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Kehoe K, Morden E, Zinyakatira N, Heekes A, Jones HE, Walter SR, Jacobs T, Murray J, Buys H, Redaniel MT, Davies MA. Lower respiratory tract infection admissions and deaths among children under 5 years in public sector facilities in the Western Cape Province, South Africa, before and during the COVID-19 pandemic (2019 - 2021). S Afr Med J 2024; 114:e1560. [PMID: 38525574 DOI: 10.7196/samj.2024.v114i3.1560] [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] [Received: 09/22/2023] [Accepted: 11/27/2023] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic resulted in the implementation of strict public health and social measures (PHSMs) (including mobility restrictions, social distancing, mask-wearing and hand hygiene), limitations on non-essential healthcare services, and public fear of COVID-19 infection, all of which potentially affected transmission and healthcare use for other diseases such as lower respiratory tract infections (LRTIs). OBJECTIVE To determine changes in LRTI hospital admissions and in-facility mortality in children aged <5 years in the Western Cape Province during the pandemic. METHODS We conducted a retrospective analysis of LRTI admissions and in-facility deaths from January 2019 to November 2021. We estimated changes in rates and trends of LRTI admissions during the pandemic compared with pre-pandemic period using interrupted time series analysis, adjusting for key characteristics. RESULTS There were 36 277 children admitted for LRTIs during the study period, of whom 58% were male and 51% were aged 28 days - 1 year. COVID-19 restrictions were associated with a 13% step reduction in LRTI admissions compared with the pre-COVID-19 period (incidence rate ratio (IRR) 0.87, 95% confidence interval (CI)) 0.80 - 0.94). The average LRTI admission trend increased on average by 2% per month during the pandemic (IRR 1.02, 95% CI 1.02 - 1.04). CONCLUSIONS The COVID-19 surges and their associated measures were linked to declining LRTI admissions and in-facility deaths, likely driven by a combination of reduced infectious disease transmission and reduced use of healthcare services, with effects diminishing over time. These findings may inform future pandemic response policies.
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Affiliation(s)
- K Kehoe
- Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape Town, South Africa; Population Health Sciences, Bristol Medical School, University of Bristol, UK; Health Intelligence Directorate, Western Cape Government Health and Wellness, South Africa.
| | - E Morden
- Health Intelligence Directorate, Western Cape Government Health and Wellness, South Africa; Division of Public Health Medicine, School of Public Health, University of Cape Town, South Africa.
| | - N Zinyakatira
- Health Intelligence Directorate, Western Cape Government Health and Wellness, South Africa; Division of Public Health Medicine, School of Public Health, University of Cape Town, South Africa.
| | - A Heekes
- Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape Town, South Africa; Health Intelligence Directorate, Western Cape Government Health and Wellness, South Africa.
| | - H E Jones
- Population Health Sciences, Bristol Medical School, University of Bristol, UK.
| | - S R Walter
- Population Health Sciences, Bristol Medical School, University of Bristol, UK; National Institute for Health and Care Research Applied Research Collaboration West (NIHR ARC West) at University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK.
| | - T Jacobs
- Health Intelligence Directorate, Western Cape Government Health and Wellness, South Africa.
| | - J Murray
- Department of Paediatrics & Neonatology, Paarl Hospital, Western Cape Government Health and Wellness, Paarl, South Africa.
| | - H Buys
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa; Red Cross War Memorial Children's Hospital, Western Cape Government Health and Wellness, Cape Town, South Africa.
| | - M T Redaniel
- Population Health Sciences, Bristol Medical School, University of Bristol, UK; National Institute for Health and Care Research Applied Research Collaboration West (NIHR ARC West) at University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK.
| | - M-A Davies
- Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape Town, South Africa; Health Intelligence Directorate, Western Cape Government Health and Wellness, South Africa.
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Van Den Berghe T, Babin D, Chen M, Callens M, Brack D, Maes H, Lievens J, Lammens M, Van Sumere M, Morbée L, Hautekeete S, Schatteman S, Jacobs T, Thooft WJ, Herregods N, Huysse W, Jaremko JL, Lambert R, Maksymowych W, Laloo F, Baraliakos X, De Craemer AS, Carron P, Van den Bosch F, Elewaut D, Jans L. Neural network algorithm for detection of erosions and ankylosis on CT of the sacroiliac joints: multicentre development and validation of diagnostic accuracy. Eur Radiol 2023; 33:8310-8323. [PMID: 37219619 DOI: 10.1007/s00330-023-09704-y] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/03/2023] [Accepted: 03/25/2023] [Indexed: 05/24/2023]
Abstract
OBJECTIVES To evaluate the feasibility and diagnostic accuracy of a deep learning network for detection of structural lesions of sacroiliitis on multicentre pelvic CT scans. METHODS Pelvic CT scans of 145 patients (81 female, 121 Ghent University/24 Alberta University, 18-87 years old, mean 40 ± 13 years, 2005-2021) with a clinical suspicion of sacroiliitis were retrospectively included. After manual sacroiliac joint (SIJ) segmentation and structural lesion annotation, a U-Net for SIJ segmentation and two separate convolutional neural networks (CNN) for erosion and ankylosis detection were trained. In-training validation and tenfold validation testing (U-Net-n = 10 × 58; CNN-n = 10 × 29) on a test dataset were performed to assess performance on a slice-by-slice and patient level (dice coefficient/accuracy/sensitivity/specificity/positive and negative predictive value/ROC AUC). Patient-level optimisation was applied to increase the performance regarding predefined statistical metrics. Gradient-weighted class activation mapping (Grad-CAM++) heatmap explainability analysis highlighted image parts with statistically important regions for algorithmic decisions. RESULTS Regarding SIJ segmentation, a dice coefficient of 0.75 was obtained in the test dataset. For slice-by-slice structural lesion detection, a sensitivity/specificity/ROC AUC of 95%/89%/0.92 and 93%/91%/0.91 were obtained in the test dataset for erosion and ankylosis detection, respectively. For patient-level lesion detection after pipeline optimisation for predefined statistical metrics, a sensitivity/specificity of 95%/85% and 82%/97% were obtained for erosion and ankylosis detection, respectively. Grad-CAM++ explainability analysis highlighted cortical edges as focus for pipeline decisions. CONCLUSIONS An optimised deep learning pipeline, including an explainability analysis, detects structural lesions of sacroiliitis on pelvic CT scans with excellent statistical performance on a slice-by-slice and patient level. CLINICAL RELEVANCE STATEMENT An optimised deep learning pipeline, including a robust explainability analysis, detects structural lesions of sacroiliitis on pelvic CT scans with excellent statistical metrics on a slice-by-slice and patient level. KEY POINTS • Structural lesions of sacroiliitis can be detected automatically in pelvic CT scans. • Both automatic segmentation and disease detection yield excellent statistical outcome metrics. • The algorithm takes decisions based on cortical edges, rendering an explainable solution.
