Recent improvements in prediction of protein structure by global optimization of a potential energy function

Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (Cα) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å Cα rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the Cα rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a Cα rmsd less than 6.0 Å. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence.

Visual habit formation in monkeys with neurotoxic lesions of the ventrocaudal neostriatum

Visual habit formation in monkeys, assessed by concurrent visual discrimination learning with 24-h intertrial intervals (ITI), was found earlier to be impaired by removal of the inferior temporal visual area (TE) but not by removal of either the medial temporal lobe or inferior prefrontal convexity, two of TE's major projection targets. To assess the role in this form of learning of another pair of structures to which TE projects, namely the rostral portion of the tail of the caudate nucleus and the overlying ventrocaudal putamen, we injected a neurotoxin into this neostriatal region of several monkeys and tested them on the 24-h ITI task as well as on a test of visual recognition memory. Compared with unoperated monkeys, the experimental animals were unaffected on the recognition test but showed an impairment on the 24-h ITI task that was highly correlated with the extent of their neostriatal damage. The findings suggest that TE and its projection areas in the ventrocaudal neostriatum form part of a circuit that selectively mediates visual habit formation.

The growth of demand will limit output growth for food over the next quarter century

The rate of growth of world food demand will be much slower for 1990–2010 than it was for the prior three decades. The major factor determining the increase in food demand is population growth. Income growth has a much smaller effect. From 1960 to 1990, population growth accounted for approximately three fourths of the growth in demand or use of grain. For 1990–2010, it is anticipated that population growth will account for nearly all of the increase in world demand for grain. The rate of population growth from 1990 to 2020 is projected to be at an annual rate of 1.3% compared with 1.9% for 1960 to 1990—a decline of more than 30%. World per capita use of grain will increase very little—perhaps by 4%. The increase in grain use is projected to be 40% less than in 1960–1990. It is anticipated that real grain prices will decline during the period, although not nearly as much as the 40% decline in the previous three decades. Concern has been expressed concerning the deterioration of the quality and productivity of the world’s farmland. A study for China and Indonesia indicates that there has been no significant change in the productive capacity of the land over the past 50 years. Contrary to numerous claims, the depth of the topsoil has not changed, indicating that erosion has had little or no impact.

Telomerase expression and activity are coupled with myocyte proliferation and preservation of telomeric length in the failing heart

The role and even the existence of myocyte proliferation in the adult heart remain controversial. Documentation of cell cycle regulators, DNA synthesis, and mitotic images has not modified the view that myocardial growth can only occur from hypertrophy of an irreplaceable population of differentiated myocytes. To improve understanding the biology of the heart and obtain supportive evidence of myocyte replication, three indices of cell proliferation were analyzed in dogs affected by a progressive deterioration of cardiac performance and dilated cardiomyopathy. The magnitude of cycling myocytes was evaluated by the expression of Ki67 in nuclei. Ki67 labeling of left ventricular myocytes increased 5-fold, 12-fold, and 17-fold with the onset of moderate and severe ventricular dysfunction and overt failure, respectively. Telomerase activity in vivo is present only in multiplying cells; this enzyme increased 2.4-fold and 3.1-fold in the decompensated heart, preserving telomeric length in myocytes. The contribution of cycling myocytes to telomerase activity was determined by the colocalization of Ki67 and telomerase in myocyte nuclei. More than 50% of Ki67-positive cells expressed telomerase in the overloaded myocardium, suggesting that these myocytes were the morphological counterpart of the biochemical assay of enzyme activity. Moreover, we report that 20–30% of canine myocytes were telomerase competent, and this value was not changed by cardiac failure. In conclusion, the enhanced expression of Ki67 and telomerase activity, in combination with Ki67-telomerase labeling of myocyte nuclei, support the notion that myocyte proliferation contributes to cardiac hypertrophy of the diseased heart.

Longevity and the genetic determination of collagen glycoxidation kinetics in mammalian senescence.

A fundamental question in the basic biology of aging is whether there is a universal aging process. If indeed such a process exists, one would expect that it develops at a higher rate in short- versus long-lived species. We have quantitated pentosidine, a marker of glycoxidative stress in skin collagen from eight mammalian species as a function of age. A curvilinear increase was modeled for all species, and the rate of increase correlated inversely with maximum life-span. Dietary restriction, a potent intervention associated with increased life-span, markedly inhibited glycoxidation rate in the rodent. On the assumption that collagen turnover rate is primarily influenced by the crosslinking due to glycoxidation, these results suggest that there is a progressive age-related deterioration of the process that controls the collagen glycoxidation rate. Thus, the ability to withstand damage due to glycoxidation and the Maillard reaction may be under genetic control.

