APPROCCI BIOINFORMATICI PER L’ANALISI DI DATI DI NEXT GENERATION SEQUENCING IN OPHRYS (ORCHIDACEAE)

Il progetto di dottorato è stato finalizzato ad ottimizzare tecniche bioinformatiche in un contesto evolutivo e di assemblare dei genomi per contribuire all’arricchimento delle banche dati per il genere non-modello Ophrys (Orchidaceae). Questo genere rappresenta una sfida aperta per i ricercatori, in quanto è caratterizzato da una rapida radiazione evolutiva che ha impedito una chiara identificazione delle specie utilizzando le tradizionali tecniche genetiche. Nel corso del Dottorato sono stati dunque affrontati due casi di studio: l’assemblaggio e l’arricchimento delle banche dati con nuovi genomi plastidiali di due specie appartenenti al genere Ophrys ed un’analisi critica più approfondita al fine di ottimizzare l’analisi dei dati GBS in un complesso di specie appartenenti al genere Ophrys. L’approccio seed-extend si è rivelato il migliore per l’assemblaggio dei genomi plastidiali. I genomi presentano 127 geni distinti di cui 25 sono duplicati perché presenti nell’Inverted Repeat. In una specie, il gene ndhF è risultato essere troncato mentre nell’altra il gene ycf1 è risultato essere parzialmente duplicato. Questo riarrangiamento ha causato lo spostamento della giunzione tra le regioni Inverted Repeat e la Small Single Copy. Entrambi i genomi plastidiali hanno 213 loci microsatellitari di cui 67 sono polimorfici e possono essere usati per analisi filogeografiche. L’analisi critica dei dati GBS è stata effettuata attraverso l’utilizzo di diverse strategie di filtraggio dei dati mancanti e dei loci eterozigoti. Usando il genoma plastidiale di una specie come riferimento, è stato possibile distinguere sei aplotipi che hanno consentito l’individuazione di due cladi filetici. Questo risultato è in linea con un’analisi filogenetica effettuata eliminando tutti i loci eterozigoti e selezionando quelli condivisi da almeno il 70% degli individui. Diversamente introducendo nell’analisi i loci eterozigoti ed analizzando quelli condivisi da almeno il 30% degli individui è stato possibile distinguere le specie. Nel complesso questi due casi di studio hanno consentito di testare e individuare strategie di analisi bioinformatica di dati genomici in un contesto evolutivo e di assemblare dei genomi per contribuire all’arricchimento delle banche dati. Tali tecniche potranno essere utilizzate per l’annotazione di genomi organellari in specie non modello e per l’analisi di dati GBS

A derivative-free approach for a simulation-based optimization problem in healthcare

Hospitals have been challenged in recent years to deliver high quality care with limited resources. Given the pressure to contain costs,developing procedures for optimal resource allocation becomes more and more critical in this context. Indeed, under/overutilization of emergency room and ward resources can either compromise a hospital's ability to provide the best possible care, or result in precious funding going toward underutilized resources. Simulation--based optimization tools then help facilitating the planning and management of hospital services, by maximizing/minimizing some specific indices (e.g. net profit) subject to given clinical and economical constraints. In this work, we develop a simulation--based optimization approach for the resource planning of a specific hospital ward. At each step, we first consider a suitably chosen resource setting and evaluate both efficiency and satisfaction of the restrictions by means of a discrete--event simulation model. Then, taking into account the information obtained by the simulation process, we use a derivative--free optimization algorithm to modify the given setting. We report results for a real--world problem coming from the obstetrics ward of an Italian hospital showing both the effectiveness and the efficiency of the proposed approach

Simple Dynamics for Plurality Consensus

We study a \emph{Plurality-Consensus} process in which each of $n$ anonymous agents of a communication network initially supports an opinion (a color chosen from a finite set $[k]$). Then, in every (synchronous) round, each agent can revise his color according to the opinions currently held by a random sample of his neighbors. It is assumed that the initial color configuration exhibits a sufficiently large \emph{bias} $s$ towards a fixed plurality color, that is, the number of nodes supporting the plurality color exceeds the number of nodes supporting any other color by $s$ additional nodes. The goal is having the process to converge to the \emph{stable} configuration in which all nodes support the initial plurality. We consider a basic model in which the network is a clique and the update rule (called here the \emph{3-majority dynamics}) of the process is the following: each agent looks at the colors of three random neighbors and then applies the majority rule (breaking ties uniformly). We prove that the process converges in time $\mathcal{O}( \min\{ k, (n/\log n)^{1/3} \} \, \log n )$ with high probability, provided that $s \geqslant c \sqrt{ \min\{ 2k, (n/\log n)^{1/3} \}\, n \log n}$. We then prove that our upper bound above is tight as long as $k \leqslant (n/\log n)^{1/4}$. This fact implies an exponential time-gap between the plurality-consensus process and the \emph{median} process studied by Doerr et al. in [ACM SPAA'11]. A natural question is whether looking at more (than three) random neighbors can significantly speed up the process. We provide a negative answer to this question: In particular, we show that samples of polylogarithmic size can speed up the process by a polylogarithmic factor only.Comment: Preprint of journal versio

