A cell-permeable tool for analysing APP intracellular domain function and manipulation of PIKfyve activity

The mechanisms for regulating PIKfyve complex activity are currently emerging. The PIKfyve complex, consisting of the phosphoinositide kinase PIKfyve (also known as FAB1), VAC14 and FIG4, is required for the production of phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2). PIKfyve function is required for homeostasis of the endo/lysosomal system and is crucially implicated in neuronal function and integrity, as loss of function mutations in the PIKfyve complex lead to neurodegeneration in mouse models and human patients. Our recent work has shown that the intracellular domain of the Amyloid Precursor Protein (APP), a molecule central to the aetiology of Alzheimer's disease binds to VAC14 and enhances PIKfyve function. Here we utilise this recent advance to create an easy-to-use tool for increasing PIKfyve activity in cells. We fused APP's intracellular domain (AICD) to the HIV TAT domain, a cell permeable peptide allowing proteins to penetrate cells. The resultant TAT-AICD fusion protein is cell permeable and triggers an increase of PI(3,5)P2. Using the PI(3,5)P2 specific GFP-ML1Nx2 probe we show that cell-permeable AICD alters PI(3,5)P2 dynamics. TAT-AICD also provides partial protection from pharmacological inhibition of PIKfyve. All three lines of evidence show that the APP intracellular domain activates the PIKfyve complex in cells, a finding that is important for our understanding of the mechanism of neurodegeneration in Alzheimer's disease.

The electroretinogram:a useful tool for evaluating age-related macular disease?

With an ageing population, the number of age-related macular disease (ARMD) cases will inevitably rise. This gives greater impetus for the need to identify the disease earlier and assess treatments to slow disease progression. Differing electroretinogram (ERG) modalities have been reviewed in relation to the objective assessment of retinal function in ARMD and for monitoring the effectiveness of clinical interventions. Conflicting results have been found with regard to the efficacy of ERG findings in the investigation of ARMD in previous years. The newer multifocal ERG paradigm provides spatial topographical information about retinal function in ARMD. It has shown promising results in monitoring effectiveness of clinical interventions and studies are continuing in this area. Better knowledge of retinal function in ARMD may lead to enhanced treatments at each phase of the disease.

Reliability management of machine tool technology: a case study of current practice

Considerable attention has been given in the literature to identifying and describing the effective elements which positively affect the improvement of product reliability. These have been perceived by many as the 'state of the art' in the manufacturing industry. The applicability, diffusion and effectiveness of such methods and philosophies, as a means of systematically improving the reliability of a product, come in the main from case studies and single and infra-industry empirical studies. These studies have both been carried out within the wider context of quality assurance and management, and taking reliability as a discipline in its own right. However, it is somewhat of a surprise that there are no recently published findings or research studies on the adoption of these methods by the machine tool industry. This may lead one to construct several hypothesised paradigms: (a) that machine tool manufacturers compared to other industries, are slow to respond to propositions given in the literature by theorists or (b) this may indicate that a large proportion of the manufacturers make little use of the reliability improvement techniques as described in the literature, with the overall perception that they will not lead to any significant improvements? On the other hand, it is evident that hypothetical verification of the operational and engineering methods of reliability achievement and improvement adopted in the machine tool industry is less widely researched. Therefore, research into this area is needed in order to explore the 'state of the art' practice in the machine tool industry. This is in terms of the status, structure and activities of the operation of the reliability function. This paper outlines a research programme being conducted with the co-operation of a leading machine tool manufacturer, whose UK manufacturing plant produces in the main Vertical Machining Centres (VMCs) and is continuously undergoing incremental transitions in product reliability improvement.

