182 research outputs found
Discrete Convex Functions on Graphs and Their Algorithmic Applications
The present article is an exposition of a theory of discrete convex functions
on certain graph structures, developed by the author in recent years. This
theory is a spin-off of discrete convex analysis by Murota, and is motivated by
combinatorial dualities in multiflow problems and the complexity classification
of facility location problems on graphs. We outline the theory and algorithmic
applications in combinatorial optimization problems
Wiretapping a hidden network
We consider the problem of maximizing the probability of hitting a
strategically chosen hidden virtual network by placing a wiretap on a single
link of a communication network. This can be seen as a two-player win-lose
(zero-sum) game that we call the wiretap game. The value of this game is the
greatest probability that the wiretapper can secure for hitting the virtual
network. The value is shown to equal the reciprocal of the strength of the
underlying graph.
We efficiently compute a unique partition of the edges of the graph, called
the prime-partition, and find the set of pure strategies of the hider that are
best responses against every maxmin strategy of the wiretapper. Using these
special pure strategies of the hider, which we call
omni-connected-spanning-subgraphs, we define a partial order on the elements of
the prime-partition. From the partial order, we obtain a linear number of
simple two-variable inequalities that define the maxmin-polytope, and a
characterization of its extreme points.
Our definition of the partial order allows us to find all equilibrium
strategies of the wiretapper that minimize the number of pure best responses of
the hider. Among these strategies, we efficiently compute the unique strategy
that maximizes the least punishment that the hider incurs for playing a pure
strategy that is not a best response. Finally, we show that this unique
strategy is the nucleolus of the recently studied simple cooperative spanning
connectivity game
Model for the hydration of non-polar compounds and polymers
We introduce an exactly solvable statistical-mechanical model of the
hydration of non-polar compounds, based on grouping water molecules in clusters
where hydrogen bonds and isotropic interactions occur; interactions between
clusters are neglected. Analytical results show that an effective strengthening
of hydrogen bonds in the presence of the solute, together with a geometric
reorganization of water molecules, are enough to yield hydrophobic behavior. We
extend our model to describe a non-polar homopolymer in aqueous solution,
obtaining a clear evidence of both ``cold'' and ``warm'' swelling transitions.
This suggests that our model could be relevant to describe some features of
protein folding.Comment: REVTeX, 6 pages, 3 figure
Structured Sparsity: Discrete and Convex approaches
Compressive sensing (CS) exploits sparsity to recover sparse or compressible
signals from dimensionality reducing, non-adaptive sensing mechanisms. Sparsity
is also used to enhance interpretability in machine learning and statistics
applications: While the ambient dimension is vast in modern data analysis
problems, the relevant information therein typically resides in a much lower
dimensional space. However, many solutions proposed nowadays do not leverage
the true underlying structure. Recent results in CS extend the simple sparsity
idea to more sophisticated {\em structured} sparsity models, which describe the
interdependency between the nonzero components of a signal, allowing to
increase the interpretability of the results and lead to better recovery
performance. In order to better understand the impact of structured sparsity,
in this chapter we analyze the connections between the discrete models and
their convex relaxations, highlighting their relative advantages. We start with
the general group sparse model and then elaborate on two important special
cases: the dispersive and the hierarchical models. For each, we present the
models in their discrete nature, discuss how to solve the ensuing discrete
problems and then describe convex relaxations. We also consider more general
structures as defined by set functions and present their convex proxies.
Further, we discuss efficient optimization solutions for structured sparsity
problems and illustrate structured sparsity in action via three applications.Comment: 30 pages, 18 figure
Decomposition algorithms for submodular optimization with applications to parallel machine scheduling with controllable processing times
In this paper we present a decomposition algorithm for maximizing a linear function over a submodular polyhedron intersected with a box. Apart from this contribution to submodular optimization, our results extend the toolkit available in deterministic machine scheduling with controllable processing times. We demonstrate how this method can be applied to developing fast algorithms for minimizing total compression cost for preemptive schedules on parallel machines with respect to given release dates and a common deadline. Obtained scheduling algorithms are faster and easier to justify than those previously known in the scheduling literature
A Fluorescent Chromatophore Changes the Level of Fluorescence in a Reef Fish
Body coloration plays a major role in fish ecology and is predominantly generated using two principles: a) absorbance combined with reflection of the incoming light in pigment colors and b) scatter, refraction, diffraction and interference in structural colors. Poikilotherms, and especially fishes possess several cell types, so-called chromatophores, which employ either of these principles. Together, they generate the dynamic, multi-color patterns used in communication and camouflage. Several chromatophore types possess motile organelles, which enable rapid changes in coloration. Recently, we described red fluorescence in a number of marine fish and argued that it may be used for private communication in an environment devoid of red. Here, we describe the discovery of a chromatophore in fishes that regulates the distribution of fluorescent pigments in parts of the skin. These cells have a dendritic shape and contain motile fluorescent particles. We show experimentally that the fluorescent particles can be aggregated or dispersed through hormonal and nervous control. This is the first description of a stable and natural cytoskeleton-related fluorescence control mechanism in vertebrate cells. Its nervous control supports suggestions that fluorescence could act as a context-dependent signal in some marine fish species and encourages further research in this field. The fluorescent substance is stable under different chemical conditions and shows no discernible bleaching under strong, constant illumination
