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Andreano E, Paciello I, Bardelli M, Tavarini S, Sammicheli C, Frigimelica E, Guidotti S, Torricelli G, Biancucci M, D’Oro U, Chandramouli S, Bottomley MJ, Rappuoli R, Finco O, Buricchi F. The respiratory syncytial virus (RSV) prefusion F-protein functional antibody repertoire in adult healthy donors. EMBO Mol Med 2021; 13:e14035. [PMID: 33998144 PMCID: PMC8185550 DOI: 10.15252/emmm.202114035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of death from lower respiratory tract infection in infants and children, and is responsible for considerable morbidity and mortality in older adults. Vaccines for pregnant women and elderly which are in phase III clinical studies target people with pre-existing natural immunity against RSV. To investigate the background immunity which will be impacted by vaccination, we single cell-sorted human memory B cells and dissected functional and genetic features of neutralizing antibodies (nAbs) induced by natural infection. Most nAbs recognized both the prefusion and postfusion conformations of the RSV F-protein (cross-binders) while a smaller fraction bound exclusively to the prefusion conformation. Cross-binder nAbs used a wide array of gene rearrangements, while preF-binder nAbs derived mostly from the expansion of B-cell clonotypes from the IGHV1 germline. This latter class of nAbs recognizes an epitope located between Site Ø, Site II, and Site V on the F-protein, identifying an important site of pathogen vulnerability.
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Affiliation(s)
- Emanuele Andreano
- Department of Life SciencesUniversity of SienaSienaItaly
- GSK VaccinesSienaItaly
- Present address:
Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
| | - Ida Paciello
- GSK VaccinesSienaItaly
- Present address:
Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
| | | | | | | | | | | | | | | | | | - Sumana Chandramouli
- GSK VaccinesRockvilleMDUSA
- Present address:
Moderna Therapeutics IncCambridgeMAUSA
| | | | - Rino Rappuoli
- GSK VaccinesSienaItaly
- Faculty of MedicineImperial CollegeLondonUK
- Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
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2
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Schneikart G, Tavarini S, Sammicheli C, Torricelli G, Guidotti S, D'Oro U, Finco O, Bardelli M. Dataset of antibody variable region sequence features inferred from a respiratory syncytial virus fusion protein-specific B cell receptor repertoire induced by natural infection of a healthy adult. Data Brief 2020; 33:106499. [PMID: 33225034 PMCID: PMC7666335 DOI: 10.1016/j.dib.2020.106499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/30/2020] [Indexed: 11/17/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the primary cause for acute lower respiratory syndrome in children younger than 5 years. Research on B cell repertoires and antibodies binding the RSV fusion protein (RSV F) is of major interest in the development of potential vaccine candidates and therapies. B cell receptors (BCRs) which have higher affinities for a specific antigen are preferentially selected for B cell clonal expansion in germinal center reactions. Consequently, antigen-specific BCR repertoires share common features, as for instance preferential variable gene usage, variable region mutation levels or lengths of the heavy chain complementarity-determining region 3. Since RSV repeatedly infects every person throughout life, memory B cells (MBC) expressing RSV F-binding BCRs circulate in the blood of healthy adults. This dataset of BCR variable region sequence features was derived from single cell-sorted RSV F-directed MBCs of a healthy adult blood donor [1]. The dataset was produced with publicly available data analysis software programs and scripts, which facilitates integration or comparison with antibody sequence repertoire data of different individuals derived with the same or comparable data analysis approaches and tools.
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Affiliation(s)
- Gerald Schneikart
- GSK, Via Fiorentina 1, 53100 Siena, Italy
- Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | | | | | | | | | - Ugo D'Oro
- GSK, Via Fiorentina 1, 53100 Siena, Italy
| | | | - Monia Bardelli
- GSK, Via Fiorentina 1, 53100 Siena, Italy
- Corresponding author.
