1
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Spasov GH, Rossi R, Vanossi A, Cottini C, Benassi A. A critical analysis of the CFD-DEM simulation of pharmaceutical aerosols deposition in upper intra-thoracic airways: Considerations on air flow. Comput Biol Med 2024; 170:107948. [PMID: 38219648 DOI: 10.1016/j.compbiomed.2024.107948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/12/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024]
Abstract
A well-corroborated numerical methodology ensuring reproducibility in the modeling of pharmaceutical aerosols deposition in the respiratory system via CFD-DEM simulations within the RANS framework is currently missing. Often, inadequately clarified assumptions and approximations and the lack of evidences on their quantitative impact on the simulated deposition phenomenology, make a direct comparison among the different theoretical studies and the limited number of experiments a very challenging task. Here, with the ultimate goal of providing a critical analysis of some crucial computational aspects of aerosols deposition, we address the issues of velocity fluctuations propagation in the upper intra-thoracic airways and of the persistence of secondary flows using the SimInhale reference benchmark. We complement the investigation by describing how methodologies used to drive the flow through a truncated lung model may affect numerical results and how small discrepancies are observed in velocity profiles when comparing simulations based on different meshing strategies.
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Affiliation(s)
- G H Spasov
- International School for Advanced Studies (SISSA), Trieste, Italy; CNR-IOM, Consiglio Nazionale delle Ricerche - Istituto Officina dei Materiali, Trieste, Italy
| | - R Rossi
- RED Fluid Dynamics, Cagliari, Italy
| | - A Vanossi
- International School for Advanced Studies (SISSA), Trieste, Italy; CNR-IOM, Consiglio Nazionale delle Ricerche - Istituto Officina dei Materiali, Trieste, Italy
| | - C Cottini
- Chiesi Farmaceutici S.p.A., Parma, Italy
| | - A Benassi
- International School for Advanced Studies (SISSA), Trieste, Italy; Chiesi Farmaceutici S.p.A., Parma, Italy.
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2
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Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Karakikes I, Wang KC, Umapathy G, Roos C, Boubli JP, Siepel A, Kundaje A, Paten B, Lindblad-Toh K, Rogers J, Marques Bonet T, Farh KKH. Identification of constrained sequence elements across 239 primate genomes. Nature 2024; 625:735-742. [PMID: 38030727 PMCID: PMC10808062 DOI: 10.1038/s41586-023-06798-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
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Affiliation(s)
- Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Jacob C Ulirsch
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Sabrina Rashid
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Mohamed Ameen
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Anthony J Cox
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Arvind Kumar
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Mareike C Janiak
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Martin Kuhlwilm
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Joseph D Orkin
- Département d'Anthropologie, Université de Montréal, Montréal, Quebec, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Lidia Agueda
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Julie Blanc
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Rede de Pesquisa em Diversidade, Conservação e Uso da Fauna da Amazônia - RedeFauna, Manaus, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica-ComFauna, Iquitos, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
- Department of Biology, Trinity University, San Antonio, TX, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | | | - Sree Kanthaswamy
- School of Interdisciplinary Forensics, Arizona State University, Phoenix, AZ, USA
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Professorship for International Animal Health/One Health, Faculty of Veterinary Medicine, Justus Liebig University, Giessen, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
- School of Geosciences, Edinburgh, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, Göttingen, Germany
| | - Ivo Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain.
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA.
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3
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Murari A, Peluso E, Spolladore L, Rossi R, Gelfusa M. Upgrades of Genetic Programming for Data-Driven Modeling of Time Series. Evol Comput 2023; 31:401-432. [PMID: 37126579 DOI: 10.1162/evco_a_00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/31/2023] [Indexed: 05/03/2023]
Abstract
In many engineering fields and scientific disciplines, the results of experiments are in the form of time series, which can be quite problematic to interpret and model. Genetic programming tools are quite powerful in extracting knowledge from data. In this work, several upgrades and refinements are proposed and tested to improve the explorative capabilities of symbolic regression (SR) via genetic programming (GP) for the investigation of time series, with the objective of extracting mathematical models directly from the available signals. The main task is not simply prediction but consists of identifying interpretable equations, reflecting the nature of the mechanisms generating the signals. The implemented improvements involve almost all aspects of GP, from the knowledge representation and the genetic operators to the fitness function. The unique capabilities of genetic programming, to accommodate prior information and knowledge, are also leveraged effectively. The proposed upgrades cover the most important applications of empirical modeling of time series, ranging from the identification of autoregressive systems and partial differential equations to the search of models in terms of dimensionless quantities and appropriate physical units. Particularly delicate systems to identify, such as those showing hysteretic behavior or governed by delayed differential equations, are also addressed. The potential of the developed tools is substantiated with both a battery of systematic numerical tests with synthetic signals and with applications to experimental data.
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Affiliation(s)
- A Murari
- Consorzio RFX (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA), Corso Stati Uniti 4, 35127 Padova, Italy Istituto per la Scienza e la Tecnologia dei Plasmi, CNR, Padova, Italy
| | - E Peluso
- Department of Industrial Engineering, University of Rome "Tor Vergata," via del Politecnico 1, Roma, Italy
| | - L Spolladore
- Department of Industrial Engineering, University of Rome "Tor Vergata," via del Politecnico 1, Roma, Italy
| | - R Rossi
- Department of Industrial Engineering, University of Rome "Tor Vergata," via del Politecnico 1, Roma, Italy
| | - M Gelfusa
- Department of Industrial Engineering, University of Rome "Tor Vergata," via del Politecnico 1, Roma, Italy
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4
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Sorcini D, Stella A, Scialdone A, Sartori S, Marra A, Rossi R, De Falco F, Adamo FM, Dorillo E, Geraci C, Arcaleni R, Rompietti C, Esposito A, Moretti L, Mameli MG, Martelli MP, Falini B, Sportoletti P. FLT3-targeted therapy restores GATA1 pathway function in NPM1/FLT3-ITD mutated acute myeloid leukaemia. EJHaem 2023; 4:1100-1104. [PMID: 38024637 PMCID: PMC10660397 DOI: 10.1002/jha2.738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 12/01/2023]
Abstract
One-third of newly diagnosed adult acute myeloid leukaemia (AML) carry FLT3 mutations, which frequently occur together with nucleophosmin (NPM1) mutations and are associated with worse prognosis. FLT3 inhibitors are widely used in clinics with limitations due to drug resistance. AML cells carrying FLT3 mutations in both mouse models and patients present low expression of GATA1, a gene involved in haematopoietic changes preceding AML. Here, we show that FLT3 inhibition induces cellular responses and restores the GATA1 pathway and functions in NPM1/FLT3-ITD mutated AML, thus providing a new mechanism of action for this drug.
