785 research outputs found
Gene expression data annotation, effective storage, and enrichment through data mining
This thesis describes the development of different bioinformatics resources and data-mining strategies for managing and analysing the large amounts of data produced by microarray gene expression experiments. Initially, this involved addressing the problem of effectively capturing gene expression microarray data and the accompanying meta-data annotations de scribing the experimental process. This is necessary for reasons of archiving, interchange and reproducibility of datasets and comparability between them. This was achieved by the development of meditor, a graphical computer programme which allows the description of microarray experimental information through the use of diagrams and ontology-driven forms, meditor adheres to the standards set by the Microarray Gene Expression Data Society (MGED), and therefore is able to capture all the experimental information describable within the standard in a platform-independent manner. Subsequently, in order to provide capabilities for the formal modelling of gene expression analysis concepts, the concepts involved in the external validation of gene expression clusterings were formalised and defined as an object model. This model was developed with the implementation of data interchange file formats in mind. This work complements the object model of the MGED Society and attempts to cover an area that has not been formalised in a platform-independent manner by the standard object model. Finally, a method was developed to allow the use of knowledge on protein functions and protein-protein interactions to identify coherent sets of co-regulated genes suggested by the clustering of gene expression profiles. This was achieved through the development of a gene expression clustering quality metric, which judges the tightness and separation of gene expression clusters, thus providing a quality measure on a clustering or a per-cluster basis. Cluster tightness and separation are assessed by harnessing the manual annotations provided by the Gene Ontology, enriched using integrated biological information available through an in-house data warehouse (BioMap). The metric was tested on a human B-cell gene expression dataset and refined on the basis of the results produced
Transient chaos and resonant phase mixing in violent relaxation
This paper explores how orbits in a galactic potential can be impacted by
large amplitude time-dependences of the form that one might associate with
galaxy or halo formation or strong encounters between pairs of galaxies. A
period of time-dependence with a strong, possibly damped, oscillatory component
can give rise to large amounts of transient chaos, and it is argued that
chaotic phase mixing associated with this transient chaos could play a major
role in accounting for the speed and efficiency of violent relaxation. Analysis
of simple toy models involving time-dependent perturbations of an integrable
Plummer potential indicates that this chaos results from a broad, possibly
generic, resonance between the frequencies of the orbits and harmonics thereof
and the frequencies of the time-dependent perturbation. Numerical computations
of orbits in potentials exhibiting damped oscillations suggest that, within a
period of 10 dynamical times t_D or so, one could achieve simultaneously both
`near-complete' chaotic phase mixing and a nearly time-independent, integrable
end state.Comment: 11 pages and 12 figures: an extended version of the original
manuscript, containing a modified title, one new figure, and approximately
one page of additional text, to appear in Monthly Notices of the Royal
Astronomical Societ
Multivariable stability margin calculation with uncertain correlated parameters
An algorithm is developed for the computation of the multivariable stability margin in the case of real uncertain system parameters which can be related to each other
Smooth potential chaos and N-body simulations
Integrations in fixed N-body realisations of smooth density distributions
corresponding to a chaotic galactic potential can be used to derive reliable
estimates of the largest (finite time) Lyapunov exponent X_S associated with an
orbit in the smooth potential generated from the same initial condition, even
though the N-body orbit is typically characterised by an N-body exponent X_N >>
X_S. This can be accomplished either by comparing initially nearby orbits in a
single N-body system or by tracking orbits with the same initial condition
evolved in two different N-body realisations of the same smooth density.Comment: 9 pages plus 7 figures, expanded version to appear in Astrophysical
Journa
Dynamics of Cuspy Triaxial Galaxies with a Supermassive Black Hole
This talk provides a progress report on an extended collaboration which has
aimed to address two basic questions, namely: Should one expect to see cuspy,
triaxial galaxies in nature? And can one construct realistic cuspy, triaxial
equilibrium models that are robust? Three technical results are described: (1)
Unperturbed chaotic orbits in cuspy triaxial potentials can be extraordinarily
sticky, much more so than orbits in many other three-dimensional potentials.
(2) Even very weak perturbations can be important by drastically reducing,
albeit not completely eliminating, this stickiness. (3) A simple toy model
facilitates a simple understanding of why black holes and cusps can serve as an
effective source of chaos. These results suggest that, when constructing models
of galaxies using Schwarzschild's method or any analogue thereof, astronomers
would be well advised to use orbital building blocks that have been perturbed
by `noise' or other weak irregularities, since such building blocks are likely
to be more nearly time-independent than orbits evolved in the absence of all
perturbations.Comment: a contributed talk at The International Conference on Stellar
Dynamics: From Classical to Modern, Sobolev Astronomical Institute, St.
Petersburg State University, August 200
Developmental Markers of Genetic Liability to Autism in Parents: A Longitudinal, Multigenerational Study
Genetic liability to autism spectrum disorder (ASD) can be expressed in unaffected relatives through subclinical, genetically meaningful traits, or endophenotypes. This study aimed to identify developmental endophenotypes in parents of individuals with ASD by examining parents' childhood academic development over the school-age period. A cohort of 139 parents of individuals with ASD were studied, along with their children with ASD and 28 controls. Parents' childhood records in the domains of language, reading, and math were studied from grades K-12. Results indicated that relatively lower performance and slower development of skills (particularly language related skills), and an uneven rate of development across domains predicted ASD endophenotypes in adulthood for parents, and the severity of clinical symptoms in children with ASD. These findings may mark childhood indicators of genetic liability to ASD in parents, that could inform understanding of the subclinical expression of AS
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