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<title>Raji Balasubramanian</title>
<copyright>Copyright (c) 2013  All rights reserved.</copyright>
<link>http://works.bepress.com/raji_balasubramanian</link>
<description>Recent documents in Raji Balasubramanian</description>
<language>en-us</language>
<lastBuildDate>Thu, 07 Feb 2013 01:39:29 PST</lastBuildDate>
<ttl>3600</ttl>


	
		
	







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<title>Common genetic variants in Peroxisome Proliferator-activated Receptor γ (PPARG) and Clinical Diabetes Risk among Women’s Health Initiative Postmenopausal Women</title>
<link>http://works.bepress.com/raji_balasubramanian/24</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/24</guid>
<pubDate>Tue, 05 Feb 2013 06:15:40 PST</pubDate>
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<author>K HK Chan et al.</author>


<category>Women&apos;s Health Initiative</category>

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<title>Detection of promoter methylation of tumor suppressor genes in serum DNA of breast cancer cases and benign breast disease controls</title>
<link>http://works.bepress.com/raji_balasubramanian/23</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/23</guid>
<pubDate>Thu, 27 Sep 2012 08:15:44 PDT</pubDate>
<description>
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	<p>Tumors are capable of shedding DNA into the blood stream. This shed DNA may be recovered from serum or plasma. The objective of this study was to evaluate whether pyrosequencing promoter DNA in a panel of 12 breast cancer-related genes (APC, BRCA1, CCND2, CDH1, ESR1, GSTP1, HIN1, P16, RARβ, RASSF1, SFRP1 and TWIST) to measure the degree of methylation would lead to a useful serum-based marker of breast cancer. Serum was obtained from women who were about to undergo a breast biopsy or mastectomy at three hospitals from 1977 to 1987 in Grand Rapids, Michigan. We compared the methylation status of 12 genes in serum DNA obtained from three groups of postmenopausal women (mean age at blood collection: 63.0 y; SD 9.9; range 35–91): breast cancer cases with lymph node-positive disease (n = 241); breast cancer cases with lymph node-negative disease (n = 63); and benign breast disease control subjects (n = 234). Overall, median levels of promoter methylation were low, typically below 5%, for all genes in all study groups. For all genes, median levels of methylation were higher (by 3.3 to 47.6%) in lymph node-positive breast cancer cases than in the controls. Comparing mean methylation level between lymph-node positive cases and controls, the most statistically significant findings, after adjustment of the false-positive rate (q-value), were for TWIST (p = 0.04), SFRP1 (p = 0.16), ESR1 (p = 0.17), P16 (p = 0.19) and APC (p = 0.19). For two of these four genes (TWIST, P16), the median methylation level was also highest in lymph-node positive cases, intermediate in lymph node-negative cases and lowest in the controls. The percent of study subjects with mean methylation scores ≥ 5% was higher among lymph node-positive cases than controls for ten genes, and significantly higher for HIN1 and TWIST (22.0 vs. 12.2%, p = 0.04 and 37.9 vs. 24.5%, p = 0.004, respectively). Despite relatively consistent variation in methylation patterns among groups, these modest differences did not provide sufficient ability to distinguish between cases and controls in a clinical setting.</p>

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</description>

<author>Susan R. Sturgeon et al.</author>


<category>Systems Biology</category>

<category>Epigenetics</category>

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<title>Systems Pharmacology, Biomarkers and Biomolecular Networks</title>
<link>http://works.bepress.com/raji_balasubramanian/22</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/22</guid>
<pubDate>Mon, 10 Sep 2012 08:09:59 PDT</pubDate>
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<author>Aram Adourian et al.</author>


<category>Systems Biology</category>

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<title>Assessing network structure in the presence of measurement error</title>
<link>http://works.bepress.com/raji_balasubramanian/21</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/21</guid>
<pubDate>Mon, 10 Sep 2012 08:07:20 PDT</pubDate>
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<author>Denise Scholtens et al.</author>


