Browsing by Subject "Investigative Techniques"
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Item A Phase II Clinical Study to Evaluate the Efficacy and Safety of rhThrombin in Subjects Undergoing Arterial Bypass Surgery and AV Graft Formation for Hemodialysis(2004-12-01) Plascencia, Xochitl; Rustin E. Reeves; Della Weis; Don PeskaThe Association of American Medical Colleges Task Force on Clinical Research defines clinical research as a component of medical and health research intended to produce knowledge essential for understanding human disease, preventing and treating illness, and promoting health (Friedman, 1998). A clinical trial is defined as a research study conducted in humans which is designed to answer specific questions using scientifically controlled conditions with specified methodologies and endpoints (Gallin, 2002). Clinical research trials are essential in determining whether or not a drug is safe and effective. There are four phases that investigational drugs go through before they are allowed to be out in the market. Before beginning phase I of a study, there is usually a pre-clinical research and development phase. During this time the initial synthesis of study drug is accomplished and animal testing takes place. Phase I is the initial introduction of an investigational new study drug into humans. Phase I is usually conducted in healthy individuals and the primary goal is to determine the safety profile of the drug. Phase II trials tend to evaluate safety and initial efficacy. Subjects enrolled in this phase tend to have the disease necessary for use of study drug. Phase III studies are conducted to gather additional information about the effectiveness and safety of the drug and to determine the overall benefit-risk relationship of the drug. Finally, phase IV studies are usually referred to as post-marketing studies. During this phase, additional safety information is identified and the drug’s safety during routine use is evaluated. Each phase can range from two to ten years depending on the complexity of the clinical trial (Gallin, 2002). A phase II, randomized, double blind study of the safety and efficacy of topical recombinant human thrombin in patients undergoing peripheral arterial bypass surgery and arterio-venous graft formation for hemodialysis is the focus of the prospective drug study to be carried out in the surgery department at The University of North Texas Health Science Center. The primary objective of this study is to evaluate the safety and efficacy of recombinant human thrombin when used in different types of surgeries. Prior to signing an informed consent, subjects will have to meet inclusion and exclusion criteria set by study protocol. Study specific assessments and procedures will be performed after the informed consent is signed and dated. If bleeding at the anastomosis is found to necessitate intervention, a single application of either rhThrombin or placebo in combination with an absorbable hemostatic sponge to each anastomosis requiring hemostasis will be applied by the surgeon. The safety and efficacy of rhThrombin will be determined by measuring the incidence and severity of adverse events and of laboratory abnormalities. Occurrence of hemostasis within 600 seconds of application of the study drug at the anastomotic surgical site, incidence of anti-rhThrombin product antibodies, and time to hemostasis will also be measured.Item A Retrospective Analysis and Curricular Mapping Assessment of Student Engagement in Research Design in Classes Offered by the College of Pharmacy at University of North Texas Health Science Center at Fort Worth(2016-12-01) Baskaran, Karthikeyan; Jerry W. Simecka; Patrick Clay; Victor V. UteshevThe purpose of this study is to perform a retrospective analysis and curricular assessment to identify classes at the University of North Texas System College of Pharmacy (UNTSCP), which provided student engagement in research design. The first stage of this quality assurance project involved the use of content analysis to review class syllabi and materials for the potential opportunity for student engagement in research design at UNTSCP. The second stage of this quality assurance project will involve the administration of online questionnaires to students and faculty of UNTSCP. The final stage of this quality assurance project will involve conducting face-to-face interviews with the faculty of UNTSCP. Upon completion of the first stage, we gained new insight into the student learning experience and found the opportunity for student engagement in research design to have been dispersed in a variety of core and elective classes at UNTSCP.Item A Study of the Efficiency of the Combined DNA Index System for the Oregon State Police(2007-08-01) Brown, Allison A.; Joseph Warren; Arthur Eisenberg; John PlanzMethod of Procedure: This project, which was conducted at the Oregon State Police Crime Laboratory, entailed following up with CODIS hits. It involved examining cases that have been worked by forensic scientists and finding explanations as to how the cases are proceeding after NDA matches are made. Failures to follow up on a CODIS hit have become a national problem in forensic laboratories all over the country. The Oregon State Police find this a very important issue that must be resolved. Currently the Oregon State Police are getting a hit, an arrest and a conviction. The only problem with all of this is that it is hard to measure the efficiency of CODIS hits with just convictions. There are several ways the cases could have been resolved such as the victim did not want to pursue the case any further, the suspect was already incarcerated for another crime, the witnesses were hard to