Automatic quantitation of multiple sclerosis lesions on MR images

A two-pronged approach for the automatic quantitation of multiple sclerosis (MS) lesions on magnetic resonance (MR) images has been developed. This method includes the design and use of a pulse sequence for improved lesion-to-tissue contrast (LTC) and seeks to identify and minimize the sources of false lesion classifications in segmented images. The new pulse sequence, referred to as AFFIRMATIVE (Attenuation of Fluid by Fast Inversion Recovery with MAgnetization Transfer Imaging with Variable Echoes), improves the LTC, relative to spin-echo images, by combining Fluid-Attenuated Inversion Recovery (FLAIR) and Magnetization Transfer Contrast (MTC). In addition to acquiring fast FLAIR/MTC images, the AFFIRMATIVE sequence simultaneously acquires fast spin-echo (FSE) images for spatial registration of images, which is necessary for accurate lesion quantitation. Flow has been found to be a primary source of false lesion classifications. Therefore, an imaging protocol and reconstruction methods are developed to generate "flow images" which depict both coherent (vascular) and incoherent (CSF) flow. An automatic technique is designed for the removal of extra-meningeal tissues, since these are known to be sources of false lesion classifications. A retrospective, three-dimensional (3D) registration algorithm is implemented to correct for patient movement which may have occurred between AFFIRMATIVE and flow imaging scans. Following application of these pre-processing steps, images are segmented into white matter, gray matter, cerebrospinal fluid, and MS lesions based on AFFIRMATIVE and flow images using an automatic algorithm. All algorithms are seamlessly integrated into a single MR image analysis software package. Lesion quantitation has been performed on images from 15 patient volunteers. The total processing time is less than two hours per patient on a SPARCstation 20. The automated nature of this approach should provide an objective means of monitoring the progression, stabilization, and/or regression of MS lesions in large-scale, multi-center clinical trials. ^

AIDS talk

The observations of Michel Foucault, noted Twentieth Century French philosopher, regarding modern power relations and orders of discourse, form the framework utilized to analyze and interpret the power struggles of AIDS activists and their opponents--the religious and radical right, and the administrative agencies of the 'Liberal' welfare State. Supported by the tools of sociolinguistic inquiry, the analysis highlights the success of a safer sex campaign in Houston, Texas to illustrate the dynamics of cultural and political change by means of discursive transformations initiated by the gay micro-culture. The KS/AIDS Foundation, allied with both the biomedical community and gay entertainment spheres, was successful in conveying biomedical cautions that resulted in altered personal behavior and modified public attitudes by using linguistic conventions consonant with the discourse of the Houston gay micro-culture. The transformation of discursive practices transgressed not only the Houston gay micro-culture's boundaries, but the city boundaries of Houston as well. In addition to cultural and political change, moderate and confrontational gay activists also sought to change the cognitive boundaries surrounding 'the gold standard' for clinical research trials.^ From a Foucauldian perspective, the same-sex community evolved from the subordinated Other to a position of power in a period of five years. Transformations in discursive practices and power relations are exemplified by the changing definitions employed by AIDS policy-makers, the public validation of community-based research and the establishment of parallel track drug studies. Finally, transformations in discursive practices surrounding the issues of HIV antibody testing are interpreted using Foucault's six points of power relations. The Montrose Clinic provides the case study for this investigation. The clinic turned the technical rationalities of the State against itself to achieve its own ends and those of the gay micro-culture--anonymous testing with pre and post test counseling. AIDS Talk portrays a dramatic transformation in discursive practices and power relations that transcends the historical moment to provide a model for future activists. Volume 2 contains copies of fugitive primary source materials largely unavailable elsewhere. Original documents are archived in the Harris County Medical Archives in the Houston Academy of Medicine located in the Texas Medical Center Library, Houston, Texas. ^

