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Lee O, Bazzi LA, Xu Y, Pearson E, Wang M, Hosseini O, Akasha AM, Choi JN, Karlan S, Pilewskie M, Kocherginsky M, Benante K, Helland T, Mellgren G, Dimond E, Perloff M, Heckman-Stoddard BM, Khan SA. A randomized Phase I pre-operative window trial of transdermal endoxifen in women planning mastectomy: Evaluation of dermal safety, intra-mammary drug distribution, and biologic effects. Biomed Pharmacother 2024; 171:116105. [PMID: 38171245 DOI: 10.1016/j.biopha.2023.116105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/17/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Breast cancer prevention only requires local exposure of the breast to active drug. However, oral preventive agents entail systemic exposure, causing adverse effects that limit acceptance by high-risk women. Drug-delivery through the breast skin is an attractive option, but requires demonstration of dermal safety and drug distribution throughout the breast. We formulated the tamoxifen metabolite (E/Z)-endoxifen for transdermal delivery and tested it in a placebo-controlled, double-blinded Phase I trial with dose escalation from 10 to 20 mg daily. The primary endpoint was dermal toxicity. Thirty-two women planning mastectomy were randomized (2:1) to endoxifen-gel or placebo-gel applied to both breasts for 3-5 weeks. Both doses of endoxifen-gel incurred no dermal or systemic toxicity compared to placebo. All endoxifen-treated breasts contained the drug at each of five sampling locations; the median per-person tissue concentration in the treated participants was 0.6 ng/g (IQR 0.4-1.6), significantly higher (p < 0.001) than the median plasma concentration (0.2 ng/mL, IQR 0.2-0.2). The median ratio of the more potent (Z)-isomer to (E)-isomer at each breast location was 1.50 (IQR 0.96-2.54, p < 0.05). No discernible effects of breast size or adiposity on tissue concentrations were observed. At the endoxifen doses and duration used, and the tissue concentration achieved, we observed a non-significant overall reduction of tumor proliferation (Ki67 LI) and significant downregulation of gene signatures known to promote cancer invasion (FN1, SERPINH1, PLOD2, PDGFA, ITGAV) (p = 0.03). Transdermal endoxifen is an important potential breast cancer prevention agent but formulations with better dermal penetration are needed.
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Affiliation(s)
- Oukseub Lee
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Latifa A Bazzi
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yanfei Xu
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Erik Pearson
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Minhua Wang
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Omid Hosseini
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Azza M Akasha
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jennifer Nam Choi
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Scott Karlan
- Saul and Joyce Brandman Breast Center, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | | | - Masha Kocherginsky
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kelly Benante
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Thomas Helland
- Hormone Laboratory, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Gunnar Mellgren
- Hormone Laboratory, Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Eileen Dimond
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Marjorie Perloff
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | | | - Seema A Khan
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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Gertsenshteyn I, Epel B, Giurcanu M, Barth E, Lukens J, Hall K, Martinez JF, Grana M, Maggio M, Miller RC, Sundramoorthy SV, Krzykawska-Serda M, Pearson E, Aydogan B, Weichselbaum RR, Tormyshev VM, Kotecha M, Halpern HJ. Corrigendum: Absolute oxygen-guided radiation therapy improves tumor control in three preclinical tumor models. Front Med (Lausanne) 2023; 10:1339872. [PMID: 38116039 PMCID: PMC10728871 DOI: 10.3389/fmed.2023.1339872] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fmed.2023.1269689.].
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Affiliation(s)
- Inna Gertsenshteyn
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Department of Radiology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Boris Epel
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
- O2M Technologies, Chicago, IL, United States
| | - Mihai Giurcanu
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, United States
| | - Eugene Barth
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - John Lukens
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Kayla Hall
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Jenipher Flores Martinez
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Mellissa Grana
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Matthew Maggio
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Richard C. Miller
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Subramanian V. Sundramoorthy
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Martyna Krzykawska-Serda
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
- Department of Biophysics and Cancer Biology, Jagiellonian University, Kraków, Poland
| | - Erik Pearson
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Bulent Aydogan
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
| | - Ralph R. Weichselbaum
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
| | | | | | - Howard J. Halpern
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging in vivo Physiology, The University of Chicago, Chicago, IL, United States
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Gertsenshteyn I, Epel B, Giurcanu M, Barth E, Lukens J, Hall K, Martinez JF, Grana M, Maggio M, Miller RC, Sundramoorthy SV, Krzykawska-Serda M, Pearson E, Aydogan B, Weichselbaum RR, Tormyshev VM, Kotecha M, Halpern HJ. Absolute oxygen-guided radiation therapy improves tumor control in three preclinical tumor models. Front Med (Lausanne) 2023; 10:1269689. [PMID: 37904839 PMCID: PMC10613495 DOI: 10.3389/fmed.2023.1269689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/28/2023] [Indexed: 11/01/2023] Open
Abstract
Background Clinical attempts to find benefit from specifically targeting and boosting resistant hypoxic tumor subvolumes have been promising but inconclusive. While a first preclinical murine tumor type showed significant improved control with hypoxic tumor boosts, a more thorough investigation of efficacy from boosting hypoxic subvolumes defined by electron paramagnetic resonance oxygen imaging (EPROI) is necessary. The present study confirms improved hypoxic tumor control results in three different tumor types using a clonogenic assay and explores potential confounding experimental conditions. Materials and methods Three murine tumor models were used for multi-modal imaging and radiotherapy: MCa-4 mammary adenocarcinomas, SCC7 squamous cell carcinomas, and FSa fibrosarcomas. Registered T2-weighted MRI tumor boundaries, hypoxia defined by EPROI as pO2 ≤ 10 mmHg, and X-RAD 225Cx CT boost boundaries were obtained for all animals. 13 Gy boosts were directed to hypoxic or equal-integral-volume oxygenated tumor regions and monitored for regrowth. Kaplan-Meier survival analysis was used to assess local tumor control probability (LTCP). The Cox proportional hazards model was used to assess the hazard ratio of tumor progression of Hypoxic Boost vs. Oxygenated Boost for each tumor type controlling for experimental confounding variables such as EPROI radiofrequency, tumor volume, hypoxic fraction, and delay between imaging and radiation treatment. Results An overall significant increase in LTCP from Hypoxia Boost vs. Oxygenated Boost treatments was observed in the full group of three tumor types (p < 0.0001). The effects of tumor volume and hypoxic fraction on LTCP were dependent on tumor type. The delay between imaging and boost treatments did not have a significant effect on LTCP for all tumor types. Conclusion This study confirms that EPROI locates resistant tumor hypoxic regions for radiation boost, increasing clonogenic LTCP, with potential enhanced therapeutic index in three tumor types. Preclinical absolute EPROI may provide correction for clinical hypoxia images using additional clinical physiologic MRI.
