A gillespie algorithm for non-markovian stochastic processes

The Gillespie algorithm provides statistically exact methods for simulating stochastic dynamics modeled as interacting sequences of discrete events including systems of biochemical reactions or earthquake occurrences, networks of queuing processes or spiking neurons, and epidemic and opinion formation processes on social networks. Empirically, the inter-event times of various phenomena obey long-tailed distributions. The Gillespie algorithm and its variants either assume Poisson processes (i.e., exponentially distributed inter-event times), use particular functions for time courses of the event rate, or work for non-Poissonian renewal processes, including the case of long-tailed distributions of inter-event times, but at a high computational cost. In the present study, we propose an innovative Gillespie algorithm for renewal processes on the basis of the Laplace transform. The algorithm makes use of the fact that a class of point processes is represented as a mixture of Poisson processes with different event rates. The method is applicable to multivariate renewal processes whose survival function of inter-event times is completely monotone. It is an exact algorithm and works faster than a recently proposed Gillespie algorithm for general renewal processes, which is exact only in the limit of infinitely many processes. We also propose a method to generate sequences of event times with a tunable amount of positive correlation between inter-event times. We demonstrate our algorithm with exact simulations of epidemic processes on networks, finding that a realistic amount of positive correlation in inter-event times only slightly affects the epidemic dynamics

Molecular regulation of muscle development and growth in Senegalese sole larvae exposed to temperature fluctuations

Author's accepted version (post-print).NOTICE: this is the author’s version of a work that was accepted for publication in Aquaculture (2014). Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Aquaculture (2014), 432. doi: http://dx.doi.org/10.1016/j.aquaculture.2014.04.035.The Senegalese sole (Solea senegalensis) is a marine flatfish that is naturally exposed to high temperature fluctuations (12 - 28 ºC) in the wild, with a life cycle predominantly estuarine during larval and juvenile phases. Farming of this species has largely improved in the past years but marked fluctuations of temperature during production still contribute to variation on growth and muscle cellularity, particularly if they occur during early stages of development. Such thermal plasticity of muscle growth must arise through changes in a multitude of physiological and molecular pathways, in which epigenetic gene regulation is likely to play an essential role. In the present work, we review recent studies addressing molecular, physiological and morphological aspects of the thermal plasticity of somatic growth in Senegalese sole larvae and early juveniles, thus aiming to improve sole rearing in aquaculture production. The present study shows that temperature during specific time frames of ontogeny has both short- and long-term effects on growth and muscle cellularity of Senegalese sole. Nevertheless, Senegalese sole also seems to rapidly adapt to environmental temperature through a set of epigenetic mechanisms and physiological responses such as regulation of feed intake, even at early developmental stages

Inheritance of resistance to Puccinia psidii G. Winter in a eucalyptus interspecific hybrid progeny evaluated under conditions of natural infection

A ferrugem, causada pelo fungo Puccinia psidii, é atualmente a mais importante doença do eucalipto. Esta doença está amplamente disseminada pelo Brasil e causa sérios danos em viveiros e plantações. A identificação de germoplasma resistente aliado ao conhecimento da base genética da resistência são os requerimentos primordiais para o sucesso de programas de melhoramento visando à produção de cultivares resistentes. Estudos anteriores sobre a herança da resistência em condições controladas sugerem tanto uma herança monogênica como a participação de pelo menos 2 genes conferindo resistência à doença. O objetivo deste estudo foi avaliar a resistência a P. psidii, em condições de campo em quatorze progênies obtidas a partir de cruzamentos e auto-cruzamentos controlados entre quatro clones híbridos de Eucalyptus grandis Hill ex Maiden x Eucalyptus urophylla ST Blake,que contrastam para a resistência ao fungo. Os resultados indicam que a resistência pode ser explicada por um loco com efeito principal e pelo menos três alelos diferentes, com interações entre os alelos, resultando no fenótipo de resistência ou suscetibilidade. Entretanto, locos com menor efeito devem influenciar a resistência, uma vez que foram observadas variações nas classes de severidade da escala utilizada. Nenhuma diferença na segregação para a resistência foi observada entre cruzamentos recíprocos, sugerindo que não existe influência citoplasmática no controle deste caráter.Rust caused by the fungus Puccinia psidii is currently the most important disease of eucalyptus. It is widely disseminated in Brazil, and causes serious damage in nurseries and plantation areas. The identification of resistant germplasm along with knowledge of the genetic basis of resistance heredity are the first requirements for the success of breeding programs aiming to develop resistant varieties. Earlier studies carried out under controlled conditions suggested a monogenic control as well as the participation of at least two genes promoting resistance to rust. The goal of this study was to evaluate the resistance to P. psidii under field conditions in fourteen progenies from controlled crosses and self-crosses among four hybrid clones of Eucalyptus grandis Hill ex Maiden x Eucalyptus urophylla ST Blake that contrast for resistance to the fungus. Results indicated that resistance could be explained by one locus with main effects and at least three different alleles. However, loci with minor effects may influence the resistance, since variation on severity classes was observed. Differences in segregation of resistance between reciprocal crosses were not observed, indicating absence of cytoplasmic effects.Votorantim Celulose e PapelConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Intersección entre la alfabetización en información y las políticas públicas educativas: formando una ciudadanía crítica y autónoma en el manejo de la información

