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1. A comparative analysis of denoising algorithms for extragalactic imaging surveys

Author

Roscani, V., Tozza, S., Castellano, M., Merlin, E., Ottaviani, D., Falcone, M., and Fontana, A.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies
Abstract

We present a comprehensive analysis of the performance of noise-reduction (``denoising'') algorithms to determine whether they provide advantages in source detection on extragalactic survey images. The methods under analysis are Perona-Malik filtering, Bilateral filter, Total Variation denoising, Structure-texture image decomposition, Non-local means, Wavelets, and Block-matching. We tested the algorithms on simulated images of extragalactic fields with resolution and depth typical of the Hubble, Spitzer, and Euclid Space Telescopes, and of ground-based instruments. After choosing their best internal parameters configuration, we assess their performance as a function of resolution, background level, and image type, also testing their ability to preserve the objects fluxes and shapes. We analyze in terms of completeness and purity the catalogs extracted after applying denoising algorithms on a simulated Euclid Wide Survey VIS image, on real H160 (HST) and K-band (HAWK-I) observations of the CANDELS GOODS-South field. Denoising algorithms often outperform the standard approach of filtering with the Point Spread Function (PSF) of the image. Applying Structure-Texture image decomposition, Perona-Malik filtering, the Total Variation method by Chambolle, and Bilateral filtering on the Euclid-VIS image, we obtain catalogs that are both more pure and complete by 0.2 magnitudes than those based on the standard approach. The same result is achieved with the Structure-Texture image decomposition algorithm applied on the H160 image. The advantage of denoising techniques with respect to PSF filtering increases at increasing depth. Moreover, these techniques better preserve the shape of the detected objects with respect to PSF smoothing. Denoising algorithms provide significant improvements in the detection of faint objects and enhance the scientific return of current and future extragalactic surveys., Comment: 30 pages, 55 figures; accepted for publication in A&A

Published
2020
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2. Incidence and Long-term Functional Outcome of Neurologic Disorders in Hospitalized Patients with COVID-19 Infected with Pre-Omicron Variants

Author

Beretta, S, Cristillo, V, Camera, G, Morotti Colleoni, C, Pellitteri, G, Viti, B, Bianchi, E, Gipponi, S, Grimoldi, M, Valente, M, Guttmann, S, Cotelli, M, Palumbo, P, Gelosa, G, Meletti, S, Schenone, C, Ottaviani, D, Filippi, M, Zini, A, Basilico, P, Tancredi, L, Cortelli, P, Braga, M, De Giuli, V, Servidei, S, Paolicelli, D, Verde, F, Caproni, S, Pisani, A, Lo Re, V, Massacesi, L, Roccatagliata, D, Manganotti, P, Spitaleri, D, Formenti, A, Piccoli, M, Marino, S, Polverino, P, Aguglia, U, Ornello, R, Perego, E, Siciliano, G, Merlo, P, Capobianco, M, Pantoni, L, Lugaresi, A, Angelocola, S, De Rosa, A, Sessa, M, Beghi, E, Agostoni, E, Monaco, S, Padovani, A, Priori, A, Silani, V, Tedeschi, G, Ferrarese, C, Beretta S., Cristillo V., Camera G., Morotti Colleoni C., Pellitteri G., Viti B., Bianchi E., Gipponi S., Grimoldi M., Valente M., Guttmann S., Cotelli M. S., Palumbo P., Gelosa G., Meletti S., Schenone C., Ottaviani D., Filippi M., Zini A., Basilico P., Tancredi L., Cortelli P., Braga M., De Giuli V., Servidei S., Paolicelli D., Verde F., Caproni S., Pisani A., Lo Re V., Massacesi L., Roccatagliata D. V., Manganotti P., Spitaleri D., Formenti A., Piccoli M., Marino S., Polverino P., Aguglia U., Ornello R., Perego E., Siciliano G., Merlo P., Capobianco M., Pantoni L., Lugaresi A., Angelocola S., De Rosa A., Sessa M., Beghi E., Agostoni E. C., Monaco S., Padovani A., Priori A., Silani V., Tedeschi G., Ferrarese C., Beretta, S, Cristillo, V, Camera, G, Morotti Colleoni, C, Pellitteri, G, Viti, B, Bianchi, E, Gipponi, S, Grimoldi, M, Valente, M, Guttmann, S, Cotelli, M, Palumbo, P, Gelosa, G, Meletti, S, Schenone, C, Ottaviani, D, Filippi, M, Zini, A, Basilico, P, Tancredi, L, Cortelli, P, Braga, M, De Giuli, V, Servidei, S, Paolicelli, D, Verde, F, Caproni, S, Pisani, A, Lo Re, V, Massacesi, L, Roccatagliata, D, Manganotti, P, Spitaleri, D, Formenti, A, Piccoli, M, Marino, S, Polverino, P, Aguglia, U, Ornello, R, Perego, E, Siciliano, G, Merlo, P, Capobianco, M, Pantoni, L, Lugaresi, A, Angelocola, S, De Rosa, A, Sessa, M, Beghi, E, Agostoni, E, Monaco, S, Padovani, A, Priori, A, Silani, V, Tedeschi, G, Ferrarese, C, Beretta S., Cristillo V., Camera G., Morotti Colleoni C., Pellitteri G., Viti B., Bianchi E., Gipponi S., Grimoldi M., Valente M., Guttmann S., Cotelli M. S., Palumbo P., Gelosa G., Meletti S., Schenone C., Ottaviani D., Filippi M., Zini A., Basilico P., Tancredi L., Cortelli P., Braga M., De Giuli V., Servidei S., Paolicelli D., Verde F., Caproni S., Pisani A., Lo Re V., Massacesi L., Roccatagliata D. V., Manganotti P., Spitaleri D., Formenti A., Piccoli M., Marino S., Polverino P., Aguglia U., Ornello R., Perego E., Siciliano G., Merlo P., Capobianco M., Pantoni L., Lugaresi A., Angelocola S., De Rosa A., Sessa M., Beghi E., Agostoni E. C., Monaco S., Padovani A., Priori A., Silani V., Tedeschi G., and Ferrarese C.

