Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

Modelling the Mechanical Behaviour of a Pharmaceutical Tablet Using PDEs.

yesDetailed design of pharmaceutical tablets is essential nowadays in order to produce robust tablets with tailor-made properties. Compressibility and compactibility are the main compaction properties involved in the design and development of solid dosage forms. The data obtained from measured forces and displacements of the punch are normally analysed using the Heckel model to assess the mechanical behaviour of pharmaceutical powders. In this paper, we present a technique for shape modelling of pharmaceutical tablets based on the PDE method. We extended the formulation of the PDE method to a higher dimensional space in order to generate a solid tablet and a cuboid mesh is created to represent the tablet¿s components. We also modelled the displacement components of a compressed PDE- based representation of a tablet by utilising the solution of the axisymmetric boundary value problem for a finite cylinder subject to a uniform axial load. The experimental data and the results obtained from the developed model are shown in Heckel plots and a good agreement is found between both.Available in full text since 5th Feb 2013 following the publisher's embargo period

A New View on Worst-Case to Average-Case Reductions for NP Problems

We study the result by Bogdanov and Trevisan (FOCS, 2003), who show that under reasonable assumptions, there is no non-adaptive worst-case to average-case reduction that bases the average-case hardness of an NP-problem on the worst-case complexity of an NP-complete problem. We replace the hiding and the heavy samples protocol in [BT03] by employing the histogram verification protocol of Haitner, Mahmoody and Xiao (CCC, 2010), which proves to be very useful in this context. Once the histogram is verified, our hiding protocol is directly public-coin, whereas the intuition behind the original protocol inherently relies on private coins

VE-cadherin and claudin-5: it takes two to tango

Endothelial barrier function requires the adhesive activity of VE-cadherin and claudin-5, which are key components of adherens and tight endothelial junctions, respectively. Emerging evidence suggests that VE-cadherin controls claudin-5 expression by preventing the nuclear accumulation of FoxO1 and -catenin, which repress the claudin-5 promoter. This indicates that a crosstalk mechanism operates between these junctional structures

Applying MAPP Algorithm for Cooperative Path Finding in Urban Environments

The paper considers the problem of planning a set of non-conflict trajectories for the coalition of intelligent agents (mobile robots). Two divergent approaches, e.g. centralized and decentralized, are surveyed and analyzed. Decentralized planner - MAPP is described and applied to the task of finding trajectories for dozens UAVs performing nap-of-the-earth flight in urban environments. Results of the experimental studies provide an opportunity to claim that MAPP is a highly efficient planner for solving considered types of tasks

Automated Analysis and Quantification of Human Mobility using a Depth Sensor

Analysis and quantification of human motion to support clinicians in the decision-making process is the desired outcome for many clinical-based approaches. However, generating statistical models that are free from human interpretation and yet representative is a difficult task. In this work, we propose a framework that automatically recognises and evaluates human mobility impairments using the Microsoft Kinect One depth sensor. The framework is composed of two parts. Firstly, it recognises motions, such as sit-to-stand or walking 4 metres, using abstract feature representation techniques and machine learning. Secondly, evaluation of the motion sequence in the temporal domain by comparing the test participant with a statistical mobility model, generated from tracking movements of healthy people. To complement the framework, we propose an automatic method to enable a fairer, unbiased approach to label motion capture data. Finally, we demonstrate the ability of the framework to recognise and provide clinically relevant feedback to highlight mobility concerns, hence providing a route towards stratified rehabilitation pathways and clinician led interventions

On the computation of zone and double zone diagrams

Classical objects in computational geometry are defined by explicit relations. Several years ago the pioneering works of T. Asano, J. Matousek and T. Tokuyama introduced "implicit computational geometry", in which the geometric objects are defined by implicit relations involving sets. An important member in this family is called "a zone diagram". The implicit nature of zone diagrams implies, as already observed in the original works, that their computation is a challenging task. In a continuous setting this task has been addressed (briefly) only by these authors in the Euclidean plane with point sites. We discuss the possibility to compute zone diagrams in a wide class of spaces and also shed new light on their computation in the original setting. The class of spaces, which is introduced here, includes, in particular, Euclidean spheres and finite dimensional strictly convex normed spaces. Sites of a general form are allowed and it is shown that a generalization of the iterative method suggested by Asano, Matousek and Tokuyama converges to a double zone diagram, another implicit geometric object whose existence is known in general. Occasionally a zone diagram can be obtained from this procedure. The actual (approximate) computation of the iterations is based on a simple algorithm which enables the approximate computation of Voronoi diagrams in a general setting. Our analysis also yields a few byproducts of independent interest, such as certain topological properties of Voronoi cells (e.g., that in the considered setting their boundaries cannot be "fat").Comment: Very slight improvements (mainly correction of a few typos); add DOI; Ref [51] points to a freely available computer application which implements the algorithms; to appear in Discrete & Computational Geometry (available online

Nestin in immature embryonic neurons affects axon growth cone morphology and Semaphorin3a sensitivity

Correct wiring in the neocortex requires that responses to an individual guidance cue vary among neurons in the same location, and within the same neuron over time. Nestin is an atypical intermediate filament expressed strongly in neural progenitors and is thus used widely as a progenitor marker. Here we show a subpopulation of embryonic cortical neurons that transiently express nestin in their axons. Nestin expression is thus not restricted to neural progenitors, but persists for 2–3 d at lower levels in newborn neurons. We found that nestin-expressing neurons have smaller growth cones, suggesting that nestin affects cytoskeletal dynamics. Nestin, unlike other intermediate filament subtypes, regulates cdk5 kinase by binding the cdk5 activator p35. Cdk5 activity is induced by the repulsive guidance cue Semaphorin3a (Sema3a), leading to axonal growth cone collapse in vitro. Therefore, we tested whether nestin-expressing neurons showed altered responses to Sema3a. We find that nestin-expressing newborn neurons are more sensitive to Sema3a in a roscovitine-sensitive manner, whereas nestin knockdown results in lowered sensitivity to Sema3a. We propose that nestin functions in immature neurons to modulate cdk5 downstream of the Sema3a response. Thus, the transient expression of nestin could allow temporal and/or spatial modulation of a neuron’s response to Sema3a, particularly during early axon guidance