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3
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Siena E, D'Aurizio R, Riley D, Tettelin H, Guidotti S, Torricelli G, Moxon ER, Medini D. In-silico prediction and deep-DNA sequencing validation indicate phase variation in 115 Neisseria meningitidis genes. BMC Genomics 2016; 17:843. [PMID: 27793092 PMCID: PMC5084427 DOI: 10.1186/s12864-016-3185-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/22/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The Neisseria meningitidis (Nm) chromosome shows a high abundance of simple sequence DNA repeats (SSRs) that undergo stochastic, reversible mutations at high frequency. This mechanism is reflected in an extensive phenotypic diversity that facilitates Nm adaptation to dynamic environmental changes. To date, phase-variable phenotypes mediated by SSRs variation have been experimentally confirmed for 26 Nm genes. RESULTS Here we present a population-scale comparative genomic analysis that identified 277 genes and classified them into 52 strong, 60 moderate and 165 weak candidates for phase variation. Deep-coverage DNA sequencing of single colonies grown overnight under non-selective conditions confirmed the presence of high-frequency, stochastic variation in 115 of them, providing circumstantial evidence for their phase variability. We confirmed previous observations of a predominance of variable SSRs within genes for components located on the cell surface or DNA metabolism. However, in addition we identified an unexpectedly broad spectrum of other metabolic functions, and most of the variable SSRs were predicted to induce phenotypic changes by modulating gene expression at a transcriptional level or by producing different protein isoforms rather than mediating on/off translational switching through frameshifts. Investigation of the evolutionary history of SSR contingency loci revealed that these loci were inherited from a Nm ancestor, evolved independently within Nm, or were acquired by Nm through lateral DNA exchange. CONCLUSIONS Overall, our results have identified a broader and qualitatively different phenotypic diversification of SSRs-mediated stochastic variation than previously documented, including its impact on central Nm metabolism.
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Affiliation(s)
| | - Romina D'Aurizio
- GSK Vaccines, 53100, Siena, Italy.,Present address: Institute of Informatics and Telematics and Institute of Clinical Physiology, National Research Council, 56124, Pisa, Italy
| | - David Riley
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Present address: Personal Genome Disgnostics inc., Baltimore, MD, 21224, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | | | | | - E Richard Moxon
- Medical Sciences Division, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, OX3 9DS, UK
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4
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Campisi E, Rinaudo CD, Donati C, Barucco M, Torricelli G, Edwards MS, Baker CJ, Margarit I, Rosini R. Serotype IV Streptococcus agalactiae ST-452 has arisen from large genomic recombination events between CC23 and the hypervirulent CC17 lineages. Sci Rep 2016; 6:29799. [PMID: 27411639 PMCID: PMC4944191 DOI: 10.1038/srep29799] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/21/2016] [Indexed: 11/10/2022] Open
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) causes life-threatening infections in newborns and adults with chronic medical conditions. Serotype IV strains are emerging both among carriers and as cause of invasive disease and recent studies revealed two main Sequence Types (STs), ST-452 and ST-459 assigned to Clonal Complexes CC23 and CC1, respectively. Whole genome sequencing of 70 type IV GBS and subsequent phylogenetic analysis elucidated the localization of type IV isolates in a SNP-based phylogenetic tree and suggested that ST-452 could have originated through genetic recombination. SNPs density analysis of the core genome confirmed that the founder strain of this lineage originated from a single large horizontal gene transfer event between CC23 and the hypervirulent CC17. Indeed, ST-452 genomes are composed by two parts that are nearly identical to corresponding regions in ST-24 (CC23) and ST-291 (CC17). Chromosome mapping of the major GBS virulence factors showed that ST-452 strains have an intermediate yet unique profile among CC23 and CC17 strains. We described unreported large recombination events, involving the cps IV operon and resulting in the expansion of serotype IV to CC23. This work sheds further light on the evolution of GBS providing new insights on the recent emergence of serotype IV.
