Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.

BACKGROUND: Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial and probabilistic methods that look for coevolving positions in nucleotide or amino acid sequences. RESULTS: We have developed a web-based platform that gives a user-friendly access to two phylogenetic-based methods implementing the Coev model: the evaluation of coevolving scores and the simulation of coevolving positions. We have also extended the capabilities of the Coev model to allow for the generalization of the alphabet used in the Markov model, which can now analyse both nucleotide and amino acid data sets. The simulation of coevolving positions is novel and builds upon the developments of the Coev model. It allows user to simulate pairs of dependent nucleotide or amino acid positions. CONCLUSIONS: The main focus of our paper is the new simulation method we present for coevolving positions. The implementation of this method is embedded within the web platform Coev-web that is freely accessible at http://coev.vital-it.ch/, and was tested in most modern web browsers.

Statistical hypothesis testing and common misinterpretations: should we abandon p-value in forensic science applications?

Many people regard the concept of hypothesis testing as fundamental to inferential statistics. Various schools of thought, in particular frequentist and Bayesian, have promoted radically different solutions for taking a decision about the plausibility of competing hypotheses. Comprehensive philosophical comparisons about their advantages and drawbacks are widely available and continue to span over large debates in the literature. More recently, controversial discussion was initiated by an editorial decision of a scientific journal [1] to refuse any paper submitted for publication containing null hypothesis testing procedures. Since the large majority of papers published in forensic journals propose the evaluation of statistical evidence based on the so called p-values, it is of interest to expose the discussion of this journal's decision within the forensic science community. This paper aims to provide forensic science researchers with a primer on the main concepts and their implications for making informed methodological choices.

Nursing intervention versus usual care to improve delirium among home-dwelling older adults receiving homecare after hospitalization: feasibility and acceptability of a Randomized Controlled Trail.

BACKGROUND: Delirium is an acute cognitive impairment among older hospitalized patients. It can persist until discharge and for months after that. Despite proof that evidence-based nursing interventions are effective in preventing delirium in acute hospitals, interventions among home-dwelling older patients is lacking. The aim was to assess feasibility and acceptability of a nursing intervention designed to detect and reduce delirium in older adults after discharge from hospital. METHODS: Randomized clinical pilot trial with a before/after design was used. One hundred and three older adults were recruited in a home healthcare service in French-speaking Switzerland and randomized into an experimental group (EG, n = 51) and a control group (CG, n = 52). The CG received usual homecare. The EG received usual homecare plus five additional nursing interventions at 48 and 72 h and at 7, 14 and 21 days after discharge. These interventions were tailored for detecting and reducing delirium and were conducted by a geriatric clinical nurse (GCN). All patients were monitored at the start of the study (M1) and throughout the month for symptoms of delirium (M2). This was documented in patients' records after usual homecare using the Confusion Assessment Method (CAM). At one month (M2), symptoms of delirium were measured using the CAM, cognitive status was measured using the Mini-Mental State Examination (MMSE), and functional status was measured using Katz and Lawton Index of activities of daily living (ADL/IADL). At the end of the study, participants in the EG and homecare nurses were interviewed about the acceptability of the nursing interventions and the study itself. RESULTS: Feasibility and acceptability indicators reported excellent results. Recruitment, retention, randomization, and other procedures were efficient, although some potentially issues were identified. Participants and nurses considered organizational procedures, data collection, intervention content, the dose-effect of the interventions, and methodology all to be feasible. Duration, patient adherence and fidelity were judged acceptable. Nurses, participants and informal caregivers were satisfied with the relevance and safety of the interventions. CONCLUSIONS: Nursing interventions to detect/improve delirium at home are feasible and acceptable. These results confirm that developing a large-scale randomized controlled trial would be appropriate. TRIAL REGESTRATION: ISRCTN registry no: 16103589 - 19 February 2016.

Worldwide trends in diabetes since 1980: a pooled analysis of 751 population-based studies with 4.4 million participants.

One of the global targets for non-communicable diseases is to halt, by 2025, the rise in the age-standardised adult prevalence of diabetes at its 2010 levels. We aimed to estimate worldwide trends in diabetes, how likely it is for countries to achieve the global target, and how changes in prevalence, together with population growth and ageing, are affecting the number of adults with diabetes. We pooled data from population-based studies that had collected data on diabetes through measurement of its biomarkers. We used a Bayesian hierarchical model to estimate trends in diabetes prevalence-defined as fasting plasma glucose of 7.0 mmol/L or higher, or history of diagnosis with diabetes, or use of insulin or oral hypoglycaemic drugs-in 200 countries and territories in 21 regions, by sex and from 1980 to 2014. We also calculated the posterior probability of meeting the global diabetes target if post-2000 trends continue. We used data from 751 studies including 4,372,000 adults from 146 of the 200 countries we make estimates for. Global age-standardised diabetes prevalence increased from 4.3% (95% credible interval 2.4-7.0) in 1980 to 9.0% (7.2-11.1) in 2014 in men, and from 5.0% (2.9-7.9) to 7.9% (6.4-9.7) in women. The number of adults with diabetes in the world increased from 108 million in 1980 to 422 million in 2014 (28.5% due to the rise in prevalence, 39.7% due to population growth and ageing, and 31.8% due to interaction of these two factors). Age-standardised adult diabetes prevalence in 2014 was lowest in northwestern Europe, and highest in Polynesia and Micronesia, at nearly 25%, followed by Melanesia and the Middle East and north Africa. Between 1980 and 2014 there was little change in age-standardised diabetes prevalence in adult women in continental western Europe, although crude prevalence rose because of ageing of the population. By contrast, age-standardised adult prevalence rose by 15 percentage points in men and women in Polynesia and Micronesia. In 2014, American Samoa had the highest national prevalence of diabetes (>30% in both sexes), with age-standardised adult prevalence also higher than 25% in some other islands in Polynesia and Micronesia. If post-2000 trends continue, the probability of meeting the global target of halting the rise in the prevalence of diabetes by 2025 at the 2010 level worldwide is lower than 1% for men and is 1% for women. Only nine countries for men and 29 countries for women, mostly in western Europe, have a 50% or higher probability of meeting the global target. Since 1980, age-standardised diabetes prevalence in adults has increased, or at best remained unchanged, in every country. Together with population growth and ageing, this rise has led to a near quadrupling of the number of adults with diabetes worldwide. The burden of diabetes, both in terms of prevalence and number of adults affected, has increased faster in low-income and middle-income countries than in high-income countries. Wellcome Trust.