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Chen, Jun
Publications (10 of 14) Show all publications
Kryvokhyzha, D., Salcedo, A., Eriksson, M. C., Duan, T., Tawari, N., Chen, J., . . . Lascoux, M. (2019). Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae). PLoS Genetics, 15(2), Article ID e1007949.
Open this publication in new window or tab >>Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
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2019 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 2, article id e1007949Article in journal (Refereed) Published
Abstract [en]

Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cbp(Cg)) and the other one from the selfing and genetically depauperate Capsella orientalis (Cbp(Co)). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (N-e), signatures of positive and negative selection, and gene expression patterns. In all three regions, N-e of the two subgenomes decreased gradually over time and the Cbp(Co) subgenome accumulated more deleterious changes than Cbp(Cg). There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the Cbp(Cg) subgenome in Europe and the Middle East, and on the Cbp(Co) subgenome in Asia. In contrast, differences in expression were limited with the Cbp(Cg) subgenome slightly more expressed than Cbp(Co) in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions. Author summary Allopolyploid species have two or more sets of chromosomes that originate from hybridization of different species. It remains largely unknown how the two genomes evolve in the same organism and how strongly their evolutionary trajectory depends on the initial differences between the two parental species and the specific demographic history of the newly formed allopolyploid species. To address these questions, we analyzed the genomic and gene expression variation of the shepherd's purse, a recent allopolyploid species, in three regions of its natural range. After approximate to 100,000 generations of co-existence within the same species, the two subgenomes had still retained part of the initial difference between the two parental species in the number of deleterious mutations reflecting a history of mating system differences. This difference, as well as differences in patterns of positive selection and levels of gene expression, also strongly depended on the specific histories of the three regions considered. Most strikingly, and unexpectedly, the allopolyploid species showed signs of hybridization with different diploid relatives or multiple origins in different parts of its range. Regardless if it was hybridization or multiple origins, this profoundly altered the relationship between the two subgenomes in different regions. Hence, our study illustrates how both the genomic structure and ecological arena interact to determine the evolutionary trajectories of allopolyploid species.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-379946 (URN)10.1371/journal.pgen.1007949 (DOI)000459970100033 ()30768594 (PubMedID)
Funder
Swedish Research Council, 2012-04999Swedish Research Council, 2015-03797
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2019-03-25 Created: 2019-03-25 Last updated: 2019-03-25Bibliographically approved
Chen, J., Yang, Y.-f., Yang, Y., Zou, P., Chen, J., He, Y., . . . Xu, J. (2018). AXL promotes Zika virus infection in astrocytes by antagonizing type I interferon signalling. Nature Microbiology, 3(3), 302-309
Open this publication in new window or tab >>AXL promotes Zika virus infection in astrocytes by antagonizing type I interferon signalling
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2018 (English)In: Nature Microbiology, E-ISSN 2058-5276, Vol. 3, no 3, p. 302-309Article in journal (Refereed) Published
Abstract [en]

Zika virus (ZIKV) is associated with neonatal microcephaly and Guillain-Barre syndrome(1,2). While progress has been made in understanding the causal link between ZIKV infection and microcephaly(3-9), the life cycle and pathogenesis of ZIKV are less well understood. In particular, there are conflicting reports on the role of AXL, a TAM family kinase receptor that was initially described as the entry receptor for ZIKV(10-22). Here, we show that while genetic ablation of AXL protected primary human astrocytes and astrocytoma cell lines from ZIKV infection, AXL knockout did not block the entry of ZIKV. We found, instead, that the presence of AXL attenuated the ZIKV-induced activation of type I interferon (IFN) signalling genes, including several type I IFNs and IFN-stimulating genes. Knocking out type I IFN receptor alpha chain (IFNAR1) restored the vulnerability of AXL knockout astrocytes to ZIKV infection. Further experiments suggested that AXL regulates the expression of SOCS1, a known type I IFN signalling suppressor, in a STAT1/STAT2-dependent manner. Collectively, our results demonstrate that AXL is unlikely to function as an entry receptor for ZIKV and may instead promote ZIKV infection in human astrocytes by antagonizing type I IFN signalling.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-350062 (URN)10.1038/s41564-017-0092-4 (DOI)000425846200011 ()29379210 (PubMedID)
Available from: 2018-05-03 Created: 2018-05-03 Last updated: 2018-05-03Bibliographically approved
Svedberg, J., Hosseini, S., Chen, J., Vogan, A. A., Mozgova, I., Hennig, L., . . . Johannesson, H. (2018). Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements. Nature Communications, 9, Article ID 4242.
Open this publication in new window or tab >>Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements
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2018 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 4242Article in journal (Refereed) Published
Abstract [en]

Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedia. Using long-read sequencing, we generated the first complete and well-annotated genome assemblies of large, highly diverged, non-recombining regions associated with meiotic drive elements. Phylogenetic analysis shows that, even though Sk-2 and Sk-3 are located in the same chromosomal region, they do not form sister clades, suggesting independent origins or at least a long evolutionary separation. We conclude that they have in a convergent manner accumulated similar patterns of tandem inversions and dense repeat clusters, presumably in response to similar needs to create linkage between genes causing drive and resistance.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-368443 (URN)10.1038/s41467-018-06562-x (DOI)000447123000018 ()30315196 (PubMedID)
Funder
Swedish Research CouncilEU, Horizon 2020, 648143Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2018-12-07 Created: 2018-12-07 Last updated: 2018-12-07Bibliographically approved
Plomion, C., Aury, J.-M., Amselem, J., Leroy, T., Murat, F., Duplessis, S., . . . Salse, J. (2018). Oak genome reveals facets of long lifespan. NATURE PLANTS, 4(7), 440-452
Open this publication in new window or tab >>Oak genome reveals facets of long lifespan
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2018 (English)In: NATURE PLANTS, ISSN 2055-026X, Vol. 4, no 7, p. 440-452Article in journal (Refereed) Published
Abstract [en]

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-364056 (URN)10.1038/s41477-018-0172-3 (DOI)000443221200016 ()29915331 (PubMedID)
Funder
EU, FP7, Seventh Framework ProgrammeEU, European Research CouncilSwedish Foundation for Strategic Research
Available from: 2018-12-07 Created: 2018-12-07 Last updated: 2018-12-07Bibliographically approved
Chen, J., Glemin, S. & Lascoux, M. (2017). Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species. Molecular biology and evolution, 34(6), 1417-1428
Open this publication in new window or tab >>Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species
2017 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 6, p. 1417-1428Article in journal (Refereed) Published
Abstract [en]

A central question in evolutionary biology is why some species have more genetic diversity than others and a no less important question is why selection efficacy varies among species. Although these questions have started to be tackled in animals, they have not been addressed to the same extent in plants. Here, we estimated nucleotide diversity at synonymous, pi(S), and nonsynonymous sites, pi(N), and a measure of the efficacy of selection, the ratio pi(N)/pi(S), in 34 animal and 28 plant species using full genome data. We then evaluated the relationship of nucleotide diversity and selection efficacy with effective population size, the distribution of fitness effect and life history traits. In animals, our data confirm that longevity and propagule size are the variables that best explain the variation in pi(S) among species. In plants longevity also plays a major role as well as mating system. As predicted by the nearly neutral theory of molecular evolution, the log of pi(N)/pi(S) decreased linearly with the log of pi(S) but the slope was weaker in plants than in animals. This appears to be due to a higher mutation rate in long lived plants, and the difference disappears when pi(S) is rescaled by the mutation rate. Differences in the distribution of fitness effect of new mutations also contributed to variation in pi(N)/pi(S) among species.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2017
Keywords
effective population size, distribution of fitness effects, purifying selection, life history traits, nearly neutral theory
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-326224 (URN)10.1093/molbev/msx088 (DOI)000402061700010 ()28333215 (PubMedID)
Funder
Swedish Research Council FormasSwedish Research CouncilSwedish Foundation for Strategic Research
Available from: 2017-07-04 Created: 2017-07-04 Last updated: 2017-07-04Bibliographically approved
Chen, J., Yang, Y.-f., Chen, J., Zhou, X., Dong, Z., Chen, T., . . . Zhu, T. (2017). Zika virus infects renal proximal tubular epithelial cells with prolonged persistency and cytopathic effects. EMERGING MICROBES & INFECTIONS, 6, Article ID e77.
Open this publication in new window or tab >>Zika virus infects renal proximal tubular epithelial cells with prolonged persistency and cytopathic effects
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2017 (English)In: EMERGING MICROBES & INFECTIONS, ISSN 2222-1751, Vol. 6, article id e77Article in journal (Refereed) Published
Abstract [en]

