Patient Characteristics and Outcomes of Gastrointestinal Stromal Tumor Patients Undergoing Imatinib Plasma Level Testing

Although gastrointestinal stromal tumor (GIST) is effectively treated with imatinib, there are a number of clinical challenges in the optimal treatment of these patients. The plasma steady-state trough level of imatinib has been proposed to correlate with clinical outcome. Plasma imatinib level may be affected by a number of patient characteristics. Additionally, the ideal plasma trough concentration of imatinib is likely to vary based on the KIT genotype (genotype determines imatinib binding affinity) of the individual patient. Patients’ genotype or plasma imatinib level may influence the type and duration of response that is appreciable by clinical evaluation. The objectives of this study were to determine effects of genotype on the type of response appreciable by current imaging criteria, to determine the distribution of plasma imatinib levels in patients with GIST, to determine factors that correlate with plasma imatinib level, to determine the incremental effects of imatinib dose escalation; and to explore the median plasma levels and outcomes of patients with various KIT mutations. We therefore obtained KIT mutation information and analyzed CT response for size and density measurement of GISTs at baseline and within the first four moths of imatinib treatment. In 126 patients with metastatic/unresectable disease, the KIT genotype of patients’ tumor was significantly associated with unique response characteristics measurable by CT. Furthermore, hepatic and peritoneal metastases differed in their response characteristics. A subgroup of patients with KIT exon 9 mutation, who received higher doses of imatinib and experienced higher trough imatinib levels, experienced improved progression-free survival similar to that of KIT exon 11 patients. Therefore, we have found that imatinib plasma levels were higher in patients with elevated Aspartate amino transferase, were women, were older, or were being treated concomitantly with CYP450 substrate drugs. As expected, CYP450 inducers correlated with a lower plasma imatinib levels in GIST patients. Renal metabolism of imatinib accounts for <10%, so it was not included in the analysis but may affect covariates. Interestingly, there was a trend for low imatinib levels and inferior progression-free survival in patients who had undergone complete gastrectomy. Patients with KIT exon 9 mutation in our cohort received higher imatinib doses, experienced higher trough imatinib levels, and experienced a PFS similar to that of KIT exon 11 patients. In conclusion, imatinib plasma levels are influenced by a number of patient characteristics. The optimal imatinib plasma level for individual patients is not known but is an area of intense investigation. Our study confirms patients with KIT exon 9 mutations benefit from high-dose imatinib and higher trough imatinib levels.

Individual, Family, and Neighborhood Characteristics and Children's Food Insecurity

A growing body of work documents the influence of neighborhood environments on child health and well-being. Food insecurity is likely linked to neighborhood characteristics via mechanisms of social disadvantage, including access to and availability of healthy foods and the social cohesion of neighbors. In this paper, we utilize restricted, geo-coded data from the Early Childhood Longitudinal Study, which allows us to link individual children with their neighborhood's census characteristics, to assess how the neighborhoods of food secure and food insecure children differ at both the kindergarten level and in third grade. The average food insecure child lives in a neighborhood with a higher proportion of black and Hispanic residents, a higher proportion of residents living in poverty, and a higher proportion of foreign-born and linguistically isolated residents. After accounting for individual and household-level characteristics, children living in neighborhoods with a high proportion of Hispanic and foreign-born residents have a significantly increased risk of food insecurity compared to children living in neighborhoods which are predominantly white and have high socioeconomic status. We argue that interventions which take neighborhood context into account may be most efficacious for curbing child food insecurity.

Commentary on "Individual, Family, and Neighborhood Characteristics and Children's Food Insecurity"

Commentary on "Individual, Family, and Neighborhood Characteristics and Children's Food Insecurity," by Rachel Kimbro, Justin Denney, and Sarita Panchang.

The type-A horizontal cell: GABAergic characteristics and role in development of the outer plexiform layer

