Astrolabe: Curating, Linking and Computing Astronomy's Dark Data

Where appropriate repositories are not available to support all relevant astronomical data products, data can fall into darkness: unseen and unavailable for future reference and re-use. Some data in this category are legacy or old data, but newer datasets are also often uncurated and could remain "dark". This paper provides a description of the design motivation and development of Astrolabe, a cyberinfrastructure project that addresses a set of community recommendations for locating and ensuring the long-term curation of dark or otherwise at-risk data and integrated computing. This paper also describes the outcomes of the series of community workshops that informed creation of Astrolabe. According to participants in these workshops, much astronomical dark data currently exist that are not curated elsewhere, as well as software that can only be executed by a few individuals and therefore becomes unusable because of changes in computing platforms. Astronomical research questions and challenges would be better addressed with integrated data and computational resources that fall outside the scope of existing observatory and space mission projects. As a solution, the design of the Astrolabe system is aimed at developing new resources for management of astronomical data. The project is based in CyVerse cyberinfrastructure technology and is a collaboration between the University of Arizona and the American Astronomical Society. Overall the project aims to support open access to research data by leveraging existing cyberinfrastructure resources and promoting scientific discovery by making potentially-useful data in a computable format broadly available to the astronomical community.Comment: Accepted for publication in the Astrophysical Journal Supplement Series, 22 pages, 2 figure

Responsibility Modeling for the Sociotechnical Risk Analysis of Coalitions of Systems

Society is challenging systems engineers by demanding ever more complex and integrated systems. With the rise of cloud computing and systems-of-systems (including cyber-physical systems) we are entering an era where mission critical services and applications will be dependent upon 'coalitions-of-systems'. Coalitions-of-systems (CoS) are a class of system similar to systems-of-systems but they differ in that they interact to further overlapping self-interests rather than an overarching mission. Assessing the sociotechnical risks associated with CoS is an open research question of societal importance as existing risk analysis techniques typically focus on the technical aspects of systems and ignore risks associated with coalition partners reneging on responsibilities or leaving the coalition. We demonstrate that a responsibility modeling based risk analysis approach enables the identification of sociotechnical risks associated with CoS. The approach identifies hazards and associated risks that may arise when relying upon a coalition of human/organizational/technical agents to provision a service or application. Through a case study of a proposed cloud IT infrastructure migration we show how the technique identifies vulnerabilities that may arise because of human, organizational or technical agents failing to discharge responsibilities.Comment: Submitted for consideration for the IEEE SMC2011 conferenc

Risks Associated with Federal Construction Projects

The rise in terrorism, corporate espionage, cyber attacks, and federal fiscal constraints play an important role in the federal construction process. The risks associated with these occurrences are studied to aid in the risk management of the military construction process. This paper presents the status of research into these areas to identify how methods, policies, applications, and information obtained from case studies can be used by stakeholders to manage risk in the United States Air Force construction process. The author reviewed research on risk associated with four essential components of the military construction process – Critical Infrastructure, Information Technology, Contracts, and Cost in the construction and related industry. This study focused on the methodology, management policy, areas of application, and case studies research of the construction and related industry

A survey on online monitoring approaches of computer-based systems

This report surveys forms of online data collection that are in current use (as well as being the subject of research to adapt them to changing technology and demands), and can be used as inputs to assessment of dependability and resilience, although they are not primarily meant for this use

