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3. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author

Tara Oceans Coordinators, Villar, E., Farrant, G. K., Follows, M., Garczarek, L., Speich, S., Audic, S., Bittner, L., Blanke, B., Brum, J. R., Brunet, C., Casotti, R., Chase, A., Dolan, J. R., d'Ortenzio, F., Gattuso, J.-P., Grima, N., Guidi, L., Hill, C. N., Jahn, O., Jamet, J.-L., Le Goff, H., Lepoivre, C., Malviya, S., Pelletier, E., Romagnan, J.-B., Roux, S., Santini, S., Scalco, E., Schwenck, S. M., Tanaka, A., Testor, P., Vannier, T., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S. G., Bork, P., Boss, E., de Vargas, C., Gorsky, G., Ogata, H., Pesant, S., Sullivan, M. B., Sunagawa, S., Wincker, P., Karsenti, E., Bowler, C., Not, F., Hingamp, P., and Iudicone, D.

Published
2015

4. Eukaryotic plankton diversity in the sunlit ocean

Author

Tara Oceans Coordinators, de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., and Karsenti, E.

Published
2015

5. Eukaryotic plankton diversity in the sunlit ocean

Author

de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Oceans Coordinators, Tara, Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., and Karsenti, E.

Published
2015

6. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author

Villar, E., Farrant, G. K., Follows, M., Garczarek, L., Speich, S., Audic, S., Bittner, L., Blanke, B., Brum, J. R., Brunet, C., Casotti, R., Chase, A., Dolan, J. R., dʼOrtenzio, F., Gattuso, J.-P., Grima, N., Guidi, L., Hill, C. N., Jahn, O., Jamet, J.-L., Le Goff, H., Lepoivre, C., Malviya, S., Pelletier, E., Romagnan, J.-B., Roux, S., Santini, S., Scalco, E., Schwenck, S. M., Tanaka, A., Testor, P., Vannier, T., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Oceans Coordinators, Tara, Acinas, S. G., Bork, P., Boss, E., de Vargas, C., Gorsky, G., Ogata, H., Pesant, S., Sullivan, M. B., Sunagawa, S., Wincker, P., Karsenti, E., Bowler, C., Not, F., Hingamp, P., and Iudicone, D.

Published
2015

12. Comparative high resolution pQCT analysis of femoral neck indicates different bone mass distribution in osteoporosis and osteoarthritis

Author

Rubinacci A. 2, Tresoldi D. 1, 4, Scalco E. 1, Villa I. 2, Adorni F. 5, Moro G.L. 3, Fraschini G.F. 3, and Rizzo G. 1

Subjects
Osteoarthritis, Osteoporosis, Femoral neck, Femoral fracture, pQCT
Abstract

Osteoarthritis is linked to a reduced risk of femoral fracture despite osteoporosis. Different bone distribution in the femoral neck in osteoarthritis and fracture was revealed using a peripheral quantitative computed tomography (pQCT) comparative analysis. Our findings sustain the presence of an adaptive mechanism of bone structure providing fracture protection in osteoarthritis. INTRODUCTION: Although osteoarthritis is associated with reduced femoral fracture risk, it does not protect from bone loss. We investigated whether adaptive mechanisms are present at the arthritic joint, leading to reduced fracture risk, despite the presence of low bone mass density. METHODS: We performed pQCT comparative analyses of human femoral neck specimens derived from 32 postmenopausal women who received hip prostheses for osteoarthritis (n=19) or femoral fracture (n=13) by applying an in-house automated software to extract bone structure descriptors, characterize trabecular and cortical bone distribution, and evaluate their mutual relationships. RESULTS: The cortical bone volume and trabecular thickness were significantly (p

Published
2012

17. Non-linear modelling of bivariate comovements in asset prices

Author

Corazza, Marco and Scalco, E.

Subjects
asset prices, Settore SECS-S/06 - Metodi mat. dell'economia e Scienze Attuariali e Finanziarie, Comonotonicity, Polynomial approximation, Comovement, Bivariate dependence, Non-linearity, t-test, Energy asset
Published
2005

