Structural Analysis of Network Traffic Flows

Network traffic arises from the superposition of Origin-Destination (OD) flows. Hence, a thorough understanding of OD flows is essential for modeling network traffic, and for addressing a wide variety of problems including traffic engineering, traffic matrix estimation, capacity planning, forecasting and anomaly detection. However, to date, OD flows have not been closely studied, and there is very little known about their properties. We present the first analysis of complete sets of OD flow timeseries, taken from two different backbone networks (Abilene and Sprint-Europe). Using Principal Component Analysis (PCA), we find that the set of OD flows has small intrinsic dimension. In fact, even in a network with over a hundred OD flows, these flows can be accurately modeled in time using a small number (10 or less) of independent components or dimensions. We also show how to use PCA to systematically decompose the structure of OD flow timeseries into three main constituents: common periodic trends, short-lived bursts, and noise. We provide insight into how the various constituents contribute to the overall structure of OD flows and explore the extent to which this decomposition varies over time.

A structural analysis of G-quadruplex/ligand interactions

This focused review article discusses in detail, all available high-resolution small molecule ligand/G-quadruplex structural data derived from crystallographic and NMR based techniques, in an attempt to understand key factors in ligand binding and to highlight the biological importance of these complexes. In contrast to duplex DNA, G-quadruplexes are four-stranded nucleic acid structures folded from guanine rich repeat sequences stabilized by the stacking of guanine G-quartets and extensive Watson-Crick/Hoogsteen hydrogen bonding. Thermally stable, these topologies can play a role in telomere regulation and gene expression. The core structures of G-quadruplexes form stable scaffolds while the loops have been shown, by the addition of small molecule ligands, to be sufficiently adaptable to generate new and extended binding platforms for ligands to associate, either by extending G-quartet surfaces or by forming additional planar dinucleotide pairings. Many of these structurally characterised loop rearrangements were totally unexpected opening up new opportunities for the design of selective ligands. However these rearrangements do significantly complicate attempts to rationally design ligands against well defined but unbound topologies, as seen for the series of napthalene diimides complexes. Drawing together previous findings and with the introduction of two new crystallographic quadruplex/ligand structures we aim to expand the understanding of possible structural adaptations available to quadruplexes in the presence of ligands, thereby aiding in the design of new selective entities. (C) 2011 Elsevier Masson SAS. All rights reserved.

Structural analysis of glycans and development of microarrays from Helcobacter pylori cell surface glycome

