'Danger Theory: The Link between AIS and IDS?'

Abstract We present ideas about creating a next generation Intrusion Detection System (IDS) based on the latest immunological theories. The central challenge with computer security is determining the difference between normal and potentially harmful activity. For half a century, developers have protected their systems by coding rules that identify and block specific events. However, the nature of current and future threats in conjunction with ever larger IT systems urgently requires the development of automated and adaptive defensive tools. A promising solution is emerging in the form of Artificial Immune Systems (AIS): The Human Immune System (HIS) can detect and defend against harmful and previously unseen invaders, so can we not build a similar Intrusion Detection System (IDS) for our computers? Presumably, those systems would then have the same beneficial properties as HIS like error tolerance, adaptation and self-monitoring. Current AIS have been successful on test systems, but the algorithms rely on self-nonself discrimination, as stipulated in classical immunology. However, immunologist are increasingly finding fault with traditional self-nonself thinking and a new 'Danger Theory' (DT) is emerging. This new theory suggests that the immune system reacts to threats based on the correlation of various (danger) signals and it provides a method of 'grounding' the immune response, i.e. linking it directly to the attacker. Little is currently understood of the precise nature and correlation of these signals and the theory is a topic of hot debate. It is the aim of this research to investigate this correlation and to translate the DT into the realms of computer security, thereby creating AIS that are no longer limited by self-nonself discrimination. It should be noted that we do not intend to defend this controversial theory per se, although as a deliverable this project will add to the body of knowledge in this area. Rather we are interested in its merits for scaling up AIS applications by overcoming self-nonself discrimination problems.

A model to achieve sustainable improvement and innovation in organisations, industries, regions and communities

The achievement and measurement of improvements and innovations is not often an overt practice in the design and delivery of government services other than in health services. There is a need for specific mechanisms proven to increase the rate and scale of improvements and innovations in organisations, communities, regions and industries. This paper describes a model for the design, measurement and management of projects and services as systems for achieving and sustaining outcomes, improvements and innovations.The development of the model involved the practice of continuous improvement and innovation within and across a number of agricultural development projects in Australia and nternationally. Key learnings from the development and use of the model are: (1) all elements and factors critical for success can be implemented, measured and managed; (2) the design of a meaningful systemic measurement framework is possible; (3) all project partners can achieve and sustain rapid improvements and innovations; (4) outcomes can be achieved from early in the life of projects; and (5) significant spill-over benefits can be achieved beyond the scope, scale and timeframe of projects

Left Ventricle Non-Compaction Myocardium and Thrombophilia in a Pregnant Woman

Non-compaction of the ventricular myocardium (NCM) is a genetic cardiomyopathy usually due to mutationof the G4.5 gene located in the Xq28 chromosomal region. This congenital disorder is characterized by pronounced trabeculations and intertrabecular recesses resulting from abnormal embryogenesis between the fifth and eighth fetal weeks. The reported prevalence in the general population is between 0.014% and 1.3%. The classic triad of complications includes heart failure, ventricular arrhythmias and systemic embolic events, although some patients have an asymptomatic form. NCM is commonly diagnosed by echocardiography, but contrast ventriculography, CT and MRI can also be used. Here we present a case of left ventricle NCM, manifested after respiratory infection, in a pregnant patient with congenital thrombophilia and a history of myocardial infarction.

‘Mo Rùn am Fearann’ – ‘My Love is the Land’: Gaelic landscapes of the 18th and 19th centuries