On the existence and implications of an inverse folding code in proteins.

The existence of a code relating the set of possible sequences at a given position in a protein backbone to the local structure at that location is investigated. It is shown that only 73% of 4-C alpha structure fragments in a sample of 114 protein structures exhibit a preference for a particular set of sequences. The remaining structures can accommodate essentially any sequence. The structures that encode specific sequence distributions include the classical "secondary" structures, with the notable exception of planar (beta) bends. It is suggested that this has implications as to the mechanism of folding in proteins with extensive sheet/barrel structure. The possible role of structures that do not encode specific sequences as mutation hot spots is noted.

A Xenopus distal-less gene in transgenic mice: conserved regulation in distal limb epidermis and other sites of epithelial-mesenchymal interaction.

In this paper, we show the conserved regulation of the homeodomain gene Distal-less-3 (Dlx-3) by analyzing the expression of a promoter from the Xenopus ortholog, Xdll-2, in transgenic mice. A 470-bp frog regulatory sequence confers appropriate expression on a lacZ reporter gene in the ectodermal component of structures derived from epithelial-mesenchymal interactions. Remarkably, this includes structures absent in Xenopus, such as the hair follicle and mammary gland, suggesting that conserved regulatory elements can be used to control the formation of structures peculiar to individual species. In addition, expression of Dlx-3 in developing limbs is highest at the most distal portion. This pattern is duplicated by the Xenopus promoter, indicating that this DNA may include sequences responsive to conserved proximodistal patterning signals in the vertebrate limb.

Avaliação da integridade estrutural de elementos de concreto armado a partir das propriedades modais obtidas por técnicas de excitações aleatórias e transientes

A análise dinâmica experimental tem sido amplamente pesquisada como uma ferramenta de avaliação de integridade de estruturas de concreto armado. Existem técnicas de identificação de danos baseadas em propriedades modais como frequências de ressonâncias, deformadas modais, curvaturas modais e amortecimento. Há também técnicas baseadas na não linearidade da resposta dinâmica, que apesar do grande potencial na detecção de danos, têm sido pouco exploradas nos últimos anos. Este trabalho tem por objetivo avaliar a integridade estrutural de vigas de concreto armado através do comportamento da resposta dinâmica. Foram realizados ensaios dinâmicos em duas vigas de concreto armado com 3,5 m de comprimento, 25 cm de largura, 35 cm de altura e idênticas taxas de armaduras, mas configuradas com barras de aço de diferentes diâmetros, 2 ϕ 16 mm e 8 ϕ 8 mm, respectivamente. Tais vigas, inicialmente íntegras, foram submetidas a ciclos de carregamento e descarregamento com intensidades crescentes até atingir a ruptura do elemento. Após cada ciclo, as propriedades dinâmicas foram avaliadas experimentalmente, com o emprego de técnicas de excitação por sinais do tipo aleatório e tipo transiente, respectivamente, visando determinar parâmetros que indiquem a deterioração gradativa do elemento. Nesses ensaios dinâmicos aplicaram-se diferentes amplitudes da força de excitação. Verificou-se que o aumento da amplitude da força dinâmica de excitação provocou reduções nos valores das frequências de ressonância de 1,1% e 2,4%, associadas, respectivamente, às excitações aleatórias e transientes; e um comportamento não linear dos índices de amortecimento, associados às excitações aleatórias, mantendo um crescimento linear com as excitações transientes. Constatou-se, ainda, que os valores das frequências de ressonância decrescem com a redução de rigidez mecânica, diminuída com o aumento do nível de fissuração induzido nos modelos. Já os valores dos índices de amortecimento, após cada ciclo, se comportaram de forma não linear e assumiram diferentes valores, conforme a técnica de excitação empregada. Acredita-se que esta não linearidade está relacionada aos danos provocados no elemento pela solicitação estrutural e, por consequência, ao processo de como a dissipação de energia é empregada no processo de instauração, configuração e propagação das fissuras nos elementos de concreto armado.

Efeito da corrosão do chapeamento do fundo do casco sobre a confiabilidade estrutural de navios.

