An approach to computing downward closures

The downward closure of a word language is the set of all (not necessarily contiguous) subwords of its members. It is well-known that the downward closure of any language is regular. While the downward closure appears to be a powerful abstraction, algorithms for computing a finite automaton for the downward closure of a given language have been established only for few language classes. This work presents a simple general method for computing downward closures. For language classes that are closed under rational transductions, it is shown that the computation of downward closures can be reduced to checking a certain unboundedness property. This result is used to prove that downward closures are computable for (i) every language class with effectively semilinear Parikh images that are closed under rational transductions, (ii) matrix languages, and (iii) indexed languages (equivalently, languages accepted by higher-order pushdown automata of order 2).Comment: Full version of contribution to ICALP 2015. Comments welcom

Safe Maneuvering Near Offshore Installations: A New Algorithmic Tool

Maneuvers of human-operated and autonomous marine vessels in the safety zone of drilling rigs, wind farms and other installations present a risk of collision. This article proposes an algorithmic toolkit that ensures maneuver safety, taking into account the restrictions imposed by ship dynamics. The algorithms can be used for anomaly detection, decision making by a human operator or an unmanned vehicle guidance system. We also consider a response to failures in the vessel's control systems and emergency escape maneuvers. Data used by the algorithms come from the vessel's dynamic positioning control system and positional survey charts of the marine installations

Signatures of arithmetic simplicity in metabolic network architecture

Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their evolutionary history and complex wiring constitutes one of the most fascinating open questions in biology, intimately related to the enigma of life's origin itself. Is the evolution of metabolism subject to general principles, beyond the unpredictable accumulation of multiple historical accidents? Here we search for such principles by applying to an artificial chemical universe some of the methodologies developed for the study of genome scale models of cellular metabolism. In particular, we use metabolic flux constraint-based models to exhaustively search for artificial chemistry pathways that can optimally perform an array of elementary metabolic functions. Despite the simplicity of the model employed, we find that the ensuing pathways display a surprisingly rich set of properties, including the existence of autocatalytic cycles and hierarchical modules, the appearance of universally preferable metabolites and reactions, and a logarithmic trend of pathway length as a function of input/output molecule size. Some of these properties can be derived analytically, borrowing methods previously used in cryptography. In addition, by mapping biochemical networks onto a simplified carbon atom reaction backbone, we find that several of the properties predicted by the artificial chemistry model hold for real metabolic networks. These findings suggest that optimality principles and arithmetic simplicity might lie beneath some aspects of biochemical complexity

Quantitative proteomic analysis of age-related subventricular zone proteins associated with neurodegenerative disease.

Aging is characterized by a progressive decline in the function of adult tissues which can lead to neurodegenerative disorders. However, little is known about the correlation between protein changes in the subventricular zone (SVZ) and neurodegenerative diseases with age. In the present study, neural stem cells (NSCs) were derived from the SVZ on postnatal 7 d, 1 m, and 12 m-old mice. With age, NSCs exhibited increased SA-β-gal activity and decreased proliferation and pool size in the SVZ zone, and were associated with elevated inflammatory chemokines and cytokines. Furthermore, quantitative proteomics and ingenuity pathway analysis were used to evaluate the significant age-related alterations in proteins and their functions. Some downregulated proteins such as DPYSL2, TPI1, ALDH, and UCHL1 were found to play critical roles in the neurological disease and PSMA1, PSMA3, PSMC2, PSMD11, and UCHL1 in protein homeostasis. Taken together, we have provided valuable insight into the cellular and molecular processes that underlie aging-associated declines in SVZ neurogenesis for the early detection of differences in gene expression and the potential risk of neurological disease, which is beneficial in the prevention of the diseases

A historical overview of the classification, evolution, and dispersion of Leishmania parasites and sandflies