44. Large scale patterns of marine diatom richness: Drivers and trends in a changing ocean

Author

Francesco d'Ovidio, Roberta Piredda, Bruno Hay Mele, Daniele Iudicone, Colomban de Vargas, Adriana Zingone, Greta Busseni, Luigi Caputi, Lucia Campese, Chris Bowler, Paul Frémont, Maurizio Ribera d'Alcalà, Eleonora Scalco, Busseni, G., Caputi, L., Piredda, R., Fremont, P., Hay Mele, B., Campese, L., Scalco, E., de Vargas, C., Bowler, C., D'Ovidio, F., Zingone, A., Ribera d'Alcala, M., Iudicone, D., Stazione Zoologica Anton Dohrn (SZN), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Tara Oceans-GOSEE (FR2022), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), European Project: 654008,H2020,H2020-INFRADEV-1-2014-1,EMBRIC(2015), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), d'Ovidio, Francesco, European Marine Biological Research Infrastructure Cluster to promote the Blue Bioeconomy - EMBRIC - - H20202015-06-01 - 2019-05-31 - 654008 - VALID, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
010504 meteorology & atmospheric sciences, Scale (ratio), Tara Oceans, richne, 01 natural sciences, diversity, 03 medical and health sciences, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Global and Planetary Change, Ecology, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, Marine diatom, diatom, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Oceanography, machine learning, metabarcoding, microscopy, Environmental science, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Aim: Plankton diversity is a pivotal element of marine ecosystem stability and functioning. A major obstacle in the assessment of diversity is the lack of consistency between patterns assessed by molecular and morphological data. This work aims to reconcile the two in a single richness measure, to investigate the environmental drivers affecting this measure, and finally to predict its spatio-temporal patterns. Location and time period: This is a global scale study, based on data collected within the 2009–2013 interval during the Tara Oceans expedition. Major taxa studied: The focus of this study is diatoms. They play an important role in several biogeochemical cycles and within marine food webs, and display high taxonomic and functional richness. Methods: We integrate measures of diatom richness across the global ocean using molecular and morphological approaches, giving particular attention to ‘the rare biosphere’. We then perform a machine-learning-based analysis of these reconciled patterns to extrapolate diatom richness at the global scale and to identify the main environmental processes governing it. Finally, we model the response of diatom richness to climate change. Results: By filtering out 0.3% of the rarest operational taxonomic units, molecular-based richness patterns show the best possible match with the morphological approach. Temperature, phosphate, chlorophyll a and the Lyapunov exponent are the major explainers of these reconciled patterns. Global scale predictions provide a first approximation of the global geography of diatom richness and of the possible impacts of climate change. Main conclusions: Our models suggest that diatom richness is controlled by different processes characteristic of distinct environmental scenarios: lateral mixing in highly dynamic regions, and both nutrient availability and temperature elsewhere. We present herein the effects of these processes on richness and how these same effects differ from other diversity indices because of the main component of richness: the rare biosphere.

Published
2020

48. Analysis of serial CT images for studying the RT effects in head-neck cancer patients

Author

Giuseppe Sanguineti, Vincenzo Valentini, Gerlinde Logghe, Elisa Scalco, Nadia Di Muzio, M.L. Belli, Sara Broggi, Riccardo Calandrino, Italo Dell'Oca, Stefano Moriconi, Claudio Fiorino, Giovanni Mauro Cattaneo, Belli, Ml, Broggi, S, Scalco, E, Cattaneo, Gm, Dell'Oca, I, Logghe, G, Moriconi, S, Sanguineti, G, Valentini, V, Di Muzio, N, Fiorino, C, and Calandrino, R.

Subjects
business.industry, Head and neck cancer, medical imaging, Cancer, Head neck cancer, medicine.disease, Xerostomia, Parotid gland, Mri image, medicine.anatomical_structure, Conventional radiotherapy, stomatognathic system, Head and Neck Neoplasms, medicine, Treatment strategy, Humans, Parotid Gland, cancer, Radiotherapy treatment, Nuclear medicine, business, Tomography, X-Ray Computed, radiotherapy, Radiotherapy, Image-Guided
Abstract

Images taken during and after RT for head and neck cancer have the potential to quantitatively assess xerostomia. Image information may be used as biomarkers of RT effects on parotid glands with significant potential to support adaptive treatment strategies. We investigated the possibility to extract information based on in-room CT images (kVCT, MVCT), acquired for daily image-guided radiotherapy treatment of head-and-neck cancer patients, in order to predict individual response in terms of toxicity. Follow-up MRI images were also used in order to investigate long term parotid gland deformation.

Published
2015

49. Evaluation of morphological and structural variations in parotid glands during radiotherapy in the head and neck district

Author

SCALCO, ELISA, Scalco, E, and MORESCO, ROSA MARIA

Subjects
MED/36 - DIAGNOSTICA PER IMMAGINI E RADIOTERAPIA, image registration, parotid gland, image analysi, Head-and-neck radiotherapy
Abstract

