The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The requested identity is verified. PTPRN2 encodes human receptor-type tyrosine-protein phosphatase N2, better known as phogrin or IA-2β. It is the IA-2-family paralog of PTPRN/IA-2/ICA512, not the same protein. The literature consistently places PTPRN2 in neuroendocrine dense-core secretory-granule membranes and describes a type-I, single-pass membrane topology with a luminal N-terminal region and cytosolic protein-tyrosine-phosphatase-like domain. This agrees with UniProt Q92932 and the listed IA-2/IA-2β, receptor IA-2, and PTP-like domains. No conflicting gene-symbol usage was found. (torii2009expressionandfunction pages 1-3, torii2009expressionandfunction pages 7-8)
The most defensible primary function is regulation of dense-core secretory-granule biology, including granule targeting/recycling, membrane phosphoinositide composition, and stimulus-coupled secretion. Native PTPRN2 is not a conventional protein-tyrosine phosphatase. One important biochemical study instead reported catalytic-cysteine-dependent phosphoinositide phosphatase activity toward PI(3)P and PI(4,5)P₂, but not PI(3,4,5)P₃. Because this lipid activity has limited independent confirmation in physiological human systems, PTPRN2 should be annotated as a PTP-like secretory-granule regulator with proposed phosphoinositide-phosphatase activity, rather than as an established broad protein phosphatase. (drake2003anovelstrategy pages 3-4, caromile2010theneurosecretoryvesicle pages 1-2, reiterer2020thedeadphosphatases pages 12-15)
| Annotation topic | Best-supported conclusion | Evidence type/model | Confidence/caveat |
|---|---|---|---|
| Identity and paralog distinction | Human PTPRN2/Q92932 encodes IA-2β/phogrin, an IA-2-family protein distinct from PTPRN, which encodes IA-2/ICA512. (torii2009expressionandfunction pages 1-3, torii2009expressionandfunction pages 8-10) | Human sequence-based classification; peer-reviewed family review | High. Literature consistently distinguishes PTPRN2/IA-2β from PTPRN/IA-2; no material symbol ambiguity was found. |
| Topology, processing, and localization | PTPRN2 is a precursor, type-I single-pass membrane protein with a luminal N-terminal pro/ectodomain, one transmembrane segment, and a cytosolic PTP-like domain. It is processed through the secretory pathway and concentrates in insulin- and hormone-containing dense-core granule membranes. (torii2009expressionandfunction pages 1-3, torii2009expressionandfunction pages 3-5) | Biochemical processing studies; immunoelectron microscopy and colocalization in neuroendocrine/β-cell models | High for topology and granule localization; exact processing products can vary by cell type and assay. |
| Conventional protein-tyrosine phosphatase activity | Native IA-2β lacks detectable activity toward conventional PTP substrates because key catalytic-region residues diverge from consensus; engineered back-mutations restore activity against artificial pNPP. (drake2003anovelstrategy pages 3-4, drake2003anovelstrategy pages 2-3) | Purified mouse IA-2β catalytic-domain mutants and enzyme kinetics | High that it is not a conventional protein-tyrosine phosphatase; an exceptionally narrow protein substrate cannot be completely excluded. |
| Phosphoinositide phosphatase activity | One primary study supports C934-dependent hydrolysis of PI(3)P and PI(4,5)P₂, but not PI(3,4,5)P₃. Purified transmembrane phogrin showed a reported specific activity of 142 mol·min⁻¹·mol⁻¹, about 75-fold above the soluble catalytic-domain fusion. (caromile2010theneurosecretoryvesicle pages 1-2, caromile2010theneurosecretoryvesicle pages 8-9) | Defined-lipid assays, immunopurified/full-length protein, catalytic C934S mutant, INS-1 and HEK293 cellular lipid measurements | Moderate. Catalytic-residue and knockdown evidence is compelling, but results are mainly from rat/mouse constructs or cultured cells; independent physiological confirmation in human β cells is limited, and expert reviews still describe the activity as proposed or unresolved. (kubota2024phogrinregulateshighfat pages 1-2, reiterer2020thedeadphosphatases pages 12-15) |
