201
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Confounding factors in identification of disease-resilient individuals. Nat Biotechnol 2016; 34:1103-1104. [PMID: 27824855 DOI: 10.1038/nbt.3684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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202
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Bertier G, Carrot-Zhang J, Ragoussis V, Joly Y. Integrating precision cancer medicine into healthcare-policy, practice, and research challenges. Genome Med 2016; 8:108. [PMID: 27776531 PMCID: PMC5075982 DOI: 10.1186/s13073-016-0362-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Precision medicine (PM) can be defined as a predictive, preventive, personalized, and participatory healthcare service delivery model. Recent developments in molecular biology and information technology make PM a reality today through the use of massive amounts of genetic, ‘omics’, clinical, environmental, and lifestyle data. With cancer being one of the most prominent public health threats in developed countries, both the research community and governments have been investing significant time, money, and efforts in precision cancer medicine (PCM). Although PCM research is extremely promising, a number of hurdles still remain on the road to an optimal integration of standardized and evidence-based use of PCM in healthcare systems. Indeed, PCM raises a number of technical, organizational, ethical, legal, social, and economic challenges that have to be taken into account in the development of an appropriate health policy framework. Here, we highlight some of the more salient issues regarding the standards needed for integration of PCM into healthcare systems, and we identify fields where more research is needed before policy can be implemented. Key challenges include, but are not limited to, the creation of new standards for the collection, analysis, and sharing of samples and data from cancer patients, and the creation of new clinical trial designs with renewed endpoints. We believe that these issues need to be addressed as a matter of priority by public health policymakers in the coming years for a better integration of PCM into healthcare.
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Affiliation(s)
- Gabrielle Bertier
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, QC, H3A 0G1, Canada. .,Université Toulouse III Paul Sabatier and Inserm UMR 102, 37 allées Jules Guesde, F-31000, Toulouse, France.
| | - Jian Carrot-Zhang
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Vassilis Ragoussis
- Sargent College, Boston University, One Silber Way, Boston, MA, 02215, USA
| | - Yann Joly
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, QC, H3A 0G1, Canada
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203
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Shashi V, Pena LD, Kim K, Burton B, Hempel M, Schoch K, Walkiewicz M, McLaughlin HM, Cho M, Stong N, Hickey SE, Shuss CM, Freemark MS, Bellet JS, Keels MA, Bonner MJ, El-Dairi M, Butler M, Kranz PG, Stumpel CT, Klinkenberg S, Oberndorff K, Alawi M, Santer R, Petrovski S, Kuismin O, Korpi-Heikkilä S, Pietilainen O, Aarno P, Kurki MI, Hoischen A, Need AC, Goldstein DB, Kortüm F, Bacino A, Lee BH, Balasubramanyam A, Burrage LC, Clark GD, Craigen WJ, Dhar SU, Emrick LT, Graham BH, Jain M, Lalani SR, Lewis RA, Moretti PM, Nicholas SK, Orange JS, Posey JE, Potocki L, Rosenfeld JA, Scott DA, Hanchard NA, Alyssa TA, Mercedes AE, Mashid AS, Bellen HJ, Yamamoto S, Wangler