Abstract

Background and ObjectivesA variety of neurologic disorders have been reported as presentations or complications of coronavirus disease 2019 (COVID-19) infection. The objective of this study was to determine their incidence dynamics and long-term functional outcome.MethodsThe Neuro-COVID Italy study was a multicenter, observational, cohort study with ambispective recruitment and prospective follow-up. Consecutive hospitalized patients presenting new neurologic disorders associated with COVID-19 infection (neuro-COVID), independently from respiratory severity, were systematically screened and actively recruited by neurology specialists in 38 centers in Italy and the Republic of San Marino. The primary outcomes were incidence of neuro-COVID cases during the first 70 weeks of the pandemic (March 2020-June 2021) and long-term functional outcome at 6 months, categorized as full recovery, mild symptoms, disabling symptoms, or death.ResultsAmong 52,759 hospitalized patients with COVID-19, 1,865 patients presenting 2,881 new neurologic disorders associated with COVID-19 infection (neuro-COVID) were recruited. The incidence of neuro-COVID cases significantly declined over time, comparing the first 3 pandemic waves (8.4%, 95% CI 7.9-8.9; 5.0%, 95% CI 4.7-5.3; 3.3%, 95% CI 3.0-3.6, respectively; p = 0.027). The most frequent neurologic disorders were acute encephalopathy (25.2%), hyposmia-hypogeusia (20.2%), acute ischemic stroke (18.4%), and cognitive impairment (13.7%). The onset of neurologic disorders was more common in the prodromic phase (44.3%) or during the acute respiratory illness (40.9%), except for cognitive impairment whose onset prevailed during recovery (48.4%). A good functional outcome was achieved by most patients with neuro-COVID (64.6%) during follow-up (median 6.7 months), and the proportion of good outcome increased throughout the study period (r = 0.29, 95% CI 0.05-0.50; p = 0.019). Mild residual symptoms were frequently reported (28.1%) while disabling s

Published
2023

3. The genomic anchors of the human major histocompatibility complex

Author

Ottaviani, D.

Subjects
572.8
Abstract

Eukaryotic chromatin is organised into a hierarchy of topologically constrained loop structures. Matrix Attachment Regions (MARs) are genomic sequences that mediate the anchoring of chromatin to the insoluble proteinaceous fraction of the nucleus known as the nuclear matrix. Since only a few MARs have been characterised so far, their role in genomic structure and function is not well understood. The aim of this thesis is to use the human Major Histocompatibility Complex (MHC) as model region to provide novel insights into the relationship between chromatin folding mediated by MARs and gene expression. This large locus contains critical genes for immunity and is associated with more diseases than any other genomic region. Classical MHC genes are expressed in a cell type specific pattern, and can be induced by cytokines such as IFN-γ. MARs were identified across the entire MHC in uninduced fibroblasts, IFN-γ induced fibroblasts and B lymphoblastoid cells. Expression array analysis showed that these cell types exhibit different MHC expression profiles. MARs were first isolated treating nuclei with hypertonic buffers followed by nuclease digestion and then mapped by hybridizing them onto a novel tiling path array for the MHC. The suitability of this array platform to study DNA-protein interactions was verified using hybridisations of CIITA-enriched DNA and DNA enriched in H3-K9/K14 acetylation. The findings reveal that MARs are unevenly distributed across the MHC, and that they can be classified into three classes: constitutive, cell type specific and transcriptiondependent. These sequences are mainly positioned in intergenic regions and in close proximity to the MHC class boundaries, subdividing the locus into physical domains. By comparing the position of MARs in uninduced fibroblasts, IFN-γ induced fibroblasts and B lymphoblastoid cells, transcriptional activation of the MHC was found to be associated with a reconfiguration of chromatin architecture resulting from the formation of additional genomic anchors. These results suggest that the dynamic tethering of chromatin is linked to transcriptional regulation.

Published
2009

6. Cognitive phenotypes in Parkinson’s disease: A latent profile analysis

Author

Barvas, E, Mattavelli, G, Zappini, F, Giardina, F, Ottaviani, D, Papagno, C, Barvas, E., Zappini, F., Giardina, F., Ottaviani, D., Barvas, E, Mattavelli, G, Zappini, F, Giardina, F, Ottaviani, D, Papagno, C, Barvas, E., Zappini, F., Giardina, F., and Ottaviani, D.

Abstract

OBJECTIVES: Neurocognitive disorders in Parkinson's disease (PD) are common and heterogeneous. The aim of this study was to use a data-driven method to describe different cognitive phenotypes in PD and to explore anxiety, depression, and motor disturbances across the different cognitive profiles. METHOD: Latent profile analysis was applied to the neuropsychological performances of 65 patients with idiopathic PD assessed by means of a battery of tests that encompass measures of attention, memory, executive functions, social cognition, language, and visuospatial abilities. RESULTS: A three-cluster model produced the best solution: Cluster A (21.54%) included patients with intact cognition or with a relatively slight cognitive impairment in memory and executive functioning; Cluster B (53.85%) included patients with an intermediate level of cognitive impairment; and Cluster C (24.61%) included patients with the most severe cognitive impairment, with greater deficit compared to Cluster B in executive functioning, and, notably, in tasks with a predominantly posterior cortical basis (naming and visuospatial abilities). The three subgroups did not differ in terms of age, gender, disease duration, motor symptom severity or side of onset, levodopa equivalent daily dose, level of anxiety, or depression; however, patients from Cluster C showed greater impairment than patients from Cluster A in measures of everyday functioning. CONCLUSIONS: We presented a qualitative description of three distinct cognitive phenotypes emerging from a sample of 65 PD patients. The three clusters seem to be related to daily functioning but are independent from the stage of disease, motor functioning, anxiety, and depression.

