MOOGLE: a metamodel-based model search engine

Models are becoming increasingly important in the software development process. As a consequence, the number of models being used is increasing, and so is the need for efficient mechanisms to search them. Various existing search engines could be used for this purpose, but they lack features to properly search models, mainly because they are strongly focused on text-based search. This paper presents Moogle, a model search engine that uses metamodeling information to create richer search indexes and to allow more complex queries to be performed. The paper also presents the results of an evaluation of Moogle, which showed that the metamodel information improves the accuracy of the search.

Three-feature model to reproduce the topology of citation networks and the effects from authors' visibility on their h-index

Various factors are believed to govern the selection of references in citation networks, but a precise, quantitative determination of their importance has remained elusive. In this paper, we show that three factors can account for the referencing pattern of citation networks for two topics, namely "graphenes" and "complex networks", thus allowing one to reproduce the topological features of the networks built with papers being the nodes and the edges established by citations. The most relevant factor was content similarity, while the other two - in-degree (i.e. citation counts) and age of publication - had varying importance depending on the topic studied. This dependence indicates that additional factors could play a role. Indeed, by intuition one should expect the reputation (or visibility) of authors and/or institutions to affect the referencing pattern, and this is only indirectly considered via the in-degree that should correlate with such reputation. Because information on reputation is not readily available, we simulated its effect on artificial citation networks considering two communities with distinct fitness (visibility) parameters. One community was assumed to have twice the fitness value of the other, which amounts to a double probability for a paper being cited. While the h-index for authors in the community with larger fitness evolved with time with slightly higher values than for the control network (no fitness considered), a drastic effect was noted for the community with smaller fitness. (C) 2012 Elsevier Ltd. All rights reserved.

Probabilistic crack growth analyses using a boundary element model: Applications in linear elastic fracture and fatigue problems

This paper addresses the numerical solution of random crack propagation problems using the coupling boundary element method (BEM) and reliability algorithms. Crack propagation phenomenon is efficiently modelled using BEM, due to its mesh reduction features. The BEM model is based on the dual BEM formulation, in which singular and hyper-singular integral equations are adopted to construct the system of algebraic equations. Two reliability algorithms are coupled with BEM model. The first is the well known response surface method, in which local, adaptive polynomial approximations of the mechanical response are constructed in search of the design point. Different experiment designs and adaptive schemes are considered. The alternative approach direct coupling, in which the limit state function remains implicit and its gradients are calculated directly from the numerical mechanical response, is also considered. The performance of both coupling methods is compared in application to some crack propagation problems. The investigation shows that direct coupling scheme converged for all problems studied, irrespective of the problem nonlinearity. The computational cost of direct coupling has shown to be a fraction of the cost of response surface solutions, regardless of experiment design or adaptive scheme considered. (C) 2012 Elsevier Ltd. All rights reserved.

Aniline-1,4-benzoquinone as a model system for the characterization of products from aniline oligomerization in low acidic media

Increase in the pH medium of aniline polymerization is used for giving products of different morphologies, which are often wrongly attributed to PANI chains. Infrared and Raman spectroscopic data, supported by quantum chemical calculations, show that aniline-1,4-benzoquinone (AnBzq) is a model system for the characterization of the products of aniline oligomerization in low acidic media. The Raman spectra excited at different laser lines reveal the bichromophoric nature of AnBzq, whose absorption bands at 550 nm and 440 nm can be attributed to pi-pi* transitions of the delocalized benzoquinone and amino-phenyl moieties, respectively. (C) 2012 Elsevier B.V. All rights reserved.

Embryonic and Fetal Development in - Pigmy Rice Rat - Oligoryzomys sp (Rodentia, Sigmodontinae) and its Significance for Being a new Experimental Model

Oligoryzomys (Cricetidae, Sigmodontinae) is a common rodent genus from South America that includes a couple of very similar species. Related species have been used as experimental model for understanding several diseases for which these species are reservoirs. In order to provide a better understanding of the embryological aspects of this group, herein we showed data on the embryonic and fetal development in Oligoryzomys sp. Eight specimens of different stages of gestation were obtained from the Collection of the Zoology Museum of University of Sao Paulo, Brazil. Gestational ages were estimated by crown-rump-length according to Evans and Sack (1973). To address our analysis after examining the gross morphology, tissues from several organs were processed for light and scanning electron microscopy. Morphological data on the systems (nervous system, cardiorespiratory system, intestinal tract and urogenital system) were described in detail. Finally, the findings were compared with what is known about embryological aspects in other rodent species in order to establish similarities and differences during the organogenesis in different species.

