
Donoso, R. A., PerezPantoja, D., & Gonzalez, B. (2011). Strict and direct transcriptional repression of the pobA gene by benzoate avoids 4hydroxybenzoate degradation in the pollutant degrader bacterium Cupriavidus necator JMP134. Environ. Microbiol., 13(6), 1590–1600.
Abstract: As other environmental bacteria, Cupriavidus necator JMP134 uses benzoate as preferred substrate in mixtures with 4hydroxybenzoate, strongly inhibiting its degradation. The mechanism underlying this hierarchical use was studied. A C. necator benA mutant, defective in the first step of benzoate degradation, is unable to metabolize 4hydroxybenzoate when benzoate is also included in the medium, indicating that this substrate and not one of its catabolic intermediates is directly triggering repression. Reverse transcription polymerase chain reaction analysis revealed that 4hydroxybenzoate 3hydroxylaseencoding pobA transcripts are nearly absent in presence of benzoate and a fusion of pobA promoter to lacZ reporter confirmed that benzoate drastically decreases the transcription of this gene. Expression of pobA driven by a heterologous promoter in C. necator benA mutant, allows growth on 4hydroxybenzoate in presence of benzoate, overcoming its repressive effect. In contrast with other bacteria, regulators of benzoate catabolism do not participate in repression of 4hydroxybenzoate degradation. Moreover, the effect of benzoate on pobA promoter can be observed in heterologous strains with the sole presence of PobR, the transcriptional activator of pobA gene, indicating that PobR is enough to fully reproduce the phenomenon. This novel mechanism for benzoate repression is probably mediated by direct action of benzoate over PobR.



Dumais, J. (2013). Modes of deformation of walled cells. J. Exp. Bot., 64(15), 4681–4695.
Abstract: The bewildering morphological diversity found in cells is one of the starkest illustrations of lifes ability to selforganize. Yet the morphogenetic mechanisms that produce the multifarious shapes of cells are still poorly understood. The shared similarities between the walled cells of prokaryotes, many protists, fungi, and plants make these groups particularly appealing to begin investigating how morphological diversity is generated at the cell level. In this review, I attempt a first classification of the different modes of surface deformation used by walled cells. Five modes of deformation were identified: inextensional bending, equiarea shear, elastic stretching, processive intussusception, and chemorheological growth. The two most restrictive modesuinextensional and equiarea deformationsuare embodied in the exine of pollen grains and the walllike pellicle of euglenoids, respectively. For these modes, it is possible to express the deformed geometry of the cell explicitly in terms of the undeformed geometry and other easily observable geometrical parameters. The greatest morphogenetic power is reached with the processive intussusception and chemorheological growth mechanisms that underlie the expansive growth of walled cells. A comparison of these two growth mechanisms suggests a possible way to tackle the complexity behind wall growth.



During, G., Josserand, C., & Rica, S. (2015). Selfsimilar formation of an inverse cascade in vibrating elastic plates. Phys. Rev. E, 91(5), 10 pp.
Abstract: The dynamics of random weakly nonlinear waves is studied in the framework of vibrating thin elastic plates. Although it has been previously predicted that no stationary inverse cascade of constant wave action flux could exist in the framework of wave turbulence for elastic plates, we present substantial evidence of the existence of a timedependent inverse cascade, opening up the possibility of selforganization for a larger class of systems. This inverse cascade transports the spectral density of the amplitude of the waves from short up to large scales, increasing the distribution of long waves despite the shortwave fluctuations. This dynamics appears to be selfsimilar and possesses a powerlaw behavior in the shortwavelength limit which significantly differs from the exponent obtained via a Kolmogorov dimensional analysis argument. Finally, we show explicitly a tendency to build a longwave coherent structure in finite time.