| Granule trafficking and insulin secretion | Luminal targeting information and cytosolic tyrosine/leucine motifs direct secretory-granule sorting, AP-adaptor-dependent endocytosis, and recycling after stimulus-coupled plasma-membrane exposure. PTPRN2 perturbation changes PI(4,5)P₂, granule abundance, and glucose-stimulated secretion. (torii2009expressionandfunction pages 5-7, torii2009expressionandfunction pages 8-10, caromile2010theneurosecretoryvesicle pages 6-8) | β-cell localization/trafficking experiments, cultured-cell perturbations, isolated islets, and mouse knockout studies | Moderate–high for trafficking and a role in regulated secretion. Direction and magnitude vary by overexpression, knockdown, and knockout design; overexpression can itself alter granule morphology and secretion. |
| Insulin-receptor–IRS2 growth axis | Following glucose-stimulated exocytosis, surface phogrin can interact with activated insulin receptor and stabilize IRS2. In 2024, β-cell-specific phogrin deficiency suppressed high-fat-diet-induced compensatory β-cell-mass expansion, supporting a stress-responsive proliferation pathway. (kubota2024phogrinregulateshighfat pages 1-2, kubota2024phogrinregulateshighfat pages 11-12) | MIN6/INS-1 interaction and proliferation experiments; β-cell-specific knockout and high-fat-diet mouse model | Moderate, preclinical. Mechanistic evidence is chiefly murine; the model involving a switch between phogrin–phogrin and phogrin–IR binding requires validation in human islets. |
| Alzheimer biomarker application | CSF PTPRN2 was useful as an amyloid-associated partner in cross-group protein pairs. GAP43–PTPRN2 classified A⁺T⁺ versus A⁻T⁻ participants with AUC 0.98 in discovery and 0.98 in validation cohorts. (mravinacova2024csfproteinratios pages 1-2, mravinacova2024csfproteinratios pages 5-7) | Antibody-array study: discovery n=213 and independent validation n=52; support-vector-machine modeling | Exploratory biomarker evidence. PTPRN2 was not independently different between groups in the cited analysis; pair performance does not establish causality or clinical utility. |
| Cancer mechanisms and genomic findings | In breast-cancer models, PTPRN2 lowered plasma-membrane PI(4,5)P₂, released cofilin for actin turnover, and promoted migration/invasion; overexpression increased these phenotypes by at least 50%. A 2023 report identified a BRAF::PTPRN2 fusion with MAPK activation in one meningioma. (sengelaub2016ptprn2andplcβ1 pages 1-2, sadagopan2023anovelbrafptprn2 pages 8-8) | Knockdown/overexpression in metastatic breast-cancer cells; clinical-expression association; single meningioma case with sequencing and pERK staining | Preclinical/exploratory. Breast-cancer perturbations support mechanism but not therapeutic efficacy; the meningioma fusion is a single case and may primarily act through retained BRAF kinase signaling rather than normal PTPRN2 function. |
| Recent metabolic epigenetics | PTPRN2 CpGs emerged during a 2023 whole-blood EWAS of adolescent NAFLD, but selected PTPRN2 loci did not validate by pyrosequencing. (melton2023differentialdnamethylation pages 1-3) | Cross-sectional EWAS in 707 adolescents, followed by targeted validation | Exploratory/negative validation. Whole-blood methylation is not evidence of altered PTPRN2 protein function in liver and does not support causality. |
Table: This table ranks the principal functional annotations for human PTPRN2/Q92932 by evidence type and confidence. It separates established identity and localization from debated enzymology and exploratory translational findings.
