1
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Claes J, Agten A, Blázquez-Moreno A, Crabbe M, Tuefferd M, Goehlmann H, Geys H, Peng CY, Neyens T, Faes C. The influence of resolution on the predictive power of spatial heterogeneity measures as biomarkers of liver fibrosis. Comput Biol Med 2024; 171:108231. [PMID: 38422965 DOI: 10.1016/j.compbiomed.2024.108231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/23/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
Spatial heterogeneity of cells in liver biopsies can be used as biomarker for disease severity of patients. This heterogeneity can be quantified by non-parametric statistics of point pattern data, which make use of an aggregation of the point locations. The method and scale of aggregation are usually chosen ad hoc, despite values of the aforementioned statistics being heavily dependent on them. Moreover, in the context of measuring heterogeneity, increasing spatial resolution will not endlessly provide more accuracy. The question then becomes how changes in resolution influence heterogeneity indicators, and subsequently how they influence their predictive abilities. In this paper, cell level data of liver biopsy tissue taken from chronic Hepatitis B patients is used to analyze this issue. Firstly, Morisita-Horn indices, Shannon indices and Getis-Ord statistics were evaluated as heterogeneity indicators of different types of cells, using multiple resolutions. Secondly, the effect of resolution on the predictive performance of the indices in an ordinal regression model was investigated, as well as their importance in the model. A simulation study was subsequently performed to validate the aforementioned methods. In general, for specific heterogeneity indicators, a downward trend in predictive performance could be observed. While for local measures of heterogeneity a smaller grid-size is outperforming, global measures have a better performance with medium-sized grids. In addition, the use of both local and global measures of heterogeneity is recommended to improve the predictive performance.
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Affiliation(s)
- Jari Claes
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium.
| | - Annelies Agten
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium
| | - Alfonso Blázquez-Moreno
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Marjolein Crabbe
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Marianne Tuefferd
- Translational Biomarkers, Infectious Diseases, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Hinrich Goehlmann
- Translational Biomarkers, Infectious Diseases, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Helena Geys
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | | | - Thomas Neyens
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium; L-BioStat, KU Leuven, Kapucijnenvoer 35, Leuven, 3000, Belgium
| | - Christel Faes
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium
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2
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Lin CP, Duan Y, Sargsyan D, Cabrera J, Livingston CM, Vogel R, Hartman J, Das M, Talloen W, Geys H, Kanoulas ED, Mohanty S. Automated Spot Counting in Microbiology. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:3703-3714. [PMID: 37725729 DOI: 10.1109/tcbb.2023.3317339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Biological samples are routinely analyzed for microbe concentration. The samples are diluted, loaded onto established host cell cultures, and incubated. If infectious agents are present in the samples, they form circular spots that do not contain the host cells. Each spot is assumed to be originated from a single microbial unit such as a bacterial colony forming unit or viral plaque forming unit. The undiluted sample concentration is estimated by counting the spots and back-calculating. Counting the number of spots by trained technicians is currently the gold standard but it is laborious, subjective, and hard to scale. This paper presents a new automated algorithm for spot counting, Localized and Sequential Thresholding (LoST). Validation studies showed that LoST performance was comparable with manual counting and outperformed several existing tools on images with overlapping spots. The LoST algorithm employs sequential thresholding through a two-stage segmentation and borrows information across all images from the same dilution series to fine-tune the count and identify right censoring. The algorithm increases the efficiency of the spot counting and the quality of the downstream analysis, especially when coupled with an appropriate statistical serial dilution model to enhance the undiluted sample concentration estimation procedure.
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3
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Agten A, Blázquez-Moreno A, Crabbe M, Tuefferd M, Goehlmann H, Geys H, Peng CY, Claes J, Neyens T, Faes C. Measures of spatial heterogeneity in the liver tissue micro-environment as predictive factors for fibrosis score. Comput Biol Med 2023; 165:107382. [PMID: 37634463 DOI: 10.1016/j.compbiomed.2023.107382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/02/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023]
Abstract
The organization and interaction between hepatocytes and other hepatic non-parenchymal cells plays a pivotal role in maintaining normal liver function and structure. Although spatial heterogeneity within the tumor micro-environment has been proven to be a fundamental feature in cancer progression, the role of liver tissue topology and micro-environmental factors in the context of liver damage in chronic infection has not been widely studied yet. We obtained images from 110 core needle biopsies from a cohort of chronic hepatitis B patients with different fibrosis stages according to METAVIR score. The tissue sections were immunofluorescently stained and imaged to determine the locations of CD45 positive immune cells and HBsAg-negative and HBsAg-positive hepatocytes within the tissue. We applied several descriptive techniques adopted from ecology, including Getis-Ord, the Shannon Index and the Morisita-Horn Index, to quantify the extent to which immune cells and different types of liver cells co-localize in the tissue biopsies. Additionally, we modeled the spatial distribution of the different cell types using a joint log-Gaussian Cox process and proposed several features to quantify spatial heterogeneity. We then related these measures to the patient fibrosis stage by using a linear discriminant analysis approach. Our analysis revealed that the co-localization of HBsAg-negative hepatocytes with immune cells and the co-localization of HBsAg-positive hepatocytes with immune cells are equally important factors for explaining the METAVIR score in chronic hepatitis B patients. Moreover, we found that if we allow for an error of 1 on the METAVIR score, we are able to reach an accuracy of around 80%. With this study we demonstrate how methods adopted from ecology and applied to the liver tissue micro-environment can be used to quantify heterogeneity and how these approaches can be valuable in biomarker analyses for liver topology.
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Affiliation(s)
- Annelies Agten
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, BE 3590 Diepenbeek, Belgium.
| | - Alfonso Blázquez-Moreno
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marjolein Crabbe
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marianne Tuefferd
- Translational Biomarkers, Infectious Diseases, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Hinrich Goehlmann
- Translational Biomarkers, Infectious Diseases, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Helena Geys
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Jari Claes
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, BE 3590 Diepenbeek, Belgium
| | - Thomas Neyens
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, BE 3590 Diepenbeek, Belgium; L-BioStat, KU Leuven, Kapucijnenvoer 35, 3000 Leuven, Belgium
| | - Christel Faes
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, BE 3590 Diepenbeek, Belgium
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4
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Rao M, Nassiri V, Alhambra C, Snoeys J, Van Goethem F, Irrechukwu O, Aleo MD, Geys H, Mitra K, Will Y. AI/ML Models to Predict the Severity of Drug-Induced Liver Injury for Small Molecules. Chem Res Toxicol 2023. [PMID: 37294641 DOI: 10.1021/acs.chemrestox.3c00098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Drug-induced liver injury (DILI), believed to be a multifactorial toxicity, has been a leading cause of attrition of small molecules during discovery, clinical development, and postmarketing. Identification of DILI risk early reduces the costs and cycle times associated with drug development. In recent years, several groups have reported predictive models that use physicochemical properties or in vitro and in vivo assay endpoints; however, these approaches have not accounted for liver-expressed proteins and drug molecules. To address this gap, we have developed an integrated artificial intelligence/machine learning (AI/ML) model to predict DILI severity for small molecules using a combination of physicochemical properties and off-target interactions predicted in silico. We compiled a data set of 603 diverse compounds from public databases. Among them, 164 were categorized as Most DILI (M-DILI), 245 as Less DILI (L-DILI), and 194 as No DILI (N-DILI) by the FDA. Six machine learning methods were used to create a consensus model for predicting the DILI potential. These methods include k-nearest neighbor (k-NN), support vector machine (SVM), random forest (RF), Naïve Bayes (NB), artificial neural network (ANN), logistic regression (LR), weighted average ensemble learning (WA) and penalized logistic regression (PLR). Among the analyzed ML methods, SVM, RF, LR, WA, and PLR identified M-DILI and N-DILI compounds, achieving a receiver operating characteristic area under the curve of 0.88, sensitivity of 0.73, and specificity of 0.9. Approximately 43 off-targets, along with physicochemical properties (fsp3, log S, basicity, reactive functional groups, and predicted metabolites), were identified as significant factors in distinguishing between M-DILI and N-DILI compounds. The key off-targets that we identified include: PTGS1, PTGS2, SLC22A12, PPARγ, RXRA, CYP2C9, AKR1C3, MGLL, RET, AR, and ABCC4. The present AI/ML computational approach therefore demonstrates that the integration of physicochemical properties and predicted on- and off-target biological interactions can significantly improve DILI predictivity compared to chemical properties alone.