GLUCAGON GENE EXPRESSION: ANALYSIS OF PREPROGLUCAGON

Glucagon is a 29 amino acid polypeptide hormone produced in the (alpha) cells of the pancreatic islets. The purpose of this research was to understand better the role of glucagon in the regulation of metabolic processes. As with other polypeptide hormones, the synthesis of glucagon is thought to involve a larger precursor, which is then enzymatically cleaved to the functional form. The specific research objectives were to obtain cloned copies of the messenger RNA (mRNA) for pancreatic glucagon, to determine their primary sequences, and from this coding information to deduce the amino acid sequence of the initial glucagon precursor. From this suggested preproglucagon sequence and prior information on possible proglucagon intermediate processing products, the overall objective of this research is to propose a possible pathway for the biosynthesis of pancreatic glucagon.^ Synthetic oligodeoxynucleotide probes of 14-nucleotides (14-mer) and 17-nucleotides (a 17-mer) complementary to codons specifying a unique sequence of mature glucagon were synthesized. The ('32)P-labeled-14-mer was hybridized with size-fractionated fetal bovine pancreatic poly(A('+))RNA bound to nitrocellulose. RNA fractions of (TURN)14S were found to hybridize specifically, resulting in an (TURN)10-fold enrichment for these sequences. These poly(A('+))RNAs were translated in a cell-free system and the products analyzed by gel electrophoresis. The translation products were found to be enriched for a protein of the putative size of mammalian preproglucagon ((TURN)21 kd). These enriched RNA fractions were used to construct a complementary DNA (cDNA) library is plasmid pBR322.^ Screening of duplicate colony filters with the ('32)P-labeled-17-mer and a ('32)P-labeled-17-mer-primed cDNA probe indicated 25 possible glucagon clones from 3100 colonies screened. Restriction mapping of 6 of these clones suggested that they represented a single mRNA species. Primary sequence analysis of one clone containing a 1200 base pair DNA insert revealed that it contained essentially a full-length copy of glucagon cDNA.^ Analaysis of the cDNA suggested that it encoded an initial translation product of 180 amino acids with an M(,r) = 21 kd. The first initiation codon (ATG, methionine) followed by the longest open reading frame of 540 nucleotides was preceded by a 5'-untranslated region of 90 nucleotides, and was followed by a longer 3'-untranslated region of 471 nucleotides, resulting in a total of 1101 nucleotides. . . . (Author's abstract exceeds stipulated maximum length. Discontinued here with permission of author.) UMI ^

The effect of the shift from HMO to PPO plans on the prevalence of hospital bad debt in the insured population: A case study in two Houston-area hospitals

In spite of the dramatic increase and general concern with U.S. hospital bad debt expense (AMNews, January 12, 2004; Philadelphia Business Journal, April 30, 2004; WSJ, July 23, 2004), there appears to be little available analysis of the precise sources and causes of its growth. This is particularly true in terms of the potential contribution of insured patients to bad debt expense in light of the recent shift in managed care from health maintenance organization (HMO) plans to preferred provider organization (PPO) plans (Kaiser Annual Survey Report, 2003). This study examines and attempts to explain the recent dramatic growth in bad debt expense by focusing on and analyzing data from two Houston-area hospital providers within one healthcare system. In contrast to prior studies in which self-pay was found to be the primary source of hospital bad debt expense (Saywell, R. M., et al., 1989; Zollinger, T. W., 1991; Weissman, Joel S., et al., 1999), this study hypothesizes that the growing hospital bad debt expense is mainly due to the shifting trend away from HMOs to PPOs as a conscious decision by employers to share costs with employees. Compared to HMO plans, the structure of PPOs includes higher co-pays, coinsurance, and deductibles for the patient-pay portion of medical bills, creating the potential for an increase in bad debt for hospital providers (from a case study). This bad debt expense has a greater impact in the community hospital than in the Texas Medical Center hospital. ^

