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Article ; Online: GLUMIP 2.0

John A. Kairalla / Christopher S. Coffey / Keith E. Muller

Journal of Statistical Software, Vol 28, Iss

SAS/IML Software for Planning Internal Pilots

2008 Volume 7

Abstract: Internal pilot designs involve conducting interim power analysis (without interim data analysis) to modify the final sample size. Recently developed techniques have been described to avoid the type~I error rate inflation inherent to unadjusted hypothesis ...

Abstract	Internal pilot designs involve conducting interim power analysis (without interim data analysis) to modify the final sample size. Recently developed techniques have been described to avoid the type~I error rate inflation inherent to unadjusted hypothesis tests, while still providing the advantages of an internal pilot design. We present GLUMIP 2.0, the latest version of our free SAS/IML software for planning internal pilot studies in the general linear univariate model (GLUM) framework. The new analytic forms incorporated into the updated software solve many problems inherent to current internal pilot techniques for linear models with Gaussian errors. Hence, the GLUMIP 2.0 software makes it easy to perform exact power analysis for internal pilots under the GLUM framework with independent Gaussian errors and fixed predictors.
Keywords	sample size re-estimation ; power ; adaptive designs ; Statistics ; HA1-4737 ; Social Sciences ; H ; DOAJ:Statistics ; DOAJ:Mathematics and Statistics
Subject code	310
Language	English
Publishing date	2008-09-01T00:00:00Z
Publisher	University of California, Los Angeles
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Multi-Site Observational Study to Assess Biomarkers for Susceptibility or Resilience to Chronic Pain

Giovanni Berardi / Laura Frey-Law / Kathleen A. Sluka / Emine O. Bayman / Christopher S. Coffey / Dixie Ecklund / Carol G. T. Vance / Dana L. Dailey / John Burns / Asokumar Buvanendran / Robert J. McCarthy / Joshua Jacobs / Xiaohong Joe Zhou / Richard Wixson / Tessa Balach / Chad M. Brummett / Daniel Clauw / Douglas Colquhoun / Steven E. Harte /

Frontiers in Medicine, Vol

The Acute to Chronic Pain Signatures (A2CPS) Study Protocol

2022 Volume 9

Abstract: Chronic pain has become a global health problem contributing to years lived with disability and reduced quality of life. Advances in the clinical management of chronic pain have been limited due to incomplete understanding of the multiple risk factors ... ...

Abstract	Chronic pain has become a global health problem contributing to years lived with disability and reduced quality of life. Advances in the clinical management of chronic pain have been limited due to incomplete understanding of the multiple risk factors and molecular mechanisms that contribute to the development of chronic pain. The Acute to Chronic Pain Signatures (A2CPS) Program aims to characterize the predictive nature of biomarkers (brain imaging, high-throughput molecular screening techniques, or “omics,” quantitative sensory testing, patient-reported outcome assessments and functional assessments) to identify individuals who will develop chronic pain following surgical intervention. The A2CPS is a multisite observational study investigating biomarkers and collective biosignatures (a combination of several individual biomarkers) that predict susceptibility or resilience to the development of chronic pain following knee arthroplasty and thoracic surgery. This manuscript provides an overview of data collection methods and procedures designed to standardize data collection across multiple clinical sites and institutions. Pain-related biomarkers are evaluated before surgery and up to 3 months after surgery for use as predictors of patient reported outcomes 6 months after surgery. The dataset from this prospective observational study will be available for researchers internal and external to the A2CPS Consortium to advance understanding of the transition from acute to chronic postsurgical pain.
Keywords	postsurgical pain ; thoracic surgery ; pain ; biomarker ; risk factors ; protocol ; Medicine (General) ; R5-920
Subject code	616
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cognition among individuals along a spectrum of increased risk for Parkinson's disease.

Lana M Chahine / Liz Urbe / Chelsea Caspell-Garcia / Dag Aarsland / Roy Alcalay / Paolo Barone / David Burn / Alberto J Espay / Jamie L Hamilton / Keith A Hawkins / Shirley Lasch / James B Leverenz / Irene Litvan / Irene Richard / Andrew Siderowf / Christopher S Coffey / Tanya Simuni / Daniel Weintraub / Parkinson’s Progression Markers Initiative

PLoS ONE, Vol 13, Iss 8, p e

2018 Volume 0201964

Abstract: INTRODUCTION:Several characteristics associated with increased risk for Parkinson's disease (PD) have been identified, including specific genotypes and various non-motor symptoms. Characterizing non-motor features, such as cognitive abilities, among ... ...