Housing Conditions and Health in Rural Nigeria: A Study of Akwa Ibom State

The study examined the relationship between housing conditions and ill health among households in Nigeria’s neglected rural areas with specific focus on rural Akwa Ibom State. The study design was based on household cross- sectional survey. Housing and Health Questionnaire (HHQ) was used to obtain the required information on 540 randomly sampled households in 90 rural communities. Housing Conditions were measured using six broad variables: Safety/Security, indoor temperature controls/ventilation, hygiene/sanitation, building condition, environmental quality and crowding. While ill health was measured by the reporting of respiratory symptoms namely Asthma, Pneumonia, Cough and Bronchitis. A stepwise multiple regression model was used to analyze the relationship between ill-health and housing conditions, controlling for other covariates. Results showed that majority of households lived in “inadequate housing” lacking facilities necessary to promote occupants health and wellbeing. About 92.3% of sampled households reported the occurrence of at least one respiratory symptom. The indoor temperature controls/ventilation and building condition were found to contribute significantly to Asthma occurrence (R2 =.669); building condition and environmental quality contributed 84.8% to the total variance in Pneumonia incidence (R2 =.848). Crowding was identified as the major determinant of cough incidence (R2 =.648) while building condition and crowding was found to jointly contribute 75.6% to the total variance in the occurrence of Bronchitis (R2 = .756). These findings highlight the need for immediate action on housing intervention as they suggest that health among the rural people could be strengthened with improved housing conditions. Keywords: Housing Conditions; Respiratory symptoms; Ill Health; Rural Areas; Akwa Ibom State

Interactive Experience Design: Integrated and Tangible Storytelling with Maritime Museum Artefacts

Museums play the role of intermediary between cultural heritage and visitors, and are often described as places and environments for education and enjoyment. The European Union also encourages innovative uses of museums to support education through the cultural heritage resources. However, the importance of visitors’ active role in museums as places for education and entertainment, on the one hand, and the growing and indispensable presence of technology in the cultural heritage domain, on the other hand, provided the initial ideas to develop the research. This thesis, presents the study and design for an interactive storytelling installation for a maritime museum. The installation is designed to integrate different museum artefacts into the storytelling system to enrich the visitors experience through tangible storytelling. The project was conducted in collaboration with another PhD student, Luca Ciotoli. His contribution was mainly focused on the narrative and storytelling features of the research, while my contribution was focused on the interaction- and technology-related features, including the design and implementation of the prototype. The research is deployed using a four-phase iterative approach. The first phase of the research, Study, deals with literature review and different studies to identify the requirements. The second phase, Design, determines the broad outlines of the project i.e., an interactive storytelling installation. The design phase includes interaction and museum experience design. We investigated different design approaches, e.g., interaction and museum experience design, to develop a conceptual design. The third phase, prototype, allows us to determine how to fulfill the tasks and meet the requirements that are established for the research. Prototyping involves content creation, storyboarding, integrating augmented artefacts into the storytelling system. Th final phase, test, refers to the evaluations that are conducted during the aforementioned phases e.g., formative and the final usability testing with users. The outcome of the research confirms previous results in the literature about how digital narratives can be enriched with the tangible dimension, moreover it shows how this dimension can enable to communicate stories and knowledge of the past that are complex, such as the art of navigating in the past, by integrating tangible objects that play different roles in the storytelling process

Virtual aids to navigation

There are many examples of master, bridge crew and pilot errors in navigation causing grounding under adverse circumstances that were known and published in official notices and records. Also dangerous are hazards to navigation resulting from dynamic changes within the marine environment, inadequate surveys and charts. This research attempts to reduce grounding and allision incidents and increase safety of navigation by expanding mariner situational awareness at and below the waterline using new technology and developing methods for the creation, implementation and display of Virtual Aids to Navigation (AtoN) and related navigation information. This approach has widespread significance beyond commonly encountered navigation situations. Increased vessel navigation activity in the Arctic and sub-Arctic regions engenders risk due, in part, to the inability to place navigational aids and buoys in constantly changing ice conditions. Similar conditions exist in tropical regions where sinker placement to moor buoys in sensitive environmental areas with coral reefs is problematic. Underdeveloped regions also lack assets and infrastructure needed to provide adequate navigation services, and infrastructure can also rapidly perish in developed regions during times of war and natural disaster. This research exploits rapidly developing advances in environmental sensing technology, evolving capabilities and improved methods for reporting real time environmental data that can substantially expand electronic navigation aid availability and improve knowledge of undersea terrain and imminent hazards to navigation that may adversely affect ship operations. This is most needed in areas where physical aids to navigation are scarce or non-existent as well as in areas where vessel traffic is congested. Research to expand related vessel capabilities is accomplished to overcome limitations in existing and planned electronic aids, expanding global capabilities and resources at relatively low-cost. New methods for sensor fusion are also explored to vi reduce overall complexity and improve integration with other navigation systems with the goal of simplifying navigation tasks. An additional goal is to supplement training program content by expanding technical resources and capabilities within the confines of existing International Convention on Standards for Training, Certification and Watchkeeping for Seafarers (STCW) requirements, while improving safety by providing new techniques to enhance situational awareness

