NGS_SNPAnalyzer: a desktop software supporting genome projects by identifying and visualizing sequence variations from next-generation sequencing data

Dong‑Jun Lee,Taesoo Kwon,Chang‑Kug Kim,Young‑Joo Seol,Dong‑Suk Park,Tae‑Ho Lee,Byung‑Ohg Ahn 한국유전학회 2020 Genes & Genomics Vol.42 No.11

Background Sequence variations such as single nucleotide polymorphisms are markers for genetic diseases and breeding. Therefore, identifying sequence variations is one of the main objectives of several genome projects. Although most genomeproject consortiums provide standard operation procedures for sequence variation detection methods, there may be differencesin the results because of human selection or error. Objective To standardize the procedure for sequence variation detection and help researchers who are not formally trainedin bioinformatics, we developed the NGS_SNPAnalyzer, a desktop software and fully automated graphical pipeline. Methods The NGS_SNPAnalyzer is implemented using JavaFX (version 1.8); therefore, it is not limited to any operatingsystem (OS). The tools employed in the NGS_SNPAnalyzer were compiled on Microsoft Windows (version 7, 10) andUbuntu Linux (version 16.04, 17.0.4). Results The NGS_SNPAnalyzer not only includes the functionalities for variant calling and annotation but also providesquality control, mapping, and filtering details to support all procedures from next-generation sequencing (NGS) data to variantvisualization. It can be executed using pre-set pipelines and options and customized via user-specified options. Additionally,the NGS_SNPAnalyzer provides a user-friendly graphical interface and can be installed on any OS that supports JAVA. Conclusions Although there are several pipelines and visualization tools available for NGS data analysis, we developedthe NGS_SNPAnalyzer to provide the user with an easy-to-use interface. The benchmark test results indicate that theNGS_SNPAnayzer achieves better performance than other open source tools.

금속 도재 수복물을 이용한 청년기 법랑질 이형성증 환자의 수복증례

김홍준,이재훈,한동후,문홍석 大韓齒科補綴學會 2012 대한치과보철학회지 Vol.50 No.3

전반적인 치아변색과 치아마모가 심한 환자들이 심미를 위해 전치부 치료를 원하는 경우가 있다. 이런 경우 법랑질 이형성증에 대해 의심해 보아야 하며 임상 검사 및 방사선 검사를 통해 확인을 해야 한다. 법랑질 이형성증으로 판단된 경우 단지 심미적 목적 하에 전치부 치료만 하는 것은 바람직하지 못하다. 본 증례는 법랑질 이형성증으로 진단된 청년기 환자에서 대부분의 치아를 금속 도재 수복물로 치료하였다. 전반적인 변색 및 마모, 치관 파절이 있었으며, 좌측 전치부와 구치부에 교차교합이 있었다. 심미적, 기능적인 개선을 목적으로 하여 치아를 수복하였다. 전치부의 교차교합은 해소하였고, 구치부의 교차교합은 해소하지 않은 채로 진행하였다. 수복 이후 환자는 심미적, 기능적으로 만족하였으며, 3개월간의 임상관찰에서 특이할 문제없이 안정적으로 유지되어 보고하고자 한다. Some patients with generalized attrition and teeth discoloration may want their anterior teeth to be treated just for esthetic improvement. Ameologenesis imperfecta, however, should be considered for such patients prior to any treatment with thorough clinical and radiographic examination. If a patient is diagnosed with amelogenesis imperfecta, the treatment on anterior teeth just for esthetic purpose is not advisable. In this case, a young man with amelogenesis imperfecta was treated with metal-ceramic restorations. The patient had generalized attrition, teeth discoloration, crown fracture, and cross-bite on the left teeth. The ultimate objective of this treatment was to enhance esthetics and masticatory function. The cross-bite on the left anterior teeth was treated with restorations, whereas the reverse horizontal overlap was maintained on the posterior. The patient was satisfied with the result esthetically and functionally, and the third month recall examination revealed no pathologic changes associated with the treatment.

