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0:ID	Type	Title	Authors	Abstract	Source	Year	CNR list	Keywords	9:DOI
388694	Software	ChromStruct v4.2 - Reconstruction of 3D chromatin structure from chromosome conformation capture data	Salerno E., Caudai C.	This Python (v.2.7.10) code provides an estimate of the 3D structure of the chromatin fibre in cell nuclei from the contact frequency data produced by a 'Chromosome conformation capture' experiment. The only input required is a text file containing a general real matrix of contact frequencies. The code features a GUI where all the tuneable parameters are made available to the user. The fibre is divided in independent segments whose structures are first estimated separately and then modelled as single elements of a lower-resolution fibre, which is treated iteratively in the same way until it cannot be divided anymore into independent segments. The full-resolution chain is then reconstructed by another iterative procedure. See the Readme file and the cited references for more detail.	2018	2018	CAUDAI CLAUDIA, SALERNO EMANUELE	Chromosome Conformation Capture, Chromatin Structure Estimation
388705	Poster	Effect of the use of chlorine usage in milking equipment cleaning procedures on raw milk microbiota	Cremonesi P., Ceccarani C., Cologna N., Goss A., Severgnini M., Mazzucchi M., Partel E., Morandi S., Castiglioni B., Tamburini A., Zanini L., Brasca M.	Aim Proper milking machine cleaning and disinfection procedures are essential to ensure milk hygienic quality, and sodium hypochlorite is generally present in commercially available products (Gleeson et al. 2012), but it has been previously demonstrated that nonchlorine detergent products give satisfactory results when used with sufficiently hot water (Teagasc et al. 2012). In addition, some studies highlighted the effect of chlorine on milk bacterial count, encouraging a deeper comprehension of the relationship between the use of chlorine products and milk microbiota, which represents a key point for raw milk cheese production (Gleeson et al. 2013). The aim of the study was to evaluate the influence of chlorine products usage for cleaning and sanitizing the milking equipment on raw milk and the deriving whey-starter microbiota in Trentingrana production. Trentingrana is a Protected Designation of Origin (PDO) hard cheese manufactured in the valleys of Trento province (eastern Italian Alps) by several small cooperative dairies linked in a consortium (Bittante et al. 2011). Materials and Methods Three farms (here named as F1, F2 and F3) located in Trentino and associated to a factory producing Trentingrana cheese, were involved in the study. The herds were composed by 55, 48 and 91 lactating cows (Italian Holstein-Friesian, Brown and Italian Simmental in different ratios). The farms were free stall barns with cubicles with mattress covered with sawdust and lactating cows were fed hay associated with concentrate. The herds were milked twice a day in DeLaval herringbone milking plants (F1 (5+5), F2 (4+4), F3 (6+6). The cleaning routine practices and products usage rates were those recommended by the producers and the water temperatures appropriate. Milk was collected thrice weekly during the sodium hypoclorite detergent usage (six-weeks period, C) and in a subsequent, analogous, nonchlorine detergent period (period NC); a 4-weeks interval was established between the two experimental periods in order to allow bacterial population adaptation to the new detergent. In the last three days of each experimental week, bulk milk was sampled from tank. The whey-starter used that day for cheese-making was sampled too. Within 12 h from collection, samples were submitted to microbiological analyses (Standard Plate Count SPC, coliforms, staphylococci coagulase positive, lactic acid bacteria LAB). For microbiome analysis, bacterial DNA was extracted from 5 ml of milk or whey-starter samples using a protocol previously described (Cremonesi et al. 2006) with some modifications. 16S rRNA gene (V3-V4 region) was amplified following standard 16S Metagenomic Sequencing Library Preparation and sequenced on a paired 2x250 bp run on Illumina MiSeq platform. Data analyses (alpha and beta diversity, taxonomical abundances) were performed using the QIIME pipeline (release 1.8.0; (Kuczynski et al., 2011). Results and Discussion Even if no microbiological significant differences were observed, higher levels of SPC and LAB in bulk milk were recorded going from period C to period NC (4,06 +-0,16 vs 4,10 +-0,20 log cfu/mL), while coliforms and staphylococci tended to be lower in NC period (1,97+-1,02 vs 1,60+-0,68 log ufc/mL and 2,17+-0,48 vs 2,07+-0,57 log cfu/mL respectively). An increase in LAB count, although not significant, was observed in LAB content in whey-starter (8,11+-0,43 log ufc/mL in period N vs 8,66 +-0,45 log cfu/mL in period NC). The microbiota composition was quite peculiar in the three farms analysed, and between C and NC periods. Alpha- and beta-diversity analyses revealed significant differences among farms (p values: 0.003 and 0.001, respectively): in fact, farm F1 and F2 microbial taxonomic composition was dominated by Firmicutes (rel. ab. respectively 60.5% and 42.8% in period C; 57.5% and 52.1% in period NC), while farm F3 showed a microbial composition dominated by Bacteriodetes (47.4% period C; 52.1% period NC). Differences in the microbiota profile (beta-diversity) between C and NC periods within each farm were found to be significant (p < 0.05). Relative abundances analysis revealed that farm F1 and F2 had a significant change in Oscillospira genus and, respectively, in Chryseobacterium and Clostridium genera; farm F3 showed Acinetobacter and Trichococcus genera significantly decreased. Though raw milk microbiota varied among farms, whey-starter bacterial composition consisted mainly of Lactobacillus genus. At a species-level, Lb. helveticus was predominant during period C (62.9% rel. ab.) and significantly reduced during period NC (31.8%), whereas Lb. delbrueckii had the exact opposite trend (28.1% period C; 58.6% period NC). Conclusion Our preliminary results report that is reasonable to further study chlorine influence on milk microbiota, in order to better understand the changes in its composition and, consequently, the possible effect on raw milk cheese production performances and overall quality.	International Bovine Mastitis Conference., Milano, 11-13/06/2018	2018	CECCARANI CAMILLA, CASTIGLIONI BIANCA MARIA ELISABETTA, BRASCA MILENA, SEVERGNINI MARCO, MORANDI STEFANO, CREMONESI PAOLA	chlorine, milking equipment, cleaning procedures, raw milk microbiota
390841	Presentazione	Ripensare la poliarchia. Il pensiero di Dahl come antidoto al malessere della democrazia	ANTONUCCI, MARIA CRISTINA	Le democrazie contemporanee appaiono oggetto di disfunzioni tanto in termini procedurali, con la difficolta di tradurre gli orientamenti elettorali espressi dai cittadini nella fase elettorale in concrete pratiche di rappresentanza politica e in politiche di governo, quanto in termini sostanziali, in ragione della generalizzata disaffezione dei cittadini alla politica e ai suoi attori, prima ancora che all'astensionismo elettorale. Le difficolta dei regimi politici democratici sono radicate dentro un contesto sociale e politico dominato da fenomeni di una complessita non prevedibile nella genesi della democrazia rappresentativa: gli effetti dei media digitali e sociali sulla formazione dell'opinione pubblica, la nuova percezione del rapporto tra cittadini, politica e istituzioni, la percezione della inefficacia dei comportamenti elettorali a fronte di forti vincoli esterni (globalizzazione economica, partecipazione ad istituzioni politiche sovranazionali cui e demandato il processo decisionale) ed interni (governance multilivello, sussidiarieta) condizionano sempre di piu spazi, orientamenti e ambiti di azione e partecipazione nelle democrazie contemporanee, ritenute, a torto o a ragione, sempre piu foriere di promesse non mantenute nei confronti dei cittadini. La formulazione di preferenze, la capacita di rendere le preferenze espresse significative nel quadro del contesto istituzionale e la possibilita che queste preferenze vengano concretamente considerate nell'ambito della formazione di politiche di governo sono i fattori di sistema che vengono posti in questione dall'attuale crisi di partecipazione politico-elettorale, dal ridotto grado di accountability politico-istituzionale, dalla rottura delle premesse ideali e fiduciarie, fondate su classe, ceto, ideologia, nei confronti degli attori partitici, transitati da un modello organizzativo di massa consolidato e diffusivo alla galassia post-ideologica di cartel party e catch all party. Nel presente contributo, si intende riportare i termini del dibattito sul malessere della democrazia alla concezione di Robert Dahl espressa nel volume Poliarchia, cercando di porre in luce i fattori istituzionali, di sviluppo socio-economico e di natura propriamente politica in grado di favorire la realizzazione di un modello poliarchico all'interno di un determinato regime politico. In particolare, appare utile ancorare ogni ragionamento sulla crisi della democrazia rappresentativa all'idea sviluppata dallo studioso statunitense di poliarchia: se la concezione di democrazia appare legata alla dimensione puramente ideale di indagine, appare piu significativo impostare l'analisi sul concetto di poliarchia, intesa come regime politico relativamente, ma incompiutamente, democratizzato. Lo scarto tra idealizzazione democratica e concretezza delle esperienze poliarchiche realizzatesi nei regimi politici indagate da Dahl, porta alla riformulazione della valutazione dei regimi politici alla luce delle condizioni che ne aumentano gli ambiti di democratizzazione: 1.livello di liberalizzazione e margine di inclusione dei cittadini; 2. ammissibilita di spazi per la contestazione delle politiche poste in essere dal governo; 3. relazione tra ordine sociale pluralista e livello di sviluppo economico atto alla diversificazione sociale; 4. capacita del sistema di produrre eguaglianza nella distribuzione di risorse politiche ed economiche; 5. possibilita di tratteggiare uno spazio specifico per le sottoculture sub-nazionali, 6. costruzione di elementi a sostegno della legittimazione istituzionale dei sistemi poliarchici. Con particolare riferimento all'ultimo tema, per la legittimazione dei sistemi poliarchici un ruolo particolare sembra affidato all'autorita dei governi, alla efficienza delle politiche, intesa come capacita di un regime di risolvere le questioni critiche, alla fiducia riposta dai cittadini nei confronti del sistema politico e dei suoi attori, alla volonta di cooperazione dei diversi soggetti sociali, economici, istituzionali e politici, all'interno del regime politico poliarchico. Nell'analisi dei problemi di salute delle poliarchie contemporanee, grande spazio appare occupato dalla inefficacia delle politiche, dalla crisi di fiducia nei confronti delle istituzioni, dalla mancanza di cooperazione e dal limitato accesso, su base di pari opportunita tra i cittadini, alle risorse politiche. Riprendere in considerazione i fattori socio-economici che determinano le condizioni politiche dei regimi poliarchici e la principale indicazione che una rilettura odierna dal pensiero di Dahl puo offrire alla odierna crisi della democrazia, specialmente in un contesto di teoria politica piu concentrato sulle cause tecnico-procedurali del malessere democratico che sulle determinanti politiche, sociali e culturali dell'inefficacia dei regimi democratici.	SOCIETA' ITALIANA DI SCIENZA POLITICA, CONVEGNO ANNUALE 2018 - Democrazia e ri-definizioni. La teoria politica e il <> della teoria democratica, pp. 1-10, TORINO - UNIVERSITA' DEGLI STUDI, 06-08/09/2018	2018	ANTONUCCI MARIA CRISTINA	DEMOCRAZIA, DAHL, POLIARCHIA, TEORIA POLITICA
392376	Presentazione	Effetto dell'impiego di cloro nella pulizia dell'impianto di mungitura sul microbiota del latte crudo	Morandi S., Cremonesi P., Ceccarani C., Cologna N., Goss A., Severgnini M., Mazzucchi M., Partel E., Castiglioni B., Tamburini A., Zanini L., Brasca M.	Lo scopo dello studio e stato quello di valutare l'influenza dell'uso di prodotti a base di cloro per la pulizia e la sanificazione delle attrezzature di mungitura sul latte crudo e del microbiota derivante dal siero nella produzione di Trentingrana. Trentingrana e un formaggio a pasta dura a denominazione di origine protetta (DOP) prodotto nelle valli della provincia di Trento (Alpi italiane orientali) da alcune piccole latterie cooperative collegate in un consorzio	6? Congresso lattiero-caseario Aitel. Latte e derivati: ricerca, innovazione e valorizzazione, Trento, 20/09/2018	2018	CECCARANI CAMILLA, CASTIGLIONI BIANCA MARIA ELISABETTA, BRASCA MILENA, SEVERGNINI MARCO, MORANDI STEFANO, CREMONESI PAOLA	Cloro, siero-innesto, metagenomica
400549	Monografia o trattato scientifico	ARE THEY WORTH A SHOT?	Andrea Grignolio	The dangerous decline in vaccinations in many developed countries is at the heart of a lively debate that confirms how important the subject is today. Vaccinations are among mankind's most important scientific discoveries, yet they continue to be viewed with suspicion by part of the public - the victims of disinformation campaigns, instrumentalization and unfounded fears. There is, however, also an evolutionary explanation for these irrational beliefs, and countering the growing social opposition will be extremely difficult without grasping it. This book, which sheds new light on the safety and importance of vaccinations, is intended both for parents and those readers who want to understand the role of vaccinations in contemporary society, where the ease of access to knowledge is both a great opportunity and a great responsibility. The chapters follow a historical progression and conclude with a discussion of the most recent cognitive theories on how to overcome this opposition to vaccinations.	Basel: Springer Nature Switzerland, 2018	2018	GRIGNOLIO ANDREA	Vaccini
400553	Postfazione	"INTRODUZIONE". VOLUME DEDICATO A GIUSEPPE LEVI	Andrea Grignolio	Introduzione al Volume dedicato a Giuseppe Levi	GIUSEPPE LEVI: A BIBLIOGRAPHY, edited by Grignolio Andrea, pp. 9-14, 2018	2018	GRIGNOLIO ANDREA	Giuseppe Levi
400596	Postfazione	Why does medicine need rhetoric? Introduction to the issue on "Argumentation and Medicine"	Zagarella, Roberta Martina	Introduction to the issue on "Argumentation and Medicine"	"Argumentation and Medicine", pp. 1-4, 2018	2018	ZAGARELLA ROBERTA MARTINA	Argumentation, Medicine	10.4396/20180600
400604	Curatela di numero monografico (di rivista o di collana)	Argumentation and medicine	Roberta Martina Zagarella	Argumentation theory, or "new rhetoric", focuses on our uses of language when a decision with an action in sight is at stake. Today, argumentation theory has proven particularly pertinent to the analysis of the role language plays in clinical practice and more generally in biomedicine - areas that increasingly involve individual choices regarding health and the body. The combination of rhetoric and medicine, however, is not a new one. The methodological affinities of the two disciplines constituted, in fact, a topos of ancient Greek thought, especially with regards to the ability of the rhetor and the physician to make good decisions; the constitutive possibility of deviating from pre-established, fixed paths by elaborating new hypotheses; as well as the importance of the individual case in both practices. The objective of this journal issue is to thematise the relationship between argumentation/rhetoric and medicine, by putting ancient tradition and the contemporary debate into dialogue. We hope to gather contributions from a variety of disciplines which will emphasise the key elements of this relationship. The interconnections between argumentation and medicine merit scrutiny from points of view that are diverse and complementary. On the one hand, this interdisciplinary approach will allow us to test a number of theoretical models of argumentation on an area of application that is less common than politics or law. Medicine entails ethically complex and continuously shifting individual situations, not least due to biomedical innovations. Furthermore, a juxtaposition of the two disciplines enables us to linger on some of their common epistemological traits, as well as on the status of proof; on the notions of credibility, trust, truth, and liberty; and finally on bioethical principles such as self-determination and autonomy. On the other hand, argumentation studies can offer tools for reflection on the era of post-paternalistic medicine, from a bioethical as well as biopolitical point of view. Moreover, a rhetorical or argumentative perspective can contribute to the contemporary need for what is called "high-quality communication" in the field of health. Finally, argumentation allows us to tackle - not only from a political, but also from a theoretical point of view - the issue of science's loss of credibility in the eyes of citizens, as seen, for instance, in the controversy over the safety and efficacy of vaccines; as well as to dissect the debate over fake news, post-truth and science communication. We welcome contributions that focus on: historical as well as theoretical reconstructions of the relationship between rhetoric and medicine; the role of persuasive language in contemporary medicine; the bioethical and biopolitical issues that underlie it; the discursive and decision-making processes that involve physicians and patients, including securing informed consent; the relationship between the word and the cure, or between discourse and biopower; the divulgation of science; the ways in which citizens understand, evaluate, and discuss medical information; the impact of fake news and the notion of post-truth. We will consider contributions which analyse the relationship between argumentation and medicine from diverse theoretical standpoints and disciplines, such as, but not limited to: argumentation theory; rhetoric; philosophy of language; linguistics; semiotics; history of ideas; bioethics; moral philosophy; philosophy of law; philosophy of science; medicine; psychoanalysis; psychology; neuroscience; sociology.	2018	2018	ZAGARELLA ROBERTA MARTINA	argumentation theory, rhetoric, medicine, bioethics
