An alternative marginal likelihood estimator for phylogenetic models

Bayesian phylogenetic methods are generating noticeable enthusiasm in the field of molecular systematics. Many phylogenetic models are often at stake and different approaches are used to compare them within a Bayesian framework. The Bayes factor, defined as the ratio of the marginal likelihoods of two competing models, plays a key role in Bayesian model selection. We focus on an alternative estimator of the marginal likelihood whose computation is still a challenging problem. Several computational solutions have been proposed none of which can be considered outperforming the others simultaneously in terms of simplicity of implementation, computational burden and precision of the estimates. Practitioners and researchers, often led by available software, have privileged so far the simplicity of the harmonic mean estimator (HM) and the arithmetic mean estimator (AM). However it is known that the resulting estimates of the Bayesian evidence in favor of one model are biased and often inaccurate up to having an infinite variance so that the reliability of the corresponding conclusions is doubtful. Our new implementation of the generalized harmonic mean (GHM) idea recycles MCMC simulations from the posterior, shares the computational simplicity of the original HM estimator, but, unlike it, overcomes the infinite variance issue. The alternative estimator is applied to simulated phylogenetic data and produces fully satisfactory results outperforming those simple estimators currently provided by most of the publicly available software

Low-cost carriers and tourism in the Italian regions: a segmented regression model

The paper analyzes the effects of air transport deregulation on international tourism flows in the Italian regions. Due to several reasons, tourist flows rarely are equally distributed within a nation. We focus on the accessibility to a territory as one of those reasons. Easy and cheap access to a destination is the prerequisite for its tourism development; in this respect, the advent of low-cost carriers has increased accessibility to many tourist destinations. We propose a segmented regression analysis to study the evolution of the share of European tourist arrivals in each region on the total European tourists visiting Italy. Accordingly, we identify which regions have gotten a higher advantage in terms of tourism growth due to the air transport deregulation

Bayesian analysis of the multivariate dependence of three transition water ecosystem classifications

The Water Framework Directive (WFD) recognizes benthic macroinvertebrates as a good biological quality element for transitional waters as they are the most exposed to natural variability patterns characteristic of these ecosystems, due to their life cycles and space-use behavior. Here, we address the ecological status classification issue for three lagoons in Apulia, using benthic macroinvertebrates and three proposed multimetric indices (namely M-AMBI, BITS and ISS), likely to respond differently to different sources of stress and natural variability. Lagoon classification is based on discretization by standard classification boundaries with only partial consideration of the natural variability of ecosystem properties and possible inaccuracies of the classification procedures. In order to investigate the possible contrasting behavior of the three classifications, we propose Bayesian hierarchical models in which the multimetric indices and their discrete counterparts are jointly modeled as function of abiotic covariates, external anthropogenic pressures indicators and spatio-temporal effects

L'arte e la scienza di imparare dai dati: la biostatistica, dalle mutazioni genetiche all'intelligenza artificiale.

La biostatistica è comunemente definita come l'applicazione di metodologie statistiche a dati di natura biologica o medica. In realtà, tale definizione è piuttosto riduttiva in quanto essa si occupa di sviluppare nuove metodologie che tengano conto della peculiarità dei dati sperimentali e che rispondano, in modo chiaro, alle domande poste dagli scienziati. In particolare, i metodi di biostatistica si sono particolarmente sviluppati per l'analisi di dati genetici che, per dimensione e per struttura di dipendenza, non possono essere analizzati con metodologie standard. La biostatistica nasce quindi come materia interdisciplinare che formalizza con un linguaggio statistico-probabilistico problemi di natura applicata e cerca di dare delle risposte che riflettano sia una significatività statistica che biologica

Two-part model with measurement error. Modello a due parti con errore di misura

In many applications, there are positive-valued phenomena which show a very high frequency at zero. One major difculty with this type of data is that the existence of a point-mass at zero makes common distributions unsuited for modeling the data. To cope with these difculties, some models have been developed. A popular example is the two-part model in which two stochastic models are assumed: the rst governs whether the response variable is zero or positive an the second, conditional on its being positive, models the level. We extend the two-part model to cope with measurement error on the dependent variables of both stochastic parts. This situation is common in many applied works

Using tt-distribution for Robust ‎Hierarchical Bayesian Small Area Estimation under Measurement Error in Covariates

Small area estimation often suffers from imprecise direct estimators due to small sample sizes. One method for giving direct estimators more strength is to use models.‎ Models ‎employ area effects and ‎include supplementary information  from extra sources as covariates to increase the accuracy of direct estimators. ‎The valid covariates are the basis of ‎the ‎small ‎area ‎estimation.‎ Therefore, measurement error (ME) in covariates can produce contradictory results, i.e., even reduce the precision of direct estimators. The Gaussian distribution with known variance is generally apply as a distribution of ME. ‏‎ ‎However‎, ‎in real problem, ‎‎there might be situations in which the normality assumption fo MEs does not hold‎. In addition, the assumption of known ME variance is restricted. To address these issues and obtain a more robust model, ‎‎we propose modeling ME using a $t$-distribution with known and unknown degrees of freedom. Model parameters are estimated using a fully Bayesian framework based on MCMC methods. We validate our proposed model using simulated data and apply it to well-known crop data and the cost and income of households living in Kurdistan province of ‎Iran.

