Towards semantics-driven modelling and simulation of context-aware manufacturing systems

Systems modelling and simulation are two important facets for thoroughly and effectively analysing manufacturing processes. The ever-growing complexity of the latter, the increasing amount of knowledge, and the use of Semantic Web techniques adhering meaning to data have led researchers to explore and combine together methodologies by exploiting their best features with the purpose of supporting manufacturing system's modelling and simulation applications. In the past two decades, the use of ontologies has proven to be highly effective for context modelling and knowledge management. Nevertheless, they are not meant for any kind of model simulations. The latter, instead, can be achieved by using a well-known workflow-oriented mathematical modelling language such as Petri Net (PN), which brings in modelling and analytical features suitable for creating a digital copy of an industrial system (also known as "digital twin"). The theoretical framework presented in this dissertation aims to exploit W3C standards, such as Semantic Web Rule Language (SWRL) and Web Ontology Language (OWL), to transform each piece of knowledge regarding a manufacturing system into Petri Net modelling primitives. In so doing, it supports the semantics-driven instantiation, analysis and simulation of what we call semantically-enriched PN-based manufacturing system digital twins. The approach proposed by this exploratory research is therefore based on the exploitation of the best features introduced by state-of-the-art developments in W3C standards for Linked Data, such as OWL and SWRL, together with a multipurpose graphical and mathematical modelling tool known as Petri Net. The former is used for gathering, classifying and properly storing industrial data and therefore enhances our PN-based digital copy of an industrial system with advanced reasoning features. This makes both the system modelling and analysis phases more effective and, above all, paves the way towards a completely new field, where semantically-enriched PN-based manufacturing system digital twins represent one of the drivers of the digital transformation already in place in all companies facing the industrial revolution. As a result, it has been possible to outline a list of indications that will help future efforts in the application of complex digital twin support oriented solutions, which in turn is based on semantically-enriched manufacturing information systems. Through the application cases, five key topics have been tackled, namely: (i) semantic enrichment of industrial data using the most recent ontological models in order to enhance its value and enable new uses; (ii) context-awareness, or context-adaptiveness, aiming to enable the system to capture and use information about the context of operations; (iii) reusability, which is a core concept through which we want to emphasize the importance of reusing existing assets in some form within the industrial modelling process, such as industrial process knowledge, process data, system modelling primitives, and the like; (iv) the ultimate goal of semantic Interoperability, which can be accomplished by adding data about the metadata, linking each data element to a controlled, shared vocabulary; finally, (v) the impact on modelling and simulation applications, which shows how we could automate the translation process of industrial knowledge into a digital manufacturing system and empower it with quantitative and qualitative analytical technics

Investigating alkyl nitrates as nitric oxide releasing precursors of multitarget acetylcholinesterase-monoamine oxidase B inhibitors

Herein we envisaged the possibility of exploiting alkyl nitrates as precursors of alcohol-bearing dual inhibitors targeting acetylcholinesterase (AChE) and monoamine oxidase B (MAO B), key enzymes in neurodegenerative syndromes such as Alzheimer's disease (AD), through biotransformation unmasking an alcoholic function upon nitric oxide (NO) release. The cooperation to neuroprotection of low fluxes of NO and target enzymes’ inhibition by the alcohol metabolites might return a multitargeting effect. The in vitro screening towards ChEs and MAOs of a collection of 21 primary alcohols disclosed a subset of dual inhibitors, among which three diverse chemotypes were selected to study the corresponding nitrates. Nitrate 14 proved to be a brain permeant, potent AChE-MAO B inhibitor by itself. Moreover, it protected human SH-SY5Y lines against rotenone and hydrogen peroxide with a poor inherent cytotoxicity and showed a slow conversion profile to its alcohol metabolite 9d that still behaved as bimodal and neuroprotective molecule

In Vivo Investigation of (2-Hydroxypropyl)-β-cyclodextrin-Based Formulation of Spironolactone in Aqueous Solution for Paediatric Use

Spironolactone (SPL), a potent anti-aldosterone steroidal drug used to treat several diseases in paediatric patients (e.g., hypertension, primary aldosteronism, Bartter’s syndrome, and congestive heart failure), is not available in child-friendly dosage forms, and spironolactone liquids have been reported to be unpalatable. Aiming to enhance SPL solubility in aqueous solution and overcome palatability, herein, the effects of (2-hydroxypropyl)-β-cyclodextrin (HP-β-CyD) were thoroughly investigated on solubilisation in water and on masking the unpleasant taste of SPL in vivo. Although the complexation of SPL with HP-β-CyD was demonstrated through phase solubility studies, Job’s plot, NMR and computational docking studies, our in vivo tests did not show significant effects on taste aversion. Our findings, on the one hand, suggest that the formation of an inclusion complex of SPL with HP-β-CyD itself is not necessarily a good indicator for an acceptable degree of palatability, whereas, on the other hand, they constitute the basis for investigating other cyclodextrin-based formulations of the poorly water-soluble steroidal drug, including solid dosage forms, such as spray-dried powders and orodispersible tablets