During, G., Josserand, C., & Rica, S. (2017). Wave turbulence theory of elastic plates. Physica D, 347, 42–73.
Abstract: This article presents the complete study of the longtime evolution of random waves of a vibrating thin elastic plate in the limit of small plate deformation so that modes of oscillations interact weakly. According to the wave turbulence theory a nonlinear wave system evolves in longtime creating a slow redistribution of the spectral energy from one mode to another. We derive step by step, following the method of cumulants expansion and multiscale asymptotic perturbations, the kinetic equation for the second order cumulants as well as the second and fourth order renormalization of the dispersion relation of the waves. We characterize the nonequilibrium evolution to an equilibrium wave spectrum, which happens to be the well known RayleighJeans distribution. Moreover we show the existence of an energy cascade, often called the KolmogorovZakharov spectrum, which happens to be not simply a power law, but a logarithmic correction to the Rayleigh Jeans distribution. We perform numerical simulations confirming these scenarii, namely the equilibrium relaxation for closed systems and the existence of an energy cascade wave spectrum. Both show a good agreement between theoretical predictions and numerics. We show also some other relevant features of vibrating elastic plates, such as the existence of a selfsimilar wave action inverse cascade which happens to blowup in finite time. We discuss the mechanism of the wave breakdown phenomena in elastic plates as well as the limit of strong turbulence which arises as the thickness of the plate vanishes. Finally, we discuss the role of dissipation and the connection with experiments, and the generalization of the wave turbulence theory to elastic shells. (C) 2017 Elsevier B.V. All rights reserved.



During, G., Picozzi, A., & Rica, S. (2009). Breakdown of weakturbulence and nonlinear wave condensation. Physica D, 238(16), 1524–1549.
Abstract: The formation of a largescale coherent structure (a condensate) as a result of the long time evolution of the initial value problem of a classical partial differential nonlinear wave equation is considered. We consider the nonintegrable and unforced defocusing NonLinear Schrodinger (NLS) equation as a representative model. In spite of the formal reversibility of the NLS equation, the nonlinear wave exhibits an irreversible evolution towards a thermodynamic equilibrium state. The equilibrium state is characterized by a homogeneous solution (condensate), with smallscale fluctuations superposed (uncondensed particles), which store the information necessary for “time reversal”. We analyze the evolution Of the cumulants of the random wave as originally formulated by DJ. Benney and P.G. Saffman [D.J. Bentley, P.G. Saffman, Proc. Roy. Soc. London A 289 (1966) 301] and A.C. Newell [A.C. Newell, Rev. Geophys. 6 (1968) 1]. This allows us to provide a selfconsistent weakturbulence theory of the condensation process, in which the nonequilibrium formation of the condensate is a natural consequence of the spontaneous regeneration of a nonvanishing firstorder cumulant in the hierarchy of the cumulants' equations. More precisely, we show that in the presence of a small condensate amplitude, all relevant statistical information is contained in the offdiagonal second order cumulant, as described by the usual weakturbulence theory. Conversely, in the presence of a highamplitude condensate, the diagonal secondorder cumulants no longer vanish in the long time limit, which signals a breakdown of the weakturbulence theory. However, we show that all asymptotic closure of the hierarchy of the cumulants' equations is still possible provided one considers the Bogoliubov's basis rather than the standard Fourier's (free particle) basis. The nonequilibrium dynamics turns out to be governed by the Bogoliubov's offdiagonal second order cumulant, while the corresponding diagonal cumulants, as well as the higher order cumulants, are shown to vanish asymptotically. The numerical discretization of the NLS equation implicitly introduces an ultraviolet frequency cutoff. The simulations are in quantitative agreement with the weak turbulence theory without adjustable parameters, despite the fact that the theory is expected to breakdown nearby the transition to condensation. The fraction of condensed particles vs energy is characterized by two distinct regimes: For small energies (H << Hc) the Bogoliubov's regime is established, whereas for H less than or similar to Hc the smallamplitude condensate regime is described by the weakturbulence theory. In both regimes we derive coupled kinetic equations that describe the coupled evolution of the condensate amplitude and the incoherent field component. The influence of finite size effects and of the dimensionality of the system are also considered. It is shown that, beyond the thermodynamic limit, wave condensation is reestablished in two spatial dimensions, in complete analogy with uniform and ideal 2D Bose gases. (C) 2009 Elsevier B.V. All rights reserved.



