The Cultural Heritage of "Black Stones" (Lapis Aequipondus/Martyrum) 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 5.6 kg each, corresponding to multiples of standard roman weights (drachma and scrupulum). These features and the presence of some grooves on the rock artefacts, probably for grappling hooks, suggest an original use as counterweight for the four black stones herein classified as amphibole-bearing serpentinites whose lithologies are far away from Recanati (probably coming from geological outcrops in Tuscany). The four serpentinite stones closely match with the so-called Lapis Aequipondus used in antiquity by the Romans as counterweights. Due to the presence of lead rings or iron hooks in these stones, Lapis Aequipondus were also used for martyrdoms during the persecution of Christians in the Roman period, attached to the necks of martyrs that were then thrown in the wells or attached to the ankles of hanging bodies. This is the reason why these stones are also known as Lapis Martyrum, venerated with the relative martyrs, in several churches of Rome. The four black stones investigated probably arrived at Recanati from Rome after the middle of the 19th century. In the past, Christians also called Lapis Martyrum the "devil's stones" (Lapis Diaboli). This could also be the reason for the popular belief that black stones cannot be touched by people, except those of the Leopardi dynasty. This work contributes to the cultural heritage of Leopardi's child home, as the four black stones had never been investigated.

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.

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. Between January 2008 to January 2018, demographics, anthropometric and post-operative data of obese patients undergone LAGB were retrospectively evaluated. To compare the postoperative outcomes, the cohort was divided in two groups according to the quantity of band filling (QBF): low band filling group (Group 1) with at most 3 ml of QBF, and patients in the high band filling group (Group 2) with at least 4 ml. 699 obese patients were considered in the analysis (351 in Group 1 and 348 in Group 2). Patients in Group 1 resulted significantly associated (p < 0.05) to higher % EWL and quality of life score (BAROS Score), 49.1 ± 11.3 vs 38.2 ± 14.2 and 5.9 ± 1.8 vs 3.8 ± 2.5, respectively. Moreover, patients with lower band filling (Group 1) complained less episodes of vomiting, epigastric pain and post-prandial reflux and significantly decreased slippage and migration rate (p < 0.001 for all parameters). LAGB is a safe and reversible procedure, whose efficacy is primarily related to correct postoperative handling. Low band filling and strict follow-up seem the success' key of this technique, which deserves full consideration among bariatric procedures.

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. To this end, several algorithms have been tested that allow for separating the characteristics and creating binary masks to be statistically analyzed and polygonized. Since our methodology aims to offer a conservator-restorer model to obtain useful graphic documentation in a short time that is usable for design and statistical purposes, this process has been implemented in a single Geographic Information Systems (GIS) application.

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 AND IMPLEMENTATION: 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.

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. RESULTS: We present a novel method, single-cell Tumor-Host Interaction tool (scTHI), to identify significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data. We apply our approach to uncover the ligand-receptor interactions in glioma using 6 publicly available human glioma datasets encompassing 57,060 gene expression profiles from 71 patients. By leveraging this large-scale collection we show that unexpected cross-talk partners are highly conserved across different datasets in the majority of the tumor samples. This suggests that shared cross-talk mechanisms exist in glioma. CONCLUSIONS: Our results provide a complete map of the active tumor-host interaction pairs in glioma that can be therapeutically exploited to reduce the immunosuppressive action of the microenvironment in brain tumor.

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. Using dual-energy X-ray absorptiometry analysis, all subjects substantially lost total body mass (-3.9 ± 1.9 kg; p < .001) and fat mass (-3.3 ± 1.3 kg; p < .001). Average lean mass was lost (-0.6 ± 1.5 kg; p < .001), but lean mass as a percentage of total body mass was not reduced. The authors observed a loss of -3.9 ± 1.9% android fat over total fat mass (p < .001), a loss of -2.2 ± 1.9% gynoid over total fat mass (p < .001), and reduced android/gynoid ratios (-0.05 ± 0.1; p < .001). Analyzing 15 preselected single-nucleotide polymorphisms in 13 metabolism-related genes revealed trending associations for thyroid state-related single-nucleotide polymorphisms rs225014 (deiodinase 2) and rs35767 (insulin-like growth factor1), and rs1053049 (PPARD). In conclusion, a short period of combined fasting and exercise leads to a substantial loss of body and fat mass without a loss of lean mass as a percentage of total mass.

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. With the aim of trying to solve the archaeological question, an archaeometric comparison among this well-known artwork and several frescoed tombs coming from Hellenistic and Lucan necropolis was carried out. The multi-analytical study was focused on the identification of peculiar features of executive techniques and raw materials since the first period of the archaeological site. The analytical investigation has been preliminary based on a non-destructive approach, performed in-situ by portable equipment including imaging diagnostics and compositional spectroscopic techniques for identifying pigments and the conservation state of original painted surface; subsequently, a further deepening by using destructive techniques was performed in-lab for the mortar-based supports characterization. Archaeometric study suggested that technological choices slightly changed in a time span of about two centuries, highlighting important markers that allow clustering the contemporary artistic productions. Moreover, a comparison with mortars from temples decorations was provided to better understand the whole artistic context. The archaeometric data showed that the Tomb of the Diver could be traced back to a local artisanal tradition and therefore is neither Etruscan nor Greek, but the first and foremost an expression of the local elite culture of Paestum.

Analytical and mathematical methods for revealing hidden details in ancient manuscripts and paintings: A review.

