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Pagani M, Zerbi V, Gini S, Alvino F, Banerjee A, Barberis A, Basson MA, Bozzi Y, Galbusera A, Ellegood J, Fagiolini M, Lerch J, Matteoli M, Montani C, Pozzi D, Provenzano G, Scattoni ML, Wenderoth N, Xu T, Lombardo M, Milham MP, Martino AD, Gozzi A. Biological subtyping of autism via cross-species fMRI. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.04.641400. [PMID: 40093106 PMCID: PMC11908180 DOI: 10.1101/2025.03.04.641400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
It is frequently assumed that the phenotypic heterogeneity in autism spectrum disorder reflects underlying pathobiological variation. However, direct evidence in support of this hypothesis is lacking. Here, we leverage cross-species functional neuroimaging to examine whether variability in brain functional connectivity reflects distinct biological mechanisms. We find that fMRI connectivity alterations in 20 distinct mouse models of autism (n=549 individual mice) can be clustered into two prominent hypo- and hyperconnectivity subtypes. We show that these connectivity profiles are linked to distinct signaling pathways, with hypoconnectivity being associated with synaptic dysfunction, and hyperconnectivity reflecting transcriptional and immune-related alterations. Extending these findings to humans, we identify analogous hypo- and hyperconnectivity subtypes in a large, multicenter resting state fMRI dataset of n=940 autistic and n=1036 neurotypical individuals. Remarkably, hypo- and hyperconnectivity autism subtypes are replicable across independent cohorts (accounting for 25.1% of all autism data), exhibit distinct functional network architecture, are behaviorally dissociable, and recapitulate synaptic and immune mechanisms identified in corresponding mouse subtypes. Our cross-species investigation, thus, decodes the heterogeneity of fMRI connectivity in autism into distinct pathway-specific etiologies, offering a new empirical framework for targeted subtyping of autism.
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Affiliation(s)
- Marco Pagani
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
- Autism Center, Child Mind Institute, New York, NY, USA
- IMT School for Advanced Studies, Lucca, Italy
| | - Valerio Zerbi
- Department of Psychiatry, University of Geneva, Switzerland
- Department of Basic Neurosciences, University of Geneva, Switzerland
| | - Silvia Gini
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
- Center for Mind and Brain Sciences (CIMeC), University of Trento, Rovereto, Italy
| | - Filomena Alvino
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | | | - Andrea Barberis
- Synaptic Plasticity of Inhibitory Networks, Istituto Italiano di Tecnologia, Genova, Italy
| | - M. Albert Basson
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, UK
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - Yuri Bozzi
- Center for Mind and Brain Sciences (CIMeC), University of Trento, Rovereto, Italy
| | - Alberto Galbusera
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Jacob Ellegood
- Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
| | | | - Jason Lerch
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Michela Matteoli
- Humanitas University, Milan, Italy
- CNR Institute of Neuroscience c/o Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Caterina Montani
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Davide Pozzi
- CNR Institute of Neuroscience c/o Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Giovanni Provenzano
- Department of Cellular, Computational and Integrative Biology. University of Trento, Trento, Italy
| | - Maria Luisa Scattoni
- Research Coordination and Support Service, Istituto Superiore di Sanità, Rome, Italy
| | | | - Ting Xu
- Center for Integrative Developing Brain, Child Mind Institute, New York, NY, USA
| | - Michael Lombardo
- Laboratory for Autism and Neurodevelopmental Disorders, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, Rovereto, Italy
| | - Michael P Milham
- Center for the Integrative Developmental Neuroscience, Child Mind Institute, New York, NY, USA
| | | | - Alessandro Gozzi
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
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Song X, Xia Z, Martinez D, Xu B, Spritzer Z, Zhang Y, Nugent E, Ho Y, Terzic B, Zhou Z. Independent genetic strategies define the scope and limits of CDKL5 deficiency disorder reversal. Cell Rep Med 2025; 6:101926. [PMID: 39855191 PMCID: PMC11866500 DOI: 10.1016/j.xcrm.2024.101926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 07/18/2024] [Accepted: 12/30/2024] [Indexed: 01/27/2025]
Abstract
Cyclin-dependent kinase-like 5 (CDKL5) deficiency disorder (CDD) is a neurodevelopmental syndrome caused by mutations in the X-linked CDKL5 gene. The early onset of CDD suggests that CDKL5 is essential during development, but post-developmental re-expression rescues multiple CDD-related phenotypes in hemizygous male mice. Since most patients are heterozygous females, studies in clinically relevant female models are essential. Here, we systematically compare phenotype reversal across age and sex using two independent mouse models of CDD. We find that early re-activation of endogenous Cdkl5 in heterozygous females reverses most phenotypes, except working memory. Later re-expression improves several traits but has limited effects on cognitive function. Seizure prevention is more effective with early intervention in heterozygous females but becomes limited after seizure onset. These findings demonstrate the robust potential of CDKL5 re-expression to reverse CDD-related phenotypes in both sexes while underscoring the critical impact of age and disease stage in designing clinical trials.