Abstract	INTRODUCTION:Several characteristics associated with increased risk for Parkinson's disease (PD) have been identified, including specific genotypes and various non-motor symptoms. Characterizing non-motor features, such as cognitive abilities, among individuals considered at-risk for PD is essential to improving prediction of future neurodegeneration. METHODS:Participants belonging to the following cohorts of the Parkinson Progression Markers Initiative (PPMI) study were included: de novo PD with dopamine transporter binding deficit (n = 423), idiopathic REM sleep behavior disorder (RBD, n = 39), hyposmia (n = 26) and non-PD mutation carrier (NMC; Leucine-rich repeat kinase 2 (LRRK2) G2019S (n = 88) and glucocerebrosidase (GBA) gene (n = 38) mutations)). Inclusion criteria enriched the RBD and hyposmia cohorts, but not the NMC cohort, with individuals with dopamine transporter binding deficit. Baseline neuropsychological performance was compared, and analyses were adjusted for age, sex, education, and depression. RESULTS:The RBD cohort performed significantly worse than the hyposmia and NMC cohorts on Symbol Digit Modality Test (mean (SD) 32.4 (9.16) vs. 41.8 (9.98), p = 0.002 and vs. 45.2 (10.9), p<0.001) and Judgment of Line Orientation (11.3 (2.36) vs.12.9 (1.87), p = 0.004 and vs. 12.9 (1.87), p<0.001). The RBD cohort also performed worse than the hyposmia cohort on the Montreal Cognitive Assessment (25.5 (4.13) vs. 27.3 (1.71), p = 0.02). Hyposmics did not differ from PD or NMC cohorts on any cognitive test score. CONCLUSION:Among individuals across a spectrum of risk for PD, cognitive function is worse among those with the characteristic most strongly associated with future risk of PD or dementia with Lewy bodies, namely RBD.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Recruitment & retention program for the NeuroNEXT SMA Biomarker Study

Amy Bartlett / Stephen J. Kolb / Allison Kingsley / Kathryn J. Swoboda / Sandra P. Reyna / Ai Sakonju / Basil T. Darras / Richard Shell / Nancy Kuntz / Diana Castro / Susan T. Iannaccone / Julie Parsons / Anne M. Connolly / Claudia A. Chiriboga / Craig McDonald / W. Bryan Burnette / Klaus Werner / Mathula Thangarajh / Perry B. Shieh /

Erika Finanger / Christopher S. Coffey / Jon W. Yankey / Merit E. Cudkowicz / Michelle M. McGovern / D. Elizabeth McNeil / W. David Arnold / John T. Kissel

Contemporary Clinical Trials Communications, Vol 11, Iss , Pp 113-

Super Babies for SMA!

2018 Volume 119

Abstract: Background/Aims: Recruitment and retention of research participants are challenging and critical components of successful clinical trials and natural history studies. Infants with spinal muscular atrophy (SMA) have been a particularly challenging ... ...

Abstract	Background/Aims: Recruitment and retention of research participants are challenging and critical components of successful clinical trials and natural history studies. Infants with spinal muscular atrophy (SMA) have been a particularly challenging population to study due to their fragile and complex medical issues, poor prognosis and, until 2016, a lack of effective therapies. Recruitment of healthy infants into clinical trials and natural history studies is also challenging and sometimes assumed to not be feasible. Methods: In 2011, our group initiated a two-year, longitudinal natural history study of infants with SMA and healthy infant controls to provide data to assist in the analysis and interpretation of planned clinical trials in infants with SMA. The recruitment goal was to enroll 27 infants less than 6 months of age with SMA and 27 age-matched healthy infants within the two-year enrollment period. A detailed recruitment and retention plan was developed for this purpose. In addition, a survey was administered to participant families to understand the determinants of participation in the study. Results: All healthy infants were recruited within the study's first year and 26 SMA infants were recruited within the two-year recruitment period. Thirty-eight participant families responded to the recruitment determinants survey. Nearly half of respondents (18/38, 48%) reported that they first heard of the study from their physician or neurologist. The most common reason to decide to enroll their infant (22/38, 58%) and to remain in the study (28/38, 74%) was their understanding of the importance of the study. Thematic recruitment tools such as a study brochure, video on social media, and presentations at advocacy meetings were reported to positively influence the decision to enroll. Conclusions: A proactive, thematic and inclusive recruitment and retention plan that effectively communicates the rationale of a clinical study and partners with patients, advocacy groups and the local communities can effectively ...
Keywords	Medicine (General) ; R5-920
Subject code	150
Language	English
Publishing date	2018-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Association of the Metabolic Syndrome with PAI-1 and t-PA Levels