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Affiliation(s)
- Thomas Van Den Berghe
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
| | - Danilo Babin
- Department of Telecommunication and Information Processing - Image Processing and Interpretation (TELIN-IPI), Faculty of Engineering and Architecture, Ghent University - IMEC, Sint-Pietersnieuwstraat 41, 9000, Ghent, Belgium
| | - Min Chen
- Department of Radiology, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Martijn Callens
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Denim Brack
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Helena Maes
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Jan Lievens
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Marie Lammens
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Maxime Van Sumere
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Lieve Morbée
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Simon Hautekeete
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Stijn Schatteman
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Tom Jacobs
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Willem-Jan Thooft
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Nele Herregods
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Wouter Huysse
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Jacob L Jaremko
- Department of Radiology and Diagnostic Imaging and Rheumatology, University of Alberta, 8440 122 Street NW, Edmonton, Alberta, T6G 2B7, Canada
| | - Robert Lambert
- Department of Radiology and Diagnostic Imaging and Rheumatology, University of Alberta, 8440 122 Street NW, Edmonton, Alberta, T6G 2B7, Canada
| | - Walter Maksymowych
- Department of Radiology and Diagnostic Imaging and Rheumatology, University of Alberta, 8440 122 Street NW, Edmonton, Alberta, T6G 2B7, Canada
| | - Frederiek Laloo
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Xenofon Baraliakos
- Rheumazentrum Ruhrgebiet Herne, Ruhr-University Bochum, Claudiusstraße 45, 44649, Herne, Germany
| | - Ann-Sophie De Craemer
- Department of Rheumatology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB) Centre for Inflammation Research (IRC), Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Philippe Carron
- Department of Rheumatology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB) Centre for Inflammation Research (IRC), Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Filip Van den Bosch
- Department of Rheumatology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB) Centre for Inflammation Research (IRC), Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Dirk Elewaut
- Department of Rheumatology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Vlaams Instituut voor Biotechnologie (VIB) Centre for Inflammation Research (IRC), Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Lennart Jans
- Department of Radiology and Medical Imaging, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
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Kehoe K, Morden E, Jacobs T, Zinyakatira N, Smith M, Heekes A, Murray J, le Roux DM, Wessels T, Richards M, Eley B, Jones HE, Redaniel MT, Davies MA. Comparison of paediatric infectious disease deaths in public sector health facilities using different data sources in the Western Cape, South Africa (2007-2021). BMC Infect Dis 2023; 23:104. [PMID: 36814192 PMCID: PMC9945739 DOI: 10.1186/s12879-023-08012-6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/17/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Routinely collected population-wide health data are often used to understand mortality trends including child mortality, as these data are often available more readily or quickly and for lower geographic levels than population-wide mortality data. However, understanding the completeness and accuracy of routine health data sources is essential for their appropriate interpretation and use. This study aims to assess the accuracy of diagnostic coding for public sector in-facility childhood (age < 5 years) infectious disease deaths (lower respiratory tract infections [LRTI], diarrhoea, meningitis, and tuberculous meningitis [TBM]) in routine hospital information systems (RHIS) through comparison with causes of death identified in a child death audit system (Child Healthcare Problem Identification Programme [Child PIP]) and the vital registration system (Death Notification [DN] Surveillance) in the Western Cape, South Africa and to calculate admission mortality rates (number of deaths in admitted patients per 1000 live births) using the best available data from all sources. METHODS The three data sources: RHIS, Child PIP, and DN Surveillance are integrated and linked by the Western Cape Provincial Health Data Centre using a unique patient identifier. We calculated the deduplicated total number of infectious disease deaths and estimated admission mortality rates using all three data sources. We determined the completeness of Child PIP and DN Surveillance in identifying deaths recorded in RHIS and the level of agreement for causes of death between data sources. RESULTS Completeness of recorded in-facility infectious disease deaths in Child PIP (23/05/2007-08/02/2021) and DN Surveillance (2010-2013) was 70% and 69% respectively. The greatest agreement in infectious causes of death were for diarrhoea and LRTI: 92% and 84% respectively between RHIS and Child PIP, and 98% and 83% respectively between RHIS and DN Surveillance. In-facility infectious disease admission mortality rates decreased significantly for the province: 1.60 (95% CI: 1.37-1.85) to 0.73 (95% CI: 0.56-0.93) deaths per 1000 live births from 2007 to 2020. CONCLUSION RHIS had accurate causes of death amongst children dying from infectious diseases, particularly for diarrhoea and LRTI, with declining in-facility admission mortality rates over time. We recommend integrating data sources to ensure the most accurate assessment of child deaths.
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Affiliation(s)
- K. Kehoe
- grid.7836.a0000 0004 1937 1151Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa ,grid.5337.20000 0004 1936 7603Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK ,Health Intelligence Directorate, Western Cape Government Health, Cape Town, South Africa
| | - E. Morden
- Health Intelligence Directorate, Western Cape Government Health, Cape Town, South Africa ,grid.7836.a0000 0004 1937 1151Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - T. Jacobs
- Health Intelligence Directorate, Western Cape Government Health, Cape Town, South Africa
| | - N. Zinyakatira
- Health Intelligence Directorate, Western Cape Government Health, Cape Town, South Africa ,grid.7836.a0000 0004 1937 1151Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - M. Smith
- grid.7836.a0000 0004 1937 1151Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa ,Health Intelligence Directorate, Western Cape Government Health, Cape Town, South Africa
| | - A. Heekes
- grid.7836.a0000 0004 1937 1151Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa ,Health Intelligence Directorate, Western Cape Government Health, Cape Town, South Africa
| | - J. Murray
- Department of Paediatrics and Neonatology, Paarl Hospital, Cape Town, South Africa
| | - D. M. le Roux
- grid.415742.10000 0001 2296 3850Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Cape Town, South Africa
| | - T. Wessels
- grid.11956.3a0000 0001 2214 904XDistrict Paediatrician Cape Town Metro East, Department of Paediatrics and Child Health, Tygerberg Hospital, Stellenbosch University, Stellenbosch, South Africa
| | - M. Richards
- grid.415742.10000 0001 2296 3850Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Cape Town, South Africa ,grid.7836.a0000 0004 1937 1151Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - B. Eley
- grid.415742.10000 0001 2296 3850Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Cape Town, South Africa ,grid.415742.10000 0001 2296 3850Paediatric Infectious Diseases Unit, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - H. E. Jones
- grid.5337.20000 0004 1936 7603Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - M. T. Redaniel
- grid.5337.20000 0004 1936 7603Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK ,grid.410421.20000 0004 0380 7336The National Institute for Health Research Applied Research Collaboration West (NIHR ARC West) at University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - M. A. Davies
- grid.7836.a0000 0004 1937 1151Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa ,Health Intelligence Directorate, Western Cape Government Health, Cape Town, South Africa ,grid.7836.a0000 0004 1937 1151Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
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Affiliation(s)
- S Lyons
- Gloucestershire Hospitals NHS Foundation Trust, Gloucester, UK
| | - L Kidd
- Gloucestershire Hospitals NHS Foundation Trust, Gloucester, UK
| | - T Jacobs
- Gloucestershire Hospitals NHS Foundation Trust, Gloucester, UK
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Heelan KA, Abbey BM, Bartee RT, Estabrooks PA, Malmkar A, Jacobs T, Hill JL. Packaging of a Pediatric Weight Management Intervention and Implementation Blueprint for Rural and Micropolitan Communities: The Nebraska CORD 3.0 Project. Child Obes 2021; 17:S62-S69. [PMID: 34569846 DOI: 10.1089/chi.2021.0171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Pediatric weight management interventions (PWMIs) have resulted in positive changes among family members and, if widely disseminated, could have an impact on pediatric weight management in rural communities. The purpose of this article is to describe a backward design approach taken to create an online packaged program and implementation blueprint for building healthy families (BHF), an effective PWMI for implementation in rural communities. The backward design process included the identification of end users: primary (facilitators to be trained through the packaged program and implementation blueprint), secondary (researchers and evaluators), terminal (caregivers and children impacted by PWMI participation), tertiary (community support organizations, funding agency promoting widespread PWMI, and payors), as well as, key outcomes for respective end user groups based on the reach, effectiveness, adoption, implementation, and maintenance (RE-AIM) framework. This process resulted in the BHF Online Training Resources and Program package and implementation blueprint that included a modular approach encompassing the interplay of training modules for program facilitators, knowledge checks to ensure mastery of program components, recruitment resources for school and clinical settings, all program materials, embedded fidelity assessments for quality assurance, and a data portal to track participant success. Next steps include preliminary product testing with potential facilitators and a type 3 effectiveness implementation trial to determine the utility of the BHF Online Training Resources and Program package with and without participation in a learning collaborative to support implementation and sustainability.
