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Biomedical subjects

Ji Zhu

Publications and source records attributed to Ji Zhu.

16 recordsLinked to original sources
PubMed2006

Methodological challenges in constructing effective treatment sequences for chronic psychiatric disorders.

Psychiatric disorders are often chronic conditions that require sequential decision making to achieve the best clinical outcomes. Sequential decisions are necessary to accommodate treatment response heterogeneity, a variable course of illness, and the often heavy burden associated with intensive or longer-term treatment. Yet, only a few studies in this field have been designed to address sequential decisions. Most of the experimental designs and data analytic methods that are best suited for improving sequential clinical decision making are often found in nonmedical fields such as engineering, computer science, and statistics. Promising designs and methods are surveyed with a focus on those areas most immediately useful for informing clinical decision making.

Chronic Disease↗
PubMed2006

Prediction of radiation induced liver disease using artificial neural networks.

OBJECTIVE: To evaluate the efficiency of predicting radiation induced liver disease (RILD) with an artificial neural network (ANN) model. METHODS AND MATERIALS: From August 2000 to November 2004, a total of 93 primary liver carcinoma (PLC) patients with single lesion and associated with hepatic cirrhosis of Child-Pugh grade A, were treated with hypofractionated three-dimensional conformal radiotherapy (3DCRT). Eight out of 93 patients were diagnosed RILD. Ninety-three patients were randomly divided into two subsets (training set and verification set). In model A, the ratio of patient numbers was 1:1 for training and verification set, and in model B, the ratio was 2:1. RESULTS: The areas under receiver-operating characteristic (ROC) curves were 0.8897 and 0.8831 for model A and B, respectively. Sensitivity, specificity, accuracy, positive prediction value (PPV) and negative prediction value (NPV) were 0.875 (7/8), 0.882 (75/85), 0.882 (82/93), 0.412 (7/17) and 0.987 (75/76) for model A, and 0.750 (6/8), 0.800 (68/85), 0.796 (74/93), 0.261 (6/23) and 0.971 (68/70) for model B. CONCLUSION: ANN was proved high accuracy for prediction of RILD. It could be used together with other models and dosimetric parameters to evaluate hepatic irradiation plans.

Algorithms↗
PubMed2006

Radiation-induced liver disease in three-dimensional conformal radiation therapy for primary liver carcinoma: the risk factors and hepatic radiation tolerance.

PURPOSE: To identify risk factors relevant to radiation-induced liver disease (RILD) and to determine the hepatic tolerance to radiation. METHODS AND MATERIALS: The data of 109 primary liver carcinomas (PLC) treated with hypofractionated three-dimensional conformal radiation therapy (3D-CRT) were analyzed. Seventeen patients were diagnosed with RILD and 13 of 17 died of it. RESULTS: The risk factors for RILD were late T stage, large gross tumor volume, presence of portal vein thrombosis, association with Child-Pugh Grade B cirrhosis, and acute hepatic toxicity. Multivariate analyses demonstrated that the severity of hepatic cirrhosis was a unique independent predictor. For Child-Pugh Grade A patients, the hepatic radiation tolerance was as follows: (1) Mean dose to normal liver (MDTNL) of 23 Gy was tolerable. (2) For cumulative dose-volume histogram, the tolerable volume percentages would be less than: V5 of 86%, V10 of 68%, V15 of 59%, V20 of 49%, V25 of 35%, V30 of 28%, V35 of 25%, and V40 of 20%. (3) Tolerable MDTNL could be estimated by MDTNL (Gy) = -1.686 + 0.023 * normal liver volume (cm3). CONCLUSION: The predominant risk factor for RILD was the severity of hepatic cirrhosis. The hepatic tolerance to radiation could be estimated by dosimetric parameters.

Adult↗
PubMed2006

Prediction of radiation-induced liver disease by Lyman normal-tissue complication probability model in three-dimensional conformal radiation therapy for primary liver carcinoma.