Modifiable risk factors associated with bronchiolitis

Background: We sought to clarify possibly modifiable risk factors related to pollution responsible for acute bronchiolitis in hospitalized infants. Methods: For this observational study, we recruited 213 consecutive infants with bronchiolitis (cases: median age: 2 months; age range: 0.5-12 months; boys: 55.4%) and 213 children aged <3 years (controls: median age: 12 months; age range: 0.5-36 months; boys: 54.5%) with a negative medical history for lower respiratory tract diseases hospitalized at 'Sapienza' University Rome and IRCCS Bambino Gesù Hospital. Infants' parents completed a standardized 53-item questionnaire seeking information on social-demographic and clinical characteristics, indoor pollution, eating habits and outdoor air pollution. Multivariate logistic regression analyses were run to assess the independent effect of risk factors, accounting for confounders and effect modifiers. Results: In the 213 hospitalized infants the questionnaire identified the following risk factors for acute bronchiolitis: breastfeeding 3/43 months (OR: 2.1, 95% confidence interval [CI]: 1.2-3.6), presence of older siblings (OR: 2.8, 95% CI: 1.7-4.7), 3/44 cohabitants (OR: 1.5, 95% CI: 1.1-2.1), and using seed oil for cooking (OR: 1.7, 95% CI: 1.2-2.6). Having renovated their home in the past 12 months and concurrently being exposed daily to smoking, involving more than 11 cigarettes and two or more smoking cohabitants, were more frequent factors in cases than in controls (p = 0.021 and 0.05), whereas self-estimated proximity to road and traffic was similar in the two groups. Conclusions: We identified several risk factors for acute bronchiolitis related to indoor and outdoor pollution, including inhaling cooking oil fumes. Having this information would help public health authorities draw up effective preventive measures - for example, teach mothers to avoid handling their child when they have a cold and eliminate exposure to second-hand tobacco smoke

Polygraphic findings in simplified Barbed Reposition Pharyngoplasty (BRP) as a treatment for OSA patients

This study aims to compare polygraphic data in patients with OSA treated with Barbed Reposition Pharyngoplasty (BRP) performed with a simplified technique compared to the standard method. Variations of technique were performed and tested with the purpose of promoting tolerability and diffusion of this simplified technique. To evaluate the efficacy of the simplified BRP method, a sample of 99 patients was divided into two groups: Group A was treated with BRP (BRP group) and Group B was treated with simplified BRP (sBRP group). The results obtained on the two groups were compared with the two sample Bootstrap t-tests method, showing a substantial overlap in polygraphic results recorded 6 months after surgery

The Role of Age on Beta-Amyloid1–42 Plasma Levels in Healthy Subjects

Beta-amyloid (Ab) plaques have been observed in the brain of healthy elderlies with frequencies strongly influenced by age. The aim of the study is to evaluate the role of age and other biochemical and hematological parameters on Ab1–42 plasma levels in cognitively and neurologically normal individuals. Two-hundred and seventy-five normal subjects stratified by age groups (&lt;35 years, 35–65 years, and &gt;65 years) were included in the study. Ab1–42 plasma levels significantly correlated with age (rs = 0.27; p &lt; 0.0001) in the whole sample, inversely correlated with age in the first age group (rs = 0.25, p = 0.01), positively correlated in the second group (rs = 0.22, p = 0.03), while there was no significant correlation in the older group (rs = 0.02, p = 0.86). Both age (b- estimate = 0.08; p &lt; 0.001) and cholesterol (b-estimate = 0.03; p = 0.009) were significantly associated with Ab1–42 plasma level in multivariable analysis. However, only the association with age survived post hoc adjustment for multiple comparisons. The different effects of age on the Ab level across age groups should be explored in further studies to better understand the age-dependent variability. This could better define the value of plasma Ab as a biomarker of the Alzheimer neuropathology

Patterns of functional diversity of macroinvertebrates across three aquatic ecosystem types, NE Mediterranean

This study is focused on investigating the variation patterns of macroinvertebrate guilds functional structure, in relation to the taxonomic one, across aquatic ecosystem types along the salinity gradient from freshwater to marine and the resulting implications on guild organization and energy flows. Synoptic samplings have been carried out using the leaf-pack technique at 30 sites of the aquatic ecosystems of the Corfu Island (Greece), including freshwater, lagoon, and marine sites. Here, we analyzed the macroinvertebrate guilds of river, lagoon, and marine ecosystems, as: i. taxonomic composition and population abundance ii. trophic guilds composition and relative abundance; and iii. body size spectra and size patterns. The following variation patterns across the three ecosystem types were observed: a. trophic guild composition and body size spectra were more conservative than taxonomic composition within and among ecosystem types, where, trophic guild and size spectra composition were more similar between river and lagoon ecosystem types than with marine ones; b. a dominance on resource exploitation of large species over smaller ones was inferred at all sites; and, c. higher body size-specific density of individuals was consistently observed in lagoon than in freshwater and marine ecosystems. Results extend previous findings suggesting a common hierarchical organization of benthic macroinvertebrate guilds in aquatic ecosystems and showing that lagoon ecosystems have higher energy density transferred to benthic macroinvertebrates than both freshwater and marine ecosystem types