197 research outputs found
A Taxonomy of Network and Computer Attack Methodologies
No full textSince the invention of computers and networks, people have found various ways to attack them. Attacks over the years have ranged from using a sledge hammer on a computer, to advanced distributed denial of service attacks. This research focuses on computer and network attacks and providing a taxonomy of them. This is to help combat new attacks, improve computer and network security and to provide consistency in language when describing attacks. A wide range of computer and network attacks are examined to provide both a survey of the field and to provide a basis on which to build the proposed taxonomy. The proposed taxonomy consists of four dimensions which provide a holistic taxonomy and to deal with inherent problems in the computer and network attack field. The first dimension covers the attack vector and the main behaviour of the attack. The second dimension allows for classification of the attack targets. Vulnerabilities are classified in the third dimension and payloads in the fourth. The taxonomy is briefly evaluated and is found to work well, with a few areas that could be improved. Acknowledgements Firstly I would like to thank my supervisor, Associate Professor Ray Hunt. This research project has been interesting and I have appreciated having you as a supervisor. Thank you to Jay Garden, Nick Lavery an
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Enhanced colour encoding of materials discrimination information for multiple view dual-energy x-ray imaging
No full textThis thesis reports an investigation into dual-energy X-ray discrimination techniques. These techniques are designed to provide colour-coded materials discrimination information in a sequence of perspective images exhibiting sequential parallax. The methods developed are combined with a novel 3D imaging technique employing depth from motion or kinetic depth effect (KDE). This technique when applied to X-ray images is termed KDEX imaging and was developed previously by the university team for luggage screening applications at security checkpoints. A primary motivation for this research is that the dual-energy X-ray techniques, which are routinely incorporated into ‘standard’ 2D luggage scanners, provide relatively crude materials discrimination information. In this work it was critical that robust materials discrimination and colour encoding process was implemented as the sequential parallax exhibited by the KDEX imagery may introduce colour changes, due to the different X-ray beam paths associated with each perspective image. Any introduction of ‘colour noise’ into the resultant image sequences could affect the perception of depth and hinder the ongoing assessment of the potential utility of the dual-energy KDEX technique. Two dual-energy discrimination methods have been developed, termed K-II and W-E respectively. Employing the total amount of attenuation measured at each energy level and the weight fraction of layered structures, a combination of the K-II and the W-E techniques enables the computation and extraction of a target objects’ effective atomic number (Zeff) and its surface density (ρS) in the presence of masking layers
The XMM-Newton long look of NGC 1365: uncovering of the obscured X-ray source
No full textWe present an analysis of the extreme obscuration variability observed during an XMM–Newton 5-d continuous monitoring of the active galactic nuclei (AGN) in NGC 1365. The source was in a reflection-dominated state in the first ∼1.5 d, then a strong increase in the 7–10 keV emission was observed in ∼10 h, followed by a symmetric decrease. The spectral analysis of the different states clearly shows that this variation is due to an uncovering of the X-ray source. From this observation, we estimate a size of the X-ray source DS < 1013 cm, a distance of the obscuring clouds R∼ 1016 cm and a density n∼ 1011 cm−3. These values suggest that the X-ray absorption/reflection originates from the broad-line region clouds. This is also supported by the resolved width of the iron narrow Kα emission line, consistent with the width of the broad Hβ line
Radio sources in the Chandra Galactic Bulge Survey
Get PDFWe discuss radio sources in the Chandra Galactic Bulge Survey region. By cross-matching the X-ray sources in this field with the NRAO VLA Sky Survey archival data, we find 12 candidate matches. We present a classification scheme for radio/X-ray matches in surveys taken in or near the Galactic plane, taking into account other multiwavelength data. We show that none of the matches found here is likely to be due to coronal activity from normal stars because the radio to X-ray flux ratios are systematically too high. We show that one of the source could be a radio pulsar, and that one could be a planetary nebula, but that the bulk of the sources are likely to be background active galactic nuclei (AGN), with many confirmed through a variety of approaches. Several of the AGN are bright enough in the near-infrared (and presumably in the optical) to use as probes of the interstellar medium in the inner Galaxy
Towards NMR analysis of the HIV-1 coreceptor CCR5 and its interaction with RANTES
Get PDFCCR5 is a chemokine receptor together with CD4 used by HIV-1 as a primary gate of cell infection. For this reason CCR5 is of great interest for medicine as a target for the anti-HIV-1 therapies. Since the binding site of its endogenous ligand RANTES overlaps with the binding site of viral envelope glycoprotein gp120, a noninflamatory RANTES derivative 5P12-RANTES has been developed as an anti-HIV-1 infection microbicide. The primary aim of this thesis was to establish an NMR-amenable system to study CCR5 and to understand better the interaction with RANTES.
