A staggered approach for the coupling of Cahn–Hilliard type diffusion and finite strain elasticity

We develop an algorithm and computational implementation for simulation of problems that combine Cahn–Hilliard type diffusion with finite strain elasticity. We have in mind applications such as the electro-chemo- mechanics of lithium ion (Li-ion) batteries. We concentrate on basic computational aspects. A staggered algorithm is pro- posed for the coupled multi-field model. For the diffusion problem, the fourth order differential equation is replaced by a system of second order equations to deal with the issue of the regularity required for the approximation spaces. Low order finite elements are used for discretization in space of the involved fields (displacement, concentration, nonlocal concentration). Three (both 2D and 3D) extensively worked numerical examples show the capabilities of our approach for the representation of (i) phase separation, (ii) the effect of concentration in deformation and stress, (iii) the effect of Electronic supplementary material The online version of this article (doi:10.1007/s00466-015-1235-1) contains supplementary material, which is available to authorized users. B P. Areias pmaa@uevora.pt 1 Department of Physics, University of Évora, Colégio Luís António Verney, Rua Romão Ramalho, 59, 7002-554 Évora, Portugal 2 ICIST, Lisbon, Portugal 3 School of Engineering, Universidad de Cuenca, Av. 12 de Abril s/n. 01-01-168, Cuenca, Ecuador 4 Institute of Structural Mechanics, Bauhaus-University Weimar, Marienstraße 15, 99423 Weimar, Germany strain in concentration, and (iv) lithiation. We analyze con- vergence with respect to spatial and time discretization and found that very good results are achievable using both a stag- gered scheme and approximated strain interpolation.

Computational resources for structural and metagenomic characterization of functions in bacteria and bacterial communities. Antimicrobial resistance, pathways for xenobiotic degradation and relationship between gut microbiome and ageing.

Prokaryotic organisms are one of the most successful forms of life, they are present in all known ecosystems. The deluge diversity of bacteria reflects their ability to colonise every environment. Also, human beings host trillions of microorganisms in their body districts, including skin, mucosae, and gut. This symbiosis is active for all other terrestrial and marine animals, as well as plants. With the term holobiont we refer, with a single word, to the systems including both the host and its symbiotic microbial species. The coevolution of bacteria within their ecological niches reflects the adaptation of both host and guest species, and it is shaped by complex interactions that are pivotal for determining the host state. Nowadays, thanks to the current sequencing technologies, Next Generation Sequencing, we have unprecedented tools for investigating the bacterial life by studying the prokaryotic genome sequences. NGS revolution has been sustained by the advancements in computational performance, in terms of speed, storage capacity, algorithm development and hardware costs decreasing following the Moore’s Law. Bioinformaticians and computational biologists design and implement ad hoc tools able to analyse high-throughput data and extract valuable biological information. Metagenomics requires the integration of life and computational sciences and it is uncovering the deluge diversity of the bacterial world. The present thesis work focuses mainly on the analysis of prokaryotic genomes under different aspects. Being supervised by two groups at the University of Bologna, the Biocomputing group and the group of Microbial Ecology of Health, I investigated three different topics: i) antimicrobial resistance, particularly with respect to missense point mutations involved in the resistant phenotype, ii) bacterial mechanisms involved in xenobiotic degradation via the computational analysis of metagenomic samples, and iii) the variation of the human gut microbiota through ageing, in elderly and longevous individuals.

Characterization of microplastics ingested by marine benthos - a methodological and field-experimental study

Microplastics have become ubiquitous pollutants in the marine environment. Ingestion of microplastics by a wide range of marine organisms has been recorded both in laboratory and field studies. Despite growing concern for microplastics, few studies have evaluated their concentrations and distribution in wild populations. Further, there is a need to identify cost-effective standardized methodologies for microplastics extraction and analysis in organisms. In this thesis I present: (i) the results of a multi-scale field sampling to quantify and characterize microplastics occurrence and distribution in 4 benthic marine invertebrates from saltmarshes along the North Adriatic Italian coastal lagoons; (ii) a comparison of the effects and cost-effectiveness of two extraction protocols for microplastics isolation on microfibers and on wild collected organisms; (iii) the development of a novel field- based technique to quantify and characterize the microplastic uptake rates of wild and farmed populations of mussels (Mytilus galloprovincialis) through the analysis of their biodeposits. I found very low and patchy amounts of microplastics in the gastrointestinal tracts of sampled organisms. The omnivorous crab Carcinus aestuarii was the species with the highest amounts of microplastics, but there was a notable variation among individuals. There were no substantial differences between enzymatic and alkaline extraction methods. However, the alkaline extraction was quicker and cheaper. Biodeposit traps proved to be an effective method to estimate mussel ingestion rates. However their performance differed significantly among sites, suggesting that the method, as currently designed, is sensible to local environmental conditions. There were no differences in the ingestion rates of microplastics between farmed and wild mussels. The estimates of microplastic ingestion and the validated procedures for their extraction provide a strong basis for future work on microplastic pollution.

