Simplifying the representation of complex free-energy landscapes using sketch-map

A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that correspond to the slow degrees of freedom. This realization informs the development of sketch-map, which endeavors to reproduce the proximity information from the high-dimensionality description in a space of lower dimensionality even when a faithful embedding is not possible.

The C*-algebra of ax+b-like groups

We describe the C*-algebras of " ax+b" -like groups in terms of algebras of operator fields defined over their dual spaces.

Invariant Information Local Sub-map Filter (IILSF) for Efficient Simultaneous Localisation and Mapping of Large Environments

This paper presents an Invariant Information Local Sub-map Filter (IILSF) as a technique for consistent Simultaneous Localisation and Mapping (SLAM) in a large environment. It harnesses the benefits of sub-map technique to improve the consistency and efficiency of Extended Kalman Filter (EKF) based SLAM. The IILSF makes use of invariant information obtained from estimated locations of features in independent sub-maps, instead of incorporating every observation directly into the global map. Then the global map is updated at regular intervals. Applying this technique to the EKF based SLAM algorithm: (a) reduces the computational complexity of maintaining the global map estimates and (b) simplifies transformation complexities and data association ambiguities usually experienced in fusing sub-maps together. Simulation results show that the method was able to accurately fuse local map observations to generate an efficient and consistent global map, in addition to significantly reducing computational cost and data association ambiguities.

Accessibility and Health: Towards Walkability Tools for Planning Practice

There is increasing research interest in how we can most effectively intervene in the built environment to change behaviours such as physical activity and improve health. Much of this work has focussed around the concept of walkability and the identification of those attributes of our cities that encourage pedestrian activity, including density, connectivity and the aesthetic of the urban realm (Saelens et al 2003, Frank et al 2010). Much of the existing research has clarified the strength of the relationships between various environmental attributes and the differential impact on different demographic groups (e.g. Panter et al 2011). This has not yet been effectively translated into tools to help integrate the concepts of walkability into decision-making by statutory authorities that can help shape the spatial development and delivery of public services which can support more active lifestyles. A key reason for this has been that standard models for transport planning and accessibility are based on networks of road infrastructure, which provides a weak basis for modelling pedestrian accessibility (Chin et al 2008).

This paper reports the findings of Knowledge Exchange project funded by UK’s Economic and Social Research Council (ES/J010588/1) and partners including Belfast and Derry City Councils and Northern Ireland’s Public Health Agency, the Department of Regional Development and Belfast Healthy Cities, that has attempted to address this problem. This project has mapped city-wide footpath networks and used these to assist partner organisations in developing the evidence base for making decisions on public services based on health impacts and pedestrian access. The paper describes the tool developed, uses a number of examples to highlight its impact on areas of decision-making and evaluates the benefits of further integrating walkability into planning and development practice.

cudaMap: a GPU accelerated program for gene expression connectivity mapping

Background: Modern cancer research often involves large datasets and the use of sophisticated statistical techniques. Together these add a heavy computational load to the analysis, which is often coupled with issues surrounding data accessibility. Connectivity mapping is an advanced bioinformatic and computational technique dedicated to therapeutics discovery and drug re-purposing around differential gene expression analysis. On a normal desktop PC, it is common for the connectivity mapping task with a single gene signature to take >2h to complete using sscMap, a popular Java application that runs on standard CPUs (Central Processing Units). Here, we describe new software, cudaMap, which has been implemented using CUDA C/C++ to harness the computational power of NVIDIA GPUs (Graphics Processing Units) to greatly reduce processing times for connectivity mapping.

Results: cudaMap can identify candidate therapeutics from the same signature in just over thirty seconds when using an NVIDIA Tesla C2050 GPU. Results from the analysis of multiple gene signatures, which would previously have taken several days, can now be obtained in as little as 10 minutes, greatly facilitating candidate therapeutics discovery with high throughput. We are able to demonstrate dramatic speed differentials between GPU assisted performance and CPU executions as the computational load increases for high accuracy evaluation of statistical significance.

Conclusion: Emerging 'omics' technologies are constantly increasing the volume of data and information to be processed in all areas of biomedical research. Embracing the multicore functionality of GPUs represents a major avenue of local accelerated computing. cudaMap will make a strong contribution in the discovery of candidate therapeutics by enabling speedy execution of heavy duty connectivity mapping tasks, which are increasingly required in modern cancer research. cudaMap is open source and can be freely downloaded from http://purl.oclc.org/NET/cudaMap.

The Map Defines the Territory: Remodelling NGO Partnerships for Knowledge Translation in Transition Contexts

The initial impetus for a theoretical exploration of organisational relationships is based on case study research on a Bulgarian NGO's implementation of values and goals into practices under a guiding relationship from a very experienced UK organisation in the same field. Findings diverged from conventional accounts of developing NGOs' dependence on more developed counterparts and that case study findings characterised the inter- dependency between the two organisations as more alike to a collaborative knowledge ...

The Map of Watchful Architecture

The international border between Northern Ireland and the South (the Republic of Ireland) came into being in 1922, but there are many important historical antecedents to the notion and expression of spatial separation in this borderland. The author identifies historical precedents and links them to recent defensive features in order to generate a 'map of watchful architecture' that includes recent and much older elements.

Fictional Ulster:A map of places created by writers

Ballybeg, the fictitious setting for Brian Friel’s plays, is more famous than most real villages in Ulster. Despite not existing, the village has a kind of cultural and geographic life. This is part of what this map is about. It locates and charts Ulster’s fictional places — places invented by writers down through the years. These places have meaning too, they are part of how Ulster pictures itself and how others picture Ulster.

