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The accuracy of Genomic Selection in Norwegian red cattle assessed by cross-validation.

https://arctichealth.org/en/permalink/ahliterature98928
Source
Genetics. 2009 Nov;183(3):1119-26
Publication Type
Article
Date
Nov-2009
Author
Tu Luan
John A Woolliams
Sigbjørn Lien
Matthew Kent
Morten Svendsen
Theo H E Meuwissen
Author Affiliation
Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Box 5003, N-1432 As, Norway. tu.luan@umb.no
Source
Genetics. 2009 Nov;183(3):1119-26
Date
Nov-2009
Language
English
Publication Type
Article
Keywords
Algorithms
Animal Husbandry - methods
Animals
Bayes Theorem
Breeding - methods
Cattle - genetics - metabolism
Female
Genome - genetics
Genome-Wide Association Study
Genotype
Male
Milk - metabolism - standards
Norway
Polymorphism, Single Nucleotide - genetics
Quantitative Trait Loci - genetics
Reproducibility of Results
Selection, Genetic
Abstract
Genomic Selection (GS) is a newly developed tool for the estimation of breeding values for quantitative traits through the use of dense markers covering the whole genome. For a successful application of GS, accuracy of the prediction of genomewide breeding value (GW-EBV) is a key issue to consider. Here we investigated the accuracy and possible bias of GW-EBV prediction, using real bovine SNP genotyping (18,991 SNPs) and phenotypic data of 500 Norwegian Red bulls. The study was performed on milk yield, fat yield, protein yield, first lactation mastitis traits, and calving ease. Three methods, best linear unbiased prediction (G-BLUP), Bayesian statistics (BayesB), and a mixture model approach (MIXTURE), were used to estimate marker effects, and their accuracy and bias were estimated by using cross-validation. The accuracies of the GW-EBV prediction were found to vary widely between 0.12 and 0.62. G-BLUP gave overall the highest accuracy. We observed a strong relationship between the accuracy of the prediction and the heritability of the trait. GW-EBV prediction for production traits with high heritability achieved higher accuracy and also lower bias than health traits with low heritability. To achieve a similar accuracy for the health traits probably more records will be needed.
PubMed ID
19704013 View in PubMed
Less detail

Archival bone marrow samples: suitable for multiple biomarker analysis.

https://arctichealth.org/en/permalink/ahliterature265165
Source
Appl Immunohistochem Mol Morphol. 2015 Jan;23(1):71-7
Publication Type
Article
Date
Jan-2015
Author
Bendik Lund
Laeya A Najmi
Agata Wesolowska-Andersen
Veslemøy M Landsem
Kirsten K Rasmussen
Louise Borst
Ramneek Gupta
Kjeld Schmiegelow
Helge Klungland
Source
Appl Immunohistochem Mol Morphol. 2015 Jan;23(1):71-7
Date
Jan-2015
Language
English
Publication Type
Article
Keywords
Adolescent
Biopsy
Bone Banks - standards
Bone Marrow - physiology
Child
Child, Preschool
DNA - analysis - isolation & purification
Denmark
Female
Fluorometry
Genome - genetics
Genotype
Humans
Male
Microsatellite Repeats - genetics
Norway
Pilot Projects
Polymorphism, Single Nucleotide
Precursor Cell Lymphoblastic Leukemia-Lymphoma - diagnosis - genetics
Specimen Handling
Spectrophotometry
Tumor Markers, Biological - analysis
Abstract
AB Archival samples represent a significant potential for genetic studies, particularly in severe diseases with risk of lethal outcome, such as in cancer. In this pilot study, we aimed to evaluate the usability of archival bone marrow smears and biopsies for DNA extraction and purification, whole genome amplification (WGA), multiple marker analysis including 10 short tandem repeats, and finally a comprehensive genotyping of 33,683 single nucleotide polymorphisms (SNPs) with multiplexed targeted next-generation sequencing. A total of 73 samples from 21 bone marrow smears and 13 bone marrow biopsies from 18 Danish and Norwegian childhood acute lymphoblastic leukemia patients were included and compared with corresponding blood samples. Samples were grouped according to the age of sample and whether WGA was performed or not. We found that measurements of DNA concentration after DNA extraction was dependent on detection method and that spectrophotometry overestimated DNA amount compared with fluorometry. In the short tandem repeat analysis, detection rate dropped slightly with longer fragments. After WGA, this drop was more pronounced. Samples stored for 0 to 3 years showed better results compared with samples stored for 4 to 10 years. Acceptable call rates for SNPs were detected for 7 of 42 archival samples. In conclusion, archival bone marrow samples are suitable for DNA extraction and multiple marker analysis, but WGA was less successful, especially when longer fragments were analyzed. Multiple SNP analysis seems feasible, but the method has to be further optimized.
PubMed ID
25621358 View in PubMed
Less detail

