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Zengli Yu,Xiaozhuan Liu,Zhan Gao,Zhitao Li,Jun Yin,Yuchang Tao,Lingling Cui,Zengli Yu 한국통합생물학회 2017 Animal cells and systems Vol.21 No.1
All-trans retinoic acid (atRA), the oxidative metabolite of retinoic acid (RA), is essential for palatogenesis. Overdose RA is capable of inducing cleft palate in mice and humans. Normal embryonic palatal mesenchymal (EPM) cell growth is crucial for shelf growth. Smad signaling is involved in many biological processes. However, it is not much clear if atRA could affect Smad signaling during EPM cells growth. In this study, the timed pregnant mice with maternal administration of 100 mg/kg body weight of RA by gastric intubation were cervical dislocation executed to evaluate growth changes of palatal shelves by hematoxylin and eosin (H&E) staining. At the same time, a primary mouse EPM (MEPM) cell culture model was also established. MEPM cells were treated with atRA (0.1, 0.5, 1, 5 and 10 μM) for 24, 48 and 72 h. The results indicated that the sizes of the shelves were smaller than those in control. AtRA inhibited MEPM cell growth with both increasing concentration and increasing incubation time, especially at 72 h in vitro. Moreover, atRA significantly increased the mRNA and protein expression levels of Smad7 (P < .05), but the mRNA and protein expression levels of PCNA were reduced (P < .05). We also found atRA inhibited phosphorylation of Smad2 compared with untreated group (P < .05). However, the protein and mRNA levels of Smad2 did not change both in atRA-treated and untreated group (P > .05). We demonstrated that RA induced inhibition of MEPM cell growth that could cause cleft palate partly by down-regulation of Smad pathway.
A Comprehensive Review of Emerging Computational Methods for Gene Identification
Yu, Ning,Yu, Zeng,Li, Bing,Gu, Feng,Pan, Yi Korea Information Processing Society 2016 Journal of information processing systems Vol.12 No.1
Gene identification is at the center of genomic studies. Although the first phase of the Encyclopedia of DNA Elements (ENCODE) project has been claimed to be complete, the annotation of the functional elements is far from being so. Computational methods in gene identification continue to play important roles in this area and other relevant issues. So far, a lot of work has been performed on this area, and a plethora of computational methods and avenues have been developed. Many review papers have summarized these methods and other related work. However, most of them focus on the methodologies from a particular aspect or perspective. Different from these existing bodies of research, this paper aims to comprehensively summarize the mainstream computational methods in gene identification and tries to provide a short but concise technical reference for future studies. Moreover, this review sheds light on the emerging trends and cutting-edge techniques that are believed to be capable of leading the research on this field in the future.
Zeng, Yu-Jie,Liu, Lu,Wu, Heng,Lai, Wei,Cao, Jie-Zhi,Xu, He-Yang,Wang, Jie,Chu, Zhong-Hua Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.10
Background: The gastroenteropancreatic neuroendocrine neoplasm (GEP-NEN) is the most common type of neuroendocrine neoplasm. We summarized data in our centre to investigate the clinicopathological features, diagnostic methods, therapeutic approaches and prognosis for this neoplasm to increase knowledge of this disease in Asian populations. Method: A total of 122 patients treated at Sun Yet-san Memorial Hospital of Sun Yat-sen University between January 2000 and December 2011 were analyzed retrospectively. Results: Pancreas was the most common site of involvement (65/122, 53.3%); this disease has no special symptoms; positive rates of chromogranin A (CgA) and synaptophysin (Syn) were 81.1% and 87.7%, respectively. The positive rate of Syn had statistical difference among the three grades, but not CgA. Some 68 patients had G1 tumors, 32 G2 tumors and 22 G3 tumors, and Chi-square test showed that higher grading was correlated with worse prognosis (${\chi}^2=32.825$, P=0.0001). A total of 32 patients presented with distant metastasis, and 8 cases emerged during following up. Cox proportional hazards regression modeling showed that the tumor grade (P=0.01), lymphatic metastasis (P=0.025) and distant metastasis (P=0.031) were predictors of unfavorable prognosis. The overall 5-year survival rate was 39.6%, the 5-year survival rate of G1 was 55.7%, and the G2 and G3 were 34.2% and 0%, respectively. Conclusions: The incidence of gastroenteropancreatic neuroendocrine tumors has risen over the last 12 years. All grades of these diseases metastasize readily, and further research regarding the treatment of patients after radical surgery is needed to prolong disease-free survival.
