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Otero-Carrasco B, Ugarte Carro E, Prieto-Santamaría L, Diaz Uzquiano M, Caraça-Valente Hernández JP, Rodríguez-González A. Identifying patterns to uncover the importance of biological pathways on known drug repurposing scenarios. BMC Genomics 2024; 25:43. [PMID: 38191292 PMCID: PMC10775474 DOI: 10.1186/s12864-023-09913-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Drug repurposing plays a significant role in providing effective treatments for certain diseases faster and more cost-effectively. Successful repurposing cases are mostly supported by a classical paradigm that stems from de novo drug development. This paradigm is based on the "one-drug-one-target-one-disease" idea. It consists of designing drugs specifically for a single disease and its drug's gene target. In this article, we investigated the use of biological pathways as potential elements to achieve effective drug repurposing. METHODS Considering a total of 4214 successful cases of drug repurposing, we identified cases in which biological pathways serve as the underlying basis for successful repurposing, referred to as DREBIOP. Once the repurposing cases based on pathways were identified, we studied their inherent patterns by considering the different biological elements associated with this dataset, as well as the pathways involved in these cases. Furthermore, we obtained gene-disease association values to demonstrate the diminished significance of the drug's gene target in these repurposing cases. To achieve this, we compared the values obtained for the DREBIOP set with the overall association values found in DISNET, as well as with the drug's target gene (DREGE) based repurposing cases using the Mann-Whitney U Test. RESULTS A collection of drug repurposing cases, known as DREBIOP, was identified as a result. DREBIOP cases exhibit distinct characteristics compared with DREGE cases. Notably, DREBIOP cases are associated with a higher number of biological pathways, with Vitamin D Metabolism and ACE inhibitors being the most prominent pathways. Additionally, it was observed that the association values of GDAs in DREBIOP cases were significantly lower than those in DREGE cases (p-value < 0.05). CONCLUSIONS Biological pathways assume a pivotal role in drug repurposing cases. This investigation successfully revealed patterns that distinguish drug repurposing instances associated with biological pathways. These identified patterns can be applied to any known repurposing case, enabling the detection of pathway-based repurposing scenarios or the classical paradigm.
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Affiliation(s)
- Belén Otero-Carrasco
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223, Spain
- ETS Ingenieros Informáticos, Universidad Politécnica de Madrid, Boadilla del Monte, 28660, Spain
| | - Esther Ugarte Carro
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223, Spain
| | - Lucía Prieto-Santamaría
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223, Spain
- ETS Ingenieros Informáticos, Universidad Politécnica de Madrid, Boadilla del Monte, 28660, Spain
| | - Marina Diaz Uzquiano
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223, Spain
| | | | - Alejandro Rodríguez-González
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223, Spain.
- ETS Ingenieros Informáticos, Universidad Politécnica de Madrid, Boadilla del Monte, 28660, Spain.
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Bacchetta J, Edouard T, Laverny G, Bernardor J, Bertholet-Thomas A, Castanet M, Garnier C, Gennero I, Harambat J, Lapillonne A, Molin A, Naud C, Salles JP, Laborie S, Tounian P, Linglart A. Vitamin D and calcium intakes in general pediatric populations: A French expert consensus paper. Arch Pediatr 2022; 29:312-325. [PMID: 35305879 DOI: 10.1016/j.arcped.2022.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/20/2022] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Nutritional vitamin D supplements are often used in general pediatrics. Here, the aim is to address vitamin D supplementation and calcium nutritional intakes in newborns, infants, children, and adolescents to prevent vitamin D deficiency and rickets in general populations. STUDY DESIGN We formulated clinical questions relating to the following categories: the Patient (or Population) to whom the recommendation will apply; the Intervention being considered; the Comparison (which may be "no action," placebo, or an alternative intervention); and the Outcomes affected by the intervention (PICO). These PICO elements were arranged into the questions to be addressed in the literature searches. Each PICO question then formed the basis for a statement. The population covered consisted of children aged between 0 and 18 years and premature babies hospitalized in neonatology. Two groups were assembled: a core working group and a voting panel from different scientific pediatric committees from the French Society of Pediatrics and national scientific societies. RESULTS We present here 35 clinical practice points (CPPs) for the use of native vitamin D therapy (ergocalciferol, vitamin D2 and cholecalciferol, vitamin D3) and calcium nutritional intakes in general pediatric populations. CONCLUSION This consensus document was developed to provide guidance to health care professionals on the use of nutritional vitamin D and dietary modalities to achieve the recommended calcium intakes in general pediatric populations. These CPPs will be revised periodically. Research recommendations to study key vitamin D outcome measures in children are also suggested.
