From Linguistic Resources to Ontology-Aware Terminologies: Minding the Representation Gap

Terminological resources have proven crucial in many applications ranging from Computer-Aided Translation tools to authoring software and multilingual and cross-lingual information retrieval systems. Nonetheless, with the exception of a few felicitous examples, such as the IATE (Interactive Terminology for Europe) Termbank, many terminological resources are not available in standard formats, such as Term Base eXchange (TBX), thus preventing their sharing and reuse. Yet, these terminologies could be improved associating the correspondent ontology-based information. The research described in the present contribution demonstrates the process and the methodologies adopted in the automatic conversion into TBX of such type of resources, together with their semantic enrichment based on the formalization of ontological information into terminologies. We present a proof-of-concept using the Italian Linguistic Resource for the Archaeological domain (developed according to Thesauri and Guidelines of the Italian Central Institute for the Catalogue and Documentation). Further, we introduce the conversion tool developed to support the process of creating ontology-aware terminologies for improving interoperability and sharing of existing language technologies and data set

Estimation of Nanoporous Au Young's Modulus from Serial Block Face-SEM 3D-Characterisation

Nanoporous Au has been subjected to serial block face-scanning electron microscopy (SBF-SEM) 3D-characterisation. Corresponding sections have been digitalized and used to evaluate the associated mechanical properties. Our investigation demonstrates that the sample is homogeneous and isotropic. The effective Young's modulus estimated by an analytical multiscale approach agrees remarkably well with the values stated in the literature

A method to search for long duration gravitational wave transients from isolated neutron stars using the generalized FrequencyHough

We describe a method to detect gravitational waves lasting $O(hours-days)$ emitted by young, isolated neutron stars, such as those that could form after a supernova or a binary neutron star merger, using advanced LIGO/Virgo data. The method is based on a generalization of the FrequencyHough (FH), a pipeline that performs hierarchical searches for continuous gravitational waves by mapping points in the time/frequency plane of the detector to lines in the frequency/spindown plane of the source. We show that signals whose spindowns are related to their frequencies by a power law can be transformed to coordinates where the behavior of these signals is always linear, and can therefore be searched for by the FH. We estimate the sensitivity of our search across different braking indices, and describe the portion of the parameter space we could explore in a search using varying fast Fourier Transform (FFT) lengths.Comment: 15 figure

Co-expression of Myoepithelial and Melanocytic Features in Carcinoma Ex Pleomorphic Adenoma

The presence of melanin pigment and melanocytic markers expression have been rarely reported in salivary gland tumors. Herein, two cases of carcinoma arising in pleomorphic adenoma of the parotid gland and showing diffuse expression of myoepithelial and melanocytic markers are described. The clinical-pathological clues useful in the differential diagnosis with melanoma are discussed. In addition, a review of the pertinent literature is also proposed, discussing the pathologic mechanisms potentially involved in this phenomenon

Toxicogenomics analysis of dynamic dose-response in macrophages highlights molecular alterations relevant for multi-walled carbon nanotube-induced lung fibrosis

Toxicogenomics approaches are increasingly used to gain mechanistic insight into the toxicity of engineered nanomaterials (ENMs). These emerging technologies have been shown to aid the translation of in vitro experimentation into relevant information on real-life exposures. Furthermore, integrating multiple layers of molecular alteration can provide a broader understanding of the toxicological insult. While there is growing evidence of the immunotoxic effects of several ENMs, the mechanisms are less characterized, and the dynamics of the molecular adaptation of the immune cells are still largely unknown. Here, we hypothesized that a multi-omics investigation of dynamic dose-dependent (DDD) molecular alterations could be used to retrieve relevant information concerning possible long-term consequences of the exposure. To this end, we applied this approach on a model of human macrophages to investigate the effects of rigid multi-walled carbon nanotubes (rCNTs). THP-1 macrophages were exposed to increasing concentrations of rCNTs and the genome-wide transcription and gene promoter methylation were assessed at three consecutive time points. The results suggest dynamic molecular adaptation with a rapid response in the gene expression and contribution of DNA methylation in the long-term adaptation. Moreover, our analytical approach is able to highlight patterns of molecular alteration in vitro that are relevant for the pathogenesis of pulmonary fibrosis, a known long-term effect of rCNTs exposure in vivo.Peer reviewe

