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1.  Knowledge of the Health Consequences of Obesity among Overweight/Obese Black and Hispanic Adults 
Patient education and counseling  2014;94(1):123-127.
To measure knowledge of the health consequences of obesity among overweight/obese Black and Hispanic adults and examine the relationship to prior weight loss.
Knowledge of the health consequences of obesity was assessed among 410 Black and Hispanic adults with BMI ≥ 25 kg/m2 enrolled in a behavior change weight loss study. The relationship between obesity risk knowledge and previous weight loss was also examined.
The majority of participants were knowledgeable of the risk of hypertension (94%), diabetes (96%), high cholesterol (91%), joint pains/arthritis (89%) and sleep apnea (89%) associated with obesity. Among post-menopausal age women, 53% were aware of the increased risk of breast cancer. There was no significant relationship between obesity risk knowledge and previous weight loss of 10 pounds or more (OR= 1.075, 95% CI: [0.808, 1.430]).
We found that knowledge of the health consequences of obesity was high, except for knowledge of the risk of breast cancer. Obesity risk knowledge was not associated with past weight loss.
Practice implications
Further health education is needed regarding the increased risk of breast cancer associated with obesity. Our data suggest that knowledge of the health consequences of obesity is not associated with weight loss success.
PMCID: PMC4059523  PMID: 24479156
obesity; patient education; health education; health behavior; minority populations
2.  The Charlson Comorbidity Index Can Be Used Prospectively to Identify Patients Who Will Incur High Future Costs 
PLoS ONE  2014;9(12):e112479.
Reducing health care costs requires the ability to identify patients most likely to incur high costs. Our objective was to evaluate the ability of the Charlson comorbidity score to predict the individuals who would incur high costs in the subsequent year and to contrast its predictive ability with other commonly used predictors.
We contrasted the prior year Charlson comorbidity index, costs, Diagnostic Cost Group (DCG) and hospitalization as predictors of subsequent year costs from claims data of fund that provides comprehensive health benefits to a large union of health care workers. Total costs in the subsequent year was the principal outcome.
Of the 181,764 predominantly Black and Latino beneficiaries, 70% were adults (mean age 45.7 years; 62% women). As the comorbidity index increased, total yearly costs increased significantly (P<.001). At lower comorbidity, the costs were similar across different chronic diseases. Using regression to predict total costs, top 5th and 10th percentile of costs, the comorbidity index, prior costs and DCG achieved almost identical explained variance in both adults and children.
Conclusions and Relevance
The comorbidity index predicted health costs in the subsequent year, performing as well as prior cost and DCG in identifying those in the top 5% or 10%. The comorbidity index can be used prospectively to identify patients who are likely to incur high costs.
Trial Registration NCT01761253
PMCID: PMC4254512  PMID: 25469987
3.  Large-Scale Genome-Wide Association Studies and Meta-Analyses of Longitudinal Change in Adult Lung Function 
Tang, Wenbo | Kowgier, Matthew | Loth, Daan W. | Soler Artigas, María | Joubert, Bonnie R. | Hodge, Emily | Gharib, Sina A. | Smith, Albert V. | Ruczinski, Ingo | Gudnason, Vilmundur | Mathias, Rasika A. | Harris, Tamara B. | Hansel, Nadia N. | Launer, Lenore J. | Barnes, Kathleen C. | Hansen, Joyanna G. | Albrecht, Eva | Aldrich, Melinda C. | Allerhand, Michael | Barr, R. Graham | Brusselle, Guy G. | Couper, David J. | Curjuric, Ivan | Davies, Gail | Deary, Ian J. | Dupuis, Josée | Fall, Tove | Foy, Millennia | Franceschini, Nora | Gao, Wei | Gläser, Sven | Gu, Xiangjun | Hancock, Dana B. | Heinrich, Joachim | Hofman, Albert | Imboden, Medea | Ingelsson, Erik | James, Alan | Karrasch, Stefan | Koch, Beate | Kritchevsky, Stephen B. | Kumar, Ashish | Lahousse, Lies | Li, Guo | Lind, Lars | Lindgren, Cecilia | Liu, Yongmei | Lohman, Kurt | Lumley, Thomas | McArdle, Wendy L. | Meibohm, Bernd | Morris, Andrew P. | Morrison, Alanna C. | Musk, Bill | North, Kari E. | Palmer, Lyle J. | Probst-Hensch, Nicole M. | Psaty, Bruce M. | Rivadeneira, Fernando | Rotter, Jerome I. | Schulz, Holger | Smith, Lewis J. | Sood, Akshay | Starr, John M. | Strachan, David P. | Teumer, Alexander | Uitterlinden, André G. | Völzke, Henry | Voorman, Arend | Wain, Louise V. | Wells, Martin T. | Wilk, Jemma B. | Williams, O. Dale | Heckbert, Susan R. | Stricker, Bruno H. | London, Stephanie J. | Fornage, Myriam | Tobin, Martin D. | O′Connor, George T. | Hall, Ian P. | Cassano, Patricia A.