Toitu Te Moananui a Toi – The Effects of the MV Rena on the Water Quality, Chemistry and Zooplankton of Otaiti (Astrolabe Reef)

Humans have had a profound effect on the world’s oceans, particularly through pollution. Marine pollution incidents are particularly important and increasingly involve both petrochemical and metal contamination. The effects of complex high level, point source pollution events such as ship wrecks on larval recruitment to reef environments is not well understood. Larval settlement is heavily influenced by chemical cues, hence pollution events could have a long term influence on reef ecology, and the likelihood that planktonic zooplankton can entrain contaminants into the reef food web is also of concern. This thesis aims to address concerns from local Tangata Whenua, government, researchers, stakeholders and the public about the long term recovery of Otaiti following the MV Rena shipwreck and subsequent reef contamination. The incident is a complex one involving metallic container debris contamination along with oil. Research focussed on assessing the effects of water borne contamination surrounding the wreck site in order to examine acute and chronic responses of planktonic invertebrates: (1) the influence of Rena and associated debris to the chemistry and quality of water in the benthic zone around the wreck, (2) the toxicity of contaminants to survivorship of zooplankton, and (3) the influence on contaminant plumes to zooplankton recruitment behaviour of Otaiti. There is a clear effect from the Rena and its associated debris field on the water quality and chemistry of Otaiti. Aluminium and copper for example, were consistently elevated in dissolved and total metal concentrations around the debris field. Laboratory based exposure of zooplankton to realistic concentration gradients of Rena contaminated sediments resulted in increased mortality with increased contaminant concentrations. Behavioural responses of pelagic and settling invertebrates to Rena pollution influenced sediment highlighted sensitivity to associated contaminant plumes. This could have significant ecological implications to the recruitment behaviour of other planktonic organisms that rely on reef conspecifics and chemical cues to initiate settlement. Ecological concepts such as ecosystem function and biodiversity dynamics (including recruitment) relate the life force and longevity of a system. Key concerns within the scope of this research were highlighted that may have implications to Tangata Whenua decision making in assessing the Mauri of Otaiti. It can be implied that the Rena continues to impact the Mauri of Otaiti due to the presence of contaminants within the debris field

“Rethinking High-Grade Serous Carcinoma: Development of new tools for deep tissue profiling”

