395 research outputs found
Substrate Deformation Predicts Neuronal Growth Cone Advance
AbstractAlthough pulling forces have been observed in axonal growth for several decades, their underlying mechanisms, absolute magnitudes, and exact roles are not well understood. In this study, using two different experimental approaches, we quantified retrograde traction force in Aplysia californica neuronal growth cones as they develop over time in response to a new adhesion substrate. In the first approach, we developed a novel method, to our knowledge, for measuring traction forces using an atomic force microscope (AFM) with a cantilever that was modified with an Aplysia cell adhesion molecule (apCAM)-coated microbead. In the second approach, we used force-calibrated glass microneedles coated with apCAM ligands to guide growth cone advance. The traction force exerted by the growth cone was measured by monitoring the microneedle deflection using an optical microscope. Both approaches showed that Aplysia growth cones can develop traction forces in the 100â102 nN range during adhesion-mediated advance. Moreover, our results suggest that the level of traction force is directly correlated to the stiffness of the microneedle, which is consistent with a reinforcement mechanism previously observed in other cell types. Interestingly, the absolute level of traction force did not correlate with growth cone advance toward the adhesion site, but the amount of microneedle deflection did. In cases of adhesion-mediated growth cone advance, the mean needle deflection was 1.05 ± 0.07 Όm. By contrast, the mean deflection was significantly lower (0.48 ± 0.06 ÎŒm) when the growth cones did not advance. Our data support a hypothesis that adhesion complexes, which can undergo micron-scale elastic deformation, regulate the coupling between the retrogradely flowing actin cytoskeleton and apCAM substrates, stimulating growth cone advance if sufficiently abundant
Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen
The past two decades have seen a worldwide resurgence in infections caused by Treponema pallidum subsp. pallidum, the syphilis spirochete. The well-recognized capacity of the syphilis spirochete for early dissemination and immune evasion has earned it the designation 'the stealth pathogen'. Despite the many hurdles to studying syphilis pathogenesis, most notably the inability to culture and to genetically manipulate T. pallidum, in recent years, considerable progress has been made in elucidating the structural, physiological, and regulatory facets of T. pallidum pathogenicity. In this Review, we integrate this eclectic body of information to garner fresh insights into the highly successful parasitic lifestyles of the syphilis spirochete and related pathogenic treponemes
Statistical tests for large tree-structured data
We develop a general statistical framework for the analysis and inference of large tree-structured data, with a focus on developing asymptotic goodness-of-fit tests. We first propose a consistent statistical model for binary trees, from which we develop a class of invariant tests. Using the model for binary trees, we then construct tests for general trees by using the distributional properties of the Continuum Random Tree, which arises as the invariant limit for a broad class of models for tree-structured data based on conditioned GaltonâWatson processes. The test statistics for the goodness-of-fit tests are simple to compute and are asymptotically distributed as Ï2 and F random variables. We illustrate our methods on an important application of detecting tumour heterogeneity in brain cancer. We use a novel approach with tree-based representations of magnetic resonance images and employ the developed tests to ascertain tumor heterogeneity between two groups of patients
Adverse prognostic and predictive significance of low DNA-dependent protein kinase catalytic subunit (DNA-PKcs) expression in early-stage breast cancers
Background: DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a serine threonine kinase belonging to the PIKK family (phosphoinositide 3-kinase-like-family of protein kinase), is a critical component of the non-homologous end joining (NHEJ) pathway required for the repair of DNA double strand breaks. DNA-PKcs may be involved in breast cancer pathogenesis. Methods: We evaluated clinicopathological significance of DNA-PKcs protein expression in 1161 tumours and DNA-PKcs mRNA expression in 1950 tumours. We correlated DNA-PKcs to other markers of aggressive phenotypes, DNA repair, apoptosis and cell cycle regulation. Results: Low DNA-PKcs protein expression was associated with higher tumour grade, higher mitotic index, tumour de-differentiation and tumour type (ps<0.05). Absence of BRCA1, low XRCC1/SMUG1/APE1/PolÎČ were also more likely in low DNA-PKcs expressing tumours (ps<0.05). Low DNA-PKcs protein expression was significantly associated with worse breast cancer specific survival (BCCS) in univariate and multivariate analysis (ps<0.01). At the mRNA level, low DNA-PKcs was associated with PAM50.Her2 and PAM50.LumA molecular phenotypes (ps<0.01) and poor BCSS. In patients with ER positive tumours who received endocrine therapy, low DNA-PKcs (protein and mRNA) was associated with poor survival. In ER negative patients, low DNA-PKcs mRNA remains significantly associated with adverse outcome. Conclusions: Our study suggests that low DNA-PKcs expression may have prognostic and predictive significance in breast cancers
Flexible graph matching and graph edit distance using answer set programming
The graph isomorphism, subgraph isomorphism, and graph edit distance problems
are combinatorial problems with many applications. Heuristic exact and
approximate algorithms for each of these problems have been developed for
different kinds of graphs: directed, undirected, labeled, etc. However,
additional work is often needed to adapt such algorithms to different classes
of graphs, for example to accommodate both labels and property annotations on
nodes and edges. In this paper, we propose an approach based on answer set
programming. We show how each of these problems can be defined for a general
class of property graphs with directed edges, and labels and key-value
properties annotating both nodes and edges. We evaluate this approach on a
variety of synthetic and realistic graphs, demonstrating that it is feasible as
a rapid prototyping approach.Comment: To appear, PADL 202
Building robust prediction models for defective sensor data using Artificial Neural Networks
Predicting the health of components in complex dynamic systems such as an
automobile poses numerous challenges. The primary aim of such predictive
systems is to use the high-dimensional data acquired from different sensors and
predict the state-of-health of a particular component, e.g., brake pad. The
classical approach involves selecting a smaller set of relevant sensor signals
using feature selection and using them to train a machine learning algorithm.
