Using multiple reference ontologies: Managing composite annotations

There are a growing number of reference ontologies available across a variety of biomedical domains and current research focuses on their construction, organization and use. An important use case for these ontologies is annotation—where users create metadata that access concepts and terms in reference ontologies. We draw on our experience in physiological modeling to present a compelling use case that demonstrates the potential complexity of such annotations. In the domain of physiological biosimulation, we argue that most annotations require the use of multiple reference ontologies. We suggest that these “composite” annotations should be retained as a repository of knowledge about post-coordination that promotes sharing and interoperation across biosimulation models

Cos’è successo a Siena il 26 maggio 1798 ? Un’iniziativa interdisciplinare per la valutazione del possibile impatto di un futuro «massimo sismico» su una città-monumento

L’importanza di un terremoto non dipende solo dalla sua intensità epicentrale. Quello del 26 maggio 1798 (Io VII MCS secondo CPTI04) non si può dire una catastrofe ma è di certo un evento «strategico». Si tratta, infatti, del massimo terremoto storico conosciuto per Siena, che è una delle maggiori attrazioni turistiche e quindi uno dei luoghi più frequentati di questo paese. Nell’ultimo ventennio il terremoto del 1798 è stato più volte studiato, sia da sismologi storici nell’ambito delle attività di revisione del catalogo PFG promosse dal GNDT e dall’ING/INGV (Castelli e Camassi, 1995; Castelli et al., 1996; Boschi et al., 1997; Boschi et al., 2000), sia da storici dell’architettura (Gennari, 2005). Siamo ancora lontani dall’aver completamente esplorato la copiosissima documentazione storica potenzialmente utile per una ricostruzione degli effetti di questo terremoto nel centro urbano senese. Tuttavia il campione reso disponibile dagli studi fatti finora è abbastanza significativo da rendere possibile l’avvio di un progetto di microzonazione del centro storico senese e di una serie di indagini miranti a comprendere cosa realmente successe a Siena il 26 maggio 1798 e, per conseguenza, quali effetti ci si possa attendere in occasione di un futuro terremoto di analoga portata. Il centro storico senese ha infatti conservato, almeno nelle grandi linee, una fisionomia molto simile a quella che aveva del 1798 e questa circostanza offre l’opportunità di attualizzare l’esperienza del terremoto del 1798 contribuendo alla identificazione delle eventuali criticità attese in caso di terremoti futuri. Si è perciò creato un gruppo di studio interdisciplinare (geofisica, architettura, sismologia storica, ingegneria sismica, geologia, ecc.) che ha cominciato a predisporre gli elementi necessari per questa ricostruzione. La base di dati storici di cui si dispone comprende descrizioni di danno più o meno dettagliate per circa seicento edifici senesi, su un migliaio da cui era composto il centro urbano nel 1798. Questo campione comprende sia edifici monumentali o comunque di vaste proporzioni (palazzi gentilizi e case di abitazione multipla, chiese, conventi, opifici) sia edifici non monumentali. Il nostro primo scopo è una ricostruzione dettagliata della distribuzione del danno del terremoto del 1798 nell’area urbana. Utilizzando cartografia storica pressoché coeva al terremoto (cfr. Gennari, 2005) e grazie all’impiego di un GIS, è stato possibile trasporre le informazioni storiche sottoforma di carte tematiche (Danno, Vulnerabilità, Interventi richiesti, eccetera). Le Figg. 1 e 2 presentano due esempi di tematismi derivati da dati archivistici. In parallelo a questa analisi verrà svolta una indagine a campione su una ventina di edifici rappresentativi per i quali si eseguiranno stime di comportamento dinamico con la tecnica del tremore sismico ambientale. A completamento della caratterizzazione della risposta sismica dei terreni nell’area del centro storico saranno svolte analisi geologiche e sismiche per definire le aree in cui l’assetto del sottosuolo rende ipotizzabili fenomeni di amplificazione del moto sismico del suolo. Tutti i risultati verranno raccolti in una base dati comune e implementati nel GIS (Figura 2) L’analisi congiunta dei dati di danno (opportunamente interpretati in termini di risposta sismica locale utilizzando il metodo proposto da Goretti e Dolce, 2004; Goretti, 2006) e delle analisi geofisiche e geologiche permetterà di individuare quelle parti del patrimonio edilizio storico più esposte a danno in caso di futuri eventi sismici