Published
2021

7. Facial expressions recognition and discrimination in Parkinson’s disease

Author

Mattavelli, G, Barvas, E, Longo, C, Zappini, F, Ottaviani, D, Malaguti, M, Pellegrini, M, Papagno, C, Mattavelli G., Barvas E., Longo C., Zappini F., Ottaviani D., Malaguti M. C., Pellegrini M., Papagno C., Mattavelli, G, Barvas, E, Longo, C, Zappini, F, Ottaviani, D, Malaguti, M, Pellegrini, M, Papagno, C, Mattavelli G., Barvas E., Longo C., Zappini F., Ottaviani D., Malaguti M. C., Pellegrini M., and Papagno C.

Abstract

Emotion processing impairment is a common non-motor symptom in Parkinson’s Disease (PD). Previous literature reported conflicting results concerning, in particular, the performance for different emotions, the relation with cognitive and neuropsychiatric symptoms and the affected stage of processing. This study aims at assessing emotion recognition and discrimination in PD. Recognition of six facial expressions was studied in order to clarify its relationship with motor, cognitive and neuropsychiatric symptoms. Sensitivity in discriminating happy and fearful faces was investigated to address controversial findings on impairment in early stages of emotion processing. To do so, seventy PD patients were tested with the Ekman 60 Faces test and compared with 46 neurologically unimpaired participants. Patients’ performances were correlated with clinical scales and neuropsychological tests. A subsample of 25 PD patients and 25 control participants were also tested with a backward masking paradigm for sensitivity in happiness and fear discrimination. Results showed that PD patients were impaired in facial emotion recognition, especially for fearful expressions. The performance correlated with perceptual, executive and general cognitive abilities, but facial expression recognition deficits were present even in cognitively unimpaired patients. In contrast, patients’ sensitivity in backward masking tasks was not reduced as compared to controls. Taken together our data demonstrate that facial emotion recognition, and fear expression in particular, is critically affected by neurodegeneration in PD and related to cognitive abilities; however, it appears before other cognitive impairments. Preserved performances in discriminating shortly presented facial expressions, suggest unimpaired early stages of emotion processing.

Published
2021

8. Presenting features and early mortality from SARS-CoV-2 infection in cancer patients during the initial stage of the COVID-19 pandemic in Europe

Author

Pinato, D, Lee, A, Biello, F, Segui, E, Aguilar-Company, J, Carbo, A, Bruna, R, Bower, M, Rizzo, G, Benafif, S, Carmona, C, Chopra, N, Cruz, C, D'Avanzo, F, Evans, J, Galazi, M, Garcia-Fructuoso, I, Pria, A, Newsom-Davis, T, Ottaviani, D, Patriarca, A, Reyes, R, Sharkey, R, Sng, C, Wong, Y, Ferrante, D, Scotti, L, Avanzi, G, Bellan, M, Castello, L, Marco-Hernandez, J, Molla, M, Pirisi, M, Ruiz-Camps, I, Sainaghi, P, Gaidano, G, Brunet, J, Tabernero, J, Prat, A, Gennari, A, Pinato D. J., Lee A. J. X., Biello F., Segui E., Aguilar-Company J., Carbo A., Bruna R., Bower M., Rizzo G., Benafif S., Carmona C., Chopra N., Cruz C. A., D'avanzo F., Evans J. S., Galazi M., Garcia-Fructuoso I., Pria A. D., Newsom-Davis T., Ottaviani D., Patriarca A., Reyes R., Sharkey R., Sng C. C. T., Wong Y. N. S., Ferrante D., Scotti L., Avanzi G. C., Bellan M., Castello L. M., Marco-Hernandez J., Molla M., Pirisi M., Ruiz-Camps I., Sainaghi P. P., Gaidano G., Brunet J., Tabernero J., Prat A., Gennari A., Pinato, D, Lee, A, Biello, F, Segui, E, Aguilar-Company, J, Carbo, A, Bruna, R, Bower, M, Rizzo, G, Benafif, S, Carmona, C, Chopra, N, Cruz, C, D'Avanzo, F, Evans, J, Galazi, M, Garcia-Fructuoso, I, Pria, A, Newsom-Davis, T, Ottaviani, D, Patriarca, A, Reyes, R, Sharkey, R, Sng, C, Wong, Y, Ferrante, D, Scotti, L, Avanzi, G, Bellan, M, Castello, L, Marco-Hernandez, J, Molla, M, Pirisi, M, Ruiz-Camps, I, Sainaghi, P, Gaidano, G, Brunet, J, Tabernero, J, Prat, A, Gennari, A, Pinato D. J., Lee A. J. X., Biello F., Segui E., Aguilar-Company J., Carbo A., Bruna R., Bower M., Rizzo G., Benafif S., Carmona C., Chopra N., Cruz C. A., D'avanzo F., Evans J. S., Galazi M., Garcia-Fructuoso I., Pria A. D., Newsom-Davis T., Ottaviani D., Patriarca A., Reyes R., Sharkey R., Sng C. C. T., Wong Y. N. S., Ferrante D., Scotti L., Avanzi G. C., Bellan M., Castello L. M., Marco-Hernandez J., Molla M., Pirisi M., Ruiz-Camps I., Sainaghi P. P., Gaidano G., Brunet J., Tabernero J., Prat A., and Gennari A.