<category>High Dimensional Data</category>

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<title>The Liver Toxicity Biomarker Study Phase 1: Markers for the Effects of Tolcapone or Entacapone</title>
<link>http://works.bepress.com/raji_balasubramanian/20</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/20</guid>
<pubDate>Wed, 15 Aug 2012 06:21:41 PDT</pubDate>
<description>
	<![CDATA[
	<p>The Liver Toxicity Biomarker Study is a systems toxicology approach to discover biomarkers that are indicative of a drug's potential to cause human idiosyncratic drug-induced liver injury. In phase I, the molecular effects in rat liver and blood plasma induced by tolcapone (a "toxic" drug) were compared with the molecular effects in the same tissues by dosing with entacapone (a "clean" drug, similar to tolcapone in chemical structure and primary pharmacological mechanism). Two durations of drug exposure, 3 and 28 days, were employed. Comprehensive molecular analysis of rat liver and plasma samples yielded marker analytes for various drug-vehicle or drug-drug comparisons. An important finding was that the marker analytes associated with tolcapone only partially overlapped with marker analytes associated with entacapone, despite the fact that both drugs have similar chemical structures and the same primary pharmacological mechanism of action. This result indicates that the molecular analyses employed in the study are detecting substantial "off-target" markers for the two drugs. An additional interesting finding was the modest overlap of the marker data sets for 3-day exposure and 28-day exposure, indicating that the molecular changes in liver and plasma caused by short- and long-term drug treatments do not share common characteristics.</p>

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</description>

<author>Robert N. McBurney et al.</author>


<category>Systems Biology</category>

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<title>Statin Use and Risk of Diabetes in Postmenopausal Women in the Women’s Health Initiative</title>
<link>http://works.bepress.com/raji_balasubramanian/19</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/19</guid>
<pubDate>Mon, 13 Aug 2012 07:00:44 PDT</pubDate>
<description>
	<![CDATA[
	<p>BACKGROUND:  This study investigates whether the incidence of new-onset diabetes mellitus (DM) is associated with statin use among postmenopausal women participating in the Women's Health Initiative (WHI).</p>
<p>METHODS:  The WHI recruited 161,808 postmenopausal women aged 50 to 79 years at 40 clinical centers across the United States from 1993 to 1998 with ongoing follow-up. The current analysis includes data through 2005. Statin use was captured at enrollment and year 3. Incident DM status was determined annually from enrollment. Cox proportional hazards models were used to estimate the risk of DM by statin use, with adjustments for propensity score and other potential confounding factors. Subgroup analyses by race/ethnicity, obesity status, and age group were conducted to uncover effect modification.</p>
<p>RESULTS:  This investigation included 153,840 women without DM and no missing data at baseline. At baseline, 7.04% reported taking statin medication. There were 10,242 incident cases of self-reported DM over 1,004,466 person-years of follow-up. Statin use at baseline was associated with an increased risk of DM (hazard ratio [HR], 1.71; 95% CI, 1.61-1.83). This association remained after adjusting for other potential confounders (multivariate-adjusted HR, 1.48; 95% CI, 1.38-1.59) and was observed for all types of statin medications. Subset analyses evaluating the association of self-reported DM with longitudinal measures of statin use in 125,575 women confirmed these findings.</p>
<p>CONCLUSIONS:  Statin medication use in postmenopausal women is associated with an increased risk for DM. This may be a medication class effect. Further study by statin type and dose may reveal varying risk levels for new-onset DM in this population.</p>

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</description>

<author>Annie L. Culver et al.</author>


<category>Women&apos;s Health Initiative</category>

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<title>Caffeinated coffee, decaffeinated coffee and endometrial cancer risk: A prospective cohort study among U.S. postmenopausal women</title>
<link>http://works.bepress.com/raji_balasubramanian/18</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/18</guid>
<pubDate>Mon, 13 Aug 2012 06:56:41 PDT</pubDate>
<description>
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	<p>There is plausible biological evidence as well as epidemiologic evidence to suggest coffee consumption may lower endometrial cancer risk. We evaluated the associations between self-reported total coffee, caffeinated coffee and decaffeinated coffee, and endometrial cancer risk using the Women’s Health Initiative Observational Study Research Materials obtained from the National Heart, Lung, and Blood Institute Biological Specimen and Data Repository Coordinating Center. Our primary analyses included 45,696 women and 427 incident endometrial cancer cases, diagnosed over a total of 342,927 person-years of follow-up. We used Cox-proportional hazard models to evaluate coffee consumption and endometrial cancer risk. Overall, we did not find an association between coffee consumption and endometrial cancer risk. Compared to non-daily drinkers (none or < 1 cup/day), the multivariable adjusted hazard ratios for women who drank ≥4 cups/day were 0.86 (95% confidence interval (CI) 0.63, 1.18) for total coffee, 0.89 (95% CI 0.63, 1.27) for caffeinated coffee, and 0.51 (95% CI 0.25, 1.03) for decaf coffee. In subgroup analyses by body mass index (BMI) there were no associations among normal-weight and overweight women for total coffee and caffeinated coffee. However among obese women, compared to the referent group (none or < 1 cup/day), the hazard ratios for women who drank ≥2 cups/day were: 0.72 (95% CI 0.50, 1.04) for total coffee and 0.66 (95% CI 0.45, 0.97) for caffeinated coffee. Hazard ratios for women who drank ≥2 cups/day for decaffeinated coffee drinkers were 0.67 (0.43–1.06), 0.93 (0.55–1.58) and 0.80 (0.49–1.30) for normal, overweight and obese women, respectively. Our study suggests that caffeinated coffee consumption may be associated with lower endometrial cancer risk among obese postmenopausal women, but the association with decaffeinated coffee remains unclear.</p>

