A practical guide to the simultaneous determination of protein structure and dynamics using metainference

Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well as with system heterogeneity. Furthermore, metainference can be implemented using the metadynamics approach, which enables the computational study of complex biological systems requiring extensive conformational sampling. In this chapter, we provide a step-by-step guide to perform and analyse metadynamic metainference simulations using the ISDB module of the open-source PLUMED library, as well as a series of practical tips to avoid common mistakes. Specifically, we will guide the reader in the process of learning how to model the structural ensemble of a small disordered peptide by combining state-of-the-art molecular mechanics force fields with nuclear magnetic resonance data, including chemical shifts, scalar couplings and residual dipolar couplings.Comment: 49 pages, 9 figure

Minichromosome maintenance proteins 2 and 5 in non-benign epithelial ovarian tumours: relationship with cell cycle regulators and prognostic implications

Minichromosome maintenance proteins (MCM) have recently emerged as novel proliferation markers with prognostic implications in several tumour types. This is the first study investigating MCM-2 and MCM-5 immunohistochemical expression in a series of ovarian adenocarcinomas and low malignant potential (LMP) tumours aiming to determine possible associations with clinicopathological parameters, the conventional proliferation index Ki-67, cell cycle regulators (p53, p27Kip1, p21WAF1 and pRb) and patients' outcome. Immunohistochemistry was applied in a series of 43 cases of ovarian LMP tumours and 85 cases of adenocarcinomas. Survival analysis was restricted to adenocarcinomas. The median MCM-2 and MCM-5 labelling indices (LIs) were significantly higher in adenocarcinomas compared to LMP tumours (P<0.0001 for both associations). In adenocarcinomas, the levels of MCM-2 and MCM-5 increased significantly with advancing tumour stage (P=0.0052 and P=0.0180, respectively), whereas both MCM-2 and MCM-5 increased significantly with increasing tumour grade (P=0.0002 and P=0.0006, respectively) and the presence of bulky residual disease (P<0.0001 in both relationships). A strong positive correlation was established between MCM-2 or MCM-5 expression level and Ki-67 LI (P<0.0001) as well as p53 protein (P=0.0038 and P=0.0500, respectively). Moreover, MCM-2 LI was inversely correlated with p27Kip−1 LI (P=0.0068). Finally, both MCM-2 and MCM-5 were associated significantly with adverse patients' outcome in both univariate (⩾20 vs >20%, P=0.0011 and ⩾25 vs <25%, P=0.0100, respectively) and multivariate (P=0.0001 and 0.0090, respectively) analysis. An adequately powered independent group of 45 patients was used in order to validate our results in univariate survival analysis. In this group, MCM-2 and MCM-5 expression retained their prognostic significance (P<0.0001 in both relationships). In conclusion, MCM-2 and MCM-5 proteins appear to be promising as prognostic markers in patients with ovarian adenocarcinomas

Beyond the Evidence of the New Hypertension Guidelines. Blood pressure measurement – is it good enough for accurate diagnosis of hypertension? Time might be in, for a paradigm shift (I)