MF, Westerfield M, Postlethwait JH, Eng CM, Yang Y, Muzny DM, Ward PA, Ramoni RB, McCray AT, Kohane IS, Holm IA, Might M, Mazur P, Splinter K, Esteves C, Shashi V, Jiang YH, Pena LD, McConkie-Rosell A, Schoch K, Spillmann RC, Sullivan JA, Walley NM, Goldstein DB, Stong N, Beggs AH, Loscalzo J, MacRae CA, Silverman EK, Stoler JM, Sweetser DA, Maas RL, Krier JB, Rodan LH, Walsh CA, Cooper CM, Pallais JC, Donnell-Fink LA, Krieg EL, Lincoln SA, Briere LC, Jacob HJ, Worthey EA, Lazar J, Strong KA, Handley LH, Newberry JS, Bick DP, Schroeder MC, Brown DM, Birch CL, Levy SE, Boone BE, Dorset DC, Jones AL, Manolio TA, Mulvihill JJ, Wise AL, Dayal JG, Eckstein DJ, Krasnewich DM, Loomis CR, Mamounas LA, Iglesias B, Martin C, Koeller DM, Metz TO, Ashley EA, Fisher PG, Bernstein JA, Wheeler MT, Zornio PA, Waggott DM, Dries AM, Kohler JN, Dipple KM, Nelson SF, Palmer CG, Vilain E, Allard P, Dell Angelica EC, Lee H, Sinsheimer JS, Papp JC, Dorrani N, Herzog MR, Barseghyan H, Adams DR, Adams CJ, Burke EA, Chao KR, Davids M, Draper DD, Estwick T, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Gordon MG, Groden CA, Gropman AL, Hackbarth ME, Hardee I, Johnston JM, Koehler AE, Latham L, Latour YL, Lau CYC, Lee PR, Levy DJ, Liebendorder AP, Macnamara EF, Maduro VV, Malicdan MV, Markello TC, McCarty AJ, Murphy JL, Nehrebecky ME, Novacic D, Pusey BN, Sadozai S, Schaffer KE, Sharma P, Soldatos AG, Thomas SP, Tifft CJ, Tolman NJ, Toro C, Valivullah ZM, Wahl CE, Warburton M, Weech AA, Wolfe LA, Yu G, Hamid R, Newman JH, Phillips JA, Cogan JD. De Novo Truncating Variants in ASXL2 Are Associated with a Unique and Recognizable Clinical Phenotype. Am J Hum Genet 2016; 99:991-999. [PMID: 27693232 PMCID: PMC5065681 DOI: 10.1016/j.ajhg.2016.08.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/24/2016] [Indexed: 12/14/2022] Open
Abstract
The ASXL genes (ASXL1, ASXL2, and ASXL3) participate in body patterning during embryogenesis and encode proteins involved in epigenetic regulation and assembly of transcription factors to specific genomic loci. Germline de novo truncating variants in ASXL1 and ASXL3 have been respectively implicated in causing Bohring-Opitz and Bainbridge-Ropers syndromes, which result in overlapping features of severe intellectual disability and dysmorphic features. ASXL2 has not yet been associated with a human Mendelian disorder. In this study, we performed whole-exome sequencing in six unrelated probands with developmental delay, macrocephaly, and dysmorphic features. All six had de novo truncating variants in ASXL2. A careful review enabled the recognition of a specific phenotype consisting of macrocephaly, prominent eyes, arched eyebrows, hypertelorism, a glabellar nevus flammeus, neonatal feeding difficulties, hypotonia, and developmental disabilities. Although overlapping features with Bohring-Opitz and Bainbridge-Ropers syndromes exist, features that distinguish the ASXL2-associated condition from ASXL1- and ASXL3-related disorders are macrocephaly, absence of growth retardation, and more variability in the degree of intellectual disabilities. We were also able to demonstrate with mRNA studies that these variants are likely to exert a dominant-negative effect, given that both alleles are expressed in blood and the mutated ASXL2 transcripts escape nonsense-mediated decay. In conclusion, de novo truncating variants in ASXL2 underlie a neurodevelopmental syndrome with a clinically recognizable phenotype. This report expands the germline disorders that are linked to the ASXL genes.
