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A 5700 year-old human genome and oral microbiome from chewed birch pitch.

https://arctichealth.org/en/permalink/ahliterature307649
Source
Nat Commun. 2019 12 17; 10(1):5520
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
12-17-2019
Author
Theis Z T Jensen
Jonas Niemann
Katrine Højholt Iversen
Anna K Fotakis
Shyam Gopalakrishnan
Åshild J Vågene
Mikkel Winther Pedersen
Mikkel-Holger S Sinding
Martin R Ellegaard
Morten E Allentoft
Liam T Lanigan
Alberto J Taurozzi
Sofie Holtsmark Nielsen
Michael W Dee
Martin N Mortensen
Mads C Christensen
Søren A Sørensen
Matthew J Collins
M Thomas P Gilbert
Martin Sikora
Simon Rasmussen
Hannes Schroeder
Author Affiliation
The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark.
Source
Nat Commun. 2019 12 17; 10(1):5520
Date
12-17-2019
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Betula - physiology
DNA, Ancient - analysis
DNA, Bacterial - analysis
Denmark
Genome, Human
Geography
Humans
Microbiota - genetics
Mouth - microbiology
Phenotype
Radiometric Dating
Sex Determination Analysis
Time Factors
Abstract
The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA.
PubMed ID
31848342 View in PubMed
Less detail
Source
Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660)
Publication Type
Article
Date
Jan-19-2015
Author
Mikkel Winther Pedersen
Søren Overballe-Petersen
Luca Ermini
Clio Der Sarkissian
James Haile
Micaela Hellstrom
Johan Spens
Philip Francis Thomsen
Kristine Bohmann
Enrico Cappellini
Ida Bærholm Schnell
Nathan A Wales
Christian Carøe
Paula F Campos
Astrid M Z Schmidt
M Thomas P Gilbert
Anders J Hansen
Ludovic Orlando
Eske Willerslev
Author Affiliation
Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark.
Source
Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660)
Date
Jan-19-2015
Language
English
Publication Type
Article
Abstract
DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
PubMed ID
25487334 View in PubMed
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Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics.

https://arctichealth.org/en/permalink/ahliterature97786
Source
Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5675-80
Publication Type
Article
Date
Mar-23-2010
Author
Paula F Campos
Eske Willerslev
Andrei Sher
Ludovic Orlando
Erik Axelsson
Alexei Tikhonov
Kim Aaris-Sørensen
Alex D Greenwood
Ralf-Dietrich Kahlke
Pavel Kosintsev
Tatiana Krakhmalnaya
Tatyana Kuznetsova
Philippe Lemey
Ross MacPhee
Christopher A Norris
Kieran Shepherd
Marc A Suchard
Grant D Zazula
Beth Shapiro
M Thomas P Gilbert
Author Affiliation
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK 1350 Copenhagen, Denmark.
Source
Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5675-80
Date
Mar-23-2010
Language
English
Publication Type
Article
Keywords
Animals
DNA - genetics - history
DNA, Mitochondrial - genetics - history
Extinction, Biological
Fossils
Genetic Variation
History, Ancient
Humans
Molecular Sequence Data
Phylogeny
Population Dynamics
Ruminants - genetics
Abstract
The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at approximately 45,000 radiocarbon years before present ((14)C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 (14)C YBP, recontracted at ca. 18,000 (14)C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations.
PubMed ID
20212118 View in PubMed
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Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians.

https://arctichealth.org/en/permalink/ahliterature148346
Source
Curr Biol. 2009 Nov 3;19(20):1758-62
Publication Type
Article
Date
Nov-3-2009
Author
Helena Malmström
M Thomas P Gilbert
Mark G Thomas
Mikael Brandström
Jan Storå
Petra Molnar
Pernille K Andersen
Christian Bendixen
Gunilla Holmlund
Anders Götherström
Eske Willerslev
Author Affiliation
Department of Evolutionary Biology, Uppsala University, Sweden.
Source
Curr Biol. 2009 Nov 3;19(20):1758-62
Date
Nov-3-2009
Language
English
Publication Type
Article
Keywords
Agriculture - history
Anthropology, Physical
DNA, Mitochondrial - chemistry
Emigration and Immigration - history
Genetic Variation
History, Ancient
Humans
Scandinavia
Abstract
The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century [1-3]. Of particular interest is whether population replacement or cultural exchange was responsible [3-5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7, 8]. The prolonged coexistence of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.
Notes
Comment In: Curr Biol. 2009 Nov 3;19(20):R948-919889371
PubMed ID
19781941 View in PubMed
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Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene.

