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Yang Zhang

Publications and source records attributed to Yang Zhang.

At least 109 records · Page 6Linked to original sources
PubMed2004

Application and evaluation of two air quality models for particulate matter for a southeastern U.S. episode.

The Models-3 Community Multiscale Air Quality (CMAQ) Modeling System and the Particulate Matter Comprehensive Air Quality Model with extensions (PMCAMx) were applied to simulate the period June 29-July 10, 1999, of the Southern Oxidants Study episode with two nested horizontal grid sizes: a coarse resolution of 32 km and a fine resolution of 8 km. The predicted spatial variations of ozone (O3), particulate matter with an aerodynamic diameter less than or equal to 2.5 microm (PM2.5), and particulate matter with an aerodynamic diameter less than or equal to 10 microm (PM10) by both models are similar in rural areas but differ from one another significantly over some urban/suburban areas in the eastern and southern United States, where PMCAMx tends to predict higher values of O3 and PM than CMAQ. Both models tend to predict O3 values that are higher than those observed. For observed O3 values above 60 ppb, O3 performance meets the U.S. Environmental Protection Agency's criteria for CMAQ with both grids and for PMCAMx with the fine grid only. It becomes unsatisfactory for PMCAMx and marginally satisfactory for CMAQ for observed O3 values above 40 ppb. Both models predict similar amounts of sulfate (SO4(2-)) and organic matter, and both predict SO4(2-) to be the largest contributor to PM2.5. PMCAMx generally predicts higher amounts of ammonium (NH4+), nitrate (NO3-), and black carbon (BC) than does CMAQ. PM performance for CMAQ is generally consistent with that of other PM models, whereas PMCAMx predicts higher concentrations of NO3-, NH4+, and BC than observed, which degrades its performance. For PM10 and PM2.5 predictions over the southeastern U.S. domain, the ranges of mean normalized gross errors (MNGEs) and mean normalized bias are 37-43% and -33-4% for CMAQ and 50-59% and 7-30% for PMCAMx. Both models predict the largest MNGEs for NO3- (98-104% for CMAQ 138-338% for PMCAMx). The inaccurate NO3- predictions by both models may be caused by the inaccuracies in the ammonia emission inventory and the uncertainties in the gas/particle partitioning under some conditions. In addition to these uncertainties, the significant PM overpredictions by PMCAMx may be attributed to the lack of wet removal for PM and a likely underprediction in the vertical mixing during the daytime.

Air Pollutants↗
PubMed2004

Application of sparse NMR restraints to large-scale protein structure prediction.

The protein structure prediction algorithm TOUCHSTONEX that uses sparse distance restraints derived from NMR nuclear Overhauser enhancement (NOE) data to predict protein structures at low-to-medium resolution was evaluated as follows: First, a representative benchmark set of the Protein Data Bank library consisting of 1365 proteins up to 200 residues was employed. Using N/8 simulated long-range restraints, where N is the number of residues, 1023 (75%) proteins were folded to a C(alpha) root-mean-square deviation (RMSD) from native <6.5 A in one of the top five models. The average RMSD of the models for all 1365 proteins is 5.0 A. Using N/4 simulated restraints, 1206 (88%) proteins were folded to a RMSD <6.5 A and the average RMSD improved to 4.1 A. Then, 69 proteins with experimental NMR data were used. Using long-range NOE-derived restraints, 47 proteins were folded to a RMSD <6.5 A with N/8 restraints and 61 proteins were folded to a RMSD <6.5 A with N/4 restraints. Thus, TOUCHSTONEX can be a tool for NMR-based rapid structure determination, as well as used in other experimental methods that can provide tertiary restraint information.

Algorithms↗
PubMed2004

Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins.

We evaluate tertiary structure predictions on medium to large size proteins by TASSER, a new algorithm that assembles protein structures through rearranging the rigid fragments from threading templates guided by a reduced Calpha and side-chain based potential consistent with threading based tertiary restraints. Predictions were generated for 745 proteins 201-300 residues in length that cover the Protein Data Bank (PDB) at the level of 35% sequence identity. With homologous proteins excluded, in 365 cases, the templates identified by our threading program, PROSPECTOR_3, have a root-mean-square deviation (RMSD) to native < 6.5 angstroms, with >70% alignment coverage. After TASSER assembly, in 408 cases the best of the top five full-length models has a RMSD < 6.5 angstroms. Among the 745 targets are 18 membrane proteins, with one-third having a predicted RMSD < 5.5 A. For all representative proteins less than or equal to 300 residues that have corresponding multiple NMR structures in the Protein Data Bank, approximately 20% of the models generated by TASSER are closer to the NMR structure centroid than the farthest individual NMR model. These results suggest that reasonable structure predictions for nonhomologous large size proteins can be automatically generated on a proteomic scale, and the application of this approach to structural as well as functional genomics represent promising applications of TASSER.