The complete genome sequence of a Neanderthal from the Altai Mountains.

https://arctichealth.org/en/permalink/ahliterature105562
Source
Nature. 2014 Jan 2;505(7481):43-9
Publication Type
Article
Date
Jan-2-2014
Author
Kay Prüfer
Fernando Racimo
Nick Patterson
Flora Jay
Sriram Sankararaman
Susanna Sawyer
Anja Heinze
Gabriel Renaud
Peter H Sudmant
Cesare de Filippo
Heng Li
Swapan Mallick
Michael Dannemann
Qiaomei Fu
Martin Kircher
Martin Kuhlwilm
Michael Lachmann
Matthias Meyer
Matthias Ongyerth
Michael Siebauer
Christoph Theunert
Arti Tandon
Priya Moorjani
Joseph Pickrell
James C Mullikin
Samuel H Vohr
Richard E Green
Ines Hellmann
Philip L F Johnson
Hélène Blanche
Howard Cann
Jacob O Kitzman
Jay Shendure
Evan E Eichler
Ed S Lein
Trygve E Bakken
Liubov V Golovanova
Vladimir B Doronichev
Michael V Shunkov
Anatoli P Derevianko
Bence Viola
Montgomery Slatkin
David Reich
Janet Kelso
Svante Pääbo
Author Affiliation
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
Source
Nature. 2014 Jan 2;505(7481):43-9
Date
Jan-2-2014
Language
English
Publication Type
Article
Keywords
Africa
Animals
Caves
DNA Copy Number Variations - genetics
Female
Fossils
Gene Flow - genetics
Gene Frequency
Genome - genetics
Heterozygote
Humans
Inbreeding
Models, Genetic
Neanderthals - classification - genetics
Phylogeny
Population Density
Siberia - ethnology
Toe Phalanges - anatomy & histology
Abstract
We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.
Notes
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Comment In: Nature. 2014 Jan 2;505(7481):32-424352230
PubMed ID
24352235 View in PubMed
Less detail

Dynamic convergence and divergence of renal genomic and biological pathways in protection from Dahl salt-sensitive hypertension.

https://arctichealth.org/en/permalink/ahliterature98608
Source
Physiol Genomics. 2010 Mar 3;41(1):63-70
Publication Type
Article
Date
Mar-3-2010
Author
Limin Lu
Peigang Li
Chun Yang
Terry Kurth
Michael Misale
Meredith Skelton
Carol Moreno
Richard J Roman
Andrew S Greene
Howard J Jacob
Jozef Lazar
Mingyu Liang
Allen W Cowley
Author Affiliation
Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
Source
Physiol Genomics. 2010 Mar 3;41(1):63-70
Date
Mar-3-2010
Language
English
Publication Type
Article
Keywords
Albuminuria - complications - genetics
Animals
Animals, Congenic
Chromosomes, Mammalian - genetics
Gene Expression Profiling
Gene Expression Regulation
Genome - genetics
Hypertension - complications - genetics - prevention & control
Inbreeding
Kidney - metabolism - pathology
Male
Phenotype
Rats
Rats, Inbred BN
Rats, Inbred Dahl
Reproducibility of Results
Signal Transduction - genetics
Thiobarbituric Acid Reactive Substances - metabolism
Abstract
Chromosome 13 consomic and congenic rat strains were analyzed to investigate the pattern of genomic pathway utilization involved in protection against salt-sensitive hypertension and renal injury. Introgression of the entire Brown-Norway chromosome 13 (consomic SS-13(BN)) or nonoverlapping segments of this chromosome (congenic strains, 16 Mbp in D13Rat151-D13Rat197 or 14 Mbp in D13Rat111-D13Got22) into the genome of the Dahl salt-sensitive rat attenuated salt-induced hypertension and proteinuria. mRNA abundance profiles in the renal cortex and the renal medulla from rats receiving 0.4% or 8% NaCl diets revealed two important features of pathway recruitment in these rat strains. First, the two congenic strains shared alterations in several pathways compared with Dahl salt-sensitive rats, despite the fact that the genomic segments introgressed in the two congenic strains did not overlap. Second, even though the genomic segment introgressed in each congenic strain was a part of the chromosome introgressed in the consomic strain, pathways altered in each congenic strain were not simply a subset of those altered in the consomic. Supporting the relevance of the mRNA data, differential expression of oxidative stress-related genes among the four strains of rats was associated with differences in urinary excretion of lipid peroxidation products. The findings suggest that different genetic alterations might converge to influence shared pathways in protection from hypertension, and that, depending on the genomic context, the same genetic alteration might diverge to affect different pathways.
PubMed ID
20009007 View in PubMed
Less detail