Abstract

We describe the outcomes in cancer patients during the initial outbreak of the COVID-19 in Europe from the retrospective, multi-center observational OnCovid study. We identified 204 cancer patients from eight centers in the United Kingdom, Italy, and Spain aged > 18 (mean = 69) and diagnosed with COVID-19 between February 26th and April 1st, 2020. A total of 127 (62%) were male, 184 (91%) had a diagnosis of solid malignancy, and 103 (51%) had non-metastatic disease. A total of 161 (79%) had > 1 co-morbidity. A total of 141 (69%) patients had > 1 COVID-19 complication. A total of 36 (19%) were escalated to high-dependency or intensive care. A total of 59 (29%) died, 53 (26%) were discharged, and 92 (45%) were in-hospital survivors. Mortality was higher in patients aged > 65 (36% versus 16%), in those with > 2 co-morbidities (40% versus 18%) and developing > 1 complication from COVID-19 (38% versus 4%, p = 0.004). Multi-variable analyses confirmed age > 65 and > 2 co-morbidities to predict for patient mortality independent of tumor stage, active malignancy, or anticancer therapy. During the early outbreak of SARS-CoV-2 infection in Europe co-morbid burden and advancing age predicted for adverse disease course in cancer patients. The ongoing OnCovid study will allow us to compare risks and outcomes in cancer patients between the initial and later stages of the COVID-19 pandemic.

Published
2020

10. DYNC2H1 hypomorphic or retina-predominant variants cause nonsyndromic retinal degeneration

Author

Vig, A, Poulter, JA, Ottaviani, D, Tavares, E, Toropova, K, Tracewska, AM, Mollica, A, Kang, J, Kehelwathugoda, O, Paton, T, Maynes, JT, Wheway, G, Arno, G, Genomics England Research Consortium, Khan, KN, McKibbin, M, Toomes, C, Ali, M, Di Scipio, M, Li, S, Ellingford, J, Black, G, Webster, A, Rydzanicz, M, Stawiński, P, Płoski, R, Vincent, A, Cheetham, ME, Inglehearn, CF, Roberts, A, and Heon, E

Subjects
bcs
Abstract

Purpose: Determining the role of DYNC2H1 variants in nonsyndromic inherited retinal disease (IRD).\ud \ud Methods: Genome and exome sequencing were performed for five unrelated cases of IRD with no identified variant. In vitro assays were developed to validate the variants identified (fibroblast assay, induced pluripotent stem cell [iPSC] derived retinal organoids, and a dynein motility assay).\ud \ud Results: Four novel DYNC2H1 variants (V1, g.103327020_103327021dup; V2, g.103055779A>T; V3, g.103112272C>G; V4, g.103070104A>C) and one previously reported variant (V5, g.103339363T>G) were identified. In proband 1 (V1/V2), V1 was predicted to introduce a premature termination codon (PTC), whereas V2 disrupted the exon 41 splice donor site causing incomplete skipping of exon 41. V1 and V2 impaired dynein-2 motility in vitro and perturbed IFT88 distribution within cilia. V3, homozygous in probands 2–4, is predicted to cause a PTC in a retina-predominant transcript. Analysis of retinal organoids showed that this new transcript expression increased with organoid differentiation. V4, a novel missense variant, was in trans with V5, previously associated with Jeune asphyxiating thoracic dystrophy (JATD).\ud \ud Conclusion: The DYNC2H1 variants discussed herein were either hypomorphic or affecting a retina-predominant transcript and caused nonsyndromic IRD. Dynein variants, specifically DYNC2H1 variants are reported as a cause of non syndromic IRD.

Published
2020

11. Camptocormia in Parkinson disease: an epidemiological and clinical study

Author

Tiple, D., Fabbrini, G., Colosimo, C., Ottaviani, D., Camerota, F., Defazio, G., and Berardelli, A.

Subjects
Parkinson's disease -- Research, Parkinson's disease -- Physiological aspects, Parkinson's disease -- Development and progression, Epidemiology -- Research, Spine -- Abnormalities, Spine -- Research, Spine -- Physiological aspects, Health, Psychology and mental health
Published
2009

12. Clinical portrait of the SARS-Cov-2 epidemic in European cancer patients

Author

Pinato DJ, Zambelli A, Aguilar-Company J, Bower M, Sng C, Salazar R, Bertuzzi A, Brunet J, Mesia R, Segui E, Biello F, Generali D, Grisanti S, Rizzo G, Libertini M, Maconi A, Harbeck N, Vincenzi B, Bertulli R, Ottaviani D, Carbo A, Bruna R, Benafif S, Marrari A, Wuerstlein R, Carmona-Garcia MC, Chopra N, Tondini C, Mirallas O, Tovazzi V, Betti M, Provenzano S, Fotia V, Cruz CA, Dalla Pria A, D'Avanzo F, Evans JS, Saoudi-Gonzalez N, Felip E, Galazi M, Garcia-Fructuoso I, Lee AJX, Newsom-Davis T, Patriarca A, Garcia-Illescas D, Reyes R, Dileo P, Sharkey R, Wong YNS, Ferrante D, Marco-Hernandez J, Sureda A, Maluquer C, Ruiz-Camps I, Gaidano G, Rimassa L, Chiudinelli L, Izuzquiza M, Cabirta A, Franchi M, Santoro A, Prat A, Tabernero J, Gennari A, Wellcome Trust, and Cancer Treatment & Research Trust

Subjects
1112 Oncology and Carcinogenesis
Abstract

The SARS-Cov-2 pandemic significantly impacted on oncology practice across the globe. There is uncertainty as to the contribution of patients' demographics and oncological features on severity and mortality from Covid-19 and little guidance as to the role of anti-cancer and anti-Covid-19 therapy in this population. In a multi-center study of 890 cancer patients with confirmed Covid-19 we demonstrated a worsening gradient of mortality from breast cancer to haematological malignancies and showed that male gender, older age, and number of co-morbidities identifies a subset of patients with significantly worse mortality rates from Covid-19. Provision of chemotherapy, targeted therapy and immunotherapy did not worsen mortality. Exposure to antimalarials was associated with improved mortality rates independent of baseline prognostic factors. This study highlights the clinical utility of demographic factors for individualized risk-stratification of patients and support further research into emerging anti-Covid-19 therapeutics in SARS-Cov-2 infected cancer patients.