The TNG Near Infrared Camera Spectrometer

NICS (acronym for Near Infrared Camera Spectrometer) is the near-infrared cooled camera-spectrometer that has been developed by the Arcetri Infrared Group at the Arcetri Astrophysical Observatory, in collaboration with the CAISMI-CNR for the TNG (the Italian National Telescope Galileo at La Palma, Canary Islands, Spain). As NICS is in its scientific commissioning phase, we report its observing capabilities in the near-infrared bands at the TNG, along with the measured performance and the limiting magnitudes. We also describe some technical details of the project, such as cryogenics, mechanics, and the system which executes data acquisition and control, along with the related software.Comment: 7 pages, 5 figures, compiled with A&A macros. A&A in pres

The Messinian "Calcare di Base" (Sicily, Italy) revisited

Three different types of carbonate deposits are included within the "Calcare di Base",commonly envisaged to record the Messinian salinity crisis onset: type 1 consists of sulphur-bearinglimestones, representing the biogenic product of bacterial sulphate reduction after original gypsum;type 2 comprises dm-thick laminated dolomitic limestones interbedded with diatomites, sapropels andmarls found at the top the Tripoli Formation; type 3, the most common variety, consists of m-thickbrecciated limestones interbedded with shales and clastic gypsum.Type 3 shows sedimentary features suggesting a clastic origin and deposition from high- to lowdensitygravity flows; thus, these deposits can be regarded as an end-member of a large variety ofevaporite-bearing gravity flow deposits, with a dominant carbonate component.The genetic and stratigraphic characterization of these carbonates has strong implications for a bettercomprehension of Messinian events; the three types of Calcare di Base seem to have formed duringdifferent stages of the Messinian salinity crisis (MSC). Type 2 formed in the first stage (5.96-5.60 Ma),and is the only type that can be regarded as the Lower Gypsum time-equivalent. Type 3 was depositedin the second stage (5.60-5.55 Ma) and its base is associated with a regional-scale hiatus and erosion(Messinian erosional surface). Type 1 formed even later, likely in post-Messinian time, throughdiagenetic processes affecting resedimented gypsum deposited during the second stage of the MSC.It follows that not all the Calcare di Base deposits record the onset of the Messinian salinity crisis, ascommonly thought. Thus, a detailed facies characterization of these carbonate deposits is fundamental for both stratigraphic reconstructions and a better comprehension of Messinian events

Isolation of a Vibrio parahaemolyticus pandemic strain from a marine water sample obtained in the northern Adriatic

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Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology

We introduce and define the Ontology of Physics for Biology (OPB), a reference ontology of physical principles that bridges the gap between bioinformatics modeling of biological structures and the biosimulation modeling of biological processes. Whereas modeling anatomical entities is relatively wellstudied, representing the physics-based semantics of biosimulation and biological processes remains an open research challenge. The OPB bridges this semantic gap--linking the semantics of biosimulation mathematics to structural bio-ontologies. Our design of the OPB is driven both by theory and pragmatics: we have applied systems dynamics theory to build an ontology with pragmatic use for annotating biosimulation models

Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies

Abstract—Current methods for annotating biomedical data resources rely on simple mappings between data elements and the contents of a variety of biomedical ontologies and controlled vocabularies. Here we point out that such simple mappings are inadequate for large-scale multiscale, multidomain integrative “virtual human” projects. For such integrative challenges, we describe a “composite annotation” schema that is simple yet sufficiently extensible for mapping the biomedical content of a variety of data sources and biosimulation models to available biomedical ontologies

Remarks on the Messinian evaporites of Zakynthos Island (Ionian Sea, Eastern Mediterranean)