Yu Wang,Yu-juan Xue,Ying-xi Zuo,Yue-ping Jia,Ai-dong Lu,Hui-min Zeng,Le-ping Zhang 대한암학회 2024 Cancer Research and Treatment Vol.56 No.3
Purpose Chemotherapy has been the primary treatment for patients with B-cell acute lymphoblastic leukemia (B-ALL). However, there are still patients who are not sensitive to chemotherapy, including those with refractory/relapse (R/R) disease and those experiencing minimal residual disease (MRD) re-emergence. Chimeric antigen receptor-T lymphocytes (CAR-T) therapy may provide a new treatment option for these patients. Materials and Methods Our institution conducted a single-arm prospective clinical trial (ChiCTR-OPN-17013507) using CAR-T-19 to treat R/R B-ALL and MRD re-emergent patients. One hundred and fifteen patients, aged 1-25 years (median age, 8 years), were enrolled, including 67 R/R and 48 MRD re-emergent CD19-positive B-ALL patients. Results All patients achieved morphologic complete remission (CR), and within 1 month after infusion, 111 out of 115 (96.5%) patients achieved MRD-negative CR. With a median follow-up time of 48.4 months, the estimated 4-year leukemia-free survival (LFS) rate and overall survival (OS) rate were 68.7%±4.5% and 70.7%±4.3%, respectively. There were no significant differences in long-term efficacy observed among patients with different disease statuses before infusion (4-year OS: MRD re-emergence vs. R/R B-ALL, 70.6%±6.6% vs. 66.5%±6.1%, p=0.755; 4-year LFS: MRD re-emergence vs. R/R B-ALL, 67.3%±7.0% vs. 63.8%±6.2%, p=0.704). R/R B-ALL patients bridging to transplantation after CAR-T treatment had a superior OS and LFS compared to those who did not. However, for MRD re-emergent patients, there was no significant difference in OS and LFS, regardless of whether they underwent hematopoietic stem cell transplantation or not. Conclusion CD19 CAR-T therapy effectively and safely cures both R/R B-ALL and MRD re-emergent patients.
Sensitization of Cervical Carcinoma Cells to Paclitaxel by an IPP5 Active Mutant
Zeng, Qi-Yan,Huang, Yu,Zeng, Lin-Jie,Huang, Min,Huang, Yong-Qi,Zhu, Qi-Fang Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.19
Paclitaxel is one of the best anticancer agents that has been isolated from plants, but its major disadvantage is its dose-limiting toxicity. In this study, we obtained evidence that the active mutant IPP5 ($8-60hIPP5^m$), the latest member of the inhibitory molecules for protein phosphatase 1, sensitizes human cervix carcinoma cells HeLa more efficiently to the therapeutic effects of paclitaxel. The combination of $8-60hIPP5^m$ with paclitaxel augmented anticancer effects as compared to paclitaxel alone as evidenced by reduced DNA synthesis and increased cytotoxicity in HeLa cells. Furthermore, our results revealed that $8-60hIPP5^m$ enhances paclitaxel-induced G2/M arrest and apoptosis, and augments paclitaxel-induced activation of caspases and release of cytochrome C. Evaluation of signaling pathways indicated that this synergism was in part related to downregulation of NF-${\kappa}B$ activation and serine/threonine kinase Akt pathways. We noted that $8-60hIPP5^m$ downregulated the paclitaxel-induced NF-${\kappa}B$ activation, $I{\kappa}B{\alpha}$ degradation, PI3-K activity and phosphorylation of the serine/threonine kinase Akt, a survival signal which in many instances is regulated by NF-${\kappa}B$. Together, our observations indicate that paclitaxel in combination with $8-60hIPP5^m$ may provide a therapeutic advantage for the treatment of human cervical carcinoma.