Phosphodiesterase 10A Upregulation Contributes to Pulmonary Vascular Remodeling
Phosphodiesterases (PDEs) modulate the cellular proliferation involved in the pathophysiology of pulmonary hypertension (PH) by hydrolyzing cAMP and cGMP. The present study was designed to determine whether any of the recently identified PDEs (PDE7-PDE11) contribute to progressive pulmonary vascular remodeling in PH. All in vitro experiments were performed with lung tissue or pulmonary arterial smooth muscle cells (PASMCs) obtained from control rats or monocrotaline (MCT)-induced pulmonary hypertensive (MCT-PH) rats, and we examined the effects of the PDE10 inhibitor papaverine (Pap) and specific small interfering RNA (siRNA). In addition, papaverine was administrated to MCT-induced PH rats from day 21 to day 35 by continuous intravenous infusion to examine the in vivo effects of PDE10A inhibition. We found that PDE10A was predominantly present in the lung vasculature, and the mRNA, protein, and activity levels of PDE10A were all significantly increased in MCT PASMCs compared with control PASMCs. Papaverine and PDE10A siRNA induced an accumulation of intracellular cAMP, activated cAMP response element binding protein and attenuated PASMC proliferation. Intravenous infusion of papaverine in MCT-PH rats resulted in a 40%–50% attenuation of the effects on pulmonary hypertensive hemodynamic parameters and pulmonary vascular remodeling. The present study is the first to demonstrate a central role of PDE10A in progressive pulmonary vascular remodeling, and the results suggest a novel therapeutic approach for the treatment of PH
Rhizobium Promotes Non-Legumes Growth and Quality in Several Production Steps: Towards a Biofertilization of Edible Raw Vegetables Healthy for Humans
The biofertilization of crops with plant-growth-promoting microorganisms is currently considered as a healthy alternative to chemical fertilization. However, only microorganisms safe for humans can be used as biofertilizers, particularly in vegetables that are raw consumed, in order to avoid sanitary problems derived from the presence of pathogenic bacteria in the final products. In the present work we showed that Rhizobium strains colonize the roots of tomato and pepper plants promoting their growth in different production stages increasing yield and quality of seedlings and fruits. Our results confirmed those obtained in cereals and alimentary oil producing plants extending the number of non-legumes susceptible to be biofertilized with rhizobia to those whose fruits are raw consumed. This is a relevant conclusion since safety of rhizobia for human health has been demonstrated after several decades of legume inoculation ensuring that they are optimal bacteria for biofertilization
Subcellular Location of PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny Dendrites
Dopamine release in the striatum has been implicated in various forms of reward dependent learning. Dopamine leads to production of cAMP and activation of protein kinase A (PKA), which are involved in striatal synaptic plasticity and learning. PKA and its protein targets are not diffusely located throughout the neuron, but are confined to various subcellular compartments by anchoring molecules such as A-Kinase Anchoring Proteins (AKAPs). Experiments have shown that blocking the interaction of PKA with AKAPs disrupts its subcellular location and prevents LTP in the hippocampus and striatum; however, these experiments have not revealed whether the critical function of anchoring is to locate PKA near the cAMP that activates it or near its targets, such as AMPA receptors located in the post-synaptic density. We have developed a large scale stochastic reaction-diffusion model of signaling pathways in a medium spiny projection neuron dendrite with spines, based on published biochemical measurements, to investigate this question and to evaluate whether dopamine signaling exhibits spatial specificity post-synaptically. The model was stimulated with dopamine pulses mimicking those recorded in response to reward. Simulations show that PKA colocalization with adenylate cyclase, either in the spine head or in the dendrite, leads to greater phosphorylation of DARPP-32 Thr34 and AMPA receptor GluA1 Ser845 than when PKA is anchored away from adenylate cyclase. Simulations further demonstrate that though cAMP exhibits a strong spatial gradient, diffusible DARPP-32 facilitates the spread of PKA activity, suggesting that additional inactivation mechanisms are required to produce spatial specificity of PKA activity
Selective phosphodiesterase inhibitors: a promising target for cognition enhancement
# The Author(s) 2008. This article is published with open access at Springerlink.com Rationale One of the major complaints most people face during aging is an impairment in cognitive functioning. This has a negative impact on the quality of daily life and is even more prominent in patients suffering from neurodegenerative and psychiatric disorders including Alzheimer’s disease, schizophrenia, and depression. So far, the majority of cognition enhancers are generally targeting one particular neurotransmitter system. However, recently phosphodiesterases (PDEs) have gained increased attention as a potential new target for cognition enhancement. Inhibition of PDEs increases the intracellular availability of the second messengers cGMP and/or cAMP. Objective The aim of this review was to provide an overvie
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