Published
2020

13. GBA-Related Parkinson’s Disease:Dissection of Genotype–Phenotype Correlates in a LargeItalian Cohort

Author

Petrucci, S., Ginevrino, M., Trezzi, I., Monfrini, E., Ricciardi, L., Albanese, A., Avenali, M., Barone, P., Bentivoglio, A. R., Bonifati, V., Bove, F., Bonanni, L., Brusa, L., Cereda, C., Cossu, G., Criscuolo, C., Dati, G., De Rosa, A., Eleopra, R., Fabbrini, G., Fadda, L., Garbellini, M., Minafra, B., Onofrj, M., Pacchetti, C., Palmieri, I., Pellecchia, M. T., Petracca, M., Picillo, M., Pisani, A., Vallelunga, A., Zangaglia, R., Di Fonzo, A., Morgante, F., Valente, E. M., Altavista, M. C., Amboni, M., Ardolino, G., Berardelli, A., Cogiamanian, F., Colosimo, C., Costanti, D., De Michele, G., Bonaventura, C. D., Di Lazzaro, G., Di Lazzaro, V., Emanuele Elia, A., Erro, R., Ferrazzano, G., Guerra, A., Ialongo, T., Malaguti, M. C., Melis, M., Moro, E., Oppo, V., Ottaviani, D., Peluso, S., Quadri, M. L., Romito, L. M., Sarchioto, M., Schirinzi, T., Sorbera, C., Stefani, A., Thomas, A., Valente, M. L., Volpe, G, ITA-GENE-PD Study, Group., Petrucci, S, Ginevrino, M, Trezzi, I, Monfrini, E, Ricciardi, L, Albanese, A, Avenali, M, Barone, P, Bentivoglio, Ar, Bonifati, V, Bove, F, Bonanni, L, Brusa, L, Cereda, C, Cossu, G, Criscuolo, C, Dati, G, De Rosa, A, Eleopra, R, Fabbrini, G, Fadda, L, Garbellini, M, Minafra, B, Onofrj, M, Pacchetti, C, Palmieri, I, Pellecchia, Mt, Petracca, M, Picillo, M, Pisani, A, Vallelunga, A, Zangaglia, R, Di Fonzo, A, Morgante, F, Valente, Em, Clinical Genetics, Erasmus MC other, and Radiology & Nuclear Medicine

Subjects
0301 basic medicine, Oncology, medicine.medical_specialty, Parkinson's disease, Genotype, genotype–phenotype correlates, Disease, Settore MED/05, Genotype phenotype, dementia, GBA, impulsive–compulsive behavior, 03 medical and health sciences, symbols.namesake, 0302 clinical medicine, Internal medicine, medicine, Dementia, Humans, Sanger sequencing, business.industry, Dissection, Parkinson Disease, medicine.disease, Phenotype, Settore MED/26 - NEUROLOGIA, 030104 developmental biology, Glucosylceramidase, Italy, Mutation, Neurology, Cohort, symbols, Neurology (clinical), business, 030217 neurology & neurosurgery
Abstract

BACKGROUND Variants in GBA are the most common genetic risk factor for Parkinson's disease (PD). The impact of different variants on the PD clinical spectrum is still unclear. OBJECTIVES We determined the frequency of GBA-related PD in Italy and correlated GBA variants with motor and nonmotor features and their occurrence over time. METHODS Sanger sequencing of the whole GBA gene was performed. Variants were classified as mild, severe, complex, and risk. β-glucocerebrosidase activity was measured. The Kaplan-Meier method and Cox proportional hazard regression models were performed. RESULTS Among 874 patients with PD, 36 variants were detected in 14.3%, including 20.4% early onset. Patients with GBA-PD had earlier and more frequent occurrence of several nonmotor symptoms. Patients with severe and complex GBA-PD had the highest burden of symptoms and a higher risk of hallucinations and cognitive impairment. Complex GBA-PD had the lowest β-glucocerebrosidase activity. CONCLUSIONS GBA-PD is highly prevalent in Italy. Different types of mutations underlie distinct phenotypic profiles. © 2020 International Parkinson and Movement Disorder Society.

Published
2020

17. Natural history of bone metastasis in colorectal cancer: final results of a large Italian bone metastases study

Author

Santini, D., Tampellini, M., Vincenzi, B., Ibrahim, T., Ortega, C., Virzi, V., Silvestris, N., Berardi, R., Masini, C., Calipari, N., Ottaviani, D., Catalano, V., Badalamenti, G., Giannicola, R., Fabbri, F., Venditti, O., Fratto, M. E., Mazzara, C., Latiano, T. P., Bertolini, F., Petrelli, F., Ottone, A., Caroti, C., Salvatore, L., Falcone, A., Giordani, P., Addeo, R., Aglietta, M., Cascinu, S., Barni, S., Maiello, E., and Tonini, G.

Published
2012
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23. A pan-European ring trial to validate an International Standard for detection of Vibrio cholerae , Vibrio parahaemolyticus and Vibrio vulnificus in seafoods

Author

Hartnell, R. E., Stockley, L., Keay, W., Rosec, J. -p., Hervio-heath, Dominique, Van Den Berg, H., Leoni, F., Ottaviani, D., Henigman, U., Denayer, S., Serbruyns, B., Georgsson, F., Krumova-valcheva, G., Gyurova, E., Blanco, C., Copin, S., Strauch, E., Wieczorek, K., Lopatek, M., Britova, A., Hardouin, G., Lombard, B., Veld, P. In'T, Leclercq, A., Baker-austin, C., Hartnell, R. E., Stockley, L., Keay, W., Rosec, J. -p., Hervio-heath, Dominique, Van Den Berg, H., Leoni, F., Ottaviani, D., Henigman, U., Denayer, S., Serbruyns, B., Georgsson, F., Krumova-valcheva, G., Gyurova, E., Blanco, C., Copin, S., Strauch, E., Wieczorek, K., Lopatek, M., Britova, A., Hardouin, G., Lombard, B., Veld, P. In'T, Leclercq, A., and Baker-austin, C.