The treatment of head and neck cancer (HNC) patients is one of the widest applications of radiation treatment. One of the main organs involved in dose delivery and playing a relevant role in the quality of life of patients treated for HNC is the parotid gland, the major salivary gland, whose damage causes a pathologic condition called xerostomia. During the treatment, HNC patients may undergo significant anatomical changes; it was generally reported that parotids shrink during RT with a shift of the center of mass (COM) toward the midline. These modifications cause a translation of the glands into the high dose region, thus the effective delivered dose on parotids is significantly higher than that planned. Therefore, the study of local changes in parotid glands due to irradiation is still an open challenge, and the exploitation of the information content in medical images acquired during the radiation treatment is of practical interest for the non-invasiveness of these techniques. The aim of this work was thus the evaluation of morphological and structural modifications induced by RT on parotid glands using image-based indices extracted from CT images acquired during the treatment. In particular, in this PhD project it was proposed to estimate morphological changes by the deformation of the glands, evaluated by applying a non-rigid registration method expressly optimized and validated on CT images of the HN district. Secondly, a method of image analysis based on textural feature extraction was proposed to characterize structural variations of parotid tissue. All these methods were evaluated and optimized for the clinical problem and all these parameters were studied in relation to dosimetric and clinical indices and to the clinical outcome, in order to better assess their contribution in this research field. Parotid deformation was here estimated through an image registration and contour propagation method, based on Free Form Deformation and Mutual Information. A deep validation of this method was performed to assess the accuracy of contour propagation method, to ensure a reliable quantification of parotid deformation. The quantification of parotid deformation was carried out starting from the estimated deformation field, by calculating the Jacobian index, while the structural characterization of parotid tissue was performed by the extraction of features related to the intensity patterns of the image, quantified by texture analysis. We evidenced that parotid shrinkage is highly related to low dose DVH values; at the same time, density variation measured after RT is significantly correlated with volume decrease, suggesting that the loss of acinar cells and the consequent increase in the percentage of the fatty component is related to the decrease in functionality. We proved that the major reduction in density is concentrated in the first half of the treatment, while the decrease in volume and in tissue complexity is quite constant during the whole treatment. Finally, we found that the most accurate prediction of parotid shrinkage is achieved by the combination of geometrical and structural variations measured in the first two weeks and that the early prediction of xerostomia score was preliminary achieved by early density and volume variation.

Published
2014

50. Density variation of parotid glands during IMRT for head-neck cancer: correlation with treatment and anatomical parameters

Author

Nadia Di Muzio, Sara Broggi, Elisa Scalco, Giovanna Rizzo, Claudio Fiorino, Vincenzo Valentini, Giuseppe Sanguineti, Francesco Ricchetti, Aldo Mejia Rodriguez, Giovanni Mauro Cattaneo, Nicola Dinapoli, Italo Dell'Oca, M.L. Belli, Riccardo Calandrino, Fiorino, C, Rizzo, G, Scalco, E, Broggi, S, Belli, Ml, Dell'Oca, I, Dinapoli, N, Ricchetti, F, Rodriguez, Am, Di Muzio, N, Calandrino, R, Sanguineti, G, Valentini, V, and Cattaneo, Gm

Subjects
Adult, Male, medicine.medical_treatment, Image-guided radiotherapy, Head neck cancer, Radiation Dosage, Risk Assessment, Tomotherapy, parotid deformation, Cohort Studies, Correlation, stomatognathic system, Hounsfield scale, Tomography spiral computed, medicine, Humans, Parotid Gland, Radiology, Nuclear Medicine and imaging, In patient, Radiometry, Aged, Neoplasm Staging, Retrospective Studies, Aged, 80 and over, business.industry, Objective measurement, Hematology, head-neck tumors, Middle Aged, Parotid gland, stomatognathic diseases, Logistic Models, Treatment Outcome, medicine.anatomical_structure, Oncology, adaptive radiotherapy, Head and Neck Neoplasms, Carcinoma, Squamous Cell, Female, Radiotherapy, Intensity-Modulated, Tomography, X-Ray Computed, business, Nuclear medicine, Tomography, Spiral Computed, Algorithms
Abstract

PURPOSE: Measuring parotid density changes in patients treated with IMRT for head-neck cancer (HNC) and assessing correlation with treatment-related parameters. PATIENTS AND MATERIALS: Data of 84 patients treated with IMRT for different HNC were pooled from three institutions. Parotid deformation and average Hounsfield number changes (?HU) were evaluated through MVCT (with Helical Tomotherapy) or diagnostic kVCT images taken at the treatment start/end. Parotids were delineated in the first image and propagated to the last using a previously validated algorithm based on elastic registration. The correlation between ?HU and several treatment-related parameters was tested; then, logistic uni- and multi-variate analyses taking "large" ?HU as end-point were carried out. Due to the better image quality, analyses were repeated considering only kVCT data. RESULTS: ?HU was negative in 116/168 parotids (69%; for kVCT patients: 72/92, 78%). The average ?HU was significantly different from zero (-7.3, 0.20-0.25HU/fraction, p

Published
2012

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