https://arctichealth.org/en/permalink/ahliterature100381
Source
Mol Ecol. 2010 Nov;19(22):4863-75
Publication Type
Article
Date
Nov-2010
Author
Paula F Campos
Tommy Kristensen
Ludovic Orlando
Andrei Sher
Marina V Kholodova
Anders Götherström
Michael Hofreiter
Dorothée G Drucker
Pavel Kosintsev
Alexei Tikhonov
Gennady F Baryshnikov
Eske Willerslev
M Thomas P Gilbert
Author Affiliation
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Source
Mol Ecol. 2010 Nov;19(22):4863-75
Date
Nov-2010
Language
English
Publication Type
Article
Abstract
Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49,500 (14) C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40,400 to 10,250 (14) C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.
PubMed ID
20874761 View in PubMed
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Ancient genomes from Iceland reveal the making of a human population.

https://arctichealth.org/en/permalink/ahliterature294280
Source
Science. 2018 06 01; 360(6392):1028-1032
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
06-01-2018
Author
S Sunna Ebenesersdóttir
Marcela Sandoval-Velasco
Ellen D Gunnarsdóttir
Anuradha Jagadeesan
Valdís B Guðmundsdóttir
Elísabet L Thordardóttir
Margrét S Einarsdóttir
Kristjan H S Moore
Ásgeir Sigurðsson
Droplaug N Magnúsdóttir
Hákon Jónsson
Steinunn Snorradóttir
Eivind Hovig
Pål Møller
Ingrid Kockum
Tomas Olsson
Lars Alfredsson
Thomas F Hansen
Thomas Werge
Gianpiero L Cavalleri
Edmund Gilbert
Carles Lalueza-Fox
Joe W Walser
Steinunn Kristjánsdóttir
Shyam Gopalakrishnan
Lilja Árnadóttir
Ólafur Þ Magnússon
M Thomas P Gilbert
Kári Stefánsson
Agnar Helgason
Author Affiliation
deCODE Genetics/AMGEN, Inc., Reykjavik Iceland. sunna@decode.is kstefan@deocde.is agnar@decode.is.
Source
Science. 2018 06 01; 360(6392):1028-1032
Date
06-01-2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Biological Evolution
DNA, Ancient
Female
Founder Effect
Gene Pool
Genetic Drift
Genome, Human
Genotype
Humans
Iceland
Male
Phenotype
Population - genetics
Abstract
Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily useful for the discovery of genotype-phenotype associations.
Notes
CommentIn: Science. 2018 Jun 1;360(6392):964-965 PMID 29853673
PubMed ID
29853688 View in PubMed
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Ancient human genome sequence of an extinct Palaeo-Eskimo.

https://arctichealth.org/en/permalink/ahliterature98088
Source
Nature. 2010 Feb 11;463(7282):757-62
Publication Type
Article
Date
Feb-11-2010
Author
Morten Rasmussen
Yingrui Li
Stinus Lindgreen
Jakob Skou Pedersen
Anders Albrechtsen
Ida Moltke
Mait Metspalu
Ene Metspalu
Toomas Kivisild
Ramneek Gupta
Marcelo Bertalan
Kasper Nielsen
M Thomas P Gilbert
Yong Wang
Maanasa Raghavan
Paula F Campos
Hanne Munkholm Kamp
Andrew S Wilson
Andrew Gledhill
Silvana Tridico
Michael Bunce
Eline D Lorenzen
Jonas Binladen
Xiaosen Guo
Jing Zhao
Xiuqing Zhang
Hao Zhang
Zhuo Li
Minfeng Chen
Ludovic Orlando
Karsten Kristiansen
Mads Bak
Niels Tommerup
Christian Bendixen
Tracey L Pierre
Bjarne Grønnow
Morten Meldgaard
Claus Andreasen
Sardana A Fedorova
Ludmila P Osipova
Thomas F G Higham
Christopher Bronk Ramsey
Thomas V O Hansen
Finn C Nielsen
Michael H Crawford
Søren Brunak
Thomas Sicheritz-Pontén
Richard Villems
Rasmus Nielsen
Anders Krogh
Jun Wang
Eske Willerslev
Author Affiliation
Centre for GeoGenetics, Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
Source
Nature. 2010 Feb 11;463(7282):757-62
Date
Feb-11-2010
Language
English
Geographic Location
Russia
Publication Type
Article
Keywords
Cryopreservation
Emigration and Immigration - history
Extinction, Biological
Genetics, Population
Genome, Human - genetics
Genomics
Genotype
Greenland
Hair
History, Ancient
Humans
Inuits - genetics
Male
Phenotype
Phylogeny
Polymorphism, Single Nucleotide - genetics
Sequence Analysis, DNA
Siberia - ethnology
Abstract
We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.
Notes
RefSource: Nature. 2010 Feb 11;463(7282):739-40
PubMed ID
20148029 View in PubMed
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Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process.