PLoS ONE  2014;9(7):e100776.
Genome-wide association studies (GWAS) have identified numerous loci influencing cross-sectional lung function, but less is known about genes influencing longitudinal change in lung function.
We performed GWAS of the rate of change in forced expiratory volume in the first second (FEV1) in 14 longitudinal, population-based cohort studies comprising 27,249 adults of European ancestry using linear mixed effects model and combined cohort-specific results using fixed effect meta-analysis to identify novel genetic loci associated with longitudinal change in lung function. Gene expression analyses were subsequently performed for identified genetic loci. As a secondary aim, we estimated the mean rate of decline in FEV1 by smoking pattern, irrespective of genotypes, across these 14 studies using meta-analysis.
The overall meta-analysis produced suggestive evidence for association at the novel IL16/STARD5/TMC3 locus on chromosome 15 (P  =  5.71 × 10-7). In addition, meta-analysis using the five cohorts with ≥3 FEV1 measurements per participant identified the novel ME3 locus on chromosome 11 (P  =  2.18 × 10-8) at genome-wide significance. Neither locus was associated with FEV1 decline in two additional cohort studies. We confirmed gene expression of IL16, STARD5, and ME3 in multiple lung tissues. Publicly available microarray data confirmed differential expression of all three genes in lung samples from COPD patients compared with controls. Irrespective of genotypes, the combined estimate for FEV1 decline was 26.9, 29.2 and 35.7 mL/year in never, former, and persistent smokers, respectively.
In this large-scale GWAS, we identified two novel genetic loci in association with the rate of change in FEV1 that harbor candidate genes with biologically plausible functional links to lung function.
PMCID: PMC4077649  PMID: 24983941
4.  Intermediate-Type Vancomycin Resistance (VISA) in Genetically-Distinct Staphylococcus aureus Isolates Is Linked to Specific, Reversible Metabolic Alterations 
PLoS ONE  2014;9(5):e97137.
Intermediate (VISA-type) vancomycin resistance in Staphylococcus aureus has been associated with a range of physiologic and genetic alterations. Previous work described the emergence of VISA-type resistance in two clonally-distinct series of isolates. In both series (the first belonging to MRSA clone ST8-USA300, and the second to ST5-USA100), resistance was conferred by a single mutation in yvqF (a negative regulator of the vraSR two-component system associated with vancomycin resistance). In the USA300 series, resistance was reversed by a secondary mutation in vraSR. In this study, we combined systems-level metabolomic profiling with statistical modeling techniques to discover specific, reversible metabolic alterations associated with the VISA phenotype.
PMCID: PMC4016254  PMID: 24817125
5.  Translating Basic Behavioral and Social Science Research to Clinical Application: The EVOLVE Mixed Methods Approach 
To describe a mixed-methods approach to develop and test a basic behavioral science-informed intervention to motivate behavior change in three high-risk clinical populations. Our theoretically-derived intervention comprised a combination of positive affect and self-affirmation (PA/SA) which we applied to three clinical chronic disease populations.
