Algorithms for Maneuvering Spacecraft Around Small Bodies

A document describes mathematical derivations and applications of autonomous guidance algorithms for maneuvering spacecraft in the vicinities of small astronomical bodies like comets or asteroids. These algorithms compute fuel- or energy-optimal trajectories for typical maneuvers by solving the associated optimal-control problems with relevant control and state constraints. In the derivations, these problems are converted from their original continuous (infinite-dimensional) forms to finite-dimensional forms through (1) discretization of the time axis and (2) spectral discretization of control inputs via a finite number of Chebyshev basis functions. In these doubly discretized problems, the Chebyshev coefficients are the variables. These problems are, variously, either convex programming problems or programming problems that can be convexified. The resulting discrete problems are convex parameter-optimization problems; this is desirable because one can take advantage of very efficient and robust algorithms that have been developed previously and are well established for solving such problems. These algorithms are fast, do not require initial guesses, and always converge to global optima. Following the derivations, the algorithms are demonstrated by applying them to numerical examples of flyby, descent-to-hover, and ascent-from-hover maneuvers

Clustering with shallow trees

We propose a new method for hierarchical clustering based on the optimisation of a cost function over trees of limited depth, and we derive a message--passing method that allows to solve it efficiently. The method and algorithm can be interpreted as a natural interpolation between two well-known approaches, namely single linkage and the recently presented Affinity Propagation. We analyze with this general scheme three biological/medical structured datasets (human population based on genetic information, proteins based on sequences and verbal autopsies) and show that the interpolation technique provides new insight.Comment: 11 pages, 7 figure

Finding undetected protein associations in cell signaling by belief propagation

External information propagates in the cell mainly through signaling cascades and transcriptional activation, allowing it to react to a wide spectrum of environmental changes. High throughput experiments identify numerous molecular components of such cascades that may, however, interact through unknown partners. Some of them may be detected using data coming from the integration of a protein-protein interaction network and mRNA expression profiles. This inference problem can be mapped onto the problem of finding appropriate optimal connected subgraphs of a network defined by these datasets. The optimization procedure turns out to be computationally intractable in general. Here we present a new distributed algorithm for this task, inspired from statistical physics, and apply this scheme to alpha factor and drug perturbations data in yeast. We identify the role of the COS8 protein, a member of a gene family of previously unknown function, and validate the results by genetic experiments. The algorithm we present is specially suited for very large datasets, can run in parallel, and can be adapted to other problems in systems biology. On renowned benchmarks it outperforms other algorithms in the field.Comment: 6 pages, 3 figures, 1 table, Supporting Informatio

Inference algorithms for gene networks: a statistical mechanics analysis

The inference of gene regulatory networks from high throughput gene expression data is one of the major challenges in systems biology. This paper aims at analysing and comparing two different algorithmic approaches. The first approach uses pairwise correlations between regulated and regulating genes; the second one uses message-passing techniques for inferring activating and inhibiting regulatory interactions. The performance of these two algorithms can be analysed theoretically on well-defined test sets, using tools from the statistical physics of disordered systems like the replica method. We find that the second algorithm outperforms the first one since it takes into account collective effects of multiple regulators