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Affiliation(s)
- Mohan Rao
- Discovery, Product Development and Supply (DPDS), Preclinical Sciences and Translational Safety (PSTS), Predictive Investigative and Translational Toxicology (PITT), Janssen Pharmaceutical Companies of Johnson and Johnson, La Jolla, California 92121, United States
| | - Vahid Nassiri
- Open Analytics, Jupiterstraat 20, 2600 Antwerpen, Belgium
| | - Cristóbal Alhambra
- Discovery, Product Development and Supply (DPDS), Preclinical Sciences and Translational Safety (PSTS), Predictive Investigative and Translational Toxicology (PITT), Janssen Pharmaceutical Companies of Johnson and Johnson, La Jolla, California 92121, United States
| | - Jan Snoeys
- Discovery, Product Development and Supply (DPDS), Preclinical Sciences and Translational Safety (PSTS), Predictive Investigative and Translational Toxicology (PITT), Janssen Pharmaceutical Companies of Johnson and Johnson, La Jolla, California 92121, United States
| | - Freddy Van Goethem
- Discovery, Product Development and Supply (DPDS), Preclinical Sciences and Translational Safety (PSTS), Predictive Investigative and Translational Toxicology (PITT), Janssen Pharmaceutical Companies of Johnson and Johnson, La Jolla, California 92121, United States
| | - Onyi Irrechukwu
- Discovery, Product Development and Supply (DPDS), Preclinical Sciences and Translational Safety (PSTS), Predictive Investigative and Translational Toxicology (PITT), Janssen Pharmaceutical Companies of Johnson and Johnson, La Jolla, California 92121, United States
| | - Michael D Aleo
- TOXinsights LLC, Boiling Springs, Pennsylvania 17007, United States
| | - Helena Geys
- Discovery, Product Development and Supply (DPDS), Preclinical Sciences and Translational Safety (PSTS), Predictive Investigative and Translational Toxicology (PITT), Janssen Pharmaceutical Companies of Johnson and Johnson, La Jolla, California 92121, United States
| | - Kaushik Mitra
- Discovery, Product Development and Supply (DPDS), Preclinical Sciences and Translational Safety (PSTS), Predictive Investigative and Translational Toxicology (PITT), Janssen Pharmaceutical Companies of Johnson and Johnson, La Jolla, California 92121, United States
| | - Yvonne Will
- Discovery, Product Development and Supply (DPDS), Preclinical Sciences and Translational Safety (PSTS), Predictive Investigative and Translational Toxicology (PITT), Janssen Pharmaceutical Companies of Johnson and Johnson, La Jolla, California 92121, United States
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5
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Barnett HY, Villar SS, Geys H, Jaki T. A novel statistical test for treatment differences in clinical trials using a response-adaptive forward-looking Gittins Index Rule. Biometrics 2023; 79:86-97. [PMID: 34669968 PMCID: PMC7614356 DOI: 10.1111/biom.13581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/30/2021] [Indexed: 11/28/2022]
Abstract
The most common objective for response-adaptive clinical trials is to seek to ensure that patients within a trial have a high chance of receiving the best treatment available by altering the chance of allocation on the basis of accumulating data. Approaches that yield good patient benefit properties suffer from low power from a frequentist perspective when testing for a treatment difference at the end of the study due to the high imbalance in treatment allocations. In this work we develop an alternative pairwise test for treatment difference on the basis of allocation probabilities of the covariate-adjusted response-adaptive randomization with forward-looking Gittins Index (CARA-FLGI) Rule for binary responses. The performance of the novel test is evaluated in simulations for two-armed studies and then its applications to multiarmed studies are illustrated. The proposed test has markedly improved power over the traditional Fisher exact test when this class of nonmyopic response adaptation is used. We also find that the test's power is close to the power of a Fisher exact test under equal randomization.
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Affiliation(s)
| | - Sofía S Villar
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | | | - Thomas Jaki
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Medical and Pharmaceutical Statistics Research Unit, Lancaster University, Lancaster, UK
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6
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Altan S, Amaratunga D, Cabrera J, Garren J, Geys H, Kolassa J, LeBlond D, Li D, Liao J, Liu J, Lubomirski M, Miro-Quesada G, Novick S, Otava M, Peterson J, Reckermann K, Schofield T, Tan C, Tatikola K, Tekle F, Thomas J, Vukovinsky K. Survey and Recommendations on the Use of P-Values Driving Decisions in Nonclinical Pharmaceutical Applications. Stat Biopharm Res 2022. [DOI: 10.1080/19466315.2022.2038258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jia Liu
- Pfizer Inc, Andover, Ma, 01810
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7
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Tresadern G, Tatikola K, Cabrera J, Wang L, Abel R, van Vlijmen H, Geys H. The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions. J Chem Inf Model 2022; 62:703-717. [DOI: 10.1021/acs.jcim.1c01214] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Kanaka Tatikola
- Nonclinical Statistics, Janssen Research & Development, 920 Route 202 South, Raritan, New Jersey 08869, United States
| | - Javier Cabrera
- Department of Statistics, Rutgers University, New Brunswick, New Jersey 08901-8554, United States
| | - Lingle Wang
- Schrödinger, Inc., New York, New York 10036, United States
| | - Robert Abel
- Schrödinger, Inc., New York, New York 10036, United States
| | - Herman van Vlijmen
- Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Helena Geys
- Nonclinical Statistics, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
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8
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Barnett HY, Geys H, Jacobs T, Jaki T. Methods for Non-Compartmental Pharmacokinetic Analysis With Observations Below the Limit of Quantification. Stat Biopharm Res 2021. [DOI: 10.1080/19466315.2019.1701546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | | | | | - Thomas Jaki
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
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9
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La Gamba F, Jacobs T, Serroyen J, Geys H, Faes C. Bayesian pooling versus sequential integration of small preclinical trials: a comparison within linear and nonlinear modeling frameworks. J Biopharm Stat 2020; 31:25-36. [PMID: 32552560 DOI: 10.1080/10543406.2020.1776312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Bayesian sequential integration is an appealing approach in drug development, as it allows to recursively update posterior distributions as soon as new data become available, thus considerably reducing the computation time. However, preclinical trials are often characterized by small sample sizes, which may affect the estimation process during the first integration steps, particularly when complex PK-PD models are used. In this case, sequential integration would not be practicable, and trials should be pooled together. This work is aimed at comparing simple Bayesian pooling with sequential integration through a simulation study. The two techniques are compared under several scenarios using linear as well as nonlinear models. The results of our simulation study encourage the use of Bayesian sequential integration with linear models. However, in the case of nonlinear models several caveats arise. This paper outlines some important recommendations and precautions in that respect.
