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Jae K Lee

Publications and source records attributed to Jae K Lee.

17 recordsLinked to original sources
PubMed2006

Effects of water deprivation for 72 hours on the pharmacokinetics of DA-7867, a new oxazolidinone, in rats.

The pharmacokinetic parameters of DA-7867 were compared after intravenous and oral administration at a dose of 10 mg/kg in control rats and in rats with water deprivation for 72 h (rat model of dehydration). After intravenous administration in the rat model of dehydration, the Cl(nr) (0.654 versus 0.992 ml/min/kg) and Cl(r) (0.0273 versus 0.0784 ml/min/kg) values were significantly slower than in the controls. The slower Cl(nr) could be due mainly to a significantly smaller total amount of unchanged DA-7867 recovered from the gastrointestinal tract at 24 h (GI(24 h): 5.16% versus 9.21% of intravenous dose) due to impaired liver function in the rat model of dehydration. The slower Cl(r) could be due mainly to a significantly smaller 24 h urinary excretion of unchanged drug (Ae(0-24 h): 4.41% versus 7.75% of intravenous dose) due to urine flow rate-dependent Cl(r) of DA-7867 in the rat model of dehydration. Hence, the Cl was significantly slower in the rat model of dehydration (0.677 versus 1.07 ml/min/kg). After intravenous administration in the rat model of dehydration, the V(ss) of DA-7867 was significantly smaller than in the controls (396 versus 506 ml/kg) due mainly to significantly smaller free (unbound to plasma proteins) fractions of DA-7867 in plasma (6.90% versus 29.2%) in the rat model of dehydration. After oral administration in the rat model of dehydration, the AUC was significantly greater than that in controls (10800 versus 7060 microg min/ml) due mainly to a significantly smaller Ae(0-24 h) than in controls (3.50% and 6.17% of oral dose).

Administration, Oral↗
PubMed2005

Effect of spinal cord injury severity on alterations of the H-reflex.

The monosynaptic motoneuron response to stimulation of Ia afferents is known to be altered by spinal cord injury (SCI). Although the Hoffman (H)-reflex is a tool that is often used to measure this reflex in patients, there has not been a systematic study investigating the effect of SCI severity and time on the H-reflex. We used a clinically relevant model of spinal cord contusion (Mild and Moderate) as well as complete surgical transection to measure the H-reflex at 1, 4 and 8 weeks after injury. The H-reflex was recorded from rat hindpaw plantar muscles in order to measure the baseline reflex amplitude and its response to increased stimulus frequency, i.e. rate depression. We correlated the reflex amplitude at each frequency to spared white matter at the injury epicenter, hindlimb function and serotonin immunoreactivity associated with retrogradely labeled plantar muscle motoneurons. The three injury groups displayed different behavioral deficits and amount of spared white matter at all three times tested. H-reflex rate depression was abnormal in all three injury groups at all three time points. At 8 weeks, transected animals displayed more H-reflex rate depression than those with a mild contusion. Baseline H-reflex amplitude was increased in both contusion groups at 4 weeks and showed a positive linear correlation with serotonin immunoreactivity. This baseline amplitude was not increased after transection. Furthermore, in the contusion group, there was a U-shaped relationship between behavioral scores and H-reflex rate depression, suggesting that an intermediate sensitivity of the motoneuronal pool to afferent input is associated with better recovery of hindlimb function.

Analysis of Variance↗
PubMed2005

Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data.

BACKGROUND: The evaluation of statistical significance has become a critical process in identifying differentially expressed genes in microarray studies. Classical p-value adjustment methods for multiple comparisons such as family-wise error rate (FWER) have been found to be too conservative in analyzing large-screening microarray data, and the False Discovery Rate (FDR), the expected proportion of false positives among all positives, has been recently suggested as an alternative for controlling false positives. Several statistical approaches have been used to estimate and control FDR, but these may not provide reliable FDR estimation when applied to microarray data sets with a small number of replicates. RESULTS: We propose a rank-invariant resampling (RIR) based approach to FDR evaluation. Our proposed method generates a biologically relevant null distribution, which maintains similar variability to observed microarray data. We compare the performance of our RIR-based FDR estimation with that of four other popular methods. Our approach outperforms the other methods both in simulated and real microarray data. CONCLUSION: We found that the SAM's random shuffling and SPLOSH approaches were liberal and the other two theoretical methods were too conservative while our RIR approach provided more accurate FDR estimation than the other approaches.