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Affiliation(s)
- Edmondo Campisi
- GSK Vaccines s.r.l., Siena, Italy.,Sapienza, Università di Roma, Rome, Italy
| | | | - Claudio Donati
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Mara Barucco
- GSK Vaccines s.r.l., Siena, Italy.,Department of physics "Enrico Fermi", University of Pisa, Pisa, Italy
| | | | - Morven S Edwards
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Carol J Baker
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Department Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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Guetto R, Mancosu M, Scherer S, Torricelli G. The Spreading of Cohabitation as a Diffusion Process: Evidence from Italy. Eur J Popul 2016; 32:661-686. [PMID: 30976224 DOI: 10.1007/s10680-016-9380-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 03/07/2016] [Indexed: 10/22/2022]
Abstract
Drawing on seminal work by Nazio and Blossfeld (Eur J Popul 19(1):47-82, 2003) and Di Giulio and Rosina (Demogr Res 16(14):441-468, 2007), this paper tests whether the recent spread of cohabitation in Italy has followed the typical pattern of diffusion of innovation processes. In doing so, we contribute to the debate on the determinants of the emergence of "new" family behaviour. Following previous literature, innovative behaviour should spread initially through direct social modelling, i.e. interpersonal communication among highly selected individuals (peer effects). At later stages, the diffusion should spread through knowledge awareness of the innovation, i.e. communication with previous generations (pre-cohort effects), so that also less selected individuals are prone to adopt the new behaviour. In the specific Italian context-a Catholic, "familistic" setting, with high normative pressure and importance of parental approval-we surmise the influence of previous generations to be dominant. We use data from the "Family and Social Subjects" survey carried out by Istat (2009) and apply Event History Analysis in the form of competing-risks exponential models to study Italian women's transition to cohabitation as first partnership. Results suggest that the most important driver of the spreading of cohabitation in Italy is represented by the degree of its diffusion among older cohorts. However, we find a positive and significant interaction between women's education and peer effects at the onset of the phenomenon, in line with the Second Demographic Transition (SDT) hypothesis. Cohabitation is also more likely if parents experienced separation/divorce and, more generally, if the environment of the family of origin can be described as "SDT-friendly".
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Affiliation(s)
- Raffaele Guetto
- 1Department of Sociology and Social Research, University of Trento, Via Verdi, 26, 38122 Trento, Italy
| | - Moreno Mancosu
- 1Department of Sociology and Social Research, University of Trento, Via Verdi, 26, 38122 Trento, Italy.,2Collegio Carlo Alberto, Via Real Collegio 30, Moncalieri, 10024 Turin, Italy
| | - Stefani Scherer
- 1Department of Sociology and Social Research, University of Trento, Via Verdi, 26, 38122 Trento, Italy
| | - Giulia Torricelli
- Duepuntozero Research, Doxa, Via Bartolomeo Panizza, 7, 20144 Milan, Italy
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Berti F, Campisi E, Toniolo C, Morelli L, Crotti S, Rosini R, Romano MR, Pinto V, Brogioni B, Torricelli G, Janulczyk R, Grandi G, Margarit I. Structure of the type IX group B Streptococcus capsular polysaccharide and its evolutionary relationship with types V and VII. J Biol Chem 2014; 289:23437-48. [PMID: 24990951 DOI: 10.1074/jbc.m114.567974] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Group B Streptococcus capsular polysaccharide type IX was isolated and purified, and the structure of its repeating unit was determined. Type IX capsule → 4)[NeupNAc-α-(2 → 3)-Galp-β-(1 → 4)-GlcpNAc-β-(1 → 6)]-β-GlcpNAc-(1 → 4)-β-Galp-(1 → 4)-β-Glcp-(1 → appears most similar to types VII and V, although it contains two GlcpNAc residues. Genetic analysis identified differences in cpsM, cpsO, and cpsI gene sequences as responsible for the differentiation between the three capsular polysaccharide types, leading us to hypothesize that type V emerged from a recombination event in a type IX background.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Guido Grandi
- From Novartis Vaccines Research, 53100 Siena, Italy
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7
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Moschioni M, Lo Sapio M, Crisafulli G, Torricelli G, Guidotti S, Muzzi A, Barocchi MA, Donati C. Sequence analysis of 96 genomic regions identifies distinct evolutionary lineages within CC156, the largest Streptococcus pneumoniae clonal complex in the MLST database. PLoS One 2013; 8:e61003. [PMID: 23593373 PMCID: PMC3625235 DOI: 10.1371/journal.pone.0061003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 03/05/2013] [Indexed: 11/19/2022] Open
Abstract