Efraimidis, I., Gaona, J., Hernandez, R., & Venegas, O. (2017). On harmonic Blochtype mappings. Complex Var. Elliptic Equ., 62(8), 1081–1092.
Abstract: Let f be a complexvalued harmonicmapping defined in the unit disk D. We introduce the following notion: we say that f is a Blochtype function if its Jacobian satisfies This gives rise to a new class of functions which generalizes and contains the wellknown analytic Bloch space. We give estimates for the schlicht radius, the growth and the coefficients of functions in this class. We establish an analogue of the theorem which, roughly speaking, states that for. analytic log. is Bloch if and only if. is univalent.



Ekman, R., Asenjo, F. A., & Zamanian, J. (2017). Relativistic kinetic equation for spin1/2 particles in the longscalelength approximation. Phys. Rev. E, 96(2), 8 pp.
Abstract: In this paper, we derive a fully relativistic kinetic theory for spin1/2 particles and its coupling to Maxwell's equations, valid in the longscalelength limit, where the fields vary on a scale much longer than the localization of the particles; we work to first order in (h) over bar. Our starting point is a FoldyWouthuysen (FW) transformation, applicable to this regime, of the Dirac Hamiltonian. We derive the corresponding evolution equation for the Wigner quasidistribution in an external electromagnetic field. Using a Lagrangian method we find expressions for the charge and current densities, expressed as free and bound parts. It is furthermore found that the velocity is nontrivially related to the momentum variable, with the difference depending on the spin and the external electromagnetic fields. This fact that has previously been discussed as “hidden momentum” and is due to that the FW transformation maps pointlike particles to particle clouds for which the prescription of minimal coupling is incorrect, as they have multipole moments. We express energy and momentum conservation for the system of particles and the electromagnetic field, and discuss our results in the context of the AbrahamMinkowski dilemma.



Espinoza, D., & Moreno, E. (2014). A primaldual aggregation algorithm for minimizing conditional valueatrisk in linear programs. Comput. Optim. Appl., 59(3), 617–638.
Abstract: Recent years have seen growing interest in coherent risk measures, especially in Conditional ValueatRisk (). Since is a convex function, it is suitable as an objective for optimization problems when we desire to minimize risk. In the case that the underlying distribution has discrete support, this problem can be formulated as a linear programming (LP) problem. Over more general distributions, recent techniques, such as the sample average approximation method, allow to approximate the solution by solving a series of sampled problems, although the latter approach may require a large number of samples when the risk measures concentrate on the tail of the underlying distributions. In this paper we propose an automatic primaldual aggregation scheme to exactly solve these special structured LPs with a very large number of scenarios. The algorithm aggregates scenarios and constraints in order to solve a smaller problem, which is automatically disaggregated using the information of its dual variables. We compare this algorithm with other common approaches found in related literature, such as an improved formulation of the full problem, cutgeneration schemes and other problemspecific approaches available in commercial software. Extensive computational experiments are performed on portfolio and general LP instances.



Espinoza, D., Goycoolea, M., & Moreno, E. (2015). The precedence constrained knapsack problem: Separating maximally violated inequalities. Discret Appl. Math., 194, 65–80.
Abstract: We consider the problem of separating maximally violated inequalities for the precedence constrained knapsack problem. Though we consider maximally violated constraints in a very general way, special emphasis is placed on induced cover inequalities and induced clique inequalities. Our contributions include a new partial characterization of maximally violated inequalities, a new safe shrinking technique, and new insights on strengthening and lifting. This work follows on the work of Boyd (1993), Park and Park (1997), van de Leensel et al. (1999) and Boland et al. (2011). Computational experiments show that our new techniques and insights can be used to significantly improve the performance of cutting plane algorithms for this problem. (C) 2015 Elsevier B.V. All rights reserved.