locate or the case was dropped because of a plea to other crimes. As part of my research I investigated each of the cases that have been worked to see if they were pursued any further after a hit to an individual. After researching these cases, it was my responsibility to put my findings into a format that made it easier for the state police to know how the cases were resolved. The information was collected using a variety of software programs. The reason that more then one computer program needed to be used in the project, is due to the fact that more of then not some of the information that should have been provided in a program was absent in one and present in another program. The California Department of Justice currently has a system that is available which allows its users to input data. In order to design such a system it was my responsibility to obtain the case information. Once this had been obtained it made it easier to combine the data into a table format so that the state police could see how each case was proceeding. Below is a table of exactly what information was obtained. Due to the confidentiality of the information, false names and false information will be used in all tables seen. Once the information for one thousand hits had been gathered it was placed into Microsoft Access so that a database could be created. Throughout the time that CODIS has been in place, crimes where DNA matches have been made but not pursued have shed light upon a common problem occurring everywhere in forensic laboratories. Dozens of cases have found matches between a suspect and a crime but there has been no pressure to pursue the case any further. In fact one unfortunate result has been multiple DNA matches of a suspect, with the suspect continuously making repeated offenses. Most of the offenses are nor pursued until the investigators realize there might be a link between the current crime and the past cases worked. Only then are the reports of the DNA matches reviewed and pursued further. In one Virginia case, this scenario occurred. A man by the name of William Orlando Smith followed a girl and raped her in the woods. Had the DNA match that the Virginia police made months earlier been pursued, the rape might have been prevented. This is not just one isolated event but a common occurrence seen in other states as well. Although this research for the Oregon State Police might not resolve a national issue, it will aid in preventing scenarios like the above from possibly occurring. By solving this problem and entering how cases are resolved into a database like Microsoft Access, it will make it easier for the investigators to process crimes. Even more important is the need for this information to be compared with other states. A study such as this will enable states to test the efficiency of CODIS.Item Alzheimer's Fibroblasts are More Susceptible to Oxidative Stress(2001-05-01) Marshall, Pamela L.; Neeraj Agarwal; Robert GracyMarshall, Pamela L., Alzheimer’s Fibroblasts Are More Susceptible to Oxidative Stress. Master’s of Science (Biomedical Sciences). May 2001. Recent evidence indicates that oxidative stress contributes to neuronal death in Alzheimer’s disease (AD). In addition, it has been suggested that AD is a systemic illness in which the development of the disease is only visible in the brain. The aim of this research is to develop experimental procedures using a simple cell model, the fibroblast, to determine if proteins derived from AD skin fibroblasts are more sensitive to oxidation by reactive oxygen species than non-AD cells, and to assess the ability of antioxidants to prevent this oxidative damage in AD fibroblasts. Preliminary findings suggest that changes in sensitivity are already detectable in fibroblasts from AD patients, probably as a consequence of genetic component as well as other risk factors. Therefore, this biochemical marker might have the potential for identifying individuals at risk for AD.Item Amplified Fragment Length Polymorphism Analysis of White Oak Tree Leaves(2005-07-01) Patel, Kaajal Devendra; John Planz; Joseph Warren; Arthur EisenbergThe AFLP technique at first seems to be a remarkable new technology that can be applied to the growing area of non-human DNA testing. The ability to identify organisms without prior genetic knowledge would be an asset to a field such as non-human DNA testing since not enough research in the area is being conducted. With any new technique or theory in science, intense scrutiny must be used to examine the applicability of the new technology. In the area of forensic science, the severe consequences of a false result extend far beyond the realm of scientific error. Errors make in forensic casework could result in life changing occurrences for the families of not only the victim, but the defendant as well. From this study it can be seen that AFLP as a technique may not stand up to the high expectations of reliability, and reproducibility required for a technique to be adopted into the field of forensic science. Several problems occurred through this study that may prevent this technology from becoming a widely accepted technique in non-human DNA testing. The initial problems with the technique were associated with reproducible results. The first several attempts were conducted under the same conditions, by the same analyst but yielded results that were no comparable. The RFUs of each experiment were inconsistent, not only between samples examined at different times, but samples examined within the same tiral as well. AFLP as a technique is supposedly insensitive to template concentrations however, it has been previously shown to produce differences in the electropherogram when the template