Morphological analysis of neonatal rabbit retina suggests that the type-A horizontal cell acts as the pioneer cell for development of the OPL. It is the first mature element of the OPL, and it forms the infrastructure upon which the OPL accrues. The role of type-A horizontal cells in influencing postnatal development of the OPL was examined.^ GABAergic characteristics of the type-A horizontal cell were defined. The type-A horizontal cell was found to possess two more GABAergic characteristics in addition to those previously demonstrated, during a short period in early postnatal development: endogenous stores of GABA and the GABA precursor, glutamate. Lesioning the type-A horizontal cell resulted in their permanent loss in addition to the disappearance of cone terminals and a dramatic increase in rod terminals within the OPL. Thus the type-A cells are not a necessary prerequisite for positioning the OPL in postnatal development, but may be necessary for establishment of the normal photoreceptor mosaic.^ Since type-A horizontal cells possess a number of GABAergic qualities during the period of cone photoreceptor cell differentiation, and there are reports of GABA's trophic action in other developing neuronal systems; the role that GABAergic type-A horizontal cells play in directing photoreceptor differentiation was examined.^ Disrupting effects of GABA-A receptor antagonists indicate that type-A horizontal cells act as postsynaptic targets for the growing cone terminals of photoreceptor cells. These trophic or synaptic interactions may involve GABA-A receptors activated by GABA released from horizontal cells. These findings are consistent with the hypothesis that type-A horizontal cells act as pioneering cells in directing the postnatal development of the OPL.^ These studies offer an in depth analysis of the structural and chemical relationship between type-A horizontal cells and other elements of the OPL from which the roles of type-A horizontal cells and the GABA system in development can be defined. They contribute to our knowledge of both structural and GABAergic mechanisms involved in central nervous system development. ^

Characteristics and experiences of past participants in the Texas Peer Assistance Program for Nurses

There are nearly 200,000 licensed practicing nurses in the state of Texas, representing one-tenth of the nations' workforce. The prevalence of substance abuse among nurses is estimated to range between six and 20 percent in this professional group.^ Since March 1987, the Texas Peer Assistance Program for Nurses (TPAPN) has offered intervention, education, support and monitoring to nurses in Texas whose practice has become impaired due to substance abuse and/or mental illness. Since then approximately 44 percent of nurses who voluntarily signed participation agreements successfully completed the program; fifty-six percent have not. One determinant of completion for those nurses identified as chemically dependent is abstinence from mood altering substances. Other helping professions report higher rates of abstinence two years following treatment.^ The purpose of this study was to investigate the relationship between relapse, demographics, treatment variables, work setting, "stress" indicators and support factors for nurses who participated in TPAPN. A questionnaire was mailed to 1000 randomly selected nurses who had signed agreements since 1987 and were no longer active in the program. More than 41% of the questionnaires were returned undeliverable.^ Recipients of the questionnaire were known only to TPAPN, never to the investigator. All information was received anonymously except when the participant chose to sign the questionnaire. A cover letter explaining the study and inviting participation was enclosed. Completion and return of the questionnaire was considered consent to participate.^ Findings demonstrated a significant relationship between relapse and opiates as the drug of choice for past participants in the Texas Peer Assistance Program for Nurses. Significant associations were found among factors such as control at work, support, physical complaints, job security, self-esteem and employment in this sample. Respondents shared copious written comments about their experiences in TPAPN. These data were analyzed using qualitative methods and compared with similar studies of recovering nurses. Further research with nurses whose practice has been affected by abuse of chemical and mental illness is warranted. ^

RNA binding characteristics and overall topology of the vaccinia virus polyadenylation complex

mRNA 3′ polyadenylation is central to mRNA biogenesis in prokaryotes and eukaryotes, and is implicated in numerous aspects of mRNA metabolism, including efficiency of mRNA export from the nucleus, message stability, and initiation of translation. However, due to the great complexity of the eukaryotic polyadenylation apparatus, the mechanisms of RNA 3 ′ end processing have remained elusive. Although the RNA processing reactions leading to polyadenylated messenger RNA have been studied in many systems, and much progress has been made, a complete understanding of the biochemistry of the poly(A) polymerase enzyme is still lacking. My research uses Vaccinia virus as a model system to gain a better understanding of this complicated polyadenylation process, which consist of RNA binding, catalysis and polymerase translocation. ^ Vaccinia virus replicates in the cytoplasm of its host cell, so it must employ its own poly(A) polymerase (PAP), a heterodimer of two virus encoded proteins, VP55 and VP39. VP55 is the catalytic subunit, adding 30 adenylates to a non-polyadenylated RNA in a rapid processive manner before abruptly changing to a slow, non-processive mode of adenylate addition and dissociating from the RNA. VP39 is the stimulatory subunit. It has no polyadenylation catalytic activity by itself, but when associated with VP55 it facilitates the semi-processive synthesis of tails several hundred adenylates in length. ^ Oligonucleotide selection and competition studies have shown that the heterodimer binds a minimal motif of (rU)2 (N)25 U, the “heterodimer binding motif”, within an oligonucleotide, and its primer selection for polyadenylation is base-type specific. ^ Crosslinking studies using photosensitive uridylate analogs show that within a VP55-VP39-primer ternary complex, VP55 comes into contact with all three required uridylates, while VP39 only contacts the downstream uridylate. Further studies, using a backbone-anchored photosensitive crosslinker show that both PAP subunits are in close proximity to the downstream −10 to −21 region of 50mer model primers containing the heterodimer binding motif. This equal crosslinking to both subunits suggests that the dimerization of VP55 and VP39 creates either a cleft or a channel between the two subunits through which this region of RNA passes. ^ Peptide mapping studies of VP39 covalently crosslinked to the oligonucleotide have identified residue R107 as the amino acid in close proximity to the −10 uridylate. This helps us project a conceptual model onto the known physical surface of this subunit. In the absence of any tertiary structural data for VP55, we have used a series of oligonucleotide selection assays, as well as crosslinking, nucleotide transfer assays, and gel shift assays to gain insight into the requirements for binding, polyadenylation and translocation. Collectively, these data allow us to put together a comprehensive model of the structure and function of the polyadenylation ternary complex consisting of VP39, VP55 and RNA. ^

