627 research outputs found
Periodic Splines and Gaussian Processes for the Resolution of Linear Inverse Problems
This paper deals with the resolution of inverse problems in a periodic
setting or, in other terms, the reconstruction of periodic continuous-domain
signals from their noisy measurements. We focus on two reconstruction
paradigms: variational and statistical. In the variational approach, the
reconstructed signal is solution to an optimization problem that establishes a
tradeoff between fidelity to the data and smoothness conditions via a quadratic
regularization associated to a linear operator. In the statistical approach,
the signal is modeled as a stationary random process defined from a Gaussian
white noise and a whitening operator; one then looks for the optimal estimator
in the mean-square sense. We give a generic form of the reconstructed signals
for both approaches, allowing for a rigorous comparison of the two.We fully
characterize the conditions under which the two formulations yield the same
solution, which is a periodic spline in the case of sampling measurements. We
also show that this equivalence between the two approaches remains valid on
simulations for a broad class of problems. This extends the practical range of
applicability of the variational method
Exclusion processes: short range correlations induced by adhesion and contact interactions
We analyze the out-of-equilibrium behavior of exclusion processes where
agents interact with their nearest neighbors, and we study the short-range
correlations which develop because of the exclusion and other contact
interactions. The form of interactions we focus on, including adhesion and
contact-preserving interactions, is especially relevant for migration processes
of living cells. We show the local agent density and nearest-neighbor two-point
correlations resulting from simulations on two dimensional lattices in the
transient regime where agents invade an initially empty space from a source and
in the stationary regime between a source and a sink. We compare the results of
simulations with the corresponding quantities derived from the master equation
of the exclusion processes, and in both cases, we show that, during the
invasion of space by agents, a wave of correlations travels with velocity v(t)
~ t^(-1/2). The relative placement of this wave to the agent density front and
the time dependence of its height may be used to discriminate between different
forms of contact interactions or to quantitatively estimate the intensity of
interactions. We discuss, in the stationary density profile between a full and
an empty reservoir of agents, the presence of a discontinuity close to the
empty reservoir. Then, we develop a method for deriving approximate
hydrodynamic limits of the processes. From the resulting systems of partial
differential equations, we recover the self-similar behavior of the agent
density and correlations during space invasion
Automatic quantification of the microvascular density on whole slide images, applied to paediatric brain tumours
Angiogenesis is a key phenomenon for tumour progression, diagnosis and
treatment in brain tumours and more generally in oncology. Presently, its
precise, direct quantitative assessment can only be done on whole tissue
sections immunostained to reveal vascular endothelial cells. But this is a
tremendous task for the pathologist and a challenge for the computer since
digitised whole tissue sections, whole slide images (WSI), contain typically
around ten gigapixels.
We define and implement an algorithm that determines automatically, on a WSI
at objective magnification , the regions of tissue, the regions
without blur and the regions of large puddles of red blood cells, and
constructs the mask of blur-free, significant tissue on the WSI. Then it
calibrates automatically the optical density ratios of the immunostaining of
the vessel walls and of the counterstaining, performs a colour deconvolution
inside the regions of blur-free tissue, and finds the vessel walls inside these
regions by selecting, on the image resulting from the colour deconvolution,
zones which satisfy a double-threshold criterion. A mask of vessel wall regions
on the WSI is produced. The density of microvessels is finally computed as the
fraction of the area of significant tissue which is occupied by vessel walls.
We apply this algorithm to a set of 186 WSI of paediatric brain tumours from
World Health Organisation grades I to IV. The segmentations are of very good
quality although the set of slides is very heterogeneous. The computation time
is of the order of a fraction of an hour for each WSI on a modest computer. The
computed microvascular density is found to be robust and strongly correlates
with the tumour grade.
This method requires no training and can easily be applied to other tumour
types and other stainings
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HAGE, a cancer/testis antigen expressed at the protein level in a variety of cancers
The search for novel tumour antigens that are either uniquely expressed or over-expressed in a wide variety of tumours is still ongoing. Because of their expression in a broad spectrum of cancers and limited expression in normal tissues, cancer/testis antigens are considered to be potentially reliable targets for immunotherapy of cancer in general. The helicase antigen HAGE has been identified as a cancer/testis antigen. However, little is known about its expression in normal and cancer tissues. Using a newly developed antibody against HAGE, specific staining of its expression by immunohistochemistry was validated and optimised on murine tumours transfected to express the HAGE protein. The antibody was subsequently used to determine HAGE expression in normal human and cancer tissue microarrays. HAGE protein expression was confirmed in 75% (12/16) of carcinomas as compared to normal tissues, which either did not express HAGE at all or expressed HAGE at very low levels with the exception of testis. Interestingly, discrepancies were also found between mRNA analysis by real time quantitative PCR (RT-qPCR) and protein analysis by immunohistochemistry, emphasising the need to validate the expression of cancer/testis antigens at the protein level prior to the development of new vaccine strategies. HAGE is therefore proposed to be a valid candidate for designing a broad spectrum vaccine against cancer
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