A comparative study of Gaussian Graphical Model approaches for genomic data

The inference of networks of dependencies by Gaussian Graphical models on high-throughput data is an open issue in modern molecular biology. In this paper we provide a comparative study of three methods to obtain small sample and high dimension estimates of partial correlation coefficients: the Moore-Penrose pseudoinverse (PINV), residual correlation (RCM) and covariance-regularized method $(\ell_{2C})$. We first compare them on simulated datasets and we find that PINV is less stable in terms of AUC performance when the number of variables changes. The two regularized methods have comparable performances but $\ell_{2C}$ is much faster than RCM. Finally, we present the results of an application of $\ell_{2C}$ for the inference of a gene network for isoprenoid biosynthesis pathways in Arabidopsis thaliana.Comment: 7 pages, 1 figure, RevTex4, version to appear in the proceedings of 1st International Workshop on Pattern Recognition, Proteomics, Structural Biology and Bioinformatics: PR PS BB 2011, Ravenna, Italy, 13 September 201

Comparison of different multivariate calibrations and ensemble methods for estimating selected soil properties with vis-NIR reflectance spectroscopy

Sustainable soil management requires a correct assessment of soil chemi- cal and physical properties. Historically, this has been gained through conventional laboratory analyses, which are considered costly and time-consuming, particularly when a large number of soil samples need to be analysed. An alternative, faster and less expensive, approach is based on the use of reflectance spectroscopy in the vis- NIR domain. This approach implies the calibration of predictive models that relate the spectral reflectance to soil properties. The goodness of the models can be partic- ularly influenced by the multivariate methods used. In this article, we compare the performance of different multivariate and statistical ensemble methods for estimating some basic soil properties, such as sand, silt, clay, and organic carbon in the specific pedo-environmental conditions of an important agricultural area in southern Italy

Role of surgical setting and patients-related factors in predicting the occurrence of postoperative pulmonary complications after abdominal surgery

OBJECTIVE: The aim of this retrospective study was to evaluate the role of surgical setting (urgent vs. elective) and approach (open vs. laparoscopic) in affecting postoperative pulmonary complications (PPCs) prevalence in patients undergoing abdominal surgery. PATIENTS AND METHODS: After local Ethical Committee approval, 409 patients who had undergone abdominal surgery between January and December 2014 were included in the final analysis. PPCs were defined as the development of one of the following new findings: respiratory failure, pulmonary infection, aspiration pneumonia, pleural effusion, pneumothorax, atelectasis on chest X-ray, bronchospasm or un-planned urgent re-intubation. RESULTS: PPCs prevalence was greater in urgent (33%) vs. elective setting (7%) (chi(2) with Yates correction: 44; p=0.0001) and in open (6%) vs. laparoscopic approach (1.9%) (chi(2) with Yates correction: 12; p=0.0006). PPCs occurrence was positively correlated with in-hospital mortality (Biserial Correlation r=0.37; p=0.0001). Logistic regression showed that urgent setting (p=0.000), Ariscat (Assess Respiratory Risk in Surgical Patients in Catalonia) score (p=0.004), and age (p=0.01) were predictors of PPCs. A cutoff of 23 for Ariscat score was also identified as determining factor for PPCs occurrence with 94% sensitivity and 29% specificity. CONCLUSIONS: Patients undergoing abdominal surgery in an urgent setting were exposed to a higher risk of PPCs compared to patients scheduled for elective procedures. Ariscat score fitted with PPCs prevalence and older patients were exposed to a higher risk of PPCs. Prospective studies are needed to confirm these result

Renewable Energy Storage System Based on a Power-to-Gas Conversion Process

Abstract The increasing penetration of renewable energy generation in the electric energy market is currently posing new critical issues, related to the generation prediction and scheduling, due to the mismatch between power production and utilization. In order to cope with these issues, the implementation of new large scale storage units on the electric network is foreseen as a key mitigation strategy. Among large scale technologies for the electric energy storage, the Power-to-Gas solution can be regarded as a long-term viable option, provided that the conversion efficiency is improved and aligned with other more conventional storage alternatives. In this study, a Power-to-Gas storage system is investigated, including as main components a high-temperature electrolyzer for hydrogen generation and a Sabatier reactor for methane production. The high-temperature Solide Oxide Electrolyser Cell (SOEC) technology, currently under development, is considered as a promising solution for hydrogen generation, due to the expected higher efficiency values, in comparison with conventional low-temperature electrolysis technologies. In order to evaluate the performance of the system and the energy efficiency, in this study a numerical model of the SOEC integrated with the Sabatier reactor has been implemented, including also the necessary additional auxiliaries, which can significantly affect the energy conversion performance. The whole energy conversion and storage system has been analyzed, taking into account different layout variants, by means of Aspen HysysTM numerical tool, based on a lumped modelling approach. The various Power-to-Gas storage configurations have been compared, with the aim to optimize both the system's efficiency and the composition of the produced gas stream

Lipid-coated zinc oxide nanocrystals as innovative ROS-generators for photodynamic therapy