Algorithms↗
PubMed2004

Phloridzin improves hyperglycemia but not hepatic insulin resistance in a transgenic mouse model of type 2 diabetes.

The chronic hyperglycemia that occurs in type 2 diabetes may cause deterioration of beta-cell function and insulin resistance in peripheral tissues. Mice that express a dominant-negative IGF-1 receptor, specifically in skeletal muscle (MKR mice), exhibit severe insulin resistance, hyperinsulinemia, dyslipidemia, and hyper-glycemia. To determine the role of hyperglycemia in the worsening of the diabetes state in these animals, MKR mice were treated with phloridzin (PHZ), which inhibits intestinal glucose uptake and renal glucose reabsorption. Blood glucose levels were decreased and urine glucose levels were increased in response to PHZ treatment in MKR mice. PHZ treatment also increased food intake in MKR mice; however, the fat mass was decreased and lean body mass did not change. Serum insulin, fatty acid, and triglyceride levels were not affected by PHZ treatment in MKR mice. Hyperinsulinemic-euglycemic clamp analysis demonstrated that glucose uptake in white adipose tissue was significantly increased in response to PHZ treatment. Despite the reduction in blood glucose following PHZ treatment, there was no improvement in insulin-stimulated whole-body glucose uptake in MKR mice and neither was there suppression of endogenous glucose production by insulin. These results suggest that glucotoxicity plays little or no role in the worsening of insulin resistance that occurs in the MKR mouse model of type 2 diabetes.

Adipose Tissue↗
PubMed2004

[Regulation of CD3, CD4 and CD8 expressions on PMA-activated human peripheral T cells].

OBJECTIVE: To investigate the effect of mitogen Phorbol 12-myristate 13-Acetate (PMA) on CD3, CD4 and CD8 expression of human T-lymphocytes. METHODS: Peripheral blood mononuclear cells from 37 blood samples stimulated in vitro with PMA at different concentrations (2,5,10,20 and 50 ng/ml for 4 hours) and time (10 ng/ml for 2,4 and 6 hours) were analyzed by 4-color flow cytometry (FCM). RESULTS: Under different PMA stimulation protocols,significant CD4 down-regulation was observed,which was negatively correlated with intracellular cytokine secretion (r= 0.601,P<.001), except for PMA stimulation at 10 ng/ml for 2-hours which showed no significant intracellular cytokine secretion. The expressions of CD3 and CD8 molecules after PMA activation were not significantly affected as compared with pre-activation. Among CD3 positive T lymphocytes, CD4/CD8 double-negative cells only account for 5.52%. CONCLUSION: PMA has a significant down-regulation effect on CD4 molecules of Th cells, without altering the CD3 and CD8 expression. For quantitative analysis of Th1/Th2 variation, indirect method such as CD3(+)CD8( ) T cells can be used to define CD4(+) Th cells stimulated by PMA in the future.

CD3 Complex↗
PubMed2004

[The study of illusion in flight on flight pilots].

OBJECTIVE: To observe the characteristics of illusion in flight in fighter pilots. METHOD: A survey about illusion in flight was performed in 81 pilots who were under physical examination for modification to equipment of high performance aircraft. RESULT: 1. Among 81 pilots, there were history of illusion in flight in 91.4% (74/81) cases. There were history of inclination illusion in 74 cases, rotation illusion in 1 case, inversion illusion in 1 case and pitch illusion in 1 case. 2. Among the 74 cases, 85.1% (63/74) claim relations with flying subjects, 81.1% (60/74) with distribution of attention, 74.3% (55/74) with light, 73.0% (54/74) with distribution of cloud layer, 71.6% (53/74) with visibility, 67.6%(50/74) with fatigue, 54.1% (40/74) with suspension of flying and 2.7%(2/74) with other factors. When illusion in flight appeared, 70 cases could easily overcome it, 4 cases felt a little difficult, but all 74 cases did not lead aircraft accident or potential accident. CONCLUSION: Instructions in health about illusion in flight have made a considerably positive achievement in airman troops, but it must be continually paid more attention, and meanwhile, the space orientation system of aircraft must be improved.