In this work, a critical review of the current nondestructive probing and image analysis approaches is presented, to revealing otherwise invisible or hardly discernible details in manuscripts and paintings relevant to cultural heritage and archaeology. Multispectral imaging, X-ray fluorescence, Laser-Induced Breakdown Spectroscopy, Raman spectroscopy and Thermography are considered, as techniques for acquiring images and spectral image sets; statistical methods for the analysis of these images are then discussed, including blind separation and false colour techniques. Several case studies are presented, with particular attention dedicated to the approaches that appear most promising for future applications. Some of the techniques described herein are likely to replace, in the near future, classical digital photography in the study of ancient manuscripts and paintings.

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. Acta, Part B, 2013, 79-80, 63-71) and the C-sigma model of Aragon and Aguilera (Aragon, C.; Aguilera, J. A. J. Quant. Spectrosc. Radiat. Trans. 2014, 149, 90-102). Both methods are based on the exploitation of self-absorbed lines for the characterization of plasmas in laser-induced breakdown spectroscopy experiments. However, although the two methods can be safely applied in many cases, their usefulness is limited in many practical cases of interest because of the intrinsic constraints of the used plasma model or because of the complexity of the numerical treatment. The two methods are presented here and critically discussed. Finally, an extended C-sigma approach is proposed to merge the advantages of the two methods, overcoming their intrinsic limitations and simplifying the numerical treatment.

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 D463H mutation. PRKCA encodes the Protein kinase C (PKC) isozyme alpha (PKCα) and is mutated in a wide range of human cancers. However the hot spot PRKCA D463H mutation was not described in other tumors. PRKCA D463H is strongly associated with the activation of protein translation initiation (EIF2) pathway. PKCαD463H mRNA levels are more abundant than wild-type PKCα transcripts, while PKCαD463H is less stable than the PCKαWT protein. Compared to PCKαWT, the PKCαD463H protein is depleted from the cell membrane. The PKCαD463H mutant enhances proliferation of astrocytes and tanycytes, the cells of origin of ChG. In conclusion, our study identifies the hallmark mutation for chordoid gliomas and provides mechanistic insights on ChG oncogenesis.

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. F3-T3 fusions are potent oncogenes that confer sensitivity to FGFR inhibitors, but the downstream oncogenic signalling pathways remain unknown. Here we show that human tumours with F3-T3 fusions cluster within transcriptional subgroups that are characterized by the activation of mitochondrial functions. F3-T3 activates oxidative phosphorylation and mitochondrial biogenesis and induces sensitivity to inhibitors of oxidative metabolism. Phosphorylation of the phosphopeptide PIN4 is an intermediate step in the signalling pathway of the activation of mitochondrial metabolism. The F3-T3-PIN4 axis triggers the biogenesis of peroxisomes and the synthesis of new proteins. The anabolic response converges on the PGC1α coactivator through the production of intracellular reactive oxygen species, which enables mitochondrial respiration and tumour growth. These data illustrate the oncogenic circuit engaged by F3-T3 and show that F3-T3-positive tumours rely on mitochondrial respiration, highlighting this pathway as a therapeutic opportunity for the treatment of tumours with F3-T3 fusions. We also provide insights into the genetic alterations that initiate the chain of metabolic responses that drive mitochondrial metabolism in cancer.

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. Four thousand LIBS spectra were acquired from an area of 10 mm2, with a 50 µm lateral resolution. The elements of interest in the mortar sample (H, C, O, Na, Mg, Al, Si, K, Ca, Ti, Mn, Fe) were detected and mapped. The collected data graphically shown as compositional images were interpreted using different statistical approaches for the determination of the chemical composition of the binder and aggregate fraction. The methods of false color imaging, blind separation, and self-organizing maps were applied and their results are discussed in this paper. In particular, the method based on the use of self-organizing maps gives well interpretable results in very short times, without any reduction in the dimensionality of the system.

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. The quantitative determination of the gold alloys used for the realization of the coins was obtained applying the fundamental parameters method to the XRF spectra; as a result, using the self-organizing maps method, we were able to classify the coins in four main groups. The main parameter determining the classification is the quantity of silver in the alloy. The results obtained shed some light about the origin of the coins under study.

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. RNA sequencing identified a recurrent in-frame SH3PXD2A-HTRA1 fusion in 12/125 (10%) cases, and genomic analysis demonstrated the mechanism as resulting from a balanced 19-Mb chromosomal inversion on chromosome 10q. The fusion was associated with male gender predominance, occurring in one out of every six men with schwannoma. Methylation profiling identified distinct molecular subgroups of schwannomas that were associated with anatomical location. Expression of the SH3PXD2A-HTRA1 fusion resulted in elevated phosphorylated ERK, increased proliferation, increased invasion and in vivo tumorigenesis. Targeting of the MEK-ERK pathway was effective in fusion-positive Schwann cells, suggesting a possible therapeutic approach for this subset of tumors.

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. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes.

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. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries.

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.

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. Analysis of dichotomies generated by the signatures results in a set of 133 samples stably classified in good prognosis group and 56 samples in poor prognosis group, whereas 43 remain unreliably classified. AKAP12, DCBLD2, NT5E and SPON1 are particularly represented in the signatures and selected for validation in vivo on two independent patients cohorts comprising 140 tumor tissues and 60 matched normal tissues. Their expression and regulatory programs are investigated in vitro. We show that the coupled expression of NT5E and DCBLD2 robustly stratifies our patients in two groups (one of which with 100% survival at five years). We show that NT5E is a target of the TNF-α signaling in vitro; the tumor suppressor PPARγ acts as a novel NT5E antagonist that positively and concomitantly regulates DCBLD2 in a cancer cell context-dependent manner.

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. 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: ceccarelli@unisannio.it; morganella@unisannio.it. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.