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Min Yao

Publications and source records attributed to Min Yao.

At least 37 records · Page 2Linked to original sources
PubMed2006

LAFIRE: software for automating the refinement process of protein-structure analysis.

Manual intervention is usually required in the multiple rounds of refinement of protein crystal structures, including linking and/or extending the fragments of the initial model and rebuilding (fitting) ill-matched residues using computer-graphics software. Such manual modification is both time-consuming and requires a great deal of expertise in crystallography. Consequently, the refinement process becomes the bottleneck for high-throughput structure analysis. A program, Local correlation coefficient-based Automatic FItting for REfinement (LAFIRE), has been developed to achieve manual intervention-free refinement. This program was designed to perform the entire process of protein structural refinement automatically using the refinement programs CNS1.1 (CNS v.1.1) or REFMAC5. The automatic process begins from an initial model, which can be approximate, fragmentary or even only main-chain, and refines it to the final model including water molecules, controlled by monitoring the R(free) factor. More than 30 structures have now been refined successfully in a fully or semi-automatic manner within a few hours or days using LAFIRE.

Animals↗
PubMed2006

Comparison of short- and mid-term outcomes between CYPHER and TAXUS stents in patients with complex lesions of the coronary arteries.

BACKGROUND: Drug-eluting stent (DES) could obviously reduce in-stent restenosis, which has been proved by international multi-center clinical trials. However, the types of the lesions for stenting were highly selected in these trials. Up to now, there has been no large scale study on the effect of DES in treating complex lesions in real world. Although REALITY trial was just reported during American College of Cardiology Congress 2005, the entry criteria for lesions were limited to one or two de novo lesions. This study was conducted to compare the short- and mid-term clinical outcomes between sirolimus-eluting stent (CYPHER stent) and paclitaxel-eluting stent (TAXUS stent) in patients with complex lesion. METHODS: This is a retrospective study. From April 2002 to June 2004, a total of 1061 patients were treated with DES in Fu Wai Hospital, of which, 611 patients (642 lesions with 698 CYPHER stents) were in CYPHER group, and 450 patients (534 lesions with 600 TAXUS stents) were in TAXUS group. There was no significant difference in clinical data and lesion types between CYPHER group and TAXUS group. RESULTS: Success rates of stent implantation were 99.2% and 98.8% in CYPHER and TAXUS stent groups respectively. The major adverse cardiac events (MACE) during in-hospital and 6-8-month follow-up were 0.7% and 2.3% in CYPHER stent group versus 1.3% and 3.2% in TAXUS stent group. There was no significant difference in MACE rate between these two groups. Restenosis rate was a little higher in TAXUS stent group than that in CYPHER stent group (14.0% vs 7.3%), but there was no significant difference. The incidence of acute occlusion of side branch after implanting DES in main vessel was 6.9% in CYPHER group and 11.9% in TAXUS group (P < 0.05). CONCLUSIONS: CYPHER and TAXUS DES were safe and effective in patients with complex lesion. Clinical outcomes of CYPHER stent were better than TAXUS stent in bifurcation lesions. There was an increasing tendency in restenosis rate and late thrombosis in TAXUS group as compared with that of CYPHER group.

Coronary Disease↗
PubMed2006

Changing failure patterns in oropharyngeal squamous cell carcinoma treated with intensity modulated radiotherapy and implications for future research.

OBJECTIVE: Review the University of Iowa experience with intensity modulated radiation treatment (IMRT) in oropharyngeal squamous cell carcinoma. METHODS: From January 2000 to July 2004, 66 patients with oropharyngeal cancer were treated with IMRT, 62 with definitive IMRT and 4 postoperative IMRT. Three target volumes (CTV1, CTV2, and CTV3) were defined. The prescribed doses to CTV1, CTV2, and CTV3 were 70 to 74 Gy, 60 Gy, and 54 Gy, respectively, for definitive IMRT, and 60 to 66 Gy, 60 Gy, and 54 Gy, respectively, for postoperative IMRT. RESULTS: Median follow-up was 27.3 months and all living patients had a follow-up of at least 11.5 months. The 3-year estimate of locoregional progression free survival was 98.8%. However, there is a high incidence of distant metastasis with a 3-year estimate of distant metastasis-free survival of 80.4%. In addition, there is a high incidence of second primary tumor. The 3-year overall survival and 3-year disease-free survival were 78.1% and 64.4%, respectively. Treatment was well tolerated with 1 death resulting from treatment toxicity. CONCLUSIONS: IMRT offers an excellent locoregional control for oropharyngeal cancer patients. Failure patterns have changed with an increased portion of patients who failed distantly, either with metastasis or second primary tumor. Therefore, survival for these patients is still poor. Future research should focus on identifying patients at high risk of distant diseases and developing effective systemic treatment and prevention for distant diseases.