Algorithms↗
PubMed2005

Robust classification modeling on microarray data using misclassification penalized posterior.

MOTIVATION: Genome-wide microarray data are often used in challenging classification problems of clinically relevant subtypes of human diseases. However, the identification of a parsimonious robust prediction model that performs consistently well on future independent data has not been successful due to the biased model selection from an extremely large number of candidate models during the classification model search and construction. Furthermore, common criteria of prediction model performance, such as classification error rates, do not provide a sensitive measure for evaluating performance of such astronomic competing models. Also, even though several different classification approaches have been utilized to tackle such classification problems, no direct comparison on these methods have been made. RESULTS: We introduce a novel measure for assessing the performance of a prediction model, the misclassification-penalized posterior (MiPP), the sum of the posterior classification probabilities penalized by the number of incorrectly classified samples. Using MiPP, we implement a forward step-wise cross-validated procedure to find our optimal prediction models with different numbers of features on a training set. Our final robust classification model and its dimension are determined based on a completely independent test dataset. This MiPP-based classification modeling approach enables us to identify the most parsimonious robust prediction models only with two or three features on well-known microarray datasets. These models show superior performance to other models in the literature that often have more than 40-100 features in their model construction. AVAILABILITY: Our MiPP software program is available at the Bioconductor website (http://www.bioconductor.org).

Algorithms↗
PubMed2005

Diagnostic plots for detecting outlying slides in a cDNA microarray experiment.

Different sources of systematic and random error variations are often observed in cDNA microarray experiments. A simple scatter plot is commonly used to examine outlying slides that have unusual expression patterns or larger variability than other slides. These outlying slides tend to have large impacts on the subsequent analyses, such as identification of differentially expressed genes and clustering analysis. However, it is difficult to select outlying slides rigorously and consistently based on subjective human pattern recognition on their scatter plots. A graphical method and a rigorous diagnostic measure are proposed to detect outlying slides. The proposed graphical method is easy to implement and shown to be quite effective in detecting outlying slides in real microarray data sets. This diagnostic measure is also informative to compare variability among slides. Two cDNA microarray data sets are carefully examined to illustrate the proposed approach. A 3840-gene microarray experiment for neuronal differentiation of cortical stem cells and a 2076-gene microarray experiment for anticancer compound time-course expression of the NCI-60 cancer cell lines.

Algorithms↗
PubMed2004

CXC chemokine receptor 3 expression by activated CD8+ T cells is associated with survival in melanoma patients with stage III disease.

Despite the presence of tumor Ag-specific CD8(+) T cells in the peripheral blood, metastatic melanoma often evades immune-mediated destruction. Even after therapeutic efforts to expand Ag-specific T-cell populations, the correlation between magnitude of response and clinical efficacy has been weak. Because the migratory phenotype of tumor Ag-specific effector T cells may determine their ability for tumor control, we hypothesized that the expression of CC or CXC chemokine receptor (CCR) molecules on activated CD8(+) T cells may define phenotypes associated with more effective control of melanoma progression and prolonged survival. In a retrospective evaluation of patient isolates, CCR expression was determined for activated CD8(+) T cells derived from the peripheral blood or tumor-involved lymph nodes of 52 patients with stage III or IV metastatic melanoma. In patients with stage III disease, expression of CXCR3 by CD8(+)CD45RO(+) cells was significantly associated with enhanced survival. This was a stage-specific effect, because it was not observed in patients with stage IV disease. In addition, CCR4 and CXCR3 were highly coexpressed and associated with enhanced survival in stage III patients; however, CXCR3 seems to be the dominant receptor associated with clinical outcome. These findings support the hypothesis that the host immune system affects cancer progression and control, and that measures of CCR status of circulating lymphocytes may have prognostic value.

CD8-Positive T-Lymphocytes↗
PubMed2004

Lipoic acid pretreatment attenuates ferric chloride-induced seizures in the rat.