Effets du dérangement par la chasse sur les oiseaux d'eau : revue de littérature

La chasse aux oiseaux d'eau, activité humaine largement pratiquée sur les zones humides du continent eurasiatique, présente deux composantes pouvant affecter la dynamique des populations de ces espèces migratrices : le prélèvement (qui concerne la mortalité) et le dérangement. Ce dernier aspect fait l'objet d'études de plus en plus nombreuses et détaillées, ici synthétisées, incluant des protocoles expérimentaux et des approches conceptuelles. Le dérangement par la chasse est considéré comme important pour une espèce lorsque les modifications qu'il induit ont un effet sur la « fitness » des individus de cette espèce (diminution de la survie et/ou du succès reproducteur). Les études montrent que le dérangement modifie presque toujours la distribution géographique des oiseaux en favorisant leur regroupement (5 à 50 fois plus) sur des espaces non chassés, induisant une sous-exploitation des ressources trophiques présentes sur les espaces chassés. Le dérangement peut aussi provoquer un accroissement du taux de renouvellement (« turnover ») des individus sur leur étape migratoire. Ces transferts d'oiseaux, bien quantifiés localement, ont un impact encore inconnu sur la taille des populations concernées, la large distribution de ces populations sur plusieurs continents rendant cette évaluation difficile. Le dérangement provoque une modification comportementale soit en favorisant des activités plus coûteuses que celles pratiquées sans dérangement, soit en diminuant le temps passé à des activités qui permettent d'acquérir de l'énergie. Les estimations ou simulations de ces pertes peuvent atteindre 25 % de la dépense énergétique journalière. Les oiseaux dérangés développent des capacités d'adaptation physiologique face aux contraintes associées au dérangement, par exemple une augmentation de la prise alimentaire, une augmentation du rendement de l'assimilation énergétique ou une augmentation de la sécrétion de corticostérone qui stimule l'activité de recherche de nourriture. L'évaluation directe du bilan énergétique de ces adaptations n'a pas encore été réalisée et l'on peut admettre qu'elles permettent à l'oiseau de maintenir un apport énergétique analogue à celui obtenu sans dérangement; mais le coût à terme de cette acquisition est élevé. Ainsi, une étude récente sur la Grande Oie des neiges Anser caerules-cens atlantica au Canada révèle que lorsque les individus sont dérangés par la chasse sur leur étape migratoire de printemps, ils sont contraints d'exploiter des sites moins riches que s'il n'y avait pas de chasse; ils sont alors dans de moins bonnes conditions corporelles (lipidiques et protéiniques) lors du départ vers leurs lieux de reproduction et ils ont finalement un moindre succès de reproduction que les individus n'ayant pas subi le dérangement par la chasse. Certes, des lacunes et des incertitudes persistent, par exemple au niveau spécifique (peu d'études sur les limicoles), mais tous les auteurs qui les ont mises en évidence s'accordent aussi pour reconnaître que, pour contrebalancer les effets du dérangement par la chasse, des mesures de protection doivent être prises.Waterbird hunting is a widespread human activity over wetlands of the Eurasian continent. It has two components that can influence the population dynamics of migratory species : mortality and disturbance. Disturbance is the focus of an increasing number of detailed studies, using both experimental and theoretical approaches. They are synthesized herein. Disturbance is considered important when induced changes influence the fitness of the individuals of a species (decrease in survival or breeding success). Studies show that disturbance almost always change the geographical distribution of birds, conducting to an under-exploitation of food resources available in hunting areas. Disturbance can also favour an increase in the turnover rate of individuals on their migratory stopover. These changes in bird distribution, although precisely quantified at a local scale, have an unknown impact on the population size of the concerned species. The wide distribution of several of these species ranging over several continents makes the precise evaluation of this impact difficult. Disturbance changes behaviour either by increasing time spent in activities more costly than those done without disturbance or by decreasing time spent gaining energy. Estimation or simulation of these lost can reach 25% of the daily energy expenses. Facing disturbance, birds can develop several physiological adaptations, for instance an increased food intake, an increased efficiency of energy assimilation or an augmentation of corticosterone secretion stimulating food searching. The direct evaluation of the energy balance of these adaptations has not been made yet and it can be acknowledged that they allow birds to maintain energy gains similar to those obtained without disturbance. However, the long-term cost of this compensation is high. A recent study of the Greater Snow Goose Anser caerulescens atlantica on their spring stopover in Canada indicates that hunting disturbance makes geese use lower quality habitats, decreases their body condition (fat and protein) when they depart to the breeding sites and decreases their breeding success relative to individuals that have not experienced hunting. Uncertainties remain, for instance at the species level (few studies on waders), but all authors that emphasized them also agree to acknowledge that protection measures must be taken to counter-balance the effects of hunting disturbance. They recommend the increase of protected areas (hunt-free areas), the elaboration of a network of reserves and the establishment of non hunted zones around existing reserves to reduce to the minimum the negative effects of disturbance on birds that use these reserves. The implementation of these management actions must favour the widening of the distribution of these populations and facilitate the local and regional increase of their numbers. These protection measures are positive responses to the recommendations of the European Union birds and habitats directives

Cancer targeting with biomolecules: a comparative study of photodynamic therapy efficacy using antibody or lectin conjugated phthalocyanine-PEG gold nanoparticles