An examination of the relationship between maternal and neighborhood-level characteristics and intrauterine growth retardation in Harris County, Texas, 1999--2001

The persistence of low birth weight and intrauterine growth retardation (IUGR) in the United States has puzzled researchers for decades. Much of the work that has been conducted on adverse birth outcomes has focused on low birth weight in general and not on IUGR. Studies that have examined IUGR specifically thus far have focused primarily on individual-level maternal risk factors. These risk factors have only been able to explain a small portion of the variance in IUGR. Therefore, recent work has begun to focus on community-level risk factors in addition to the individual-level maternal characteristics. This study uses Social Ecology to examine the relationship of individual and community-level risk factors and IUGR. Logistic regression was used to establish an individual-level model based on 155, 856 births recorded in Harris County, TX during 1999-2001. IUGR was characterized using a fetal growth ratio method with race/ethnic and sex specific mean birth weights calculated from national vital records. The spatial distributions of 114,460 birth records spatially located within the City of Houston were examined using choropleth, probability and density maps. Census tracts with higher than expected rates of IUGR and high levels of neighborhood disadvantage were highlighted. Neighborhood disadvantage was constructed using socioeconomic variables from the 2000 U.S. Census. Factor analysis was used to create a unified single measure. Lastly, a random coefficients model was used to examine the relationship between varying levels of community disadvantage, given the set of individual-level risk factors for 152,997 birth records spatially located within Harris County, TX. Neighborhood disadvantage was measured using three different indices adapted from previous work. The findings show that pregnancy-induced hypertension, previous preterm infant, tobacco use and insufficient weight gain have the highest association with IUGR. Neighborhood disadvantage only slightly further increases the risk of IUGR (OR 1.12 to 1.23). Although community level disadvantage only helped to explain a small proportion of the variance of IUGR, it did have a significant impact. This finding suggests that community level risk factors should be included in future work with IUGR and that more work needs to be conducted. ^

Simulation study of joint transition and Weibull survival model with shared parameters

This study investigates a theoretical model where a longitudinal process, that is a stationary Markov-Chain, and a Weibull survival process share a bivariate random effect. Furthermore, a Quality-of-Life adjusted survival is calculated as the weighted sum of survival time. Theoretical values of population mean adjusted survival of the described model are computed numerically. The parameters of the bivariate random effect do significantly affect theoretical values of population mean. Maximum-Likelihood and Bayesian methods are applied on simulated data to estimate the model parameters. Based on the parameter estimates, predicated population mean adjusted survival can then be calculated numerically and compared with the theoretical values. Bayesian method and Maximum-Likelihood method provide parameter estimations and population mean prediction with comparable accuracy; however Bayesian method suffers from poor convergence due to autocorrelation and inter-variable correlation. ^

Association of pellicle growth morphological characteristics and clinical presentation of Mycobacterium tuberculosis isolates