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Affiliation(s)
- D Sorcini
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - A Stella
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - A Scialdone
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - S Sartori
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - A Marra
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - R Rossi
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - F De Falco
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - FM Adamo
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - E Dorillo
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - C Geraci
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - R Arcaleni
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - C Rompietti
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - A Esposito
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - L Moretti
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - MG Mameli
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - MP Martelli
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - B Falini
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
| | - P Sportoletti
- Department of Medicine and SurgeryCentro di Ricerca Emato‐OncologicheUniversity of PerugiaPerugiaItaly
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5
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La Rocca E, Rancati T, Rossi R, Rossi G, Benini A, Volpi G, Cavedon C, Mazzarotto R. Study of a Geometric Score to Identify the Increased Risk of Local Failure after SBRT for Locally Advanced Pancreatic Cancer (LAPC). Int J Radiat Oncol Biol Phys 2023; 117:e311. [PMID: 37785123 DOI: 10.1016/j.ijrobp.2023.06.2338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) A previous analysis on an institutional cohort of LAPC patients, treated with intensive induction chemotherapy followed by SBRT, proved that local failures (LFs) predominantly occurred within the RT field. This suggests a specific efficacy of a complete covering of the macroscopic (GTV) aggressive disease with high doses (i.e., simultaneous boost [SIB] doses). Still, this is often not feasible due to the proximity of extremely radiosensitive organs at risk (OARs), which forces the use of "Simultaneous Integrated Protection" (SIP), limiting the dose to safe values in a portion of the GTV. This analysis aimed to quantitatively assess the role of GTV size and incomplete GTV covering with SIB in increasing the risk of LF. MATERIALS/METHODS We included 51 consecutive LAPC pts treated with SBRT (Nov 2016 - Nov 2019): 30 Gy in 5 fractions to the tumor PTV, 50 Gy SIB to the region of vessel abutment/encasement, 25 Gy SIP to the overlap between tumor PTV, and the Planning OAR volumes. We used univariate/multivariable survival analysis (UVA/MVA, Cox regression, Kaplan-Meier Curves, Log-Rank test) to assess the association of LF with the GTV size and the amount of the GTV which the SIB did not cover. Specifically, we defined a set of incomplete GTV-covering levels: GTV75 (= yes if less than 75% of the GTV was included in the 50 Gy SIB isodose), GTV70, GTV50 and GTV30. Variables with p≤0.2 at UVA were included for MVA assessment. MVA models were considered relevant if their likelihood was significantly higher when compared to UVA. RESULTS With a median follow-up of 17 months (range 1.4-47) 12 pts experienced LF. The GTV size (p = 0.007, risk factor for LF, Hazard Ratio [HR] 1.04 for 1 cc increase in GTV size) and GTV70 (p = 0.2, risk factor, HR = 3.73 for GTV70 = yes) were selected at UVA and included in MVA. To build a simple decision tool, we dichotomized the GTV size as below/above 25 cc (selected from Youden Index on the ROC curve): HR = 9.3 if GTV>25 cc. We used dichotomized GTV size and GTV70 to build a 3-level Geometric Score for the prediction of the risk of LF: [Low Risk (LR)] if "GTV<25cc AND GTV70 = no"; [Intermediate Risk (IR)] if "GTV>25cc OR GTV70 = yes"; [High Risk (HiR)] if "GTV>25cc AND GTV70 = yes". Pts classified at HiR had a significantly higher probability of LF: HR = 6.9 (95% CI 1.5-32.9) compared to LR, and HR = 13.2 (95% CI 3.6-48.4) when compared to IR. 10/12 LFs are in the HiR group. CONCLUSION A large GTV size, coupled with an incomplete (<70%) covering of GTV from the SIB, highly increases the risk of LF: 62% actuarial probability in the HiR group vs 7% in the LR/IR groups. Full coverage of the GTV with SIB would be of clinical relevance for pts with large macroscopic tumors. The Geometric Score could be used to select pts that would effectively benefit from online tumor tracking (e.g., with an MRI-Linac), allowing a reduction of the SIP volume and a consequent decrease in the amount of GTV left uncovered by the SIB.
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Affiliation(s)
- E La Rocca
- Department of Radiation Oncology, University of Verona Hospital Trust, Verona, Italy
| | - T Rancati
- Fondazione IRCCS Istituto Nazionale dei Tumori, Data Science Unit, Milan, Italy
| | - R Rossi
- Department of Radiation Oncology, University of Verona Hospital Trust, Verona, Italy
| | - G Rossi
- Department of Radiation Oncology, University of Verona Hospital Trust, Verona, Italy
| | - A Benini
- Department of Radiation Oncology, University of Verona Hospital Trust, Verona, Italy
| | - G Volpi
- Department of Radiation Oncology, University of Verona Hospital Trust, Verona, Italy
| | - C Cavedon
- Medical Physics Unit, University of Verona Hospital Trust, Verona, Italy
| | - R Mazzarotto
- Department of Radiation Oncology, University of Verona Hospital Trust, Verona, Italy
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6
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Luciano M, Sampogna G, D'Ambrosio E, Rampino A, Amore M, Calcagno P, Rossi A, Rossi R, Carmassi C, Dell'Osso L, Bianciardi E, Siracusano A, Della Rocca B, Di Vincenzo M, Fiorillo A. One-year efficacy of a lifestyle behavioural intervention on physical and mental health in people with severe mental disorders: results from a randomized controlled trial. Eur Arch Psychiatry Clin Neurosci 2023:10.1007/s00406-023-01684-w. [PMID: 37665401 DOI: 10.1007/s00406-023-01684-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/14/2023] [Indexed: 09/05/2023]
Abstract
This multicentric randomized controlled trial (RCT), carried out in six Italian University mental health sites, aims to test the efficacy of a six-month psychosocial intervention (LYFESTYLE) on Body Mass Index (BMI), body weight, waist circumference, fasting glucose, triglycerides, cholesterol, Framingham and HOmeostasis Model Assessment of insulin resistance (HOMA-IR) indexes in patients with schizophrenia, bipolar disorder, and major depression. Moreover, the efficacy of the intervention has also been tested on several other physical and mental health domains. Patients were randomly allocated to receive the six-month experimental intervention (LIFESTYLE) or a behavioural control intervention. All enrolled patients were assessed at baseline and after one year. We recruited 401 patients (206 in the experimental and 195 in the control group) with a diagnosis of schizophrenia or other psychotic disorder (29.9%), bipolar disorder (43.3%), or major depression (26.9%). At one year, patients receiving the experimental intervention reported an improvement in body mass index, body weight, waist circumference, HOMA-IR index, anxiety and depressive symptoms and in quality of life. Our findings confirm the efficacy of the LIFESTYLE intervention in improving physical and mental health-related outcomes in patients with severe mental illnesses after one year.
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Affiliation(s)
- M Luciano
- Department of Psychiatry, University of Campania "L. Vanvitelli", Largo Madonna Delle Grazie 80039, Naples, Italy.
| | - G Sampogna
- Department of Psychiatry, University of Campania "L. Vanvitelli", Largo Madonna Delle Grazie 80039, Naples, Italy
| | - E D'Ambrosio
- Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari "Aldo Moro", Bari, Italy
| | - A Rampino
- Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari "Aldo Moro", Bari, Italy
| | - M Amore
- Section of Psychiatry, Department of Neuroscience, Ophthalmology, Genetics and Infant-Maternal Science, University of Genoa, Genoa, Italy
| | - P Calcagno
- Section of Psychiatry, Department of Neuroscience, Ophthalmology, Genetics and Infant-Maternal Science, University of Genoa, Genoa, Italy
| | - A Rossi
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - R Rossi
- Department of System Medicine, University of Rome Tor Vergata, Rome, Italy
| | - C Carmassi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - L Dell'Osso
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - E Bianciardi
- Department of System Medicine, University of Rome Tor Vergata, Rome, Italy
| | - A Siracusano
- Department of System Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Bianca Della Rocca
- Department of Psychiatry, University of Campania "L. Vanvitelli", Largo Madonna Delle Grazie 80039, Naples, Italy
| | - M Di Vincenzo
- Department of Psychiatry, University of Campania "L. Vanvitelli", Largo Madonna Delle Grazie 80039, Naples, Italy
| | - A Fiorillo
- Department of Psychiatry, University of Campania "L. Vanvitelli", Largo Madonna Delle Grazie 80039, Naples, Italy
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7
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Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Marques Bonet T. A global catalog of whole-genome diversity from 233 primate species. Science 2023; 380:906-913. [PMID: 37262161 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
Abstract
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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Affiliation(s)
- Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria
| | - Joseph D Orkin
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | | | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
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8
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKH. The landscape of tolerated genetic variation in humans and primates. Science 2023; 380:eabn8153. [PMID: 37262156 DOI: 10.1126/science.abn8197] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/22/2023] [Indexed: 06/03/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | | | - Petko P Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Balick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Joseph D Orkin
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para, Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação "Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N F da Silva
- Instituto Nacional de Pesquisas da Amazonia, Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso, Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University, New Haven, CT 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, PoB 16316, Addis Ababa 1000, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald - Insei Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore 168582, Republic of Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, 08010 Barcelona, Spain
| | - Amanda Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
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9
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath J, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Batallion T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O’Donnell A, Rehm H, Xu J, Rogers J, Marques-Bonet T, Kai-How Farh K. The landscape of tolerated genetic variation in humans and primates. bioRxiv 2023:2023.05.01.538953. [PMID: 37205491 PMCID: PMC10187174 DOI: 10.1101/2023.05.01.538953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence Summary Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Joshua G. Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Anastasia Dietrich
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Petko Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Lukas Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Daniel Balick
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna; Djerassiplatz 1, 1030, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna; 1030, Vienna, Austria
| | - Joseph D. Orkin
