Improved Detection of Mycobacterium bovis Infection in Bovine Lymph Node Tissue Using Immunomagnetic Separation (IMS)-Based Methods

Immunomagnetic separation (IMS) can selectively isolate and concentrate Mycobacterium bovis cells from lymph node tissue to facilitate subsequent detection by PCR (IMS-PCR) or culture (IMS-MGIT). This study describes application of these novel IMS-based methods to test for M. bovis in a survey of 280 bovine lymph nodes (206 visibly lesioned (VL), 74 non-visibly lesioned (NVL)) collected at slaughter as part of the Northern Ireland bovine TB eradication programme. Their performance was evaluated relative to culture. Overall, 174 (62.1%) lymph node samples tested positive by culture, 162 (57.8%) by IMS-PCR (targeting IS6110), and 196 (70.0%) by IMS-MGIT culture. Twelve (6.9%) of the 174 culture positive lymph node samples were not detected by either of the IMS-based methods. However, an additional 78 M. bovis positive lymph node samples (26 (12.6%) VL and 54 (73.0%) NVL) were detected by the IMS-based methods and not by culture. When low numbers of viable M. bovis are present in lymph nodes (e.g. in NVLs of skin test reactor cattle) decontamination prior to culture may adversely affect viability, leading to false negative culture results. In contrast, IMS specifically captures whole M. bovis cells (live, dead or potentially dormant) which are not subject to any deleterious treatment before detection by PCR or MGIT culture. During this study only 2.7% of NVL lymph nodes tested culture positive, whereas 73% of the same samples tested M. bovis positive by the IMS-based tests. Results clearly demonstrate that not only are the IMS-based methods more rapid but they have greater detection sensitivity than the culture approach currently used for the detection of M. bovis infection in cattle.. Adoption of the IMS-based methods for lymph node testing would have the potential to improve M. bovis detection in clinical samples.

Defending the Irish Border: The Map of Watchful Architecture

This chapter offers an analysis of a map of the Irish border. The Map of Watchful Architecture charts the history of defensive structures in the border region.

Mycobacterium chelonae keratitis:Resolution after debridement and presoaked collagen shields

We report a case of Mycobacterium chelonae keratitis following corneal injury by a foreign body. Diagnosis was made by Ziehl-Neelsen staining and Lowenstein-Jensen culture of corneal scrapings. On the basis of the in vitro susceptibility testing, the patient was treated with topical fortified amikacin. Given the lack of response to this therapy, we decided to carry out a debridement of the infiltrative areas to eliminate infected tissue, and to use an amikacin-soaked collagen shield supplemented every 4 h with topical fortified amikacin to promote healing of the debrided area and to potentiate the effects of the antibiotic therapy. After this treatment, clinical resolution was observed and a further acid-fast stain and culture for mycobacterium were negative. Debridement of the infiltrative areas could be used in cases of mycobacterium keratitis when early diagnosis is made and before the corneal infection has become widespread.

Demonstrating the Transferability and the Descriptive Power of Sketch-Map

Increasingly, it is recognized that new automated forms of analysis are required to understand the high-dimensional output obtained from atomistic simulations. Recently, we introduced a new dimensionality reduction algorithm, sketch-map, that was designed specifically to work with data from molecular dynamics trajectories. In what follows, we provide more details on how this algorithm works and on how to set its parameters. We also test it on two well-studied Lennard-Jones clusters and show that the coordinates we extract using this algorithm are extremely robust. In particular, we demonstrate that the coordinates constructed for one particular Lennard-Jones cluster can be used to describe the configurations adopted by a second, different cluster and even to tell apart different phases of bulk Lennard-Jonesium.

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

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.

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.

Field-Isolated Genotypes of Mycobacterium bovis Vary in Virulence and Influence Case Pathology but Do Not Affect Outbreak Size

Strains of many infectious agents differ in fundamental epidemiological parameters including transmissibility, virulence and pathology. We investigated whether genotypes of Mycobacterium bovis (the causative agent of bovine tuberculosis, bTB) differ significantly in transmissibility and virulence, combining data from a nine-year survey of the genetic structure of the M. bovis population in Northern Ireland with detailed records of the cattle population during the same period. We used the size of herd breakdowns as a proxy measure of transmissibility and the proportion of skin test positive animals (reactors) that were visibly lesioned as a measure of virulence. Average breakdown size increased with herd size and varied depending on the manner of detection (routine herd testing or tracing of infectious contacts) but we found no significant variation among M. bovis genotypes in breakdown size once these factors had been accounted for. However breakdowns due to some genotypes had a greater proportion of lesioned reactors than others, indicating that there may be variation in virulence among genotypes. These findings indicate that the current bTB control programme may be detecting infected herds sufficiently quickly so that differences in virulence are not manifested in terms of outbreak sizes. We also investigated whether pathology of infected cattle varied according to M. bovis genotype, analysing the distribution of lesions recorded at post mortem inspection. We concentrated on the proportion of cases lesioned in the lower respiratory tract, which can indicate the relative importance of the respiratory and alimentary routes of infection. The distribution of lesions varied among genotypes and with cattle age and there were also subtle differences among breeds. Age and breed differences may be related to differences in susceptibility and husbandry, but reasons for variation in lesion distribution among genotypes require further investigation. © 2013 Wright et al.

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.