A three dimensional surface measurement and reconstruction system for respiratory function analysis

Respiration is a complex activity. If the relationship between all neurological and skeletomuscular interactions was perfectly understood, an accurate dynamic model of the respiratory system could be developed and the interaction between different inputs and outputs could be investigated in a straightforward fashion. Unfortunately, this is not the case and does not appear to be viable at this time. In addition, the provision of appropriate sensor signals for such a model would be a considerable invasive task. Useful quantitative information with respect to respiratory performance can be gained from non-invasive monitoring of chest and abdomen motion. Currently available devices are not well suited in application for spirometric measurement for ambulatory monitoring. A sensor matrix measurement technique is investigated to identify suitable sensing elements with which to base an upper body surface measurement device that monitors respiration. This thesis is divided into two main areas of investigation; model based and geometrical based surface plethysmography. In the first instance, chapter 2 deals with an array of tactile sensors that are used as progression of existing and previously investigated volumetric measurement schemes based on models of respiration. Chapter 3 details a non-model based geometrical approach to surface (and hence volumetric) profile measurement. Later sections of the thesis concentrate upon the development of a functioning prototype sensor array. To broaden the application area the study has been conducted as it would be fore a generically configured sensor array. In experimental form the system performance on group estimation compares favourably with existing system on volumetric performance. In addition provides continuous transient measurement of respiratory motion within an acceptable accuracy using approximately 20 sensing elements. Because of the potential size and complexity of the system it is possible to deploy it as a fully mobile ambulatory monitoring device, which may be used outside of the laboratory. It provides a means by which to isolate coupled physiological functions and thus allows individual contributions to be analysed separately. Thus facilitating greater understanding of respiratory physiology and diagnostic capabilities. The outcome of the study is the basis for a three-dimensional surface contour sensing system that is suitable for respiratory function monitoring and has the prospect with future development to be incorporated into a garment based clinical tool.

A flexible cost function model with risk

In examining bank cost efficiency in banking inclusion of risk-taking of banks is very important. In this paper we depart from the standard modeling approach and view risk intimately related to the technology. Thus, instead of controlling for risk by viewing them as covariates in the standard cost function we argue that the technology differs with risk, thereby meaning that the parameters of the parametric cost function changes with risk in a fully flexible manner. This is accomplished by viewing the parameters of the cost function as nonparametric functions of risk. We also control for country-specific effects in a fully flexible manner by using them as arguments of the nonparametric functions along with the risk variable. The resulting cost function then becomes semiparametric. The standard parametric model becomes a special case of our semiparametric model. We use the above modeling approach for banks in the EU countries. Actually, European financial integration is seen as a stepping stone for the development of a competitive single EU market that promotes efficiency and increases consumer welfare, changing the risk profile of the European banks. Particularly, financial integration allows more risk diversification and permits banks to use more advanced risk management instruments and systems, however it has at the same time increased the probability of systematic risks. Financial integration has increased the risk of contagion and changed its nature and scope. Consequently the bank’s risk seems to be an important issue to be investigated.

Saccharomyces Cerevisiae as a biotechnological tool for ageing research:studies on translation and metabolism

The yeast Saccharomyces cerevisiae is an important model organism for the study of cell biology. The similarity between yeast and human genes and the conservation of fundamental pathways means it can be used to investigate characteristics of healthy and diseased cells throughout the lifespan. Yeast is an equally important biotechnological tool that has long been the organism of choice for the production of alcoholic beverages, bread and a large variety of industrial products. For example, yeast is used to manufacture biofuels, lubricants, detergents, industrial enzymes, food additives and pharmaceuticals such as anti-parasitics, anti-cancer compounds, hormones (including insulin), vaccines and nutraceuticals. Its function as a cell factory is possible because of the speed with which it can be grown to high cell yields, the knowledge that it is generally recognized as safe (GRAS) and the ease with which metabolism and cellular pathways, such as translation can be manipulated. In this thesis, these two pathways are explored in the context of their biotechnological application to ageing research: (i) understanding translational processes during the high-yielding production of membrane protein drug targets and (ii) the manipulation of yeast metabolism to study the molecule, L-carnosine, which has been proposed to have anti-ageing properties. In the first of these themes, the yeast strains, spt3?, srb5?, gcn5? and yTHCBMS1, were examined since they have been previously demonstrated to dramatically increase the yields of a target membrane protein (the aquaporin, Fps1) compared to wild-type cells. The mechanisms underlying this discovery were therefore investigated. All high yielding strains were shown to have an altered translational state (mostly characterised by an initiation block) and constitutive phosphorylation of the translational initiation factor, eIF2a. The relevance of the initiation block was further supported by the finding that other strains, with known initiation blocks, are also high yielding for Fps1. A correlation in all strains between increased Fps1 yields and increased production of the transcriptional activator protein, Gcn4, suggested that yields are subject to translational control. Analysis of the 5´ untranslated region (UTR) of FPS1 revealed two upstream open reading frames (uORFs). Mutagenesis data suggest that high yielding strains may circumvent these control elements through either a leaky scanning or a re-initiation mechanism. In the second theme, the dipeptide L-carnosine (ß-alanyl-L-histidine) was investigated: it has previously been shown to inhibit the growth of cancer cells but delay senescence in cultured human fibroblasts and extend the lifespan of male fruit flies. To understand these apparently contradictory properties, the effects of L-carnosine on yeast were studied. S. cerevisiae can respire aerobically when grown on a non-fermentable carbon source as a substrate but has a respiro-fermentative metabolism when grown on a fermentable carbon source; these metabolisms mimic normal cell and cancerous cell metabolisms, respectively. When yeast were grown on fermentable carbon sources, in the presence of L-carnosine, a reduction in cell growth and viability was observed, which was not apparent for cells grown on a non-fermentable carbon source. The metabolism-dependent mechanism was confirmed in the respiratory yeast species Pichia pastoris. Further analysis of S. cerevisiae yeast strains with deletions in their nutrient-sensing pathway, which result in an increase in respiratory metabolism, confirmed the metabolism-dependent effects of L-carnosine.