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Affiliation(s)
- Kate A Heelan
- Kinesiology and Sports Sciences Department, University of Nebraska at Kearney, Kearney, NE, USA
| | - Bryce M Abbey
- Kinesiology and Sports Sciences Department, University of Nebraska at Kearney, Kearney, NE, USA
| | - Roderick T Bartee
- Kinesiology and Sports Sciences Department, University of Nebraska at Kearney, Kearney, NE, USA
| | - Paul A Estabrooks
- Department of Health Promotion, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ali Malmkar
- Kinesiology and Sports Sciences Department, University of Nebraska at Kearney, Kearney, NE, USA
| | - Tom Jacobs
- Custom Thinking Media LLC, Eugene, OR, USA
| | - Jennie L Hill
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE, USA
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Broadbent R, Wheatley R, Stajer S, Jacobs T, Lamarca A, Hubner R, Valle J, Amir E, McNamara M. P-53 Prognostic factors for relapse in resected gastroenteropancreatic neuroendocrine neoplasms: A systematic review and meta-analysis. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.108] [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: 11/28/2022] Open
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Edeline J, Lamarca A, McNamara M, Jacobs T, Hubner R, Palmer D, Johnson P, Guiu B, Valle J. P-229 Systematic review and pooled analysis of locoregional therapies in patients with intrahepatic cholangiocarcinoma. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.283] [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: 11/27/2022] Open
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Abstract
Objectives Severe COVID-19 (SvC19) is a syndrome of acute lung injury, respiratory failure, cytokine storm, distributive shock, multi-system organ failure and high mortality. SvC19 disproportionately impacts the elderly, who are also at risk for micronutrient deficiency. After observing a beneficial response to micronutrient repletion (MR) in a 69 year-old male with SvC19, we hypothesized that nutritional deficiencies were linked to the pathogenesis and that correcting them could be beneficial. In this report we detail a case series of 18 older patients with SvC19 treated with MR. Methods All patients had SvC19 requiring mechanical ventilation, elevated levels of CRP, D-dimer and neutrophil to lymphocyte ratio. MR consisted of daily parenteral ascorbate, thiamine, pyridoxine and multivitamins, as well as daily ergocalciferol, zinc and carnitine via nasogastric tube. Results The average age was 63.3 years. Six patients were male, 12 female. Disease severity was comparable based on SOFA score. A partial response was observed in 10 of the 18 patients (55.5%). Six (33.3%) were able to wean off blood pressure support. Five (27.7%) had improvement in gas exchange. Four (22.2) were able to wean off ventilator support. Three patients (37.5%) showed improvement in renal dysfunction. Conclusions MR shows potential promise as an adjunctive treatment for severe COVID-19, particularly in older patients or those with chronic illness in whom nutritional deficiencies are more probable. Funding Sources None
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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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Zhang Y, Bash JO, Roselle SJ, Shatas A, Repinsky A, Mathur R, Hogrefe C, Piziali J, Jacobs T, Gilliland A. Unexpected air quality impacts from implementation of green infrastructure in urban environments: A Kansas City case study. Sci Total Environ 2020; 744:140960. [PMID: 32711327 PMCID: PMC7802588 DOI: 10.1016/j.scitotenv.2020.140960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/09/2020] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
Green infrastructure (GI) implementation can benefit an urban environment by reducing the impacts of urban stormwater on aquatic ecosystems and human health. However, few studies have systematically analyzed the biophysical effects on regional meteorology and air quality that are triggered by changes in the urban vegetative coverage. In this study we use a state-of-the-art high-resolution air quality model to simulate the effects of a hypothetically feasible vegetation-focused GI implementation scenario in Kansas City, MO/KS on regional meteorology and air quality. Full year simulations are conducted for both the base case and GI land use scenarios using two different land surface models (LSMs) schemes inside the meteorological model. While the magnitudes of the changes in air quality due to the GI implementation differ using the two LSMs, the model outputs consistently showed increases in summertime PM2.5 (1.1 μg m-3, approximately 10% increase using NOAH LSM), which occurred mostly during the night and arose from the primary components, due to the cooler surface temperatures and the decreased planetary boundary layer height (PBLH). Both the maximum daily 8-hour average ozone and 1 h daily maximum O3 during summertime, decreased over the downtown areas (maximum decreases of 0.9 and 1.4 ppbv respectively). The largest ozone decreases were simulated to happen during the night, mainly caused by the titration effect of increased NOx concentration from the lower PBLH. These results highlight the region-specific non-linear process feedback from GI on regional air quality, and further demonstrate the need for comprehensive coupled meteorological-air quality modeling systems and necessity of accurate land surface model for studying these impacts.
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Affiliation(s)
- Yuqiang Zhang
- Oak Ridge Institute for Science and Education (ORISE) Fellowship Participant at U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States of America; Nicholas School of the Environment, Duke University, Durham, NC 27708, United States of America.
| | - Jesse O Bash
- Computational Exposure Division, National Exposure Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States of America
| | - Shawn J Roselle
- Computational Exposure Division, National Exposure Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States of America
| | - Angie Shatas
- Outreach Information Division, Office of Air Quality Planning and Standards, Office of Air and Radiation, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States of America
| | - Andrea Repinsky
- Research Services Department, Mid-America Regional Council, Kansas City, MO 64105, United States of America
| | - Rohit Mathur
- Computational Exposure Division, National Exposure Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States of America
| | - Christian Hogrefe
- Computational Exposure Division, National Exposure Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States of America
| | - Jamie Piziali
- Water Permits Division, Office of Wastewater Management, Office of Water, U.S. Environmental Protection Agency, Washington, DC 20460, United States of America
| | - Tom Jacobs
- Transportation and Environment, Mid-America Regional Council, Kansas City, MO 64105, United States of America
| | - Alice Gilliland
- National Risk Management Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH 45268, United States of America
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Tan M, Nyamundanda G, Fontana E, Hazell S, Ragulan C, Jones K, Abah B, Jacobs T, Bowes J, Sadanandam A, Huddart R. PO-1207: Exploring molecular subtype as a biomarker of radiation response in muscle-invasive bladder cancer. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)01225-1] [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: 11/15/2022]
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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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13
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Vamos CA, Griner SB, Kirchharr C, Green SM, DeBate R, Daley EM, Quinonez RB, Boggess KA, Jacobs T, Christiansen S. The development of a theory-based eHealth app prototype to promote oral health during prenatal care visits. Transl Behav Med 2019; 9:1100-1111. [PMID: 31009536 PMCID: PMC6875649 DOI: 10.1093/tbm/ibz047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Poor maternal oral health during pregnancy is associated with adverse maternal and child outcomes, including preterm birth and early childhood caries. Subsequently, professional associations have developed prenatal oral health guidelines, but significant gaps exist in implementing guidelines into clinical practice. The purpose of this study was to develop and test the usability of an innovative, theory-driven, eHealth application ("app") to facilitate prenatal providers' (nurse practitioners and midwives) implementation of oral health promotion during prenatal care visits. App development was guided by previous research, an integrated conceptual framework, Scientific Advisory Board input, and consumer-engaged iterative processes utilizing mixed-methods (observations, surveys, in-depth interviews) among providers (n = 4) during 10 unique prenatal care visits at a federally qualified health care center. Triangulation of quantitative and qualitative data analysis produced descriptive frequencies and salient themes. Concepts and principles from the following theoretical frameworks informed intervention development and testing: Consolidated Framework for Implementation Research; Information-Motivation-Behavioral Skills Model; Health Literacy; and Brief Motivational Interviewing. Overall, providers reported the app was effective at providing the information, motivation, and behavioral skills needed to integrate oral health promotion (e.g., easy to use; provided cues to action via scripts and tailored education; and documented findings into the patient's record). Although providers reported high usability, time constraints and detailed patient counseling scripts were identified areas for improvement. Findings suggest that the eHealth app could serve as an innovative mechanism to assist providers in implementing the prenatal oral health guidelines into practice. Future research is needed to continue app development efforts and to determine efficacy and effectiveness in practice settings.