400609	Rapporto tecnico	R11 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0061896/2018, 2018	2018	ADAMO GIORGIA	Research Integrity
400610	Rapporto tecnico	R12 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0016955/2018, 2018	2018	ADAMO GIORGIA	Research Integrity
400612	Annual report	R13 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0016960/2018, 2018	2018	ADAMO GIORGIA	Research Integrity
400614	Rapporto tecnico	R14 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0039081/2018, 2018	2018	ADAMO GIORGIA	Research Integrity
400615	Rapporto tecnico	R15 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	2018	2018	ADAMO GIORGIA	Research Integrity
400616	Rapporto tecnico	R23 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo, Cinzia Caporale	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0028546/2018, 2018	2018	ADAMO GIORGIA	Research Integrity
400617	Rapporto tecnico	R36 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Adamo Giorgia	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0062334/2018, 2018	2018	ADAMO GIORGIA	Research Integrity
400618	Rapporto tecnico	R37 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0039080/2018, 2018	2018	ADAMO GIORGIA	Research Integrity
400619	Rapporto tecnico	R39 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0062341/2018, 2018	2018	ADAMO GIORGIA	Research Integrity
400620	Rapporto tecnico	R40 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0062345/2018, 2018	2018	ADAMO GIORGIA	Research Integrity
400621	Rapporto tecnico	R41 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0032907/2018, 2018	2018	ADAMO GIORGIA	Research Integrity
400688	Rapporto tecnico	R32 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Paola Grisanti	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0077229/2018, 2018	2018	GRISANTI PAOLA	Research Integrity, Research Misconduct
400690	Rapporto tecnico	R33 - Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Paola Grisanti	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n. 0077231/2018, 2018	2018	GRISANTI PAOLA	Research Integrity, Research Misconduct
400881	Recensione in rivista	Book Review "Capitali regionali" on Contemporary Italian Politics	ANTONUCCI M		Bulletin of Italian politics 11 (2019): 104-105.	2019	ANTONUCCI MARIA CRISTINA	italian politics, regions, elections, political subcultures	10.1080/23248823.2019.1577002
409080	Sito web	www.gemma-project.eu	Matteo Gnocchi, Marco Moscatelli, Alessandra Mezzelani	Portale Scientifico del Progetto Europeo Gemma	2019	2019	MEZZELANI ALESSANDRA MARIA, GNOCCHI MATTEO, MOSCATELLI MARCO	Portale, Unione Europea, wordpress, Gemma-Project
409083	Rapporto tecnico	GEMMA EU PROJECT INFRASTRUCTURE	Matteo Gnocchi, Marco Moscatelli, Alessandra Mezzelani	Descrizione della infrastruttura IT implementata nell'ambito del progetto europeo GEMMA	2019	2019	MEZZELANI ALESSANDRA MARIA, GNOCCHI MATTEO, MOSCATELLI MARCO	gemma-project
396211	Poster	Confronto tra la biodiversita del microbioma del latte delle razze Frisona Italiana e Rendena	Paola Cremonesi1, Camilla Ceccarani2, 3, Giulio Curone4, Marco Severgnini2, Claudia Pollera4, Valerio Bronzo4, Federica Riva4, Maria Filippa Addis4, Joel Filipe4, Massimo Amadori5, Erminio Trevisi6, Daniele Vigo4, Paolo Moroni4, 7, Bianca Castiglioni1	Il periodo del periparto rappresenta una delle fasi piu critiche per la salute delle mammelle nei bovini, specialmente nelle razze altamente produttive, come la Frisona Italiana, mentre alcune razze autoctone, come la Rendena (REN), attualmente diffusa maggiormente nelle province di Padova, Trento, Vicenza e Verona, hanno una prevalenza inferiore di mastite o di altre malattie. In questo studio abbiamo pertanto confrontato il microbiota del latte di 6 vacche di razza Frisona Italiana con quello di 3 animali di razza Rendena, allevati tutti nello stesso luogo e con le stesse condizioni, allo scopo di definire la prevalenza d quei gruppi batterici che potrebbero avere un effetto sulla salute della ghiandola mammaria. Sono stati considerati quattro punti temporali (asciutta, 1 giorno dopo il parto, 7-10 giorni dopo il parto e 30 giorni dopo il parto). Abbiamo caratterizzato, attraverso il sequenziamento del gene rRNA 16S, il microbioma di 117 campioni di latte raccolti durante il periodo sperimentale soltanto dai quarti sani con una conta delle cellule somatiche (SCC) inferiore a 200.000 cellule / ml. Le popolazioni microbiche presenti nel latte delle due razze sono risultate profondamente diverse in tutto il periodo, con il latte della razza Rendena che mostrava una biodiversita microbica significativamente piu bassa. I profili tassonomici di entrambe le razze cosmopolite e locali erano dominati dai Firmicutes, per lo piu rappresentati dal genere Streptococcus, sebbene in proporzioni molto diverse (27,5 nella razza Frisona, 68,6% nella razza Rendena). Infine, solo il latte delle bovine di razza Frisona ha mostrato cambiamenti significativi nella composizione microbica durante il periodo di transizione, mentre il latte della razza Rendena ha mantenuto un microbiota piu stabile. In conclusione, le significative differenze riscontrate nel microbioma del latte delle due razze potrebbero anche avere un impatto sulla salute della ghiandola mammaria, oltre ad un'influenza sulle caratteristiche finali dei prodotti caseari delle due razze.	6? Congresso lattiero-caseario Aitel. Latte e derivati: ricerca, innovazione e valorizzazione, Trento, 20/09/2018	2018	CECCARANI CAMILLA, CASTIGLIONI BIANCA MARIA ELISABETTA, SEVERGNINI MARCO, CREMONESI PAOLA	microbioma, latte, bovina
405968	Poster	Effect of the use of chlorine usage in milking equipment cleaning procedures on raw milk microbiota	Cremonesi P, Morandi S, Ceccarani C, Cologna N, Goss A, Severgnini M, Mazzucchi M, Partel E, Castiglioni B, Tamburini A, Zanini L, Brasca M	Background: Sodium hypochlorite (NaClO) is generally used for disinfection of milking equipment ensuring milk hygienic quality. Different studies showed that the chlorine can affect milk microbial population, encouraging the comprehension of the relationship between the use of chlorine products and milk microbiota, which represents a key point for raw milk cheese production. Objectives: The aim of the study was to evaluate the influence of NaClO on raw milk microbiota and the deriving whey-starter bacterial composition in Trentingrana PDO cheese production. Methods: Three farms were involved in the study. Milk was collected thrice weekly during the NaClO usage (six-weeks period, C) and in a subsequent, analogous, nonchlorine detergent period (NC). Fourweeks interval was established between the two experimental periods. The deriving whey-starter was sampled too. Samples were submitted to microbiological analyses (Standard Plate Count, coliforms, staphylococci, Lactic Acid Bacteria) and to metagenomic analysis. To this aim, 16S rRNA gene (V3-V4 region) was sequenced by Illumina MiSeq platform. Data analyses were performed with QIIME pipeline. Results: No significant differences were observed but higher SPC and LAB counts were recorded in milk going from period C to period NC. The metagenomic analysis of milk showed a distinctive microbiota composition for the three farms during the whole experimental period, moreover we evidenced a significant difference in microbial population related to chlorine use. The use of chlorine was found to affect the whey-starter population; Lactobacillus helveticus was predominant during period C and significantly reduced during period NC, whereas Lb. delbrueckii had the exact opposite trend.	8th Congress of European Microbiologist (FEMS), pp. 1569-1569, Glasgow (UK), 7-11/07/2019	2019	CECCARANI CAMILLA, CASTIGLIONI BIANCA MARIA ELISABETTA, BRASCA MILENA, SEVERGNINI MARCO, MORANDI STEFANO, CREMONESI PAOLA	Chlorine, Raw milk, Whey culture, milking equipment, Trentingrana
406069	Abstract in atti di convegno	Comparison among four different bacterial DNA extraction protocols for analysing milk metagenomics	Paola Cremonesi1, Marco Severgnini2, Alicia Romano3, 4, Mario Luini3, Bianca Castiglioni1	Bovine udder is colonized by a huge number of microorganisms that constitute the intramammary ecosystem, with a specific role in modulating not only the udder homeostasis and mastitis susceptibility but also the quality of the dairy products. Therefore, information on milk microbiota composition will facilitate the dairy industry in the production of safe and high-quality products. However, generating high-quality bacterial DNA could be critical. In the present study, bacterial DNA from healthy milk samples was isolated by four different protocols to evaluate the effect of the extraction procedures on milk microbiota composition. For the characterization of the milk microbiota by 16S deep sequencing, 500 ml of bulk tank milk samples were aseptically collected from three different farms and bacterial DNA was extracted by using an internal laboratory protocol and three commercial kits. Bacterial DNA was then amplified using the primers for the V3-V4 hypervariable regions and sequenced in one MiSeq (Illumina) run with 2x250-base paired-end reads. Data analysis was performed by using QIIME suite and SILVA 132 as reference database for taxonomy. The results showed that the four extraction kits performed very differently and showed a significant separation on both microbial richness (alpha-diversity) and composition (beta-diversity). In particular, the relative abundance of some genera (e.g.: Lactobacillus, Acinetobacter and Microbacterium) were consistently altered by the extraction method. Based on these data, then, particular attention must be kept in choosing the proper extraction method, for example, carefully evaluating eventual biases towards or against bacterial genera of interest. Moreover, we believe that, in order to define which kit best resembles the original bacterial community, an additional set of experiments with a mock community with known composition should be performed.	23? Congresso dell'Associazione per la Scienza e le Produzioni Animali (ASPA), Sorrento, Italy, 11/06/2019, 14/06/2019	2019	CASTIGLIONI BIANCA MARIA ELISABETTA, SEVERGNINI MARCO, CREMONESI PAOLA	bovine milk, DNA extraction, milk microbiome	10.1080/1828051X.2019.1622269
406138	Abstract in atti di convegno	NeoHiC: a web application for the analysis of Hi-C data	D. D'Agostino, I. Merelli, M. Aldinucci, P. Lio	High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of chromatin interactions and 3D chromosome folding on a larger scale. A graph-based representation of Hi-C data is very important for a proper visualization of the spatial pattern they represent, in particular for comparing different experiments or for re-mapping omics-data in a space-aware context. But the size of these graphs can be very large, and this prevents the straightforward use of current available graph visualization tools and libraries. In this paper, we present the first version of NeoHIC, a web application for the progressive graph visualization of Hi-C data based on the use of the Neo4j graph database.	Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2019), pp. 29-32, Bergamo, Italy, 4-6/9/2019	2019	D'AGOSTINO DANIELE, MERELLI IVAN	Hi-C, graph databases, web application, graph visualization
401232	Comunicazione in rivista (Letter - Letter to editor)	Seeking a standardized normalization method for the quantification of microRNA expression	Nuzziello N., Liguori M.		Muscle & nerve (Print) (2019).	2019	NUZZIELLO NICOLETTA, LIGUORI MARIA	microRNA, HT-NGS, qPCR, standardization	10.1002/mus.26455
409554	Poster	Raw milk microbiota modifications as affected by different cleaning procedures: the Trentingrana case. Interbational Conference on raw milk.	Battelli G., Cremonesi P., Ceccarani C., Cologna N., Goss A., Severgnini M., Mazzucchi M., Partel E., Morandi S., Castiglioni B., Tamburini A., Zanini L., Brasca M.	x	International conference on raw milk., Valencia, Spain, 24-25/10/2019	2019	CECCARANI CAMILLA, BATTELLI GIOVANNA, CASTIGLIONI BIANCA MARIA ELISABETTA, BRASCA MILENA, SEVERGNINI MARCO, MORANDI STEFANO, CREMONESI PAOLA	raw milk, cheese, microbiome, sanitizing products
421744	Presentazione	Presentation of National Research Council (CNR) Institute for Biomedical Technologies (ITB) as LifeTime Associated Partner	Alessandra Mezzelani	CNR-ITB is the largest public institute of its kind in Italy It pioneers new types of cross-disciplinary biomedical research by bringing biology, engineering, medicine, and the basic sciences together. It counts on collaborations between industry and basic scientists and clinicians from a broad range of disciplines. CNR-ITB: Platforms, Infrastructures and Units related to LifeTime Bioinformatics, Stem Cell - 3D Organoid Technologies Unit, BMI1 is studied at the SC-transcriptomics level as novel therapeutic targetin lung cancer, Clinical Proteomics Laboratory, Epigenetics, Genomics, Research ethics, Bioethics and Biolaw UNIT, Proposed involvement and expertise CNR-ITB is the largest public institute of its kind in Italy It pioneers new types of cross-disciplinary biomedical research by bringing biology, engineering, medicine, and the basic sciences together. It counts on collaborations between industry and basic scientists and clinicians from a broad range of disciplines.	LifeTime UnConference: Single-cell Multi-omics and Imaging and Data Science, Artificial Intelligence and Machine Learning., Barcellona, 22- 23 July 2019.	2019	MEZZELANI ALESSANDRA MARIA	single cell analysis, LifeTime, European initiative
416885	Editoriale in rivista	Latest advances in parallel, distributed, and network-based processing	I. Merelli, P. Lio, I. Kotenko, D. D'Agostino		Concurrency and computation (Online) 32 (2020): e5683.	2020	D'AGOSTINO DANIELE, MERELLI IVAN	parallel computing, distributed computing, network-based computing	10.1002/cpe.5683
426212	Poster	Linked-read whole genome sequencing reveals undetected variants in autism spectrum disorder	F.A. Cupaioli1, E Mosca1, N. Di Nanni1, P. Pelucchi1, L. Milanesi1, M.E. Raggi2, M.L. Villa2, A. Mezzelani1	Abstract Introduction: Autism Spectrum Disorder (ASD) is a neurodevelopmental condition with complex etiology. Although genetics play a key role in ASD, causative or predisposing genetic variants have been detected only in 30% of patients. Here, for the first time, linked-read whole genome sequencing of ASD patients is used to access disease associated regions unmappable by short-reads NGS. Materials and Methods: 10 children with ASD, including 3 couples of affected siblings, were enrolled and HMW DNA isolated from peripheral blood. DNA was submitted to 10Xgenomics microfluidics partitioning and barcoding, library preparation and Illumina WG-NGS. Data were analyzed through 10x Long Ranger pipelines to find SNVs, in/dels and larger structural variants in comparison to 1000 genomes, genome aggregation database and NHLBI-ESP populations. Genes affected by variants were compared with those already known to be associated with ASD (SFARI database, large-scale sequencing studies, bioinformatics predictions). Results: this approach successfully produced sequences up to 9mln bp in length. Among the detected variants, 405 were listed in SFARI, 43 confirmed bioinformatics predictions and 3,210 were new. Among the latter variants, 22 were homozygous in all the 3 couples of siblings. Conclusion: this powerful approach deciphered underlying genomic heterogeneity and missing variations in ASD. Further studies will be performed to validate the new ASD variants in a large size of samples and in public data. Data integration will be also performed to identify pathways and gene networks involved in the disorder to understand disease mechanisms and design target-driven treatment. Acknowledgements: EU project GEMMA (grant agreement No 825033).	European Human Genetics Virtual Conference ESHG 2020.2, JUNE 6-9, 2020	2020	DI NANNI NOEMI, MEZZELANI ALESSANDRA MARIA, PELUCCHI PARIDE, MOSCA ETTORE, CUPAIOLI FRANCESCA ANNA	whole genome sequencing, autism spectrum disorder, linked read