Zika virus (ZIKV) infection can cause fetal developmental abnormalities and Guillain-Barre syndrome in adults. Although progress has been made in understanding the link between ZIKV infection and microcephaly, the pathology of ZIKV, particularly the viral reservoirs in human, remains poorly understood. Several studies have shown that compared to serum samples, patients' urine samples often have a longer duration of ZIKV persistency and higher viral load. This finding suggests that an independent viral reservoir may exist in the human urinary system. Despite the clinical observations, the host cells of ZIKV in the human urinary system are poorly characterized. In this study, we demonstrate that ZIKV can infect renal proximal tubular epithelial cells (RPTEpiCs) in immunodeficient mice in vivo and in both immortalized and primary human renal proximal tubular epithelial cells (hRPTEpiCs) in vitro. Importantly, ZIKV infection in mouse kidneys caused caspase-3-mediated apoptosis of renal cells. Similarly, in vitro infection of immortalized and primary hRPTEpiCs resulted in notable cytopathic effects. Consistent with the clinical observations, we found that ZIKV infection can persist with prolonged duration in hRPTEpiCs. RNA-Seq analyses of infected hRPTEpiCs revealed a large number of transcriptional changes in response to ZIKV infection, including type I interferon signaling genes and anti-viral response genes. Our results suggest that hRPTEpiCs are a potential reservoir of ZIKV in the human urinary system, providing a possible explanation for the prolonged persistency of ZIKV in patients' urine.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2017
Keywords
cytopathic effects, prolonged persistency, renal proximal tubular epithelial cells, urinary system, Zika virus
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-335710 (URN)10.1038/emi.2017.67 (DOI)000409365800005 ()28831192 (PubMedID)
Available from: 2017-12-11 Created: 2017-12-11 Last updated: 2017-12-11Bibliographically approved
Chen, J., Källman, T., Ma, X.-F., Zaina, G., Morgante, M. & Lascoux, M. (2016). Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies. G3: Genes, Genomes, Genetics, 6(7), 1979-1989
Open this publication in new window or tab >>Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies
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2016 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 7, p. 1979-1989Article in journal (Refereed) Published
Abstract [en]

The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower F-ST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both F-ST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI.

Keywords
pooled sequencing, F-ST, allele frequencies, local adaptation
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-300546 (URN)10.1534/g3.116.028753 (DOI)000379590200018 ()27172202 (PubMedID)
Funder
EU, European Research CouncilSwedish Research Council Formas
Available from: 2016-08-10 Created: 2016-08-09 Last updated: 2017-11-28Bibliographically approved
Tsuda, Y., Chen, J., Stocks, M., Källman, T., Sonstebo, J. H., Parducci, L., . . . Lascoux, M. (2016). The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?. Molecular Ecology, 25(12), 2773-2789
Open this publication in new window or tab >>The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?
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2016 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 12, p. 2773-2789Article in journal (Refereed) Published
Abstract [en]

Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive STRUCTURE plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.

Keywords
divergence, Eurasia, introgression, phylogeography, spruce
National Category
Botany Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-300075 (URN)10.1111/mec.13654 (DOI)000378941800010 ()27087633 (PubMedID)
Funder
Swedish Research Council FormasEU, European Research Council, KBBE-289119
Available from: 2016-08-02 Created: 2016-08-02 Last updated: 2017-11-28Bibliographically approved
Kryvokhyzha, D., Holm, K., Chen, J., Cornille, A., Glemin, S., Wright, S. I., . . . Lascoux, M. (2016). The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae). Molecular Ecology, 25(5), 1106-1121
Open this publication in new window or tab >>The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)
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2016 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 5, p. 1106-1121Article in journal (Refereed) Published
Abstract [en]

