Stationary scattering from a nonlinear network

Transmission through a complex network of nonlinear one-dimensional leads is discussed by extending the stationary scattering theory on quantum graphs to the nonlinear regime. We show that the existence of cycles inside the graph leads to a large number of sharp resonances that dominate scattering. The latter resonances are then shown to be extremely sensitive to the nonlinearity and display multistability and hysteresis. This work provides a framework for the study of light propagation in complex optical networks.

The interplay between microscopic and mesoscopic structures in complex networks

Understanding a complex network's structure holds the key to understanding its function. The physics community has contributed a multitude of methods and analyses to this cross-disciplinary endeavor. Structural features exist on both the microscopic level, resulting from differences between single node properties, and the mesoscopic level resulting from properties shared by groups of nodes. Disentangling the determinants of network structure on these different scales has remained a major, and so far unsolved, challenge. Here we show how multiscale generative probabilistic exponential random graph models combined with efficient, distributive message-passing inference techniques can be used to achieve this separation of scales, leading to improved detection accuracy of latent classes as demonstrated on benchmark problems. It sheds new light on the statistical significance of motif-distributions in neural networks and improves the link-prediction accuracy as exemplified for gene-disease associations in the highly consequential Online Mendelian Inheritance in Man database. © 2011 Reichardt et al.

Communities and emerging semantics in semantic link network:discovery and learning

The World Wide Web provides plentiful contents for Web-based learning, but its hyperlink-based architecture connects Web resources for browsing freely rather than for effective learning. To support effective learning, an e-learning system should be able to discover and make use of the semantic communities and the emerging semantic relations in a dynamic complex network of learning resources. Previous graph-based community discovery approaches are limited in ability to discover semantic communities. This paper first suggests the Semantic Link Network (SLN), a loosely coupled semantic data model that can semantically link resources and derive out implicit semantic links according to a set of relational reasoning rules. By studying the intrinsic relationship between semantic communities and the semantic space of SLN, approaches to discovering reasoning-constraint, rule-constraint, and classification-constraint semantic communities are proposed. Further, the approaches, principles, and strategies for discovering emerging semantics in dynamic SLNs are studied. The basic laws of the semantic link network motion are revealed for the first time. An e-learning environment incorporating the proposed approaches, principles, and strategies to support effective discovery and learning is suggested.

New Directions in Commercial Secrecy and Encryption Protocols

Secure transmission of bulk data is of interest to many content providers. A commercially-viable distribution of content requires technology to prevent unauthorised access. Encryption tools are powerful, but have a performance cost. Without encryption, intercepted data may be illicitly duplicated and re-sold, or its commercial value diminished because its secrecy is lost. Two technical solutions make it possible to perform bulk transmissions while retaining security without too high a performance overhead. These are: 1. a) hierarchical encryption - the stronger the encryption, the harder it is to break but also the more computationally expensive it is. A hierarchical approach to key exchange means that simple and relatively weak encryption and keys are used to encrypt small chunks of data, for example 10 seconds of video. Each chunk has its own key. New keys for this bottom-level encryption are exchanged using a slightly stronger encryption, for example a whole-video key could govern the exchange of the 10-second chunk keys. At a higher level again, there could be daily or weekly keys, securing the exchange of whole-video keys, and at a yet higher level, a subscriber key could govern the exchange of weekly keys. At higher levels, the encryption becomes stronger but is used less frequently, so that the overall computational cost is minimal. The main observation is that the value of each encrypted item determines the strength of the key used to secure it. 2. b) non-symbolic fragmentation with signal diversity - communications are usually assumed to be sent over a single communications medium, and the data to have been encrypted and/or partitioned in whole-symbol packets. Network and path diversity break up a file or data stream into fragments which are then sent over many different channels, either in the same network or different networks. For example, a message could be transmitted partly over the phone network and partly via satellite. While TCP/IP does a similar thing in sending different packets over different paths, this is done for load-balancing purposes and is invisible to the end application. Network and path diversity deliberately introduce the same principle as a secure communications mechanism - an eavesdropper would need to intercept not just one transmission path but all paths used. Non-symbolic fragmentation of data is also introduced to further confuse any intercepted stream of data. This involves breaking up data into bit strings which are subsequently disordered prior to transmission. Even if all transmissions were intercepted, the cryptanalyst still needs to determine fragment boundaries and correctly order them. These two solutions depart from the usual idea of data encryption. Hierarchical encryption is an extension of the combined encryption of systems such as PGP but with the distinction that the strength of encryption at each level is determined by the "value" of the data being transmitted. Non- symbolic fragmentation suppresses or destroys bit patterns in the transmitted data in what is essentially a bit-level transposition cipher but with unpredictable irregularly-sized fragments. Both technologies have applications outside the commercial and can be used in conjunction with other forms of encryption, being functionally orthogonal.