This research is based on the premise that the Uruguayan Educational System does not provide individuals sufficient tools to acquire skills and competencies in the management of information, being that one of the reasons that explain the difficulties to improve the levels of academic performance of the students. It seeks to justify that the inclusion of Information Literacy into the Educational Public Policies, that guide the Uruguayan Educational System, would contribute to solve the identified problem, since, the Information Literacy is the process by which the students could acquire the information tools that are necessary to have a good information management, adopting a critical stance toward it, and achieving more autonomy. In this way, the student would be more able to graduate from the Educational System, being a citizen more suitable for the decision-making and to exercise the full enjoyment of their rights. It considered that a citizenship with these characteristics possess the ability to deal with the social problems in a more conscious and responsible way, collaborating with the contraction of a more just and egalitarian society. To achieve the above stated objective, the research was developed with a purely qualitative and analytical deductive methodology, in which was elaborated a conceptual framework with great bibliographical support, with the development of the key research concepts by the research team. After that, a set of interviews were held with qualified informants in each of the themes that are treated in the development of this research. Reinforcing these interviews was made a focus group in which participated only actors that make up the Uruguayan Educational System from various roles (students, teachers, authorities, etc.) that facilitated the establishment of the status of situation of that system from all the possible perspectives, Developed these three instances of the investigation, was carried up a theoretical discussion of the problem identified and the proposal established to contribute to solve it, nurturing that discussion with theoretical concepts and the testimonies gathered in the previous stages of the research. After that, were settled some conclusions and reflections that confirm the hypothesis raised by the research team and consequently the achieving of the objectives that were established by him. Finally were exposed some recommendations taking into account the results obtain. Concluding that, indeed, the inclusion of Information Literacy in Educational Public Policies that rules the Uruguayan Education System would contribute to improve the educational performance of students, since that would give them the necessary tools to develop skills and competencies in the information management, which also will favour his development within society

Enhancement of the magnetic anisotropy of nanometer-sized Co clusters: influence of the surface and of the inter-particle interactions

We study the magnetic properties of spherical Co clusters with diameters between 0.8 nm and 5.4 nm (25 to 7500$ atoms) prepared by sequential sputtering of Co and Al2O3. The particle size distribution has been determined from the equilibrium susceptibility and magnetization data and it is compared to previous structural characterizations. The distribution of activation energies was independently obtained from a scaling plot of the ac susceptibility. Combining these two distributions we have accurately determined the effective anisotropy constant Keff. We find that Keff is enhanced with respect to the bulk value and that it is dominated by a strong anisotropy induced at the surface of the clusters. Interactions between the magnetic moments of adjacent layers are shown to increase the effective activation energy barrier for the reversal of the magnetic moments. Finally, this reversal is shown to proceed classically down to the lowest temperature investigated (1.8 K).Comment: 13 figures submitted to Phys. Rev.

Anisotropic Superparamagnetism of Monodispersive Cobalt-Platinum Nanocrystals

Based on the high-temperature organometallic route (Sun et al. Science 287, 1989 (2000)), we have synthesized powders containing CoPt_3 single crystals with mean diameters of 3.3(2) nm and 6.0(2) nm and small log-normal widths sigma=0.15(1). In the entire temperature range from 5 K to 400 K, the zero-field cooled susceptibility chi(T) displays significant deviations from ideal superparamagnetism. Approaching the Curie temperature of 450(10) K, the deviations arise from the (mean-field) type reduction of the ferromagnetic moments, while below the blocking temperature T_b, chi(T) is suppressed by the presence of energy barriers, the distributions of which scale with the particle volumes obtained from transmission electron microscopy (TEM). This indication for volume anisotropy is supported by scaling analyses of the shape of the magnetic absorption chi''(T,omega) which reveal distribution functions for the barriers being also consistent with the volume distributions observed by TEM. Above 200 K, the magnetization isotherms M(H,T) display Langevin behavior providing 2.5(1) mu_B per CoPt_3 in agreement with reports on bulk and thin film CoPt_3. The non-Langevin shape of the magnetization curves at lower temperatures is for the first time interpreted as anisotropic superparamagnetism by taking into account an anisotropy energy of the nanoparticles E_A(T). Using the magnitude and temperature variation of E_A(T), the mean energy barriers and 'unphysical' small switching times of the particles obtained from the analyses of chi''(T,omega) are explained. Below T_b hysteresis loops appear and are quantitatively described by a blocking model, which also ignores particle interactions, but takes the size distributions from TEM and the conventional field dependence of E_A into account.Comment: 12 pages with 10 figures and 1 table. Version accepted for publication in Phys. Rev. B . Two-column layou