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204
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Prabhu AV, Luu W, Li D, Sharpe LJ, Brown AJ. DHCR7: A vital enzyme switch between cholesterol and vitamin D production. Prog Lipid Res 2016; 64:138-151. [PMID: 27697512 DOI: 10.1016/j.plipres.2016.09.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/29/2016] [Accepted: 09/29/2016] [Indexed: 01/07/2023]
Abstract
The conversion of 7-dehydrocholesterol to cholesterol, the final step of cholesterol synthesis in the Kandutsch-Russell pathway, is catalyzed by the enzyme 7-dehydrocholesterol reductase (DHCR7). Homozygous or compound heterozygous mutations in DHCR7 lead to the developmental disease Smith-Lemli-Opitz syndrome, which can also result in fetal mortality, highlighting the importance of this enzyme in human development and survival. Besides serving as a substrate for DHCR7, 7-dehydrocholesterol is also a precursor of vitamin D via the action of ultraviolet light on the skin. Thus, DHCR7 exerts complex biological effects, involved in both cholesterol and vitamin D production. Indeed, we argue that DHCR7 can act as a switch between cholesterol and vitamin D synthesis. This review summarizes current knowledge about the critical enzyme DHCR7, highlighting recent findings regarding its structure, transcriptional and post-transcriptional regulation, and its links to vitamin D synthesis. Greater understanding about DHCR7 function, regulation and its place within cellular metabolism will provide important insights into its biological roles.
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Affiliation(s)
- Anika V Prabhu
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Winnie Luu
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Dianfan Li
- National Center for Protein Sciences, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Laura J Sharpe
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Andrew J Brown
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.
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205
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Bacchelli C, Williams HJ. Opportunities and technical challenges in next-generation sequencing for diagnosis of rare pediatric diseases. Expert Rev Mol Diagn 2016; 16:1073-1082. [PMID: 27560481 DOI: 10.1080/14737159.2016.1222906] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Rare pediatric diseases are clinically severe with high rates of mortality and morbidity. This paper outlines how next-generation sequencing (NGS) can be used to greatly advance identification of the underlying genetic causes. Areas covered: This manuscript is a blend of evidence obtained from literature searches from PubMed and rare disease related websites, laboratory experience and the author's opinions. The paper covers the current state of the field and identifies where the challenges lie and how they are being overcome, using up-to-date references. Expert commentary: The field of NGS is still relatively new but it has already transformed the field of rare disease research. Technological advances in instrumentation, computational hardware and software have resulted in the identification of many causative genes, but as sequencing moves into population-scale initiatives standardisation and data sharing is going to be of paramount importance to ensure we derive the maximum benefit for patients.
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Affiliation(s)
- Chiara Bacchelli
- a Head of Experimental & Personalised Medicine Section , Genetics and Genomic Medicine Programme, UCL GOS Institute of Child Health , London , England
| | - Hywel J Williams
- b GOSgene, Genetics and Genomic Medicine Programme , UCL GOS Institute of Child Health , London , England
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206
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Cirulli ET, Ginsburg GS. Studying genetic resilience to improve human health. Oral Dis 2016; 23:685-688. [PMID: 27510747 DOI: 10.1111/odi.12567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E T Cirulli
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - G S Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
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207
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Hu JX, Thomas CE, Brunak S. Network biology concepts in complex disease comorbidities. Nat Rev Genet 2016; 17:615-29. [PMID: 27498692 DOI: 10.1038/nrg.2016.87] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The co-occurrence of diseases can inform the underlying network biology of shared and multifunctional genes and pathways. In addition, comorbidities help to elucidate the effects of external exposures, such as diet, lifestyle and patient care. With worldwide health transaction data now often being collected electronically, disease co-occurrences are starting to be quantitatively characterized. Linking network dynamics to the real-life, non-ideal patient in whom diseases co-occur and interact provides a valuable basis for generating hypotheses on molecular disease mechanisms, and provides knowledge that can facilitate drug repurposing and the development of targeted therapeutic strategies.