Shared action spaces:a basis function framework for social re-calibration of sensorimotor representations supporting joint action

The article explores the possibilities of formalizing and explaining the mechanisms that support spatial and social perspective alignment sustained over the duration of a social interaction. The basic proposed principle is that in social contexts the mechanisms for sensorimotor transformations and multisensory integration (learn to) incorporate information relative to the other actor(s), similar to the "re-calibration" of visual receptive fields in response to repeated tool use. This process aligns or merges the co-actors' spatial representations and creates a "Shared Action Space" (SAS) supporting key computations of social interactions and joint actions; for example, the remapping between the coordinate systems and frames of reference of the co-actors, including perspective taking, the sensorimotor transformations required for lifting jointly an object, and the predictions of the sensory effects of such joint action. The social re-calibration is proposed to be based on common basis function maps (BFMs) and could constitute an optimal solution to sensorimotor transformation and multisensory integration in joint action or more in general social interaction contexts. However, certain situations such as discrepant postural and viewpoint alignment and associated differences in perspectives between the co-actors could constrain the process quite differently. We discuss how alignment is achieved in the first place, and how it is maintained over time, providing a taxonomy of various forms and mechanisms of space alignment and overlap based, for instance, on automaticity vs. control of the transformations between the two agents. Finally, we discuss the link between low-level mechanisms for the sharing of space and high-level mechanisms for the sharing of cognitive representations. © 2013 Pezzulo, Iodice, Ferraina and Kessler.

GEO Label – quality information interrogation tool for geospatial datasets:towards effective visualization of quality metadata

Although the importance of dataset fitness-for-use evaluation and intercomparison is widely recognised within the GIS community, no practical tools have yet been developed to support such interrogation. GeoViQua aims to develop a GEO label which will visually summarise and allow interrogation of key informational aspects of geospatial datasets upon which users rely when selecting datasets for use. The proposed GEO label will be integrated in the Global Earth Observation System of Systems (GEOSS) and will be used as a value and trust indicator for datasets accessible through the GEO Portal. As envisioned, the GEO label will act as a decision support mechanism for dataset selection and thereby hopefully improve user recognition of the quality of datasets. To date we have conducted 3 user studies to (1) identify the informational aspects of geospatial datasets upon which users rely when assessing dataset quality and trustworthiness, (2) elicit initial user views on a GEO label and its potential role and (3), evaluate prototype label visualisations. Our first study revealed that, when evaluating quality of data, users consider 8 facets: dataset producer information; producer comments on dataset quality; dataset compliance with international standards; community advice; dataset ratings; links to dataset citations; expert value judgements; and quantitative quality information. Our second study confirmed the relevance of these facets in terms of the community-perceived function that a GEO label should fulfil: users and producers of geospatial data supported the concept of a GEO label that provides a drill-down interrogation facility covering all 8 informational aspects. Consequently, we developed three prototype label visualisations and evaluated their comparative effectiveness and user preference via a third user study to arrive at a final graphical GEO label representation. When integrated in the GEOSS, an individual GEO label will be provided for each dataset in the GEOSS clearinghouse (or other data portals and clearinghouses) based on its available quality information. Producer and feedback metadata documents are being used to dynamically assess information availability and generate the GEO labels. The producer metadata document can either be a standard ISO compliant metadata record supplied with the dataset, or an extended version of a GeoViQua-derived metadata record, and is used to assess the availability of a producer profile, producer comments, compliance with standards, citations and quantitative quality information. GeoViQua is also currently developing a feedback server to collect and encode (as metadata records) user and producer feedback on datasets; these metadata records will be used to assess the availability of user comments, ratings, expert reviews and user-supplied citations for a dataset. The GEO label will provide drill-down functionality which will allow a user to navigate to a GEO label page offering detailed quality information for its associated dataset. At this stage, we are developing the GEO label service that will be used to provide GEO labels on demand based on supplied metadata records. In this presentation, we will provide a comprehensive overview of the GEO label development process, with specific emphasis on the GEO label implementation and integration into the GEOSS.

