Nmag micromagnetic simulation tool - software engineering lessons learned

We review design and development decisions and their impact for the open source code Nmag from a software engineering in computational science point of view. We summarise lessons learned and recommendations for future computational science projects. Key lessons include that encapsulating the simulation functionality in a library of a general purpose language, here Python, provides great flexibility in using the software. The choice of Python for the top-level user interface was very well received by users from the science and engineering community. The from-source installation in which required external libraries and dependencies are compiled from a tarball was remarkably robust. In places, the code is a lot more ambitious than necessary, which introduces unnecessary complexity and reduces main- tainability. Tests distributed with the package are useful, although more unit tests and continuous integration would have been desirable. The detailed documentation, together with a tutorial for the usage of the system, was perceived as one of its main strengths by the community.Comment: 7 pages, 5 figures, Software Engineering for Science, ICSE201

Spectrum-to-spectrum methods for the generation of elastic floor acceleration spectra

In seismic codes, the acceleration demand of nonstructural components is commonly expressed in terms of floor response spectra and estimated by means of simple predictive equations. By using the latter, response-history analysis of the structure is not required, being floor spectra calculated directly from the peak ground acceleration expected at the site. The price for this simplicity in the method used for the estimation of floor spectra is the generally poor approximation of the obtained predictions. Codes’ equations, in fact, do not explicitly account for important factors influencing floor spectra, such as the contribution of the higher modes of vibration of the structure and the actual value of the nonstructural components’ damping ratio. Alternative spectrum-to-spectrum methods for direct generation of floor spectra have been proposed, which include these factors and improve the accuracy of the predictions. Different approaches have been used and several methods developed. Despite large research effort, however, a comparative evaluation of the currently available proposals is still lacking. The objective of this paper is to fill this gap, by reviewing selected proposals representative of practice-oriented spectrum-to-spectrum methods. A case study consisting in a six-story frame is analyzed and predictions obtained with the investigated methods are compared with exact floor spectra derived from time-history analyses of the structure, as well as spectra calculated using the Eurocode 8 equation

A systematic approach to multiphysics extensions of finite-element-based micromagnetic simulations: Nmag

Extensions of the basic micromagnetic model that include effects such as spin-current interaction, diffusion of thermal energy or anisotropic magnetoresistance are often studied by performing simulations that use case-specific ad-hoc extensions of widely used software packages such as OOMMF or Magpar. We present the novel software framework 'Nmag' that handles specifications of micromagnetic systems at a sufficiently abstract level to enable users with little programming experience to automatically translate a description of a large class of dynamical multifield equations plus a description of the system's geometry into a working simulation. Conceptually, this is a step towards a higher-level abstract notation for classical multifield mutliphysics simulations, similar to the change from assembly language to a higher level human-and-machine-readable formula notation for mathematical terms (FORTRAN) half a century ago. We demonstrate the capability of this approach through two examples, showing 1) a reduced dimensionality model coupling two copies of the micromagnetic sector and 2) the computation of a spatial current density distribution for anisotropic magnetoresistance (AMR). For cross-wise validation purposes, we also show how Nmag compares to the OOMMF and Magpar packages on a selected micromagnetic toy system. We furthermore, briefly discuss the limiations of our framework and related conceptual questions

Comparative assessment of strut models for the modelling of in-plane seismic response of infill walls

The influence of infills on the seismic response of frame structures has long been recognised. Typically, stiffness and strength of the infill and connections between infill and frame are such that the infill affects the global seismic behaviour of the structure. Hence, the presence of infills should be considered in the analysis and design of new buildings and in the seismic assessment of existing ones. To this aim, simple models for infill walls, such as the equivalent diagonal no-tension strut model, have been developed in the last decades. The objective of the present study is to assess the validity of different strut models. To this aim, 162 experimental tests available in the literature are considered. The data set includes both reinforced concrete and steel frames, as well as confined masonry structures. The mechanical characteristics of masonry and the boundary conditions between frames and infills of the test specimens take into account a large set of situations, reflecting the great variability in the materials and in the construction techniques adopted in different countries. Moreover, the type of tests and the related results are not uniform; in some cases monotonic experiments are performed, whereas in other cases cyclic tests are carried out. As expected, the presence of different types of infill-frame systems results in a large scatter of the data. However, the comparison between experimental results and predictions show that, on the average, the infill strength can be adequately estimated by resorting to the strut model whereas major uncertainties are found for the stiffness prediction

