Gene co-expression analyses: an overview from microarray collections in Arabidopsis thaliana

4noBioinformatics web-based resources and databases are precious references for most biological laboratories worldwide. However, the quality and reliability of the information they provide depends on them being used in an appropriate way that takes into account their specific features. Huge collections of gene expression data are currently publicly available, ready to support the understanding of gene and genome functionalities. In this context, tools and resources for gene co-expression analyses have flourished to exploit the ‘guilty by association' principle, which assumes that genes with correlated expression profiles are functionally related. In the case of Arabidopsis thaliana, the reference species in plant biology, the resources available mainly consist of microarray results. After a general overview of such resources, we tested and compared the results they offer for gene co-expression analysis. We also discuss the effect on the results when using different data sets, as well as different data normalization approaches and parameter settings, which often consider different metrics for establishing co-expression. A dedicated example analysis of different gene pools, implemented by including/excluding mutant samples in a reference data set, showed significant variation of gene co-expression occurrence, magnitude and direction. We conclude that, as the heterogeneity of the resources and methods may produce different results for the same query genes, the exploration of more than one of the available resources is strongly recommended. The aim of this article is to show how best to integrate data sources and/or merge outputs to achieve robust analyses and reliable interpretations, thereby making use of diverse data resources an opportunity for added value.openembargoed_20170219Di Salle, Pasquale; Incerti, Guido; Colantuono, Chiara; Chiusano, Maria LuisaDi Salle, Pasquale; Incerti, Guido; Colantuono, Chiara; Chiusano, Maria Luis

Prevalence of temporomandibular disorders in adult obstructive sleep apnoea patients: A cross-sectional controlled study

Background: Obstructive sleep apnoea (OSA) is characterised by partial or complete obstruction of the upper airways during sleep and it has been associated with temporomandibular disorders (TMDs) on the basis of several pathophysiological hypotheses. Objectives:To assess the prevalence of TMDs in a population of patients affected by OSA compared to a control group of subjects not affected by OSA. MethodsA cross-sectional controlled study was conducted on a group subjects studied by polygraphy (PG) at the snoring section of the ENT department, Sant'Orsola-Malpighi Hospital - University of Bologna. Patients who received a diagnosis of OSA were included in the study group and subjects with a negative PG diagnosis for Sleep Disordered Breathing and PG respiratory pattern that did not suggest the occurrence of sleep disorders were enrolled in the control group. Both the subjects included in the study group and the control group underwent an examination following the Diagnostic Criteria for Temporomandibular Disorders Axis I and II. Results: Forty-three OSA patients (29 M, 16 F, mean age 52.26 +/- 11.40) and 43 healthy controls (25 M, 18 F, mean age 49.95 +/- 7.59) were included in the study. No significant differences were found between groups in demographic data. TMD prevalence and Axis II results did not differ between groups. Conclusions: This paper does not highlight a higher prevalence of TMDs in adults with OSA compared to healthy controls. Further high-quality studies are needed to confirm the results and to give possible pathophysiological explanations, providing reliable evidence

Plant–environment interactions through a functional traits perspective: a review of Italian studies

Italy is among the European countries with the greatest plant diversity due to both a great environmental heterogeneity and a long history of man–environment interactions. Trait-based approaches to ecological studies have developed greatly over recent decades worldwide, although several issues concerning the relationships between plant functional traits and the environment still lack sufficient empirical evaluation. To draw insights on the association between plant functional traits and direct and indirect human and natural pressures on the environmental drivers, this article summarizes the existing knowledge on this topic by reviewing the results of studies performed in Italy adopting a functional trait approach on vascular plants, bryophytes and lichens. Although we recorded trait measurements for 1418 taxa, our review highlighted some major gaps in plant traits knowledge: Mediterranean ecosystems are poorly represented; traits related to belowground organs are still overlooked; traits measurements for bryophytes and lichens are lacking. Finally, intraspecific variation has been little studied at community level so far. We conclude by highlighting the need for approaches evaluating trait–environment relationship at large spatial and temporal scales and the need of a more effective contribution to online databases to tie more firmly Italian researchers to international scientific networks on plant traits

Analisi FEM 3D d'interazione terreno-struttura: effetti dello scavo di una galleria sotto edifici in muratura

