Exploring knowledge transfer mechanisms: The case of a UK-based group within a high-tech global corporation

Jasimuddin, Sajjad, 'Exploring knowledge transfer mechanisms: The case of a UK-based group within a high-tech global corporation', International Journal of Information Management (2007) 27(4) pp.294-300 RAE2008

Coordination changes in magnesium silicate glasses

Wilding, Martin; Benmore, C.J.; Tangeman, J.A.; Sampath, S., (2004) 'Coordination changes in magnesium silicate glasses', Europhysics Letters 67 pp.212-218 RAE2008

Liquid alumina: detailed atomic coordination determined from neutron diffraction data using empirical potential structure refinement

Greaves, George; Jenkins, T.E.; Landron, C.; Hennet, L., (2001) 'Liquid alumina: detailed atomic coordination determined from neutron diffraction data using empirical potential structure refinement', Physical Review Letters 86 pp.4839-4842 RAE2008

Regulation of yeast oscillatory dynamics

Douglas B. Murray, Manfred Beckmann, and Hiroaki Kitano. (2007). Regulation of yeast oscillatory dynamics. Proceedings of the National Academy of Sciences of the USA, 104 (7), 2241-2246 Sponsorship: Solution-Oriented Research for Science and Technology Agency to the Systems Biology Institute /21st Century Center of Excellence Program and Special Coordination Program of the Ministry of Education, Sports, Culture, Science, and Technology to Keio University RAE2008

The Terrorism Virus: Contemporary Traits and Mechanisms

In order to present and understand the nature of modern terrorism it is important to realize its key properties as well the mechanisms that shape terrorism. Selected properties and mechanisms shaping modern terrorism which can be exemplified by the following: evolutionary nature of terrorism, asymmetry of terrorism, interferentiality of terrorism, multitude of components of terrorism, diffusion of terrorism, duality of terrorism, positive dimension of terrorism, terrorist as the system, diversity of terrorist activity goals, changeability of terrorist threat, the broad and narrow dimension of terrorism, counter-anti-terrorism, the confrontational and cooperational character of relations, calculation and operational strategy, disintegrational nature of terrorism, multidisciplinarity of terrorism, horizontal and vertical dimension of terrorism and a the few other traits or mechanisms.

Detour-Based Mobility Coordination in DTNs

Commonly, research work in routing for delay tolerant networks (DTN) assumes that node encounters are predestined, in the sense that they are the result of unknown, exogenous processes that control the mobility of these nodes. In this paper, we argue that for many applications such an assumption is too restrictive: while the spatio-temporal coordinates of the start and end points of a node's journey are determined by exogenous processes, the specific path that a node may take in space-time, and hence the set of nodes it may encounter could be controlled in such a way so as to improve the performance of DTN routing. To that end, we consider a setting in which each mobile node is governed by a schedule consisting of a ist of locations that the node must visit at particular times. Typically, such schedules exhibit some level of slack, which could be leveraged for DTN message delivery purposes. We define the Mobility Coordination Problem (MCP) for DTNs as follows: Given a set of nodes, each with its own schedule, and a set of messages to be exchanged between these nodes, devise a set of node encounters that minimize message delivery delays while satisfying all node schedules. The MCP for DTNs is general enough that it allows us to model and evaluate some of the existing DTN schemes, including data mules and message ferries. In this paper, we show that MCP for DTNs is NP-hard and propose two detour-based approaches to solve the problem. The first (DMD) is a centralized heuristic that leverages knowledge of the message workload to suggest specific detours to optimize message delivery. The second (DNE) is a distributed heuristic that is oblivious to the message workload, and which selects detours so as to maximize node encounters. We evaluate the performance of these detour-based approaches using extensive simulations based on synthetic workloads as well as real schedules obtained from taxi logs in a major metropolitan area. Our evaluation shows that our centralized, workload-aware DMD approach yields the best performance, in terms of message delay and delivery success ratio, and that our distributed, workload-oblivious DNE approach yields favorable performance when compared to approaches that require the use of data mules and message ferries.