426789	Poster	Microbiota Profile in Autism Spectrum Disorder: Different Metagenomics Approaches to analyze 16S and 18S rRNA	Chiappori F, Cupaioli F.A., Milanesi L., Raggi M.E., Mezzelani A.	Abstract Introduction: Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by communication impairments, limited social interaction, restricted interests, repetitive behaviors and stereotypies. It manifests within the first 3 years of age and lasts for a lifetime with dramatic personal, familial and social consequences. ASD affects much more males than females (male:female=5:1) and its prevalence, that is continuously increasing, interests 2.24% of children and 1% of the general population [1,3]. Although genetics play a key role in ASD, its etiology is complex. Since most of individuals with ASD suffer from additional comorbidities including gastrointestinal disorders, intestinal permeability, inflammation and allergies, a gene-environment interaction has been proposed as ASD triggering [3]. Dysbiosis has been frequently associated with many neurological disorders including ASD. Thanks to the last advances in metagenomics, much progress has been made in the knowledge of gut microbiota profile and role, especially the prokaryotic one, but literature lacks of studies about eukaryotic colonizer of human intestine and their role in human health. Aims Here, employing different bioinformatics tools, we propose a metagenomics pilot study to define the prokaryotic and eukaryotic gut microbiota of children with ASD and neurotypical controls. The aims are to test different metagenomics pipelines and set up the more performing bioinformatics conditions to identify ASD microbial biomarkers useful for patient stratification and personalized treatments. Materials and Methods: We isolated DNA from stools collected from 6 children with ASD (5 males and 1 female) and 6 neurotypical controls matching for age and sex. Both 16S and 18S were amplified for each DNA and Illumina libraries prepared. NGS was performed by Illunima MiSeq platform coupled with Flowcell V3 2X300 and forward and reverse reading, reaching about 22Milion of sequences. As for bioinformatics analysis, three different software with several pipelines were applied: the automatic pipeline of SILVAngs analysis platform (https://ngs.arb-silva.de/silvangs/) [4], the MiSeq SOP pipeline of Mothur (https://mothur.org/) [5], and two pipelines of Qiime2 (https://qiime2.org/) [6]. The latter includes the Dada2 pipeline and the Deblur one. All the analyses were performed against SILVAv132 database [7], the only one that includes both 16s and 18S reference database. Results: The results obtained from the four tools are superimposable, also at different level of taxonomy detail. Restricting to Bacteria results, the identified genera are comparable with literature data [8]. As for Fungi, this first round of analysis doesn't return relevant differences between patients and controls. Further studies are needed to set up a pipeline specifically for the 18S datasets. Acknowledgements: EU project GEMMA (grant agreement No 825033), EPTRI and CNRBiOmics. Istituto San Vincenzo Erba and Albese, Italy	EPTRI open meeting 2020, virtuale (causa Covid19), April 2-3, 2020	2020	CUPAIOLI FRANCESCA ANNA, MEZZELANI ALESSANDRA MARIA, CHIAPPORI FEDERICA CATERINA	microbiota, metagenomics, gene-environment interaction, autism
421675	Altro prodotto	Autismo: il coordinatore del progetto GEMMA alla conferenza internazionale "Dr. Roger's Prize"	Alessandra Mezzelani	comunicato stampa inerente il progetto europeo GEMMA, di cui il CNR e partner, attraverso le news CNR	2019	2019	MEZZELANI ALESSANDRA MARIA	GEMMA, Dr. Roger's Prize
421672	Altro prodotto	GEMMA, progetto europeo per identificare i biomarcatori dell'autismo	Alessandra Mezzelani	Comunicato stampa pubblicato sulla pagina News del sito web CNR: presentazione del progetto europeo GEMMA	2019	2019	MEZZELANI ALESSANDRA MARIA	GEMMA, progetto europeo, autismo multi-omics
421673	Altro prodotto	Il progetto europeo GEMMA continua il reclutamento dei bambini a rischio di sviluppare autismo	Alessandra Mezzelani	Comunicato stampa pubblicato sulle News del sito web CNR inerente il progetto europeo GEMMA, di cui sono responsabile per il CNR,	2019	2019	MEZZELANI ALESSANDRA MARIA	peogetto europeo GEMMA, autismo, reclutamento
426825	Rassegna della letteratura scientifica in rivista (Literature review)	Biomarkers for Early Cancer Diagnosis: Prospects for Success through the Lens of Tumor Genetics	Dragani, Tommaso A., Matarese, Valerie, Colombo, Francesca	Thousands of candidate cancer biomarkers have been proposed, but so far, few are used in cancer screening. Failure to implement these biomarkers is attributed to technical and design flaws in the discovery and validation phases, but a major obstacle stems from cancer biology itself. Oncogenomics has revealed broad genetic heterogeneity among tumors of the same histology and same tissue (or organ) from different patients, while tumors of different tissue origins also share common genetic mutations. Moreover, there is wide intratumor genetic heterogeneity among cells within any single neoplasm. These findings seriously limit the prospects of finding a single biomarker with high specificity for early cancer detection. Current research focuses on developing biomarker panels, with data assessment by machine-learning algorithms. Whether such approaches will overcome the inherent limitations posed by tumor biology and lead to tests with true clinical value remains to be seen.	BioEssays 42 (2020).	2020	COLOMBO FRANCESCA	biomarkers, clinical validation, discovery pipeline, early diagnosis, genetic heterogeneity, genome sequencing, oncogenomics, screening	10.1002/bies.201900122
426848	Poster	Proteins and miRNA in feline renal amyloid deposits	Genova F, Nonnis S, Maffioli E, Grassi Scalvini, Di Nanni N, Cupaioli F, Mosca E, Mezzelani A, Sironi G, Lyons LA, Tedeschi G, Longeri M.	Amyloidosis is a group of diseases occurring in humans and animals, due to the deposition of misfolding proteins in different organs. In humans, deposits were characterized using proteomics and more recently the role of miRNAs in the pathogenesis was proposed. In Abyssinian cat the main target is the kidney. Little is known on the mechanisms underlying the disease. The aim of this study is to profile proteins and miRNAs in healthy and affected Abyssinian cats, to evaluate their differential expression and clarify the pathogenesis mechanisms. Formalin-fixed paraffin-embedded kidney slices were collected from 7 affected and 5 healthy Abyssinians and used for proteomic and miRNAs analyzes. Peptides were analyzed with an LTQ-Orbitrap Velos mass spectrometer (MS). MS spectra were searched against the F.catus NCBI sequence database (release31.01.2017) by MaxQuant. Bioinformatic analysis was performed with DAVID and Panther softwares. MiRNAs were sequenced on the Illumina NextSeq500 platform. MiRDeep2 was used to map reads on the genome vs9.0, identify putative miRNAs, quantify their expression and identify homologous. Filtered proteins and miRNs statistically different were identified using a student t-test and a moderate t-test respectively (p- value<=.05). Part of the proteins was exclusively detected in the affected (n.175), part in the healthy (n.47) and part were common to the two groups (n.160). A fraction of the latter resulted upregulated (n.16) or down regulated (n.18) in affected compared to the healthy cats (p-value<=.05). Annotation and functional grouping suggested an effect on extracellular matrix and macromolecular complex subunit organization. MiRNA analysis detected 341 representatives, 22 differentially expressed between affected and healthy (p<.05). Six miRNAs out of 22 (four with a P-value<.009) are known to be involved in Alzheimer Disease. Interestingly, miR-26a-5p (P-value 0.120) is involved in the human immunoglobulin light chain amyloidosis onset. This study identified different miRNA and protein renal compositions in Abyssinian affected and healthy cats. The pathways involving these molecules are under investigation, providing new insights for the pathogenesis understanding.	ISAG 2019 - 37th International Society for Animal Genetics Conference, Lleida, Spain, 07/07/2019 - 12/07/2019	2019	CUPAIOLI FRANCESCA ANNA, DI NANNI NOEMI, MEZZELANI ALESSANDRA MARIA, MOSCA ETTORE	Amyloidosis, MiRNA, protein, Transcriptomics, Proteomics
426853	Poster	Identification of miRNAs and evaluation of their differential expression in Abyssinian cat amyloidosis	Genova F 1, Mosca E 2, Di Nanni N 2, Cupaioli F 2, Mezzelani A 2, Longeri M. 1	Introduction: Domestic felids represent one of the main species in which amyloidosis occurs. The disease is caused by the presence of protein complexes, known as amyloids, which form insoluble deposits in different organs. However, little is known about the pathogenic pathway and the genetic of the disease is still under exploration. Among cat breeds, amyloidosis particularly affects Abyssinian/Somali and Siamese/Oriental cats, where the main target organs for the deposit are kidneys and liver, respectively. Objective: The aim of this study is i) to detect miRNAs expressed in amyloidosis affected and healthy Abyssinian kidneys ii) to evaluate their possible differential expression iii) to identify miRNAs potentially involved in the disease onset or in the regulation of its pathogenesis. Materials & Methods: miRNAs were extracted from Formalin Fixed Paraffin Embedded (FFPE) kidney slides collected from 6 affected and 4 healthy Abyssinians using the miRNeasy Mini Kit (Qiagen). The sequencing of miRNAs was carried out by smallRNA-seq kit (Illumina) and Illumina NextSeq500 platform, and its quality was assessed with FastQC. Cutadapter was used to remove the adapter sequences from the high-throughput sequencing reads. MiRDeep2 was then used to map reads against the cat reference genome (Felis catus, genome assembly version 9.0), identify putative miRNAs, quantify their expression and identify homologous human miRNAs. MiRNAs with less than 10 reads for each sample were filtered out. Raw counts were normalized with TMM method (Trimmed mean of M values) and expressed as log2 CPM (counts per million). Differential expression was assessed with a moderated t test (limma) and nominal p values were adjusted by Benjamini-Hochberg method. Results: A total of 854 miRNAs were detected, and 341 miRNAs were selected as representative after filtering. A total of 22 miRNAs showed significant expression difference between affected and healthy Abyssinians (p<0.05), but none of this was significant after p-value correction for multiple hypotheses. A total of 6 (out of 22) are known to be involved in the development of Alzheimer Disease (AD), four of which with a P-value < 0.009. Suggestively, within the not significantly associated to amyloidosis miRNAs (p>0.05), miR- 26a-5p (P-value 0.120) is one of the main miRNAs involved in the human immunoglobulin light chain (AL) amyloidosis onset. Conclusions: recent studies in humans have been focusing on disclosing the potential role of miRNAs in the accumulation of amyloid fibrils, especially in AD. It was shown that miRNAs dysregulation plays an important role in the disease alterations, although it cannot be considered the main trigger of the AD itself. Some of the identified miRNAs in the present study were already known to be associated with human AD. These results are encouraging and will help understanding the pathogenesis of feline amyloidosis. The genes directly regulated and involved in these pathways are under investigation and further evidences will be obtained with an integrative approach through a proteomic analysis.	10th Conference of canine and feline genetics and genomics 2019, Kursaal, Bern, Switzerland, 26/05/2019 - 29/05/2019	2019	CUPAIOLI FRANCESCA ANNA, DI NANNI NOEMI, MEZZELANI ALESSANDRA MARIA, MOSCA ETTORE	Amyloidosis, miRNA, Transcriptomics
426874	Comunicazione in rivista (Letter - Letter to editor)	Differential lung tissue gene expression in males and females: implications for the susceptibility to develop COPD	van den Berge, Maarten, Brandsma, Corry Anke, Faiz, Alen, de Vries, Maaike, Rathnayake, Senani N.H., Pare, Peter D., Sin, Don D., Bosse, Yohan, Laviolette, Michel, Nickle, David C., Hao, Ke, Obeidat, Ma'en, Dragani, Tommaso A., Colombo, Francesca, Timens, Wim, Postma, Dirkje S.		The European respiratory journal 54 (2019).	2019	COLOMBO FRANCESCA	transcriptome, lung parenchyma, chronic obstructive pulmonary disease, sex differences	10.1183/13993003.02567-2017
426880	Comunicazione in rivista (Letter - Letter to editor)	Response to comments on 'Malignant mesothelioma diagnosed at a younger age is associated with heavier asbestos exposure' by Farioli et al. and Oddone et al.	Dragani, Tommaso A., Colombo, Francesca, Pavlisko, Elizabeth N., Roggli, Victor L.		Carcinogenesis (N.Y., Print) 40 (2019): 490-491.	2019	COLOMBO FRANCESCA	pleural malignant mesothelioma, age at diagnosis, asbestos exposure	10.1093/carcin/bgy145
426882	Comunicazione in rivista (Letter - Letter to editor)	Corrigendum: Malignant mesothelioma diagnosed at a younger age is associated with heavier asbestos exposure (Carcinogenesis (bgy145) DOI: 10.1093/carcin/bgy145)	Dragani, Tommaso A., Colombo, Francesca, Pavlisko, Elizabeth N., Roggli, Victor L.		Carcinogenesis (N.Y., Print) 40 (2019): 492.	2019	COLOMBO FRANCESCA	age at diagnosis, pleural malignant mesothelioma, asbestos exposure	10.1093/carcin/bgz037
426884	Rassegna della letteratura scientifica in rivista (Literature review)	Prolonged activity and toxicity of sirolimus in a patient with metastatic renal perivascular epithelioid cell tumor: A case report and literature review	Raimondi, Alessandra, Colombo, Francesca, Pintarelli, Giulia, Morosi, Carlo, Renne, Salvatore L., Frezza, Anna M., Saponara, Maristella, Dei Tos, Angelo P., Mazzocchi, Arabella, Provenzano, Salvatore, Casali, Paolo G., Stacchiotti, Silvia	Perivascular epithelioid cell tumor (PEComa) is a family of mesenchymal tumors. Conventional chemotherapy has little activity in this disease, but case reports are available on the activity of mammalian target of rapamycin inhibitors (e.g. sirolimus and temsirolimus). Pharmacokinetic assays of sirolimus are available as this drug has a precise therapeutic window and blood levels might be influenced by CYP3A4 polymorphisms and drug interactions. We report on a case of a patient with metastatic, progressive PEComa who started sirolimus at a dose of 5 mg/day with evidence of grade (G) 3 mucositis, G2 thrombocytopenia, and G1 leucopenia 10 days after the treatment started, in absence of concomitant medications or prohibited food assumption. Elevated sirolimus blood levels were detected (156.8 ng/ml). Sirolimus was stopped, and toxicity resolved in 5 weeks. Computed tomography scan 2 months after the treatment started showed a partial response (RECIST). After toxicity resolution, the patient restarted sirolimus at a dose of 1 mg/day, with blood levels in the range of 10-20 ng/ml. Tumor response was confirmed and maintained, and the patient is still under treatment 18 months later, with no additional adverse effects. Genetic analysis of five selected polymorphisms (rs2740574, rs776746, rs1128503, rs2032582, and rs1045642) in drug metabolism enzymes and transporters did not provide a clear explanation of the observed unusual pharmacokinetic. This case confirms the activity of mammalian target of rapamycin inhibitors in PEComa and strengthens the importance of pharmacokinetic drug blood levels monitoring in patients treated with sirolimus. In our patient, after dose adjustment, sirolimus could be restarted with a prolonged clinical benefit and no additional toxicity.	Anti-cancer drugs 29 (2018): 589-595.	2018	COLOMBO FRANCESCA	chemotherapy, drug metabolizing enzyme, drug monitoring, mammalian target of rapamycin inhibitor, perivascular epithelioid cell tumor, pharmacokinetics, polymorphism, sarcoma, sirolimus, toxicity	10.1097/CAD.0000000000000634
408133	Rassegna della letteratura scientifica in rivista (Literature review)	The MicroRNA Centrism in the Orchestration of Neuroinflammation in Neurodegenerative Diseases.	Nicoletta Nuzziello and Maria Liguori	MicroRNAs (miRNAs) are small non-coding RNAs with a unique ability to regulate the transcriptomic profile by binding to complementary regulatory RNA sequences. The ability of miRNAs to enhance (proinflammatory miRNAs) or restrict (anti-inflammatory miRNAs) inflammatory signalling within the central nervous system is an area of ongoing research, particularly in the context of disorders that feature neuroinflammation, including neurodegenerative diseases (NDDs). Furthermore, the discovery of competing endogenous RNAs (ceRNAs) has led to an increase in the complexity of miRNA-mediated gene regulation, with a paradigm shift from a unidirectional to a bidirectional regulation, where miRNA acts as both a regulator and is regulated by ceRNAs. Increasing evidence has revealed that ceRNAs, including long non-coding RNAs, circular RNAs, and pseudogenes, can act as miRNA sponges to regulate neuroinflammation in NDDs within complex cross-talk regulatory machinery, which is referred to as ceRNA network (ceRNET). In this review, we discuss the role of miRNAs in neuroinflammatory regulation and the manner in which cellular and vesicular ceRNETs could influence neuroinflammatory dynamics in complex multifactorial diseases, such as NDDs.	Cells (2019).	2019	NUZZIELLO NICOLETTA, LIGUORI MARIA	EVs; NDDs; ceRNAs; competing endogenous RNAs; extracellular vesicles; miRNA; microRNA; neurodegenerative diseases; neuroinflammation	10.3390/cells8101193