PTPRN2 is also called IA-2β, phogrin—“phosphatase homologue in granules of insulinoma”—and islet-cell-autoantigen-related protein. PTPRN, by contrast, encodes IA-2/ICA512. Both are evolutionarily conserved, neuroendocrine-enriched members of the IA-2 subfamily of receptor-type PTP-like proteins. Thus, results reported exclusively for IA-2/ICA512 cannot automatically be assigned to PTPRN2. (torii2009expressionandfunction pages 1-3, torii2009expressionandfunction pages 8-10)
The precursor has the expected type-I membrane organization: an N-terminal luminal pro-region, a mature luminal/secretory-granule ectodomain, one transmembrane helix, and a C-terminal cytosolic PTP-like domain. The protein is synthesized as an approximately 100–120-kDa rough-ER precursor, undergoes glycosylation and other secretory-pathway processing to approximately 110–130 kDa, and is proteolytically converted into mature products commonly reported around 60–70 kDa. Processing products vary between studies and cellular contexts. (torii2009expressionandfunction pages 1-3)
This architecture aligns with the supplied InterPro assignments: IA-2/IA-2β-specific regions and receptor-IA-2 ectodomain characterize the luminal portion, while the PTP-like/catalytic-domain assignments describe the cytosolic C terminus. Importantly, a structural PTP-domain assignment does not by itself imply ordinary protein-tyrosine-phosphatase activity.
PTPRN2 expression is concentrated in neuronal and endocrine/neuroendocrine cells, with prominent expression in brain and pancreatic islets. Immunoelectron microscopy in pancreatic β-cell models showed phogrin colocalized with insulin on dense-core insulin-secretory granules. This is the principal intracellular site at which its established biology should be interpreted. (torii2009expressionandfunction pages 3-5)
Granule targeting uses information on both sides of the membrane. The luminal pro-region contributes to entry into the regulated secretory pathway, while cytosolic tyrosine- and leucine-based motifs engage clathrin-adaptor machinery, including AP-1/AP-2-associated pathways. During stimulated exocytosis, granule membrane PTPRN2 becomes transiently exposed at the plasma membrane and can be endocytosed through endosomal compartments for return to the granule pathway. (torii2009expressionandfunction pages 5-7, torii2009expressionandfunction pages 8-10, torii2009expressionandfunction pages 3-5)
Accordingly, “receptor type” is structurally correct but potentially misleading: PTPRN2 is not primarily a constitutive plasma-membrane receptor. Its steady-state location is the membrane of intracellular dense-core vesicles, with stimulus-dependent surface exposure.
Native IA-2β contains substitutions in key catalytic-region residues and has little or no detectable activity against conventional PTP substrates. In a 2003 Biochemical Journal study, wild-type IA-2β and a single WPD-loop Y898P mutant had no measurable activity against the artificial substrate pNPP. Combined “back-mutations” toward active PTP consensus residues restored catalysis: the engineered S762Y/Y898P/D933A domain had a reported Kₘ of 1.6 mM, kcat of 11.8 s⁻¹, and kcat/Kₘ of 7,440 M⁻¹s⁻¹. These experiments show that the domain retains a PTP-compatible fold but that the native sequence is catalytically impaired for ordinary PTP chemistry. They do not identify a native protein substrate. Publication: July 2003; https://doi.org/10.1042/bj20021851. (drake2003anovelstrategy pages 3-4, drake2003anovelstrategy pages 2-3)
An unusually narrow protein substrate remains theoretically possible, but no reproducibly established physiological phosphoprotein substrate was found. Therefore, assigning EC 3.1.3.48 should be accompanied by a qualification that conventional protein-tyrosine-phosphatase activity is not established under physiological conditions.
