Towards Automatic Model Completion: from Requirements to SysML State Machines

Even if model-driven techniques have been enabled the centrality of the models in automated development processes, the majority of the industrial settings does not embrace such a paradigm due to the procedural complexity of managing model life cycle. This paper proposes a semi-automatic approach for the completion of high-level models of critical systems. The proposal suggests a specification guidelines that starts from a partial SysML (Systems Modeling Language) model of a system and on a set of requirements, expressed in the well-known Behaviour-Driven Design paradigm. On the base of such requirements, the approach enables the automatic generation of SysML state machines fragments. Once completed, the approach also enables the modeller to check the results improving the quality of the model and avoiding errors both coming from the mis-interpretation of the tool and from the modeller himself/herself. An example taken from the railway domain shows the approach.Comment: Editor: Ib\'eria Medeiros. 18th European Dependable Computing Conference (EDCC 2022), September 12-15, 2022, Zaragoza, Spain. Student Forum Proceedings - EDCC 202

Early impairment of endothelial structure and function in young normal-weight women with polycystic ovary syndrome

The aim of this study was to evaluate the presence of early vascular damage in young normal-weight women with polycystic ovary syndrome (PCOS).Thirty young normal-weight women with PCOS, who had no additional metabolic or cardiovascular diseases, and 30 healthy women (controls) matched for age and body mass index were studied. A complete hormonal assay was performed in each subject. Serum insulin and glucose levels were measured at baseline and after the oral glucose tolerance test. Plasma endothelin-1 levels and serum lipid profile were also assessed. The endothelial function was studied by flow-mediated dilation on the brachial artery, and arterial structure was evaluated by intima-media thickness measurement using Doppler ultrasound of both common carotid arteries.A significant (P < 0.05) difference in flow-mediated dilation (14.3 +/- 1.9% vs. 18.1 +/- 2.0% for PCOS patients and controls, respectively) and in intima-media thickness (0.53 +/- 0.09 mm vs. 0.39 +/- 0.08 mm for PCOS patients and controls, respectively) was found between PCOS and control subjects. Serum endothelin-1 levels were also significantly (P < 0.05) higher in PCOS patients compared with controls (1.1 +/- 0.4 pmol/liter vs. 0.5 +/- 0.2 pmol/liter for PCOS patients and controls, respectively).In conclusion, our data show that young, normal-weight, nondyslipidemic, nonhypertensive women with PCOS have an early impairment of endothelial structure and function

Allele Specific Locked Nucleic Acid Quantitative PCR (ASLNAqPCR): An Accurate and Cost-Effective Assay to Diagnose and Quantify KRAS and BRAF Mutation

The use of tyrosine kinase inhibitors (TKIs) requires the testing for hot spot mutations of the molecular effectors downstream the membrane-bound tyrosine kinases since their wild type status is expected for response to TKI therapy. We report a novel assay that we have called Allele Specific Locked Nucleic Acid quantitative PCR (ASLNAqPCR). The assay uses LNA-modified allele specific primers and LNA-modified beacon probes to increase sensitivity, specificity and to accurately quantify mutations. We designed primers specific for codon 12/13 KRAS mutations and BRAF V600E, and validated the assay with 300 routine samples from a variety of sources, including cytology specimens. All were analyzed by ASLNAqPCR and Sanger sequencing. Discordant cases were pyrosequenced. ASLNAqPCR correctly identified BRAF and KRAS mutations in all discordant cases and all had a mutated/wild type DNA ratio below the analytical sensitivity of the Sanger method. ASLNAqPCR was 100% specific with greater accuracy, positive and negative predictive values compared with Sanger sequencing. The analytical sensitivity of ASLNAqPCR is 0.1%, allowing quantification of mutated DNA in small neoplastic cell clones. ASLNAqPCR can be performed in any laboratory with real-time PCR equipment, is very cost-effective and can easily be adapted to detect hot spot mutations in other oncogenes

Progetto FATA: From Awareness To Action. Rafforzare la conoscenza e la cooperazione pubblico-privata contro le nuove forme della contraffazione online

Questo studio rappresenta il primo tentativo in Italia di analizzare in modo sistematico gli schemi e i modi operandi della contraffazione online