However, this fails to address two prominent problems: (1) sensors are
susceptible to failure when exposed to extreme conditions over a long periods
of time; (2) sensors are electrical devices that can be affected by noise or
electrical interference. Using the failed and noisy sensor signals as inputs
largely reduce the prediction accuracy. To tackle this problem, it is
advantageous to use the information from all sensor signals, so that the
failure of one sensor can be compensated by another. In this work, we propose
an Artificial Neural Network (ANN) based framework to exploit the information
from a large number of signals. Secondly, our framework introduces a data
augmentation approach to perform accurate predictions in spite of noisy
signals. The plausibility of our framework is validated on real life industrial
application from Robert Bosch GmbH.Comment: 16 pages, 7 figures. Currently under review. This research has
obtained funding from the Electronic Components and Systems for European
Leadership (ECSEL) Joint Undertaking, the framework programme for research
and innovation Horizon 2020 (2014-2020) under grant agreement number
662189-MANTIS-2014-
Information measures and classicality in quantum mechanics
We study information measures in quantu mechanics, with particular emphasis
on providing a quantification of the notions of classicality and
predictability. Our primary tool is the Shannon - Wehrl entropy I. We give a
precise criterion for phase space classicality and argue that in view of this
a) I provides a measure of the degree of deviation from classicality for closed
system b) I - S (S the von Neumann entropy) plays the same role in open systems
We examine particular examples in non-relativistic quantum mechanics. Finally,
(this being one of our main motivations) we comment on field classicalisation
on early universe cosmology.Comment: 35 pages, LATE
Barut-Girardello coherent states for u(p,q) and sp(N,R) and their macroscopic superpositions
The Barut-Girardello coherent states (BG CS) representation is extended to
the noncompact algebras u(p,q) and sp(N,R) in (reducible) quadratic boson
realizations. The sp(N,R) BG CS take the form of multimode ordinary
Schr\"odinger cat states. Macroscopic superpositions of 2^{n-1} sp(N,R) CS (2^n
canonical CS, n=1,2,...) are pointed out which are overcomplete in the N-mode
Hilbert space and the relation between the canonical CS and the u(p,q) BG-type
CS representations is established. The sets of u(p,q) and sp(N,R) BG CS and
their discrete superpositions contain many states studied in quantum optics
(even and odd N-mode CS, pair CS) and provide an approach to quadrature
squeezing, alternative to that of intelligent states. New subsets of weakly and
strongly nonclassical states are pointed out and their statistical properties
(first- and second-order squeezing, photon number distributions) are discussed.
For specific values of the angle parameters and small amplitude of the
canonical CS components these states approaches multimode Fock states with one,
two or three bosons/photons. It is shown that eigenstates of a squared
non-Hermitian operator A^2 (generalized cat states) can exhibit squeezing of
the quadratures of A.Comment: 29 pages, LaTex, 5 figures. Improvements in text, corrections in some
formulas. To appear in J. Phys. A, v. 3
On D3-brane Potentials in Compactifications with Fluxes and Wrapped D-branes
We study the potential governing D3-brane motion in a warped throat region of
a string compactification with internal fluxes and wrapped D-branes. If the
Kahler moduli of the compact space are stabilized by nonperturbative effects, a
D3-brane experiences a force due to its interaction with D-branes wrapping
certain four-cycles. We compute this interaction, as a correction to the warped
four-cycle volume, using explicit throat backgrounds in supergravity. This
amounts to a closed-string channel computation of the loop corrections to the
nonperturbative superpotential that stabilizes the volume. We demonstrate for
warped conical spaces that the superpotential correction is given by the
embedding equation specifying the wrapped four-cycle, in agreement with the
general form proposed by Ganor. Our approach automatically provides a solution
to the problem of defining a holomorphic gauge coupling on wrapped D7-branes in
a background with D3-branes. Finally, our results have applications to
cosmological inflation models in which the inflaton is modeled by a D3-brane
moving in a warped throat.Comment: 45 pages, 1 figure; v2: added reference, clarified notatio
Kinetic Monte Carlo Simulation of Strained Heteroepitaxial Growth with Intermixing
An efficient method for the simulation of strained heteroepitaxial growth
with intermixing using kinetic Monte Carlo is presented. The model used is
based on a solid-on-solid bond counting formulation in which elastic effects
are incorporated using a ball and spring model. While idealized, this model
nevertheless captures many aspects of heteroepitaxial growth, including
nucleation, surface diffusion, and long range effects due elastic interaction.
The algorithm combines a fast evaluation of the elastic displacement field with
an efficient implementation of a rejection-reduced kinetic Monte Carlo based on
using upper bounds for the rates. The former is achieved by using a multigrid
method for global updates of the displacement field and an expanding box method
for local updates. The simulations show the importance of intermixing on the
growth of a strained film. Further the method is used to simulate the growth of
self-assembled stacked quantum dots
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