We employed a sequential mixed methods model (EVOLVE) to design and test the PA/SA intervention in order to increase physical activity in people with coronary artery disease (post-percutaneous coronary intervention [PCI]) or asthma (ASM), and to improve medication adherence in African Americans with hypertension (HTN). In an initial qualitative phase, we explored participant values and beliefs. We next pilot tested and refined the intervention, and then conducted three randomized controlled trials (RCTs) with parallel study design. Participants were randomized to combined PA/SA vs. an informational control (IC) and followed bimonthly for 12 months, assessing for health behaviors and interval medical events.
Over 4.5 years, we enrolled 1,056 participants. Changes were sequentially made to the intervention during the qualitative and pilot phases. The three RCTs enrolled 242 PCI, 258 ASM and 256 HTN participants (n=756). Overall, 45.1% of PA/SA participants versus 33.6% of IC participants achieved successful behavior change (p=0.001). In multivariate analysis PA/SA intervention remained a significant predictor of achieving behavior change (p<0.002, OR=1.66, 95% CI 1.22–2.27), controlling for baseline negative affect, comorbidity, gender, race/ethnicity, medical events, smoking and age.
The EVOLVE method is a means by which basic behavioral science research can be translated into efficacious interventions for chronic disease populations.
PMCID: PMC3578179  PMID: 22963594
Behavioral intervention; behavioral risk reduction; health behavior; mixed methods; translational research
6.  Improvement in Asthma Quality of Life in Patients Enrolled in a Prospective Study to Increase Lifestyle Physical Activity 
Asthma patients know the benefits of exercise but often avoid physical activity because they are concerned it will exacerbate asthma. The objective of this analysis was to assess longitudinal asthma status in 256 primary care patients in New York City enrolled in a trial to increase lifestyle physical activity.
Patients were randomized to two protocols to increase physical activity during 12 months. At enrollment patients completed the Asthma Quality of Life Questionnaire (AQLQ) and the Asthma Control Questionnaire (ACQ), and received asthma self-management instruction through an evaluative test and workbook. Exercise and self-management were reinforced every 2 months. The AQLQ was repeated every 4 months and the ACQ was repeated at 12 months.
The mean age was 43 years and 75% were women. At 12 months there were clinically important increases in physical activity with no differences between groups; thus data were pooled for asthma analyses. The enrollment AQLQ score was 5.0±1.3 and increased to 5.9±1.1; corresponding to a clinically important difference. Correlations between AQLQ and physical activity were approximately 0.35 (p<.0001) at each time point. In a mixed effects model, variables associated with improvement in AQLQ scores over time were male sex, less severe asthma, not taking maintenance asthma medications, fewer depressive symptoms, and increased physical activity (all variables p<0.03). According to the ACQ, asthma was well controlled in 38% at enrollment and in 60% at 12 months (p<.0001).
In conclusion, with attention to self management, increased physical activity did not compromise asthma control and was associated with improved asthma.
PMCID: PMC3567614  PMID: 23173979
exercise; energy expenditure; kcal/week; asthma control; asthma self-management
7.  Mediators and moderators of behavior change in patients with chronic cardiopulmonary disease: the impact of positive affect and self-affirmation 
Among patients with chronic cardiopulmonary disease, increasing healthy behaviors improves outcomes, but such behavior changes are difficult for patients to make and sustain over time. This study aims to demonstrate how positive affect and self-affirmation improve health behaviors compared with a patient education control group. The patient education (PE control) patients completed a behavioral contract, promising to increase their physical activity or their medication adherence and received an educational guide. In addition to the contract and guide, the positive affect/self-affirmation intervention (PA intervention) patients also learned to use positive affect and self-affirmation to facilitate behavior change. Follow-up was identical. In 756 patients, enrolled in three randomized trials, the PA intervention resulted in increased positive affect and more success in behavior change than the PE control (p < .01). Behavior-specific self-efficacy also predicted success (p < .01). Induction of positive affect played a critical role in buffering against the adverse behavioral consequences of stress. Patients who experienced either negative psychosocial changes (p < .05) or interval negative life events (p < .05) fared better with the PA intervention than without it. The PA intervention increased self-efficacy and promoted success in behavior change by buffering stress.
