BENCHMARKING AND IMPLEMENTATION OF A NEW INDEPENDENT MONTE CARLO DOSE CALCULATION QUALITY ASSURANCE AUDIT TOOL FOR CLINICAL TRIALS

Introduction Commercial treatment planning systems employ a variety of dose calculation algorithms to plan and predict the dose distributions a patient receives during external beam radiation therapy. Traditionally, the Radiological Physics Center has relied on measurements to assure that institutions participating in the National Cancer Institute sponsored clinical trials administer radiation in doses that are clinically comparable to those of other participating institutions. To complement the effort of the RPC, an independent dose calculation tool needs to be developed that will enable a generic method to determine patient dose distributions in three dimensions and to perform retrospective analysis of radiation delivered to patients who enrolled in past clinical trials. Methods A multi-source model representing output for Varian 6 MV and 10 MV photon beams was developed and evaluated. The Monte Carlo algorithm, know as the Dose Planning Method (DPM), was used to perform the dose calculations. The dose calculations were compared to measurements made in a water phantom and in anthropomorphic phantoms. Intensity modulated radiation therapy and stereotactic body radiation therapy techniques were used with the anthropomorphic phantoms. Finally, past patient treatment plans were selected and recalculated using DPM and contrasted against a commercial dose calculation algorithm. Results The multi-source model was validated for the Varian 6 MV and 10 MV photon beams. The benchmark evaluations demonstrated the ability of the model to accurately calculate dose for the Varian 6 MV and the Varian 10 MV source models. The patient calculations proved that the model was reproducible in determining dose under similar conditions described by the benchmark tests. Conclusions The dose calculation tool that relied on a multi-source model approach and used the DPM code to calculate dose was developed, validated, and benchmarked for the Varian 6 MV and 10 MV photon beams. Several patient dose distributions were contrasted against a commercial algorithm to provide a proof of principal to use as an application in monitoring clinical trial activity.

Comparison of cost and outcome of care in patients with low back pain who are managed by physicians or physical therapists in private practice

The purpose of this study was to determine if there were differences in the cost and outcome of care in patients with low back pain who were managed by physicians or physical therapists in private practice in the state of Arizona. A secondary purpose was to describe the current status of private practice physical therapy clinicians who treat patients with low back pain.^ A Survey on Practice was mailed to 194 physical therapists who were listed by the American Physical Therapy Association as being in private practice in Arizona. Eighty-three percent of the surveys were returned after three attempts. Of those which were returned, 72 were complete and included in the analysis.^ The 72 practices were screened to determine those eligible for the second phase of the study. Those eligible for the second phase numbered 52 clinics. Twenty-six practices agreed to participate; however, only 21 did participate. Clinics which participated were sent packets of information which were to be kept on each patient seen with a complaint of low back pain during a three month period. Packets contained a patient-oriented survey on functional activity to be completed before and after the physical therapy course of treatment, as well as a log which was completed by the physical therapist on the type of care given to the patient and an assessment of the outcome of treatment. The patient was asked to fill out a satisfaction survey relative to the care received from the physical therapist and physician, if applicable.^ Although 259 patients were entered into the study, 210 patient logs were available for analysis. Results indicated that generally, there was no difference in cost or outcome as measured by the final functional score, change between the initial and final functional scores, or the therapist-rated outcome between the patients who were managed by physicians or physical therapists when controlling for age and length of time the patient was experiencing pain. Patients were more satisfied with care received from physical therapists as compared to physicians. Age and length of pain were good predictors of the type of referral patients received according to a logistic regression procedure. The initial disability score (IRS) and the time spent in the facility predicted therapist-rated outcome, a good or poor final disability score (FRS), and a good or poor change score. In addition, age predicted FRS and change scores. The time that the therapist spent in direct contact with the patient also predicted the change score.^ These findings of no difference in the cost and outcome of care were discussed as they relate to the practice of medicine and physical therapy. ^

A study of the cost and effect of newborn screening for Congenital Adrenal Hyperplasia in Texas