Statistical learning of random probability measures

The study of random probability measures is a lively research topic that has attracted interest from different fields in recent years. In this thesis, we consider random probability measures in the context of Bayesian nonparametrics, where the law of a random probability measure is used as prior distribution, and in the context of distributional data analysis, where the goal is to perform inference given avsample from the law of a random probability measure. The contributions contained in this thesis can be subdivided according to three different topics: (i) the use of almost surely discrete repulsive random measures (i.e., whose support points are well separated) for Bayesian model-based clustering, (ii) the proposal of new laws for collections of random probability measures for Bayesian density estimation of partially exchangeable data subdivided into different groups, and (iii) the study of principal component analysis and regression models for probability distributions seen as elements of the 2-Wasserstein space. Specifically, for point (i) above we propose an efficient Markov chain Monte Carlo algorithm for posterior inference, which sidesteps the need of split-merge reversible jump moves typically associated with poor performance, we propose a model for clustering high-dimensional data by introducing a novel class of anisotropic determinantal point processes, and study the distributional properties of the repulsive measures, shedding light on important theoretical results which enable more principled prior elicitation and more efficient posterior simulation algorithms. For point (ii) above, we consider several models suitable for clustering homogeneous populations, inducing spatial dependence across groups of data, extracting the characteristic traits common to all the data-groups, and propose a novel vector autoregressive model to study of growth curves of Singaporean kids. Finally, for point (iii), we propose a novel class of projected statistical methods for distributional data analysis for measures on the real line and on the unit-circle.

Multi-scale analysis of active landslides using two-pass differential interferometry

Landslides are common features of the landscape of the north-central Apennine mountain range and cause frequent damage to human facilities and infrastructure. Most of these landslides move periodically with moderate velocities and, only after particular rainfall events, some accelerate abruptly. Synthetic aperture radar interferometry (InSAR) provides a particularly convenient method for studying deforming slopes. We use standard two-pass interferometry, taking advantage of the short revisit time of the Sentinel-1 satellites. In this paper we present the results of the InSAR analysis developed on several study areas in central and Northern Italian Apennines. The aims of the work described within the articles contained in this paper, concern: i) the potential of the standard two-pass interferometric technique for the recognition of active landslides; ii) the exploration of the potential related to the displacement time series resulting from a two-pass multiple time-scale InSAR analysis; iii) the evaluation of the possibility of making comparisons with climate forcing for cognitive and risk assessment purposes. Our analysis successfully identified more than 400 InSAR deformation signals (IDS) in the different study areas corresponding to active slope movements. The comparison between IDSs and thematic maps allowed us to identify the main characteristics of the slopes most prone to landslides. The analysis of displacement time series derived from monthly interferometric stacks or single 6-day interferograms allowed the establishment of landslide activity thresholds. This information, combined with the displacement time series, allowed the relationship between ground deformation and climate forcing to be successfully investigated. The InSAR data also gave access to the possibility of validating geographical warning systems and comparing the activity state of landslides with triggering probability thresholds.

Correlation Between The Friedman Staging System And The Upper Airway Volume In Patients With Obstructive Sleep Apnea.

This study was designed to evaluate the correlation between computed tomography findings and data from the physical examination and the Friedman Staging System (FSS) in patients with obstructive sleep apnea (OSA). We performed a retrospective evaluation by reviewing the medical records of 33 patients (19 male and 14 female patients) with a mean body mass index of 30.38 kg/m(2) and mean age of 49.35 years. Among these patients, 14 presented with severe OSA, 7 had moderate OSA, 7 had mild OSA, and 5 were healthy. The patients were divided into 2 groups according to the FSS: Group A comprised patients with FSS stage I or II, and group B comprised patients with FSS stage III. By use of the Fisher exact test, a positive relationship between the FSS stage and apnea-hypopnea index (P = .011) and between the FSS stage and body mass index (P = .012) was found. There was no correlation between age (P = .55) and gender (P = .53) with the FSS stage. The analysis of variance test comparing the upper airway volume between the 2 groups showed P = .018. In this sample the FSS and upper airway volume showed an inverse correlation and were useful in analyzing the mechanisms of airway collapse in patients with OSA.

