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Qiang Yang

Publications and source records attributed to Qiang Yang.

18 recordsLinked to original sources

Graph embedding and extensions: a general framework for dimensionality reduction.

Over the past few decades, a large family of algorithms - supervised or unsupervised; stemming from statistics or geometry theory - has been designed to provide different solutions to the problem of dimensionality reduction. Despite the different motivations of these algorithms, we present in this paper a general formulation known as graph embedding to unify them within a common framework. In graph embedding, each algorithm can be considered as the direct graph embedding or its linear/kernel/tensor extension of a specific intrinsic graph that describes certain desired statistical or geometric properties of a data set, with constraints from scale normalization or a penalty graph that characterizes a statistical or geometric property that should be avoided. Furthermore, the graph embedding framework can be used as a general platform for developing new dimensionality reduction algorithms. By utilizing this framework as a tool, we propose a new supervised dimensionality reduction algorithm called Marginal Fisher Analysis in which the intrinsic graph characterizes the intraclass compactness and connects each data point with its neighboring points of the same class, while the penalty graph connects the marginal points and characterizes the interclass separability. We show that MFA effectively overcomes the limitations of the traditional Linear Discriminant Analysis algorithm due to data distribution assumptions and available projection directions. Real face recognition experiments show the superiority of our proposed MFA in comparison to LDA, also for corresponding kernel and tensor extensions.

Algorithms↗

Fourier domain preconditioned conjugate gradient algorithm for atmospheric tomography.

By 'atmospheric tomography' we mean the estimation of a layered atmospheric turbulence profile from measurements of the pupil-plane phase (or phase gradients) corresponding to several different guide star directions. We introduce what we believe to be a new Fourier domain preconditioned conjugate gradient (FD-PCG) algorithm for atmospheric tomography, and we compare its performance against an existing multigrid preconditioned conjugate gradient (MG-PCG) approach. Numerical results indicate that on conventional serial computers, FD-PCG is as accurate and robust as MG-PCG, but it is from one to two orders of magnitude faster for atmospheric tomography on 30 m class telescopes. Simulations are carried out for both natural guide stars and for a combination of finite-altitude laser guide stars and natural guide stars to resolve tip-tilt uncertainty.

Journal Article↗

Modeling, simulation, and open-loop control of a continuous facesheet MEMS deformable mirror.

We introduce a coupled system of nonlinear partial differential equations (PDEs) to model a particular microelectromechanical systems (MEMS) deformable mirror consisting of a continuous facesheet coupled with electrostatic plate-driven actuators. To make the problem computationally tractable, we reduced the system to a single linear PDE for the facesheet coupled with nonlinear algebraic constraints for each of the actuators. We also introduce a nonlinearly constrained quadratic optimization problem for open-loop control of the MEMS mirror. Numerical simulation and control results are presented, and shortcomings of the model are discussed.

Journal Article↗

Wavefront correction with high-order curvature adaptive optics systems.

We demonstrate the existence of higher-order curvature adaptive optics (AO) systems and compare their performance with the current 85-element system being built at the Institute for Astronomy at the University of Hawaii. Simulation results show that systems with in excess of 500 actuators are possible with actuator patterns that are simple extensions of the 85-element design. The attenuation of residual phase error within the Nyquist frequency of the deformable mirror (DM) satisfies the (-5/6) power law. A high-order system is also analyzed in which the pattern of wavefront sensor is synthesized from square pixels and the curvature actuators of the DM are also rectangular. The Strehl performance is approximately 2% worse than its annular analog.

Journal Article↗

[Expressions and correlation with radiotherapy's effect of five kinds of genes in nasopharyngeal carcinoma].

OBJECTIVE: To investigate the expressions of E-cadherin, CD44H, matrix metalloproteinase-3 (MMP-3), nm23H1 and vascular endothelial growth factor (VEGF) in nasopharyngeal carcinoma and its relationship to the effect of radiotherapy. Furthermore, to analyze the predict value of radiotherapy effect. METHODS: The expressions of E-cadherin, CD44H, MMP-3, nm23H1 and VEGF in 62 patients with nasopharyngeal carcinoma were determined by immunohistochemical SP method. There were 62 patients (17 to 70 years old) with nasopharyngeal carcinoma which were treated by radiotherapy from March 1995 to October 1995 and the period of follow-up had full 10 years. RESULTS: The expressions of CD44H (chi2 = 18.739, P = 0.028) and VEGF (chi2 = 18.523, P = 0.030) were closely related with short-term effect after radiotherapy in nasopharyngeal carcinoma. The short-term effect was descent along with enhancement of their expressions. In the group of low expressions in CD44H and nm23H1, 3-year overall survival rate were 65.5% and 45.5%, and 5-year overall survival rate were 47.3% and 22.7%. In the group of high expressions in CD44H and nm23H1, 3-year overall survival rate were 54.6% and 75.9%, and 5-year overall survival rate were 27.8% and 53.2%. There were respectively significant difference between two group of expressions in CD44H (chi2 = 7.31, P = 0.0069) and nm23H1 (chi2 = 15.64, P = 0.0001). CONCLUSIONS: These findings indicated that to detect the expressions of CD44H and VEGF gene may predict short-term effect of radiotherapy. Furthermore, to detect the expressions of CD44H and nm23H1 gene may predict long-term effect of radiotherapy in nasopharyngeal carcinoma.