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Affiliation(s)
- Fabiola La Gamba
- Department of Quantitative Sciences, Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium.,Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Tom Jacobs
- Department of Quantitative Sciences, Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Jan Serroyen
- Department of Quantitative Sciences, Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Helena Geys
- Department of Quantitative Sciences, Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium.,Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Christel Faes
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
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10
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van der Leede B, Weiner S, Van Doninck T, De Vlieger K, Schuermans A, Tekle F, Geys H, van Heerden M, De Jonghe S, Van Gompel J. Testing of acetaminophen in support of the international multilaboratory in vivo rat Pig-a assay validation trial. Environ Mol Mutagen 2020; 61:508-525. [PMID: 32187737 PMCID: PMC7317746 DOI: 10.1002/em.22368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
Acetaminophen, a nonmutagenic compound as previously concluded from bacteria, in vitro mammalian cell, and in vivo transgenic rat assays, presented a good profile as a nonmutagenic reference compound for use in the international multilaboratory Pig-a assay validation. Acetaminophen was administered at 250, 500, 1,000, and 2,000 mg·kg-1 ·day-1 to male Sprague Dawley rats once daily in 3 studies (3 days, 2 weeks, and 1 month with a 1-month recovery group). The 3-Day and 1-Month Studies included assessments of the micronucleus endpoint in peripheral blood erythrocytes and the comet endpoint in liver cells and peripheral blood cells in addition to the Pig-a assay; appropriate positive controls were included for each assay. Within these studies, potential toxicity of acetaminophen was evaluated and confirmed by inclusion of liver damage biomarkers and histopathology. Blood was sampled pre-treatment and at multiple time points up to Day 57. Pig-a mutant frequencies were determined in total red blood cells (RBCs) and reticulocytes (RETs) as CD59-negative RBC and CD59-negative RET frequencies, respectively. No increases in DNA damage as indicated through Pig-a, micronucleus, or comet endpoints were seen in treated rats. All positive controls responded as appropriate. Data from this series of studies demonstrate that acetaminophen is not mutagenic in the rat Pig-a model. These data are consistent with multiple studies in other nonclinical models, which have shown that acetaminophen is not mutagenic. At 1,000 mg·kg-1 ·day-1 , Cmax values of acetaminophen on Day 28 were 153,600 ng/ml and 131,500 ng/ml after single and repeat dosing, respectively, which were multiples over that of clinical therapeutic exposures (2.6-6.1 fold for single doses of 4,000 mg and 1,000 mg, respectively, and 11.5 fold for multiple dose of 4,000 mg) (FDA 2002). Data generated were of high quality and valid for contribution to the international multilaboratory validation of the in vivo Rat Pig-a Mutation Assay.
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Affiliation(s)
| | - Sandy Weiner
- Janssen Research & DevelopmentSpring House, PennsylvaniaUSA
| | | | | | | | - Fetene Tekle
- Janssen Research & DevelopmentBeerse, AntwerpBelgium
| | - Helena Geys
- Janssen Research & DevelopmentBeerse, AntwerpBelgium
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11
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Van der Elst W, Alonso AA, Geys H, Meyvisch P, Bijnens L, Sengupta R, Molenberghs G. Univariate Versus Multivariate Surrogates in the Single-Trial Setting. Stat Biopharm Res 2019. [DOI: 10.1080/19466315.2019.1575276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Wim Van der Elst
- The Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | | | - Helena Geys
- The Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | | | - Luc Bijnens
- The Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Rudradev Sengupta
- The Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
| | - Geert Molenberghs
- I-BioStat, KU Leuven & UHasselt, Leuven, Belgium and Hasselt, Belgium
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12
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Affiliation(s)
- Sammy Chebon
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Christel Faes
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | | | - Helena Geys
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
- Janssen Pharmaceutica NV, Beerse, Belgium
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13
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La Gamba F, Jacobs T, Geys H, Jaki T, Serroyen J, Ursino M, Russu A, Faes C. Bayesian sequential integration within a preclinical pharmacokinetic and pharmacodynamic modeling framework: Lessons learned. Pharm Stat 2019; 18:486-506. [PMID: 30932327 DOI: 10.1002/pst.1941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 11/09/2018] [Accepted: 02/02/2019] [Indexed: 12/25/2022]
Abstract
The present manuscript aims to discuss the implications of sequential knowledge integration of small preclinical trials in a Bayesian pharmacokinetic and pharmacodynamic (PK-PD) framework. While, at first sight, a Bayesian PK-PD framework seems to be a natural framework to allow for sequential knowledge integration, the scope of this paper is to highlight some often-overlooked challenges while at the same time providing some guidances in the many and overwhelming choices that need to be made. Challenges as well as opportunities will be discussed that are related to the impact of (1) the prior specification, (2) the choice of random effects, (3) the type of sequential integration method. In addition, it will be shown how the success of a sequential integration strategy is highly dependent on a carefully chosen experimental design when small trials are analyzed.