Association between metabolic syndrome, obesity, diabetes mellitus and oncological outcomes of bladder cancer. A systematic review

Metabolic syndrome is a cluster of several metabolic abnormalities, its prevalence is increasing worldwide. To summarize the most recent evidence regarding the relationship between metabolic syndrome, its components and the oncological outcomes in bladder cancer patients, a National Center for Biotechnology Information PubMed search for relevant articles either published or e-published up to March 2014 was carried out by combining the following Patient population, Intervention, Comparison, Outcome terms: metabolic syndrome, obesity, body mass index, hyperglycemia, insulin resistance, diabetes, hypertension, dyslipidemia, bladder cancer, risk, mortality, cancer specific survival, disease recurrence and progression. Metabolic syndrome is a complex, highly prevalent disorder, and central obesity, insulin resistance, dyslipidemia and hypertension are its main components. Published findings would suggest that metabolic syndrome per se might be associated with an increased risk of bladder cancer in male patients, but it did not seem to confer a risk of worse prognosis. Considering the primary components of metabolic syndrome (hypertension, obesity and dyslipidemia), available data are uncertain, and it is no possible to reach a conclusion yet on either a direct or an indirect association with bladder cancer risk and prognosis. Only with regard to type 2 diabetes mellitus, available data would suggest a potential negative correlation. However, as the evaluation of bladder cancer risk and prognosis in patients with metabolic disorders is certainly complex, further studies are urgently required to better assess the actual role of these metabolic disorders

Presence and severity of lower urinary tract symptoms are inversely correlated with the risk of prostate cancer on prostate biopsy

BACKGROUND: The assessment of lower urinary tract symptoms (LUTS) is common part of urological investigation. Furthermore, patients bother of prostate cancer (PCa) when they are affected of LUTS. This study was aimed to determine whether the presence and severity of LUTS, as assessed by the International Prostate Symptoms Score (IPSS), could help to identify patients at higher risk of prostate cancer (PCa) on prostate biopsy (PBx). In this effort, an initial PCa predictive model was calculated and IPSS was subsequently added. The diagnostic accuracy of both models was compared. METHODS: The analysis of prospectively collected data of patients scheduled for PBx at four academic hospitals between January 2012 and June 2015 was performed. Univariate and multivariate analysis assessed the correlation between the IPSS and the risk of being diagnosed with PCa; Receiver operator characteristic curve (ROC) analysis evaluated the predictive models including or not the IPSS. RESULTS: Of the 1366 enrolled patients, 706 (52%) were diagnosed with PCa. Patients with PCa had a significantly lower IPSS (10.6 +/- 7.4 vs. 12.7 +/- 8.1) than those with benign diagnosis. Multivariate logistic regression analysis showed that age, prostate-specific antigen (PSA), prostate volume and IPSS were the most significant predictors of PBx outcome, (OR 1.61, P=0.001; OR 1.20, P=0.001; OR 0.97, P=0.001; OR 0.74, P=0.004; respectively). ROC curve analysis showed that the addition of IPSS to the predictive model based on age, PSA, DRE and prostate volume significantly improved the model diagnostic accuracy (AUC: 0.776 vs. 0.652; P=0.001). CONCLUSIONS: Presence and severity of LUTS are inversely correlated with the risk of being diagnosed with PCa at PBx. Incorporating the IPSS into predictive models may reduce the risk of unnecessary PBxs.info:eu-repo/semantics/publishedVersio

Structure-Based Design and Optimization of Multitarget-Directed 2H-Chromen-2-one Derivatives as Potent Inhibitors of Monoamine Oxidase B and Cholinesterases

The multifactorial nature of Alzheimer’s disease calls for the development of multitarget agents addressing key pathogenic processes. To this end, by following a docking-assisted hybridization strategy, a number of aminocoumarins were designed, prepared, and tested as monoamine oxidases (MAOs) and acetyl- and butyryl-cholinesterase (AChE and BChE) inhibitors. Highly flexible N-benzyl-N-alkyloxy coumarins 2–12 showed good inhibitory activities at MAO-B, AChE, and BChE but low selectivity. More rigid inhibitors, bearing meta- and para-xylyl linkers, displayed good inhibitory activities and high MAO-B selectivity. Compounds 21, 24, 37, and 39, the last two featuring an improved hydrophilic/lipophilic balance, exhibited excellent activity profiles with nanomolar inhibitory potency toward hMAO-B, high hMAO-B over hMAO-A selectivity and submicromolar potency at hAChE. Cell-based assays of BBB permeation, neurotoxicity, and neuroprotection supported the potential of compound 37 as a BBB-permeant neuroprotective agent against H2O2-induced oxidative stress with poor interaction as P-gp substrate and very low cytotoxicity