Adolescent↗

Experimental tests of a homology model for OxlT, the oxalate transporter of Oxalobacter formigenes.

Using the x-ray structure of the glycerol 3-phosphate transporter (GlpT), we devised a model for the distantly related oxalate transporter, OxlT. The model accommodates all earlier biochemical information on OxlT, including the idea that Lys-355 lies on the permeation pathway, and predicts that Lys-355 and a second positive center, Arg-272, comprise the binding site for divalent oxalate. Study of R272K, R272A, and R272Q derivatives verifies that Arg-272 is essential, and comparisons with GlpT show that both anion transporters bind substrates within equivalent domains. In 22 single-cysteine variants in TM7 and TM8, topology as marked by accessibility to Oregon green maleimide is predicted by the model, with similar concordance for 52 positions probed earlier. The model also reconciles cross-linking of a cysteine pair placed near the periplasmic ends of TM2 and TM7, and retrospective study of TM2 and TM11 confirms that positions supporting disulfide trapping lie at a helical interface. Our work describes a pathway to the modeling of OxlT and other transporters in the major facilitator superfamily and outlines simple experimental tests to evaluate such proposals.

Bacterial Proteins↗

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry.

SUMMARY: Research in proteomics requires powerful database-searching software to automatically identify protein sequences in a complex protein mixture via tandem mass spectrometry. In this paper, we describe a novel database-searching software system called pFind (peptide/protein Finder), which employs an effective peptide-scoring algorithm that we reported earlier. The pFind server is implemented with the C++ STL, .Net and XML technologies. As a result, high speed and good usability of the software are achieved.

Algorithms↗

Hysteresis correction in the curvature adaptive optics system.

An enhancing Coleman-Hodgdon model is introduced to describe the hysteresis curves of the bimorph deformable mirror (DM). Hysteresis curves are measured from a bimorph DM and then experiment is set up for the correction of hysteresis. Finally, step response and transfer functions of a curvature adaptive optics (AO) system are compared in three cases: with DM hysteresis, without hysteresis, and with hysteresis but corrected. Simulation results show that the bandwidth of a curvature AO system is improved significantly under different loop gains after hysteresis of the DM is corrected.

Journal Article↗

[Simultaneous determination of 25 persistent organic pollutants in rice by gas chromatography-mass spectrometry with selected ion monitoring mode].

A multi-residue analytical method for the simultaneous determination of persistent organic pollutants (POPs) in rice samples was developed. POPs were extracted from rice with ethyl acetate/n-hexane (80:20, v/v) by sonication, and determined by gas chromatography with electron impact mass spectrometric detection in the selected ion monitoring mode. A fused silica capillary column DB-35MS (30 m x 0.25 mm i.d. x 0.25 microm) was employed. Operating conditions were as follows: injector port temperature, 300 degrees C; column temperature, programming; carrier gas, helium; flow rate, 1.0 mL/min; sample size, 1 microL with splitless injection. The mass spectrometric detector (MSD) was operated in electron impact ionization mode with an ionizing energy of 70 eV. Analysis was performed with selected ion monitoring (SIM) using one target and one or two qualifier ion. POPs were confirmed by their retention times, their qualifier and target ions, and their qualifier/target abundance ratios. Recovery studies were performed at 0.05, 0.1, and 0.5 mg/L spiked levels of each POPs, and the recoveries obtained ranged from 81.99% to 100.60% with relative standard deviations between 2.37% and 18.48%. The detection limits of the method ranged from 0.1 to 5 ng/g for the different POPs except endrin, trans-chlordane and cis-chlordane. The results show that the method developed is sensitive and reliable.

Chlordan↗

Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry.

MOTIVATION: The correlation among fragment ions in a tandem mass spectrum is crucial in reducing stochastic mismatches for peptide identification by database searching. Until now, an efficient scoring algorithm that considers the correlative information in a tunable and comprehensive manner has been lacking. RESULTS: This paper provides a promising approach to utilizing the correlative information for improving the peptide identification accuracy. The kernel trick, rooted in the statistical learning theory, is exploited to address this issue with low computational effort. The common scoring method, the tandem mass spectral dot product (SDP), is extended to the kernel SDP (KSDP). Experiments on a dataset reported previously demonstrate the effectiveness of the KSDP. The implementation on consecutive fragments shows a decrease of 10% in the error rate compared with the SDP. Our software tool, pFind, using a simple scoring function based on the KSDP, outperforms two SDP-based software tools, SEQUEST and Sonar MS/MS, in terms of identification accuracy. SUPPLEMENTARY INFORMATION: http://www.jdl.ac.cn/user/yfu/pfind/index.html

Algorithms↗

[Expression and correlation with metastasis of E-cadherin, CD44H, matrix metalloproteinase-3, nm23H1 and VEGF in nasopharyngeal carcinoma].