Trehalose dimycolate (TDM) is a mycobacterial glycolipid that is released from the surface of virulent M. tuberculosis. We evaluated the rate of growth, colony characteristics and production of TDM by Mycobacterium tuberculosis strains isolated from different clinical sites. Since detergent removes TDM from organisms, we analyzed growth rate and colony morphology of 79 primary clinical isolates grown as pellicles on the surface of detergent free Middlebrook 7H9 media. The genotype of each had been previously characterized. TDM production was measured by thin layer chromatography on 32 of these isolates. We found that strains isolated from pulmonary sites produced large amounts of TDM, grew rapidly as thin spreading pellicles, showed early cording (<1 week) and climbed the sides of the dish. In contrast, the extrapulmonary isolates (lymph node and bone marrow) produced less TDM (p<0.01), grew as discrete patches with little tendency to spread or climb the walls (p<0.02). The Beijing pulmonary (BP) isolates produced more TDM than non Beijing pulmonary isolates. The largest differences were observed in Beijing strains. The Beijing pulmonary isolates produced more TDM and grew faster than the Beijing extrapulmonary isolates (p<0.01). This was true even when the pulmonary and extrapulmonary isolates were derived from the same clade. These growth characteristics were consistently observed only on the first passage after primary isolation. This suggests that the differences in growth rate and TDM production observed reflect differences in gene expression patterns of pulmonary and extrapulmonary infections, that Mycobacterium tuberculosis in the lung grows more rapidly and produces more TDM than it does in extrapulmonary sites. This provides new opportunities to investigate gene expression of Mycobacterium tuberculosis in human.^

Suspected outbreak of dengue fever in Houston: Clinical characteristics and determination of autochthonous transmission between 2003 and 2005

Houston, Texas maintains the appropriate climate and mosquito populations to support the circulation of dengue viruses. The city is susceptible to the introduction and subsequent local transmission of dengue virus with its proximity to dengue-endemic Mexico and the high degree of international travel routed through its airports. In 2008, a study at the University of Texas School of Public Health identified 58 suspected dengue fever cases that presented at hospitals and clinics in the Houston area. Serum or CSF samples of the 58 samples tested positive or equivocal for the presence of anti-dengue IgM antibodies (Rodriguez, 2008). Here, we present the results of an investigation aimed to describe the clinical characteristics of the 58 suspected dengue fever cases and to determine if local transmission had occurred. Data from medical record abstractions and personal telephone interviews were used to describe clinical characteristics and travel history of the suspected cases. Our analysis classified six probable dengue fever cases based on the case definition from the World Health Organization. Three of the probable cases for which we were able to obtain travel history had not recently traveled to an endemic area prior to onset of symptoms suggesting the illnesses were locally acquired in Houston. Further analysis led us to hypothesize that additional cases of dengue fever are present in our study population. Fifty-one percent of the study population was diagnosed with meningitis and/or encephalitis. Sixty percent of the individuals who received a lumbar puncture had abnormal CSF. Together these findings indicate viral infection with neurological involvement, which has been reported to occur with dengue fever. Among the individuals who received liver enzyme analysis, 54% had evidence of abnormal liver enzyme levels, a clinical sign commonly observed with dengue. Our results indicate that a suspected outbreak of dengue fever with autochthonous transmission occurred in the Houston area between 2003 and 2005. ^

The association between classroom characteristics and student physical activity in physical education classrooms

Background. With the rapid rise in childhood obesity, physical activity participation among young children has become the subject of much recent attention. Physical education classes have been specifically targeted as a method of providing opportunities for all children to be active. Unfortunately, student participation in moderate-to-vigorous physical activity during these classes still falls far below the current recommendations. While some research to date has reported the levels of activity among elementary-aged children, research is limited on the relationship between these activity levels and the environmental characteristics that exist within the PE classroom. ^ Purpose. The purpose of this study is to examine the association between specific classroom characteristics and contextual characteristics (lesson context, class size, class location, teacher gender, and teacher encouragement for PA) with elementary aged children's moderate-to-vigorous activity during PE class. ^ Methods. A secondary analysis of 211 3rd, 4th and 5th grade physical education classes amongst 39 elementary schools in Harris County, TX and 35 elementary schools in Travis County, TX was conducted using cross-sectional data from the evaluation of a school-based health program. Lesson context and student activity levels were measured using a direct observation measurement tool. Additionally, these variables were further analyzed against a number of classroom characteristics to determine any significant associations. ^ Results. Overall, elementary PE classes are still participating in low levels of moderate-to-vigorous physical activity averaging only 38% of class time. Additionally, close to 25% of class time is spent in classroom management. Male directed classes spent significantly more time in game activities and female directed classes spent more time in fitness, knowledge, and skill activities. Classes that took place outdoors were more active and spent more time in games than those that took place indoors. Significant correlations were demonstrated between class size and time spent in management context. Time spent in management context was also correlated with time spent sitting and standing. Additionally, positive correlations were demonstrated between time very active and teachers that praised students and encouraged physical activity among their classes.^