The functionalisation of therapeutic nanoparticle constructs with cancer-specific biomolecules can enable selective tumour accumulation and targeted treatment. Water soluble gold nanoparticles (ca. 4 nm) stabilised by a mixed monolayer of a hydrophobic zinc phthalocyanine photosensitiser (C11Pc) and hydrophilic polyethylene glycol (PEG) have been prepared. The C11Pc-PEG gold nanoparticle constructs were further functionalised with jacalin, a lectin specific for the cancer-associated Thomsen–Friedenreich (T) carbohydrate antigen, or with monoclonal antibodies specific for the human epidermal growth factor receptor-2 (HER-2). The two biofunctionalised nanoparticle conjugates produced similar levels of singlet oxygen upon irradiation at 633 nm. Importantly, both nanoparticle conjugates demonstrated extensive, yet comparable, phototoxicity in HT-29 colorectal adenocarcinoma cells (80–90%) and in SK-BR-3 breast adenocarcinoma cells (>99%). Non-conjugated C11Pc-PEG gold nanoparticles were only minimally phototoxic. Lysosomal colocalisation studies performed with the HT-29 colon cancer cells and the SK-BR-3 breast cancer cells revealed that both nanoparticle conjugates were partially localised within acidic organelles, which is typical of receptor-mediated endocytosis. The similarity of the targeted PDT efficacy of the two biofunctionalised C11Pc-PEG gold nanoparticles is discussed with respect to targeting ligand binding affinity and cell surface antigen density as key determinants of targeting efficiency. This study highlights how targeting small cell-surface molecules, such as the T antigen, can mediate a selective photodynamic treatment response which is similar to that achieved when targeting overexpressed protein receptors, such as HER-2. The high prevalence of the T antigen present on the cellular surface of primary tumours emphasises the broad potential applications for lectin-targeted therapies

Beyond inverse Ising model: structure of the analytical solution for a class of inverse problems

I consider the problem of deriving couplings of a statistical model from measured correlations, a task which generalizes the well-known inverse Ising problem. After reminding that such problem can be mapped on the one of expressing the entropy of a system as a function of its corresponding observables, I show the conditions under which this can be done without resorting to iterative algorithms. I find that inverse problems are local (the inverse Fisher information is sparse) whenever the corresponding models have a factorized form, and the entropy can be split in a sum of small cluster contributions. I illustrate these ideas through two examples (the Ising model on a tree and the one-dimensional periodic chain with arbitrary order interaction) and support the results with numerical simulations. The extension of these methods to more general scenarios is finally discussed.Comment: 15 pages, 6 figure

First astronomical unit scale image of the GW Ori triple. Direct detection of a new stellar companion

Young and close multiple systems are unique laboratories to probe the initial dynamical interactions between forming stellar systems and their dust and gas environment. Their study is a key building block to understanding the high frequency of main-sequence multiple systems. However, the number of detected spectroscopic young multiple systems that allow dynamical studies is limited. GW Orionis is one such system. It is one of the brightest young T Tauri stars and is surrounded by a massive disk. Our goal is to probe the GW Orionis multiplicity at angular scales at which we can spatially resolve the orbit. We used the IOTA/IONIC3 interferometer to probe the environment of GW Orionis with an astronomical unit resolution in 2003, 2004, and 2005. By measuring squared visibilities and closure phases with a good UV coverage we carry out the first image reconstruction of GW Ori from infrared long-baseline interferometry. We obtain the first infrared image of a T Tauri multiple system with astronomical unit resolution. We show that GW Orionis is a triple system, resolve for the first time the previously known inner pair (separation $\rho\sim$1.4 AU) and reveal a new more distant component (GW Ori C) with a projected separation of $\sim$8 AU with direct evidence of motion. Furthermore, the nearly equal (2:1) H-band flux ratio of the inner components suggests that either GW Ori B is undergoing a preferential accretion event that increases its disk luminosity or that the estimate of the masses has to be revisited in favour of a more equal mass-ratio system that is seen at lower inclination. Accretion disk models of GW Ori will need to be completely reconsidered because of this outer companion C and the unexpected brightness of companion B.Comment: 5 pages, 9 figures, accepted Astronomy and Astrophysics Letters. 201

Reverse Engineering Gene Networks with ANN: Variability in Network Inference Algorithms

Motivation :Reconstructing the topology of a gene regulatory network is one of the key tasks in systems biology. Despite of the wide variety of proposed methods, very little work has been dedicated to the assessment of their stability properties. Here we present a methodical comparison of the performance of a novel method (RegnANN) for gene network inference based on multilayer perceptrons with three reference algorithms (ARACNE, CLR, KELLER), focussing our analysis on the prediction variability induced by both the network intrinsic structure and the available data. Results: The extensive evaluation on both synthetic data and a selection of gene modules of "Escherichia coli" indicates that all the algorithms suffer of instability and variability issues with regards to the reconstruction of the topology of the network. This instability makes objectively very hard the task of establishing which method performs best. Nevertheless, RegnANN shows MCC scores that compare very favorably with all the other inference methods tested. Availability: The software for the RegnANN inference algorithm is distributed under GPL3 and it is available at the corresponding author home page (http://mpba.fbk.eu/grimaldi/regnann-supmat