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1.  Appropriate treatment strategies improve survival of hepatocellular carcinoma patients with portal vein tumor thrombus 
World Journal of Gastroenterology : WJG  2014;20(45):17141-17147.
AIM: To evaluate the survival benefits of different treatment strategies for hepatocellular carcinoma (HCC) patients with portal vein tumor thrombus (PVTT) and to determine the prognosis factors.
METHODS: Between 2007 and 2009, 338 HCC patients treated for PVTT were retrospectively studied. The patients were divided into 4 groups that underwent different treatments: the conservative treatment group (n = 75), the transarterial chemoembolization (TACE) group (n = 86), the hepatic resection group (n = 90), and the hepatic resection associated with postoperative TACE group (n = 87). Survival rates were determined using the Kaplan-Meier method and differences between the groups were identified through log-rank analysis. Cox’s proportional hazard model was used to identify the risk factors for survival.
RESULTS: The mean survival periods for patients in the conservative treatment, TACE, hepatic resection and hepatic resection associated with postoperative TACE groups were 3.8, 7, 8.2 and 15.1 mo, respectively. Significant differences were observed in the survival rates. For the surgical resection associated with postoperative TACE group, the survival rates after 1, 2 and 3 years were 49%, 37% and 19%, respectively. These results were significantly higher than those of the other groups (P < 0.05). Meanwhile, the 1, 2 and 3 year survival rates for the surgical resection group were 28%, 20% and 15%, whereas those for the TACE group were 17.5%, 0% and 0%, respectively. These values significantly increased after hepatic resection compared with those after TACE (P < 0.05).
CONCLUSION: Surgical resection is the most effective therapeutic strategy for HCC patients with PVTT and results in high hepatic functional reserve. For patients who can tolerate the procedure, postoperative TACE is necessary to prevent recurrence and prolong the survival period.
PMCID: PMC4258584  PMID: 25493028
Hepatocellular carcinoma; Portal vein tumor thrombosis; Conservative treatment; Transarterial chemoembolization; Surgical resection; Postoperative transarterial chemoembolization
2.  Effectiveness and safety profile of S-1-based chemotherapy compared with capecitabine-based chemotherapy for advanced gastric and colorectal cancer: A meta-analysis 
The aim of the present analysis was to compare the efficacy and safety profile of S-1-based chemotherapy (SBCT) versus capecitabine-based chemotherapy (CBCT) for advanced gastric cancer (AGC) and advanced colorectal cancer (ACRC). A meta-analysis was performed, which included eligible randomized controlled trials (RCTs) that were identified using RevMan 5.1.0 software. A total of 1,064 patients from 11 RCTs, comprising of 527 patients in the SBCT group and 537 patients in the CBCT group, were included in the analysis. For AGC, the meta-analysis of overall survival (OS) [hazard ratio (HR), 0.98; 95% confidence interval (CI), 0.85–1.12], time to progression (HR, 0.95; 95% CI, 0.80–1.12) and overall response rate (ORR) [odds ratio (OR), 1.06; 95% CI, 0.72–1.55] of patients in the SBCT group indicated no statistical significance when compared with those in the CBCT group. Furthermore, for ACRC, a pooled analysis demonstrated no significant difference between the SBCT and CBCT groups (OS: HR, 0.82; 95% CI, 0.61–1.10; progression-free survival: HR, 0.79; 95% CI=0.60–1.04; ORR: OR, 1.27; 95% CI, 0.91–1.78). The statistically significant differences identified in the overall meta-analysis indicated a low incidence of grade 3–4 hand-foot-syndrome (OR, 0.15; 95% CI, 0.06–0.36) in the SBCT group; however no statistically significant difference was observed in the incidence of grade 3–4 anemia, thrombocytopenia, leucopenia, neutropenia, diarrhea, stomatitis or nausea/vomiting. The SBCT treatment exhibited similar efficacy and an approximately equivalent safety profile compared with the CBCT treatment and was an alternative to CBCT for patients with AGC or ACRC; however, further investigation is required to provide confirmation.