Qing Li / Jason H. Moore / Folkert W. Asselbergs / Hans L. Hillege / Patricia R. Hebert / Christopher S. Coffey / Wiek H. van Gilst

Cardiology Research and Practice, Vol

2011 Volume 2011

Keywords	Diseases of the circulatory (Cardiovascular) system ; RC666-701 ; Specialties of internal medicine ; RC581-951 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Cardiovascular ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
Language	English
Publishing date	2011-01-01T00:00:00Z
Publisher	Hindawi Publishing Corporation
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Association of the Metabolic Syndrome with PAI-1 and t-PA Levels

Christopher S. Coffey / Folkert W. Asselbergs / Patricia R. Hebert / Hans L. Hillege / Qing Li / Jason H. Moore / Wiek H. van Gilst

Cardiology Research and Practice, Vol

2011 Volume 2011

Keywords	Diseases of the circulatory (Cardiovascular) system ; RC666-701 ; Specialties of internal medicine ; RC581-951 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Cardiovascular ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
Language	English
Publishing date	2011-01-01T00:00:00Z
Publisher	Hindawi Publishing Corporation
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cardiovascular risk associated with interactions among polymorphisms in genes from the renin-angiotensin, bradykinin, and fibrinolytic systems.

John P Bentley / Folkert W Asselbergs / Christopher S Coffey / Patricia R Hebert / Jason H Moore / Hans L Hillege / Wiek H van Gilst

PLoS ONE, Vol 5, Iss 9, p e

2010 Volume 12757

Abstract: Vascular fibrinolytic balance is maintained primarily by interplay of tissue plasminogen activator (t-PA) and plasminogen activator inhibitor type 1 (PAI-1). Previous research has shown that polymorphisms in genes from the renin-angiotensin (RA), ... ...

Abstract	Vascular fibrinolytic balance is maintained primarily by interplay of tissue plasminogen activator (t-PA) and plasminogen activator inhibitor type 1 (PAI-1). Previous research has shown that polymorphisms in genes from the renin-angiotensin (RA), bradykinin, and fibrinolytic systems affect plasma concentrations of both t-PA and PAI-1 through a set of gene-gene interactions. In the present study, we extend this finding by exploring the effects of polymorphisms in genes from these systems on incident cardiovascular disease, explicitly examining two-way interactions in a large population-based study.Data from the population-based PREVEND study in Groningen, The Netherlands (n = 8,138) were analyzed. The effects of the polymorphisms and their interactions on cardiovascular events were analyzed via Cox proportional hazards models. There was no association between five of the six polymorphisms singly and risk of cardiovascular disease. There was a significant main effect for the ACE I/D polymorphism for both dominant and additive coding schemes. There were significant interactions between the following polymorphism pairs even after adjustment for known risk factors: ACE I/D & PAI-1 4G/5G (p = 0.012), BDKRB2 C181T & ACE I/D (p = 0.016), BDKRB2 C58T & ACE I/D (p = 0.025), BDKRB2 exon 1 I/D & AT1R A1166C (p = 0.017), and BDKRB2 C58T & AT1R A1166C (p = 0.015).This study suggests possible interactions between genes from the RA, bradykinin, and fibrinolytic systems on the risk of cardiovascular disease, extending previous research that has demonstrated that interactions among genes from these systems influence plasma concentrations of both t-PA and PAI-1. Further explorations of these interactions are needed.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2010-09-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Missing data in randomized clinical trials for weight loss

Mai A Elobeid / Miguel A Padilla / Theresa McVie / Olivia Thomas / David W Brock / Bret Musser / Kaifeng Lu / Christopher S Coffey / Renee A Desmond / Marie-Pierre St-Onge / Kishore M Gadde / Steven B Heymsfield / David B Allison

PLoS ONE, Vol 4, Iss 8, p e

scope of the problem, state of the field, and performance of statistical methods.

2009 Volume 6624

Abstract: Dropouts and missing data are nearly-ubiquitous in obesity randomized controlled trails, threatening validity and generalizability of conclusions. Herein, we meta-analytically evaluate the extent of missing data, the frequency with which various analytic ...

