When the path is never shortest: a reality check on shortest path biocomputation

Shortest path problems are a touchstone for evaluating the computing performance and functional range of novel computing substrates. Much has been published in recent years regarding the use of biocomputers to solve minimal path problems such as route optimisation and labyrinth navigation, but their outputs are typically difficult to reproduce and somewhat abstract in nature, suggesting that both experimental design and analysis in the field require standardising. This chapter details laboratory experimental data which probe the path finding process in two single-celled protistic model organisms, Physarum polycephalum and Paramecium caudatum, comprising a shortest path problem and labyrinth navigation, respectively. The results presented illustrate several of the key difficulties that are encountered in categorising biological behaviours in the language of computing, including biological variability, non-halting operations and adverse reactions to experimental stimuli. It is concluded that neither organism examined are able to efficiently or reproducibly solve shortest path problems in the specific experimental conditions that were tested. Data presented are contextualised with biological theory and design principles for maximising the usefulness of experimental biocomputer prototypes.Comment: To appear in: Adamatzky, A (Ed.) Shortest path solvers. From software to wetware. Springer, 201

Arzner, Dorothy (1897–1979)

Dorothy Arzner was the only American woman that was successful in both the silent and the sound era. She was the only woman director working for Hollywood in the 1930s and one of the very few female Hollywood directors that have been successful from the 1920s to the 1940s. Arzner in fact came to symbolize everything that women could achieve in cinema and her work had a great influence on later women directors such as Ida Lupino, Joan Micklin Silver, and Elaine May. Her films were reclaimed by feminist scholars during the 1970s as texts that subvert patriarchal constructions of gender. In particular, feminist film critics often quote Arzner\u27s Dance, Girl, Dance (1940) as a film that actively critiques the culture of the spectacle where the woman is objectified by the gaze of the camera. Overall, although Arzner uses the “master\u27s tools,” she still manages to dismantle “the master\u27s house” by denaturalizing the gender conventions of her era

Development and application of the GIM code for the Cyber 203 computer

The GIM computer code for fluid dynamics research was developed. Enhancement of the computer code, implicit algorithm development, turbulence model implementation, chemistry model development, interactive input module coding and wing/body flowfield computation are described. The GIM quasi-parabolic code development was completed, and the code used to compute a number of example cases. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and implicit finite difference scheme were also added. Development was completed on the interactive module for generating the input data for GIM. Solutions for inviscid hypersonic flow over a wing/body configuration are also presented

Assessment of Grass Production and Efficiency of Utilisation on Three Northern Ireland Dairy Farms

Recent research has shown that grazed grass can be an expensive forage for milk production, particularly if herbage production is low or utilisation is inefficient. There is very limited data on the level of herbage grown and utilised on commercial farms. The objective of this project was to quantify grass production and efficiency of utilisation on farm to substantiate the potential of grazed grass for profitable milk production

Cellular automata modelling of slime mould actin network signalling

© 2016, The Author(s). Actin is a cytoskeletal protein which forms dense, highly interconnected networks within eukaryotic cells. A growing body of evidence suggests that actin-mediated intra- and extracellular signalling is instrumental in facilitating organism-level emergent behaviour patterns which, crucially, may be characterised as natural expressions of computation. We use excitable cellular automata modelling to simulate signal transmission through cell arrays whose topology was extracted from images of Watershed transformation-derived actin network reconstructions; the actin networks sampled were from laboratory experimental observations of a model organism, slime mould Physarum polycephalum. Our results indicate that actin networks support directional transmission of generalised energetic phenomena, the amplification and trans-network speed of which of which is proportional to network density (whose primary determinant is the anatomical location of the network sampled). Furthermore, this model also suggests the ability of such networks for supporting signal-signal interactions which may be characterised as Boolean logical operations, thus indicating that a cell’s actin network may function as a nanoscale data transmission and processing network. We conclude by discussing the role of the cytoskeleton in facilitating intracellular computing, how computation can be implemented in such a network and practical considerations for designing ‘useful’ actin circuitry

Geometric quantum computation using fictitious spin- 1/2 subspaces of strongly dipolar coupled nuclear spins

Geometric phases have been used in NMR, to implement controlled phase shift gates for quantum information processing, only in weakly coupled systems in which the individual spins can be identified as qubits. In this work, we implement controlled phase shift gates in strongly coupled systems, by using non-adiabatic geometric phases, obtained by evolving the magnetization of fictitious spin-1/2 subspaces, over a closed loop on the Bloch sphere. The dynamical phase accumulated during the evolution of the subspaces, is refocused by a spin echo pulse sequence and by setting the delay of transition selective pulses such that the evolution under the homonuclear coupling makes a complete $2\pi$ rotation. A detailed theoretical explanation of non-adiabatic geometric phases in NMR is given, by using single transition operators. Controlled phase shift gates, two qubit Deutsch-Jozsa algorithm and parity algorithm in a qubit-qutrit system have been implemented in various strongly dipolar coupled systems obtained by orienting the molecules in liquid crystal media.Comment: 37 pages, 17 figure

