Multi-study factor regression model: an application in nutritional epidemiology

Diet is a risk factor for many diseases. In nutritional epidemiology, studying reproducible dietary patterns is critical to reveal important associations with health. However, it is challenging: diverse cultural and ethnic backgrounds may critically impact eating patterns, showing heterogeneity, leading to incorrect dietary patterns and obscuring the components shared across different groups or populations. Moreover, covariate effects generated from observed variables, such as demographics and other confounders, can further bias these dietary patterns. Identifying the shared and group-specific dietary components and covariate effects is essential to drive accurate conclusions. To address these issues, we introduce a new modeling factor regression, the Multi-Study Factor Regression (MSFR) model. The MSFR model analyzes different populations simultaneously, achieving three goals: capturing shared component(s) across populations, identifying group-specific structures, and correcting for covariate effects. We use this novel method to derive common and ethnic-specific dietary patterns in a multi-center epidemiological study in Hispanic/Latinos community. Our model improves the accuracy of common and group dietary signals and yields better prediction than other techniques, revealing significant associations with health. In summary, we provide a tool to integrate different groups, giving accurate dietary signals crucial to inform public health policy

The Impact of Exercise Intervention with Rhythmic Auditory Stimulation to Improve Gait and Mobility in Parkinson Disease: An Umbrella Review

Difficulties in walking, controlling balance, and performing activities of daily living are common problems encountered by individuals affected by Parkinson disease. Scientific evidence suggests that exercise performed with music or auditory or rhythmical cues facilitates movement and improves balance, gait, mobility, and activities of daily living (ADL) performance in patients with PD. The aim of this umbrella review was to summarize available high-quality evidence from systematic reviews and meta-analyses on the effectiveness of rhythmically cued exercise to improve gait, mobility, and ADL performance in individuals with PD. PubMed, Cochrane, and Embase databases were searched from January 2010 to October 2020 for systematic reviews and meta-analyses which had to be (1) written in English, (2) include studies on populations of males and females with PD of any age, (3) analyze outcomes related to gait, mobility, and ADL, and (4) apply exercise interventions with music or auditory or rhythmical cues. Two independent authors screened potentially eligible studies and assessed the methodological quality of the studies using the AMSTAR 2 tool. Four studies, two systematic reviews and meta-analyses, one a systematic review, and one a meta-analysis, were selected. Overall results indicated positive effects for gait and mobility of the use of rhythmic auditory cueing with exercise and suggested that it should be incorporated into a regular rehabilitation program for patients affected by PD. Nonetheless, more primary level research is needed to address the identified gaps regarding the application of this method to physical exercise interventions

Multi-study factor models for high-dimensional biological data

High-throughput assays are transforming the study of biology, and are generating a rich, complex and diverse collection of high-dimensional data sets. Building systematic knowledge from this data is a cumulative process, which requires analyses that integrate multiple sources, studies, and technologies. The increased availability of ensembles of studies on related clinical populations, assaying technologies, and genomic features poses two categories of very important multi-study statistical components: 1) common factors shared across multiple studies; 2) study-specific factors. To capture these two different quantities, in this thesis we propose a novel class of factor analysis models, both under a frequentist and Bayesian approach. In the frequentist approach an ECM algorithm is provided to obtain the maximum likelihood estimates. Moreover, we propose a Bayesian approach to apply the method to settings with more variables than subjects. In modeling dependencies among many variables, a sparse structure underlying the associations among genes is assumed. Both methods allow to perform joint analysis of multiple high-throughput studies. The results are helpful for combining multiple studies, identifying reproducible biology across studies and interesting study-specific components, and removing idiosyncratic variation that lacks cross-study reproducibility

Bayesian Ordinal Quantile Regression with a Partially Collapsed Gibbs Sampler

Unlike standard linear regression, quantile regression captures the relationship between covariates and the conditional response distribution as a whole, rather than only the relationship between covariates and the expected value of the conditional response. However, while there are well-established quantile regression methods for continuous variables and some forms of discrete data, there is no widely accepted method for ordinal variables, despite their importance in many medical contexts. In this work, we describe two existing ordinal quantile regression methods and demonstrate their weaknesses. We then propose a new method, Bayesian ordinal quantile regression with a partially collapsed Gibbs sampler (BORPS). We show superior results using BORPS versus existing methods on an extensive set of simulations. We further illustrate the benefits of our method by applying BORPS to the Fragile Families and Child Wellbeing Study data to tease apart associations with early puberty among both genders. Software is available at: GitHub.com/igrabski/borps

Ability of Lactobacillus kefiri LKF01 (DSM32079) to colonize the intestinal environment and modify the gut microbiota composition of healthy individuals