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Affiliation(s)
- Inna Gertsenshteyn
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Department of Radiology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Boris Epel
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
- O2M Technologies, Chicago, IL, United States
| | - Mihai Giurcanu
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, United States
| | - Eugene Barth
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - John Lukens
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Kayla Hall
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Jenipher Flores Martinez
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Mellissa Grana
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Matthew Maggio
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Richard C. Miller
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Subramanian V. Sundramoorthy
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Martyna Krzykawska-Serda
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
- Department of Biophysics and Cancer Biology, Jagiellonian University, Kraków, Poland
| | - Erik Pearson
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
| | - Bulent Aydogan
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
| | - Ralph R. Weichselbaum
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
| | | | | | - Howard J. Halpern
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States
- Center for EPR Imaging In Vivo Physiology, The University of Chicago, Chicago, IL, United States
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Northwood K, Pearson E, Arnautovska U, Kisely S, Pawar M, Sharma M, Vitangcol K, Wagner E, Warren N, Siskind D. Optimising plasma clozapine levels to improve treatment response: an individual patient data meta-analysis and receiver operating characteristic curve analysis. Br J Psychiatry 2023; 222:241-245. [PMID: 36994656 DOI: 10.1192/bjp.2023.27] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
BACKGROUND Although clozapine is the most efficacious medication for treatment-refractory schizophrenia, not all patients will have an adequate response. Optimising clozapine dose using therapeutic drug monitoring could therefore maximise response. AIMS Using individual patient data, we undertook a receiver operating characteristic (ROC) curve analysis to determine an optimal therapeutic range for clozapine levels to guide clinical practice. METHOD We conducted a systematic review of PubMed, PsycINFO and Embase for studies that provided individual participant level data on clozapine levels and response. These data were analysed using ROC curves to determine the prediction performance of plasma clozapine levels for treatment response. RESULTS We included data on 294 individual participants from nine studies. ROC analysis yielded an area under the curve of 0.612. The clozapine level at the point of optimal diagnostic benefit was 372 ng/mL; at this level, the response sensitivity was 57.3%, and specificity 65.7%. The interquartile range for treatment response was 223-558 ng/mL. There was no improvement in ROC performance with mixed models including patient gender, age or length of trial. Clozapine dose and clozapine concentration to dose ratio did not provide significantly meaningful prediction of response to clozapine. CONCLUSIONS Clozapine dose should be optimised based on clozapine therapeutic levels. We found that a range between 250 and 550 ng/mL could be recommended, while noting that a level of >350 ng/mL is the most optimal for response. Although some patients may not respond without clozapine levels >550 ng/mL, the benefits should be weighed against the increased risk of adverse drug reactions.
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Affiliation(s)
- Korinne Northwood
- Metro South Addiction and Mental Health Service, Metro South Health, Australia and Faculty of Medicine, University of Queensland, Australia
| | - E Pearson
- College of Medicine and Public Health, Flinders University, Australia
| | - U Arnautovska
- Metro South Addiction and Mental Health Service, Metro South Health, Australia and Faculty of Medicine, University of Queensland, Australia
| | - S Kisely
- Metro South Addiction and Mental Health Service, Metro South Health, Australia and Faculty of Medicine, University of Queensland, Australia
| | - M Pawar
- Metro South Addiction and Mental Health Service, Metro South Health, Australia
| | - M Sharma
- Department of Mental Health, Monash Health, Australia
| | - K Vitangcol
- Faculty of Medicine, University of Queensland, Australia
| | - E Wagner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Germany
| | - N Warren
- Metro South Addiction and Mental Health Service, Metro South Health, Australia and Faculty of Medicine, University of Queensland, Australia
| | - Dan Siskind
- Metro South Addiction and Mental Health Service, Metro South Health, Australia and Faculty of Medicine, University of Queensland, Australia
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Ni K, Xu Z, Culbert A, Luo T, Guo N, Yang K, Pearson E, Preusser B, Wu T, La Riviere P, Weichselbaum RR, Spiotto MT, Lin W. Author Correction: Synergistic checkpoint-blockade and radiotherapy–radiodynamic therapy via an immunomodulatory nanoscale metal–organic framework. Nat Biomed Eng 2022; 6:1449-1450. [DOI: 10.1038/s41551-022-00966-3] [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: 11/13/2022]
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6