FACTORS INFLUENCING THE PATTERNS OF PHYSICIAN VISITS TO NURSING HOME RESIDENTS

This study was designed to identify some of the factors related to patterns of physician visits to nursing home residents. The relationship of ten resident and organizational characteristics to patterns of physician visits was investigated through secondary analysis of data abstracted from the 1973-74 National Nursing Home Survey of the National Center for Health Statistics. The study sample was composed of 11,135 of the 19,013 nursing home residents who participated in the survey.^ The analytic results revealed that all ten variables had a statistically significant relationship to patterns of physician visits, mainly due to the large sample size. The degrees of association between the variables, measured by the Cramer's V statistic, ranged from moderate to very weak.^ Certification status of the nursing home under Medicare and/or Medicaid was shown to be most strongly related to patterns of physician visits, followed by primary source of payment for nursing home care, and residence prior to nursing home admission. Several variables thought to be related to patterns of physician visits were found to have a very weak relationship: age of the resident, marital status, length of stay, primary diagnosis, number of chronic conditions, activities of daily living status, and levels of care.^ In order to get a more precise picture of the relative influence of certification status and primary source of payment when the other variables were statistically controlled, these two variables were combined into a single variable. The results revealed that the combined effects of certification status and primary source of payment were sustained, regardless of differences in the residents' personal, utilization, and health status characteristics, and the levels of care that they received. The results also indicated that the five groups created by combining the two variables differed in patterns of physician visits. For example, private pay residents in intermediate care facilities (ICF's) and non-certified facilities were more likely to receive unscheduled visits than private pay residents in skilled nursing homes (SNH's), residents in SNH's supported by Medicare or Medicaid, and residents in ICF's supported by Medicaid. ^

Estimation of male-to-female ratios of mutation rate in primates and rodents

Haldane (1935) developed a method for estimating the male-to-female ratio of mutation rate ($\alpha$) by using sex-linked recessive genetic disease, but in six different studies using hemophilia A data the estimates of $\alpha$ varied from 1.2 to 29.3. Direct genomic sequencing is a better approach, but it is laborious and not readily applicable to non-human organisms. To study the sex ratios of mutation rate in various mammals, I used an indirect method proposed by Miyata et al. (1987). This method takes advantage of the fact that different chromosomes segregate differently between males and females, and uses the ratios of mutation rate in sequences on different chromosomes to estimate the male-to-female ratio of mutation rate. I sequenced the last intron of ZFX and ZFY genes in 6 species of primates and 2 species of rodents; I also sequenced the partial genomic sequence of the Ube1x and Ube1y genes of mice and rats. The purposes of my study in addition to estimation of $\alpha$'s in different mammalian species, are to test the hypothesis that most mutations are replication dependent and to examine the generation-time effect on $\alpha$. The $\alpha$ value estimated from the ZFX and ZFY introns of the six primate specise is ${\sim}$6. This estimate is the same as an earlier estimate using only 4 species of primates, but the 95% confidence interval has been reduced from (2, 84) to (2, 33). The estimate of $\alpha$ in the rodents obtained from Zfx and Zfy introns is ${\sim}$1.9, and that deriving from Ube1x and Ube1y introns is ${\sim}$2. Both estimates have a 95% confidence interval from 1 to 3. These two estimates are very close to each other, but are only one-third of that of the primates, suggesting a generation-time effect on $\alpha$. An $\alpha$ of 6 in primates and 2 in rodents are close to the estimates of the male-to-female ratio of the number of germ-cell divisions per generation in humans and mice, which are 6 and 2, respectively, assuming the generation time in humans is 20 years and that in mice is 5 months. These findings suggest that errors during germ-cell DNA replication are the primary source of mutation and that $\alpha$ decreases with decreasing length of generation time. ^

Household risk factors and the health and nutritional status of children in rural Honduras