https://arctichealth.org/en/permalink/ahliterature265418
Source
Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130373
Publication Type
Article
Date
Jan-19-2015
Author
Helena Malmström
Anna Linderholm
Pontus Skoglund
Jan Storå
Per Sjödin
M Thomas P Gilbert
Gunilla Holmlund
Eske Willerslev
Mattias Jakobsson
Kerstin Lidén
Anders Götherström
Source
Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130373
Date
Jan-19-2015
Language
English
Publication Type
Article
Keywords
Agriculture - history
Base Sequence
Computational Biology
DNA Primers - genetics
DNA, Mitochondrial - genetics - history
Gene Flow
Genetic Variation
Genetics, Population
High-Throughput Nucleotide Sequencing
History, Ancient
Human Migration - history
Humans
Models, Genetic
Molecular Sequence Data
Population Dynamics
Real-Time Polymerase Chain Reaction
Sweden
Abstract
The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers.
Notes
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PubMed ID
25487325 View in PubMed
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Arctic-adapted dogs emerged at the Pleistocene-Holocene transition.

https://arctichealth.org/en/permalink/ahliterature305477
Source
Science. 2020 06 26; 368(6498):1495-1499
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
06-26-2020
Author
Mikkel-Holger S Sinding
Shyam Gopalakrishnan
Jazmín Ramos-Madrigal
Marc de Manuel
Vladimir V Pitulko
Lukas Kuderna
Tatiana R Feuerborn
Laurent A F Frantz
Filipe G Vieira
Jonas Niemann
Jose A Samaniego Castruita
Christian Carøe
Emilie U Andersen-Ranberg
Peter D Jordan
Elena Y Pavlova
Pavel A Nikolskiy
Aleksei K Kasparov
Varvara V Ivanova
Eske Willerslev
Pontus Skoglund
Merete Fredholm
Sanne Eline Wennerberg
Mads Peter Heide-Jørgensen
Rune Dietz
Christian Sonne
Morten Meldgaard
Love Dalén
Greger Larson
Bent Petersen
Thomas Sicheritz-Pontén
Lutz Bachmann
Øystein Wiig
Tomas Marques-Bonet
Anders J Hansen
M Thomas P Gilbert
Author Affiliation
The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. mhssinding@gmail.com tomas.marques@upf.edu ajhansen@sund.ku.dk tgilbert@sund.ku.dk.
Source
Science. 2020 06 26; 368(6498):1495-1499
Date
06-26-2020
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Adaptation, Physiological - genetics
Animals
Apolipoproteins - genetics
Arctic Regions
Dogs - genetics
Fatty Acids - metabolism
Genome
Greenland
Haplotypes
Mitochondrial Membrane Transport Proteins - genetics
Selective Breeding
Sequence Analysis, DNA
Siberia
Triglycerides - metabolism
Wolves - genetics
Abstract
Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
PubMed ID
32587022 View in PubMed
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Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus).

https://arctichealth.org/en/permalink/ahliterature301069
Source
Science. 2019 06 21; 364(6446):
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
06-21-2019
Author
Zeshan Lin
Lei Chen
Xianqing Chen
Yingbin Zhong
Yue Yang
Wenhao Xia
Chang Liu
Wenbo Zhu
Han Wang
Biyao Yan
Yifeng Yang
Xing Liu
Kjersti Sternang Kvie
Knut Håkon Røed
Kun Wang
Wuhan Xiao
Haijun Wei
Guangyu Li
Rasmus Heller
M Thomas P Gilbert
Qiang Qiu
Wen Wang
Zhipeng Li
Author Affiliation
Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China.
Source
Science. 2019 06 21; 364(6446):
Date
06-21-2019
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Abstract
The reindeer is an Arctic species that exhibits distinctive biological characteristics, for which the underlying genetic basis remains largely unknown. We compared the genomes of reindeer against those of other ruminants and nonruminant mammals to reveal the genetic basis of light arrhythmicity, high vitamin D metabolic efficiency, the antler growth trait of females, and docility. We validate that two reindeer vitamin D metabolic genes (CYP27B1 and POR) show signs of positive selection and exhibit higher catalytic activity than those of other ruminants. A mutation upstream of the reindeer CCND1 gene endows an extra functional binding motif of the androgen receptor and thereby may result in female antlers. Furthermore, a mutation (proline-1172?threonine) in reindeer PER2 results in loss of binding ability with CRY1, which may explain circadian arrhythmicity in reindeer.
Notes
CommentIn: Science. 2019 Jun 21;364(6446):1130-1131 PMID 31221843
PubMed ID
31221829 View in PubMed
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27 records – page 1 of 3.