86 research outputs found
Structure tensor total variation
This is the final version of the article. Available from Society for Industrial and Applied Mathematics via the DOI in this record.We introduce a novel generic energy functional that we employ to solve inverse imaging problems
within a variational framework. The proposed regularization family, termed as structure tensor
total variation (STV), penalizes the eigenvalues of the structure tensor and is suitable for both
grayscale and vector-valued images. It generalizes several existing variational penalties, including
the total variation seminorm and vectorial extensions of it. Meanwhile, thanks to the structure
tensor’s ability to capture first-order information around a local neighborhood, the STV functionals
can provide more robust measures of image variation. Further, we prove that the STV regularizers
are convex while they also satisfy several invariance properties w.r.t. image transformations. These
properties qualify them as ideal candidates for imaging applications. In addition, for the discrete
version of the STV functionals we derive an equivalent definition that is based on the patch-based
Jacobian operator, a novel linear operator which extends the Jacobian matrix. This alternative
definition allow us to derive a dual problem formulation. The duality of the problem paves the
way for employing robust tools from convex optimization and enables us to design an efficient
and parallelizable optimization algorithm. Finally, we present extensive experiments on various
inverse imaging problems, where we compare our regularizers with other competing regularization
approaches. Our results are shown to be systematically superior, both quantitatively and visually
Dynamic Bayesian Combination of Multiple Imperfect Classifiers
Classifier combination methods need to make best use of the outputs of
multiple, imperfect classifiers to enable higher accuracy classifications. In
many situations, such as when human decisions need to be combined, the base
decisions can vary enormously in reliability. A Bayesian approach to such
uncertain combination allows us to infer the differences in performance between
individuals and to incorporate any available prior knowledge about their
abilities when training data is sparse. In this paper we explore Bayesian
classifier combination, using the computationally efficient framework of
variational Bayesian inference. We apply the approach to real data from a large
citizen science project, Galaxy Zoo Supernovae, and show that our method far
outperforms other established approaches to imperfect decision combination. We
go on to analyse the putative community structure of the decision makers, based
on their inferred decision making strategies, and show that natural groupings
are formed. Finally we present a dynamic Bayesian classifier combination
approach and investigate the changes in base classifier performance over time.Comment: 35 pages, 12 figure
Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus.
BACKGROUND: Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires) have long been debated. While it is now generally agreed that Rodentia constitutes a monophyletic sister-group of Lagomorpha and that this clade (Glires) is sister to Primates and Dermoptera, higher-level relationships within Rodentia remain contentious. RESULTS: We have sequenced and performed extensive evolutionary analyses on the mitochondrial genome of the scaly-tailed flying squirrel Anomalurus sp., an enigmatic rodent whose phylogenetic affinities have been obscure and extensively debated. Our phylogenetic analyses of the coding regions of available complete mitochondrial genome sequences from Euarchontoglires suggest that Anomalurus is a sister taxon to the Hystricognathi, and that this clade represents the most basal divergence among sampled Rodentia. Bayesian dating methods incorporating a relaxed molecular clock provide divergence-time estimates which are consistently in agreement with the fossil record and which indicate a rapid radiation within Glires around 60 million years ago. CONCLUSION: Taken together, the data presented provide a working hypothesis as to the phylogenetic placement of Anomalurus, underline the utility of mitochondrial sequences in the resolution of even relatively deep divergences and go some way to explaining the difficulty of conclusively resolving higher-level relationships within Glires with available data and methodologies
Cardiac hypertrophy is inhibited by a local pool of cAMP regulated by phosphodiesterase 2
Rationale: Chronic elevation of 3'-5'-cyclic adenosine monophosphate (cAMP) levels has been associated with cardiac remodelling and cardiac hypertrophy. However, enhancement of particular aspects of cAMP/protein kinase A (PKA) signalling appears to be beneficial for the failing heart. cAMP is a pleiotropic second messenger with the ability to generate multiple functional outcomes in response to different extracellular stimuli with strict fidelity, a feature that relies on the spatial segregation of the cAMP pathway components in signalling microdomains.
Objective: How individual cAMP microdomains impact on cardiac pathophysiology remains largely to be established. The cAMP-degrading enzymes phosphodiesterases (PDEs) play a key role in shaping local changes in cAMP. Here we investigated the effect of specific inhibition of selected PDEs on cardiac myocyte hypertrophic growth.
Methods and Results: Using pharmacological and genetic manipulation of PDE activity we found that the rise in cAMP resulting from inhibition of PDE3 and PDE4 induces hypertrophy whereas increasing cAMP levels via PDE2 inhibition is anti-hypertrophic. By real-time imaging of cAMP levels in intact myocytes and selective displacement of PKA isoforms we demonstrate that the anti-hypertrophic effect of PDE2 inhibition involves the generation of a local pool of cAMP and activation of a PKA type II subset leading to phosphorylation of the nuclear factor of activated T cells (NFAT).
