Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit.

Computational modeling has become a widely used tool for unraveling the mechanisms of higher level cooperative cell behavior during vascular morphogenesis. However, experimenting with published simulation models or adding new assumptions to those models can be daunting for novice and even for experienced computational scientists. Here, we present a step-by-step, practical tutorial for building cell-based simulations of vascular morphogenesis using the Tissue Simulation Toolkit (TST). The TST is a freely available, open-source C++ library for developing simulations with the two-dimensional cellular Potts model, a stochastic, agent-based framework to simulate collective cell behavior. We will show the basic use of the TST to simulate and experiment with published simulations of vascular network formation. Then, we will present step-by-step instructions and explanations for building a recent simulation model of tumor angiogenesis. Demonstrated mechanisms include cell-cell adhesion, chemotaxis, cell elongation, haptotaxis, and haptokinesis.

Long-tailed trapping times and Lévy flights in a self-organized critical granular system

We present a continuous time random walk model for the scale-invariant transport found in a self-organized critical rice pile [K. Christensen et al., Phys. Rev. Lett. 77, 107 (1996)]. From our analytical results it is shown that the dynamics of the experiment can be explained in terms of Lvy flights for the grains and a long-tailed distribution of trapping times. Scaling relations for the exponents of these distributions are obtained. The predicted microscopic behavior is confirmed by means of a cellular automaton model.

Prospectiva de la llengua a Catalunya: simulació amb autòmats cel·lulars

L'artilce aborda l'aplicació d'eines informàtiques de simulació en l'àmbit psicosocial a la situació de la llengua a Catalunya per extreure'n escenaris de futur. En primer lloc, aborda el context metodològic de la simulació social amb autòmats cel·lulars. En segon lloc, s'aplica el mètode i el sistema als resultats de l''Enquesta d'Usos Lingüístics de Població 2008' i se n'extreuen resultats. Finalment, s'apunten algunes conclusions.

Prospectiva de la llengua a Catalunya: simulació amb autòmats cel·lulars

L"article aborda l"aplicació d"eines informàtiques de simulació en l"àmbit psicosocial a la situació de la llengua a Catalunya per extreure"n escenaris de futur. En primer lloc, s"aborda el context metodològic de la simulació social amb autòmats cel·lulars. En segon lloc, s"aplica el mètode i el sistema als resultats de l"Enquesta d"usos lingüístics de la població 2008 i se n"extreuen resultats. Finalment, s"apunten unes conclusions.

Proceedings of JAC 2010. Journées Automates Cellulaires

The second Symposium on Cellular Automata “Journ´ees Automates Cellulaires” (JAC 2010) took place in Turku, Finland, on December 15-17, 2010. The first two conference days were held in the Educarium building of the University of Turku, while the talks of the third day were given onboard passenger ferry boats in the beautiful Turku archipelago, along the route Turku–Mariehamn–Turku. The conference was organized by FUNDIM, the Fundamentals of Computing and Discrete Mathematics research center at the mathematics department of the University of Turku. The program of the conference included 17 submitted papers that were selected by the international program committee, based on three peer reviews of each paper. These papers form the core of these proceedings. I want to thank the members of the program committee and the external referees for the excellent work that have done in choosing the papers to be presented in the conference. In addition to the submitted papers, the program of JAC 2010 included four distinguished invited speakers: Michel Coornaert (Universit´e de Strasbourg, France), Bruno Durand (Universit´e de Provence, Marseille, France), Dora Giammarresi (Universit` a di Roma Tor Vergata, Italy) and Martin Kutrib (Universit¨at Gie_en, Germany). I sincerely thank the invited speakers for accepting our invitation to come and give a plenary talk in the conference. The invited talk by Bruno Durand was eventually given by his co-author Alexander Shen, and I thank him for accepting to make the presentation with a short notice. Abstracts or extended abstracts of the invited presentations appear in the first part of this volume. The program also included several informal presentations describing very recent developments and ongoing research projects. I wish to thank all the speakers for their contribution to the success of the symposium. I also would like to thank the sponsors and our collaborators: the Finnish Academy of Science and Letters, the French National Research Agency project EMC (ANR-09-BLAN-0164), Turku Centre for Computer Science, the University of Turku, and Centro Hotel. Finally, I sincerely thank the members of the local organizing committee for making the conference possible. These proceedings are published both in an electronic format and in print. The electronic proceedings are available on the electronic repository HAL, managed by several French research agencies. The printed version is published in the general publications series of TUCS, Turku Centre for Computer Science. We thank both HAL and TUCS for accepting to publish the proceedings.

