A co-operative formation-based collision avoidance approach for a group of autonomous vehicles (Special Issue on Adaptive Control and Signal Processing in Marine System)

This paper employs a unique decentralised cooperative control method to realise a formation-based collision avoidance strategy for a group of autonomous vehicles. In this approach, the vehicles' role in the formation and their alert and danger areas are first defined, and the formation-based intra-group and external collision avoidance methods are then proposed to translate the collision avoidance problem into the formation stability problem. The extension–decomposition–aggregation formation control method is next employed to stabilise the original and modified formations, whilst manoeuvring, and subsequently solve their collision avoidance problem indirectly. Simulation study verifies the feasibility and effectiveness of the intra-group and external collision avoidance strategy. It is demonstrated that both formation control and collision avoidance problems can be simultaneously solved if the stability of the expanded formation including external obstacles can be satisfied.

Stability of Short-span Bridges Subject to Overtopping during Floods: Case Studies from UK and the USA

As a consequence of increased levels of flooding, largely attributable to urbanization of watersheds (and perhaps climate change, more frequent extreme rainfall events are occurring and threatening existing critical infrastructure. Many of which are short-span bridges over relatively small waterways (e.g., small rivers, streams and canals). Whilst these short-span bridges were designed, often many years ago, to pass relatively minor the then standard return-period floods, in recenttimes the failure incidence of such short-span bridges has been noticeably increasing. This is suggestive of insufficient hydraulic capacity or alternative failure mechanism not envisaged at the time of design e.g. foundation scour or undermining. This paper presen ts, and draws lessons, from bridge failures in Ireland and the USA. For example, in November 2009, the UK and Ireland were subjected to extraordinarily severe weather conditions for several days. The resulting flooding led to the collapse of three UK bridges that were generally 19th century masonry arch bridges, withrelatively shallow foundations. Parallel failure events have been observed in the USA. To date, knowledge of the combined effect of waterway erosion, bridge submergence, and geotechnical collapse has not been adequately studied. Recent research carried out considered the hydraulic analysis of short span bridges under flood conditions, but no consideration was given towards the likely damage to these structures due to erosive coupling of hydraulic and geotechnical factors. Some work has been done to predict the discharge downstream of an inundated arch, focusing onpredicting afflux, as opposed to bridge scour, under both pressurized and free-surface flows, but no ! predictive equation for scour under pressurized conditions was ever considered. The case studies this paper presents will be augmented by the initial findings from the laboratory experiments investigating the effects of surcharged flow and subsequent scour within the vicinity of single span arch bridges. Velocities profiles will be shown within the vicinity of the arch, in addition to the depth of consequent scour, for a series of flows and model spans. The data will be presented and correlated to the most recent predictive equations for submerged contraction and abutment scour. The accuracy of these equations is examined, and the findings used as a basis for developing further studies in relation to short span bridges.

O-GlcNAc transferase integrates metabolic pathways to regulate the stability of c-MYC in human prostate cancer cells

Metabolic disruptions that occur widely in cancers offer an attractive focus for generalized treatment strategies. The hexosamine biosynthetic pathway (HBP) senses metabolic status and produces an essential substrate for O-linked β-N-acetylglucosamine transferase (OGT), which glycosylates and thereby modulates the function of its target proteins. Here, we report that the HBP is activated in prostate cancer cells and that OGT is a central regulator of c-Myc stability in this setting. HBP genes were overexpressed in human prostate cancers and androgen regulated in cultured human cancer cell lines. Immunohistochemical analysis of human specimens (n = 1987) established that OGT is upregulated at the protein level and that its expression correlates with high Gleason score, pT and pN stages, and biochemical recurrence. RNA interference-mediated siliencing or pharmacologic inhibition of OGT was sufficient to decrease prostate cancer cell growth. Microarray profiling showed that the principal effects of OGT inhibition in prostate cancer cells were related to cell-cycle progression and DNA replication. In particular, c-MYC was identified as a candidate upstream regulator of OGT target genes and OGT inhibition elicited a dose-dependent decrease in the levels of c-MYC protein but not c-MYC mRNA in cell lines. Supporting this relationship, expression of c-MYC and OGT was tightly correlated in human prostate cancer samples (n = 1306). Our findings identify HBP as a modulator of prostate cancer growth and c-MYC as a key target of OGT function in prostate cancer cells.