During this cross-sectional study, both quantitative and qualitative research methods were used to elucidate the role that household environment and sanitation play in the nutritional status of children in a rural Honduran community. Anthropometric measurements were taken as measures of nutritional status among children under five years of age, while interviews regarding the household environment were conducted with their primary caregivers. Community participatory activities were conducted with primary caregivers, and results from water quality testing were analyzed for E. coli contamination. Anthropometric results were compared using the 1977 NCHS Growth Charts and the 2006 WHO Child Growth Standard to examine the implications of using the new WHO standard. The references showed generally good or excellent agreement between z-score categories, except among height-for-age classifications for males 24-35.9 months and weight-for-age classifications for males older than 24 months. Comparing the proportion of stunted, underweight, and wasted children, using the WHO standard generally resulted in higher proportions of stunting, lower underweight proportions, and higher overweight proportions. Logistic regression was used to determine which household and sanitation factors most influenced the growth of children. Results suggest only having water from a spring, stream, or other type of surface water as the primary source of drinking water is a significant risk factor for stunting. A protective association was seen between the household wealth index and stunting. Through participatory activities, the community provided insight on health issues important for improving child health. These activities yielded findings to be harnessed as a powerful resource to unify efforts for change. The qualitative findings were triangulated with the quantitative interview and water testing results to provide intervention recommendations for the community and its primary health care clinic. Recommendations include educating the community on best water consumption practices and encouraging the completion of at least some primary education for primary caregivers to improve child health. It is recommended that a community health worker program be developed to support and implement community interventions to improve water use and household sanitation behaviors and to encourage the involvement of the community in targeting and guiding successful interventions. ^

Nitrogen dioxide exposures among a selected group of residents of substandard housing in Houston, Texas

Nitrogen dioxide (NO$\sb2)$ levels in sixteen substandard houses located in Houston, Texas were examined. The classification of the houses as substandard was based on an assessment of structural integrity which would affect air exchange rates. In these homes, unvented gas space heaters were operated as the primary source of heat.^ The Ogawa passive sampling device was used to measure NO$\sb2$ concentrations over 24 to 48-hour periods during generally cold weather. A sampler was placed in the kitchen and bedroom of each house. The female head of household was asked to wear a monitor during area monitoring to assess her personal exposure. Outdoor levels of NO$\sb2$ were also measured.^ Mean (standard deviation) levels of kitchen, bedroom and personal exposures were 280 (125) ppb, 256 (155) ppb and 164 (102) ppb, respectively. Additional short-term ($<$24 hours) samples were measured in three houses. The mean level of NO$\sb2$ measured outdoors was 51 ppb over the course of the study.^ The measurements obtained with the Ogawa sampler were compared to those levels obtained using a reference method (chemiluminescence). Outdoor levels measured with the diffusion samplers were 48% higher.^ These results suggest that wintertime NO$\sb2$ levels within substandard houses using gas appliances for heating and cooking are extremely elevated. Further work is needed to investigate the prevalence of possible health effects associated with these exposures. ^

Analysis of primary Wilms tumors for WT1 RNA processing alterations

Wilms tumor (WT) is an embryonal renal tumor with a heterogeneous genetic etiology that serves as a valuable model for studying tumorigenesis. Biallelic inactivation of the tumor suppressor gene WT1, a zinc-finger transcriptional regulator located at 11p13, is critical for the development of some Wilms tumors. Interestingly, WT1 genomic analysis has demonstrated mutations in less than 20% of WT cases. This suggests either other genes play a more major role in Wilms tumorigenesis or WT1 is functionally altered by mechanisms other than DNA mutation. Previous observations in rat and in WT xenograft cell lines have suggested that abnormal WT1 RNA processing (exon 6 RNA editing and aberrant exon 2 splicing, respectively) is a potential mechanism of altering WT1 function in the absence of a WT1 DNA mutation. However, the role of this abnormal RNA processing has not previously been assessed in primary Wilms tumors. ^ To test the hypothesis that abnormal WT1 RNA processing is a mechanism of WT1alteration during tumor development, WT1 RNA from 85 primary tumors was analyzed using reverse transcription and polymerase chain reaction amplification (RT-PCR). Although no evidence for WT1 RNA editing was observed, variable levels (5% to 50%) of aberrant WT1 exon 2 splicing were detected for 11 tumors in the absence of a detectable WT1 DNA mutation. Also, alteration of normal WT1 alternative splicing, observed as RNA isoform loss, was detected in five tumors with no apparent WT1 genomic alteration, although no consistent pattern of RNA isoform loss was detected. This abnormal WT1 splicing, detected by either loss of exon 2 from some of the transcripts or loss of RNA isoforms, is statistically correlated with relapse (p = 0.005). These studies demonstrate that abnormal WT1 RNA processing is not a common mechanism of abrogating normal WT1 function in primary tumors. However, in those cases in which abnormal WTI splicing is present, these data indicate that it may serve as a useful prognostic marker for relapse in WT patients. ^