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</description>

<author>Ayush Giri et al.</author>


<category>Women&apos;s Health Initiative</category>

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<title>Determinants of Racial/Ethnic Disparities in Incidence of Clinical Diabetes in Postmenopausal Women in the United States: The Women’s Health Initiative 1993-2009</title>
<link>http://works.bepress.com/raji_balasubramanian/17</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/17</guid>
<pubDate>Sun, 12 Aug 2012 11:59:01 PDT</pubDate>
<description>
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	<p>OBJECTIVE To examine determinants of racial/ethnic differences in diabetes incidence among postmenopausal women participating in the Women's Health Initiative.</p>
<p>RESEARCH DESIGN AND METHODS Data on race/ethnicity, baseline diabetes prevalence, and incident diabetes were obtained from 158,833 women recruited from 1993-1998 and followed through August 2009. The relationship between race/ethnicity, other potential risk factors, and the risk of incident diabetes was estimated using Cox proportional hazards models from which hazard ratios (HRs) and 95% CIs were computed.</p>
<p>RESULTS Participants were aged 63 years on average at baseline. The racial/ethnic distribution was 84.1% non-Hispanic white, 9.2% non-Hispanic black, 4.1% Hispanic, and 2.6% Asian. After an average of 10.4 years of follow-up, compared with whites and adjusting for potential confounders, the HRs for incident diabetes were 1.55 for blacks (95% CI 1.47-1.63), 1.67 for Hispanics (1.54-1.81), and 1.86 for Asians (1.68-2.06). Whites, blacks, and Hispanics with all factors (i.e., weight, physical activity, dietary quality, and smoking) in the low-risk category had 60, 69, and 63% lower risk for incident diabetes. Although contributions of different risk factors varied slightly by race/ethnicity, most findings were similar across groups, and women who had both a healthy weight and were in the highest tertile of physical activity had less than one-third the risk of diabetes compared with obese and inactive women.</p>
<p>CONCLUSIONS Despite large racial/ethnic differences in diabetes incidence, most variability could be attributed to lifestyle factors. Our findings show that the majority of diabetes cases are preventable, and risk reduction strategies can be effectively applied to all racial/ethnic groups.</p>

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</description>

<author>Yunsheng Ma et al.</author>


<category>Women&apos;s Health Initiative</category>

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<title>Sleep duration and endometrial cancer risk</title>
<link>http://works.bepress.com/raji_balasubramanian/16</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/16</guid>
<pubDate>Sun, 12 Aug 2012 11:53:41 PDT</pubDate>
<description>
	<![CDATA[
	<p>PURPOSE:  Recent data indicate that night shift work is associated with increased endometrial cancer risk, perhaps through a pathway involving lower melatonin production. Melatonin is an antiestrogenic hormone, with production in a circadian pattern that is dependent on presence of dark at night. Sleep duration is positively associated with melatonin production and may be an indicator of melatonin levels in epidemiologic studies.</p>
<p>METHODS:  We evaluated associations between self-reported sleep duration and endometrial cancer risk using publicly available prospective data on 48,725 participants in the Women's Health Initiative Observational Study, among whom 452 adjudicated incident cases of endometrial cancer were diagnosed over approximately 7.5 years of follow-up. Sleep duration was self-reported at baseline. Cox proportional hazards regression was used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for endometrial cancer risk with adjustment for potential confounders.</p>
<p>RESULTS:  Most women reported sleeping ≤ 6 (33.3%) or 7 (38.5%) h each night; fewer reported sleeping 8 (23.4%) or ≥ 9 (4.8%) h each night. In adjusted analyses, there was an indication of reduced risk associated with longer sleep duration, though no statistically significant association was observed. Women who slept ≥ 9 h had a nonsignificant reduced risk of endometrial cancer compared with women who slept ≤ 6 h (HR = 0.87; 95% CI = 0.51-1.46).</p>
<p>CONCLUSIONS:  We found weak evidence of an association between sleep duration and endometrial cancer risk. Self-reported sleep duration may not adequately represent melatonin levels, thus further studies utilizing urinary melatonin levels are necessary to establish the mechanism by which night shift work increases endometrial cancer risk.</p>