Genomic analysis of expressed sequence tags in American black bear Ursus americanus.

https://arctichealth.org/en/permalink/ahliterature97574
Source
BMC Genomics. 2010;11:201
Publication Type
Article
Date
2010
Author
Sen Zhao
Chunxuan Shao
Anna V Goropashnaya
Nathan C Stewart
Yichi Xu
Øivind Tøien
Brian M Barnes
Vadim B Fedorov
Jun Yan
Author Affiliation
CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
Source
BMC Genomics. 2010;11:201
Date
2010
Language
English
Publication Type
Article
Keywords
Alaska
Alternative Splicing
Amino Acid Sequence
Animals
Evolution, Molecular
Expressed Sequence Tags
Gene Expression Profiling
Gene Expression Regulation
Genome - genetics
Humans
Models, Molecular
Molecular Sequence Data
Organ Specificity
Phylogeny
Protein Structure, Tertiary
Sequence Alignment
Ursidae - genetics
Abstract
BACKGROUND: Species of the bear family (Ursidae) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (Ursus americanus). RESULTS: Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (PLN), cysteine glycine-rich protein 3 (CSRP3) and Troponin I type 3 (TNNI3), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (BPHL) and CSRP3, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes. CONCLUSION: We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes.
PubMed ID
20338065 View in PubMed
Less detail

Murine gammaretrovirus group G3 was not found in Swedish patients with myalgic encephalomyelitis/chronic fatigue syndrome and fibromyalgia.

https://arctichealth.org/en/permalink/ahliterature130237
Source
PLoS One. 2011;6(10):e24602
Publication Type
Article
Date
2011
Author
Amal Elfaitouri
Xingwu Shao
Johan Mattsson Ulfstedt
Shaman Muradrasoli
Agnes Bölin Wiener
Sultan Golbob
Christina Ohrmalm
Michael Matousek
Olof Zachrisson
Carl-Gerhard Gottfries
Jonas Blomberg
Author Affiliation
Section of Clinical Virology, Department of Medical Sciences, University of Uppsala, Uppsala, Sweden.
Source
PLoS One. 2011;6(10):e24602
Date
2011
Language
English
Publication Type
Article
Keywords
Animals
Base Sequence
Computational Biology
Fatigue Syndrome, Chronic - complications - virology
Fibromyalgia - complications - virology
Gammaretrovirus - genetics - isolation & purification
Gene Products, env - genetics
Gene Products, gag - genetics
Genome - genetics
Histones - metabolism
Humans
Mice
Mice, Inbred C57BL
Molecular Sequence Data
Nucleic Acids - genetics
Phylogeny
Polymerase Chain Reaction
Proviruses - genetics - isolation & purification
Real-Time Polymerase Chain Reaction
Recombination, Genetic - genetics
Sensitivity and specificity
Sequence Alignment
Sweden
Abstract
The recent report of gammaretroviruses of probable murine origin in humans, called xenotropic murine retrovirus related virus (XMRV) and human murine leukemia virus related virus (HMRV), necessitated a bioinformatic search for this virus in genomes of the mouse and other vertebrates, and by PCR in humans.
Three major groups of murine endogenous gammaretroviruses were identified. The third group encompassed both exogenous and endogenous Murine Leukemia Viruses (MLVs), and most XMRV/HMRV sequences reported from patients suffering from myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Two sensitive real-time PCRs for this group were developed. The predicted and observed amplification range for these and three published XMRV/HMRV PCRs demonstrated conspicuous differences between some of them, partly explainable by a recombinatorial origin of XMRV. Three reverse transcription real-time PCRs (RTQPCRs), directed against conserved and not overlapping stretches of env, gag and integrase (INT) sequences of XMRV/HMRV were used on human samples. White blood cells from 78 patients suffering from ME/CFS, of which 30 patients also fulfilled the diagnostic criteria for fibromyalgia (ME/CFS/FM) and in 7 patients with fibromyalgia (FM) only, all from the Gothenburg area of Sweden. As controls we analyzed 168 sera from Uppsala blood donors. We controlled for presence and amplifiability of nucleic acid and for mouse DNA contamination. To score as positive, a sample had to react with several of the XMRV/HMRV PCRs. None of the samples gave PCR reactions which fulfilled the positivity criteria.
XMRV/HMRV like proviruses occur in the third murine gammaretrovirus group, characterized here. PCRs developed by us, and others, approximately cover this group, except for the INT RTQPCR, which is rather strictly XMRV specific. Using such PCRs, XMRV/HMRV could not be detected in PBMC and plasma samples from Swedish patients suffering from ME/CFS/FM, and in sera from Swedish blood donors.
Notes
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PubMed ID
22022360 View in PubMed
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Reconstructing the genetic history of late Neanderthals.