DESIGN OF SWEPT SOURCE OPTICAL COHERENCE TOMOGRAPHY

openPresentation on the state of the art of optical coherence tomography (OCT) and design of a tomograph based on a swept-type laser source centered at 1305 nm

Can Greater Flamingo Recognize Fertile <i>vs.</i> Infertile Egg? A Single Case Study

Fertility of captive flamingos varies between flocks, species and seasons. Individuating infertile eggs could be helpful to facilitate important decisions. Wild animals could be encouraged to abandon the nest or not, whereas in captivity removing non-viable egg would lead birds to lay a new one. The aim of this study was to investigate the parental behaviour of a pair of greater flamingos (Phoenicopterus roseus ) in the presence of a fertile and an infertile egg. Data on the posture and behaviours of the pair on the nest were collected over two different periods: first period\u2014an infertile egg was laid; second period\u2014a fertile egg was laid. For each period, 28 ten-minute sessions per flamingo partner were run. Results revealed that female flamingo spent significantly more time standing on the nest in the first than in the second period (P = 0.010). Moreover, when standing on the nest, the female performed significantly more egg-care behaviour (attention to the egg, egg rotation/moving) in the first than in the second period (P = 0.010). No significant differences between periods emerged in the male flamingo posture on the nest and behaviours. Findings from this study suggest that female flamingos stand on the nest longer if the egg is infertile, paying more attention and examining it deeply. This study provides new insights into greater flamingo parent-embryo communication. Future research is needed to improve our knowledge on this topic, as well as on the husbandry of this species in the controlled environment

Multiphysics simulations of magnetic nanostructures

Multiphysics simulations of magnetic nanostructures by Matteo Franchin.In recent years the research on magnetism has seen a new trend emerging, characterised by considerable effort in developing new nanostructures and finding new ways to control and manipulate their magnetisation, such as using spin polarised currents or light pulses. The field of magnetism is thus moving towards the multiphysics direction, since it is increasingly studied in conjunction with other types of physics, such as electric and spin transport, electromagnetic waves generation and absorption, heat generation and diffusion. Understanding these new phenomena is intriguing and may lead to major technological advances. Computer simulations are often invaluable to such research, since they offer a way to predict and understand the physics of magnetic nanostructures and help in the design and optimisation of new devices.For the preparation of this thesis the Nmag multiphysics micromagnetic simulation package has been further developed and improved by the author. The software has also been extended in order to model exchange spring systems. Using Nmag, we carried out micromagnetic simulations in order to characterise the magnetisation dynamics in exchange spring systems and derived analytical models to validate and gain further insight into the numerical results. We found that the average magnetisation moves in spiral trajectories near equilibrium and becomes particularly soft (low oscillation frequency and damping, high amplitude) when the applied field is close to a particular value, called the bending field.We studied spin transport in exchange spring systems and investigated new geometries and setups in order to maximise the interaction between spin polarised current and magnetisation. We found that by engineering a trilayer exchange spring system in the form of a cylindrical nanopillar, it is possible to obtain microwave emission with frequencies of 5-35 GHz for applied current densities between 0.5-2.0 x 1011 A/m2 and without the need for an externally applied magnetic field. We proposed a one dimensional analytical model and found a formula which relates the emission frequency to the geometrical parameters and the current density

In vivo and in vitro activity of isolated compounds from Brazilian propolis on the modulation of the inflammatory process