PURPOSE: To describe the probability of RILD by application of the Lyman-Kutcher-Burman normal-tissue complication (NTCP) model for primary liver carcinoma (PLC) treated with hypofractionated three-dimensional conformal radiotherapy (3D-CRT). METHODS AND MATERIALS: A total of 109 PLC patients treated by 3D-CRT were followed for RILD. Of these patients, 93 were in liver cirrhosis of Child-Pugh Grade A, and 16 were in Child-Pugh Grade B. The Michigan NTCP model was used to predict the probability of RILD, and then the modified Lyman NTCP model was generated for Child-Pugh A and Child-Pugh B patients by maximum-likelihood analysis. RESULTS: Of all patients, 17 developed RILD in which 8 were of Child-Pugh Grade A, and 9 were of Child-Pugh Grade B. The prediction of RILD by the Michigan model was underestimated for PLC patients. The modified n, m, TD50 (1) were 1.1, 0.28, and 40.5 Gy and 0.7, 0.43, and 23 Gy for patients with Child-Pugh A and B, respectively, which yielded better estimations of RILD probability. The hepatic tolerable doses (TD5) would be MDTNL of 21 Gy and 6 Gy, respectively, for Child-Pugh A and B patients. CONCLUSIONS: The Michigan model was probably not fit to predict RILD in PLC patients. A modified Lyman NTCP model for RILD was recommended.

Adult↗
PubMed2005

Improved classification of mass spectrometry database search results using newer machine learning approaches.

Manual analysis of mass spectrometry data is a current bottleneck in high throughput proteomics. In particular, the need to manually validate the results of mass spectrometry database searching algorithms can be prohibitively time-consuming. Development of software tools that attempt to quantify the confidence in the assignment of a protein or peptide identity to a mass spectrum is an area of active interest. We sought to extend work in this area by investigating the potential of recent machine learning algorithms to improve the accuracy of these approaches and as a flexible framework for accommodating new data features. Specifically we demonstrated the ability of boosting and random forest approaches to improve the discrimination of true hits from false positive identifications in the results of mass spectrometry database search engines compared with thresholding and other machine learning approaches. We accommodated additional attributes obtainable from database search results, including a factor addressing proton mobility. Performance was evaluated using publically available electrospray data and a new collection of MALDI data generated from purified human reference proteins.

Amino Acid Sequence↗
PubMed2005

An in vivo model to study osteogenic gene regulation: targeting an avian retroviral receptor (TVA) to bone with the bone sialoprotein (BSP) promoter.

UNLABELLED: To study bone development in vivo, a transgenic mouse model was established in which an avian retroviral receptor (TVA) gene driven by the BSP promoter was selectively expressed in skeletal tissues. The model was validated by showing suppressed BSP expression and delayed bone and tooth formation after infection with a virus expressing a mutated Cbfa1/Runx2 gene. INTRODUCTION: Tissue-specific expression of the avian retroviral (TVA) receptor can be used to efficiently target ectopic expression of genes in vivo. To determine the use of this approach for studies of osteogenic differentiation and bone formation at specific developmental stages, transgenic mice expressing the TVA receptor under the control of a 5-kb bone sialoprotein (BSP) promoter were generated. The mice were first analyzed for tissue-specific expression of the TVA gene and then, after infection with a viral construct, for the effects of a dominant-negative form of the Cbfa1/Runx2 transcription factor on bone formation. MATERIALS AND METHODS: We first generated transgenic mice (BSP/TVA) in which the TVA gene was expressed under the control of a 4.9-kb mouse BSP promoter. The tissue-specific expression of the TVA gene was analyzed by RT-PCR, in situ hybridization, and immunohistochemistry and compared with the expression of the endogenous BSP gene. A 396-bp fragment of mutated Cbfa1/Runx2 (Cbfa1mu) encoding the DNA-binding domain was cloned into a RCASBP (A) viral vector, which was used to infect neonatal BSP/TVA mice. RESULTS AND CONCLUSION: Expression of the TVA receptor mRNA and protein in the transgenic mice was consistent with the expression of endogenous BSP. Four days after systemic infection with the Cbfa1mu-RCASBP (A) vector, RT-PCR analyses revealed that the expression of BSP mRNA in tibia and mandibles was virtually abolished, whereas a 30% reduction was seen in calvarial bone. After 9 days, BSP expression in the tibia and mandible was reduced by 45% in comparison with control animals infected with an empty RCASBP vector, whereas BSP expression in the membranous bone of calvariae was decreased approximately 15%. However, after 4 and 8 weeks, there was almost no change in BSP expression in any of the bone tissues. In comparison, a reduction in osteopontin expression was only observed 9 days after viral transfection in the three bones. Histomorphological examination revealed that bone formation and tooth development were delayed in some of the mice infected with mutated Cbfa1. These studies show that BSP/TVA transgenic mice can be used to target genes to sites of osteogenesis, providing a unique system for studying molecular events associated with bone formation in vivo.