Espinoza, D., Goycoolea, M., Moreno, E., & Newman, A. (2013). MineLib: a library of open pit mining problems. Ann. Oper. Res., 206(1), 93–114.
Abstract: Similar to the mixedinteger programming library (MIPLIB), we present a library of publicly available test problem instances for three classical types of open pit mining problems: the ultimate pit limit problem and two variants of open pit production scheduling problems. The ultimate pit limit problem determines a set of notional threedimensional blocks containing ore and/or waste material to extract to maximize value subject to geospatial precedence constraints. Open pit production scheduling problems seek to determine when, if ever, a block is extracted from an open pit mine. A typical objective is to maximize the net present value of the extracted ore; constraints include precedence and upper bounds on operational resource usage. Extensions of this problem can include (i) lower bounds on operational resource usage, (ii) the determination of whether a block is sent to a waste dump, i.e., discarded, or to a processing plant, i.e., to a facility that derives salable mineral from the block, (iii) average grade constraints at the processing plant, and (iv) inventories of extracted but unprocessed material. Although open pit mining problems have appeared in academic literature dating back to the 1960s, no standard representations exist, and there are no commonly available corresponding data sets. We describe some representative open pit mining problems, briefly mention related literature, and provide a library consisting of mathematical models and sets of instances, available on the Internet. We conclude with directions for use of this newly established mining library. The library serves not only as a suggestion of standard expressions of and available data for open pit mining problems, but also as encouragement for the development of increasingly sophisticated algorithms.



Farhan, A., Scholl, A., Petersen, C. F., Anghinolfi, L., Wuth, C., Dhuey, S., et al. (2016). Thermodynamics of emergent magnetic charge screening in artificial spin ice. Nat. Commun., 7, 6 pp.
Abstract: Electric charge screening is a fundamental principle governing the behaviour in a variety of systems in nature. Through reconfiguration of the local environment, the Coulomb attraction between electric charges is decreased, leading, for example, to the creation of polaron states in solids or hydration shells around proteins in water. Here, we directly visualize the realtime creation and decay of screened magnetic charge configurations in a twodimensional artificial spin ice system, the dipolar dice lattice. By comparing the temperature dependent occurrence of screened and unscreened emergent magnetic charge defects, we determine that screened magnetic charges are indeed a result of local energy reduction and appear as a transient minimum energy state before the system relaxes towards the predicted ground state. These results highlight the important role of emergent magnetic charges in artificial spin ice, giving rise to screened charge excitations and the emergence of exotic lowtemperature configurations.



FeoValero, M., GarciaMenendez, L., & GarridoHidalgo, R. (2011). Valuing Freight Transport Time using Transport Demand Modelling: A Bibliographical Review. Transp. Rev., 31(5), 625–651.
Abstract: The value of time for freight transport is of major importance in infrastructurerelated costbenefit analysis and yet its study has been largely neglected when compared with its passenger counterpart. In fact, one of the attributes that could decide the profitability of a project is how much can be saved if freight vehicles use new infrastructure. Despite being the primary benefit of most investments in transport infrastructure, researchers have not yet reached agreement over either the size or the nature of the values of time that should be used when evaluating projects. This article provides a review of the estimation of freight value of time through transport demand modelling and extant empirical evidence on this topic. Similarly, the bibliographic review of studies undertaken has allowed us to pinpoint the most critical issues when modelling freight transport demand and the position of various research teams regarding these aspects. Such issues include identifying the decisionmaker, heterogeneity in the transport flows and transport attributes considered by decisionmakers.



