Chancellery Research - Research Publications

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    plyranges: a grammar of genomic data transformation
    Lee, S ; Cook, D ; Lawrence, M (BMC, 2019-01-04)
    Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there are gaps in the API that prevent its general use. By recognizing that the GRanges class follows "tidy" data principles, we create a grammar of genomic data transformation, defining verbs for performing actions on and between genomic interval data and providing a way of performing common data analysis tasks through a coherent interface to existing Bioconductor infrastructure. We implement this grammar as a Bioconductor/R package called plyranges.
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    Simulated in vivo Electrophysiology Experiments Provide Previously Inaccessible Insights into Visual Physiology.
    Quiroga, M ; Price, NSC ( 2016)
    Lecture content and practical laboratory classes are ideally complementary. However, the types of experiments that have led to our detailed understanding of sensory neuroscience are often not amenable to classroom experimentation as they require expensive equipment, time-consuming surgeries, specialized experimental techniques, and the use of animals. While sometimes feasible in small group teaching, these experiments are not suitable for large cohorts of students. Previous attempts to expose students to sensory neuroscience experiments include: the use of electrophysiology preparations in invertebrates, data-driven simulations that do not replicate the experience of conducting an experiment, or simply observing an experiment in a research laboratory. We developed an online simulation of a visual neuroscience experiment in which extracellular recordings are made from a motion sensitive neuron. Students have control over stimulation parameters (direction and contrast) and can see and hear the action potential responses to stimuli as they are presented. The simulation provides an intuitive way for students to gain insight into neurophysiology, including experimental design, data collection and data analysis. Our simulation allows large cohorts of students to cost-effectively "experience" the results of animal research without ethical concerns, to be exposed to realistic data variability, and to develop their understanding of how sensory neuroscience experiments are conducted.
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    IL-23 costimulates antigen-specific MAIT cell activation and enables vaccination against bacterial infection
    Wang, H ; Kjer-Nielsen, L ; Shi, M ; D'Souza, C ; Pediongco, TJ ; Cao, H ; Kostenko, L ; Lim, XY ; Eckle, SBG ; Meehan, BS ; Zhu, T ; Wang, B ; Zhao, Z ; Mak, JYW ; Fairlie, DP ; Teng, MWL ; Rossjohn, J ; Yu, D ; de St Groth, BF ; Lovrecz, G ; Lu, L ; McCluskey, J ; Strugnell, RA ; Corbett, AJ ; Chen, Z (AMER ASSOC ADVANCEMENT SCIENCE, 2019-11-01)
    Mucosal-associated invariant T (MAIT) cells are activated in a TCR-dependent manner by antigens derived from the riboflavin synthesis pathway, including 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), bound to MHC-related protein-1 (MR1). However, MAIT cell activation in vivo has not been studied in detail. Here, we have found and characterized additional molecular signals required for optimal activation and expansion of MAIT cells after pulmonary Legionella or Salmonella infection in mice. We show that either bone marrow–derived APCs or non–bone marrow–derived cells can activate MAIT cells in vivo, depending on the pathogen. Optimal MAIT cell activation in vivo requires signaling through the inducible T cell costimulator (ICOS), which is highly expressed on MAIT cells. Subsequent expansion and maintenance of MAIT-17/1-type responses are dependent on IL-23. Vaccination with IL-23 plus 5-OP-RU augments MAIT cell–mediated control of pulmonary Legionella infection. These findings reveal cellular and molecular targets for manipulating MAIT cell function under physiological conditions.
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    DIALOGUE / COLLABORATION
    Andrew, B ; Walter, T ; Maidment, S ; Ryan, J (National Gallery of Victoria, 2017)
    The text focusses on key moments in Brook Andrew’s 25-year career, and looking at the artist’s fascination with archival materials and strong interest in process that remain central to his practice. A point of focus is Andrew’s interdisciplinary and collaborative approach which encompasses mediums of photography, video, neon, text, collage, printmaking, assemblage, sculpture, painting and installation.
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    'Knowing Whether' in Proper Epistemic Knowledge Bases
    Miller, T ; Felli, P ; Muise, C ; Pearce, AR ; Sonenberg, L (AAAI Press, 2016)
    Proper epistemic knowledge bases (PEKBs) are syntactic knowledge bases that use multi-agent epistemic logic to represent nested multi-agent knowledge and belief. PEKBs have certain syntactic restrictions that lead to desirable computational properties; primarily, a PEKB is a conjunction of modal literals, and therefore contains no disjunction. Sound entailment can be checked in polynomial time, and is complete for a large set of arbitrary formulae in logics Kn and KDn. In this paper, we extend PEKBs to deal with a restricted form of disjunction: 'knowing whether.' An agent i knows whether Q iff agent i knows Q or knows not Q; that is, []Q or []not(Q). In our experience, the ability to represent that an agent knows whether something holds is useful in many multi-agent domains. We represent knowing whether with a modal operator, and present sound polynomial-time entailment algorithms on PEKBs with the knowing whether operator in Kn and KDn, but which are complete for a smaller class of queries than standard PEKBs.
