Inference for dynamics of continuous variables: the Extended Plefka Expansion with hidden nodes

We consider the problem of a subnetwork of observed nodes embedded into a larger bulk of unknown (i.e. hidden) nodes, where the aim is to infer these hidden states given information about the subnetwork dynamics. The biochemical networks underlying many cellular and metabolic processes are important realizations of such a scenario as typically one is interested in reconstructing the time evolution of unobserved chemical concentrations starting from the experimentally more accessible ones. We present an application to this problem of a novel dynamical mean field approximation, the Extended Plefka Expansion, which is based on a path integral description of the stochastic dynamics. As a paradigmatic model we study the stochastic linear dynamics of continuous degrees of freedom interacting via random Gaussian couplings. The resulting joint distribution is known to be Gaussian and this allows us to fully characterize the posterior statistics of the hidden nodes. In particular the equal-time hidden-to-hidden variance -- conditioned on observations -- gives the expected error at each node when the hidden time courses are predicted based on the observations. We assess the accuracy of the Extended Plefka Expansion in predicting these single node variances as well as error correlations over time, focussing on the role of the system size and the number of observed nodes.Comment: 30 pages, 6 figures, 1 Appendi

New delivery model for non-profit organisations: shared computing services

Abstract: The current economic climate of funding stringency has intensified the need for non-profit organisations (NPOs) to find new delivery models of their services as a way of creating greater efficiencies and reducing costs. Consideration of improvement to their back-office operations is one way of addressing overheads associated with delivery functions of NPOs so that they can continue to focus on their core business activities. The overheads for back-office functions are much larger for smaller NPOs (by about 10-15 percent) than the larger ones and interest in sharing services could appeal to that sector. One approach to reduce overhead costs is for two or more NPOs to collaborate in sharing office space and office equipment and, in some instances, outsourcing some functions, for example, human resources and information technology. Currently, in New Zealand, there is very little engagement by NPOs in sharing services, particularly back office computing services. It was against this background that meetings with representatives of eight NPOs in Wellington, New Zealand, identified the challenges they were facing. These included funding, client management, compliance with reporting (financial and non-financial), financial management and control, governance, marketing and promotion and retention and management of staff and volunteers. Wellington City Council, as a significant funding agent of some local NPOs, commissioned an online survey with the aim of understanding the interest and readiness of NPOs in adopting shared computing services. The survey was developed collaboratively with the council, a computing charitable trust and a local university. The objectives of the survey were: to provide a snapshot of computing usage within the organisations, identify significant issues challenging the sector and understand their perceptions of shared computing services. The perceptions of the Wellington region NPO representatives (147 valid surveys) regarding shared services are reported in this paper. Results reveal the factors that drive the uptake of shared services within the non-profit sector, the benefits, barriers and priorities of sharing computing services and respondents’ views on their willingness to pay for a shared services arrangement. NPOs were positive regarding potential benefits of a shared services arrangement but recognised potential barriers of privacy and security, a need for contractual relationships, shared vision and compliance and standardisation. Priorities for a proposed shared services model were identified as finance and management of data and knowledge. The majority of respondents indicated they were willing to pay up to five percent of their budget for a shared services arrangement. These results provide a basis for further study as to the type of shared services model that organisations would find acceptable and render efficiencies and cost savings.Authors: Barbara Crump, Raja Peter Massey University, Wellington, New Zealand.Paper to be presented at the 7th European Conference on Information Management and Evaluation, Gdansk, 23-24 September 2013

Effect of mechanical soil treatment in blueberry orchards

From June 2004 onwards a trial was conducted on a blueberry farm in the Lüneburg Heath, Northern Germany, in which methods of mechanical soil cultivation were compared with mulching. The aim was to determine how far the mechanical methods and equipment established for soil management in viniculture and pomiculture can be adapted to blueberry cultivation, and can be improved. The results showed a clear advantage of the methods based on mulch technology in the shape of increased yields. Whilst the mechanical treatments provided acceptable weed control, they cannot be recommended for routine use at present because of strong yield reductions associated with damage to the shallow root system of highbush blueberry shrubs