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Affiliation(s)
- Jessica Xin Hu
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Cecilia Engel Thomas
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen DK-2200, Denmark.,Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
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208
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Song Z, Laleve A, Vallières C, McGeehan JE, Lloyd RE, Meunier B. Human Mitochondrial Cytochrome b Variants Studied in Yeast: Not All Are Silent Polymorphisms. Hum Mutat 2016; 37:933-41. [PMID: 27291790 PMCID: PMC5094555 DOI: 10.1002/humu.23024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/24/2016] [Indexed: 11/12/2022]
Abstract
Variations in mitochondrial DNA (mtDNA) cytochrome b (mt‐cyb) are frequently found within the healthy population, but also occur within a spectrum of mitochondrial and common diseases. mt‐cyb encodes the core subunit (MT‐CYB) of complex III, a central component of the oxidative phosphorylation system that drives cellular energy production and homeostasis. Despite significant efforts, most mt‐cyb variations identified are not matched with corresponding biochemical data, so their functional and pathogenic consequences in humans remain elusive. While human mtDNA is recalcitrant to genetic manipulation, it is possible to introduce human‐associated point mutations into yeast mtDNA. Using this system, we reveal direct links between human mt‐cyb variations in key catalytic domains of MT‐CYB and significant changes to complex III activity or drug sensitivity. Strikingly, m.15257G>A (p.Asp171Asn) increased the sensitivity of yeast to the antimalarial drug atovaquone, and m.14798T>C (p.Phe18Leu) enhanced the sensitivity of yeast to the antidepressant drug clomipramine. We demonstrate that while a small number of mt‐cyb variations had no functional effect, others have the capacity to alter complex III properties, suggesting they could play a wider role in human health and disease than previously thought. This compendium of new mt‐cyb‐biochemical relationships in yeast provides a resource for future investigations in humans.
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Affiliation(s)
- Zehua Song
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
| | - Anaïs Laleve
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
| | - Cindy Vallières
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
| | - John E McGeehan
- Molecular Biophysics Laboratories, Institute of Biomedical and Biomolecular Science, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Rhiannon E Lloyd
- Brain Tumour Research Centre, Institute of Biomedical and Biomolecular Science, School of Pharmacy and Biomedicine, University of Portsmouth, Portsmouth, UK
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
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209
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Chaitankar V, Karakülah G, Ratnapriya R, Giuste FO, Brooks MJ, Swaroop A. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res 2016; 55:1-31. [PMID: 27297499 DOI: 10.1016/j.preteyeres.2016.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 02/08/2023]
Abstract
The advent of high throughput next generation sequencing (NGS) has accelerated the pace of discovery of disease-associated genetic variants and genomewide profiling of expressed sequences and epigenetic marks, thereby permitting systems-based analyses of ocular development and disease. Rapid evolution of NGS and associated methodologies presents significant challenges in acquisition, management, and analysis of large data sets and for extracting biologically or clinically relevant information. Here we illustrate the basic design of commonly used NGS-based methods, specifically whole exome sequencing, transcriptome, and epigenome profiling, and provide recommendations for data analyses. We briefly discuss systems biology approaches for integrating multiple data sets to elucidate gene regulatory or disease networks. While we provide examples from the retina, the NGS guidelines reviewed here are applicable to other tissues/cell types as well.
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Affiliation(s)
- Vijender Chaitankar
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Gökhan Karakülah
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Felipe O Giuste
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Matthew J Brooks
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
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210
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Finding the resilient few. Nat Rev Genet 2016; 17:316. [DOI: 10.1038/nrg.2016.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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211
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Brand A, Evangelatos N, Satyamoorthy K. Public Health Genomics: the essential part for good governance in public health. Int J Public Health 2016; 61:401-3. [PMID: 27177507 PMCID: PMC4909794 DOI: 10.1007/s00038-016-0828-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 04/28/2016] [Indexed: 11/29/2022] Open
Affiliation(s)
- Angela Brand
- Faculty of Humanities and Sciences, MERIT (Maastricht Economic and Social Research Institute on Innovation and Technology), Maastricht University, Boschstraat 24, 6211AX, Maastricht, The Netherlands.
| | - Nikolaos Evangelatos
- Faculty of Humanities and Sciences, MERIT (Maastricht Economic and Social Research Institute on Innovation and Technology), Maastricht University, Boschstraat 24, 6211AX, Maastricht, The Netherlands
- University Clinic for Emergency and Intensive Care Medicine, Paracelsus Medical University (PMU), Nuremberg, Germany
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212
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Mystery factors protect lucky few from severe genetic disorders. Nature 2016. [DOI: 10.1038/nature.2016.19719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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213
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