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Kavak AG, Surucu M, Ahn KH, Pearson E, Aydogan B. Impact of respiratory motion on lung dose during total marrow irradiation. Front Oncol 2022; 12:924961. [PMID: 36330489 PMCID: PMC9622752 DOI: 10.3389/fonc.2022.924961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/16/2022] [Indexed: 11/21/2022] Open
Abstract
We evaluated the impact of respiratory motion on the lung dose during linac-based intensity-modulated total marrow irradiation (IMTMI) using two different approaches: (1) measurement of doses within the lungs of an anthropomorphic phantom using thermoluminescent detectors (TLDs) and (2) treatment delivery measurements using ArcCHECK where gamma passing rates (GPRs) and the mean lung doses were calculated and compared with and without motion. In the first approach, respiratory motions were simulated using a programmable motion platform by using typical published peak-to-peak motion amplitudes of 5, 8, and 12 mm in the craniocaudal (CC) direction, denoted here as M1, M2, and M3, respectively, with 2 mm in both anteroposterior (AP) and lateral (LAT) directions. TLDs were placed in five selected locations in the lungs of a RANDO phantom. Average TLD measurements obtained with motion were normalized to those obtained with static phantom delivery. The mean dose ratios were 1.01 (0.98–1.03), 1.04 (1.01–1.09), and 1.08 (1.04–1.12) for respiratory motions M1, M2, and M3, respectively. To determine the impact of directional respiratory motion, we repeated the experiment with 5-, 8-, and 12-mm motion in the CC direction only. The differences in average TLD doses were less than 1% when compared with the M1, M2, and M3 motions indicating a minimal impact from CC motion on lung dose during IMTMI. In the second experimental approach, we evaluated extreme respiratory motion 15 mm excursion in only the CC direction. We placed an ArcCHECK device on a commercial motion platform and delivered the clinical IMTMI plans of five patients. We compared, with and without motion, the dose volume histograms (DVHs) and mean lung dose calculated with the ArcCHECK-3DVH tool as well as GPR with 3%, 5%, and 10% dose agreements and a 3-mm constant distance to agreement (DTA). GPR differed by 11.1 ± 2.1%, 3.8 ± 1.5%, and 0.1 ± 0.2% with dose agreement criteria of 3%, 5%, and 10%, respectively. This indicates that respiratory motion impacts dose distribution in small and isolated parts of the lungs. More importantly, the impact of respiratory motion on the mean lung dose, a critical indicator for toxicity in IMTMI, was not statistically significant (p > 0.05) based on the Student’s t-test. We conclude that most patients treated with IMTMI will have negligible dose uncertainty due to respiratory motion. This is particularly reassuring as lung toxicity is the main concern for future IMTMI dose escalation studies.
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Affiliation(s)
- Ayse Gulbin Kavak
- Department of Radiation Oncology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Murat Surucu
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, United States
| | - Kang-Hyun Ahn
- Department of Radiation and Cellular Oncology, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
- Department of Radiation Oncology, University of Illinois at Chicago Medical Center, Chicago, IL, United States
| | - Erik Pearson
- Department of Radiation and Cellular Oncology, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
| | - Bulent Aydogan
- Department of Radiation and Cellular Oncology, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
- Department of Radiation Oncology, University of Illinois at Chicago Medical Center, Chicago, IL, United States
- *Correspondence: Bulent Aydogan, ;
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Cruz-Bastida JP, Pearson E, Al-Hallaq H. Toward understanding deep learning classification of anatomic sites: lessons from the development of a CBCT projection classifier. J Med Imaging (Bellingham) 2022; 9:045002. [PMID: 35903414 PMCID: PMC9311487 DOI: 10.1117/1.jmi.9.4.045002] [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: 11/01/2021] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
Purpose: Deep learning (DL) applications strongly depend on the training dataset and convolutional neural network architecture; however, it is unclear how to objectively select such parameters. We investigate the classification performance of different DL models and training schemes for the anatomic classification of cone-beam computed tomography (CBCT) projections. Approach: CBCT scans from 1055 patients were collected and manually classified into five anatomic classes and used to develop DL models to predict the anatomic class from single x-ray projections. VGG-16, Xception, and Inception v3 architectures were trained with 75% of the data, and the remaining 25% was used for testing and evaluation. To study the dependence of the classification performance on dataset size, training data was downsampled to various dataset sizes. Gradient-weighted class activation maps (grad-CAM) were generated using the model with highest classification performance, to identify regions with strong influence on CNN decisions. Results: The highest precision and recall values were achieved with VGG-16. One of the best performing combinations was the VGG-16 trained with 90 deg projections (mean class precision = 0.87). The training dataset size could be reduced to ∼ 50 % of its initial size, without compromising the classification performance. For correctly classified cases, Grad-CAM were more heavily weighted for anatomically relevant regions. Conclusions: It was possible to determine those dependencies with a higher influence on the classification performance of DL models for the studied task. Grad-CAM enabled the identification of possible sources of class confusion.