Clustering of chronic hepatitis B screening intentions in social networks of Moroccan immigrants in the Netherlands

Background Early detection, identification, and treatment of chronic hepatitis B through screening is vital for those at increased risk, e.g. born in hepatitis B endemic countries. In the Netherlands, Moroccan immigrants show low participation rates in health-related screening programmes. Since social networks influence health behaviour, we investigated whether similar screening intentions for chronic hepatitis B cluster within social networks of Moroccan immigrants. Methods We used respondent-driven sampling (RDS) where each participant ("recruiter") was asked to complete a questionnaire and to recruit three Moroccans ("recruitees") from their social network. Logistic regression analyses were used to analyse whether the recruiters' intention to request a screening test was similar to the intention of their recruitees. Results We sampled 354 recruiter-recruitee pairs: for 154 pairs both participants had a positive screening intention, for 68 pairs both had a negative screening intention, and the remaining 132 pairs had a discordant intention to request a screening test. A tie between a recruiter and recruitee was associated with having the same screening intention, after correction for sociodemographic variables (OR 1.70 [1.15-2.51]). Conclusions The findings of our pilot study show clustering of screening intention among individuals in the same network. This provides opportunities for social network interventions to encourage participation in hepatitis B screening initiatives

Long chain polyunsaturated fatty acid synthesis in a marine vertebrate: Ontogenetic and nutritional regulation of a fatty acyl desaturase with Delta4 activity

Solea senegalensis is an unusual marine teleost as it has very low dietary requirement for long-chain polyunsaturated fatty acids (LC-PUFA) during early development. Aquaculture is rapidly becoming the main source of health-beneficial fish products for human consumption. This, associated with limited supply of LC-PUFA-rich ingredients for fish feeds, render S. senegalensis a highly interesting species in which to study the LC-PUFA biosynthesis pathway. We have cloned and functionally characterized fatty acyl desaturase and elongase cDNAs corresponding to D4fad (with some D5 activity for the n-3 series) and elovl5 with the potential to catalyze docosahexaenoic acid (DHA) biosynthesis from eicosapentaenoic acid (EPA). Changes in expression of both transcripts were determined during embryonic and early larval development, and transcriptional regulation in response to higher or lower dietary n-3 LC-PUFA was assessed during larval and post-larval stages. There was a marked pattern of regulation during early ontogenesis, with both transcripts showing peak expression coinciding with the start of exogenous feeding. Although elovl5 transcripts were present in fertilized eggs, D4fad only appeared at hatching. However, eggs have high proportions of DHA (~ 20%) and high DHA/EPA ratio (~ 11) to meet the high demands for early embryonic development. The fatty acid profile of larvae after the start of exogenous feeding closely reflected dietary composition. Nonetheless, D4fad was significantly up-regulated in response to LC-PUFA-poor diets, which may suggest biological relevance of this pathway in reducing LC-PUFA dietary requirements in this species, compared to other marine teleosts. These results indicate that sole is capable of synthesizing DHA from EPA through a Sprecher-independent pathway

X-ray tomography for fully-3D time-resolved reconstruction of bubbling fluidized beds

A new X-ray computed tomography technique for the purpose of imaging fluidized beds is presented. It consists of an experimental set-up with three stationary X-ray source and flat panel detector pairs, a geometric calibration and data processing workflow, and an image reconstruction algorithm. The technique enables sparse-angular tomographic reconstruction in large 3D regions of fluidized beds at framerates up to 200 Hz, and therefore images bubbles along their whole trajectories through the volume. It allows for a unique analysis of bubble dynamics in fluidized beds, including bubble velocities, bubble transformations, i.e., time evolution of the bubble distributions in space, and bubble\xe2\x80\x93bubble interactions. In this article, we first analyze the main limitation of the technique, the sparse angular resolution, through numerical simulations. We then test the experimental set-up through imaging a series of phantoms. Lastly, we demonstrate results from a Geldart B bubbling fluidized bed

Dynamics of air transport networks: A review from a complex systems perspective

Air transport systems are highly dynamic at temporal scales from minutes to years. This dynamic behavior not only characterizes the evolution of the system but also affect the system's functioning. Understanding the evolutionary mechanisms is thus fundamental in order to better design optimal air transport networks that benefits companies, passengers and the environment. In this review, we briefly present and discuss the state-of-the-art on time-evolving air transport networks. We distinguish the structural analysis of sequences of network snapshots, ideal for long-term network evolution (e.g. annual evolution), and temporal paths, preferred for short-term dynamics (e.g. hourly evolution). We emphasize that most previous research focused on the first modeling approach (i.e. long-term) whereas only a few studies look at high-resolution temporal paths. We conclude the review highlighting that much research remains to be done, both to apply already available methods and to develop new measures for temporal paths on air transport networks. In particular, we identify that the study of delays, network resilience and optimization of resources (aircraft and crew) are critical topics