414907	Rassegna della letteratura scientifica in rivista (Literature review)	Precision Medicine in Neurodegenerative Diseases: Some Promising Tips Coming from the microRNAs' World.	Nuzziello N, Ciaccia L, Liguori M.	Novel insights in the development of a precision medicine approach for treating the neurodegenerative diseases (NDDs) are provided by emerging advances in the field of pharmacoepigenomics. In this context, microRNAs (miRNAs) have been extensively studied because of their implication in several disorders related to the central nervous system, as well as for their potential role as biomarkers of diagnosis, prognosis, and response to treatment. Recent studies in the field of neurodegeneration reported evidence that drug response and efficacy can be modulated by miRNA-mediated mechanisms. In fact, miRNAs seem to regulate the expression of pharmacology target genes, while approved (conventional and non-conventional) therapies can restore altered miRNAs observed in NDDs. The knowledge of miRNA pharmacoepigenomics may offers new clues to develop more effective treatments by providing novel insights into interindividual variability in drug disposition and response. Recently, the therapeutic potential of miRNAs is gaining increasing attention, and miRNA-based drugs (for cancer) have been under observation in clinical trials. However, the effective use of miRNAs as therapeutic target still needs to be investigated. Here, we report a brief review of representative studies in which miRNAs related to therapeutic effects have been investigated in NDDs, providing exciting potential prospects of miRNAs in pharmacoepigenomics and translational medicine.	Cells (2019).	2019	NUZZIELLO NICOLETTA, LIGUORI MARIA	drug response; epidrug; microRNA; neurodegenerative diseases; pharmacoepigenomic; precision medicine	10.3390/cells9010075
434840	Abstract in rivista	Analysis of cortical gene expression variability in a mouse model of X-linked Infantile spsms syndrome	Verrillo L, Tuccillo M, Drongitis D, Mangano E, Franco C, Terrone G, Canzoniero MT, Del Giudice E, Bordoni R, Poeta L, Miano MG.	None	Translational medicine @ UniSa (2019).	2019	DRONGITIS DENISE, TUCCILLO MARIACARMINE, VERRILLO LUCIA, BORDONI ROBERTA, MIANO MARIA GIUSEPPINA, MANGANO ELEONORA	Single-cell RNAseq, primary cells, embryonic brain
435608	Poster	Evaluation of the effectiveness of a preventive program focused on cognitive stimulation and physical exercise in virtual reality in people with mild cognitive impairment or subjective cognitive decline	Flaminia Franchini, Beatrice Filipputti, Federica Ratto, Matilde Luchi, Sara Arlati, Sarah Tabbozzi, C Caltagirone, Massimo Musicco, Simona Gabriella di Santo	TARGETS: An association exists between vascular and lifestyle modifiable risk factors and incident dementia. Many clinical trials have been started to provide evidence of the effectiveness of interventions aimed at these risk factors in preventing or postponing dementia onset, and multidomain approaches seem to be more effective than single-factor strategies. Virtual Reality (VR) is an innovative approach in neuroscience, that could be feasible and effective for intervention. GR-2013-02356043 is a RCT with 2X2 factorial design, to evaluate the separate and combined effect of cognitive stimulation (CS) and physical exercise (PE) in VR in delaying dementia onset or reduce cognitive and functional progression in 320 people with MCI OR SCD. METHODS: Here we present the results of analyses that compared the sub-samples subjected to training in VR and the outpatient control group (80 participants aged a?JPY 60 yrs). Each subject was twice randomized to receive CS/NO CS and PE/NO PE. The training provided twice-weekly sessions of CS and/or PE for 12 weeks. A complete neuropsychological and functional evaluation was performed at baseline (t0), post-training (t1) and 4 months after (t2). Mixed factor ANOVA (4 groups, 3 times) on ITT-LOCF data were conducted, corrected for demographics and baseline MMSE scores. RESULTS: 59 (73.8%) and 44 (55,0%) participants underwent t1 and t2 evaluations. Analyses showed significant group differences in Immediate and delayed recall of a short story (IR and DR: F3,74 = 2.94; p = 0.04 and F 3,74 = 3.11; p = 0.03) scores. Planned contrasts revealed significant differences at t2 between controls and CS+PE groups in IR (T(38) = 2,76; p < 0,01) and DR scores (t(38) = 2.00; p = 00.45) and between controls and CS groups in DR (T(38) = 2.15; p = 0.03). CONCLUSIONS: CS and CS+PE seem to exert mild effects ON memory performances that appear after a time from treatment. Caution in the interpretation is required due to high drop-out rates; however, the conservativeness of statistical analyses it presumably implies an underestimation of these effects, compared to their real extent.	XV Convegno Nazionale Sindem, Siena (Virtual Conference), 5-7/11/2020	2020	DI SANTO SIMONA GABRIELLA, TABOZZI SARAH ANTONELLA, ARLATI SARA, MUSICCO MASSIMO	cognitive training, physical exercise, virtual reality, mild cognitive impairment
412873	Abstract in atti di convegno	Biotic stress trigger plant endogenous short non-coding RNAs that regulate components of photosynthetic machinery	Leonetti P., Gazemzadeh A., Gursinsky T., Consiglio A., Behrens S.E., Pantaleo V.	A massive and diverse population of short non-coding (s)RNAs accumulates in plant tissues. sRNAs drive RNA silencing-based gene repression. Besides their role in tissue and organ development, differentiation and in the maintenance of genome integrity, sRNA play crucial roles in host response to a wide range of environmental conditions, including biotic stresses. By image data augmentation technique, we have selected Brassica rapa (turnip) and B. napus (canola) plant tissues infected by cauliflower mosaic virus (CaMV) showing mosaic and yellowing symptoms. sRNA populations associated to CaMV-infected tissues of the two crops were characterized by sequencing and bioinformatics and compared with those from the model pathosystem CaMV-Arabidopsis. We revealed orthologues genes producing endogenous sRNAs shared out among turnip, canola and Arabidopsis. In the three plant species, the majority of these siRNAs were from protein coding genes encoding components of the photosynthetic machinery, such as LHCB1.3, LHCB1.4, LHCA1, and FBA1. By quantitative real time PCR we revealed a significant down-regulation of transcripts generating the endogenous RNA in the two crops. Moreover, by in vitro assays we have proved the functionality of selected sRNAs in cleaving the corresponding RNA targets upon incorporation into specific core proteins of the class of "Argonautes". The results herein suggested that the generation of sRNA regulators from specific gene clusters of the photosynthetic machinery is an unifying qualitative feature among plant species of the Brassicaceae family under biotic stress.	Biophysics-of-Phenosynthesis from molecules to the field, pp. 115-115, Accademia dei Lincei, Roma, 2-4/10/2019	2019	PANTALEO VITANTONIO, LEONETTI PAOLA, CONSIGLIO ARIANNA	sRNA, biotic stress, photosynthesis
416339	Rapporto di progetto (Project report)	Nestore - D4.2 - First prototype of the DSS	Orte S., Subias P., Dauwalder S., Roecke C., Guye S., Palumbo F., Rizzo G.	The D4.2 is the software that conforms the first prototype of the Decision Support System. As the DSS is merely designed and implemented in form of a Software as a Service platform, and it does not have any graphical user interface, this document is intended to report a description of the DSS first prototype main features with a particular focus on the architecture, functionalities and technical implementation. Therefore, the aim of this document is to provide a picture of the actual development of the DSS starting from the scientific background from which it is grounded and going through the different elements that form the DSS. The DSS main objective is to help users in selecting coaching plans by proposing personalised recommendations based on users' behaviours and preferences. Recognising such behaviours and their evolution over time is therefore a crucial element for tailoring the interaction of the system with the user. A three-layer system composed of pathways, coaching activity plans, and coaching events, constitutes the so-called coaching timeline on which the analysis is grounded. Various techniques are used to model and personalise the recommendations and feedback. Firstly, the indicators are extracted from disparate data sources, then these are modelled through a profiling system and, finally, recommendations on the pathways and coaching plans are performed through a tagging system. With the aim of developing and testing the models and workflow prior to the pilot starting date, two simulators are also being implemented and reported in this document.	Project report, Nestore, Deliverable D4.2, 2019	2019	RIZZO GIOVANNA, PALUMBO FILIPPO	Decision Support System, Architecture, Functionalities, Data Processing, Data Sources, Scoring System, Tagging System, Scheduler, Pathway, Coaching Activity Plan, Coaching Event, API Services, Data Simulators
416345	Rapporto di progetto (Project report)	D6.3.2 - NESTORE Platform Shared components & Architecture	Candea C., Staicu M., Candea G., Zgripcea C., Orte S., Kniestedt I., Segato D., Radeva P, Crivello A., Palumbo F., Pillitteri L., Miori V., Rizzo G., Rocke C.	Present document aims to describe in detail the NESTORE ecosystem architecture and explains its technical specifications on both the implementation criteria and the requirements. NESTORE adopt an evolutionary architecture approach: "An evolutionary architecture designs for incremental change in an architecture as a first principle. Evolutionary architectures are appealing because change has historically been difficult to anticipate and expensive to retrofit. If evolutionary change is built into the architecture, change becomes easier and cheaper, allowing changes to development practices, release practices, and overall agility".	Project report, Nestore, Deliverable D6.3.2, 2019	2019	PILLITTERI LOREDANA, RIZZO GIOVANNA, MIORI VITTORIO, PALUMBO FILIPPO, CRIVELLO ANTONINO	NESTORE Architecture, Shared Component, End User, API, Sensors, IOT, Platform, Cloud, Applications
425410	Poster	GOBLET: fostering international collaboration for advanced Learning, Education and Training in Computational Biology and Bioinformatics	Javier De Las Rivas (1), Domenica D'Elia (2), Eija Korpelainen (3), Annette McGrath (4), Asif M. Khan (5), Michelle D. Brazas (6), Teresa K. Attwood (7), Celia Van Gelder (8)	In the current era of Big Data production and Artificial Intelligence development, one of the fastest growing scientific and professional areas that is generating petabytes of data is Life Sciences. In this context, many scientific and educational institutions recognize that it is no longer possible to carry out adequate studies and research in this area without well-trained computational biologists and bioinformaticians. GOBLET is an international organization, established in 2012, with the mission to cultivate a global community of bioinformatics trainers who support learning, education and training. GOBLET's mission was defined under the vision that there is a clear worldwide need to harmonize bioinformatics training activities and to unite, inspire and equip bioinformatics trainers. This can only be achieved by developing active linkages and collaborations with many national and international institutions that work in the field of Life Sciences. Relevant activities conducted last year by GOBLET members, together with other international experts, include the initiation of a series of assets, standards and guidelines, to define competencies, promote best practices and provide high-quality resources for learning, education and training in bioinformatics and computational biology, worldwide. GOBLET's new website offers a comprehensive portal, providing many materials and resources for the international bioinformatics community.	ISMB 2020 - 28th Conference on Intelligent Systems for Molecular Biology, Virtual - Montreal (Canada), 13-16 July, 2020	2020	D'ELIA DOMENICA	Education, Bioinformatics
425411	Presentazione	GOBLET- The Global Organisation for Bioinformatics Learning, Education & Training	Domenica D'Elia	GOBLET, the Global Organisation for Bioinformatics Learning, Education and Training, is a legally registered foundation whose mission is to cultivate the global bioinformatics trainer community, set standards and provide high-quality resources to support learning, education and training. GOBLET main objectives are: for the training portal to become both a pull mechanism and repository; to offer training for trainers and end-users; to develop training material and course standards; to provide training resources (surveys, best-practice guidelines, etc.); to raise funds to be able to meet our objectives; to offer a network/community forum; to give further consideration to mechanisms for trainer recognition.	ISCB 2020 - 28th Conference on Intelligent Systems for Molecular Biology, Virtual - Montreal (Canada), 13/07/2020, 16/07/2020	2020	D'ELIA DOMENICA	Education, Training, Learning, Bioinformatics
433252	Comunicazione in rivista (Letter - Letter to editor)	Standards Make The World Go Round	Domenica D'Elia1, Chris Evelo2, 3, Babette Regierer 4, 5, Susanne Hollmann 4, 6		EMBnet journal 25 (2020): 1-2.	2020	D'ELIA DOMENICA	standard, standard operating procedure, life science, omics, NGS	10.14806/ej.25.0.931
434884	Poster	Analysis of transcriptome landscapes in the epileptogenic cortex of the Arx(GCG)7/Y mouse	Tuccillo M, Verrillo L, Drongitis D, Mangano E, Consolandi C, Franco C, Mallardo M, Cankaya I, M. T. Canzoniero, Poeta L, Bordoni R, Miano MG.	The X-linked Aristaless-related homeobox gene (ARX) encodes an interneuron-specific transcription factor (TF) with a key role in mammalian corticogenesis and GABAergic sub-type specification. Elongations in two of its four polyalanine (PolyA) tracts have been found in incurable neurodevelopmental disorders (NDDs), such as intellectual disability (XLID) and infantile spasms, a catastrophic chronic epilepsy resistant to standard cures. Here we report on a single-cell RNA sequencing (scRNA-Seq) study aimed to identify transcriptome landscapes in an epileptogenic niche of the Arx(GCG)7/Y mouse compared to the Wild Type (WT) one. Understanding all these aspects may help us to identify cell-specific epileptic-biomarkers linked to the disease-response that could be used as druggable molecules in anti-epileptic drug discovery research.	19th International Workshop on Fragile X and other Neurodevelopmental Disorders, Sorrento, Naples, Italy, 18-21 September 2019	2019	POETA LOREDANA, DRONGITIS DENISE, MALLARDO MARIO, TUCCILLO MARIACARMINE, VERRILLO LUCIA, BORDONI ROBERTA, MIANO MARIA GIUSEPPINA, CONSOLANDI CLARISSA, MANGANO ELEONORA	ARX, corticogenesis, scRNA-Seq, 10x Genomics
434897	Poster	Exploring transcriptional single-cell signatures in a mouse model of epilepsy caused by a polyalanine expansion mutation in Aristaless-related homeobox gene.	Tuccillo M, Mangano E, Verrillo L, Poeta L, Consolandi C, Padula A, Franco C, Drongitis D, Mallardo M, Cervicato G, Canzoniero L M T, Bordoni R, Miano MG.	The X-linked Aristaless-related homeobox gene (ARX) encodes an interneuron-specific transcription factor (TF) with a key role in mammalian corticogenesis and GABAergic sub-type specification. Elongations in two of its four polyalanine (PolyA) tracts have been found in incurable neurodevelopmental disorders (NDDs), such as intellectual disability (XLID) and infantile spasms, a catastrophic chronic epilepsy resistant to standard cures. Our main objective is to disclose cell-to-cell expression variability, in terms of transcriptomic dynamics, underlying cellular heterogeneity and cell populations that bulk the Arx polyA epileptic brain. Understanding all these aspects may help us to identify cell-specific epileptic-biomarkers linked to the disease-response that could be used as druggable molecules in anti-epileptic drug discovery research.	EMBO Workshop- From epigenome towards epitranscriptome in cell fate choice, Capri, Nplaes, Italy, 14 -17 October 2018	2018	POETA LOREDANA, PADULA AGNESE, CERVICATO GIUSEPPE, DRONGITIS DENISE, MALLARDO MARIO, TUCCILLO MARIACARMINE, VERRILLO LUCIA, BORDONI ROBERTA, MIANO MARIA GIUSEPPINA, CONSOLANDI CLARISSA, MANGANO ELEONORA	ARX, single-cell signatures, polialanine expansion mutation