Animals↗
PubMed2005

[Cloning of human obesity gene and its expression in E. coli].

OBJECTIVE: To clone the obesity gene of Chinese and express human leptin in E.coli. METHOD: The obesity gene was amplified from the total RNA isolated from cultured human adipocytes of Chinese by reverse transcriptional PCR, inserted into TA-vector and cloned into the expression plasmid pBV220 after sequence identification. RESULTS: DNA sequencing confirmed that the isolated obesity gene was identical to the previously reported sequence. The recombinant plasmid pBV220-OB was constructed and leptin successfully expressed in E.coli. CONCLUSION: Successful cloning and expression of human obesity gene in E.coli may facilitate further research of the mechanism of fat metabolism and adipocyte differentiation.

Adipocytes↗
PubMed2005

[Application of green fluorescent protein gene in study of adipocyte differentiation].

OBJECTIVE: To establish a model for dynamic detection of adipocyte differentiation in vivo by green fluorescent protein (GFP). METHODS: The promoter of peroxisome proliferators-activated receptor gamma 2 (PPARgamma2) gene was amplified by PCR from the genomic DNA of human preadipocytes, inserted into the eukaryotic expression vector pEGFP-1 and transferred into NIH3T3 fibroblasts and preadipocytes which were induced to differentiate into adipocyte. RESULTS: Upon induction with insulin, dexamethasone and 3-isobutyl-1-methyl xanthine, the transformed human preadipocytes differentiated into mature adipocytes and expressed GFP, but NIH3T3 fibroblasts could not differentiate into adipocytes or express GFP. CONCLUSION: Transformation of human preadipocytes with the recombinant of PPARgamma2 promoter with GFP gene can be employed to dynamically detect the differentiation of adipocytes in vivo.

Adipocytes↗
PubMed2004

Classification of gene microarrays by penalized logistic regression.

Classification of patient samples is an important aspect of cancer diagnosis and treatment. The support vector machine (SVM) has been successfully applied to microarray cancer diagnosis problems. However, one weakness of the SVM is that given a tumor sample, it only predicts a cancer class label but does not provide any estimate of the underlying probability. We propose penalized logistic regression (PLR) as an alternative to the SVM for the microarray cancer diagnosis problem. We show that when using the same set of genes, PLR and the SVM perform similarly in cancer classification, but PLR has the advantage of additionally providing an estimate of the underlying probability. Often a primary goal in microarray cancer diagnosis is to identify the genes responsible for the classification, rather than class prediction. We consider two gene selection methods in this paper, univariate ranking (UR) and recursive feature elimination (RFE). Empirical results indicate that PLR combined with RFE tends to select fewer genes than other methods and also performs well in both cross-validation and test samples. A fast algorithm for solving PLR is also described.

Algorithms↗
PubMed2003

Catalysis and nanoscience.

The development of synthetic catalysts is inspired by nature's use of enzymes to achieve high reaction rates and 100% selectivity. These natural catalysts often contain inorganic nanoclusters at the active site, and it is an understanding of the activity and selectivity of these nanoclusters and their interaction with the surrounding protein, which can aid in the design of synthetic catalysts. Since natural and synthetic catalysts are composed of these nanoclusters, the fields of catalysis and nanoscience are inextricably linked.