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</description>

<author>Susan R. Sturgeon et al.</author>


<category>Women&apos;s Health Initiative</category>

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<title>Depressive symptoms, Antidepressant Use and Diabetes in a Large Multiethnic National Sample of Postmenopausal Women</title>
<link>http://works.bepress.com/raji_balasubramanian/15</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/15</guid>
<pubDate>Sun, 12 Aug 2012 11:51:04 PDT</pubDate>
<description>
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	<p>OBJECTIVE:To examine elevated depressive symptoms and antidepressant use in relation to diabetes incidence in the Women's Health Initiative.</p>
<p>RESEARCH DESIGN AND METHODS: A total of 161,808 postmenopausal women were followed for over an average of 7.6 years. Hazard ratios (HRs) estimating the effects of elevated depressive symptoms and antidepressant use on newly diagnosed incident diabetes were obtained using Cox proportional hazards models adjusted for known diabetes risk factors.</p>
<p>RESULTS: Multivariable-adjusted HRs indicated an increased risk of incident diabetes with elevated baseline depressive symptoms (HR 1.13 [95% CI 1.07-1.20]) and antidepressant use (1.18 [1.10-1.28]). These associations persisted through year 3 data, in which respective adjusted HRs were 1.23 (1.09-1.39) and 1.31 (1.14-1.50).</p>
<p>CONCLUSIONS: Postmenopausal women with elevated depressive symptoms who also use antidepressants have a greater risk of developing incident diabetes. In addition, longstanding elevated depressive symptoms and recent antidepressant medication use increase the risk of incident diabetes.</p>

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</description>

<author>Yunsheng Ma et al.</author>


<category>Women&apos;s Health Initiative</category>

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<title>A systems biology approach to understanding elevated serum alanine transaminase levels in a clinical trial with ximelagatran</title>
<link>http://works.bepress.com/raji_balasubramanian/14</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/14</guid>
<pubDate>Sun, 05 Aug 2012 08:20:07 PDT</pubDate>
<description>
	<![CDATA[
	<p>Ximelagatran was developed for the prevention and treatment of thromboembolic conditions. However, in long-term clinical trials with ximelagatran, the liver injury marker, alanine aminotransferase (ALT) increased in some patients. Analysis of plasma samples from 134 patients was carried out using proteomic and metabolomic platforms, with the aim of finding predictive biomarkers to explain the ALT elevation. Analytes that were changed after ximelagatran treatment included 3-hydroxybutyrate, pyruvic acid, CSF1R, Gc-globulin, L-glutamine, protein S and alanine, etc. Two of these analytes (pyruvic acid and CSF1R) were studied further in human cell cultures in vitro with ximelagatran. A systems biology approach applied in this study proved to be successful in generating new hypotheses for an unknown mechanism of toxicity.</p>

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</description>

<author>U Andersson et al.</author>


<category>Systems Biology</category>

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<title>The Liver Toxicity Biomarker Study: Phase I Design and Preliminary Results</title>
<link>http://works.bepress.com/raji_balasubramanian/13</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/13</guid>
<pubDate>Sun, 05 Aug 2012 07:59:40 PDT</pubDate>
<description>
	<![CDATA[
	<p>Drug-induced liver injury (DILI) is the primary adverse event that results in withdrawal of drugs from the market and a frequent reason for the failure of drug candidates in development. The Liver Toxicity Biomarker Study (LTBS) is an innovative approach to investigate DILI because it compares molecular events produced in vivo by compound pairs that (a) are similar in structure and mechanism of action, (b) are associated with few or no signs of liver toxicity in preclinical studies, and (c) show marked differences in hepatotoxic potential. The LTBS is a collaborative preclinical research effort in molecular systems toxicology between the National Center for Toxicological Research and BG Medicine, Inc., and is supported by seven pharmaceutical companies and three technology providers. In phase I of the LTBS, entacapone and tolcapone were studied in rats to provide results and information that will form the foundation for the design and implementation of phase II. Molecular analysis of the rat liver and plasma samples combined with statistical analyses of the resulting datasets yielded marker analytes, illustrating the value of the broad-spectrum, molecular systems analysis approach to studying pharmacological or toxicological effects.</p>