The Map of Connections 3.1: Unofficial and previously unmapped Irish border crossings

I charted unofficial border-crossings along Ireland's border, those not found on any other map.

During many surveys of Ireland's border I discovered that it is often perforated. Gates are set in hedgerows for the convenience of farmers, stepping stones and community-built bridges span rivers, walkers’ routes and muddy by-ways go wherever they please. These kinds of connections have always been there, although I think it is fair to say that their numbers have increased during the Peace Process. Roads blocked or cratered during the Troubles are being re-connected at a rate too fast for the Ordnance Survey to keep up with. On the local level cross-border movement is quietly happening, unchecked and often unmapped, until now.

This map attempts to throw the borderline in perpendicular, showing it as a place of connection rather than division.

The Map of Watchful Architecture 2.0:Defensive forms along Ireland's border

For The Map of Watchful Architecture I only concerned myself with defensive architecture along the Border. As the map followed a border it came out as a wavy line of points. This was largely artificial, I only charted architecture within the Border corridor, but was not entirely artificial. That linear landscape has long been staked-out by the regularity of certain kinds of architecture. The 1st/2nd century Black Pig’s Dyke and Dorsey correspond with today’s Border. The concentration of souterrains in north Louth indicate that it may have been a volatile interface zone in later centuries. In 1618 Londonderry and its walls were built. Further north and two centuries later, Martello Towers were constructed to watch over Lough Foyle. During the Second World War pillboxes and observation posts were manned along the Border, close to what was now an international frontier. Then came the Operation Banner installations built during The Troubles. All this adds up to be one of the longest unbroken traditions of defensive architecture anywhere in Western Europe, a tradition some thought finally broken as the last of the Operation Banner towers were de-installed in 2007. But, take a bus south across the Border and you will often be pulled over by the Garda Síochána. They ID check the passengers in an attempt to stop illegal immigration via the UK. What about illegal immigrants who walk through the fields or along quiet lanes? They will have understood the Border is not really how it seems on most maps. It is not a solid line, it is a row of points.

Integrated Earth Resistivity Tomography (ERT) and Multilevel Gas Sampling: A Tool to Map Geogenic and Anthropogenic Methane Accumulation on Brownfield Sites

Soil gas emissions of methane and carbon dioxide on brownfield sites are usually attributed to anthropogenic activities; however geogenic sources of soil gas are often not considered during site investigation and risk management strategies. This paper presents a field study at a redeveloped brownfield site on a flood plain to identify accumulations of methane biogas trapped in underlying sediments. The investigation is based on a multidisciplinary approach using direct multi-level sampling measurements and Earth resistivity tomography . Resistivity imaging was applied to evaluate the feasibility of identifying the size and spatial continuity of soil gas accumulations in anthropogenic and naturally occurring deposits. As a result, biogas accumulations are described within both anthropogenic deposits and pristine organic sediments. This result is important to identify the correct approaches to identify and manage risks associated with soil gas emissions on brownfield and pristine sites. The organic-rich sediments in Quaternary fluvial environments of São Paulo Basin in particular the Tietê River, biogas reservoirs can be generated and trapped beneath geogenic and anthropogenic layers, potentially requiring the management of brownfield developments across this region.

Optimizing the efficiency of the sub-map technique for large-scale simultaneous localization and mapping

A technique for optimizing the efficiency of the sub-map method for large-scale simultaneous localization and mapping (SLAM) is proposed. It optimizes the benefits of the sub-map technique to improve the accuracy and consistency of an extended Kalman filter (EKF)-based SLAM. Error models were developed and engaged to investigate some of the outstanding issues in employing the sub-map technique in SLAM. Such issues include the size (distance) of an optimal sub-map, the acceptable error effect caused by the process noise covariance on the predictions and estimations made within a sub-map, when to terminate an existing sub-map and start a new one and the magnitude of the process noise covariance that could produce such an effect. Numerical results obtained from the study and an error-correcting process were engaged to optimize the accuracy and convergence of the Invariant Information Local Sub-map Filter previously proposed. Applying this technique to the EKF-based SLAM algorithm (a) reduces the computational burden of maintaining the global map estimates and (b) simplifies transformation complexities and data association ambiguities usually experienced in fusing sub-maps together. A Monte Carlo analysis of the system is presented as a means of demonstrating the consistency and efficacy of the proposed technique.

Sets of multiplicity and closable multipliers on group algebras

We undertake a detailed study of the sets of multiplicity in a second countable locally compact group G and their operator versions. We establish a symbolic calculus for normal completely bounded maps from the space B(L-2(G)) of bounded linear operators on L-2 (G) into the von Neumann algebra VN(G) of G and use it to show that a closed subset E subset of G is a set of multiplicity if and only if the set E* = {(s,t) is an element of G x G : ts(-1) is an element of E} is a set of operator multiplicity. Analogous results are established for M-1-sets and M-0-sets. We show that the property of being a set of multiplicity is preserved under various operations, including taking direct products, and establish an Inverse Image Theorem for such sets. We characterise the sets of finite width that are also sets of operator multiplicity, and show that every compact operator supported on a set of finite width can be approximated by sums of rank one operators supported on the same set. We show that, if G satisfies a mild approximation condition, pointwise multiplication by a given measurable function psi : G -> C defines a closable multiplier on the reduced C*-algebra G(r)*(G) of G if and only if Schur multiplication by the function N(psi): G x G -> C, given by N(psi)(s, t) = psi(ts(-1)), is a closable operator when viewed as a densely defined linear map on the space of compact operators on L-2(G). Similar results are obtained for multipliers on VN(C).