The period of the 18th and 19th centuries was one of great change in the Highlands and Islands of Scotland. Improvement, the Jacobite Rebellions, and the Clearances transformed its communities and landscapes. These events have rightly been a focus of research. However, archaeological approaches have often sought simply to illustrate these processes, rather than create new narratives about life in the past. The resulting picture of the period can over-emphasise economic change whilst failing to reflect the richness and variety of everyday life. This thesis aims to suggest a new approach to the place and period, one which addresses matters often ignored in previous work. Whilst it has an archaeological sensibility, it draws on ideas from outside archaeology, such as landscape theory and on Gaelic oral tradition, an underused resource, to create a novel and broad-based approach to the period. An important part of the method is a synchronic approach that seeks to reconstruct the experience of the landscape at very particular times, engaging fully with the everyday experience of landscape rather than grand historical narratives. Two Hebridean case studies are utilised: Hiort (St Kilda) and Loch Aoineart, South Uist. Thematic discussions drawn from these landscapes are intended as critical assessments of the efficacy of the approach, as well as new narratives about life in the past in themselves. The thesis concludes by comparing the two case studies, reflecting on the merits of the approach, discussing recurrent themes in the work, and considering its wider context and implications. It is concluded that taking a novel approach to the case study landscapes can create narratives that often contrast or expand upon those produced by previous scholars, allow for a more detailed consideration of everyday life in the period, and open up new areas for archaeological enquiry. The extensive and critical use of evidence from Gaelic oral tradition is highlighted as crucial in understanding life and society in the period. The thesis questions the utility of grand historical narratives as a framework for archaeological study of post-medieval Gaeldom and suggests that our understanding of the past is best served by approaching the evidence in ways which allows for many different voices and stories from the past to emerge.

Predictors of stress and depressive mood in portuguese middle-aged women

This cross-sectional study investigates the predictors of psychological symptoms-stress and depressive mood-in a sample of middle-aged women. A community sample of 1,003 women filled in the questionnaires and instruments, which included the Depression, Anxiety and Stress Scales and the Life Events Survey; sociodemographic, health, and menopause-related and lifestyle information was also collected. Structural equation modeling was used to build the model that had stress and depressive mood as dependent variables. Health status (both physical and psychological), recent life events, income and menopausal phase were significantly associated with the frequency of stress and depressive symptoms. Additionally, educational level and parity were also significant predictors of depressive mood. This study emphasizes that psychological symptoms occurrence in midlife depends not only on personal variables (such as health and menopausal status) but also on contextual ones (including recent stressful events) that can be a strong influence on how middle-aged women feel.

Learning Binary Code Representations for Effective and Efficient Image Retrieval

The size of online image datasets is constantly increasing. Considering an image dataset with millions of images, image retrieval becomes a seemingly intractable problem for exhaustive similarity search algorithms. Hashing methods, which encodes high-dimensional descriptors into compact binary strings, have become very popular because of their high efficiency in search and storage capacity. In the first part, we propose a multimodal retrieval method based on latent feature models. The procedure consists of a nonparametric Bayesian framework for learning underlying semantically meaningful abstract features in a multimodal dataset, a probabilistic retrieval model that allows cross-modal queries and an extension model for relevance feedback. In the second part, we focus on supervised hashing with kernels. We describe a flexible hashing procedure that treats binary codes and pairwise semantic similarity as latent and observed variables, respectively, in a probabilistic model based on Gaussian processes for binary classification. We present a scalable inference algorithm with the sparse pseudo-input Gaussian process (SPGP) model and distributed computing. In the last part, we define an incremental hashing strategy for dynamic databases where new images are added to the databases frequently. The method is based on a two-stage classification framework using binary and multi-class SVMs. The proposed method also enforces balance in binary codes by an imbalance penalty to obtain higher quality binary codes. We learn hash functions by an efficient algorithm where the NP-hard problem of finding optimal binary codes is solved via cyclic coordinate descent and SVMs are trained in a parallelized incremental manner. For modifications like adding images from an unseen class, we propose an incremental procedure for effective and efficient updates to the previous hash functions. Experiments on three large-scale image datasets demonstrate that the incremental strategy is capable of efficiently updating hash functions to the same retrieval performance as hashing from scratch.