VERIFICATION OF DNA PREDICTED PROTEIN SEQUENCES BY ENZYME HYDROLYSIS AND MASS SPECTROMETRIC ANALYSIS

The focus of this thesis lies in the development of a sensitive method for the analysis of protein primary structure which can be easily used to confirm the DNA sequence of a protein's gene and determine the modifications which are made after translation. This technique involves the use of dipeptidyl aminopeptidase (DAP) and dipeptidyl carboxypeptidase (DCP) to hydrolyze the protein and the mass spectrometric analysis of the dipeptide products.^ Dipeptidyl carboxypeptidase was purified from human lung tissue and characterized with respect to its proteolytic activity. The results showed that the enzyme has a relatively unrestricted specificity, making it useful for the analysis of the C-terminal of proteins. Most of the dipeptide products were identified using gas chromatography/mass spectrometry (GC/MS). In order to analyze the peptides not hydrolyzed by DCP and DAP, as well as the dipeptides not identified by GC/MS, a FAB ion source was installed on a quadrupole mass spectrometer and its performance evaluated with a variety of compounds.^ Using these techniques, the sequences of the N-terminal and C-terminal regions and seven fragments of bacteriophage P22 tail protein have been verified. All of the dipeptides identified in these analysis were in the same DNA reading frame, thus ruling out the possibility of a single base being inserted or deleted from the DNA sequence. The verification of small sequences throughout the protein sequence also indicates that no large portions of the protein have been removed after translation. ^

An analysis of the function of region 1.2 of the primary sigma factor, sigma 70, from Escherichia coli

The sigma (σ) subunit of eubacterial RNA polymerase is required for recognition of and transcription initiation from promoter DNA sequences. One family of sigma factors includes those related to the primary sigma factor from E. coli, σ70. Members of the σ70 family have four highly conserved domains, of which regions 2 through 4 are present in all members. Region 1 can be subdivided into regions 1.1 and 1.2. Region 1.1 affects DNA binding by σ 70 alone, as well as transcription initiation by holoenzyme. Region 1.2, present and highly conserved in most sigma factors, has not yet been assigned a putative function, although previous work demonstrated that it is not required for either association with the core subunits of RNA polymerase or promoter specific binding by holoenzyme. This study primarily investigates the functional role of region 1.2 during transcription initiation. In vivo and in vitro characterization of thirty-two single amino acid substitutions targeted to region 1.2 of E. coli σ70 as well as a deletion of region 1.2, revealed that mutations in region 1.2 can affect promoter binding, open complex formation, initiated complex formation, and the transition from abortive transcription to elongation. The relative degree of solvent exposure of several positions in region 1.2 has been determined, with positions 116 and 122 likely to be located near the surface of σ70. ^ During the course of this study, the existence of two “wild type” variants of E. coli σ70 was discovered. The identity of amino acid 149 has been reported variably as either arginine or aspartic acid in published articles and in online databases. In vivo and in vitro characterization of the two reported variations of E. coli σ70 (N149 and D149) has determined that the two variants are functionally equivalent. However, in vivo and in vitro characterization of single amino acid substitutions and a region 1.2 deletion in the context of each variant background revealed that the behavior of some mutations are greatly affected by the identity of amino acid 149. ^