Adult↗
PubMed2006

A molecular mimic demonstrates that phosphorylated human prolactin is a potent anti-angiogenic hormone.

S179D prolactin (PRL) is an experimentally useful mimic of naturally phosphorylated human prolactin. S179D PRL, but not unmodified PRL, was found to be anti-angiogenic in both the chorioallantoic membrane and corneal assays. Further investigation using human endothelial in vitro models showed reduced cell number, reduced tubule formation in Matrigel, and reduced migration and invasion, as a function of treatment with S179D PRL. Analysis of growth factors in human endothelial cells in response to S179D PRL showed: a decreased expression or release of endogenous PRL, heme-oxygenase-1, basic fibroblast growth factor (bFGF), angiogenin, epidermal growth factor and vascular endothelial growth factor; and an increased expression of inhibitors of matrix metalloproteases. S179D PRL also blocked signaling from bFGF in these cells. We conclude that this molecular mimic of a pituitary hormone is a potent anti-angiogenic protein, partly as a result of its ability to reduce utilization of several well-established endothelial autocrine growth loops, partly by its ability to block signaling from bFGF and partly because of its ability to decrease endothelial migration. These findings suggest that circulating levels of phosphorylated PRL may influence the progression of cancer and, furthermore, that S179D PRL may be a useful anti-angiogenic therapeutic.

Angiogenesis Inhibitors↗
PubMed2006

Crystallization and preliminary X-ray studies of the DNA-binding domain of hepatocyte nuclear factor-6alpha complexed with DNA.

Hepatocyte nuclear factor 6 (HNF-6)/OC-1, a part of liver-enriched transcription factor, controls pancreas and liver development and regulates expression of several hepatic genes. DNA-binding region of HNF-6alpha bound to a 14-mer DNA fragment has been crystallized by the hanging drop vapor diffusion method. The crystals belong to space group P2 with unit cell parameters of a = 73.0 A, b = 39.0 A, c = 106.5 A, beta = 107.6 degrees. X-ray diffraction data were collected to 2.0 A resolution.

Base Sequence↗
PubMed2006

[Clinical outcomes of treating bifurcation lesions with two drug-eluting stent techniques].

OBJECTIVE: To evaluate the clinical outcomes of treating bifurcation lesions with two drug-eluting stent (DES) techniques. METHODS: From October 2003 to February 2005, Seventy-one patients with 72 bifurcation lesions (the ostium of side branch > 2.5 mm in diameter) were treated by two DES. Forty-five of the bifurcation lesions were located in LAD/Diagonal (62.5%), 20 in distal left main coronary arteries (27.8%), 6 in LCX/OM (8.3%) and 1 distal RCA (1.4%). The Crush or modified Crush technique was used in 42, "T" technique in 19, modified "Y" technique in 5, "V" technique in 3 and Culotta technique in 3 bifurcation lesions, respectively. Fifty-nine Cypher or Cypher Select stents, 48 TAXUS stents, 25 Firebird stents and 24 bare metal stents were used for 144 lesions. Final kissing balloon inflation was performed in 60 bifurcation lesions (83.3%) after stenting procedure. RESULTS: Success rate of PCI procedure for the bifurcation lesions was 100%. One patient developed subacute stent thrombosis and underwent successful urgent revascularization. In-hospital major adverse cardiac events (MACE, death, AMI, revascularization) rate was 1.4% (1/71). Six months follow-up was made in 16 patients. No death and AMI occurred during the follow-up period in these patients. Total occlusion in ostium of the diagonal vessel was found in one patient with LAD/Diagonal bifurcation lesion 6 months post procedure. MACE rate during the follow-up was 6.3% (1/16). CONCLUSION: This study showed that the use of two DES techniques for the treatment of bifurcation lesions was safe and effective. The short-term outcome for this strategy was very satisfactory and primary data of 6-month follow-up also showed satisfactory results.