Rail passenger crowding, stress, health and safety in Britain

There has long been a question as to whether crowding in rail passenger transport poses a threat to passenger health related to the experience of stress. A review of the scientific literature was conducted. Little rail-specific empirical research was identified. The more general research that does exist suggests that high-density environments are not necessarily perceived as crowded and that stress-related physiological, psychological and behavioural reactions do not necessarily follow from exposure to such environments. Several factors are identified that may moderate the impact of a high-density environment on perceptions of crowding and the subsequent experience and effects of stress. These include, inter alia, perceptions of control and predictability of events. However, if caused, the experience and effects of stress may be made worse by inadequate coach design that gives rise to discomfort. The model that emerges from these findings offers a suitable framework for the development of research questions that should help translate emerging knowledge into practical interventions, for the reduction of any adverse health outcomes associated with crowding.

A VOICE OF THEIR OWN: MUSIC AND SOCIAL COHESION IN TURKISH ALEVI LIFE

This dissertation examines the role that music has played in the expression of identity and revitalization of culture of the Alevis in Turkey, since the start of their sociocultural revival movement in the late 1980s. Music is central to Alevi claims of ethnic and religious difference—singing and playing the bağlama (Turkish folk lute) constitutes an expressive practice in worship and everyday life. Based on research conducted from 2012 to 2014, I investigate and present Alevi music through the lens of discourses on the construction of identity as a social and musical process. Alevi musicians perform a revived repertoire of the ritual music and folk songs of Anatolian bards and dervish-lodge poets that developed over several centuries. Contemporary media and performance contexts have blurred former distinctions between sacred and secular, yet have provided new avenues to build community in an urban setting. I compare music performances in the worship services of urban and small-town areas, and other community events such as devotional meetings, concerts, clubs, and broadcast and social media to illustrate the ways that participation—both performing and listening—reinforces identity and solidarity. I also examine the influence of these different contexts on performers’ musical choices, and the power of music to evoke a range of responses and emotional feelings in the participants. Through my investigation I argue that the Alevi music repertoire is not only a cultural practice but also a symbol of power and collective action in their struggle for human rights and self-determination. As Alevis have faced a redefined Turkish nationalism that incorporates Sunni Muslim piety, this music has gained even greater potency in their resistance to misrecognition as a folkloric, rather than a living, tradition.

Preoperative assessment of deep myometrial and cervical invasion in endometrial carcinoma: comparison of magnetic resonance imaging and histopathologic evaluation

This study aimed to evaluate the accuracy of magnetic resonance imaging (MRI) in the detection of deep myometrial invasion and cervical extension by endometrial carcinoma. This prospective study included 101 patients with histologically documented endometrial carcinoma, between July 1998 and April 2004. The findings of preoperative pelvic MRI were compared with histological diagnosis. From 101 cases studied by pelvic MRI, 43 were classified as deep myometrial invasion (50% of myometrium), where the pathological evaluation confirmed as having deep myometrial invasion. Cervical extension in the MRI study was found in 19 cases. Pathologic study found cervical extension and/or invasion in 31 cases including all cases identified by MRI. The accuracy, sensitivity and specificity of MRI were 95%, 89%, 100%, detecting deep myometrial invasion and 88%, 61%, 100%, detecting cervical invasion, respectively. The high accuracy achieved makes MRI an adequate method for determine the depth of myometrial and cervical invasion in endometrial carcinoma.

Danger theory: the link between AIS and IDS?

We present ideas about creating a next generation Intrusion Detection System (IDS) based on the latest immunological theories. The central challenge with computer security is determining the difference between normal and potentially harmful activity. For half a century, developers have protected their systems by coding rules that identify and block specific events. However, the nature of current and future threats in conjunction with ever larger IT systems urgently requires the development of automated and adaptive defensive tools. A promising solution is emerging in the form of Artificial Immune Systems (AIS): The Human Immune System (HIS) can detect and defend against harmful and previously unseen invaders, so can we not build a similar Intrusion Detection System (IDS) for our computers? Presumably, those systems would then have the same beneficial properties as HIS like error tolerance, adaptation and self-monitoring. Current AIS have been successful on test systems, but the algorithms rely on self-nonself discrimination, as stipulated in classical immunology. However, immunologist are increasingly finding fault with traditional self-nonself thinking and a new ‘Danger Theory’ (DT) is emerging. This new theory suggests that the immune system reacts to threats based on the correlation of various (danger) signals and it provides a method of ‘grounding’ the immune response, i.e. linking it directly to the attacker. Little is currently understood of the precise nature and correlation of these signals and the theory is a topic of hot debate. It is the aim of this research to investigate this correlation and to translate the DT into the realms of computer security, thereby creating AIS that are no longer limited by self-nonself discrimination. It should be noted that we do not intend to defend this controversial theory per se, although as a deliverable this project will add to the body of knowledge in this area. Rather we are interested in its merits for scaling up AIS applications by overcoming self-nonself discrimination problems.

