Localizing the Latent Structure Canonical Uncertainty: Entropy Profiles for Hidden Markov Models

This report addresses state inference for hidden Markov models. These models rely on unobserved states, which often have a meaningful interpretation. This makes it necessary to develop diagnostic tools for quantification of state uncertainty. The entropy of the state sequence that explains an observed sequence for a given hidden Markov chain model can be considered as the canonical measure of state sequence uncertainty. This canonical measure of state sequence uncertainty is not reflected by the classic multivariate state profiles computed by the smoothing algorithm, which summarizes the possible state sequences. Here, we introduce a new type of profiles which have the following properties: (i) these profiles of conditional entropies are a decomposition of the canonical measure of state sequence uncertainty along the sequence and makes it possible to localize this uncertainty, (ii) these profiles are univariate and thus remain easily interpretable on tree structures. We show how to extend the smoothing algorithms for hidden Markov chain and tree models to compute these entropy profiles efficiently.Comment: Submitted to Journal of Machine Learning Research; No RR-7896 (2012

Update on the ICUD-SIU consultation on multi-parametric magnetic resonance imaging in localised prostate cancer

Introduction: Prostate cancer (PCa) imaging is a rapidly evolving field. Dramatic improvements in prostate MRI during the last decade will probably change the accuracy of diagnosis. This chapter reviews recent current evidence about MRI diagnostic performance and impact on PCa management. Materials and methods: The International Consultation on Urological Diseases nominated a committee to review the literature on prostate MRI. A search of the PubMed database was conducted to identify articles focussed on MP-MRI detection and staging protocols, reporting and scoring systems, the role of MP-MRI in diagnosing PCa prior to biopsy, in active surveillance, in focal therapy and in detecting local recurrence after treatment. Results: Differences in opinion were reported in the use of the strength of magnets [1.5 Tesla (T) vs. 3T] and coils. More agreement was found regarding the choice of pulse sequences; diffusion-weighted MRI (DW-MRI), dynamic contrast-enhanced MRI (DCE MRI), and/or MR spectroscopy imaging (MRSI) are recommended in addition to conventional T2-weighted anatomical sequences. In 2015, the Prostate Imaging Reporting and Data System (PI-RADS version 2) was described to standardize image acquisition and interpretation. MP-MRI improves detection of clinically significant PCa (csPCa) in the repeat biopsy setting or before the confirmatory biopsy in patients considering active surveillance. It is useful to guide focal treatment and to detect local recurrences after treatment. Its role in biopsy-naive patients or during the course of active surveillance remains debated. Conclusion: MP-MRI is increasingly used to improve detection of csPCa and for the selection of a suitable therapeutic approach

Analysis of dynamical corrections to baryon magnetic moments

We present and analyze QCD corrections to the baryon magnetic moments in terms of the one-, two-, and three-body operators which appear in the effective field theory developed in our recent papers. The main corrections are extended Thomas-type corrections associated with the confining interactions in the baryon. We investigate the contributions of low-lying angular excitations to the moments quantitatively and show that they are completely negligible. When the QCD corrections are combined with the non-quark model contributions of the meson loops, we obtain a model which describes the moments within a mean deviation of 0.04 $\mu_N$. The nontrivial interplay of the two types of corrections to the quark-model moments is analyzed in detail, and explains why the quark model is so successful. In the course of these calculations, we parametrize the general spin structure of the $j={1/2}^+$ baryon wave functions in a form which clearly displays the symmetry properties and the internal angular momentum content of the wave functions, and allows us to use spin-trace methods to calculate the many spin matrix elements which appear in the expressions for the moments. This representation may be useful elsewhere.Comment: 32 pages, 3 figures, submitted to Phys. Rev.

Cooling Tests of the NectarCAM camera for the Cherenkov Telescope Array

The NectarCAM is a camera proposed for the medium-sized telescopes in the framework of the Cherenkov Telescope Array (CTA), the next-generation observatory for very-high-energy gamma-ray astronomy. The cameras are designed to operate in an open environment and their mechanics must provide protection for all their components under the conditions defined for the CTA observatory. In order to operate in a stable environment and ensure the best physics performance, each NectarCAM will be enclosed in a slightly overpressurized, nearly air-tight, camera body, to prevent dust and water from entering. The total power dissipation will be ~7.7 kW for a 1855-pixel camera. The largest fraction is dissipated by the readout electronics in the modules. We present the design and implementation of the cooling system together with the test bench results obtained on the NectarCAM thermal demonstrator.Comment: In Proceedings of the 34th International Cosmic Ray Conference (ICRC2015), The Hague, The Netherlands. All CTA contributions at arXiv:1508.0589