Fernandes, D., Pitie, F., Caceres, G., & Baeyens, J. (2012). Thermal energy storage: “How previous findings determine current research priorities”. Energy, 39(1), 246–257.
Abstract: Thermal energy storage is an expanding field within the subject of renewable energy technologies. After a listing of the different possibilities available for energy storage, this paper provides a comparison of various materials for High Temperature Thermal Energy Storage (HTTS). Several attributes and needs of each solution are listed. One in particular is using the latent heat as one of the most efficient ways to store thermal energy. The mixture of phase change material (PCM) embedded in a metal foam is optimising the thermal properties of the material for latent heat energy storage. The results of previous studies show that mechanical and thermal properties of foam were extensively studied separately. This paper highlights the potential for an advanced study of thermomechanical properties of metal foams embedded with PCM. (c) 2012 Elsevier Ltd. All rights reserved.



Fernandez, C., Valle, C., Saravia, F., & Allende, H. (2012). Behavior analysis of neural network ensemble algorithm on a virtual machine cluster. Neural Comput. Appl., 21(3), 535–542.
Abstract: Ensemble learning has gained considerable attention in different learning tasks including regression, classification, and clustering problems. One of the drawbacks of the ensemble is the high computational cost of training stages. Resampling local negative correlation (RLNC) is a technique that combines two wellknown methods to generate ensemble diversityresampling and error negative correlationand a finegrain parallel approach that allows us to achieve a satisfactory balance between accuracy and efficiency. In this paper, we introduce a structure of the virtual machine aimed to test diverse selection strategies of parameters in neural ensemble designs, such as RLNC. We assess the parallel performance of this approach on a virtual machine cluster based on the full virtualization paradigm, using speedup and efficiency as performance metrics, for different numbers of processors and training data sizes.



Fierro, R., Leiva, V., & Balakrishnan, N. (2015). Statistical Inference on a Stochastic Epidemic Model. Commun. Stat.Simul. Comput., 44(9), 2297–2314.
Abstract: In this work, we develop statistical inference for the parameters of a discretetime stochastic SIR epidemic model. We use a Markov chain for describing the dynamic behavior of the epidemic. Specifically, we propose estimators for the contact and removal rates based on the maximum likelihood and martingale methods, and establish their asymptotic distributions. The obtained results are applied in the statistical analysis of the basic reproduction number, a quantity that is useful in establishing vaccination policies. In order to evaluate the population size for which the results are useful, a numerical study is carried out. Finally, a comparison of the maximum likelihood and martingale estimators is conducted by means of Monte Carlo simulations.



Fierro, R., Leiva, V., & Moller, J. (2015). The Hawkes Process With Different Exciting Functions And Its Asymptotic Behavior. J. Appl. Probab., 52(1), 37–54.
Abstract: The standard Hawkes process is constructed from a homogeneous Poisson process and uses the same exciting function for different generations of offspring. We propose an extension of this process by considering different exciting functions. This consideration may be important in a number of fields; e.g. in seismology, where main shocks produce aftershocks with possibly different intensities. The main results are devoted to the asymptotic behavior of this extension of the Hawkes process. Indeed, a law of large numbers and a central limit theorem are stated. These results allow us to analyze the asymptotic behavior of the process when unpredictable marks are considered.



Filker, S., Forster, D., Weinisch, L., MoraRuiz, M., Gonzalez, B., Farias, M. E., et al. (2017). Transition boundaries for protistan species turnover in hypersaline waters of different biogeographic regions. Environ. Microbiol., 19(8), 3186–3200.
Abstract: The identification of environmental barriers which govern species distribution is a fundamental concern in ecology. Even though salt was previously identified as a major transition boundary for micro and macroorganisms alike, the salinities causing species turnover in protistan communities are unknown. We investigated 4.5 million highquality protistan metabarcodes (V4 region of the SSU rDNA) obtained from 24 shallow salt ponds (salinities 4%44%) from South America and Europe. Statistical analyses of protistan community profiles identified four salinity classes, which strongly selected for different protistan communities: 49%, 1424%, 2736% and 3844%. The proportion of organisms unknown to science is highest in the 1424% salinity class, showing that environments within this salinity range are an unappreciated reservoir of as yet undiscovered organisms. Distinct higherrank taxon groups dominated in the four salinity classes in terms of diversity. As increasing salinities require different cellular responses to cope with salt, our results suggest that different evolutionary lineages of protists have evolved distinct haloadaptation strategies. Salinity appears to be a stronger selection factor for the structuring of protistan communities than geography. Yet, we find a higher degree of endemism in shallow salt ponds compared with less isolated ecosystems such as the open ocean. Thus, rules for biogeographic structuring of protistan communities are not universal, but depend on the ecosystem under consideration.