Background: High-grade serous ovarian cancer (HGSOC) is the most frequently occurring and most fatal epithelial ovarian cancer (EOC) subtype. The reciprocal interplay of the different components encompassed within the tumour microenvironment (TME) are fundamental for tumour growth, advancement, and therapy response. It is therefore important to be able to deeply characterize the complex and diverse TME with multidimensional approaches. Aims: The main aim of this project was to establish novel multiparametric mass cytometry panels and thoroughly characterise the HGSOC TME. Methods: We first developed a novel 35-marker ovarian TME-based Cytometry by time-of-flight (CyTOF) panel (pan-tumour panel) and utilized it to examine the effects of six different tissue dissociation methods on cell surface antigen expression profiles in HGSOC tumour samples (Paper I). We further established an unique immune panel (pan-immune) for the detailed immunophenotyping of chemo-naïve HGSOC patients. The individual tumour immune microenvironments were characterized with tailored computational analysis (Paper II). With the use of an established merging algorithm— CyTOFmerge—the pan-tumour and pan-immune datasets were merged for a more in- depth immune delineation of the ten ovarian chemo-naïve TME profiles in addition to tumour and stromal cell phenotyping (Paper III). Results: We have established a novel ovarian TME-based CyTOF panel for HGSOC that is capable of delineating the immune, tumour, and stromal cells of the TME. Utilizing this panel, we demonstrated that, although the six tissue dissociation methods have a certain level of influence on the TME antigen expression profiles, inter-patient differences between the tumour samples are still clear. In addition, we identified a previously undescribed stem-like cell subset (Paper I). We have developed a unique 34-marker immune panel and have provided a detailed characterization of the ovarian tumour immune microenvironment of chemo-naïve patients. We identified a high degree of interpatient immune cell heterogenicity and discovered an abundance of conventional dendritic cells (DC), natural killer (NK) cells, and unassigned hematopoietic cells. Certain monocyte and dendritic cell (DC) clusters have shown prognostic relevance within the ovarian TME (Paper II). The merged dataset analysis revealed a new level of complexity with a more in-depth immune (myeloid cells) delineation in addition to tumour and stromal (fibroblast subsets) cell phenotypes. We identified an even higher degree of interpatient TME heterogenicity and a novel tumour cell metacluster, CD45-CD56-(EpCAM-FOLR1-CD24-). As a benefit of integrating the datasets, we identified even higher clinical associations (from 12 [pan-tumour dataset] to 20 [merged dataset]). Furthermore, most of these observed associations were majorly between PFS, OS, and infiltrating immune cell subsets (Paper III). Conclusions and consequences: (Paper I) In conclusion, the panel represents a promising profiling tool for the in-depth phenotyping of the HGSOC TME cell subsets. Although the tissue dissociation methods have influence on the TME antigen expression profiles, inter-patient differences are still clear. (Paper II) Our findings revealed a high degree of heterogeneity and identified phenotypic profiles that can be explored for use in HGSOC phenotypic profiling. (Paper III) Together, the merged sketching illustrates that comprehensive individual TME mapping for HGSOC patients can contribute to a better understanding each patient’s unique micromilieu given the need for more personalized treatment approaches.Doktorgradsavhandlin

Robust peer-to-peer systems

textPeer-to-peer (p2p) approaches are an increasingly effective way to deploy services. Popular examples include BitTorrent, Skype, and KaZaA. These approaches are attractive because they can be highly fault-tolerant, scalable, adaptive, and less expensive than a more centralized solution. Cooperation lies at the heart of these strengths. Yet, in settings where working together is crucial, a natural question is: "What if users stop cooperating?" After all, cooperative services are typically deployed over multiple administrative domains, and thus vulnerable to Byzantine failures and users who may act selfishly. This dissertation explores how to construct p2p systems to tolerate Byzantine participants while also incentivizing selfish participants to contribute resources. We describe how to balance obedience against choice in building a robust p2p live streaming system. Imposing obedience is desirable as it leaves little room for peers to attack or cheat the system. However, providing choice is also attractive as it allows us to engineer flexible and efficient solutions. We first focus on obedience by using Nash equilibria to drive the design of BAR Gossip, the first gossip protocol that is resilient to Byzantine and selfish nodes. BAR Gossip relies on verifiable pseudo-random partner selection to eliminate non-determinism, which can be used to game the system, while maintaining the robustness and rapid convergence of traditional gossip. A novel fair enough exchange primitive entices cooperation among selfish peers on short timescales, thereby avoiding the need for distributed reputation schemes. We next focus on tempering obedience with choice by using approximate equilibria to guide the construction of a novel p2p live streaming system. These equilibria allow us to design incentives to limit selfish behavior rigorously, yet provide sufficient flexibility to build practical systems. We show the advantages of using an [element of]-Nash equilibrium, instead of an exact Nash, to design and implement FlightPath, our live streaming system that uses bandwidth efficiently, absorbs flash crowds, adapts to sudden peer departures, handles churn, and tolerates malicious activity.Computer Science