Utilização da discriminação grafica de Fisher para indicação dos dermatoglifos como referencial de potencialidade de atletas de basquetebol

Universidade Estadual de Campinas. Faculdade de Educação Física

Gametogenesis in Madracis decactis Lyman, 1859 (Cnidaria, Scleractinia) from Ilha Grande Bay (Rio de Janeiro), southeastern Brazil

Collections were made every two months in Ilha Grande Bay, Rio de Janeiro, for 21 months (August/2004-May/2006) to study the gametogenesis of Madracis decactis Lyman, 1859. A total of 1800 polyps were examined using standard histological techniques. Madracis decactis is a hermaphroditic species whose male and female gametes develop within different mesenteries. Oogenesis begins in October, while spermatogenesis begins at the end of February, both reaching maturity at the end of April. The peak of reproductive activity occurred between February and April, when all the polyps were fertile, containing mainly stage III oocytes. Examination of fertile polyps indicated the simultaneous presence of stages I, II and III for oogenesis and I, II, III and IV for spermatogenesis. No embryos or planulae were observed in the histological sections. The gametes or planulae spawning may occur between April and May.

Análise morfométrica da transição esôfago-gástrica de eqüinos submetidos a diferentes manejos alimentares e atividade física

O objetivo deste trabalho foi identificar se diferentes tipos de manejo físico e alimentar determinaram mudanças adaptativas na morfometria da região de transição esôfago-gástrica (TEG) em eqüinos. Foram utilizados 15 conjuntos de animais adultos com raça, sexo e idade não identificados, divididos em três grupos de acordo com a dieta e a atividade física: grupo I - composto por cinco conjuntos da TEG de eqüinos em treinamento intensivo e alimentados principalmente à base de concentrado; grupo II - com cinco conjuntos da TEG de eqüinos que não desempenhavam atividade física intensa e eram alimentados principalmente à base de concentrado, e o grupo III - composto por cinco conjuntos da TEG de eqüinos mantidos a pasto e que não desempenhavam atividade física intensa. A região de transição esôfago-gástrica teve a estrutura do seu epitélio avaliada morfometricamente, onde foram feitas mensurações para identificar a espessura do epitélio estratificado pavimentoso queratinizado. A espessura do grupo I teve como média 122,3µm, do grupo II foi de 173,4µm e do grupo III foi de 281,7µm. Os resultados encontrados para a espessura do epitélio estratificado pavimentoso queratinizado dos eqüinos mostraram a existência de diferenças estatisticamente significativas dos eqüinos do grupo I, quando comparados aos eqüinos do grupo III.

The B0.5 IVe CoRoT target HD 49330 II. Spectroscopic ground-based observations

Context. We present spectroscopic ground-based observations of the early Be star HD 49330 obtained simultaneously with the CoRoT-LRA1 run just before the burst observed in the CoRoT data. Aims. Ground-based spectroscopic observations of the early Be star HD 49330 obtained during the precursor phase and just before the start of an outburst allow us to disantangle stellar and circumstellar contributions and identify modes of stellar pulsations in this rapidly rotating star. Methods. Time series analysis (TSA) is performed on photospheric line profiles of He I and Si III by means of the least squares method. Results. We find two main frequencies f1 = 11.86 c d(-1) and f2 = 16.89 c d(-1) which can be associated with high order p-mode pulsations. We also detect a frequency f3 = 1.51 c d(-1) which can be associated with a low order g-mode. Moreover we show that the stellar line profile variability changed over the spectroscopic run. These results are in agreement with the results of the CoRoT data analysis, as shown in Huat et al. (2009). Conclusions. Our study of mid-and short-term spectroscopic variability allows the identification of p-and g-modes in HD 49330. It also allows us to display changes in the line profile variability before the start of an outburst. This brings new constraints for the seimic modelling of this star.