Adult↗
PubMed2004

[The expression of mTOR and its substrates in oral squamous cell carcinoma].

OBJECTIVE: The aim of this study was to observe the expression of mTOR (mammalian target of rapamycin) and its substrates in oral squamous cell carcinoma. METHODS: mTOR and its substrates alpha1, alpha2, beta1, beta2 isoforms of p70 S6 kinase (p70S6k) and 4EBP1 were examined by means of RT-PCR, Western-blot test. RESULTS: The result of RT-PCR showed that in poorly differentiated tissue, the expression level of mTOR and its substrates alpha1, alpha2, beta1, beta2 isoforms of p70S6k increased obviously, while that of 4EBP1 decreased, while that in well differentiated tissue was second to it, the normal oral tissue was the last. The expression of Western-blot was the same as the RT-PCR. CONCLUSION: The expression of mTOR and its substrates differs in different types of oral squamous cell carcinoma. The result suggests that mTOR, p70S6K and 4EBP1 might play important roles in oral squamous cell carcinoma. It may be an important target protein to treat tumor in the future.

Adaptor Proteins, Signal Transducing↗
PubMed2004

[Cloning of human angiogenesis inhibitor METH1 and its expression in mammalian cells].

OBJECTIVE: To get the full length of human METH1 cDNA and express it steadily in mammalian cell stably. METHODS: METH1 was amplified by RT-PCR, and cloned into pCDNA3.0 after confirmed by sequence analysis. HepG2 cells were transfected by Lipofectamine reagent and then selected in medium with G418. The expression level of METH1 was detected by RT-PCR and Western blot. RESULTS: METH1 with expected length was effectively amplified, and completely matched the published sequence of encoding mature peptide [GI:5725505] as shown by sequence analysis. Eukaryotic vector expressing METH1 was obtained by gene cloning, cells expressing METH1 was got by selection with G418 at 3 weeks after transfection. RT-PCR and Western blot showed high level expression of METH1. CONCLUSION: Full length of human METH1 gene is cloned successfully and expressed in HepG2 steadily, The results set up a basis for the study of effects of METH1 on hypertrophic scar angiogenesis.

ADAM Proteins↗
PubMed2004

[Effect of fluorided etching fluid on the shear bond strength and the deposition on the surface of enamel.].

PURPOSE: The aim of this study was to find the best concentration of fluorided etching acid in the dental clinic which had both the best shear bond strength and the maximal anti-caries effect. METHODS: 84 extracted human premolars were divided into four groups of 21 teeth each. The enamel of each group was conditioned with 35% phosphoric acid containing 0%, 1.23%, 2%, 3% NaF. The shear bond strength was tested by bond strength machine and the enamel morphology was observed by scanning electron microscopy at once, 1 week, 4 weeks, 12 weeks, 24 weeks after etching. The shear bond strength was statistically analyzed by SPSS10.0 software. RESULTS: The shear bond strength of the group whose acid containing 3% NaF was less than the others significantly (P<0.05); and there was no significant difference among the other groups (P>0.05). The amount of the deposition on the surface of enamel after etching was increased with the time after etching and the concentration of NaF increasing. CONCLUSIONS: 2% NaF added to 35% phosphoric acid has both the best bond strength and the best effect of preventing enamel from caries.

Acid Etching, Dental↗
PubMed2004

Circulating IGF-1 and its role in cancer: lessons from the IGF-1 gene deletion (LID) mouse.

Recent epidemiological studies have suggested a statistical connection between serum IGF-1 levels in the upper quartile of the normal range and the relative risk of developing certain cancers. Our studies have focused on mouse models where circulating IGF-1 levels are reduced, while tissue expression of IGF-1 is normal. These mice show a lower risk for the development of colon and breast cancers and metastases when compared with control mice, and lend support to the hypothesis that circulating IGF-1 may be linked to cancer cell growth.

Animals↗
PubMed2004

[Gemcitabine plus cisplatin versus gemcitabine plus vinorelbine in treatment of advanced non-small cell lung cancer (NSCLC)].

