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Biomedical subjects

Song Yang

Publications and source records attributed to Song Yang.

29 records · Page 2Linked to original sources
PubMed2005

Imputation of missing data when measuring physical activity by accelerometry.

PURPOSE: We consider the issue of summarizing accelerometer activity count data accumulated over multiple days when the time interval in which the monitor is worn is not uniform for every subject on every day. The fact that counts are not being recorded during periods in which the monitor is not worn means that many common estimators of daily physical activity are biased downward. METHODS: Data from the Trial for Activity in Adolescent Girls (TAAG), a multicenter group-randomized trial to reduce the decline in physical activity among middle-school girls, were used to illustrate the problem of bias in estimation of physical activity due to missing accelerometer data. The effectiveness of two imputation procedures to reduce bias was investigated in a simulation experiment. Count data for an entire day, or a segment of the day were deleted at random or in an informative way with higher probability of missingness at upper levels of body mass index (BMI) and lower levels of physical activity. RESULTS: When data were deleted at random, estimates of activity computed from the observed data and those based on a data set in which the missing data have been imputed were equally unbiased; however, imputation estimates were more precise. When the data were deleted in a systematic fashion, the bias in estimated activity was lower using imputation procedures. Both imputation techniques, single imputation using the EM algorithm and multiple imputation (MI), performed similarly, with no significant differences in bias or precision. CONCLUSIONS: Researchers are encouraged to take advantage of software to implement missing value imputation, as estimates of activity are more precise and less biased in the presence of intermittent missing accelerometer data than those derived from an observed data analysis approach.

Acceleration↗
PubMed2004

Bis(micro-4-chlorobenzoato-kappa(2)O:O)bis[(2-aminopyridine-kappaN)silver(I)].

The title compound, [Ag(2)(C(7)H(4)ClO(2))(2)(C(5)H(6)N(2))(2)], lies about an inversion centre and the Ag atom is three-coordinated by two O atoms and one N atom from three different ligands. The 4-chlorobenzoate anion acts as a monodonor ligand, bridging two inversion-related Ag atoms of the compound into a dimer. There are weak intermolecular N-H.O hydrogen bonds in the structure.

Journal Article↗
PubMed2004

A map of WW domain family interactions.

WW domains are protein modules that bind proline-rich ligands. WW domain-ligand complexes are of importance as they have been implicated in several human diseases such as muscular dystrophy, cancer, hypertension, Alzheimer's, and Huntington's diseases. We report the results of a protein array aimed at mapping all the human WW domain protein-protein interactions. Our biochemical approach integrates parallel synthesis of peptides, protein expression, and high-throughput screening methodology combined with tools of bioinformatics. The results suggest that the majority of the bioinformatically predicted WW peptide ligands and most WW domains are functional, and that only about 10% of the measured domain-ligand interactions are positive. The analysis of the WW domain protein arrays also underscores the importance of the amino acid residues surrounding the WW ligand core motifs for specific binding to WW domains. In addition, the methodology presented here allows for the rapid elucidation of WW domain-ligand interactions with multiple applications including prediction of exact WW ligand binding sites, which can be applied to the mapping of other protein signaling domain families. Such information can be applied to the generation of protein interaction networks and identification of potential drug targets. To our knowledge, this report describes the first protein-protein interaction map of a domain in the human proteome.

Amino Acid Motifs↗
PubMed2004

Biomedical informatics: development of a comprehensive data warehouse for clinical and genomic breast cancer research.

The Windber Research Institute is an integrated high-throughput research center employing clinical, genomic and proteomic platforms to produce terabyte levels of data. We use biomedical informatics technologies to integrate all of these operations. This report includes information on a multi-year, multi-phase hybrid data warehouse project currently under development in the Institute. The purpose of the warehouse is to host the terabyte-level of internal experimentally generated data as well as data from public sources. We have previously reported on the phase I development, which integrated limited internal data sources and selected public databases. Currently, we are completing phase II development, which integrates our internal automated data sources and develops visualization tools to query across these data types. This paper summarizes our clinical and experimental operations, the data warehouse development, and the challenges we have faced. In phase III we plan to federate additional manual internal and public data sources and then to develop and adapt more data analysis and mining tools. We expect that the final implementation of the data warehouse will greatly facilitate biomedical informatics research.

Breast Neoplasms↗
PubMed2004

[Synthesis and antifungal activity of novel triazole antifungal agents].

AIM: A series of triazole antifungal agents were synthesized to search for novel triazole antifungal agents with more potent activity, less toxicity and broader spectrum. METHODS: Twenty-one 1-(1H-1, 2, 4-triazolyl)-2-(2, 4-diflurophenyl)-3-(4-substituted-1-piperazinyl)-2-propanols were synthesized, on the basis of the three dimensional structure of P450 cytochrome 14alpha-sterol demethylase (CYP51) and their antifungal activities were also evaluated. RESULTS: Results of preliminary biological tests showed that most of title compounds exhibited activity against the eight common pathogenic fungi to some extent and the activities against deep fungi were higher than that against shallow fungi. In general, phenyl and pyridinyl analogues showed higher antifungal activity than that of the phenylacyl analogues. CONCLUSION: Several title compounds showed higher antifungal activities than fluconazole and terbinafine. Compound VIII-1, 4, 5 and IX-3 showed the best antifungal activity with broad antifungal spectrum and were chosen for further study.

