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Maitra M, Mitsuhashi H, Rahimian R, Chawla A, Yang J, Fiori LM, Davoli MA, Perlman K, Aouabed Z, Mash DC, Suderman M, Mechawar N, Turecki G, Nagy C. Cell type specific transcriptomic differences in depression show similar patterns between males and females but implicate distinct cell types and genes. Nat Commun 2023; 14:2912. [PMID: 37217515 PMCID: PMC10203145 DOI: 10.1038/s41467-023-38530-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
Major depressive disorder (MDD) is a common, heterogenous, and potentially serious psychiatric illness. Diverse brain cell types have been implicated in MDD etiology. Significant sexual differences exist in MDD clinical presentation and outcome, and recent evidence suggests different molecular bases for male and female MDD. We evaluated over 160,000 nuclei from 71 female and male donors, leveraging new and pre-existing single-nucleus RNA-sequencing data from the dorsolateral prefrontal cortex. Cell type specific transcriptome-wide threshold-free MDD-associated gene expression patterns were similar between the sexes, but significant differentially expressed genes (DEGs) diverged. Among 7 broad cell types and 41 clusters evaluated, microglia and parvalbumin interneurons contributed the most DEGs in females, while deep layer excitatory neurons, astrocytes, and oligodendrocyte precursors were the major contributors in males. Further, the Mic1 cluster with 38% of female DEGs and the ExN10_L46 cluster with 53% of male DEGs, stood out in the meta-analysis of both sexes.
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Affiliation(s)
- Malosree Maitra
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Haruka Mitsuhashi
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Reza Rahimian
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Anjali Chawla
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Jennie Yang
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Laura M Fiori
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Maria Antonietta Davoli
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Kelly Perlman
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Zahia Aouabed
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Deborah C Mash
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Ft. Lauderdale, FL, USA
| | - Matthew Suderman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Naguib Mechawar
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada.
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada.
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada.
| | - Corina Nagy
- McGill Group for Suicide Studies, Douglas Institute, Verdun, QC, Canada.
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada.
- Douglas Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada.
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Gadepalli VS, Kim H, Liu Y, Han T, Cheng L. XDeathDB: a visualization platform for cell death molecular interactions. Cell Death Dis 2021; 12:1156. [PMID: 34907160 PMCID: PMC8669630 DOI: 10.1038/s41419-021-04397-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/07/2021] [Accepted: 11/09/2021] [Indexed: 12/23/2022]
Abstract
Lots of cell death initiator and effector molecules, signalling pathways and subcellular sites have been identified as key mediators in both cell death processes in cancer. The XDeathDB visualization platform provides a comprehensive cell death and their crosstalk resource for deciphering the signaling network organization of interactions among different cell death modes associated with 1461 cancer types and COVID-19, with an aim to understand the molecular mechanisms of physiological cell death in disease and facilitate systems-oriented novel drug discovery in inducing cell deaths properly. Apoptosis, autosis, efferocytosis, ferroptosis, immunogenic cell death, intrinsic apoptosis, lysosomal cell death, mitotic cell death, mitochondrial permeability transition, necroptosis, parthanatos, and pyroptosis related to 12 cell deaths and their crosstalk can be observed systematically by the platform. Big data for cell death gene-disease associations, gene-cell death pathway associations, pathway-cell death mode associations, and cell death-cell death associations is collected by literature review articles and public database from iRefIndex, STRING, BioGRID, Reactom, Pathway's commons, DisGeNET, DrugBank, and Therapeutic Target Database (TTD). An interactive webtool, XDeathDB, is built by web applications with R-Shiny, JavaScript (JS) and Shiny Server Iso. With this platform, users can search specific interactions from vast interdependent networks that occur in the realm of cell death. A multilayer spectral graph clustering method that performs convex layer aggregation to identify crosstalk function among cell death modes for a specific cancer. 147 hallmark genes of cell death could be observed in detail in these networks. These potential druggable targets are displayed systematically and tailoring networks to visualize specified relations is available to fulfil user-specific needs. Users can access XDeathDB for free at https://pcm2019.shinyapps.io/XDeathDB/ .
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Affiliation(s)
- Venkat Sundar Gadepalli
- Research Information Technology, College of Medicine, Ohio State University, 1585 Neil Ave, Columbus, OH, 43210, USA
| | - Hangil Kim
- 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Yueze Liu
- The Grainger College of Engineering, The University of Illinois-Urbana-Champaign, Urbana and Champaign, Champaign, IL, 61801, USA
| | - Tao Han
- 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Lijun Cheng
- 1Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA.