Zeng-Yu Yao,Jian-Hua Qi 강원대학교 산림과학연구소 2016 Journal of Forest Science Vol.32 No.3
Xanthoceras sorbifolia seed coat (XSSC) is a processing residue of the bioenergy crop. This work aimed to evaluate the applicability of using the steam explosion to modify the residue for dye biosorption from aqueous solutions by using methylene blue as a model cationic dye. Equilibrium, kinetic and thermodynamic parameters for the biosorption of methylene blue on the steam-exploded XSSC (SE-XSSC) were evaluated. The kinetic data followed the pseudo-second- order model, and the rate-limiting step was the chemical adsorption. Intraparticle diffusion was one of the rate-controlling factors. The equilibrium data agreed well with the Langmuir isotherm, and the biosorption was favorable. The steam-explosion pretreatment strongly affected the biosorption in some respects. It reduced the adsorption rate constant and the initial sorption rate of the pseudo-second-order model. It enhanced the adsorption capacity of methylene blue at higher temperatures while reduced the capacity at lower ones. It changed the biosorption from an exothermic process driven by both the enthalpy and the entropy to an endothermic one driven by entropy only. It increased the surface area and decreased the pH point of zero charge of the biomass. Compared with the native XSSC, SE-XSSC is preferable to MB biosorption from warmer dye effluents.
Deep Learning in Genomic and Medical Image Data Analysis: Challenges and Approaches
Yu, Ning,Yu, Zeng,Gu, Feng,Li, Tianrui,Tian, Xinmin,Pan, Yi Korea Information Processing Society 2017 Journal of information processing systems Vol.13 No.2
Artificial intelligence, especially deep learning technology, is penetrating the majority of research areas, including the field of bioinformatics. However, deep learning has some limitations, such as the complexity of parameter tuning, architecture design, and so forth. In this study, we analyze these issues and challenges in regards to its applications in bioinformatics, particularly genomic analysis and medical image analytics, and give the corresponding approaches and solutions. Although these solutions are mostly rule of thumb, they can effectively handle the issues connected to training learning machines. As such, we explore the tendency of deep learning technology by examining several directions, such as automation, scalability, individuality, mobility, integration, and intelligence warehousing.
Zeng, Qi-Yan,Zeng, Lin-Jie,Huang, Yu,Huang, Yong-Qi,Zhu, Qi-Fang,Liao, Zhi-Hong Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.9
Protein phosphatase 1 (PP1) is a major serine/threonine phosphatase that controls gene expression and cell cycle progression. The active mutant IPP5 ($8-60hIPP5^m$), the latest member of the inhibitory molecules for PP1, has been shown to inhibit the growth of human cervix carcinoma cells (HeLa). In order to elucidate the underlying mechanisms, the present study assessed overexpression of $8-60hIPP5^m$ in HeLa cells. Flow cytometric and biochemical analyses showed that overexpression of $8-60hIPP5^m$ induced G2/M-phase arrest, which was accompanied by the upregulation of cyclin B1 and phosphorylation of G2/M-phase proteins ATM, p53, $p21^{cip1/waf1}$ and Cdc2, suggesting that $8-60hIPP5^m$ induces G2/M arrest through activation of the ATM/p53/$p21^{cip1/waf1}$/Cdc2/cyclin B1 pathways. We further showed that overexpression of $8-60hIPP5^m$ led to delayed nuclear translocation of cyclin B1. $8-60hIPP5^m$ also could translocate to the nucleus in G2/M phase and interact with $pp1{\alpha}$ and Cdc2 as demonstrated by co-precipitation assay. Taken together, our data demonstrate a novel role for $8-60hIPP5^m$ in regulation of cell cycle in HeLa cells, possibly contributing to the development of new therapeutic strategies for cervix carcinoma.