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d’anthropologie, Université de Montréal; 3150 Jean-Brillant, Montréal, QC, H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University; Aarhus, 8000, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development; Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Faculty of Sciences, Department of Organismal Biology, Unit of Evolutionary Biology and Ecology, Université Libre de Bruxelles (ULB); Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
| | | | - Julie Horvath
- North Carolina Museum of Natural Sciences; Raleigh, North Carolina, 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University; Durham, North Carolina , 27707, USA
- Department of Biological Sciences, North Carolina State University; Raleigh, North Carolina , 27695, USA
- Department of Evolutionary Anthropology, Duke University; Durham, North Carolina , 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabricio Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah; Salt Lake City, Utah, 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para; Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development; Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia – RedeFauna; Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica – ComFauna; Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação “Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N. F. da Silva
- Instituto Nacional de Pesquisas da Amazonia; Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso; Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University; San Antonio, Texas, 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | | | - Joe H. Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University; New Haven, Connecticut, 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | | | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen; Copenhagen, DK-2100, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center; 1369 West Wenyi Road, Hangzhou, 311121, China
- Women’s Hospital, School of Medicine, Zhejiang University; 1 Xueshi Road, Shangcheng District, Hangzhou, 310006, China
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office; P.O.Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health; 17493 Greifswald - Isle of Riems, Germany
| | - Minh D. Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University; Hanoi, 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart; 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Av. Doctor Aiguader, N88, Barcelona, 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation; C. Wellington 30, Barcelona, 08005, Spain
| | - Thomas Batallion
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune; Nho Quan District, Ninh Binh Province, 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature; 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre; Singapore 168582, Republic of Singapore
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland; Chambers Street, Edinburgh, EH1 1JF, UK
- School of Geosciences, University of Edinburgh; Drummond Street, Edinburgh, EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research; 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen; 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Amanda Melin
- Leibniz Science Campus Primate Cognition; 37077 Göttingen, Germany
- Department of Anthropology & Archaeology and Department of Medical Genetics
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
- Alberta Children’s Hospital Research Institute; University of Calgary; 2500 University Dr NW T2N 1N4, Calgary, Alberta, Canada
| | | | - Robin M. D. Beck
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Christian Roos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH8 9XP, UK
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Monkol Lek
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research; Kellnerweg 4, 37077 Göttingen, Germany
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Genetics, Yale School of Medicine; New Haven, Connecticut, 06520, USA
| | - Anne O’Donnell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Heidi Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Toyota Technological Institute at Chicago; Chicago, Illinois, 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
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Spasov G, Rossi R, Vanossi A, Cottini C, Benassi A. A critical analysis of the CFD-DEM simulation of pharmaceutical aerosols deposition in extra-thoracic airways. Int J Pharm 2022; 629:122331. [DOI: 10.1016/j.ijpharm.2022.122331] [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] [Received: 07/27/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022]
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11
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Mietto M, Neri M, Ricci F, Rossi R, Margutti A, Nagliati V, Selvatici R, Ferlini A, Falzarano M. VP.22 Dystrophin transcript profile in urinary stem cells allows to study the impact of missense mutations. Neuromuscul Disord 2022. [DOI: 10.1016/j.nmd.2022.07.122] [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: 11/05/2022]
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12
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Jannini T, Rossi R, Sconci V, Bonanni R, De Michele F, Cavallo G, Siracusano A, Rossi A, Di Lorenzo G, Jannini E, Ciocca G. Italian validation of Arizona Sexual Experience (ASEX) on patients suffering from psychotic spectrum disorders. Eur Psychiatry 2022. [PMCID: PMC9566763 DOI: 10.1192/j.eurpsy.2022.325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Introduction Many forms of mental disorders, especially psychotic disorders are characterized also by a worsening of sexual functioning. Sexual dysfunction has been shown to significantly correlate with a longer duration of untreated psychosis and with heavier psychotic symptomatology. Objectives The aim of this study is to validate the Italian version of the Arizona Sexual Experience (ASEX), a very handy and reliable tool to assess sexual dysfunction, in a population of people suffering from psychotic spectrum disorders. Methods Seventy-three psychiatric patients were recruited and assessed for mental illness and sexual functioning. We administered the Italian version of ASEX, adequately translated by two expert bilinguals. After 15 days we administered once again the test for test-retest reliability. Results Validation of ASEX revealed Cronbach’s coefficients >0.70 in both single items as in the total score. In addition, the test-retest reliability revealed Pearson’s coefficients >0.50 in the various domains. Confirmatory factor analysis revealed good fit indexes for the two factors model of ASEX (SRMR=0.54; CFI=0.974; RMSEA=0.135). Conclusions
This study represents the first validation in the Italian psychiatric context of a very useful specific tool for the sexual assessment in people suffering from mental illness. Our analysis revealed good psychometric characteristics in terms of confirmatory factor analysis, internal consistency, and test-retest reliability. Disclosure No significant relationships.
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Janiak MC, Silva FE, Beck RMD, de Vries D, Kuderna LFK, Torosin NS, Melin AD, Marquès-Bonet T, Goodhead IB, Messias M, da Silva MNF, Sampaio I, Farias IP, Rossi R, de Melo FR, Valsecchi J, Hrbek T, Boubli JP. 205 newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Mol Ecol 2022; 31:3888-3902. [PMID: 35638312 PMCID: PMC9546496 DOI: 10.1111/mec.16554] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022]
Abstract
Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.
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Affiliation(s)
- Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Felipe E Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Brazil.,Department of Evolutionary Biology and Ecology, Université Libre de Bruxelles, Belgium
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Lukas F K Kuderna
- Ilumina Inc., Hayward, CA, USA.,Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Nicole S Torosin
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Amanda D Melin
- Department of Anthropology & Archaeology and Department of Medical Genetics, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Barcelona, Spain
| | - Ian B Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom
| | - Mariluce Messias
- Department of Biology, Universidade Federal de Rondônia, Porto Velho, Brazil
| | - Maria N F da Silva
- Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Brazil
| | | | - Izeni P Farias
- Laboratory of Evolution and Animal Genetics, Universidade Federal do Amazonas, Brazil
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Brazil
| | - Fabiano R de Melo
- Department of Forestry Engineering, Universidade Federal de Viçosa, Brazil
| | - João Valsecchi
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Brazil
| | - Tomas Hrbek
- Department of Biology, Trinity University, San Antonio, TX, USA
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford, United Kingdom.,Coleção de Mamíferos, Instituto Nacional de Pesquisas da Amazônia, Brazil
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Gräff I, Pin M, Ehlers P, Seidel M, Hossfeld B, Dietz-Wittstock M, Rossi R, Gries A, Ramshorn-Zimmer A, Reifferscheid F, Reinhold T, Band H, Kuhl KH, König MK, Kasberger J, Löb R, Krings R, Schäfer S, Wienen IM, Strametz R, Wedler K, Mach C, Werner D, Schacher S. Empfehlungen zum strukturierten Übergabeprozess in der zentralen Notaufnahme. Notf Rett Med 2022. [DOI: 10.1007/s10049-020-00810-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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15
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Boeckelmann M, Glaser N, Dejas F, Östreicher I, Grüner J, Höche A, Akanbi S, Thiemig D, Rossi R. „Pediatric inflammatory multisystem syndrome“ – Erfahrungen aus einer Berliner Kinderklinik. Monatsschr Kinderheilkd 2022; 170:139-145. [PMID: 35079175 PMCID: PMC8773388 DOI: 10.1007/s00112-021-01394-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2021] [Indexed: 12/14/2022]
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16
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Nimbi FM, Magno S, Agostini L, Di Micco A, Maggiore C, De Cesaris BM, Rossi R, Galizia R, Simonelli C, Tambelli R. Sexuality in breast cancer survivors: sexual experiences, emotions, and cognitions in a group of women under hormonal therapy. Breast Cancer 2022; 29:419-428. [PMID: 34988885 DOI: 10.1007/s12282-021-01320-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Earlier diagnosis and improved treatments have led to better outcomes in breast cancer, making quality of life a key issue. Sexuality represents a pillar of quality of life, although it is often neglected by both healthcare providers and patients when it comes to cancer. This study aims to explore the differences in sexual functioning, distress, psychopathology, emotions, and cognitions between breast cancer patients under hormonal treatment and controls. METHODS Seventy-nine women (age range between 24 and 69 years) in hormonal therapy for breast cancer completed a self-reported protocol. A matched control group of 103 women was randomly extracted from an Italian general population database. Eight self-report questionnaires exploring biopsychosocial factors were administered. RESULTS The current study showed an impaired sexuality in breast cancer patients compared to controls. Breast cancer women under hormonal treatment were characterized by diminished or absent sexual activity (chi2 = 36.16; p < 0.001), lower level of sexual functioning in all areas except for pain (F(1,180) = 8.1; p < 0.01), higher sexual (F(1,180) = 10.08; p < 0.001) and psychological distress (F(1,180) = 6.23; p < 0.05), higher scores in Difficulties in Identifying Feelings (F(1,180) = 7.31; p < 0.01) and Externally Oriented Thinking (F(1,180) = 6.64; p < 0.05), higher level of negative emotions related to sexuality (F(1,180) = 11.13; p < 0.001), and more rigid cognition towards peculiar aspects of sexuality, such as Failure Disengagement Thoughts (F(1,180) = 22.01; p < 0.001) and Age related Beliefs (F(1,180) = 5.7; p < 0.05). CONCLUSIONS Health care providers do not usually assess those issues in their routine practice, so that sexuality remains an unmet need with remarkable effects on general health and quality of life.