Adult↗
PubMed2006

[A randomized comparative study of using enoxaparin or UFH adjunctive to percutaneous coronary intervention in patients with CHD (ROUTE)].

OBJECTIVE: To evaluate the efficacy and safety of using Enoxaparin instead of UFH for patients with coronary heart disease (CHD) underwent coronary angiogram with or without percutaneous coronary intervention (PCI). METHODS: From Oct. 2003 to Feb. 2005, 966 patients with CHD underwent coronary angiogram (CAG) were randomized to receive enoxaparin (1 mg/kg subcutaneously, Q12 h, at least twice before CAG and the sheath was withdrawn immediately after the procedure, n = 484) or UFH (25 mg, iv, before CAG with additional 65 mg iv if PCI indicated and the sheath was withdrawn 4 hours after the procedure, n = 482). RESULTS: (1) PCI was not performed in 511 patients due to mild lesions or patients were suitable for CABG. In 455 patients underwent PCI (227 in enoxaparin and 228 in UFH group), 1 patient in enoxaparin group developed acute thrombosis and resulted in AMI during PCI and underwent successful urgent revascularization. The incidence of in-hospital major adverse cardiac events were 0.44% in the enoxaparin group and 0 in the UFH group. (2) Hematoma at the puncture site happened in 8 patients (3.5%) in enoxaparin group and in 20 patients (8.8%, P < 0.05) in UFH group. (3) One patient had AMI caused by subacute thrombosis in UFH group during 1 month follow-up. CONCLUSIONS: Our results suggest that the effects and safety are comparable for enoxaparin and UFH, it is also safe and efficient to give enoxaparin at least twice before CAG/PCI and the sheath can be withdrawn immediately after PCI. For ACS patients received more than twice enoxaparin and the last dose was given within 8 hours before PCI, PCI could be performed directly without additional UFH.

Angioplasty, Balloon, Coronary↗
PubMed2006

Abnormal expression of HSP gp96 associated with HBV replication in human hepatocellular carcinoma.

BACKGROUND: Heat shock protein (HSP) gp96 is a member of the HSP90 family and presumably overexpresses as a result of stimulation by mutated or abnormal proteins. Its abnormal expression correlates with carcinogenesis, progression and prognosis of hepatocellular carcinoma (HCC). In this study, we investigated the pathological characteristics of liver gp96 expression and its relationship with hepatitis B virus (HBV) replication in HCC patients. METHODS: Tumor specimens were prospectively collected from 30 HCC patients undergoing liver resection. Total RNAs were extracted from HCC or their non-cancerous tissues. The distribution of gp96 expression in hepatocytes was investigated by streptavidin peroxidase (S-P) immunohistochemistry and tissue HBV-DNA was detected by the in situ molecular hybridization technique. The association of gp96 expression with HBV replication, and the histopathological characteristics of HCC were analyzed. RESULTS: The gp96 was strongly expressed in HCC (73.3%, 22 of 30) and weakly (46.7%, 14 of 30) in non-cancerous tissues. The gp96 expression in HCC tissues was correlated with degree of tumor differentiation and tumor size, but not with tumor number (P>0.05). Immunohistochemical analysis showed that 17 of 19 HCC patients with HBV-DNA-positive were strongly expressed for gp96, whereas only 5 of 11 patients with HBV-DNA-negative were positive for gp96. A significant difference was found between the two groups (89.5% vs. 45.5%, P<0.05). CONCLUSIONS: The abnormal expressions of HSP gp96 in HCC tissues are associated with HBV replication. This finding indicates that HBV infection plays an important role in the development of HCC.

Adult↗
PubMed2005

Elemene displays anti-cancer ability on laryngeal cancer cells in vitro and in vivo.