Abstract

Globally, vibrios represent an important and well-established group of bacterial foodborne pathogens. The European Commission (EC) mandated the Comite de European Normalisation (CEN) to undertake work to provide validation data for 15 methods in microbiology to support EC legislation. As part of this mandated work programme, merging of ISO/TS 21872–1:2007, which specifies a horizontal method for the detection of V. parahaemolyticus and V. cholerae, and ISO/TS 21872–2:2007, a similar horizontal method for the detection of potentially pathogenic vibrios other than V. cholerae and V. parahaemolyticus) was proposed. Both parts of ISO/TS 21872 utilized classical culture-based isolation techniques coupled with biochemical confirmation steps. The work also considered simplification of the biochemical confirmation steps. In addition, because of advances in molecular based methods for identification of human pathogenic Vibrio spp. classical and real time PCR options were also included within the scope of the validation. These considerations formed the basis of a multi-laboratory validation study with the aim of improving the precision of this ISO technical specification and providing a single ISO standard method to enable detection of these important foodborne Vibrio spp.. To achieve this aim, an international validation study involving 13 laboratories from 9 countries in Europe was conducted in 2013. The results of this validation have enabled integration of the two existing technical specifications targeting the detection of the major foodborne Vibrio spp., simplification of the suite of recommended biochemical identification tests and the introduction of molecular procedures that provide both species level identification and discrimination of putatively pathogenic strains of V. parahaemolyticus by the determination of the presence of theromostable direct and direct related haemolysins. The method performance characteristics generated in this have been included in revised

Published
2019
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24. Removal of deep-sea sponges by bottom trawling in the Flemish Cap area: conservation, ecology and economic assessment

Author

Pham, Christopher K., Murillo, Francisco Javier, Lirette, Camille, Maldonado, Manuel, Colaço, Ana, Ottaviani, D., Kenchington, Ellen L. R., Pham, Christopher K., Murillo, Francisco Javier, Lirette, Camille, Maldonado, Manuel, Colaço, Ana, Ottaviani, D., and Kenchington, Ellen L. R.

Abstract

Deep-sea sponge grounds are vulnerable marine ecosystems, which through their benthic-pelagic coupling of nutrients, are of functional relevance to the deep-sea realm. The impact of fishing bycatch is here evaluated for the first time at a bathyal, sponge-dominated ecosystem in the high seas managed by the Northwest Atlantic Fisheries Organization. Sponge biomass surfaces created from research survey data using both random forest modeling and a gridded surface revealed 231,140 t of sponges in the area. About 65% of that biomass was protected by current fisheries closures. However, projections of trawling tracks estimated that the sponge biomass within them would be wiped out in just 1 year by the current level of fishing activity if directed on the sponges. Because these sponges filter 56,143 ± 15,047 million litres of seawater daily, consume 63.11 ± 11.83 t of organic carbon through respiration, and affect the turnover of several nitrogen nutrients, their removal would likely affect the delicate ecological equilibrium of the deep-sea benthic ecosystem. We estimated that, on Flemish Cap, the economic value associated with seawater filtration by the sponges is nearly double the market value of the fish catch. Hence, fishery closures are essential to reach sponge conservation goals as economic drivers cannot be relied upon.

Published
2019

30. Erratum: Natural History of Non-Small-Cell Lung Cancer with Bone Metastases (Scientific Reports (2015) 5 (18670) DOI: 10.1038/srep18670)

Author

Santini D., Barni S., Intagliata S., Falcone A., Ferrau F., Galetta D., Moscetti L., La Verde N., Ibrahim T., Petrelli F., Vasile E., Ginocchi L., Ottaviani D., Longo F., Ortega C., Russo A., Badalamenti G., Collova E., Lanzetta G., Mansueto G., Adamo V., De Marinis F., Satolli M. A., Cantile F., Mancuso A., Tanca F. M., Addeo R., Russano M., Sterpi M., Pantano F., Vincenzi B., Tonini G., Santini D., Barni S., Intagliata S., Falcone A., Ferrau F., Galetta D., Moscetti L., La Verde N., Ibrahim T., Petrelli F., Vasile E., Ginocchi L., Ottaviani D., Longo F., Ortega C., Russo A., Badalamenti G., Collova E., Lanzetta G., Mansueto G., Adamo V., De Marinis F., Satolli M.A., Cantile F., Mancuso A., Tanca F.M., Addeo R., Russano M., Sterpi M., Pantano F., Vincenzi B., and Tonini G.

Subjects
Non-Small-Cell Lung Cancer, Multidisciplinary, Settore MED/06 - Oncologia Medica
Abstract

Erratum for Natural History of Non-Small-Cell Lung Cancer with Bone Metastases

Published
2016

36. Improving resolution and depth of astronomical observations via modern mathematical methods for image analysis

Author

Castellano, M., Ottaviani, D., adriano fontana, Merlin, E., Pilo, S., and Falcone, M.

Subjects
FOS: Physical sciences, Astrophysics - Instrumentation and Methods for Astrophysics, Instrumentation and Methods for Astrophysics (astro-ph.IM)
Abstract

In the past years modern mathematical methods for image analysis have led to a revolution in many fields, from computer vision to scientific imaging. However, some recently developed image processing techniques successfully exploited by other sectors have been rarely, if ever, experimented on astronomical observations. We present here tests of two classes of variational image enhancement techniques: "structure-texture decomposition" and "super-resolution" showing that they are effective in improving the quality of observations. Structure-texture decomposition allows to recover faint sources previously hidden by the background noise, effectively increasing the depth of available observations. Super-resolution yields an higher-resolution and a better sampled image out of a set of low resolution frames, thus mitigating problematics in data analysis arising from the difference in resolution/sampling between different instruments, as in the case of EUCLID VIS and NIR imagers., Comment: 4 pages, contributed paper at the ADASS XXIV conference (Calgary, Oct. 2014). To be published in ASP conference series