https://arctichealth.org/en/permalink/ahliterature294406
Source
Nature. 2018 03 29; 555(7698):652-656
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Date
03-29-2018
Author
Mateja Hajdinjak
Qiaomei Fu
Alexander Hübner
Martin Petr
Fabrizio Mafessoni
Steffi Grote
Pontus Skoglund
Vagheesh Narasimham
Hélène Rougier
Isabelle Crevecoeur
Patrick Semal
Marie Soressi
Sahra Talamo
Jean-Jacques Hublin
Ivan Gušic
Željko Kucan
Pavao Rudan
Liubov V Golovanova
Vladimir B Doronichev
Cosimo Posth
Johannes Krause
Petra Korlevic
Sarah Nagel
Birgit Nickel
Montgomery Slatkin
Nick Patterson
David Reich
Kay Prüfer
Matthias Meyer
Svante Pääbo
Janet Kelso
Author Affiliation
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
Source
Nature. 2018 03 29; 555(7698):652-656
Date
03-29-2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Keywords
Africa - ethnology
Animals
Bone and Bones
DNA, Ancient - analysis
Europe - ethnology
Female
Gene Flow
Genetics, Population
Genome - genetics
Genomics
Humans
Hypochlorous Acid
Male
Neanderthals - classification - genetics
Phylogeny
Siberia - ethnology
Tooth
Abstract
Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA. Here we use hypochlorite treatment of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.
Notes
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PubMed ID
29562232 View in PubMed
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Salmonid genomes have a remarkably expanded akirin family, coexpressed with genes from conserved pathways governing skeletal muscle growth and catabolism.