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</description>

<author>Robert N. McBurney et al.</author>


<category>Systems Biology</category>

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<title>Correlation Network Analysis for Data Integration and Biomarker Selection</title>
<link>http://works.bepress.com/raji_balasubramanian/12</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/12</guid>
<pubDate>Sun, 05 Aug 2012 07:52:55 PDT</pubDate>
<description>
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	<p>This work demonstrates the application of correlation networks to a systems-based investigation of drug-induced hepatotoxicity and the identification of specific and relevant biomarkers in this context.</p>

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</description>

<author>Aram Adourian et al.</author>


<category>Systems Biology</category>

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<title>Ruling out (160,54,18) difference sets in some nonabelian groups</title>
<link>http://works.bepress.com/raji_balasubramanian/11</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/11</guid>
<pubDate>Sun, 05 Aug 2012 07:39:15 PDT</pubDate>
<description>
	<![CDATA[
	<p>We prove the following theorems.  Theorem A. Let G be a group of order 160 satisfying one of the following conditions. (1) G has an image isomorphic to D20 ×  Z2(for example, if G ≃ D20 × K). (2) G has a normal 5-Sylow subgroup and an elementary abelian 2-Sylow subgroup. (3) G has an abelian image of exponent 2, 4, 5, or 10 and order greater than 20. Then G cannot contain a (160, 54, 18) difference set.</p>
<p>Theorem B. Suppose G is a nonabelian group with 2-Sylow subgroup S and 5-Sylow subgroup T and contains a (160, 54, 18) difference set. Then we have one of three possibilities. (1) T is normal, |ϕ(S)| = 8, and one of the following is true: (a) G = S × T and S is nonabelian; (b) G has a D10image; or (c) G has a Frobenius image of order 20. (2) G has a Frobenius image of order 80. (3) G is of index 6 in A Γ L(1, 16).</p>
<p>To prove the first case of Theorem A, we find the possible distribution of a putative difference set with the stipulated parameters among the cosets of a normal subgroup using irreducible representations of the quotient; we show that no such distribution is possible. The other two cases are due to others. In the second (due to Pott) irreducible representations of the elementary abelian quotient of order 32 give a contradiction. In the third (due to an anonymous referee), the contradiction derives from a theorem of Lander together with Dillon's “dihedral trick.” Theorem B summarizes the open nonabelian cases based on this work.</p>

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</description>

<author>Jason Alexander et al.</author>


<category>Mathematics</category>

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<title>Maternal Toxicity and Pregnancy Outcome According to Antiretroviral Therapy during Pregnancy: An analysis of the PACTG 316 Study</title>
<link>http://works.bepress.com/raji_balasubramanian/10</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/10</guid>
<pubDate>Mon, 26 Mar 2012 08:16:52 PDT</pubDate>
<description>
	<![CDATA[
	<p>BACKGROUND: Antiretroviral therapy (ART) during pregnancy reduces the risk of perinatal transmission of HIV-1 but may increase the risk of pregnancy complications. Pregnancy may enhance toxicity of ART. We evaluated rates of maternal toxicity, adverse pregnancy outcomes, and maternal peripartum morbidity according to the type and duration of ART taken during pregnancy.</p>
<p>METHODS: PACTG 316 evaluated if the addition of intrapartum/neonatal nevirapine to established ART during pregnancy reduced perinatal transmission of HIV-1. Detailed data were collected on maternal ART use throughout pregnancy. For this analysis, women were categorized into 1 of 6 groups based on type of therapy during pregnancy (monotherapy [monoRx], combination without protease inhibitor [PI], combination with PI) and start date (early = before pregnancy or during first trimester, late = begun second or third trimester). Outcomes were determined from signs/symptoms, diagnoses, laboratory results forms prospectively completed on study at enrollment, delivery and 6 wks postpartum.</p>
<p>RESULTS: A total 1,409 women were included in the analysis: 290 monoRx early, 34 monoRx late, 175 combo no PI early, 327 combo no PI late, 263 combo PI early, and 320 combo PI late. The most common symptoms anytime during pregnancy (moderate grade or higher) were vaginal bleeding 5.5%, nausea/vomiting 2.7%, and headache 2.2%. The most frequent lab abnormalities were anemia ( 2.5 x ULN) 1.1%. Mean gestational age at delivery was 38.1 wks and mean birth weight was 3078 g. Stillbirth occurred in 0.4%. Bacterial pneumonia occurred in 3% of women and AIDS-associated pneumonia in 2% during pregnancy or the postpartum period. Peripartum complication rates were low and depended on delivery mode. Event rates did not differ by antiretroviral group or study treatment assignment.</p>
<p>CONCLUSIONS: In this population of HIV-infected women receiving prenatal care and ART, adverse events were uncommon and did not differ by type and duration of ART. Pneumonia occurred relatively frequently during pregnancy.</p>