PURPOSE: The goal of this study is to investigate the inhibitory effects and mechanism of elemene on the growth of laryngeal cancer cells in vitro and in vivo. METHODS: Laryngeal cancer cells (HEp-2 cells) were grown in elemene, cisplatin, or a combination of the drugs. The cytotoxic, or apoptotic, effects of elemene on the cells were evaluated by a 3-[4,5-dimethylthiazol-2yl]-2,5-diphenyltetrazolium bromide assay, flow cytometry, and a caspase-3 activity assay. A Western blot was used to semi-quantify the protein expression of eukaryotic initiation factors (eIF4E and eIF4G), basic fibroblast growth factor (bFGF), and vascular endothelial growth factor (VEGF); RT-PCR analysis semi-quantified the mRNA transcript expression of bFGF and VEGF. The HEp-2 cells were transplanted subcutaneously to BALB/c nude mice to produce solid tumors. Elemene and cisplatin were administered to the mice either as individual drugs or in combination. The tumors were excised and immunostained to determine the effect each drug had on tumor size, eIF levels, angiogenic factors, and microvessel density (MVD). RESULTS: Elemene inhibited the growth of HEp-2 cells in vitro in a dose- and time-dependent manner with an IC(50) of 346.5 microM (24 h incubation). Increased apoptosis was observed in elemene-administered cells. Elemene is suspected to enhance caspase-3 activity, and thus inhibit protein expression of eIFs (4E, 4G), bFGF, and VEGF. In vivo, the growth of HEp-2 cell-transplanted tumors in nude mice was inhibited by intraperitoneal injection of elemene. Compared with control groups, elemene significantly inhibited the protein expression of eIFs (4E and 4G), bFGF, and VEGF and decreased the MVD. CONCLUSIONS: Elemene inhibits the growth of HEp-2 cells in vitro and in vivo. These data provide useful information for further clinical study on the treatment of LSCC by elemene.

Animals↗
PubMed2005

Intensity-modulated radiation treatment for head-and-neck squamous cell carcinoma--the University of Iowa experience.

PURPOSE: To review the University of Iowa experience with intensity-modulated radiotherapy (IMRT) in the treatment of head-and-neck squamous cell carcinoma. METHODS AND MATERIALS: From October 1999 to April 2004, 151 patients with head-and-neck squamous cell carcinoma were treated with IMRT for curative intent. One patient was lost to follow-up 2 months after treatment and therefore excluded from analysis. Of the remaining 150 patients, 99 were treated with definitive IMRT, and 51 received postoperative IMRT. Sites included were nasopharynx, 5; oropharynx, 56; larynx, 33; oral cavity, 29; hypopharynx, 8; nasal cavity/paranasal sinus, 8; and unknown primary, 11. None of the patients treated with postoperative IMRT received chemotherapy. Of 99 patients who had definitive IMRT, 68 patients received concurrent cisplatin-based chemotherapy. One patient received induction cisplatin-based chemotherapy, but no concurrent chemotherapy was given. Three clinical target volumes (CTV1, CTV2, and CTV3) were defined. The prescribed doses to CTV1, CTV2, and CTV3 in the definitive cohort were 70-74 Gy, 60 Gy, and 54 Gy, respectively. For high-risk postoperative IMRT, the prescribed doses to CTV1, CTV2, and CTV3 were 64-66 Gy, 60 Gy, and 54 Gy, respectively. For intermediate-risk postoperative IMRT, the prescribed doses to CTV1, CTV2, and CTV3 were 60 Gy, 60 Gy, and 54 Gy. RESULTS: The median follow-up was 18 months (range, 2-60 months). All living patients were followed for at least 6 months. There were 11 local-regional failures: 7 local failures, 3 regional failures, and 1 failure both in the primary tumor and regional lymph node. There were 16 patients who failed distantly, either with distant metastasis or new lung primaries. The 2-year overall survival, local progression-free survival, locoregional progression-free survival, and distant disease-free survival rates were 85%, 94%, 92%, and 87%, respectively. The median time from treatment completion to local-regional recurrence was 4.7 months (range, 1.8 to 15.6 months). Only one marginal failure was noted in a patient who had extensive tonsil cancer with tumor extension into the orbit and cavernous sinus. Patients with oropharyngeal cancer did significantly better than patients with oral cavity and laryngeal cancer, with a 2-year local-regional control rate of 98%, compared with 78% for oral cavity cancer and 85% for laryngeal cancer (p = 0.005). There was no significant difference in local-regional control for patients who received postoperative radiation or definitive radiation (p = 0.339) and for patients who had chemotherapy or not (p = 0.402). Neither T stage nor N stage had a significant effect on local-regional control (p = 0.722 and 0.712, respectively). CONCLUSIONS: Our results have confirmed the effectiveness of IMRT in head-and-neck cancer. It offers excellent outcomes in local-regional control and overall survival. More studies are necessary to further improve the outcomes of laryngeal cancer as well as oral cavity cancer.