PARTITIONED ANALYSIS FOR DIMENSIONALLY-HETEROGENEOUS HYDRAULIC NETWORKS

In this work an iterative strategy is developed to tackle the problem of coupling dimensionally-heterogeneous models in the context of fluid mechanics. The procedure proposed here makes use of a reinterpretation of the original problem as a nonlinear interface problem for which classical nonlinear solvers can be applied. Strong coupling of the partitions is achieved while dealing with different codes for each partition, each code in black-box mode. The main application for which this procedure is envisaged arises when modeling hydraulic networks in which complex and simple subsystems are treated using detailed and simplified models, correspondingly. The potentialities and the performance of the strategy are assessed through several examples involving transient flows and complex network configurations.

Musical genres: beating to the rhythms of different drums

Online music databases have increased significantly as a consequence of the rapid growth of the Internet and digital audio, requiring the development of faster and more efficient tools for music content analysis. Musical genres are widely used to organize music collections. In this paper, the problem of automatic single and multi-label music genre classification is addressed by exploring rhythm-based features obtained from a respective complex network representation. A Markov model is built in order to analyse the temporal sequence of rhythmic notation events. Feature analysis is performed by using two multi-variate statistical approaches: principal components analysis (unsupervised) and linear discriminant analysis (supervised). Similarly, two classifiers are applied in order to identify the category of rhythms: parametric Bayesian classifier under the Gaussian hypothesis (supervised) and agglomerative hierarchical clustering (unsupervised). Qualitative results obtained by using the kappa coefficient and the obtained clusters corroborated the effectiveness of the proposed method.

A vaccination game based on public health actions and personal decisions

Susceptible-infective-removed (SIR) models are commonly used for representing the spread of contagious diseases. A SIR model can be described in terms of a probabilistic cellular automaton (PCA), where each individual (corresponding to a cell of the PCA lattice) is connected to others by a random network favoring local contacts. Here, this framework is employed for investigating the consequences of applying vaccine against the propagation of a contagious infection, by considering vaccination as a game, in the sense of game theory. In this game, the players are the government and the susceptible newborns. In order to maximize their own payoffs, the government attempts to reduce the costs for combating the epidemic, and the newborns may be vaccinated only when infective individuals are found in their neighborhoods and/or the government promotes an immunization program. As a consequence of these strategies supported by cost-benefit analysis and perceived risk, numerical simulations show that the disease is not fully eliminated and the government implements quasi-periodic vaccination campaigns. (C) 2011 Elsevier B.V. All rights reserved.

Australia’s Lily Brayton: Performer and theatre artist

Recognition is the aim of this account of an artist who is now remembered largely for her beauty, her wide iconic fame achieved by mass distribution of her image via photography and postcards, and her professional association with a internationally prominent producer who was also her husband. It is however a historically situated study, confining itself to readings of the kind of theatrical, social and cultural work performed by Brayton's presence in a rapidly-modernising Australia during the period between Federation in 1901 and the first World War, which event marks a disjuncture in the patterns of entertainment and cultural discourse in the new nation. Pre-war Australian theatre and vaudeville managements competed vigorously to secure the most acclaimed artists, seeing it as a kind of service and duty to boost their country's prestige along with their own coffers. Meanwhile, local playwrights and producers promoted a burgeoning repertoire of Australian dramas and films which played alongside the imported products in a complex network of cultural codes and affects.

Bone Deposition, Bone Resorption, and Osteosarcoma

Bone deposition and bone resorption are ongoing dynamic processes, constituting bone remodeling. Some bone tumors, such as osteosarcoma (OS), stimulate focal bone deposition. OS is the most common primary bone tumor in children and young adults. A complex network of genes regulates bone remodeling and alterations in its expression levels can influence the genesis and progression of bone diseases, including OS. We hypothesized that the expression profiles of bone remodeling regulator genes would be correlated with OS biology and clinical features. We used real-time PCR to evaluate the mRNA levels of the tartrate-resistant acid phosphatase (ACP5), colony stimulating factor-1 (CSF1R), bone morphogenetic protein 7 (BMP7), collagen, type XI, alpha 2 (COL11A2), and protein tyrosine phosphatases zeta 1 (PTPRZ1) genes, in 30 OS tumor samples and correlated with clinical and histological data. All genes analyzed, except CSF1R, were differentially expressed when compared with normal bone expression profiles. In our results, OS patients with high levels of COL11A2 mRNA showed worse overall (p = 0.041) and event free survival (p = 0.037). Also, a trend for better overall survival was observed in patients with samples showing higher expression of BMP7 (p =0.067). COL11A2 overexpression and BMP7 underexpression could collaborate to OS tumor growth, through its central role in bone remodeling process. (C) 2010 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 28:1142-1148, 2010

Development of human minor salivary glands: expression of mucins according to stage of morphogenesis