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Affiliation(s)
- Juan P Cruz-Bastida
- University of Chicago, Department of Radiology, Chicago, Illinois, United States.,University of Chicago, Department of Radiation and Cellular Oncology, Chicago, Illinois, United States
| | - Erik Pearson
- University of Chicago, Department of Radiation and Cellular Oncology, Chicago, Illinois, United States
| | - Hania Al-Hallaq
- University of Chicago, Department of Radiation and Cellular Oncology, Chicago, Illinois, United States
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8
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Liu X, Van Slyke AL, Pearson E, Shoniyozov K, Redler G, Wiersma RD. Improving the efficiency of small animal 3D-printed compensator IMRT with beamlet intensity total variation regularization. Med Phys 2022; 49:5400-5408. [PMID: 35608256 DOI: 10.1002/mp.15764] [Citation(s) in RCA: 1] [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] [Received: 09/25/2021] [Revised: 02/23/2022] [Accepted: 05/11/2022] [Indexed: 12/30/2022] Open
Abstract
PURPOSE There is growing interest in the use of modern 3D printing technology to implement intensity-modulated radiation therapy (IMRT) on the preclinical scale that is analogous to clinical IMRT. However, current 3D-printed IMRT methods suffer from complex modulation patterns leading to long delivery times, excess filament usage, and less accurate compensator fabrication. In this work, we have developed a total variation regularization (TVR) approach to address these issues. METHODS TVR-IMRT was used to optimize the beamlet intensity map, which was then converted to a thickness of the corresponding compensator attenuation region in copper-doped polylactic acid (PLA) filament. IMRT and TVR-IMRT heart and lung plans were generated for two different mice using three, five, or seven gantry angles. The total compensator thickness, total variation of compensator beamlet thicknesses, total variation of beamlet intensities, and exposure time were compared. The individual field doses and composite dose were delivered to film for one plan and gamma analysis was performed. RESULTS In total, 12 mice heart and lung plans were generated for both IMRT and TVR-IMRT cases. Across all cases, it was found that TVR-IMRT reduced the total variation of compensator beamlet thicknesses and beamlet intensities by 54 ± 4 % $54\pm 4\%$ and 50 ± 3 % $50\pm 3\%$ on average when compared to standard 3D-printed compensator IMRT. On average, the total mass of compensator material consumed and radiation beam-on time were reduced by 45 ± 6 % $45\pm 6\%$ and 24 ± 4 % $24\pm 4\%$ , respectively, whereas dose metrics remained comparable. Heart plan compensators were printed and delivered to film and subsequent gamma analysis performed for each of the single fields as well as the composite dose. For the composite delivery, a passing rate of 89.1% for IMRT and 95.4% for TVR-IMRT was achieved for a 3 % / 0.3 $3\%/0.3$ mm criterion. CONCLUSIONS TVR can be applied to small animal IMRT beamlet intensities to produce fluence maps and subsequent 3D-printed compensator patterns with significantly less complexity while still maintaining similar dose conformity to traditional IMRT. This can simplify/accelerate the 3D printing process, reduce the amount of filament required, and reduce overall beam-on time to deliver a plan.
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Affiliation(s)
- Xinmin Liu
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexander L Van Slyke
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erik Pearson
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois, USA
| | - Khayrullo Shoniyozov
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gage Redler
- Moffitt Cancer Center, Department of Radiation Oncology, Tampa, Florida, USA
| | - Rodney D Wiersma
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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9
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Ni K, Xu Z, Culbert A, Luo T, Guo N, Yang K, Pearson E, Preusser B, Wu T, La Riviere P, Weichselbaum RR, Spiotto MT, Lin W. Synergistic checkpoint-blockade and radiotherapy–radiodynamic therapy via an immunomodulatory nanoscale metal–organic framework. Nat Biomed Eng 2022; 6:144-156. [DOI: 10.1038/s41551-022-00846-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/12/2022] [Indexed: 12/20/2022]
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10
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Pearson E, Nielsen E, Kita S, Groves L, Nelson L, Moss J, Oliver C. Low speech rate but high gesture rate during conversational interaction in people with Cornelia de Lange syndrome. J Intellect Disabil Res 2021; 65:601-607. [PMID: 33694205 DOI: 10.1111/jir.12829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/28/2021] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cornelia de Lange syndrsome (CdLS) is a rare genetic syndrome with notable impaired expressive communication characterised by reduced spoken language. We examined gesture use to refine the description of expressive communication impairments in CdLS. METHODS During conversations, we compared gesture use in people with CdLS to peers with Down syndrome (DS) matched for receptive language and adaptive ability, and typically developing (TD) individuals of similar chronological age. RESULTS As anticipated the DS and CdLS groups used fewer words during conversation than TD peers (P < .001). However, the CdLS group used twice the number of gestures per 100 words compared with the DS and TD groups (P = .003). CONCLUSIONS Individuals with CdLS have a significantly higher gesture rate than expected given their level of intellectual disability and chronological age. This result indicates the cause of reduced use of spoken language does not extend to all forms of expressive communication.
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Affiliation(s)
- E Pearson
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
- School of Psychology, College of Health and Life Sciences, Aston University, Birmingham, UK
| | - E Nielsen
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - S Kita
- Department of Psychology, University of Warwick, Coventry, UK
| | - L Groves
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - L Nelson
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
- Royal Derby Hospital, Derby, UK
| | - J Moss
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
- School of Psychology, University of Surrey, Surrey, UK
| | - C Oliver
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
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11
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Eaton C, Tarver J, Shirazi A, Pearson E, Walker L, Bird M, Oliver C, Waite J. A systematic review of the behaviours associated with depression in people with severe-profound intellectual disability. J Intellect Disabil Res 2021; 65:211-229. [PMID: 33426741 DOI: 10.1111/jir.12807] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 11/09/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
The assessment of depression in people with severe to profound intellectual disability (severe-profound ID) is challenging, primarily due to inability to report internal states such as mood, feelings of worthlessness and suicidal ideation. This group also commonly presents with challenging behaviours (e.g. aggression and self-injury) with debate about whether these behaviours should be considered 'depressive equivalents' or are sensitive for, but not specific to, depression in severe-profound ID. We conducted a systematic review exploring behaviours associated with depression and low mood in individuals with severe-profound ID. The review was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (2009) guidelines. Three electronic databases were searched (Embase, PsycINFO and Ovid MEDLINE), and 13 studies were included and rated for quality. Few studies were rated as having high methodological quality. Behaviours captured by standard diagnostic schemes for depression (e.g. Diagnostic and Statistical Manual of Mental Disorders and International Classification of Diseases) showed a relationship with depression in severe-profound ID, including the two core symptoms (depressed affect and anhedonia), as well as irritability, sleep disturbance, psychomotor agitation, reduced appetite and fatigue. Challenging behaviours such as aggression, self-injury, temper tantrums, screaming and disruptive behaviour were associated with depression. Challenging behaviours show a robust relationship with depression. Whilst these behaviours may suggest an underlying depression, study limitations warrant caution in labelling them as 'depressive equivalents'. These limitations include not controlling for potential confounds (autism, other affective disorders and pain) and bias associated with comparing depressed/non-depressed groups on the same behavioural criteria used to initially diagnose and separate these groups. Future studies that use depressive measures designed for ID populations, which control for confounds and which explore low mood irrespective of psychiatric diagnosis, are warranted to better delineate the behaviours associated with depression in this population (PROSPERO 2018: CRD42018103244).