Congenital Adrenal Hyperplasia (CAH), due to 21-Hydroxylase deficiency, has an estimated incidence of 1:15,000 births and can result in death, salt-wasting crisis or impaired growth. It has been proposed that early diagnosis and treatment of infants detected from newborn screening for CAH will decrease the incidence of mortality and morbidity in the affected population. The Texas Department of Health (TDH) began mandatory screening for CAH in June, 1989 and Texas is one of fourteen states to provide neonatal screening for the disorder.^ The purpose of this study was to describe the cost and effect of screening for CAH in Texas during 1994 and to compare cases first detected by screen and first detected clinically between January 1, 1990 and December 31, 1994. This study used a longitudinal descriptive research design. The data was secondary and previously collected by the Texas Department of Health. Along with the descriptive study, an economic analysis was done. The cost of the program was defined, measured and valued for four phases of screening: specimen collection, specimen testing, follow-up and diagnostic evaluation.^ There were 103 infants with Classical CAH diagnosed during the study and 71 of the cases had the more serious Salt-Wasting form of the disease. Of the infants diagnosed with Classical CAH, 60% of the cases were first detected by screen and 40% were first detected because of clinical findings before the screening results were returned. The base case cost of adding newborn screening to an existing program (excluding the cost of specimen collection) was $357,989 for 100,000 infants. The cost per case of Classical CAH diagnosed, based on the number of infants first detected by screen in 1994, was \$126,892. There were 42 infants diagnosed with the more benign Nonclassical form of the disease. When these cases were included in the total, the cost per infant to diagnose Congenital Adrenal/Hyperplasia was $87,848. ^

Homology Cloning, Heterologous Expression and Characterization of a New Channelrhodopsin

Channelrhodopsins are phototaxis receptors in the plasma membranes of motile unicellular algae. They function as light-gated cation channels and this channel activity has been exploited to trigger action potentials in neurons with light to control neural circuits (“optogenetics"). Four channelrhodopsins were identified in two algal species, Chlamydomonas reinhardtii and Volvox carteri, with known genome sequences; each species contains 2 channelrhodopsins, one absorbing at longer wavelengths and one at shorter wavelengths, named CrChR1 and CrChR2, respectively. Our goals are to expand knowledge of channelrhodopsin mechanisms and also to identify new channelrhodopsins from various algal species with improved properties for optogenetic use. For these aims we are targeting algae from extreme environments to establish the natural diversity of their properties. We cloned a new channelrhodopsin from the psychrophilic (cold-loving) alga, Chlamydomonas augustae, with degenerate primers based on the 4 known homologs. The new protein is 48% and 52% identical to CrChR1 and CrChR2, respectively. We expressed the channelrhodopsin in HEK293 cells and measured light-induced currents to assess their kinetics and action spectrum. Based on the primary structure, kinetics of light-induced photocurrents in HEK293 cells, and action spectrum maximum of 520 nm near that of the two previously found CrChR1, we named the new channelrhodopsin CaChR1. The properties of robust channel activity at physiological pH, fast on-and-off kinetics, and greatly red-shifted action spectrum maximum from that of CrChR2, make CaChR1 advantageous as an optogenetic tool. To know this new channelrhodopsin better, we expressed His-tagged CaChR1 in Pichia pastoris and the yield is about 6 mg/L. The purified His-tagged CaChR1 exhibited an absorption spectrum identical to the action spectrum of CaChR1-generated photocurrents. The future work will be measurement of the photocycles of CaChR1 by flash photolysis, crystallization of CaChR1 for the structure and mutagenesis of CaChR1 to find the critical amino acids accounting for red-shifted spectra, slow inactivation and rapid on-and-off kinetics. Seven new channelrhodopsins including CaChR1 from different algal species have been cloned in our lab at this time, bringing the total known to 13. The work of cloning of these new channelrhodopsins along with the expression of CaChR1 was published in Photochemistry and Photobiology in January 2012

Evaluation of PRESAGE® dosimeters for brachytherapy sources and the 3D dosimetry and characterization of the new AgX100 125I seed model