A Cost-Effectiveness-Assessing Model of Vaccination for Varicella and Zoster

A decision analytical model is presented and analysed to assess the effectiveness and cost-effectiveness of routine vaccination against varicella and herpes-zoster, or shingles. These diseases have as common aetiological agent the varicella-zoster virus (VZV). Zoster can more likely occur in aged people with declining cell-mediated immunity. The general concern is that universal varicella vaccination might lead to more cases of zoster: with more vaccinated children exposure of the general population to varicella infectives become smaller and thus a larger proportion of older people will have weaker immunity to VZV, leading to more cases of reactivation of zoster. Our compartment model shows that only two possible equilibria exist, one without varicella and the other one where varicella arid zoster both thrive. Threshold quantities to distinguish these cases are derived. Cost estimates on a possible herd vaccination program are discussed indicating a possible tradeoff choice.

Degradation of the resin-dentin bonds after simulated and inhibited cariogenic challenge in an in situ model

The aim of this study was to evaluate the resindentin bonds of two simplified etch-and-rinse adhesive after simulated cariogenic and inhibited cariogenic challenge in situ. Dental cavities (4 mm wide, 4 mm long, and 1.5 mm deep) were prepared in 60 bovine teeth with enamel margins. Restorations were bonded with either adhesive Adper Single Bond 2 (3MESPE) or Optibond Solo Plus (Kerr). Forty restorations were included in an intra-oral palatal appliance that was used for 10 adult volunteers while the remaining 20 dental blocks were not submitted to any cariogenic challenge [NC group] and tested immediately. For the simulated cariogenic challenge [C+DA], each volunteer dropped 20% sucrose solution onto all blocks four times a day during 14 days and distilled water twice a day. In the inhibited cariogenic challenge group [C + FA], the same procedure was done, but slurry of fluoride dentifrice (1.100 ppm) was applied instead of water. The restored bovine blocks were sectioned to obtain a slice for cross-sectional Vickers microhardness evaluation and resindentin bonded sticks (0.8 mm2) for resindentin microtensile evaluation. Data were evaluated by two-way ANOVA and Tukey's tests (a = 0.05). Statistically lower microhardness values and degradation of the resindentin bonds were only found in the C + DW group for both adhesives. The in situ model seems to be a suitable short-term methodology to investigate the degradation of the resindentin bonds under a more realistic condition. (c) 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 100B: 14661471, 2012.

The r-matrix of the Alday-Arutyunov-Frolov model

We investigate the classical integrability of the Alday-Arutyunov-Frolov model, and show that the Lax connection can be reduced to a simpler 2 x 2 representation. Based on this result, we calculate the algebra between the L-operators and find that it has a highly non-ultralocal form. We then employ and make a suitable generalization of the regularization technique proposed by Mail let for a simpler class of non-ultralocal models, and find the corresponding r- and s-matrices. We also make a connection between the operator-regularization method proposed earlier for the quantum case, and the Mail let's symmetric limit regularization prescription used for non-ultralocal algebras in the classical theory.

Application of magnetically induced hyperthermia in the model protozoan Crithidia fasciculata as a potential therapy against parasitic infections

