319 research outputs found

    Computation of protein geometry and its applications: Packing and function prediction

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    This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure

    Personal goals, group performance and ‘social’ networks: participants’ negotiation of virtual and embodied relationships in the ‘Workplace Challenge’ physical activity programme

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    County Sports Partnerships (CSPs) epitomise the growing reliance upon building networks and partnerships sports delivery. This study investigated how social networks were created and contested in a CSP-led programme entitled the ‘Workplace Challenge’ (WPC). The WPC used a web-platform to encourage workplace-based teams to engage in physical activity by self-recording their activity over an eight-week period. Points were awarded for activity completed and a peer-challenge facility was promoted via online league tables, prizes and the opportunity to ‘challenge’ other users. Semi-structured interviews were conducted with a total of seventeen participants recruited from one public and one private sector workplace and from a sample of participants registered as individuals. Two programme planners employed by the CSP also took part. A figurational framework was utilised to investigate participants’ negotiation of networks of embodied and virtual relationships within the programme. Findings suggest the messages promoted in the WPC were disseminated and transformed according to the organizational structure of these networks. Embodied social relationships within workplaces reinforced peer support in professional I-we identities, whereas virtual networks sometimes highlighted participants’ isolation. Moreover, emphasis upon competition within and between teams caused some to question their performance. Often, competition motivated engagement. For less active participants, constant comparison could prove discouraging, particularly if participants felt they had let their colleagues down. Planners of similar programmes must be cognizant of the uneven manner of programme dissemination. Contextual differences at the point of delivery including existing organizational structures and power hierarchies have an impact upon participants’ perceptions of a programme

    Scale-free memory model for multiagent reinforcement learning. Mean field approximation and rock-paper-scissors dynamics

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    A continuous time model for multiagent systems governed by reinforcement learning with scale-free memory is developed. The agents are assumed to act independently of one another in optimizing their choice of possible actions via trial-and-error search. To gain awareness about the action value the agents accumulate in their memory the rewards obtained from taking a specific action at each moment of time. The contribution of the rewards in the past to the agent current perception of action value is described by an integral operator with a power-law kernel. Finally a fractional differential equation governing the system dynamics is obtained. The agents are considered to interact with one another implicitly via the reward of one agent depending on the choice of the other agents. The pairwise interaction model is adopted to describe this effect. As a specific example of systems with non-transitive interactions, a two agent and three agent systems of the rock-paper-scissors type are analyzed in detail, including the stability analysis and numerical simulation. Scale-free memory is demonstrated to cause complex dynamics of the systems at hand. In particular, it is shown that there can be simultaneously two modes of the system instability undergoing subcritical and supercritical bifurcation, with the latter one exhibiting anomalous oscillations with the amplitude and period growing with time. Besides, the instability onset via this supercritical mode may be regarded as "altruism self-organization". For the three agent system the instability dynamics is found to be rather irregular and can be composed of alternate fragments of oscillations different in their properties.Comment: 17 pages, 7 figur

    Induction of T Lymphocytes Specific for Bovine Viral Diarrhea Virus in Calves with Maternal Antibody

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    Passive antibody to bovine viral diarrhea virus (BVDV) acquired through colostrum intake may interfere with the development of a protective immune response by calves to this virus. The objective of this study was to determine if calves, with a high level of maternal antibody to bovine viral diarrhea virus (BVDV), develop CD4+, CD8+, or γΎ T lymphocyte responses to BVDV in the absence of a measurable humoral immune response. Colostrum or milk replacer fed calves were challenged with virulent BVDV at 2-5 weeks of age and/or after maternal antibody had waned. Calves exposed to BVDV while passive antibody levels were high did not mount a measurable humoral immune response to BVDV. However, compared to nonexposed animals, these animals had CD4+, CD8+, and γΎ T lymphocytes that were activated by BVDV after exposure to in vitro BVDV. The production of IFNγ by lymphocytes after in vitro BVDV exposure was also much greater in lymphocytes from calves exposed to BVDV in the presence of maternal antibody compared to the nonexposed calves. These data indicate that calves exposed to BVDV while maternal antibody levels are high can develop antigen specific CD4+, CD8+, and γΎ T lymphocytes in the absence of an active antibody response. A manuscript presented separately demonstrates that the calves with T lymphocytes specific for BVDV in this study were also protected from virulent BVDV genotype 2 challenge after maternal antibody became undetectable

    Using statistical and artificial neural networks to predict the permeability of loosely packed granular materials

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    Well-known analytical equations for predicting permeability are generally reported to overestimate this important property of porous media. In this work, more robust models developed from statistical (multivariable regression) and Artificial Neural Network (ANN) methods utilised additional particle characteristics [‘fines ratio’ (x50/x10) and particle shape] that are not found in traditional analytical equations. Using data from experiments and literature, model performance analyses with average absolute error (AAE) showed error of ~40% for the analytical models (Kozeny–Carman and Happel–Brenner). This error reduces to 9% with ANN model. This work establishes superiority of the new models, using experiments and mathematical techniques

    Scavenging in the Anthropocene: Human impact drives vertebrate scavenger species richness at a global scale

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    Understanding the distribution of biodiversity across the Earth is one of the most challenging questions in biology. Much research has been directed at explaining the species latitudinal pattern showing that communities are richer in tropical areas; however, despite decades of research, a general consensus has not yet emerged. In addition, global biodiversity patterns are being rapidly altered by human activities. Here, we aim to describe large‐scale patterns of species richness and diversity in terrestrial vertebrate scavenger (carrion‐consuming) assemblages, which provide key ecosystem functions and services. We used a worldwide dataset comprising 43 sites, where vertebrate scavenger assemblages were identified using 2,485 carcasses monitored between 1991 and 2018. First, we evaluated how scavenger richness (number of species) and diversity (Shannon diversity index) varied among seasons (cold vs. warm, wet vs. dry). Then, we studied the potential effects of human impact and a set of macroecological variables related to climatic conditions on the scavenger assemblages. Vertebrate scavenger richness ranged from species‐poor to species rich assemblages (4–30 species). Both scavenger richness and diversity also showed some seasonal variation. However, in general, climatic variables did not drive latitudinal patterns, as scavenger richness and diversity were not affected by temperature or rainfall. Rainfall seasonality slightly increased the number of species in the community, but its effect was weak. Instead, the human impact index included in our study was the main predictor of scavenger richness. Scavenger assemblages in highly human‐impacted areas sustained the smallest number of scavenger species, suggesting human activity may be overriding other macroecological processes in shaping scavenger communities. Our results highlight the effect of human impact at a global scale. As speciesrich assemblages tend to be more functional, we warn about possible reductions in ecosystem functions and the services provided by scavengers in human‐dominated landscapes in the Anthropocene
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