Preferential Field Coverage Through Detour-Based Mobility Coordination

Controlling the mobility pattern of mobile nodes (e.g., robots) to monitor a given field is a well-studied problem in sensor networks. In this setup, absolute control over the nodes’ mobility is assumed. Apart from the physical ones, no other constraints are imposed on planning mobility of these nodes. In this paper, we address a more general version of the problem. Specifically, we consider a setting in which mobility of each node is externally constrained by a schedule consisting of a list of locations that the node must visit at particular times. Typically, such schedules exhibit some level of slack, which could be leveraged to achieve a specific coverage distribution of a field. Such a distribution defines the relative importance of different field locations. We define the Constrained Mobility Coordination problem for Preferential Coverage (CMC-PC) as follows: given a field with a desired monitoring distribution, and a number of nodes n, each with its own schedule, we need to coordinate the mobility of the nodes in order to achieve the following two goals: 1) satisfy the schedules of all nodes, and 2) attain the required coverage of the given field. We show that the CMC-PC problem is NP-complete (by reduction to the Hamiltonian Cycle problem). Then we propose TFM, a distributed heuristic to achieve field coverage that is as close as possible to the required coverage distribution. We verify the premise of TFM using extensive simulations, as well as taxi logs from a major metropolitan area. We compare TFM to the random mobility strategy—the latter provides a lower bound on performance. Our results show that TFM is very successful in matching the required field coverage distribution, and that it provides, at least, two-fold query success ratio for queries that follow the target coverage distribution of the field.

How Does Binocular Rivalry Emerge from Cortical Mechanisms of 3D Vision?

Under natural viewing conditions, a single depthful percept of the world is consciously seen. When dissimilar images are presented to corresponding regions of the two eyes, binocular rivalyr may occur, during which the brain consciously perceives alternating percepts through time. How do the same brain mechanisms that generate a single depthful percept of the world also cause perceptual bistability, notably binocular rivalry? What properties of brain representations correspond to consciously seen percepts? A laminar cortical model of how cortical areas V1, V2, and V4 generate depthful percepts is developed to explain and quantitatively simulate binocualr rivalry data. The model proposes how mechanisms of cortical developement, perceptual grouping, and figure-ground perception lead to signle and rivalrous percepts. Quantitative model simulations include influences of contrast changes that are synchronized with switches in the dominant eye percept, gamma distribution of dominant phase durations, piecemeal percepts, and coexistence of eye-based and stimulus-based rivalry. The model also quantitatively explains data about multiple brain regions involved in rivalry, effects of object attention on switching between superimposed transparent surfaces, and monocular rivalry. These data explanations are linked to brain mechanisms that assure non-rivalrous conscious percepts. To our knowledge, no existing model can explain all of these phenomena.

Neural Dynamics of Saccadic and Smooth Pursuit Eye Movement Coordination during Visual Tracking of Unpredictably Moving Targets

How does the brain use eye movements to track objects that move in unpredictable directions and speeds? Saccadic eye movements rapidly foveate peripheral visual or auditory targets and smooth pursuit eye movements keep the fovea pointed toward an attended moving target. Analyses of tracking data in monkeys and humans reveal systematic deviations from predictions of the simplest model of saccade-pursuit interactions, which would use no interactions other than common target selection and recruitment of shared motoneurons. Instead, saccadic and smooth pursuit movements cooperate to cancel errors of gaze position and velocity, and thus to maximize target visibility through time. How are these two systems coordinated to promote visual localization and identification of moving targets? How are saccades calibrated to correctly foveate a target despite its continued motion during the saccade? A neural model proposes answers to such questions. The modeled interactions encompass motion processing areas MT, MST, FPA, DLPN and NRTP; saccade planning and execution areas FEF and SC; the saccadic generator in the brain stem; and the cerebellum. Simulations illustrate the model’s ability to functionally explain and quantitatively simulate anatomical, neurophysiological and behavioral data about SAC-SPEM tracking.

Neural Control of Interlimb Coordination and Gait Timing in Bipeds and Quadrupeds