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Affiliation(s)
- Cheryl A Vamos
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Stacey B Griner
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Claire Kirchharr
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Shana M Green
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Rita DeBate
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Ellen M Daley
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Rocio B Quinonez
- Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - Kim A Boggess
- School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Tom Jacobs
- Custom Thinking Media, LLC, Eugene, OR, USA
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14
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Mancuso R, Fryatt G, Cleal M, Obst J, Pipi E, Monzón-Sandoval J, Ribe E, Winchester L, Webber C, Nevado A, Jacobs T, Austin N, Theunis C, Grauwen K, Daniela Ruiz E, Mudher A, Vicente-Rodriguez M, Parker CA, Simmons C, Cash D, Richardson J. CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice. Brain 2019; 142:3243-3264. [PMID: 31504240 PMCID: PMC6794948 DOI: 10.1093/brain/awz241] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 11/12/2022] Open
Abstract
Neuroinflammation and microglial activation are significant processes in Alzheimer's disease pathology. Recent genome-wide association studies have highlighted multiple immune-related genes in association with Alzheimer's disease, and experimental data have demonstrated microglial proliferation as a significant component of the neuropathology. In this study, we tested the efficacy of the selective CSF1R inhibitor JNJ-40346527 (JNJ-527) in the P301S mouse tauopathy model. We first demonstrated the anti-proliferative effects of JNJ-527 on microglia in the ME7 prion model, and its impact on the inflammatory profile, and provided potential CNS biomarkers for clinical investigation with the compound, including pharmacokinetic/pharmacodynamics and efficacy assessment by TSPO autoradiography and CSF proteomics. Then, we showed for the first time that blockade of microglial proliferation and modification of microglial phenotype leads to an attenuation of tau-induced neurodegeneration and results in functional improvement in P301S mice. Overall, this work strongly supports the potential for inhibition of CSF1R as a target for the treatment of Alzheimer's disease and other tau-mediated neurodegenerative diseases.
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Affiliation(s)
- Renzo Mancuso
- Biological Sciences, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Gemma Fryatt
- Biological Sciences, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Madeleine Cleal
- Biological Sciences, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Juliane Obst
- Biological Sciences, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Elena Pipi
- Biological Sciences, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Jimena Monzón-Sandoval
- Department of Physiology Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
- UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Elena Ribe
- Department of Physiology Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
| | - Laura Winchester
- Department of Physiology Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
| | - Caleb Webber
- Department of Physiology Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
- UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Alejo Nevado
- Department of Physiology Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
| | - Tom Jacobs
- Janssen Research and Development, Turnhoutseweg 30, box 270, 2340 Beerse 1, Belgium
| | - Nigel Austin
- Janssen Research and Development, Turnhoutseweg 30, box 270, 2340 Beerse 1, Belgium
| | - Clara Theunis
- Janssen Neuroscience Research and Development, Janssen Pharmaceutical Companies of Johnson and Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Karolien Grauwen
- Janssen Neuroscience Research and Development, Janssen Pharmaceutical Companies of Johnson and Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Eva Daniela Ruiz
- Biological Sciences, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Amrit Mudher
- Biological Sciences, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Marta Vicente-Rodriguez
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Christine A Parker
- Experimental Medicine Imaging, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Camilla Simmons
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Diana Cash
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Jill Richardson
- Neurosciences Therapeutic Area, GlaxoSmithKline R&D, Stevenage, UK
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15
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McNamara M, Jacobs T, Frizziero M, Pihlak R, Lamarca A, Hubner R, Valle J, Amir E. Prognostic and predictive impact of high tumor mutation burden (TMB) in solid tumors: A systematic review and meta-analysis. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz239] [Citation(s) in RCA: 2] [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: 11/14/2022] Open
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16
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Jatana C, Jacobs T, Towning C, Guo X, Ni A, Towning L. The Addition of Platelet-Rich-Fibrin in Socket Preservation for Future Dental Implant Placement: A Randomized Controlled Clinical Trial. J Oral Maxillofac Surg 2019. [DOI: 10.1016/j.joms.2019.06.045] [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: 10/26/2022]
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17
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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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18
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Jaki T, Gordon A, Forster P, Bijnens L, Bornkamp B, Brannath W, Fontana R, Gasparini M, Hampson LV, Jacobs T, Jones B, Paoletti X, Posch M, Titman A, Vonk R, Koenig F. Response to comments on Jaki et al., A proposal for a new PhD level curriculum on quantitative methods for drug development. Pharm Stat 17(5):593-606, Sep/Oct 2018., DOI: https://doi.org/10.1002/pst.1873. Pharm Stat 2019; 18:284-286. [PMID: 30868716 DOI: 10.1002/pst.1942] [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] [Received: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Thomas Jaki
- Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom
| | - Allan Gordon
- Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom
| | - Pamela Forster
- Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom
| | | | | | - Werner Brannath
- KKSB and IfS Faculty 3 - Mathematics/ComputerScience, University of Bremen, Bremen, Germany
| | - Roberto Fontana
- Department of Mathematical Sciences, Politechnico di Torino, Turin, Italy
| | - Mauro Gasparini
- Department of Mathematical Sciences, Politechnico di Torino, Turin, Italy
| | | | - Tom Jacobs
- Janssen Pharmaceutica N.V., Beerse, Belgium
| | | | - Xavier Paoletti
- INSERM CESP-OncoStat Institut Gustave Roussy & Université Paris-Saclay UVSQ & Service de Biostatistique etd' Epidémiologie, Gustave Roussy, Villejuif, France
| | - Martin Posch
- Center for Medical Statistics, Informatics, and Intelligent Systems; Medical University Vienna, Vienna, Austria
| | - Andrew Titman
- Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom
| | | | - Franz Koenig
- Center for Medical Statistics, Informatics, and Intelligent Systems; Medical University Vienna, Vienna, Austria
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19
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Erhardt EM, Ursino M, Biewenga J, Jacobs T, Gasparini M. Bayesian knowledge integration for an in vitro-in vivo correlation model. Biom J 2018; 61:1104-1119. [PMID: 30259557 DOI: 10.1002/bimj.201700263] [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] [Received: 11/15/2017] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 11/11/2022]
Abstract
The primary goal of "in vitro-in vivo correlation" (IVIVC) is the reliable prediction of the in vivo serum concentration-time course, based on the in vitro drug dissolution or release profiles. IVIVC methods are particularly appropriate for formulations that are released over an extended period of time or with a lag in absorption and may support approving a change in formulation of a drug without additional bioequivalence trials in human subjects. Most of the current IVIVC models are assessed using frequentist methods, such as linear regression, based on averaged data and entail complex and potentially unstable mathematical deconvolution. The proposed IVIVC approach includes (a) a nonlinear-mixed effects model for the in vitro release data; (b) a population pharmacokinetic (PK) compartment model for the in vivo immediate release (IR) data; and (c) a system of ordinal differential equations (ODEs), containing the submodels (a) and (b), which approximates and predicts the in vivo controlled release (CR) data. The innovation in this paper consists of splitting the parameter space between submodels (a) and (b) versus (c). Subsequently, the uncertainty on these parameters is accounted for using a Bayesian framework, that is estimates from the first two submodels serve as priors for the Bayesian hierarchical third submodel. As such, the Bayesian method explained ensures a natural integration and transfer of knowledge between various sources of information, balancing possible differences in sample size and parameter uncertainty of in vitro and in vivo studies. Consequently, it is a very flexible approach yielding results for a broad range of data situations. The application of the method is demonstrated for a transdermal patch (TD).
