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2. A Note on Using Discretized Simulated Data to Estimate Implicit Likelihoods in Bayesian Analyses

Author

Hamada, M. S., Graves, T. L., Hengartner, N. W., Higdon, D. M., Huzurbazar, A. V., Lawrence, E. C., Linkletter, C. D., Reese, C. S., Scott, D. W., Sitter, R. R., Warr, R. L., and Williams, B. J.

Subjects
Statistics - Methodology
Abstract

This article presents a Bayesian inferential method where the likelihood for a model is unknown but where data can easily be simulated from the model. We discretize simulated (continuous) data to estimate the implicit likelihood in a Bayesian analysis employing a Markov chain Monte Carlo algorithm. Three examples are presented as well as a small study on some of the method's properties.

Published
2020

6. Analysis of human mRNAs with the reference genome sequence reveals potent errors, polymorphisms, and RNA editing

Author

Furey, T S, Diekhans, M, Lu, Y T, Graves, T A, Oddy, L, Randall-Maher, J, Hillier, L W, Wilson, R K, and Haussler, D

Subjects
human mRNAs, SNPs, RNA editing
Abstract

The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of similar to30,000 nonredundant human mRNA sequences with identified coding regions representing 17,000 distinct loci. These high-quality mRNA sequences allow for the identification of transcribed regions in the human genome sequence, and many researchers accept them as the correct representation of each defined gene sequence. Computational comparison of these mRNA sequences and the recently published essentially finished human genome sequence reveals several thousand undocumented nonsynonymous substitution and frame shift discrepancies between the two resources. Additional analysis is undertaken to verify that the euchromatic human genome is sufficiently complete-containing nearly the whole mRNA collection, thus allowing for a comprehensive analysis to be undertaken. Many of the discrepancies will prove to be genuine polymorphisms in the human population, somatic cell genomic variants, or examples of RNA editing. It is observed that the genome sequence variant has significant additional support from other mRNAs and ESTs, almost four times more often than does the mRNA variant, suggesting that the genome sequence is more accurate. In similar to15% of these cases, there is substantial support for both variants, suggestive of an undocumented polymorphism. An initial screening against a 24-individual genomic DNA diversity panel verified 60% of a small set of potential single nucleotide polymorphisms from which successful results could be obtained. We also find statistical evidence that a few of these discrepancies are due to RNA editing. Overall, these results suggest that the mRNA collections may contain a substantial number of errors. For current and future mRNA collections, it may be prudent to fully reconcile each genome sequence discrepancy, classifying each as a polymorphism, site of RNA editing or somatic cell variation, or genome sequence error.

Published
2004

8. Genome Project Standards in a New Era of Sequencing

Author

Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., Cole, J. R., Ding, Y., Dugan, S., Field, D., Garrity, G. M., Gibbs, R., Graves, T., Han, C. S., Harrison, S. H., Highlander, S., Hugenholtz, P., Khouri, H. M., Kodira, C. D., Kolker, E., Kyrpides, N. C., Lang, D., Lapidus, A., Malfatti, S. A., Markowitz, V., Metha, T., Nelson, K. E., Parkhill, J., Pitluck, S., Qin, X., Read, T. D., Schmutz, J., Sozhamannan, S., Sterk, P., Strausberg, R. L., Sutton, G., Thomson, N. R., Tiedje, J. M., Weinstock, G., Wollam, A., and Detter, J. C.

Published
2009
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21. Using simulation to handle implicit likelihoods in a Bayesian analysis

Author

Hamada, M. S., primary, Graves, T. L., additional, Hengartner, N. W., additional, Higdon, D. M., additional, Huzurbazar, A. V., additional, Lawrence, E., additional, Linkletter, C. D., additional, Reese, C. S., additional, Scott, D. W., additional, Sitter, R. R., additional, Warr, R. L., additional, and Williams, B. J., additional

Published
2021
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24. Novel GDF2 Loss of Function Variant in a Family with HHT and PAVMs Expands the Phenotype Associated with BMP9 Dysfunction