BACKGROUND & OBJECTIVE: Although platin-based chemotherapy has become a standard treatment for non-small cell lung cancer (NSCLC), its severe toxicities limit clinical application, and a new replacement is required. The study was to evaluate the efficacy, survival rate and toxicity between the combination of gemcitabine and cisplatin (GP arm) and the combination of gemcitabine and vinorelbine (GN arm) in the treatment of advanced NSCLC. METHODS: Eighty-two patients with locally advanced or metastatic NSCLC were enrolled into this study. 42 patients and 40 patients were randomized into GP group and GN group respectively. The patients' characteristics were similar between the two groups. They were treated with gemcitabine (1 000 mg/m(2) d(1), d(8)) plus cisplatin (80 mg/m(2), d(1)) in GP group, or gemcitabine plus vinorelbine (25 mg/m(2) d(1), d(8)) in GN group. The chemotherapy was repeated every 3 weeks as a cycle. Every patient was treated two cycles at least. RESULTS: An objective response rate of 28.6% was observed in GP arm versus 25% in GN arm (P=0.346). The 1-year survival rate was 64% in GP arm and 66% in GN arm. The median survival time was 9.87 months for GN arm and 8.78 months for GP arm. Nausea and vomiting were the major dose-limiting toxicity. The incidence of grade III/IV nausea and vomiting was significantly higher in the GP arm than in the GN arm (P=0.000). The Leukopenia incidence was similar in two groups (P=0.130). CONCLUSION: The efficacy of GN regimen (platinum-free regimen) was similar to that of GP regimen, but the toxicity of GN regimen is lighter than that of GP regimen.

Adenocarcinoma↗
PubMed2004

[Phase III randomized clinical trial of intratumoral injection of E1B gene-deleted adenovirus (H101) combined with cisplatin-based chemotherapy in treating squamous cell cancer of head and neck or esophagus].

BACKGROUND & OBJECTIVE: H101 is an E1B-55 kDa gene-deleted replication-selective adenovirus, which showed a significant antitumor activity. This study was to compare effects and toxicities of intratumoral H101 injection combined with cisplatin plus 5-fluorouracil (PF) regimen or adriamycin plus 5-fluorouracil (AF) regimen versus PF or AF regimen alone in treating patients with head and neck or esophagus squamous cell cancer. METHODS: A total of 160 patients were recruited. PF regimen (cisplatin 20 mg/m(2) ivgtt, qd x 5d; 5-fluorouracil 500 mg/m(2) ivgtt, qd x 5d) was administered to patients have no history of PF chemotherapy,or sensitive to PF chemotherapy,while AF regimen (adriamycin 50 mg/m(2) iv,d1; 5-fluorouracil 500 mg/m(2) ivgtt, qd x 5d) was administered to patients didn't response to PF regimen. All patients were randomized to either receive intratumoral H101 injection (5.0 x 10(11)-1.5 x 10(12) VP/day for 5 consecutive days every 3 weeks) or not. Treatment repeated every 3 weeks,all patients have to receive at least 2 cycles of chemotherapy. RESULTS: Among 123 accordant patients,overall response rate of PF plus H101 group (group A1) was 78.8% (41/52),of PF alone group (group B1) was 39.6% (21/53),of AF plus H101 group (group A2) was 50.0% (7/14),of AF alone group (group B2) was 50.0% (2/4). Differences of response rates between group A1 and group B1,between group A1+A2 and group B1+B2 were significant (P=0.000). Main side effects were fever (45.7%), injection site reaction (28.3%),and influenza-like symptoms (9.8%). CONCLUSION: Intratumoral H101 injection showed a distinct efficacy in patients with squamous cell cancer of head and neck or esophagus,and was relatively safe.

Adenoviridae↗
PubMed2004

[DMSO arrested hybridoma cells for enhanced antibody production].

Dimethyl sulfoxide (DMSO), a well-known differentiation inducer in several myeloid cells, induces G1 phase arrest in many cell lines. In this study, we investigated the possibility of using DMSO to arrest H18 hybridoma cells to the G1 phase and monitor whether the arrest improves antibody production. We showed that DMSO in concentration ranging between 0.3% and 0.6% efficiently arrested H18 hybridoma cells in G1 phase. In our experiment, > 80% of cells grown for 36h in presence of the 0.6% DMSO were arrested in G1. Furthermore, expression levels of P27 were up-regulated tow fold during the G1 phase. Higher concentration of DMSO at 0.9% leads to cytotoxicity. Herein we show a simple way, a two-stage process for antibody production, which consists of a proliferation phase leading to the desired cell density, followed by an extended production phase during which the cells remain at G1 phase. Our observation that the addition of DMSO results in increase antibody production is of significance in further use of hybridoma cells in high density large scale cell culture.

Animals↗
PubMed2003

TOUCHSTONEX: protein structure prediction with sparse NMR data.