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Affiliation(s)
- Elvira M Erhardt
- Department of Mathematical Sciences, Politecnico di Torino, 10129, Torino, Italy
| | - Moreno Ursino
- INSERM, UMRS 1138, team 22, CRC, University Paris Descartes, Sorbonne University, Paris, France
| | - Jeike Biewenga
- Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, 2340, Beerse, Belgium
| | - Tom Jacobs
- Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, 2340, Beerse, Belgium
| | - Mauro Gasparini
- Department of Mathematical Sciences, Politecnico di Torino, 10129, Torino, Italy
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20
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Jaki T, Gordon A, Forster P, Bijnens L, Bornkamp B, Brannath W, Fontana R, Gasparini M, Hampson L, Jacobs T, Jones B, Paoletti X, Posch M, Titman A, Vonk R, Koenig F. A proposal for a new PhD level curriculum on quantitative methods for drug development. Pharm Stat 2018; 17:593-606. [PMID: 29984474 PMCID: PMC6174936 DOI: 10.1002/pst.1873] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 01/23/2018] [Accepted: 05/22/2018] [Indexed: 12/30/2022]
Abstract
This paper provides an overview of "Improving Design, Evaluation and Analysis of early drug development Studies" (IDEAS), a European Commission-funded network bringing together leading academic institutions and small- to large-sized pharmaceutical companies to train a cohort of graduate-level medical statisticians. The network is composed of a diverse mix of public and private sector partners spread across Europe, which will host 14 early-stage researchers for 36 months. IDEAS training activities are composed of a well-rounded mixture of specialist methodological components and generic transferable skills. Particular attention is paid to fostering collaborations between researchers and supervisors, which span academia and the private sector. Within this paper, we review existing medical statistics programmes (MSc and PhD) and highlight the training they provide on skills relevant to drug development. Motivated by this review and our experiences with the IDEAS project, we propose a concept for a joint, harmonised European PhD programme to train statisticians in quantitative methods for drug development.
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Affiliation(s)
- T. Jaki
- Lancaster UniversityDepartment of Mathematics and StatisticsLancasterUK
| | - A. Gordon
- Lancaster UniversityDepartment of Mathematics and StatisticsLancasterUK
| | - P. Forster
- Lancaster UniversityDepartment of Mathematics and StatisticsLancasterUK
| | | | | | - W. Brannath
- University of BremenKKSB and IfS Faculty 3 – Mathematics/Computer ScienceBremenGermany
| | | | | | | | - T. Jacobs
- Janssen Pharmaceutica NVBeerseBelgium
| | - B. Jones
- Novartis Pharma AGBaselSwitzerland
| | - X. Paoletti
- INSERM CESP‐OncoStat Institut Gustave Roussy & Université Paris‐Saclay UVSQ & Service de Biostatistique et d'EpidémiologieGustave RoussyVillejuifFrance
| | - M. Posch
- Medical University of ViennaCenter for Medical Statistics, Informatics, and Intelligent SystemsViennaAustria
| | - A. Titman
- Lancaster UniversityDepartment of Mathematics and StatisticsLancasterUK
| | | | - F. Koenig
- Medical University of ViennaCenter for Medical Statistics, Informatics, and Intelligent SystemsViennaAustria
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21
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Vamos CA, Green SM, Griner S, Daley E, DeBate R, Jacobs T, Christiansen S. Identifying Implementation Science Characteristics for a Prenatal Oral Health eHealth Application. Health Promot Pract 2018; 21:246-258. [PMID: 30153742 DOI: 10.1177/1524839918793628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 11/15/2022]
Abstract
Background. Oral health is a significant public health issue; yet barriers to implementing the prenatal oral health guidelines into practice remain. This formative research aimed to identify key implementation science characteristics to inform the development of an eHealth application (app) to assist providers in implementing the prenatal oral health guidelines during prenatal visits. Method. Guided by the Consolidated Framework for Implementation Research, the clinic's infrastructure, workflow, and contextual factors were assessed via clinic observation, technology assessment, prenatal provider interviews (n = 4), clinic staff interviews (n = 8), and two focus groups with oral health providers (n = 16). Results. System-level factors influencing future implementation were identified regarding structural characteristic, networks/communication, culture, external policy/incentives, relative advantage, complexity, design quality/packaging, knowledge/beliefs, and personal attributes. Discussion. Findings provided vital information and will directly inform the design and implementation of an eHealth app that aims to facilitate the translation of the interprofessional prenatal oral health guidelines into clinical prenatal oral health practices.
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Affiliation(s)
| | | | | | | | | | - Tom Jacobs
- Custom Thinking Media, LLC, Eugene, OR, USA
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22
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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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23
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Affiliation(s)
| | | | | | - Thomas Jaki
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
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24
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Borghys H, Van Broeck B, Dhuyvetter D, Jacobs T, de Waepenaert K, Erkens T, Brooks M, Thevarkunnel S, Araujo JA. Young to Middle-Aged Dogs with High Amyloid-β Levels in Cerebrospinal Fluid are Impaired on Learning in Standard Cognition tests. J Alzheimers Dis 2018; 56:763-774. [PMID: 28035921 PMCID: PMC5271428 DOI: 10.3233/jad-160434] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Understanding differences in Alzheimer’s disease biomarkers before the pathology becomes evident can contribute to an improved understanding of disease pathogenesis and treatment. A decrease in amyloid-β (Aβ)42 in cerebrospinal fluid (CSF) is suggested to be a biomarker for Aβ deposition in brain. However, the relevance of CSF Aβ levels prior to deposition is not entirely known. Dogs are similar to man with respect to amyloid-β protein precursor (AβPP)-processing, age-related amyloid plaque deposition, and cognitive dysfunction. In the current study, we evaluated the relation between CSF Aβ42 levels and cognitive performance in young to middle-aged dogs (1.5–7 years old). Additionally, CSF sAβPPα and sAβPPβ were measured to evaluate AβPP processing, and CSF cytokines were measured to determine the immune status of the brain. We identified two groups of dogs showing consistently low or high CSF Aβ42 levels. Based on prior studies, it was assumed that at this age no cerebral amyloid plaques were likely to be present. The cognitive performance was evaluated in standard cognition tests. Low or high Aβ concentrations coincided with low or high sAβPPα, sAβPPβ, and CXCL-1 levels, respectively. Dogs with high Aβ concentrations showed significant learning impairments on delayed non-match to position (DNMP), object discrimination, and reversal learning compared to dogs with low Aβ concentrations. Our data support the hypothesis that high levels of CSF Aβ in dogs coincide with lower cognitive performance prior to amyloid deposition. Further experiments are needed to investigate this link, as well as the relevance with respect to Alzheimer’s disease pathology progression.
