two distinct forms of protein prenylation, farnesylation and geranylgeranylation, are both required for cellular adaptation to stress, as well as full virulence in animal infection models. Here, we establish that the C. neoformans RAM1 gene encoding the farnesyltransferase β-subunit, though not strictly essential for growth under permissive in vitro conditions, is absolutely required for cryptococcal pathogenesis. We also identify and characterize postprenylation protease and carboxyl methyltransferase enzymes in C. neoformans. In contrast to the prenyltransferases, deletion of the genes encoding the Rce1 protease and Ste14 carboxyl methyltransferase results in subtle defects in stress response and only partial reductions in virulence. These postprenylation modifications, as well as the prenylation events themselves, do play important roles in mating and hyphal transitions, likely due to their regulation of peptide pheromones and other proteins involved in development. IMPORTANCE Cryptococcus neoformans is an important human fungal pathogen that causes disease and death in immunocompromised individuals. The growth and morphogenesis of this fungus are controlled by conserved Ras-like GTPases, which are also important for its pathogenicity. Many of these proteins require proper subcellular localization for full function, and they are directed to cellular membranes through a posttranslational modification process known as prenylation. These studies investigate the roles of one of the prenylation enzymes, farnesyltransferase, as well as the postprenylation processing enzymes in C. neoformans. We demonstrate that the postprenylation processing steps are dispensable for the localization of certain substrate proteins. However, both protein farnesylation and the subsequent postprenylation processing steps are required for full pathogenesis of this fungus.

Benchmarking a modified version of the civ3 nonrelativistic atomic-structure code within Na-like-tungsten R -matrix calculations

In this work we explore the validity of employing a modified version of the nonrelativistic structure code civ3 for heavy, highly charged systems, using Na-like tungsten as a simple benchmark. Consequently, we present radiative and subsequent collisional atomic data compared with corresponding results from a fully relativistic structure and collisional model. Our motivation for this line of study is to benchmark civ3 against the relativistic grasp0 structure code. This is an important study as civ3 wave functions in nonrelativistic R-matrix calculations are computationally less expensive than their Dirac counterparts. There are very few existing data for the W LXIV ion in the literature with which we can compare except for an incomplete set of energy levels available from the NIST database. The overall accuracy of the present results is thus determined by the comparison between the civ3 and grasp0 structure codes alongside collisional atomic data computed by the R-matrix Breit-Pauli and Dirac codes. It is found that the electron-impact collision strengths and effective collision strengths computed by these differing methods are in good general agreement for the majority of the transitions considered, across a broad range of electron temperatures.

Mise en évidence de dysfonctions liées au développement de l'endométriose péritonérale Contributions angio-inflammatoires des cytokines et prostaglandines

L’endométriose est une maladie gynécologique, touchant les femmes en âge de procréer. Cette pathologie est caractérisée par la présence de tissu endométrial ectopique, c’est-à-dire en dehors de la cavité utérine. Des dysfonctions du système immunitaire sont de plus en plus souvent suspectées comme étant un des éléments responsables de la pathogenèse de cette maladie. L’objectif général de ce projet a donc été d’étudier les mécanismes cellulaires de molécules pro-inflammatoires aux propriétés variées et à l’expression anormalement élevée dans cette pathologie, que sont MIF et les prostaglandines PGE2 et PGF2α, dans les anomalies inflammatoires et invasives en cause dans cette pathologie. La première partie de nos travaux a porté sur l’étude d’un modèle murin de l’endométriose déficient du gène MIF. Le nombre et le volume des lésions collectées à partir des souris déficientes pour le gène MIF sont significativement inférieurs à ceux mesurés dans des souris sauvages utilisées comme contrôle. L’analyse par PCR des cellules isolées des lésions de souris déficientes du gène MIF a révélé une expression réprimée des protéines d’adhésion, d’inflammation et d’angiogenèse. Ces données démontrent pour la première fois que le MIF agit directement sur la croissance et la progression de lésions d’endométriose in vivo. Une partie de nos travaux a porté sur les molécules nécessaires au métabolisme de PGE2 et PGF2α dans l’endomètre eutopique des femmes normales et l’endomètre eutopique et ectopique des femmes atteintes d’endométriose. Selon nos données, l’expression de certains de ces facteurs est perturbée durant cette maladie, ce qui peut avoir des effets délétères sur la physiologie de la procréation. La stimulation des cellules ectopiques par PGF2α entraîne une libération accrue de VEGF et CXCL-8, ceci via l’induction de COX-2 et des deux variants d’épissage du récepteur FP. De plus, la PKC joue un rôle dans ce phénomène, dépendamment et indépendamment de la PLC. Par son effet inducteur sur la libération de VEGF et CXCL-8, PGF2α pourrait favoriser l’aspect inflammatoire et le développement ectopique des lésions d’endométriose, notamment par des phénomènes d’angiogenèse et de prolifération cellulaire accrus. L’effet de PGF2α sur la libération de VEGF et CXCL-8 par les cellules endométriales ectopiques pourrait également expliquer les quantités élevées de ces cytokines dans le liquide péritonéal des femmes atteintes d’endométriose, un phénomène suspecté dans l’infertilité et les douleurs associées à cette maladie. Nos derniers résultats obtenus à partir du liquide péritonéal montrent un profil cytokinique en faveur de l’angiogenèse et la prolifération des lésions d’endométriose, avec une forte augmentation des facteurs suivants : EGF, FGF-2, IL-1α, MIP-1β, TGFα, PDGF-AA, PDGF-BB, MCP-3, sCD40L, Gro Pan, IL-17α, MDC et Rantes, confortant nos observations préalables redéfinissant la maladie comme étant d’origine angio-inflammatoire. L’endométriose et ses symptômes sont des phénomènes complexes ayant probablement plus qu’une seule origine. Parmi les nombreux facteurs à l’expression altérée dans l’endométriose, notre étude montre que MIF, PGE2 et PGF2α, ainsi qu’une pléthore de facteurs pro-angiogéniques pourraient être de ceux jouant un rôle dans l’infertilité et les douleurs reliées à cette maladie.