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Affiliation(s)
- Fabiola La Gamba
- Department of Quantitative Sciences, Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Beerse, Belgium.,Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Tom Jacobs
- Department of Quantitative Sciences, Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Helena Geys
- Department of Quantitative Sciences, Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Beerse, Belgium.,Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Thomas Jaki
- Department of Mathematics and Statistics, Lancaster University, Lancaster, England
| | - Jan Serroyen
- Department of Quantitative Sciences, Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Moreno Ursino
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Paris, France
| | - Alberto Russu
- Department of Quantitative Sciences, Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Christel Faes
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
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14
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La Gamba F, Jacobs T, Geys H, Ver Donck L, Faes C. A Bayesian K-PD model for synergy: A case study. Pharm Stat 2018; 17:674-684. [DOI: 10.1002/pst.1887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 03/28/2018] [Accepted: 06/09/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Fabiola La Gamba
- Janssen Research & Development; Turnhoutseweg 30 Beerse B-2340 Belgium
- I-BioStat; Hasselt University; Agoralaan building D Diepenbeek B-3590 Belgium
| | - Tom Jacobs
- Janssen Research & Development; Turnhoutseweg 30 Beerse B-2340 Belgium
| | - Helena Geys
- Janssen Research & Development; Turnhoutseweg 30 Beerse B-2340 Belgium
- I-BioStat; Hasselt University; Agoralaan building D Diepenbeek B-3590 Belgium
| | - Luc Ver Donck
- Janssen Research & Development; Turnhoutseweg 30 Beerse B-2340 Belgium
| | - Christel Faes
- I-BioStat; Hasselt University; Agoralaan building D Diepenbeek B-3590 Belgium
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15
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Affiliation(s)
| | | | | | - Thomas Jaki
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
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16
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Barnett HY, Geys H, Jacobs T, Jaki T. Comparing sampling methods for pharmacokinetic studies using model averaged derived parameters. Stat Med 2017; 36:4301-4315. [DOI: 10.1002/sim.7436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 07/12/2017] [Accepted: 07/21/2017] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Thomas Jaki
- Department of Mathematics and Statistics; Lancaster University; Lancaster U.K
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17
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Chebon S, Faes C, Cools F, Geys H. Models for zero-inflated, correlated count data with extra heterogeneity: when is it too complex? Stat Med 2017; 36:345-361. [PMID: 27734514 DOI: 10.1002/sim.7142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 07/30/2016] [Accepted: 09/16/2016] [Indexed: 11/10/2022]
Abstract
Statistical analysis of count data typically starts with a Poisson regression. However, in many real-life applications, it is observed that the variation in the counts is larger than the mean, and one needs to deal with the problem of overdispersion in the counts. Several factors may contribute to overdispersion: (1) unobserved heterogeneity due to missing covariates, (2) correlation between observations (such as in longitudinal studies), and (3) the occurrence of many zeros (more than expected from the Poisson distribution). In this paper, we discuss a model that allows one to explicitly take each of these factors into consideration. The aim of this paper is twofold: (1) investigate whether we can identify the cause of overdispersion via model selection, and (2) investigate the impact of a misspecification of the model on the power of a covariate. The paper is motivated by a study of the occurrence of drug-induced arrhythmia in beagle dogs based on electrocardiogram recordings, with the objective to evaluate the effect of potential drugs on the heartbeat irregularities. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Sammy Chebon
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, 3590, Belgium
| | - Christel Faes
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, 3590, Belgium
| | - Frank Cools
- Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Helena Geys
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, 3590, Belgium.,Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse, 2340, Belgium
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18
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Faes C, Aerts M, Geys H, Bijnens L, Ver Donck L, Lammers WJEP. GLMM approach to study the spatial and temporal evolution of spikes in the small intestine. STAT MODEL 2016. [DOI: 10.1177/1471082006071851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mixed models can be applied in a wide range of settings. Probably, they are most commonly used to handle grouping in the data. In addition, mixed models can be used for smoothing purposes as well. When dealing with non-normal data, the use of smoothing methods within the generalized linear mixed models (GLMM) framework is less familiar. We explore the use of GLMM for smoothing purposes in both spatial and longitudinal dimensions. The methodology is illustrated by analysis of spike potentials in the small intestine of different cats. Spatio-temporal models that use two-dimensional smoothing splines across the spatial dimension and random effects to account for the correlations during successive slow-waves are developed. A major advantage of the mixed-model approach is that it can handle smoothing together with grouping (or other types of correlations) in a unified model. In this way, areas with high spike incidence compared with other areas can be detected. Also, the temporal and spatial characteristics of spikes during successive slow-waves can be identified.
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Affiliation(s)
| | - Marc Aerts
- Center for Statistics, Hasselt University, Belgium
| | - Helena Geys
- Center for Statistics, Hasselt University, Belgium, Janssen
Pharmaceutica, Beerse, Belgium
| | | | | | - Wim JEP Lammers
- Department of Physiology, Faculty of Medicine and Health Sciences, UAE
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19
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Faes C, Geys H, Aerts M, Molenberghs G. Use of fractional polynomials for dose-response modelling and quantitative risk assessment in developmental toxicity studies. STAT MODEL 2016. [DOI: 10.1191/1471082x03st051oa] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Developmental toxicity studies are designed to assess the potential adverse effects of an exposure on developing fetuses. Safe dose levels can be determined using dose-response modelling. To this end, it is important to investigate the effect of misspecifying the dose-response model on the safe dose. Since classical polynomial predictors are often of poor quality, there is a clear need for alternative specifications of the predictors, such as fractional polynomials. By means of simulations, we will show how fractional polynomial predictors may resolve possible model misspecifications and may thus yield more reliable estimates of the benchmark doses.
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Affiliation(s)
- Christel Faes
- Center for Statistics, Biostatistics, Limburgs Universitair Centrum,
Diepenbeek, Belgium,
| | - Helena Geys
- Center for Statistics, Biostatistics, Limburgs Universitair Centrum,
Diepenbeek, Belgium
| | - Marc Aerts
- Center for Statistics, Biostatistics, Limburgs Universitair Centrum,
Diepenbeek, Belgium
| | - Geert Molenberghs
- Center for Statistics, Biostatistics, Limburgs Universitair Centrum,
Diepenbeek, Belgium
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20
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Abstract
Finite mixture models have been used to model population heterogeneity and to relax distributional assumptions. These models are also convenient tools for clustering and classification of complex data such as, for example, repeated-measurements data. The performance of model-based clustering algorithms is sensitive to influential and outlying observations. Methods for identifying outliers in a finite mixture model have been described in the literature. Approaches to identify influential observations are less common. In this paper, we apply local-influence diagnostics to a finite mixture model with known number of components. The methodology is illustrated on real-life data.
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Affiliation(s)
| | - Geert Molenberghs
- 1 I-BioStat, Universiteit Hasselt, Hasselt, Belgium.,2 I-Biostat, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Geert Verbeke
- 1 I-BioStat, Universiteit Hasselt, Hasselt, Belgium.,2 I-Biostat, Katholieke Universiteit Leuven, Leuven, Belgium
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21
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Abstract
Latent growth modeling approaches, such as growth mixture models, are used to identify meaningful groups or classes of individuals in a larger heterogeneous population. But when applied to multivariate repeated measures computational problems are likely, due to the high dimension of the joint distribution of the random effects in these mixed-effects models. This article proposes a cluster algorithm for multivariate repeated data, using pseudo-likelihood and ideas based on k-means clustering, to reveal homogenous subgroups. The algorithm was demonstrated on an electro-encephalogram dataset set quantifying the effect of psychoactive compounds on the brain activity in rats.
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Affiliation(s)
| | - Geert Molenberghs
- a I-BioStat , Universiteit Hasselt , Diepenbeek , Belgium.,b I-BioStat , Katholieke Universiteit Leuven , Leuven , Belgium
| | - Pim Drinkenburg
- c Janssen Research & Development , Division of Janssen Pharmaceutica NV , Beerse , Belgium
| | - Helena Geys
- a I-BioStat , Universiteit Hasselt , Diepenbeek , Belgium.,c Janssen Research & Development , Division of Janssen Pharmaceutica NV , Beerse , Belgium
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22
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Chebon S, Faes C, Smedt AD, Geys H. Flexible modelling of simultaneously interval censored and truncated time-to-event data. Pharm Stat 2015; 14:311-21. [PMID: 25953423 DOI: 10.1002/pst.1687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/12/2015] [Accepted: 04/10/2015] [Indexed: 11/06/2022]
Abstract
This paper deals with the analysis of data from a HET-CAM(VT) experiment. From a statistical perspective, such data yield many challenges. First of all, the data are typically time-to-event like data, which are at the same time interval censored and right truncated. In addition, one has to cope with overdispersion as well as clustering. Traditional analysis approaches ignore overdispersion and clustering and summarize the data into a continuous score that can be analysed using simple linear models. In this paper, a novel combined frailty model is developed that simultaneously captures all of the aforementioned statistical challenges posed by the data.
