Resequencing 295 accessions of heuristic and Korean breeding rice deciphers the milestones for breeding and domestication history of Korean rice

Qiang He,Byung-Kook Yun,Min-Young Yoon,Xiao-Qiang Wang,Feng-Peng Li,Aye-Aye Khaing,Won-Hee Ra,Win Htet Oo,Cheol-Soon Park,Sun-Kyung Min,Wei Tong,Jie Yu,Bu-Woong Choi,Eun-Beom Heo,Khandakar Md.Rayhanul 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

As one of the most important crop, rice is not only a staple food of half world’s population but a wonderful model plant, which has been leading the evolution and functional genomics study. The next-generation sequencing technology are expediting rice genomic study, by providing a simple but powerful way. In this study, we re-sequenced a core collection of 137 rice accessions from all over the world along with 158 Korean breeding varieties. Finally, 6.3G uniquely mapped reads were obtained, and about 10 million SNPs and ~1.2 million InDels were identified with average sequencing depth of 7.5X. These will help us to maximize our germplasm utilization and assists all the deep research in population dynamics and functional studies. Here, we’d like to show the approaches applied to resequencing data mining and on-going activities.

Study on Safety of Up-righting Project for a Capsized Ship Model Based on Cable Tensions, Theoretical Model and NumericalMethod Accounting for Dynamic Effect

Yu-Qiang Sun,De-Jun Jia 국제이네비해양경제학회 2018 International Journal of e-Navigation and Maritime Vol.10 No.1

During an up-righting project for a capsized ship, the dynamic effect enlarges the tensions of cables. The cable tensions which are calculated based on statics and the safety evaluation which is based on these tensions cannot ensure the safety of the up-righting project. Due to the above reasons, a numerical simulation project is applied to investigate the dynamic effect on cable tensions of up-righting projects and evaluate the safety of up-righting project in current research. Firstly, a theoretical equation of the quasi-static up-righting project model is established in current research and is solved. Subsequently, the precision of the numerical simulation method applied in current research is checked by comparing cable tensions which are calculated by theoretical model and numerical simulation method. The cable tensions in different cases are solved by the numerical simulation method which accounts for dynamic effect in order to investigate the relationship between cable tensions and capsized ship weights, cable stiffness and winding-in speed. Finally, the safety of up-righting project is evaluated based on all the cable tensions calculated. It is pointed out that cable tension increases with the value of capsized ship weight, cable stiffness or winding-in speed approximately. The safety coefficients of cable in some high winding-in speeds are bellow 1.0. The results indicate that the dynamic effect is significant and should be accounted for during the up-righting project.

Comparison of Liver Transplantation and Liver Resection for Hepatocellular Carcinoma Patients with Portal Vein Tumor Thrombus Type I and Type II

Jia-Yu Lv,Ning-Ning Zhang,Ya-Wei Du,Ying Wu,Tian-Qiang Song,Ya-Min Zhang,Yan Qu,Yu-Xin Liu,Jie Gu,Ze-Yu Wang,Yi-Bo Qiu,Bing Yang,Da-Zhi Tian,Qing-Jun Guo,Li Zhang,Ji-San Sun,Yan Xie,Zheng-Lu Wang,Xin 연세대학교의과대학 2021 Yonsei medical journal Vol.62 No.1

Purpose: The aim of this study was to compare the efficacy of liver transplantation (LT) and liver resection (LR) for hepatocellularcarcinoma (HCC) patients with portal vein tumor thrombus (PVTT) and to investigate risk factors affecting prognosis. Materials and Methods: A total of 94 HCC patients with PVTT type I (segmental PVTT) and PVTT type II (lobar PVTT) were involvedand divided into LR (n=47) and LT groups (n=47). Recurrence-free survival (RFS) and overall survival (OS) were comparedbefore and after inverse probability of treatment weighting (IPTW). Prognostic factors for RFS and OS were explored. Results: Two treatment groups were well-balanced using IPTW. In the entire cohort, LT provided a better prognosis than LR. Among patients with PVTT type I, RFS was better with LT (p=0.039); OS was not different significantly between LT and LR(p=0.093). In subgroup analysis of PVTT type I patients with α-fetoprotein (AFP) levels >200 ng/mL, LT elicited significantly longermedian RFS (18.0 months vs. 2.1 months, p=0.022) and relatively longer median OS time (23.6 months vs. 9.8 months, p=0.065). Among patients with PVTT type II, no significant differences in RFS and OS were found between LT and LR (p=0.115 and 0.335,respectively). Multivariate analyses showed treatment allocation (LR), tumor size (>5 cm), AFP and aspartate aminotransferase(AST) levels to be risk factors of RFS and treatment allocation (LR), AFP and AST as risk factors for OS. Conclusion: LT appeared to afford a better prognosis for HCC with PVTT type I than LR, especially in patients with AFP levels>200 ng/mL.