Author

Balachandar, S., primary, Graves, T., additional, Shimonty, A., additional, Xiao, S., additional, Slade, R., additional, Sroya, M., additional, Mohammed, M., additional, Alikian, M., additional, Curetean, E., additional, Thomas, E., additional, Kilner, J., additional, Kerr, K., additional, Mcconnell, V., additional, McKee, S., additional, Boardman-Pretty, F., additional, Devereau, A., additional, McDonagh, E., additional, Scott, R., additional, Fowler, T., additional, Caulfield, M., additional, Alton, E., additional, Ferguson, T., additional, Redhead, J., additional, McKnight, A., additional, Thomas, G., additional, Genomics England Research Consortium and Respirato, R.G., additional, Aldred, M., additional, and Shovlin, C., additional

Published
2020
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25. Evidence-based pain medicine for primary care physicians

Author

Brian M. Bruel, Graves T. Owen, C. M. Schade, Maxim S. Eckmann, Mitchell P. Engle, and Erik C. Hustak

Subjects
Biopsychosocial model, medicine.medical_specialty, Evidence-based practice, business.industry, Pain medicine, Best practice, Chronic pain, Psychological intervention, Review, General Medicine, medicine.disease, 03 medical and health sciences, 0302 clinical medicine, Pharmacotherapy, Opioid, medicine, 030212 general & internal medicine, Intensive care medicine, business, 030217 neurology & neurosurgery, medicine.drug
Abstract

The last several decades have seen a marked increase in both the recognition and treatment of chronic pain. Unfortunately, patients frequently misunderstand both the nature of pain and the best practices for its treatment. Because primary care physicians treat the majority of chronic pain, they are ideally situated to provide evidence-based pain care. The majority of the medical evidence supports a biopsychosocial model of pain that integrates physical, emotional, social, and cultural variables. The goal of this primer is to assist primary care physicians in their understanding of pain, evaluation of the chronic pain patient, and ability to direct evidence-based care. This article will discuss the role of physical rehabilitation, pain psychology, pharmacotherapy, and procedural interventions in the treatment of chronic pain. Given the current epidemic of drug-related deaths, particular emphasis is placed on the alternatives to opioid therapy. Unfortunately, death is not the only significant complication from opioid therapy, and this article discusses many of the most common side effects. This article provides general guidelines on the most appropriate utilization of opioids with emphasis on the recent Centers for Disease Control and Prevention guidelines, risk stratification, and patient monitoring. Finally, the article concludes with the critical role that a pain medicine specialist can play in the management of patients with chronic pain.

Published
2018
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28. Genome Project Standards in a New Era of Sequencing

Author

Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., Cole, J. R., Ding, Y., Dugan, S., Field, D., Garrity, G. M., Gibbs, R., Graves, T., Han, C. S., Harrison, S. H., Highlander, S., Hugenholtz, P., Khouri, H. M., Kodira, C. D., Kolker, E., Kyrpides, N. C., Lang, D., Lapidus, A., Malfatti, S. A., Markowitz, V., Metha, T., Nelson, K. E., Parkhill, J., Pitluck, S., Qin, X., Read, T. D., Schmutz, J., Sozhamannan, S., Sterk, P., Strausberg, R. L., Sutton, G., Thomson, N. R., Tiedje, J. M., Weinstock, G., Wollam, A., and Detter, J. C.

Published
2009

33. A platform in the use of medicines to treat chronic hepatitis C (PLATINUM C): protocol for a prospective treatment registry of real-world outcomes for hepatitis C

Author

Ramsay, J, Marsh, J, Pedrana, A, Andric, N, Norman, R, Cheng, W, Webb, S, Zeps, N, Bellgard, M, Graves, T, Hellard, M, Snelling, T, Ramsay, J, Marsh, J, Pedrana, A, Andric, N, Norman, R, Cheng, W, Webb, S, Zeps, N, Bellgard, M, Graves, T, Hellard, M, and Snelling, T