Bcl-xL (S49) and (S62) sequential phosphorylation/dephosphorylation during mitosis prevents chromosome instability and aneuploidy

Une caractéristique intéressante de la protéine Bcl-xL est la présence d'un domaine en boucle non-structurée entre les hélices α1 and α2 de la protéine. Ce domaine protéique n'est pas essentiel pour sa fonction anti-apoptotique et absent chez CED-9, la protéine orthologue chez Caenorhabditis elegans. A l'intérieur de ce domaine, Bcl-xL subit une phosphorylation et déphosphorylation dynamique sur les résidus Ser49 et Ser62 en phase G2 du cycle cellulaire et lors de la mitose. Lorsque ces résidus sont mutés et les protéines exprimées dans des cellules cancéreuses, les cellules démontrent plusieurs défauts mitotiques liés à l'instabilité chromosomique. Pour analyser les effets de Bcl-xL Ser49 et Ser62 dans les cellules normales, les présentes études ont été réalisées dans des cellules diploïdes humaines normales, et in vivo chez Caenorhabditis elegans. Dans une première étude, nous avons utilisé la lignée cellulaire de cellules fibroblastiques diploïdes humaines normales BJ, exprimant Bcl-xL (type sauvage), (S49A), (S49D), (S62A), (S62D) et les double (S49/62A) et (S49/62D) mutants. Les cellules exprimant les mutants de phosphorylation ont montré des cinétiques de doublement de la population cellulaire réduites. Ces effets sur la cinétique de doublement de la population cellulaire corrèle avec l'apparition de la sénescence cellulaire, sans impact sur les taux de mort cellulaire. Ces cellules sénescentes affichent des phénotypes typiques de sénescence associés notamment à haut niveau de l'activité β-galactosidase associée à la sénescence, la sécrétion d' interleukine-6, l'activation de p53 et de p21WAF1/ Cip1, un inhibiteur des complexes kinase cycline-dépendant, ainsi que la formation de foyers de chromatine nucléaire associés à γH2A.X. Les analyses de fluorescence par hybridation in situ et des caryotypes par coloration au Giemsa ont révélé que l'expression des mutants de phosphorylation de Bcl-xL provoquent de l'instabilité chromosomique et l'aneuploïdie. Ces résultats suggèrent que les cycles de phosphorylation et déphosphorylation dynamiques de Bcl-xL Ser49 et Ser62 sont importants dans le maintien de l'intégrité des chromosomes lors de la mitose dans les cellules normales. Dans une deuxième étude, nous avons entrepris des expériences chez Caenorhabditis elegans pour comprendre l'importance des résidus Ser49 et Ser62 de Bcl-xL in vivo. Les vers transgéniques portant les mutations de Bcl-xL (S49A, S62A, S49D, S62D et S49/62A) ont été générés et leurs effets ont été analysés sur les cellules germinales des jeunes vers adultes. Les vers portant les mutations de Bcl-xL ont montré une diminution de ponte et d'éclosion des oeufs, des variations de la longueur de leurs régions mitotiques et des zones de transition, des anomalies chromosomiques à leur stade de diplotène, et une augmentation de l'apoptose des cellules germinales. Certaines de ces souches transgéniques, en particulier les variants Ser/Ala, ont également montré des variations de durée de vie par rapport aux vers témoins. Ces observations in vivo ont confirmé l'importance de Ser49 et Ser62 à l'intérieur du domaine à boucle de Bcl-xL pour le maintien de la stabilité chromosomique. Ces études auront une incidence sur les futures stratégies visant à développer et à identifier des composés qui pourraient cibler non seulement le domaine anti-apoptotique de la protéine Bcl-xL, mais aussi son domaine mitotique pour la thérapie du cancer.