Yu-lian Tang,Xiao-ming Zhang,Zhi-gang Yang,Yu-cheng Huang,Tian-wu Chen,Yan-li Chen,Fan Chen,Nan-lin Zeng,Rui Li,Jiani Hu 대한영상의학회 2017 Korean Journal of Radiology Vol.18 No.4
Objective: To explore the association between the blood oxygenation T2* values of resectable esophageal squamous cell carcinomas (ESCCs) and tumor stages. Materials and Methods: This study included 48 ESCC patients and 20 healthy participants who had undergone esophageal T2*-weighted imaging to obtain T2* values of the tumors and normal esophagi. ESCC patients underwent surgical resections less than one week after imaging. Statistical analyses were performed to identify the association between T2* values of ESCCs and tumor stages. Results: One-way ANOVA and Student-Newman-Keuls tests revealed that the T2* value could differentiate stage T1 ESCCs (17.7 ± 3.3 ms) from stage T2 and T3 tumors (24.6 ± 2.7 ms and 27.8 ± 5.6 ms, respectively; all ps < 0.001). Receiver operating curve (ROC) analysis showed the suitable cutoff T2* value of 21.3 ms for either differentiation. The former statistical tests demonstrated that the T2* value could not differentiate between stages T2 and T3 (24.6 ± 2.7 ms vs. 27.8 ± 5.6 ms, respectively, p > 0.05) or between N stages (N1 vs. N2 vs. N3: 24.7 ± 6.9 ms vs. 25.4 ± 4.5 ms vs. 26.8 ± 3.9 ms, respectively; all ps > 0.05). The former tests illustrated that the T2* value could differentiate anatomic stages I and II (18.8 ± 4.8 ms and 26.9 ± 5.9 ms, respectively) or stages I and III (27.3 ± 3.6 ms). ROC analysis depicted the same cutoff T2* value of 21.3 ms for either differentiation. In addition, the Student’s t test revealed that the T2* value could determine grouped T stages (T0 vs. T1–3: 17.0 ± 2.9 ms vs. 25.2 ± 6.2 ms; T0–1 vs. T2–3: 17.3 ± 3.0 ms vs. 27.1 ± 5.3 ms; and T0–2 vs. T3: 18.8 ± 4.2 ms vs. 27.8 ± 5.6 ms, all ps < 0.001). ROC analysis indicated that the T2* value could detect ESCCs (cutoff, 20 ms), and discriminate between stages T0–1 and T2–3 (cutoff, 21.3 ms) and between T0–2 and T3 (cutoff, 20.4 ms). Conclusion: The T2* value can be an additional quantitative indicator for detecting ESCC except for stage T1 cancer, and can preoperatively discriminate between some T stages and between anatomic stages of this tumor.
曾育榮(Zeng Yu-rong) 경북대학교 아시아연구소 2011 아시아연구 Vol.- No.13
五代시기, 吏部에서 6品 이하의 官員을 選任할 때는 대체적으로 庸代의 銓選제도를 답습하였다. 그러나 五代시기는 戰亂이 끊이지 않아 사회가 안정되지 않아 장기간 銓選제도가 규범화 되지 않았기 때문에 매우 혼탁하였다. 이와 같은 상황을 변화시키기 위해 後唐시기부터 各朝는 모두 여러 가지 조치를 취하여 吏部選人文書에 眞僞가 섞인 상황을 변화시키고자 하였다. 그 중 가장 중요한 조치의 하나가 吏部에서 選人文書에 대한 심사를 더욱 엄격히 하는 것이었다. 그래서 選人文書의 종류가 9種으로 늘어났고 이것은 唐代에 비해 훨씬 많아진 것이었다. 그 중에서도 選人의 기본적인 자질에 대한 자료가 매우 상세해졌다. 구체적으로 보면, 첫째, 초기 선택단계에서 選人이 제출해야 하는 문서는 네 가지가 있었다. ⓛ 解狀으로, 여기에는 選人의 출신, 3대의 가족상황, 鄕貫, 骨肉, 在朝親情, 年齒形貌, 考覈資序, 優劣課最, 罷職年月 등이 포함된 官員 개인 이력을 상세히 나타낸 문서였다. 매년 5월에는 選格科限에 부합하는 選人은 “銓狀”이라는 申請表를 써서 本郡 혹은 任所에 보내 府川 혹은 本司 장관이 吏部의 選格樣式에 따라 심사의견을 쓴 다음 다시 選人에게 주었다. ② 歷子로서, 이것은 吏部에서 官員이 역임할 때 주는 사인과 도장을 찍은 문서를 말하는데, 여기에는 관원이 上任하는 月日과 累任하는 月日 및 임기의 治積 등이 적혀있다. ③ 解由로서, 이것은 관원이 罷任될 때 각 지역 州府의 관리와 여러 司의 長官들이 제출하는 문서로서, 여기에는 罷任月日, 戶口增減과 세금 수금 액수 등이 적혀있다. ④ 考牒으로, 이것은 관원의 역대 考課 등급 기록으로서 관원이 일정시기 사업한 실적의 최종 평가결과이다. 둘째, 注判 단계에 選人이 제출해야할 문서에는 세 가지가 있다. ① 告身, 즉 吏部가 官員에게 수여하는 일종의 憑證으로서 後唐시기인 長興元年(930년) 5월에 시작하였다. 여기에는 選人이 銓司에게 제공한 告身, 注明하여 보관해야할 名銜, 選人의 三代情況, 有無出身, 歷任告敕, 逐任考數 등이 포함되어 있다. ② 告敕, 즉 官員의 위임장으로서 注判 전에 選人이 歷任告敕을 告身 내에 붙여서 吏部南曹에게 바쳐 審覈을 받는다. ③ 公憑, 이것은 選人이 문서를 분실 했을 때의 증명이거나, 州府의 長官이 冤案을 심리할 때 縣官이 작성한 증명이거나, 관련 기구에서 官員에게 보낸 減選증명이거나, 吏部 南曹가 選人이 바친 歷任사실을 나타내는 문서를 받고나서 떼어준 수거이다. 