For this purpose CCR5 expressed in insect cells was characterized in detail with regards to its secondary structure, oligomeric state, particle size, stability, posttranslational modifications and functionality. In contrast to the previous results, carefully performed detergent screening revealed that FosCholine-12, a detergent which allows high yield purification, does not support CCR5 recognition by 2D7 and cannot be used for studying CCR5 interactions with ligands. Therefore for the functional studies the receptor was solubilized with a milder detergent mixture DDM/CHAPS/CHS, which was shown to support native CCR5 tertiary structure.
Using this setup it could be shown by SPR that 5P12-RANTES binds with higher affinity than another potent RANTES variant PSC-RANTES (Morin et al., manuscript in preparation). This explains why 5P12-RANTES, which unlike PSC-RANTES does not cause CCR5 internalization, is an equally effective anti-HIV-1 microbicide. On the other hand, the wild-type RANTES was shown to aggregate on the receptor micelle using a mechanism compatible with the linear oligomerization, a process that is proposed to serve local chemokine preconcentration.
To obtain an access to a cost-efficient source of isotope-labeled samples, an E. coli expression system was established for CCR5 (Wiktor et al., 2012, J Biomol NMR, in revision). The expression was facilitated by fusing the N-terminus of CCR5 to well expressing protein domains e.g. thioredoxin. The C-terminal CCR5 truncation and the mutation of cysteines increased the protein yield up to 10 mg/L and improved the sample stability. Due to the engineered thrombin proteolytic site the N-terminal fusion partner i.e. thioredoxin could be quantitatively cleaved and removed by size exclusion chromatography. The FC-12-purified receptor was abundant in alpha-helical secondary structure but could bind RANTES, MIP-1beta and conformation-dependent antibody 2D7 only when solubilized by a DDM/CHAPS/CHS mixture. Using 15N,13C,2H-labeled CCR5 2D and 3D NMR experiments were recorded but only about 80 backbone resonances could be resolved. The spectral quality was jeopardized by large overlap and line-broadening and needs further improvements to allow the assignment and the structural investigation.
To study 5P12-RANTES by NMR the backbone assignment was completed. The HSQC spectrum revealed that, unlike wild-type RANTES and other chemokines, 5P12-RANTES does not form dimers. The secondary chemical shift analysis suggest that the overall structure of 5P12-RANTES is similar to the wild-type RANTES, with the exception of the mutated N-terminus, which does not participate in the intermolecular beta-sheet and was shown to be highly flexible. Another important observation was that RANTES secondary structure is perturbed by Fos-Choline detergents, whereas maltosides shift the RANTES monomer:dimmer equilibrium towards its monomeric form.
The last part of the thesis present an independent study, where using ubiquitin as an example the mechanism of protein unfolding is studied (Vajpai et al., 2012, Proc Natl Acad Sci USA, in revision) manuscript submitted for publication). The secondary chemical shift analysis showed that the alcohol-denatured ubiquitin structure closely resembles the cold- and pressure denatured structure. This suggests that alcohol, low temperature and pressure unfold proteins by reducing the hydrophobic effect, the cost of exposing hydrophobic residues.
The data of this thesis will be presented in the following publications:
1. Wiktor, M., Morin, S., Sass, H-J., Kebbel, F., Grzesiek, S. (2012) Biophysical and structural investigation of bacterially expressed and engineered CCR5, a G protein-coupled receptor. J Biomol NMR (2012, in revision).
2. Vajpai, N., Nisius, L., Wiktor, M., Grzesiek, S. (2012) High pressure NMR reveals close similarity between cold and alcohol protein denaturation due to a reduction of the hydrophobic effect. Proc Natl Acad Sci USA (in revision).