Helicobacter pylori is a bacterial pathogen that affects more than half of the world’s population with gastro-intestinal diseases and is associated with gastric cancer. The cell surface of H. pylori is decorated with lipopolysaccharides (LPSs) composed of three distinct regions: a variable polysaccharide moiety (O-chain), a structurally conserved core oligosaccharide, and a lipid A region that anchors the LPS to the cell membrane. The O-chain of H. pylori LPS, exhibits unique oligosaccharide structures, such as Lewis (Le) antigens, similar to those present in the gastric mucosa and are involved in interactions with the host. Glucan, heptoglycan, and riban domains are present in the outer core region of some H. pylori LPSs. Amylose-like glycans and mannans are also constituents of some H. pylori strains, possibly co-expressed with LPSs. The complexity of H. pylori LPSs has hampered the establishment of accurate structure-function relationships in interactions with the host, and the design of carbohydrate-based therapeutics, such as vaccines. Carbohydrate microarrays are recent powerful and sensitive tools for studying carbohydrate antigens and, since their emergence, are providing insights into the function of carbohydrates and their involvement in pathogen-host interactions. The major goals of this thesis were the structural analysis of LPSs from H. pylori strains isolated from gastric biopsies of symptomatic Portuguese patients and the construction of a novel pathogen carbohydrate microarray of these LPSs (H. pylori LPS microarray) for interaction studies with proteins. LPSs were extracted from the cell surface of five H. pylori clinical isolates and one NCTC strain (26695) by phenol/water method, fractionated by size exclusion chromatography and analysed by gas chromatography coupled to mass spectrometry. The oligosaccharides released after mild acid treatment of the LPS were analysed by electrospray mass spectrometry. In addition to the conserved core oligosaccharide moieties, structural analyses revealed the presence of type-2 Lex and Ley antigens and N-acetyllactosamine (LacNAc) sequences, typically found in H. pylori strains. Also, the presence of O-6 linked glucose residues, particularly in LPSs from strains 2191 and NCTC 26695, pointed out to the expression of a 6-glucan. Other structural domains, namely ribans, composed of O-2 linked ribofuranose residues were observed in the LPS of most of H. pylori clinical isolates. For the LPS from strain 14382, large amounts of O-3 linked galactose units, pointing to the occurrence of a galactan, a domain recently identified in the LPS of another H. pylori strain. A particular feature to the LPSs from strains 2191 and CI-117 was the detection of large amounts of O-4 linked N-acetylglucosamine (GlcNAc) residues, suggesting the presence of chitin-like glycans, which to our knowledge have not been described for H. pylori strains. For the construction of the H. pylori LPS microarray, the structurally analysed LPSs, as well as LPS-derived oligosaccharide fractions, prepared as neoglycolipid (NGL) probes were noncovalently immobilized onto nitrocellulosecoated glass slides. These were printed together with NGLs of selected sequence defined oligosaccharides, bacterial LPSs and polysaccharides. The H. pylori LPS microarray was probed for recognition with carbohydratebinding proteins (CBPs) of known specificity. These included Le and blood group-related monoclonal antibodies (mAbs), plant lectins, a carbohydratebinding module (CBM) and the mammalian immune receptors DC-SIGN and Dectin-1. The analysis of these CBPs provided new information that complemented the structural analyses and was valuable in the quality control of the constructed microarray. Microarray analysis revealed the occurrence of type-2 Lex and Ley, but not type-1 Lea or Leb antigens, supporting the results obtained in the structural analysis. Furthermore, the H. pylori LPSs were recognised by DC-SIGN, a mammalian lectin known to interact with this bacterium through fucosylated Le epitopes expressed in its LPSs. The -fucose-specific lectin UEA-I, showed restricted binding to probes containing type-2 blood group H sequence and to the LPSs from strains CI-117 and 14382. The presence of H-type-2, as well Htype- 1 in the LPSs from these strains, was confirmed using specific mAbs. Although H-type-1 determinant has been reported for H. pylori LPSs, this is the first report of the presence of H-type-2 determinant. Microarray analysis also revealed that plant lectins known to bind 4-linked GlcNAc chitin oligosaccharide sequences bound H. pylori LPSs. STL, which exhibited restricted and strong binding to 4GlcNAc tri- and pentasaccharides, differentially recognised the LPS from the strain CI-117. The chitin sequences recognised in the LPS could be internal, as no binding was detected to this LPS with WGA, known to be specific for nonreducing terminal of 4GlcNAc sequence. Analyses of the H. pylori LPSs by SDS-PAGE and Western blot with STL provided further evidence for the presence of these novel domains in the O-chain region of this LPS. H. pylori LPS microarray was also applied to analysis of two human sera. The first was from a case infected with H. pylori (H. pylori+ CI-5) and the second was from a non-infected control.The analysis revealed a higher IgG-reactivity towards H. pylori LPSs in the H. pylori+ serum, than the control serum. A specific IgG response was observed to the LPS isolated from the CI-5 strain, which caused the infection. The present thesis has contributed to extension of current knowledge on chemical structures of LPS from H. pylori clinical isolates. Furthermore, the H. pylori LPS microarray constructed enabled the study of interactions with host proteins and showed promise as a tool in serological studies of H. pyloriinfected individuals. Thus, it is anticipated that the use of these complementary approaches may contribute to a better understanding of the molecular complexity of the LPSs and their role in pathogenesis.