브랜드 인지도와 광고가 콘택트렌즈의 착용감과 가격만족도에 미치는 영향

임동규 ; 신상준 ; 한지선 ; 이익한 ; 김진숙 김천대학교 2016 김천대학교 논문집 Vol.36 No.-

The purpose of this research was to analyze the effects of brand awareness and brand advertising on price satisfaction and comfort in contact lens. We did a survey with 200 university students (85 male, 115 female) who have experience of wearing contact lens from April to May in 2015. The brand awareness of contact lens influences to purchasing intention of contact lens, it effects women more than men. Many respondents(53%) replied that the reliability is the most important elements of the advertising. This survey indicates that there is no statistically significant correlation between the brand awareness and advertisement with price satisfaction in contact lens. Therefore we could confirm they have dissatisfaction for prices of contact lens regardless to brand awareness or advertisement. The brand and advertising dependence group have more comfort of contact lens than non-dependence group when they are long time wear of contact lens. Therefore, there is statistically significant correlation between the brand awareness and advertisement with comfort of contact lens. As a result, brand awareness and reliability of advertising influences to purchasing intention of contact lens. But there is no statistically significant correlation with price satisfaction in contact lens. Whereas, brand awareness and advertisement have a statistically significant correlation with comfort of contact lens.

구순 구개열 환아의 수유 보조 장치에 대한 증례보고

최형준,손흥규,최병재,박동석 大韓小兒齒科學會 1995 大韓小兒齒科學會誌 Vol.22 No.2

Cleft lip, cleft palate, cleft lip and palate are the most common congenital anomalies in cranio-orofacial region. These anomalies lead to esthetic problem as well as to difficulties in feeding and speech and also to chronic infection of upper airway and to disturbance of jaw growth during growing up. Especially, some difficulties during feeding make parents to be confused and puts infants in dangerous position. But these difficulties can be controlled by proper feeding methods according to pattern of cleft lip and palate. Among these feeding methods, feeding appliance is the most safe and relatively easy to manufacture. Early wearing of this appliance makes cleft lip and palate infants to a normal feeding and weight gain. As a member of team approach for the treatment of cleft lip and palate, a pediatric dentist should solve the feeding problems which cleft lip and palate infants and its parents are confronted and help in receiving further treatment.

흰쥐에서 염화비닐 폭로수준에 따른 소변내 thiodiglycolic acid 농도의 변화

왕승준,차봉석,노재훈,신동천,김명수,전근재 大韓産業醫學會 1999 대한직업환경의학회지 Vol.11 No.4

Objectives : It is the objective of this research to identify the variation of thiodiglycolic acid(TdGA) in urine with vinyl chloride monamer(VCM) exposure levels through methylation. Methods : After rats were exposed to vinyl chloride monomer of 4 levels, 0㎎/㎥, 50㎎/㎥, 150㎎/㎥, 500㎎/㎥, respectively, of which urine was sampled in each sampling time of 0 hour, 2 hours, 4 hours, 8 hours, 16 hours, 36 hours, 48 hours. After urine had been methylated with diazomethane in the preliminary experiment and the peak of 146 m/z had been verified, the main experiment was done. Results : In the variation of TdGA with sampling times, concentration of TdGA increased rapidly in 4 hours and then decreased after 8 hours. When the variation of urinary TdGA concentration in urine according to exposure level of VGM was verified through Kruskal-Wallis statistical method at each sampling time, the significant increment with the exposure levels at 2 hours, 4 hours, 8 hours after exposure was clarified. Conclusion : TdGA concentration in urine with increment of VCM exposure level increased, especially significantly at 2 hours, 4 hours, 8 hours of sampling time.