Traumatic brain injury (TBI) is often complicated by the occurrence of seizures, which adversely affect clinical outcome. The risk of seizures increases to the extent that the injury is associated with sub-arachnoid hemorrhage and hematoma. A likely mechanism of seizure development post-TBI is decompartmentalization of iron from extravasated hemoglobin (Hb). It is well known that iron can catalyze formation of reactive oxygen species (ROS). Based on this proposed mechanism, a descriptive model of TBI-induced seizures, using intracortical injection of iron salts, was developed by Willmore. We have added modifications to enhance the quantifiability of seizure activity and have used the model to examine the therapeutic efficacy of lipoic acids (ROS-scavenging antioxidants). Male SD rats were pretreated with alpha-lipoic acid (ALA) and dihydrolipoic acid (DHLA) or appropriate vehicles. Under anesthesia, unilateral intracortical infusions of ferric chloride were performed stereotaxically. EEG was recorded via extradural electrodes. EEG was sampled for 10 s of every 60-s interval over a 24-h period following injection of ferric chloride. We measured the number of seconds of epileptiform discharges or seizure activity in every 10-s EEG sample during the 24 h. The EEGs of rats pretreated with ALA and DHLA exhibited 55% less seizure activity than vehicle-treated ferric chloride-injected animals, suggesting that lipoic acids may be of use in preventing or attenuating TBI-induced seizures.

Animals↗
PubMed2004

Bayesian hierarchical error model for analysis of gene expression data.

MOTIVATION: Analysis of genome-wide microarray data requires the estimation of a large number of genetic parameters for individual genes and their interaction expression patterns under multiple biological conditions. The sources of microarray error variability comprises various biological and experimental factors, such as biological and individual replication, sample preparation, hybridization and image processing. Moreover, the same gene often shows quite heterogeneous error variability under different biological and experimental conditions, which must be estimated separately for evaluating the statistical significance of differential expression patterns. Widely used linear modeling approaches are limited because they do not allow simultaneous modeling and inference on the large number of these genetic parameters and heterogeneous error components on different genes, different biological and experimental conditions, and varying intensity ranges in microarray data. RESULTS: We propose a Bayesian hierarchical error model (HEM) to overcome the above restrictions. HEM accounts for heterogeneous error variability in an oligonucleotide microarray experiment. The error variability is decomposed into two components (experimental and biological errors) when both biological and experimental replicates are available. Our HEM inference is based on Markov chain Monte Carlo to estimate a large number of parameters from a single-likelihood function for all genes. An F-like summary statistic is proposed to identify differentially expressed genes under multiple conditions based on the HEM estimation. The performance of HEM and its F-like statistic was examined with simulated data and two published microarray datasets-primate brain data and mouse B-cell development data. HEM was also compared with ANOVA using simulated data. AVAILABILITY: The software for the HEM is available from the authors upon request.

Algorithms↗
PubMed2004

Developing optimal prediction models for cancer classification using gene expression data.

Microarrays can provide genome-wide expression patterns for various cancers, especially for tumor sub-types that may exhibit substantially different patient prognosis. Using such gene expression data, several approaches have been proposed to classify tumor sub-types accurately. These classification methods are not robust, and often dependent on a particular training sample for modelling, which raises issues in utilizing these methods to administer proper treatment for a future patient. We propose to construct an optimal, robust prediction model for classifying cancer sub-types using gene expression data. Our model is constructed in a step-wise fashion implementing cross-validated quadratic discriminant analysis. At each step, all identified models are validated by an independent sample of patients to develop a robust model for future data. We apply the proposed methods to two microarray data sets of cancer: the acute leukemia data by Golub et al. and the colon cancer data by Alon et al. We have found that the dimensionality of our optimal prediction models is relatively small for these cases and that our prediction models with one or two gene factors outperforms or has competing performance, especially for independent samples, to other methods based on 50 or more predictive gene factors. The methodology is implemented and developed by the procedures in R and Splus. The source code can be obtained at http://hesweb1.med.virginia.edu/bioinformatics.

Colonic Neoplasms↗
PubMed2004

GeneX Va: VBC open source microarray database and analysis software.