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</description>

<author>H D. Watts et al.</author>


<category>HIV</category>

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<title>The Impact of Race/Ethnicity on Mother-to-Child HIV Transmission in the U.S. in Pediatric AIDS Clinical Trials Group Protocol 316</title>
<link>http://works.bepress.com/raji_balasubramanian/9</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/9</guid>
<pubDate>Mon, 26 Mar 2012 08:07:59 PDT</pubDate>
<description>
	<![CDATA[
	<p>The present analysis was designed to determine whether race/ethnicity was independently associated with mother-to-child HIV-1 transmission risk in subjects enrolled in a trial of 2-dose intra-partum nevirapine in combination with standard antiretroviral therapy and to determine what factors, including race/ethnicity, predicted maternal viral suppression at the time of delivery. Women enrolled in Pediatric AIDS Clinical Trials Group (PACTG) 316 from sites in the United States and Puerto Rico were included. Distribution of selected maternal disease and treatment characteristics was assessed by race/ethnicity category. Logistic regression models were fit to evaluate possible association of factors with HIV transmission and with viral load at delivery. Variables associated with the outcome at P < 0.05 level were retained in the final models. Of 1052 women randomized at PACTG sites, 891 were included in the present analysis: 572 (64%) were black; 206 (23%) were Hispanic; and 113 (13%) were white. All women who had infected infants were black or Hispanic (11/572 and 3/206, respectively), whereas none of the women identified as white had an infected infant (0/113). This difference was not statistically significant (P = 0.54). White women had higher entry CD4 cell counts and lower HIV-1 RNA at delivery than women of other races/ethnicities. Black and Hispanic women were more likely than white women to start therapy during their current pregnancy but did not initiate prenatal care later. In bivariate models that included antiretroviral type and variables that had values of P < or = 0.25 in univariate analysis, time of antiretroviral initiation, time of prenatal care initiation, and race/ethnicity each retained significance in predicting viral suppression at delivery. Race/ethnicity remained predictive of viral suppression at delivery in a multivariate model incorporating all of these variables (P = 0.01). Higher HIV-1 RNA and lower CD4 cell counts in women identified as black or Hispanic have significant implications for the health of these women and their newborns. Race/ethnicity is significant in predicting viral suppression at the time of delivery.</p>

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</description>

<author>C K. Cunningham et al.</author>


<category>HIV</category>

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<title>The impact of storage effects in biobanks on biomarker discovery in systems biology studies</title>
<link>http://works.bepress.com/raji_balasubramanian/8</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/8</guid>
<pubDate>Tue, 20 Mar 2012 08:53:17 PDT</pubDate>
<description>
	<![CDATA[
	<p>Sample handling and storage conditions in specimens frozen over long periods of time can severely impact marker levels. If laboratory technologies, practices and related protocols change over time, biomarker studies are potentially biased and report erroneous results. These issues and pitfalls are often overlooked in system biology studies using previously collected and stored materials, and are likely to be one notable cause for biomarker candidates failing to be validated. We present results from simulation studies quantifying the loss in statistical power to detect true biomarkers, due to diminishing concentration of analytes in samples subject to poor handling and storage conditions.</p>