TOUCHSTONEX, a new method for folding proteins that uses a small number of long-range contact restraints derived from NMR experimental NOE (nuclear Overhauser enhancement) data, is described. The method employs a new lattice-based, reduced model of proteins that explicitly represents C(alpha), C(beta), and the sidechain centers of mass. The force field consists of knowledge-based terms to produce protein-like behavior, including various short-range interactions, hydrogen bonding, and one-body, pairwise, and multibody long-range interactions. Contact restraints were incorporated into the force field as an NOE-specific pairwise potential. We evaluated the algorithm using a set of 125 proteins of various secondary structure types and lengths up to 174 residues. Using N/8 simulated, long-range sidechain contact restraints, where N is the number of residues, 108 proteins were folded to a C(alpha)-root-mean-square deviation (RMSD) from native below 6.5 A. The average RMSD of the lowest RMSD structures for all 125 proteins (folded and unfolded) was 4.4 A. The algorithm was also applied to limited experimental NOE data generated for three proteins. Using very few experimental sidechain contact restraints, and a small number of sidechain-main chain and main chain-main chain contact restraints, we folded all three proteins to low-to-medium resolution structures. The algorithm can be applied to the NMR structure determination process or other experimental methods that can provide tertiary restraint information, especially in the early stage of structure determination, when only limited data are available.

Algorithms↗
PubMed2003

BlmIII and BlmIV nonribosomal peptide synthetase-catalyzed biosynthesis of the bleomycin bithiazole moiety involving both in cis and in trans aminoacylation.

Cloning and sequence analysis of the bleomycin (BLM) biosynthetic gene cluster predicted that the two nonribosomal peptide synthetases (NRPSs), BlmIV and BlmIII, are responsible for the biosynthesis of the BLM bithiazole moiety. BlmIV is a seven domain (C(2)-A(2)-PCP(2)-Cy(1)-A(1)-PCP(1)-Cy(0)) NRPS, and BlmIII is a three domain (A(0)-PCP(0)-Ox) NRPS. The three domains of Cy(1)-A(1)-PCP(1) residing on the BlmIV subunit, the four domains of Cy(0) residing on the BlmIV subunit, and A(0)-PCP(0)-Ox residing on the BlmIII subunit constitute the two thiazole-forming NRPS-1 and NRPS-0 modules, respectively. BlmIII-A(0) was predicted to be nonfunctional, raising the question of how the NRPS-0 module activates and loads the Cys substrate to its cognate BlmIII-PCP(0). The NRPS-0 module consists of domains residing on two different subunits, requiring precise protein-protein interaction. Here, we report the production of the BlmIV and BlmIII NRPSs as an excised domain(s), module, or intact subunit form and biochemical characterizations of the resultant enzymes in vitro for their roles in BLM bithiazole biosynthesis. Our results (a) confirm that BlmIII-A(0) is a naturally occurring nonfunctional mutant, (b) demonstrate that BlmIV-A(1) activates Cys and catalyzes both in cis aminoacylation of BlmIV-PCP(1) (for NRPS-1) and in trans aminoacylation of BlmIII-PCP(0) (for NRPS-0), and (c) reveal that the C-terminus of the BlmIV subunit, characterized by the unprecedented AGHDDD(G) and PGHDDG repeats, is absolutely required for in trans aminoacylation of BlmIII-PCP(0). These findings underscore the flexibility and versatility of NRPSs in both structure and mechanism for natural product biosynthesis and provide an outstanding opportunity to study the molecular recognition and protein-protein interaction mechanism in NRPS assembly line enzymology.

Acylation↗
PubMed2003

Solvent-dependent chemoselectivities in Ce(IV)-mediated oxidative coupling reactions.

The oxidative coupling of 1,3-diketones, beta-keto esters, and beta-keto silyl enol ethers with allyl trimethylsilane in the presence of CTAN was investigated. In the case of acyclic diketones and esters, different chemoselectivities were observed in CH(3)CN and CH(2)Cl(2) leading to good yields of allylation and dihydrofuran products, respectively. [reaction: see text]

Journal Article↗
PubMed2003

Mechanistic investigation of substrate oxidation by Ce(IV) reagents in acetonitrile.

Rates and activation parameters for the Ce(4+)-mediated oxidation of a beta-keto ester, a beta-diketone, and a beta-keto silyl enol ether were determined in acetonitrile. In the case of the dicarbonyls, the enol content of the substrate impacts the rate of oxidation by Ce(4+), predominantly through contributions from DeltaH(). For the silyl enol ether, the transition state for oxidation by Ce(4+) is substantially more ordered than it is for the beta-keto ester or the beta-diketone.

Journal Article↗