A Search for Muon Neutrinos in Coincidence with Gamma-Ray Bursts in the Southern Hemisphere Sky Using the IceCube Neutrino Observatory

The origin of observed ultra-high energy cosmic rays (UHECRs, energies in excess of $10^{18.5}$ eV) remains unknown, as extragalactic magnetic fields deflect these charged particles from their true origin. Interactions of these UHECRs at their source would invariably produce high energy neutrinos. As these neutrinos are chargeless and nearly massless, their propagation through the universe is unimpeded and their detection can be correlated with the origin of UHECRs. Gamma-ray bursts (GRBs) are one of the few possible origins for UHECRs, observed as short, immensely bright outbursts of gamma-rays at cosmological distances. The energy density of GRBs in the universe is capable of explaining the measured UHECR flux, making them promising UHECR sources. Interactions between UHECRs and the prompt gamma-ray emission of a GRB would produce neutrinos that would be detected in coincidence with the GRB’s gamma-ray emission. The IceCube Neutrino Observatory can be used to search for these neutrinos in coincidence with GRBs, detecting neutrinos through the Cherenkov radiation emitted by secondary charged particles produced in neutrino interactions in the South Pole glacial ice. Restricting these searches to be in coincidence with GRB gamma-ray emis- sion, analyses can be performed with very little atmospheric background. Previous searches have focused on detecting muon tracks from muon neutrino interactions fromthe Northern Hemisphere, where the Earth shields IceCube’s primary background of atmospheric muons, or spherical cascade events from neutrinos of all flavors from the entire sky, with no compelling neutrino signal found. Neutrino searches from GRBs with IceCube have been extended to a search for muon tracks in the Southern Hemisphere in coincidence with 664 GRBs over five years of IceCube data in this dissertation. Though this region of the sky contains IceCube’s primary background of atmospheric muons, it is also where IceCube is most sensitive to neutrinos at the very highest energies as Earth absorption in the Northern Hemisphere becomes relevant. As previous neutrino searches have strongly constrained neutrino production in GRBs, a new per-GRB analysis is introduced for the first time to discover neutrinos in coincidence with possibly rare neutrino-bright GRBs. A stacked analysis is also performed to discover a weak neutrino signal distributed over many GRBs. Results of this search are found to be consistent with atmospheric muon backgrounds. Combining this result with previously published searches for muon neutrino tracks in the Northern Hemisphere, cascade event searches over the entire sky, and an extension of the Northern Hemisphere track search in three additional years of IceCube data that is consistent with atmospheric backgrounds, the most stringent limits yet can be placed on prompt neutrino production in GRBs, which increasingly disfavor GRBs as primary sources of UHECRs in current GRB models.

Distinct immune responses of juvenile and adult oysters (Crassostrea gigas) to viral and bacterial infections

Since 2008, massive mortality events of Pacific oysters (Crassostrea gigas) have been reported worldwide and these disease events are often associated with Ostreid herpesvirus type 1 (OsHV-1). Epidemiological field studies have also reported oyster age and other pathogens of the Vibrio genus are contributing factors to this syndrome. We undertook a controlled laboratory experiment to simultaneously investigate survival and immunological response of juvenile and adult C. gigas at different time-points post-infection with OsHV-1, Vibrio tasmaniensis LGP32 and V. aestuarianus. Our data corroborates epidemiological studies that juveniles are more susceptible to OsHV-1, whereas adults are more susceptible to Vibrio. We measured the expression of 102 immune-genes by high-throughput RT-qPCR, which revealed oysters have different transcriptional responses to OsHV-1 and Vibrio. The transcriptional response in the early stages of OsHV-1 infection involved genes related to apoptosis and the interferon-pathway. Transcriptional response to Vibrio infection involved antimicrobial peptides, heat shock proteins and galectins. Interestingly, oysters in the later stages of OsHV-1 infection had a transcriptional response that resembled an antibacterial response, which is suggestive of the oyster's microbiome causing secondary infections (dysbiosis-driven pathology). This study provides molecular evidence that oysters can mount distinct immune response to viral and bacterial pathogens and these responses differ depending on the age of the host.