OBJECTIVE: To investigate the expression of E-cadherin, CD44H, matrix metalloproteinase-3, nm23H1 and VEGF in nasopharyngeal carcinoma and its relationship to the metastasis. METHOD: The expression of E-cadherin, CD44H, matrix metalloproteinase-3, nm23H1 and VEGF in 62 patients with nasopharyngeal carcinoma was detected by immunohistochemical SP method. RESULT: In the group of nasopharyngeal carcinoma with lymph node metastasis, the expression of E-cadherin and nm23H1 reduced and the expression of CD44H and MMP-3 increased, and there were respectively significant difference compared to the group of non-lymph node metastasis, but there wasn't significant difference between the two groups in VEGF. Furthermore, expression of E-cadherin was inversely correlated with that of CD44H and MMP-3, and the expression of CD44H was positively correlated with that of MMP-3. In the group of nasopharyngeal carcinoma with distant metastasis, the expression of E-cadherin and nm23H1 also increased and the expression of CD44H, MMP-3 and VEGF all increased. Compared with the group of negative distant metastasis, there were respectively significant difference. In addition, there was a positive correlation between the expression of CD44H and VEGF. CONCLUSION: E-cadherin, CD44H, matrix metalloproteinase-3 and nm23H1 genes are closely related with lymph node and distant metastasis of nasopharyngeal carcinoma, while VEGF gene only relates to lymph node metastasis. They are important factors acting on metastasis of neoplasms.

Adolescent↗

[Purification of eutrophicated water body by Vetiveria zizanioids].

Studies on the purification efficiency of eutrophicated water body by Vetiveria Zizanioids on floating-beds showed that V. zizanioids had a great ability to remove TN, NH4(+)-N, TP, PO4(3-), COD, and BOD, and had a significant effect on improving water quality. It was proved that V. zizanioids could be used to purify the eutrophicated water body.

Eutrophication↗

[Evaluation of noninvasive positive pressure ventilation in treatment for patients with severe acute respiratory syndrome].

OBJECTIVE: To analyze the effects of noninvasive positive pressure ventilation (NIPPV) on oxygenation of severe acute respiratory syndrome (SARS) patients, and to discuss the timing point for mechanical ventilation. METHODS: Twenty-five SARS patients with respiratory dysfunction treated with NIPPV were studied retrospectively in order to evaluate the influences within 24 hours after initiation of ventilatory support on their physiological indices and oxygenation. Patients with SARS were divided into two groups: survivor group (n=13) and non-survivor group (n=12). We compared the acute physiology and chronic health evaluation (APACHEII) score, respiratory rate (RR),saturation of oxygen (SpO(2)) and modificative respiratory index (MRI) for the survivors and non-survivors before NIPPV and after NIPPV for twenty-four hours, respectively. RESULTS: Although NIPPV administered via full-face masks might be an effective treatment for rapidly improving vital signs and gas exchange and sense of dyspnea in both groups during the initial 24 hours of ventilatory support, the patients in non-survivor group had higher APACHEII score, respiratory rates and lower SpO(2), MRI than the patients in survivor group (P<0.05) at the same intervals after initiation of support. CONCLUSION: Noninvasive ventilation should be used as a substitutive tool for endotracheal intubation an alternative treatment for acute respiratory failure related to SARS. Therefore, we should make efforts to avoid missing the time point for NIPPV or intubation, and we should not be restricted to the available indications for NIPPV or IPPV.

Adult↗

[Pharmacokinetics of scutellarin in rabbits].

An RP-HPLC was established to determine scutellarin in rabbit plasma and to study pharmacokinetics of breviscapine in rabbits. The analytical column was DiamonsilTM C18(4.6 mm x 250 mm, 5 microns), the mobile phase consisted of methanol, 0.02 mol/L phosphate buffer(adjusted by phosphoric acid to pH 3.0) and acetonitrile (65:35:10), the flow rate was 1.0 ml.min-1, the column temperature was 25 degrees C and the detection wavelength was 334 nm. The results of the pharmacokinetics study showed that the concentration-time curve of scutellarin was conformed to two-compartment model, the chief pharmacokinetic parameters were as follows: t1/2 alpha 1.29 +/- 0.53 min, t1/2 beta 10.40 +/- 1.97 min, Vc148.1 +/- 118.6 ml, and CL 57.5 +/- 31.7 ml.min-1.