In vivo investigation of (2-hydroxypropyl)-β-cyclodextrin-based formulation of spironolactone in aqueous solution for paediatric use

Spironolactone (SPL), a potent anti-aldosterone steroidal drug used to treat several diseases in paediatric patients (e.g., hypertension, primary aldosteronism, Bartter’s syndrome, and congestive heart failure), is not available in child-friendly dosage forms, and spironolactone liquids have been reported to be unpalatable. Aiming to enhance SPL solubility in aqueous solution and overcome palatability, herein, the effects of (2-hydroxypropyl)-β-cyclodextrin (HP-β-CyD) were thoroughly investigated on solubilisation in water and on masking the unpleasant taste of SPL in vivo. Although the complexation of SPL with HP-β-CyD was demonstrated through phase solubility studies, Job’s plot, NMR and computational docking studies, our in vivo tests did not show significant effects on taste aversion. Our findings, on the one hand, suggest that the formation of an inclusion complex of SPL with HP-β-CyD itself is not necessarily a good indicator for an acceptable degree of palatability, whereas, on the other hand, they constitute the basis for investigating other cyclodextrin-based formulations of the poorly water-soluble steroidal drug, including solid dosage forms, such as spray-dried powders and orodispersible tablets

How future surgery will benefit from SARS-COV-2-related measures: a SPIGC survey conveying the perspective of Italian surgeons

COVID-19 negatively affected surgical activity, but the potential benefits resulting from adopted measures remain unclear. The aim of this study was to evaluate the change in surgical activity and potential benefit from COVID-19 measures in perspective of Italian surgeons on behalf of SPIGC. A nationwide online survey on surgical practice before, during, and after COVID-19 pandemic was conducted in March-April 2022 (NCT:05323851). Effects of COVID-19 hospital-related measures on surgical patients' management and personal professional development across surgical specialties were explored. Data on demographics, pre-operative/peri-operative/post-operative management, and professional development were collected. Outcomes were matched with the corresponding volume. Four hundred and seventy-three respondents were included in final analysis across 14 surgical specialties. Since SARS-CoV-2 pandemic, application of telematic consultations (4.1% vs. 21.6%; p < 0.0001) and diagnostic evaluations (16.4% vs. 42.2%; p < 0.0001) increased. Elective surgical activities significantly reduced and surgeons opted more frequently for conservative management with a possible indication for elective (26.3% vs. 35.7%; p < 0.0001) or urgent (20.4% vs. 38.5%; p < 0.0001) surgery. All new COVID-related measures are perceived to be maintained in the future. Surgeons' personal education online increased from 12.6% (pre-COVID) to 86.6% (post-COVID; p < 0.0001). Online educational activities are considered a beneficial effect from COVID pandemic (56.4%). COVID-19 had a great impact on surgical specialties, with significant reduction of operation volume. However, some forced changes turned out to be benefits. Isolation measures pushed the use of telemedicine and telemetric devices for outpatient practice and favored communication for educational purposes and surgeon-patient/family communication. From the Italian surgeons' perspective, COVID-related measures will continue to influence future surgical clinical practice

Transglutaminase-mediated modification of proteins: Molecular mechanisms and metal-labelling of proteins