Abstract Background Probiotics have been observed to positively influence the host's health, but to date few data about the ability of probiotics to modify the gut microbiota composition exist. Aims To evaluate the ability of Lactobacillus kefiri LKF01 DSM32079 (LKEF) to colonize the intestinal environment of healthy subjects and modify the gut microbiota composition. Methods Twenty Italian healthy volunteers were randomized in pre-prandial and post-prandial groups. Changes in the gut microbiota composition were detected by using a Next Generation Sequencing technology (Ion Torrent Personal Genome Machine). Results L. kefiri was recovered in the feces of all volunteers after one month of probiotic administration, while it was detected only in three subjects belonging to the pre-prandial group and in two subjects belonging to the post-prandial group one month after the end of probiotic consumption. After one month of probiotic oral intake we observed a reduction of Bilophila, Butyricicomonas, Flavonifractor, Oscillibacter and Prevotella. Interestingly, after the end of probiotic administration Bacteroides, Barnesiella, Butyricicomonas, Clostridium, Haemophilus, Oscillibacter, Salmonella, Streptococcus, Subdoligranolum, and Veillonella were significantly reduced if compared to baseline samples. Conclusion L. kefiri LKF01 showed a strong ability to modulate the gut microbiota composition, leading to a significant reduction of several bacterial genera directly involved in the onset of pro-inflammatory response and gastrointestinal diseases

Who chooses alternative sources of information about childhood vaccinations? A cross-sectional study

Introduction: Vaccine hesitancy can lead to problematic outcomes in terms of public health. A factor playing a fundamental role in this dynamic is the source of information considered by parents in the decision-making progress that leads to the acceptance or refusal of childhood vaccinations. This study aims to investigate the sources of information considered by the parents of children attending primary and secondary schools in two large Italian cities and to identify predictors that led to choosing alternative sources of information. Methods: An online questionnaire was administered to the parents of students attending elementary, middle, and high schools in Rome and Turin. Two validated tools were used: the Parent Attitudes about Childhood Vaccines Survey and the Vaccine Health Literacy of adults in Italian. Sources of information about vaccinations, trust toward the healthcare system, hesitancy and attitudes about COVID-19 vaccinations, were also investigated. A multivariable logistic regression model was built to identify predictors of the preferred sources of information on the topic. Results: Totally, 2,301 answers to the survey were collected from June to October 2021. Of these, 1,127 came from parents in Rome (49%) and 1,174 from parents based in Turin (51%) with a mean age of 47.7 years (±6.4). The majority of the respondents were mothers (81%), married (73%), with two or more children (70.5%). The multivariable logistic regression model results showed that fathers were more inclined than mothers to use alternative sources of information (OR 1.48, 95% CI 1.29–2.00). Moreover, a higher level of vaccine hesitancy was a strong predictor for choosing alternative sources of information (OR 2.45, 95% CI 1.73–3.46). The HLVa-it scores show that parents with a lower Vaccine Literacy (VL) were more inclined to use alternative sources of information. Discussion: Addressing health literacy issues and changing the official forms of communication could help improving vaccine acceptance. This study shows the importance of rebuilding a trusting relationship between patients and health care providers, which is fundamental in the fight against vaccine hesitancy

Agminated Spitzoid Naevi after Remission of Langerhans Cell Histiocytosis: First Italian Case and Literature Review.

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Risk perception, knowledge about SARS-CoV-2, and perception towards preventive measures in Italy: a nationwide cross-sectional study

Introduction: After COVID-19 outbreak, governments adopted several containment measures. Risk perception and knowledge may play a crucial role since they can affect compliance with preventive measures. This study aimed to explore the extent and the associated factors of risk perception, knowledge regarding SARS-CoV2, and perception towards preventive measures among the Italian population. Methods: A nationwide cross-sectional study involving adults was conducted in April-May 2021: an online survey was distributed through social media. The outcomes were: Knowledge Score (KS) (0 to 100%: higher scores correspond to higher COVID-19-related knowledge); Risk Perception Score (RPS) (1 to 4: higher values indicate higher concern); Preventive measures Perception Score (PPS) (1 to 4: higher values indicate higher confidence). Multivariable regression models were performed. Results: A total of 1120 participants were included. Median KS was 79.5%  (IQR=72.7%-86.4%). Lower education and poor economic conditions were negatively associated with the KS.  Median RPS was 2.8 (IQR=2.4-3.2). Female gender, sharing house with a fragile person, suffering from a chronic disease, having a family member/close friend who contracted SARS-CoV-2 infection were positively associated with the RPS. Median PPS was 3.1 (IQR=2.8-3.4). Lower educational level was negatively associated with the PPS. Vaccine hesitancy was negatively associated with all three outcomes. The three scores were positively associated with each other. Conclusions: Fair levels of knowledge, risk perception and perception towards preventive measures were reported. Reciprocal relationships between the outcomes and a relevant relationship with vaccine hesitancy were highlighted. Further investigations should be focused on studying underlying determinants and consequences