55 research outputs found
Principal components analysis in the space of phylogenetic trees
Phylogenetic analysis of DNA or other data commonly gives rise to a
collection or sample of inferred evolutionary trees. Principal Components
Analysis (PCA) cannot be applied directly to collections of trees since the
space of evolutionary trees on a fixed set of taxa is not a vector space. This
paper describes a novel geometrical approach to PCA in tree-space that
constructs the first principal path in an analogous way to standard linear
Euclidean PCA. Given a data set of phylogenetic trees, a geodesic principal
path is sought that maximizes the variance of the data under a form of
projection onto the path. Due to the high dimensionality of tree-space and the
nonlinear nature of this problem, the computational complexity is potentially
very high, so approximate optimization algorithms are used to search for the
optimal path. Principal paths identified in this way reveal and quantify the
main sources of variation in the original collection of trees in terms of both
topology and branch lengths. The approach is illustrated by application to
simulated sets of trees and to a set of gene trees from metazoan (animal)
species.Comment: Published in at http://dx.doi.org/10.1214/11-AOS915 the Annals of
Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical
Statistics (http://www.imstat.org
An L^2-Index Theorem for Dirac Operators on S^1 * R^3
An expression is found for the -index of a Dirac operator coupled to a
connection on a vector bundle over . Boundary
conditions for the connection are given which ensure the coupled Dirac operator
is Fredholm. Callias' index theorem is used to calculate the index when the
connection is independent of the coordinate on . An excision theorem due
to Gromov, Lawson, and Anghel reduces the index theorem to this special case.
The index formula can be expressed using the adiabatic limit of the
-invariant of a Dirac operator canonically associated to the boundary. An
application of the theorem is to count the zero modes of the Dirac operator in
the background of a caloron (periodic instanton).Comment: 14 pages, Latex, to appear in the Journal of Functional Analysi
Foundations of the Wald Space for Phylogenetic Trees
Evolutionary relationships between species are represented by phylogenetic
trees, but these relationships are subject to uncertainty due to the random
nature of evolution. A geometry for the space of phylogenetic trees is
necessary in order to properly quantify this uncertainty during the statistical
analysis of collections of possible evolutionary trees inferred from biological
data. Recently, the wald space has been introduced: a length space for trees
which is a certain subset of the manifold of symmetric positive definite
matrices. In this work, the wald space is introduced formally and its topology
and structure is studied in detail. In particular, we show that wald space has
the topology of a disjoint union of open cubes, it is contractible, and by
careful characterization of cube boundaries, we demonstrate that wald space is
a Whitney stratified space of type (A). Imposing the metric induced by the
affine invariant metric on symmetric positive definite matrices, we prove that
wald space is a geodesic Riemann stratified space. A new numerical method is
proposed and investigated for construction of geodesics, computation of
Fr\'echet means and calculation of curvature in wald space. This work is
intended to serve as a mathematical foundation for further geometric and
statistical research on this space.Comment: 42 pages, 15 figure
Types of Stickiness in BHV Phylogenetic Tree Spaces and Their Degree
It has been observed that the sample mean of certain probability
distributions in Billera-Holmes-Vogtmann (BHV) phylogenetic spaces is confined
to a lower-dimensional subspace for large enough sample size. This non-standard
behavior has been called stickiness and poses difficulties in statistical
applications when comparing samples of sticky distributions. We extend previous
results on stickiness to show the equivalence of this sampling behavior to
topological conditions in the special case of BHV spaces. Furthermore, we
propose to alleviate statistical comparision of sticky distributions by
including the directional derivatives of the Fr\'echet function: the degree of
stickiness.Comment: 8 Pages, 1 Figure, conference submission to GSI 202
Virology Experts in the Boundary Zone Between Science, Policy and the Public: A Biographical Analysis
This article aims to open up the biographical black box of three experts working in the boundary zone between science, policy and public debate. A biographical-narrative approach is used to analyse the roles played by the virologists Albert Osterhaus, Roel Coutinho and Jaap Goudsmit in policy and public debate. These figures were among the few leading virologists visibly active in the Netherlands during the revival of infectious diseases in the 1980s. Osterhaus and Coutinho in particular are still the key figures today, as demonstrated during the outbreak of novel influenza A (H1N1). This article studies the various political and communicative challenges and dilemmas encountered by these three virologists, and discusses the way in which, strategically or not, they handled those challenges and dilemmas during the various stages of the fieldās recent history. Important in this respect is their pursuit of a public role that is both effective and credible. We will conclude with a reflection on the H1N1 pandemic, and the historical and biographical ties between emerging governance arrangements and the experts involved in the development of such arrangements
CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice
Neuroinflammation and microglial activation are significant processes in Alzheimerās disease pathology. Recent genome-wide association studies have highlighted multiple immune-related genes in association with Alzheimerās disease, and experimental data have demonstrated microglial proliferation as a significant component of the neuropathology. In this study, we tested the efficacy of the selective CSF1R inhibitor JNJ-40346527 (JNJ-527) in the P301S mouse tauopathy model. We first demonstrated the anti-proliferative effects of JNJ-527 on microglia in the ME7 prion model, and its impact on the inflammatory profile, and provided potential CNS biomarkers for clinical investigation with the compound, including pharmacokinetic/pharmacodynamics and efficacy assessment by TSPO autoradiography and CSF proteomics. Then, we showed for the first time that blockade of microglial proliferation and modification of microglial phenotype leads to an attenuation of tau-induced neurodegeneration and results in functional improvement in P301S mice. Overall, this work strongly supports the potential for inhibition of CSF1R as a target for the treatment of Alzheimerās disease and other tau-mediated neurodegenerative diseases
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