PMCID: PMC3991506  PMID: 24940424
S-1; capecitabine; advanced gastric cancer; advanced colorectal cancer; meta-analysis
3.  Erlotinib: An enhancer of radiation therapy in nasopharyngeal carcinoma 
The aim of this study was to explore the effects of erlotinib combined with radiation on human nasopharyngeal carcinoma (NPC) radiosensitivity using the CNE1 and CNE2 cell lines. Human NPC cells were treated with erlotinib and/or radiation. The effect of erlotinib on the radiosensitivity of the cells was detected using a clonogenic cell survival assay. The rate of apoptosis and the cell cycle were evaluated using flow cytometry. An NPC xenograft model in NOD-SCID mice was used to evaluate the efficacy of the combination therapy of erlotinib with radiation. Erlotinib enhanced the sensitivity of the CNE1 and CNE2 cells to radiation, with sensitization enhancement ratios (SERs) of 1.076 and 1.109, respectively. Erlotinib combined with radiation induced G2/M phase cell cycle arrest in the two cell lines. The mouse tumor model demonstrated a significant reduction in NPC tumor volume in mice treated with erlotinib in combination with radiation when compared with that in mice treated with radiation alone. Erlotinib combined with radiation provoked G2-M phase cell cycle arrest, thereby enhancing the sensitivity of the NPC cells to radiation.
PMCID: PMC3797307  PMID: 24137317
nasopharyngeal carcinoma; radiation; erlotinib
4.  Anti-Inflammation of Spirocyclopiperazinium Salt Compound LXM-10 Targeting α7 nAChR and M4 mAChR and Inhibiting JAK2/STAT3 Pathway in Rats 
PLoS ONE  2013;8(6):e66895.
The present study aims to investigate the therapeutic effects of LXM-10 by intragastric administration in both acute and chronic inflammatory models, and to explore the underlying molecular mechanisms. The results showed that LXM-10 produced significant anti-inflammatory effects on carrageenan induced paw edema and complete Freund's adjuvant (CFA) induced arthritis, in which LXM-10 inhibited paw swelling in a dose- and time-dependent manner. ELISA analysis showed the production of pro-inflammatory cytokines including TNF-α and IL-6 was decreased by LXM-10. Western blot analysis showed that LXM-10 significantly reduced phosphorylation of Janus kinase 2 (JAK2) and further blunted phosphorylation of signal transducer and activator of transcription-3 (STAT3). The effects that LXM-10 had shown were attenuated by methyllycaconitine citrate (an α7 nicotinic acetylcholine receptor antagonist) or tropicamide (an M4 muscarinic acetylcholine receptor antagonist) in vivo. In conclusion, the studies showed that intragastric administration of LXM-10 exerted significant anti-inflammation effects in acute and chronic models, which may be attribute to the activation of α7 nicotinic acetylcholine receptor and M4 muscarinic acetylcholine receptor, thereby inhibiting the JAK2/STAT3 signal pathway, and ultimately reducing the production of pro-inflammatory cytokines of TNF-α and IL-6.
PMCID: PMC3695990  PMID: 23840548
5.  Effects of ACE inhibition on endothelial progenitor cell mobilization and prognosis after acute myocardial infarction in type 2 diabetic patients 
Clinics  2013;68(5):665-673.
We aimed to assess the chemotactic response of endothelial progenitor cells to angiotensin-converting enzyme inhibitors in T2DM patients after acute myocardial infarction, as well as the associated prognosis.
Sixty-eight T2DM patients with acute myocardial infarction were randomized to either receive or not receive daily oral perindopril 4 mg, and 36 non-diabetic patients with acute myocardial infarction were enrolled as controls. The numbers of circulating CD45−/low+CD34+CD133+KDR+ endothelial progenitor cells, as well as the stromal cell-derived factor-α and high-sensitivity C reactive protein levels, were measured before acute percutaneous coronary intervention and on days 1, 3, 5, 7, 14, and 28 after percutaneous coronary intervention. Patients were followed up for 6 months. Chinese Clinical Trial Registry: ChiCTR-TRC-12002599.
T2DM patients had lower circulating endothelial progenitor cell counts, decreased plasma vascular endothelial growth factor and α levels, and higher plasma high-sensitivity C reactive protein levels compared with non-diabetic controls. After receiving perindopril, the number of circulating endothelial progenitor cells increased from day 3 to 7, as did the plasma levels of vascular endothelial growth factor and stromal cell-derived factor-α, compared with the levels in T2DM controls. Plasma high-sensitivity C reactive protein levels in the treated group decreased to the same levels as those in non-diabetic controls. Furthermore, compared with T2DM controls, the perindopril-treated T2DM patients had lower cardiovascular mortality and occurrence of heart failure symptoms (p<0.05) and better left ventricle function (p<0.01).
The use of angiotensin-converting enzyme inhibitors represents a novel approach for improving cardiovascular repair after acute myocardial infarction in T2DM patients.