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Affiliation(s)
- C Eaton
- The Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
- Department of Child Life and Health, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - J Tarver
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - A Shirazi
- The Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - E Pearson
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - L Walker
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - M Bird
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - C Oliver
- The Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - J Waite
- School of Life and Health Sciences, Aston University, Birmingham, UK
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12
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Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber M, Best AA, DeJongh M, Kimbrel JA, D’haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res 2021; 49:D575-D588. [PMID: 32986834 PMCID: PMC7778927 DOI: 10.1093/nar/gkaa746] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/25/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical 'Rosetta Stone' to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org/biochem and KBase.
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Affiliation(s)
- Samuel M D Seaver
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Qizhi Zhang
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - James Jeffryes
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Janaka N Edirisinghe
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Aaron A Best
- Department of Biology, Hope College, Holland, MI 49423, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, MI 49423, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Patrik D’haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean R McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jay R Bolton
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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13
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Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber ME, Best AA, DeJongh M, Kimbrel JA, D'haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res 2021; 49:D1555. [PMID: 33179751 DOI: 10.1101/2020.03.31.018663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
ABSTRACTFor over ten years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions;; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical “Rosetta Stone” to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies, and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.
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Affiliation(s)
- Samuel M D Seaver
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Qizhi Zhang
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - James Jeffryes
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Janaka N Edirisinghe
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Aaron A Best
- Department of Biology, Hope College, Holland, MI 49423, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, MI 49423, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean R McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jay R Bolton
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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14
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Redler G, Pearson E, Liu X, Gertsenshteyn I, Epel B, Pelizzari C, Aydogan B, Weichselbaum R, Halpern HJ, Wiersma RD. Small Animal IMRT Using 3D-Printed Compensators. Int J Radiat Oncol Biol Phys 2020; 110:551-565. [PMID: 33373659 DOI: 10.1016/j.ijrobp.2020.12.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 11/17/2020] [Accepted: 12/13/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE Preclinical radiation replicating clinical intensity modulated radiation therapy (IMRT) techniques can provide data translatable to clinical practice. For this work, treatment plans were created for oxygen-guided dose-painting in small animals using inverse-planned IMRT. Spatially varying beam intensities were achieved using 3-dimensional (3D)-printed compensators. METHODS AND MATERIALS Optimized beam fluence from arbitrary gantry angles was determined using a verified model of the XRAD225Cx treatment beam. Compensators were 3D-printed with varied thickness to provide desired attenuation using copper/polylactic-acid. Spatial resolution capabilities were investigated using printed test-patterns. Following American Association of Physicists in Medicine TG119, a 5-beam IMRT plan was created for a miniaturized (∼1/8th scale) C-shape target. Electron paramagnetic resonance imaging of murine tumor oxygenation guided simultaneous integrated boost (SIB) plans conformally treating tumor to a base dose (Rx1) with boost (Rx2) based on tumor oxygenation. The 3D-printed compensator intensity modulation accuracy and precision was evaluated by individually delivering each field to a phantom containing radiochromic film and subsequent per-field gamma analysis. The methodology was validated end-to-end with composite delivery (incorporating 3D-printed tungsten/polylactic-acid beam trimmers to reduce out-of-field leakage) of the oxygen-guided SIB plan to a phantom containing film and subsequent gamma analysis. RESULTS Resolution test-patterns demonstrate practical printer resolution of ∼0.7 mm, corresponding to 1.0 mm bixels at the isocenter. The miniaturized C-shape plan provides planning target volume coverage (V95% = 95%) with organ sparing (organs at risk Dmax < 50%). The SIB plan to hypoxic tumor demonstrates the utility of this approach (hypoxic tumor V95%,Rx2 = 91.6%, normoxic tumor V95%,Rx1 = 95.7%, normal tissue V100%,Rx1 = 7.1%). The more challenging SIB plan to boost the normoxic tumor rim achieved normoxic tumor V95%,Rx2 = 90.9%, hypoxic tumor V95%,Rx1 = 62.7%, and normal tissue V100%,Rx2 = 5.3%. Average per-field gamma passing rates using 3%/1.0 mm, 3%/0.7 mm, and 3%/0.5 mm criteria were 98.8% ± 2.8%, 96.6% ± 4.1%, and 90.6% ± 5.9%, respectively. Composite delivery of the hypoxia boost plan and gamma analysis (3%/1 mm) gave passing results of 95.3% and 98.1% for the 2 measured orthogonal dose planes. CONCLUSIONS This simple and cost-effective approach using 3D-printed compensators for small-animal IMRT provides a methodology enabling preclinical studies that can be readily translated into the clinic. The presented oxygen-guided dose-painting demonstrates that this methodology will facilitate studies driving much needed biologic personalization of radiation therapy for improvements in patient outcomes.
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Affiliation(s)
- Gage Redler
- Moffitt Cancer Center, Department of Radiation Oncology, Tampa, Florida.
