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Zuofeng Li

Publications and source records attributed to Zuofeng Li.

13 recordsLinked to original sources
PubMed2006

PlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information.

We have designed and implemented a web-based database system, called PlantQTL-GE, to facilitate quantitatine traits locus (QTL) based candidate gene identification and gene function analysis. We collected a large number of genes, gene expression information in microarray data and expressed sequence tags (ESTs) and genetic markers from multiple sources of Oryza sativa and Arabidopsis thaliana. The system integrates these diverse data sources and has a uniform web interface for easy access. It supports QTL queries specifying QTL marker intervals or genomic loci, and displays, on rice or Arabidopsis genome, known genes, microarray data, ESTs and candidate genes and similar putative genes in the other plant. Candidate genes in QTL intervals are further annotated based on matching ESTs, microarray gene expression data and cis-elements in regulatory sequences. The system is freely available at http://www.scbit.org/qtl2gene/new/.

Arabidopsis↗
PubMed2006

Characterization of the porcine alpha interferon multigene family.

The availability of data on the pig genome sequence prompted us to characterize the porcine IFN-alpha (PoIFN-alpha) multigene family. Fourteen functional PoIFN-alpha genes and two PoIFN-alpha pseudogenes were detected in the porcine genome. Multiple sequence alignment revealed a C-terminal deletion of eight residues in six subtypes. A phylogenetic tree of the porcine IFN-alpha gene family defined the evolutionary relationship of the various subtypes. In addition, analysis of the evolutionary rate and the effect of positive selection suggested that the C-terminal deletion is a strategy for preservation in the genome. Eight PoIFN-alpha subtypes were isolated from the porcine liver genome and expressed in BHK-21 cells line. We detected the level of transcription by real-time quantitative RT-PCR analysis. The antiviral activities of the products were determined by WISH cells/Vesicular Stomatitis Virus (VSV) and PK 15 cells/Pseudorabies Virus (PRV) respectively. We found the antiviral activities of intact PoIFN-alpha genes are approximately 2-50 times higher than those of the subtypes with C-terminal deletions in WISH cells and 15-55 times higher in PK 15 cells. There was no obvious difference between the subtypes with and without C-terminal deletion on acid susceptibility.

Amino Acid Sequence↗
PubMed2006

Measurement of LINAC 90 degrees head leakage radiation TVL values.

One of the key components in modern LINAC room shielding design is the amount of 90 degrees head leakage radiation levels. With the general clinical acceptance of intensity-modulated radiation therapy (IMRT) technique, accurate knowledge of this quantity has become even more important. Measurement of 90 degrees head leakage radiation of medical linear accelerators can be technically challenging due to the low dose rate causing poor signal-to-noise ratios in most detectors. 90 degrees leakage tenth-value layer (TVL) values in concrete have not been reported for the Elekta linear accelerators. This report describes our measurements of 90 degrees leakage TVL values for 6, 10, and 18 MV x-ray beams for an Elekta Precise Treatment System. A large-volume (1000 cm3) unpressurized ionization chamber and a high sensitivity electrometer, together with a separate chamber bias power supply, were used in these measurements in order to maximize the signal-to-noise ratio. A lead enclosure, of minimum thickness 10 cm, was constructed inside the treatment room to house the ion chamber to reduce the influence of room-scattered radiation. A square aperture of 10 X 10 cm2 area was left in the shield and aimed towards the accelerator head. Measurements were performed with the chamber placed at approximately 2 m from the accelerator isocenter. Concrete slabs with individual dimensions of approximately 40 X 40 cm2 cross-sectional area and 5 cm thickness were placed between the accelerator head and the ion chamber for these measurements. The measurements were performed with total concrete thickness of up to 80 cm, so that values up to the third TVL were measured. These measurements showed thatthe first concrete TVL values are 22, 23, and 28 cm (8.6, 9.1, and 10.5 in.) for 6, 10, and 18 MV beams, while the average of the first 3 TVL's were 25, 26, and 29 cm (9.9, 10.2, and 11.5 in.). Measured values agreed to within 10% of previously reported values for Varian linear accelerators for equivalent radiation beam qualities.