Orientador: Pedro Luiz RosalenTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Odontologia de PiracicabaResumo: O objetivo deste estudo foi avaliar a atividade e possíveis mecanismos de ação dos compostos isolados de própolis brasileiras sobre a modulação do processo inflamatório. As atividades anti-inflamatórias dos compostos vestitol e neovestitol, isolados da própolis vermelha brasileira e do cinamoiloxi-mammeisina (CNM), isolado da geoprópolis de Melipona scutellaris, foram avaliadas e os seguintes resultados obtidos: 1) O composto vestitol apresentou atividade inibitória sobre a migração de neutrófilos induzido por LPS ou mBSA, bem como sobre a liberação das quimiocinas CXCL1/KC e CXCL2/MIP-2 in vivo e in vitro. Foi também observado que o tratamento com vestitol reduziu o rolamento e adesão de leucócitos na microcirculação mesentérica de camundongos. Quanto à sua atividade em neutrófilos in vitro, o vestitol reduziu a quimiotaxia de neutrófilos induzida por CXCL2/MIP-2 e LTB4 e bloqueou o influxo de cálcio nestas células. Não foi constatada alteração da expressão do receptor CXCR2 com o pré-tratamento de vestitol. 2) Em relação ao composto neovestitol, foi verificada que a sua administração reduziu a migração de neutrófilos, o rolamento e adesão de leucócitos e a expressão de ICAM-1 em camundongos desafiados com LPS. No que diz respeito à liberação de TNF-?, CXCL1/KC e CXCL2/MIP-2, não foi constatada atividade do neovestitol sobre estes mediadores inflamatórios. Além disso, o composto não alterou a expressão de ICAM-1 in vitro. Por outro lado, foi observado que a administração de um inibidor da óxido nítrico sintetase, aboliu o efeito anti-inflamatório do neovestitol sobre a migração de neutrófilos. No modelo de artrite induzida por colágeno, a administração diária do neovestitol pelo período de 12 dias, reduziu o escore clinico de artrite dos animais, as lesões articulares e a liberação de IL-6. 3) Em relação aos resultados obtidos com o composto CNM, foi observado que a sua administração reduziu a migração de neutrófilos na cavidade peritoneal e articular, bem como a liberação de TNF-? e CXCL2/MIP-2 in vivo e in vitro. Foi verificado também, que o CNM reduziu a expressão das proteínas fosforiladas ERK 1/2, JNK, p38 MAPK e c-jun em macrófagos RAW 264.6. Da mesma forma, o CNM reduziu a ativação de NF-?B, entretanto, não alterou a degradação de I?B? e a translocação de p65 nuclear. Portanto, conclui-se que a própolis brasileira é uma importante fonte de compostos ativos com potencial biológico e que os compostos isolados delas como vestitol, neovestitol e CNM, são promissores agentes anti-inflamatórios com mecanismos distintos e de interesses para os desfechos de processos inflamatórios agudos ou crônicos, com possibilidades de uso terapêuticoAbstract: The objective of this study was to evaluate the activity and possible mechanisms of action of compounds isolated from Brazilian propolis on modulation of the inflammatory process. The anti-inflammatory activities of vestitol and neovestitol, isolated from Brazilian red propolis and cinnamoyloxy-mammeisin (CNM), isolated from Melipona scutellaris geopropolis were evaluated and the following results were observed: 1) Vestitol had inhibitory activity against LPS or mBSA induced neutrophil migration as well as on the release of chemokines CXCL1/KC and CXCL2/MIP-2 in vivo and in vitro. It was also found that treatment with vestitol reduced leukocytes rolling and adhesion in mice mesenteric microcirculation. Regarding the activity on neutrophil in vitro, vestitol reduced CXCL2/MIP-2 and LTB4 induced neutrophils chemotaxis and blocked the calcium influx in these cells. No change was observed in CXCR2 receptor expression with vestitol pretreatment. 2) The administration of neovestitol reduced neutrophil migration, leukocytes rolling and adhesion and ICAM-1 expression in mice challenged with LPS. Despite the release of TNF-?, CXCL1/KC and CXCL2/MIP-2, we found no activity of neovestitol on these inflammatory mediators. Furthermore, the compound did not alter the in vitro ICAM-1expression. Moreover, it was observed that administration of a nitric oxide sintase inhibitor abolished the anti-inflammatory effect of neovestitol neutrophils migration. In the of collagen-induced arthritis model, it was found that the daily administration of neovestitol for 12 days, reduced the clinical arthritis score of the animals, joint injury and IL-6 release. 3) Regarding the results obtained with CNM, it was found that administration reduced neutrophil migration into the peritoneal and joint cavity, as well as TNF-? and CXCL2/MIP-2 release in vivo and in vitro. Concerning mechanism of action, it was found that CNM reduced the expression of the phosphorylated proteins ERK 1/2, JNK, p38 MAPK and c-jun in RAW 264.6 macrophages. Furthermore, it was observed that CNM reduced NF-kB activation, however, did not affect the I?B? degradation and p65 nuclear translocation. Thus, we conclude that Brazilian propolis is an important source of active compounds with biological potential. Also, some of isolated compounds such as vestitol, neovestitol and CNM are promising anti-inflammatory agents with distinct mechanisms of action with possible therapeutic use in acute or chronic inflammatory processesDoutoradoFarmacologia, Anestesiologia e TerapeuticaDoutor em Odontologia2012/01365-0, 2012/22378-2FAPES