A engenharia é a ciência que transforma os conhecimentos das disciplinas básicas aplicadas a fatos reais. Nosso mundo está rodeado por essas realizações da engenharia, e é necessário que as pessoas se sintam confortáveis e seguras nas mesmas. Assim, a segurança se torna um fator importante que deve ser considerado em qualquer projeto. Na engenharia naval, um apropriado nível de segurança e, em consequência, um correto desenho estrutural é baseado, atualmente, em estudos determinísticos com o objetivo de obter estruturas capazes de suportar o pior cenário possível de solicitações durante um período de tempo determinado. A maior parte das solicitações na estrutura de um navio se deve à ação da natureza (ventos, ondas, correnteza e tempestades), ou, ainda, aos erros cometidos por humanos (explosões internas, explosões externas e colisões). Devido à aleatoriedade destes eventos, a confiabilidade estrutural de um navio deveria ser considerada como um problema estocástico sob condições ambientais bem caracterizadas. A metodologia probabilística, baseada em estatística e incertezas, oferece uma melhor perspectiva dos fenômenos reais que acontecem na estrutura dos navios. Esta pesquisa tem como objetivo apresentar resultados de confiabilidade estrutural em projetos e planejamento da manutenção para a chapa do fundo dos cascos dos navios, as quais são submetidas a esforços variáveis pela ação das ondas do mar e da corrosão. Foram estudados modelos estatísticos para a avaliação da estrutura da viga-navio e para o detalhe estrutural da chapa do fundo. Na avaliação da estrutura da viga-navio, o modelo desenvolvido consiste em determinar as probabilidades de ocorrência das solicitações na estrutura, considerando a deterioração por corrosão, com base numa investigação estatística da variação dos esforços em função das ondas e a deterioração em função de uma taxa de corrosão padrão recomendada pela DET NORSKE VERITAS (DNV). A abordagem para avaliação da confiabilidade dependente do tempo é desenvolvida com base nas curvas de resistências e solicitações (R-S) determinadas pela utilização do método de Monte Carlo. Uma variação estatística de longo prazo das adversidades é determinada pelo estudo estatístico de ondas em longo prazo e ajustada por uma distribuição com base numa vida de projeto conhecida. Constam no trabalho resultados da variação da confiabilidade ao longo do tempo de um navio petroleiro. O caso de estudo foi simplificado para facilitar a obtenção de dados, com o objetivo de corroborar a metodologia desenvolvida.

Changes in Access to Health Services of the Immigrant and Native-Born Population in Spain in the Context of Economic Crisis

Aim: To analyze changes in access to health care and its determinants in the immigrant and native-born populations in Spain, before and during the economic crisis. Methods: Comparative analysis of two iterations of the Spanish National Health Survey (2006 and 2012). Outcome variables were: unmet need and use of different healthcare levels; explanatory variables: need, predisposing and enabling factors. Multivariate models were performed (1) to compare outcome variables in each group between years, (2) to compare outcome variables between both groups within each year, and (3) to determine the factors associated with health service use for each group and year. Results: unmet healthcare needs decreased in 2012 compared to 2006; the use of health services remained constant, with some changes worth highlighting, such as the decline in general practitioner visits among autochthons and a narrowed gap in specialist visits between the two populations. The factors associated with health service use in 2006 remained constant in 2012. Conclusion: Access to healthcare did not worsen, possibly due to the fact that, until 2012, the national health system may have cushioned the deterioration of social determinants as a consequence of the financial crisis. Further studies are necessary to evaluate the effects of health policy responses to the crisis after 2012.

Understanding sickness presenteeism through the experience of immigrant workers in a context of economic crisis

Background: Previous economic recessions show that immigrant workers may experience longer periods of unemployment, a situation that may lead employees to presenteeism, the act of working in spite of a health problem. This study explored perceptions about the factors that lead to presenteeism in immigrant workers considering the context of economic crisis. Methods: Six focus group discussions were held (February 2012), with men and women from Colombia, Ecuador, and Morocco (n = 44) living in Spain and selected by theoretical sample. A qualitative content analysis was performed. Results: Four categories were identified as factors that influence the occurrence of presenteeism in a context of economic crisis: poor employment conditions, fear of unemployment, employer/employee relationship, and difficulties in finding temporary replacement workers. Furthermore, musculoskeletal, respiratory, and mental problems were related to presenteeism. Conclusions: It is important to develop strategies to protect workers from negative working conditions that are associated with deterioration of health.