Abstract	Dropouts and missing data are nearly-ubiquitous in obesity randomized controlled trails, threatening validity and generalizability of conclusions. Herein, we meta-analytically evaluate the extent of missing data, the frequency with which various analytic methods are employed to accommodate dropouts, and the performance of multiple statistical methods.We searched PubMed and Cochrane databases (2000-2006) for articles published in English and manually searched bibliographic references. Articles of pharmaceutical randomized controlled trials with weight loss or weight gain prevention as major endpoints were included. Two authors independently reviewed each publication for inclusion. 121 articles met the inclusion criteria. Two authors independently extracted treatment, sample size, drop-out rates, study duration, and statistical method used to handle missing data from all articles and resolved disagreements by consensus. In the meta-analysis, drop-out rates were substantial with the survival (non-dropout) rates being approximated by an exponential decay curve (e(-lambdat)) where lambda was estimated to be .0088 (95% bootstrap confidence interval: .0076 to .0100) and t represents time in weeks. The estimated drop-out rate at 1 year was 37%. Most studies used last observation carried forward as the primary analytic method to handle missing data. We also obtained 12 raw obesity randomized controlled trial datasets for empirical analyses. Analyses of raw randomized controlled trial data suggested that both mixed models and multiple imputation performed well, but that multiple imputation may be more robust when missing data are extensive.Our analysis offers an equation for predictions of dropout rates useful for future study planning. Our raw data analyses suggests that multiple imputation is better than other methods for handling missing data in obesity randomized controlled trials, followed closely by mixed models. We suggest these methods supplant last observation carried forward as the primary method of analysis.
Keywords	Medicine ; R ; Science ; Q
Subject code	310
Language	English
Publishing date	2009-08-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Alterations in Lipoxygenase and Cyclooxygenase-2 Catalytic Activity and mRNA Expression in Prostate Carcinoma

Scott B. Shappell / Suzanne Manning / William E. Boeglin / You-Fei Guan / Richard L. Roberts / Linda Davis / Sandra J. Olson / Gregory S. Jack / Christopher S. Coffey / Thomas M. Wheeler / Matthew D. Breyer / Alan R. Brash

Neoplasia : An International Journal for Oncology Research, Vol 3, Iss 4, Pp 287-

2001 Volume 303

Abstract: Recent studies in prostate tissues and especially cell lines have suggested roles for arachidonic acid (AA) metabolizing enzymes in prostate adenocarcinoma (Pca) development or progression. The goal of this study was to more fully characterize ... ...

Abstract	Recent studies in prostate tissues and especially cell lines have suggested roles for arachidonic acid (AA) metabolizing enzymes in prostate adenocarcinoma (Pca) development or progression. The goal of this study was to more fully characterize lipoxygenase (LOX) and cyclooxygenase-2 (COX-2) gene expression and AA metabolism in benign and malignant prostate using snap-frozen tissues obtained intraoperatively and mRNA analyses and enzyme assays. Formation of 15-hydroxyeicosatetraenoic acid (15-HETE) was detected in 23/29 benign samples and 15-LOX-2 mRNA was detected in 21/25 benign samples. In pairs of pure benign and Pca from the same patients, 15-HETE production and 15-LOX-2 mRNA were reduced in Pca versus benign in 9/14 (P=.04) and 14/17 (P=.002), respectively. Under the same conditions, neither 5HETE nor 12-HETE formation was detectable in 29 benign and 24 tumor samples; with a more sensitive assay, traces were detected in some samples, but there was no clear association with tumor tissue. COX-2 mRNA was detected by nuclease protection assay in 7/16 benign samples and 5/16 tumors. In benign and tumor pairs from 10 patients, COX-2 was higher in tumor versus benign in only 2, with similar results by in situ hybridization. Paraffin immunoperoxidase for COX2 was performed in whole mount sections from 87 additional radical prostatectomy specimens, with strong expression in ejaculatory duct as a positive control and corroboration with in situ hybridization. No immunostaining was detected in benign prostate or tumor in 45% of cases. Greater immunostaining in tumor versus benign was present in only 17% of cases, and correlated with high tumor grade (Gleason score 8 and 9 vs. 5 to 7). In conclusion, reduced 15-LOX-2 expression and 15-HETE formation is the most characteristic alteration of AA metabolism in Pca. Increased 12-HETE and 5-HETE formation in Pca were not discernible. Increased COX-2 expression is not a typical abnormality in Pca in general, but occurs in high-grade tumors.
Keywords	arachidonic acid ; eicosanoids ; HETEs ; 15-lipoxygenase-2 ; cyclooxygenase ; Medicine ; R ; Internal medicine ; RC31-1245 ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282
Publishing date	2001-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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