Uncovering the Social Deficits in the Autistic Brain. A Source-Based Morphometric Study

Autism is a neurodevelopmental disorder that mainly affects social interaction and communication. Evidence from behavioral and functional MRI studies supports the hypothesis that dysfunctional mechanisms involving social brain structures play a major role in autistic symptomatology. However, the investigation of anatomical abnormalities in the brain of people with autism has led to inconsistent results. We investigated whether specific brain regions, known to display functional abnormalities in autism, may exhibit mutual and peculiar patterns of covariance in their gray-matter concentrations. We analyzed structural MRI images of 32 young men affected by autistic disorder (AD) and 50 healthy controls. Controls were matched for sex, age, handedness. IQ scores were also monitored to avoid confounding. A multivariate Source-Based Morphometry (SBM) was applied for the first time on AD and controls to detect maximally independent networks of gray matter. Group comparison revealed a gray-matter source that showed differences in AD compared to controls. This network includes broad temporal regions involved in social cognition and high-level visual processing, but also motor and executive areas of the frontal lobe. Notably, we found that gray matter differences, as reflected by SBM, significantly correlated with social and behavioral deficits displayed by AD individuals and encoded via the Autism Diagnostic Observation Schedule scores. These findings provide support for current hypotheses about the neural basis of atypical social and mental states information processing in autism

Maximum Principle and generalized principal eigenvalue for degenerate elliptic operators

We characterize the validity of the Maximum Principle in bounded domains for fully nonlinear degenerate elliptic operators in terms of the sign of a suitably defined generalized principal eigenvalue. Here, the maximum principle refers to the property of non-positivity of viscosity subsolutions of the Dirichlet problem. The new notion of generalized principal eigenvalue that we introduce here allows us to deal with arbitrary type of degeneracy of the elliptic operators. We further discuss the relations between this notion and other natural generalizations of the classical notion of principal eigenvalue, some of which have been previously introduced for particular classes of operators

Rotational arherectomy in the distal left anterior descending coronary artery through an internal mammary artery graft.

We report the case of a 53-year-old white man who began complaining of dyspnoea and angina 19 months after coronary artery bypass graft surgery. Coronary angiography revealed the presence of a long and critical stenosis in the native left anterior descending coronary artery, shortly after distal anastomosis of the left internal mammary artery. After failed predilatations with standard or cutting balloons, we successfully used the rotablator system, which allowed us to implant a bare-metal stent in the native left anterior descending coronary artery. However, stent deployment caused long linear graft dissection, which was reduced by drug-eluting stent implantation in the proximal and distal segments of the left internal mammary artery

Sviluppo di una micro CT con sorgente Quasi-Monocromatica Multi-Energy per lo studio in vivo della crescita e della metastasi tumorale

Un innovativo micro scanner CT per piccolo animali – basato su di una sorgente che genera una coppia di fasci X Quasi-Monocromatici paralleli con diverse energie selezionabili – è in corso di installazione e caratterizzazione al Dipartimento di Fisica dell’Università di Bologna. Lo scopo della ricerca è quello di effettuare l’imaging radiologico in vivo del tessuto tumorale e/o dei pattern di neo-angiogenesi in una fase diagnostica precoce realizzando la separazione del tessuto patologico da quello sano per mezzo della tecnica multi-energy che consiste nell’utilizzo di due o più fasci di raggi X quasi-monocromatici in sostituzione dell’unico fascio policromatico utilizzato nella radiologia convenzionale. Lo strumento consentirà inoltre lo studio, sui topi, della crescita tumorale e della formazione delle metastasi per differenti tipologie di tumore. Per la diagnosi precoce del tumore è essenziale essere in grado di rivelare i cambiamenti tissutali precancerosi, come la neo-angiogenesi. Si tratta di un meccanismo che si verifica in una fase iniziale dello sviluppo della patologia ed è dovuto alla produzione di molecole che stimolano la creazione di nuovi vasi sanguigni per alimentare la crescita delle cellule cancerose. Come dimostrato in precedenti studi di fattibilità [1], un sistema di imaging basato su due fasci di raggi X quasi-monocromatici di differenti energie fornisce maggiore sensibilità nella rivelazione di basse concentrazioni di mezzo di contrasto iodato rispetto ai tradizionali apparati RX con fascio policromatico. La K-edge dual energy radiology è una tecnologia potenzialmente in grado di rivelare il processo di neo-angiogenesi tumorale in uno stadio precoce quando la strumentazione convenzionale non dispone di sufficiente sensibilità. Inoltre, la possibilità di selezionare le energie dei fasci quasi-monocromatici consente l’applicazione della Multi-Energy Quasi-MonochromaticRadiology: selezionando opportunamente le energie è possibile esaltare le differenze fra i coefficienti di attenuazione lineare del tessuto patologico rispetto a quello sano aumentando il contrasto della patologia. Infatti, la tecnica multi-energy consente di ricostruire il numero atomico efficace e persino la composizione chimica del tessuto irradiato. Tuttavia, per ottenere questo risultato, si dovrebbero conoscere le bande di energia in cui l’assorbimento dei raggi X da parte del tessuto tumorale eventualmente differisce significativamente da quello dei tessuti sani. Per questo motivo è stata iniziata una sistematica caratterizzazione radiologica di molti tipi di tessuti sani e neoplastici, murini e umani allo scopo di costituire un catalogo delle finestre di energia in cui sarà possibile applicare la metodica multi-energy