A chloroplast variation map generated using whole genome re-sequencing of Korean landrace rice reveals phylogenetic relationships among Oryza sativa subspecies

Wei Tong,Qiang He,Xiao-Qiang Wang,Min-Young Yoon,Won-Hee Ra,Feng Peng Li,Jie Yu,Win Htet Oo,Sun-Kyung Min,Buung Choi,Eun-Beom Heo,Byoung-Kook Yun,Kyu-Won Kim,Tae-Sung Kim,Chang-Yong Lee,Yong-Jin Park 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07

Although the overall structure of the chloroplast genome is generally conserved, a number of sequence variations have been identified, which are valuable for plant population and evolutionary studies. Here, we constructed a chloroplast variation map of 30 landrace rice strains of Korean origin, using the Oryza rufipogon chloroplast genome (Genbank: NC_017835) as a reference. Differential distribution of single nucleotide polymorphisms (SNPs) and indels across the rice chloroplast genome is suggestive of a region-specific variation. Population structure clustering revealed the existence of two clear subgroups (indica and japonica) and an admixture group (aus). Phylogenetic analysis of the 30 landrace rice strains and six rice chloroplast references suggested and supported independent evolution of O. sativa indica and japonica. Interestingly, two “aus” type accessions, which were thought to be indica type, shared a closer relationship with the japonica type. One hypothesis is that “Korean aus” was intentionally introduced and may have obtained japonica chloroplasts during cultivation. We also calculated the nucleotide diversity of 30 accessions and compared to six rice chloroplast references, which shown a higher diversity in the indica and aus groups than in the japonica group in lower level substitution diversity.

Pathologic Response During Chemo-radiotherapy and Variation of Serum VEGF Levels Could Predict Effects of Chemo-Radiotherapy in Patients with Esophageal Cancer

Yu, Jing-Ping,Lu, Wen-Bin,Wang, Jian-Lin,Ni, Xin-Chu,Wang, Jian,Sun, Zhi-Qiang,Sun, Su-Ping Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.3

Background: To investigate the relationship between pathologic tumor response to concurrent chemoradiotherapy and variation of serum VEGF in patients with esophageal cancer. Materials and Methods: Forty six patients with esophageal cancer who were treated with concurrent chemo-radiotherapy were enrolled. Endoscopic and pathologic examination was conducted before and four weeks afterwards. Serum level of VEGF was documented before, four weeks later and after chemo-radiotherapy. The relationship between pathologic response and the variation of serum level of VEGF and its influence on the prognosis were investigated. Results: Serum level of VEGF decreased remarkably during and after chemo-radiotherapy in patients whose pathologic response was severe (F=5.393, 4.587, P(0.05). There were no statistical differences of serum VEGF level before, during and after chemo-radiotherapy for patients whose pathologic response was moderate or mild. There were 18 (85.7%), 7 (53.8%) and 6 patients (50.0%) whose serum VEGF level dropped in the severe, moderate and mild group, respectively, with significant differences among these groups (p=0.046). Two year survival rates of patients with severe, moderate and mild pathologic response were 61.9%, 53.8% and 33.3% respectively, and no statistically difference between severe and mild group regarding OS (p=0.245) was tested. Conclusions: Tumor pathologic response during chemo-radiotherapy and the changes of serum VEGF lever could predict curative effects of chemo-radiotherapy in patients with esophageal cancer.

The Uneven Distribution of Mating Type Genes in Natural and Cultivated Truffle Orchards Contributes to the Fructification of Tuber indicum

( Qiang Li ),( Yu Fu ),( Qun Sun ),( Pierre Sourzat ),( Mei Yang ),( Chengyi Liu ),( Hao Tan ),( Lei Ye ),( Jie Zou ),( Chenguang Wu ),( Bo Zhang ),( Xiaolin Li ) 한국균학회 2018 Mycobiology Vol.46 No.1

The aim of this study was to investigate the pattern of distribution of mating type (MAT) genes of Tuber indicum in ectomycorhizosphere soils from natural T. indicum-producing areas and cultivated truffle orchards and ascocarp samples from different regions. Quantitative real-time PCR and multiplex PCR were used to weight the copy numbers of MAT1-1-1 and MAT1-2-1 in natural truffle soils and cultivated orchard soils. The effect of limestone on the pattern of truffle MAT genes and the correlation between soil properties and the proportion of MAT genes were also assessed. These results indicated that an uneven and nonrandom distribution of MAT genes was common in truffle-producing areas, cultivated truffle orchards, and ascocarps gleba. The competition between the two mating type genes and the expansion of unbalanced distribution was found to be closely related to truffle fructification. Limestone treatments failed to alter the proportion of the two mating type genes in the soil. The content of available phosphorus in soil was significantly correlated with the value of MAT1-1-1/MAT1-2-1 in cultivated and natural ectomycorhizosphere soils. The application of real-time quantitative PCR can provide reference for monitoring the dynamic changes of mating type genes in soil. This study investigates the distributional pattern of T. indicum MAT genes in the ectomycorhizosphere soil and ascocarp gleba from different regions, which may provide a foundation for the cultivation of T. indicum.