Multi-Locus Sequence Typing (MLST) of Streptococcus pneumoniae is based on the sequence of seven housekeeping gene fragments. The analysis of MLST allelic profiles by eBURST allows the grouping of genetically related strains into Clonal Complexes (CCs) including those genotypes with a common descent from a predicted ancestor. However, the increasing use of MLST to characterize S. pneumoniae strains has led to the identification of a large number of new Sequence Types (STs) causing the merger of formerly distinct lineages into larger CCs. An example of this is the CC156, displaying a high level of complexity and including strains with allelic profiles differing in all seven of the MLST loci, capsular type and the presence of the Pilus Islet-1 (PI-1). Detailed analysis of the CC156 indicates that the identification of new STs, such as ST4945, induced the merging of formerly distinct clonal complexes. In order to discriminate the strain diversity within CC156, a recently developed typing schema, 96-MLST, was used to analyse 66 strains representative of 41 different STs. Analysis of allelic profiles by hierarchical clustering and a minimum spanning tree identified ten genetically distinct evolutionary lineages. Similar results were obtained by phylogenetic analysis on the concatenated sequences with different methods. The identified lineages are homogenous in capsular type and PI-1 presence. ST4945 strains were unequivocally assigned to one of the lineages. In conclusion, the identification of new STs through an exhaustive analysis of pneumococcal strains from various laboratories has highlighted that potentially unrelated subgroups can be grouped into a single CC by eBURST. The analysis of additional loci, such as those included in the 96-MLST schema, will be necessary to accurately discriminate the clonal evolution of the pneumococcal population.
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Affiliation(s)
- Monica Moschioni
- Research Center, Novartis Vaccines and Diagnostics, Siena, Italy.
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Abstract
Silicon clusters were produced by gas aggregation in vacuum and co-deposited with water vapour onto a cold target where the water vapour froze. Melting of the ice yielded fluorescent silicon nanoparticles suspended in water which were investigated by photoluminescence spectroscopy (PL) and atomic force microscopy (AFM). The PL spectrum showed a prominent band at 420 nm and other, less intense bands at shorter wavelengths. No fluorescence was observed below 275 nm. The shortest wavelength observed was related to a silicon cluster diameter of 0.9 nm using a simple particle-in-a-box model. Drops of the suspension were also deposited on freshly cleaved HOPG and investigated by AFM. The images showed single and agglomerated clusters with heights of typically 0.6 up to 2 nm. The sizes displayed by our measurements are not correlated to the average sizes that result from gas aggregation, indicating a size-selecting effect of the water suspension. The cluster-cluster interaction in water is governed by repulsion due to thermal energy and attraction due to van der Waals forces. For very small clusters repulsion dominates; at 3 nm diameter the two forces are balanced. We identify this stable phase of small clusters as the origin of exceptionally stable fluorescence.
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Affiliation(s)
- G Torricelli
- Department of Physics and Astronomy, University of Leicester, Leicester, UK
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Torricelli G, Carapelli A, Convey P, Nardi F, Boore JL, Frati F. High divergence across the whole mitochondrial genome in the "pan-Antarctic" springtail Friesea grisea: evidence for cryptic species? Gene 2009; 449:30-40. [PMID: 19782734 DOI: 10.1016/j.gene.2009.09.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 09/14/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
Abstract
Collembola are one of the few hexapod groups adapted to live in the harsh environmental conditions of Antarctic terrestrial ecosystems. Diversity is limited to a few species that can be very abundant in coastal deglaciated sites. A remarkable lack of overlap in Collembola species composition is evident between Western and Eastern Antarctica, and Friesea grisea is currently the only species whose distribution is thought to span these two main regions of the continent. However, our analysis of the complete sequences of the mitochondrial genomes from specimens obtained from each of the two regions showed unexpected genetic divergence, well above the average levels observed between populations belonging to the same species, and so indicating that these are actually separate species, despite their lack of distinguishing morphology. Detailed analysis of the two genomes showed the presence of a non-coding region observed between trnS(uga) and nad1. Other features of these mitochondrial genomes, such as base compositional bias, secondary structure features of tRNAs and the presence of regulatory elements in the control region, are described and discussed from an evolutionary standpoint.