400608	Rapporto tecnico	R1 - rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Giorgia Adamo, Cinzia Caporale	Rapporto tecnico relativo alla verifica di fabbricazione/falsificazione e/o plagio di dati, immagini e testi	Prot. n: 0032254/2018, 2018	2018	CAPORALE CINZIA, ADAMO GIORGIA	Research integrity
401902	Monografia o trattato scientifico	Verita e cura. Dalla diagnosi al placebo, l'etica dell'inganno in medicina	Marco Annoni	Deve il medico dire sempre la verita ai pazienti? Oppure il dovere di veridicita dei medici puo essere sospeso quando la differenza tra bugia e verita equivale alla differenza tra la vita e la morte? E mai permissibile mentire in ambito clinico per compassione o per sfruttare i benefici dell'effetto placebo? E se si, come distinguere i casi in cui e moralmente giustificabile ingannare un paziente "a fin di bene" - e cioe, per ragioni paternalistiche - da quei casi in cui, invece, occorre essere onesti? Queste domande sono fondamentali per chiunque si trovi a prestare o ricevere delle cure perche "la verita" puo a volte segnare in modo indelebile il destino di una persona e di chi la assiste. Eppure, l'etica medica contemporanea ha finora dedicato scarsa attenzione a questa problematica cosi centrale. Se a cio si aggiunge che la formazione etica degli operatori sanitari e spesso inadeguata, e che i nostri giudizi morali tendono a essere intrinsecamente sbilanciati, esistono inoltre fondate ragioni per ritenere che ancora oggi i medici omettano e distorcano la verita ai pazienti molto piu di quanto essi stessi siano portati a credere e, sfortunatamente, anche piu di quanto sia eticamente giustificabile. In tale contesto, questo saggio propone e difende la teoria secondo cui il dovere di veridicita dei medici deve essere concepito come prima facie, e cioe come un dovere che occorre sempre rispettare a meno che cio non contrasti con il piu generale obbligo di prendersi cura del bene dei pazienti e a patto che si segua un processo di deliberazione morale adeguato. Perche la verita e sempre importante, ma non tutte le verita sono buone ai fini della cura, cosi come non tutti gli inganni sono necessariamente contrari al bene dei pazienti.	Pisa: Edizioni ETS, 2019	2019	ANNONI MARCO ANGELO MARIA	Etica medica, Placebo, Bioetica
406463	Poster	Antarctic Dry Valleys melt water systems analogues of Martian gullies: characterization of microbial communities and soil properties	Fabiana Canini 1, 2, Laura Zucconi 1, Jozsef Geml 2, 3, Luigi Paolo D'Acqui 4, Marco Severgnini 5, Giacomo Mele 6, Valentina Raimondi 7, Lorenzo Palombi 7, Clarissa Consolandi 5, Tania Camboni 5, Silvano Onofri 1, Laura Selbmann 1, 8, Alessia Cassaro 1, Claudia Pacelli 1, 9, Stefano Ventura 4, 10	Antarctic McMurdo Dry Valleys (MDVs) are characterized by extremely low temperatures, strong desiccating winds, very low precipitation, aridity, high solar irradiation, and locally high salt concentrations. The majority of the MDVs surface is unconsolidated sediment, with an ice-cemented permafrost with neither wet nor dry active layers, as soil temperature generally never rises above 0 ?C. For these characteristics, these soils are regarded as one of the closest terrestrial analogues of the cold arid Martian regolith. Despite cold and dry conditions, gullies and streams occur in a broad zone distal to the ephemeral streams, as dark bands, commonly on north-facing slopes, from surface top-down melting of snow and ice, due to enhanced summer solar insolation. They host a biological activity that can persist even after surface water flow in the channel has ceased, surviving long periods of desiccation and extreme cold in a cryptobiotic state. MDVs hydrological system may provide important insights into the potential configuration of Mars climate, in which MDV-like ephemeral streams and rivers could have originated through processes related to the presence of liquid water in the recent geological past and could have hosted life forms remained trapped within the gully (Levy et al., 2012). NASA has chosen Jezero Crater as the landing site for Mars 2020 rover mission, as it is located on the western edge of Isidis Planitia, a giant basin, once home of a river delta. This area could have preserved organic molecules and other potential signs of a hypothetical microbial life from the water and sediments that flowed into the crater billions of years ago. During the XXXI (2015/16) Italian Antarctic expedition, soil samples have been collected in MDVs, in the areas surrounding three Antarctic lakes, namely Lake Fryxell, Lake Hoare and Lake Joyce. Although soil communities of these areas have already been deeply studied, here we propose a new multidisciplinary approach that could lead to characterize the microbiota and the environmental conditions determining the colonization in such limiting environment, and to provide parameters that could be uniquely descriptive of the presence and the type of colonization. To achieve these goals, both fungal and bacterial diversity have been characterized via metabarcoding next-generation sequencing. In these samples, we found 21987 and 292 OTUs for Bacteria and Fungi, respectively, with richness ranging from 2962 to 4859 OTUs and from 7 and 122 OTUs, respectively. Main bacterial phyla within Lake Hoare and Lake Joyce communities were Bacteroidetes and Firmicutes (accounting for >80% of the relative abundance), whereas, Lake Fryxell samples showed 27% Cyanobacteria and 3% Deinococcus-Thermus, that were nearly absent in the other two sites. Instead for fungal communities, we highlighted a dominance of saprotrophic and lichen forming organisms in all the samples. Soil edaphic parameters (pH, relative moisture, C, N, P, Na, K, Mg and Ca content and cation exchange capacity) and granulometry have been characterized, to relate communities diversity and composition to soil characteristics. Laser induced fluorescence spectra were also acquired in situ by using an in-house developed instrument to detect accessory pigments and contribute to the characterization of soil communities. Additionally, the DRIFT (Diffuse Reflectance Infrared Spectroscopy) spectra and colorimetric data have been recorded for soil samples, in order to be associated to specific communities and edaphic characteristics. In this view, our data could be of interest for future Martian explorations, focused on the search of signs of past or present life forms, as they could describe composition, soil parameters or specific color spectra that could be descriptive of living or extinct biological colonization. Levy, J. (2012). Icarus, 219(1), 1-4.	EANA 2019: 19th EANA Astrobiology Conference, Orleans, France, 3rd-6th September 2019	2019	CAMBONI TANIA, D'ACQUI LUIGI PAOLO, MELE GIACOMO, RAIMONDI VALENTINA, CONSOLANDI CLARISSA, SEVERGNINI MARCO, PALOMBI LORENZO, VENTURA STEFANO	Astrobiology, Antarctica, bacteria, fungi, soil
448182	Rapporto tecnico	Dal web al desktop: come creare applicazioni ibride	Matteo Gnocchi e Marco Moscatelli	descrive come sviluppare, partendo da una applicazione web basata sul framework Angular, un eseguibile installabile ed utilizzabile sui maggiori sistemi operativi in commercio; in particolare:	Protocollo N 0002368 del 14/11/2019, 2019	2019	GNOCCHI MATTEO, MOSCATELLI MARCO	Wen application, Desktop application
448179	Rapporto tecnico	Nuova Directory Nazionale BBMRI.it	Matteo Gnocchi e Marco Moscatelli	Descrizione della nuova directory nazionale BBMRI.it sviluppata con il framework javascript Angular (prossima alla release 3.X)	Protocollo N 0002330 del 6/10/2018, 2018	2018	GNOCCHI MATTEO, MOSCATELLI MARCO	BBMRI.it, Angular, Biobank directory
448195	Rapporto tecnico	Realizzazione di una piattaforma di High Performance Computing	M. Moscatelli, M. Gnocchi	L'infrastruttura descritta si basa sull'utilizzo di un sistema di provisioning per l'installazione dei diversi servizi. La piattaforma di High Performance Computing e composta principalmente da 3 Servizi: Identity Management, Storage e Job Scheduler system. L'identity Management consiste di un ambiente in cui vengono immagazzinate le informazioni relative agli utenti e ai servizi; per il corretto funzionamento del sistema, la sincronizzazione del timestamp e per l'autenticazione ai sistemi sono configurati anche i server NTP, DNS e Kerberos. Inoltre grazie al server Kerberos viene implementato il sistema di Single Sign On (SSO). Lo storage viene reso fruibile ai diversi server tramite l'esportazione di file system Lustre; per permettere un'alta disponibilita del sistema ed un'elevata efficienza di accesso ai dati vengono configurate due coppie di nodi. La prima coppia (MDS nodes) e responsabile dell'accesso ai metadati e quindi all'identificazione della posizione dei dati veri e propri; i dati sono provisionati dalla seconda coppia di nodi (ODS nodes) che rendono accessibili i dati ai client. Infine, il sistema di Scheduling viene gestito da un server Master affiancato da un sistema di Backup in caso di failure. I dati e l'accounting sono salvati su un apposito server con funzione di database. Al cluster e possibile accedere tramite appositi nodi di Login che permettono la sottomissione di job nel cluster.	Protocollo N 0 000924/2020 del 26/05/2020, 2020	2020	GNOCCHI MATTEO, MOSCATELLI MARCO	Ansible, SSO, Kerberos, LDAP, HPC
448199	Rapporto tecnico	Design E Prototipazione Di Una Piattaforma Per La Gestione Di Progetti Single Cell	M. Moscatelli, M. Gnocchi	Il prototipo descritto permette di centralizzare l'accesso ai principali servizi necessari alla gestione di un progetto di analisi "Single Cell". L'infrastruttura garantisce l'accesso ad un ampio spettro di risorse (dati, calcolo, applicazioni, etc ...) nascondendo all'utente la complessita dell'interazione con un ambiente eterogeneo. Tramite l'applicazione client l'utente puo accedere facilmente ed in modo ordinato ai dati suddivisi per progetto garantendo allo stesso tempo un pieno controllo di quel che succede agli amministratori di sistema. Le tecnologie implementate permettono di gestire una grande quantita di dati da qualsiasi dispositivo senza limitare le performance garantendo un accesso in mobilita.	Protocollo N 0000676/2020 del 01/04/2020, 2020	2020	GNOCCHI MATTEO, MOSCATELLI MARCO	Single Cell, HPC, Web app
448496	Presentazione	COST Action CHARME (CA15110) - Harmonising standardisation strategies to increase efficiency and competitiveness of European Life Science Research	Domenica D'Elia	The COST Action CHARME: a European initiative for the harmonisation of standards for life-science research Open Science (OS) describes the ongoing transitions in the way research is performed, i.e. researchers collaborate, knowledge is shared, and science is organised. OS is driven by digital technologies and by the growth of data, globalisation, enlargement of the scientific community and the need to address societal challenges. It has now widely been recognised that making research results more accessible contributes to more efficient science and innovation in the public and private sectors. To unlock that potential, data needs to be made computer readable and interoperable. Therefore, they must be generated, formatted and stored according to Standard Operating Procedures and Data Management Plans included as an integral part of any projects. Although several initiatives are actives in different life science research fields, they are still too much fragmented. A significant barrier hindering the implementation of FAIR (findable, accessible, interoperable and reusable) data principles is the lack of awareness and insufficient education of scientists and other stakeholders in the process of producing, handling, publishing and transferring knowledge to biotech applications. CHARME: "Harmonising standardisation strategies to increase the efficiency and competitiveness of European life-science research", is an Action funded through COST (European Cooperation in Science and Technology). CHARME aims to identify needs and gaps in standards, teaming up with other initiatives and organisations, and proposing new strategies for successful assimilation of standards into the daily work-flow of researchers. This presentation underlines the scenario in which CHARME moves and actions needed to increase the efficiency and competitiveness of life-science research.	ISCB-LA SOIBIO EMBnet 2018 Conference, Vina del Mar, Chile, Nov 5 - 9, 2018	2018	D'ELIA DOMENICA	Standards, Standard Operating Procedure, Bioinformatics, Reproducibility, Open Access, Quality Control
448497	Poster	The COST Action CHARME A European Initiative for the Harmonisation of Standards for Life Sciences Research (CA15110)	Domenica D'Elia	Standardisation and quality management are important drivers in the life sciences and biotechnology, as only data generated with minimum quality assurance can be easily implemented into industrial applications. Standards assure and ensure that data become easily accessible, shareable and comparable along the value chain. Reproducibility, standards and standard operating procedures (SOPs) in data generation and analysis are challenging topics of modern research and bioinformatics. Only by the use of common standards life science research will improve its efficiency and competitiveness. CHARME aims to identify needs and gaps in standards, teaming up with other initiatives and organisations, and proposing new strategies for the successful assimilation of standards into the daily work-flow of researchers. Currently, 30 EU countries are involved in this initiative, which makes it one of the most widely recognised Actions among all COST initiatives.	ISCB-LA SOIBIO EMBnet 2018 Conference, pp. A17, Vina del Mar, Chile, 5-9 November, 2018	2018	D'ELIA DOMENICA	Standards, COST Action, Standard Operating Procedure, Big Data Storage
449037	Sito web	Sito Web EPICOViD19	Matteo Gnocchi	Il progetto EPICOVID19 si propone di raggiungere ogni fascia adulta della popolazione, e stato approvato dal Comitato Etico dell'Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani I.R.C.C.S.	2020	2020	ADORNI FULVIO DANIELE, GNOCCHI MATTEO	COVID19, EPIDEMIOLOGIA
449179	Rapporto tecnico	Using community events to increase quality and adoption of standards: the case of Bioschemas	Giuseppe Profiti, Rafael C. Jimenez, Federico Zambelli, Ivan Mi?eti?, Vito Flavio Licciulli, Matteo Chiara, Silvio Tosatto, Rita Casadio, Graziano Pesole	We present how a workshop for the local Italian ELIXIR community steered an improvement of the quality and adoption of Bioschemas, a series of semantic annotation templates for tools, data and samples developed by the ELIXIR Interoperability platform. Gathering a small number of different end-users and having them focus on applying Bioschemas specification to their tools and data resulted in recruitment of early adopters, eight annotated resources, Bioschemas examples for future users and more than ten suggestions for specification improvement. This approach could be applied to other open specifications, promoting a wider adoption and the integration of suggestions in a bottom-up fashion.	2018	2018	LICCIULLI VITO FLAVIO	Bioschemas, Elixir, schema.org
452134	Materiale didattico	Quaderno delle sfide	Fabrizio Bianchi, Cinzia Caporale, Liliana Cori, Luana Gasparini, Pietro Greco, Carla Guerriero, Patrizia Lucialli, Elena Mancini, Federica Manzoli, Maria Grazia Petronio, Elisa Pollini, Meri Scaringi	Il quaderno si inserisce tra i risultati del progetto GOCONDA. I GIOVANI CONTANO NELLE DECISIONI su AMBIENTE e SALUTE, ed e dedicato ad una educazione ambientale innovativa e partecipata.	2018	2018	MANZOLI FEDERICA, CORI LILIANA, CAPORALE CINZIA, MANCINI ELENA, BIANCHI FABRIZIO	diritti ambientali, salute a ambiente, sviluppo sostenibile e cittadinanza
402332	Editoriale in rivista	The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes	P. Romano, A. Ceol, A. Drager, A. Fiannaca, R. Giugno, M. La Rosa, L. Milanesi, U. Pfeffer, R. Rizzo, S.Y. Shin, J. Xia, A. Urso		BMC bioinformatics 20 (2019).	2019	RIZZO RICCARDO, URSO ALFONSO, MILANESI LUCIANO, FIANNACA ANTONINO, LA ROSA MASSIMO	NETTAB 2017	10.1186/s12859-019-2681-0