Published
2015
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37. Anhedonia and cognitive impairment in Parkinson's disease: Italian validation of the Snaith-Hamilton Pleasure Scale and its application in the clinical routine practice during the PRIAMO study

Author

Santangelo, G, Morgante, L, Savica, R, Marconi, R, Grasso, L, Antonini, A, De Gaspari, D, Ottaviani, D, Tiple, D, Simoni, L, Barone, P, Priamo, Sg, Colosimo, C, Benincasa, D, Biguzzi, S, Braga, M, Capecci, M, Caravona, N, De Falco, Fa, Pezzoli, G, Di Giovanni, M, Floris, G, Gallerini, S, Gurgone, G, Kiferle, L, Meoni, S, Moschella, V, Morgante, F, Pepe, F, Petretta, V, Randisi, Mg, Romeno, M, Ianniciello, M, Sciortino, G, Guzzardi, Po, Sorbello, V, Fabbrini, G, Guidubaldi, A, Muoio, R, Toni, V, Ferrari, Po, Logi, C, Ciacci, G, Ulivelli, M, Perini, M, Lanfranchi, S, Griffini, S, Troianiello, B, Baratti, M, Amidei, S, Consoli, D, Iellamo, M, Cuomo, T, Scaglioni, A, Medici, D, Abbruzzese, Giovanni, Di Brigida, G, Cocco, Ga, Agnetti, V, Cossu, G, Deriu, M, Abrignani, M, Modica, C, Albani, G, Milan, E, Martinelli, P, Scaglione, C, Mucchiut, M, Zanini, S, Pennisi, F, Soliveri, P, Albanese, A, Bartolomei, L, L'Erario, R, Capus, L, Ferigo, L, Marano, R, Nastasi, V, Luciano, R, Maiello, L, Simone, P, Fogli, D, Lopiano, L, Pesare, M, Molinette, As, Nordera, G, Pilleri, E, Scaravilli, T, Giaccaglini, E, Alesi, C, Corbetta, T, Dumitriu, A, Ingelheim, B, Sgarbi, S, Rapisarda, A, Rizzoli, S, Zanoli, L, Manfredi, A., Santangelo, Gabriella, Morgante, L, Savica, R, Marconi, R, Grasso, L, Antonini, A, De Gaspari, D, Ottaviani, D, Tiple, D, Simoni, L, Barone, P, PRIAMO Study, Group, Santangelo, G, Barone, Paolo, and PRIAMO Study, G. r. o. u. p.

Subjects
Male, medicine.medical_specialty, Parkinson's disease, media_common.quotation_subject, Multilingualism, Pilot Projects, Test validity, Affect (psychology), behavioral disciplines and activities, Aged, Aged, 80 and over, Cognition Disorders, diagnosis/epidemiology/psychology, Depressive Disorder, Major, diagnosis/epidemiology/psychology, Female, Humans, Italy, epidemiology, Male, Middle Aged, Multilingualism, Parkinson Disease, diagnosis/epidemiology/psychology, Pilot Projects, Psychiatric Status Rating Scales, standards, Reproducibility of Results, Pleasure, medicine, 80 and over, Humans, Psychiatry, Depression (differential diagnoses), media_common, Aged, Aged, 80 and over, Psychiatric Status Rating Scales, Depressive Disorder, Major, Depressive Disorder, Parkinsonism, Anhedonia, Reproducibility of Results, Parkinson Disease, Middle Aged, medicine.disease, Test (assessment), Neurology, Italy, standards, Female, epidemiology, Neurology (clinical), Geriatrics and Gerontology, medicine.symptom, Psychology, Cognition Disorders, diagnosis/epidemiology/psychology, Clinical psychology
Abstract

To assess the psychometric properties of the Italian version of the Snaith-Hamilton Pleasure Scale (SHAPS) and to study the relationship between anhedonia, depression and cognitive impairment in patients with Parkinson's disease (PD).The SHAPS (14 items) was translated into Italian and pre-tested in a pilot study. Two items evaluating physical anhedonia related to sexual issues were added. The Italian version of SHAPS was validated in 274 consecutive PD patients, divided into patients with major depression according to DSM-IV criteria (dPD) and patients without depression (nPD), and in healthy subjects. To test the feasibility of the instrument and to determine whether clinical data affect anhedonia, we also administered SHAPS to 1307 patients with different types of parkinsonism.The Italian SHAPS proved to be easy to understand as regards the question and answer modes. Intraclass coefficient for test-retest reliability was 0.65 for the total score. KR index was 0.61. ANOVA of the SHAPS total score revealed that scores were higher in dPD patients than in healthy controls and nPD (p0.05). In the 1307 patients with various types of parkinsonism, the SHAPS data showed that anhedonia was related to age, type of parkinsonism, apathy, depression and cognitive impairment. Anhedonia was correlated with frontal dysfunctions in supranuclear palsy and PD patients (r=-0.682 and -0.264 respectively, p0.05).The Italian version of the SHAPS is a reliable tool with which to assess anhedonia in patients with PD and other forms of parkinsonism.

Published
2009

39. Halobacteriovorax isolated from marine water of the Adriatic sea, Italy, as an effective predator of Vibrio parahaemolyticus, non‐O1/O139 V. cholerae, V. vulnificus.

Author

Ottaviani, D., Chierichetti, S., Angelico, G., Forte, C., Rocchegiani, E., Manuali, E., and Leoni, F.

