127 research outputs found
The ACIGA Data Analysis programme
The Data Analysis programme of the Australian Consortium for Interferometric
Gravitational Astronomy (ACIGA) was set up in 1998 by the first author to
complement the then existing ACIGA programmes working on suspension systems,
lasers and optics, and detector configurations. The ACIGA Data Analysis
programme continues to contribute significantly in the field; we present an
overview of our activities.Comment: 10 pages, 0 figures, accepted, Classical and Quantum Gravity,
(Proceedings of the 5th Edoardo Amaldi Conference on Gravitational Waves,
Tirrenia, Pisa, Italy, 6-11 July 2003
Multiple feedback loops through cytokinin signaling control stem cell number within the Arabidopsis shoot meristem
A central unanswered question in stem cell biology, both in plants and in animals, is how the spatial organization of stem cell niches are maintained as cells move through them. We address this question for the shoot apical meristem (SAM) which harbors pluripotent stem cells responsible for growth of above-ground tissues in flowering plants. We find that localized perception of the plant hormone cytokinin establishes a spatial domain in which cell fate is respecified through induction of the master regulator WUSCHEL as cells are displaced during growth. Cytokinin-induced WUSCHEL expression occurs through both CLAVATA-dependent and CLAVATA-independent pathways. Computational analysis shows that feedback between cytokinin response and genetic regulators predicts their relative patterning, which we confirm experimentally. Our results also may explain how increasing cytokinin concentration leads to the first steps in reestablishing the shoot stem cell niche in vitro
Squeezed light in a frontal-phase-modulated signal-recycled interferometer
The application of squeezed Light to a frontal-phase-modulated signal-recycled interferometer is considered. We present a simple model to understand the required spectrum of squeezing so as to make the interferometer more sensitive. In particular we analyze the broad-and narrow-band cases for signal recycling and fmd that the sensitivity of the detector can be enhanced provided an appropriate input squeezed spectrum is used. We also discuss the effect of using squeezed light on the bandwidth of the detector
Predicting Pancreas Cell Fate Decisions and Reprogramming with a Hierarchical Multi-Attractor Model
Cell fate reprogramming, such as the generation of insulin-producing β cells from other pancreas cells, can be achieved by external modulation of key transcription factors. However, the known gene regulatory interactions that form a complex network with multiple feedback loops make it increasingly difficult to design the cell reprogramming scheme because the linear regulatory pathways as schemes of causal influences upon cell lineages are inadequate for predicting the effect of transcriptional perturbation. However, sufficient information on regulatory networks is usually not available for detailed formal models. Here we demonstrate that by using the qualitatively described regulatory interactions as the basis for a coarse-grained dynamical ODE (ordinary differential equation) based model, it is possible to recapitulate the observed attractors of the exocrine and β, δ, α endocrine cells and to predict which gene perturbation can result in desired lineage reprogramming. Our model indicates that the constraints imposed by the incompletely elucidated regulatory network architecture suffice to build a predictive model for making informed decisions in choosing the set of transcription factors that need to be modulated for fate reprogramming
Cytokinin signaling as a positional cue for patterning the apical-basal axis of the growing Arabidopsis shoot meristem
Bridging Time Scales in Cellular Decision Making with a Stochastic Bistable Switch
Cellular transformations which involve a significant phenotypical change of
the cell's state use bistable biochemical switches as underlying decision
systems. In this work, we aim at linking cellular decisions taking place on a
time scale of years to decades with the biochemical dynamics in signal
transduction and gene regulation, occuring on a time scale of minutes to hours.
We show that a stochastic bistable switch forms a viable biochemical mechanism
to implement decision processes on long time scales. As a case study, the
mechanism is applied to model the initiation of follicle growth in mammalian
ovaries, where the physiological time scale of follicle pool depletion is on
the order of the organism's lifespan. We construct a simple mathematical model
for this process based on experimental evidence for the involved genetic
mechanisms. Despite the underlying stochasticity, the proposed mechanism turns
out to yield reliable behavior in large populations of cells subject to the
considered decision process. Our model explains how the physiological time
constant may emerge from the intrinsic stochasticity of the underlying gene
regulatory network. Apart from ovarian follicles, the proposed mechanism may
also be of relevance for other physiological systems where cells take binary
decisions over a long time scale.Comment: 14 pages, 4 figure
Purity of Gaussian states: measurement schemes and time-evolution in noisy channels
We present a systematic study of the purity for Gaussian states of
single-mode continuous variable systems. We prove the connection of purity to
observable quantities for these states, and show that the joint measurement of
two conjugate quadratures is necessary and sufficient to determine the purity
at any time. The statistical reliability and the range of applicability of the
proposed measurement scheme is tested by means of Monte Carlo simulated
experiments. We then consider the dynamics of purity in noisy channels. We
derive an evolution equation for the purity of general Gaussian states both in
thermal and squeezed thermal baths. We show that purity is maximized at any
given time for an initial coherent state evolving in a thermal bath, or for an
initial squeezed state evolving in a squeezed thermal bath whose asymptotic
squeezing is orthogonal to that of the input state.Comment: 9 Pages, 6 Figures; minor errors correcte
Inverse bifurcation analysis: application to simple gene systems
BACKGROUND: Bifurcation analysis has proven to be a powerful method for understanding the qualitative behavior of gene regulatory networks. In addition to the more traditional forward problem of determining the mapping from parameter space to the space of model behavior, the inverse problem of determining model parameters to result in certain desired properties of the bifurcation diagram provides an attractive methodology for addressing important biological problems. These include understanding how the robustness of qualitative behavior arises from system design as well as providing a way to engineer biological networks with qualitative properties. RESULTS: We demonstrate that certain inverse bifurcation problems of biological interest may be cast as optimization problems involving minimal distances of reference parameter sets to bifurcation manifolds. This formulation allows for an iterative solution procedure based on performing a sequence of eigen-system computations and one-parameter continuations of solutions, the latter being a standard capability in existing numerical bifurcation software. As applications of the proposed method, we show that the problem of maximizing regions of a given qualitative behavior as well as the reverse engineering of bistable gene switches can be modelled and efficiently solved
Searching for gravitational waves from known pulsars
We present upper limits on the amplitude of gravitational waves from 28
isolated pulsars using data from the second science run of LIGO. The results
are also expressed as a constraint on the pulsars' equatorial ellipticities. We
discuss a new way of presenting such ellipticity upper limits that takes
account of the uncertainties of the pulsar moment of inertia. We also extend
our previous method to search for known pulsars in binary systems, of which
there are about 80 in the sensitive frequency range of LIGO and GEO 600.Comment: Accepted by CQG for the proceeding of GWDAW9, 7 pages, 2 figure
Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells
Generation of induced pluripotent stem cells (iPSCs) opens a new avenue in regenerative medicine. One of the major hurdles for therapeutic applications is to improve the efficiency of generating iPSCs and also to avoid the tumorigenicity, which requires searching for new reprogramming recipes. We present a systems biology approach to efficiently evaluate a large number of possible recipes and find those that are most effective at generating iPSCs. We not only recovered several experimentally confirmed recipes but we also suggested new ones that may improve reprogramming efficiency and quality. In addition, our approach allows one to estimate the cell-state landscape, monitor the progress of reprogramming, identify important regulatory transition states, and ultimately understand the mechanisms of iPSC generation
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