Background The aim of this study is to describe the major evolutionary historical events among Leishmania, sandflies, and the associated animal reservoirs in detail, in accordance with the geographical evolution of the Earth, which has not been previously discussed on a large scale. Methodology and Principal Findings Leishmania and sandfly classification has always been a controversial matter, and the increasing number of species currently described further complicates this issue. Despite several hypotheses on the origin, evolution, and distribution of Leishmania and sandflies in the Old and New World, no consistent agreement exists regarding dissemination of the actors that play roles in leishmaniasis. For this purpose, we present here three centuries of research on sandflies and Leishmania descriptions, as well as a complete description of Leishmania and sandfly fossils and the emergence date of each Leishmania and sandfly group during different geographical periods, from 550 million years ago until now. We discuss critically the different approaches that were used for Leishmana and sandfly classification and their synonymies, proposing an updated classification for each species of Leishmania and sandfly. We update information on the current distribution and dispersion of different species of Leishmania (53), sandflies (more than 800 at genus or subgenus level), and animal reservoirs in each of the following geographical ecozones: Palearctic, Nearctic, Neotropic, Afrotropical, Oriental, Malagasy, and Australian. We propose an updated list of the potential and proven sandfly vectors for each Leishmania species in the Old and New World. Finally, we address a classical question about digenetic Leishmania evolution: which was the first host, a vertebrate or an invertebrate? Conclusions and Significance We propose an updated view of events that have played important roles in the geographical dispersion of sandflies, in relation to both the Leishmania species they transmit and the animal reservoirs of the parasites

Charge Fractionalization in nonchiral Luttinger systems

One-dimensional metals, such as quantum wires or carbon nanotubes, can carry charge in arbitrary units, smaller or larger than a single electron charge. However, according to Luttinger theory, which describes the low-energy excitations of such systems, when a single electron is injected by tunneling into the middle of such a wire, it will tend to break up into separate charge pulses, moving in opposite directions, which carry definite fractions $f$ and $(1-f)$ of the electron charge, determined by a parameter $g$ that measures the strength of charge interactions in the wire. (The injected electron will also produce a spin excitation, which will travel at a different velocity than the charge excitations.) Observing charge fractionalization physics in an experiment is a challenge in those (nonchiral) low-dimensional systems which are adiabatically coupled to Fermi liquid leads. We theoretically discuss a first important step towards the observation of charge fractionalization in quantum wires based on momentum-resolved tunneling and multi-terminal geometries, and explain the recent experimental results of H. Steinberg {\it et al.}, Nature Physics {\bf 4}, 116 (2008).Comment: 31 pages, final version to appear in Annals of Physic

In situ size sorting in CVD synthesis of Si microspheres

[EN] Silicon microspheres produced in gas-phase by hot-wall CVD offer unique quality in terms of sphericity, surface smoothness, and size. However, the spheres produced are polydisperse in size, which typically range from 0.5 mu m to 5 mu m. In this work we show through experiments and calculations that thermophoretic forces arising from strong temperature gradients inside the reactor volume effectively sort the particles in size along the reactor. These temperature gradients are shown to be produced by a convective gas flow. The results prove that it is possible to select the particle size by collecting them in a particular reactor region, opening new possibilities towards the production by CVD of size-controlled high-quality silicon microspheres.The authors acknowledge financial support from the following projects: ENE2013-49984-EXP, MAT2012-35040, MAT2015-69669-P and ESP2014-54256-C4-2-R of the Spanish Ministry of Economy and Competitiveness (MINECO), and PROMETEOII/2014/026 of the Regional Valencian Government.Garín Escrivá, M.; Fenollosa Esteve, R.; Kowalski, L. (2016). In situ size sorting in CVD synthesis of Si microspheres. Scientific Reports. 6:1-10. https://doi.org/10.1038/srep38719S110

Quantum Rings in Electromagnetic Fields

This is the author accepted manuscript. The final version is available from Springer via the DOI in this recordThis chapter is devoted to optical properties of so-called Aharonov-Bohm quantum rings (quantum rings pierced by a magnetic flux resulting in AharonovBohm oscillations of their electronic spectra) in external electromagnetic fields. It studies two problems. The first problem deals with a single-electron AharonovBohm quantum ring pierced by a magnetic flux and subjected to an in-plane (lateral) electric field. We predict magneto-oscillations of the ring electric dipole moment. These oscillations are accompanied by periodic changes in the selection rules for inter-level optical transitions in the ring allowing control of polarization properties of the associated terahertz radiation. The second problem treats a single-mode microcavity with an embedded Aharonov-Bohm quantum ring which is pierced by a magnetic flux and subjected to a lateral electric field. We show that external electric and magnetic fields provide additional means of control of the emission spectrum of the system. In particular, when the magnetic flux through the quantum ring is equal to a half-integer number of the magnetic flux quanta, a small change in the lateral electric field allows for tuning of the energy levels of the quantum ring into resonance with the microcavity mode, thus providing an efficient way to control the quantum ring-microcavity coupling strength. Emission spectra of the system are discussed for several combinations of the applied magnetic and electric fields