과량의 인슐린 투여로 인한 인위성 저혈당증 1예

김준우,안철우,남주영,김똘미,김영균,추적금,박종숙,박진아,조승현,김동연,김도연,윤수지,이경열,차봉수,김경래,임승길,이현철,허갑범 대한당뇨병학회 2002 임상당뇨병 Vol.3 No.2

본 저자들은 인위적인 인슐린 투여로 인한 인간성 저혈당증 1예에서 보존적인 치료로 의식기능은 회복하였으나, 현저한 인지능력 저하를 하였기에 문헌고찰과 함께 보고하는 바이다. Factitious hypoglycemia is a covert attempt to lower the blood glucose concentration with insulin or a sulfonylurea agent. This attempt is mainly performed by the patients themselves. In a large series of diabetics who had overdosed on drug, less than 5% had used insulin for suicidal or homicidal purposes. Additionally, 4 of 204 hypoglycemic episodes were due to a suicide attempt with insulin. The onset of insulin action, its peak level, and duration, and the degree of hypoglycemia, are determined by insulin's pharmacokinetics. However, the final outcomes are not associated with the amount of insulin used. The complications related to insulin overdose are cerebral damage and hypokalemia. Other complications include, pulmonary edema attributed to congestive heart failure and hypertensive crisis, as well as respiratory insufficiency. We report this case with a review of the literature.

보리등겨로 제조한 간장의 향기성분

권오준,이은정,최웅규,손동화,이석일,정연건,지원대 한국위생과학회 2002 한국위생과학회지 Vol.8 No.2

새로운 장류제품으로서 보리등겨의 이용방안을 모색하기 위하여 간장을 만들어 연구하였다. 보리로 제조한 간장의 갈색화는 점차적으로 증가 하였으며 완만한 변화를 보였다. 향기성분으로는 4-vinyl-2-methoxy-phenol, benzeneacetaldehyde, palmitic acid, 2-furancatboxaldehyde, methyl-9, 12-octadecadienoate, di-(2-ethylhexyl)phthalate, diethyl phtalate, dibytyl-1,2-benzenedicatboxylate, 5-methyl-2-furancarboxaldehyde, 3,4-dimethyl-1h-pyrazole, phenylethyl alcohol, dioctyl-hexanedioate, dimethyl-1,2-benzenedicatboxylate, benzaldehyde, methional, 2-methoxy-phenol, n-furfurylidene-3-methylbutyl amine, 1-furfuryl-2-formyl pyrrole, tetradrcanoic acid, 5-methyl-pyrimidine, 4-methyl-5-hydroxymethyl-imidazole, maltol, 5-(5-methyl-2-furanyl)methyl-2-furancarboxaldehyde 순으로 높은 함량을 차지 하였다. For investigation of new utilization as jang-products, kanjang was prepared using barely bran. This study was conducted to investigate flavor components of kanjang during fermentation time. The optical density was gradually increased. Among the flavor components identified in kanjang made with barley bran, the contents of 4-viny1-2-methoxy-phenol was the most in quantity followed by benzeneacetaldehyde, palmitic acid, 2-furancarboxaldehyde, methyl-9,12-octadecadienoate, di-(2-ethylhexyl)phthalate, diethyl phtalate, dibutyl-1,2-benzendicarboxylate, 5-methyl-2-furancarboxaldehyde, 3,4-dimethyl-1h-pyrazole, phenylethyl alcohol, dioctyl-hexanedioate, dimethyl-1,2-benzenedicarboxylate, benzaldehyde, methional, 2-methoxy-phenol, n-furfurylidene-3-methylbutyl amine, 1-furfuryl-2-formyl pyrrole, tetradecanoic acid, 5-methyl-pyrimidine, 4-methyl-5-hydroxymethyl-imidazole, maltol and 5-(5-methyl-2-furanyl)methyl-2-furancarboxaldegyde.

부여-함평분지에 분포하는 백악기 퇴적암에 대한 고지자기연구

홍준표,석동우 한양대학교 이학기술연구소 2004 이학기술연구지 Vol.7 No.

