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Oh CS, Kim MJ, Kim YS, Min S, Oh KT, Lee SD, Shin DH. Revealing Joseon period People's single nucleotide polymorphism associated with lactase gene by ancient DNA analysis of human remains from archaeological sites in Korea. Anat Cell Biol 2023; 56:54-60. [PMID: 36450657 PMCID: PMC9989794 DOI: 10.5115/acb.22.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
Lactase non-persistence (LNP), one of the causes of lactose intolerance, is related to lactase gene associated single nucleotide polymorphisms (SNPs). Since the frequency of LNP varies by ethnic group and country, the research to reveal the presence or absence of LNP for specific people has been conducted worldwide. However, in East Asia, the study of lactase gene associated SNPs have not been sufficiently examined so far using ancient human specimens from archaeological sites. In our study of Joseon period human remains (n=14), we successfully revealed genetic information of lactase gene associated SNPs (rs1679771596, rs41525747, rs4988236, rs4988235, rs41380347, rs869051967, rs145946881 and rs182549), further confirming that as for eight SNPs, the pre-modern Korean people had a lactase non-persistent genotype. Our report contributes to the establishment of LNP associated SNP analysis technique that can be useful in forthcoming studies on human bones and mummy samples from East Asian archaeological sites.
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Affiliation(s)
- Chang Seok Oh
- Department of Mortuary Science, College of Bio-Convergence, Eulji University, Seongnam, Korea
| | - Myeung Ju Kim
- Department of Anatomy, Dankook University College of Medicine, Cheonan, Korea
| | - Yi-Suk Kim
- Catholic Institute for Applied Anatomy, Department of Anatomy, Colllege of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sori Min
- Nuri Institute of Archaeology, Gongju, Korea
| | | | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea.,Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea
| | - Dong Hoon Shin
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea.,Department of Anatomy and Cell Biology, Seoul National University College of Medicine, Seoul, Korea
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Ancient DNA of Metagonimus yokogawai Recovered from Joseon Period Human Remains Newly Discovered at Goryeong County in South Korea. Acta Parasitol 2022; 67:539-545. [PMID: 34731404 DOI: 10.1007/s11686-021-00487-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]
Abstract
PURPOSE Metagonimiasis, commonly seen in East Asian countries, is a parasitic disorder caused by definitive hosts' ingestion of undercooked freshwater fishes. Recently, genetic analysis has proved 28S rRNA and cytochrome c oxidase subunit I (COI) mtDNA gene to be a successful marker differentiating species of the genus Metagonimus. In the present study, using specimens from the newly discovered Joseon Dynasty human remains of Goryeong, we obtained updated genetic data on genus Metagonimus, which was also prevalent during the Joseon period. METHODS The ancient DNA (aDNA) was retrieved from the coprolite sample of the seventeenth century, half-mummified individual discovered at Goryeong Country, South Korea. Cloning and sequencing were performed on PCR-amplified amplicons for M. yokogawai 28S rRNA and COI mtDNA gene. The consensus sequences were used for species identification and phylogenetic analysis using NCBI/BLAST and MEGA X software. RESULTS Based on the COI mtDNA gene region, the Goryeong sequence was confirmed as belonging to M. yokogawai, as it was shown to form a separate cluster with other M. yokogawai taxa that are distinct also from M. takahashii and M. miyatai. CONCLUSION In a series of our genetic analyses on genus Metagonimus using samples retrieved from Joseon-period cases, aDNA sequences of genus Metagonimus revealed in South Korea thus far are those of M. yokogawai, but not of M. miyatai or M. takahashii yet.
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Hong JH, Seo M, Oh CS, Chai JY, Shin DH. Metagonimus yokogawai Ancient DNA Recovered from 16th- to 17th-Century Korean Mummy Feces of the Joseon Dynasty. J Parasitol 2021; 106:802-808. [PMID: 33351947 DOI: 10.1645/20-42] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Metagonimiasis is foodborne intestinal parasitism occurring by the definitive hosts' ingestion of raw or undercooked fish, mostly commonly sweetfish. Most Metagonimus infection is caused by Metagonimus yokogawai but also rarely by Metagonimus takahashii as well as Metagonimus miyatai. Despite recent molecular work on Metagonimus spp., there are still insufficient data to reveal the genetic characteristics of ancient M. yokogawai in a wide geo-historical scope. In this study, we were successful in the analysis of M. yokogawai ancient DNA (aDNA) using coprolite samples retrieved from 16th- to 17th-century Korean mummies. In BLAST and phylogenetic analyses, M. yokogawai 28S rDNA of Korean mummies were clustered along with the 28S rDNA taxa of M. takahashii and M. miyatai in GenBank. Conversely, the cytochrome c oxidase subunit I (COI) of M. yokogawai aDNA from Korean mummies was distinctly clustered apart from M. takahashii and M. miyatai sequences. This study is the first report of its kind to identify M. yokogawai aDNA retrieved from the archaeological specimens and confirms the usefulness of COI in molecular diagnosis of M. yokogawai. Considering the rarity of reports on the genetics of genus Metagonimus spp., our study will be fundamental for the future study of M. yokogawai paleogenetics.