Microarray Data Preprocessing: From Experimental Design to Differential Analysis

DNA microarray data preprocessing is of utmost importance in the analytical path starting from the experimental design and leading to a reliable biological interpretation. In fact, when all relevant aspects regarding the experimental plan have been considered, the following steps from data quality check to differential analysis will lead to robust, trustworthy results. In this chapter, all the relevant aspects and considerations about microarray preprocessing will be discussed. Preprocessing steps are organized in an orderly manner, from experimental design to quality check and batch effect removal, including the most common visualization methods. Furthermore, we will discuss data representation and differential testing methods with a focus on the most common microarray technologies, such as gene expression and DNA methylation.Peer reviewe

Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment

The COVID-19 disease led to an unprecedented health emergency, still ongoing worldwide. Given the lack of a vaccine or a clear therapeutic strategy to counteract the infection as well as its secondary effects, there is currently a pressing need to generate new insights into the SARS-CoV-2 induced host response. Biomedical data can help to investigate new aspects of the COVID-19 pathogenesis, but source heterogeneity represents a major drawback and limitation. In this work, we applied data integration methods to develop a Unified Knowledge Space (UKS) and used it to identify a new set of genes associated with SARS-CoV-2 host response, both in vitro and in vivo. Functional analysis of these genes reveals possible long-term systemic effects of the infection, such as vascular remodelling and fibrosis. Finally, we identified a set of potentially relevant drugs targeting proteins involved in multiple steps of the host response to the virus.Peer reviewe

Aging related changes of circadian rhythmicity of cytotoxic lymphocyte subpopulations

<p>Abstract</p> <p>Background</p> <p>Immunosenescence is a process that affects all cell compartments of the immune system and the contribution of the immune system to healthy aging and longevity is still an open question. Lymphocyte subpopulations present different patterns of circadian variation and in the elderly alteration of circadian rhythmicity has been evidenced. The aim of our study was to analyze the dynamics of variation of specific cytotoxic lymphocyte subsets in old aged subjects.</p> <p>Methods</p> <p>Lymphocyte subpopulation analyses were performed and cortisol serum levels were measured on blood samples collected every four hours for 24 hours from fifteen healthy male young-middle aged subjects (age range 36-55 years) and fifteen healthy male old aged subjects (age range 67-79 years).</p> <p>Results</p> <p>In healthy young-middle aged subjects CD20 were higher and at 06:00 h CD8+ dim correlated positively with CD16+ and positively with γδTCR+ cells, CD16 correlated positively with γδTCR+ cells At 18:00 h CD8+ dim correlated positively with CD16+ and positively with γδTCR+ cells, CD16+ correlated positively with γδTCR+ cells and a clear circadian rhythm was validated for the time-qualified changes of CD3+, CD4+, CD20+, CD25+ and HLA-DR+ cells with acrophase during the night and for the time-qualified changes of CD8+, CD8+ bright, CD8+ dim, CD16+ and γδTCR+ cells with acrophase during the day. In old aged subjects CD25, DR+ T cells and cortisol serum levels were higher, but there was no statistically significant correlation among lymphocyte subpopulations and a clear circadian rhythm was evidenced for time-qualified changes of CD3+ and CD25+ cells with acrophase during the night and for the time-qualified changes of CD8+ cells and cortisol with acrophase during the day.</p> <p>Conclusion</p> <p>Our study has evidenced aging-related changes of correlation and circadian rhythmicity of variation of cytotoxic lymphocyte subpopulations that might play a role in the alteration of immune system function in the elderly.</p