Background: Magnetic hyperthermia is currently a clinical therapy approved in the European Union for treatment of tumor cells, and uses magnetic nanoparticles (MNPs) under time-varying magnetic fields (TVMFs). The same basic principle seems promising against trypanosomatids causing Chagas disease and sleeping sickness, given that the therapeutic drugs available have severe side effects and that there are drug-resistant strains. However, no applications of this strategy against protozoan-induced diseases have been reported so far. In the present study, Crithidia fasciculata, a widely used model for therapeutic strategies against pathogenic trypanosomatids, was targeted with Fe3O4 MNPs in order to provoke cell death remotely using TVMFs. Methods: Iron oxide MNPs with average diameters of approximately 30 nm were synthesized by precipitation of FeSO4 in basic medium. The MNPs were added to C. fasciculata choanomastigotes in the exponential phase and incubated overnight, removing excess MNPs using a DEAE-cellulose resin column. The amount of MNPs uploaded per cell was determined by magnetic measurement. The cells bearing MNPs were submitted to TVMFs using a homemade AC field applicator (f = 249 kHz, H = 13 kA/m), and the temperature variation during the experiments was measured. Scanning electron microscopy was used to assess morphological changes after the TVMF experiments. Cell viability was analyzed using an MTT colorimetric assay and flow cytometry. Results: MNPs were incorporated into the cells, with no noticeable cytotoxicity. When a TVMF was applied to cells bearing MNPs, massive cell death was induced via a nonapoptotic mechanism. No effects were observed by applying TVMF to control cells not loaded with MNPs. No macroscopic rise in temperature was observed in the extracellular medium during the experiments. Conclusion: As a proof of principle, these data indicate that intracellular hyperthermia is a suitable technology to induce death of protozoan parasites bearing MNPs. These findings expand the possibilities for new therapeutic strategies combating parasitic infection.

Soil carbon balance in a tropical grassland: Estimation of soil respiration and its partitioning using a semi-empirical model

In savannah and tropical grasslands, which account for 60% of grasslands worldwide, a large share of ecosystem carbon is located below ground due to high root:shoot ratios. Temporal variations in soil CO2 efflux (R-S) were investigated in a grassland of coastal Congo over two years. The objectives were (1) to identify the main factors controlling seasonal variations in R-S and (2) to develop a semi-empirical model describing R-S and including a heterotrophic component (R-H) and an autotrophic component (R-A). Plant above-ground activity was found to exert strong control over soil respiration since 71% of seasonal R-S variability was explained by the quantity of photosynthetically active radiation absorbed (APAR) by the grass canopy. We tested an additive model including a parameter enabling R-S partitioning into R-A and R-H. Assumptions underlying this model were that R-A mainly depended on the amount of photosynthates allocated below ground and that microbial and root activity was mostly controlled by soil temperature and soil moisture. The model provided a reasonably good prediction of seasonal variations in R-S (R-2 = 0.85) which varied between 5.4 mu mol m(-2) s(-1) in the wet season and 0.9 mu mol m(-2) s(-1) at the end of the dry season. The model was subsequently used to obtain annual estimates of R-S, R-A and R-H. In accordance with results reported for other tropical grasslands, we estimated that R-H accounted for 44% of R-S, which represented a flux similar to the amount of carbon brought annually to the soil from below-ground litter production. Overall, this study opens up prospects for simulating the carbon budget of tropical grasslands on a large scale using remotely sensed data. (C) 2012 Elsevier B.V. All rights reserved.

3,4-Methylenedioxymethamphetamine (Ecstasy) Decreases Inflammation and Airway Reactivity in a Murine Model of Asthma

Objective:3,4-Methylenedioxymethamphetamine(MDMA), or ecstasy, is a synthetic drug used recreationally, mainly by young people. It has been suggested that MDMA has a Th cell skewing effect, in which Th1 cell activity is suppressed and Th2 cell activity is increased. Experimental allergic airway inflammation in ovalbumin (OVA)-sensitized rodents is a useful model to study Th2 response; therefore, based on the Th2 skewing effect of MDMA, we studied MDMA in a model of allergic lung inflammation in OVA-sensitized mice. Methods: We evaluated cell trafficking in the bronchoalveolar lavage fluid, blood and bone marrow; cytokine production; L-selectin expression and lung histology. We also investigated the effects of MDMA on tracheal reactivity in vitro and mast cell degranulation. Results: We found that MDMA given prior to OVA challenge in OVA-sensitized mice decreased leukocyte migration into the lung, as revealed by a lower cell count in the bronchoalveolar lavage fluid and lung histologic analysis. We also showed that MDMA decreased expression of both Th2-like cytokines (IL-4, IL-5 and IL-10) and adhesion molecules (L-selectin). Moreover, we showed that the hypothalamus-pituitary-adrenal axis is partially involved in the MDMA-induced reduction in leukocyte migration into the lung. Finally, we showed that MDMA decreased tracheal reactivity to methacholine as well as mast cell degranulation in situ. Conclusions:Thus, we report here that MDMA given prior to OVA challenge in OVA-sensitized allergic mice is able to decrease lung inflammation and airway reactivity and that hypothalamus-pituitary-adrenal axis activation is partially involved. Together, the data strongly suggest an involvement of a neuroinnmune mechanism in the effects of MDMA on lung inflammatory response and cell recruitment to the lungs of allergic animals. Copyright (C) 2012 S. Karger AG, Basel