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Affiliation(s)
- J Bacchetta
- Centre de Référence des Maladies Rares du Calcium et du Phosphore, Service de Néphrologie Rhumatologie Dermatologie Pédiatriques, Filières Santé Maladies Rares OSCAR, ORKID et ERKNet, Hôpital Femme Mère Enfant, 59 Boulevard Pinel, Bron 69677 CEDEX, France; INSERM U1033, LYOS, Prévention des Maladies Osseuses, Lyon, France; Faculté de Médecine Lyon Est, Université de Lyon, Lyon, France.
| | - T Edouard
- Centre de Référence des Maladies Rares du Calcium et du Phosphore, Unité d'Endocrinologie, Génétique et Pathologies Osseuses, Filières Santé Maladies Rares OSCAR et BOND, Hôpital des Enfants, Toulouse, France
| | - G Laverny
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch, France
| | - J Bernardor
- INSERM U1033, LYOS, Prévention des Maladies Osseuses, Lyon, France; Département de Pédiatrie, CHU de Nice, Nice, France
| | - A Bertholet-Thomas
- Centre de Référence des Maladies Rares du Calcium et du Phosphore, Service de Néphrologie Rhumatologie Dermatologie Pédiatriques, Filières Santé Maladies Rares OSCAR, ORKID et ERKNet, Hôpital Femme Mère Enfant, 59 Boulevard Pinel, Bron 69677 CEDEX, France; INSERM U1033, LYOS, Prévention des Maladies Osseuses, Lyon, France
| | - M Castanet
- Centre de Référence des Maladies Rares du Calcium et du Phosphore, Département de Pédiatrie, Filière Santé Maladies Rares OSCAR, CHU Rouen, Rouen, France
| | - C Garnier
- Centre de Référence des Maladies Rares du Calcium et du Phosphore, Service de Néphrologie Rhumatologie Dermatologie Pédiatriques, Filières Santé Maladies Rares OSCAR, ORKID et ERKNet, Hôpital Femme Mère Enfant, 59 Boulevard Pinel, Bron 69677 CEDEX, France
| | - I Gennero
- Centre de Référence des Maladies Rares du Calcium et du Phosphore, Unité d'Endocrinologie, Génétique et Pathologies Osseuses, Filières Santé Maladies Rares OSCAR et BOND, Hôpital des Enfants, Toulouse, France
| | - J Harambat
- Centre de Référence Maladies Rénales Rares, Unité de Néphrologie Pédiatrique, Hôpital Pellegrin-Enfants, Bordeaux, France; INSERM U1219, Bordeaux, France
| | - A Lapillonne
- Service de Pédiatrie et Réanimation Néonatales, EHU 7328 Université de Paris, Hôpital Necker- Enfants Malades, Paris, France; CNRC, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - A Molin
- Centre de Référence des Maladies Rares du Calcium et du Phosphore, Département de Génétique, Filière Santé Maladies Rares OSCAR, CHU Caen, Caen, France
| | - C Naud
- Centre de Référence des Maladies Rares du Calcium et du Phosphore, Service de Néphrologie Rhumatologie Dermatologie Pédiatriques, Filières Santé Maladies Rares OSCAR, ORKID et ERKNet, Hôpital Femme Mère Enfant, 59 Boulevard Pinel, Bron 69677 CEDEX, France
| | - J P Salles
- Centre de Référence des Maladies Rares du Calcium et du Phosphore, Unité d'Endocrinologie, Génétique et Pathologies Osseuses, Filières Santé Maladies Rares OSCAR et BOND, Hôpital des Enfants, Toulouse, France
| | - S Laborie
- Service de Réanimation Néonatale, Hôpital Femme Mère Enfant, Bron, France