BRAF and MLH1 Analysis Algorithm for the Evaluation of Lynch Syndrome Risk in Colorectal Carcinoma Patients: Evidence-Based Data from the Analysis of 100 Consecutive Cases

settingsOrder Article Reprints Open AccessFeature PaperArticle BRAF and MLH1 Analysis Algorithm for the Evaluation of Lynch Syndrome Risk in Colorectal Carcinoma Patients: Evidence-Based Data from the Analysis of 100 Consecutive Cases by Thais Maloberti 1,2,†ORCID,Antonio De Leo 1,2,†ORCID,Viviana Sanza 2,Lidia Merlo 2,Michela Visani 1ORCID,Giorgia Acquaviva 1,Sara Coluccelli 1,2ORCID,Annalisa Altimari 2,3,Elisa Gruppioni 2,3,Stefano Zagnoni 2,3,Daniela Turchetti 4,Sara Miccoli 4,Michelangelo Fiorentino 5,6ORCID,Antonietta D’Errico 3ORCID,Dario de Biase 7,*,‡ORCID andGiovanni Tallini 1,2,‡ORCID 1 Department of Experimental, Diagnostic and Specialty Medicine, Anatomic Pathology Unit-University of Bologna Medical Center, 40138 Bologna, Italy 2 Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy 3 Department of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy 4 Unit of Medical Genetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico), Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy 5 Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy 6 Pathology Department, Maggiore Hospital, 40133 Bologna, Italy 7 Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy * Author to whom correspondence should be addressed. † These authors contributed equally to this work. ‡ These authors contributed equally to this work. J. Mol. Pathol. 2022, 3(3), 115-124; https://doi.org/10.3390/jmp3030011 Received: 30 March 2022 / Revised: 27 May 2022 / Accepted: 21 June 2022 / Published: 25 June 2022 (This article belongs to the Collection Feature Papers in Journal of Molecular Pathology) Download Browse Figures Versions Notes Abstract Several causes may lead to CRC, either extrinsic (sporadic forms) or genetic (hereditary forms), such as Lynch syndrome (LS). Most sporadic deficient mismatch repair (dMMR) CRC cases are characterized by the methylation of the MLH1 promoter gene and/or BRAF gene mutations. Usually, the first test performed is the mismatch repair deficiency analysis. If a tumor shows a dMMR, BRAF mutations and then the MLH1 promoter methylation status have to be assessed, according to the ACG/ASCO screening algorithm. In this study, 100 consecutive formalin-fixed and paraffin-embedded samples of dMMR CRC were analyzed for both BRAF mutations and MLH1 promoter methylation. A total of 47 (47%) samples were BRAF p.V600E mutated, while MLH1 promoter methylation was found in 77 cases (77.0%). The pipeline “BRAF-followed-by-MLH1-analysis” led to a total of 153 tests, while the sequence “MLH1-followed-by-BRAF-analysis” resulted in a total of 123 tests. This study highlights the importance of performing MLH1 analysis in LS screening of BRAF-WT specimens before addressing patients to genetic counseling. We show that MLH1 analysis performs better as a first-line test in the screening of patients with LS risk than first-line BRAF analysis. Our data indicate that analyzing MLH1 methylation as a first-line test is more cost-effective

Multi-Gene Next-Generation Sequencing Panel for Analysis of BRCA1/BRCA2 and Homologous Recombination Repair Genes Alterations Metastatic Castration-Resistant Prostate Cancer

: Despite significant therapeutic advances, metastatic CRPC (mCRPC) remains a lethal disease. Mutations in homologous recombination repair (HRR) genes are frequent in mCRPC, and tumors harboring these mutations are known to be sensitive to PARP inhibitors. The aim of this study was to verify the technical effectiveness of this panel in the analysis of mCRPC, the frequency and type of mutations in the BRCA1/BRCA2 genes, as well as in the homologous recombination repair (HRR) genes. A total of 50 mCRPC cases were analyzed using a multi-gene next-generation sequencing panel evaluating a total of 1360 amplicons in 24 HRR genes. Of the 50 cases, 23 specimens (46.0%) had an mCRPC harboring a pathogenic variant or a variant of uncertain significance (VUS), whereas in 27 mCRPCs (54.0%), no mutations were detected (wild-type tumors). BRCA2 was the most commonly mutated gene (14.0% of samples), followed by ATM (12.0%), and BRCA1 (6.0%). In conclusion, we have set up an NGS multi-gene panel that is capable of analyzing BRCA1/BRCA2 and HRR alterations in mCRPC. Moreover, our clinical algorithm is currently being used in clinical practice for the management of patients with mCRPC

Bone Marrow Edema: Overview of Etiology and Treatment Strategies

➤: Bone marrow edema (BME) is a nonspecific but relevant finding, usually indicating the presence of an underlying pathology. ➤: The gold standard technique for detecting BME is magnetic resonance imaging (MRI), as it allows for a correct diagnosis to be made, which is extremely important given the heterogeneity of BME-related diseases. ➤: Depending on the severity of painful symptomatology and the MRI evidence, different treatment strategies can be followed: physical modalities, pharmacological options, and surgical therapy