Abstract Transglutaminase (TGase) is a 331-residue monomeric microbial enzyme produced by recombinant methods, easily available from a commercial source and well characterized in structural terms. TGase catalyzes the reaction between the γ-amido group of a protein-bound Gln residue (–CONH2, the acceptor) and an amino group (–NH2, the donor) of an alkyl-amine. This enzymatic approach appears to be mild and specific for glutamine (Gln) and lysine (Lys) residues of a protein. Indeed, initial experiments have already established that TGase can be used for an effective modification of proteins. In this PhD project we have used microbial TGase for the site-specific modification of proteins at the level of Gln or Lys residue(s) by using different substrates for the enzymatic reaction. In particular, we aimed also to prepare protein derivatives containing covalently-bound peptide moieties capable of chelating metals and radionuclides. The TGase-mediated labelling of proteins has been examined in detail using protein substrates of known 3D structure and dynamics in order to unravel the conformational and dynamic features that dictate preferential or specific protein modification by TGase. Avidin and apo-α-lactalbumin were respectively modified with carbobenzoxy-glutaminyl-glycine (ZQG) and dansyl-cadaverine. In both cases, modified proteins were purified by RP-HPLC and analyzed by mass spectrometry (MS) in order to identify the sites of the modification. The results of these analyses indicated that in the case of avidin there is a double modification of the protein, while in the case of apo-α-lactalbumin there is only one site of modification. Interestingly, both proteins are derivatised by TGase at the level of Gln or Lys residues located at flexible regions of their structure, as deduced from the crystallographically determined B-factor profile along the polypeptide chain of the protein. Moreover, it was shown that there is a correlation between sites of TGase attack and sites of limited proteolysis, indicating that both TGase and a protease require some local unfolding of the protein substrate for their selective enzymatic reactions. We have also designed and synthesised two peptides that can function as suitable metal-chelating agents. These chelating peptides contain a cysteine (Cys) residue at the C-terminus that can coordinate metals as technetium (99mTc) or rhenium (186/188Re) with the thiol group and C-terminal carboxylic group acting as ligands for the metal. Moreover, these peptides contain a Lys or Gln residue that can be exploited for their TGase-mediated conjugation to proteins. The complexes of these peptides with 99mTc and 185/187Re were purified and characterised in terms of metal binding properties. Experiments are now in progress in order to use TGase for the site-specific conjugation of these metal-chelating peptides to proteins that can be used as imaging agents.RIASSUNTO La transglutaminasi (TGase) microbica è un enzima di 331 residui amminoacidici prodotta con metodi ricombinanti, facilmente reperibili da una fonte commerciale e ben caratterizzata in termini strutturali. La TGase catalizza la reazione tra il gruppo γ-ammidico di un residuo di glutammina (Gln) (-CONH2, accettore) ed un gruppo amminico (-NH2, donatore) di una alchil-ammina, ad es., il gruppo -amminico di una lisina (Lys). Le reazioni mediate da TGase avvengono in condizioni blande ed inoltre con notevole specificità, soprattutto per i residui di Gln. La TGase può essere utilizzata per la modifica enzimatica di proteine a livello di Gln, ma anche di Lys. Lo Schema illustra la possibilità di utilizzare nella reazione di una proteina con TGase un ligando in grado di mimare sia la catena laterale di Gln che Lys, potendo in tal modo, con opportuni ligandi, introdurre covalentemente in una proteina un gruppo fluorescente, un farmaco o anche un complesso metallo-peptide. In questa Tesi di dottorato la TGase è stata usata per la modifica di proteine modello, tra cui -lattalbumina, avidina ed apomioglobina (apoMb). Lo scopo della ricerca è stato quello di comprendere i motivi strutturali che determinano la specificità di azione della TGase. Inoltre, la modifica di proteine con TGase è stata condotta utilizzando substrati peptidici in grado di legare metalli e radionuclidi. La modifica di proteine con TGase è stata esaminata in dettaglio utilizzando proteine di struttura 3D e dinamiche note, al fine di individuare le caratteristiche conformazionali e dinamiche che determinano la modifica preferenziale o specifica. L’avidina e l’apo-α-lattalbumina sono state modificate utilizzando carbobenzoxy-glutaminyl-glicina (ZQG) (donatore) e dansyl-cadaverina (accettore). Le proteine modificate sono state purificate mediante RP-HPLC ed analizzate mediante spettrometria di massa (MS) al fine di individuare i siti di modifica. I risultati di queste analisi hanno indicato che le modifiche di queste proteine avvengono a livello di residui di Gln e Lys localizzati in regioni flessibili della loro struttura, come si deduce dai valori di fattore-B (parametro di flessibilità) della loro catena polipeptidica. Inoltre, è stato dimostrato che esiste una correlazione tra i siti di attacco di TGase ed i siti di proteolisi limitata, indicando che sia la TGase che una proteasi richiedono una certa flessibilità del substrato polipeptidico affinchè la reazione possa avvenire. Sono stati anche progettati e sintetizzati due peptidi in grado di fare complessi con metalli. Questi peptidi, contenendo una cisteina (Cys) quale residuo al C-terminale, sono in grado di coordinare metalli con il gruppo tiolo ed il gruppo carbossilico, tra cui tecnezio (99mTc) o renio (186/188Re). Inoltre, questi peptidi contenevano un residuo di Gln o Lys, ai fini di un riconoscimento da parte della TGase per la loro coniugazione covalente ad una proteina. I complessi di questi peptidi con 99mTc e 185/187Re sono stati purificati e caratterizzati in termini di proprietà leganti per i metalli ed utilizzati per la modifica di proteine. Ulteriori esperimenti sono in corso al fine di utilizzare la TGase per la modifica sito-specifica di proteine con questi metallo-peptidi, al fine di sviluppare una strategia di produzione di proteine marcate da usare per analisi di imagin