https://arctichealth.org/en/permalink/ahliterature144232
Source
Physiol Genomics. 2010 Jun;42(1):134-48
Publication Type
Article
Date
Jun-2010
Author
Daniel J Macqueen
Bjarni K Kristjánsson
Ian A Johnston
Author Affiliation
Scottish Ocean Institute, School of Biology, University of St Andrews, St Andrews, United Kingdom. djm59@st-andrews.ac.uk
Source
Physiol Genomics. 2010 Jun;42(1):134-48
Date
Jun-2010
Language
English
Publication Type
Article
Keywords
Amino Acid Sequence
Animals
Base Sequence
Cluster analysis
Fish Proteins - classification - genetics
Gene Expression Profiling
Gene Expression Regulation, Developmental
Genome - genetics
Humans
Molecular Sequence Data
Muscle, Skeletal - growth & development - metabolism
Phylogeny
Reverse Transcriptase Polymerase Chain Reaction
Salmon - genetics - growth & development
Sequence Homology, Amino Acid
Sequence Homology, Nucleic Acid
Signal Transduction - genetics
Trout - genetics - growth & development
Abstract
Metazoan akirin genes regulate innate immunity, myogenesis, and carcinogenesis. Invertebrates typically have one family member, while most tetrapod and teleost vertebrates have one to three. We demonstrate an expanded repertoire of eight family members in genomes of four salmonid fishes, owing to paralog preservation after three tetraploidization events. Retention of paralogs secondarily lost in other teleosts may be related to functional diversification and posttranslational regulation. We hypothesized that salmonid akirins would be transcriptionally regulated in fast-twitch skeletal muscle during activation of conserved pathways governing catabolism and growth. The in vivo nutritional state of Arctic charr (Salvelinus alpinus L.) was experimentally manipulated, and transcript levels for akirin family members and 26 other genes were measured by quantitative real-time PCR (qPCR), allowing the establishment of a similarity network of expression profiles. In fasted muscle, a class of akirins was upregulated, with one family member showing high coexpression with catabolic genes coding the NF-kappaB p65 subunit, E2 ubiquitin-conjugating enzymes, E3 ubiquitin ligases, and IGF-I receptors. Another class of akirin was upregulated with subsequent feeding, coexpressed with 14-3-3 protein genes. There was no similarity between expression profiles of akirins with IGF hormones or binding protein genes. The level of phylogenetic relatedness of akirin family members was not a strong predictor of transcriptional responses to nutritional state, or differences in transcript abundance levels, indicating a complex pattern of regulatory evolution. The salmonid akirins epitomize the complexity linking the genome to physiological phenotypes of vertebrates with a history of tetraploidization.
Notes
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PubMed ID
20388840 View in PubMed
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Sharing reference data and including cows in the reference population improve genomic predictions in Danish Jersey.

https://arctichealth.org/en/permalink/ahliterature279473
Source
Animal. 2016 Jun;10(6):1067-75
Publication Type
Article
Date
Jun-2016
Author
G. Su
P. Ma
U S Nielsen
G P Aamand
G. Wiggans
B. Guldbrandtsen
M S Lund
Source
Animal. 2016 Jun;10(6):1067-75
Date
Jun-2016
Language
English
Publication Type
Article
Keywords
Animals
Breeding
Cattle - classification - genetics
Denmark
Female
Fertility - genetics
Genome - genetics
Genomics - methods - standards
Genotype
Linear Models
Male
Models, Genetic
Phenotype
Reference Standards
Reproducibility of Results
United States
Abstract
Small reference populations limit the accuracy of genomic prediction in numerically small breeds, such like Danish Jersey. The objective of this study was to investigate two approaches to improve genomic prediction by increasing size of reference population in Danish Jersey. The first approach was to include North American Jersey bulls in Danish Jersey reference population. The second was to genotype cows and use them as reference animals. The validation of genomic prediction was carried out on bulls and cows, respectively. In validation on bulls, about 300 Danish bulls (depending on traits) born in 2005 and later were used as validation data, and the reference populations were: (1) about 1050 Danish bulls, (2) about 1050 Danish bulls and about 1150 US bulls. In validation on cows, about 3000 Danish cows from 87 young half-sib families were used as validation data, and the reference populations were: (1) about 1250 Danish bulls, (2) about 1250 Danish bulls and about 1150 US bulls, (3) about 1250 Danish bulls and about 4800 cows, (4) about 1250 Danish bulls, 1150 US bulls and 4800 Danish cows. Genomic best linear unbiased prediction model was used to predict breeding values. De-regressed proofs were used as response variables. In the validation on bulls for eight traits, the joint DK-US bull reference population led to higher reliability of genomic prediction than the DK bull reference population for six traits, but not for fertility and longevity. Averaged over the eight traits, the gain was 3 percentage points. In the validation on cows for six traits (fertility and longevity were not available), the gain from inclusion of US bull in reference population was 6.6 percentage points in average over the six traits, and the gain from inclusion of cows was 8.2 percentage points. However, the gains from cows and US bulls were not accumulative. The total gain of including both US bulls and Danish cows was 10.5 percentage points. The results indicate that sharing reference data and including cows in reference population are efficient approaches to increase reliability of genomic prediction. Therefore, genomic selection is promising for numerically small population.
PubMed ID
26330119 View in PubMed
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