FOREIGN INVESTMENT AND THE BRAZILIAN REAL ESTATE MARKET

This article discusses the main aspects of the Brazilian real estate market in order to illustrate if it would be attractive for a typical American real estate investor to buy office-building portfolios in Brazil. The article emphasizes: [i] - the regulatory frontiers, comparing investment securitization, using a typical American REIT structure, with the Brazilian solution, using the Fundo de Investimento Imobiliario - FII; [ii] - the investment quality attributes in the Brazilian market, using an office building prototype, and [iii] - the comparison of [risk vs. yield] generated by an investment in the Brazilian market, using a FII, benchmarked against an existing REIT (OFFICE SUB-SECTOR) in the USA market. We conclude that investing dollars exchanged for Reais [the Brazilian currency] in a FII with a triple A office-building portfolio in the Sao Paulo marketplace will yield an annual income and a premium return above an American REIT investment. The highly aggressive scenario, along with the strong persistent exchange rate detachment to the IGP-M variations, plus instabilities affecting the generation of income, and even if we adopt a 300-point margin for the Brazil-Risk level, demonstrates that an investment opportunity in the Brazilian market, in the segment we have analyzed, outperforms an equivalent investment in the American market.

Ocular abnormalities in chronic schizophrenia: clinical implications

Objective: As part of a randomised double-blind study of a new atypical antipsychotic we sought to determine both the levels of visual acuity and the occurrence of toxic side-effects in a group of patients treated for many years on a variety of antipsychotics. Method: Twenty-three inpatients with a DSM-III-R diagnosis of chronic schizophrenia from two separate hospital locations who met the criteria for the double-blind trial were examined for ocular abnormalities at both baseline and at trial completion. Results: At baseline a high prevalence of abnormalities was identified: 19 patients (82.6%) were found to have one or more ocular abnormalities, including lens opacities/cataracts and corneal pigmentation; three patients, with delusions related to the sun, were noted to have solar burns; a high proportion (almost 70%) of patients had untreated visual acuity problems. No further changes were observed at the follow-up examinations. Conclusions: The possible causes of ocular disturbance in schizophrenia and the reasons for the relatively high ocular morbidity in this group are thought to result from both illness-related factors and the effects of antipsychotic medication. Causality is confounded by a number of issues such as the high prevalence of smoking, poor general health and the variety of antipsychotic medications used in the treatment of psychosis as well as substance abuse. The clinical implications are considered in this paper in relation to the move towards community-based psychiatric services.

Depersonalization and personality in panic disorder

Background: Prevalence and clinical correlates of depersonalization symptoms have been associated with panic disorder. Personality traits might increase the likelihood of experiencing depersonalization symptoms or depersonalization disorder in panic patients. Aims: The objectives of this study are to establish the prevalence of depersonalization symptoms during the panic attack and in depersonalization disorder and to examine the personality factors associated with the presence of depersonalization in patients with panic disorder. Methods: The sample comprised 104 consecutive adult outpatients with panic disorder, diagnosed according to the Semistructured Clinical Interview for DSM-IV (Axis I/II disorders). Participants were assessed with the Cambridge Depersonalization Scales, the Temperament and Character Inventory, and the Panic and Agoraphobia Scale. Results: Forty-eight percent of the sample had depersonalization symptoms during the panic attack, whereas 20% of patients had a depersonalization disorder. Women presented more depersonalization disorders than did men (P = .036). Patients with panic disorder with depersonalization disorder had a more severe panic disorder (P = .002). Logistic regression analysis showed that self-transcendence trait (odds ratio, 1.089; 95% confidence interval, 1.021-1.162; P = .010) and severity of panic (odds ratio, 1.056; 95% confidence interval, 1.005-1.110; P = .032) were independently associated with depersonalization disorder. Conclusions: A high prevalence of depersonalization symptoms and depersonalization disorder was confirmed in patients with panic disorder, supporting a dosage effect model for understanding depersonalization pathology. Self-transcendence trait and severity of panic disorder were reported as risk factors for depersonalization disorder. (C) 2011 Elsevier Inc. All rights reserved.

Relationship between endosomes and lysosomes

Delivery of endocytosed macromolecules to lysosomes occurs by means of direct fusion of late endosomes with lysosomes. This has been formally demonstrated in a cell-free content mixing assay using late endosomes and lysosomes from rat liver. There is evidence from electron microscopy Studies that the same process occurs in intact cells. The fusion process results in the formation of hybrid organelles from which lysosomes are reformed. The discovery of the hybrid organelle has opened up three areas of investigation: (i) the mechanism of direct fusion of late endosomes and lysosomes, (ii) the mechanism of re-formation of lysosomes from the hybrid organelle, and (iii) the function of the hybrid organelle. Fusion has analogies with homotypic vacuole fusion in yeast. It requires syntaxin 7 as part of the functional trans-SNARE [SNAP receptor, where SNAP is soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein] complex and the release of lumenal calcium to achieve membrane fusion. Reformation of lysosomes from the hybrid organelle occurs by a maturation process involving condensation of lumenal content and probably removal of some membrane proteins by vesicular traffic. Lysosomes may thus be regarded as a type of secretory granule, storing acid hydrolases in between fusion events with late endosomes. The hybrid organelle is predicted to function as a 'cell stomach', acting as a major site of hydrolysis of endocytosed macromolecules.