The formation of salivary glands entails the proliferation of epithelial cells from the stomatodeum into the underlying ectomesenchyme, culminating in a complex network of ducts and acinar bulbs. The extent to which mucins regulate this process is unknown, but they appear to mediate luminal space formation and maturation. Our aim was to examine mucin expression patterns during the morphogenesis of human salivary glands. Mucin expression - MUC1, 2, 3, 4, 5AC, 5B, 6, and 16 - was analyzed in specimens of developing human salivary glands, obtained from fetuses at 4-24 weeks` gestation, and fully developed salivary glands by immunohistochemistry. Expression patterns were analyzed qualitatively according to the development stage of the salivary glands. Mucins 1, 3, 4, 5B, and 16 were expressed during salivary gland development - being stronger in all ductal segments by the final phases of branching morphogenesis and in mature glands. Acinar cells were negative for most mucins, including MUC1 in mature salivary glands. Mucins 2, 5AC, and 6 were not expressed. Mucins MUC1, 3, 4, 5B, and 16 are expressed in developing human salivary glands and in mature glands, suggesting important roles in the maturation and maintenance of the ductal network.

Transthyretin Amyloidosis: Chaperone Concentration Changes and Increased Proteolysis in the Pathway to Disease

Transthyretin amyloidosis is a conformational pathology characterized by the extracellular formation of amyloid deposits and the progressive impairment of the peripheral nervous system. Point mutations in this tetrameric plasma protein decrease its stability and are linked to disease onset and progression. Since non-mutated transthyretin also forms amyloid in systemic senile amyloidosis and some mutation bearers are asymptomatic throughout their lives, non-genetic factors must also be involved in transthyretin amyloidosis. We discovered, using a differential proteomics approach, that extracellular chaperones such as fibrinogen, clusterin, haptoglobin, alpha-1-anti-trypsin and 2-macroglobulin are overrepresented in transthyretin amyloidosis. Our data shows that a complex network of extracellular chaperones are over represented in human plasma and we speculate that they act synergistically to cope with amyloid prone proteins. Proteostasis may thus be as important as point mutations in transthyretin amyloidosis.

Multiresponsive supramolecular systems for information processing at the molecular level

Dissertação para obtenção do Grau de Doutor em Química Sustentável

Study of the role of wall teichoic acids in the localization Staphylococcus aureus cell wall synthesis protein PBP4

The cell wall of Staphylococcus aureus is a highly complex network mainly composed of highly cross-linked peptidoglycan (PG) and teichoic acids (TAs), both important for the maintenance of the integrity and viability of bacteria. The penicillin binding proteins (PBPs), which catalyse the final stage of PG biosynthesis, are targets of β-lactam antibiotics and have been a key focus of antibacterial research. S. aureus has four native PBPs, PBP1-4 carried by both methicillin-sensitive (MSSA) and –resistant (MRSA) strains. PBP4 is required for the synthesis of the highly cross-linked PG and, as shown in recent studies, is essential for the expression of β-lactam resistance in community-acquired strains (CA-MRSA). This protein has a septal localization that seems to be spatially and temporally regulated by an unknown intermediate of the wall teichoic acids (WTA) biosynthesis pathway. Therefore, if WTA synthesis is compromised, PBP4 becomes dispersed throughout the entire cell membrane. The aim of this project was to identify the WTA precursor responsible for the septal recruitment of PBP4. In order to do so, inducible mutants of tarB and tarL genes in the background of NCTCPBP4-YFP were constructed allowing for the study of PBP4 localization in the presence and absence of these specific tar genes.With this work we were able to show that the absence of TarB or TarL leads to the delocalization of PBP4, indicating that TarL or a protein/WTA precursor whose localization/synthesis is dependent on TarL is responsible for the recruitment of PBP4.

The role of IFNγ in higher brain function: in health and under chronic stress

Tese de Doutoramento em Ciências da Saúde

Cellular and genetic mechanisms involved in the generation of protective and pathogenic immune responses in human Chagas disease

Perhaps one of the most intriguing aspects of human Chagas disease is the complex network of events that underlie the generation of protective versus pathogenic immune responses during the chronic phase of the disease. While most individuals do not develop patent disease, a large percentage may develop severe forms that eventually lead to death. Although many efforts have been devoted to deciphering these mechanisms, there is still much to be learned before we can fully understand the pathogenesis of Chagas disease. It is clear that the host's immune response is decisive in this process. While characteristics of the parasite influence the immune response, it is becoming evident that the host genetic background plays a fundamental role in the establishment of pathogenic versus protective responses. The involvement of three complex organisms, host, parasite and vector, is certainly one of the key aspects that calls for multidisciplinary approaches towards the understanding of Chagas disease. We believe that now, one hundred years after the discovery of Chagas disease, it is imperative to continue with highly interactive research in order to elucidate the immune response associated with disease evolution, which will be essential in designing prophylactic or therapeutic interventions.