Finding recurrent copy number alterations preserving within-sample homogeneity

Abstract Motivation: Copy number alterations (CNAs) represent an important component of genetic variation and play a significant role in many human diseases. Development of array comparative genomic hybridization (aCGH) technology has made it possible to identify CNAs. Identification of recurrent CNAs represents the first fundamental step to provide a list of genomic regions which form the basis for further biological investigations. The main problem in recurrent CNAs discovery is related to the need to distinguish between functional changes and random events without pathological relevance. Within-sample homogeneity represents a common feature of copy number profile in cancer, so it can be used as additional source of information to increase the accuracy of the results. Although several algorithms aimed at the identification of recurrent CNAs have been proposed, no attempt of a comprehensive comparison of different approaches has yet been published. Results: We propose a new approach, called Genomic Analysis of Important Alterations (GAIA), to find recurrent CNAs where a statistical hypothesis framework is extended to take into account within-sample homogeneity. Statistical significance and within-sample homogeneity are combined into an iterative procedure to extract the regions that likely are involved in functional changes. Results show that GAIA represents a valid alternative to other proposed approaches. In addition, we perform an accurate comparison by using two real aCGH datasets and a carefully planned simulation study. Availability: GAIA has been implemented as R/Bioconductor package. It can be downloaded from the following page http://bioinformatics.biogem.it/download/gaia Contact: [email protected]; [email protected] Supplementary Information: Supplementary data are available at Bioinformatics online

Geopolymers as a potential material for preservation and restoration of Urban Build Heritage: an overview

Since the introduction of the term 'geopolymer' by Davidovits in 1978, many works have been published, sometimes providing clear and concise indications, and other times creating confusion about what are a geopolymer. What seems interesting beyond the terminology discourse is the advantage of low CO2 emissions, the use of waste industrial byproducts in their implementation and the resistance to air pollution and aggressive agents. Playing on the combination of the different precursors and alkaline activators, geopolymers can reach competitive mechanical properties and significant environmental benefits. The materials, with specially designed formulations, can be fireproof, breathable, resistant to rising salts and acid rain, as well as products with low emission of carbon dioxide. Furthermore, a further advantage is the ability to imitate natural, artificial and stone materials. There are hundreds of papers about characteristics, properties both of precursors and final product, but only a few of them about the Cultural Heritage Application. Despite this, the data shown by the few publications present to date give hope for a use of these materials for the consolidation, conservation and restoration of the heritage built within the historical centres, where the low CO2 emissions and the characteristics shown by the geopolymers could bring a huge benefit to the environment and the protection of the structures themselves. In this work, we briefly review the bibliography available on the applications of these materials to Cultural Heritage, hypothesising future uses aimed at specific urban contexts, where the application could play a key role in the future projects to restore the built heritage

The chemical-physical knowledge before the restoration: The case of "The Plague in Lucca", a masterpiece of Lorenzo Viani (1882-1936)

Background: "The Plague in Lucca", a masterpiece of the contemporary painter Lorenzo Viani, was studied by multianalytical techniques (Multiband, IR and UV fluorescence imaging, micro-Raman spectroscopy, direct exposure-mass spectrometry, gas chromatography-mass spectrometry and energy dispersive X-ray fluorescence) in view of its restoration at the Gallery of Modern and Contemporary Art (GAMC) of Palazzo delle Muse in Viareggio (Lucca, Italy). The analysis allowed to obtain a better understanding of the artistic technique of the painter and to underline critical conservation aspects. Results: At first, non-invasive techniques, such as the Multiband Imaging, Infrared Reflectometry, UV Fluorescence and X-ray Fluorescence, have been applied in order to characterize the conservation state of the painting surface and determining the more representative zones of the painting for the taking of micro-samples to be analysed in the laboratory. The destructive chemical analysis of these micro-samples, performed using mass (DEMS and GC/MS) and infrared spectroscopy (micro-Raman), permitted to reveal the nature of the organic and inorganic materials present in the painting. Conclusions: The use of different physical and chemical diagnostic techniques allowed us to obtain precious information about the palette and the technique used by Lorenzo Viani for the realization of "La Peste a Lucca". Furthermore, this approach permit to characterize paintings, to understand the nature and origin of materials used by the artist and to develop the appropriate restoration procedure

A multidisciplinary approach to the investigation of "La Caverna dell'Antimateria" (1958–1959) by Pinot Gallizio