is excessively diluted (26). Vos et al. (1995) determined that high dilutions yielding template DNA concentrations below 1 pg could result in irreproducible fingerprints. In this study 27.5 ng of template DNA was added to each digestion-ligation reaction, yet the resulting quantity of amplified fragments varied. These variations in quantities of amplified product could be due to PCR inefficiencies when comparing samples from different trials, but it does not explain instances where duplicate trials were inconsistent with each other (10, 22). When new ligase was introduced the resulting electropherograms did produce considerably higher RFUs for each peak, but the lack of interpretable peaks observed previously may not have been solely due to inefficient ligase. In an inter-laboratory study, Jones et al. (1997) noted that several laboratories encountered problems in obtaining complete AFLP profiles. For several groups, up to 50% of the bands were missing during the preliminary testing. Though this problem subsided with successive attempts, this approach to achieving successful results may not be feasible in a forensic setting. Often the evidence received from a crime scene may be insufficient to allow for multiple testing. In addition, multiple attempts to obtain results may open up areas for scrutiny and attack by the defense counsel. Repetitive testing may appear to be a biased search for condemning evidence against the questioned party, rather than the production of reliable results. Repetitive testing may also not be possible since laboratory reagents and time involved in the production of these results may not be within the constraints of a crime laboratory. In this study, capillary electrophoresis was used to visualize the fluorescent dyes attached to each fragment however, laboratories could use radioisotopes and polyacrylamide gels instead. This method of visualizing AFLP fingerprints is not only costly, but time consuming as well. Conducting repetitive tests in order to obtain a sample with sufficiently intense bands for analysis may not be feasible. These limitations may therefore restricts the use of the AFLP technique from only being conducted in laboratories with sufficient time and funds to conduct repetitive testing as is needed (10). Despite the potential cost in time and funds, the technique was able to produce AFLP fingerprints that were consistent with each other when the electropherograms were compared. The major source of error resulted from the method used to determine the presence of peaks within the designated categories. Since not all peaks crossed the 50 RFU detection threshold, they were not identified by the Genotyper macros. However, when the actual electropherograms were compared, these peaks were present. It has been suggested that to verify whether each peak is present in the pre-designated categories a scan of the electropherogram should be done and any peaks that were not called by the macro should be manually entered into the binary table or should be reanalyzed (Heather Coyle, personal communications). Although this method could potentially aid in the correct genotyping of each sample, it requires a considerable amount of user intervention. A considerable amount of time is needed to examine each electropherogram for the presence of peaks that are below the 50 RFU threshold. Without a redefined interpretation threshold, the analysis of each electropherogram can be highly subjective. Peaks that are relatively low need to be distinguished from peaks that may be associated with background noise. Therefore, in order to eliminate analyst bias a peak detection threshold must be established. Generally the interpretation threshold is established by a validation study of the analysis technique. In this study the lower threshold was previously established at 50 RFU for the instrument being used, but this threshold was insufficient for the recognition of all peaks present during the AFLP analysis. The question then becomes to what extend the peaks can or should be called in order to correctly identify each organism without errors. The exclusion of some peaks could lead to discrepancies, such as those observed during the blind study, which could result in an initial false match or exclusion. The interlaboratory study by Jones et al. found only one scoring difference associated with the absence of one band out of a total of 172 in the AFLP profiles. This error was later associated with experimental errors that incurred during the AFLP procedure. Discrepancies such as this can lead to an erroneous identification of samples that could have severe consequences in a criminal case. At this time, the utilization of AFLP technique for further testing of other organisms such as Cannabis sativa does not seem feasible. A variety of adjustments in the technique need to be addressed before this technology should be further applied to organisms in forensic casework. In order for AFLP typing to be used for forensic casework, major improvements in the technique need to be made. Consistency in obtaining reliable electropherograms with peaks well above the RFU detection threshold must be resolved in order to allow for accurate sample interpretation. This will not only allow for greater consistency between replicates, but will also help in establishing new databases for organisms that are being tested. As with any type of forensic DNA analysis, a database must be established for each organism being tested. Without a reliable database, accurate identification of crime scene evidence cannot be established. A major improvement that is required for the utilization of AFLP typing is the process by which genotypes are identified. Utilizing the macros