A Methodological Framework to Discover Pharmacogenomic Interactions Based on Random Forests

The identification of genomic alterations in tumor tissues, including somatic mutations, deletions, and gene amplifications, produces large amounts of data, which can be correlated with a diversity of therapeutic responses. We aimed to provide a methodological framework to discover pharmacogenomic interactions based on Random Forests. We matched two databases from the Cancer Cell Line Encyclopaedia (CCLE) project, and the Genomics of Drug Sensitivity in Cancer (GDSC) project. For a total of 648 shared cell lines, we considered 48,270 gene alterations from CCLE as input features and the area under the dose-response curve (AUC) for 265 drugs from GDSC as the outcomes. A three-step reduction to 501 alterations was performed, selecting known driver genes and excluding very frequent/infrequent alterations and redundant ones. For each model, we used the concordance correlation coefficient (CCC) for assessing the predictive performance, and permutation importance for assessing the contribution of each alteration. In a reasonable computational time (56 min), we identified 12 compounds whose response was at least fairly sensitive (CCC > 20) to the alteration profiles. Some diversities were found in the sets of influential alterations, providing clues to discover significant drug-gene interactions. The proposed methodological framework can be helpful for mining pharmacogenomic interactions

Pharmacogenomics: A Step forward Precision Medicine in Childhood Asthma

Personalized medicine, an approach to care in which individual characteristics are used for targeting interventions and maximizing health outcomes, is rapidly becoming a reality for many diseases. Childhood asthma is a heterogeneous disease and many children have uncontrolled symptoms. Therefore, an individualized approach is needed for improving asthma outcomes in children. The rapidly evolving fields of genomics and pharmacogenomics may provide a way to achieve asthma control and reduce future risks in children with asthma. In particular, pharmacogenomics can provide tools for identifying novel molecular mechanisms and biomarkers to guide treatment. Emergent high-throughput technologies, along with patient pheno-endotypization, will increase our knowledge of several molecular mechanisms involved in asthma pathophysiology and contribute to selecting and stratifying appropriate treatment for each patient

Radiation Recall Pneumonitis Anticipates Bilateral Immune-Induced Pneumonitis in Non-Small Cell Lung Cancer

Radiation recall pneumonitis (RRP) is a rare inflammatory reaction that occurs in previously irradiated fields, and it may be caused by various triggering agents. Immunotherapy has been reported to potentially be one of these triggers. However, precise mechanisms and specific treatments have not been explored yet due to a lack of data in this setting. Here, we report a case of a patient who received radiation therapy and immune checkpoint inhibitor therapy for non-small cell lung cancer. He developed first radiation recall pneumonitis and subsequently immune-checkpoint inhibitor-induced pneumonitis (IIP). After presenting the case, we discuss the currently available literature on RRP and the challenges of differential diagnosis between RRP, IIP, and other forms of pneumonitis. We believe that this case is of particular clinical value since it highlights the importance of including RRP in a differential diagnosis of lung consolidation during immunotherapy. Furthermore, it suggests that RRP might anticipate more extensive ICI-induced pneumonitis

Custo de implantação dos sistemas intensivos de criação de suínos confinado e ao ar livre.

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What to do in an oncology department to face the new COVID-19 era challenges?

9noItaly was the first European country to be hit by COVID-19 pandemic. As a consequence, Italian oncologists had to guarantee essential treatments although minimizing exposure to the virus, and accidental infection, of patients and healthcare professionals. As Department of Medical Oncology of the University Hospital of Udine, in this short report, we describe the measures that we have taken, and gradually updated, since February 26, 2020. All accesses to our Oncology facilities are currently regulated by entrance check-points where patients are screened for infections following dedicated algorithms. Up to date, after 6 weeks of systematic execution of swabs no physician, nurse or other individual of the staff has been found positive to COVID-19. Only one patient admitted for therapy has been identified as COVID-19 positive. The aim of our work is to propose a model, made up of a set of operative procedures, that may be adopted by all the oncologists that daily struggle to guarantee safety and care in Oncology during this COVID-19 emergency.openopenGarattini S.K.; Bin A.; Donato R.; Mansutti M.; Rizzato S.; Troiero G.; Candoni A.; Fanin R.; Fasola G.Garattini, S. K.; Bin, A.; Donato, R.; Mansutti, M.; Rizzato, S.; Troiero, G.; Candoni, A.; Fanin, R.; Fasola, G

Complexity of biogeographic pattern in the endangered crayfish Austropotamobius italicus in northern Italy: molecular insights of conservation concern.