본 연구에서는 부여분지와 함평분지에 분포하는 백악기 퇴적암에 대한 고지자기 연구를 수행하였다. 한반도 남서부에 분포하는 백악기 퇴적분지인 부여, 함평분지에 생성된 백악기 퇴적암에 대한 특성잔류자화 방향을 정립하기 위하여 충 279개의시료를 준비하였으며, 열소자와 교류 소자를 실시한 후 특성잔류자화 방향을 추출하였다. 부석분지의 경우 총 13개 site에서 120개의 정향시료를 채취하여 측정한 결과 경사보정 후의 방향으로 계산된 고지자기극은 Lat./Long.=69.9˚N/193.7˚E (dp=11.5˚, dm=15.1˚)으로 한반도 중기 백악기의 극과 유사하다. 또한 함평분지의 경우 총 20개 site에서 159개의 정향시료를 채취하여 측정한 결과 경사보정후의 방향으로 계산된 고지자기극의 위치는 Lat/Long.=63.7˚N/205.2˚E(dp=8.8˚, dm=12.4˚)로 한반도 중기 백악기의 고지자기극의 위치와 가장 유사하므로 암석의 생성 시기는 중기 백악기라고 사료되며 이들 분지가 중기 백악기에 생성된 이후 유라시아 대륙의 한 부분으로서 현재의 상대적 위치를 크게 벗어나지 않았음을 알 수 있다. This study is a paieomagnetic investigation for the Cretaceous sedimentary rocks in the Buyeo and Hampyeong basins. A total of 279 independently oriented core samples were collected from the Buyeo and Hampyeong Basins for this study. Typical stepwise AF and thermal demagnetization and measurement methods to determine the directions of characteristic remanent magnetization (ChRM) were used. The paleomagnetic pole position calculated from the mean direction for a total of 120 samples from 13 sites of the Buyeo Basin after bedding correction is at Lat./Long.=69.9˚N/193.7˚E (dp=11.5˚, dm=15.1˚), which is statistically similar to the Cretaceous pole of the Kyongsang Basin. The paleomagnetic pole position of the Hampyeong Basin calculated from the mean CWM after bedding correction for a total of 159 independently oriented samples from 20 sites in the Hampyeong Basin is at Lat/Long.=63.7˚N/205.2˚E(dp=8.8˚, dm=12.4˚), which is similar to the paleomagnetic pole (Lat/Long.=66.4˚N/204.5˚N, A%=2.8˚) of the Cretaceous rocks in the Kyongsang Basin, suggesting that the Hampyeong Basin is stable since the Cretaceous period.

연령증가에 따른 혈압요소들의 좌심실비대 및 관동맥질환과의 관련성

박재석,박창규,박미영,박재형,김용현,나진오,신성희,서순용,홍순준,박성미,임홍의,김응주,서홍석,오동주,노영무 대한순환기학회 2004 Korean Circulation Journal Vol.34 No.2

골유착성 치과 임플란트의 성공률에 대한 임상적 연구

김영석,이동근,민승기,이준,문철 대한악안면성형재건외과학회 2002 Maxillofacial Plastic Reconstructive Surgery Vol.24 No.2

The purpose of this study is to review the prognosis of the endosteal osseointegrated dental implants placed in the total and partial edentulous area of mandible and maxilla and to suspect the possible causes leading to failure. 301 osseointegrated dental implants that had been inserted between 1992 thru 2000 were followed up for over one year (average follow up : three years) in function. Medical records and radiographs included CT were evaluated and analyzed by the overall success rate, gender and age factor, general disease, implant fixture length and diameter, surface status of implant, bone density, and the stage of removal. Chi squire test was used statistically. Of the 301 osseointegrated dental implants, 18 dental implants (6.0%) were removed and cumulative survival rate was 94%. No significant difference in the failure rate were found between male (5.4%) and female (6.5%). The failure rate were 8.0% in the fifties, 7.3% in the forties, 5.2% in the thirties, 4.6% in the sixties. Patients who had systemic disease were highly related with failure rate (25%), and cumulative survival rate was 75%. Success rate was the highest in the premolar area than anterior and molar area (p<0.05). The failure rate was highest in the D4 bone (12.5%). High failure rate was found in the wide diameter implant (9.7%) and 7∼9㎜ short implant (12.5%). No significant difference in the failure rate were found between implant surface condition. Stages of removal were pre-prosthetic (16 implants) and post-prosthetic (2 implanrs) stage. The failure rate in the conventional technique was 5.1%, 19.1% in the GBR, 10% in the sinus lifting. Marginal bone resorption around the implants were found 0.15㎜ in the 3 months. 0.4㎜ in the 6 months. 0.71㎜ in the 1 year, 0.9㎜ in the 2 years and 1.06㎜ in the 3 years.