Function interval arithmetic

We propose an arithmetic of function intervals as a basis for convenient rigorous numerical computation. Function intervals can be used as mathematical objects in their own right or as enclosures of functions over the reals. We present two areas of application of function interval arithmetic and associated software that implements the arithmetic: (1) Validated ordinary differential equation solving using the AERN library and within the Acumen hybrid system modeling tool. (2) Numerical theorem proving using the PolyPaver prover. © 2014 Springer-Verlag.

Polynomial function intervals for floating-point software verification

The focus of our work is the verification of tight functional properties of numerical programs, such as showing that a floating-point implementation of Riemann integration computes a close approximation of the exact integral. Programmers and engineers writing such programs will benefit from verification tools that support an expressive specification language and that are highly automated. Our work provides a new method for verification of numerical software, supporting a substantially more expressive language for specifications than other publicly available automated tools. The additional expressivity in the specification language is provided by two constructs. First, the specification can feature inclusions between interval arithmetic expressions. Second, the integral operator from classical analysis can be used in the specifications, where the integration bounds can be arbitrary expressions over real variables. To support our claim of expressivity, we outline the verification of four example programs, including the integration example mentioned earlier. A key component of our method is an algorithm for proving numerical theorems. This algorithm is based on automatic polynomial approximation of non-linear real and real-interval functions defined by expressions. The PolyPaver tool is our implementation of the algorithm and its source code is publicly available. In this paper we report on experiments using PolyPaver that indicate that the additional expressivity does not come at a performance cost when comparing with other publicly available state-of-the-art provers. We also include a scalability study that explores the limits of PolyPaver in proving tight functional specifications of progressively larger randomly generated programs. © 2014 Springer International Publishing Switzerland.

Projected sequential Gaussian processes:a C++ tool for interpolation of large datasets with heterogeneous noise

Heterogeneous datasets arise naturally in most applications due to the use of a variety of sensors and measuring platforms. Such datasets can be heterogeneous in terms of the error characteristics and sensor models. Treating such data is most naturally accomplished using a Bayesian or model-based geostatistical approach; however, such methods generally scale rather badly with the size of dataset, and require computationally expensive Monte Carlo based inference. Recently within the machine learning and spatial statistics communities many papers have explored the potential of reduced rank representations of the covariance matrix, often referred to as projected or fixed rank approaches. In such methods the covariance function of the posterior process is represented by a reduced rank approximation which is chosen such that there is minimal information loss. In this paper a sequential Bayesian framework for inference in such projected processes is presented. The observations are considered one at a time which avoids the need for high dimensional integrals typically required in a Bayesian approach. A C++ library, gptk, which is part of the INTAMAP web service, is introduced which implements projected, sequential estimation and adds several novel features. In particular the library includes the ability to use a generic observation operator, or sensor model, to permit data fusion. It is also possible to cope with a range of observation error characteristics, including non-Gaussian observation errors. Inference for the covariance parameters is explored, including the impact of the projected process approximation on likelihood profiles. We illustrate the projected sequential method in application to synthetic and real datasets. Limitations and extensions are discussed. © 2010 Elsevier Ltd.