A qualitative analysis of leadership styles and the selection of quality improvement in primary care practice

In the Practice Change Model, physicians act as key stakeholders, people who have both an investment in the practice and the capacity to influence how the practice performs. This leadership role is critical to the development and change of the practice. Leadership roles and effectiveness are an important factor in quality improvement in primary care practices.^ The study conducted involved a comparative case study analysis to identify leadership roles and the relationship between leadership roles and the number and type of quality improvement strategies adopted during a Practice Change Model-based intervention study. The research utilized secondary data from four primary care practices with various leadership styles. The practices are located in the San Antonio region and serve a large Hispanic population. The data was collected by two ABC Project Facilitators from each practice during a 12-month period including Key Informant Interviews (all staff members), MAP (Multi-method Assessment Process), and Practice Facilitation field notes. This data was used to evaluate leadership styles, management within the practice, and intervention tools that were implemented. The chief steps will be (1) to analyze if the leader-member relations contribute to the type of quality improvement strategy or strategies selected (2) to investigate if leader-position power contributes to the number of strategies selected and the type of strategy selected (3) and to explore whether the task structure varies across the four primary care practices.^ The research found that involving more members of the clinic staff in decision-making, building bridges between organizational staff and clinical staff, and task structure are all associated with the direct influence on the number and type of quality improvement strategies implemented in primary care practice.^ Although this research only investigated leadership styles of four different practices, it will offer future guidance on how to establish the priorities and implementation of quality improvement strategies that will have the greatest impact on patient care improvement. ^

Pathway analysis of genome-wide association study data in primary biliary cirrhosisa

Genome-wide association studies (GWAS) have successfully identified several genetic loci associated with inherited predisposition to primary biliary cirrhosis (PBC), the most common autoimmune disease of the liver. Pathway-based tests constitute a novel paradigm for GWAS analysis. By evaluating genetic variation across a biological pathway (gene set), these tests have the potential to determine the collective impact of variants with subtle effects that are individually too weak to be detected in traditional single variant GWAS analysis. To identify biological pathways associated with the risk of development of PBC, GWAS of PBC from Italy (449 cases and 940 controls) and Canada (530 cases and 398 controls) were independently analyzed. The linear combination test (LCT), a recently developed pathway-level statistical method was used for this analysis. For additional validation, pathways that were replicated at the P <0.05 level of significance in both GWAS on LCT analysis were also tested for association with PBC in each dataset using two complementary GWAS pathway approaches. The complementary approaches included a modification of the gene set enrichment analysis algorithm (i-GSEA4GWAS) and Fisher's exact test for pathway enrichment ratios. Twenty-five pathways were associated with PBC risk on LCT analysis in the Italian dataset at P<0.05, of which eight had an FDR<0.25. The top pathway in the Italian dataset was the TNF/stress related signaling pathway (p=7.38×10 -4, FDR=0.18). Twenty-six pathways were associated with PBC at the P<0.05 level using the LCT in the Canadian dataset with the regulation and function of ChREBP in liver pathway (p=5.68×10-4, FDR=0.285) emerging as the most significant pathway. Two pathways, phosphatidylinositol signaling system (Italian: p=0.016, FDR=0.436; Canadian: p=0.034, FDR=0.693) and hedgehog signaling (Italian: p=0.044, FDR=0.636; Canadian: p=0.041, FDR=0.693), were replicated at LCT P<0.05 in both datasets. Statistically significant association of both pathways with PBC genetic susceptibility was confirmed in the Italian dataset on i-GSEA4GWAS. Results for the phosphatidylinositol signaling system were also significant in both datasets on applying Fisher's exact test for pathway enrichment ratios. This study identified a combination of known and novel pathway-level associations with PBC risk. If functionally validated, the findings may yield fresh insights into the etiology of this complex autoimmune disease with possible preventive and therapeutic application.^