Health inequality between immigrants and natives in Spain: the loss of the healthy immigrant effect in times of economic crisis

Background: The immigrant population living in Spain grew exponentially in the early 2000s but has been particularly affected by the economic crisis. This study aims to analyse health inequalities between immigrants born in middle- or low-income countries and natives in Spain, in 2006 and 2012, taking into account gender, year of arrival and socioeconomic exposures. Methods: Study of trends using two cross-sections, the 2006 and 2012 editions of the Spanish National Health Survey, including residents in Spain aged 15–64 years (20 810 natives and 2950 immigrants in 2006, 14 291 natives and 2448 immigrants in 2012). Fair/poor self-rated health, poor mental health (GHQ-12 > 2), chronic activity limitation and use of psychotropic drugs were compared between natives and immigrants who arrived in Spain before 2006, adjusting robust Poisson regression models for age and socioeconomic variables to obtain prevalence ratios (PR) and 95% confidence interval (CI). Results: Inequalities in poor self-rated health between immigrants and natives tend to increase among women (age-adjusted PR2006 = 1.39; 95% CI: 1.24–1.56, PR2012 = 1.56; 95% CI: 1.33–1.82). Among men, there is a new onset of inequalities in poor mental health (PR2006 = 1.10; 95% CI: 0.86–1.40, PR2012 = 1.34; 95% CI: 1.06–1.69) and an equalization of the previously lower use of psychotropic drugs (PR2006 = 0.22; 95% CI: 0.11–0.43, PR2012 = 1.20; 95% CI: 0.73–2.01). Conclusions: Between 2006 and 2012, immigrants who arrived in Spain before 2006 appeared to worsen their health status when compared with natives. The loss of the healthy immigrant effect in the context of a worse impact of the economic crisis on immigrants appears as potential explanation. Employment, social protection and re-universalization of healthcare would prevent further deterioration of immigrants’ health status.

Electrochemical reactions of catechol, methylcatechol and dopamine at tetrahedral amorphous carbon (ta-C) thin film electrodes

The electrochemical reactions of dopamine, catechol and methylcatechol were investigated at tetrahedral amorphous carbon (ta-C) thin film electrodes. In order to better understand the reaction mechanisms of these molecules, cyclic voltammetry with varying scan rates was carried out at different pH values in H2SO4 and PBS solutions. The results were compared to the same redox reactions taking place at glassy carbon (GC) electrodes. All three catechols exhibited quasi-reversible behavior with sluggish electron transfer kinetics at the ta-C electrode. At neutral and alkaline pH, rapid coupled homogeneous reactions followed the oxidation of the catechols to the corresponding o-quinones and led to significant deterioration of the electrode response. At acidic pH, the extent of deterioration was considerably lower. All the redox reactions showed significantly faster electron transfer kinetics at the GC electrode and it was less susceptible toward surface passivation. An EC mechanism was observed for the oxidation of dopamine at both ta-C and GC electrodes and the formation of polydopamine was suspected to cause the passivation of the electrodes.

The beginning of a new political cycle: the results and consequences of a nomination summit. EPC Post-Summit Analysis, 30 June 2014

Despite a broader agenda, the June 2014 European Council was dominated by the decision of EU leaders – taken by qualified majority – to propose to the European Parliament Jean-Claude Juncker as the next Commission President. In this post-summit analysis Janis A. Emmanouilidis argues that recent developments could have four consequences: increasing politicisation at European level; opposition from the side of national governments to what they consider to be an unjustifiable shift of power; further complication, maybe even deterioration of the relationship between London and ‘Brussels; and ‘consolidation’ as the predominant political attitude in the beginning of a new political cycle. Aside from all this, the Summit adopted a Strategic Agenda for the years to come, agreed to new strategic guidelines for the Area of Freedom, Security and Justice, postponed the decision on a new energy and climate framework to October, concluded the fourth European Semester with the adoption of country-specific recommendations, and, last but not least, EU leaders finally signed the Association Agreements with Georgia, Moldova and Ukraine demonstrating that the Union and these countries are ready to deepen political and economic ties.

The challenge of freedom in the Southeastern Europe. OSW Report, July 2015

Over the past few decades substantial progress has been achieved in the democratisation and modernisation of the countries of Southeastern Europe. The formal democratic institutions were introduced, a liberalisation of trade resulted in the reintegration of the region into the global economy and some of them successfully applied to join the EU and NATO. But the transformation process is far from over. In the past years the achievements of the political and economic transformation have been rolled back and the quality of governance has declined in many countries. To avoid a further deterioration of the situation in the region the new impulse for institutional transformation and a change of the development model are needed. This report is the outcome of a discussion held during the conference “The Freedom Challenge in Southeastern Europe – Implications for Poland”. This joint event was developed by the Centre for Eastern Studies and Ideas Lab – the President’s Expert Programme at the Chancellery of the President of the Republic of Poland. The chapters of the report reflect the main three subjects debated during the conference. In the first chapter Spasimir Domaradzki assesses the rule of law and its influence on the consolidation of democracy in the region. In the second chapter Marta Szpala focuses on economic development in Southeastern Europe. The third chapter is written by Adam Balcer and analyses the key instruments Russia is using to build influence in this region.