A hybrid strategy for comprehensive annotation of the protein coding genes in prokaryotic genome

Jia-Feng Yu,Jing Guo,Qing-Bin Liu,Yue Hou,Ke Xiao,Qing-Li Chen,Ji-Hua Wang,Xiao Sun 한국유전학회 2015 Genes & Genomics Vol.37 No.4

Protein coding gene annotation errors in prokaryotic genomes are accumulating continually in bioinformatics databases, while the update rate of genome annotation can not keep up with the explosive increasing genome sequences in most cases. Hence it is critical to manually rectify the genome annotation errors. In this paper, a hybrid strategy by combing the gene ab initio predicting programs and the over annotated gene re-annotation programs is proposed for re-annotation of the protein coding genes in prokaryotic genomes. Based on this strategy, the protein coding genes in Geobacter sulfurreducens PCA is comprehensively re-annotated. As a consequence, 16 hypothetical genes are annotated as non-coding sequences and 104 missing genes are retrieved as protein coding genes. Subsequent function analysis and sequences analysis show that the predicting results are much reliable and robust. Further application to other genomes show that this work can provide alternative tools for later post-process of prokaryotic genome annotations.

Low Counts of γδ T Cells in Peritumoral Liver Tissue are Related to More Frequent Recurrence in Patients with Hepatocellular Carcinoma after Curative Resection

Cai, Xiao-Yan,Wang, Jia-Xing,Yi, Yong,He, Hong-Wei,Ni, Xiao-Chun,Zhou, Jian,Cheng, Yun-Feng,Jin, Jian-Jun,Fan, Jia,Qiu, Shuang-Jian Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.2

Objectives: TCR-gamma-delta+T cells (${\gamma}{\delta}$ T cells) are non-conventional T lymphocytes that can recognize and eradicate tumor cells. Our previous studies showed that infiltration and function of ${\gamma}{\delta}$ T cells were substantially attenuated in hepatocellular carcinoma (HCC). However, their prognostic value was not clarified. Methods: The association between ${\gamma}{\delta}$ T cells and the clinical outcomes was determined by immunohistochemistry (IHC) in a HCC patient cohort (n = 342). Results:Immunohistochemistry showed decreased infiltration of ${\gamma}{\delta}$ T cells in tumoral tissues compared with paired peritumoral tissues. The counts of ${\gamma}{\delta}$ T cells in peritumoral tissues were negatively correlated with tumor size (P = 0.005). Survival analysis showed that the levels of peritumoral ${\gamma}{\delta}$T cells were related to both time to recurrence (TTR) and overall survival (OS) (P = 0.010 and P = 0.036, respectively) in univariate analysis, and related to TTR in multivariate analysis (P = 0.014, H.R. [95% CI] = 0.682 [0.502-0.927]). Furthermore, the level of peritumoral ${\gamma}{\delta}$ T cells showed independent prognostic value for TTR in Barcelona Clinic Liver Cancer (BCLC) stage A patients (P = 0.038, H.R. [95% CI] = 0.727 [0.537-0.984]). However, tumoral ${\gamma}{\delta}$ T cells did not show independent prognostic value for either TTR or OS in HCC patients. Conclusions: Low counts of ${\gamma}{\delta}$ T cells in peritumoral liver tissue are related to a higher incidence of recurrence in HCC and can predict postoperative recurrence, especially in those with early-stage HCC.

Bioremediation of Coastal Saline-Alkali Marshy Soil by the Irrigation with Pulp & Paper Wastewater

LI Jia-liang,LU Zhao-hua,TIAN Jia-yi,WANG Lin,LI Peng-hui,XIAO Zhong-feng 대전대학교 환경문제연구소 2009 환경문제연구소 논문집 Vol.13 No.-

Based on the importance of coastal saline-alkali soil remediation in Yellow River Delta, China, the Cl-、Na+ transferring tendency in soil and the saline-alkali soil eco-remediation effects were researched by measuring soil Cl-、Na+ 、soluble salt、soil respire rate and dry biomass weight of reed, etc. periodically. The results shows: the concentration of irrigated soil Cl-、Na+ and soluble salt were decreased 57.7-70%、45.7-47.1% and 53.2-59.7%, respectively, and soil salt decreasing level were little influenced by the hydraulic load, inundation depth varies in some degree, but it was influenced by dry-wet alternative irrigating mode The concentration of soil total nitrogen、organic mass、microbial respire rate, and the reed biomass above ground were increased averagely to 2.17、1.20、1.46 and 1.34 multiple respectively afterirrigation with wastewater, which have complex remediation effects on the coastal saline-alkali wetland, but there are some differences among the different irrigating crafts.