Developed by the Virginia Bioinformatics Consortium (VBC), GeneX Va is an open source, freeware database and bioinformatics analysis software for archiving and analyzing Affymetrix GeneChip data. It provides an integrated framework for management, documentation, and analysis of microarray experiments and data to support a range of users, from individual research laboratories to institutional microarray facilities. GeneX Va also provides web-based access to a PostgreSQL relational database system with a comprehensive security system. Data can be extracted from the database and delivered to interactive or scriptable statistical analysis protocols. The security system allows each investigator to manage their own array data and analysis output files and also provides custom access privileges for other users, groups, and internal/external collaborators. The analysis interface uses "Analysis Trees," an innovative user interface that allows researchers to interactively create a tree-structured flow chart of analysis routines. The latest GeneX Va software is available from and can be freely downloaded at the Sourceforge web site http://va-genex.sourceforge.net. To allow researchers to access the database and analysis capabilities of the GeneX Va system, microarray data from many VBC GeneChip experiments have been deposited into a public section of the GeneX Va system at the University of Virginia. The VBC GeneX Va sites, which include documentation, are at http://genes.med.virginia.edu/ of the University of Virginia and at http://genex.csbc.vcu.edu/ of the Virginia Commonwealth University.

Computer Security↗
PubMed2003

Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells.

Microarray gene-expression profiles are generally validated one gene at a time by real-time RT-PCR. We describe here a different approach based on simultaneous mutual validation of large numbers of genes using two different expression-profiling platforms. The result described here for the NCI-60 cancer cell lines is a consensus set of genes that give similar profiles on spotted cDNA arrays and Affymetrix oligonucleotide chips. Global concordance is parameterized by a 'correlation of correlations' coefficient.

Algorithms↗
PubMed2003

Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays.

Because most potential molecular markers and targets are proteins, proteomic profiling is expected to yield more direct answers to functional and pharmacological questions than does transcriptional profiling. To aid in such studies, we have developed a protocol for making reverse-phase protein lysate microarrays with larger numbers of spots than previously feasible. Our first application of these arrays was to profiling of the 60 human cancer cell lines (NCI-60) used by the National Cancer Institute to screen compounds for anticancer activity. Each glass slide microarray included 648 lysate spots representing the NCI-60 cell lines plus controls, each at 10 two-fold serial dilutions to provide a wide dynamic range. Mouse monoclonal antibodies and the catalyzed signal amplification system were used for immunoquantitation. The signal levels from the >30,000 data points for our first 52 antibodies were analyzed by using p-scan and a quantitative dose interpolation method. Clustered image maps revealed biologically interpretable patterns of protein expression. Among the principal early findings from these arrays were two promising pathological markers for distinguishing colon from ovarian adenocarcinomas. When we compared the patterns of protein expression with those we had obtained for the same genes at the mRNA level by using both cDNA and oligonucleotide arrays, a striking regularity appeared: cell-structure-related proteins almost invariably showed a high correlation between mRNA and protein levels across the NCI-60 cell lines, whereas non-cell-structure-related proteins showed poor correlation.

Blotting, Western↗
PubMed2003

Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays.

MOTIVATION: In microarray studies gene discovery based on fold-change values is often misleading because error variability for each gene is heterogeneous under different biological conditions and intensity ranges. Several statistical testing methods for differential gene expression have been suggested, but some of these approaches are underpowered and result in high false positive rates because within-gene variance estimates are based on a small number of replicated arrays. RESULTS: We propose to use local-pooled-error (LPE) estimates and robust statistical tests for evaluating significance of each gene's differential expression. Our LPE estimation is based on pooling errors within genes and between replicate arrays for genes in which expression values are similar. We have applied our LPE method to compare gene expression in naïve and activated CD8+ T-cells. Our results show that the LPE method effectively identifies significant differential-expression patterns with a small number of replicated arrays. AVAILABILITY: The methodology is implemented with S-PLUS and R functions available at http://hesweb1.med.virginia.edu/bioinformatics

Algorithms↗
PubMed2003

Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling.