Structural analysis of Turtle mountain (Alberta) using digital elevation model: Toward a progressive failure

In 1903, the eastern slope of Turtle Mountain (Alberta) was affected by a 30 M m3-rockslide named Frank Slide that resulted in more than 70 casualties. Assuming that the main discontinuity sets, including bedding, control part of the slope morphology, the structural features of Turtle Mountain were investigated using a digital elevation model (DEM). Using new landscape analysis techniques, we have identified three main joint and fault sets. These results are in agreement with those sets identified through field observations. Landscape analysis techniques, using a DEM, confirm and refine the most recent geology model of the Frank Slide. The rockslide was initiated along bedding and a fault at the base of the slope and propagated up slope by a regressive process following a surface composed of pre-existing discontinuities. The DEM analysis also permits the identification of important geological structures along the 1903 slide scar. Based on the so called Sloping Local Base Level (SLBL) an estimation was made of the present unstable volumes in the main scar delimited by the cracks, and around the south area of the scar (South Peak). The SLBL is a method permitting a geometric interpretation of the failure surface based on a DEM. Finally we propose a failure mechanism permitting the progressive failure of the rock mass that considers gentle dipping wedges (30°). The prisms or wedges defined by two discontinuity sets permit the creation of a failure surface by progressive failure. Such structures are more commonly observed in recent rockslides. This method is efficient and is recommended as a preliminary analysis prior to field investigation.

Structural analysis of the Paint Lake Deformation Zone, Northern Ontario /

The Paint Lake Deformation Zone (PLDZ), located within the Superior Province of Canada, demarcates a major structural and lithological break between the Onaman-Tashota Terrane to the north and the Beardmore-Geraldton Belt to the south. The PLDZ is an east-west trending lineament, approximately 50 km in length and up to 1 km in width, comprised of an early ductile component termed the Paint Lake Shear Zone and a late brittle component known as the Paint Lake Fault. Structures associated with PLDZ development including S-, C- and C'-fabrics, stretching lineations, slickensides, C-C' intersection lineations, Z-folds and kinkbands indicate that simple shear deformation dominated during a NW-SE compressional event. Movement along the PLDZ was in a dextral sense consisting of an early differential motion with southside- down and a later strike-slip motion. Although the locus of the PLDZ may in part be lithologically controlled, mylonitization which accompanied shear zone development is not dependent on the lithological type. Conglomerate, intermediate and mafic volcanic units exhibit similar mesoscopic and microscopic structures where transected by the PLDZ. Field mapping, supported by thin section analysis, defines five strain domains increasing in intensity of deformation from shear zone boundary to centre. A change in the dominant microstructural deformation mechanism from dislocation creep to diffusion creep is observed with increasing strain during mylonitization. C'-fabric development is temporally associated with this change. A decrease in the angular relationship between C- and C'-fabrics is observed upon attaining maximum strain intensity. Strain profiling of the PLDZ demonstrates the presence of an outer primary strain gradient which exhibits a simple profile and an inner secondary strain gradient which exhibits a more complex profile. Regionally metamorphosed lithologies of lower greenschist facies outside the PLDZ were subjected to retrograde metamorphism during deformation within the PLDZ.

Structural analysis of interior layered deposits in north and south Coprates Chasma, Mars

Interior layered deposits within an embayment in the northern as well as near the southern wall of Coprates Chasma in the Valles Marineris, Mars are studied using HRSC, CTX, HiRISE and CRISM data. In the northern embayment, layered deposits outcrop in three separate locations (a western deposit, a central deposit and an eastern deposit). The central layered deposit in the north has a stratigraphic thickness of 2 km. The western layered deposit abuts against the chasma wall appearing to have a relatively un-eroded depositional surface. The eastern deposit is near a landslide scar which appears to have exposed basement layering showing downward displacement. This northern embayment is suggested to have been an ancestral basin. The triangular edged deposit near the southern wall of Coprates Chasma has an elongated mound protruding from the central edge and is suggested to be the outer limits of a fault block which is back rotated 6° south. The rotation may be the result of the Valles Marineris opening.