Prognosis of Eight Chinese Cases of Primary Vaginal Yolk Sac Tumor with a Review of the Literature

Tang, Qiong-Lan,Jiang, Xue-Feng,Yuan, Xiao-Ping,Liu, Yong,Zhang, Lin,Tang, Xiao-Feng,Zhou, Jia-Jia,Li, Hai-Gang,Fang, Jian-Pei,Xue, Lin Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.21

Background: Primary vaginal yolk sac tumor is a rare malignancy in the pediatric population, and a diagnostic challenge and appropriate initial treatment remains unsolved. The aim of this study was to investigate the clinicopathologic features, treatment and prognosis of this tumor. Materials and Methods: Eight cases of primary vaginal yolk sac tumor were reported with a literature review. Results: There were 4 pure yolk sac tumor cases and four mixed germ cell tumors containing yolk sac tumor element, including two cases with embryonal carcinoma and two cases with embryonal carcinoma and dysgerminoma. Partial vaginectomy was performed in four cases and all patients received chemotherapy. 85 cases in literatures were reviewed and 9 cases were misdiagnosed. Follow-up data was available in 77 cases and 5-year overall survival rate was 87.6%. 5-year survival rate of biopsy with chemotherapy, conservative surgery with chemotherapy and radical surgery with chemotherapy was 91.1%, 100% and 28.6%, respectively (p<0.001). Compared to cases without relapse or metastasis after initial treatment, patients with relapse or metastasis had a shorter overall survival (35.6% vs 96.6%, p<0.001). Conclusions: Mixed germ cell tumor containing yolk sac tumor element was not uncommon and partial vaginectomy may be a good choice for primary vaginal mixed yolk sac tumor type to eradicate local tumor cells and provide complete information for pathological diagnosis and postoperative adjuvant therapy.

N-Carbamylglutamate in Combination with Vitamin C Show Synergistic Role to Anti-Heat Stress in Sows

Feng Tao,Bai Jia-hua,Xu Xiao-ling,Huang Zheng,Guo Yong,Liu Yan 한국동물생명공학회(구 한국동물번식학회) 2014 한국동물번식학회 한중일 심포지엄 Vol.2014 No.1

Regulated differentiation of stem cells into an artificial 3D liver as a transplantable source

Feng Chen,Hua Wang,Jia Xiao 대한간학회 2020 Clinical and Molecular Hepatology(대한간학회지) Vol.26 No.2

End-stage liver disease is one of the leading causes of death around the world. Since insufficient sources of transplantable liver and possible immune rejection severely hinder the wide application of conventional liver transplantation therapy, artificial three-dimensional (3D) liver culture and assembly from stem cells have become a new hope for patients with end-stage liver diseases, such as cirrhosis and liver cancer. However, the induced differentiation of single-layer or 3D-structured hepatocytes from stem cells cannot physiologically support essential liver functions due to the lack of formation of blood vessels, immune regulation, storage of vitamins, and other vital hepatic activities. Thus, there is emerging evidence showing that 3D organogenesis of artificial vascularized liver tissue from combined hepatic cell types derived from differentiated stem cells is practical for the treatment of end-stage liver diseases. The optimization of novel biomaterials, such as decellularized matrices and natural macromolecules, also strongly supports the organogenesis of 3D tissue with the desired complex structure. This review summarizes new research updates on novel differentiation protocols of stem cell-derived major hepatic cell types and the application of new supportive biomaterials. Future biological and clinical challenges of this concept are also discussed.

Processing, digestion property and structure characterization of slowly digestible gorgon nut starch

Jia-cheng Zeng,Pin-Jian Xiao,Li-Juan Ling,Li Zhang,Dao-Bang Tang,Qing-Feng Zhang,Jiguang Chen,Jing-En Li,Zhongping Yin 한국식품과학회 2022 Food Science and Biotechnology Vol.31 No.1

Slowly digestible gorgon nut starch (GN-SDS) was prepared by heating–cooling treatment (HCT), meanwhile its morphological and structural features were characterized in detail by SEM, DSC, XRD and IR detection. The optimized parameters of GN-SDS processing were as following: starch milk (20%) was heated at 100 °C for 20 min, and then cooled under 4 °C for 24 h. Under the optimized parameters, the SDS content increased from 20.49 to 61.74%. GN-SDS showed typical SDS characteristics in in vivo digestion with a low postprandial blood glucose. SEM images suggested that GN-S particles changed from uniform regular polyhedron with smooth surface to irregular gravel-like particles with coarse surface and obvious layered structure inside after HCT. The results of SEM, DSC, XRD and IR determination indicated that HCT changed the granule morphology, interior structure, gelatinization temperature and crystal type (A to B-type) of GN-S, and therefore made it hard to be digested accordingly.