Caromile and colleagues reported that phogrin hydrolyzes PI(3)P and PI(4,5)P₂, but not PI(3,4,5)P₃. Purified full-length transmembrane phogrin showed a specific activity of 142 mol substrate·min⁻¹·mol enzyme⁻¹—approximately 75-fold above a soluble catalytic-domain fusion—suggesting that membrane context or noncatalytic regions strongly affect activity. The reaction depended on the active-site cysteine, corresponding to C934 in the construct studied. Publication: April 2010; https://doi.org/10.1074/jbc.M109.066563. (caromile2010theneurosecretoryvesicle pages 1-2, caromile2010theneurosecretoryvesicle pages 8-9)
Cellular perturbations supported PI(4,5)P₂ as a relevant substrate. In INS-1 cells, wild-type phogrin reduced PI(4,5)P₂ whereas C934S did not; approximately 94% knockdown of endogenous phogrin produced a threefold increase in PI(4,5)P₂. At the highest overexpression level, plasma-membrane PI(4,5)P₂ fell by about 70%. Wild-type overexpression reduced glucose-stimulated insulin secretion by approximately 83–90% without decreasing insulin content, predominantly affecting the second phase; the C934S mutant did not reproduce the inhibition. (caromile2010theneurosecretoryvesicle pages 6-8, caromile2010theneurosecretoryvesicle pages 8-9)
These are strong construct-level and cellular observations, but chiefly from rat INS-1, mouse-related constructs, and HEK293 systems rather than primary human β cells. Later expert reviews consequently describe PTPRN2 as a pseudophosphatase or as having proposed/limited phosphoinositide activity whose physiological significance remains unresolved. The enzyme annotation should retain this uncertainty. (kubota2024phogrinregulateshighfat pages 1-2, reiterer2020thedeadphosphatases pages 12-15)
PTPRN2 contributes to the identity and trafficking of hormone-containing secretory granules. Sorting motifs direct it into granules and mediate retrieval after exocytosis. Mouse disruption studies report impaired glucose tolerance, reduced glucose-stimulated insulin secretion, and fewer dense-core vesicles, supporting an in-vivo role in maintaining the releasable hormone-granule system. However, different knockdown, knockout, and overexpression designs have produced variable effects on secretion, indicating that dosage, chronic compensation, and experimental context matter. (torii2009expressionandfunction pages 8-10, kubota2024phogrinregulateshighfat pages 1-2, reiterer2020thedeadphosphatases pages 12-15)
The lipid-phosphatase model supplies a plausible biochemical mechanism: phogrin could help maintain compartment-specific PI(4,5)P₂ levels in granule or recycling membranes. Because PI(4,5)P₂ controls actin, docking, priming, and membrane-fusion machinery, either excessive depletion or loss of phogrin-mediated turnover could disturb secretion. This model is consistent with the preferential effect on sustained/second-phase insulin release, but the exact membrane on which endogenous catalysis occurs remains unsettled. (caromile2010theneurosecretoryvesicle pages 6-8, caromile2010theneurosecretoryvesicle pages 8-9)
After glucose-stimulated granule fusion, surface-exposed phogrin can interact with activated insulin receptor and support IRS2 stability, linking exocytosis to autocrine insulin signaling and β-cell proliferation. A January 2024 mouse study found that β-cell-specific phogrin deficiency suppressed compensatory β-cell-mass expansion during high-fat feeding. Phogrin–insulin-receptor complexes were observed in high-fat-diet mouse islets and proliferating β-cell lines, while intercellular surface phogrin binding under confluent conditions inhibited this interaction. The authors propose a binding-partner switch: phogrin–IR favors IRS2-dependent proliferation during metabolic stress, whereas phogrin–phogrin contact helps terminate growth as cell density recovers. Publication: January 2024; https://doi.org/10.3390/nu16010169. (kubota2024phogrinregulateshighfat pages 1-2, kubota2024phogrinregulateshighfat pages 11-12)
This pathway is mechanistically informative but remains preclinical. It has not yet established an equivalent quantitative role in human islet adaptation.