Contributions to 3D Data Registration and Representation

Nowadays, new computers generation provides a high performance that enables to build computationally expensive computer vision applications applied to mobile robotics. Building a map of the environment is a common task of a robot and is an essential part to allow the robots to move through these environments. Traditionally, mobile robots used a combination of several sensors from different technologies. Lasers, sonars and contact sensors have been typically used in any mobile robotic architecture, however color cameras are an important sensor due to we want the robots to use the same information that humans to sense and move through the different environments. Color cameras are cheap and flexible but a lot of work need to be done to give robots enough visual understanding of the scenes. Computer vision algorithms are computational complex problems but nowadays robots have access to different and powerful architectures that can be used for mobile robotics purposes. The advent of low-cost RGB-D sensors like Microsoft Kinect which provide 3D colored point clouds at high frame rates made the computer vision even more relevant in the mobile robotics field. The combination of visual and 3D data allows the systems to use both computer vision and 3D processing and therefore to be aware of more details of the surrounding environment. The research described in this thesis was motivated by the need of scene mapping. Being aware of the surrounding environment is a key feature in many mobile robotics applications from simple robotic navigation to complex surveillance applications. In addition, the acquisition of a 3D model of the scenes is useful in many areas as video games scene modeling where well-known places are reconstructed and added to game systems or advertising where once you get the 3D model of one room the system can add furniture pieces using augmented reality techniques. In this thesis we perform an experimental study of the state-of-the-art registration methods to find which one fits better to our scene mapping purposes. Different methods are tested and analyzed on different scene distributions of visual and geometry appearance. In addition, this thesis proposes two methods for 3d data compression and representation of 3D maps. Our 3D representation proposal is based on the use of Growing Neural Gas (GNG) method. This Self-Organizing Maps (SOMs) has been successfully used for clustering, pattern recognition and topology representation of various kind of data. Until now, Self-Organizing Maps have been primarily computed offline and their application in 3D data has mainly focused on free noise models without considering time constraints. Self-organising neural models have the ability to provide a good representation of the input space. In particular, the Growing Neural Gas (GNG) is a suitable model because of its flexibility, rapid adaptation and excellent quality of representation. However, this type of learning is time consuming, specially for high-dimensional input data. Since real applications often work under time constraints, it is necessary to adapt the learning process in order to complete it in a predefined time. This thesis proposes a hardware implementation leveraging the computing power of modern GPUs which takes advantage of a new paradigm coined as General-Purpose Computing on Graphics Processing Units (GPGPU). Our proposed geometrical 3D compression method seeks to reduce the 3D information using plane detection as basic structure to compress the data. This is due to our target environments are man-made and therefore there are a lot of points that belong to a plane surface. Our proposed method is able to get good compression results in those man-made scenarios. The detected and compressed planes can be also used in other applications as surface reconstruction or plane-based registration algorithms. Finally, we have also demonstrated the goodness of the GPU technologies getting a high performance implementation of a CAD/CAM common technique called Virtual Digitizing.

Enterococcus faecalis prophage dynamics and contributions to pathogenic traits

Polylysogeny is frequently considered to be the result of an adaptive evolutionary process in which prophages confer fitness and/or virulence factors, thus making them important for evolution of both bacterial populations and infectious diseases. The Enterococcus faecalis V583 isolate belongs to the high-risk clonal complex 2 that is particularly well adapted to the hospital environment. Its genome carries 7 prophage-like elements (V583-pp1 to -pp7), one of which is ubiquitous in the species. In this study, we investigated the activity of the V583 prophages and their contribution to E. faecalis biological traits. We systematically analyzed the ability of each prophage to excise from the bacterial chromosome, to replicate and to package its DNA. We also created a set of E. faecalis isogenic strains that lack from one to all six non-ubiquitous prophages by mimicking natural excision. Our work reveals that prophages of E. faecalis V583 excise from the bacterial chromosome in the presence of a fluoroquinolone, and are able to produce active phage progeny. Intricate interactions between V583 prophages were also unveiled: i) pp7, coined EfCIV583 for E. faecalis chromosomal island of V583, hijacks capsids from helper phage 1, leading to the formation of distinct virions, and ii) pp1, pp3 and pp5 inhibit excision of pp4 and pp6. The hijacking exerted by EfCIV583 on helper phage 1 capsids is the first example of molecular piracy in Gram positive bacteria other than staphylococci. Furthermore, prophages encoding platelet-binding-like proteins were found to be involved in adhesion to human platelets, considered as a first step towards the development of infective endocarditis. Our findings reveal not only a role of E. faecalis V583 prophages in pathogenicity, but also provide an explanation for the correlation between antibiotic usage and E. faecalis success as a nosocomial pathogen, as fluoriquinolone may provoke release of prophages and promote gene dissemination among isolates.