Evaluation of anti-inflammatory and antinociceptive potential of geopropolis of Melipona scutellaris

Orientador: Pedro Luiz RosalenDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Odontologia de PiracicabaResumo: O objetivo deste estudo foi avaliar a atividade anti-inflamatória e antinociceptiva do extrato etanólico de geoprópolis (EEGP) de Melipona scutellaris e frações químicas, bem como possíveis mecanismos de ação. Além disso, caracterizar quimicamente o EEGP e frações bioativas. Para avaliação da atividade anti-inflamatória foram aplicados os ensaios de recrutamento de neutrófilos na cavidade peritoneal, microscopia intravital e edema de pata induzido por carragenina. A via do óxido nítrico (NO) foi avaliada através da administração de inibidores desta via, além da avaliação da expressão das moléculas de adesão intercelular tipo 1 (ICAM-1) e quantificação de nitritos. A análise química do EEGP e fração bioativa foram realizadas pelos métodos de cromatografia gasosa com espectrometria de massas (CG/EM) e cromatografia líquida de alta eficiência em fase reversa (CLAE-FR). Para avaliação da atividade antinociceptiva, foram aplicados os ensaios de contorções abdominais induzida por ácido acético, teste da formalina, hipernocicepção inflamatória mecânica induzida por carragenina e quantificação das citocinas IL-1 ? e TNF-?. A composição química do EEGP e frações bioativas foram avaliadas pela quantificação de fenóis e flavonóides totais. Conforme os resultados nos ensaios anti-inflamatórios, foi verificado que o EEGP e sua fração aquosa diminuíram a migração de neutrófilos na cavidade peritoneal induzido por carragenina, como também diminuíram a interação dos leucócitos (rolamento e adesão) com as células endoteliais. A administração de inibidores da via do NO suprimiu a atividade inibitória do EEGP e da fração aquosa sobre a migração de neutrófilos. A expressão de ICAM-1 apresentou-se diminuída, e os níveis de nitritos aumentados após o tratamento com EEGP e fração aquosa. No modelo de edema de pata induzido por carragenina, o EEGP e a fração aquosa apresentaram atividade anti-edematogênica. Nenhum padrão de ácido fenólico ou flavonóide, comumente encontrado em amostra de própolis de Apis mellifera, pôde ser detectado nas amostras de EEGP e da fração aquosa pelas técnicas de CG/EM e CLAE-FR. Nos ensaios de atividade antinociceptiva foi verificado que o EEGP e as frações hexânica e aquosa diminuíram o número de contorções abdominais induzida por ácido acético. No teste da formalina, o EEGP e a fração aquosa inibiram ambas as fases (neurogênica e inflamatória), e a fração hexânica apenas a fase neurogênica. Foi evidenciada atividade do EEGP e fração aquosa na hipernocicepção inflamatória mecânica induzida por carragenina, como também foi constatado níveis diminuídos de IL-1? e TNF-?. Para as amostras de EEGP e frações hexânica e aquosa foi verificada a presença de compostos fenólicos e ausência de flavonóides. Estes resultados indicam que as frações bioativas encontradas possuem substâncias promissoras como novos agentes terapêuticos para o controle da inflamação e dorAbstract: The aim of this study was to evaluate the anti-inflammatory and antinociceptive geopropolis of ethanolic extract (EEGP) of Melipona scutellaris and fractions, as well as a possible mechanism of actions. In addition, to characterize chemically EEGP and bioactive fractions. To evaluate the anti-inflammatory activity we used the recruitment of neutrophils into the peritoneal cavity, intravital microscopy and paw edema induced by carrageenan. The pathway of nitric oxide (NO) was demonstrated by administration of antagonists of this pathway, but also evaluated by the expression of intercellular adhesion molecule type 1 (ICAM-1) and quantification of nitrites. Reversed-phase high-performance liquid chromatography (RP-HPLC) and gas chromatography/mass spectrometry (GC/MS) were used the phytochemical analyses. The tests used to evaluate the antinociceptive activity were abdominal contortions induced by acetic acid, formalin test, carrageenan-induced mechanical inflammatory hypernociception and quantification of IL-1 ? and TNF-?. The quantification of total phenols and flavonoids was also determined in the EEGP and the bioactive fractions. In the anti-inflammatory tests the EEGP and the aqueous fraction decreased the neutrophil migration into the peritoneal cavity induced by carrageenan and also decreased the interaction of leukocytes (rolling and adhesion) with endothelial cells. The route of administration of inhibitors of NO abolished the inhibitory activity of the aqueous fraction and EEGP on neutrophil migration. The expression of ICAM-1 was reduced and nitrite levels increased after treatment with EEGP and aqueous fraction. In the paw edema induced by carrageenan, both EEGP and aqueous fraction showed anti-edema activity. No standards of flavonoid or phenolic acid commonly found in a sample of propolis of Apis mellifera could be detected in any samples of aqueous fraction or EEGP by GC/MS and RP-HPLC techniques. In tests to evaluate the antinociceptive activity was determined that EEGP, hexane and aqueous fractions decreased the number of abdominal constrictions induced by acetic acid. In the formalin test, the aqueous fraction and EEGP inhibited both phases (neurogenic and inflammatory), and the hexane fraction only neurogenic phase. The EEGP and the aqueous fraction showed activity in the carrageenan-induced mechanical inflammatory hypernociception model, as also observed decreased levels of IL-1? and TNF-?. The EEGP, hexane and aqueous fractions was verified the presence of phenolic compounds and absence of flavonoids. These results indicate that the bioactive fractions in the present study showed substances that could be promising new therapeutic agents to control inflammation and painMestradoFarmacologia, Anestesiologia e TerapeuticaMestre em Odontologi