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Affiliation(s)
- Sammy Chebon
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Christel Faes
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Ann De Smedt
- Janssen Pharmaceutica NV., Turnhoutseweg 30, Beerse, Belgium
| | - Helena Geys
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.,Janssen Pharmaceutica NV., Turnhoutseweg 30, Beerse, Belgium
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23
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Teuns G, Geys H, Geuens S, Meert T. Predictability of preclinical drug abuse liability testing procedures: Four validation studies with methylphenidate. J Pharmacol Toxicol Methods 2014. [DOI: 10.1016/j.vascn.2014.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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De Jonghe S, Proctor J, Vinken P, Feyen B, Wynant I, Marien D, Geys H, Mamidi RNVS, Johnson MD. Carcinogenicity in rats of the SGLT2 inhibitor canagliflozin. Chem Biol Interact 2014; 224:1-12. [PMID: 25289773 DOI: 10.1016/j.cbi.2014.09.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/29/2014] [Accepted: 09/23/2014] [Indexed: 12/20/2022]
Abstract
The carcinogenicity potential of canagliflozin, an inhibitor of SGLT2, was evaluated in a 2-year rat study (10, 30, and 100 mg/kg). Rats showed an increase in pheochromocytomas, renal tubular tumors, and testicular Leydig cell tumors. Systemic exposure multiples at the highest dose relative to the maximum clinical dose were 12- to 21-fold. Pheochromocytomas and renal tubular tumors were noted in both sexes at 100 mg/kg. Leydig cell tumors were observed in males in all dose groups and were associated with increased luteinizing hormone levels. Hyperplasia was increased in the adrenal medulla at 100 mg/kg, but only a limited increase in simple tubular hyperplasia was observed in the kidney of males at 100 mg/kg. Hyperostosis occurred and was accompanied by substantial effects on calcium metabolism, including increased urinary calcium excretion and decreased levels of calcium regulating hormones (1,25-dihydroxyvitamin D and parathyroid hormone). A separate study with radiolabeled calcium confirmed that increased urinary calcium excretion was mediated via increased calcium absorption from the gastrointestinal tract. It was hypothesized that, at high doses, canagliflozin might have inhibited glucose absorption in the intestine via SGLT1 inhibition that resulted in glucose malabsorption, which increased calcium absorption by stimulating colonic glucose fermentation and reducing intestinal pH. Pheochromocytomas and adrenal medullary hyperplasia were attributed to altered calcium homeostasis, which have a known relationship in the rat. In conclusion, Leydig cell tumors were associated with increased luteinizing hormone levels and pheochromocytomas were most likely related to glucose malabsorption and altered calcium homeostasis. Renal tubular tumors may also have been linked to glucose malabsorption.
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Affiliation(s)
- Sandra De Jonghe
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Jim Proctor
- Janssen Research & Development, LLC, 1000 Route 202 South, Raritan, NJ 08869, United States
| | - Petra Vinken
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Bianca Feyen
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Inneke Wynant
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Dirk Marien
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Helena Geys
- Janssen Research & Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Rao N V S Mamidi
- Janssen Research & Development, LLC, 1000 Route 202 South, Raritan, NJ 08869, United States
| | - Mark D Johnson
- Janssen Research & Development, LLC, 1000 Route 202 South, Raritan, NJ 08869, United States.
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25
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Ewart L, Aylott M, Deurinck M, Engwall M, Gallacher DJ, Geys H, Jarvis P, Ju H, Leishman D, Leong L, McMahon N, Mead A, Milliken P, Suter W, Teisman A, Van Ammel K, Vargas HM, Wallis R, Valentin JP. The Concordance between Nonclinical and Phase I Clinical Cardiovascular Assessment from a Cross-Company Data Sharing Initiative. Toxicol Sci 2014; 142:427-35. [DOI: 10.1093/toxsci/kfu198] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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De Schaepdrijver L, Delille P, Geys H, Boehringer-Shahidi C, Vanhove C. In vivo longitudinal micro-CT study of bent long limb bones in rat offspring. Reprod Toxicol 2014; 46:91-7. [DOI: 10.1016/j.reprotox.2014.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/24/2014] [Accepted: 03/04/2014] [Indexed: 01/08/2023]
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27
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Cools F, Dhuyvetter D, Vanlommel A, Janssens S, Borghys H, Geys H, Gallacher DJ. A translational assessment of preclinical versus clinical tools for the measurement of cardiac contractility: Comparison of LV dP/dtmax with echocardiography in telemetry implanted beagle dogs. J Pharmacol Toxicol Methods 2014; 69:17-23. [DOI: 10.1016/j.vascn.2013.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/02/2013] [Accepted: 10/08/2013] [Indexed: 11/29/2022]
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28
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Affiliation(s)
| | - Christel Faes
- a I-BioStat , Universiteit Hasselt , Diepenbeek , Belgium
| | - Geert Molenberghs
- a I-BioStat , Universiteit Hasselt , Diepenbeek , Belgium
- b I-BioStat , Katholieke Universiteit Leuven , Leuven , Belgium
| | | | - Helena Geys
- a I-BioStat , Universiteit Hasselt , Diepenbeek , Belgium
- c Janssen Pharmaceutica , Beerse , Belgium
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29
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Ghebretinsae AH, Faes C, Molenberghs G, Geys H, Van der Leede BJ. Joint modeling of hierarchically clustered and overdispersed non-gaussian continuous outcomes for comet assay data. Pharm Stat 2012; 11:449-55. [DOI: 10.1002/pst.1533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Christel Faes
- I-BioStat; Universiteit Hasselt; B-3590 Diepenbeek Belgium
| | - Geert Molenberghs
- I-BioStat; Universiteit Hasselt; B-3590 Diepenbeek Belgium
- I-BioStat; Katholieke Universiteit Leuven; B-3000 Leuven Belgium
| | - Helena Geys
- I-BioStat; Universiteit Hasselt; B-3590 Diepenbeek Belgium
- Janssen Pharmaceutica; Turnhoutseweg 40 B-2430 Beerse Belgium
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30
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Kimpe A, Moesen E, Geys H, Peeters T. Comparison of the cardiovascular profile of sotalol in two conscious dog models, the sling and telemetry model. J Pharmacol Toxicol Methods 2012. [DOI: 10.1016/j.vascn.2012.08.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Bijnens L, Van den Bergh A, Sinha V, Geys H, Molenberghs G, Verbeke T, Kasim A, Straetemans R, De Ridder F, Balmain-Mackie C. A Meta-Analytical Framework to Include Historical Data in Allometric Scaling. Stat Biopharm Res 2012. [DOI: 10.1080/19466315.2012.707493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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Affiliation(s)
- Christel Faes