Fomin, F. V., Golovach, P. A., Kratochvil, J., Nisse, N., & Suchan, K. (2010). Pursuing a fast robber on a graph. Theor. Comput. Sci., 411(79), 1167–1181.
Abstract: The Cops and Robbers game as originally defined independently by Quilliot and by Nowakowski and Winkler in the 1980s has been Much Studied, but very few results pertain to the algorithmic and complexity aspects of it. In this paper we prove that computing the minimum number of cops that are guaranteed to catch a robber on a given graph is NPhard and that the parameterized version of the problem is W[2]hard; the proof extends to the case where the robber moves s time faster than the cops. We show that on split graphs, the problem is polynomially solvable if s = 1 but is NPhard if s = 2. We further prove that on graphs of bounded cliquewidth the problem is polynomially solvable for s <= 2. Finally, we show that for planar graphs the minimum number of cops is unbounded if the robber is faster than the cops. (C) 2009 Elsevier B.V. All rights reserved.



Formenti, E., Goles, E., & Martin, B. (2012). Computational Complexity of Avalanches in the Kadanoff Sandpile Model. Fundam. Inform., 115(1), 107–124.
Abstract: This paper investigates the avalanche problem AP for the Kadanoff sandpile model (KSPM). We prove that (a slight restriction of) AP is in NC1 in dimension one, leaving the general case open. Moreover, we prove that AP is Pcomplete in dimension two. The proof of this latter result is based on a reduction from the monotone circuit value problem by building logic gates and wires which work with an initial sand distribution in KSPM. These results are also related to the known prediction problem for sandpiles which is in NC1 for onedimensional sandpiles and Pcomplete for dimension 3 or higher. The computational complexity of the prediction problem remains open for the Bak's model of twodimensional sandpiles.



FraVazquez, A., Morales, N., Figueroa, M., del Rio, A. V., Regueiro, L., Campos, J. L., et al. (2016). Bacterial community dynamics in longterm operation of a pilot plant using aerobic granular sludge to treat pig slurry. Biotechnol. Prog., 32(5), 1212–1221.
Abstract: Aerobic granular sludge represents an interesting approach for simultaneous organic matter and nitrogen removal in wastewater treatment plants. However, the information about microbial communities in aerobic granular systems dealing with industrial wastewater like pig slurry is limited. Herein, bacterial diversity and dynamics were assessed in a pilot scale plant using aerobic granular sludge for organic matter and nitrogen elimination from swine slurry during more than 300 days. Results indicated that bacterial composition evolved throughout the operational period from flocculent activated sludge, used as inoculum, to mature aerobic granules. Bacterial diversity increased at the beginning of the granulation process and then declined due to the application of transient organic matter and nitrogen loads. The operational conditions of the pilot plant and the degree of granulation determined the microbial community of the aerobic granules. Brachymonas, Zoogloea and Thauera were attributed with structural function as they are able to produce extracellular polymeric substances to maintain the granular structure. Nitrogen removal was justified by partial nitrification (Nitrosomonas) and denitrification (Thauera and Zoogloea), while Comamonas was identified as the main organic matter oxidizing bacteria. Overall, clear links between bacterial dynamics and composition with process performance were found and will help to predict their biological functions in wastewater ecosystems improving the future control of the process. (c) 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:12121221, 2016

