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Ambroa-Conde A, Casares de Cal MA, Gómez-Tato A, Robinson O, Mosquera-Miguel A, de la Puente M, Ruiz-Ramírez J, Phillips C, Lareu MV, Freire-Aradas A. Inference of tobacco and alcohol consumption habits from DNA methylation analysis of blood. Forensic Sci Int Genet 2024; 70:103022. [PMID: 38309257 DOI: 10.1016/j.fsigen.2024.103022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/22/2023] [Accepted: 01/25/2024] [Indexed: 02/05/2024]
Abstract
DNA methylation has become a biomarker of great interest in the forensic and clinical fields. In criminal investigations, the study of this epigenetic marker has allowed the development of DNA intelligence tools providing information that can be useful for investigators, such as age prediction. Following a similar trend, when the origin of a sample in a criminal scenario is unknown, the inference of an individual's lifestyle such as tobacco use and alcohol consumption could provide relevant information to help in the identification of DNA donors at the crime scene. At the same time, in the clinical domain, prediction of these trends of consumption could allow the identification of people at risk or better identification of the causes of different pathologies. In the present study, DNA methylation data from the UK AIRWAVE study was used to build two binomial logistic models for the inference of smoking and drinking status. A total of 348 individuals (116 non-smokers, 116 former smokers and 116 smokers) plus a total of 237 individuals (79 non-drinkers, 79 moderate drinkers and 79 drinkers) were used for development of tobacco and alcohol consumption prediction models, respectively. The tobacco prediction model was composed of two CpGs (cg05575921 in AHRR and cg01940273) and the alcohol prediction model three CpGs (cg06690548 in SLC7A11, cg0886875 and cg21294714 in MIR4435-2HG), providing correct classifications of 86.49% and 74.26%, respectively. Validation of the models was performed using leave-one-out cross-validation. Additionally, two independent testing sets were also assessed for tobacco and alcohol consumption. Considering that the consumption of these substances could underlie accelerated epigenetic ageing patterns, the effect of these lifestyles on the prediction of age was evaluated. To do that, a quantile regression model based on previous studies was generated, and the potential effect of tobacco and alcohol consumption with the epigenetic age was assessed. The Wilcoxon test was used to evaluate the residuals generated by the model and no significant differences were observed between the categories analyzed.
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Affiliation(s)
- A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M A Casares de Cal
- CITMAga (Center for Mathematical Research and Technology of Galicia), University of Santiago de Compostela, Spain
| | - A Gómez-Tato
- CITMAga (Center for Mathematical Research and Technology of Galicia), University of Santiago de Compostela, Spain
| | - O Robinson
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - J Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain.
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Freire-Aradas A, Tomsia M, Piniewska-Róg D, Ambroa-Conde A, Casares de Cal MA, Pisarek A, Gómez-Tato A, Álvarez-Dios J, Pośpiech E, Parson W, Kayser M, Phillips C, Branicki W. Development of an epigenetic age predictor for costal cartilage with a simultaneous somatic tissue differentiation system. Forensic Sci Int Genet 2023; 67:102936. [PMID: 37783021 DOI: 10.1016/j.fsigen.2023.102936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 10/04/2023]
Abstract
Age prediction from DNA has been a topic of interest in recent years due to the promising results obtained when using epigenetic markers. Since DNA methylation gradually changes across the individual's lifetime, prediction models have been developed accordingly for age estimation. The tissue-dependence for this biomarker usually necessitates the development of tissue-specific age prediction models, in this way, multiple models for age inference have been constructed for the most commonly encountered forensic tissues (blood, oral mucosa, semen). The analysis of skeletal remains has also been attempted and prediction models for bone have now been reported. Recently, the VISAGE Enhanced Tool was developed for the simultaneous DNA methylation analysis of 8 age-correlated loci using targeted high-throughput sequencing. It has been shown that this method is compatible with epigenetic age estimation models for blood, buccal cells, and bone. Since when dealing with decomposed cadavers or postmortem samples, cartilage samples are also an important