PMCID: PMC3958599  PMID: 24653772
Behavior change; Self-efficacy; Stress; Positive affect; Self-affirmation
8.  A novel community-based study to address disparities in hypertension and colorectal cancer: a study protocol for a randomized control trial 
Trials  2013;14:287.
Black men have the greatest burden of premature death and disability from hypertension (HTN) in the United States, and the highest incidence and mortality from colorectal cancer (CRC). While several clinical trials have reported beneficial effects of lifestyle changes on blood pressure (BP) reduction, and improved CRC screening with patient navigation (PN), the effectiveness of these approaches in community-based settings remains understudied, particularly among Black men.
MISTER B is a two-parallel-arm randomized controlled trial that will compare the effect of a motivational interviewing tailored lifestyle intervention (MINT) versus a culturally targeted PN intervention on improvement of BP and CRC screening among black men aged ≥50 with uncontrolled HTN who are eligible for CRC screening. Approximately 480 self-identified black men will be randomly assigned to one of the two study conditions. This innovative research design allows each intervention to serve as the control for the other. Specifically, the MINT arm is the control condition for the PN arm, and vice-versa. This novel, simultaneous testing of two community-based interventions in a randomized fashion is an economical and yet rigorous strategy that also enhances the acceptability of the project. Participants will be recruited during scheduled screening events at barbershops in New York City. Trained research assistants will conduct the lifestyle intervention, while trained community health workers will deliver the PN intervention. The primary outcomes will be 1) within-patient change in systolic and diastolic BP from baseline to six months and 2) CRC screening rates at six months.
This innovative study will provide a unique opportunity to test two interventions for two health disparities simultaneously in community-based settings. Our study is one of the first to test culturally targeted patient navigation for CRC screening among black men in barbershops. Thus, our study has the potential to improve the reach of hypertension control and cancer prevention efforts within a high-risk population that is under-represented in primary care settings.
Trial registration, NCT01092078
PMCID: PMC3844539  PMID: 24011142
Hypertension; Patient navigation; African Americans; Barbershops
9.  Extreme value theory in analysis of differential expression in microarrays where either only up- or down-regulated genes are relevant or expected 
Genetics research  2008;90(4):347-361.
We propose an empirical Bayes method based on the extreme value theory (EVT) (BE) for the analysis of data from spotted microarrays where the interest of the investigator (e.g. to identify up-regulated gene markers of a disease) or the design of the experiment (e.g. in certain ‘wild-type versus mutant’ experiments) limits identification of differentially expressed genes to those regulated in a single direction (either up or down). In such experiments, unlike in genome-wide microarrays, analysis is restricted to the tail of the distribution (extremes) of all the genes in the genome. The EVT provides a platform to account for this extreme behaviour, and is therefore a natural candidate for inference about differential expression. We compared the performance of the developed BE method with two other empirical Bayes methods on two real ‘wild-type versus mutant’ datasets where a single direction of regulation was expected due to experimental design, and in a simulation study. The BE method appears to have a better fit to the real data. In the analysis of simulated data, the BE method showed better accuracy and precision while being robust to different characteristics of microarray experiments. The BE method, therefore, seems promising and useful for inference about differential expression in microarrays where either only up- or down-regulated genes are relevant or expected.
PMCID: PMC3722073  PMID: 18840309
10.  Randomized Controlled Trial of Positive Affect Induction to Promote Physical Activity After Percutaneous Coronary Intervention 
Archives of internal medicine  2012;172(4):329-336.