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Affiliation(s)
- Xie Song
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA; Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, China
| | - Zijie Xia
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA
| | - Dayne Martinez
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA
| | - Bing Xu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA; Department of Urology, The First Affiliated Hospital of Shandong First Medical University & Shandong Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Organ Transplantation and Nephrosis, Shandong Institute of Nephrology, Jinan, Shandong 250000, China
| | - Zachary Spritzer
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA
| | - Yanjie Zhang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA
| | - Erin Nugent
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA
| | - Yugong Ho
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA
| | - Barbara Terzic
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA; Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19102, USA; The Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19102, USA.
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Martinez D, Jiang E, Zhou Z. Overcoming genetic and cellular complexity to study the pathophysiology of X-linked intellectual disabilities. J Neurodev Disord 2024; 16:5. [PMID: 38424476 PMCID: PMC10902969 DOI: 10.1186/s11689-024-09517-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/04/2024] [Indexed: 03/02/2024] Open
Abstract
X-linked genetic causes of intellectual disability (ID) account for a substantial proportion of cases and remain poorly understood, in part due to the heterogeneous expression of X-linked genes in females. This is because most genes on the X chromosome are subject to random X chromosome inactivation (XCI) during early embryonic development, which results in a mosaic pattern of gene expression for a given X-linked mutant allele. This mosaic expression produces substantial complexity, especially when attempting to study the already complicated neural circuits that underly behavior, thus impeding the understanding of disease-related pathophysiology and the development of therapeutics. Here, we review a few selected X-linked forms of ID that predominantly affect heterozygous females and the current obstacles for developing effective therapies for such disorders. We also propose a genetic strategy to overcome the complexity presented by mosaicism in heterozygous females and highlight specific tools for studying synaptic and circuit mechanisms, many of which could be shared across multiple forms of intellectual disability.
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Affiliation(s)
- Dayne Martinez
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Evan Jiang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Intellectual and Developmental Disabilities Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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Sampedro-Castañeda M, Baltussen LL, Lopes AT, Qiu Y, Sirvio L, Mihaylov SR, Claxton S, Richardson JC, Lignani G, Ultanir SK. Epilepsy-linked kinase CDKL5 phosphorylates voltage-gated calcium channel Cav2.3, altering inactivation kinetics and neuronal excitability. Nat Commun 2023; 14:7830. [PMID: 38081835 PMCID: PMC10713615 DOI: 10.1038/s41467-023-43475-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) are a group of rare childhood disorders characterized by severe epilepsy and cognitive deficits. Numerous DEE genes have been discovered thanks to advances in genomic diagnosis, yet putative molecular links between these disorders are unknown. CDKL5 deficiency disorder (CDD, DEE2), one of the most common genetic epilepsies, is caused by loss-of-function mutations in the brain-enriched kinase CDKL5. To elucidate CDKL5 function, we looked for CDKL5 substrates using a SILAC-based phosphoproteomic screen. We identified the voltage-gated Ca2+ channel Cav2.3 (encoded by CACNA1E) as a physiological target of CDKL5 in mice and humans. Recombinant channel electrophysiology and interdisciplinary characterization of Cav2.3 phosphomutant mice revealed that loss of Cav2.3 phosphorylation leads to channel gain-of-function via slower inactivation and enhanced cholinergic stimulation, resulting in increased neuronal excitability. Our results thus show that CDD is partly a channelopathy. The properties of unphosphorylated Cav2.3 closely resemble those described for CACNA1E gain-of-function mutations causing DEE69, a disorder sharing clinical features with CDD. We show that these two single-gene diseases are mechanistically related and could be ameliorated with Cav2.3 inhibitors.