Equipment Design↗
PubMed2005

Dose distribution outside of a sphere of P-32 chromic phosphorous colloid.

PURPOSE: To evaluate the dose distribution outside of a cyst instilled with phosphorous-32 (P-32, an electron emitter with a short effective range of 2-8 mm and average energy of 0.69 MeV, used to treat cystic craniopharyngioma) as a function of cyst size with and without plating (migration and adhesion of P-32 to the cyst surface). METHODS AND MATERIALS: A cystic craniopharyngioma treated with instillation of P-32 was approximated by a sphere of uniformly distributed and plated chromic P-32 colloid. The percent depth dose was calculated along a radial position vector exterior to the sphere with a three-dimensional convolution integral and a dose point kernel. RESULTS: The percent depth dose variation of surface or volume source external to a family of spheres was plotted. Complex cyst geometry is amenable to evaluation by approximation with simple spheres. Error estimates are calculated for the dose outside of truncated sphere segments. Plating might occur and raise the dose outside the cyst by more than a factor of 5.0. This has the potential to cause damage to adjacent tissues, including the optic chiasm. CONCLUSION: Clinicians are faced with a number of treatment options for cystic craniopharyngioma, including intracystic instillation of colloid P-32. Unfortunately, plating might occur and potentially damage adjacent normal tissues. It is recommended that the propensity for a craniopharyngioma to plate be evaluated before full treatment, especially after previous treatment.

Algorithms↗
PubMed2005

Detecting correlation between sequence and expression divergences in a comparative analysis of human serpin genes.

Physiological functions and characteristic structures of the serpin gene superfamily have been studied extensively, yet the evolution of the serpin genes remains unclear. Gene duplication in this superfamily may shed light on this issue. Two models are used to predict the preservation of duplicated genes: the classical model and the duplication-degeneration-complementation (DDC) model. In this study, we analyzed the phylogenetic relationships of 33 human serpin genes and the expression data of some members of the serpin superfamily from a DNA microarray of human leukemia U937 cells with stably inducible expression of the leukemia-related AML1-ETO gene. We then determined the utility of the DDC model by mapping serpin superfamily expression data to the phylogenetic tree. The correlation between sequence and expression divergences as measured by the Pearson correlation coefficient indicated that human serpin genes evolved under the DDC model. Our study provides a new strategy for comparative analysis of gene sequences and microarray data.

Cell Line, Tumor↗
PubMed2005

An improved internal mammary irradiation technique in radiation treatment of locally advanced breast cancers.

The purpose of the present study was to compare a new internal mammary irradiation technique with traditional techniques for locally advanced breast cancers in terms of sparing ipsilateral lung and heart and reducing the "cold" and "hot spots"in breast tissue. The new technique uses wide tangential fields for the first eight fractions of treatment. A medial internal mammary field (IMF) of electrons matched with narrowed tangential fields is used for the remaining fractions. Intensity-modulated radiation therapy (IMRT) by means of segmented multileaf collimation (SMLC) is used in the narrowed tangential fields to improve the match between the electron and the photon fields. Treatment planning was performed to compare this technique to a wide-tangential-only technique and to a traditional oblique IMF technique for three patients with differing habitus. Film dosimetry was performed in a solid water phantom to confirm the planning results. For all three patients, the mean doses of the ipsilateral lung and the heart were significantly reduced with the new technique. The lung and the heart volumes were remarkably reduced at lowdose levels (< or =12 Gy) compared to the traditional IMF technique, and significantly reduced at all dose levels compared to the wide tangential technique. The new technique also reduced the "cold" and "hot spots" along the match plane between the IMF and the tangential fields compared to the traditional IMF technique. In conclusion, the new IMF technique shows dosimetric improvement compared to the traditional IMF technique in terms of the critical organ sparing and target dose uniformity.

Body Burden↗
PubMed2005

Detecting horizontal gene transfer with T-REX and RHOM programs.