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Affiliation(s)
- Jong Ha Hong
- Institute of Korean Archaeology and Ancient History, Kyung Hee University, Seoul, South Korea.,Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, South Korea
| | - Min Seo
- Department of Parasitology, Dankook University College of Medicine, Cheonan, South Korea
| | - Chang Seok Oh
- Department of Mortuary Science, Eulji University, Seongnam-Si, Gyeonggi-Do, South Korea.,Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Jong-Yil Chai
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul, South Korea
| | - Dong Hoon Shin
- Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea
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Ancient to modern secular changes in the cranial/cephalic index in Korea: historical brachycephalization and recent debrachycephalization. Anat Sci Int 2020; 95:363-373. [PMID: 32086765 DOI: 10.1007/s12565-020-00529-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/03/2020] [Indexed: 10/25/2022]
Abstract
We investigated changes in the cranial/cephalic index of the Korean population in millennia, centuries, and recent decades. Secular changes of Korean's cephalic index in history were studied using the data of archaeology literature and our measurement data of different adult skull sets for the fifteenth-nineteenth century Joseon people, the Korean War victims (1950-1953), and the Korean skeletons collected by medical schools in the 1960s. A change in head shape during the last century was also estimated by the analysis on Korean cephalometric datasets of Korean Research Institute of Standards and Science. In brief, over the past 2000 years, the crania of Korean people have steadily changed from mesocephalic to brachycephalic, mainly due to the cranial length shortening. Brachycephalization accelerated at the beginning of the twentieth century and continued until the early twenty-first century, largely caused by increased cephalic breadth. We also note that debrachycephalization began in birth cohorts around 1965 for males and around 1970 for females. Taken together, we figure out that the head shape of Korean people has been gradually shortened over millennia and then has undergone dramatic shortening in the last century. In recent decades, however, the changing pattern has reversed to debrachycephalization, for which we discussed about the possible causes in the present report.
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Hong JH, Oh CS, Chai JY, Seo M, Shin DH. Cytochrome C Oxidase Subunit 1, Internal Transcribed Spacer 1, Nicotinamide Adenine Dinucleotide Hydrogen Dehydrogenase Subunits 2 and 5 of Clonorchis sinensis Ancient DNA Retrieved from Joseon Dynasty Mummy Specimens. J Korean Med Sci 2019; 34:e149. [PMID: 31124326 PMCID: PMC6535405 DOI: 10.3346/jkms.2019.34.e149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
We analyzed Clonorchis sinensis ancient DNA (aDNA) acquired from the specimens of the Joseon mummies. The target regions were cytochrome C oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase subunits 2 (NAD2) and 5 (NAD5). The sequences of C. sinensis aDNA was completely or almost identical to modern C. sinensis sequences in GenBank. We also found that ITS1, NAD2 and NAD5 could be good markers for molecular diagnosis between C. sinensis and the other trematode parasite species. The current result could improve our knowledge about genetic history of C. sinensis.
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Affiliation(s)
- Jong Ha Hong
- Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Seok Oh
- Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, Korea
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Yil Chai
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul, Korea
- Institute of Parasitic Diseases, Korean Association of Health Promotion, Seoul, Korea
| | - Min Seo
- Department of Parasitology, Dankook University College of Medicine, Cheonan, Korea.
| | - Dong Hoon Shin
- Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, Korea
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea.
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Hong JH, Oh CS, Seo M, Shin DH. Analysis of COI and ITS2 regions of DNA obtained from Paragonimus westermani eggs in ancient coprolites on Joseon dynasty mummies. Mem Inst Oswaldo Cruz 2019; 114:e180595. [PMID: 31116227 PMCID: PMC6524962 DOI: 10.1590/0074-02760180595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/04/2019] [Indexed: 11/22/2022] Open
Abstract
The genetic information of ancient Paragonimus westermani, the oriental lung fluke infecting over 20 million people worldwide, has not been thoroughly investigated thus far. We analysed genetic markers (COI and ITS2) of P. westermani from coprolite specimens (n = 6) obtained from 15th to 18th century Korean mummies. Our results indicated that all P. westermani sequences were generally distinct from the other species of the genus Paragonimus. The sequences were clustered into three groups: Group I for East Asia; Group II for South and Southeast Asia; and Group III for India and Sri Lanka. In this study, we found that ancient P. westermani sequences in Korea belong to Group I, adding invaluable information to the existing knowledge of Paragonimus paleogenetics.