La presente tesi ha riguardato lo studio numerico con un modello 3D dell' interazione tra lo scavo di una galleria urbana e un edificio esistente in muratura, la Stazione di Ferrara Porta Reno (risalente ai primi del '900). A tale scopo è stato utilizzato il programma di calcolo agli elementi finiti Plaxis 3D. Nello studio numerico, per il terreno è stato adottato un modello costitutivo avanzato elasto-plastico con incrudimento isotropo, l’Hardening soil model with small strain stiffness, mentre per la muratura e stato utilizzato il criterio di Mohr-Coulomb. Inoltre, lo scavo della galleria è stato simulato con una procedura per passi, tenendo in conto i principali aspetti del processo. La subsidenza in superficie è stata controllata applicando una contrazione fittizia lungo lo scudo. E’ stata svolta un'analisi numerica in condizione di campo libero, ossia in assenza di strutture, al fine di valutare i movimenti del terreno indotti dal processo di scavo; successivamente sono state eseguite diverse analisi accoppiate, in condizioni di simmetria e con eccentricità della costruzione rispetto all'asse della galleria, per studiare il complesso fenomeno di interazione galleria-terreno-struttura. I risultati di tali analisi accoppiate sono stati utilizzati per effettuare una stima del livello di danno atteso per l'edificio. Le analisi numeriche condotte hanno messo in luce, confermando quanto già noto in letteratura, che la presenza di un edificio a piano campagna interagente con l’opera di scavo modifica la forma del profilo dei cedimenti relativa alle condizioni di campo libero. Tale modifica, che dipende dalle specifiche caratteristiche di rigidezza e peso della struttura presa in esame, generalmente si traduce in una riduzione del cedimento differenziale che può influenzare in modo significativo la stima del danno sull’edificio. Ciò è tanto più evidente, quanto maggiore è la perdita di volume indotta dallo scavo della galleria

Dentoskeletal effects of oral appliance wear in obstructive sleep apnoea and snoring patients

OBJECTIVES: To evaluate the dentoskeletal changes associated with long-term and continuous mandibular advancement device (MAD) use in sleep-related breathing disorder patients. METHODS: Cephalometric measurements and three-dimensional model analysis were performed at baseline and after 3.5 ± 1.1 years in 20 snoring and obstructive sleep apnoea patients treated with the Silensor® appliance. Intra-group differences were compared using paired t-test or Wilcoxon signed-rank test. A regression analysis was performed for variables that showed a statistically significant difference between time points to evaluate the influence of treatment time and patient's initial characteristics on their variations. The statistical significance was set at P < 0.05. RESULTS: At cephalometric assessment, the maxilla revealed a significant decrease in horizontal position (SNA: -0.4 ± 0.72 degree, P = 0.021) and a significant retroclination of the upper incisor (-1.59 ± 1.07 degree, P < 0.001), while the mandible displayed a significant downward rotation (0.88 ± 1.28 degree, P = 0.006) and a proclination of the lower incisor (2.27 ± 1.38 degree, P < 0.001). Model analysis showed a decrease in upper total space discrepancy (-0.66 ± 0.72 mm, P < 0.002), overjet (OJ; -0.34 ± 0.47 mm, P < 0.011), and overbite (-0.4 ± 0.52 mm, P < 0.004). In the regression analysis, treatment time influenced the lower incisor inclination (Beta = -0.713, P = 0.018) and OJ (Beta = -0.218, P = 0.018); patients' initial characteristics had an effect on OJ (Beta = -0.195, P = 0.011). LIMITATIONS: A larger sample size could increase the generalizability of the findings. CONCLUSION: MAD wear after a mean of 3.5 years determines statistically significant but clinically irrelevant dentoskeletal changes. Their potential occurrence should be thoroughly discussed with patients; regular follow-up visits by a specialist experienced in dental sleep medicine are also mandatory during treatment in addition to polysomnographic examinations

New sustainable binders based on waste valorization for civil engineering applications

This research investigates different kinds of waste as possible new binder components for the production of cement based mortar and concrete. Waste types have been selected on the basis of availability in the Emilia Romagna Region. In particular, three different wastes (i.e., waste from rectified porcelain gres tile, sea shell fragments and eggshell waste from agri-food industry) are explored as a possible substitution of a certain fraction of cement in order to evaluate their effect. Chemical properties and physical behavior of the waste are studied, and the activity index of the waste is investigated. A series of mortar specimens with normalized silica sand and a binder compositional ratio of cement (CEM I) at 75 wt.% and waste at 25 wt.% is prepared. The physical and mechanical behavior of the mortar is investigated at different curing time (i.e., 2, 7, 28 and 90 days). This research shows first preliminary results of the MATER-SOS Project, funded by the Emilia Romagna Region, Italy (POR FESR 2014-2020), aimed at implementing circular economy processes in the constructions industry