to identify control and variable peaks to create the binary table was a quick and easy method, however it was not always able to identify the correct genotype. The overlapping of electropherograms in GeneScan ultimately was the best method for accurate identification of the blind samples, but in a real case scenario it would not be feasible to compare each evidentiary electropherogram with those in a database. Advancements in technology will continually introduce new techniques and procedures that could be applicable to the field of forensic science. As with any new technique, the methods and theories must be validated in order to determine whether they can be used in a criminal case. The field of non-human DNA testing is growing and with the advent of new technology such as AFLP, the possibility for establishing a non-human DNA identification method may be on the horizon.Item An Analytical Study of the Perceptions, Prevention Strategies, Treatment and Economic Impact of Equine West Nile Virus(2004-06-01) Galvan, Robert; Lurie, Sue; Singh, Karan; Gonzalez, AdelaGalvan, Robert, M.P.H., M.S. An Analytical Study of the Perceptions, Prevention Strategies, Treatment and Economic Impact of Equine West Nile Virus. Doctor of Public Health, Social and Behavioral Sciences, June 2004, 109 pp., 16 Tables, 15 Figures, 47 Titles. Since the introduction of the West Nile Virus (WNV) in the United State in 1999, WNV has been the cause of disease and deaths in humans, wild birds, zoo birds, and horses. In 2002, more than 15,000 equines in 40 states were diagnosed with illness associated with WNV. Approximately one third of those horses died or were euthanized (Campbell et al, 2002). Horses are infected with the WNV more often than humans or any other mammal. It is becoming on e of the fastest growing health threats to horses nationwide. Texas responded to the discovery of WNV by expanding their surveillance systems in the eastern counties of the state (Texas Department of Health, 2003). Positive reports for WNV were announced in 2002, which prompted an increase in public education and equine vaccination recommendations. Although much has been reported on the economic impact WNV has on human health and hospital care facilities, documentation is lacking on these issues in the equine population. Understanding the biology, epidemiology, economic impact, and how WNV affects the equine industry are important aspects to public health programs and prevention activities. The objectives of this study are to: (1) examine WNV cases in the equine population in Texas in order to better understand the distribution of clinical disease, signs, treatments and outcomes; (2) to provide information regarding the perceptions, knowledge, concerns, and treatment of the WNV by Texas veterinarians; and (3) to determine the economic impact of the WNV on the equine population in the state. A 14 question survey was mailed to licensed veterinarians in Texas in an effort to gather information about their perceptions and beliefs of the WNV, recommended treatment preferences, and the estimated cost of treatment. Outcomes included case fatality rate, descriptive data, veterinarians’ knowledge of WNV, veterinarians’ beliefs/perceptions of WNV, and the economic impact of WNV. Descriptive analyses were performed by using SPSS version 11. The methods used for analysis of WNV data were primarily simple descriptive statistics including summations and frequencies. A cross-tabulation was performed between the results of Questions 1, 2, and 3 and a variable created to approximate the number of veterinarians that actually treated cases of WNV (treat). A cross-tabulation and Chi-square analysis was performed between the treatment variables (treat) and derived variables of Questions 1, 2, and 3 to examine differing beliefs and knowledge between veterinarians who had treated WNV and those who had not. Seven hundred of 4,177 surveys returned yielded a response rate of 16.8 percent. Among the veterinarians, 73.4% (514/691) believed that they are receiving or received enough training and/or education concerning WNV. The vaccination regimen is believed to be effective and reliable by 56.1% (393/691) of the respondents. There were 1,256 cases of equine WNV reported confirmed via laboratory testing. There were also 766 cases reported that were not confirmed via laboratory testing. Among the 2,022 diagnosed cases, 257 were vaccinated against WNV prior to illness; and, 159 cases were vaccinated after signs of illness. A total of 441 horses died as either a direct cause of the disease or by owner or veterinarian elected euthanasia. The most common criteria used to decide euthanasia in these horses was prolonged recumbency as reported by 44.2% (87/197) or the veterinarians. Fifty-two percent (233/488) of the veterinarians did not recommend prevention strategies to equine owners. The cost of vaccination regimen was reported by 63% (269/434) of the veterinarians to be $25 or less. The results of the survey suggest that there could be a need for WVN education among veterinarians in areas of prevention, control, and treatment. Future studies should be conducted to examine owner perceptions, knowledge and beliefs of WNV vaccinations and prevention strategies. Values for lost horses were not solicited in the survey, thus, a total economic impact could not be completely estimated. However, a formula to approximate the aggregate economic impact of the WNV on the Texas equine industry was employed.Item An Evaluation of Muscle Biopsies in a Managed Care Organization(2001-05-01) Saad, Jill Moore; S. Dan Dimitrijevich; Roderick HookerSaad, Jill Moore., An Evaluation of Muscle Biopsies in a Managed Care Organization. Master of Science (Biomedical Sciences), May 2001, 16 pp., 7 illustrations, Reference List, 17 titles. Objective: The goal of this study was to assess the use of the percutaneous muscle biopsy in diagnosing inflammatory muscle diseases and to examine the benefit of centralizing inflammatory myopathies under one department-rheumatology-within a large health maintenance organization. Methods: A retrospective review of 363 muscle biopsies and histopathology reports, spanning 25 years, formed the basis of this study. The databases used in this study were the medical record, an institutional rheumatology registry, and histopathology reports. Cytoarchitectural abnormalities, necrosis and regeneration formed the basis of muscle disease classification. The histopathology findings were interpreted against the patient’s clinical history, examination, and clinical tests to develop a final diagnosis. Results: Rheumatologists in this location performed two-thirds of the biopsies percutaneously using an intervertebral rongeur and surgeons performed one-third open biopsies. Over time open biopsies were phased out due to preference for the percutaneous method. The average age of all muscle biopsy patients was 45 (3 months to 88 years old) and 55% were male. Polymyositis was the most frequently identified myositis (62%), followed by dermatomyositis (19%), and inclusion body myositis (7%). Conclusion: The use of percutaneous muscle biopsies using an intervertebral rongeur is the method of choice because of convenience, quality of specimen, low morbidity, and limited discomfort. Centralizing inflammatory muscle diseases within one organization contributes to the efficiency and effectiveness of inflammatory muscle disease management.Item An Initial Comparison of Applied Biosystems Quantifiler Duo and Promega Plexor HY Real-time PCR DNA Quantification Systems(2008-05-01) Cole, Sarah Kathleen; Arthur Eisenberg; John Planz; Joseph WarrenObjective 1: Sensitive Study: This study was designed to determine the quantity of template DNA below which amplification is not expected to yield a DNA profile. Dilution series of male and female stock DNA ranging from 0.003 ng/μl will independently be run with both Quantifiler Duo and Plexor HY. These samples will be run in duplicate per plate, with duplicate plates being run. We want to determine if the published lowest detection thresholds (0.023 ng/μl for Duo; 0.0032 ng/μl for HY) are concordant with the data obtained. Objective 2: Mixture Study: The purpose of this study is to obtain quantification results for mixtures of male and female DNA, which should allow for calculations of autosomal:Y ratios that can be helpful in determining what type of genetic analysis to pursue (autosomal STR, Y-STR, or both). Mixtures of female and male DNA ranging from 1:1 to 1024:1 (female: male) will be run in duplicate per plate, with duplicate plates being run. We want to find out how minor of a contributor the male can be in an excess of female DNA and still be detected. This is especially important in sexual assault cases where the major contributor is usually female or when the offender is a vasectomized male. Objective 3: Concordance Study: The purpose of this study is to compare quantification results from Quantifiler Duo and Plexor HY with those from Quantifiler Human, specifically in cases when samples are degraded. The majority of these samples originate from unidentified human remains. Patterns of overestimation or underestimation of DNA concentration can help determine which system will be most beneficial in these cases. This is where the new amplicons size featured in Quantifiler Duo is important in comparing the values with previous results for Quantifiler Human. Sample choice will be at the discretion of the laboratory technical leader and Unidentified Human Remains section analysts. These samples will be the ones that are known to be degraded and have previously yielded overestimated results from the Quantifiler Human quantification system, resulting in poor STR data.Item An Open-Label Pilot Study Evaluating the Effects of Travoprost on Eyebrow Regrowth Among Patients Undergoing Chemotherapy for Cancer(2005-12-01) Habib, Nausheen; Jamboor Vishwanatha; Harold J. Sheedlo; Michael W. MartinHabib, Nausheen. Master of Science, Biomedical Sciences, December 2005, An Open-Label Pilot Study Evaluating the Effects of Travoprost on Eyebrow Regrowth Among Patients Undergoing Chemotherapy for Cancer. The primary objective of this study is to determine the effect of eyebrow hair growth of a twice daily application of travoprost among patients undergoing chemotherapy or those who have already completed chemotherapy. Travoprost, used clinically in the treatment of glaucoma, is topically and unilaterally applied to a total of 15 patients to induce eyebrow hair growth. This is an ongoing pilot study in which the screening, treatment and follow-up visits are scheduled on day 0, week 4, week 8, week 12, and week 14. After an eight week treatment period, 69% of the patients demonstrated increased eyebrow density. This increase in eyebrow hair is consistent with travoprost’s ability to prolong the anagen or growing phase of the hair cycle.Item Analysis of Low Copy Number DNA Using Profiler Plus at Increased Amplification Cycles and Modifications in Sample Injection Parameters(2003-08-01) Hynds, Jody Lynn; Arthur Eisenberg; John Planz; Joseph WarrenThere are many DNA testing techniques that can be utilized for samples with low quantities of DNA. Mitochondrial DNA testing is designed for successful DNA sequencing of hair shafts, degraded and burned samples. Newly developed SNP (single nucleotide polymorphisms) testing is also designed for the analysis of challenging