| | - P Tounian
- Service de Nutrition et Gastroentérologie Pédiatriques, Hôpital Trousseau, Faculté de Médecine Sorbonne Université, Paris, France
| | - A Linglart
- AP-HP, Centre de Référence des Maladies Rares du Calcium et du Phosphore, Service d'Endocrinologie et diabète de l'enfant, Filières Santé Maladies Rares OSCAR, ERN endoRARE et BOND, Plateforme d'expertise des maladies rares Paris Saclay, Hôpital Bicêtre Paris-Saclay, Université Paris Saclay, INSERM U1185, Le Kremlin Bicêtre, France
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Yin M, Chen M, Yanagisawa T, Matsuoka R, Zhang L, Qiu W, Tao N, Xi Y, Wang X. A comparative study on the nutritional evaluation of the head, meat, roe, and viscera of rainbow smelt (Osmerus mordax). J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Defective mineralization of the growth plate and preformed osteoid result in rickets and osteomalacia, respectively. The leading cause of rickets worldwide is solar vitamin D deficiency and/or dietary calcium deficiency collectively termed as nutritional rickets. Vitamin D deficiency predominates in high-latitude countries in at-risk groups (dark skin, reduced sun exposure, infants and pregnant and lactating women) but is emerging in some tropical countries due to sun avoidance behaviour. Calcium deficiency predominates in tropical countries, especially in the malnourished population. Nutritional rickets can have devastating health consequences beyond bony deformities (swollen wrist and ankle joints, rachitic rosary, soft skull, stunting and bowing) and include life-threatening hypocalcaemic complications of seizures and, in infancy, heart failure due to dilated cardiomyopathy. In children, diagnosis of rickets (always associated with osteomalacia) is confirmed on radiographs (cupping and flaring of metaphyses) and should be suspected in high risk individuals with the above clinical manifestations in the presence of abnormal blood biochemistry (high alkaline phosphatase and parathyroid hormone, low 25-hydroxyvitamin D and calcium and/or low phosphate). In adults or adolescents with closed growth plates, osteomalacia presents with non-specific symptoms (fatigue, malaise and muscle weakness) and abnormal blood biochemistry, but only in extreme cases, it is associated with radiographic findings of Looser's zone fractures. Bone biopsies could confirm osteomalacia at earlier disease stages, for definitive diagnosis. Treatment includes high-dose cholecalciferol or ergocalciferol daily for a minimum of 12 wk or stoss therapy in exceptional circumstances, each followed by lifelong maintenance supplementation. In addition, adequate calcium intake through diet or supplementation should be ensured. Preventative approaches should be tailored to the population needs and incorporate multiple strategies including targeted vitamin D supplementation of at-risk groups and food fortification with vitamin D and/or calcium. Economically, food fortification is certainly the most cost-effective way forward.