biological source, an age prediction model for cartilage has been generated in the present study based on methylation data collected using the VISAGE Enhanced Tool. In this way, we have developed a forensic cartilage age prediction model using a training set composed of 109 samples (19-74 age range) based on DNA methylation levels from three CpGs in FHL2, TRIM59 and KLF14, using multivariate quantile regression which provides a mean absolute error (MAE) of ± 4.41 years. An independent testing set composed of 72 samples (19-75 age range) was also analyzed and provided an MAE of ± 4.26 years. In addition, we demonstrate that the 8 VISAGE markers, comprising EDARADD, TRIM59, ELOVL2, MIR29B2CHG, PDE4C, ASPA, FHL2 and KLF14, can be used as tissue prediction markers which provide reliable blood, buccal cells, bone, and cartilage differentiation using a developed multinomial logistic regression model. A training set composed of 392 samples (n = 87 blood, n = 86 buccal cells, n = 110 bone and n = 109 cartilage) was used for building the model (correct classifications: 98.72%, sensitivity: 0.988, specificity: 0.996) and validation was performed using a testing set composed of 192 samples (n = 38 blood, n = 36 buccal cells, n = 46 bone and n = 72 cartilage) showing similar predictive success to the training set (correct classifications: 97.4%, sensitivity: 0.968, specificity: 0.991). By developing both a new cartilage age model and a tissue differentiation model, our study significantly expands the use of the VISAGE Enhanced Tool while increasing the amount of DNA methylation-based information obtained from a single sample and a single forensic laboratory analysis. Both models have been placed in the open-access Snipper forensic classification website.
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Affiliation(s)
- A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.
| | - M Tomsia
- Department of Forensic Medicine and Forensic Toxicology, Medical University of Silesia, Katowice, Poland
| | - D Piniewska-Róg
- Department of Forensic Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - M A Casares de Cal
- CITMAga (Center for Mathematical Research and Technology of Galicia), University of Santiago de Compostela, Spain
| | - A Pisarek
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland
| | - A Gómez-Tato
- CITMAga (Center for Mathematical Research and Technology of Galicia), University of Santiago de Compostela, Spain
| | - J Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, Spain
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Poland
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Austria; Forensic Science Program, Pennsylvania State University, PA, USA
| | - M Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - W Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland; Institute of Forensic Research, Kraków, Poland.
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Ambroa-Conde A, Girón-Santamaría L, Mosquera-Miguel A, Phillips C, Casares de Cal M, Gómez-Tato A, Álvarez-Dios J, de la Puente M, Ruiz-Ramírez J, Lareu M, Freire-Aradas A. Epigenetic age estimation in saliva and in buccal cells. Forensic Sci Int Genet 2022; 61:102770. [DOI: 10.1016/j.fsigen.2022.102770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/04/2022]
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Freire-Aradas A, Girón-Santamaría L, Mosquera-Miguel A, Ambroa-Conde A, Phillips C, Casares de Cal M, Gómez-Tato A, Álvarez-Dios J, Pospiech E, Aliferi A, Syndercombe Court D, Branicki W, Lareu M. A common epigenetic clock from childhood to old age. Forensic Sci Int Genet 2022; 60:102743. [DOI: 10.1016/j.fsigen.2022.102743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/04/2022]
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Freire-Aradas A, Pośpiech E, Aliferi A, Girón-Santamaría L, Mosquera-Miguel A, Pisarek A, Ambroa-Conde A, Phillips C, Casares de Cal MA, Gómez-Tato A, Spólnicka M, Woźniak A, Álvarez-Dios J, Ballard D, Court DS, Branicki W, Carracedo Á, Lareu MV. A Comparison of Forensic Age Prediction Models Using Data From Four DNA Methylation Technologies. Front Genet 2020; 11:932. [PMID: 32973877 PMCID: PMC7466768 DOI: 10.3389/fgene.2020.00932] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