Antifungal Agents↗
PubMed2003

[Relationship among the XhaI and EcoRI locus polymorphisms of apolipoprotein B gene, serum lipid metabolism and gallstone disease].

OBJECTIVES: To explore the relationship between the XbaI and EcoRI locus polymorphisms of apolipoprotein B gene and gallstone disease. METHODS: Restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) technique was used to analyze the genotype of the ApoB gene in 106 patients and 105 controls, according to the design of case control study. RESULTS: The frequencies of X+X- and X-X- of XbaI locus polymorphism were significantly different between the patients and controls and the frequency of X+ allele in the patients was significantly higher than that in the controls (0.104 vs 0.052). Meanwhile, the levels of LDLc and ApoB in the patients were significantly higher than those in the controls among the group of X+X- genotype. The frequencies of E+E- and E+E+ of EcoRI locus polymorphism were significantly different between the patients and controls and the frequency of E-allele in the patients was significantly higher than that the in controls, and the level of LDLc with E+E- genotype was higher than that with E+E+ genotype among the patients. CONCLUSION: ApoB gene X+ allele of XbaI locus and E-allele of EcoRI locus may be the susceptible genes for gallstone disease, and variation of X+ and E-alleles may affect serum lipid metabolism and formation of gallstone.

Adult↗
PubMed2003

Structure-based de novo design, synthesis, and biological evaluation of non-azole inhibitors specific for lanosterol 14alpha-demethylase of fungi.

The active site of lanosterol 14alpha-demethylase (CYP51) was investigated via MCSS functional group mapping and LUDI calculations. Several non-azole lead molecules were obtained by coupling structure-based de novo design with chemical synthesis and biological evaluation. All of the lead molecules exhibited a strong inhibitory effect on CYP51 of Candida albicans. They occupy the substrate-binding site and interfere with the binding of azole antifungal agents in a competitive manner. The mode of action of the lead molecules was validated by spectrophotomeric analysis and SAR studies. This is the first successful example reported for the inhibitor design of the cytochrome P450 superfamily using the de novo design strategy. Because the affinity of the lead molecules for CYP51 was mainly attributed to their nonbonding interaction with the apoprotein, the studies presented here afford the opportunity to develop novel antifungal agents that specifically interact with the residues in the active site and avoid the serious toxicity arising from coordination binding with the heme of mammalian P450s.

Antifungal Agents↗
PubMed2003

[Synthesis and antifungal activity of 1-(1,2,4-triazolyl-1H-1-yl)-2-(2,4-diflurophenyl)-3-(4-substituted benzyl-1-piperazinyl)-2-propanols].

AIM: A series of triazole antifungals were synthesized to search for novel triazole antifungals with more potent activity, less toxicity and broader spectrum. METHODS: Nineteen 1-(1,2,4-triazolyl-1H-1-yl)-2-(2,4-diflurophenyl)-3-(4-substituted benzyl-1-piperazinyl)-2-propanols were designed and synthesized, on basis of the three dimensional structure of P450 cytochrome 14 alpha-sterol demethylase (CYP51) and their antifungal activities were also evaluated. RESULTS: All the title compounds were first reported. Results of preliminary biological tests showed that most of the title compounds exhibited high activity against the eight common pathogenic fungi and the activities against deep fungi were higher than that against shallow fungi. CONCLUSION: Most of the title compounds showed higher antifungal activities than Fluconazole and Terbinafine. Compound VIII-1, 10, 12, 17 showed best antifungal activity with broad antifungal spectrum and were chosen for further development.

Antifungal Agents↗
PubMed2003

[Assay of haemolymph protein concentration in Anopheles stephensi].

OBJECTIVE: To ascertain the changes of haemolymph protein concentration in adult Anopheles stephensi mosquitoes under different feeding conditions. METHODS: Haemolymph samples from four groups of adult An. stephensi, fed with sucrose solution, normal blood, plasmodium-infected blood and nitroquine, respectively, were collected by expulsion method. The concentration of haemolymph protein was examined by Bradford method. The results were analyzed automatically by Excel program. RESULTS: The level of protein concentration in the infected blood-fed group was higher than the sucrose solution group and normal blood group at day 8 after Plasmodium yoelii infection, the average concentration was 4.436, 3.080 and 3.092 micrograms/microliter, respectively. The haemolymph protein concentration (2.264 micrograms/microliter) in the nitroquine-administered mosquitoes was lower than the infected blood-fed mosquitoes. CONCLUSION: The haemolymph protein concentration of the adult An. stephensi decreases after the nitroquine administration, indicating that the haemolymph proteins may be involved in the melantotic encapsulation reaction of plasmodial oocysts.

Animals↗