Within 1 year after percutaneous coronary intervention, more than 20% of patients experience new adverse events. Physical activity confers a 25% reduction in mortality; however, physical activity is widely underused. Thus, there is a need for more powerful behavioral interventions to promote physical activity. Our objective was to motivate patients to achieve an increase in expenditure of 336 kcal/wk or more at 12 months as assessed by the Paffenbarger Physical Activity and Exercise Index.
Two hundred forty-two patients were recruited immediately after percutaneous coronary intervention between October 2004 and October 2006. Patients were randomized to 1 of 2 groups. The patient education (PE) control group (n=118) (1) received an educational workbook, (2) received a pedometer, and (3) set a behavioral contract for a physical activity goal. The positive affect/self-affirmation (PA) intervention group (n=124) received the 3 PE control components plus (1) a PA workbook chapter, (2) bimonthly induction of PA by telephone, and (3) small mailed gifts. All patients were contacted with standardized bimonthly telephone follow-up for 12 months.
Attrition was 4.5%, and 2.1% of patients died. Significantly more patients in the PA intervention group increased expenditure by 336 kcal/wk or more at 12 months, our main outcome, compared with the PE control group (54.9% vs 37.4%, P=.007). The PA intervention patients were 1.7 times more likely to reach the goal of a 336-kcal/wk or more increase by 12 months, controlling for demographic and psychosocial measures. In multivariate analysis, the PA intervention patients had nearly double the improvement in kilocalories per week at 12 months compared with the PE control patients (602 vs 328, P=.03).
Patients who receive PA intervention after percutaneous coronary intervention are able to achieve a sustained and clinically significant increase in physical activity by 12 months.
Trial Registration Identifier: NCT00248846
PMCID: PMC3717982  PMID: 22269589
11.  Factors Associated with Resistance to Schistosoma mansoni Infection in an Endemic Area of Bahia, Brazil 
Detailed knowledge of factors associated with resistance to Schistosoma mansoni infection in endemic areas might facilitate more effective schistosomiasis control. We conducted a cross-sectional study of persons resistant to schistosomiasis and found no association between socioeconomic status and resistance to infection. Mononuclear cells of resistant subjects produced higher levels of interleukin-5 (IL-5), IL-13 and interferon-γ upon stimulation with soluble egg antigen (SEA) compared with infected persons. When stimulated with Sm21.6 or Sm22.6, levels of IL-10 were higher in cell culture of resistant persons. Levels of IgE against soluble adult worm antigen (SWAP) and against interleukin-4–inducing principle from S. mansoni eggs (IPSE) and levels of IgG4 against SWAP, SEA, and Sm22.6 were lower in the resistant group compared with the susceptible group. Our data suggest that socioeconomic status could not fully explain resistance to S. mansoni infection observed in the studied area. However, a mixture of Th1 and Th2 immune responses and low levels of specific IgG4 against parasite antigens could be mediating resistance to infection.
PMCID: PMC3269284  PMID: 22302866
12.  Attrition in longitudinal randomized controlled trials: home visits make a difference 
Participant attrition in longitudinal studies can introduce systematic bias, favoring participants who return for follow-up, and increase the likelihood that those with complications will be underestimated. Our aim was to examine the effectiveness of home follow-up (Home F/U) to complete the final study evaluation on potentially “lost” participants by: 1) evaluating the impact of including and excluding potentially “lost” participants (e.g., those who required Home F/U to complete the final evaluation) on the rates of study complications; 2) examining the relationship between timing and number of complications on the requirement for subsequent Home F/U; and 3) determining predictors of those who required Home F/U.
We used data from a randomized controlled trial (RCT) conducted from 1991–1994 among coronary artery bypass graft surgery patients that investigated the effect of High mean arterial pressure (MAP) (intervention) vs. Low MAP (control) during cardiopulmonary bypass on 5 complications: cardiac morbidity/mortality, neurologic morbidity/mortality, all-cause mortality, neurocognitive dysfunction and functional decline. We enhanced completion of the final 6-month evaluation using Home F/U.