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Affiliation(s)
- F M Nimbi
- Department of Dynamic, Clinical and Health Psychology (Ex Department of Dynamic and Clinical Psychology), Sapienza University of Rome, Rome, Italy.
| | - S Magno
- University Hospital Foundation A Gemelli IRCCS, Rome, Italy
| | - L Agostini
- University Hospital Foundation A Gemelli IRCCS, Rome, Italy
| | - A Di Micco
- University Hospital Foundation A Gemelli IRCCS, Rome, Italy
| | - C Maggiore
- University Hospital Foundation A Gemelli IRCCS, Rome, Italy
| | - B M De Cesaris
- University Hospital Foundation A Gemelli IRCCS, Rome, Italy
| | - R Rossi
- Institute of Clinical Sexology, Rome, Italy
| | - R Galizia
- Department of Dynamic, Clinical and Health Psychology (Ex Department of Dynamic and Clinical Psychology), Sapienza University of Rome, Rome, Italy
| | - C Simonelli
- Department of Dynamic, Clinical and Health Psychology (Ex Department of Dynamic and Clinical Psychology), Sapienza University of Rome, Rome, Italy
| | - R Tambelli
- Department of Dynamic, Clinical and Health Psychology (Ex Department of Dynamic and Clinical Psychology), Sapienza University of Rome, Rome, Italy
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Boncinelli V, Barbero G, Lenzi E, Genazzani A, Mori G, Molo M, Piaggi P, Rossetto C, Rossi R, Tampelli A, Tomà F, Veglia F, Caruso S. Corrélation entre l’imaginaire érotique et le désir sexuel d’un échantillon d’hommes et de femmes italiens : une étude observationnelle de la Fédération italienne de sexologie scientifique (FISS). Sexologies 2021. [DOI: 10.1016/j.sexol.2021.11.003] [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: 10/19/2022]
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18
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Selvatici R, Rossi R, Fang M, Lu J, Sansone V, Falzarano M, Gualandi F, Bello L, Pegoraro E, Ferlini A. DMD/BMD - GENETICS. Neuromuscul Disord 2021. [DOI: 10.1016/j.nmd.2021.07.142] [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: 11/28/2022]
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19
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Longo L, Jannini T, Merlo M, Bombacci C, Biancolino M, Rossi R, Carlo ED, Niolu C, Siracusano A, Lorenzo GD. Suicidality and relation with dissociation and alexithymia in PNES and conversion disorder. Eur Psychiatry 2021. [PMCID: PMC9479824 DOI: 10.1192/j.eurpsy.2021.1576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Introduction Amongst different subtypes of Conversion Disorder (CD), DSM-V lists the Psychogenic Non-epileptic seizures (PNES). PNES are defined as episodes that visually resemble epileptic seizures but, etiologically, they are not due to electrical discharges in the brain. Objectives Our study aims to explore the differences between PNES and other CDs. In particular, we studied the suicidality and its correlations with dissociation and alexithymia. Methods Patients, recruited from the Psychiatry and Clinical Psychology Unit of the Fondazione Policlinico Tor Vergata, Rome, Italy, were diagnosed with PNES (n=22) and CD (n=16) using the DSM-5 criteria. Patients underwent the following clinical assessments: HAM-D, BDI, DES, BHS, TAS, CTQ. Results PNES showed significantly higher scores than CD in all assessments, except for BDI-somatic (p=0.39), BHS-feeling (p=0.86), and the presence of childhood trauma. PNES also showed significantly higher suicidality (p = 0.003). By controlling for the confounding factor “depression”, in PNES suicidality (and in particular the BHS-loss of motivation) appears to be correlated with DES-total score (p = 0.008), DES-amnesia (p = 0.002) and DES -derealization-depersonalization (p = 0.003). On the other hand, in CDs, the BHS-total score shows a correlation with the TAS-total score (p = 0.03) and BHS-Feelings with TAS-Externally-Oriented Thinking (p = 0.035), while only the BHS-Loss of motivation appears correlated with DES-Absorption (p = 0.011). Conclusions Our study shows significant differences between PNES and CD, in several symptomatologic dimensions, including suicidality. Indeed, in PNES suicidality appears to be related to dissociation, while in CDs it appears mainly to be correlated with alexithymia.
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Longo L, Jannini T, Merlo M, Cecora V, Gagliano M, D’Imperia B, Daverio A, Monaco L, Rossi R, Niolu C, Siracusano A, Lorenzo GD. Suicidality in post-traumatic stress disorder (PTSD) and complex PTSD (CPTSD). Eur Psychiatry 2021. [PMCID: PMC9471773 DOI: 10.1192/j.eurpsy.2021.390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
IntroductionInternational Classification of Diseases 11th Revision (ICD-11) has inserted complex post-traumatic stress disorder (cPTSD) as a clinically distinct disorder, different from PTSD. The diagnosis of cPTSD has the same requirements for the one of PTSD, in addition to disturbances of self-organization (DSO – e.g., disturbances in relationships, affect dysregulation, and negative self-concept).ObjectivesThis study aimed to explore suicidality in PTSD and cPTSD. We examined also the association between clinical dimensions of hopelessness (feelings, loss of motivation, future expectations) and other symptomatologic variables.MethodsThe sample, recruited at the Fondazione Policlinico Tor Vergata, Rome, Italy, consisted of 189 subjects, 132 diagnosed with PTSD, and 57 with cPTSD, according to the ICD-11 criteria. Participants underwent the following clinical assessments: Clinician-Administered PTSD Scale (CAPS), Impact of Event Scale-Revised (IES), Beck Depression Inventory (BDI), Symptom Checklist-90-Revised (SCL-90), Dissociative Experience Scale (DES), Beck Hopelessness Scale (BHS).ResultscPTSD showed significantly higher BHS-total (p = 0.01) and BHS-loss of motivation subscale (p <0.001) scores than PTSD. Besides, cPTSD showed significantly higher scores in all clinical variables except for the IES-intrusive subscale. By controlling for the confounding factor “depression”, suicidality in cPTSD (and in particular the BHS-total) appears to be correlated with IES-total score (p = 0.042) and with DES-Absorption (p = 0.02). Differently, no such correlations are found in PTSD.ConclusionsOur study shows significant symptomatologic differences between PTSD and cPTSD, including suicidality. Indeed, suicidality in cPTSD appears to be correlated with the “loss of motivation” dimension, which fits well within the ICD-11 criteria of DSO.DisclosureNo significant relationships.