Adult↗
PubMed2005

Absolute configuration of the hydroxyfarnesylethyl group of haem A, determined by X-ray structural analysis of bovine heart cytochrome c oxidase using methods applicable at 2.8 Angstrom resolution.

The absolute configuration of haem A, the prosthetic group of cytochrome c oxidase, was determined to be S by analysis of the bond angles surrounding the chiral centre of haem A after refinement with X-PLOR starting from respective initial structures with R and S configurations under absolute configuration constraints at 1.8 Angstrom resolution. The same result was obtained by refinement at 1.8 Angstrom resolution without the absolute configuration constraints. Both of these methods were applicable down to a resolution of about 2.8 Angstrom. The constrained refinement converges more quickly than the unconstrained refinement.

Animals↗
PubMed2005

The CGL2612 protein from Corynebacterium glutamicum is a drug resistance-related transcriptional repressor: structural and functional analysis of a newly identified transcription factor from genomic DNA analysis.

The emergence of antibiotic-resistant bacteria often causes serious clinical problems. The TetR family is one of the major transcription factor families that regulate expression of genes involved in bacterial antimicrobial resistance systems. CGL2612 protein is a transcription factor newly identified by genomic DNA analysis on Corynebacterium glutamicum, which belongs to the mycolic acid-containing Actinomycetales, including the well known pathogens Corynebacterium diphtheriae and Mycobacterium tuberculosis. Crystal structure analysis showed that the CGL2612 protein exhibits significant structural similarity to the multidrug resistance (MDR)-related transcription factor QacR from Staphylococcus aureus, despite poor amino acid sequence similarity between these proteins. Binding DNA sequence analysis of CGL2612 protein using the systematic evolution of ligands by the exponential enrichment (systematic evolution of ligands by exponential enrichment, or SELEX) method revealed that this protein is a new member of the TetR family, which regulates expression of the immediately upstream gene, cgl2611, probably encoding a major facilitator superfamily permease. Subsequent functional analyses confirmed a function of the CGL2612 as a transcriptional repressor responsible for the antimicrobial resistance system in C. glutamicum. The strategy used in the present study is one of the most convenient and powerful methods to analyze functionally unknown transcription factors, and the results obtained here will contribute to our understanding of the drug resistance mechanism not only in C. glutamicum but also in the related bacteria, C. diphtheriae and M. tuberculosis.

Amino Acid Sequence↗
PubMed2005

Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P protein Rpp21.

Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the removal of 5' leader sequences from tRNA precursors (pre-tRNA). The human protein Rpp21 is essential for human RNase P activity in tRNA processing in vitro. The crystal structure of Ph1601p from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, the archaeal homologue of Rpp21, was determined using the multiple anomalous dispersion (MAD) method with the aid of anomalous scattering in zinc and selenium at 1.6 A resolution. Ph1601p comprises an N-terminal domain (residues 1-55), a central linker domain (residues 56-79), and a C-terminal domain (residues 80-120), forming an L-shaped structure. The N-terminal domain consists of two long alpha-helices, while the central and C-terminal domains fold in a zinc ribbon domain. The electrostatic potential representation indicates the presence of positively charged clusters along the L arms, suggesting a possible role in RNA binding. A single zinc ion binds the well-ordered binding site that consists of four Cys residues (Cys68, Cys71, Cys97, and Cys100) and appears to stabilize the relative positions of the N- and C-domains. Mutations of Cys68 and Cys71 or Cys97 and Cys100 to Ser destabilize the protein structure, which results in inactivation of the RNase P activity. In addition, site-directed mutagenesis suggests that Lys69 at the central loop and Arg86 and Arg105 at the zinc ribbon domain are strongly involved in the functional activity, while Arg22, Tyr44, Arg65, and Arg84 play a modest role in the activity.