Programmable Self-Assembly: Constructing Global Shape using Biologically-inspire

In this thesis I present a language for instructing a sheet of identically-programmed, flexible, autonomous agents (``cells'') to assemble themselves into a predetermined global shape, using local interactions. The global shape is described as a folding construction on a continuous sheet, using a set of axioms from paper-folding (origami). I provide a means of automatically deriving the cell program, executed by all cells, from the global shape description. With this language, a wide variety of global shapes and patterns can be synthesized, using only local interactions between identically-programmed cells. Examples include flat layered shapes, all plane Euclidean constructions, and a variety of tessellation patterns. In contrast to approaches based on cellular automata or evolution, the cell program is directly derived from the global shape description and is composed from a small number of biologically-inspired primitives: gradients, neighborhood query, polarity inversion, cell-to-cell contact and flexible folding. The cell programs are robust, without relying on regular cell placement, global coordinates, or synchronous operation and can tolerate a small amount of random cell death. I show that an average cell neighborhood of 15 is sufficient to reliably self-assemble complex shapes and geometric patterns on randomly distributed cells. The language provides many insights into the relationship between local and global descriptions of behavior, such as the advantage of constructive languages, mechanisms for achieving global robustness, and mechanisms for achieving scale-independent shapes from a single cell program. The language suggests a mechanism by which many related shapes can be created by the same cell program, in the manner of D'Arcy Thompson's famous coordinate transformations. The thesis illuminates how complex morphology and pattern can emerge from local interactions, and how one can engineer robust self-assembly.

Interaction of Mycoplasma genitalium with host cells: evidence for nuclear localization

Mycoplasma genitalium (Mg) is a mollicute that causes a range of human urogenital infections. A hallmark of these bacteria is their ability to establish chronic infections that can persist despite completion of appropriate antibiotic therapies and intact and functional immune systems. Intimate adherence and surface colonization of mycoplasmas to host cells are important pathogenic features. However, their facultative intracellular nature is poorly understood, partly due to difficulties in developing and standardizing cellular interaction model systems. Here, we characterize growth and invasion properties of two Mg strains (G37 and 1019V). Mg G37 is a high-passage laboratory strain, while Mg 1019V is a low-passage isolate recovered from the cervix. The two strains diverge partially in gene sequences for adherence-related proteins and exhibit subtle variations in their axenic growth. However, with both strains and consistent with our previous studies, a subset of adherent Mg organisms invade host cells and exhibit perinuclear targeting. Remarkably, intranuclear localization of Mg proteins is observed, which occurred as early as 30 min after infection. Mg strains deficient in adherence were markedly reduced in their ability to invade and associate with perinuclear and nuclear sites.

FAST, PARALLEL AND SECURE CRYPTOGRAPHY ALGORITHM USING LORENZ`S ATTRACTOR

A novel cryptography method based on the Lorenz`s attractor chaotic system is presented. The proposed algorithm is secure and fast, making it practical for general use. We introduce the chaotic operation mode, which provides an interaction among the password, message and a chaotic system. It ensures that the algorithm yields a secure codification, even if the nature of the chaotic system is known. The algorithm has been implemented in two versions: one sequential and slow and the other, parallel and fast. Our algorithm assures the integrity of the ciphertext (we know if it has been altered, which is not assured by traditional algorithms) and consequently its authenticity. Numerical experiments are presented, discussed and show the behavior of the method in terms of security and performance. The fast version of the algorithm has a performance comparable to AES, a popular cryptography program used commercially nowadays, but it is more secure, which makes it immediately suitable for general purpose cryptography applications. An internet page has been set up, which enables the readers to test the algorithm and also to try to break into the cipher.