Individual age estimation can be applied to criminal, legal, and anthropological investigations. DNA methylation has been established as the biomarker of choice for age prediction, since it was observed that specific CpG positions in the genome show systematic changes during an individual’s lifetime, with progressive increases or decreases in methylation levels. Subsequently, several forensic age prediction models have been reported, providing average age prediction error ranges of ±3–4 years, using a broad spectrum of technologies and underlying statistical analyses. DNA methylation assessment is not categorical but quantitative. Therefore, the detection platform used plays a pivotal role, since quantitative and semi-quantitative technologies could potentially result in differences in detected DNA methylation levels. In the present study, we analyzed as a shared sample pool, 84 blood-based DNA controls ranging from 18 to 99 years old using four different technologies: EpiTYPER®, pyrosequencing, MiSeq, and SNaPshotTM. The DNA methylation levels detected for CpG sites from ELOVL2, FHL2, and MIR29B2 with each system were compared. A restricted three CpG-site age prediction model was rebuilt for each system, as well as for a combination of technologies, based on previous training datasets, and age predictions were calculated accordingly for all the samples detected with the previous technologies. While the DNA methylation patterns and subsequent age predictions from EpiTYPER®, pyrosequencing, and MiSeq systems are largely comparable for the CpG sites studied, SNaPshotTM gives bigger differences reflected in higher predictive errors. However, these differences can be reduced by applying a z-score data transformation.
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Affiliation(s)
- A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - A Aliferi
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - L Girón-Santamaría
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - A Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - M A Casares de Cal
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, Spain
| | - A Gómez-Tato
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, Spain
| | - M Spólnicka
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - A Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - J Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, Spain
| | - D Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - D Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - W Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.,Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.,Fundación Pública Galega de Medicina Xenómica - CIBERER-IDIS, Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
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Freire-Aradas A, Phillips C, Mosquera-Miguel A, Girón-Santamaría L, Gómez-Tato A, Casares de Cal M, Álvarez-Dios J, Ansede-Bermejo J, Torres-Español M, Schneider PM, Pośpiech E, Branicki W, Carracedo Á, Lareu MV. Development of a methylation marker set for forensic age estimation using analysis of public methylation data and the Agena Bioscience EpiTYPER system. Forensic Sci Int Genet 2016; 24:65-74. [PMID: 27337627 DOI: 10.1016/j.fsigen.2016.06.005] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 01/24/2023]
Abstract
Individual age estimation has the potential to provide key information that could enhance and extend DNA intelligence tools. Following predictive tests for externally visible characteristics developed in recent years, prediction of age could guide police investigations and improve the assessment of age-related phenotype expression patterns such as hair colour changes and early onset of male pattern baldness. DNA methylation at CpG positions has emerged as the most promising DNA tests to ascertain the individual age of the donor of a biological contact trace. Although different methodologies are available to detect DNA methylation, EpiTYPER technology (Agena Bioscience, formerly Sequenom) provides useful characteristics that can be applied as a discovery tool in localized regions of the genome. In our study, a total of twenty-two candidate genomic regions, selected from the assessment of publically available data from the Illumina HumanMethylation 450 BeadChip, had a total of 177 CpG sites with informative methylation patterns that were subsequently investigated in detail. From the methylation analyses made, a novel age prediction model based on a multivariate quantile regression analysis was built using the seven highest age-correlated loci of ELOVL2, ASPA, PDE4C, FHL2, CCDC102B, C1orf132 and chr16:85395429. The detected methylation levels in these loci provide a median absolute age prediction error of ±3.07years and a percentage of prediction error relative to the age of 6.3%. We report the predictive performance of the developed model using cross validation of a carefully age-graded training set of 725 European individuals and a test set of 52 monozygotic twin pairs. The multivariate quantile regression age predictor, using the CpG sites selected in this study, has been placed in the open-access Snipper forensic classification website.