Among 248 participants, 61 (25%) required Home F/U and the remaining 187 (75%) received Routine F/U. By employing Home F/U, we detected 11 additional complications at 6 months: 1 major neurologic complication, 6 cases of neurocognitive dysfunction and 4 cases of functional decline. Follow-up of 61 additional Home F/U participants enabled us to reach statistical significance on our main trial outcome. Specifically, the High MAP group had a significantly lower rate of the Combined Trial Outcome compared to the Low MAP group, 16.1% vs. 27.4% (p=0.032). In multivariate analysis, participants who were ≥ 75 years (OR=3.23, 95% CI 1.52-6.88, p=0.002) or on baseline diuretic therapy (OR=2.44, 95% CI 1.14-5.21, p=0.02) were more likely to require Home F/U. In addition, those in the Home F/U group were more likely to have sustained 2 or more complications (p=0.05).
Home visits are an effective approach to reduce attrition and improve accuracy of study outcome reporting. Trial results may be influenced by this method of reducing attrition. Older participants, those with greater medical burden and those who sustain multiple complications are at higher risk for attrition.
PMCID: PMC3536670  PMID: 23176384
Loss to follow-up; Coronary artery bypass graft (CABG) surgery; Cardiovascular disease; Epidemiological methods; Dropouts; Non-response bias; Non respondents; Home visit; Predictors of attrition; Strategies to reduce attrition
13.  Pregnancy Induces Transcriptional Activation of the Peripheral Innate Immune System and Increases Oxidative DNA Damage among Healthy Third Trimester Pregnant Women 
PLoS ONE  2012;7(11):e46736.
Pregnancy induces physiological adaptations that may involve, or contribute to, alterations in the genomic landscape. Pregnancy also increases the nutritional demand for choline, an essential nutrient that can modulate epigenomic and transcriptomic readouts secondary to its role as a methyl donor. Nevertheless, the interplay between human pregnancy, choline and the human genome is largely unexplored.
Methodology/Principal Findings
As part of a controlled feeding study, we assessed the influence of pregnancy and choline intake on maternal genomic markers. Healthy third trimester pregnant (n = 26, wk 26–29 gestation) and nonpregnant (n = 21) women were randomized to choline intakes of 480 mg/day, approximating the Adequate Intake level, or 930 mg/day for 12-weeks. Blood leukocytes were acquired at study week 0 and study week 12 for microarray, DNA damage and global DNA/histone methylation measurements. A main effect of pregnancy that was independent of choline intake was detected on several of the maternal leukocyte genomic markers. Compared to nonpregnant women, third trimester pregnant women exhibited higher (P<0.05) transcript abundance of defense response genes associated with the innate immune system including pattern recognition molecules, neutrophil granule proteins and oxidases, complement proteins, cytokines and chemokines. Pregnant women also exhibited higher (P<0.001) levels of DNA damage in blood leukocytes, a genomic marker of oxidative stress. No effect of choline intake was detected on the maternal leukocyte genomic markers with the exception of histone 3 lysine 4 di-methylation which was lower among pregnant women in the 930 versus 480 mg/d choline intake group.
Pregnancy induces transcriptional activation of the peripheral innate immune system and increases oxidative DNA damage among healthy third trimester pregnant women.
PMCID: PMC3487782  PMID: 23133592
14.  Folate network genetic variation, plasma homocysteine, and global genomic methylation content: a genetic association study 
BMC Medical Genetics  2011;12:150.
Sequence variants in genes functioning in folate-mediated one-carbon metabolism are hypothesized to lead to changes in levels of homocysteine and DNA methylation, which, in turn, are associated with risk of cardiovascular disease.
330 SNPs in 52 genes were studied in relation to plasma homocysteine and global genomic DNA methylation. SNPs were selected based on functional effects and gene coverage, and assays were completed on the Illumina Goldengate platform. Age-, smoking-, and nutrient-adjusted genotype--phenotype associations were estimated in regression models.