samples. The increased interest in the analysis of low copy number DNA samples using STR testing is necessitated since the national database CODIS (Combined Data Index System) currently only accepts the DNA profiles analyzed with the 13 core STR loci. CODIS contains DNA profiles of evidence found at crime scenes, convicted offender and missing persons DNA profiles (4). The goal of this project is to develop methodologies to increase the success rate of LCN DNA samples using STR testing. The experimental design for this study involved the amplification of DNA isolated from buccal swabs using the Profiler Plus multiplex kit at two different DNA input quantities: 0/0156ng (15.6pg) and 0.0312ng (31.2pg). Four separate amplifications of these DNA samples were done at: 28, 30, 32 and 34 cycles. The manufacturer’s recommended cycle number for AmpFISTR Profiler Plus is 28 cycles. These samples were analyzed on both the ABI Prism 310 Genetic Analyzer and the ABI Prism 3100 Genetic Analyzer using OCD standard protocols for loading samples. The injection time and voltage were modified for each of the number of PCR cycles. The best combination of cycle number and injection parameters was chosen for the low copy number reproducibility study.Item Approaches to mitochondrial genome sequencing using the oxford nanopore minion device(2017-05-01) Thorson, Kelcie C.; John V. Planz; Rance E. Berg; J. Thomas CunninghamCurrent DNA sequencing methods rely on polymerase chain reaction (PCR) to create sufficient copies of targeted DNA fragments to serve as a library. PCR and subsequent clean-up steps add considerable time and cost to the process and provide opportunity for introduction of amplification errors or contamination. The aim of this study was to develop a reliable method for mitochondrial genome sequencing sans PCR using the Oxford Nanopore MinION. Our hypothesis was that results generated from native DNA sequencing would be concordant to sequencing results generated from PCR-enriched libraries. Error-rates of 1.47% (enriched) and 1.26% (native) were observed when sequencing the control DNA. Consensus sequences generated from native and PCR-enriched libraries show an average of 98.7% identity between the two methods.Item Automatable Virtual Array Screening System for Rapid Analysis of Mitochondrial DNA Polymorphism(2002-05-01) Campbell, Rowan Stewart; Arthur J. Eisenberg; Bruce Budowle; John PlanzCampbell, Rowan Stewart, Automatable Virtual Array Screening System For Rapid Analysis of Mitochondrial DNA Polymorphism. Doctor of Philosophy (Biomedical Sciences), May, 2002, 156 pp., 11 tables, 48 illustrations, bibliography, 96 titles. The goal of this research project was to develop alternative methods to traditional forensic mtDNA sequence analysis. Conventional forensic mtDNA analysis requires the direct sequencing of Hypervariable Region I and Hypervariable Region II in both the forward and reverse directions. This method is time consuming, labor intensive and expensive. Two methods for determining mtDNA haplotypes through the direct interrogation of Single Nucleotide Polymorphisms with HVI and HVII have been developed. A Sequence Specific Oligonucleotide Hybridization assay was developed on the Luminex 100™ flow cytometer, as well as a Single Base Extension assay developed for the ABI Prism® 310 Genetic Analyzer. The SNP typing of mtDNA sequences can provide a significant benefit in many forensic and human identification cases. The reassociation of mass disaster remains, mass grave analysis, and the screening of large numbers of crime scene samples are examples of their potential application. Their inclusion as a standard screening tool would be high beneficial since more extensive DNA analysis would be reserved for those samples that possess the greatest evidentiary value. In a blind study of 50 samples, the Sequence Specific Oligonucleotide Hybridization assay incorrectly identified the mtDNA haplotypes in 7 samples, whereas the Single Base Extension assay correctly identified each of the SNP positions interrogated. The SNaPshot™ primer extension assay was approximately 20-25 times more sensitive than the standard sequencing approach. This would suggest that this system could be a viable alternative to sequence analysis when samples are limited, as well as being more robust in detection and typing of heteroplasmic sites. A statistical evaluation of the SNP panels revealed that the genetic diversity estimated for the 50 Southwestern Hispanic samples tested was 0.9624 for the primer extension array and 0.9559 for the hybridization-based array. The probability of two randomly selected individuals from a population group having the same mtDNA haplotype was 0.0568 for the Single Base Extension assay and 0.0632 for the Sequence Specific Oligonucleotide Hybridization assay. A forensic mtDNA SNP array consisting of the positions evaluated in this study could provide a reasonable alternative to the full sequencing of the HVI and HVII regions.Item Barriers to Completion of a Family Health History Tool and Increasing Subject Retention(2016-12-01) Bennett, Margarett A.; Robert T. MalletFamily Health Histories (FHH) are crucial for identifying disease risk factors, and such information is paramount to the diagnosis, treatment, and long term care of patients. Many if not most human diseases include a hereditary component. Despite the recognized importance of health history information, the FHH of many Americans remains uncaptured. This study examined impediments to FHH completion and evaluated a strategy for increasing completion. Participants were givenreminder prompts, offers of assistance, and surveyed to identify barriers and effective methods to improve FHH completion. The