1) A large body of behavioral data conceming animal and human gaits and gait transitions is simulated as emergent properties of a central pattern generator (CPG) model. The CPG model incorporates neurons obeying Hodgkin-Huxley type dynamics that interact via an on-center off-surround anatomy whose excitatory signals operate on a faster time scale than their inhibitory signals. A descending cornmand or arousal signal called a GO signal activates the gaits and controL their transitions. The GO signal and the CPG model are compared with neural data from globus pallidus and spinal cord, among other brain structures. 2) Data from human bimanual finger coordination tasks are simulated in which anti-phase oscillations at low frequencies spontaneously switch to in-phase oscillations at high frequencies, in-phase oscillations can be performed both at low and high frequencies, phase fluctuations occur at the anti-phase in-phase transition, and a "seagull effect" of larger errors occurs at intermediate phases. When driven by environmental patterns with intermediate phase relationships, the model's output exhibits a tendency to slip toward purely in-phase and anti-phase relationships as observed in humans subjects. 3) Quadruped vertebrate gaits, including the amble, the walk, all three pairwise gaits (trot, pace, and gallop) and the pronk are simulated. Rapid gait transitions are simulated in the order--walk, trot, pace, and gallop--that occurs in the cat, along with the observed increase in oscillation frequency. 4) Precise control of quadruped gait switching is achieved in the model by using GO-dependent modulation of the model's inhibitory interactions. This generates a different functional connectivity in a single CPG at different arousal levels. Such task-specific modulation of functional connectivity in neural pattern generators has been experimentally reported in invertebrates. Phase-dependent modulation of reflex gain has been observed in cats. A role for state-dependent modulation is herein predicted to occur in vertebrates for precise control of phase transitions from one gait to another. 5) The primary human gaits (the walk and the run) and elephant gaits (the amble and the walk) are sirnulated. Although these two gaits are qualitatively different, they both have the same limb order and may exhibit oscillation frequencies that overlap. The CPG model simulates the walk and the run by generating oscillations which exhibit the same phase relationships. but qualitatively different waveform shapes, at different GO signal levels. The fraction of each cycle that activity is above threshold quantitatively distinguishes the two gaits, much as the duty cycles of the feet are longer in the walk than in the run. 6) A key model properly concerns the ability of a single model CPG, that obeys a fixed set of opponent processing equations to generate both in-phase and anti-phase oscillations at different arousal levels. Phase transitions from either in-phase to anti-phase oscillations, or from anti-phase to in-phase oscillations, can occur in different parameter ranges, as the GO signal increases.

Frequency-Dependent Phase Transitions in the Coordination of Human Bimanual Tasks

The 2-channel Ellias-Grossberg neural pattern generator of Cohen, Grossberg, and Pribe [1] is shown to simulate data from human bimanual coordination tasks in which anti-phase oscillations at low frequencies spontaneously switch to in-phase oscillations at high frequencies, in-phase oscillations can be performed at both low and high frequencies, phase fluctuations occur at the anti-phase to in-phase transition, and a "seagull effect" of larger errors occurs at intermediate phases.

Does Binocular Rivalry Emerge from Cortical Mechanisms of 3D Vision

Under natural viewing conditions, a single depthful percept of the world is consciously seen. When dissimilar images are presented to corresponding regions of the two eyes, binocular rivalry may occur, during which the brain consciously perceives alternating percepts through time. Perceptual bistability can also occur in response to a single ambiguous figure. These percepts raise basic questions: What brain mechanisms generate a single depthful percept of the world? How do the same mechanisms cause perceptual bistability, notably binocular rivalry? What properties of brain representations correspond to consciously seen percepts? How do the dynamics of the layered circuits of visual cortex generate single and bistable percepts? A laminar cortical model of how cortical areas V1, V2, and V4 generate depthful percepts is developed to explain and quantitatively simulate binocular rivalry data. The model proposes how mechanisms of cortical development, perceptual grouping, and figure-ground perception lead to single and rivalrous percepts.

Plasmid biology of natural Lactococcus lactis strains and molecular mechanisms of bacteriophage-host interaction

Lacticin 3147, enterocin AS-48, lacticin 481, variacin, and sakacin P are bacteriocins offering promising perspectives in terms of preservation and shelf-life extension of food products and should find commercial application in the near future. The studies detailing their characterization and bio-preservative applications are reviewed. Transcriptomic analyses showed a cell wall-targeted response of Lactococcus lactis IL1403 during the early stages of infection with the lytic bacteriophage c2, which is probably orchestrated by a number of membrane stress proteins and involves D-alanylation of membrane lipoteichoic acids, restoration of the physiological proton motive force disrupted following bacteriophage infection, and energy conservation. Sequencing of the eight plasmids of L. lactis subsp. cremoris DPC3758 from raw milk cheese revealed three anti-phage restriction/modification (R/M) systems, immunity/resistance to nisin, lacticin 481, cadmium and copper, and six conjugative/mobilization regions. A food-grade derivative strain with enhanced bacteriophage resistance was generated via stacking of R/M plasmids. Sequencing and functional analysis of the four plasmids of L. lactis subsp. lactis biovar. diacetylactis DPC3901 from raw milk cheese revealed genes novel to Lactococcus and typical of bacteria associated with plants, in addition to genes associated with plant-derived lactococcal strains. The functionality of a novel high-affinity regulated system for cobalt uptake was demonstrated. The bacteriophage resistant and bacteriocin-producing plasmid pMRC01 places a metabolic burden on lactococcal hosts resulting in lowered growth rates and increased cell permeability and autolysis. The magnitude of these effects is strain dependent but not related to bacteriocin production. Starters’ acidification capacity is not significantly affected. Transcriptomic analyses showed that pMRC01 abortive infection (Abi) system is probably subjected to a complex regulatory control by Rgg-like ORF51 and CopG-like ORF58 proteins. These regulators are suggested to modulate the activity of the putative Abi effectors ORF50 and ORF49 exhibiting topology and functional similarities to the Rex system aborting bacteriophage λ lytic growth.