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Affiliation(s)
| | - Lucas L Baltussen
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Laboratory for the Research of Neurodegenerative Diseases (VIB-KU Leuven), Department of Neurosciences, ON5 Herestraat 49, 3000, Leuven, Belgium
| | - André T Lopes
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Yichen Qiu
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, Queen Square House, London, WC1N 3BG, UK
| | - Liina Sirvio
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simeon R Mihaylov
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Suzanne Claxton
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jill C Richardson
- Neuroscience, MSD Research Laboratories, 120 Moorgate, London, EC2M 6UR, UK
| | - Gabriele Lignani
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, Queen Square House, London, WC1N 3BG, UK
| | - Sila K Ultanir
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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Pagani M, Gutierrez-Barragan D, de Guzman AE, Xu T, Gozzi A. Mapping and comparing fMRI connectivity networks across species. Commun Biol 2023; 6:1238. [PMID: 38062107 PMCID: PMC10703935 DOI: 10.1038/s42003-023-05629-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Technical advances in neuroimaging, notably in fMRI, have allowed distributed patterns of functional connectivity to be mapped in the human brain with increasing spatiotemporal resolution. Recent years have seen a growing interest in extending this approach to rodents and non-human primates to understand the mechanism of fMRI connectivity and complement human investigations of the functional connectome. Here, we discuss current challenges and opportunities of fMRI connectivity mapping across species. We underscore the critical importance of physiologically decoding neuroimaging measures of brain (dys)connectivity via multiscale mechanistic investigations in animals. We next highlight a set of general principles governing the organization of mammalian connectivity networks across species. These include the presence of evolutionarily conserved network systems, a dominant cortical axis of functional connectivity, and a common repertoire of topographically conserved fMRI spatiotemporal modes. We finally describe emerging approaches allowing comparisons and extrapolations of fMRI connectivity findings across species. As neuroscientists gain access to increasingly sophisticated perturbational, computational and recording tools, cross-species fMRI offers novel opportunities to investigate the large-scale organization of the mammalian brain in health and disease.
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Affiliation(s)
- Marco Pagani
- Functional Neuroimaging Laboratory, Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy
- Autism Center, Child Mind Institute, New York, NY, USA
- IMT School for Advanced Studies, Lucca, Italy
| | - Daniel Gutierrez-Barragan
- Functional Neuroimaging Laboratory, Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - A Elizabeth de Guzman
- Functional Neuroimaging Laboratory, Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - Ting Xu
- Center for the Integrative Developmental Neuroscience, Child Mind Institute, New York, NY, USA
| | - Alessandro Gozzi
- Functional Neuroimaging Laboratory, Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy.
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Petitpierre G, Dind J, De Blasio C. Olfactive short-term habituation in children and young people with profound intellectual and multiple disabilities. RESEARCH IN DEVELOPMENTAL DISABILITIES 2023; 140:104569. [PMID: 37473626 DOI: 10.1016/j.ridd.2023.104569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 06/21/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Despite its importance for learning, the existence of the habituation process and its characteristics in people with profound intellectual and multiple disabilities (PIMD) remains understudied. Habituation is, however, considered the simplest form of learning, and a significant neuroadaptive mechanism. Even though habituation occurs in all sensory modalities, the olfactory system is where it manifests itself very visibly. AIM This study explores the olfactory short-term habituation abilities of children and young people with PIMD. METHOD Twenty children and young people with PIMD (7-18 years) were presented six times successively with a 30-second habituating olfactory stimulus. The interstimulus interval was 15 s. A new odour was presented on the seventh trial. The scenario was carried out two times with two pairs of stimuli. The participants' head alignment duration on the odour was measured. RESULTS Seventeen participants out of 20 manifested a decline in response, which reached about 50 % between the first and sixth presentation of the habituation odour. All habituators also showed a distinctive response when exposed to a novel odour. The participants who did not habituate showed a strong, non-fluctuating response to the stimulus throughout the presentations. Three participants only habituated to one of the two habituation stimuli. CONCLUSION AND IMPLICATIONS The results raise theoretical, scientific, and practical issues. They question the factors explaining olfactory habituation mechanisms, namely the stimulus properties and the severity of impairment, reveal the need for points of comparison for interpreting this population's responses, and point to the consequences of stimuli repetition and or variety in therapeutic or educational settings for these individuals' learning and cognitive functioning.