Petals of Resonance: A performance system for the transformation of small body sounds

A system of software and hardware that combines signal processing and contact microphones using normally inaudible body sounds, including heartbeat/pulse, respiration and internal sounds from the vocal tract that can be heard internally by the performer but not externally by others, to drive resonant filters. Performance at SARC Sonic Lab, Belfast, 19 Feb 2015 in collaboration with Birgit Ulher.

High-temperature stability study of 1 nm Al2O3 deposited on InAs surfaces investigated by synchrotron radiation based photoemission spectroscopy

High-resolution soft x-ray photoemission spectroscopy (SXPS) has been used to study the high-temperature thermal stability of ultra-thin atomic layer deposited (ALD) Al2O3 layers (~1 nm) on sulfur passivated and native oxide covered InAs surfaces. While the arsenic oxides were removed from both interfaces following a 600 °C anneal, a residual indium oxide signal remained. No significant differences were observed between the sulfur passivated and native oxide surfaces other than the thickness of the interfacial oxide layer while the Al2O3 stoichiometry remained unaffected by the anneals. The energy band offsets were determined for the Al2O3 on the sulfur passivated InAs surface using both valence band edge and shallow core-level photoemission measurements.

Inexact-aware architecture design for ultra-low power bio-signal analysis

This study introduces an inexact, but ultra-low power, computing architecture devoted to the embedded analysis of bio-signals. The platform operates at extremely low voltage supply levels to minimise energy consumption. In this scenario, the reliability of static RAM (SRAM) memories cannot be guaranteed when using conventional 6-transistor implementations. While error correction codes and dedicated SRAM implementations can ensure correct operations in this near-threshold regime, they incur in significant area and energy overheads, and should therefore be employed judiciously. Herein, the authors propose a novel scheme to design inexact computing architectures that selectively protects memory regions based on their significance, i.e. their impact on the end-to-end quality of service, as dictated by the bio-signal application characteristics. The authors illustrate their scheme on an industrial benchmark application performing the power spectrum analysis of electrocardiograms. Experimental evidence showcases that a significance-based memory protection approach leads to a small degradation in the output quality with respect to an exact implementation, while resulting in substantial energy gains, both in the memory and the processing subsystem.

Reference clock design for low power and low phase noise with temperature compensation

Thesis (Ph.D.)--University of Washington, 2016-03

An embedded 1149.4 extension to support mixed-signal debugging

Debugging electronic circuits is traditionally done with bench equipment directly connected to the circuit under debug. In the digital domain, the difficulties associated with the direct physical access to circuit nodes led to the inclusion of resources providing support to that activity, first at the printed circuit level, and then at the integrated circuit level. The experience acquired with those solutions led to the emergence of dedicated infrastructures for debugging cores at the system-on-chip level. However, all these developments had a small impact in the analog and mixed-signal domain, where debugging still depends, to a large extent, on direct physical access to circuit nodes. As a consequence, when analog and mixed-signal circuits are integrated as cores inside a system-on-chip, the difficulties associated with debugging increase, which cause the time-to-market and the prototype verification costs to also increase. The present work considers the IEEE1149.4 infrastructure as a means to support the debugging of mixed-signal circuits, namely to access the circuit nodes and also an embedded debug mechanism named mixed-signal condition detector, necessary for watch-/breakpoints and real-time analysis operations. One of the main advantages associated with the proposed solution is the seamless migration to the system-on-chip level, as the access is done through electronic means, thus easing debugging operations at different hierarchical levels.

The Role of Small RNAs and Ribonucleases in the Control of Gene Expression in Salmonella Typhimurium

Dissertation presented to obtain the Ph.D degree in Biology

Practical signal-to-noise ratio quantification for sensitivity encoding: Application to coronary MR angiography.