IA-2β/phogrin is a major islet autoantigen, and antibodies against IA-2-family proteins can precede clinical type 1 diabetes. Its autoantigen status is clinically relevant to risk-assessment panels, but IA-2β-specific assays must be distinguished from the much more commonly discussed IA-2/PTPRN antibody assays. The autoimmune role does not demonstrate that autoantibodies inhibit PTPRN2’s cellular function. (torii2009expressionandfunction pages 7-8)
In metastatic breast-cancer models, PTPRN2 and PLCβ1 independently lowered plasma-membrane PI(4,5)P₂. Reduced PI(4,5)P₂ released cofilin from inhibitory membrane sequestration, increased actin turnover, and promoted migration. PTPRN2 depletion reduced transwell and scratch-assay migration, while overexpression in less-metastatic cells increased migration and invasion by at least 50%; proliferation and viability were not materially altered. This provides mechanistic evidence for a PI(4,5)P₂–cofilin–actin pathway, although it does not yet constitute a validated therapeutic application. Publication: November 2016; https://doi.org/10.15252/embj.201591973. (sengelaub2016ptprn2andplcβ1 pages 1-2)
A December 2023 case report identified an in-frame BRAF::PTPRN2 fusion in a WHO-grade-1 meningioma, accompanied by elevated pERK staining and complex chromosome-7 alterations. As a single case, this is hypothesis-generating; the likely oncogenic output may derive chiefly from altered BRAF/MAPK signaling rather than normal phogrin function. https://doi.org/10.1186/s40478-023-01668-w. (sadagopan2023anovelbrafptprn2 pages 8-8)
A February 2024 CSF study measured 49 proteins in a discovery cohort of 213 participants—148 amyloid/tau negative and 65 positive—and validated its protein-pair approach in 52 additional participants. PTPRN2 belonged to an amyloid-associated protein cluster. GAP43–PTPRN2 achieved an AUC of 0.98 (95% CI 0.93–1.00) in discovery and 0.98 (0.94–1.00) in validation. SNCB–PTPRN2 reached AUCs of 0.93 and 1.00, respectively. Publication: February 2024; https://doi.org/10.1186/s13024-024-00705-z. (mravinacova2024csfproteinratios pages 1-2, mravinacova2024csfproteinratios pages 5-7)
This is promising analytical-biomarker evidence, not proof that PTPRN2 causes Alzheimer pathology. PTPRN2 was not individually different between diagnostic groups in the cited analysis; performance arose from ratios or pairs that may normalize interindividual variation. Relative antibody-array quantification and modest validation size also limit immediate clinical implementation. (mravinacova2024csfproteinratios pages 5-7, mravinacova2024csfproteinratios pages 4-5)
A 2023 whole-blood EWAS studied 707 adolescents assessed by ultrasound at age 17. PTPRN2 CpGs emerged during discovery and three loci were selected for pyrosequencing, but the validated NAFLD associations involved ANK1 and MIR10A, not PTPRN2. Thus, this study should not be cited as validated evidence that PTPRN2 methylation causes adolescent NAFLD. Publication: February 2023; https://doi.org/10.1007/s12072-022-10469-7. (melton2023differentialdnamethylation pages 1-3)
A conservative functional annotation is:
PTPRN2/phogrin is a neuroendocrine type-I dense-core-secretory-granule membrane protein and PTP-family pseudoenzyme that regulates granule trafficking, phosphoinositide homeostasis, stimulus-coupled secretion, and context-dependent β-cell insulin-receptor/IRS2 signaling. It lacks established conventional protein-tyrosine-phosphatase activity. C934-dependent hydrolysis of PI(3)P and PI(4,5)P₂ has been demonstrated in biochemical and cultured-cell systems, but its endogenous physiological importance and substrate range in human cells remain incompletely validated.
Confidence is high for identity, domain architecture, processing, neuroendocrine expression, and dense-core-granule localization; moderate for a direct role in granule abundance and regulated secretion; and moderate-to-limited for phosphoinositide phosphatase activity as the universal primary mechanism. The 2024 β-cell-growth pathway is compelling but murine, while Alzheimer biomarker, tumor-fusion, methylation, and other disease associations remain exploratory or preclinical rather than established clinical uses.
References
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(drake2003anovelstrategy pages 3-4): Paul G. DRAKE, Günther H. PETERS, Henrik Sune ANDERSEN, Wiljan HENDRIKS, and Niels Peter H. MØLLER. A novel strategy for the development of selective active-site inhibitors of the protein tyrosine phosphatase-like proteins islet-cell antigen 512 (ia-2) and phogrin (ia-2beta). Jul 2003. URL: https://doi.org/10.1042/bj20021851, doi:10.1042/bj20021851. This article has 24 citations and is from a domain leading peer-reviewed journal.
(caromile2010theneurosecretoryvesicle pages 1-2): Leslie A. Caromile, Anush Oganesian, Scott A. Coats, Ronald A. Seifert, and Daniel F. Bowen-Pope. The neurosecretory vesicle protein phogrin functions as a phosphatidylinositol phosphatase to regulate insulin secretion. Apr 2010. URL: https://doi.org/10.1074/jbc.m109.066563, doi:10.1074/jbc.m109.066563. This article has 66 citations and is from a domain leading peer-reviewed journal.