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Affiliation(s)
- Herman Borghys
- Janssen Research & Development, a division of Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Bianca Van Broeck
- Janssen Research & Development, a division of Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Deborah Dhuyvetter
- Janssen Research & Development, a division of Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Tom Jacobs
- Janssen Research & Development, a division of Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Katja de Waepenaert
- Janssen Research & Development, a division of Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Tim Erkens
- Janssen Research & Development, a division of Janssen Pharmaceutica N.V., Beerse, Belgium
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25
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Rappaport S, Vanderburg A, Jacobs T, LaCourse D, Jenkins J, Kraus A, Rizzuto A, Latham DW, Bieryla A, Lazarevic M, Schmitt A. Likely Transiting Exocomets Detected By Kepler. Mon Not R Astron Soc 2018; 474:1453-1468. [PMID: 29755143 PMCID: PMC5943639 DOI: 10.1093/mnras/stx2735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present the first good evidence for exocomet transits of a host star in continuum light in data from the Kepler mission. The Kepler star in question, KIC 3542116, is of spectral type F2V and is quite bright at Kp = 10. The transits have a distinct asymmetric shape with a steeper ingress and slower egress that can be ascribed to objects with a trailing dust tail passing over the stellar disk. There are three deeper transits with depths of ≃ 0.1% that last for about a day, and three that are several times more shallow and of shorter duration. The transits were found via an exhaustive visual search of the entire Kepler photometric data set, which we describe in some detail. We review the methods we use to validate the Kepler data showing the comet transits, and rule out instrumental artefacts as sources of the signals. We fit the transits with a simple dust-tail model, and find that a transverse comet speed of ∼35-50 km s-1 and a minimum amount of dust present in the tail of ∼ 1016 g are required to explain the larger transits. For a dust replenishment time of ∼10 days, and a comet lifetime of only ∼300 days, this implies a total cometary mass of ≳ 3 × 1017 g, or about the mass of Halley's comet. We also discuss the number of comets and orbital geometry that would be necessary to explain the six transits detected over the four years of Kepler prime-field observations. Finally, we also report the discovery of a single comet-shaped transit in KIC 11084727 with very similar transit and host-star properties.
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Affiliation(s)
- S Rappaport
- Department of Physics, and Kavli Institute for Astrophysics and Space Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - A Vanderburg
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 USA
- Department of Astronomy, The University of Texas at Austin, 2515 Speedway, Stop C1400, Austin, TX 78712
- NASA Sagan Fellow
| | - T Jacobs
- 12812 SE 69th Place Bellevue, WA 98006, USA
| | - D LaCourse
- 7507 52nd Place NE Marysville, WA 98270, USA
| | - J Jenkins
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - A Kraus
- Department of Astronomy, University of Texas, Austin, 78712-1205, USA
| | - A Rizzuto
- Department of Astronomy, University of Texas, Austin, 78712-1205, USA
| | - D W Latham
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 USA
| | - A Bieryla
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 USA
| | - M Lazarevic
- Department of Physics, Northeastern University, 100 Forsyth St, Boston, MA 02115
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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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Abstract
Most ischemic strokes are managed on the ward or on designated stroke units. A significant proportion of patients with ischemic stroke require more specialized care. Several studies have shown improved outcomes for patients with acute ischemic stroke when neurocritical care services are available. Features of acute ischemic stroke patients requiring intensive care unit-level care include airway or respiratory compromise; large cerebral or cerebellar hemisphere infarction with swelling; infarction with symptomatic hemorrhagic transformation; infarction complicated by seizures; and a large proportion of patients require close management of blood pressure after thrombolytics. In this chapter, we discuss aspects of acute ischemic stroke care that are of particular relevance to a neurointensivist, covering neuropathology, neurodiagnostics and imaging, blood pressure management, glycemic control, temperature management, and the selection and timing of antithrombotics. We also focus on the care of patients who have received intravenous thrombolysis or mechanical thrombectomy. Complex clinical decision making in decompressive hemicraniectomy for hemispheric infarction and urgent management of basilar artery thrombosis are specifically addressed.
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Affiliation(s)
- M McDermott
- Stroke Program, University of Michigan, Ann Arbor, MI, USA.
| | - T Jacobs
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, USA
| | - L Morgenstern
- Stroke Program, University of Michigan, Ann Arbor, MI, USA
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Schulte P, Bhattacharya A, Butler C, Chun H, Jacklitsch B, Jacobs T, Kiefer M, Lincoln J, Pendergrass S, Shire J, Watson J, Wagner G. Advancing the framework for considering the effects of climate change on worker safety and health. J Occup Environ Hyg 2016; 13:847-65. [PMID: 27115294 PMCID: PMC5017900 DOI: 10.1080/15459624.2016.1179388] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In 2009, a preliminary framework for how climate change could affect worker safety and health was described. That framework was based on a literature search from 1988-2008 that supported seven categories of climate-related occupational hazards: (1) increased ambient temperature; (2) air pollution; (3) ultraviolet radiation exposure; (4) extreme weather; (5) vector-borne diseases and expanded habitats; (6) industrial transitions and emerging industries; and (7) changes in the built environment. This article reviews the published literature from 2008-2014 in each of the seven categories. Additionally, three new topics related to occupational safety and health are considered: mental health effects, economic burden, and potential worker safety and health impacts associated with the nascent field of climate intervention (geoengineering). Beyond updating the literature, this article also identifies key priorities for action to better characterize and understand how occupational safety and health may be associated with climate change events and ensure that worker health and safety issues are anticipated, recognized, evaluated, and mitigated. These key priorities include research, surveillance, risk assessment, risk management, and policy development. Strong evidence indicates that climate change will continue to present occupational safety and health hazards, and this framework may be a useful tool for preventing adverse effects to workers.
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Affiliation(s)
- P.A. Schulte
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Education and Infomation Division, Cincinnati, Ohio
- CONTACT P.A. Schulte National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 1090 Tusculum Avenue, MS C-14, Cincinnati, OH45226
| | - A. Bhattacharya
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Education and Infomation Division, Cincinnati, Ohio
| | - C.R. Butler
- Western States Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Denver, Colorado
| | - H.K. Chun
- Georgia Southern University, College of Public Health, Statesboro, Georgia
| | - B. Jacklitsch
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Education and Infomation Division, Cincinnati, Ohio
| | - T. Jacobs
- Division of Surveillance, Hazard Evaluations, and Field Studies, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio
| | - M. Kiefer
- Western States Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Denver, Colorado
| | - J. Lincoln
- Western States Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Anchorage, Alaska
| | - S. Pendergrass
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Education and Infomation Division, Cincinnati, Ohio
| | - J. Shire
- Division of Surveillance, Hazard Evaluations, and Field Studies, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio
| | - J. Watson
- Western States Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Spokane, Washington
| | - G.R. Wagner
- Office of the Director, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention; Washington, D.C.
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Dixon CA, Ammerman RT, Dexheimer JW, Meyer B, Jung H, Johnson BL, Elliott J, Jacobs T, Pomerantz WJ, Mahabee-Gittens EM. Development of iBsafe: A Collaborative, Theory-based Approach to Creating a Mobile Game Application for Child Safety. AMIA Annu Symp Proc 2014; 2014:477-485. [PMID: 25954352 PMCID: PMC4419895] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Unintentional injury is a leading cause of death worldwide, and the number one cause of child death in the United States. The American Academy of Pediatrics promotes safety recommendations to decrease child injury risk, however the majority of educational programs delivering these strategies are school-based or in community campaigns. Mobile technology provides an opportune platform to deliver pediatric injury prevention programs given its massive global reach and underrepresentation within the current mobile health market. This paper describes the development of iBsafe, a novel mobile safety game application designed to prevent injury in 5- to 6- year old children. Our multidisciplinary team utilized a step-wise approach to create an innovative child game application which is based in behavioral theory and promotes evidence-based safety recommendations. Results and future directions for iBsafe aim to interactively educate children on how to be safe and ultimately improve their safety behaviors.