Relationship between Fractional Exhaled Nitric Oxide Level and Efficacy of Inhaled Corticosteroid in Asthma-COPD Overlap Syndrome Patients with Different Disease Severity

Jia-Xi Feng,Yun Lin,Jian Lin,Su-Su He,Mei-Fang Chen,Xiao-Mai Wu,You-Zu Xu 대한의학회 2017 Journal of Korean medical science Vol.32 No.3

This study explored the relationship between the fractional exhaled nitric oxide (FeNO) level and the efficacy of inhaled corticosteroid (ICS) in asthma-chronic obstructive pulmonary disease (COPD) overlap syndrome (ACOS) patients with different disease severity. A total of 127 ACOS patients with ACOS (case group) and 131 healthy people (control group) were enrolled in this study. Based on the severity of COPD, the ACOS patients were divided into: mild ACOS; moderate ACOS; severe ACOS; and extremely severe ACOS groups. We compared FeNO levels, pulmonary function parameters including percentage of forced expiratory volume in 1 second (FEV1) to predicted value (FEV1%pred), ratio of FEV1 to forced vital capacity (FEV1/FVC), inspiratory capacity to total lung capacity (IC/TLC) and residual volume to total lung capacity (RV/TLC), arterial blood gas parameters, including PH, arterial partial pressure of oxygen (PaO2) and arterial partial pressure of carbon dioxide (PaCO2), total serum immunoglobulin E (IgE), induced sputum eosinophil (EOS), plasma surfactant protein A (SP-A), plasma soluble receptor for advanced glycation end products (sRAGE), sputum myeloperoxidase (MPO), sputum neutrophil gelatinase-associated lipocalin (NGAL) and Asthma Control Test (ACT) scores, and COPD Assessment Test (CAT) scores. Compared with pre-treatment parameters, the FeNO levels, RV/TLC, PaCO2, total serum IgE, induced sputum EOS, plasma SP-A, sputum MPO, sputum NGAL, and CAT scores were significantly decreased after 6 months of ICS treatment, while FEV1%pred, FEV1/FVC, IC/TLC, PH, PaO2, plasma sRAGE, and ACT scores were significantly increased in ACOS patients with different disease severity after 6 months of ICS treatment. This finding suggests that the FeNO level may accurately predict the efficacy of ICS in the treatment of ACOS patients.

Agglomeration of particles during coal combustion in multistage spouted fluidized tower

Jia-Xun Liu,Jian-Min Gao,Xiao-Feng Wang,Shao-Hua Wu,Ji-Hui Gao 한국화학공학회 2009 Korean Journal of Chemical Engineering Vol.26 No.3

An experimental platform of spray agglomeration has been designed and built for removing small fly ash particles (PM10) from coal combustion. Systematic experiments were conducted in a multistage spouted tower using kinds of agglomerant solutions. The particle concentration increases greatly from the first stage to the second stage of the tower. With the increase of flue gas flow rate the oscillation of impulse signal response curves increases and the internal circulation of the tower intensifies. The influencing factors such as the surfactant, PH value, flow rate of the agglomerant solutions and inlet flue gas temperature were analyzed. SEM was used to analyze the microstructure of the particles. Final results indicate that the special shape of a multistage spouted fluidized tower has significant influences on the effect of agglomeration. The findings from this work will be helpful to form the basis, and provide guidance for, further studies on the control of fine particles such as PM2.5 or even smaller.

Post-fire Study on Mechanical Properties of Damaged Ultra-high Strength Concrete

Xiao Lyu,Guang-Hao Jia,Gan-Ping Shu,Xin Zhang,Er-Feng Du,Wen-Ming Wang 한국강구조학회 2022 International Journal of Steel Structures Vol.22 No.6

In order to study the eff ect of steel tube, pre-load and temperature on residual performance of heated ultra-high strength concrete (UHSC), an experimental program was carried out to investigate the physical and mechanical properties of UHSC post-fi re in room temperature. With total of 54 standard cylindrical concrete specimens subjected to various temperatures ranging from 62 °C to 496 °C, their residual compressive strength, elastic modulus, peak strain was measured after natural cooling down. By comparing the test results of standard cylindrical concrete specimens with the results of the bare specimens in and after fi re, it is known that the residual compressive strength of standard cylindrical concrete specimens decayed more serious after exposing to same temperature. Seen from the results, the temperature which the specimens suff ered was found to be responsibility to the reduction of the compressive strength, elastic modulus, peak strain. As the temperature up to 300 °C, the strength reduction coeffi cient of UHSC was 0.67 ~ 0.68 and the elastic modulus reduction coeffi cient of UHSC was 0.41 ~ 0.51 with peak strain coeffi cient ε cr ( T ) /ε 0 1.57 ~ 1.67. Finally, based on the analysis of test results, simple formulae were proposed to describe the eff ect of temperature on residual performance of heated UHSC which infi lled the steel tube.