Disease, sanitation and the 'lower orders' : perception and reality in Sydney, 1875-1881

This is a study in human relationships - of the way in which the ignorance and subsequent fears and prejudices which shape human perceptions of one another are incorporated into the social ties binding together the community as a whole. The thesis is confined geographically to the inner city area within the administrative boundaries of the Sydney City Council.! It takes as its core-period the years between the disease alarms early in 1875 and the smallpox epidemic during the second half of 1881, and from that perspective views the broader sweep of time from mid-century until the early 1890s. It shows an urban community in whose expanding economy and aggregation of population were contained forces of fragmentation and division - geographical, social, and psychological. City growth at a rate faster than the enactment of regulatory controls and provision of local services had been accompanied by a proliferation of aesthetic and sanitary nuisances, caused for example by the expansion of industry, and deficiencies in garbage collection, in drainage and water services. Networks of abutting courts and passageways developed off City main streets, crowded with insanitary tenements and groups of decaying cottage-dwellings, relics from the city's past. The consequent anxieties about city ill-health, and recurring alarms about the likely appearance of epidemic disease, were expressed in a generally-felt dissatisfaction with the achievements of local government sanitary administration. As the experiences of CHOs in attempting to remedy sanitary nuisances make plain, the City Corporation's performance in the field of public health was limited by its powerlessness to undertake necessary sanitary initiatives independently of Parliament. Many outside critics however, aware only of the continuing deficiencies in City health regulation, called for the City Council's replacement by a more energetic metropolitan municipal council, or for its subordination to the directions of government-appointed experts on a board of health. Contemporary understanding of the nature of disease, influenced by miasmic or filth-based explanations of illness, focused community anxieties about disease upon the working class districts of the inner City. The resulting sanitary investigations of these little-known neighbourhoods presented a generalised picture of squalor and unwholesomeness. Apprehensions about disease, together with middle class rationalisations for the existence of poverty, and at the individual level a psychological need among people of all classes to have someone else to look down upon, in turn produced a distorting, stereotyped image of an alien and menacing subgroup of debased humanity within the community - the urban lower orders. The emergence and subsequent impact of the image of the lower orders upon the direction of sanitary endeavour and of public health policy in Sydney forms the core of this thesis. This is the first doctoral thesis to have been based upon the manuscript material on city health in the Sydney Town Hall archives. The City Council's sanitary staff has never before been studied. The CHOs are largely forgotten men. In their many hundreds of reports, however, there lies an invaluable source of information on life - and death - in a nineteenth century city. A chronicle of the principal events dealt with in the thesis may be found in Appendix Eleven

Automating Vehicles by Deep Reinforcement Learning using Task Separation with Hill Climbing

Within the context of autonomous driving a model-based reinforcement learning algorithm is proposed for the design of neural network-parameterized controllers. Classical model-based control methods, which include sampling- and lattice-based algorithms and model predictive control, suffer from the trade-off between model complexity and computational burden required for the online solution of expensive optimization or search problems at every short sampling time. To circumvent this trade-off, a 2-step procedure is motivated: first learning of a controller during offline training based on an arbitrarily complicated mathematical system model, before online fast feedforward evaluation of the trained controller. The contribution of this paper is the proposition of a simple gradient-free and model-based algorithm for deep reinforcement learning using task separation with hill climbing (TSHC). In particular, (i) simultaneous training on separate deterministic tasks with the purpose of encoding many motion primitives in a neural network, and (ii) the employment of maximally sparse rewards in combination with virtual velocity constraints (VVCs) in setpoint proximity are advocated.Comment: 10 pages, 6 figures, 1 tabl

Accelerated placental aging in early onset preeclampsia pregnancies identified by DNA methylation.

Aim: To determine whether dynamic DNA methylation changes in the human placenta can be used to predict gestational age. Materials & methods: Publicly available placental DNA methylation data from 12 studies, together with our own dataset, using Illumina Infinium Human Methylation BeadChip arrays. Results & conclusion: We developed an accurate tool for predicting gestational age of placentas using 62 CpG sites. There was a higher predicted gestational age for placentas from early onset preeclampsia cases, but not term preeclampsia, compared with their chronological age. Therefore, early onset preeclampsia is associated with placental aging. Gestational age acceleration prediction from DNA methylation array data may provide insight into the molecular mechanisms of pregnancy disorders.Benjamin T Mayne, Shalem Y Leemaqz, Alicia K Smith, James Breen, Claire T Roberts, Tina Bianco-Miott