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</description>

<author>Raji Balasubramanian et al.</author>


<category>High Dimensional Data</category>

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<title>Comparative evaluation of classifiers in the presence of statistical interaction between features in high-dimensionality data settings</title>
<link>http://works.bepress.com/raji_balasubramanian/7</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/7</guid>
<pubDate>Tue, 20 Mar 2012 08:49:45 PDT</pubDate>
<description>
	<![CDATA[
	<p>Background: A central challenge in high dimensional data settings in biomedical investigations involves the estimation of an optimal prediction algorithm to distinguish between different disease phenotypes. A significant complicating aspect in these analyses can be attributed to the presence of features that exhibit statistical interactions. Indeed, in several clinical investigations such as genetic studies of complex diseases, it is of interest to specifically identify such features. In this paper, we compare the performance of four commonly used classifiers (K-Nearest Neighbors, Prediction Analysis for Microarrays, Random Forests and Support Vector Machines) in settings involving high dimensional datasets including statistically interacting feature subsets. We evaluate the performance of these classifiers under conditions of varying sample size, levels of signal-to-noise ratio and strength of statistical interactions among features. We summarize two datasets from studies in diabetes and cardiovascular disease involving gene expression, metabolomics and proteomics measurements and compare results obtained using the four classifiers.</p>
<p>Results: Simulation studies revealed that the classifier Prediction Analysis of Microarrays had the highest classification accuracy in the absence of noise, statistical interactions and when feature distributions were multivariate Gaussian within each class. In the presence of statistical interactions, modest effect sizes and the absence of noise, Support Vector Machines achieved the best performance followed closely by Random Forests. Random Forests was optimal in settings that included both significant levels of high dimensional noise features and statistical interactions between biomarker pairs. The data applications revealed similar trends in the relative performances of each classifier.</p>
<p>Conclusion: Random Forests had the highest classification accuracy among the four classifiers and was successful in incorporating interaction effects between features in the presence of noise in high dimensional datasets.</p>

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</description>

<author>Yu Guo et al.</author>


<category>High Dimensional Data</category>

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<item>
<title>A graph-theoretic approach to testing associations between disparate sources of functional genomics data</title>
<link>http://works.bepress.com/raji_balasubramanian/6</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/6</guid>
<pubDate>Mon, 19 Mar 2012 15:06:52 PDT</pubDate>
<description>
	<![CDATA[
	<p>Motivation: The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data sources, or lack thereof, can shed light on the mechanisms that govern cellular function. A central challenge for bioinformatics research is to develop a unified framework for combining the multiple sources of functional genomics information and testing associations between them, thus obtaining a robust and integrated view of the underlying biology.</p>
<p>Results: We present a graph-theoretic approach to test the significance of the association between multiple disparate sources of functional genomics data by proposing two statistical tests, namely edge permutation and node label permutation tests. We demonstrate the use of the proposed tests by finding significant association between a Gene Ontology-derived predictome and data obtained from mRNA expression and phenotypic experiments for Saccharomyces cerevisiae. Moreover, we employ the graph-theoretic framework to recast a surprising discrepancy presented elsewhere between gene expression and knockout phenotype, using expression data from a different set of experiments.</p>
<p>Availability: An R software package, GraphAT, containing the data and statistical procedures is available from Bioconductor: http://www.bioconductor.org</p>

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</description>

<author>Raji Balasubramanian et al.</author>


<category>High Dimensional Data</category>

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<item>
<title>Estimating HIV Incidence Based on Combined Prevalence Testing</title>
<link>http://works.bepress.com/raji_balasubramanian/5</link>
<guid isPermaLink="true">http://works.bepress.com/raji_balasubramanian/5</guid>
<pubDate>Mon, 19 Mar 2012 15:01:54 PDT</pubDate>
<description>
	<![CDATA[
	<p>Knowledge of incidence rates of HIV and other infectious diseases is important in evaluating the state of an epidemic as well as for designing interventional studies. Estimation of disease incidence from longitudinal studies can be expensive and time consuming. Alternatively, Janssen et al. (1998, Journal of the American Medical Association 280, 42–48) proposed the estimation of HIV incidence at a single point in time based on the combined use of a standard and “detuned” antibody assay. This article frames the problem from a longitudinal perspective, from which the maximum likelihood estimator of incidence is determined and compared with the Janssen estimator. The formulation also allows estimation for general situations, including different batteries of tests among subjects, inclusion of covariates, and a comparative evaluation of different test batteries to help guide study design. The methods are illustrated with data from an HIV interventional trial and a seroprevalence survey recently conducted in Botswana.</p>

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</description>

<author>Raji Balasubramanian et al.</author>


<category>General Biostatistics</category>

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