Biomedical subjects

Chaoyang Zhang

Publications and source records attributed to Chaoyang Zhang.

9 recordsLinked to original sources

PubMed2006

Investigation on the correlation between the interaction energies of all substituted groups and the molecular stabilities of nitro compounds.

A model, similar to an isodesmic reaction, is for the first time presented in this paper for describing, defining, and calculating the interaction energies of the indirectly linked groups or atoms within one molecule. Its applications to nitro substitutes of methane, benzene, and cubane verify its validity for a separate group of closely related compounds by the reasonable correlation between the calculated interaction energies of all substituted groups and the molecular stabilities or experimental impact sensitivities. Comparing with some existing rules of assessing the molecular stability, this so-called interaction energy is calculated using a model considering the chemical structures, that is, the electronic environments of compounds, and can be well related with the stabilities of nitro compounds. All investigation results show that the so-called interaction energy is a new, quantitative, and useful tool to evaluate the stabilities of nitro compounds.

Journal Article↗

PubMed2006

Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06).

The first symposium of computations in bioinformatics and bioscience (SCBB06) was held in Hangzhou, China on June 21-22, 2006. Twenty-six peer-reviewed papers were selected for publication in this special issue of BMC Bioinformatics. These papers cover a broad range of topics including bioinformatics theories, algorithms, applications and tool development. The main technical topics contain gene expression analysis, sequence analysis, genome analysis, phylogenetic analysis, gene function prediction, molecular interaction and system biology, genetics and population study, immune strategy, protein structure prediction and proteomics.

Biological Science Disciplines↗

PubMed2006

Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data.

BACKGROUND: Multicategory Support Vector Machines (MC-SVM) are powerful classification systems with excellent performance in a variety of data classification problems. Since the process of generating models in traditional multicategory support vector machines for large datasets is very computationally intensive, there is a need to improve the performance using high performance computing techniques. RESULTS: In this paper, Parallel Multicategory Support Vector Machines (PMC-SVM) have been developed based on the sequential minimum optimization-type decomposition method for support vector machines (SMO-SVM). It was implemented in parallel using MPI and C++ libraries and executed on both shared memory supercomputer and Linux cluster for multicategory classification of microarray data. PMC-SVM has been analyzed and evaluated using four microarray datasets with multiple diagnostic categories, such as different cancer types and normal tissue types. CONCLUSION: The experiments show that the PMC-SVM can significantly improve the performance of classification of microarray data without loss of accuracy, compared with previous work.

Algorithms↗

PubMed2006

Identification of new members of hydrophobin family using primary structure analysis.

BACKGROUND: Hydrophobins are fungal proteins that can turn into amphipathic membranes at hydrophilic/hydrophobic interfaces by self-assembly. The assemblages by Class I hydrophobins are extremely stable and possess the remarkable ability to change the polarity of the surface. One of its most important industrial applications is its usage as paint. Without detailed knowledge of the 3D structure and self-assembly principles of hydrophobins, it is difficult to make significant progress in furthering its research. RESULTS: In order to provide useful information to hydrophobin researchers, we analyzed primary structure of hydrophobins to gain more insight about these proteins. In this paper, we presented an in-depth primary sequence analysis using batch BLAST search of the database, sequence filtering by programming and motif finding by MEME. We used batch BLAST to find similar sequences in the NCBI nr database. Then we used MEME to find out motifs. Based on the newly found motifs and the well-known C-CC-C-C-CC-C pattern we used MAST to search the entire nr database. At the end, domain search and phylogenetic analysis were conducted to confirm the result. After searching the nr database with the new PSSM-format motifs identified by MEME, many sequences from various species were found by MAST. Filtering process by pattern, domain and length left 9 qualified candidates. CONCLUSION: All of 9 newly identified potential hydrophobins possess the common pattern and hydrophobin domain. From the multiple sequence alignment result, we can see that some of them are grouped very close to other known hydrophobins, which means their phylogenetic relationship is very close and it is highly plausible that they are indeed hydrophobin proteins.

Amino Acid Sequence↗

PubMed2006

A Fourier transformation based method to mine peptide space for antimicrobial activity.

BACKGROUND: Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every living organism, it is possible to discover new candidate peptides using the available genomic and proteomic data. High throughput computational techniques could also be used to virtually scan the entire peptide space for discovering out new candidate antimicrobial peptides. RESULT: We have identified a unique indexing method based on biologically distinct characteristic features of known antimicrobial peptides. Analysis of the entries in the antimicrobial peptide databases, based on our indexing method, using Fourier transformation technique revealed a distinct peak in their power spectrum. We have developed a method to mine the genomic and proteomic data, for the presence of peptides with potential antimicrobial activity, by looking for this distinct peak. We also used the Euclidean metric to rank the potential antimicrobial peptides activity. We have parallelized our method so that virtually any given protein space could be data mined, in search of antimicrobial peptides. CONCLUSION: The results show that the Fourier transform based method with the property based coding strategy could be used to scan the peptide space for discovering new potential antimicrobial peptides.