Amino Acid Sequence↗
PubMed2005

[Short and long-term therapeutic effects of rapamycin-eluting stent and paclitaxel-eluting stent in treatment of coronary disease with complicated lesions].

OBJECTIVE: To compare the short and long-term clinical outcomes of rapamycin (sirolimus)-eluting stent (DES) (CYPHER stent) and paclitaxel-DES (TAXUS stent) in treatment of coronary heart disease (CHD) patients with complicated lesions. METHODS: 611 CHD patients with 642 lesions, were treated with 698 CYPHER stents, and 450 sex, age, clinical data and lesion type-matched patients, with 534 lesions, were treated with 600 TAXUS stents by means of percutaneous coronary intervention. The short and long term outcomes were compared between these 2 groups. RESULTS: The success rate of stent implantation was 99.2% (606/611) and 98.8% (445/450) in the CYPHER stent and TAXUS stent groups respectfully. The overall rate of major cardiac events, including death, acute myocardial infarction (AMI) target lesion revascularization (TLR), and major adverse cardiac event (MACE), during hospitalization and 6 - 8 month' follow-up were 0.65% and 2.3% in the CYPHER stent group, not significantly different from those of the TAXUS stent group (1.3% and 3.2% respectively). The restenosis rate of the TAXUS stent group was 7.3%, a little higher than that of the CYPHER stent group (14%), but without significant difference. CONCLUSION: CYPHER and TAXUS DES are both safe and effective in CHD patients with complicated lesions. There is an increasing tendency of restenosis rate in the TAXUS stent group in comparison with the CYPHER stent.

Angioplasty, Balloon, Coronary↗
PubMed2005

The role of FDG PET in management of neck metastasis from head-and-neck cancer after definitive radiation treatment.

PURPOSE: The role of neck dissection after definitive radiation for head-and-neck cancer is controversial. We select patients for neck dissection based on postradiation therapy (post-RT), computed tomography (CT), and [18F] fluorodeoxyglucose positron emission tomography (FDG PET). We summarize the clinical outcomes of patients treated with this policy to further elucidate the role of FDG PET in decision making for neck dissection after primary radiotherapy. METHODS AND MATERIALS: Between December 1999 and February 2004, 53 eligible patients were identified. These patients had stage N2A or higher head-and-neck squamous cell carcinoma and had complete response of the primary tumor after definitive radiation with or without chemotherapy. PET or computed tomography (CT) scans were performed within 6 months after treatment. Neck dissection was performed in patients with residual lymphadenopathy (identified by clinical examination or CT) and a positive PET scan. Those without residual lymph nodes and a negative PET were observed without neck dissection. For patients with residual lymphadenopathy, but a negative PET scan, neck dissection was performed at the discretion of the attending surgeon and decision of the patient. There was a total of 70 heminecks available for analysis (17 patients had bilateral neck disease). RESULTS: There were 21 heminecks with residual lymphadenopathy identified on CT imaging or clinical examination and negative PET. Of these, 4 had neck dissection and were pathologically negative. The remaining 17 were observed without neck dissection. There was a total of 42 heminecks without residual lymph nodes on post-RT CT imaging or clinical examination with a negative PET. They were also observed without neck dissection. Seven heminecks had a positive PET scan and residual lymphadenopathy. Six of them had neck dissection and 1 had fine-needle aspiration of a residual node; 3 contained residual viable cancer and 4 were pathologically negative. At median follow up of 26 months (range, 12-57 months), no regional failure was identified. The negative predictive value of PET was 100% and positive predictive value was 43%. CONCLUSION: For patients who have no evidence of residual lymphadenopathy and a negative FDG PET scan 12 weeks after definitive radiation, neck dissection can be safely withheld. Even in cases in which small residual lymphadenopathy was observed, regional recurrences have not occurred when the post-RT PET scan was negative and neck dissection was withheld. For patients with large residual lymphadenopathy (greater than 2.0-3.0 cm in size) but a negative post-RT FDG PET, further studies with longer follow-up are necessary to determine the appropriateness of withholding neck dissection.

Adult↗