As the Human Genome Project and other genome projects experience remarkable success and a flood of biological data is produced by means of high-throughout sequencing techniques, detection of horizontal gene transfer (HGT) becomes a promising field in bioinformatics. This review describes two freeware programs: T-REX for MS Windows and RHOM for Linux. T-REX is a graphical user interface program that offers functions to reconstruct the HGT network among the donor and receptor hosts from the gene and species distance matrices. RHOM is a set of command-line driven programs used to detect HGT in genomes. While T-REX impresses with a user-friendly interface and drawing of the reticulation network, the strength of RHOM is an extensive statistical framework of genome and the graphical display of the estimated sequence position probabilities for the candidate horizontally transferred genes.

Algorithms↗
PubMed2004

A simple method of independent treatment time verification in gamma knife radiosurgery using integral dose.

The purpose of this study is to develop a simple independent dose calculation method to verify treatment plans for Leksell Gamma Knife radiosurgery. Our approach uses the total integral dose within the skull as an end point for comparison. The total integral dose is computed using a spreadsheet and is compared to that obtained from Leksell GammaPlan. It is calculated as the sum of the integral doses of 201 beams, each passing through a cylindrical volume. The average length of the cylinders is estimated from the Skull-Scaler measurement data taken before treatment. Correction factors are applied to the length of the cylinder depending on the location of a shot in the skull. The radius of the cylinder corresponds to the collimator aperture of the helmet, with a correction factor for the beam penumbra and scattering. We have tested our simple spreadsheet program using treatment plans of 40 patients treated with Gamma Knife in our center. These patients differ in geometry, size, lesion locations, collimator helmet, and treatment complexities. Results show that differences between our calculations and treatment planning results are typically within +/-3%, with a maximum difference of +/-3.8%. We demonstrate that our spreadsheet program is a convenient and effective independent method to verify treatment planning irradiation times prior to implementation of Gamma Knife radiosurgery.

Algorithms↗
PubMed2003

Thermoluminescent dosimetry of the SourceTech Medical model STM1251 125I seed.

Many new models of 125I seeds are being introduced, mainly due to the increase in prostate seed implants. We have evaluated the SourceTech Medical (STM), model STM1251, 125I seed using thermoluminescent dosimeters (TLDs) in a solid water phantom. TLD cubes, LiF TLD-100, with dimension 1 mm on each edge, were irradiated at various distances, 1, 2, 3, and 5 cm, at angles ranging from 0 degrees to 90 degrees in 10 degrees increments. Sensitivity calibration of the TLDs was achieved by irradiation to 10 cGy with 6 MV x rays from a clinical linear accelerator, Clinac 600C. Concurrent with the 125I seed exposures, several TLDs were also exposed to 10 cGy with the 600C as a control set. Dose rates per unit air kerma strength were determined based on the 1999 NIST traceable standard for the STM1251 seed. They are presented as a function of distance r and angle theta. The TG-43 parameters, including the dose rate constant, lambda, anisotropy function, F(r,theta), radial dose function, g(r), anisotropy factor, phian(r), and anisotropy constant, phi, were obtained for use in radiation treatment planning software. The value of lambda was determined as 1.07 +/- 5.5% cGy U(-1) h(-1), which is comparable to model 6702 and to the value determined using the point extrapolation method by Kirov and Williamson. We also find agreement between our TLD data and their Monte Carlo results for g(r), F(r,theta), phian(r), and phi. Additionally, agreement is found with the TLD data of Li and Williamson for lambda and g(r).

Anisotropy↗
PubMed2003

Surface and buildup dose characteristics for 6, 10, and 18 MV photons from an Elekta Precise linear accelerator.