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Ahnaou A, Huysmans H, Jacobs T, Drinkenburg W. Cortical EEG oscillations and network connectivity as efficacy indices for assessing drugs with cognition enhancing potential. Neuropharmacology 2014; 86:362-77. [DOI: 10.1016/j.neuropharm.2014.08.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/18/2014] [Accepted: 08/20/2014] [Indexed: 10/24/2022]
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Borghys H, Jacobs T, Van Broeck B, Dillen L, Dhuyvetter D, Gijsen H, Mercken M. Comparison of two different methods for measurement of amyloid-β peptides in cerebrospinal fluid after BACE1 inhibition in a dog model. J Alzheimers Dis 2014; 38:39-48. [PMID: 23948925 DOI: 10.3233/jad-130599] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 11/15/2022]
Abstract
Beta-secretase is the first cleavage enzyme of amyloid-β protein precursor (AβPP) in the amyloidogenic pathway, leading to the formation of the plaque forming Amyloid-β (Aβ)1-42 peptide. BACE (beta-site AβPP cleaving enzyme) 1 inhibition is therefore considered to be a promising disease modifying therapy for Alzheimer's disease. An early assessment of the in vivo activity of BACE inhibitors was done in dogs since AβPP processing is the same as in humans and this species easily enables longitudinal cerebrospinal fluid (CSF) sampling. Aβ changes in CSF compared to baseline are used to evaluate target engagement of the compounds. Levels of Aβ1-37, Aβ1-38, Aβ1-40, and Aβ1-42 in CSF are measured with immunoassay (Mesoscale electrochemiluminescence technology) and with an ultra high-performance liquid chromatography mass spectrometry (UPLC-MS/MS). Two experimental BACE inhibitors were evaluated. With the immunoassay, a dose dependent decrease is observed for all four Aβ peptides. Measurements with the UPLC-MS/MS are in line with the immunoassay for Aβ1-37, Aβ1-38, and Aβ1-40, however, for Aβ1-42, differences are sometimes observed when comparing to changes seen in the other peptides with UPLC-MS/MS and with immunoassay results. Generally lower concentrations are measured with immunoassay. The reason for these differences is still unknown. Aβ1-42 is more prone to form aggregates compared to the other peptides. One hypothesis could be that while the immunoassay only measures free Aβ, bound and aggregated Aβ peptides are at least partially dissolved with the UPLC-MS/MS method, since acetonitrile is added to the CSF samples. This increases variability in the concentration of Aβ peptide measured with UPLC-MS/MS, especially for Aβ1-42, potentially masking the compound effect on Aβ1-42 levels.
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Affiliation(s)
- Herman Borghys
- Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium
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Streyer W, Law S, Rooney G, Jacobs T, Wasserman D. Strong absorption and selective emission from engineered metals with dielectric coatings. Opt Express 2013; 21:9113-9122. [PMID: 23572000 DOI: 10.1364/oe.21.009113] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We demonstrate strong-to-perfect absorption across a wide range of mid-infrared wavelengths (5-12µm) using a two-layer system consisting of heavily-doped silicon and a thin high-index germanium dielectric layer. We demonstrate spectral control of the absorption resonance by varying the thickness of the dielectric layer. The absorption resonance is shown to be largely polarization-independent and angle-invariant. Upon heating, we observe selective thermal emission from our materials. Experimental data is compared to an analytical model of our structures with strong agreement.
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Affiliation(s)
- W Streyer
- Department of Electrical and Computer Engineering, Micro and Nanotechnology Lab, University of Illinois Urbana Champaign, 208 N. Wright St., Urbana, IL 61801, USA
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Van Loock M, Hombrouck A, Jacobs T, Winters B, Meersseman G, Van Acker K, Clayton RF, Malcolm BA. Reporter gene expression from LTR-circles as tool to identify HIV-1 integrase inhibitors. J Virol Methods 2012. [PMID: 23178583 DOI: 10.1016/j.jviromet.2012.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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
Early HIV-1 integrase inhibitors, such as compounds containing a β-diketo acid moiety, were identified by extensive high-throughput screening campaigns. Traditionally, in vitro biochemical assays, measuring the catalytic activities of integrase, have been used for this purpose. However, these assays are confounded by the absence of cellular processes or cofactors that play a role in the integration of HIV-1 DNA in the cellular genome. In contrast to regular cell-based virus inhibition assays, which targets all steps of the viral replication cycle, a novel cellular screening assays was developed to enable the specific identification of integrase inhibitors, employing a readout that is linked with the inhibition of integrase activity. Therefore, a HIV-1 lentiviral vector equipped with the enhanced green fluorescent protein (eGFP) reporter gene was used to detect expression from extrachromosomal viral DNA (1- or 2-long terminal repeat circles), formed when integration of vector DNA into the cellular genome is prevented by an integrase inhibitor. In this assay, eGFP expression from the low residual level of transcriptional activity of extrachromosomal DNA was measured via high-throughput flow cytometry. An algorithm for analysis of eGFP expression histograms enabled the specific identification of integrase inhibitors. This assay is amenable for high throughput screening to identify inhibitors of HIV-1 integrase.
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Affiliation(s)
- M Van Loock
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
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Verbinnen T, Jacobs T, Vijgen L, Ceulemans H, Neyts J, Fanning G, Lenz O. Replication capacity of minority variants in viral populations can affect the assessment of resistance in HCV chimeric replicon phenotyping assays. J Antimicrob Chemother 2012; 67:2327-37. [DOI: 10.1093/jac/dks234] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Abstract
Brivaracetam is a novel high-affinity SV2A ligand currently in clinical development for epilepsy. The objective was to characterize its disposition in patients with renal impairment. A single oral dose of 200 mg brivaracetam was administered to 9 patients with severe renal impairment not requiring dialysis (creatinine clearance <15 mL/min, n = 6; 15-29 mL/min, n = 3) and 9 matched healthy controls. Plasma and urinary concentrations of brivaracetam and 3 pharmacologically inactive metabolites (acid, hydroxy, and hydroxyacid) were determined up to 72 hours postdose, and noncompartmental pharmacokinetic parameters were derived. The C(max) of brivaracetam was unchanged relative to healthy controls, whereas AUC was slightly increased (mean ratio, 1.21; 90% confidence interval, 1.01-1.45). Nonrenal and renal clearances of brivaracetam decreased from 47 and 4.5 to 41 and 1.7 mL/min/1.73 m(2). Exposure to the acid, hydroxy, and hydroxyacid metabolites was markedly increased: C(max) by 2.4-, 2.0-, and 11.7-fold and AUC by 3.2-, 4.1-, and 21.5-fold. Renal clearance of these rapidly cleared metabolites was decreased 10-fold in patients with severe renal impairment. Nonclinical toxicology studies concluded to the absence of safety issues related to the increased levels of metabolites. These observations suggest that dose adjustment of brivaracetam should not be required at any stage of renal dysfunction.
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Jacobs T, Hardie MJ. Self-assembly of metal trischelates to afford extended structures for porous applications. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311087678] [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: 11/10/2022] Open
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37
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Jacobs T. Book Review: Neurologic Emergencies. Neurology 2011. [DOI: 10.1212/wnl.0b013e3182299fba] [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: 11/15/2022] Open
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Jacobs T, Straetemans R, Molenberghs G, Adriaan Bouwknecht J, Bijnens L. A latent pharmacokinetic time profile to model dose-response survival data. J Biopharm Stat 2011; 20:759-67. [PMID: 20496204 DOI: 10.1080/10543401003618249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The accelerating rotarod test is a preclinical pharmacodynamic test to assess the effect of a treatment on an animal's motor coordination. Two models are proposed to analyze the dose-response time-to-event data that typically result from such experiments: (1) a linear regression model and (2) an E(max) model with latent drug concentration at the site of action. Both cope with the survival character of the data. The latter model allows a direct comparison of compounds, but raises the question of whether the study design would benefit from the inclusion of additional mice for plasma concentration sampling on the one hand or whether additional time-to-event data without plasma concentration sampling should be ascertained from these additional mice on the other hand. A simulation study explores the impact on operational characteristics of this change of study design.
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Affiliation(s)
- Tom Jacobs
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Universiteit Hasselt, Diepenbeek, Belgium.