| | - Erik Pearson
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Xinmin Liu
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Inna Gertsenshteyn
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Boris Epel
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Charles Pelizzari
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Bulent Aydogan
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Ralph Weichselbaum
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Howard J Halpern
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Rodney D Wiersma
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania
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15
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Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber ME, Best AA, DeJongh M, Kimbrel JA, D'haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res 2020; 49:D1555. [PMID: 33179751 PMCID: PMC7778962 DOI: 10.1093/nar/gkaa1143] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Samuel M D Seaver
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Qizhi Zhang
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - James Jeffryes
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Janaka N Edirisinghe
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Aaron A Best
- Department of Biology, Hope College, Holland, MI 49423, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, MI 49423, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean R McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jay R Bolton
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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16
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Crouthamel B, Dixit A, Pearson E, Menzel J, Paul D, Shakhider A, Silverman J, Averbach S. P14 Intimate partner violence is associated with self-managed abortion in Bangladesh. Contraception 2020. [DOI: 10.1016/j.contraception.2020.07.033] [Citation(s) in RCA: 1] [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: 10/23/2022]
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17
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Day CPF, Miloserdov A, Wildish-Jones K, Pearson E, Carruthers AE. Quantifying the hygroscopic properties of cyclodextrin containing aerosol for drug delivery to the lungs. Phys Chem Chem Phys 2020; 22:11327-11336. [PMID: 32406900 DOI: 10.1039/d0cp01385d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aerosol dynamics is important to quantify in drug delivery to the lungs with the aim of delivering therapeutics to a target location and optimising drug efficacy. The macrocycle (2-hydroxypropyl)-β-cyclodextrin (2-HP-β-CD) is thought to alleviate symptoms associated with neurodegenerative diseases when inhaled but the hygroscopic response is not well understood. Here we measure the hygroscopic growth of individual aqueous aerosol containing 2-HP-β-CD in optical tweezers through analysis of morphology-dependent resonances arising in Raman spectra. Droplets are analysed in the size range of 3-5 μm in radius. The evolving radius and refractive index of each droplet are measured in response to change in relative humidity from 98-20% to determine mass and radius based hygroscopic growth factors, and compared with dynamic vapour sorption measurements. Bulk solution refractive index and density measurements were used in accordance with the self-consistent Lorenz-Lorentz rule to determine melt solute and droplet properties. The refractive index of 2-HP-β-CD was determined to be 1.520 ± 0.002 with a density of 1.389 ± 0.005 g cm-3. To our knowledge, we show the first aerosol measurements of 2-HP-β-CD and determine hygroscopicity. By quantifying the hygroscopic growth and physicochemical properties of 2-HP-β-CD, the impact of aerosol dynamics can be accounted for in tailoring drug formulations and informing models used to predict drug deposition patterns within the respiratory system.
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Affiliation(s)
- C P F Day
- Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
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18
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Wu T, Pearson E, Chmura S, Weichselbaum R, Aydogan B. Advance SBRT approaches for patients with oligometastases. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.05.058] [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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19
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Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 2018; 36:566-569. [PMID: 29979655 PMCID: PMC6870991 DOI: 10.1038/nbt.4163] [Citation(s) in RCA: 684] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Nomi L Harris
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rick L Stevens
- Computer Science Department and Computation Institute, University of Chicago, Chicago, Illinois, USA.,Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Sergei Maslov
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Paramvir Dehal
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Fernando Perez
- Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Berkeley Institute for Data Science, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Shane Canon
- National Energy Research Scientific Computing Center, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael W Sneddon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew L Henderson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - William J Riehl
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Dan Murphy-Olson
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Stephen Y Chan
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Roy T Kamimura
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Meghan M Drake
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Thomas S Brettin
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Elizabeth M Glass
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Dylan Chivian
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Dan Gunter
- Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Benjamin H Allen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jason Baumohl
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aaron A Best
- Department of Biology, Hope College, Holland, Michigan, USA
| | - Ben Bowen
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Christopher C Bun
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jer-Ming Chia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Ric Colasanti
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Neal Conrad
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - James J Davis
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Brian H Davison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, Michigan, USA
| | - Scott Devoid
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Emily Dietrich
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Inna Dubchak
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Janaka N Edirisinghe
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.,Computation Institute, University of Chicago, Chicago, Illinois, USA
| | - Gang Fang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - José P Faria
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Paul M Frybarger
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Wolfgang Gerlach
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Annette Greiner
- National Energy Research Scientific Computing Center, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - James Gurtowski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Holly L Haun
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Fei He
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Rashmi Jain
- Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcin P Joachimiak
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kevin P Keegan
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Shinnosuke Kondo
- Department of Computer Science, Hope College, Holland, Michigan, USA
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Miriam L Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Folker Meyer
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Marissa Mills
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Taeyun Oh
- Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Gary J Olsen
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Robert Olson
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Bruce Parrello
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sarah S Poon
- Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Gavin A Price
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Srividya Ramakrishnan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Pamela C Ronald
- Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Samuel M D Seaver
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Maulik Shukla
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Roman A Sutormin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mustafa H Syed
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - James Thomason
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Nathan L Tintle
- Department of Mathematics, Hope College, Holland, Michigan, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Daifeng Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Fangfang Xia
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Hyunseung Yoo
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Shinjae Yoo
- Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA
| | - Dantong Yu
- Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
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Al-Talabany S, Weir-McCall J, Mohan M, Singh J, Mordi I, Gandy S, Khan F, Choy A, Houston G, Pearson E, George J, Struthers A, Lang C. PO022 Metformin and Dapagliflozin Effects On Epicardial Adipose Tissue Area In Prediabetes and Type 2 Diabetes Patients: MRI Evaluation Studies. Glob Heart 2018. [DOI: 10.1016/j.gheart.2018.09.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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21
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Mordi I, Li T, Tee A, Palmer C, Pearson E, McCrimmon R, Doney A, Lang CC. P2783Diabetic retinopathy is associated with echocardiographic structural abnormalities and both heart failure with reduced and preserved ejection fraction. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p2783] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- I Mordi
- University of Dundee, Dundee, United Kingdom
| | - T Li
- University of Dundee, Dundee, United Kingdom
| | - A Tee
- University of Dundee, Dundee, United Kingdom
| | - C Palmer
- University of Dundee, Dundee, United Kingdom
| | - E Pearson
- University of Dundee, Dundee, United Kingdom
| | - R McCrimmon
- University of Dundee, Dundee, United Kingdom
| | - A Doney
- University of Dundee, Dundee, United Kingdom
| | - C C Lang
- University of Dundee, Dundee, United Kingdom
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22
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Barras M, Pearson E, Cousin I, Le Rouzic C, Thepaut M, Gentric JC, Roue JM, Yevich S, de Vries P. Renal artery embolization in a child with delayed hemodynamic instability from penetrating knife wound. Arch Pediatr 2018; 25:S0929-693X(18)30113-1. [PMID: 29909939 DOI: 10.1016/j.arcped.2018.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 02/22/2018] [Accepted: 05/20/2018] [Indexed: 11/24/2022]
Abstract
Penetrating laceration injury in the pediatric population may present as an acute or delayed life-threatening injury. Although emergent intra-arterial embolization is commonly utilized in adults, few cases have been reported for children. Surgical treatment for severe renal laceration injuries may require complete nephrectomy; an unfortunate outcome for a pediatric patient if a renal-preserving alternative is feasible. We present a case of penetrating renal laceration in a 10-year-old boy treated with intra-arterial embolization of the lacerated dominant renal artery and subsequent renal perfusion by an uninjured accessory renal artery allowing for renal preservation.