Purpose: To develop and evaluate a practical method for the quantification of signal-to-noise ratio (SNR) on coronary MR angiograms (MRA) acquired with parallel imaging.Materials and Methods: To quantify the spatially varying noise due to parallel imaging reconstruction, a new method has been implemented incorporating image data acquisition followed by a fast noise scan during which radio-frequency pulses, cardiac triggering and navigator gating are disabled. The performance of this method was evaluated in a phantom study where SNR measurements were compared with those of a reference standard (multiple repetitions). Subsequently, SNR of myocardium and posterior skeletal muscle was determined on in vivo human coronary MRA.Results: In a phantom, the SNR measured using the proposed method deviated less than 10.1% from the reference method for small geometry factors (<= 2). In vivo, the noise scan for a 10 min coronary MRA acquisition was acquired in 30 s. Higher signal and lower SNR, due to spatially varying noise, were found in myocardium compared with posterior skeletal muscle.Conclusion: SNR quantification based on a fast noise scan is a validated and easy-to-use method when applied to three-dimensional coronary MRA obtained with parallel imaging as long as the geometry factor remains low.

Localisation et fonction de CHK2 en mitose

Les centrosomes dont le rôle principal est d’organiser le cytosquelette de microtubules et le fuseau mitotique servent aussi de sites d’interaction pour plusieurs protéines régulatrices du cycle cellulaire et de la réponse aux dommages à l’ADN. Une de ces protéines est la kinase CHK2 et plusieurs publications montrent une sous-population de CHK2 localisée aux centrosomes dans les cellules en interphase et en mitose. Toutefois, la localisation de CHK2 aux centrosomes demeure controversée, car des doutes subsistent en ce qui concerne la spécificité des anticorps utilisés en immunocytochimie. En utilisant des lignées cellulaires du cancer du côlon, les cellules HCT116 sauvages et HCT116 CHK2-/- ainsi que différentes lignées d’ostéosarcome humain dans lesquelles l’expression de CHK2 a été inhibée par ARN interférence, nous montrons que les anticorps anti-CHK2 qui donnent un signal centrosomal sont non spécifiques et reconnaissent un antigène inconnu sur les centrosomes. Cependant, par des expériences d’immunofluorescence réalisées avec des cellules U2OS qui expriment les protéines de fusion GFP-CHK2 ou FLAG-CHK2, nous révélons une localisation centrosomale de CHK2 dans les cellules en mitose, mais pas en interphase. Ce résultat a été confirmé par vidéomicroscopie dans les cellules vivantes exprimant GFP-CHK2. Pour déterminer le ou les rôles potentiels de CHK2 en mitose nous avons réalisé des expériences pour explorer le rôle de CHK2 dans la progression de la mitose, la nucléation des microtubules aux centrosomes et la progression de la mitose en présence de problèmes d’attachement des chromosomes où de lésions génotoxiques. Nos données suggèrent que CHK2 n’est pas impliquée dans la régulation de la mitose dans les cellules U2OS.

Étude de la régulation des activités transcriptionnelle, réplicative et de l’instabilité de la protéine régulatrice E2 des papillomavirus