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    Planning for a Single Agent in a Multi-Agent Environment Using FOND
    Muise, C ; Felli, P ; Miller, T ; Pearce, AR ; Sonenberg, L ; Kambhampati, S (AAAI Press, 2016)
    Single-agent planning in a multi-agent environment is challenging because the actions of other agents can affect our ability to achieve a goal. From a given agent's perspective, actions of others can be viewed as non-deterministic outcomes of that agent's actions. While simple conceptually, this interpretation of planning in a multi-agent environment as non-deterministic planning remains challenging, not only due to the non-determinism resulting from others' actions, but because it is not clear how to compactly model the possible actions of others in the environment. In this paper, we cast the problem of planning in a multiagent environment as one of Fully-Observable Non-Deterministic (FOND) planning. We extend a non-deterministic planner to plan in a multi-agent setting, allowing non-deterministic planning technology to solve a new class of planning problems. To improve the efficiency in domains too large for solving optimally, we propose a technique to use the goals and possible actions of other agents to focus the search on a set of plausible actions. We evaluate our approach on existing and new multiagent benchmarks, demonstrating that modelling the other agents' goals improves the quality of the resulting solutions.
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    Social planning for social HRI
    Sonenberg, E ; Miller, T ; Pearce, AR ; Felli, P ; Muise, CJ ; Dignum, F ; Baxter, P ; Trafton, G ; Lemaignan, S (arxiv, 2016)
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    Social Planning for Trusted Autonomy
    Miller, T ; Pearce, AR ; Sonenberg, L ; Abbass, HA ; Scholz, J ; Reid, DJ (Springer International Publishing, 2018)
    In this chapter, we describe social planning mechanisms for constructing and representing explainable plans in human-agent interactions, addressing one aspect of what it will take to meet the requirements of a trusted autonomous system. Social planning is automated planning in which the planning agent maintains and reasons with an explicit model of the other agents, human or artificial, with which it interacts, including the humans’ goals, intentions, and beliefs, as well as their potential behaviours. The chapter includes a brief overview of the challenge of planning in human-agent teams, and an introduction to a recent body of technical work in multi-agent epistemic planning. The benefits of planning in the presence of nested belief reasoning and first-person multi-agent planning are illustrated in two scenarios, hence indicating how social planning could be used for planning human-agent interaction explicitly as part of an agent’s deliberation.
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    Uteroplacental insufficiency in rats induces renal apoptosis and delays nephrogenesis completion
    Cuffe, JSM ; Briffa, JF ; Rosser, S ; Siebel, AL ; Romano, T ; Hryciw, DH ; Wlodek, ME ; Moritz, KM (WILEY, 2018-03)
    AIM: Uteroplacental insufficiency in rats reduces nephron endowment, leptin concentrations and programmes cardiorenal disease in offspring. Cross-fostering growth-restricted (Restricted) offspring onto a mother with normal lactation restores leptin concentrations and nephron endowment. This study aimed to determine whether the reduced nephron endowment in Restricted offspring is due to delayed glomerular formation and dysregulation of renal genes regulating branching morphogenesis, apoptosis or leptin signalling. Furthermore, we aimed to investigate whether cross-fostering Restricted offspring onto Control mothers could improve glomerular maturation and restore renal gene abundance. METHODS: Uteroplacental insufficiency was induced by bilateral uterine vessel ligation (Restricted) or sham (Control) surgery on gestation day 18 (E18). Kidneys were collected at E20, postnatal day 1 (PN1) and PN7. An additional cohort was cross-fostered onto separate mothers at birth and kidneys collected at PN7. RESULTS: Kidneys were lighter in the Restricted group, but weight was restored with cross-fostering. At E20, abundance of Bax, Flt1 and Vegfa was increased in Restricted offspring, while Ret and Bcl2 transcripts were increased only in Restricted females. At PN7, abundance of Gdnf and Ret was higher in Restricted offspring, as was Casp3. Restricted offspring had a wider nephrogenic zone with more immature glomeruli suggesting a delayed or extended nephrogenic period. Cross-fostering had subtle effects on gene abundance and glomerular maturity. CONCLUSION: Uteroplacental insufficiency induced apoptosis in the developing kidney and delayed and extended nephrogenesis. Cross-fostering Restricted offspring onto Control mothers had beneficial effects on kidney growth and renal maturity, which may contribute to the restoration of nephron endowment.
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    Detection of Toscana virus from an adult traveler returning to Australia with encephalitis.
    Arden, KE ; Heney, C ; Shaban, B ; Nimmo, GR ; Nissen, MD ; Sloots, TP ; Mackay, IM (Wiley, 2017-10)
    Toscana virus (TOSV) is identified in sandflies, animals, and humans around the Mediterranean Sea. TOSV has not been reported in Australia. During investigations of cerebrospinal fluid samples from patients with encephalitis, TOSV genetic sequences were identified in a traveler returning to Australia from Europe. TOSV should be considered, especially during May to October, in travelers to Australia who embarked in countries in and around the Mediterranean Sea and who subsequently present for medical care because of neurological symptoms.