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Affiliation(s)
- M Barras
- Pediatric surgery department, CHU de Brest, 2, avenue Foch, 29609 Brest cedex, France.
| | - E Pearson
- Interventional Radiology department, CHU de Brest, boulevard Tanguy-Prigent, 29000 Brest, France
| | - I Cousin
- Pediatric surgery department, CHU de Brest, 2, avenue Foch, 29609 Brest cedex, France
| | - C Le Rouzic
- Pediatric surgery department, CHU de Brest, 2, avenue Foch, 29609 Brest cedex, France
| | - M Thepaut
- Pediatric surgery department, CHU de Brest, 2, avenue Foch, 29609 Brest cedex, France
| | - J-C Gentric
- Interventional Radiology department, CHU de Brest, boulevard Tanguy-Prigent, 29000 Brest, France
| | - J-M Roue
- Pediatric department, CHU de Brest, 2, avenue Foch, 29609 Brest cedex, France
| | - S Yevich
- Gustave Roussy Cancer Campus Grand Paris, Interventional Radiology department, 114, rue Edouard-Vaillant, 94805 Villejuif, France
| | - P de Vries
- Pediatric surgery department, CHU de Brest, 2, avenue Foch, 29609 Brest cedex, France
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23
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Senderowicz LG, Pearson E, Francis J. Quality of family planning counseling and the ability to realize fertility intentions in Tanzania. Contraception 2017. [DOI: 10.1016/j.contraception.2017.07.142] [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: 10/18/2022]
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24
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Zhang Z, Han X, Pearson E, Pelizzari C, Sidky EY, Pan X. Artifact reduction in short-scan CBCT by use of optimization-based reconstruction. Phys Med Biol 2016; 61:3387-406. [PMID: 27046218 DOI: 10.1088/0031-9155/61/9/3387] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Increasing interest in optimization-based reconstruction in research on, and applications of, cone-beam computed tomography (CBCT) exists because it has been shown to have to potential to reduce artifacts observed in reconstructions obtained with the Feldkamp-Davis-Kress (FDK) algorithm (or its variants), which is used extensively for image reconstruction in current CBCT applications. In this work, we carried out a study on optimization-based reconstruction for possible reduction of artifacts in FDK reconstruction specifically from short-scan CBCT data. The investigation includes a set of optimization programs such as the image-total-variation (TV)-constrained data-divergency minimization, data-weighting matrices such as the Parker weighting matrix, and objects of practical interest for demonstrating and assessing the degree of artifact reduction. Results of investigative work reveal that appropriately designed optimization-based reconstruction, including the image-TV-constrained reconstruction, can reduce significant artifacts observed in FDK reconstruction in CBCT with a short-scan configuration.
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Affiliation(s)
- Zheng Zhang
- Department of Radiology, The University of Chicago, Chicago, IL, USA
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25
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Abstract
BACKGROUND Patient dose from image guidance in radiotherapy is small compared to the treatment dose. However, the imaging beam is untargeted and deposits dose equally in tumor and healthy tissues. It is desirable to minimize imaging dose while maintaining efficacy. OBJECTIVE Image guidance typically does not require full image quality throughout the patient. Dynamic filtration of the kV beam allows local control of CT image noise for high quality around the target volume and lower quality elsewhere, with substantial dose sparing and reduced scatter fluence on the detector. METHODS The dynamic Intensity-Weighted Region of Interest (dIWROI) technique spatially varies beam intensity during acquisition with copper filter collimation. Fluence is reduced by 95% under the filters with the aperture conformed dynamically to the ROI during cone-beam CT scanning. Preprocessing to account for physical effects of the collimator before reconstruction is described. RESULTS Reconstructions show image quality comparable to a standard scan in the ROI, with higher noise and streak artifacts in the outer region but still adequate quality for patient localization. Monte Carlo modeling shows dose reduction by 10-15% in the ROI due to reduced scatter, and up to 75% outside. CONCLUSIONS The presented technique offers a method to reduce imaging dose by accepting increased image noise outside the ROI, while maintaining full image quality inside the ROI.