Journal Article↗
PubMed2003

A modified restriction display PCR method in sample-labelling of DNA microarray.

The restriction display PCR is a useful technique for studying the diversity of gene expression. This method involves ligating the digested genes with adapters and amplifying the gene fragments by PCR using universal and selective primers. In this study, we improved this restriction display PCR method by using Cy3-UP, a fluorescently labelled universal primer, in place of Cy3-dCTP in sample-labelling for DNA microarray. The results show that this new method increases significantly the sensitivity of the assay, and will have a wide application in the DNA microarray field.

Carbocyanines↗
PubMed2002

[Analysis with DNA chips of the changes of gene expressions in K562 cells in response to As2O3 treatment].

OBJECTIVE: To investigate differential gene expression in apoptotic cells induced by As(2)O(3), and identify novel apoptosis-related genes. METHOD: Apoptosis of K562 cells cultured in RPMI 1640 medium supplemented with 10 % calf serum was induced by As(2)O(3). Total RNA of the apoptotic and normal cells were then extracted, purified and subject to reverse transcription into first-strand cDNA, labeled with Cy3/Cy5. Placenta DNA microarrays containing 348 DNA fragments were used to analyze the changes in gene expressions in the cells treated with As(2)O(3). RESULT: Eleven differentially expressed genes were identified in the apoptotic cells in comparison with the normal cells, 3 of which were associated with apoptosis, while the others were related to cell growth and proliferation. CONCLUSION: The placenta DNA microarrays we constructed may well apply to the analysis of the differentially expressed genes.

Antineoplastic Agents↗
PubMed2002

[Preliminary study of development of gene chips for HIV diagnosis].

OBJECTIVE: To study the technology for establishing DNA chips for the diagnosis of HIV. METHODS: HIV 1U26942 DNA fragments were isolated by restriction display-PCR (RD-PCR) and printed onto aminosilane-coated glass slides by Pixsys 5500 arrayer as probes to prepare the gene chips. HIV samples, after labeled with Cy3, were hybridized with the microarray followed by scanning for analysis of hybridization kinetics of the RD fragments. RESULTS: The experimental condition for preparing the gene chips was investigated and 12 RD fragments were screened as probes for further study. CONCLUSION: The technique established in this study for preparing DNA chips is specific and applicable.

Diagnostic Techniques and Procedures↗
PubMed2002

[A method for construction of restriction cDNA library].

A kind of cDNA library constructed according to Restriction Display PCR(RD-PCR) technology setup in our lab,which was called restriction cDNA library,was introduced in this paper. In the construction of cDNA library, cDNA was digested with restriction endonuclease, linked with special adaptor, amplified with PCR in groups. Each group of the restriction cDNA library contained special cDNAs. The method greatly reduced the repetitive frequency and accelerated the speed of identification.

English Abstract↗
PubMedDate not supplied

Mesoporous silicates as nanoreactors for carbon nanotube production in the absence of transition metal catalysts.

Carbon nanotubes were produced from either a template or the polymer-filled pore systems of mesoporous silicates of various structures and dimensions by heat treatment in the absence of air. Successful synthesis was done when the template molecules contained little or no oxygen. For SBA-15 material, where the structure-directing molecule used for synthesis of mesoporous silicate was polyethylene oxide-polypropylene oxide-polyethylene oxide triblock copolymer, no carbon nanostructures were formed. A peculiar carbon nanostructure was generated from the template for pore expanded MCM-41. To demonstrate carbon nanotube formation from polymer in the mesoporous silicates, the mesopores of MCM-41, MCM-48, and SBA-15 silicates were filled with divinyl-benzene polymer and then graphitized at 1300 K. The polymer was successfully transformed into carbon nanotubes for the MCM class silicate but not the SBA-15 silicate.

Catalysis↗