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Affiliation(s)
- Jong Ha Hong
- Seoul National University College of Medicine, Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul, South Korea
| | - Chang Seok Oh
- Seoul National University College of Medicine, Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul, South Korea.,Seoul National University College of Medicine, Institute of Forensic Science, Seoul, South Korea
| | - Min Seo
- Dankook University College of Medicine, Department of Parasitology, Cheonan, South Korea
| | - Dong Hoon Shin
- Seoul National University College of Medicine, Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul, South Korea.,Seoul National University College of Medicine, Institute of Forensic Science, Seoul, South Korea
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WOO EUNJIN, KIM JAEHYUN, LEE WONJOON, CHO HELEN, PAK SUNYOUNG. Syphilitic infection in a pre-modern population from South Korea (19th century AD). ANTHROPOL SCI 2019. [DOI: 10.1537/ase.181122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- EUN JIN WOO
- Department of History, College of Liberal Art, Sejong University, Seoul
| | - JAE-HYUN KIM
- Department of Archaeology and Art History, College of Humanities, Dong-A University, Busan
| | - WON-JOON LEE
- National Forensic Service Seoul Institute, Seoul
| | - HELEN CHO
- Department of Anthropology, Davidson College, Davidson
| | - SUNYOUNG PAK
- Department of Anthropology, College of Social Sciences, Seoul National University, Seoul
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The Use and Effectiveness of Triple Multiplex System for Coding Region Single Nucleotide Polymorphism in Mitochondrial DNA Typing of Archaeologically Obtained Human Skeletons from Premodern Joseon Tombs of Korea. BIOMED RESEARCH INTERNATIONAL 2015; 2015:850648. [PMID: 26345190 PMCID: PMC4544719 DOI: 10.1155/2015/850648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/16/2015] [Indexed: 11/18/2022]
Abstract
Previous study showed that East Asian mtDNA haplogroups, especially those of Koreans, could be successfully assigned by the coupled use of analyses on coding region SNP markers and control region mutation motifs. In this study, we tried to see if the same triple multiplex analysis for coding regions SNPs could be also applicable to ancient samples from East Asia as the complementation for sequence analysis of mtDNA control region. By the study on Joseon skeleton samples, we know that mtDNA haplogroup determined by coding region SNP markers successfully falls within the same haplogroup that sequence analysis on control region can assign. Considering that ancient samples in previous studies make no small number of errors in control region mtDNA sequencing, coding region SNP analysis can be used as good complimentary to the conventional haplogroup determination, especially of archaeological human bone samples buried underground over long periods.
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Oh CS, Koh BJ, Yoo DS, Park JB, Min SR, Kim YS, Lee SS, Ge J, Seo SB, Shin DH. Joseon funerary texts tested using ancient DNA analysis of a Korean mummy. Anat Rec (Hoboken) 2015; 298:1191-207. [PMID: 25998652 DOI: 10.1002/ar.23142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 01/30/2015] [Indexed: 01/23/2023]
Abstract
In Korea, ancient DNA (aDNA) analysis has been applied to investigations into the genetic affiliations of mummies found in Joseon Dynasty tombs (1392-1910 CE), becoming now indispensable tool for researches studying human remains from archaeological sites. In the course of our recent examinations on a Korean mummy of Joseon Dynasty, we discovered many teeth contained in a pouch. And in fact, the historical literature on the topic of Joseon funerals contain general accounts of pouches in which an individual's lost teeth were collected over the course of a lifetime and, after death, placed in the coffin with the body. To test the veracity of the historical texts, the present study undertook aDNA analyses and compared the results between specifically questioned (Q) samples (teeth) and known (K) samples (brain and bone) from the mummy to ensure that they came from the same individual. Although the Q-K comparison of autosomal short tandem repeat results did not show full concordance due to allelic drop-outs in some loci, our statistical calculation indicated that the teeth in the pouch are highly likely those of the mummy. Additionally, Q-K comparison of mitochondrial DNA sequence results showed 100% matches between samples. There results, in short, could not gainsay the conjecture that the teeth samples originated from the person buried in the tomb; and if so, he must have kept his teeth for a long time after their loss. As the application of aDNA analysis to Korean mummy studies develops, there will be other opportunities to test historical documents, particularly those referring to funerary rites.