FLOOD RISK ASSESSMENT UNDER HISTORICAL AND PREDICTED LAND USE CHANGE USING CONTINUOUS HYDROLOGIC MODELING

Current procedures for flood risk estimation assume flood distributions are stationary over time, meaning annual maximum flood (AMF) series are not affected by climatic variation, land use/land cover (LULC) change, or management practices. Thus, changes in LULC and climate are generally not accounted for in policy and design related to flood risk/control, and historical flood events are deemed representative of future flood risk. These assumptions need to be re-evaluated, however, as climate change and anthropogenic activities have been observed to have large impacts on flood risk in many areas. In particular, understanding the effects of LULC change is essential to the study and understanding of global environmental change and the consequent hydrologic responses. The research presented herein provides possible causation for observed nonstationarity in AMF series with respect to changes in LULC, as well as a means to assess the degree to which future LULC change will impact flood risk. Four watersheds in the Midwest, Northeastern, and Central United States were studied to determine flood risk associated with historical and future projected LULC change. Historical single framed aerial images dating back to the mid-1950s were used along with Geographic Information Systems (GIS) and remote sensing models (SPRING and ERDAS) to create historical land use maps. The Forecasting Scenarios of Future Land Use Change (FORE-SCE) model was applied to generate future LULC maps annually from 2006 to 2100 for the conterminous U.S. based on the four IPCC-SRES future emission scenario conditions. These land use maps were input into previously calibrated Soil and Water Assessment Tool (SWAT) models for two case study watersheds. In order to isolate effects of LULC change, the only variable parameter was the Runoff Curve Number associated with the land use layer. All simulations were run with daily climate data from 1978-1999, consistent with the 'base' model which employed the 1992 NLCD to represent 'current' conditions. Output daily maximum flows were converted to instantaneous AMF series and were subsequently modeled using a Log-Pearson Type 3 (LP3) distribution to evaluate flood risk. Analysis of the progression of LULC change over the historic period and associated SWAT outputs revealed that AMF magnitudes tend to increase over time in response to increasing degrees of urbanization. This is consistent with positive trends in the AMF series identified in previous studies, although there are difficulties identifying correlations between LULC change and identified change points due to large time gaps in the generated historical LULC maps, mainly caused by unavailability of sufficient quality historic aerial imagery. Similarly, increases in the mean and median AMF magnitude were observed in response to future LULC change projections, with the tails of the distributions remaining reasonably constant. FORE-SCE scenario A2 was found to have the most dramatic impact on AMF series, consistent with more extreme projections of population growth, demands for growing energy sources, agricultural land, and urban expansion, while AMF outputs based on scenario B2 showed little changes for the future as the focus is on environmental conservation and regional solutions to environmental issues.

Alchemy and Symbolism in the Work of Carlos Estevez

The purpose of this thesis was to explore how alchemy has influenced Carlos Estevez’s work through a study of the symbolic repertoire and the philosophical concepts associated with it in his art, particularly how these are expressed in his artworks and how alchemy has evolved thematically in his oeuvre. The study of alchemy influenced this artist so deeply that even pieces that were not primarily inspired by this philosophical system show traces of it, essentially by representing the concept of transformation, crucial to understanding the alchemical process. This thesis is based on Carl Gustav Jung’s idea of metaphysical transformation as one of the main aspects of alchemy, and on his theory of active imagination as a tool to represent thoughts through artworks. Alchemy transformed Estevez’s art, and by extension the way he approaches life, making him conscious of the importance of transmutation and alchemical concepts.