Avaliação do crescimento de ocupação da bacia do rio Pitimbu com subsídios para estudos de possíveis impactos sobre os recursos hidricos

The Pitimbu River Watershed (PRW), belonging to Potiguar capital metropolitan area, State of Rio Grande do Norte, contributes, among other purposes, to human using and animal watering. This watershed is extremely important because, besides filling up with freshwater approximately 30% of the south part of Natal (South, East and West Zones), contributes to the river shore ecosystem equilibrium. Face to the current conjuncture, this study aims to evaluate the urban development dynamics in the PRW, applying Cellular Automata as a modeling instrument, and to simulate future urban scenarios, between 2014 and 2033, using the simulation program SLEUTH. In the calibration phase, urban spots for 1 984, 1992, 2004 and 2013 years were used, with resolution from 100 meters. After the simulation, it was found a predominance of organic growth, expanding the BHRP from existing urban centers. The spontaneous growth occurred through the fullest extent of the watershed, however the probability of effective growth should not exceed 21%. It was observed that, there was a 68% increase for the period between 2014 and 2033, corresponding to an expansion area of 1,778 ha. For 2033, the source of Pitimbu River area and the Jiqui Lake surroundings will increase more than 78%. Finally, it was seen an exogenous urban growth tendency in the watershed (outside-in). As a result of this growth, hydraulics resources will become scarcer

Use of Adipose Tissue-Derived Mesenchymal Stem Cells for Experimental Tendinitis Therapy in Equines

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

ASSESSING THE SUITABILITY of STERILE INSECT TECHNIQUE APPLIED TO AEDES AEGYPTI

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Enhanced multiwavelength holographic profilometry by laser mode selection

A method for improving the accuracy of surface shape measurement by multiwavelength holography is presented. In our holographic setup, a Bi12TiO20 photorefractive crystal was the holographic recording medium, and a multimode diode laser emitting in the red region was the light source in a two-wave mixing scheme. on employing such lasers the resulting holographic image appears covered with interference fringes corresponding to the object relief, and the interferogram spatial frequency is proportional to the diode laser's free spectral range (FSR). Our method consists in increasing the effective free spectral range of the laser by positioning a Fabry-Perot etalon at the laser output for mode selection. As larger effective values of the laser FSR were achieved, higher-spatial-frequency interferograms were obtained and therefore more sensitive and accurate measurements were performed. The quantitative evaluation of the interferograms was made through the phase-stepping technique, and the phase map unwrapping was carried out through the cellular-automata method. For a given surface, shape measurements with different interferogram spatial frequencies were performed and compared with respect to measurement noise and visual inspection. (c) 2007 Society of Photo-Optical Instrumentation Engineers.

Multi-wavelength holographic profilometry - art. no. 60272L

A novel method for surface profilometry by holography is presented. We used a diode laser emitting at many wavelengths simultaneously as the light source and a Bi12TiO20 (BTO) crystal as the holographic medium in single exposure processes. The employ of multi-wavelength, large free spectral range (FSR) lasers leads to holographic images covered of interference fringes corresponding to the contour lines of the studied surface. In order to obtain the relief of the studied surface, the fringe analysis was performed by the phase stepping technique (PST) and the phase unwrapping was carried out by the Cellular-automata method. We analysed the relief of a tilted flat metallic bar and a tooth prosthesis.

Enhanced multi-wavelength holographic profilometry by laser mode selection

The application of multi-wavelength holography for surface shape measurement is presented. In our holographic setup a Bi12TiO 20 (BTO) photorefractive crystal was the holographic recording medium and a multimode diode laser emitting in the red region was the light source in a two-wave mixing scheme. The holographic imaging with multimode lasers results in multiple holograms in the BTO. By employing such lasers the resulting holographic image appears covered of interference fringes corresponding to the object relief and the interferogram spatial frequency is proportional to the diode laser free spectral range (FSR). We used a Fabry-Perot étalon at the laser output for laser mode selection. Thus, larger effective values of the laser FSR were achieved, leading to higher-spatial frequency interferograms and therefore to more sensitive and accurate measurements. The quantitative evaluation of the interferograms was performed through the phase stepping technique (PST) and the phase map unwrapping was carried out through the Cellular-Automata method. For a given surface, shape measurements with different interferogram spatial frequencies were performed and compared, concerning measurement noise and visual inspection.