most frequently cited barrier was that the participant did not remember being part of the study or anything about the study. Although the reminder phone prompts produced a modest increase in participation, this strategy was time consuming and inefficient. The possibilities that providing additional information during the recruitment process and earlier reminder phone calls after registration may improve FHH participation and completion rates warrants further investigation.Item Benefits, Challenges, and Future Directions: Making the Case for eTMF in Clinical Research(2016-12-01) Beckham, Amber C.; Patricia A. Gwirtz; Stephen O. MathewIn clinical research there are many documents that must be retained in order to evaluate a trial, known as essential documents and collectively held in a trial master file. A trial master file can show if a trial was conducted according to regulatory standards. Traditionally this file has contained all paper documents, but with the advancement of technology, an electronic trial master file is now available. Although the technology of electronic trial master files exists, some organizations are still reluctant to make the switch from paper to electronic. This practicum aims to measure current opinions about the use of an electronic trial master file, as well as determine what benefits and challenges are associated with using an electronic trial master file. Finally, this project aims to show the promising future and usefulness of an electronic trial master file in order to make the case for using an electronic trial master file in clinical research. This project will use a survey of clinical research professionals working at a CRO and an illustrative comparison in order to support the hypothesis that the benefits of using an electronic trial master file compared to a paper trial master file outweigh the challenges. Participants of this project are generally in favor of using an electronic trial master file over a paper one, and they believe that using and electronic trial master file has positively impacted the role they have in clinical research. Although respondents view electronic trial master files as a good investment, they are also aware that there is room for improvement and have used their industry knowledge and experience to suggest future directions for the continued adoption and use of electronic trial master files.Item Beta Testing and the Population Genetics of Promega's Prototype PowerPlex Y Kit(2004-08-01) Kirkendoll, Ross A.; Joseph Warren; John Planz; Arthur EisenbergDevelopmental validation is typically done by the manufacturer of the technique or technology. According to National Standards, the manufacturer must test for human specificity to ensure compliance with standards. In addition, the PowerPlex Y kit must be shown to have male specificity because all of the loci are located on the Y-chromosome. Other necessary studies include mixture both male/female and male/male mixture studies, stability studies to show stability in the presence of environmental insults, and the focus of this study the construction of a popular database. In order to satisfy both the requirement of the National Standards and the scrutiny of the legal system, Promega Corporation assembled a collaboration of different laboratories to assist with the developmental validation of the PowerPlex Y Kit. This project was a small part of that collaboration. The DNA Identify Laboratory was chosen by Promega to assist with the construction of a population database because of the number of samples available and the need for confirmed father/son pairs. The objectives of the study were to type ~200 father/son pairs from each of the Caucasian and African American races, and then determine the haplotype frequencies, haplotype diversities, and mutation rates for each race.Item Cardiovascular Fitness and Lung Function of Adult Men and Women in the United States: NHANES 1999-2002.(2008-12-01) Jackson, HannahThere is a distinct disparity between adult males and females in lung function and cardiovascular fitness in the United States. This study utilizes a nationally representative sample in order to determine predictors of lung function between men and women. Simple means analysis, logistic and linear regressions were utilized in order to determine predictors of lung function between genders. Continuous analyses of lung function reveal that sex and BMI are the most important predictors of VO2 max. However, analyses of clinical cut-points of cardiovascular fitness indicate that gender was not a significant predictor.Item Cell line authentication and contamination assessment for human cell cultures(2015-05-01) Ormos, Andrea; Arthur J. Eisenberg; Rhonda Roby; John V. PlanzCell line authentication is an essential step in ensuring the integrity and reproducibility of biomedical research. The major contaminants in cell cultures are fungi, viruses, bacteria and contamination from other cell lines of the same or different species. Contaminants alter the physiology and properties of cells, compromising the results of experiments. In this study, an improved multiplex assay was developed, detecting mycoplasma and mouse cell line contamination, while performing DNA typing. The assay was tested on cell cultures, the reproducibility of the assay was verified, sample collection and procedures were optimized and limit of detection for contaminants were determined. A survey was conducted to assess the interest in an in-house cell line authentication and contamination assessment service.Item Clinical Internship with the Division of Gynecologic Oncology at UT Southwestern Medical Center: Carboplatin and Doxil for Gynecologic Cancers(2003-12-01) Epps, Camitria