New approach of fragment charge correlations in 129Xe+(nat)Sn central collisions

A previous analysis of the charge (Z) correlations in the $\Delta Z-$ plane for Xe+Sn central collisions at 32 MeV/u has shown an enhancement in the production of equally sized fragments (low $\Delta Z$) which was interpreted as an evidence for spinodal decomposition. However the signal is weak and rises the question of the estimation of the uncorrelated yield. After a critical analysis of its robustness, we propose in this paper a new technique to build the uncorrelated yield in the charge correlation function. The application of this method to Xe+Sn central collision data at 32, 39, 45 and 50 MeV/u does not show any particular enhancement of the correlation function in any $\Delta Z$ bin.Comment: 23 pages, 9 figures, revised version with an added figure and minor changes. To appear in Nuclear Physics

Impact of mesh resolution for MISMIP and MISMIP3d experiments using Elmer/Ice

International audienceThe dynamical contribution of marine ice sheets to sea level rise is largely controlled by grounding line (GL) dynamics. Two marine ice sheet model intercomparison exercises , namely MISMIP and MISMIP3d, have been proposed to the community to test and compare the ability of models to capture the GL dynamics. Both exercises are known to present a discontinuity of the friction at the GL, which is believed to increase the model sensitivity to mesh resolution. Here, using Elmer/Ice, the only Stokes model which completed both intercomparisons, the sensitivity to the mesh resolution is studied from an extended MISMIP experiment in which the friction continuously decreases over a transition distance and equals zero at the GL. Using this MISMIP-like setup, it is shown that the sensitivity to the mesh resolution is not improved for a vanishing friction at the GL. For the original MISMIP experiment, i.e. for a discontinuous friction at the GL, we further show that the results are moreover very sensitive to the way the friction is interpolated in the close vicinity of the GL. In the light of these new insights, and thanks to increased computing resources, new results for the MISMIP3d experiments obtained for higher resolutions than previously published are made available for future comparisons as the Supplement

Retinitis pigmentosa: rapid neurodegeneration is governed by slow cell death mechanisms

For most neurodegenerative diseases the precise duration of an individual cell's death is unknown, which is an obstacle when counteractive measures are being considered. To address this, we used the rd1 mouse model for retinal neurodegeneration, characterized by phosphodiesterase-6 (PDE6) dysfunction and photoreceptor death triggered by high cyclic guanosinemono-phosphate (cGMP) levels. Using cellular data on cGMP accumulation, cell death, and survival, we created mathematical models to simulate the temporal development of the degeneration. We validated model predictions using organotypic retinal explant cultures derived from wild-type animals and exposed to the selective PDE6 inhibitor zaprinast. Together, photoreceptor data and modeling for the first time delineated three major cell death phases in a complex neuronal tissue: (1) initiation, taking up to 36 h, (2) execution, lasting another 40 h, and finally (3) clearance, lasting about 7 h. Surprisingly, photoreceptor neurodegeneration was noticeably slower than necrosis or apoptosis, suggesting a different mechanism of death for these neurons. Cell Death and Disease (2013) 4, e488; doi: 10.1038/cddis.2013.12; published online 7 February 201

New electron source concept for single-shot sub-100 fs electron diffraction in the 100 keV range

We present a method for producing sub-100 fs electron bunches that are suitable for single-shot ultrafast electron diffraction experiments in the 100 keV energy range. A combination of analytical results and state-of-the-art numerical simulations show that it is possible to create 100 keV, 0.1 pC, 20 fs electron bunches with a spotsize smaller than 500 micron and a transverse coherence length of 3 nm, using established technologies in a table-top set-up. The system operates in the space-charge dominated regime to produce energy-correlated bunches that are recompressed by established radio-frequency techniques. With this approach we overcome the Coulomb expansion of the bunch, providing an entirely new ultrafast electron diffraction source concept

Hydrodynamic lift on bound vesicles

Bound vesicles subject to lateral forces such as arising from shear flow are investigated theoretically by combining a lubrication analysis of the bound part with a scaling approach to the global motion. A minor inclination of the bound part leads to significant lift due to the additive effects of lateral and tank-treading motions. With increasing shear rate, the vesicle unbinds from the substrate at a critical value. Estimates are in agreement with recent experimental data.Comment: 9 pages, one figur