Population structure is a potential problem when testing for adaptive phenotypic differences among populations. The observed phenotypic differences among populations can simply be due to genetic drift, and if the genetic distance between them is not considered, the differentiation may be falsely interpreted as adaptive. Conversely, adaptive and demographic processes might have been tightly associated and correcting for the population structure may lead to false negatives. Here, we evaluated this problem in the cosmopolitan weed Capsella bursa-pastoris. We used RNA-Seq to analyse gene expression differences among 24 accessions, which belonged to a much larger group that had been previously characterized for flowering time and circadian rhythm and were genotyped using genotyping-by-sequencing (GBS) technique. We found that clustering of accessions for gene expression retrieved the same three clusters that were obtained with GBS data previously, namely Europe, the Middle East and Asia. Moreover, the three groups were also differentiated for both flowering time and circadian rhythm variation. Correction for population genetic structure when analysing differential gene expression analysis removed all differences among the three groups. This may suggest that most differences are neutral and simply reflect population history. However, geographical variation in flowering time and circadian rhythm indicated that the distribution of adaptive traits might be confounded by population structure. To bypass this confounding effect, we compared gene expression differentiation between flowering ecotypes within the genetic groups. Among the differentially expressed genes, FLOWERING LOCUS C was the strongest candidate for local adaptation in regulation of flowering time.

Keywords
adaptation, circadian rhythm, genetic drift, neutrality, population structure, RNA-Seq, transcriptome
National Category
Biochemistry and Molecular Biology Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-282478 (URN)10.1111/mec.13537 (DOI)000371433400007 ()26797895 (PubMedID)
Funder
Swedish Research Council
Available from: 2016-04-05 Created: 2016-04-05 Last updated: 2018-02-13Bibliographically approved
Lind, M., Kallman, T., Chen, J., Ma, X.-F., Bousquet, J., Morgante, M., . . . Stenlid, J. (2014). A Picea abies Linkage Map Based on SNP Markers Identifies QTLs for Four Aspects of Resistance to Heterobasidion parviporum Infection. PLoS ONE, 9(7), e101049
Open this publication in new window or tab >>A Picea abies Linkage Map Based on SNP Markers Identifies QTLs for Four Aspects of Resistance to Heterobasidion parviporum Infection
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2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 7, p. e101049-Article in journal (Refereed) Published
Abstract [en]

A consensus linkage map of Picea abies, an economically important conifer, was constructed based on the segregation of 686 SNP markers in a F-1 progeny population consisting of 247 individuals. The total length of 1889.2 cM covered 96.5% of the estimated genome length and comprised 12 large linkage groups, corresponding to the number of haploid P. abies chromosomes. The sizes of the groups (from 5.9 to 9.9% of the total map length) correlated well with previous estimates of chromosome sizes (from 5.8 to 10.8% of total genome size). Any locus in the genome has a 97% probability to be within 10 cM from a mapped marker, which makes the map suited for QTL mapping. Infecting the progeny trees with the root rot pathogen Heterobasidion parviporum allowed for mapping of four different resistance traits: lesion length at the inoculation site, fungal spread within the sapwood, exclusion of the pathogen from the host after initial infection, and ability to prevent the infection from establishing at all. These four traits were associated with two, four, four and three QTL regions respectively of which none overlapped between the traits. Each QTL explained between 4.6 and 10.1% of the respective traits phenotypic variation. Although the QTL regions contain many more genes than the ones represented by the SNP markers, at least four markers within the confidence intervals originated from genes with known function in conifer defence; a leucoanthocyanidine reductase, which has previously been shown to upregulate during H. parviporum infection, and three intermediates of the lignification process; a hydroxycinnamoyl CoA shikimate/quinate hydroxycinnamoyltransferase, a 4-coumarate CoA ligase, and a R2R3-MYB transcription factor.

National Category
Genetics Botany
Identifiers
urn:nbn:se:uu:diva-231301 (URN)10.1371/journal.pone.0101049 (DOI)000339615200012 ()25036209 (PubMedID)
Available from: 2014-09-08 Created: 2014-09-07 Last updated: 2017-12-05Bibliographically approved
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