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Affiliation(s)
- A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - L Girón-Santamaría
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Gómez-Tato
- Faculty of Mathematics, University of Santiago de Compostela, Spain
| | - M Casares de Cal
- Faculty of Mathematics, University of Santiago de Compostela, Spain
| | - J Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, Spain
| | - J Ansede-Bermejo
- Spanish National Genotyping Center-USC-PRB2-ISCIII, Santiago de Compostela, Spain
| | - M Torres-Español
- Spanish National Genotyping Center-USC-PRB2-ISCIII, Santiago de Compostela, Spain
| | - P M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - E Pośpiech
- Institute of Zoology, Faculty of Biology and Earth Sciences, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - W Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Á Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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Ribas L, Robledo D, Gómez-Tato A, Viñas A, Martínez P, Piferrer F. Comprehensive transcriptomic analysis of the process of gonadal sex differentiation in the turbot (Scophthalmus maximus). Mol Cell Endocrinol 2016; 422:132-149. [PMID: 26586209 DOI: 10.1016/j.mce.2015.11.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/03/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022]
Abstract
The turbot is a flatfish with a ZW/ZZ sex determination system but with a still unknown sex determining gene(s), and with a marked sexual growth dimorphism in favor of females. To better understand sexual development in turbot we sampled young turbot encompassing the whole process of gonadal differentiation and conducted a comprehensive transcriptomic study on its sex differentiation using a validated custom oligomicroarray. Also, the expression profiles of 18 canonical reproduction-related genes were studied along gonad development. The expression levels of gonadal aromatase cyp19a1a alone at three months of age allowed the accurate and early identification of sex before the first signs of histological differentiation. A total of 56 differentially expressed genes (DEG) that had not previously been related to sex differentiation in fish were identified within the first three months of age, of which 44 were associated with ovarian differentiation (e.g., cd98, gpd1 and cry2), and 12 with testicular differentiation (e.g., ace, capn8 and nxph1). To identify putative sex determining genes, ∼4.000 DEG in juvenile gonads were mapped and their positions compared with that of previously identified sex- and growth-related quantitative trait loci (QTL). Although no genes mapped to the previously identified sex-related QTLs, two genes (foxl2 and 17βhsd) of the canonical reproduction-related genes mapped to growth-QTLs in linkage group (LG) 15 and LG6, respectively, suggesting that these genes are related to the growth dimorphism in this species.
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Affiliation(s)
- L Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003, Barcelona, Spain
| | - D Robledo
- Departamento de Genética. Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - A Gómez-Tato
- Departamento de Matemática Aplicada, Facultad de Matemáticas, Universidad de Santiago de Compostela, 15781, Santiago de Compostela, Spain
| | - A Viñas
- Departamento de Genética. Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - P Martínez
- Departamento de Genética. Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - F Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003, Barcelona, Spain.
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Barbazan J, Muinelo-Romay L, Vieito M, Candamio S, Díaz-López A, Cano A, Gómez-Tato A, Casares de Cal M, Abal M, López-López R. 978: A multimarker panel for circulating tumor cells detection predicts patient outcome and therapy response in metastatic colorectal cancer. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50867-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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McNevin D, Santos C, Gómez-Tato A, Álvarez-Dios J, de Cal MC, Daniel R, Phillips C, Lareu M. An assessment of Bayesian and multinomial logistic regression classification systems to analyse admixed individuals. Forensic Science International: Genetics Supplement Series 2013. [DOI: 10.1016/j.fsigss.2013.10.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Phillips C, Salas A, Sánchez J, Fondevila M, Gómez-Tato A, Álvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu M, Carracedo Á. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 2007; 1:273-80. [DOI: 10.1016/j.fsigen.2007.06.008] [Citation(s) in RCA: 218] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 06/25/2007] [Accepted: 06/27/2007] [Indexed: 10/22/2022]
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