Conclusions: Different cAMP pools have opposing effects on cardiac myocyte cell size. PDE2 emerges as a novel key regulator of cardiac hypertrophy in vitro and in vivo and its inhibition may have therapeutic applications
A combined first and second order variational approach for image reconstruction
In this paper we study a variational problem in the space of functions of
bounded Hessian. Our model constitutes a straightforward higher-order extension
of the well known ROF functional (total variation minimisation) to which we add
a non-smooth second order regulariser. It combines convex functions of the
total variation and the total variation of the first derivatives. In what
follows, we prove existence and uniqueness of minimisers of the combined model
and present the numerical solution of the corresponding discretised problem by
employing the split Bregman method. The paper is furnished with applications of
our model to image denoising, deblurring as well as image inpainting. The
obtained numerical results are compared with results obtained from total
generalised variation (TGV), infimal convolution and Euler's elastica, three
other state of the art higher-order models. The numerical discussion confirms
that the proposed higher-order model competes with models of its kind in
avoiding the creation of undesirable artifacts and blocky-like structures in
the reconstructed images -- a known disadvantage of the ROF model -- while
being simple and efficiently numerically solvable.Comment: 34 pages, 89 figure
A CANDLE for a deeper in-vivo insight
A new Collaborative Approach for eNhanced Denoising under Low-light Excitation (CANDLE) is introduced for the processing of 3D laser scanning multiphoton microscopy images. CANDLE is designed to be robust for low signal-to-noise ratio (SNR) conditions typically encountered when imaging deep in scattering biological specimens. Based on an optimized non-local means filter involving the comparison of filtered patches, CANDLE locally adapts the amount of smoothing in order to deal with the noise inhomogeneity inherent to laser scanning fluorescence microscopy images. An extensive validation on synthetic data, images acquired on microspheres and in vivo images is presented. These experiments show that the CANDLE filter obtained competitive results compared to a state-of-the-art method and a locally adaptive optimized non-local means filter, especially under low SNR conditions (PSNR < 8 dB). Finally, the deeper imaging capabilities enabled by the proposed filter are demonstrated on deep tissue in vivo images of neurons and fine axonal processes in the Xenopus tadpole brain.We want to thank Florian Luisier for providing free plugin of his PureDenoise filter. We also want to thank Markku Makitalo for providing the code of their OVST. This study was supported by the Canadian Institutes of Health Research (CIHR, MOP-84360 to DLC and MOP-77567 to ESR) and Cda (CECR)-Gevas-OE016. MM holds a fellowship from the Deutscher Akademischer Austasch Dienst (DAAD) and a McGill Principal's Award. ESR is a tier 2 Canada Research Chair. This work has been partially supported by the Spanish Health Institute Carlos III through the RETICS Combiomed, RD07/0067/2001. This work benefited from the use of ImageJ.Coupé, P.; Munz, M.; Manjón Herrera, JV.; Ruthazer, ES.; Collins, DL. (2012). A CANDLE for a deeper in-vivo insight. Medical Image Analysis. 16(4):849-864. https://doi.org/10.1016/j.media.2012.01.002S84986416
Differential Inhibitory Effects of CysLT1 Receptor Antagonists on P2Y6 Receptor-Mediated Signaling and Ion Transport in Human Bronchial Epithelia
BACKGROUND: Cysteinyl leukotriene (CysLT) is one of the proinflammatory mediators released by the bronchi during inflammation. CysLTs exert their biological effects via specific G-protein-coupled receptors. CysLT(1) receptor antagonists are available for clinical use for the treatment of asthma. Recently, crosstalk between CysLT(1) and P2Y(6) receptors has been delineated. P2Y receptors are expressed in apical and/or basolateral membranes of virtually all polarized epithelia to control the transport of fluid and electrolytes. Previous research suggests that CysLT(1) receptor antagonists inhibit the effects of nucleotides acting at P2Y receptors. However, the detailed molecular mechanism underlying the inhibition remains unresolved. METHODOLOGY/PRINCIPAL FINDINGS: In this study, western blot analysis confirmed that both CysLT(1) and P2Y(6) receptors were expressed in the human bronchial epithelial cell line 16HBE14o-. All three CysLT(1) antagonists inhibited the uridine diphosphate (UDP)-evoked I(SC), but only montelukast inhibited the UDP-evoked [Ca(2+)](i) increase. In the presence of forskolin or 8-bromoadenosine 3'5' cyclic monophosphate (8-Br-cAMP), the UDP-induced I(SC) was potentiated but was reduced by pranlukast and zafirlukast but not montelukast. Pranlukast inhibited the UDP-evoked I(SC) potentiated by an Epac activator, 8-(4-Chlorophenylthio)-2'-O-methyladenosine-3',5'-cyclic monophosphate (8-CPT-2'-O-Me-cAMP), while montelukast and zafirlukast had no such effect. Pranlukast inhibited the real-time increase in cAMP changes activated by 8-CPT-2'-O-Me-cAMP as monitored by fluorescence resonance energy transfer imaging. Zafirlukast inhibited the UDP-induced I(SC) potentiated by N(6)-Phenyladenosine-3',5'-cyclic monophosphorothioate, Sp-isomer (Sp-6-Phe-cAMP; a PKA activator) and UDP-activated PKA activity. CONCLUSIONS/SIGNIFICANCE: In summary, our data strongly suggest for the first time that in human airway epithelia, the three specific CysLT(1) receptor antagonists exert differential inhibitory effects on P2Y(6) receptor-coupled Ca(2+) signaling pathways and the potentiating effect on I(SC) mediated by cAMP and Epac, leading to the modulation of ion transport activities across the epithelia
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