Subjects
*HALOBACTERIOVORAX, *BDELLOVIBRIO, *VIBRIO parahaemolyticus, *SEAWATER
Abstract

Abstract: Aim: To detect marine Bdellovibrio and like organisms (BALOs) which are able to infect Vibrio parahaemolyticus from seawater of the Adriatic, Italy. To test, prey specificity and predation efficiency of our Halobacteriovorax isolate, named HBXCO1, towards 17 Vibrio and 7 non‐Vibrio strains linked to the Adriatic sea, Italy. Methods and Results: Double layer agar plating technique was used to enumerate BALOs and to evaluate their prey specificity and predation efficiency. Transmission electron microscopy and 16S rRNA analysis were used to identify them. Means of BALOs counts ranged from 5·0 PFU per ml (March 2017) to 98·6 PFU per ml (August 2016). HBXCO1 had the ability to attack all tested prey strains of V. parahaemolyticus, Vibrio cholerae non‐O1/O139 and Vibrio vulnificus, but it did not prey on non‐Vibrio strains and V. alginolyticus under the tested conditions. Conclusions: Bdellovibrio and like organisms capable of infecting pathogenic vibrios are naturally present in seawater of the Adriatic, Italy. Isolate HBXCO1 shows prey specificity preferentially for the Vibrio genus and high predatory efficiency towards a wide range of pathogenic strains. Significance and Impact of the Study: The public impact of V. parahaemolyticus, non‐O1/O139 V. cholerae and V. vulnificus in bivalves is relevant and current decontamination processes are not always effective. We believe that the predator HBXCO1 represents a potential candidate for the development of strategies of biocontrol of pathogenic vibrios in bivalves from harvesting to trade. [ABSTRACT FROM AUTHOR]

Published
2018
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40. Normal-release oral morphine starting dose in cancer patients with pain

Author

Ripamonti, Ci, Campa, T, Fagnoni, E, Brunelli, C, Luzzani, M, Maltoni, M, De Conno, F, MERITO Study Group: De Conno, F, Ripamonti, C, Bertetto, O, Ciuffreda, L, Ottaviani, D, Amadori, D, Modonesi, C, Fabbri, L, Arcuri, E, Tirelli, W, Brogi, A, Criscuolo, S, Camaioni, D, Bosco, M, Cascinu, S, Berardi, R, Comella, G, Daponte, A, Dini, D, Massidda, B, Capra, D, Montrone, V, Longo, V, Paccagnella, A, Mastromauro, C, Peruselli, C, Sbanotto, A, Varrassi, G, Paladini, Antonella, Marinangeli, Franco, Zucco, F, and Rusconi, M. G.

Published
2009

42. Caratteristiche Cliniche

Author

Amboni, M, Berardelli, A, Ceravolo, R, Colosimo, C, Glorioso, M, Guidi, M, Manni, R, Marconi, R, Ottaviani, D, Pacchetti, C, Pellecchia, Mt, Pellicano, C, Pierantozzi, M, Pontieri, F, Stanzione, P, and Zangaglia, R

Published
2008

43. The MERITO Study: a multicentre trial of the analgesic effect and tolerability of normal-release oral morphine during 'titration phase' in patients with cancer pain

Author

De Conno, F, Ripamonti, C, Fagnoni, E, Brunelli, C, Luzzani, M, Maltoni, M, Arcuri, E, Bertetto, O, MERITO Study Group, Campa, T, Ciuffreda, L, Ottaviani, D, Amadori, D, Modonesi, C, Fabbri, L, Tirelli, W, Brogi, A, Criscuolo, S, Camaioni, D, Bosco, M, Cascinu, S, Berardi, R, Comella, G, Daponte, A, Dini, D, Massidda, B, Capra, D, Montrone, V, Longo, V, Paccagnella, A, Mastromauro, C, Peruselli, C, Sbanotto, A, Varrassi, G, Paladini, Antonella, Marinangeli, Franco, Zucco, F, and Rusconi, M. G.

Published
2008

47. Comparison of different biochemical and molecular methods for the identification of Vibrio parahaemolyticus

Author

Croci, L., Suffredini, E., Cozzi, L., Toti, L., Ottaviani, D., Pruzzo, Carla, Serratore, P., Fischetti, R., Goffredo, E., Loffredo, G., Mioni, R., Vibrio parahaemolyticus Working Group, L. Croci, E. Suffredini, L. Cozzi, L. Toti, D. Ottaviani, C. Pruzzo, P. Serratore, R. Fischetti, E. Goffredo, G. Loffredo, and R. Mioni and the Vibrio parahaemolyticus Working Group

Subjects
Identification methods, DNA, Bacterial, Concordance, BIOCHEMICAL METHODS, Applied Microbiology and Biotechnology, Polymerase Chain Reaction, MOLECULAR METHODS, Microbiology, law.invention, Bacterial Proteins, Vibrionaceae, law, False Positive Reactions, Polymerase chain reaction, Bacteriological Techniques, Chromatography, biology, Vibrio parahaemolyticus, General Medicine, equipment and supplies, biology.organism_classification, DNA-Binding Proteins, Genes, Bacterial, Biotechnology, Transcription Factors
Abstract

Aims: Multicentre evaluation of biochemical and molecular methods for the identification of Vibrio parahaemolyticus. Methods and Results: For the biochemical identification methods, API 20E and API 20NE and Alsina's scheme were evaluated in intra- and interlaboratory tests in order to determine the accuracy and concordance of each method. Both in intra- and interlaboratory tests, the Alsina's scheme showed the highest sensitivity (86% of correct identifications in the interlaboratory test). False-positive results were obtained by all methods (specificity was 95% for API 20E, 73% for API 20NE and 84% for Alsina's scheme) and concordance varied from 65% of API 20NE to 84% of API 20E. For the molecular identifications, polymerase chain reaction (PCR) for the detection of toxR gene, tl gene and pR72H fragment were tested on 30 strains by two laboratories. The PCR for toxR showed the highest inclusivity (96%), exclusivity (100%) and concordance (97%). Conclusions: Among the biochemical identification methods tested, the Alsina's scheme gave more reliable results; however, in order to avoid false-positive results, all the biochemical identifications should be confirmed by means of molecular methods. Significance and Impact of the Study: Availability of an efficient identification method of Vibrio parahaemolyticus to use in official control of fisheries products.

Published
2006

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