Molecular analysis of virulence mechanisms associated with adherent-invasive Escherichia coli (AIEC)

Crohn's Disease (CD) is a chronic inflammatory bowel disease of unknown etiology. Recent work has shown that a new pathotype of Escherichia coli, Adherent Invasive E. coli (AIEC) may be associated with CD. AIEC has been shown to adhere to and invade epithelial cells and to replicate within macrophages (together this is called the AIEC phenotype). In this thesis, the AIEC phenotype of 84 E. coli strains were determined in order to identify the prevalence of this phenotype within the E. coli genus. This study showed that a significant proportion of E. coli strains (approx. 5%) are capable of adhering to and invading epithelial cells and undergoing intramacrophage replication. Moreover, the results presented in this study indicate a correlation between survival in macrophage and resistance to grazing by amoeba supporting the coincidental evolution hypothesis that resistance to amoebae could be a driving force in the evolution of pathogenicity in some bacteria, such as AIEC. In addition, this study has identified an important regulatory role for the CpxA/R two component system (TCS) in the invasive abilities of AIEC HM605, a colonic mucosa-associated CD isolate. A mutation in cpxR was shown to be defective in the invasion of epithelial cells and this defect was shown to be independent of motility or the expression of Type 1 fimbriae, factors that have been shown to be involved in the invasion of another strain of AIEC, isolated from a patient with ileal CD, called LF82. The CpxA/R TCS responds to disturbances in the cell envelope and has been implicated in the virulence of a number of Gram negative pathogens. In this study it is shown that the CpxA/R TCS regulates the expression of a potentially novel invasin called SinH. SinH is found in a number of invasive strains of E. coli and Salmonella. Moreover work presented here shows that a critical mechanism underpinning AIEC persistence in macrophages is the repair of DNA bases damaged by macrophage oxidants. Together these findings provide evidence to suggest that AIEC are a diverse group of E. coli and possess diverse molecular mechanisms and virulence factors that contribute to the AIEC phenotype. In addition, AIEC may have gone through different evolutionary histories acquiring various molecular mechanisms ultimately culminating in the AIEC phenotype. The gastrointestinal (GI) tract harbors a diverse microbiota; most are symbiotic or commensal however some bacteria have the potential to cause disease (pathobiont). The work presented here provides evidence to support the model that AIEC are pathobionts. AIEC strains can be carried as commensals in healthy guts however, when the intestinal homeostasis is disrupted, such as in the compromised gut of CD patients, AIEC may behave as opportunistic pathogens and cause and/or contribute to disease by driving intestinal inflammation.

Molecular characterisation of the mechanisms of compatible solute accumulation in Listeria monocytogenes

The ability of the Gram-positive foodborne pathogen Listeria monocytogenes to survive and grow in environments of elevated osmolarity can be attributed, at least in part, to the accumulation of a restricted range of low molecular mass solutes compatible with cellular function. Accumulated to high internal concentrations in hyper-saline environments, compatible solutes, either transported into the cell or synthesized de novo, play a dual role: helping to stabilize protein structure and function while also counterbalancing external osmotic strength, thus preventing water loss from the cell and plasmolysis. While previous physiological investigations identified glycine betaine, carnitine, and proline as the principal compatible solutes in the listerial osmostress response, genetic alanysis of the uptake/synthesis systems governing the accumulation of these compounds has, until now, remained largely unexplored. Representing the first genetic analysis of compatible solute accumulation in L. monocytogenes, this thesis describes the molecular characterization of BetL; a highly specific secondary glycine betaine transport system, OpuC; a multicomponent carnitine/glycine betaine transporter, and finally proBA; a two-gene operon encoding the first two enzymes of the listerial proline piosynthesis pathway. In addition to their role in osmotolerance, the potential of each system in contributing to listerial pathogenesis was investigated. While mutations in each gene cluster exhibited dramatic reductions in listerial osmotolerance, OpuC- mutants were additionally shown to exhibit reduced virulence when admisistered via the oral route. This represents the first direct link between the salt stress response and virulence in L. monocytogenes.