Interacting model for the cosmological dark sector

We discuss a new interacting model for the cosmological dark sector in which the attenuated dilution of cold dark matter scales as a(-3)f(a), where f(a) is an arbitrary function of the cosmic scale factor a. From thermodynamic arguments, we show that f(a) is proportional to the entropy source of the particle creation process. In order to investigate the cosmological consequences of this kind of interacting models, we expand f(a) in a power series, and viable cosmological solutions are obtained. Finally, we use current observational data to place constraints on the interacting function f(a).

MODEL PARTITIONS AND COMPACT TEST CASE SUITES

We present a generalized test case generation method, called the G method. Although inspired by the W method, the G method, in contrast, allows for test case suite generation even in the absence of characterization sets for the specification models. Instead, the G method relies on knowledge about the index of certain equivalences induced at the implementation models. We show that the W method can be derived from the G method as a particular case. Moreover, we discuss some naturally occurring infinite classes of FSM models over which the G method generates test suites that are exponentially more compact than those produced by the W method.

A Poisson mixed model with nonnormal random effect distribution

In this paper, we propose a random intercept Poisson model in which the random effect is assumed to follow a generalized log-gamma (GLG) distribution. This random effect accommodates (or captures) the overdispersion in the counts and induces within-cluster correlation. We derive the first two moments for the marginal distribution as well as the intraclass correlation. Even though numerical integration methods are, in general, required for deriving the marginal models, we obtain the multivariate negative binomial model from a particular parameter setting of the hierarchical model. An iterative process is derived for obtaining the maximum likelihood estimates for the parameters in the multivariate negative binomial model. Residual analysis is proposed and two applications with real data are given for illustration. (C) 2011 Elsevier B.V. All rights reserved.

The protein LJM 111 from Lutzomyia longipalpis Salivary Gland Extract (SGE) accounts for the SGE-inhibitory effects upon inflammatory parameters in experimental arthritis model

Several studies have pointed out the immunomodulatory properties of the Salivary Gland Extract (SGE) from Lutzomyia longipalpis. We aimed to identify the SGE component (s) responsible for its effect on ovalbumin (OVA)-induced neutrophil migration (NM) and to evaluate the effect of SGE and components in the antigen-induced arthritis (AIA) model. We tested the anti-arthritic activities of SGE and the recombinant LJM111 salivary protein (rLJM111) by measuring the mechanical hypernociception and the NM into synovial cavity. Furthermore, we measured IL-17, TNF-alpha and IFN-gamma released by lymph nodes cells stimulated with mBSA or anti-CD3 using enzyme-linked immunosorbent assay (ELISA). Additionally, we tested the effect of SGE and rLJM111 on co-stimulatory molecules expression (MHC-II and CD-86) by flow cytometry. TNF-alpha and IL-10 production (ELISA) of bone marrow-derived dendritic cells (BMDCs) stimulated with LPS, chemotaxis and actin polymerization from neutrophils. Besides, the effect of SGE on CXCR2 and GRK-2 expression on neutrophils was investigated. We identified one plasmid expressing the protein LJM111 that prevented NM in OVA-challenged immunized mice. Furthermore, both SGE and rLJM111 inhibited NM and pain sensitivity in AIA and reduced IL-17, TNF-alpha and IFN-gamma. SGE and rLJM111 also reduced MHC-II and CD-86 expression and TNF-alpha whereas increased IL-10 release by LPS-stimulated BMDCs. SGE, but not LJM 111, inhibited neutrophils chemotaxis and actin polymerization. Additionally, SGE reduced neutrophil CXCR2 expression and increased GRK-2. Thus, rLJM111 is partially responsible for SGE mechanisms by diminishing DC function and maturation but not chemoattraction of neutrophils. (C) 2012 Elsevier B.V. All rights reserved.