- Christel Faes is Postdoctoral Fellow , Helena Geys is Professor, Geert Molenberghs is Professor, and Marc Aerts is Professor, Center for Statistics, Hasselt University, Diepenbeek, Belgium. Carmen Cadarso-Suárez is Professor, Department of Statistics and Operations Research, and Carlos Acuña is Professor, Department of Physiology, University Hospital, University of Santiago de Compostela, Spain. Mónica Cano is Postdoctoral Fellow, Department of Psychology, University of Connecticut, Storrs, CT 06269
| | - Helena Geys
- Christel Faes is Postdoctoral Fellow , Helena Geys is Professor, Geert Molenberghs is Professor, and Marc Aerts is Professor, Center for Statistics, Hasselt University, Diepenbeek, Belgium. Carmen Cadarso-Suárez is Professor, Department of Statistics and Operations Research, and Carlos Acuña is Professor, Department of Physiology, University Hospital, University of Santiago de Compostela, Spain. Mónica Cano is Postdoctoral Fellow, Department of Psychology, University of Connecticut, Storrs, CT 06269
| | - Geert Molenberghs
- Christel Faes is Postdoctoral Fellow , Helena Geys is Professor, Geert Molenberghs is Professor, and Marc Aerts is Professor, Center for Statistics, Hasselt University, Diepenbeek, Belgium. Carmen Cadarso-Suárez is Professor, Department of Statistics and Operations Research, and Carlos Acuña is Professor, Department of Physiology, University Hospital, University of Santiago de Compostela, Spain. Mónica Cano is Postdoctoral Fellow, Department of Psychology, University of Connecticut, Storrs, CT 06269
| | - Marc Aerts
- Christel Faes is Postdoctoral Fellow , Helena Geys is Professor, Geert Molenberghs is Professor, and Marc Aerts is Professor, Center for Statistics, Hasselt University, Diepenbeek, Belgium. Carmen Cadarso-Suárez is Professor, Department of Statistics and Operations Research, and Carlos Acuña is Professor, Department of Physiology, University Hospital, University of Santiago de Compostela, Spain. Mónica Cano is Postdoctoral Fellow, Department of Psychology, University of Connecticut, Storrs, CT 06269
| | - Carmen Cadarso-Suárez
- Christel Faes is Postdoctoral Fellow , Helena Geys is Professor, Geert Molenberghs is Professor, and Marc Aerts is Professor, Center for Statistics, Hasselt University, Diepenbeek, Belgium. Carmen Cadarso-Suárez is Professor, Department of Statistics and Operations Research, and Carlos Acuña is Professor, Department of Physiology, University Hospital, University of Santiago de Compostela, Spain. Mónica Cano is Postdoctoral Fellow, Department of Psychology, University of Connecticut, Storrs, CT 06269
| | - Carlos Acuña
- Christel Faes is Postdoctoral Fellow , Helena Geys is Professor, Geert Molenberghs is Professor, and Marc Aerts is Professor, Center for Statistics, Hasselt University, Diepenbeek, Belgium. Carmen Cadarso-Suárez is Professor, Department of Statistics and Operations Research, and Carlos Acuña is Professor, Department of Physiology, University Hospital, University of Santiago de Compostela, Spain. Mónica Cano is Postdoctoral Fellow, Department of Psychology, University of Connecticut, Storrs, CT 06269
| | - Mónica Cano
- Christel Faes is Postdoctoral Fellow , Helena Geys is Professor, Geert Molenberghs is Professor, and Marc Aerts is Professor, Center for Statistics, Hasselt University, Diepenbeek, Belgium. Carmen Cadarso-Suárez is Professor, Department of Statistics and Operations Research, and Carlos Acuña is Professor, Department of Physiology, University Hospital, University of Santiago de Compostela, Spain. Mónica Cano is Postdoctoral Fellow, Department of Psychology, University of Connecticut, Storrs, CT 06269
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33
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Jarvis P, Saul J, Aylott M, Bate S, Geys H, Sherington J. An assessment of the statistical methods used to analyse toxicology studies. Pharm Stat 2011; 10:477-84. [DOI: 10.1002/pst.527] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Philip Jarvis
- Discovery Statistics; AstraZeneca R&D; Alderley Park Macclesfield Cheshire UK
| | - Jim Saul
- Covance Laboratories; Otley Road Harrogate UK
| | - Mike Aylott
- Statistical Sciences Europe; GlaxoSmithKline; Harlow UK
| | - Simon Bate
- Huntingdon Life Sciences; Huntingdon Cambridgeshire UK
| | - Helena Geys
- Janssen Pharmaceutica; Johnson and Johnson; Beerse Belgium
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34
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Abstract
In 2010, the Statisticians in the Pharmaceutical Industry (PSI) Toxicology Special Interest Group met to discuss the design and analysis of the Comet assay. The Comet assay is one potential component of the package of safety studies required by regulatory bodies. As these studies usually involve a three-way nested experimental design and as the distribution of the measured response is usually either lognormal or lognormal plus a point mass at zero, the analysis is not straightforward. This has led to many different types of analysis being proposed in the literature, with several different methods applied within the pharmaceutical industry itself. This article summarises the PSI Toxicology Group's discussions and recommendations around these issues.
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Affiliation(s)
- Jonathan Bright
- Discovery Statistics, AstraZeneca R&D, Macclesfield, Cheshire, UK.
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35
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Abstract
The reliability of multi-item scales has received a lot of attention in the psychometric literature, where a myriad of measures like the Cronbach's α or the Spearman-Brown formula have been proposed. Most of these measures, however, are based on very restrictive models that apply only to unidimensional instruments. In this article, we introduce two measures to quantify the reliability of multi-item scales based on a more general model. We show that they capture two different aspects of the reliability problem and satisfy a minimum set of intuitive properties. The relevance and complementary value of the measures is studied and earlier approaches are placed in a broader theoretical framework. Finally, we apply them to investigate the reliability of the Positive and Negative Syndrome Scale, a rating scale for the assessment of the severity of schizophrenia.
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Affiliation(s)
- Ariel Alonso
- Center for Statistics, Hasselt University, Diepenbeek, Belgium.
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36
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Abstract
The Morris water maze, developed by Morris (J Neurosci Methods 1984: 11: 47-60), is a behavioral experiment designed to test the spatial memory. When repeating the experiment several times, the changes in time (latency) and distance (path) taken to reach the platform are indicators for the learning and memory abilities of the rat. In juvenile toxicity studies, it is of interest to test whether dosing juvenile rats with some compound of interest has an effect on its learning ability. The traditional analysis uses non-parametric tests to check for a possible dose-effect. However, due to the many tests performed, this approach lacks power. Here, an alternative method is proposed, accounting for the longitudinal design of the study, the right-censoring of observations when animals did not find the platform and the correlation between the time and distance taken to reach the platform.
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Affiliation(s)
- Christel Faes
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Universiteit Hasseld and Katholieke Universiteit, Leuven, Belgium.