Lições de Direito e Processo Penal, 2012/2013

§ Parte I A: DIREITO PENAL: CAPÍTULO I – CONCEITO DE DIREITO PENAL, COM ESPECIAL RELEVO DA DIFERENCIAÇÃO ENTRE DIREITO PENAL CLÁSSICO, DIREITO PENAL ECONÓMICO E SOCIAL E DIREITO DAS CONTRA-ORDENAÇÕES; CAPÍTULO II – O PROBLEMA DOS FINS DAS PENAS; CAPÍTULO III – BREVE ABORDAGEM DA EVOLUÇÃO HISTÓRICA DO DIREITO PENAL; CAPÍTULO IV – TEORIA GERAL DA LEI CRIMINAL; CAPÍTULO V – TEORIA GERAL DA INFRACÇÃO CRIMINAL: A) ELEMENTOS; B) CONSTRUÇÕES; C) ANÁLISE: 1) ACÇÃO; 2) TIPICIDADE; 3) ILICITUDE; 4) CULPA; 5) PUNIBILIDADE; CAPÍTULO VI – FORMAS DO CRIME:A) TENTATIVA; B) AUTORIA E COMPARTICIPAÇÃO; C) CONCURSO DE CRIMES § Parte I BDIREITO PROCESSUAL PENAL; CAPÍTULO I – A DELIMITAÇÃO DO DIREITO PROCESSUAL PENAL; CAPÍTULO II – OS PRINCÍPIOS FUNDAMENTAIS DO PROCESSO PENAL; CAPÍTULO III - A LEI PROCESSUAL PENAL E A SUA APLICAÇÃO; Parte II: CAPÍTULO I- OS SUJEITOS DO PROCESSO; CAPÍTULO II - O OBJECTO DO PROCESSO; CAPÍTULO III - AS MEDIDAS DE COACÇÃO E DE GARANTIA PATRIMONIAL; CAPÍTULO IV - TRAMITAÇÃO PROCESSUAL PENAL. § § Part I: CRIMINAL LAW: CHAPTER I - CONCEPT OF CRIMINAL LAW, WITH SPECIAL RELIEF OF THE DIFFERENTIATION BETWEEN CLASSIC CRIMINAL LAW, ECONOMIC AND SOCIAL CRIMINAL LAW AND THE “AGAINST ORDINANCES” LAW ("LAW OFFENSES"); CHAPTER II - THE PROBLEM OF THE ENDS OF THE PENALTIES; CHAPTER III - BRIEF OVERVIEW OF THE EVOLUTION HISTORY OF CRIMINAL LAW; CHAPTER IV - GENERAL THEORY OF THE CRIMINAL LAW; CHAPTER V - GENERAL THEORY OF THE CRIMINAL INFRACTION: A) ELEMENTS; B) CONSTRUCTIONS; C) ANALYSIS: 1) ACTION; 2) VAGUENESS DOCTRINE; 3) ILLEGALITY; 4) GUILT (FAULT); 5) PUNISHMENT; CHAPTER VI - FORMS OF THE CRIME: A) ATTEMPT; B) AUTHORSHIP AND "CO-PARTICIPATION"; C) CUMULATION OF OFFENCES. § Part I - B: CRIMINAL PROCEDURAL LAW: CHAPTER I - THE DELIMITATION OF THE CRIMINAL PROCEDURAL LAW; CHAPTER II - THE BASIC PRINCIPLES OF THE CRIMINAL PROCEDURE; CHAPTER III - THE CRIMINAL PROCEDURE LAW AND ITS APPLICATION; Part II: CHAPTER I - THE FIGURES OF THE PROCESS; CHAPTER II - THE OBJECT OF THE PROCESS; CHAPTER III - THE MEASURES OF COERCION AND PATRIMONIAL GUARANTEE (WARRANTY); CHAPTER IV - CRIMINAL PROCEDURE.