Abstract

BACKGROUND: Safe, highly curative, short course, direct acting antiviral (DAA) therapies are now available to treat chronic hepatitis C. DAA therapy is freely available to all adults chronically infected with the hepatitis C virus (HCV) in Australia. If left untreated, hepatitis C may lead to progressive hepatic fibrosis, cirrhosis and hepatocellular carcinoma. Australia is committed to eliminating hepatitis as a public health threat by 2030 set by the World Health Organization. However, since the introduction of funded DAA treatment, uptake has been suboptimal. Australia needs improved strategies for testing, treatment uptake and treatment completion to address the persisting hepatitis C public health problem. PLATINUM C is a HCV treatment registry and research platform for assessing the comparative effectiveness of alternative interventions for achieving virological cure. METHODS: PLATINUM C will prospectively enrol people with active HCV infection confirmed by recent detection of HCV ribonucleic acid (RNA) in blood. Those enrolled will agree to allow standardised collection of demographic, lifestyle, treatment, virological outcome and other relevant clinical data to better inform the future management of HCV infection. The primary outcome is virological cure evidenced by sustained virological response (SVR), which is defined as a negative HCV PCR result 6 to 18 months after initial prescription of DAA therapy and no less than 12 weeks after the completion of treatment. Study participants will be invited to opt-in to medication adherence monitoring and quality of life assessments using validated self-reported instruments (EQ-5D-5L). DISCUSSION: PLATINUM C is a treatment registry and platform for nesting pragmatic trials. Data collected will inform the design, development and implementation of pragmatic trials. The digital infrastructure, study procedures and governing systems established by the registry will allow PLATINUM C to support a wider research platform in

Published
2020

34. The Controversy over Group Rewards in Cooperative Classrooms.

Author

Graves, T

Abstract

Suggests ways to minimize the negative effects of extrinsic group rewards in cooperative classrooms, explains how to use intrinsic rewards, and outlines conditions calling for extrinsic rewards. The "social rewards" of working cooperatively probably enhance intrinsic motivation and are among the great advantages of employing cooperative learning strategies. (20 references) (MLH)

Published
1991

47. Urine Drug Testing: Current Recommendations and Best Practices

Author

Allen W. Burton, Burton, Houston Tx, Graves T. Owen, Steve Passik, and C. M. Schade

Subjects
medicine.medical_specialty, Pathology, Urinalysis, medicine.diagnostic_test, business.industry, Best practice, Pain medicine, Chronic pain, Alternative medicine, MEDLINE, medicine.disease, Test (assessment), Anesthesiology and Pain Medicine, Family medicine, Medicine, business, Risk management
Abstract

Background: The precise role of urine drug testing (UDT) in the practice of pain medicine is currently being defined. Confusion exists as to best practices, and even to what constitutes standard of care. A member survey by our state pain society revealed variability in practice and a lack of consensus. Objective: The authors sought to further clarify the importance of routine UDT as an important part of an overall treatment plan that includes chronic opioid prescribing. Further, we wish to clarify best practices based on consensus and data where available. Methods: A 20-item membership survey was sent to Texas Pain Society members. A group of chronic pain experts from the Texas Pain Society undertook an effort to review the best practices in the literature. The rationale for current UDT practices is clarified, with risk management strategies outlined, and recommendations for UDT outlined in detail. A detailed insight into the limitations of point-of-care (enzyme-linked immunosorbent assay, test cups, test strips) versus the more sensitive and specific laboratory methods is provided. Limitations: Our membership survey was of a limited sample size in one geographic area in the United States and may not represent national patterns. Finally, there is limited data as to the efficacy of UDT practices in improving compliance and curtailing overall medication misuse. Conclusions: UDT must be done routinely as part of an overall best practice program in order to prescribe chronic opioid therapy. This program may include risk stratification; baseline and periodic UDT; behavioral monitoring; and prescription monitoring programs as the best available tools to monitor chronic opioid compliance. Key words: Urine drug screening, urine toxicology screening, urine drug testing, chronic pain, addiction, forensic testing

Published
2012
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