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Affiliation(s)
- Chang Seok Oh
- Anthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul, 110-799, Korea
| | - Bou-Ja Koh
- Dankook University, 152, Jukjeon-Ro, Suji-Gu, Yongin-Si, Gyeonggi-Do, 448-701, Korea
| | - Dong Soo Yoo
- Department of Radiology, Dankook University College of Medicine, San 29, Anseo-Dong, Chonan City, Chungcheongnam-Do, 330-715, Korea
| | - Jun Bum Park
- Seoul Institute of Cultural Heritages, 833, Tongil-Ro, Eunpyeong-Gu, Seoul, 122-842, Korea
| | - So Ri Min
- Korean Institute for Archaeology and Environment, 26, Mogwanamu-1 Gil, Jochiwon-Eup, Sejong-Si, 339-806, Korea
| | - Yi-Suk Kim
- Department of Anatomy, Graduate School of Medicine, Ewha Womans University, 911-1, Mok-Dong, Yangcheon-Gu, Seoul, 158-710, Korea
| | - Sang Sup Lee
- National Forensic Service, 331-1 Shinwol 7-Dong, Yangcheon-Gu, Seoul, 158-707, Korea
| | - Jianye Ge
- Department of Forensic and Investigative Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Seung Bum Seo
- Department of Forensic and Investigative Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Dong Hoon Shin
- Anthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul, 110-799, Korea
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Yu JA, Oh CS, Hong JH, Min SR, Oh SW, Kim YS, Park JB, Shin DH. Stable isotope analysis of Joseon people skeletons from the cemeteries of Old Seoul City, the capital of Joseon Dynasty. Anat Cell Biol 2014; 47:244-52. [PMID: 25548722 PMCID: PMC4276898 DOI: 10.5115/acb.2014.47.4.244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/14/2014] [Accepted: 11/25/2014] [Indexed: 12/03/2022] Open
Abstract
Stable carbon and nitrogen isotope analysis reveals the diets of different human populations in history. In this study, we performed stable isotope analysis on human skeletons from Joseon-period cemeteries discovered around Old Seoul City (Hansung). Our data clearly showed that Joseon individuals consumed more C3-based than C4-based foods as the main staples, and that the proteins they ate were mainly of terrestrial, but not of marine origin. Stable isotope values exhibited unique patterns in each of our sample subgroups. Whereas the δ13C values did not show any statistical differences among the subgroups, significantly higher values of δ15N were found in males than in females, which might reflect dietary differences between the sexes. For a fuller understanding of the dietary patterns of pre-industrial (pre-20th century) Koreans, additional studies on Joseon samples from Korean archaeological sites will be necessary.
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Affiliation(s)
- Jeong-A Yu
- Department of Anatomy, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Seok Oh
- Department of Anatomy, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Ha Hong
- Department of Anatomy, Seoul National University College of Medicine, Seoul, Korea
| | - So Ri Min
- Department of Anatomy, Ehwa Womans University School of Medicine, Seoul, Korea
| | - Seugn Whan Oh
- Hangang Institute of Cultural Heritage, Seoul, Korea
| | - Yi-Suk Kim
- Department of Anatomy, Ehwa Womans University School of Medicine, Seoul, Korea
| | | | - Dong Hoon Shin
- Department of Anatomy, Seoul National University College of Medicine, Seoul, Korea
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Kim DK, Kim MJ, Kim YS, Oh CS, Lee SS, Lim SB, Ki HC, Shin DH. Long bone fractures identified in the Joseon Dynasty human skeletons of Korea. Anat Cell Biol 2013; 46:203-9. [PMID: 24179696 PMCID: PMC3811853 DOI: 10.5115/acb.2013.46.3.203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/20/2013] [Accepted: 05/02/2013] [Indexed: 11/28/2022] Open
Abstract
Fracture is one of the pathological signs most frequently encountered in archaeologically obtained bones. To expand the paleopathological knowledge on traumatic injuries, it is desirable to secure data on long bone fractures from as wide a geographic and temporal range as possible. We present, for the first time, evidence of long bone fractures in a 16th-18th century Joseon skeletal series (n=96). In this study, we found 3 Colles' fractures of the radius in 2 individual cases. The pattern of fractures was unique. Although previous reports show that the ulna is broken more often than the radius, ulnar fracture associated with fending off a blunt attack was rare in our series (1/7 cases). Transverse fractures, typically caused by intentional violence, were also very rare (1/7 cases) in this study. These results may reflect the relatively tranquil lives of the Joseon people in 16th-18th century Korea. We also found post-fracture complications such as deformations, bone length shortening, and osteomyelitis. The present study would be of interest to medical scientists in related fields because it is one of the few studies conducted on long bone fractures among pre-modern societies in East Asian countries, thus far.
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Affiliation(s)
- Deog Kyeom Kim
- Department of Internal Medicine, Seoul National University Boramae Hospital, Seoul National University College of Medicine, Seoul, Korea. ; Department of Anatomy, Seoul National University College of Medicine, Seoul, Korea
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