Thermo-Structural Analysis of 3D Composites

Three dimensional (3D) composites are strong contenders for the structural applications in situations like aerospace,aircraft and automotive industries where multidirectional thermal and mechanical stresses exist. The presence of reinforcement along the thickness direction in 3D composites,increases the through the thickness stiffness and strength properties.The 3D preforms can be manufactured with numerous complex architecture variations to meet the needs of specific applications.For hot structure applications Carbon-Carbon(C-C) composites are generally used,whose property variation with respect to temperature is essential for carrying out the design of hot structures.The thermomechanical behavior of 3D composites is not fully understood and reported.The methodology to find the thermomechanical properties using analytical modelling of 3D woven,3D 4-axes braided and 3D 5-axes braided composites from Representative Unit Cells(RUC's) based on constitutive equations for 3D composites has been dealt in the present study.High Temperature Unidirectional (UD) Carbon-Carbon material properties have been evaluated using analytical methods,viz.,Composite cylinder assemblage Model and Method of Cells based on experiments carried out on Carbon-Carbon fabric composite for a temparature range of 300 degreeK to 2800degreeK.These properties have been used for evaluating the 3D composite properties.From among the existing methods of solution sequences for 3D composites,"3D composite Strength Model" has been identified as the most suitable method.For thegeneration of material properies of RUC's od 3D composites,software has been developed using MATLAB.Correlaton of the analytically determined properties with test results available in literature has been established.Parametric studies on the variation of all the thermomechanical constants for different 3D performs of Carbon-Carbon material have been studied and selection criteria have been formulated for their applications for the hot structures.Procedure for the structural design of hot structures made of 3D Carbon-Carbon composites has been established through the numerical investigations on a Nosecap.Nonlinear transient thermal and nonlinear transient thermo-structural analysis on the Nosecap have been carried out using finite element software NASTRAN.Failure indices have been established for the identified performs,identification of suitable 3D composite based on parametric studies on strength properties and recommendation of this material for Nosecap of RLV based on structural performance have been carried out in this Study.Based on the 3D failure theory the best perform for the Nosecap has been identified as 4-axis 15degree braided composite.

Structural analysis of narratives produced by normal-hearing and deaf children

This dissertation presents two experiments investigating the structural analysis of narratives produced by normal-hearing and hearing-impaired children. The results suggest that the evaluation of deaf children’s language at a discourse level is both possible and more relevant to academic achievement than traditional assessment procedures that focus on assessing language at a word, phrase or sentence level.

First structural analysis of a naphthalene-based poly(ether ketone): Crystal and molecular simulation from X-ray powder data and diffraction modeling

Polycondensation of 2,6-dihydroxynaphthalene with 4,4'-bis(4"-fluorobenzoyl)biphenyl affords a novel, semicrystalline poly(ether ketone) with a melting point of 406 degreesC and glass transition temperature (onset) of 168 degreesC. Molecular modeling and diffraction-simulation studies of this polymer, coupled with data from the single-crystal structure of an oligomer model, have enabled the crystal and molecular structure of the polymer to be determined from X-ray powder data. This structure-the first for any naphthalene-containing poly(ether ketone)-is fully ordered, in monoclinic space group P2(1)/b, with two chains per unit cell. Rietveld refinement against the experimental powder data gave a final agreement factor (R-wp) of 6.7%.

Structural analysis of PEO-PBO copolymer monolayers at the air-water interface

X-ray reflectivity (XR) and grazing incidence X-ray diffraction (GIXD) have been used to examine an oxyethylene-b-oxybutylene (E23B8) copolymer film at the air-water interface. The XR data were fitted using both a one- and a two-layer model that outputted the film thickness, roughness, and electron density. The best fit to the experimental data was obtained using a two-layer model (representing the oxyethylene and oxybutylene blocks, respectively), which showed a rapid thickening of the copolymer film at pressures above 7 mN/m. The large roughness values found indicate a significant degree of intermixing between the blocks and back up the GIXD data, which showed no long range lateral ordering within the layer. It was found from the electron density model results that there is a large film densification at 7 mN/m, possibly suggesting conformational changes within the film, even though no such change occurs on the pressure-area isotherm at the same surface pressure.