With continuous new improvements in brachytherapy source designs and techniques, method of 3D dosimetry for treatment dose verifications would better ensure accurate patient radiotherapy treatment. This study was aimed to first evaluate the 3D dose distributions of the low-dose rate (LDR) Amersham 6711 OncoseedTM using PRESAGE® dosimeters to establish PRESAGE® as a suitable brachytherapy dosimeter. The new AgX100 125I seed model (Theragenics Corporation) was then characterized using PRESAGE® following the TG-43 protocol. PRESAGE® dosimeters are solid, polyurethane-based, 3D dosimeters doped with radiochromic leuco dyes that produce a linear optical density response to radiation dose. For this project, the radiochromic response in PRESAGE® was captured using optical-CT scanning (632 nm) and the final 3D dose matrix was reconstructed using the MATLAB software. An Amersham 6711 seed with an air-kerma strength of approximately 9 U was used to irradiate two dosimeters to 2 Gy and 11 Gy at 1 cm to evaluate dose rates in the r=1 cm to r=5 cm region. The dosimetry parameters were compared to the values published in the updated AAPM Report No. 51 (TG-43U1). An AgX100 seed with an air-kerma strength of about 6 U was used to irradiate two dosimeters to 3.6 Gy and 12.5 Gy at 1 cm. The dosimetry parameters for the AgX100 were compared to the values measured from previous Monte-Carlo and experimental studies. In general, the measured dose rate constant, anisotropy function, and radial dose function for the Amersham 6711 showed agreements better than 5% compared to consensus values in the r=1 to r=3 cm region. The dose rates and radial dose functions measured for the AgX100 agreed with the MCNPX and TLD-measured values within 3% in the r=1 to r=3 cm region. The measured anisotropy function in PRESAGE® showed relative differences of up to 9% with the MCNPX calculated values. It was determined that post-irradiation optical density change over several days was non-linear in different dose regions, and therefore the dose values in the r=4 to r=5 cm regions had higher uncertainty due to this effect. This study demonstrated that within the radial distance of 3 cm, brachytherapy dosimetry in PRESAGE® can be accurate within 5% as long as irradiation times are within 48 hours.

Prevalence and trends of substance abuse in Harris County, Texas, 1989 to 1991

In the late 1980s, Harris County, Texas began experiencing an escalation of drug-related activities. Various indicators used in this analysis tracked drug-related trends from 1989 to 1991 to determine patterns for comparison of local (Houston/Harris County, Texas) to national levels.^ An important indicator of the drug scenario was drug-related activities among youths, which increased during the period of this study. The Harris County Juvenile Probation Department showed that among arrests for drug-related activities, felonies increased from 25% in 1988 to 53% in 1991. With the rise in drug-related crimes, and substance abuse among the student body, school districts were forced to institute drug education programs in an effort to curtail such activities.^ Law enforcement agencies in the county saw increased demands for their services as a result of drug activities. Harris County Sheriffs Department reported a 32% plus increase in drug-related charges between 1986 and 1991. Houston Police Department reported an increase of 109% for the same period.^ Data from the Harris County Medical Examiner, the National Institute of Justice's Drug Use Forecasting System (Houston), and drug treatment facilities around Houston/Harris County, Texas indicated similar drug usage trends. Over a four-year period (1988-91), the drugs most frequently detected during blood and urine analyses were cocaine, followed by marijuana, heroin, LSD, and methamphetamines.^ From 1988 to 1991, most drug rehabilitation organizations experienced increased demands for their services by approximately 35%. Several other organizations experienced as much as a 70 percent increase. Males accounted for roughly 70% and females about 30% of persons seeking treatment. However, the number of females pursuing treatment increased, thereby reducing the gender gap.^ Blacks in Houston/Harris County were at higher risk for drug usage among the general population, but sought treatment more readily than other ethnic groups. Whites sought treatment in similar numbers as Blacks, but overall the risk appeared smaller because they made up a larger portion of the Houston/Harris County population.^ This analysis concluded that drug trends for the Houston/Harris County, Texas did not follow national trends, but showed patterns of its own. It was recommended that other communities carry out similar studies to determine drug use trends particular to their local. ^

The application of principal component analysis on human development indicators: Temporal approach from 1999 to 2010