Photodynamic Therapy (PDT) is a medical treatment that combines the administration of a nontoxic drug, called photosensitizer (PS), with light irradiation of the targeted region. It has been proposed as a new cancer therapy, promising better selectivity and fewer side-effects compared to traditional chemo- and radio-therapies. PSs indeed can accumulate specifically within the region of interest so that when the light is directly focused only in that region the therapeutic effect is highly localized. Traditional PSs, like chlorins and porphyrins, suffer from several drawbacks such as aggregation in biological media and poor biocompatibility. Thus, the development of innovative photosensitizers able to overcome these issues is crucial to the therapeutic action of PDT. Among the others, nanostructured Zinc Oxide (ZnO) has been recently proposed as new therapeutic agent and PS thanks to its semiconducting properties, biocompatible features, and ease of functionalization [1]. Nevertheless, further efforts are needed in order to improve its colloidal stability in biological media and to unravel the effective therapeutic mechanism. Here, we propose the synthesis and characterization of lipid-coated ZnO nanoparticles as new photosensitizer for cancer PDT [2]. First, by Dynamic Light Scattering (DLS) experiments, we show that the lipid-coating increases the colloidal stability of the ZnO NPs in Phosphate buffered saline (PBS). Then, using Electron Paramagnetic Resonance (EPR) coupled with the spin-trapping technique, we demonstrate and characterize the ability of bare and lipid-coated ZnO NPs to generate Reactive Oxygen Species (ROS) in water only when remotely actuated via light irradiation. Interestingly, our results aware that the surface chemistry of the NPs greatly influence the type of photo-generated ROS. Finally, we show that our NPs are effectively internalized inside human epithelial carcinoma cells (HeLa) via a lysosomal pathway and that they are able to generate ROS inside cancer cells. [1] B. Dumontel, M. Canta, H. Engelke, A. Chiodoni, L. Racca, A. Ancona, T. Limongi, G. Canavese and V. Cauda, ‎J. Mater. Chem. B. under revision. [2] A. Ancona, H. Engelke, N. Garino, B. Dumontel, W.Fazzini and V. Cauda, to be submitted. The support from ERC Starting Grant – Project N. 678151 “Trojananohorse” is gratefully acknowledged

Fluidized bed gasification of biomass from plant-assisted bioremediation: Fate of contaminants

Fluidized-bed gasification (FBG) of Phyto-assisted Bioremediation (PABR) biomass is analyzed focusing on the contaminants' dispersion. Poplar pruning coming from an area contaminated by polychlorinated biphenyls (PCBs) and heavy metals (HM) are considered. The biomass analysis showed relevant contents in HMs, especially Cd and Cr, and no significant PCB content. FBG process was analyzed to: a) track pollutants, b) detect contaminants in the FBG and c) investigate the HMs concentration in the produced streams. The results showed that most of the metals are concentrated in the ashes collected in the bottom of the reactor (Pb, Cd, Cu, Cr), or in the cyclone (B, Na, Mg, Al, K and Fe). Interestingly, metals are also released by the olivine bed (Mg, Fe, Ni and Al) and transported downstream. Consistent fractions of Zn and Fe (also Cu) were detected in the fugitive ashes. As for the Volatile Organic Compounds (VOC) concentration, we noted similarities between PABR and virgin biomass syngas streams. A reduced-scale process was carried out in TGA-DTA to investigate the potential of such technique in reproducing the main features of the FBG process. Comparable results were obtained, thus suggesting its possible application for small-scale preliminary assessment of FBG process

Combined effects of compost and medicago sativa in recovery a PCB contaminated soil

The effectiveness of adding compost and the plant Medicago sativa in improving the quality of a soil historically contaminated by polychlorinated biphenyls (PCBs) was tested in greenhouse microcosms. Plant pots, containing soil samples from an area contaminated by PCBs, were treated with the compost and the plant, separately or together. Moreover, un-treated and un-planted microcosms were used as controls. At fixed times (1, 133 and 224 days), PCBs were analysed and the structure (cell abundance, phylogenetic characterization) and functioning (cell viability, dehydrogenase activity) of the natural microbial community were also measured. The results showed the effectiveness of the compost and plant in increasing the microbial activity, cell viability, and bacteria/fungi ratio, and in decreasing the amount of higher-chlorinated PCBs. Moreover, a higher number of ff-Proteobacteria, one of the main bacterial groups involved in the degradation of PCBs, was found in the compost and plant co-presence

Behavioral types in programming languages

A recent trend in programming language research is to use behav- ioral type theory to ensure various correctness properties of large- scale, communication-intensive systems. Behavioral types encompass concepts such as interfaces, communication protocols, contracts, and choreography. The successful application of behavioral types requires a solid understanding of several practical aspects, from their represen- tation in a concrete programming language, to their integration with other programming constructs such as methods and functions, to de- sign and monitoring methodologies that take behaviors into account. This survey provides an overview of the state of the art of these aspects, which we summarize as the pragmatics of behavioral types