Using a nominal P ≤ 0.005 threshold for statistical significance, 20 SNPs were associated with plasma homocysteine, 8 with Alu methylation, and 1 with LINE-1 methylation. Using a more stringent false discovery rate threshold, SNPs in FTCD, SLC19A1, and SLC19A3 genes remained associated with plasma homocysteine. Gene by vitamin B-6 interactions were identified for both Alu and LINE-1 methylation, and epistatic interactions with the MTHFR rs1801133 SNP were identified for the plasma homocysteine phenotype. Pleiotropy involving the MTHFD1L and SARDH genes for both plasma homocysteine and Alu methylation phenotypes was identified.
No single gene was associated with all three phenotypes, and the set of the most statistically significant SNPs predictive of homocysteine or Alu or LINE-1 methylation was unique to each phenotype. Genetic variation in folate-mediated one-carbon metabolism, other than the well-known effects of the MTHFR c.665C>T (known as c.677 C>T, rs1801133, p.Ala222Val), is predictive of cardiovascular disease biomarkers.
PMCID: PMC3266217  PMID: 22103680
16.  Variable selection for large p small n regression models with incomplete data: Mapping QTL with epistases 
BMC Bioinformatics  2008;9:251.
Identifying quantitative trait loci (QTL) for both additive and epistatic effects raises the statistical issue of selecting variables from a large number of candidates using a small number of observations. Missing trait and/or marker values prevent one from directly applying the classical model selection criteria such as Akaike's information criterion (AIC) and Bayesian information criterion (BIC).
We propose a two-step Bayesian variable selection method which deals with the sparse parameter space and the small sample size issues. The regression coefficient priors are flexible enough to incorporate the characteristic of "large p small n" data. Specifically, sparseness and possible asymmetry of the significant coefficients are dealt with by developing a Gibbs sampling algorithm to stochastically search through low-dimensional subspaces for significant variables. The superior performance of the approach is demonstrated via simulation study. We also applied it to real QTL mapping datasets.
The two-step procedure coupled with Bayesian classification offers flexibility in modeling "large p small n" data, especially for the sparse and asymmetric parameter space. This approach can be extended to other settings characterized by high dimension and low sample size.
PMCID: PMC2435550  PMID: 18510743
17.  Genome Wide Analysis Reveals Inositol, not Choline, as the Major Effector of Ino2p-Ino4p and Unfolded Protein Response Target Gene Expression in Yeast 
The Journal of biological chemistry  2004;280(10):9106-9118.
In the yeast Saccharomyces cerevisiae the transcription of many genes encoding enzymes of phospholipid biosynthesis are repressed in cells grown in the presence of the phospholipid precursors inositol and choline. A genome-wide approach using cDNA microarray technology was utilized to profile the changes in the expression of all genes in yeast that respond to the exogenous presence of inositol and choline. We report that the global response to inositol is completely distinct from the effect of choline. Whereas the effect of inositol on gene expression was primarily repressing, the effect of choline on gene expression was activating. Moreover, the combination inositol and choline increased the number of repressed genes compared to inositol alone and enhanced the repression levels of a subset of genes that responded to inositol. In all, 110 genes were repressed in the presence of inositol and choline. Two distinct sets of genes exhibited differential expression in response to inositol or the combination of inositol and choline in wild type cells. One set of genes contained the UASINO sequence and were bound by Ino2p and Ino4p. Many of these genes were also negatively regulated by OPI1, suggesting a common regulatory mechanism for Ino2p, Ino4p, and Opi1p. Another non-overlapping set of genes were coregulated by the unfolded protein response pathway, an ER-localized stress response pathway, but were not dependent on OPI1 and did not show further repression when choline was present together with inositol. These results suggest that inositol is the major effector of target gene expression, while choline plays a minor role.
PMCID: PMC1352320  PMID: 15611057
Microarray; Lipid Metabolism; Inositol; Choline; Unfolded Protein Response

Results 1-17 (17)