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37
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Vangeneugden T, Molenberghs G, Laenen A, Geys H, Beunckens C, Sotto C. Marginal Correlation in Longitudinal Binary Data Based on Generalized Linear Mixed Models. COMMUN STAT-THEOR M 2010. [DOI: 10.1080/03610920903249568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Tilahun A, Lin D, Shkedy Z, Geys H, Alonso A, Peeters P, Talloen W, Drinkenburg W, Göhlmann H, Gorden E, Bijnens L, Molenberghs G. Genomic Biomarkers for Depression: Feature-Specific and Joint Biomarkers. Stat Biopharm Res 2010. [DOI: 10.1198/sbr.2009.08091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Wouters K, Abrahantes JC, Molenberghs G, Geys H, Ahnaou A, Drinkenburg WHIM, Bijnens L. Correction for Model Selection Bias Using a Modified Model Averaging Approach for Supervised Learning Methods Applied to EEG Experiments. J Biopharm Stat 2010; 20:768-86. [DOI: 10.1080/10543401003618744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Kristien Wouters
- a Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Universiteit Hasselt , Diepenbeek, Belgium
| | - José Cortiñas Abrahantes
- a Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Universiteit Hasselt , Diepenbeek, Belgium
| | - Geert Molenberghs
- a Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Universiteit Hasselt , Diepenbeek, Belgium
| | - Helena Geys
- a Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Universiteit Hasselt , Diepenbeek, Belgium
- b Johnson & Johnson Pharmaceutical Research and Development , Beerse, Belgium
| | - Abdellah Ahnaou
- b Johnson & Johnson Pharmaceutical Research and Development , Beerse, Belgium
| | | | - Luc Bijnens
- b Johnson & Johnson Pharmaceutical Research and Development , Beerse, Belgium
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40
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Torremans A, Ahnaou A, Van Hemelrijck A, Straetemans R, Geys H, Vanhoof G, Meert TF, Drinkenburg WH. Effects of phosphodiesterase 10 inhibition on striatal cyclic AMP and peripheral physiology in rats. Acta Neurobiol Exp (Wars) 2010; 70:13-9. [PMID: 20407482 DOI: 10.55782/ane-2010-1769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Phosphodiesterases (PDEs) form a family of enzymes involved in the hydrolysis of cyclic adenosine and guanosine monophosphate (cAMP and cGMP). PDE10A is a member of this family that is almost exclusively expressed in the striatum. Increasing cAMP/cGMP levels via inhibition of PDE10A is under consideration as a novel therapeutic avenue in the discovery of antipsychotics. Papaverine has been used as a pharmacological tool to establish the possible clinical use of PDE10A inhibitors as antipsychotics. Papaverine is known to increase cAMP levels in striatum and to decrease blood pressure, body temperature and locomotor activity after systemic administration. In this study, the effects of papaverine are compared to those of a more specific PDE10A inhibitor MP10. Papaverine raised striatal cAMP levels with hypothermia, hypoactivity and decreased cardiovascular responses. The more selective MP10 had significantly less effects on body temperature and cardiovascular functions, but reduced locomotor activity to a similar extend as papaverine.
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Affiliation(s)
- An Torremans
- Johnson & Johnson Pharmaceutical Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
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Maringwa JT, Geys H, Shkedy Z, Faes C, Molenberghs G, Aerts M, Van Ammel K, Teisman A, Bijnens L. Analysis of cross-over designs with serial correlation within periods using semi-parametric mixed models. Stat Med 2009; 27:6009-33. [PMID: 18613252 DOI: 10.1002/sim.3363] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The use of semi-parametric mixed models has proven useful in a wide variety of settings. Here, we focus on the application of the methodology in the particular case of a cross-over design with relatively long sequences of repeated measurements within each treatment period and for each subject. Other than an overall measure of the difference between each one of the experimental groups and the control group, specific time point comparisons may also be of interest. To that effect, we propose the use of flexible semi-parametric mixed models, enabling the construction of simulation-based simultaneous confidence bands. The bands take into account both between- and within-subject variabilities, while simultaneously correcting for multiple time point comparisons. Owing to the relatively long sequences of measurements per subject, the presence of serially correlated errors is anticipated and investigated. We illustrate how several formulations of semi-parametric mixed models can be fitted and the construction of simulation-based simultaneous confidence bands using SAS PROC MIXED.
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Affiliation(s)
- John T Maringwa
- Center for Statistics, Hasselt University, BE3590 Diepenbeek, Belgium.
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Maringwa JT, Faes C, Geys H, Molenberghs G, Cadarso-Suárez C, Pardo-Vázquez JL, Leborán V, Acunña C. Application of penalized splines in analyzing neuronal data. Biom J 2009; 51:203-16. [PMID: 19197962 DOI: 10.1002/bimj.200810501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neuron experiments produce high-dimensional data structures. Therefore, application of smoothing techniques in the analysis of neuronal data from electrophysiological experiments has received considerable attention of late. We investigate the use of penalized splines in the analysis of neuronal data. This is first illustrated when interested in the temporal trend of a single neuron. An approach to investigate the maximal firing rate, based on the penalizedspline model is proposed. Determination of the time of maximal firing rate is based on non-linear optimization of the objective function with the corresponding confidence intervals constructed based on the first-order derivative function. To distinguish between the curves from different experimental conditions in a moment-by-moment sense, bias adjusted simulation-based simultaneous confidence bands leading to global inference in the time domain are constructed. The bands are an extension of the approach proposed by Ruppert et al. (2003). These methods are in a second step extended towards the analysis of a population of neurons via a marginal or population-averaged model.
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Affiliation(s)
- John T Maringwa
- Center for Statistics, Hasselt University, Diepenbeek, Belgium.
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Faes C, Aerts M, Molenberghs G, Geys H, Teuns G, Bijnens L. A high-dimensional joint model for longitudinal outcomes of different nature. Stat Med 2009; 27:4408-27. [PMID: 18551509 DOI: 10.1002/sim.3314] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In repeated dose-toxicity studies, many outcomes are repeatedly measured on the same animal to study the toxicity of a compound of interest. This is only one example in which one is confronted with the analysis of many outcomes, possibly of a different type. Probably the most common situation is that of an amalgamation of continuous and categorical outcomes. A possible approach towards the joint analysis of two longitudinal outcomes of a different nature is the use of random-effects models (Models for Discrete Longitudinal Data. Springer Series in Statistics. Springer: New York, 2005). Although a random-effects model can easily be extended to jointly model many outcomes of a different nature, computational problems arise as the number of outcomes increases. To avoid maximization of the full likelihood expression, Fieuws and Verbeke (Biometrics 2006; 62:424-431) proposed a pairwise modeling strategy in which all possible pairs are modeled separately, using a mixed model, yielding several different estimates for the same parameters. These latter estimates are then combined into a single set of estimates. Also inference, based on pseudo-likelihood principles, is indirectly derived from the separate analyses. In this paper, we extend the approach of Fieuws and Verbeke (Biometrics 2006; 62:424-431) in two ways: the method is applied to different types of outcomes and the full pseudo-likelihood expression is maximized at once, leading directly to unique estimates as well as direct application of pseudo-likelihood inference. This is very appealing when interested in hypothesis testing. The method is applied to data from a repeated dose-toxicity study designed for the evaluation of the neurofunctional effects of a psychotrophic drug. The relative merits of both methods are discussed.
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Affiliation(s)
- Christel Faes
- Center for Statistics, Hasselt University, Agoralaan, Diepenbeek, Belgium.