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Collazzoni A, Imburgia L, Talevi D, Pacitti F, Gregori E, Stratta P, Socci V, Rossi R. Childhood family stress and adult resilience in a sample of depressed patients. J Affect Disord 2021; 282:255-257. [PMID: 33418375 DOI: 10.1016/j.jad.2020.12.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND The aim of this study is to explore the effect of childhood family stress on depression, personal, and social resilience in depressed patients. METHODS We assessed childhood family stress (RFQ), depression (BSI, depression subscale), and resilience (RSA) in 152 depressed patients, 70 males, and 82 females. We calculated the 33rd and 66th percentiles of RFQ scores to divide the sample among Low, Medium, and High RFQ subgroups. A one-way ANOVA has been carried out to explore the differences between the variables in the subgroups. Finally, two regression analyses with depression, as the dependent variable, and resilience, divided for stress-sensitive and no stress-sensitive factors as independent variables, have been implemented. RESULTS The one-way ANOVA showed that the Low subgroup had a positive profile, the Medium had an intermediate profile, while the High had a negative one for depression, personal (structured style and social competence), and interpersonal (social resources) resilience. The other factors (perception of self, planned future, and family cohesion) did not show differences in the subgroups, suggesting they are no stress sensitive. Regression analysis showed that no stress-sensitive factors have a constant and significant predictive value for depression in all subgroups; while, stress-sensitive ones showed a growing predictive value for depression from Low to Medium, but not in High, suggesting a ceiling effect. LIMITATIONS The use of self-report measures, the cross-sectional nature of the study, and the lack of a non-clinical and/or outpatient samples. CONCLUSIONS This study provides a contribution to the understanding of the effect of childhood family stress on adult resilience and depression.
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Affiliation(s)
- A Collazzoni
- Department of Biotechnological and Applied Clinical Sciences (DISCAB), University of L'Aquila, Via Vetoio, Coppito II, 67100, L'Aquila, Italy; Renewed Freedom Center for Rapid Anxiety Relief, Division of Strategic Cognitive Behavioral Institute, Los Angeles, CA, USA.
| | - L Imburgia
- Department of Biotechnological and Applied Clinical Sciences (DISCAB), University of L'Aquila, Via Vetoio, Coppito II, 67100, L'Aquila, Italy
| | - D Talevi
- Department of Biotechnological and Applied Clinical Sciences (DISCAB), University of L'Aquila, Via Vetoio, Coppito II, 67100, L'Aquila, Italy
| | - F Pacitti
- Department of Biotechnological and Applied Clinical Sciences (DISCAB), University of L'Aquila, Via Vetoio, Coppito II, 67100, L'Aquila, Italy
| | - E Gregori
- Department of Biotechnological and Applied Clinical Sciences (DISCAB), University of L'Aquila, Via Vetoio, Coppito II, 67100, L'Aquila, Italy
| | - Paolo Stratta
- Department of Mental Health, ASL1, Via Capo Croce 1, 67100, L'Aquila, Italy
| | - Valentina Socci
- Department of Biotechnological and Applied Clinical Sciences (DISCAB), University of L'Aquila, Via Vetoio, Coppito II, 67100, L'Aquila, Italy
| | - R Rossi
- Department of Systems Medicine, PhD program, Tor Vergata University of Rome, Via Cracovia 50, 00133 Roma, Italy
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Cinotti E, Tognetti L, Campoli M, Liso F, Cicigoi A, Cartocci A, Rossi R, Rubegni P, Perrot JL. Super-high magnification dermoscopy can aid the differential diagnosis between melanoma and atypical naevi. Clin Exp Dermatol 2021; 46:1216-1222. [PMID: 33486758 DOI: 10.1111/ced.14566] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/21/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND Dermoscopy is the most widely used noninvasive imaging technique for the clinical diagnosis of melanoma (MM). Super-high (× 400) magnification dermoscopy (D400) has recently been developed; compared with traditional dermoscopy, it can reveal additional features, down to the identification of single melanocytes in the skin. OBJECTIVES To evaluate which structures are visible at D400 and to compare them in atypical naevi and MMs. METHODS A prospective observational multicentre study was conducted. We enrolled patients who were identified as having atypical melanocytic skin lesions by clinical and/or × 20 magnification dermoscopy (D20) examination, and who were assigned to either excision or follow-up. Lesions were imaged by videodermoscopy at D20 and D400. The presence of pigmented cells and their features were assessed at D400. RESULTS In total, there were 79 patients with 57 naevi and 31 MMs. Of the total 88 lesions, 63 (71.6%) were given a histological diagnosis, while the others were followed up for ≥ 12 months, during which they showed no change and were all diagnosed as naevi. Pigmented cells were identified in > 90% of the lesions at D400. Compared with naevi, MMs had a higher frequency of scattered, large, irregular (in shape and size), dendritic/roundish, violet/blue pigmented cells under D400 (P < 0.001). Moreover, dots (P < 0.01), out-of-focus blue structureless areas (P < 0.01) and vessels (P < 0.001) were also more frequent in MMs than in naevi at D400. CONCLUSIONS This study showed that D400 can reveal many elements not otherwise visible in traditional D20 dermoscopy, such as pigmented cells and their morphology, which could be useful for the diagnosis of MM.
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Affiliation(s)
- E Cinotti
- Section of Dermatology, University of Siena, Santa Maria alle Scotte Hospital, Siena, Italy
| | - L Tognetti
- Section of Dermatology, University of Siena, Santa Maria alle Scotte Hospital, Siena, Italy
| | - M Campoli
- Section of Dermatology, University of Siena, Santa Maria alle Scotte Hospital, Siena, Italy
| | - F Liso
- Section of Dermatology, University of Siena, Santa Maria alle Scotte Hospital, Siena, Italy
| | - A Cicigoi
- Section of Dermatology, University of Siena, Santa Maria alle Scotte Hospital, Siena, Italy
| | - A Cartocci
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - R Rossi
- Department of Dermatology, Skin Center Senigallia, Senigallia, Italy
| | - P Rubegni
- Section of Dermatology, University of Siena, Santa Maria alle Scotte Hospital, Siena, Italy
| | - J L Perrot
- Department of Dermatology Department, University Hospital of Saint-Etienne, Saint-Etienne, France
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Palazzo M, Vizzarri F, Arvay J, D'Alessandro A, Martemucci G, Casamassima D, Ratti S, Corino C, Rossi R. Dietary effect of dried bay leaves (Laurus nobilis) meal on selected productive performances and on quality meat traits in growing rabbits. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Galaverni M, Chendi A, Trojani V, Bertolini M, Botti A, Ciammella P, Ruggieri M, Giaccherini L, Blandino G, Manicone M, Rossi R, Timon G, Cozzi S, Bardoscia L, Solla S, Orlandi M, Fioroni F, Spaggiari L, Iori M, Iotti C. Radiomics Analysis of Stereotactic Body Radiation Therapy Patients with Lung Cancer as a Toxicity Biomarker. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1338] [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: 11/15/2022]
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Rossi R, FOCA F, Tontini L, Micheletti S, Romeo A, Altini M, Nanni O, Maltoni M. A New Integrated Healthcare Model: Radiotherapy and Palliative Care (RaP) Outpatient Clinic. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Rossi R, Falzarano M, Pinotti M, Balestra D, Neri M, Fortunato F, Mercuri E, Pane M, Gualandi F, Selvatici R, Ferlini A. NEW GENES AND DISEASES / NGS & RELATED TECHNIQUES. Neuromuscul Disord 2020. [DOI: 10.1016/j.nmd.2020.08.322] [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: 11/16/2022]
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Falzarano M, Spedicato N, Margutti A, Dani RE, Rossi R, Zia S, Reschiglian P, Roda B, Grilli A, Bicciato S, Ferlini A. MUSCLE FUNCTION & HOMEOSTASIS / MOLECULAR THERAPEUTIC APPROACHES. Neuromuscul Disord 2020. [DOI: 10.1016/j.nmd.2020.08.072] [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: 10/23/2022]
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Falzarano M, Spedicato N, Rossi R, Dani RE, Margutti A, Morgan J, Ala P, Torelli S, Montanaro F, Muntoni F, Ferlini A. DMD – BIOMARKERS & OUTCOME MEASURES. Neuromuscul Disord 2020. [DOI: 10.1016/j.nmd.2020.08.127] [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: 10/23/2022]
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Gabusi A, Rossi R, Gissi DB. Malignant transformation of a clinically and histologically healed lichenoid lesion after amalgam removal: A case report and literature review. J Stomatol Oral Maxillofac Surg 2020; 122:208-211. [PMID: 32659410 DOI: 10.1016/j.jormas.2020.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/06/2020] [Indexed: 12/01/2022]
Abstract
Lichenoid contact lesions (LCLs) frequently develop in close contact with amalgam restorations and may regress after amalgam removal, especially when patch testing is positive to amalgam components. However, established criteria to define true LCLs healing are missing and clinical disappearance of the lesion may not always correspond to a complete regression of histological lichenoid tissue reaction. Similarly to other lichenoid lesions of the oral cavity, LCLs are included among potentially malignant disorders although its malignant transformation remains controversial. As a result, with no clear indications for neoplastic risk assessment, the management of patients with LCLs may be challenging. The present report describes the unusual case of an oral squamous cell carcinoma (OSCC) arising in the same site where 6 years before an amalgam-associated LCL had clinically and histologically healed after restoration replacement. A review of the few literature reports of amalgam-associated LCLs developing to OSCC is also provided.