PMCID: PMC3654302  PMID: 23778412
Endothelial Progenitor Cells; Endothelial Progenitor Cell Inhibitors; Prognosis; Type 2 Diabetes Mellitus; Acute Myocardial Infarction
6.  Synthetic N-Alkylated Iminosugars as New Potential Immunosuppressive Agents 
ACS Medicinal Chemistry Letters  2011;2(9):682-686.
The new emerging immunosuppressive effects displayed by iminosugars have not been much investigated so far. Several new N-alkyl dideoxy iminoalditols were designed and synthesized to explore their immunosuppressive effects. These iminosugars inhibited the proliferation of mouse splenocytes and the secretion of both IFN-γ and IL-4, which are the hallmark cytokines of Th1 and Th2 cells, respectively. Some compounds exerted good inhibitory effects. More importantly, the synthetic iminosugars prolonged the allograft survival in the mouse skin transplantation experiment. Our results provide a lead for further elucidation of the structure–activity relationships and modifications of iminosugars for better immunosuppressive agents.
PMCID: PMC4018160  PMID: 24900363
Iminosugar; immunosuppressive agent; mouse skin allograft; synthesis
7.  Methyl 5-hy­droxy-3-phenyl-1,2-oxazolidine-5-carboxyl­ate 
In the title compound, C11H13NO4, the isoxazolidine ring has an envelope conformation with the O atom as the flap. In the crystal, mol­ecules are liked via N—H⋯O and bifurcated O—H⋯(O,N) hydrogen bonds forming chains propagating along [010]. There are also C—H⋯O inter­actions present.
PMCID: PMC3344639  PMID: 22590401
8.  Computational Study of Coordinated Ni(II) Complex with High Nitrogen Content Ligands 
ISRN organic chemistry  2011;2011:920753.
Density functional computations were performed on two tetracoordinated Ni(II) complexes as high nitrogen content energetic materials (1: dinickel bishydrazine ter[(1H-Tetrazol-3-yl)methan-3yl]-1H-tetrazole and 2: dinickel tetraazide ter[(1H-Tetrazol-3-yl)methan-3yl]-1H-tetrazolate). The geometrical structures, relative stabilities and sensitivities, and thermodynamic properties of the complexes were investigated. The energy gaps of frontier molecular orbital (HOMO and LUMO) and vibrational spectroscopies were also examined. There are minor Jahn-Teller distortions in both complexes 1 and 2, with two long Ni–N bond lengths and two short ones. The enthalpies of combustion for both complexes are over 3600 kJ/mol. The N–N bond lengths in the moieties of hydrazine and azide ligands increase in the coordination process compared to those of the isolated molecules.
PMCID: PMC3765799  PMID: 24052834
9.  The diploid genome sequence of an Asian individual 
Nature  2008;456(7218):60-65.
Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.
PMCID: PMC2716080  PMID: 18987735
10.  Anti-tumor effect of Liqi, a traditional Chinese medicine prescription, in tumor bearing mice 
Liqi, an herbal preparation used in traditional Chinese medicine, has been used to treat cancer in China for centuries. We investigated the anti-tumor effects of liqi and their mechanisms in mice that had been xenografted with tumors.
Sarcoma 180 tumor, Lewis lung carcinoma, and SGC-7901 cells were implanted in BALB/c mice, C57BL/6 mice, and BALB/c nude mice, respectively. Liqi was administered to subgroups of these mice. The tumor weight and size were measured. Cell cycle analysis and T lymphocyte subsets were determined by flow cytometry. The activity of NK cells and TNF was tested using cytotoxicity assay on YAC-1 cells and L929 cells, respectively, and the activity of IL-2 was tested with an IL-2-dependent CTLL-2 cell proliferation assay. Platelet aggregation was monitored by measuring electric impedance, and the levels of thromboxane A2 (TXA2) and prostacyclin (PGI2) in blood were measured by 125I-TXB2 and 125I-Keto-PGF1α radioimmunoassay.
The results showed that liqi inhibited tumor growth in tumor-implanted mice and arrested the cell proliferation in the G0/G1 phase and reduced the portion of cells in S and G2/M phase for SGC-7901 cells. Liqi increased the activity of NK cells and TNF-α, stimulated IL-2 production and activity, and regulated T lymphocyte subpopulations. Liqi inhibited the Lewis lung carcinoma metastasis by inhibiting platelet aggregation and normalizing the balance between TXA2 and PGI2.
All these findings demonstrated that liqi has an anti-tumor effect in vivo. The mechanism may be related to immune regulation and anticoagulation effects.
PMCID: PMC2720913  PMID: 19570195
11.  WEGO: a web tool for plotting GO annotations 
Nucleic Acids Research  2006;34(Web Server issue):W293-W297.
Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many tools have been created for use with the GO ontologies. WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results. Different from other commercial software for creating chart, WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results. WEGO has been used widely in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO, along with the two other tools, namely External to GO Query and GO Archive Query, are freely available for all users at . There are two available mirror sites at and . Any suggestions are welcome at
PMCID: PMC1538768  PMID: 16845012
12.  ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun 
PLoS Computational Biology  2005;1(4):e43.
We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.
Transposable elements (TEs) are a major component of the genomes of multicellular organisms. They are parasitic creatures that invade the genome, insert multiple copies of themselves, and then die. All we see now are the decayed remnants of their ancestral sequences. Reconstruction of these ancestral sequences can bring dead TEs back to life. Algorithms for detecting TEs compare present-day sequences to a library of ancestral sequences. Unknown to many, pervasive use of whole genome shotgun (WGS) methods in large-scale sequencing have made TE reconstructions increasingly problematic. To minimize assembly errors, WGS methods must reject the highly repetitive sequences that characterize most TEs, especially the most recent TEs, which are the least diverged from their ancestral sequences (and most informative for reconstruction). This is acceptable to many, because the most important parts of the genes are not repetitive, but for the TE aficionados, it is a problem. ReAS is a novel algorithm that does TE reconstruction using only the unassembled reads of a WGS. Tested against the WGS for japonica rice, it is shown to produce a library that is superior to the manually curated Repbase database of known ancestral TEs.
PMCID: PMC1232128  PMID: 16184192
14.  The Genomes of Oryza sativa: A History of Duplications 
Yu, Jun | Wang, Jun | Lin, Wei | Li, Songgang | Li, Heng | Zhou, Jun | Ni, Peixiang | Dong, Wei | Hu, Songnian | Zeng, Changqing | Zhang, Jianguo | Zhang, Yong | Li, Ruiqiang | Xu, Zuyuan | Li, Shengting | Li, Xianran | Zheng, Hongkun | Cong, Lijuan | Lin, Liang | Yin, Jianning | Geng, Jianing | Li, Guangyuan | Shi, Jianping | Liu, Juan | Lv, Hong | Li, Jun | Wang, Jing | Deng, Yajun | Ran, Longhua | Shi, Xiaoli | Wang, Xiyin | Wu, Qingfa | Li, Changfeng | Ren, Xiaoyu | Wang, Jingqiang | Wang, Xiaoling | Li, Dawei | Liu, Dongyuan | Zhang, Xiaowei | Ji, Zhendong | Zhao, Wenming | Sun, Yongqiao | Zhang, Zhenpeng | Bao, Jingyue | Han, Yujun | Dong, Lingli | Ji, Jia | Chen, Peng | Wu, Shuming | Liu, Jinsong | Xiao, Ying | Bu, Dongbo | Tan, Jianlong | Yang, Li | Ye, Chen | Zhang, Jingfen | Xu, Jingyi | Zhou, Yan | Yu, Yingpu | Zhang, Bing | Zhuang, Shulin | Wei, Haibin | Liu, Bin | Lei, Meng | Yu, Hong | Li, Yuanzhe | Xu, Hao | Wei, Shulin | He, Ximiao | Fang, Lijun | Zhang, Zengjin | Zhang, Yunze | Huang, Xiangang | Su, Zhixi | Tong, Wei | Li, Jinhong | Tong, Zongzhong | Li, Shuangli | Ye, Jia | Wang, Lishun | Fang, Lin | Lei, Tingting | Chen, Chen | Chen, Huan | Xu, Zhao | Li, Haihong | Huang, Haiyan | Zhang, Feng | Xu, Huayong | Li, Na | Zhao, Caifeng | Li, Shuting | Dong, Lijun | Huang, Yanqing | Li, Long | Xi, Yan | Qi, Qiuhui | Li, Wenjie | Zhang, Bo | Hu, Wei | Zhang, Yanling | Tian, Xiangjun | Jiao, Yongzhi | Liang, Xiaohu | Jin, Jiao | Gao, Lei | Zheng, Weimou | Hao, Bailin | Liu, Siqi | Wang, Wen | Yuan, Longping | Cao, Mengliang | McDermott, Jason | Samudrala, Ram | Wang, Jian | Wong, Gane Ka-Shu | Yang, Huanming
PLoS Biology  2005;3(2):e38.
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.
Comparative genome sequencing of indica and japonica rice reveals that duplication of genes and genomic regions has played a major part in the evolution of grass genomes
PMCID: PMC546038  PMID: 15685292

Results 1-14 (14)