Understanding head scatter characteristics of photon beams is vital to properly commission treatment planning (TP) algorithms. Simultaneously, having definitive surface and buildup region dosimetry is important to optimize bolus. The Elekta Precise linacs have unique beam flattening filter configurations for each photon beam (6, 10, and 18 MV) in terms of material and location. We performed a comprehensive set of surface and buildup dose measurements with a thin window parallel-plate (PP) chamber to examine effects of field size (FS), source-to-skin distance (SSD), and attenuating media. Relative ionization data were converted to fractional depth dose (FDD) after correcting for bias effects and using the Gerbi method to account for chamber characteristics. Data were compared with a similar vintage Varian linac. At short SSDs the surface and buildup dose characteristics were similar to published data for Varian and Elekta accelerators. The FDD at surface (FDD(0)) for 6, 10, and 18 MV photons was 0.171, 0.159, and 0.199, respectively, for a 15x15 cm2, 100 cm SSD field. A blocking tray increased FDD(0) to 0.200, 0.200, and 0.256, while the universal wedge decreased FDD(0) to 0.107, 0.124, and 0.176. FDD(0) increased linearly with FS (approximately 1.16%/cm). FDD(0) decreased exponentially for 10 and 18 MV with increasing SSD. However, the 6 MV FDD(0) actually increased slightly with increasing SSD. This is likely due to the unique distal flattening filter for 6 MV. The measured buildup curves have been used to optimize TP calculations and guide bolus decisions. Overall the FDD(0) and buildup doses were very similar to published data. Of interest were the relatively low 10 MV surface doses, and the 6 MV FDD(0)'s dependence on SSD.

Dose Fractionation, Radiation↗
PubMed2002

Monte Carlo calculations of dosimetry parameters of the urocor prostaseed 125I source.

This report presents the results of Monte Carlo calculations of the dosimetric parameters of the Urocor ProstaSeed 1251 seed source. This source contains five spherical silver markers, of 0.5 mm diameter, with 1251 deposited on the spheres through ion exchange. The silver spheres are then encapsulated within a 0.8 mm in diameter and 4.5 mm long cylindrical shell of titanium, as is common to this type of sources. Physical dimensions of the source are confirmed by measurement. Four (4) geometric models of the source, based on different assumptions on the locations of the silver spheres within the seed, were used in dose rate calculations. Monte Carlo photon transport simulation was used to calculate the dosimetric parameters of dose rate constant, radial dose function, and anisotropy function using these geometric models of the source. The Monte Carlo calculated dose rate constant of the ProstaSeed source was found equal to 0.925 cGy/Uh with approximate uncertainties of 5%. Radial dose function values and anisotropy function values were derived from the relative dose distribution around the source calculated by the Monte Carlo code. The calculated values of these dosimetric parameters agree with previously published thermoluminescence-dosimeter-measured values for this source after consideration of measurement and calculation uncertainties.

Anisotropy↗
PubMed2002

Application of imaging-derived parameters to dosimetry of intravascular brachytherapy sources: perturbation effects of residual plaque burden.

The dosimetric effect of geometric and material heterogeneities on intravascular brachytherapy dose delivery has been studied recently. Residual plaque within the coronary vessel appears to have an impact on the uniform delivery of radiation dose to the arterial tissue. In this study, we have examined the effect of residual plaque burden and post-PCI (percutaneous coronary intervention) plaque configuration on the dose to the arterial wall from clinical intravascular brachytherapy beta-emitting sources containing 32P and 90Sr/90Y. Monte Carlo simulations using the MCNP4B code were performed for these catheter-based sources with residual plaque burden ranging between 25% and 50%. The residual plaque burden values were derived from post-PCI data provided in several recent clinical studies. Dose calculations were performed for three different values of plaque density (1.45 g cm(-3), 2.20 g cm(-3), and 3.1 g cm(-3)) and three different plaque morphologies for the same residual plaque burden. The dose perturbation factor (DPF), defined as the ratio of dose at 2 mm radial distance for a given case to the dose at the same radial distance in homogeneous water medium, was determined for each of the three different plaque densities. The range of DPF values was 0.81-1.01, 0.62-0.99, and 0.41-0.97 for different plaque densities for the 32P source. Corresponding DPF values for the 90Sr/90Y source were 0.90-1.01, 0.84-1.01, and 0.62-1.01. The results indicate the need for accurate assessment of post-PCI clinical measurements such as minimal lumen diameter and residual plaque burden and incorporation of these values into dose calculations.

Brachytherapy↗