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Affiliation(s)
- A Gabusi
- Section of oral sciences, department of biomedical and neuromotor sciences, university of Bologna, via San Vitale, 59, 40159 Bologna, Italy.
| | - R Rossi
- Section of oral sciences, department of biomedical and neuromotor sciences, university of Bologna, via San Vitale, 59, 40159 Bologna, Italy.
| | - D B Gissi
- Section of oral sciences, department of biomedical and neuromotor sciences, university of Bologna, via San Vitale, 59, 40159 Bologna, Italy.
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von Soosten H, Rother S, von Bismarck S, Rossi R. Das Modell der Berliner Kinderschutzambulanzen. Monatsschr Kinderheilkd 2020. [DOI: 10.1007/s00112-019-0651-2] [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: 10/27/2022]
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Spinella A, Macripo’ P, Cocchiara E, Galli E, Lumetti F, Magnani L, Coppi F, Mattioli AV, Rossi R, Boriani G, Salvarani C, Giuggioli D. AB0611 STRAIN ANALYSIS OF THE RIGHT VENTRICLE USING 2D-SPECKLE TRACKING ECHOCARDIOGRAPHY IN A COHORT OF PATIENTS WITH SYSTEMIC SCLEROSIS. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.2962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:Systemic Sclerosis (SSc) is a rare and life-threatening connective tissue disease with multiple organ impairment. Cardio-pulmonary involvement is common: pulmonary fibrosis, pulmonary hypertension (PH), and electrical disorders are the most serious complications and causes of increased mortality.Objectives:We evaluated features related with the onset and development of PH in a cohort of SSc patients. We further studied ecocardiographic abnormalities, by means of 2D-speckle tracking echocardiography (STE) with specific reference to the right ventricular strain measure (RV-strain).Methods:We analyzed data from 50 SSc patients (pts) referred to our University-based Rheumatology Centre and SSc Unit from January 2007 to June 2019 (F/M 45/5; lc/dcSSc 45/5; mean age 59.20±14.357 years; mean disease duration 12.08±8.75 years). All pts underwent general and cardio-pulmonary assessment in our Cardio-Rheumatology Clinic. The following parameters were considered: blood exams, in particular inflammation indexes, uric acid test and serum autoantibodies; pulmonary function tests; high resolution scan of the lungs (HRCT); standard electrocardiogram (ECG) and RV-strain measured by 2D-STE. These examinations were performed according to clinical picture and current methodologies. We compared SSc subjects with (10/50) and without (40/50) PH diagnosis during follow-up regardless of treatments.Results:SSc pts with PH didn’t show significant alterations concerning RV-strain if compared with pts without PH (p=0.707). Nevertheless, RV-strain value was modified in relation to TAPSE alterations in all pts but this data correlated with right ventricular dilatation only in PH subjects. Furthermore, interesting significant values about dilatation of right and left atria (p=0.007, p=0.048), dilatation of inferior vena cava (p=0.037) and right ventricle (p=0.023) were observed. Left ventricular hypertrophy (p=0.012) as well as valvular insufficiencies (mitral and aortic) were more frequent in PH group too (p=0.016). These pts showed higher incidence of skin ulcers (p=0.0001), higher values of blood pressure (p=0.004), elevated uric acid levels (p=0,027) and anti-centromere antibodies positivity (p=0.0001).Conclusion:Our research provides further evidence of the prognostic value of echocardiographic findings in SSc subjects, with focus on PH. Population enlargement is ongoing in order to identify more accurate results about RV-strain, considering the efficacy of PH treatments on cardiac contractility. Speckle tracking echocardiography proves to be a sensitive, low-cost, non-invasive and reliable tool to detect early cardiac impairment in Ssc, full of potential future prospects.Disclosure of Interests:None declared
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Goretti E, Pallottini M, Rossi R, La Porta G, Gardi T, Cenci Goga BT, Elia AC, Galletti M, Moroni B, Petroselli C, Selvaggi R, Cappelletti D. Heavy metal bioaccumulation in honey bee matrix, an indicator to assess the contamination level in terrestrial environments. Environ Pollut 2020; 256:113388. [PMID: 31662258 DOI: 10.1016/j.envpol.2019.113388] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/10/2019] [Accepted: 10/11/2019] [Indexed: 05/13/2023]
Abstract
The most significant risk factor for organisms living in an environment contaminated by heavy metals is the metal bioavailability. Therefore, an efficient ecotoxicological approach to metal contamination is the measure of bioaccumulation level in target organisms. In this work, we characterized the heavy metal bioaccumulation in honey bees, Apis mellifera ligustica, collected at 35 sites from Umbria (Central Italy). The comparison of our data with selected Italian investigations revealed metal bioaccumulation in honey bee matrix of the same order of magnitude, with Cd showing a higher variability. To generalize the results, we developed a Honeybee Contamination Index (HCI) based on metal bioaccumulation in honey bees. An application of the HCI to the present dataset revealed cases of low (sixteen sites), intermediate (eighteen sites), and high (one site) metal contaminations. The comparison of HCI values from the Umbrian dataset with values calculated for other Italian and European metadata showed that most of the Umbrian sites fell in the portion of low and intermediate contamination conditions. HCI represented a reliable tool that provided a piece of concise information on metal contamination in terrestrial environments. Parallel to this effort, we have determined, the metal concentrations in the airborne particulate matter (PM10) at three regional background-monitoring stations in Umbria. These stations are representative of the average air quality of the areas of the investigated apiaries. A comparative analysis of metal enrichment factors in PM10, and honey bees suggested that the contamination in the bees was related to the PM10 values only to a minor extent. On the other side, a clear enrichment of metals such as Cd, Mn, Zn, and Cu in the honey bees appeared to depend on very local conditions and was probably related to the use of pesticides and fertilizers, and the resuspension of the locally contaminated soils and agriculture residues.
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Affiliation(s)
- E Goretti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce Di Sotto 8, 06123 Perugia, Italy.