The protection of freshwater biodiversity has become a priority task for conservation practices, as freshwater ecosystems host high levels of cryptic diversity, while also record similarly high rates of extinction. The Italian white-clawed crayfish Austropotamobius italicus is an endemic freshwater crustacean, threatened by several anthropogenic impacts such as habitat fragmentation, pol- lution, invasion of exotics, and climate change. Previous phylogenetic studies conducted in Italy pointed out a complex phylogeographic framework for the species, with four different subspecies currently recognized. Conserva- tion efforts, particularly when involving restocking and reintroduction, require a detailed knowledge of their pop- ulation genetics. In this study we describe the genetic structure of A. italicus populations in northern Italy (Lombardy Alpine foothills and northern Apennines) by using the informative mitochondrial marker cytochrome c oxidase subunit I, in order to assess their current evolu- tionary diversity and past phylogeographic history from a conservation perspective. Our results contribute to the mapping of the contact area among A. i. carsicus and A. i. carinthiacus in the Orobie Larian Prealps. Moreinterestingly, we highlight the existence of two deeply differentiated evolutionary lineages within A. i. carsicus, showing alternative phylogeographic patterns and past demographic trends. We propose to consider these two clades as distinct molecular operational taxonomic units for the conservation of this endangered crayfish

Short-term effects of air pollution on cardiovascular hospitalizations in the pisan longitudinal study

Air pollution effects on cardiovascular hospitalizations in small urban/suburban areas have been scantly investigated. Such effects were assessed among the participants in the analytical epidemiological survey carried out in Pisa and Cascina, Tuscany, Italy (2009-2011). Cardiovascular hospitalizations from 1585 subjects were followed up (2011-2015). Daily mean pollutant concentrations were estimated through random forests at 1 km (particulate matter: PM10, 2011-2015; PM2.5, 2013-2015) and 200 m (PM10, PM2.5, NO2, O3, 2013-2015) resolutions. Exposure effects were estimated using the case-crossover design and conditional logistic regression (odds ratio-OR-and 95% confidence interval-CI-for 10 μg/m3 increase; lag 0-6). During the period 2011-2015 (137 hospitalizations), a significant effect at lag 0 was observed for PM10 (OR = 1.137, CI: 1.023-1.264) at 1 km resolution. During the period 2013-2015 (69 hospitalizations), significant effects at lag 0 were observed for PM10 (OR = 1.268, CI: 1.085-1.483) and PM2.5 (OR = 1.273, CI: 1.053-1.540) at 1 km resolution, as well as for PM10 (OR = 1.365, CI: 1.103-1.690), PM2.5 (OR = 1.264, CI: 1.006-1.589) and NO2 (OR = 1.477, CI: 1.058-2.061) at 200 m resolution; significant effects were observed up to lag 2. Larger ORs were observed in males and in subjects reporting pre-existent cardiovascular/respiratory diseases. Combining analytical and routine epidemiological data with high-resolution pollutant estimates provides new insights on acute cardiovascular effects in the general population and in potentially susceptible subgroups living in small urban/suburban areas

Assessing repeatability and reproducibility of Anterior Active Rhinomanometry (AAR) in children

BACKGROUND: Repeatability and reproducibility are essential for clinicians for several purposes. Although discouraged, use of the Coefficient of Variation (CV) for assessing repeatability and reproducibility, rather than the Intraclass Correlation Coefficient (ICC), is still widespread. The aim of the present study was to highlight how using inappropriate indices may lead to misleading results, and this is done by simulation study and using real data on Anterior Active Rhinomanometry (AAR) in both healthy children and ones with rhinitis. METHODS: A simulation study was carried out to highlight how using inappropriate indices could be misleading. Then a comparison was made between CV and ICC to assess repeatability and reproducibility of AAR, for which previous studies have given underestimated results. AAR is recommended as the gold standard tool for measuring nasal resistance in clinical practice. RESULTS: A simulation study showed that the ICCs estimated from data generated assuming a true CV yielded results in agreement with estimated CVs; by contrast, if data were generated assuming a true ICC, CVs yielded conflicting results. For AAR, ICCs showed good repeatability, whereas CVs showed unacceptable repeatability. AUC and 95% CI for AAR showed good performance in predicting current symptoms of rhinitis in the overall study population. CONCLUSIONS: The present study focused on the importance of the choice of appropriate indices of repeatability and reproducibility, demonstrating the repeatability of AAR in both healthy children and ones with rhinitis