Extended Plefka Expansion for Stochastic Dynamics

We propose an extension of the Plefka expansion, which is well known for the dynamics of discrete spins, to stochastic differential equations with continuous degrees of freedom and exhibiting generic nonlinearities. The scenario is sufficiently general to allow application to e.g. biochemical networks involved in metabolism and regulation. The main feature of our approach is to constrain in the Plefka expansion not just first moments akin to magnetizations, but also second moments, specifically two-time correlations and responses for each degree of freedom. The end result is an effective equation of motion for each single degree of freedom, where couplings to other variables appear as a self-coupling to the past (i.e. memory term) and a coloured noise. This constitutes a new mean field approximation that should become exact in the thermodynamic limit of a large network, for suitably long-ranged couplings. For the analytically tractable case of linear dynamics we establish this exactness explicitly by appeal to spectral methods of Random Matrix Theory, for Gaussian couplings with arbitrary degree of symmetry

Delineating neuroinflammation, parasite CNS invasion, and blood-brain barrier dysfunction in an experimental murine model of human African trypanosomiasis

Although Trypanosoma brucei spp. was first detected by Aldo Castellani in CSF samples taken from sleeping sickness patients over a century ago there is still a great deal of debate surrounding the timing, route and effects of transmigration of the parasite from the blood to the CNS. In this investigation, we have applied contrast-enhance magnetic resonance imaging (MRI) to study the effects of trypanosome infection on the blood-brain barrier (BBB) in the well-established GVR35 mouse model of sleeping sickness. In addition, we have measured the trypanosome load present in the brain using quantitative Taqman PCR and assessed the severity of the neuroinflammatory reaction at specific time points over the course of the infection. Contrast enhanced – MRI detected a significant degree of BBB impairment in mice at 14 days following trypanosome infection, which increased in a step-wise fashion as the disease progressed. Parasite DNA was present in the brain tissue on day 7 after infection. This increased significantly in quantity by day 14 post-infection and continued to rise as the infection advanced. A progressive increase in neuroinflammation was detected following trypanosome infection, reaching a significant level of severity on day 14 post-infection and rising further at later time-points. In this model stage-2 disease presents at 21 days post-infection. The combination of the three methodologies indicates that changes in the CNS become apparent prior to the onset of established stage-2 disease. This could in part account for the difficulties associated with defining specific criteria to distinguish stage-1 and stage-2 infections and highlights the need for improved staging diagnostics

Smoking related disease risk, area deprivation and health behaviours

Acknowledgements We thank Professor Luke Vale, Dr Diane Stockton and participants at the Faculty of Public Health conference, Aviemore, Scotland, November 2011 and UK Society for Behavioural Medicine conference, Stirling, Scotland, December 2011 for helpful comments. Funding This work was supported by the Medical Research Council National Preventive Research Initiative Phase 2 [G0701874]; see http://www.npri.org.uk. The Funding Partners relevant to this award are: British Heart Foundation; Cancer Research UK; Department of Health; Diabetes UK; Economic and Social Research Council; Medical Research Council; Research and Development Office for the Northern Ireland Health and Social Services; Chief Scientist Office; Scottish Government Health Directorates; The Stroke Association; Welsh Assembly Government and World Cancer Research Fund. The Health Economics Research Unit is funded by the Chief Scientist Office of the Scottish Government Health and Social Care DirectoratePeer reviewedPostprin

Mobility of core water in Bacillus subtilis spores by 2^2H NMR

Bacterial spores in a metabolically dormant state can survive long periods without nutrients under extreme environmental conditions. The molecular basis of spore dormancy is not well understood, but the distribution and physical state of water within the spore is thought to play an important role. Two scenarios have been proposed for the spore's core region, containing the DNA and most enzymes. In the gel scenario, the core is a structured macromolecular framework permeated by mobile water. In the glass scenario, the entire core, including the water, is an amorphous solid and the quenched molecular diffusion accounts for the spore's dormancy and thermal stability. Here, we use $^2$H magnetic relaxation dispersion to selectively monitor water mobility in the core of Bacillus subtilis spores in the presence and absence of core Mn$^{2+}$ ions. We also report and analyze the solid-state $^2$H NMR spectrum from these spores. Our NMR data clearly support the gel scenario with highly mobile core water (~ 25 ps average rotational correlation time). Furthermore, we find that the large depot of manganese in the core is nearly anhydrous, with merely 1.7 % on average of the maximum sixfold water coordination.Comment: 11 pages, 5 figure

Exploring the relationship between task, teacher actions, and student learning

We are examining actions that teachers take to convert tasks into learning opportunities. In this paper, we contrast ways that three teachers convert the same task into lessons, and the way that their lessons reflect their intent. We found that the teachers did what they intended to do, that this was connected to their appreciation of the mathematics involved, and directly influenced the learning opportunities of the students. To the extent that the potential of the task was reduced, this seemed due to the lack of mathematical confidence in the case of two of the teachers