3. Morin, S., Wiktor, M., Sass, H-J., Hartley, O., Grzesiek, S. (2012) Modulation of RANTES binding to CCR5 by modifications in the N-terminus and C-terminus (in preparation)
Ordering of organic molecules on templated surfaces
Get PDFThis thesis describes the controlled growth of molecular nanostructures using modified metallic and semiconductor surfaces. The Ag/Si(lll)-(root3 x root3),the Sn/Cu(100) surface alloy system and the Bi/Si(100) nanolines and (2xn) surfaces were all investigated as suitable substrates for the controlled growth of pentacene, (C22H14) or trimesic acid, (C6H3(COOH)3) organic molecules. The following techniques were used in this study; Scanning Tunnelling Microscopy (STM), Low Energy Electron Diffraction (LEED), Normal Incident X-Ray Standing Waves (NIXSW) and Temperature Programmed Desorption (TPD).
The room temperature growth and ordering of trimesic acid on the AgfSi(ll1)-(root3 x root3) surface was investigated. An oblique unit cell was determined and a model proposed for the highly ordered close-packed domains.
The discovery of a new submonolayer phase on Sn/Cu(100) and the re-examined known phase are discussed. New models for these reconstructions are proposed. Adsorption of trimesic acid at room temperature on the clean substrate the lowest Sn coverage phase were studied. Two new Sn coverage dependent structures were discovered and bonding schemes in upright and flat orientations are discussed.
BifSi(100)-(2xn) surface was exploited as a template for the ordered growth of pentacene, which exhibited orientation specific adsorption. The Bi/Si(100)-(2xn) single domain surface created on vicinal silicon was used to test the suitable of Daresbury 4.2 beamline for NIXSW Imaging experiments and the quality of the results are discussed
Neolithic Human Diet Based on Studies of Coprolites from the Swifterbant Culture Sites, the Netherlands: Micro-CT scanning analysis
No full textIn recent years, several researchers have illustrated the potential of X-ray micro-computed tomography (micro-CT) in the study of archaeological soils and artefacts. Hunt et al., Huisman et al., Wang et al., Qvarnström et al., and Shillito et al. have already foreseen and even demonstrated the added value of the technique for the investigation of ancient coprolites.114 Coprolites contain partially digested macro-food remains which can be distinguished on a micro-CT scan when they are large enough and contrast sufficiently in terms of X-ray attenuation values and/or patterns with the faecal mass. The scans of coprolites provide a direct and non-destructive way to assess diets from the past.Geo-engineerin
Management of Severe Asthma
Get PDFIn this summary of therapy for severe asthma there is no mention of etiologic factors. The author presumes that if infection is the primary factor in the progression to severe asthma that this will be recognized and appropriately treated. A chest x-ray must be an initial laboratory study for the recognition of pneumonia or complicating pneumothorax. However, unlike respiratory failure due to emphysema, here the specific therapy of the altered pulmonary physiology is of paramount importance
Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse
Get PDFabstract: Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.The final version of this article, as published in Structural Dynamics, can be viewed online at: http://aca.scitation.org/doi/10.1063/1.491939
The FRE Gripper with Planar Grasp Stability, using Spatial Form-Closure
No full textFin Ray Effect (FRE) grippers have proven versatile and effective in pick & place automation applications. However, spherical and lateral round objects are still a challenge for the state-of-the-art, as solutions are unstable when placing those objects off-centre from the longitudinal line. Resulting in large and heavy FRE gripper assemblies. The object often shoots out of the grip, since the gripper cannot counteract the lateral forces from the object with normal forces from the structure, but instead has to rely on friction forces. In this paper, a new spatially designed FRE based gripper is proposed that form-closes around the spherical object, providing a stable grip. The design variables, such as structural variations and different thicknesses of segments, are modelled using LiveLinks between SolidWorks, COMSOL and MATLAB, resulting in an optimal design. The optimal design is then compared to a basic FRE gripper design, using the model, and the stability of both is validated in the real world by an experiment. The new design shows improved performance compared to the Basic FRE grippers, and even shows centering capabilities for frictionless objects.Mechanical Engineerin
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