426380	Presentazione	Neurotossicita dell'ocratossina A: effetti epigenetici e di accumulo	Mezzelani A, Cupaioli FA, Raggi ME, Brera C, De Santis B, Milanesi L.	L'ocratossina A (OTA) e una micotossina prodotta da funghi ubiquitari dei generi Aspergillus e Penicillium che contamina i prodotti alimentari e i mangimi in tutto il mondo. In un recente studio pilota, l'OTA e risultata associata all'autismo, un disturbo del neurosviluppo che colpisce prevalentemente i soggetti di sesso maschile caratterizzato da difficolta nell'interazione sociale, interessi ristretti e comportamenti ripetitivi. L'autismo e quasi sempre associato ad altri disturbi come l'aumento dei livelli di infiammazione e dello stress ossidativo. L'OTA e nefrotossica, epatotossica e neurotossica soprattutto nei maschi che sono carenti dell'enzima CYP4A3 che la metabolizza. Essa esercita la sua tossicita inducendo stress ossidativo, infiammazione e fibrosi attraverso meccanismi epigenetici e aumentando il rapporto fenilalanina (phe)/tirosina. L'OTA e infatti composta da una molecola di isocumarina e da una di phe. Quest'ultima compete nella sintesi di neurotrasmettitori con la phe libera come substrato per la phe idrossilasi (che idrolizza la phe in tirosina, precursore della L-DOPA) con conseguente accumulo di phe e riduzione di L-DOPA e dei neurotrasmettitori che ne derivano. Inoltre, un accumulo di phe nel cervello forma fibrille simil-amilode. A livello epigenetico, l'OTA modula l'espressione di alcuni microRNA: diminuisce il mir-29b, inibitore della produzione del collagene, che si traduce in un aumento di quest'ultimo, alterazione fibrotica e nefropatia. Una diminuzione del mir-29b inoltre aumenta l'espressione della alpha-secretase (BACE1), l'enzima coinvolto nella produzione di beta-amiloide, il cui accumulo causa amiloidosi tra cui l'Alzheimer. L'OTA stimola anche la sintesi di mir-132 come si verifica in alcune condizioni neuro-psichiatriche e nello stress ossidativo. Il mir-132 agisce nella regolazione reciproca dei geni correlati all'autismo MEeCP2 e PTEN e diminuisce l'antiossidante Nrf2 aumentando i livelli di ossidanti (ROS). I ROS, a loro volta, aumentano l'espressione del mir-200c che altera ulteriormente i meccanismi antiossidativi e la plasticita sinaptica attraverso la inibizone dell'eme ossigenasi e della neuroligina4X (NLGN4X). Sia MECP2 che NLGN4X sono coinvolti in disordini dello sviluppo neurologico, incluso l'autismo, e sono mappati sul cromosoma X cosa che potrebbe spiegare la prevalenza maschile di questo disturbo. Sono necessari ulteriori studi in vitro e in vivo, da condurre separatamente nei due sessi, per ottenere un quadro completo degli effetti epigenetici dell'OTA e per prevenirli o contrastarli. Fondi: Interomix-OTANEXT-AUT.	Nutrigenomica e alimentazione, Bari, 12/10/2018 - 13/10/2018	2018	CUPAIOLI FRANCESCA ANNA, MEZZELANI ALESSANDRA MARIA, MILANESI LUCIANO	Autism, ocratoxin, inflammation, microRNA, oxidative stress
426464	Poster	Linked read sequencing reveals new genetic variants in autism	Cupaioli FA, Di Nanni N, Pelucchi P, Cifola I, Villa L, Raggi ME, Milanesi L, Mosca M, Mezzelani A	Autism spectrum disorder (ASD) is a complex neurodevelopmental condition, prevalence is 1:68. Although genetics plays a key role in ASD etiology, only 30% of patients exhibit ASD associated genetic variants that are detectable by CGH, GWAS and/or exome NGS approach and hundreds of genes have been involved. Here, we tested the hypothesis that variants in non-coding and/or NGS unmappable regions could be involved in ASD and detected by long-reads whole-genome sequencing (LR-WGS). This approach allows to probe previously unreadable genomic tracts and discover disease-associated phased loci across very long haplotype blocks. Thus, we performed LR-WGS, by 10XGenomics technology, on genomic DNA isolated from 10 children with ASD (7 males and 3 females, including 2 couples of male siblings and 1 couple of male-female siblings) followed by bioinformatics analysis performed by 10X-Long Ranger pipeline. All the sequences passed the QC test, and the longest phase block reached 9M bp in length. We first looked at large structural variants (SVs) detectable only by long-read approach. We found a total of 204 hetero- or homo-zygous large SVs (deletions, duplications, inversions and breakends), up to 30 per subject and affecting 52 distinct genomic regions of 10^5 bp in average within almost all chromosomes. Interestingly, each SV affected from 1 up to 10 subjects and 51 out of 53 SVs involved genes that have never been associated with autism (not listed in SFARI database). All genes were submitted to DAVID 6.8 and METASCAPE gene enrichment tools evidencing some pathways including that of immune response and olfactory transduction. These SVs will be validated on an independent set of DNA samples previously collected from children with ASD and healthy controls. Resulting data will be integrated with clinical data to find genotype-phenotype associations. Small variants will be analyzed and validated, too. In conclusion, LR-WGS successfully discovered 51 new gene variants in 10 patients with ASD that, if confirmed, could explain some pathogenetic mechanisms of the disorder and represent possible diagnostic biomarkers for patient stratification and personalized medicine approaches.	Neurogenetics, Nature Conferences, Virtual (Covid19), 29/07/2020	2020	DI NANNI NOEMI, MEZZELANI ALESSANDRA MARIA, CIFOLA INGRID, PELUCCHI PARIDE, MILANESI LUCIANO, MOSCA ETTORE, CUPAIOLI FRANCESCA ANNA	linked reads, autism, whole genome sequencing, large structural variants
426699	Abstract in rivista	Association of Haptoglobin-1 allele with Autism	Mezzelani, A., Cupaioli, F. A., Mosca, E., Magri, C., Gennarelli, M., Raggi, M. E., Landini, M., Galluccio, N., Chiappori, F., Moscatelli, M., Gnocchi, M., Villa, C., Molteni, M., Bonfanti, A., Ciceri, F., Marabotti, A., Milanesi, L.	Gene-environment interaction, through abnormal intestinal adsorption, has been proposed as possible mechanism for autism pathogenesis in those patients lacking of causative genetic variants. Haptoglobin (HP) is a haemoglobin binding and acute-phase plasma protein, encoded by two co-dominant alleles, HP-1 and HP-2, producing pre-HP-1 and pre-HP-2 proteins that mature in HP-1 and HP-2, respectively. Due to a 1.7Kb copy number variation in the HP gene, the HP-2 allele has two extra exons with respect to HP-1. Thus the HP protein is a dimer in homozygous subjects for HP-1 allele and is multimer in homozygous HP-2. Endogenous pre-HP-2 protein deregulates intestinal tight-junctions through EGFR and PAR2 activation, increases intestinal permeability and has been associated with autoimmune and inflammatory diseases as well as with psychiatric conditions (Fasano, 2011; Sturgeon and Fasano, 2016). Since the association between HP alleles and autism has just been investigated in a very small sample size of patients and controls (Rose et al., 2018), we genotyped, by PCR analysis, HP in a cohort of Italian patients with autism (n=406) and in controls (n=367). The aim was to evaluate the possible association of HP-2 and autism spectrum disorder (ASD). Contrary to what we expected, HP-1 allele distribution was different between patients and controls (36.3% and 29.4%, respectively) and significantly associated with autism (P=0.0041). Since a subgroup of patients and controls have already been genotyped by Illumina Human Omni-15-8 v.1.0 and Affy-6.0 chips, respectively, we are trying to impute HP alleles from flanking SNP haplotypes. HP alleles will therefore be predicted in publicly available large cohorts of patients with autism.	European journal of human genetics 27 (2019): 280-281.	2019	CHIAPPORI FEDERICA, CUPAIOLI FRANCESCA ANNA, LANDINI MARTINA, GALLUCCIO NADIA, MOSCATELLI MARCO, MEZZELANI ALESSANDRA MARIA, MILANESI LUCIANO, GNOCCHI MATTEO, MOSCA ETTORE	Autism spectrum disorders, Haptoglobin, intestinal permeability	10.1038/s41431-019-0404-7
426706	Poster	Association of Haptoglobin-1 allele with Autism.	Mezzelani A, Cupaioli F, Mosca E, Magri C, Gennarelli M, Raggi ME, Landini M, Galluccio N, Chiappori F, Moscatelli M, Gnocchi M, Villa CL, Molteni M, Bonfanti A, Ciceri F, Marabotti A, Milanesi L.	Gene-environment interaction, through abnormal intestinal adsorption, has been proposed as possible mechanism for autism pathogenesis in those patients lacking of causative genetic variants. Haptoglobin (HP) is a haemoglobin binding and acute-phase plasma protein, encoded by two co-dominant alleles, HP-1 and HP-2, producing pre-HP-1 and pre-HP-2 proteins that mature in HP-1 and HP-2, respectively. Due to a 1.7Kb copy number variation in the HP gene, the HP-2 allele has two extra exons with respect to HP-1 (Fig. 1). Thus the HP protein is a dimer in homozygous subjects for HP-1 allele and is multimer in homozygous HP-2. Endogenous pre-HP-2 protein deregulates intestinal tight-junctions through EGFR and PAR2 activation, increases intestinal permeability and has been associated with autoimmune and inflammatory diseases as well as with psychiatric conditions (Fasano, 2011; Sturgeon and Fasano, 2016). Since the association between HP alleles and autism has just been investigated in a very small sample size of patients and controls (Rose et al., 2018), we genotyped, by PCR analysis, HP in a cohort of Italian patients with autism (n=406) and in controls (n=367). The aim was to evaluate the possible association of HP-2 and autism spectrum disorder (ASD). Contrary to what we expected, HP-1 allele distribution was different between patients and controls (36.3% and 29.4%, respectively) and significantly associated with autism (P=0.0041). Since a subgroup of patients and controls have already been genotyped by Illumina Human Omni-15-8 v.1.0 and Affy-6.0 chips, respectively, we are trying to impute HP alleles from flanking SNP haplotypes. HP alleles will therefore be predicted in publicly available large cohorts of patients with autism.	European Conference of Human Genetics 2018, Milano, Italy, 16/06/2018 - 19/06/2018	2018	CHIAPPORI FEDERICA, CUPAIOLI FRANCESCA ANNA, LANDINI MARTINA, GALLUCCIO NADIA, MOSCATELLI MARCO, MEZZELANI ALESSANDRA MARIA, MILANESI LUCIANO, GNOCCHI MATTEO	Autism spectrum disorders, Haptoglobin, Zonulin, intestinal permeability
426810	Presentazione	Autism Spectrum Disorder: Linked-Read Sequencing Reveals New and Undetected Variants	F.A. Cupaioli, E. Mosca, N. Di Nanni, P. Pelucchi, L. Milanesi, M.E. Raggi, L. Villa, A. Mezzelani	Introduction Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by limited social interaction, communication impairments, restricted interests and repetitive behaviors. It occurs in pediatric age, within the first 3 years of life, and lasts for a lifetime with severe consequences for the individual and his/her family and with very high social costs. In the last decades, ASD has increased dramatically reaching the prevalence of 1:68. Although genetics play a key role in ASD, its etiology is complex and recent studies hypothesize a gene-environment interaction. Indeed, causative or predisposing genetic variants have been detected only in 30% of patients and thousands of genes are involved. Here, for the first time, linked-read whole genome sequencing of ASD patients is used to access disease associated regions unmappable by short-reads NGS. Materials and Methods Ten children suffering from ASD (diagnosed by ADOS 2 and ADI-R), including 3 couples of affected siblings, were enrolled, peripheral blood collected and HMW DNA isolated. All the procedures had been approved by Ethical Committee as well as clinical data collected according to current privacy laws. HMW DNA, 50 kb in size or greater, was submitted to 10Xgenomics microfluidics partitioning and barcoding and then to Illumina library preparation and whole genome-next generation sequencing. Data were analyzed through 10x Long Ranger pipelines to find SNVs, in/del and larger structural variants in comparison to 1,000 genomes, genome aggregation database and NHLBI-ESP populations. Genes affected by variants were compared with those already associated with ASD: SFARI database, large-scale sequencing studies, bioinformatics predictions. Results The linked-read sequencing approach successfully produced sequences up to 9mln bps in length haplo-blocks. This technique allowed to detect variants in whole genome of ASD patients. We found genes affected by mutations already listed in SFARI and previously predicted by bioinformatics analysis and discovered hundreds of new variants. Among these latter, we focused on those homozygous in the 3 couples of siblings and found that some of them are related to neuro-development and -physiology or to xenobiotic metabolism. Conclusion For the first time, we applied the linked-read sequencing technology for studying ASD genomics. This powerful approach allowed us deciphering the genomics heterogeneity in ADS and highlighting variations otherwise undetectable by classic NGS. Indeed, we identified homozygous variants within genes or regulatory regions common to 3 couples of affected siblings. Further studies will be performed to validate the new ASD variations by PCR amplification and Sanger sequencing in a large size of ASD samples and in public data; then, the new biomarkers will be used to stratify ASD patients population. Data integration will be also performed to identify pathways and gene networks involved in the disorder to understand disease mechanisms and design target-driven personalized treatment. Acknowledgements: EU project GEMMA (grant agreement No 825033), EPTRI and CNRBiOmics.	EPTRI (European Paediatric Translational Research Infrastructure) open meeting 2020, virtual meeting, 02/04/2020 - 03/04/2020	2020	DI NANNI NOEMI, MEZZELANI ALESSANDRA MARIA, PELUCCHI PARIDE, MILANESI LUCIANO, MOSCA ETTORE, CUPAIOLI FRANCESCA ANNA	Autism Spectrum Disorder, linked reads, whole genome sequencing, biomarkers, patients stratification
432991	Poster	CXCL10 binding mode to CXCR3 isoforms: different behaviors	Carisetti M, Moscatelli M, Milanesi L, Mezzelani A, Chiappori F	CXCR3 is a G-protein coupled receptor expressed principally on leukocytes, monocytes and epithelial cells; it is involved in leukocyte traffic, integrin activation, cytoskeletal changes and chemotactic migration, by binding to its classical ligands, CXCL-9/10/11 (1). Three splicing variants of CXCR3 are known: CXCR3a, the most common isoform, consisting of 368 amino acid residues; CXCR3b resulting from an alternative splicing of the CXCR3 mRNA with a 52 aa extended N-terminal domain when compared to the isoform a, while CXCR3-alt is a significantly truncated variant not involved in classical ligand binding (1). CXCL10, the interferon-?-inducible protein (IP-10) belongs to the CXC family of chemokines and acts as an immunoinflammatory mediator, inhibits angiogenesis and displays antitumor properties (2). Several studies indicated that the CXCR3 N-terminal domain plays a key role in determining binding affinity, receptor selectivity, and also in regulating allosteric signalling through the receptor (3). Moreover, tyrosine sulfation in chemokine receptors is emerging as a post-translational modification that contributes substantially to ligand binding (2). Tyr 27 and 29, two of the N- terminal tyrosine can be sulfonated. Finally, Kleist and co-workers hypothesize a "two-step" model, where receptor binding and activation can be dissociated (4). In the first step, the chemokine binds to the N-term domain of the receptor. In the second, residues on IP10 N-terminal bind to the binding cavity on the TM domain of the receptor and induce the allosteric communication to the cytosol. In this work, we analyse by a supervised molecular dynamics (SuMD) (5) simulation, the binding mechanism of IP10 on CXCR3. We explored the binding site in order to evaluate the residue- residue interactions between the chemockine and its receptor. Starting from the same equilibrated system, 3 runs of supervised MD were performed using the same conditions. A residue selection from the CXCR3 N-term domain and all the Extra-Cellular Loop (ECL) were considered for the binding interface, instead the entire chemokine was treated as ligand in order to perform the supervision on the distance between the receptor (CXCR3) and the ligand (CXCL10). They resulted with consistent similarity in both ligand-receptor contacts and interaction energies. Simulations didn't had identical durations (30.8 ns for simulation 1, 31.2 ns for simulation 2 and 36.6 ns for simulation 3), but all of them reached the ligand correctly positioned in the binding site in 15ns. Simulations 2 and 3 presented overlapping situations of decreasing energies related to minor R-L distances and of contacts, involving both residues from the CXCR3-N- term and the Extra-cellular ?-sheet, which has been described as an important player for the receptor activation. The next step will be the evaluation of the effect of tyrosine sulfation (Y27 and Y29) on binding mode and affinity.	CDDD 2019, Roma, 28-29/03/2019	2019	MEZZELANI ALESSANDRA MARIA, MILANESI LUCIANO, MOSCATELLI MARCO, CHIAPPORI FEDERICA CATERINA	CXCR3, IP10, supervised molecular dynamics, protein-protein interaction, post-translational modifications