Animals↗

Cinnamomin, a type II ribosome-inactivating protein, is a storage protein in the seed of the camphor tree (Cinnamomum camphora).

Cinnamomin is a novel type II ribosome-inactivating protein (RIP) isolated in our laboratory from the seed of the camphor tree (Cinnamomum camphora). In this paper the physiological role it plays in the plant cell was studied. Northern and Western blotting revealed that cinnamomin was expressed specifically in cotyledons. It accumulated in large amounts simultaneously with other proteins at the post-stages of seed development. Cinnamomin degraded rapidly during the early stages of seed germination. Endopeptidase was proved to play an important role in the degradation of cinnamomin. Western blotting of total proteins from the protein body with antibodies against cinnamomin demonstrated that it only existed in this specific cellular organelle as a storage protein. The similar properties of cinnamomin and other seed storage proteins of dicotyledons were compared. We conclude that cinnamomin is a special storage protein in the seed of C. camphora.

Algal Proteins↗

Studies of three genes encoding Cinnamomin (a type II RIP) isolated from the seeds of camphor tree and their expression patterns.

Cinnamomin, which has three isoforms, is a type II ribosome-inactivating protein (RIP) purified from the mature seeds of camphor tree (Cinnamomum camphora). In a previous study, an incomplete cDNA that encoded the A- and B-chain of Cinnamomin but lacked signal peptide sequence was cloned. In the present paper, its full-length cDNA was obtained by 5' rapid amplification of cDNA ends (5'RACE). Subsequently, polymerase chain reaction (PCR) amplification of its genomic DNA was performed. Unexpectedly, sequence analysis of the PCR products revealed three cinnamomin genes with >98.0% sequence identity. One of them corresponded to the published cDNA and was designated as cinnamomin I, whereas the other two genes were named as cinnamomin II and cinnamomin III, respectively. RT-PCR amplification of the cDNAs of cinnamomin II and III manifested that these two genes were functional. The three genes have no intron. Three Cinnamomin precursors that were inferred from the cDNA sequence of three cinnamomin genes exhibited relatively high sequence homology with other type II RIPs. Northern blot analysis demonstrated that the cinnamomin genes only expressed in cotyledons of C. camphora seeds and the acmes of expression emerged at 75-90 DAF when seeds were close to maturity. It is proposed that the three cinnamomin genes may encode three isoforms of Cinnamomin. The physiological function of Cinnamomin in C. camphora seeds is briefly discussed.

Algal Proteins↗

Purification and characterization of an ethylene-induced antifungal protein from leaves of guilder rose (Hydrangea macrophylla).

An ethylene-induced, chitin-binding protein (designated as HM30) from leaves of Hydrangea macrophylla was identified and purified to apparent homogeneity by chitin affinity chromatography followed by FPLC on a Superose 12 column. The molecular mass of HM30 was 30,010.0 Da determined by mass spectrometry and its isoelectric point of 8.4 was estimated by isoelectric focusing. The amino acid composition of HM30 was also determined. The initial 15 amino acid residues of the N-terminal were found to be N-S-M-E-R-V-E-E-L-R-K-K-L-Q-D by automatic Edman degradation. This chitin-binding protein showed antifungal activity toward several crop fungal pathogens. Knowledge of properties of HM30 should be useful for its potential application as a plant fungicidal agent.

Amino Acid Sequence↗

Purification of alpha-sarcin and an antifungal protein from mold (Aspergillus giganteus) by chitin affinity chromatography.

A simple method for preparation of alpha-sarcin and an antifungal protein (AFP) from mold (Aspergillus giganteus MDH 18894) has been developed. alpha-Sarcin and AFP were purified simultaneously by chitin affinity column chromatography and gel filtration. By this method, 4.5 mg of pure alpha-sarcin and 6.9 mg of pure AFP were obtained from 2 liters of culture medium. Compared with other purification methods such as ion-exchange column chromatography, this procedure was very simple and specific. The purified alpha-sarcin and AFP were homogeneous as characterized by SDS-polyacrylamide gel electrophoresis. Both alpha-sarcin and AFP exhibited the binding activity to generated chitin. Soluble glycochitin decreased the intensity of fluorescence of alpha-sarcin and made the lambda(em)m shift from 340 to 347 nm. Titration of alpha-sarcin with N-bromosuccinimide under native conditions revealed that two tryptophans (Trps) were all located in the core part of alpha-sarcin molecule. This indicated that Trps were not involved in the binding of alpha-sarcin to chitin. Glycochitin in the culture medium increased the expression of alpha-sarcin, while it had no effect on the expression of AFP. Unlike other ligands such as Cibacron blue for the affinity purification of alpha-sarcin and AFP, glycochitin increased the nuclease activity of alpha-sarcin.

Animals↗