Generalized Beamforming Design for Cooperative MIMO Multirelay Networks with Infinite Constraints and Imperfect CSI

Yu, Haiyang,Duan, Wei,Sun, Qiang,Wang, Xia,Wang, Jue,Li, Jun,Choi, Jaeho Hindawi Limited 2018 Mathematical problems in engineering Vol.2018 No.-

<P>A generalized base station-relay-user equipment (BS-Relay-UE) beamforming design is investigated for a cooperative multiple-input multiple-output (MIMO) multirelay networks with imperfect channel state information (CSI). In order to minimize the worst-case mean square error (MSE) which is subject to a semi-infinite (SI) relay power constraints, a generalized optimal beamforming structure for the relay amplifying matrix is effectively proposed, and then the SI relay power constraints are converted into linear matrix inequalities (LMIs) version. In such conversion, the objective problem recasts as a decoupled biconvex semidefinite programming (SDP) one which can be efficiently solved by the proposed alternating algorithm. The system performance has been verified in terms of worst-case MSE using a set of qualitative analyses. The results show us that the proposed beamforming method outperforms the conventional schemes and can also effectively reduce the computational complexity when it is compared to the cutting-set schemes and also to the nonrobust ones.</P>

Research on method of constraint conversion in feature-based data exchange between heterogeneous CAD systems

Wei Sun,Tie-qiang MA,Yu-jun Huang 대한기계학회 2009 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.23 No.1

Data exchange between heterogeneous CAD systems is the key problem in the field of CAD, and the popular solution to this problem is a feature-based method. Aiming at keeping the consistency of design intent in data exchange between heterogeneous CAD systems, this research focuses on the method of constraint conversion. First, two kinds of basic feature transformation ways are summarized, and this is the foundation of constraint conversion. Second, a novel identification of geometric elements based on the improved geometric certificate is proposed, and the identifier of geometric element is used to recognize the acting object of constraint. Third, the principles of constraint conversion are put forward, and the method of constraint conversion for a single feature is proposed according to the principles. Fourth, an algorithm of constraint conversion for the whole process of CAD data exchange is designed. Finally, the contrast experiment of CAD data exchange is completed, and the result of the experiment shows that the approach mentioned above is effective.

Case Reports : Surgical Treatment for 11 Cases of Penile Verrucous Carcinoma

( Chuan Yu Sun ),( Xu Ke ),( Zheng Jie ),( Guo Wei Xia ),( Zu Jun Fang ),( Qiang Ding ) 대한피부과학회 2011 Annals of Dermatology Vol.23 No.3s

Penile verrucous carcinoma is a rare, well-differentiated and low-grade tumor. The surgeons are deficiently aware about the biological behavior and the clinicopathological characteristic of this disease, which raises difficulties during the treatment. In our present study, the clinical and pathological data of 11 patients with penile verrucous carcinoma, aged between 49 to 85 years was retrospectively analyzed. The tumors exhibited exophytic, papillary, caulifower-like or verrucose lesions of great dimensions measuring between 2 to 10 cm on the penises. The tumors were located at glans in 6 cases, invaded the coronoid sulcus in 4 cases and invaded the shaft of the penis in 1 case. Eight cases underwent partial penectomy, while the other 3 were treated with local excision. The diagnosis of penile verrucous carcinoma was confirmed by histopathologic examination of the specimens with the negative surgical margins in all the cases. Within the period of 12 to 60 months of follow-up, all the patients were disease-free with no case of recurrence and metastasis. The novel knowledge and experience of the treatment of penile verrucous carcinoma will be a useful clinical guide for surgeons in the future. (Ann Dermatol 23(S3) S346~S349, 2011)

High Temperature Oxidation Resistance of NiCoCrAl High Entropy Alloy Coating on the TiAl Alloy

Yuanyuan Sun,Qiang Miao,Wenping Liang,Kai Zang,Yuting Wu,Haiyang Yu,Mengjuan Yin,Xiguang Gao,Yindong Song 대한금속·재료학회 2024 METALS AND MATERIALS International Vol.30 No.1

The high entropy alloy coating is considered as one of the most promising methods to improve the high-temperature oxidationresistance of titanium aluminum alloys due to its fine mechanical property and thermal stability. However, the high entropyalloy coating prepared so far has poor coating quality, and low coating forming efficiency and there are certain requirementsfor the substrate alloys. To this end, a NiCoCrAl high entropy alloy coating was developed using the double glow plasmaalloying technique on the TiAl alloy. The morphology, phase structure, and high temperature oxidation resistance of thecoating were comprehensively studied. The results indicate that a uniform and dense coating with a single solid solution offace-centered cube phase formed on the alloy surface. Furthermore, isothermal oxidation test was performed, and the oxidationfailure process of the TiAl substrate and the NiCoCrAl-coated sample with different oxidation times was analyzed. It isfound that the coating efficiently prevented the TiAl alloy from degeneration for up to 100 h at 900 °C.