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Tilahun A, Maringwa JT, Geys H, Alonso A, Raeymaekers L, Molenberghs G, Kieboom GVD, Drinkenburg P, Bijnens L. Investigating Association Between Behavior, Corticosterone, Heart Rate, and Blood Pressure in Rats Using Surrogate Marker Evaluation Methodology. J Biopharm Stat 2009; 19:133-49. [DOI: 10.1080/10543400802527924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Abel Tilahun
- a Center for Statistics , Hasselt University , Diepenbeek, Belgium
| | - John T. Maringwa
- a Center for Statistics , Hasselt University , Diepenbeek, Belgium
| | - Helena Geys
- b Johnson and Johnson Pharmaceutical Research and Development , A Division of Janssen Pharmaceutica , Beerse, Belgium
| | - Ariel Alonso
- a Center for Statistics , Hasselt University , Diepenbeek, Belgium
| | - Leen Raeymaekers
- b Johnson and Johnson Pharmaceutical Research and Development , A Division of Janssen Pharmaceutica , Beerse, Belgium
| | | | - Gerd Van Den Kieboom
- b Johnson and Johnson Pharmaceutical Research and Development , A Division of Janssen Pharmaceutica , Beerse, Belgium
| | - Pim Drinkenburg
- b Johnson and Johnson Pharmaceutical Research and Development , A Division of Janssen Pharmaceutica , Beerse, Belgium
| | - Luc Bijnens
- b Johnson and Johnson Pharmaceutical Research and Development , A Division of Janssen Pharmaceutica , Beerse, Belgium
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Maringwa JT, Geys H, Shkedy Z, Faes C, Molenberghs G, Aerts M, Ammel KV, Teisman A, Bijnens L. Application of Semiparametric Mixed Models and Simultaneous Confidence Bands in a Cardiovascular Safety Experiment with Longitudinal Data. J Biopharm Stat 2008; 18:1043-62. [DOI: 10.1080/10543400802368881] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- John T. Maringwa
- a Center for Statistics , Universiteit Hasselt , Diepenbeek, Belgium
| | - Helena Geys
- a Center for Statistics , Universiteit Hasselt , Diepenbeek, Belgium
- b Johnson and Johnson Pharmaceutical Research and Development , Beerse, Belgium
| | - Ziv Shkedy
- a Center for Statistics , Universiteit Hasselt , Diepenbeek, Belgium
| | - Christel Faes
- a Center for Statistics , Universiteit Hasselt , Diepenbeek, Belgium
| | - Geert Molenberghs
- a Center for Statistics , Universiteit Hasselt , Diepenbeek, Belgium
| | - Marc Aerts
- a Center for Statistics , Universiteit Hasselt , Diepenbeek, Belgium
| | - Karel Van Ammel
- b Johnson and Johnson Pharmaceutical Research and Development , Beerse, Belgium
| | - Ard Teisman
- b Johnson and Johnson Pharmaceutical Research and Development , Beerse, Belgium
| | - Luc Bijnens
- b Johnson and Johnson Pharmaceutical Research and Development , Beerse, Belgium
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Ahnaou A, Dautzenberg FM, Geys H, Imogai H, Gibelin A, Moechars D, Steckler T, Drinkenburg WHIM. Modulation of group II metabotropic glutamate receptor (mGlu2) elicits common changes in rat and mice sleep-wake architecture. Eur J Pharmacol 2008; 603:62-72. [PMID: 19046965 DOI: 10.1016/j.ejphar.2008.11.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 10/07/2008] [Accepted: 11/10/2008] [Indexed: 11/16/2022]
Abstract
Compiling pharmacological evidence implicates metabotropic glutamate mGlu(2) receptors in the regulation of emotional states and suggests positive modulators as a novel therapeutic approach of Anxiety/Depression and Schizophrenia. Here, we investigated subcutaneous effects of the metabotropic glutamate mGlu(2/3) agonist (LY354740) on sleep-wake architecture in rat. To confirm the specific effects on rapid eye movement (REM) sleep were mediated via metabotropic glutamate mGlu(2) receptors, we characterized the sleep-wake cycles in metabotropic glutamate mGlu(2) receptor deficient mice (mGlu(2)R(-/-)) and their arousal response to LY354740. We furthermore examined effects on sleep behavior in rats of the positive allosteric modulator, biphenyl-indanone A (BINA) alone and in combination with LY354740 at sub-effective doses. LY354740 (1, 3 and 10 mg/kg) dose-dependently suppressed REM sleep and prolonged its onset latency. Metabotropic glutamate mGlu(2)R(-/-) and their wild type (WT) littermates exhibited similar spontaneous sleep-wake phenotype, while LY354740 (10 mg/kg) significantly affected REM sleep variables in WT but not in the mutant. In rats, BINA (1, 3, 10, 20, 40 mg/kg) dose-dependently suppressed REM sleep, lengthened its onset latency and slightly enhanced passive waking. Additionally, combined treatment elicited a synergistic action on REM sleep variables. Our findings show common changes of REM sleep variables following modulation of metabotropic glutamate mGlu(2) receptor and support an active role of this receptor in the regulation of REM sleep. The synergistic action of BINA on LY354740's effects on sleep pattern implies that positive modulators would tune the endogenous glutamate tone suggesting potential benefit in the treatment of psychiatric disorders, in which REM sleep overdrive is manifested.
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Affiliation(s)
- Abdellah Ahnaou
- Dept. Neuroscience, A Division of Janssen Pharmaceutica NV, Johnson & Johnson Pharmaceutical Research and Development, RED Europe, Beerse, Belgium.
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Vangeneugden T, Molenberghs G, Laenen A, Alonso A, Geys H. Generalizability in NonGaussian Longitudinal Clinical Trial Data Based on Generalized Linear Mixed Models. J Biopharm Stat 2008; 18:691-712. [DOI: 10.1080/10543400802071386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Tony Vangeneugden
- a Tibotec, Johnson & Johnson , Mechelen, Belgium
- b Center for Statistics, Hasselt University , Diepenbeek, Belgium
| | | | | | - Ariel Alonso
- b Center for Statistics, Hasselt University , Diepenbeek, Belgium
| | - Helena Geys
- b Center for Statistics, Hasselt University , Diepenbeek, Belgium
- c Janssen Pharmaceutica, Johnson & Johnson , Beerse, Belgium
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Alonso A, Molenberghs G, Burzykowski T, Renard D, Geys H, Shkedy Z, Tibaldi F, Abrahantes JC, Buyse M. The authors replied as follows:. Biometrics 2007. [DOI: 10.1111/j.1541-0420.2007.00852_2.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abrahantes JC, Aerts M, van Everbroeck B, Saegerman C, Berkvens D, Geys H, Mintiens K, Roels S, Cras P. Classification of sporadic Creutzfeldt-Jakob disease based on clinical and neuropathological characteristics. Eur J Epidemiol 2007; 22:457-65. [PMID: 17587185 DOI: 10.1007/s10654-007-9146-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Accepted: 05/27/2007] [Indexed: 10/23/2022]
Abstract
Creutzfeldt-Jakob disease (CJD) is a rare and fatal neurodegenerative disease of unknown cause. Patients are usually aged between 50 and 75 and typical clinical features include rapidly progressive dementia associated with myoclonus and a characteristic electroencephalographic pattern. Neuropathological examination reveals cortical spongiform change, hence the term 'spongiform encephalopathy'. Several statistical techniques were applied to classify patients with sporadic CJD (sCJD), based on clinical and neuropathological investigation. We focus on the classification of neuropathologically confirmed sCJD patients. In order to obtain a classification rule that correctly classifies this type of patients and at the same time controls the overall error rate, we apply several classification techniques, which in general, produce comparable results. The boosting method produces the best results and the variable 14-3-3 protein in cerebrospinal fluid plays the most important role in the prediction of neuropathologically confirmed sCJD.
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Marringwa JT, Faes C, Aerts M, Geys H, Teuns G, Van Den Poel B, Bijnens L. On the Use of Historical Control Data in Pre-Clinical Safety Studies. J Biopharm Stat 2007; 17:493-509. [PMID: 17479396 DOI: 10.1080/10543400701216355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A number of methods to formally incorporate historical control information in pre-clinical safety evaluation studies have been proposed in literature. However, it remains unclear when one should use historical data. Focusing on the logistic-normal model, we investigate situations where historical studies may prove to be useful. Aspects of estimation (precision and bias) and testing (power) for treatment effect are investigated under different conditions such as the number of historical control studies, the degree of homogeneity amongst them, the level of treatment effect and different control rates. The possibility to use a selected subset of historical control studies is also explored.
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Affiliation(s)
- J T Marringwa
- Center for Statistics, Universiteit Hasselt, Diepenbeek, Belgium.
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