Les papillomavirus sont de petits virus à ADN double brin qui infectent les cellules de l’épithélium de la peau et des muqueuses d’une variété de vertébrés causant des lésions bénignes telles des verrues. Certains de ces virus sont également associés au développement de lésions malignes, notamment le cancer du col utérin. La protéine régulatrice E2 des papillomavirus est impliquée dans diverses fonctions contribuant à l’établissement de l’infection par ces virus. Entre autre, E2 régule la transcription des gènes viraux, participe à l’initiation de la réplication de l’ADN viral en s’associant à l’hélicase virale E1 et est responsable du maintien et de la ségrégation de l’épisome viral au cours de la division cellulaire. Toutes ces activités sont attribuables à la capacité de E2 à s’associer au génome viral et à interagir avec des protéines virales et cellulaires. De plus, ces fonctions sont elles-mêmes régulées par des modifications post-traductionnelles de la protéine E2. Plusieurs études ont été réalisées afin de découvrir les mécanismes de régulation des fonctions de E2 mais le rôle exact des différents domaines de E2 dans ces contrôles reste à être défini. En premier lieu, nous nous sommes intéressés à l’interaction entre E2 et Brd4(L) qui avait été définie comme étant essentielle à la ségrégation de l’épisome. Plusieurs caractéristiques associées à la protéine Brd4(L) telles que sa capacité à lier les lysines acétylées des histones, son interaction avec le complexe Mediator et sa participation à l’activation de la transcription en formant un complexe avec pTEFb, nous ont permis d’émettre l’hypothèse que l’interaction E2-Brd4(L) est nécessaire à l’activité transcriptionnelle de E2. Nous avons démontré que la protéine Brd4(L) interagit avec le domaine de transactivation de E2 de divers types de papillomavirus. De plus, cette interaction implique les résidus de E2 essentiels à son activité transcriptionnelle. Ainsi, ces résultats proposent que l’association E2-Brd4(L) serve à la régulation de la transcription des gènes viraux. Dans un second temps, nos recherches se sont concentrées sur l’existence d’une interface de dimérisation au sein du domaine de transactivation de E2 et de son implication dans les activités transcriptionnelles et réplicatives de la protéine. Nos études ont aussi mis en évidence que l’intégrité de la structure de ce domaine contribue au bon fonctionnement de la réplication du génome viral. Cette découverte suggère que la dimérisation de E2 peut réguler l’initiation de la réplication et propose l’existence d’un niveau de régulation additionnel impliquant l’état de la structure quaternaire de la protéine E2 et une modulation de l’interaction entre E1 et E2 à cette étape du cycle viral. Finalement, l’étude de l’instabilité de la protéine E2 nous a permis de définir une région importante dans le domaine flexible de la protéine, nécessaire à sa dégradation par le protéasome. De plus, la présence de résidus conservés localisés dans ce domaine, sont associés à la dégradation et portent la signature d’un signal de localisation nucléaire de type PY-NLS, suggérant que la stabilité de la protéine E2 est régulée par sa localisation au sein de la cellule. Ces études démontrent l’existence de nouvelles stratégies de régulation des activités transcriptionnelle et réplicative de la protéine E2 des papillomavirus. La compréhension de ces mécanismes nous permet de mieux cerner les étapes favorisant l’établissement et la progression du cycle viral et d’identifier de nouvelles cibles thérapeutiques contre les infections aux papillomavirus.

Interpretation of the centromere epigenetic mark to maintain genome stability

Le centromère est la région chromosomique où le kinétochore s'assemble en mitose. Contrairement à certaines caractéristiques géniques, la séquence centromérique n'est ni conservée entre les espèces ni suffisante à la fonction centromérique. Il est donc bien accepté dans la littérature que le centromère est régulé épigénétiquement par une variante de l'histone H3, CENP-A. KNL-2, aussi connu sous le nom de M18BP1, ainsi que ces partenaires Mis18α et Mis18β sont des protéines essentielles pour l'incorporation de CENP-A nouvellement synthétisé aux centromères. Des évidences expérimentales démontrent que KNL-2, ayant un domaine de liaison à l'ADN nommé Myb, est la protéine la plus en amont pour l'incorporation de CENP-A aux centromères en phase G1. Par contre, sa fonction dans le processus d'incorporation de CENP-A aux centromères n'est pas bien comprise et ces partenaires de liaison ne sont pas tous connus. De nouveaux partenaires de liaison de KNL-2 ont été identifiés par des expériences d'immunoprécipitation suivies d'une analyse en spectrométrie de masse. Un rôle dans l'incorporation de CENP-A nouvellement synthétisé aux centromères a été attribué à MgcRacGAP, une des 60 protéines identifiées par l'essai. MgcRacGAP ainsi que les protéines ECT-2 (GEF) et la petite GTPase Cdc42 ont été démontrées comme étant requises pour la stabilité de CENP-A incorporé aux centromères. Ces différentes observations ont mené à l'identification d'une troisième étape au niveau moléculaire pour l'incorporation de CENP-A nouvellement synthétisé en phase G1, celle de la stabilité de CENP-A nouvellement incorporé aux centromères. Cette étape est importante pour le maintien de l'identité centromérique à chaque division cellulaire. Pour caractériser la fonction de KNL-2 lors de l'incorporation de CENP-A nouvellement synthétisé aux centromères, une technique de microscopie à haute résolution couplée à une quantification d'image a été utilisée. Les résultats générés démontrent que le recrutement de KNL-2 au centromère est rapide, environ 5 minutes après la sortie de la mitose. De plus, la structure du domaine Myb de KNL-2 provenant du nématode C. elegans a été résolue par RMN et celle-ci démontre un motif hélice-tour-hélice, une structure connue pour les domaines de liaison à l'ADN de la famille Myb. De plus, les domaines humain (HsMyb) et C. elegans (CeMyb) Myb lient l'ADN in vitro, mais aucune séquence n'est reconnue spécifiquement par ces domaines. Cependant, il a été possible de démontrer que ces deux domaines lient préférentiellement la chromatine CENP-A-YFP comparativement à la chromatine H2B-GFP par un essai modifié de SIMPull sous le microscope TIRF. Donc, le domaine Myb de KNL-2 est suffisant pour reconnaître de façon spécifique la chromatine centromérique. Finalement, l'élément reconnu par les domaines Myb in vitro a potentiellement été identifié. En effet, il a été démontré que les domaines HsMyb et CeMyb lient l'ADN simple brin in vitro. De plus, les domaines HsMyb et CeMyb ne colocalisent pas avec CENP-A lorsqu'exprimés dans les cellules HeLa, mais plutôt avec les corps nucléaires PML, des structures nucléaires composées d'ARN. Donc, en liant potentiellement les transcrits centromériques, les domaines Myb de KNL-2 pourraient spécifier l'incorporation de CENP-A nouvellement synthétisé uniquement aux régions centromériques.