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Nicholson DN, Greene CS. Constructing knowledge graphs and their biomedical applications. Comput Struct Biotechnol J 2020; 18:1414-1428. [PMID: 32637040 PMCID: PMC7327409 DOI: 10.1016/j.csbj.2020.05.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 12/31/2022] Open
Abstract
Knowledge graphs can support many biomedical applications. These graphs represent biomedical concepts and relationships in the form of nodes and edges. In this review, we discuss how these graphs are constructed and applied with a particular focus on how machine learning approaches are changing these processes. Biomedical knowledge graphs have often been constructed by integrating databases that were populated by experts via manual curation, but we are now seeing a more robust use of automated systems. A number of techniques are used to represent knowledge graphs, but often machine learning methods are used to construct a low-dimensional representation that can support many different applications. This representation is designed to preserve a knowledge graph's local and/or global structure. Additional machine learning methods can be applied to this representation to make predictions within genomic, pharmaceutical, and clinical domains. We frame our discussion first around knowledge graph construction and then around unifying representational learning techniques and unifying applications. Advances in machine learning for biomedicine are creating new opportunities across many domains, and we note potential avenues for future work with knowledge graphs that appear particularly promising.
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Affiliation(s)
- David N. Nicholson
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, United States
| | - Casey S. Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, United States
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Piñero J, Ramírez-Anguita JM, Saüch-Pitarch J, Ronzano F, Centeno E, Sanz F, Furlong LI. The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res 2020; 48:D845-D855. [PMID: 31680165 PMCID: PMC7145631 DOI: 10.1093/nar/gkz1021] [Citation(s) in RCA: 780] [Impact Index Per Article: 195.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 02/07/2023] Open
Abstract
One of the most pressing challenges in genomic medicine is to understand the role played by genetic variation in health and disease. Thanks to the exploration of genomic variants at large scale, hundreds of thousands of disease-associated loci have been uncovered. However, the identification of variants of clinical relevance is a significant challenge that requires comprehensive interrogation of previous knowledge and linkage to new experimental results. To assist in this complex task, we created DisGeNET (http://www.disgenet.org/), a knowledge management platform integrating and standardizing data about disease associated genes and variants from multiple sources, including the scientific literature. DisGeNET covers the full spectrum of human diseases as well as normal and abnormal traits. The current release covers more than 24 000 diseases and traits, 17 000 genes and 117 000 genomic variants. The latest developments of DisGeNET include new sources of data, novel data attributes and prioritization metrics, a redesigned web interface and recently launched APIs. Thanks to the data standardization, the combination of expert curated information with data automatically mined from the scientific literature, and a suite of tools for accessing its publicly available data, DisGeNET is an interoperable resource supporting a variety of applications in genomic medicine and drug R&D.
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Affiliation(s)
- Janet Piñero
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Juan Manuel Ramírez-Anguita
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Josep Saüch-Pitarch
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Francesco Ronzano
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Emilio Centeno
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Laura I Furlong
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
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Cellular and molecular characterization of multiplex autism in human induced pluripotent stem cell-derived neurons. Mol Autism 2019; 10:51. [PMID: 31893020 PMCID: PMC6936127 DOI: 10.1186/s13229-019-0306-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is a neurodevelopmental disorder with pronounced heritability in the general population. This is largely attributable to the effects of polygenic susceptibility, with inherited liability exhibiting distinct sex differences in phenotypic expression. Attempts to model ASD in human cellular systems have principally involved rare de novo mutations associated with ASD phenocopies. However, by definition, these models are not representative of polygenic liability, which accounts for the vast share of population-attributable risk. Methods Here, we performed what is, to our knowledge, the first attempt to model multiplex autism using patient-derived induced pluripotent stem cells (iPSCs) in a family manifesting incremental degrees of phenotypic expression of inherited liability (absent, intermediate, severe). The family members share an inherited variant of uncertain significance (VUS) in GPD2, a gene that was previously associated with developmental disability but here is insufficient by itself to cause ASD. iPSCs from three first-degree relatives and an unrelated control were differentiated into both cortical excitatory (cExN) and cortical inhibitory (cIN) neurons, and cellular phenotyping and transcriptomic analysis were conducted. Results cExN neurospheres from the two affected individuals were reduced in size, compared to those derived from unaffected related and unrelated individuals. This reduction was, at least in part, due to increased apoptosis of cells from affected individuals upon initiation of cExN neural induction. Likewise, cIN neural progenitor cells from affected individuals exhibited increased apoptosis, compared to both unaffected individuals. Transcriptomic analysis of both cExN and cIN neural progenitor cells revealed distinct molecular signatures associated with affectation, including the misregulation of suites of genes associated with neural development, neuronal function, and behavior, as well as altered expression of ASD risk-associated genes. Conclusions We have provided evidence of morphological, physiological, and transcriptomic signatures of polygenic liability to ASD from an analysis of cellular models derived from a multiplex autism family. ASD is commonly inherited on the basis of additive genetic liability. Therefore, identifying convergent cellular and molecular phenotypes resulting from polygenic and monogenic susceptibility may provide a critical bridge for determining which of the disparate effects of rare highly deleterious mutations might also apply to common autistic syndromes.
