Unsupervised Single-Cell Clustering with Asymmetric Within-Sample Transformation and Per-Cluster Supervised Features Selection.

This chapter shows applying the Asymmetric Within-Sample Transformation to single-cell RNA-Seq data matched with a previous dropout imputation. The asymmetric transformation is a special winsorization that flattens low-expressed intensities and preserves highly expressed gene levels. Before a standard hierarchical clustering algorithm, an intermediate step removes noninformative genes according to a threshold applied to a per-gene entropy estimate.

The Cultural Heritage of "Black Stones" (/) of Leopardi's Child Home (Recanati, Italy).

A macroscopic lithological study and physical (hardness, size, weight) investigations, coupled with laser-induced breakdown spectroscopy (LIBS) and X-ray fluorescence (XRF) chemical analyses of three egg- and one pear-shaped polished black stones, exposed in the library of the child home of the famous poet Giacomo Leopardi, at Recanati (Italy), were carried out. They are characterized by different sizes: two with the same weight of 16.9 kg and the two smaller ones of 5.

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.

It is really time to retire laparoscopic gastric banding? Positive outcomes after long-term follow-up: the management is the key.

After the initial widespread diffusion, laparoscopic adjustable gastric banding (LAGB) has been progressively abandoned and laparoscopic sleeve gastrectomy (LSG) has become the worldwide most adopted procedure. Nevertheless, recent reports raised concerns about the long-term weight regain after different bariatric techniques. Considering the large LAGB series recorded in our multicentric bariatric database, we analysed the anthropometric and surgical outcomes of obese patients underwent LAGB at a long-term follow-up, focusing on LAGB management.

Analysis of Diagnostic Images of Artworks and Feature Extraction: Design of a Methodology.

Digital images represent the primary tool for diagnostics and documentation of the state of preservation of artifacts. Today the interpretive filters that allow one to characterize information and communicate it are extremely subjective. Our research goal is to study a quantitative analysis methodology to facilitate and semi-automate the recognition and polygonization of areas corresponding to the characteristics searched.

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.

A map of tumor-host interactions in glioma at single-cell resolution.

Background: Single-cell RNA sequencing is the reference technique for characterizing the heterogeneity of the tumor microenvironment. The composition of the various cell types making up the microenvironment can significantly affect the way in which the immune system activates cancer rejection mechanisms. Understanding the cross-talk signals between immune cells and cancer cells is of fundamental importance for the identification of immuno-oncology therapeutic targets.

Short-Term, Combined Fasting and Exercise Improves Body Composition in Healthy Males.

Fasting enhances the beneficial metabolic outcomes of exercise; however, it is unknown whether body composition is favorably modified on the short term. A baseline-follow-up study was carried out to assess the effect of an established protocol involving short-term combined exercise with fasting on body composition. One hundred seven recreationally exercising males underwent a 10-day intervention across 15 fitness centers in the Netherlands involving a 3-day gradual decrease of food intake, a 3-day period with extremely low caloric intake, and a gradual 4-day increase to initial caloric intake, with daily 30-min submaximal cycling.

The Tomb of the Diver and the frescoed tombs in Paestum (southern Italy): New insights from a comparative archaeometric study.

The Tomb of the Diver has been subject for many decades of fierce debate among archaeologists and classicists. Since its discovery in 1968, some scholars have considered it a unique example of the lost tradition of Greek painting, others have emphasized Etruscan or Italic parallels. More recently, a possible local production has been suggested.

Exploiting Self-Absorption for Plasma Characterization in Laser-Induced Breakdown Spectroscopy Experiments: A Comparison of Two Recent Approaches.

In this article, we compare two analytical methods that have been recently proposed: the columnar density Saha-Boltzmann plot method of Cristoforetti and Tognoni (Cristoforetti, G.; Tognoni, E. Spectrochim.

A recurrent point mutation in PRKCA is a hallmark of chordoid gliomas.

Chordoid glioma (ChG) is a characteristic, slow growing, and well-circumscribed diencephalic tumor, whose mutational landscape is unknown. Here we report the analysis of 16 ChG by whole-exome and RNA-sequencing. We found that 15 ChG harbor the same PRKCA mutation.

A metabolic function of FGFR3-TACC3 gene fusions in cancer.

Chromosomal translocations that generate in-frame oncogenic gene fusions are notable examples of the success of targeted cancer therapies. We have previously described gene fusions of FGFR3-TACC3 (F3-T3) in 3% of human glioblastoma cases. Subsequent studies have reported similar frequencies of F3-T3 in many other cancers, indicating that F3-T3 is a commonly occuring fusion across all tumour types.

Micro-Laser-Induced Breakdown Spectroscopy (Micro-LIBS) Study on Ancient Roman Mortars.

The laser-induced breakdown spectroscopy (LIBS) technique was used for analyzing the composition of an ancient Roman mortar (5th century A.D.), exploiting an experimental setup which allows the determination of the compositions of binder and aggregate in few minutes, without the need for sample treatment.

The genomic landscape of schwannoma.

Schwannomas are common peripheral nerve sheath tumors that can cause debilitating morbidities. We performed an integrative analysis to determine genomic aberrations common to sporadic schwannomas. Exome sequence analysis with validation by targeted DNA sequencing of 125 samples uncovered, in addition to expected NF2 disruption, recurrent mutations in ARID1A, ARID1B and DDR1.

X-Ray Fluorescence Analysis and Self-Organizing Maps Classification of the Etruscan Gold Coin Collection at the Monetiere of Florence.

The "Monetiere" of Florence hosts the most important collection of Etruscan coins in the world. In the framework of the longstanding collaboration between the Monetiere and the Applied Laser and Spectroscopy Laboratory in Pisa, the Etruscan gold coin collection of the museum was studied. The measurements were performed at the Monetiere, using a portable energy-dispersive X-ray fluorescence (XRF) instrument.

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.

Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length.

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.

The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers.

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.

Ensemble of gene signatures identifies novel biomarkers in colorectal cancer activated through PPARγ and TNFα signaling.

We describe a novel bioinformatic and translational pathology approach, gene Signature Finder Algorithm (gSFA) to identify biomarkers associated with Colorectal Cancer (CRC) survival. Here a robust set of CRC markers is selected by an ensemble method. By using a dataset of 232 gene expression profiles, gSFA discovers 16 highly significant small gene signatures.

Finding recurrent copy number alterations preserving within-sample homogeneity.

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.