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Affiliation(s)
- Suma Uday
- Department of Endocrinology & Diabetes, Birmingham Women's & Children's NHS Foundation Trust; Institute of Metabolism & Systems Research, University of Birmingham, Edgbaston, Birmingham, UK
| | - Wolfgang Högler
- Institute of Metabolism & Systems Research, University of Birmingham, Edgbaston, Birmingham, UK; Department of Paediatrics & Adolescent Medicine, Johannes Kepler University, Kepler University Hospital, Med Campus IV, Linz, Austria
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Metagenomic analysis of the gut microbiome composition associated with vitamin D supplementation in Taiwanese infants. Sci Rep 2021; 11:2856. [PMID: 33536562 PMCID: PMC7859236 DOI: 10.1038/s41598-021-82584-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
Early childhood is a critical stage for the foundation and development of the gut microbiome, large amounts of essential nutrients are required such as vitamin D. Vitamin D plays an important role in regulating calcium homeostasis, and deficiency can impair bone mineralization. In addition, most people know that breastfeeding is advocated to be the best thing for a newborn; however, exclusively breastfeeding infants are not easily able to absorb an adequate amount of vitamin D from breast milk. Understanding the effects of vitamin D supplementation on gut microbiome can improve the knowledge of infant health and development. A total of 62 fecal sample from healthy infants were collected in Taiwan. Of the 62 infants, 31 were exclusively breastfed infants and 31 were mixed- or formula-fed infants. For each feeding type, one subgroup of infants received 400 IU of vitamin D per day, and the remaining infants received a placebo. In total, there are 15 breastfed and 20 formula-fed infants with additional vitamin D supplementation, and 16 breastfed and 11 formula-fed infants belong to control group, respectively. We performed a comparative metagenomic analysis to investigate the distribution and diversity of infant gut microbiota among different types of feeding regimes with and without vitamin D supplementation. Our results reveal that the characteristics of infant gut microbiota not only depend on the feeding types but also on nutrients intake, and demonstrated that the vitamin D plays an important role in modulating the infant gut microbiota, especially increase the proportion of probiotics in breast-fed infants.
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Vitamin D deficiency in Western Australia. J Paediatr Child Health 2020; 56:1484-1485. [PMID: 32949208 DOI: 10.1111/jpc.2_14855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/13/2020] [Accepted: 02/24/2020] [Indexed: 11/30/2022]
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Lin EL, Gottesman GS, McAlister WH, Bijanki VN, Mack KE, Griffin DM, Mumm S, Whyte MP. Healing of vitamin D deficiency rickets complicating hypophosphatasia suggests a role beyond circulating mineral sufficiency for vitamin D in musculoskeletal health. Bone 2020; 136:115322. [PMID: 32200022 DOI: 10.1016/j.bone.2020.115322] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 12/17/2022]
Abstract
Hypophosphatasia (HPP) is the metabolic bone disease caused by loss-of-function mutation(s) of the ALPL gene that encodes the cell-surface tissue-nonspecific isoenzyme of alkaline phosphatase (TNSALP). In HPP, extracellular accumulation of inorganic pyrophosphate (PPi), a TNSALP natural substrate and inhibitor of biomineralization, often leads to rickets or osteomalacia despite normal or sometimes elevated circulating levels of calcium (Ca) and inorganic phosphate (Pi). We report an infant girl with vitamin D deficiency rickets subsequently healed by cholecalciferol administration alone before receiving TNSALP-replacement therapy for accompanying HPP. Throughout her clinical course, circulating Ca and Pi levels were normal or elevated. At presentation with failure-to-thrive at age six months, radiographs revealed severe rickets and serum 25(OH)D was 8 ng/mL (Nl, 30-100), yet low ALP activity 55 U/L (Nl, 124-341), normal Ca 9.3 mg/dL (Nl, 8.5-10.1) and Pi 6.4 mg/dL (Nl, 3.5-7.0), and low-normal parathyroid hormone 21 pg/mL (Nl, 14-72) were instead consistent with HPP. At age nine months, after 1000 IU of cholecalciferol orally each day for six weeks, serum 25(OH)D was 86 ng/mL, strength markedly better, and radiographs documented significant improvement of rickets. At age 18 months, with fully healed vitamin D deficiency rickets, findings of underlying HPP included a waddling gait and Gower sign, metaphyseal "tongues" of radiolucency, elevated serum pyridoxal 5'-phosphate 121 ng/mL (Nl, 2-33), and bi-allelic ALPL missense mutations. Then, nearly complete restoration of strength and radiographic healing of her remaining skeletal disease from HPP occurred during asfotase alfa enzyme replacement treatment. At no time, including presentation, were circulating Ca or Pi levels compromised. Instead, and in keeping with HPP, high-normal or elevated serum Ca and Pi concentrations were consistently documented. Thus, our findings suggest some role for vitamin D in musculoskeletal health beyond assuring circulating mineral sufficiency.