마지막으로 引驗 단계에서 銓司勘覈한 選人文書에는 두 종류가 있다. ① 家狀, 즉 選人의 郡縣鄕里, 父祖官名, 內外族姻, 年齒形式 등을 적은 家庭證明이다. ② 保狀, 즉 選人 상호간에 보증한 문서와 選人을 잘 아는 京官이 제출한 보증 문서이다. During the Five Dynasty, Ministry of Personnel still adopted the Tang Dynasty’s Personnel Selecting System for those official personnel whose positions were lower than Liuping position. However, as a result of the war affairs and the turbulent and unsafe social situation, the phenomena of forgery candidates and cheating in the selection were very common as the Personnel Selecting System was not supervised properly for a long period. Every Dynasty had taken some measures to punish and prevent such cheating behaviors in order to make the Personnel Selecting System step into the right path since the Later Tang Dynasty. Among those measures, the most significant one was to check Candidates’ testing paper in a more stringent process. The kinds of Selection Testing Paper had been increased to nine, which were much more than the number of Dang Dynasty. And it had required candidates to supply the detailed personal information. To put it more specifically, at the first phase of selection, a candidate should supply four types of credentials. ① Xiezhuang, it included political achievements, financial contribution to the government, and final evaluation during his term of office. For the personal information, it contained a candidate’s family status, his ancestor’s basic information, his off springs, and his relatives who were working in the government, personal image description, the job he had applied for, his advantages and disadvantages, and his resignation date. Every May, those qualified candidates would fill in the application forms, and then the leaders of the local government would give the comments in those forms. ② Lizi, it was a kind of credential, which was presented by the Ministry of Personnel. It contained the date when the candidate should proceed to take up one’s post and when he should leave the post. It also included the candidate’s historic achievements. ③ Jieyou, it was a kind of credential, which was given by the candidate’s higher-ups. The content still was about the candidate’s performing achievements during his term of office. ④ Kaodie, it was a kind of credential which was about the candidate’s historic testing records and working evalutions in his previous term of the office. Then, at the second phase of selection, the candidates should submit 3 types of credentials. They are specifically ① Gaoshen, a kind of certificate conferred by the Ministry of Official Personnel Affairs. Since the May of the first year of Changxing reign of Later Tang Dynasty, the Gaoshen submitted by the candidates to Quansi(the officials in charge of selection) should state clearly information such as the official title, the family condition within three generations, the social connections, and so forth. ② Gaochi, namely the credential of appointment. The candidate should submit Gaoshen with Gaochi of successive posts attached to Ministry of Official Affairs for examination and verification. ③ Gongping, the testimony for missing certificates or the testimony for grievance cases issued by the top officials of the prefecture or the receipt issued by the Ministry of the Official Affairs for receiving candidates’ documents of successive posts. Finally, two types of credentials should be submitted at the final phase of the selection: ① Jiangzhuang, the record of such family information as the predecessers’ officials titles, marriages within and beyond the clan and so forth. ② Baozhuang, the surety document presented by other candidates or the superior officials who are familiar the candidate.