Despite widespread availability of a large body of evidence in the area of hypertension, the translation of that evidence into viable recommendations aimed at improving the quality of health care is very difficult, sometimes to the point of questionable acceptability and overall credibility of the guidelines advocating those recommendations. The scientific community world-wide and especially professionals interested in the topic of hypertension are witnessing currently an unprecedented debate over the issue of appropriateness of using different drugs/drug classes for the treatment of hypertension. An endless supply of recent and less recent "drug-news", some in support of, others against the current guidelines, justifying the use of selected types of drug treatment or criticising other, are coming out in the scientific literature on an almost weekly basis. The latest of such debate (at the time of writing this paper) pertains the safety profile of ARBs vs ACE inhibitors. To great extent, the factual situation has been fuelled by the new hypertension guidelines (different for USA, Europe, New Zeeland and UK) through, apparently small inconsistencies and conflicting messages, that might have generated substantial and perpetuating confusion among both prescribing physicians and their patients, regardless of their country of origin. The overwhelming message conveyed by most guidelines and opinion leaders is the widespread use of diuretics as first-line agents in all patients with blood pressure above a certain cut-off level and the increasingly aggressive approach towards diagnosis and treatment of hypertension. This, apparently well-justified, logical and easily comprehensible message is unfortunately miss-obeyed by most physicians, on both parts of the Atlantic. Amazingly, the message assumes a universal simplicity of both diagnosis and treatment of hypertension, while ignoring several hypertension-specific variables, commonly known to have high level of complexity, such as: - accuracy of recorded blood pressure and the great inter-observer variability, - diversity in the competency and training of diagnosing physician, - individual patient/disease profile with highly subjective preferences, - difficulty in reaching consensus among opinion leaders, - pharmaceutical industry's influence, and, nonetheless, - the large variability in the efficacy and safety of the antihypertensive drugs. The present 2-series article attempts to identify and review possible causes that might have, at least in part, generated the current healthcare anachronism (I); to highlight the current trend to account for the uncertainties related to the fixed blood pressure cut-off point and the possible solutions to improve accuracy of diagnosis and treatment of hypertension (II)

Avaliação da alimentação de idosos de município paulista: aplicação do Índice de Alimentação Saudável

OBJETIVO: avaliar a qualidade da dieta da população idosa do município de Avaré (SP) através do Índice de Alimentação Saudável (IAS) MÉTODOS: trata-se de um estudo de corte transversal de base populacional realizado por meio de entrevista domiciliar. A amostra constou de 73 indivíduos, sorteados aleatoriamente dos idosos integrados ao Sistema Público de Saúde do Município. O consumo alimentar foi medido por meio de 3 Recordatórios de 24 horas. Para avaliação, foi aplicado o IAS adaptado para a população brasileira. Parte-se do princípio que o presente estudo constitui o primeiro no Brasil a aplicar o IAS utilizando 3 inquéritos do tipo recordatório de 24 horas em população idosa. Optou-se por esta metodologia, pois como descrito na literatura, um único dia não representa a ingestão habitual de um indivíduo devido à elevada variabilidade intrapessoal do consumo. RESULTADOS: Foram encontrados 32,9% de idosos com uma dieta de má qualidade; 60,3% necessitando de melhorias e 6,8% com uma dieta de boa qualidade. CONCLUSÃO: Pode-se concluir que os idosos estudados precisam de melhorias na alimentação, o que ressalta a importância de política de incentivo voltado à alimentação saudável na terceira idade.The scope of this paper was to evaluate the quality of the diet of the elderly in the city of Avaré, São Paulo state, using the Healthy Eating Index (HEI). A cross-sectional population-based study was conducted by home interviews. The sample consisted of 73 individuals, randomly selected among elderly people from the public health system in the city. Food consumption was measured by 3 24-hour recalls. The HEI adapted to the Brazilian population was applied for evaluation purposes. It is believed that this study is the first in Brazil to apply the HEI using 3 surveys of the 24-hour recall type among the elderly population. This methodology was chosen because, as described in the literature, a single day does not accurately reflect the usual intake of an individual due to the high interpersonal variance in consumption. It was found that 32.9% of elderly people were on a poor quality diet, 60.3% needed adjustments and 6.8% had a good quality diet. The conclusion that can be drawn is that the elderly population studied need to improve their diet, which emphasizes the importance of policies geared to encouraging healthy eating in old age.Universidade Estadual de São Paul

Predicting Return Outcomes to Shareholders from Companies Entering Chapter 11 Bankruptcy

In this paper we develop a model for predicting whether shareholders either lose all their investment, or receive some value, on a firm s exit from Chapter 11 bankruptcy proceedings. Using both firm-specific and market-wide predictor covariates, we employ the proportional hazards model to estimate the hazard that firms will exit from Chapter 11 without returning value to shareholders, and the survival probability that this will not happen. Furthermore, we also estimate how this probability varies over the time that a company may stay in Chapter 11. We develop two models, one using firm-specific covariates only and the other using market-wide and firm-specific covariates. Receiver operating characteristic (ROC) curves are used to examine the predictive ability of the models. Both models were found to have equivalent predictive ability