Amino Acid Sequence↗

PubMed2005

A new method to evaluate the stability of the covalent compound: by the charges on the common atom or group.

A new method of comparing and analyzing the electrostatic potential (ESP) charges of the common atom or group to evaluate and compare the stabilities of covalent compounds was introduced. That is, covalent compounds will become more stable when the electron acceptors accept adequate electrons and possess adequate negative charges, and the electron donors donate adequate electrons and possess adequate positive charges accordingly. All calculations were performed by density functional theory (DFT) and the general gradient approximation (GGA) method with the Beck-LYP hybrid functional and the DNP basis set in Acceryls' code Dmol3. Calculation results verified the method considering the molecular structure is well applied in the covalent molecule systems of hydrides, oxides, alkyl radicals, and nitro compounds. Furthermore, the method has good operability, for the charges can be easily obtained by simple calculation.

Journal Article↗

PubMed2005

Investigation of correlation between impact sensitivities and nitro group charges in nitro compounds.

A new method of calculating the Mulliken net charges of the nitro group, Q(NO)()2, to assess impact sensitivities for nitro compounds is established. All calculations including optimizations and Mulliken population and frequency analyses are performed by density functional theory (DFT) and the general gradient approximation (GGA) method in Acceryls' code Dmol(3) with the Beck-LYP hybrid functional and the DNP basis set. As a result, the charges on nitro group can be regarded as a structural parameter to estimate the impact sensitivity on the bond strength, oxygen balance, and molecular electrostatic potential. The compound with more -Q(NO)()2 will be insensitive and gives a large value of impact sensitivity H(50)(). This method considering the molecular structure is applicable for almost all nitro compounds when the C-NO(2), N-NO(2), or O-NO(2) bond is the weakest in the molecule. According to the results in this paper, the compounds with -Q(NO)()2 >0.23e show H(50)() </= 0.4 m.

Journal Article↗

PubMed2005

Detection of single and multiple targets in tissue phantoms with fluorescence-enhanced optical imaging: feasibility study.

PURPOSE: To evaluate the feasibility of reconstructing single and multiple targets by using fluorescence-enhanced tomography of a breast tissue phantom. MATERIALS AND METHODS: Frequency-domain fluorescence measurements were performed in cup-shaped tissue phantoms of clinically relevant size (diameter, 10 cm) in which single or multiple 0.5-1.0-cm(3) targets that contained micromolar concentrations of indocyanine green with 1:0 and 100:1 target-to-background (T:B) contrast ratios had been embedded. Rapid acquisition of time-dependent fluorescent light measurements was performed at the phantom surface in response to point illumination of excitation light by using a gain-modulated intensified charge-coupled device detection system. Boundary surface measurements were used to tomographically reconstruct the interior targets located with various experimental conditions. RESULTS: Single 1.0-cm(3) targets located between 1.43 and 2.82 cm deep from the phantom surface at a T:B contrast ratio of 100:1 and three approximately 0.55-cm(3) targets located about 1.30 cm deep at a T:B contrast ratio of 1:0 were reconstructed with minimal or no artifacts by using boundary surface fluorescence measurements and an approximate extended Kalman filter algorithm. CONCLUSION: It is feasible to detect single or multiple fluorescent targets in tissue phantoms of clinically relevant size by using fluorescence-enhanced optical tomography.

Algorithms↗

PubMed2003

Fluorescence-enhanced optical imaging in large tissue volumes using a gain-modulated ICCD camera.

A novel image-intensified charge-coupled device (ICCD) imaging system has been developed to perform 3D fluorescence tomographic imaging in the frequency-domain using near-infrared contrast agents. The imager is unique since it (i) employs a large tissue-mimicking phantom, which is shaped and sized to resemble a female breast and part of the extended chest-wall region, and (ii) enables rapid data acquisition in the frequency-domain by using a gain-modulated ICCD camera. Diffusion model predictions are compared to experimental measurements using two different referencing schemes under two different experimental conditions of perfect and imperfect uptake of fluorescent agent into a target. From these experimental measurements, three-dimensional images of fluorescent absorption were reconstructed using a computationally efficient variant of the approximate extended Kalman filter algorithm. The current work represents the first time that 3D fluorescence-enhanced optical tomographic reconstructions have been achieved from experimental measurements of the time-dependent light propagation on a clinically relevant breast-shaped tissue phantom using a gain-modulated ICCD camera.

Biophysical Phenomena↗