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Jacobs T, Carbone E, Morent R, De Geyter N, Reniers F, Leys C. Surface modification of polymer films with a remote atmospheric pressure d.c. glow discharge: influence of substrate location. SURF INTERFACE ANAL 2010. [DOI: 10.1002/sia.3319] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Jacobs T, Valero T, Naumann M, Kintzios S, Hauptmann P. Electrical impedance spectroscopy of gel embedded neuronal cells based on a novel impedimetric biosensor. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.proche.2009.07.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Jacobs T, Kutzner C, Kropp M, Brokmann G, Lang W, Steinke A, Kienle A, Hauptmann P. Combination of a novel perforated thermoelectric flow and impedimetric sensor for monitoring chemical conversion in micro fluidic channels. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.proche.2009.07.281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Jacobs T, Maschke M, Klawe C. Aseptische Meningitis bei intrathekaler Triamcinolontherapie bei Patienten mit progressiver Encephalomyelitis disseminata. Akt Neurol 2009. [DOI: 10.1055/s-0029-1238576] [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: 10/20/2022]
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Valero T, Jacobs T, Moschopoulou G, Naumann M, Hauptmann P, Kintzios S. Electrical impedance analysis of N2a neuroblastoma cells in gel matrices after ACh-receptor triggering with an impedimetric biosensor. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.proche.2009.07.183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Jacobs T, Rossenu S, Dunne A, Molenberghs G, Straetemans R, Bijnens L. Combined Models for Data from In Vitro–In Vivo Correlation Experiments. J Biopharm Stat 2008; 18:1197-211. [DOI: 10.1080/10543400802369061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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)
- Tom Jacobs
- a Interuniversity Institute for Biostatistics and Statistical Bioinformatics, University Hasselt , Diepenbeek, Belgium
- b Katholieke Universiteit Leuven , Belgium
| | - Stefaan Rossenu
- d Johnson and Johnson Pharmaceutical Research and Development, A Division of Janssen Pharmaceutica N.V. , Beerse, Belgium
| | - Adrian Dunne
- c UCD School of Mathematical Sciences, University College Dublin , Dublin, Ireland
| | - Geert Molenberghs
- a Interuniversity Institute for Biostatistics and Statistical Bioinformatics, University Hasselt , Diepenbeek, Belgium
- b Katholieke Universiteit Leuven , Belgium
| | - Roel Straetemans
- d Johnson and Johnson Pharmaceutical Research and Development, A Division of Janssen Pharmaceutica N.V. , Beerse, Belgium
| | - Luc Bijnens
- d Johnson and Johnson Pharmaceutical Research and Development, A Division of Janssen Pharmaceutica N.V. , Beerse, Belgium
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Jacobs T, De Ridder F, Rusch S, Van Peer A, Molenberghs G, Bijnens L. Including Information on the Therapeutic Window in Bioequivalence Acceptance. Pharm Res 2008; 25:2628-38. [DOI: 10.1007/s11095-008-9680-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 06/30/2008] [Indexed: 11/25/2022]
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Causeret F, Terao M, Jacobs T, Nishimura YV, Yanagawa Y, Obata K, Hoshino M, Nikolic M. The p21-activated kinase is required for neuronal migration in the cerebral cortex. ACTA ACUST UNITED AC 2008; 19:861-75. [PMID: 18701438 DOI: 10.1093/cercor/bhn133] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The normal formation and function of the mammalian cerebral cortex depend on the positioning of its neurones, which occurs in a highly organized, layer-specific manner. The correct morphology and movement of neurones rely on synchronized regulation of their actin filaments and microtubules. The p21-activated kinase (Pak1), a key cytoskeletal regulator, controls neuronal polarization, elaboration of axons and dendrites, and the formation of dendritic spines. However, its in vivo role in the developing nervous system is unclear. We have utilized in utero electroporation into mouse embryo cortices to reveal that both loss and gain of Pak1 function affect radial migration of projection neurones. Overexpression of hyperactivated Pak1 predominantly caused neurones to arrest in the intermediate zone (IZ) with apparently misoriented and disorganized leading projections. Loss of Pak1 disrupted the morphology of migrating neurones, which accumulated in the IZ and deep cortical layers. Unexpectedly, a significant number of neurones with reduced Pak1 expression aberrantly entered into the normally cell-sparse marginal zone, suggesting their inability to cease migrating that may be due to their impaired dissociation from radial glia. Our findings reveal the in vivo importance of temporal and spatial regulation of the Pak1 kinase during key stages of cortical development.
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Affiliation(s)
- Frédéric Causeret
- Department of Cellular and Molecular Neuroscience, Imperial College School of Medicine, London, UK
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Grenningloh R, Darj A, Bauer H, zur Lage S, Chakraborty T, Jacobs T, Weiss S. Liposome-encapsulated antigens induce a protective CTL response against Listeria monocytogenes independent of CD4+ T cell help. Scand J Immunol 2008; 67:594-602. [PMID: 18433404 DOI: 10.1111/j.1365-3083.2008.02112.x] [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: 11/29/2022]
Abstract
Protection against intracellular pathogens is usually mediated by cytotoxic T lymphocytes (CTL). Induction of a protective CTL response for vaccination purposes has proven difficult because of the limited access of protein antigens or attenuated pathogens to the MHC class I presentation pathway. We show here that pH-sensitive PE/CHEMS liposomes can be used as a vehicle to efficiently deliver intact proteins for presentation by MHC class I. Mice immunized with listerial proteins encapsulated in such liposomes launched a strong CTL response and were protected against a subsequent challenge with L. monocytogenes. Remarkably, the CTL response was induced independently of detectable CD4(+) T cell help.
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Affiliation(s)
- R Grenningloh
- Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Kolligs F, Zech C, Schönberg S, Schirra J, Thasler W, Graeb C, Beuers U, Wilkowski R, Jacobs T, Böck S, Berster J, Heinemann V, Schäfer C. Interdisziplinäre Diagnostik und Therapie von Gallengangskarzinomen. Z Gastroenterol 2008; 46:58-68. [DOI: 10.1055/s-2007-963530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kasteleijn-Nolst Trenité DGA, Genton P, Parain D, Masnou P, Steinhoff BJ, Jacobs T, Pigeolet E, Stockis A, Hirsch E. Evaluation of brivaracetam, a novel SV2A ligand, in the photosensitivity model. Neurology 2007; 69:1027-34. [PMID: 17785672 DOI: 10.1212/01.wnl.0000271385.85302.55] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [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: 11/15/2022] Open
Abstract
OBJECTIVE To assess the activity of brivaracetam, a novel SV2A ligand, in the photosensitivity model as a proof-of-principle of efficacy in patients with epilepsy. METHODS A subject-blind placebo-controlled study in patients with photosensitive epilepsy was performed to investigate the effect of single-dose brivaracetam (10, 20, 40, or 80 mg) on photosensitive responses. Each patient was exposed to intermittent photic stimulation that evoked a generalized photoparoxysmal EEG response. Individual standard photosensitivity ranges (SPRs) were recorded post-placebo (day -1) and post-brivaracetam until return to baseline (day 1 to 3). Plasma concentrations of brivaracetam and any concomitant antiepileptic drugs were determined. RESULTS Of the 18 evaluable patients, none achieved SPR abolishment post-placebo, whereas 14 (78%) achieved complete abolishment post-brivaracetam. Decrease in SPR was seen in 8 patients (44%) post-placebo compared to 17 (94%) post-brivaracetam. Duration of response was twice as long post-brivaracetam 80 mg (59.5 hours) compared with lower doses, although the overall effect was not dose-dependent. Time to maximal photosensitive response was dose-related with the shortest time interval observed at the highest dose (0.5 hours post-brivaracetam 80 mg). The area under the effect curve (SPR change from pre-dose vs time) appeared linearly correlated with the area under the plasma concentration curve. Brivaracetam was well tolerated. The most common adverse events were dizziness and somnolence. CONCLUSIONS Our findings show that brivaracetam clearly suppresses generalized photoparoxysmal EEG response. As such, investigations of the antiepileptic properties and tolerability of brivaracetam are warranted in further clinical studies of patients with epilepsy.
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