FUNCTIONS OF DEADENYLATION FACTORS IN MRNA DECAY AND MRNA PROCESSING BODY FORMATION

Most newly synthesized messenger RNAs possess a 5’ cap and a 3’ poly(A) tail. The process of poly(A) tail shortening, also termed deadenylation, is important for post-transcriptional gene regulation, because deadenylation not only leads to mRNA translational inhibition but also is the first step of major mRNA degradation. Translationally inhibited mRNAs can be stored and/or degraded in dynamic cytoplasmic foci termed mRNA processing bodies, or P bodies, which are conserved in eukaryotes. To shed new light on the mechanisms of P body formation and P body functions, I focused on the link between deadenylation factors and P bodies. I found that the two major deadenylation complexes, Pan3-Pan2 and Ccr4-Caf1, can both be enriched in P bodies. The deadenylase activity of the Ccr4-Caf1 complex is prerequisite for P body formation. Pan3, but not the deadenylase Pan2, is essential for P body formation. While the C-terminal domain of Pan3 is important for interaction with Pan2, Pan3 N-terminal domain is important for Pan3 to form cytoplasmic foci colocalizing with P bodies and to promote mRNA decay. Interestingly, Pan3 N-terminal domain may be phosphorylated to regulate Pan3 localization and functions. Aside from the functions of the two deadenylation complexes in P bodies, I also studied all reported human P body proteins as a whole using bioinformatics. This effort not only has generated a comprehensive picture of the functions of and interactions among human P body proteins, but also has predicted proteins that may regulate P body formation and/or functions. In summary, my study has established a direct link between mRNA deadenylation and P body formation and has also led to new hypotheses to guide future research on how P body dynamics are controlled.

Characteristics of a spina bifida population including North American Caucasian and Hispanic individuals.

BACKGROUND: Meningomyelocele (MM) is a common human birth defect. MM is a disorder of neural development caused by contributions from genes and environmental factors that result in the NTD and lead to a spectrum of physical and neurocognitive phenotypes. METHODS: A multidisciplinary approach has been taken to develop a comprehensive understanding of MM through collaborative efforts from investigators specializing in genetics, development, brain imaging, and neurocognitive outcome. Patients have been recruited from five different sites: Houston and the Texas-Mexico border area; Toronto, Canada; Los Angeles, California; and Lexington, Kentucky. Genetic risk factors for MM have been assessed by genotyping and association testing using the transmission disequilibrium test. RESULTS: A total of 509 affected child/parent trios and 309 affected child/parent duos have been enrolled to date for genetic association studies. Subsets of the patients have also been enrolled for studies assessing development, brain imaging, and neurocognitive outcomes. The study recruited two major ethnic groups, with 45.9% Hispanics of Mexican descent and 36.2% North American Caucasians of European descent. The remaining patients are African-American, South and Central American, Native American, and Asian. Studies of this group of patients have already discovered distinct corpus callosum morphology and neurocognitive deficits that associate with MM. We have identified maternal MTHFR 667T allele as a risk factor for MM. In addition, we also found that several genes for glucose transport and metabolism are potential risk factors for MM. CONCLUSIONS: The enrolled patient population provides a valuable resource for elucidating the disease characteristics and mechanisms for MM development.

Psychosocial job characteristics as predictors of overall health: Results from a community-based cross-sectional study conducted in southeast Texas in 2001 and 2002

Stress at the workplace exposes people to increased risk for poor physical and/or mental health. Recently psychological and social disadvantages have been proven to place the worker at risk for mental or physical health outcomes. The overall purpose of this study was to study full time employed study subjects and (1) describe the various psychosocial job characteristics in a population of low income individuals stratified by race/ethnicity residing in Houston and Brownsville, Texas and (2) examine the associations between psychosocial job characteristics and physical, mental, and self rated health. It was observed that having a low level of education is associated with having very little or no control, security, and social support at the workplace. Being Mexican American was associated with having good job control, job security, job social support and having a less demanding job. Furthermore, the psychosocial job characteristics were associated with mental health outcomes but not with physical and self rated health. ^