| | - M Pallottini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce Di Sotto 8, 06123 Perugia, Italy
| | - R Rossi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce Di Sotto 8, 06123 Perugia, Italy
| | - G La Porta
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce Di Sotto 8, 06123 Perugia, Italy
| | - T Gardi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università degli Studi di Perugia, Borgo XX giugno 74, 06121 Perugia, Italy
| | - B T Cenci Goga
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, Via San Costanzo 4, 06126 Perugia, Italy
| | - A C Elia
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce Di Sotto 8, 06123 Perugia, Italy
| | - M Galletti
- ARPA Umbria, Unità Operativa Laboratorio Multisito Terni, 05022 Terni, Italy
| | - B Moroni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce Di Sotto 8, 06123 Perugia, Italy
| | - C Petroselli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce Di Sotto 8, 06123 Perugia, Italy
| | - R Selvaggi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce Di Sotto 8, 06123 Perugia, Italy
| | - D Cappelletti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce Di Sotto 8, 06123 Perugia, Italy
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Habberstad R, Frøseth T, Aass N, Bjerkeset E, Abramova T, Garcia-Alonso E, Caputo M, Rossi R, Boland J, Brunelli C, Lund JÅ, Kaasa S, Klepstad P. Clinical predictors for analgesic response to radiotherapy in patients with painful bone metastases. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz261.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Falzarano M, Spedicato N, Margutti A, El Dani R, Rossi R, Gualandi F, Selvatici R, Fang M, Lu Z, Zia S, Reschiglian P, Roda B, Grilli A, Bicciato S, Ferlini A. P.134Physical and transcriptional characterization of human urinary stem cell populations. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.190] [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: 10/25/2022]
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Rossi R, Trabanelli C, Falzarano M, Sabatelli P, Grilli A, Bicciato S, D'Amico A, Ferlini A, Gualandi F. P.386Genome and transcriptome analysis of COLVI genes and characterization of a new promising cellular model. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.548] [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: 11/16/2022]
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Giorgio D, Di Trana A, Di Napoli MA, Sepe L, Cecchini S, Rossi R, Claps S. Comparison of cheeses from goats fed 7 forages based on a new health index. J Dairy Sci 2019; 102:6790-6801. [PMID: 31178182 DOI: 10.3168/jds.2018-15857] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/12/2019] [Indexed: 12/28/2022]
Abstract
This study proposed the General Health Index of Cheese (GHIC) as an indicator for the presence of health-promoting compounds in cheese and compared the antioxidant capacity and phenolic and fatty acid contents of cheeses from goats consuming 7 forage species. Ninety-one homogeneous Red Syrian goats were randomly assigned to 1 of 7 feeding treatments (Festuca arundinacea, Hordeum vulgare, Triticosecale, Pisum sativum, Trifolium alexandrinum, Vicia sativa, and Vicia faba minor). The housed goat groups received the scheduled forage ad libitum. Forage species affected the antioxidant capacity, the phenolic and fatty acid contents, the Health Promoting Index, and the GHIC. Trifolium alexandrinum, Triticosecale, and Hordeum vulgare showed a clear advantage in terms of beneficial fatty acids content in goat cheese. Cheese from the Triticosecale group also showed a high antioxidant capacity value even if its polyphenol content was intermediate compared with others. Trifolium alexandrinum and Triticosecale had the highest value of the new index GHIC. This comparison suggests that there are important differences in fatty acid profile and polyphenol content among cheeses from goats fed grasses and legumes commonly used in the Mediterranean area. In this first approach, GHIC index, which combines the positive components found in cheese, seems to be a useful tool to provide an indication concerning the general health value of the product.
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Affiliation(s)
- D Giorgio
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Viale dell'Ateneo Lucano 10-85100, Italy
| | - A Di Trana
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Viale dell'Ateneo Lucano 10-85100, Italy.
| | - M A Di Napoli
- CREA Research Centre for Animal Production and Acquaculture, Bella Muro (PZ), S.S. 7 Via Appia-85051, Italy
| | - L Sepe
- CREA Research Centre for Animal Production and Acquaculture, Bella Muro (PZ), S.S. 7 Via Appia-85051, Italy
| | - S Cecchini
- Department of Sciences, University of Basilicata, Potenza, Viale dell'Ateneo Lucano 10-85100, Italy
| | - R Rossi
- CREA Research Centre for Animal Production and Acquaculture, Bella Muro (PZ), S.S. 7 Via Appia-85051, Italy
| | - S Claps
- CREA Research Centre for Animal Production and Acquaculture, Bella Muro (PZ), S.S. 7 Via Appia-85051, Italy
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O'Neill D, Griffin E, Doyle KM, Power S, Brennan P, Sheehan M, O'Hare A, Looby S, da Silva Santos AM, Rossi R, Thornton J. A Standardized Aspiration-First Approach for Thrombectomy to Increase Speed and Improve Recanalization Rates. AJNR Am J Neuroradiol 2019; 40:1335-1341. [PMID: 31320463 DOI: 10.3174/ajnr.a6117] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/31/2019] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Direct aspiration is a recognized technique for revascularization in large-vessel ischemic strokes. There is ongoing debate regarding its efficacy compared with stent retrievers. Every delay in achieving revascularization and a decrease in reperfusion rates reduces the likelihood of patients achieving functional independence. We propose a standardized setup technique for aspiration-first for all anterior circulation thrombectomy procedures for increasing speed and recanalization rates. MATERIALS AND METHODS We analyzed 127 consecutive patients treated by a standardized approach to thrombectomy with an intention to perform aspiration-first compared with 127 consecutive patients treated with a stent retriever-first approach. Key time metrics evaluated included groin to first angiogram, first angiogram to reperfusion, groin to first reperfusion, and length of the procedure. The degree of successful recanalization (TICI 2b-3) and the number of passes were compared between the 2 groups. RESULTS In 127 patients who underwent the standardized technique, the median time from groin puncture to first reperfusion was 18 minutes compared with 26 minutes (P < .001). The duration of the procedure was shorter compared with the stent retriever group (26 minutes in the aspiration first group versus 47 minutes, P < .001) and required fewer passes (mean, 2.4 versus 3.1; P < .05). A higher proportion of patients had a TICI score of 2b-3 in the aspiration-first group compared with stent retriever group (96.1% versus 85.8%, P < .005). CONCLUSIONS Our study highlights the increasing speed and recanalization rates achieved with fewer passes in a standardized approach to thrombectomy with an intention to attempt aspiration-first. Any attempt to reduce revascularization time and increase successful recanalization should be used.
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Affiliation(s)
- D O'Neill
- From the Interventional Neuroradiology Service (D.O., E.G., S.P., P.B., M.S., A.O., S.L., J.T.), Department of Radiology, Beaumont Hospital, Dublin, Ireland
| | - E Griffin
- From the Interventional Neuroradiology Service (D.O., E.G., S.P., P.B., M.S., A.O., S.L., J.T.), Department of Radiology, Beaumont Hospital, Dublin, Ireland .,Royal College of Surgeons (E.G., J.T.), Dublin, Ireland
| | - K M Doyle
- Department of Physiology (K.M.D., A.M.d.S.S., R.R.), School of Medicine, National University of Ireland, Galway, Ireland
| | - S Power
- From the Interventional Neuroradiology Service (D.O., E.G., S.P., P.B., M.S., A.O., S.L., J.T.), Department of Radiology, Beaumont Hospital, Dublin, Ireland
| | - P Brennan
- From the Interventional Neuroradiology Service (D.O., E.G., S.P., P.B., M.S., A.O., S.L., J.T.), Department of Radiology, Beaumont Hospital, Dublin, Ireland
| | - M Sheehan
- From the Interventional Neuroradiology Service (D.O., E.G., S.P., P.B., M.S., A.O., S.L., J.T.), Department of Radiology, Beaumont Hospital, Dublin, Ireland
| | - A O'Hare
- From the Interventional Neuroradiology Service (D.O., E.G., S.P., P.B., M.S., A.O., S.L., J.T.), Department of Radiology, Beaumont Hospital, Dublin, Ireland
| | - S Looby
- From the Interventional Neuroradiology Service (D.O., E.G., S.P., P.B., M.S., A.O., S.L., J.T.), Department of Radiology, Beaumont Hospital, Dublin, Ireland
| | - A M da Silva Santos
- Department of Physiology (K.M.D., A.M.d.S.S., R.R.), School of Medicine, National University of Ireland, Galway, Ireland
| | - R Rossi
- Department of Physiology (K.M.D., A.M.d.S.S., R.R.), School of Medicine, National University of Ireland, Galway, Ireland
| | - J Thornton
- From the Interventional Neuroradiology Service (D.O., E.G., S.P., P.B., M.S., A.O., S.L., J.T.), Department of Radiology, Beaumont Hospital, Dublin, Ireland.,Royal College of Surgeons (E.G., J.T.), Dublin, Ireland