Comparison between balloon angioplasty and additional coronary stent implantation for the treatment of drug-eluting stent restenosis: 18-month clinical outcomes

OBJECTIVE: To evaluate the long-term outcomes after different modalities of treatment of drug-eluting stent (DES) in-stent restenosis (ISR) in a 'real world' setting. METHODS: Actually, few and conflicting data are available about the management of in-stent restenosis (ISR) after DES implantation. In our 'real world' registry 1082 consecutive patients who received a DES implantation were included. At 9-month angiographic follow-up, 93 patients presented a DES ISR that was treated with 'homo-DES' (HMD) (N = 27), 'hetero-DES' (HTD) (N = 19) and conventional balloon angioplasty (POBA) (N = 47). We evaluated the clinical outcomes in terms of major adverse cardiac event (MACE) (death, myocardial infarction and target vessel revascularization) at 18 months. RESULTS: There was no difference for clinical and angiographic characteristics between the three groups, except for the presence of silent ischaemia as clinical presentation (7.7 HMD vs. 2.2% POBA; P = 0.0001). No late stent thrombosis was found. At 18-month clinical follow-up patients treated with HMD, HTD and POBA presented a rate of MACE of 10.2, 0 and 8.7%, respectively (P = NS). Kaplan-Meier survival probability showed that HTD and POBA treatment tended to have more favourable outcomes at 18 months than the HMD treatment. CONCLUSION: In our registry, POBA seems to be as effective as other DES implantations in cases of DES ISR, especially in cases of focal type (Mehran classification IA, IC), in terms of long-term outcomes

The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids

Sexually deceptive orchids of the genus Ophrys may rapidly evolve by adaptation to pollinators. However, understanding of the genetic basis of potential changes and patterns of relationships is hampered by a lack of genomic information. We report the complete plastid genome sequences of Ophrys iricolor and O. sphegodes, representing the two most species-rich lineages of the genus Ophrys. Both plastomes are circular DNA molecules (146754 bp for O. sphegodes and 150177 bp for O. iricolor) with the typical quadripartite structure of plastid genomes and within the average size of photosynthetic orchids. 213 Simple Sequence Repeats (SSRs) (31.5% polymorphic between O. iricolor and O. sphegodes) were identified, with homopolymers and dipolymers as the most common repeat types. SSRs were mainly located in intergenic regions but SSRs located in coding regions were also found, mainly in ycf1 and rpoC2 genes. The Ophrys plastome is predicted to encode 107 distinct genes, 17 of which are completely duplicated in the Inverted Repeat regions. 83 and 87 putative RNA editing sites were detected in 25 plastid genes of the two Ophrys species, all occurring in the first or second codon position. Comparing the rate of nonsynonymous (dN) and synonymous (dS) substitutions, 24 genes (including rbcL and ycf1) display signature consistent with positive selection. When compared with other members of the orchid family, the Ophrys plastome has a complete set of 11 functional ndh plastid genes, with the exception of O. sphegodes that has a truncated ndhF gene. Comparative analysis showed a large co-linearity with other related Orchidinae. However, in contrast to O. iricolor and other Orchidinae, O. sphegodes has a shift of the junction between the Inverted Repeat and Small Single Copy regions associated with the loss of the partial duplicated gene ycf1 and the truncation of the ndhF gene. Data on relative genomic coverage and validation by PCR indicate the presence, with a different ratio, of the two plastome types (i.e. with and without ndhF deletion) in both Ophrys species, with a predominance of the deleted type in O. sphegodes. A search for this deleted plastid region in O. sphegodes nuclear genome shows that the deleted region is inserted in a retrotransposon nuclear sequence. The present study provides useful genomic tools for studying conservation and patterns of relationships of this rapidly radiating orchid genus