N.; Victoria Rudick; David S. Miller; Barbara RichardsonEpps, Camitria N., Master of Science, Clinical Research Management, December 2003, Carboplatin and Doxil for Gynecologic Cancers, 107 Pages, 9 Tables, 42 titles in Bibliography. Objective: To examine the safety and efficacy of administering the drugs carboplatin and doxil in combination chemotherapy for the treatment of gynecologic cancers, mainly endometrial and ovarian cancer. Materials and Methods: Carboplatin and doxil were previously administered intravenously to 6 patients. Each patient received 3 to 8 cycles of chemotherapy. Doses of carboplatin ranged from 310 mg to 665 mg. The doses of doxil ranged from 54 mg to 80 mg. This is a retrospective study. The 6 patient’s medical charts were reviewed. Data was extracted and a spreadsheet formatted database was created. Results: Data were extracted and a spreadsheet formatted database was created. Results: Due to the small number of patients the results are not statistically significant. 2 patients showed tumor progression while receiving treatment. All patients tolerated doses very well and experienced minimal toxicities. Conclusion: Carboplatin plus doxil combination chemotherapy given intravenously has a potent effect on endometrial and ovarian cancers. Studies using this chemotherapy for the treatment of gynecologic cancers should be conducted on a wider scale to access the statistical significance of the treatment.Item Comparison of DNA Extraction Methods From Bone to be Used With the DNA IQ System on the Maxwell 16 for Human Identification(2008-08-01) Lopez, Kristen; John Planz; Arthur Eisenberg; Joseph WarrenLopez, Kristen M., Comparison of DNA Extraction Methods From Bone to be Used with the DNA IQ System on the Maxwell 16 for Human Identification . Masters of Science (Graduate School of Biomedical Sciences), August, 2008, 52 pp., 11 tables, 15 figures, bibliography, 24 titles. Extraction and purification of DNA from human bones is essential for correctly identifying the remains through DNA analysis. Current DNA extraction methods include a demineralization step, which extracts calcium and phosphate from the bone matrix, inactivation of DNAses, and the removal of Polymerase Chain Reaction (PCR) inhibitors. These methods often use harsh chemicals and may allow for residual DNA to be discarded in various wash steps. To assess the effectiveness of DNA extraction from bone samples, two extraction protocols were compared. The first method included a bone demineralization pretreatment solution of Sodium N-Laurylsarcosinate, 0.5 M EDTA, and Proteinase K (20 mg/ml). The second included a pretreatment using a Bone Incubation Buffer by Promega Corporation, with an addition of Proteinase K (18mg/ml). Various incubation times were included to assess the extraction at different time intervals. All extracted samples were purified with the DNA IQ Reference Sample Kit on the automated Maxwell 16 Instrument (Promega Corp.). Full and partial profiles were obtained from samples extracted with the Bone Incubation pretreatment, regardless of incubation time. Profiles were not observed with the standard demineralization pretreatment when amplified at 28 cycles, with partial profiles present in a few samples when amplified at 32 cycles.Item Construction of a Cost Effective Nested-PCR Reaction for Use with the Applied Biosystems AmpFLSTR Identifiler Kit(2005-12-01) Mikeska, Margo M.; John Planz; Joseph Warren; Arthur EisenbergHuman STR analysis has greatly increased the ability to perform identity testing for many different situations. These situations include, but are not limited to, the identification of individuals involved in violent crimes, establishing paternity, and identification of unknown human remains. The most common type of DNA information currently used for identity testing is the short tandem repeat, or STR. STR testing utilizes the number of repeating units in the DNA to assign an allele. Alleles from several different loci are used to establish a genetic profile. Currently, the United States used a standard of 13 different DNA loci to establish identity. These 13 loci can be typed by using a number of different multiplex kits such as the Applied Biosystems Profiler Plus, Cofiler, and Identifiler Kits [1,2]. The 13 loci were selected based on a number of parameters. Each locus was required to be polymorphyic, and a tetranucleotide repeat. The loci also could not display any linkage between each other and extensive population studies had to be conducted to both verify the absence of linkage and to establish allelic frequencies [1]. The goal of this research was the construction of a more cost effective method of utilizing the Applied Biosystems Identifiler Kit. Across the country there is a large backlog of samples that need to be processed in order to obtain a genetic profile. If these samples could be tested using a more cost effective method, more funding could be directed to other endeavors. Paternity testing, as well as some research endeavors could be conducted at a fraction of the cost, leaving resources for other projects or additional staff. Although it would be inadvisable to use this technique on forensic samples, the implications on paternity and research samples would be positive. This research attempted to design a nested PCR reaction and subsequently dilute the Applied Biosystems Primers in order to reduce the cost. The first step was to design new primers for the first round of PCR, followed by testing of those primers. The new primers then required optimization so that they all worked effectively together. After optimization was accomplished, the Identifiler primers were diluted until loci began dropping out of the genetic profile.