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Cinotti E, Rossi R, Ferrara G, Tognetti L, Rubegni P, Perrot JL. Image Gallery: Super-high magnification dermoscopy can identify pigmented cells: correlation with reflectance confocal microscopy. Br J Dermatol 2019; 181:e1. [PMID: 31259403 DOI: 10.1111/bjd.17781] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E Cinotti
- Department of Medical, Surgical and Neurological Science, Dermatology Section, University of Siena, S. Maria alle Scotte Hospital, Viale Bracci 16, 53100, Siena, Italy
| | - R Rossi
- Department of Dermatology, Skin Center Senigallia, 60019, Senigallia, Italy
| | - G Ferrara
- Department of Anatomic Pathology, Macerata Hospital, 62100, Macerata, Italy
| | - L Tognetti
- Department of Medical, Surgical and Neurological Science, Dermatology Section, University of Siena, S. Maria alle Scotte Hospital, Viale Bracci 16, 53100, Siena, Italy
| | - P Rubegni
- Department of Medical, Surgical and Neurological Science, Dermatology Section, University of Siena, S. Maria alle Scotte Hospital, Viale Bracci 16, 53100, Siena, Italy
| | - J L Perrot
- Department of Dermatology, University Hospital of Saint-Etienne, 42055, Saint-Etienne, France
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Giami A, Rossi R, Domenech-Dorca G. Sexualités LGBT : nouvelles approches. Sexologies 2019. [DOI: 10.1016/j.sexol.2019.06.010] [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: 11/30/2022]
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Eleuteri S, Rossi R, Simonelli C. Comment aborder le travail clinique avec les clients bisexuels âgés et leurs partenaires ? Sexologies 2019. [DOI: 10.1016/j.sexol.2019.05.010] [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: 10/26/2022]
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Monteiro A, Dourmad J, Sitanaka N, Moreira C, Rossi R, Sangali C, Castilha L, Pozza P. PSVII-35 Using observed data as inputs of life cycle assessment provides a better approach to evaluate the dietary crude protein reduction for starting pigs. J Anim Sci 2018. [DOI: 10.1093/jas/sky404.834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A Monteiro
- Universidade Estadual de Maringá, Maringá,Parana, Brazil
| | | | - N Sitanaka
- Universidade Estadual de Maringá, Maringá,Parana, Brazil
| | - C Moreira
- Universidade Estadual de Maringá, Maringá,Parana, Brazil
| | - R Rossi
- Universidade Estadual de Maringá, Maringá,Parana, Brazil
| | - C Sangali
- Centro Universitário Integrado, Campo Mourão,Parana, Brazil
| | - L Castilha
- Universidade Estadual de Maringá, Maringá, Brazil
| | - P Pozza
- Universidade Estadual de Maringá, Maringá, Brazil
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Filice S, Rossi R, Pinardi C. 262. Assessment of occupational exposure to electromagnetic field around 1.5 T and 3.0 T MRI scanners. Phys Med 2018. [DOI: 10.1016/j.ejmp.2018.04.272] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Perrot JL, Biron A, Couty E, Tognetti L, Couzan C, Rossi R, Rubegni P, Cinotti E. Premiers cas de corrélation parfaite à l’échelle cellulaire entre image de microscopie confocale in vivo et dermatoscopie. Ann Dermatol Venereol 2018. [DOI: 10.1016/j.annder.2018.09.261] [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: 10/27/2022]
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Perrot JL, Biron A, Couty E, Tognetti L, Couzan C, Rossi R, Rubegni P, Cinotti E. Comparaison dermatoscopie × 400/microscopie confocale in vivo à propos de 36 lésions pigmentés génitales : premiers cas rapportés. Ann Dermatol Venereol 2018. [DOI: 10.1016/j.annder.2018.09.265] [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: 10/27/2022]
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Maddalo M, Moschini I, Benecchi G, Calabri E, Rossi R, Losardo P, Bergamini M, Dell’Anna C, Ceccon G, Grondelli C, Nurmahomed S, Gianni S, Rossi R, Manicone M, Andreani S, Ghetti F, Salaroli F, Ghetti C, D’Abbiero N. 42. The role of emphysema on radiation-induced lung toxicity and the feasibility of a “functional treatment plan”. Phys Med 2018. [DOI: 10.1016/j.ejmp.2018.04.052] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Maddalo M, Benecchi G, Grondelli C, Calabri E, Rossi R, Losardo P, Bergamini M, Dell’Anna C, Ceccon G, Nurmahomed S, Gianni S, Rossi R, Manicone M, Andreani S, Ghetti F, Salaroli F, Ghetti C, D’Abbiero N. 172. Predictors of cardiac dose reduction achieved with deep inspiration breath hold technique over free breathing technique in left breast radiotherapy. Phys Med 2018. [DOI: 10.1016/j.ejmp.2018.04.183] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Saluti G, Diamanti I, Giusepponi D, Pucciarini L, Rossi R, Moretti S, Sardella R, Galarini R. Simultaneous determination of aminoglycosides and colistins in food. Food Chem 2018; 266:9-16. [DOI: 10.1016/j.foodchem.2018.05.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/03/2018] [Accepted: 05/24/2018] [Indexed: 11/28/2022]
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Ortenzia O, Rossi R, Bertolini M, Nitrosi A, Ghetti C. PHYSICAL CHARACTERISATION OF FOUR DIFFERENT COMMERCIAL DIGITAL BREAST TOMOSYNTHESIS SYSTEMS. Radiat Prot Dosimetry 2018; 181:277-289. [PMID: 29462366 DOI: 10.1093/rpd/ncy024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/25/2018] [Indexed: 06/08/2023]
Abstract
The aim of this article was to characterise the performance of four different digital breast tomosynthesis (DBT) systems in terms of dose and image quality parameters. One of them, GE Pristina, has never been tested before. Average glandular doses were measured both in DBT and 2D full field digital mammography mode. Several phantoms were employed to perform signal difference to noise ratio, slice sensitivity profile, slice to slice incrementation, chest wall offset, z-axis geometry, artefact spread function, low contrast detectability, contrast detail evaluations, image uniformity and in-plane MTF in chest wall-nipple and in tube-travel directions. There are many differences in DBT systems explored: the angular range, detector type, reconstruction algorithms, and the presence or not of the grid. Even if it is not simple to calculate a global figure of merit, the analysis of all the collected data can be useful in a contest of a quality assurance program to define a set of values that could be used as benchmarks.
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Affiliation(s)
- O Ortenzia
- Department of Medical Physics, University Hospital of Parma, Parma, Italy
| | - R Rossi
- Department of Medical Physics, University Hospital of Parma, Parma, Italy
| | - M Bertolini
- Department of Medical Physics, Santa Maria Nuova Hospital of Reggio Emilia, Reggio Emilia, Italy
| | - A Nitrosi
- Department of Medical Physics, Santa Maria Nuova Hospital of Reggio Emilia, Reggio Emilia, Italy
| | - C Ghetti
- Department of Medical Physics, University Hospital of Parma, Parma, Italy
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Giusti R, Scarpi E, Cannita K, Silva R, Filetti M, Mazzotta M, Rossi R, Cocciolone V, Sidoni T, Tudini M, Ficorella C, Botticelli A, Marchetti P, Porzio G, Verna L. Clinical and psychometric validation of the BreSAS questionnaire for symptom assessment among breast cancer survivors. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy300.095] [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: 11/14/2022] Open
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Rossi R, Ohgoe T, Van Houcke K, Werner F. Resummation of Diagrammatic Series with Zero Convergence Radius for Strongly Correlated Fermions. Phys Rev Lett 2018; 121:130405. [PMID: 30312043 DOI: 10.1103/physrevlett.121.130405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/26/2018] [Indexed: 06/08/2023]
Abstract
We demonstrate that a summing up series of Feynman diagrams can yield unbiased accurate results for strongly correlated fermions even when the convergence radius vanishes. We consider the unitary Fermi gas, a model of nonrelativistic fermions in three-dimensional continuous space. Diagrams are built from partially dressed or fully dressed propagators of single particles and pairs. The series is resummed by a conformal-Borel transformation that incorporates the large-order behavior and the analytic structure in the Borel plane, which are found by the instanton approach. We report highly accurate numerical results for the equation of state in the normal unpolarized regime, and reconcile experimental data with the theoretically conjectured fourth virial coefficient.
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Affiliation(s)
- R Rossi
- Laboratoire de Physique Statistique, Ecole Normale Supérieure-Université PSL, CNRS, Sorbonne Université, Université Paris Diderot, 75005 Paris, France
| | - T Ohgoe
- Department of Applied Physics, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - K Van Houcke
- Laboratoire de Physique Statistique, Ecole Normale Supérieure-Université PSL, CNRS, Sorbonne Université, Université Paris Diderot, 75005 Paris, France
| | - F Werner
- Laboratoire Kastler Brossel, Ecole Normale Supérieure-Université PSL, CNRS, Sorbonne Université, Collège de France, 75005 Paris, France
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