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Affiliation(s)
- Geneviève Petitpierre
- Université de Fribourg, Département de Pédagogie spécialisée, R. St Pierre Canisius 21, Fribourg CH-1700, Switzerland.
| | - Juliane Dind
- Université de Fribourg, Département de Pédagogie spécialisée, R. St Pierre Canisius 21, Fribourg CH-1700, Switzerland
| | - Catherine De Blasio
- Université de Fribourg, Département de Pédagogie spécialisée, R. St Pierre Canisius 21, Fribourg CH-1700, Switzerland
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Tassinari M, Uguagliati B, Trazzi S, Cerchier CB, Cavina OV, Mottolese N, Loi M, Candini G, Medici G, Ciani E. Early-onset brain alterations during postnatal development in a mouse model of CDKL5 deficiency disorder. Neurobiol Dis 2023; 182:106146. [PMID: 37164289 DOI: 10.1016/j.nbd.2023.106146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/12/2023] Open
Abstract
Mutations in the CDKL5 gene are the cause of CDKL5 deficiency disorder (CDD), a rare and severe neurodevelopmental condition characterized by early-onset epilepsy, motor impairment, intellectual disability, and autistic features. A mouse model of CDD, the Cdkl5 KO mouse, that recapitulates several aspects of CDD symptomology, has helped to highlight brain alterations leading to CDD neurological defects. Studies of brain morphogenesis in adult Cdkl5 KO mice showed defects in dendritic arborization of pyramidal neurons and in synaptic connectivity, a hypocellularity of the hippocampal dentate gyrus, and a generalized microglia over-activation. Nevertheless, no studies are available regarding the presence of these brain alterations in Cdkl5 KO pups, and their severity in early stages of life compared to adulthood. A deeper understanding of the CDKL5 deficient brain during an early phase of postnatal development would represent an important milestone for further validation of the CDD mouse model, and for the identification of the optimum time window for treatments that target defects in brain development. In sight of this, we comparatively evaluated the dendritic arborization and spines of cortical pyramidal neurons, cortical excitatory and inhibitory connectivity, microglia activation, and proliferation and survival of granule cells of the hippocampal dentate gyrus in hemizygous Cdkl5 KO male (-/Y) mice aged 7, 14, 21, and 60 days. We found that most of the structural alterations in Cdkl5 -/Y brains are already present in pups aged 7 days and do not worsen with age. In contrast, the difference in the density of excitatory and inhibitory terminals between Cdkl5 -/Y and wild-type mice changes with age, suggesting an age-dependent cortical excitatory/inhibitory synaptic imbalance. Confirming the precocious presence of brain defects, Cdkl5 -/Y pups are characterized by an impairment in neonatal sensory-motor reflexes.
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Affiliation(s)
- Marianna Tassinari
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126 Bologna, Italy
| | - Beatrice Uguagliati
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126 Bologna, Italy
| | - Stefania Trazzi
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126 Bologna, Italy.
| | - Camilla Bruna Cerchier
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126 Bologna, Italy
| | - Ottavia Vera Cavina
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126 Bologna, Italy
| | - Nicola Mottolese
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126 Bologna, Italy
| | - Manuela Loi
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126 Bologna, Italy
| | - Giulia Candini
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126 Bologna, Italy
| | - Giorgio Medici
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126 Bologna, Italy
| | - Elisabetta Ciani
- Department of Biomedical and Neuromotor Science, University of Bologna, 40126 Bologna, Italy.
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