Detailed mapping of the Neogene deposits on Zakynthos Island shows that the Messinian primary evaporite basins, formed over Ionian basement, are delimited by the westernmost outcrop of the Triassic evaporitic diapirs, located west of the Kalamaki-Argasi Messinian gypsum unit. The post-Miocene external Ionian thrust is emplaced west of the Triassic diapirs. Planktonic foraminifera biostratigraphy indicates that primary evaporite accumulation took place probably during the first stage of the Messinian salinity crisis (5.96-5.60 Ma), in shallower parts of a foreland basin, formed over the Pre-Apulian and the Ionian zone basement. Establishment of these depositional environments, before the Ionian thrust emplacement, was probably due to the particularities of the foreland basin, which extended from the external Ionian to the internal Pre-Apulian zone. Field observations, borehole data and an onshore seismic profile show that the Neogene sediments over the Pre-Apulian basement correspond to the foredeep through forebulge domain of the foreland basin, as it is documented from their spatial thickness distribution. In contrast, the Neogene sediments over the Ionian basement correspond to the wedge top of the foreland basin, which was less subsiding, as it is deduced by their reduced thickness. This lower subsidence rate was the result of the concurrent diapiric movements of the Ionian Triassic evaporites. In Agios Sostis area, located over Pre-Apulian basement, the Neogene sequence is intercalated by decametre-thick resedimented blocks consisting of shallow water selenite. To the southeast, this mass-wasting Messinian gypsum passes to mainly gypsum turbidite. In Kalamaki-Argasi area, located over Ionian basement, the shallow water environment led to the deposition of the observed primary gypsum. Erosion of the primary gypsum of both forebulge and wedge top supplied the foreland basin’s depocenter with gypsum turbidites. Η λεπτομερής χαρτογράφηση των Νεογενών αποθέσεων της Ζακύνθου δείχνει ότι οι λεκάνες πρωτογενούς Μεσσήνιας εβαποριτικής απόθεσης, που σχηματίστηκαν πάνω σε Ιόνιο υπόβαθρο, οριοθετούνται από τη δυτικότερη εμφάνιση των Τριαδικών εβαποριτικών διάπειρων (δυτικά της Μεσσήνιας ενότητας γύψου Καλαμάκι-Αργάσι). Η μετα-Μειοκαινική εξωτερική Ιόνια επώθηση τοποθετείται δυτικά αυτών των Τριαδικών διάπειρων. Βιοστρωματογραφική ανάλυση των συναθροίσεων πλαγκτονικών τρηματοφόρων στα Νεογενή ιζήματα δείχνει ότι η συσσώρευση πρωτογενούς εβαπορίτη έλαβε χώρα πιθανά κατά το πρώτο στάδιο της κρίσης αλμυρότητας του Μεσσηνίου (5.96-5.60 Εκατ.χρ.), στα αβαθέστερα τμήματα της λεκάνης προχώρας, η οποία σχηματίστηκε πάνω στο Προ-Απούλιο και Ιόνιο αλπικό υπόβαθρο. Ο σχηματισμός των περιβαλλόντων ιζηματογένεσης, πριν από την Ιόνια επώθηση, πιθανά οφείλεται στις ιδιαιτερότητες της λεκάνης προχώρας, η οποία εκείνο το διάστημα εκτείνονταν από την εξωτερική Ιόνια ως την εσωτερική Προ-Απούλια ζώνη. Νέα δεδομένα υπαίθρου, σε συνδυασμό με τη βιοστρωματογραφία, τα στοιχεία γεωτρήσεων και μία διαθέσιμη σεισμική τομή δείχνουν ότι τα Νεογενή ιζήματα πάνω στο Προ-Απούλιο υπόβαθρο αντιστοιχούν στον τμήμα της λεκάνης προχώρας, από το προβύθισμα (foredeep) ως την πρόσθια ανύψωση (forebulge), όπως αυτό διαπιστώνεται από την χωρική κατανομή του πάχους τους. Αντίθετα, τα Νεογενή ιζήματα πάνω στο Ιόνιο υπόβαθρο αντιστοιχούν στο τμήμα της λεκάνης προχώρας που βρίσκεται πάνω στο μετωπικό πρίσμα της ορογένεσης (wedge top), το οποίο βυθίζονταν λιγότερο όπως συνάγεται από το ελαττωμένο πάχος των ιζημάτων. Ο μικρότερος ρυθμός βύθισης οφείλεται στις διαπειρικές κινήσεις των Τριαδικών εβαποριτών. Στη Νεογενή ακολουθία, που βρίσκεται πάνω σε Προ-Απούλιο υπόβαθρο (περιοχή Άγιος Σώστης), παρεμβάλλονται επανιζηματοποιημένα μπλοκ δεκαμετρικού πάχους αποτελούμενα από σεληνίτη μικρού βάθους απόθεσης. Προς νότο, αυτή η βαρυτικά μεταφερόμενη μάζα της Μεσσήνιας γύψου μεταπίπτει κυρίως σε τουρβιδιτική γύψο. Στην περιοχή Καλαμάκι-Αργάσι που βρίσκεται πάνω σε Ιόνιο υπόβαθρο, το αβαθές περιβάλλον οδήγησε στην απόθεση της παρατηρούμενης πρωτογενούς γύψου. Η διάβρωση της πρωτογενούς γύψου τόσο της πρόσθιας ανύψωσης όσο και του μετωπικού πρίσματος επώθησης τροφοδότησαν το προβύθισμα της λεκάνης προχώρας με τουρβιδίτες γύψου