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Affiliation(s)
- Elizabeth L Lin
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospitals for Children, St. Louis, MO 63110, USA; Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Gary S Gottesman
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospitals for Children, St. Louis, MO 63110, USA.
| | - William H McAlister
- Mallinckrodt Institute of Radiology, Washington University School of Medicine at St. Louis Children's Hospital, St. Louis, MO 63110, USA.
| | - Vinieth N Bijanki
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospitals for Children, St. Louis, MO 63110, USA.
| | - Karen E Mack
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospitals for Children, St. Louis, MO 63110, USA.
| | - Donna M Griffin
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospitals for Children, St. Louis, MO 63110, USA.
| | - Steven Mumm
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospitals for Children, St. Louis, MO 63110, USA; Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Michael P Whyte
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospitals for Children, St. Louis, MO 63110, USA; Division of Bone and Mineral Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Bouillon R, Antonio L. Nutritional rickets: Historic overview and plan for worldwide eradication. J Steroid Biochem Mol Biol 2020; 198:105563. [PMID: 31809867 DOI: 10.1016/j.jsbmb.2019.105563] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/10/2019] [Accepted: 12/02/2019] [Indexed: 02/01/2023]
Abstract
Rickets was first described in great detail in the mid 17th century and was affecting a great number of children in major European cities. The disease, however, existed already in the Roman times. The etiology of this disease remained enigmatic until the 1920s when two different mechanisms, lack of exposure to sunlight and lack of a dietary factor were finally solved by the discovery of vitamin D and its dual origin. Soon thereafter, the implementation of vitamin D supplementation for all infants and small children largely eliminated nutritional rickets in Europe and North America. It took nearly a century to elucidate the complex chemistry, metabolism, mode and spectrum of activity of the vitamin D endocrine system. Nutritional rickets, whether due to simple vitamin D or calcium deficiency or both, remains widely ravaging many infants and children around the world. Asian countries and the Middle East are mainly confronted with vitamin D deficiency whereas many African and some Asian countries face calcium deficiency rickets. Immigrants and refugees or in general people with a darker skin living in moderate climate zone are also confronted with this disease. There is great consensus how this disease could be prevented or cured. In collaboration with most international professional societies, we prepare a memorandum, in line with the successful battle against iodine deficiency disorders, to convince the World Health Organization and its member states to start an implementation program to eradicate nutritional rickets by 2030.
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Affiliation(s)
- Roger Bouillon
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Ageing, KU, Leuven, Belgium.
| | - Leen Antonio
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Ageing, KU, Leuven, Belgium
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Abstract
The maintenance of extracellular calcium levels within a narrow range is necessary for normal function of the nervous system, muscle, and coagulation, to maintain mineralization of the skeleton but to avoid calcification of soft tissues. Accordingly, absorption and excretion of calcium is closely regulated, and adult humans can adapt to a wide range of calcium intakes from 300 to 2,000 mg/day. The evidence that low calcium intakes contribute to osteoporosis development is weak, as is evidence that increasing these intakes significantly changes fracture risk. Consistent with this view, the United States Preventive Services Task Force does not support the use of calcium supplements in healthy community-dwelling adults. While some groups continue to recommend that supplements of calcium and vitamin D are given with drug treatments for osteoporosis, this view is not supported by clinical trials which demonstrate anti-fracture efficacy of estrogens and bisphosphonates in the absence of such supplementation. Thus, calcium supplements have only a minor place in contemporary medical practice.
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Affiliation(s)
- Ian R Reid
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
- Auckland District Health Board, Auckland, New Zealand.
| | - Sarah M Bristow
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
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Reid IR, Bolland MJ. Controversies in medicine: the role of calcium and vitamin D supplements in adults. Med J Aust 2019; 211:468-473. [DOI: 10.5694/mja2.50393] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ian R Reid
- University of Auckland Auckland New Zealand
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