432989	Poster	Gliadin peptide deamidation: effects on CXCR3 binding and signal transmission	Carisetti M, Moscatelli M, Milanesi L, Mezzelani A, Chiappori F	Gluten is a complex molecule made of gliadin and glutenins. During digestion, gliadin is reduced into small peptides of about 20 amino acids enriched in glutamine and prolines. In the intestinal epithelium the CXCR3 (CX-Chemokine Receptor Type 3, a G-Protein Coupled Receptor - GPCR) binds two of the gliadin peptides (pep 111-130 QQQQQQQQQQQQILQQILQQ and pep 151-170 QVLQQSTYQLLQELCCQHLW). Moreover, it is involved in celiac disease (CD) development inducing an increase of intestinal permeability, resulting in zonulin release, which is induced and activated through the MyD88-pathway. Two of the three splicing variants of CXCR3 are involved in CD: CXCR3-A and CXCR3-B. Furthermore, it is known that gliadin peptides are modified by tissue transglutaminase (tTG) converting specific glutamine (Q) residues into glutamic acid (E): pep 111-130E QQQQQQQQQQQQILQQILQE and pep 151-170E QVLQESTYQLLQELCCQHLW. Evaluate differences between deamidated and non-modified gliadin peptides bound to both CXCR3 a and b isoforms The selected conformations resulting from the Autodock CG simulations (Table 1) correspond to the complexes with the lowest binding energy if considering peptide 111-130; instead, for peptide 151-170, the chosen conformations result the second in terms of binding energy and the first in terms of cluster numerosity, since the lowest binding energy conformation displays a backward orientation of the peptide. HADDOCK run (Table 2) returned up to 14 clusters for each protein-peptide docking simulation, displaying different score ranges between deamidated and normal peptides. Instead, regarding energy values they display overlapping results except for Cxcr3b-pep111 complexes. The model with the lowest score and/or the lowest binding energy (VdW, Electrostatic and Desolvation) from each run was selected for MD simulations. MD trajectories analysis suggested either a change in CXCR3 TM-helices or in C- ter flexibility when comparing non-modified peptides to deamidated ones. Therefore, what we expect to understand is the effect of the gliadin deamidation, first on binding to CXCR3, secondly on the signal transmission to the cytoplasmic domain. Accordingly, an H-bond analysis was performed on MD trajectories. Results displayed an uninterrupted H-bond network from the binding cavity to the C-ter helix in the CXCR3a/111-130 (Fig. 2a) and CXCR3b/111-130E (Fig. 2b) complexes. But, the two complexes differ for the receptor residues involved in peptide binding (in blue in Fig.2), since the deamidated peptide binds charged residues, while the non-modified interacts with non-charged residues. Likewise, also the resulting Hbond networks involve different residues. The other CXCR3 complexes display several H-bond network stops before the C-ter. Haddock docking simulations did not allow a discrimination between non-modified and deamidated peptides while Autodock CG application displays a preference for CXCR3 a or b isoforms by deamidated peptides 111-130 and 151-170, respectively. H-bond analysis let us evaluate the effects of deamidation on the binding mode and on the affinity with CXCR3 isoforms, concluding that deamidation actively influences the binding to the receptor. Furthermore, we did not observe any substantial differences in signal transduction for peptide 151-170 (Fig. 2c), while peptide 111-130 displayed two distinct networks for each isoform (Fig. 2a and 2b). Given that CXCR3 is a GPCR, so the C-ter is involved in the activation of the G-coupled protein, these results suggest pep 111-130 as favoured ligand than pep 151-170, both for CXCR3 a and b.	BITS 2018, Torino, 27-29/06/2018	2018	MEZZELANI ALESSANDRA MARIA, MILANESI LUCIANO, MOSCATELLI MARCO, CHIAPPORI FEDERICA CATERINA	CXCR3, gliadin, protein/peptide modeling, protein-peptide docking
433002	Presentazione	CXCL10-CXCR3 complex formation, different isoforms result in different binding modes	M. Carisetti, M. Moscatelli, L. Milanesi, A. Mezzelani, F. Chiappori	CXCR3 is a G-protein coupled receptor expressed principally on leukocytes, monocytes and epithelial cells; it is involved in leukocyte traffic, integrin activation, cytoskeletal changes and chemotactic migration, by binding to its classical ligands, CXCL-9/10/11 (1). Three splicing variants of CXCR3 are known: CXCR3a, the most common isoform, consisting of 368 amino acid residues; CXCR3b resulting from an alternative splicing of the CXCR3 mRNA with a 52 aa extended N-terminal domain when compared to the isoform a, instead CXCR3-alt is a significantly truncated variant not involved in classical ligand binding (1). CXCL10, the interferon-?-inducible protein (IP-10) belongs to the CXC family of chemokines and acts as an immunoinflammatory mediator, inhibits angiogenesis and displays antitumor properties (2). Several studies indicated that the CXCR3 N-terminal domain plays a key role in determining binding affinity, receptor selectivity, and also in regulating allosteric signaling through the receptor (3). Moreover, sulfation of tyrosine in chemokine receptors is emerging as a post-translational modification that substantially contributes to ligand binding (2). Tyr 27 and 29, two of the N-terminal tyrosine can be sulfonated. Additionally, CXCR3b displays two other potential sulfonable tyrosines in the extended N-term domain, at position 6 and 40; these differences may affect the binding mechanism and the receptor activation of CXCR3b rather than CXCR3a (4). Finally, Kleist and co-workers hypothesize a "two-step" model, where receptor binding and activation can be dissociated (5). In the first step, the chemokine binds to the N-term domain of the receptor. In the second, residues on IP10 N-terminal bind to the binding cavity on the transmembrane domain of the receptor and induce the allosteric communication to the cytosol. In this work, we analyse by molecular dynamics (MD) simulation the binding mechanism of CXCL10 on CXCR3, evaluating the effect of tyrosine sulfonation and taking into account different sulfotyrosine combinations, on binding mode and affinity. In parallel, we analyse variations between CXCR3 isoforms a and b to highlight the different allosteric communication toward the cytoplasmic C-term domain, responsible of G-protein binding. We modelled CXCR3a and b isoforms, both were included in a double layer membrane with CHARMM-GUI server (http://www.charmm-gui.org/) and through the MD we optimized the structure conformation. The binding between CXCL10 and CXCR3 representative conformation was simulated employing a supervised MD approach (6). Several simulations were collected for each complex, in order to obtain a consistent result. In particular, the supervised MD was performed in 3 runs, using the same conditions, starting from the same equilibrated system. A list of selected residues from the N-term of CXCR3 and all the extra-cellular loop were adopted for the computation of the binding site instead the entire chemokine was considered as ligand in order to perform the supervision on the distance between the receptor (CXCR3) and the ligand (CXCL10). All simulations return the CXCL10 correctly positioned in CXCR3a binding site within the first 15ns (fig 1a). While, CXCR3b simulations doesn't reach the complex formation due to the closing up of the N-term domain, and interrupt at 9 A of ligand-receptor distance (fig 1b). CXCR3a complex simulations resulted consistent in both ligand-receptor decreasing energies, related to minor R-L distances and similarities in pattern of contacts, involving both residues from the CXCR3 N-terminal and the extra-cellular ?-sheet, which has been described as an important player for the receptor activation. A second round of supervised MD will be performed to evaluate the second step of the "two-step" model. The next step will be the evaluation of the effect of tyrosine sulfation (Y27, Y29 for both receptors and Y6, Y40 only for CXCR3b) (fig 1c) on binding mode and affinity.	BITS 2019, Palermo, 26-28/06/2019	2019	MEZZELANI ALESSANDRA MARIA, MILANESI LUCIANO, MOSCATELLI MARCO, CHIAPPORI FEDERICA CATERINA	CXCR3, CXCL10, IP10, protein-protein binding, supervised molecular dynamics
443504	Abstract in rivista	DEVELOPMENT AND VALIDATION OF A NOVEL EPS-METABOLOMIC SIGNATURE FOR THE DIAGNOSIS OF CLINICALLY SIGNIFICANT PROSTATE CANCER.	Andolfo, Annapaola, Drago, Denise, Cucchiara, Vito, Nocera, Luigi, Mosca, Ettore, Orro, Alessandro, Bellone, Matteo, Montorsi, Francesco, Briganti, Alberto	None	The Journal of urology 201 (2019): E220-E220.	2019	ORRO ALESSANDRO, MOSCA ETTORE	metabolomics, prostate cancer, expressed prostatic secretion
448977	Abstract in atti di convegno	Network diffusion for the integrative analysis of multiple "-omics": case studies on breast cancer	Di Nanni, N., Appierto, V., De Marco, C., Ortolan, E., Milanesi, L., Daidone, M., Mosca, E.	None	51st European Society of Human Genetics Conference, pp. 570-570, 16-19/06/2018	2019	DI NANNI NOEMI, MILANESI LUCIANO, MOSCA ETTORE	breast cancer, multiple omics, biological network	10.1038/s41431-019-0404-7
448984	Abstract in atti di convegno	Functional gene networks underlying somatic mutations in Breast Cancer Initiating Cells	Ettore Mosca1, Valentina Appierto2, Noemi Di Nanni1, 3, Cinzia De Marco2, Luciano Milanesi1, Maria Grazia Daidone2	None	CSC 2018 - Cancer Stem Cells: impact on treatment, 11-15/12/2018	2018	DI NANNI NOEMI, MILANESI LUCIANO, MOSCA ETTORE	Breast cancer initiating cells, somatic mutations, whole-exome sequencing, gene networks
449027	Abstract in atti di convegno	Network diffusion-based gene prioritization integrating multiple omics and gene networks	Noemi Di Nanni1, 2, Luciano Milanesi1, Ettore Mosca1	None	15th Annual Meeting of the Bioinformatics Italian Society, 27-29/06/2018	2018	DI NANNI NOEMI, MILANESI LUCIANO, MOSCA ETTORE	Data Integration, Molecular Networks, Multi-omics, Network Diffusion
449029	Abstract in atti di convegno	Integrative analysis of multiple "-omics" with network diffusion	N. Di Nanni1, 2, M. Gnocchi1, M. Moscatelli1, L. Milanesi1, E. Mosca1	None	VI National Congress of Bioengineering, 25-27/06/2018	2018	DI NANNI NOEMI, MILANESI LUCIANO, GNOCCHI MATTEO, MOSCA ETTORE, MOSCATELLI MARCO	Integrative analysis, Breast Cancer, Omics data, Molecular networks
449032	Software	isma - integrative somatic mutation analysis	Di Nanni, Noemi, Moscatelli, Marco, Gnocchi, Matteo, Milanesi, Luciano, Mosca, Ettore	We developed isma (integrative somatic mutation analysis), an R package for the integrative analysis of somatic mutations detected by multiple pipelines for matched tumor-normal samples. The package provides a series of functions to quantify the consensus, estimate the variability, underline outliers, integrate evidences from publicly available mutation catalogues and filter sites.	2019	2019	DI NANNI NOEMI, MILANESI LUCIANO, GNOCCHI MATTEO, MOSCA ETTORE, MOSCATELLI MARCO	Somatic mutations, Next-generation sequencing, Cancer, Data integration
449228	Abstract in atti di convegno	MicroRNA and transcription factor co-regulatory network analysis: a combined bioinformatics and molecular strategy for uncovering genetic hub regulatory elements in multiple sclerosis pathogenesis	Nuzziello, N., Vilardo, L., Pelucchi, P., Consiglio, A., Trojano, M., Liguori, M.	Introduction: As the main regulators of gene expression, microRNAs (miRNAs) and transcription factors (TFs) play key roles in complex multifactorial diseases like Multiple Sclerosis (MS). Recently, miRNA/TF-based feed-forward loops (FFLs) have been identified as key elements of biological network motifs in MS. Objectives: Starting from preliminary results obtained by a High-Throughput Next-Generation Sequencing (HT-NGS) approach on an independent MS patients cohort, we aimed to search for miRNA-TF co-regulatory networks involved as hub genetic elements in MS pathogenesis. Methods: The study was performed on peripheral blood samples belonging to 58 MS patients and 20 healthy controls (HCs).To validate the differential expressed (DE) miRNAs resulted from HT-NGS analysis, total RNA extraction was followed by microfluidic qPCR. The subsequent analysis included: miRNA-target gene interaction evaluation using experimentally validated miRNA-target interaction databases (DIANA-Tarbase and miRTarBase) and the output of 5 algorithms (miRanda, DIANA-microT-CDS, RNA22, miRDB and TargetScan) for target genes prediction; miRNA-target experimentally validation using dual luciferase reporter assay; TF-miRNA co-regulatory network identification using miRNA-TF interaction tools (Harmonizome and TransmiR) and a gene-TF interaction database (TRRUST); pathway enrichment analysis using DAVID tool. Results: Microfluidic qPCR analysis revealed 6 significantly DE miRNAs (miR-320a, miR-125a-5p, miR-652-3p, miR-185-5p, miR-942-5p and miR-25-3p) in MS patients compared to HCs. The integrated analysis of miRNAs and computationally predicted mRNAs uncovered 638 miRNA-target pairs validated by reporter gene assays and/or predicted by at least 4 of the 5 interaction tools. Luciferase reporter assays indicated that miR-125a-5p was able to target and modulate DIP2A, ADD2 and E2F2 expression, thus confirming that the in silico predicted target were effectively subjected to miRNA-mediated post-transcriptional modulation. In addition, 409 TF-miRNA interactions were identified, including 198 miRNA-TF FFLs. Furthermore, the enrichment analysis categorized in functional pathways revealed significant representations of networks mostly related to neurotrophin signalling pathway, ErbB signalling pathway and axon guidance. Conclusions: These results uncovered several hub regulatory elements allowing to shed further lights in the gene regulation mechanisms that may underlie the pathogenesis of MS.	European Committee for Treatment and Research in Multiple Sclerosis (ECTRIMS 2018), pp. 593-593, Berlin, Germany, 10-12/10/2018	2018	NUZZIELLO NICOLETTA, LIGUORI MARIA, PELUCCHI PARIDE, CONSIGLIO ARIANNA, VILARDO LAURA	microRNA, Multiple sclerosis, transcription factor
450046	Toolkit metodologico	Incidental Findings nella ricerca scientifica. Criteri e indicazioni per le scienze e tecnologie -omiche	Giuseppe Testa, Cinzia Caporale, Elena Mancini, Marco Annoni, Luca Marelli	Ethical Toolkit per l'identificazione, analisi e comunicazione degli incidental findings nella ricerca	2018	2018	CAPORALE CINZIA, MANCINI ELENA, ANNONI MARCO ANGELO MARIA	incidental finding, etica della ricerca, consenso informato, diritto di non sapere
454170	Presentazione	Un anno di COVID-19 : luci ed ombre della risposta sanitaria e lezioni apprese	Galli M, Adorni F	Clinica ed epidemiologia. Testing, tracing, treating. Medicina territoriale. ICT nella ricerca e nel SSN	MedExpo. Innovation in infobiomedical technologies and telemedicine, Virtual Conference, 20-22 May 2021	2021	ADORNI FULVIO DANIELE	Covid-19, epidemiologia, sanita pubblica
455188	Presentazione	Medicina Comunitaria, Sorveglianza Sanitaria, Epidemiologia	Adorni F	Epidemiologia e prevenzione primaria, secondaria e terziaria. ICT nella ricerca e nel SSN	eGeH'21 e-GOVERNMENT & e-HEALTH, XVIII INTERNATIONAL CONFERENCE, Webinar, 8-9 July 2021	2021	ADORNI FULVIO DANIELE	epidemiologia, sanita pubblica, malattie trasmissibili, malattie cronico-degenerative, prevenzione
455131	Poster	Estrogenic hormones counteract FSHD features in a muose model of muscle regeneration	Moretti F, Di Blasio G, Manni I, Teveroni E, Maiullari F, Rizzi R, Ricci E, Luvisetto S, Deidda G	The wide range of clinical symptoms in FSHD patients suggests the presence of modifying factors, still partially explored. Our group demonstrated that estrogens improve in vitro muscle differentiation of myoblasts from FSHD patients. Estrogens, through estrogen receptor beta (ER?), displace DUX4 from its target promoters and antagonize its transcriptional pathogenetic activity during myoblast differentiation. In this work, we confirm these data in vivo by analyzing the effect of estrogen on the regenerative potential of human muscle-precursor cells (PVCs) derived from healthy individuals and engineered to express DUX4 (DUX4-PVCs) or derived from FSHD patients. DUX4-PVCs were implanted into injured hindlimb muscle of NOD-scid-gamma (NSG) mice treated with 17?-estradiol (E2), 3?-diol (a specific ligand of ER? present in males), or EtOH (vehicle). Animals were monitored by a functional treadmill test and at the molecular levels by immunohistochemistry, gene, and protein expression. Our data demonstrate that human PVCs participate in mouse muscle regeneration and form functional heterokaryon muscle fibers that increase run ability recovery. The expression of DUX4 impairs this function and determines the increased formation of fibrotic tissue. Of relevance, both E2 and 3?-diol rescue this impairment, enhancing muscle formation and reducing the fibrotic response. Accordingly, both mouse hormone treatments rescue functional running ability reduced by DUX4 expression. Overall, these results suggest that estrogen hormones improve DUX4-PVCs regeneration ability and support the hypothesis of their beneficial activity in humans. In addition, our data substantiate the usefulness of the implantation/regeneration system here developed as an FSHD experimental model	28th Annual FSHD Society, International Research Congress, webinar online, 24-25/06/2021	2021	DEIDDA GIANCARLO, RIZZI ROBERTO, LUVISETTO SIRO, MORETTI FABIOLA	FSHD, Estrogens, muscle regeneration