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Christensen NR, Čalyševa J, Fernandes EFA, Lüchow S, Clemmensen LS, Haugaard‐Kedström LM, Strømgaard K. PDZ Domains as Drug Targets. ADVANCED THERAPEUTICS 2019; 2:1800143. [PMID: 32313833 PMCID: PMC7161847 DOI: 10.1002/adtp.201800143] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/25/2019] [Indexed: 12/14/2022]
Abstract
Protein-protein interactions within protein networks shape the human interactome, which often is promoted by specialized protein interaction modules, such as the postsynaptic density-95 (PSD-95), discs-large, zona occludens 1 (ZO-1) (PDZ) domains. PDZ domains play a role in several cellular functions, from cell-cell communication and polarization, to regulation of protein transport and protein metabolism. PDZ domain proteins are also crucial in the formation and stability of protein complexes, establishing an important bridge between extracellular stimuli detected by transmembrane receptors and intracellular responses. PDZ domains have been suggested as promising drug targets in several diseases, ranging from neurological and oncological disorders to viral infections. In this review, the authors describe structural and genetic aspects of PDZ-containing proteins and discuss the current status of the development of small-molecule and peptide modulators of PDZ domains. An overview of potential new therapeutic interventions in PDZ-mediated protein networks is also provided.
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Affiliation(s)
- Nikolaj R. Christensen
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Jelena Čalyševa
- European Molecular Biology Laboratory (EMBL)Structural and Computational Biology UnitMeyerhofstraße 169117HeidelbergGermany
- EMBL International PhD ProgrammeFaculty of BiosciencesEMBL–Heidelberg UniversityGermany
| | - Eduardo F. A. Fernandes
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Susanne Lüchow
- Department of Chemistry – BMCUppsala UniversityBox 576SE75123UppsalaSweden
| | - Louise S. Clemmensen
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Linda M. Haugaard‐Kedström
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Kristian Strømgaard
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
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Almasi SM, Hu T. Measuring the importance of vertices in the weighted human disease network. PLoS One 2019; 14:e0205936. [PMID: 30901770 PMCID: PMC6430629 DOI: 10.1371/journal.pone.0205936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 02/26/2019] [Indexed: 12/11/2022] Open
Abstract
Many human genetic disorders and diseases are known to be related to each other through frequently observed co-occurrences. Studying the correlations among multiple diseases provides an important avenue to better understand the common genetic background of diseases and to help develop new drugs that can treat multiple diseases. Meanwhile, network science has seen increasing applications on modeling complex biological systems, and can be a powerful tool to elucidate the correlations of multiple human diseases. In this article, known disease-gene associations were represented using a weighted bipartite network. We extracted a weighted human diseases network from such a bipartite network to show the correlations of diseases. Subsequently, we proposed a new centrality measurement for the weighted human disease network (WHDN) in order to quantify the importance of diseases. Using our centrality measurement to quantify the importance of vertices in WHDN, we were able to find a set of most central diseases. By investigating the 30 top diseases and their most correlated neighbors in the network, we identified disease linkages including known disease pairs and novel findings. Our research helps better understand the common genetic origin of human diseases and suggests top diseases that likely induce other related diseases.
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Affiliation(s)
| | - Ting Hu
- Department of Computer Science, Memorial University, St. John’s, NL, Canada
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Gutiérrez-Sacristán A, Hernández-Ferrer C, González JR, Furlong LI. psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes. Bioinformatics 2017; 33:4004-4006. [PMID: 28961763 PMCID: PMC5860088 DOI: 10.1093/bioinformatics/btx506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 08/04/2017] [Accepted: 08/08/2017] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Psychiatric disorders have a great impact on morbidity and mortality. Genotype-phenotype resources for psychiatric diseases are key to enable the translation of research findings to a better care of patients. PsyGeNET is a knowledge resource on psychiatric diseases and their genes, developed by text mining and curated by domain experts. RESULTS We present psygenet2r, an R package that contains a variety of functions for leveraging PsyGeNET database and facilitating its analysis and interpretation. The package offers different types of queries to the database along with variety of analysis and visualization tools, including the study of the anatomical structures in which the genes are expressed and gaining insight of gene's molecular function. Psygenet2r is especially suited for network medicine analysis of psychiatric disorders. AVAILABILITY AND IMPLEMENTATION The package is implemented in R and is available under MIT license from Bioconductor (http://bioconductor.org/packages/release/bioc/html/psygenet2r.html). CONTACT juanr.gonzalez@isglobal.org or laura.furlong@upf.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alba Gutiérrez-Sacristán
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carles Hernández-Ferrer
- Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Juan R González
- Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Laura I Furlong
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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