Genomes and Genes
Chap T Le
Affiliation: University of Minnesota
- A solution for the most basic optimization problem associated with an ROC curveChap T Le
School of Public Health, Division of Biostatistics and Cancer Center, University of Minnesota, MMC 303, Minneapolis 55455, USA
Stat Methods Med Res 15:571-84. 2006..The difficulty lies in our failure to define and justify a criterion for optimality. In this paper, we will propose a solution by maximizing a well-known parameter--the Youden's Index--within the framework of the ROC curve...
- Estimation of cancer drug potencies and relative potencies from in vitro dataT Le Chap
Division of Biostatistics, University of Minnesota, School of Public Health, Minneapolis, Minnesota 55455, USA
J Biopharm Stat 15:903-12. 2005..A simulation study illustrates substantial gains in efficiency in the estimation of the median effective dose...
- Design and analysis of in vitro experiments for combination chemotherapyT Le Chap
School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, USA
J Biopharm Stat 15:179-86. 2005..We then propose a statistical framework, a simple experimental design, and a statistical test for use with this widely accepted methodology. The test we propose is a score test based on the linear logistic regression model...
- Quality control and the identification of vaccine responders using ELISA-derived antibody dataChap T Le
School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
Stat Med 22:2935-42. 2003..The goal is to show that these two issues are inter-related, so that investigators could reduce misclassification which would interfere with the eventual comparison of immunogenicity results...
- Cap-dependent translation blockade and fixed dose-rate gemcitabine: interaction in an in vitro bioreactor systemBrent W Williams
Department of Experimental and Clinical Pharmacology, College of Pharmacy and Comprehensive Cancer Center, University of Minnesota, 717 Delaware St SE, Minneapolis, MN 55414, USA
Cancer Lett 284:37-46. 2009..We conclude that cap-dependent translation blockade and fixed dose rate infusion gemcitabine treatment results in a significant interaction affecting cell viability in vitro...
- Relationships between cigarette consumption and biomarkers of tobacco toxin exposureAnne M Joseph
Section of General Internal Medicine 111 0, VA Medical Center, One Veterans Drive, Minneapolis, MN 55417, USA
Cancer Epidemiol Biomarkers Prev 14:2963-8. 2005....
- A two-part mixed effects model for cigarette purchase task dataTingting Zhao
Division of Biostatistics, School of Public Health, University of Minnesota
J Exp Anal Behav 106:242-253. 2016..Monte Carlo simulations showed that the proposed model provides better fits than an existing model. We note that the proposed methodology is applicable to other purchase task data, for example, drugs of abuse...
- A mixture model approach to detecting differentially expressed genes with microarray dataWei Pan
Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo, MMC 303, 420 Delaware Street SE, Minneapolis, MN 55455 0378, USA
Funct Integr Genomics 3:117-24. 2003..Several methods are proposed to effectively control the false positives. The methodology is applied to a data set containing expression levels of 1,176 genes of rats with and without pneumococcal middle ear infection...
- Donors with group B KIR haplotypes improve relapse-free survival after unrelated hematopoietic cell transplantation for acute myelogenous leukemiaSarah Cooley
University of Minnesota, Minneapolis, USA
Blood 113:726-32. 2009..KIR genotyping of prospective donors, in addition to HLA typing, should be performed to identify HLA-matched donors with B KIR haplotypes...
- Does the hematopoietic cell transplantation specific comorbidity index predict transplant outcomes? A validation study in a large cohort of umbilical cord blood and matched related donor transplantsNavneet S Majhail
Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, Minnesota 55455, USA
Biol Blood Marrow Transplant 14:985-92. 2008..The HCT-CI, although a useful tool for capturing pretransplant comorbidity and risk-assessment, needs to be further validated prior to adopting it for routine clinical use...
- Smoking reduction fails to improve clinical and biological markers of cardiac disease: a randomized controlled trialAnne M Joseph
Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55414, USA
Nicotine Tob Res 10:471-81. 2008..These results emphasize the importance of abstinence for smokers with heart disease to minimize health risks from tobacco...
- How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approachWei Pan
Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware Street, Minneapolis, MN 55455 0378, USA
Genome Biol 3:research0022. 2002..Here, we discuss how to calculate the number of replicates in the context of applying a nonparametric statistical method, the normal mixture model approach, to detect changes in gene expression...
- Toxicant exposure in cigarette reducers versus light smokersDorothy K Hatsukami
Tobacco Use Research Center, University of Minnesota, 2701 University Avenue Southeast, 201, Minneapolis, MN 55414, USA
Cancer Epidemiol Biomarkers Prev 15:2355-8. 2006..The goal of this study is to investigate the occurrence of compensatory smoking in reducers compared with light smokers by measuring toxicant exposure...
- Model-based cluster analysis of microarray gene-expression dataWei Pan
Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455 0378, USA
Genome Biol 3:RESEARCH0009. 2002..Here, we introduce and illustrate its use in detecting differentially expressed genes. In particular, we do not cluster gene-expression patterns but a summary statistic, the t-statistic...
- Preliminary study on reducing oral moist snuff useDorothy K Hatsukami
University of Minnesota, Tobacco Use Research Center, 2701 University Ave SE, 210, Minneapolis 55414, USA
Drug Alcohol Depend 70:215-20. 2003..This pilot study examined whether reducing ST use using various methods can be achieved and whether this reduction results in lower exposure to carcinogens...