Colon and ovarian cancers can be difficult to distinguish in the abdomen, and the distinction is important because it determines which drugs will be used for therapy. To identify molecular markers for that differential diagnosis, we developed a multistep protocol starting with the 60 human cancer cell lines used by the National Cancer Institute to screen for new anticancer agents. The steps included: (a) identification of candidate markers using cDNA microarrays; (b) verification of clone identities by resequencing; (c) corroboration of transcript levels using Affymetrix oligonucleotide chips; (d) quantitation of protein expression by "reverse-phase" protein microarray; and (e) prospective validation of candidate markers on clinical tumor sections in tissue microarrays. The two best candidates identified were villin for colon cancer cells and moesin for ovarian cancer cells. Because moesin stained stromal elements in both types of cancer, it would probably not have been identified as a marker if we had started with mRNA or protein profiling of bulk tumors. Villin appears at least as useful as the currently used colon cancer marker cytokeratin 20, and moesin also appears to have utility. The multistep process introduced here has the potential to produce additional markers for cancer diagnosis, prognosis, and therapy.

Adenocarcinoma↗
PubMed2002

Gene expression profile of mouse myocardium with transgenic overexpression of A1 adenosine receptors.

Transgenic mice with cardiac-specific overexpression of adenosine A(1) receptors (A(1)AR) have demonstrated metabolic and functional tolerance to myocardial ischemia. We utilized cDNA microarrays to test the hypothesis that the cardioprotective mechanism(s) of A(1) overexpression involves altered gene expression. Total RNA extracted from the left ventricles from A(1) transgenic (n = 4) and wild-type (n = 6) mice was hybridized to Affymetrix mgU74A chips. Comparison of RNA expression levels in transgenic to wild-type myocardium revealed approximately 636 known genes with expression significantly altered by greater than 25%. We observed increased expressions of genes including NADH dehydrogenase, the GLUT4 glucose transporter, Na-K-ATPase, sarcolemmal K(ATP) channels, and Bcl-xl in A(1)AR-overexpressing hearts. We also observed decreased expression of pro-apoptotic genes including a 50% reduction in message level of caspase-8. Protein expression of GLUT4 and caspase-8 was also altered comparable to the differences in gene expression. These data illustrate genes with chronically altered patterns of expression in A(1) transgenic mouse myocardium that may be related to adenosine receptor overexpression-mediated cardioprotection.

Adenosine Triphosphate↗
PubMedDate not supplied

Radiation dose to the operator during vertebroplasty: prospective comparison of the use of 1-cc syringes versus an injection device.

BACKGROUND AND PURPOSE: Percutaneous vertebroplasty procedures require relatively long durations of fluoroscopic guidance, which might lead to substantial radiation dose to operators. Specialized injection devices have been proposed to limit operator exposure. Our purpose was to compare the radiation dose to the operator's hands during vertebroplasty when using 1-cc syringes versus that when using an injection device. METHODS: Radiation dosimeters were worn on the left wrist during 39 vertebroplasty injection procedures in 25 patients. Cases were alternated between the use of 1-cc syringes (19 procedures) and the use of an injection device (20 procedures). For each procedure, one dosimeter was worn throughout the procedure, both during needle placement and injection, and a second dosimeter was worn during the injection phase only. Mean doses for the whole case and mean doses for the injection procedure alone were compared between groups. RESULTS: Mean whole case dose was 128 +/- 161 mrem (range, 0-660 mrem) for the 1-cc syringe group versus 98 +/- 90 mrem (range, 0-340 mrem) for the injection device group (P =.23). Mean dose during injection was 100 +/- 145 mrem (range, 0-660 mrem) for the 1-cc syringe group versus 55 +/- 43 mrem (range, 0-130 mrem) for the injection device group (P =.09). Three of 19 1-cc syringe cases yielded zero dose, compared with four of 20 injection device cases. Duration of injection was markedly different between groups, with mean injection times of 4.2 and 7.5 min for 1-cc syringe and injection device cases, respectively (P <.00002). Mean injection dose per minute of lateral fluoroscopy was 23.6 and 7.3 mrem for the 1-cc syringe and injection device groups, respectively (P =.002). CONCLUSION: The use of an injection device significantly decreased the radiation dose to the operator's extremity per unit time of injection. However, total dose per injection was equivalent between groups because of significantly longer injection duration for the injection device cohort.

Bone Cements↗