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(torii2009expressionandfunction pages 3-5): Seiji TORII. Expression and function of ia-2 family proteins, unique neuroendocrine-specific protein-tyrosine phosphatases. Endocrine journal, 56 5:639-48, Jan 2009. URL: https://doi.org/10.1507/endocrj.k09e-157, doi:10.1507/endocrj.k09e-157. This article has 75 citations and is from a peer-reviewed journal.
(drake2003anovelstrategy pages 2-3): Paul G. DRAKE, Günther H. PETERS, Henrik Sune ANDERSEN, Wiljan HENDRIKS, and Niels Peter H. MØLLER. A novel strategy for the development of selective active-site inhibitors of the protein tyrosine phosphatase-like proteins islet-cell antigen 512 (ia-2) and phogrin (ia-2beta). Jul 2003. URL: https://doi.org/10.1042/bj20021851, doi:10.1042/bj20021851. This article has 24 citations and is from a domain leading peer-reviewed journal.
(caromile2010theneurosecretoryvesicle pages 8-9): Leslie A. Caromile, Anush Oganesian, Scott A. Coats, Ronald A. Seifert, and Daniel F. Bowen-Pope. The neurosecretory vesicle protein phogrin functions as a phosphatidylinositol phosphatase to regulate insulin secretion. Apr 2010. URL: https://doi.org/10.1074/jbc.m109.066563, doi:10.1074/jbc.m109.066563. This article has 66 citations and is from a domain leading peer-reviewed journal.
(kubota2024phogrinregulateshighfat pages 1-2): Chisato Kubota, Ryoko Torii, Masahiro Hosaka, Toshiyuki Takeuchi, Hiroshi Gomi, and Seiji Torii. Phogrin regulates high-fat diet-induced compensatory pancreatic β-cell growth by switching binding partners. Nutrients, 16:169, Jan 2024. URL: https://doi.org/10.3390/nu16010169, doi:10.3390/nu16010169. This article has 0 citations.
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(kubota2024phogrinregulateshighfat pages 11-12): Chisato Kubota, Ryoko Torii, Masahiro Hosaka, Toshiyuki Takeuchi, Hiroshi Gomi, and Seiji Torii. Phogrin regulates high-fat diet-induced compensatory pancreatic β-cell growth by switching binding partners. Nutrients, 16:169, Jan 2024. URL: https://doi.org/10.3390/nu16010169, doi:10.3390/nu16010169. This article has 0 citations.
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(melton2023differentialdnamethylation pages 1-3): Phillip E. Melton, M. A. Burton, K. A. Lillycrop, K. M. Godfrey, S. Rauschert, D. Anderson, G. C. Burdge, T. A. Mori, L. J. Beilin, O. T. Ayonrinde, J. M. Craig, J. K. Olynyk, J. D. Holbrook, C. E. Pennell, W. H. Oddy, E. K. Moses, L. A. Adams, and R. C. Huang. Differential dna methylation of steatosis and non-alcoholic fatty liver disease in adolescence. Hepatology International, 17:584-594, Feb 2023. URL: https://doi.org/10.1007/s12072-022-10469-7, doi:10.1007/s12072-022-10469-7. This article has 17 citations and is from a peer-reviewed journal.
(mravinacova2024csfproteinratios pages 4-5): Sára Mravinacová, Vilma Alanko, Sofia Bergström, Claire Bridel, Yolande Pijnenburg, Göran Hagman, Miia Kivipelto, Charlotte Teunissen, Peter Nilsson, Anna Matton, and Anna Månberg. Csf protein ratios with enhanced potential to reflect alzheimer’s disease pathology and neurodegeneration. Molecular Neurodegeneration, Feb 2024. URL: https://doi.org/10.1186/s13024-024-00705-z, doi:10.1186/s13024-024-00705-z. This article has 34 citations and is from a highest quality peer-reviewed journal.