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Affiliation(s)
- Giulia Torricelli
- Department of Evolutionary Biology, University of Siena, 53100 Siena, Italy.
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Abstract
Time-resolved x-ray experiments require intensity modulation at high frequencies (advanced rotating choppers have nowadays reached the kHz range). We here demonstrate that a silicon microlever oscillating at 13 kHz with nanometric amplitude can be used as a high frequency x-ray chopper. We claim that using micro-and nanoelectromechanical systems (MEMS and NEMS), it will be possible to achieve higher frequencies in excess of hundreds of megahertz. Working at such a frequency can open a wealth of possibilities in chemistry, biology and physics time-resolved experiments.
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Affiliation(s)
- A Siria
- Institut Néel, CNRS-Université Joseph Fourier Grenoble, Grenoble Cedex 9, France
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11
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Siria A, Rodrigues MS, Dhez O, Schwartz W, Torricelli G, Ledenmat S, Rochat N, Auvert G, Bikondoa O, Metzger TH, Wermeille D, Felici R, Comin F, Chevrier J. X-ray pushing of a mechanical microswing. Nanotechnology 2008; 19:445501. [PMID: 21832730 DOI: 10.1088/0957-4484/19/44/445501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We report here for the first time the combination of x-ray synchrotron light and a micro-electro-mechanical system (MEMS). We show how it is possible to modulate in real time a MEMS mass distribution to induce a nanometric and tunable mechanical oscillation. The quantitative experimental demonstration we present here uses periodic thermal dilatation of a Ge microcrystal attached to a Si microlever, induced by controlled absorption of an intensity modulated x-ray microbeam. The mechanism proposed can be envisaged either for the detection of small heat flux or for the actuation of a mechanical system.
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Affiliation(s)
- A Siria
- Institut Néel, CNRS-Université Joseph Fourier Grenoble, BP 166, F-38042 Grenoble Cedex 9, France. CEA-LETI, 17 Avenue des Martyrs, F-38054 Grenoble Cedex 9, France
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Pastorelli A, Torricelli G, Scabia M, Biagi E, Masotti L. A real-time 2-D vector Doppler system for clinical experimentation. IEEE Trans Med Imaging 2008; 27:1515-1524. [PMID: 18815103 DOI: 10.1109/tmi.2008.927337] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A real-time hardware software 2-D vector Doppler system has been realized by means of the FEMMINA platform. The system operates by performing two independent 1-D Doppler estimations on the scan plane of a linear array probe along different directions; the probe is connected to a commercial scanner. The reconstructed velocity is presented in real-time as superposition on the conventional B-mode images. Two different scanning techniques have been implemented, in order to carry out the 2-D Doppler investigation in the area of interest. These techniques allow to use the system both in vivo and in vivo. An extensive set of simulations has been performed in order to establish a gold standard regarding vector Doppler 2-D techniques, and to be able to assess the performance of the 2-D Doppler system by comparing simulated and experimental results. The whole real-time 2-D vector Doppler system is fully certified as hospital equipment, and thus it can be employed to carry out an experimental characterization of the 2-D Doppler technique in the clinical environment.
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Affiliation(s)
- A Pastorelli
- Electronics and Telecommunication Department, University of Florence, 50139 Florence, Italy.
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Schmithusen F, Belakhovsky M, Bletry M, de Boissieu M, Chevrier J, Comin F, Faigel G, Marchesini S, Tegze M, Torricelli G. How perfect can a quasicrystal be? Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302085781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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