Background: This study concerns the application of non-invasive and micro-invasive analyses for the study of a contemporary artwork entitled La Caverna dell'Antimateria ("The Cave of Antimatter") which was created by Pinot Gallizio in 1958–1959. The work represents one of the most significant examples of industrial painting. It consists of a total of 145 meters of painted canvas, designed in order to cover the entire floor plan of the Rene Drouin gallery in Paris, where it was displayed for the first time. Gallizio wanted to create an environment in which visitors could find themselves immersed in painting, in what he termed as a "work-environment". Non-invasive (Fibre Optic Reflectance Spectroscopy) and micro-invasive analyses (Fourier Transform Infrared and micro-Raman Spectroscopies, Pyrolysis-Gas Chromatography and Gas Chromatography/Mass Spectrometry) were performed on three of the canvases which constitute this work of art in order to obtain information regarding the artistic materials used by Gallizio. Results: Pigments and unconventional materials (such as metal wires, sand) are present in the canvases that form the ceiling. The colours are unevenly distributed on the surface, thus revealing large areas of the white preparation below. In the canvas of the wall, instead, the paint is applied more uniformly and gives a dark colour cast. The analytical results led to the identification of many of the materials used by Gallizio. The pictorial palette consists of both inorganic and organic pigments, while polyvinylacetate, pure or mixed with a siccative oil, was identified as a binder thus confirming what was reported by the artist in his notes. Conclusions: The results of this research provide information concerning the artistic technique used by Pinot Gallizio. The analyses were successfully performed both in situ and on micro-samples in order to characterise the pigments of the coloured area, the ground layer and the organic binders

Comparison between invasive breast cancer with extensive peritumoral vascular invasion and inflammatory breast carcinoma: a clinicopathologic study of 161 cases.

Objectives: Extensive peritumoral neoplastic lymphovascular invasion (ePVI) is a marker of aggressiveness in invasive breast carcinoma (BC). Methods: We explored the impact of ePVI on different BC subtypes. In a total of 2,116 BCs, 91 ePVI-BCs, 70 inflammatory breast carcinomas (IBCs), and 114 casual BCs as a control group (CG-BC) were recruited. Results: Patients affected by ePVI-BC were younger, had larger tumors, higher histologic grade, elevated Ki-67 score, Her2/neu overexpressed, and more lymph node metastases compared with CG-BC ( P < .001). Interestingly, only younger mean age at diagnosis differentiated patients with ePVI-BC from patients affected by IBC. ePVI-BC showed a clinical outcome intermediate between the prognoses of IBC and CG-BC. Conclusions: Results suggest that ePVI-BC and IBC may share some pathologic processes, providing a novel perspective on the heterogeneity of BC. Epidemiologic data and molecular studies on gene expression features are needed to rationally classify these tumors into their identified subtypes

L'individuazione dei valori anomali con strumenti di grafica dinamica

Dottorato di ricerca in statistica computazionale e applicazioni. 6. cicloConsiglio Nazionale delle Ricerche - Biblioteca Centrale - P.le Aldo Moro, 7, Rome; Biblioteca Nazionale Centrale - P.za Cavalleggeri, 1, Florence / CNR - Consiglio Nazionale delle RichercheSIGLEITItal

massiveGST: A Mann–Whitney–Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis

Gene-set enrichment analysis is the key methodology for obtaining biological information from transcriptomic space’s statistical result. Since its introduction, Gene-set Enrichment analysis methods have obtained more reliable results and a wider range of application. Great attention has been devoted to global tests, in contrast to competitive methods that have been largely ignored, although they appear more flexible because they are independent from the source of gene-profiles. We analyzed the properties of the Mann–Whitney–Wilcoxon test, a competitive method, and adapted its interpretation in the context of enrichment analysis by introducing a Normalized Enrichment Score that summarize two interpretations: a probability estimate and a location index. Two implementations are presented and compared with relevant literature methods: an R package and an online web tool. Both allow for obtaining tabular and graphical results with attention to reproducible research

Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles

MOTIVATION: Data transformations are an important step in the analysis of RNA-seq data. Nonetheless, the impact of transformation on the outcome of unsupervised clustering procedures is still unclear.RESULTS: Here, we present an Asymmetric Winsorization per Sample Transformation (AWST), which is robust to data perturbations and removes the need for selecting the most informative genes prior to sample clustering. Our procedure leads to robust and biologically meaningful clusters both in bulk and in single-cell applications.AVAILABILITY: The AWST method is available at https://github.com/drisso/awst. The code to reproduce the analyses is available at https://github.com/drisso/awst_analysis.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online