PREDICTION OF DNA METHYLATION BASED ON GENOMIC ARCHITECTURE AND APPLICATIONS OF POSITIONAL WEIGHT MATRICES

Gene silencing due to epigenetic mechanisms shows evidence of significant contributions to cancer development. We hypothesis that the genetic architecture based on retrotransposon elements surrounding the transcription start site, plays an important role in the suppression and promotion of DNA methylation. In our investigation we found a high rate of SINE and LINEs retrotransposon elements near the transcription start site of unmethylated genes when compared to methylated genes. The presence of these elements were positively associated with promoter methylation, contrary to logical expectations, due to the malicious effects of retrotransposon elements which insert themselves randomly into the genome causing possible loss of gene function. In our genome wide analysis of human genes, results suggested that 22% of the genes in cancer were predicted to be methylation-prone; in cancer these genes are generally down-regulated and function in the development process. In summary, our investigation validated our hypothesis and showed that these widespread genomic elements in cancer are highly associated with promoter DNA methylation and may further participate in influencing epigenetic regulation.

When Policy Opportunity is not Enough: College Access and Enrollment Patterns among Texas Percent Plan Eligible Students

In 1998, Texas initiated a bold new statewide university admission policy aimed at increasing college access for traditionally underserved students in the state. House Bill 588 (known as the Texas Top 10 Percent Plan (TTPP)) guaranteed automatic admission to the college or university of their choice for all top performing students in Texas public high schools. Fourteen years after the plan’s implementation, we see great strides and complexities in understanding student outcomes as a result of the percent plan. However, the legal controversy over the percent plan both in Texas and other states incorporating similar yet distinctly motivated alternative admissions plans continues to play out from institutional decision boards to the highest court in the nation. This study seeks to add to that discussion by exploring two questions. Descriptively, what are the admission and enrollment patterns within racial/ethnic groups of percent plan eligible students, over time, for Texas elite, emergent elite, and remaining public institutions? Given that all eligible percent plan students may enter the institution of choice in Texas, does which type of institution a TTPP student chooses relate to their race/ethnicity? The descriptive story told by the admission and enrollment distributions of equally eligible TTPP students is a complex but compelling one. Fundamentally, it identifies that statistically different application and enrollment patterns exist for Hispanic and especially African American TTPP beneficiaries relative to their White and Asian American counterparts.

Commentary on "When Policy Opportunity is not Enough: College Access and Enrollment Patterns among Texas Percent Plan Eligible Students"

Invited commentary on "When Policy Opportunity is not Enough: College Access and Enrollment Patterns among Texas Percent Plan Eligible Students" by Catherine Horn and Stella Flores.

Patterns of care and outcomes for pregnant inmates and their infants in Texas state prisons: Epidemiologic and ethnographic analyses

Female inmates make up the fastest growing segment in our criminal justice system today. The rapidly increasing trend for female prisoners calls for enhanced efforts to strategically plan the correctional facilities that address the needs of this growing population, and to work with communities to prevent crime in women. The incarcerated women in the U.S. have an estimated 145,000 minor children who are predisposed to unique psychosocial problems as a result of parental incarceration.^ This study examined the patterns of care and outcomes for pregnant inmates and their infants in Texas state prisons between 1994 and 1996. The study population consists of 202 pregnant inmates who delivered in a 2-year period, and a randomly sampled comparison cohort of 804 women from general Texas population, matched on race and educational levels. Both quantitative and qualitative data were used to elucidate the inmates' risk-factor profile, delivery/birth outcomes, and the patterns of care during pregnancy. The continuity-of-care issues for this population were also explored.^ Epidemiologic data were derived from multiple record systems to establish the comparison between two cohorts. A significantly great proportion of the inmates have prior lifestyle risk-factors (smoking, alcohol, and illicit drug abuse), poorer health status, and worse medical history. However, most of these existing risk-factors seem to show little manifestation in their current pregnancy. On the basis of maternal labor/delivery outcome and a number of neonatal indicators, this study found some evidence of a better pregnancy outcome for the inmate cohort when compared to the comparison group. Some possible explanations of this paradox were discussed. Seventeen percent of inmates gave birth to infants with suspected congenital syphilis. The placement patterns for the infants' care immediately after birth were elucidated.^ In addition to the quantitative data, an ethnographic approach was used to collect qualitative data from a subset of the inmate cohort (n = 20) and 12 care providers. The qualitative data were analyzed for their contents and themes, giving rise to a detailed description of the inmates' pregnancy experience. Eleven themes emerged from the study's thematic analysis, which provides the context for interpreting the epidemiologic data.^ Meaningful findings in this study were presented in a three-dimensional matrix to shed light on the apparent relationship between outcome indicators and their potential determinants. The suspected "linkages" between the outcome and their determinants can be used to generate hypotheses for future studies. ^

Estimated current patterns of food consumption and perceived changes among patients with lymphoma

Usual food choices during the past year, self-reported changes in consumption of three important food groups, and weight changes or stability were the questions addressed in this cross-sectional survey and retrospective review. The subjects were 141 patients with Hodgkin's disease or other B-cell types of lymphoma within their first three years following completion of initial treatments for lymphoma at the University of Texas M. D. Anderson Cancer Center in Houston, Texas. ^ The previously validated Block-98 Food Frequency Questionnaire was used to estimate usual food choices during the past year. Supplementary questions asked about changes breads and cereals (white or whole grain) and relative amounts of fruits and vegetables compared with before diagnosis and treatment. Over half of the subjects reported consuming more whole grains, fruits, and/or vegetables and almost three quarters of those not reporting such changes had been consuming whole grains before diagnosis and treatment. ^ Various dietary patterns were defined in order to learn whether proportionately more patients who changed in healthy directions fulfilled recognized nutritional guidelines such as 5-A-day fruits and vegetables and Dietary Reference Intakes (DRIB) for selected nutrients. ^ Small sizes of dietary pattern sub-groups limited the power of this study to detect differences in meeting recommended dietary guidelines. Nevertheless, insufficient and excessive intakes were detected among individuals with respect to fruits and vegetables, fats, calcium, selenium, iron, folate, and Vitamin A. The prevalence of inadequate or excess intakes of foods or nutrients even among those who perceived that they had increased or continued to eat whole grains and/or fruits and vegetables is of concern because of recognized effects upon general health and potential cancer related effects. ^ Over half of the subjects were overweight or obese (by BMI category) on their first visit to this cancer center and that proportion increased to almost three-quarters by their last follow-up visits. Men were significantly heavier than women, but no other significant differences in BMI measures were found even after accounting for prescribed steroids and dietary patterns. ^