456617	Abstract in rivista	Association between dietary patterns and neuroimaging markers: a systematic review	R.F. Townsend1, J.V. Woodside1, 2, F. Prinelli3, C.T. McEvoy1, 2	Neuroimaging techniques can sensitively measure brain health and may elucidate potential diet-related mechanisms of cognitive ageing. Emerging evidence for a protective role of dietary patterns (DPs) on brain changes is inconsistent(1,2). We are currently conducting a systematic review to improve our understanding of the relationship between DPs and brain ageing; in this abstract we present the studies reporting neuroimaging outcomes. The review was registered with PROSPERO (CRD42020181423). EMBASE and MEDLINE databases were searched for studies published up to March 2020. Eligible studies for inclusion in the review were prospective studies in non-demented adults that examined whole DPs in relation to >=1 neuroimaging markers and published in the English language. Risk of bias was assessed using the Newcastle-Ottawa Scale (NOS). From 9216 articles screened, 9 prospective studies involving 2540 participants from mid to older life met inclusion criteria: 7 assessed the Mediterranean dietary pattern (MeDi), 1 assessed adherence to the Alternative Healthy Eating Index (AHEI) and 1 used a-posteriori derived DPs. Eight studies examined the relationship between DPs and brain structure (e.g. grey matter[GMV]/ white matter[WMV]/hippocampal [HCV]/total brain volumes[TBV]/cortical thickness[CT]/white matter hyper intensities[WMH]/ infarcts and white matter microstructure integrity[WMI]. Three studies examined MeDi in relation to brain functional measures including beta-amyloid (A?) load (N = 3) and brain glucose metabolism (N = 2). Among the prospective studies assessing neuroimaging at 1 time point; MeDi was not associated with subsequent GMV, WMV, TBV or WMH (N = 3). However, 2 studies found an association between higher MeDi adherence, decreased odds of cerebral infarcts 5.8 years later (OR: 0.89; 95% CI: 0.80, 0.99) and improved WMI 8.9 years later. From studies assessing change in neuroimaging markers; MeDi was not associated with change in GMV or CT over 2-3 years (N = 3), but higher MeDi adherence was associated with reduced TBV atrophy across 3 years (N = 1). Two out of three studies found an association between lower MeDi adherence and increased A? load across 2-3 years, and 2 found an association between lower MeDi adherence and increased rate of decline in brain glucose metabolism. From those examining a-posteriori DPs, one found an association between higher AHEI and greater HCV and one found a positive association between a prudent diet and greater HCV, but not with 4-year change in HCV. Given the heterogeneity of these data, meta-analysis was not performed. All studies were rated fair (N = 7) or good (N = 2) using NOS. This review reveals conflicting evidence on the association between DPs and structural markers. Findings, whilst limited, were more consistent between MeDi and functional markers; this could be because functional changes may precede structural changes(3). Future research should consider the use of multimodal neuroimaging and investigate DPs other than MeDi.	Proceedings of the Nutrition Society (Online) 80 (2021): 102-102.	2021	PRINELLI FEDERICA	dietary patterns, neuroimaging markers, systematic review	10.1017/S0029665121002251
457819	Comunicazione in rivista (Letter - Letter to editor)	SELP Asp603Asn and severe thrombosis in COVID-19 males	Fallerini, Chiara, Daga, Sergio, Benetti, Elisa, Picchiotti, Nicola, Zguro, Kristina, Catapano, Francesca, Baroni, Virginia, Lanini, Simone, Bucalossi, Alessandro, Marotta, Giuseppe, Colombo, Francesca, Baldassarri, Margherita, Fava, Francesca, Beligni, Giada, Di Sarno, Laura, Alaverdian, Diana, Palmieri, Maria, Croci, Susanna, Isidori, Andrea M., Furini, Simone, Frullanti, Elisa, Renieri, Alessandra, Mari, Francesca		Journal of hematology & oncology 14 (2021).	2021	COLOMBO FRANCESCA	Anti-selectin P monoclonal antibodies, COVID-19, P-selectin, Thromboembolism, Thrombus, Venous thromboembolism	10.1186/s13045-021-01136-9
454877	Editoriale in rivista	Loss of Neurologic Reserve in Progressive Multiple Sclerosis: A Paradigm Shift?	Joep Killestein and Maria Liguori		Neurology. Clinical practice (Online) (2021).	2021	LIGUORI MARIA	progressive multiple sclerosis, neurologic reserve	10.1212/CPJ.0000000000001106
457820	Altro prodotto	ProteomiX Stargate	M.G. Giuffrida e P.L. Mauri	Gruppo di discussione su tematiche inerenti il proteoma	2021	2021	GIUFFRIDA MARIA GABRIELLA, MAURI PIETRO LUIGI	proteomica
454708	Altro prodotto	ProteomiX Stargate	M.G. Giuffrida, P.L. Mauri, A. Facchiano	Gruppo di discussione su tematiche inerenti il proteoma	2020	2020	GIUFFRIDA MARIA GABRIELLA, FACCHIANO ANGELO, MAURI PIETRO LUIGI	proteomica
455157	Altro prodotto	ProteomiX International - "Mix your knowledge to get more!"	Giuffrida Maria Gabriella, Mauri Pierluigi	Gruppo internazionale di discussione su tematiche di proteoma	2018	2018	GIUFFRIDA MARIA GABRIELLA, MAURI PIETRO LUIGI	proteomica
454700	Altro prodotto	Restrizione Calorica e Salute	Prof. Giuseppe Matarese, Dr. Pierluigi Mauri, Prof. Marco Salvetti, Prof. Franco Berrino, Dr. Gianfranco Caselli, Prof. Vincenzo Lionetti, Prof. Silvia Migliaccio, Dr. Franco Molteni, Prof. Andrea Salmaggi	Presentazione studio "Caloric Restriction Promotes Immunometabolic Reprogramming Leading to Protection from Tuberculosis" e tavola rotonda su Alimentazione e Salute - dalla Ricerca alla Clinica	2021	2021	MAURI PIETRO LUIGI	caloric restriction, Proteomics, Neurology, Oncology, Inflammation, Nutrition
457821	Altro prodotto	SMAU 2021 - PROFILI MOLECOLARI PER LA SALUTE	Pierluigi Mauri	Partecipazione con postazione PC e collegamento Zoom presso lo stand di Cluster TAV	2021	2021	MAURI PIETRO LUIGI	proteomica, salute, profili molecolari
464101	Abstract in atti di convegno	The effects of the COVID-19 pandemic and quarantine measures on the lifestyles and mental health of older adults at increased risk of dementia	Di Santo, Simona Gabriella, Franchini, Flaminia, Martone, Angela, Sannino, Serena, Beltrami, Roberta, Adorni, Fulvio, Caltagirone, Carlo	None	WCN 2021 - XXV World Congress of Neurology, Virtuale, 3-7 Ottobre 2021	2021	ADORNI FULVIO DANIELE	COVID-19, Mental health, Dementia, Lifestyles	10.1016/j.jns.2021.119800
467872	Working paper	Report of the ML4Microbiome workshop 2021 - Statistical and Machine Learning Techniques for Microbiome Data Analysis	Eliana Ibrahimi1, 2, Ilze Elbere3, 4, Magali Berland5, Domenica D'Elia6	The bacteria living in and on us, over 100 trillion, are essential for human development, immunity and nutrition and ultimately for human health. Researchers awareness of the importance of the microbiome for human wellbeing brought in the latest decade to the flourishing of new and numerous projects focused on the human microbiome, increasing the number of large microbiome datasets available. As a result, statistical and machine learning techniques to solve microbiome data analysis challenges are in high demand. The workshop "Statistical and Machine Learning Techniques for Microbiome Data Analysis" was organised by the COST Action ML4Microbiome to introduce the main concepts of study design and statistical/machine learning techniques used in human microbiome studies to a broad community of researchers and to foster connections between the discovery-oriented microbiome and statistical/machine learning researchers inside and outside the ML4Microbiome COST Action. To this aim, the workshop was organised as part of the training programme of the GOBLET & EMBnet Annual General Meeting 2021. This allowed ML4Microbiome to reach a broad and multidisciplinary community of scientists working in Bioinformatics and Computational Biology research and education from all over the world. The workshop attracted more than 80 participants from 40 different countries. In this paper, we report about the main topics treated and discuss the attendants' feedback regarding their level of satisfaction and their specific needs/demands for possible improvement of the training offer of ML4Microbiome in the microbiome research field. Under the authors' permission, presentations were recorded and are available as an ML4Microbiome playlist on YouTube (https://www.youtube.com/channel/UCiFVD1SsJzIdPRLdJ79SNcA). The programme and presentations files are available at the ML4Microbiome website (https://www.ml4microbiome.eu/activities-and-events/ml4microbiome-workshop-on-statistical-and-machine-learning-techniques-for-microbiome-data-analysis/).	pp.e1012, 2022	2022	D'ELIA DOMENICA	Report, Workshop, COST Action, ML4Microbiome, Microbiome analysis
468003	Abstract in atti di convegno	A survival genome-wide association study to identify variants associated with COVID-19 risk of death	Francesca Minnai, Filippo Biscarini, Tommaso A. Dragani, Chiara Fallerini, Kristina Zguro, Simone Furini, Gen-Covid Multicenter Study, Alessandra Renieri, Francesca Colombo	None	European Human Genetics Conference, pp. P26.006.C, Vienna, 11/06/2022 - 14/06/2022	2022	BISCARINI FILIPPO	covid-19, survival analysis, gwas, genetic variants
462251	Rapporto di progetto (Project report)	D1.2 Specifiche tecniche	Sara Arlati, Vera Colombo, Le Anh Dao, Luca Greci, Matteo Malosio, Marta Mondellini, Davide Felice Redaelli, Francesca Santini, Daniele Spoladore, Giovanni Tauro, Alfonso Mastropietro, Ilena Pirovano, Giovanna Rizzo, Mattia Chiappini, Gianluigi Reni, Fabio Storm	In questo deliverable si descrive la progettazione del simulatore di Rip@rto, focalizzando l'attenzione sulle sue componenti principali: la piattaforma meccatronica e l'abitacolo, l'ambiente virtuale e la sensoristica associata. Nel dettaglio: il Capitolo 1 introduce la tematica trattata nel deliverable, ossia la progettazione, dal punto di vista tecnico, del simulatore del progetto Rip@rto. Il Capitolo 2 descrive brevemente il valutatore FIAT, ossia lo strumento attualmente a disposizione presso il Centro Protesi di Budrio per la valutazione delle capacita di guida. Il Capitolo 3 presenta il lavoro fatto fino a questo momento per la definizione delle specifiche tecniche del simulatore, in particolare per quello che riguarda le sue componenti principali: la piattaforma meccatronica e l'abitacolo (?3.13.2), l'ambiente virtuale (?3.2), i sensori (?3.3); questi ultimi sono distinti in sistema EEG per la misura del carico cognitivo (?3.3.1) e sensori indossabili per la misura dello stress (?3.3.2). Il Capitolo 4 presenta le specifiche tecniche dell'altro risultato del progetto Rip@rto, ossia il sistema a supporto delle decisioni, che aiutera l'operatore nella scelta migliore degli ausili. Infine, il Capitolo 5 trae le conclusioni del lavoro svolto e delinea le azioni future.	2021	2021	MALOSIO MATTEO, SPOLADORE DANIELE, COLOMBO VERA MARIA, MONDELLINI MARTA, DAO LE ANH, PIROVANO ILEANA, SANTINI FRANCESCA, TAURO GIOVANNI, REDAELLI DAVIDE FELICE, RIZZO GIOVANNA, GRECI LUCA, MASTROPIETRO ALFONSO, ARLATI SARA	Simulatore, realta virtuale, piattaforma meccatronica, disabilita
471792	Altro prodotto	It's all relative, just look at the ratios!	Maria Lea Correa Leite	This is a blog post (7/02/2022) included in the "Nutrition Society Paper of the Month Collection" - CambridgeCore blog	2022	2022	CORREA LEITE MARIA LEA	dietary data, compositional data, log-ratio transformations
454704	Altro prodotto	Medicina di Precisione in Pediatria - Biotecnologie e applicazioni per lo sviluppo e la salute	Ferrante Giuliana, La Grutta Stefania, Liguori Maria, Mauri Pierluigi, Montirosso Rosario	Evento per la presentazione di alcune tecnologie innovative, applicate alla biomedicina, e particolarmente interessanti nell'ambito pediatrico. Le presentazioni, tenute da relatori esperti nelle tematiche selezionate, non vogliono essere esaustive degli argomenti, ma come stimolo per sviluppare l'integrazione tra metodologie innovative e applicazioni in pediatria. Tra le tecnologie verranno presentate quelle riguardanti la gestione del campione, dalla raccolta alla conservazione e gestione, le metodologie omiche, in grado di definire profili molecolari (big data), aumentando notevolmente la precisione nella caratterizzazione degli stati fiso-patologici; inoltre, si tratteranno nuovi sistemi di delivery, particolarmente indicati per i bambini. Negli ultimi anni un numero crescente di ricerche pediatriche ha applicato tecniche molecolari ad alta risoluzione e analisi epigenetiche ai disturbi del neurosviluppo. Questa sezione si propone di presentare alcune aree di applicazione della biologia molecolare e computazionale alle patologie del neurosviluppo e nei neonati ad alto rischio di neurosviluppo atipico. La Medicina di Precisione nel campo della pneumologia pediatrica ha ricevuto un notevole impulso nel corso degli ultimi anni anche grazie allo sviluppo e all'applicazione delle metodologie omiche. In tale contesto saranno affrontate tematiche innovative relative all'uso delle biotecnologie basate sulle scienze omiche e utili ad una gestione personalizzata del bambino con malattie respiratorie croniche in ambito predittivo, diagnostico e terapeutico. Verranno inoltre affrontati temi di grande attualita nell'ambito delle malattie neuropsichiatriche quali: l'impiego delle omiche per la diagnosi, e le nuove terapie geniche, nelle malattie neuromuscolari dell'eta evolutiva; la ricerca di biomarcatori per il monitoraggio delle malattie neuroinfiammatorie del bambino, nella prospettiva dello sviluppo di una Medicina Personalizzata.	2021	2021	LIGUORI MARIA, LA GRUTTA STEFANIA, MAURI PIETRO LUIGI	Medicina di precisione
467635	Rapporto di progetto (Project report)	D4.1 Protocollo di sperimentazione	Sara Arlati, Vera Colombo, Luca Greci, Matteo Malosio, Marta Mondellini, Giovanni Tauro, Alfonso Mastropietro, Ileana Pirovano, Carla Dei, Mattia Chiappini, Gianluigi Reni, Fabio Storm	In questo deliverable si riportano i protocolli di alcuni studi gia condotti o da finalizzare nel corso del progetto Rip@rto. Il deliverable sara poi aggiornato piu avanti quando sara possibile stilare il protocollo completo per la validazione del prototipo di Rip@rto. A causa dei ritardi nell'approvvigionamento della piattaforma, infatti, il gruppo di lavoro ha deciso di pianificare e svolgere una serie di esperimenti preliminari volti allo studio di singole componenti del sistema. Questi studi, oltre ad offrire uno spunto per la scelta di alcune tecnologie e sensori, consentono anche di valutare l'influenza del setup sui segnali fisiologici di interesse e di fare alcune valutazioni preliminari rispetto all'interazione dell'utente con la tecnologia, sia dal punto di vista oggettivo, sia dal punto di vista soggettivo.	2022	2022	COLOMBO VERA MARIA, MONDELLINI MARTA, PIROVANO ILEANA, TAURO GIOVANNI, MALOSIO MATTEO, GRECI LUCA, MASTROPIETRO ALFONSO, ARLATI SARA	simulatore, guida, sperimentazione, EEG, sensori
468924	Nota a sentenza	Author Correction: Genome sequencing of Prototheca zopfii genotypes 1 and 2 provides evidence of a severe reduction in organellar genomes (Scientific Reports, (2018), 8, 1, (14637), 10.1038/s41598-018-32992-0)	Severgnini, Marco, Lazzari, Barbara, Capra, Emanuele, Chessa, Stefania, Luini, Mario, Bordoni, Roberta, Castiglioni, Bianca, Ricchi, Matteo, Cremonesi, Paola	The original version of this Article contained errors in the Materials and Methods section where the donation of the P. zopfii genotype 2 (SAG 2021) was incorrectly attributed to Dr. Jagielski, University of Warsaw (Poland). In the Materials and Methods section, under the subheading 'Strains and culture conditions', "P. zopfii genotype 1 (SAG 2063) was obtained from the Culture Collection of Algae at Gottingen University ("Sammlung von Algenkulturen der Universitat Gottingen", SAG, Gottingen, Germany). P. zopfii genotype 2 (SAG 2021) was kindly donated by Dr. Jagielski, University of Warsaw (Poland)." now reads: "P. zopfii genotype 1 (SAG 2063) and P. zopfii genotype 2 (SAG 2021) were obtained from the Culture Collection of Algae at Gottingen University ("Sammlung von Algenkulturen der Universitat Gottingen", SAG, Gottingen, Germany)."	Scientific reports (Nature Publishing Group) 12 (2022).	2022	CASTIGLIONI BIANCA MARIA ELISABETTA, BORDONI ROBERTA, SEVERGNINI MARCO, CREMONESI PAOLA, CHESSA STEFANIA, CAPRA EMANUELE	Prototheca, Organelles, sequencing	10.1038/s41598-022-09754-0
467637	Rapporto di progetto (Project report)	D.5.1 Rapporto I anno	Sara Arlati, Vera Colombo, Le Anh Dao, Luca Greci, Matteo Malosio, Marta Mondellini, Davide Felice Redaelli, Francesca Santini, Daniele Spoladore, Giovanni Tauro, Alfonso Mastropietro, Ileana Pirovano, Mattia Chiappini, Gianluigi Reni, Fabio Storm	Rapporto delle attivita svolte nel corso del primo anno del progetto Rip@rto.	2021	2021	SPOLADORE DANIELE, COLOMBO VERA MARIA, MONDELLINI MARTA, DAO LE ANH, PIROVANO ILEANA, SANTINI FRANCESCA, TAURO GIOVANNI, REDAELLI DAVIDE FELICE, MALOSIO MATTEO, GRECI LUCA, MASTROPIETRO ALFONSO, ARLATI SARA	simulatore, guida, realta virtuale, EEG, sensori
477372	Rapporto tecnico	Implementation of a drug discovery pipeline on the D4Science platform	Orro A., D'Ursi P., Fossa P., Candela L., Panichi G.	This report documents the implementation of drug discovery pipeline in the D4Science platform realised in the context of the EOSC-Pillar project. In particular, it documents the pipeline and its constituents. Moreover, it describes how this pipeline has been integrated into the D4Science platform and exploited to create a dedicated Virtual Research Environment facilitating its exploitation and promoting a collaborative oriented approach for screening activities.	ISTI Technical Report, ISTI-2023-TR/001, 2023	2023	CANDELA LEONARDO, ORRO ALESSANDRO, PANICHI GIANCARLO, D'URSI PASQUALINA	Drug Discovery, D4Science, Virtual Research Environment