- Diminished neo-antigen response to keyhole limpet hemocyanin (KLH) vaccines in patients after treatment with chemotherapy or hematopoietic cell transplantationJeffrey S Miller
Divisions of Medical and Pediatric Hematology Oncology and Transplantation, The Blood and Marrow Transplant Program, Department of Biostatistics, and The University of Minnesota Cancer Center, MN 55455, USA
Clin Immunol 117:144-51. 2005..KLH vaccines are safe and require only a single injection to test neo-antigen responses providing an optimal platform for definitive testing of strategies to improve diminished immune recovery after chemotherapy or post-HCT...
- Some statistical methods for investigating the date of birth as a disease indicatorChap T Le
School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
Stat Med 22:2127-35. 2003....
- Donor selection for natural killer cell receptor genes leads to superior survival after unrelated transplantation for acute myelogenous leukemiaSarah Cooley
Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
Blood 116:2411-9. 2010..Adopting this practice could result in superior disease-free survival for patients with AML...
- Effect of cigarette smoking on urinary 2-hydroxypropylmercapturic acid, a metabolite of propylene oxideAdam T Zarth
Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, MN 55455, USA Electronic address
J Chromatogr B Analyt Technol Biomed Life Sci 953:126-31. 2014..The method presented here can be used to rapidly quantify an individual's exposure to propylene oxide via tobacco smoke or other sources. ..
- Short versus continuous gemcitabine treatment of non-small cell lung cancer in an in vitro cell culture bioreactor systemMark N Kirstein
Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
Lung Cancer 58:196-204. 2007..0085). In conclusion, gemcitabine infused by this novel method induced apoptosis after both the short and continuous infusions, and long-term survival was significantly diminished following continuous compared with the short infusion...
- A prospectively measured serum biomarker for a tobacco-specific carcinogen and lung cancer in smokersTimothy R Church
Division of Environmental Health Sciences, University of Minnesota School of Public Health, Minneapolis, Minnesota, USA
Cancer Epidemiol Biomarkers Prev 18:260-6. 2009..Its metabolites, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol and its glucuronides (total NNAL), have been studied as biomarkers of exposure to NNK. We studied the relation of prospectively measured NNK biomarkers to lung cancer risk...
- Carcinogenicity and DNA adduct formation of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone and enantiomers of its metabolite 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol in F-344 ratsSilvia Balbo
Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
Carcinogenesis 35:2798-806. 2014..The results of this study clearly demonstrate the potent pulmonary carcinogenicity of both enantiomers of NNAL in rats and provide important new information regarding DNA damage by these compounds in lung and pancreas. ..
- Analysis of 4-hydroxy-1-(3-pyridyl)-1-butanone (HPB)-releasing DNA adducts in human exfoliated oral mucosa cells by liquid chromatography-electrospray ionization-tandem mass spectrometryIrina Stepanov
Masonic Cancer Center and Division of Environmental Health Sciences, University of Minnesota, Mayo Mail Code 806, 420 Delaware Street SE, Minneapolis, Minnesota 55455, United States
Chem Res Toxicol 26:37-45. 2013..73, p < 0.0001). Potentially, the method can be applied in studies of individual susceptibility to tobacco-induced cancers in humans. ..
- Analysis of cigarette purchase task instrument data with a left-censored mixed effects modelWenjie Liao
Division of Biostatistics, School of Public Health and Department of Sociology, University of Minnesota, USA
Exp Clin Psychopharmacol 21:124-32. 2013..Theoretical implications of the findings, limitations of the proposed method, and future directions of research are also discussed...
- Efficacy of an osmotic pump delivered, GM-CSF-based tumor vaccine in the treatment of upper aerodigestive squamous cell carcinoma in ratsHamid R Djalilian
Department of Otolaryngology, University of Minnesota, Minneapolis, MN 55455, USA
Cancer Immunol Immunother 56:1207-14. 2007..We presently tested the efficacy of granulocyte macrophage-colony stimulating factor (GM-CSF) delivered via 28-day continuous infusion pump, in combination with irradiated tumor cells, in a flank model of UADT cancer...
- Reduced nicotine distribution from mother to fetal brain in rats vaccinated against nicotine: time course and influence of nicotine dosing regimenDaniel E Keyler
Minneapolis Medical Research Foundation, Hennepin County Medical Center, Minneapolis, MN 55415, USA
Biochem Pharmacol 69:1385-95. 2005..These data comment on the safety of vaccination against nicotine during pregnancy, and suggest that vaccination may reduce the distribution of nicotine to fetal brain under some nicotine dosing conditions...
- Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesionsEbbing P de Jong
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
PLoS ONE 5:e11148. 2010..A test for proteins, ones found in non-invasively-collected whole saliva and whose abundances distinguish these lesion types, would meet this critical need...
- Purulent otitis media in children and adultsMuhammet Tekin
The Otitis Media Research Center, Department of Otolaryngology, University of Minnesota Medical School, Minneapolis, USA
Eur Arch Otorhinolaryngol 259:67-72. 2002..Our findings suggest the need to monitor children carefully under the age of 2 years who have POM...