Seismic risk of infrastructure systems with treatment of and sensitivity to epistemic uncertainty

Modern society’s very existence is tied to the proper and reliable functioning of its Critical Infrastructure (CI) systems. In the seismic risk assessment of an infrastructure, taking into account all the relevant uncertainties affecting the problem is crucial. While both aleatory and epistemic uncertainties affect the estimate of seismic risk to an infrastructure and should be considered, the focus herein is on the latter. After providing an up-to-date literature review about the treatment of and sensitivity to epistemic uncertainty, this paper presents a comprehensive framework for seismic risk assessment of interdependent spatially distributed infrastructure systems that accounts for both aleatory and epistemic uncertainties and provides confidence in the estimate, as well as sensitivity of uncertainty in the output to the components of epistemic uncertainty in the input. The logic tree approach is used for the treatment of epistemic uncertainty and for the sensitivity analysis, whose results are presented through tornado diagrams. Sensitivity is also evaluated by elaborating the logic tree results through weighted ANOVA. The formulation is general and can be applied to risk assessment problems involving not only infrastructural but also structural systems. The presented methodology was implemented into an open-source software, OOFIMS, and applied to a synthetic city composed of buildings and a gas network and subjected to seismic hazard. The gas system’s performance is assessed through a flow-based analysis. The seismic hazard, the vulnerability assessment and the evaluation of the gas system’s operational state are addressed with a simulation-based approach. The presence of two systems (buildings and gas network) proves the capability to handle system interdependencies and highlights that uncertainty in models/parameters related to one system can affect uncertainty in the output related to dependent systems