Background and Objective. Ever since the human development index was published in 1990 by the United Nations Development Programme (UNDP), many researchers started searching and corporative studying for more effective methods to measure the human development. Published in 1999, Lai’s “Temporal analysis of human development indicators: principal component approach” provided a valuable statistical way on human developmental analysis. This study presented in the thesis is the extension of Lai’s 1999 research. ^ Methods. I used the weighted principal component method on the human development indicators to measure and analyze the progress of human development in about 180 countries around the world from the year 1999 to 2010. The association of the main principal component obtained from the study and the human development index reported by the UNDP was estimated by the Spearman’s rank correlation coefficient. The main principal component was then further applied to quantify the temporal changes of the human development of selected countries by the proposed Z-test. ^ Results. The weighted means of all three human development indicators, health, knowledge, and standard of living, were increased from 1999 to 2010. The weighted standard deviation for GDP per capita was also increased across years indicated the rising inequality of standard of living among countries. The ranking of low development countries by the main principal component (MPC) is very similar to that by the human development index (HDI). Considerable discrepancy between MPC and HDI ranking was found among high development countries with high GDP per capita shifted to higher ranks. The Spearman’s rank correlation coefficient between the main principal component and the human development index were all around 0.99. All the above results were very close to outcomes in Lai’s 1999 report. The Z test result on temporal analysis of main principal components from 1999 to 2010 on Qatar was statistically significant, but not on other selected countries, such as Brazil, Russia, India, China, and U.S.A.^ Conclusion. To synthesize the multi-dimensional measurement of human development into a single index, the weighted principal component method provides a good model by using the statistical tool on a comprehensive ranking and measurement. Since the weighted main principle component index is more objective because of using population of nations as weight, more effective when the analysis is across time and space, and more flexible when the countries reported to the system has been changed year after year. Thus, in conclusion, the index generated by using weighted main principle component has some advantage over the human development index created in UNDP reports.^

Spatial analysis of pertussis cases in Harris County from 2005-2010

Objective: This study examined the recent trends and characteristics of reported pertussis in Harris County from 2005-2010. ^ Methods: The study population included surveillance data from all reported pertussis cases from January 1, 2005 to December 31, 2010 to Harris County Public Health and Environmental Services (HCPHES). We calculated incidence and attack rates for varying age groups, race/ethnicity, and gender. Spatial analyses were conducted of hot spot and cluster of incident cases in Harris County census tracts. Maps were constructed using geographic information system. ^ Results: Age-specific incidence rates of reported cases of pertussis were highest among infants under a year of age and lowest among adults age 20 and older. Hispanics represented the most cases reported compared to any other race or ethnic group (42% of 483 cases). Age-adjusted rates were highest in 2009 at 9.81 cases per 100,000 population. Only 31.2% of people received at least four of the recommended five doses of vaccine. Spatial analyses revealed statistically significant clusters within the northeast region of Harris County. ^ Conclusions: Hispanic infants are the most at risk group for pertussis. Although 70% of cases had a history of immunization, 41.8% of infants were appropriately vaccinated for their age. Increased vaccination coverage may decrease the incidence of pertussis.^

Estimating the mean and standard deviation of concentration distributions using censored samples

Environmental data sets of pollutant concentrations in air, water, and soil frequently include unquantified sample values reported only as being below the analytical method detection limit. These values, referred to as censored values, should be considered in the estimation of distribution parameters as each represents some value of pollutant concentration between zero and the detection limit. Most of the currently accepted methods for estimating the population parameters of environmental data sets containing censored values rely upon the assumption of an underlying normal (or transformed normal) distribution. This assumption can result in unacceptable levels of error in parameter estimation due to the unbounded left tail of the normal distribution. With the beta distribution, which is bounded by the same range of a distribution of concentrations, $\rm\lbrack0\le x\le1\rbrack,$ parameter estimation errors resulting from improper distribution bounds are avoided. This work developed a method that uses the beta distribution to estimate population parameters from censored environmental data sets and evaluated its performance in comparison to currently accepted methods that rely upon an underlying normal (or transformed normal) distribution. Data sets were generated assuming typical values encountered in environmental pollutant evaluation for mean, standard deviation, and number of variates. For each set of model values, data sets were generated assuming that the data was distributed either normally, lognormally, or according to a beta distribution. For varying levels of censoring, two established methods of parameter estimation, regression on normal ordered statistics, and regression on lognormal ordered statistics, were used to estimate the known mean and standard deviation of each data set. The method developed for this study, employing a beta distribution assumption, was also used to estimate parameters and the relative accuracy of all three methods were compared. For data sets of all three distribution types, and for censoring levels up to 50%, the performance of the new method equaled, if not exceeded, the performance of the two established methods. Because of its robustness in parameter estimation regardless of distribution type or censoring level, the method employing the beta distribution should be considered for full development in estimating parameters for censored environmental data sets. ^