Characterization of Selected Photonic Materials and Systems Using Photoacoustic Technique

The photoacoustic investigations carried out on different photonic materials are presented in this thesis. Photonic materials selected for the investigation are tape cast ceramics, muItilayer dielectric coatings, organic dye doped PVA films and PMMA matrix doped with dye mixtures. The studies are performed by the measurement of photoacoustic signal generated as a result of modulated cw laser irradiation of samples. The gas-microphone scheme is employed for the detection of photoacoustic signal. The different measurements reported here reveal the adaptability and utility of the PA technique for the characterization of photonic materials.Ceramics find applications in the field of microelectronics industry. Tape cast ceramics are the building blocks of many electronic components and certain ceramic tapes are used as thermal barriers. The thermal parameters of these tapes will not be the same as that of thin films of the same materials. Parameters are influenced by the presence of foreign bodies in the matrix and the sample preparation technique. Measurements are done on ceramic tapes of Zirconia, Zirconia-Alumina combination, barium titanate, barium tin titanate, silicon carbide, lead zirconate titanateil'Z'T) and lead magnesium niobate titanate(PMNPT). Various configurations viz. heat reflection geometry and heat transmission geometry of the photoacoustic technique have been used for the evaluation of different thermal parameters of the sample. Heat reflection geometry of the PA cell has been used for the evaluation of thermal effusivity and heat transmission geometry has been made use of in the evaluation of thermal diffusivity. From the thermal diffusivity and thermal effusivity values, thermal conductivity is also calculated. The calculated values are nearly the same as the values reported for pure materials. This shows the feasibility of photoacoustic technique for the thermal characterization of ceramic tapes.Organic dyes find applications as holographic recording medium and as active media for laser operations. Knowledge of the photochemical stability of the material is essential if it has to be used tor any of these applications. Mixing one dye with another can change the properties of the resulting system. Through careful mixing of the dyes in appropriate proportions and incorporating them in polymer matrices, media of required stability can be prepared. Investigations are carried out on Rhodamine 6GRhodamine B mixture doped PMMA samples. Addition of RhB in small amounts is found to stabilize Rh6G against photodegradation and addition of Rh6G into RhB increases the photosensitivity of the latter. The PA technique has been successfully employed for the monitoring of dye mixture doped PMMA sample. The same technique has been used for the monitoring of photodegradation ofa laser dye, cresyl violet doped polyvinyl alcohol also.Another important application of photoacoustic technique is in nondestructive evaluation of layered samples. Depth profiling capability of PA technique has been used for the non-destructive testing of multilayer dielectric films, which are highly reflecting in the wavelength range selected for investigations. Eventhough calculation of thickness of the film is not possible, number of layers present in the system can be found out using PA technique. The phase plot has clear step like discontinuities, the number of which coincides with the number of layers present in the multilayer stack. This shows the sensitivity of PA signal phase to boundaries in a layered structure. This aspect of PA signal can be utilized in non-destructive depth profiling of reflecting samples and for the identification of defects in layered structures.