May car washing represent a risk for Legionella infection?

Background. Legionella is a ubiquitous Gram-negative bacterium naturally found in aquatic environments. It can pose a health problem when it grows and spreads in man-made water systems. Legionella pneumophila is the most common cause of Legionnaires\u2019 disease nowadays, a community-acquired pneumonia with pulmonary symptoms and chest radiography no different from any other form of infectious pneumonia. Legionella monitoring is important for public health reasons, including the identification of unusual environmental sources of Legionella. Methods. We report two cases of Legionnaires\u2019 disease associated with two different car wash installations in the province of Vicenza, in the Veneto region, northeastern Italy. Patients were not employees of the car wash installations, but users of the service. In both cases, Legionella antigen was detected in urine using the Alere BinaxNOW\uae Legionella Urinary Antigen, and Legionella antibodies were detected in serum using SERION ELISA classic Legionella pneumophila 1-7 IgG and IgM. Water samples were also analyzed as part of the surveillance program for Legionella prevention and control in compliance with the Italian guidelines. Results. Both patients had clinical symptoms and chest radiography compatible with pneumonia, and only one of them had diabetes as a risk factor. Legionella urinary antigen and serological test on serum samples were positive for Legionella in both patients, even if much slighter in the case A due to the retrospective serological investigation performed a year later the episode and after the second clinical case occurred in the same district. The environmental investigations highlighted two different car wash plants as potential source of infection. A certified company using shock hyperchlorination was asked to disinfect the two plants and, subsequently, control samples resulted negative for Legionella pneumophila. Conclusions. Any water source producing aerosols should be considered at risk for the transmission of Legionella bacteria, including car wash installations frequently used by a large number of customers and where poor maintenance probably creates favorable conditions for Legionella overgrowth and spreading. Additional research is needed to ascertain optimal strategies for Legionella monitoring and control, but environmental surveillance, paying careful attention to possible unconventional sources, should remain an important component of any Legionnaires\u2019 disease prevention program. Additionally, all available diagnostic methods would be recommended for the confirmation of all cases even in the event of non-serogroup 1 Legionella pneumophila infection, probably underestimated at this time

Radiation test and application of FPGAs in the ATLAS Level 1 Trigger

The front-end system of the Silicon Drift Detectors (SDDs) of the ALICE experiment is made of two ASICs. The first chip performs the preamplification, temporary analogue storage and analogue-to-digital conversion of the detector signals. The second chip is a digital buffer that allows for a significant reduction of the connection from the front-end module to the outside world. In this paper, the results achieved on the first complete prototype of the front-end system for the SDDs of ALICE are presented