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Affiliation(s)
- Erik Pearson
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
- Present Address: Princess Margaret Cancer Center, UHN, Toronto, ON, Canada
| | - Xiaochuan Pan
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
- Department of Radiology, The University of Chicago, Chicago, IL, USA
| | - Charles Pelizzari
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA
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26
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Abstract
PURPOSE The use of medical technology capable of tracking patient motion or positioning patients along 6 degree-of-freedom (6DOF) has steadily increased in the field of radiation therapy. However, due to the complex nature of tracking and performing 6DOF motion, it is critical that such technology is properly verified to be operating within specifications in order to ensure patient safety. In this study, a robotic motion phantom is presented that can be programmed to perform highly accurate motion along any X (left-right), Y (superior-inferior), Z (anterior-posterior), pitch (around X), roll (around Y), and yaw (around Z) axes. In addition, highly synchronized motion along all axes can be performed in order to simulate the dynamic motion of a tumor in 6D. The accuracy and reproducibility of this 6D motion were characterized. METHODS An in-house designed and built 6D robotic motion phantom was constructed following the Stewart-Gough parallel kinematics platform archetype. The device was controlled using an inverse kinematics formulation, and precise movements in all 6 degrees-of-freedom (X, Y, Z, pitch, roll, and yaw) were performed, both simultaneously and separately for each degree-of-freedom. Additionally, previously recorded 6D cranial and prostate motions were effectively executed. The robotic phantom movements were verified using a 15 fps 6D infrared marker tracking system and the measured trajectories were compared quantitatively to the intended input trajectories. The workspace, maximum 6D velocity, backlash, and weight load capabilities of the system were also established. RESULTS Evaluation of the 6D platform demonstrated translational root mean square error (RMSE) values of 0.14, 0.22, and 0.08 mm over 20 mm in X and Y and 10 mm in Z, respectively, and rotational RMSE values of 0.16°, 0.06°, and 0.08° over 10° of pitch, roll, and yaw, respectively. The robotic stage also effectively performed controlled 6D motions, as well as reproduced cranial trajectories over 15 min, with a maximal RMSE of 0.04 mm translationally and 0.04° rotationally, and a prostate trajectory over 2 min, with a maximal RMSE of 0.06 mm translationally and 0.04° rotationally. CONCLUSIONS This 6D robotic phantom has proven to be accurate under clinical standards and capable of reproducing tumor motion in 6D. Such functionality makes the robotic phantom usable for either quality assurance or research purposes.
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Affiliation(s)
- Andrew H Belcher
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, Illinois 60637-1470
| | - Xinmin Liu
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, Illinois 60637-1470
| | - Zachary Grelewicz
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, Illinois 60637-1470
| | - Erik Pearson
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, Illinois 60637-1470
| | - Rodney D Wiersma
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, Illinois 60637-1470
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27
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Davis A, Pearson E, Pan X, Pelizzari C. SU-E-I-02: Characterizing Low-Contrast Resolution for Non-Circular CBCT Trajectories. Med Phys 2015. [DOI: 10.1118/1.4923999] [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: 11/07/2022] Open
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de Baere T, Tselikas L, Pearson E, Yevitch S, Boige V, Malka D, Ducreux M, Goere D, Elias D, Nguyen F, Deschamps F. Interventional oncology for liver and lung metastases from colorectal cancer: The current state of the art. Diagn Interv Imaging 2015; 96:647-54. [DOI: 10.1016/j.diii.2015.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 04/08/2015] [Indexed: 02/07/2023]
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Han X, Pearson E, Pelizzari C, Al-Hallaq H, Sidky EY, Bian J, Pan X. Algorithm-enabled exploration of image-quality potential of cone-beam CT in image-guided radiation therapy. Phys Med Biol 2015; 60:4601-33. [PMID: 26020490 DOI: 10.1088/0031-9155/60/12/4601] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Kilo-voltage (KV) cone-beam computed tomography (CBCT) unit mounted onto a linear accelerator treatment system, often referred to as on-board imager (OBI), plays an increasingly important role in image-guided radiation therapy. While the FDK algorithm is currently used for reconstructing images from clinical OBI data, optimization-based reconstruction has also been investigated for OBI CBCT. An optimization-based reconstruction involves numerous parameters, which can significantly impact reconstruction properties (or utility). The success of an optimization-based reconstruction for a particular class of practical applications thus relies strongly on appropriate selection of parameter values. In the work, we focus on tailoring the constrained-TV-minimization-based reconstruction, an optimization-based reconstruction previously shown of some potential for CBCT imaging conditions of practical interest, to OBI imaging through appropriate selection of parameter values. In particular, for given real data of phantoms and patient collected with OBI CBCT, we first devise utility metrics specific to OBI-quality-assurance tasks and then apply them to guiding the selection of parameter values in constrained-TV-minimization-based reconstruction. The study results show that the reconstructions are with improvement, relative to clinical FDK reconstruction, in both visualization and quantitative assessments in terms of the devised utility metrics.
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Affiliation(s)
- Xiao Han
- Department of Radiology, The University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637, USA
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Pearson E, Pan X, Pelizzari C. TH-A-18C-10: Dynamic Intensity Weighted Region of Interest Imaging. Med Phys 2014. [DOI: 10.1118/1.4889569] [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: 11/07/2022] Open
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31
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Sensakovic W, Pearson E, Letter H. SU-E-J-262: Segmentation in Therapy: Impact of Display. Med Phys 2014. [DOI: 10.1118/1.4888316] [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: 11/07/2022] Open
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Abstract
A stratified approach to medicine aims to identify subgroups of patients who should be managed differently from others. Diabetes is a condition that offers considerable potential for stratification, in areas of drug response, complication risk and rate of progression amongst others. Approaches to stratification can be simple, using clinical phenotyping, or more complex involving genomic and other '-omic' technologies. In this review, I will highlight the utility of measuring endogenous insulin production to aid in diagnosis and appropriate treatment; outline key advances in monogenic diabetes where determining genetic aetiology can result in dramatic changes in treatment, and describe the developments in the field of pharmacogenetics in Type 2 diabetes.
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Affiliation(s)
- E Pearson
- Division of Cardiovascular and Diabetes Medicine, Medical Research Institute, University of Dundee, Dundee, UK
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Genu A, Koch G, Colin D, Aho S, Pearson E, Ben Salem D. Factors influencing the occurrence of a T2-STIR hypersignal in the lumbosacral adipose tissue. Diagn Interv Imaging 2014; 95:283-8. [DOI: 10.1016/j.diii.2013.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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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Pearson E, Belcher A, Grelewicz Z, Wiersma R, Pelizzari C. WE-G-141-04: Use of a Dynamic KV X-Ray Collimator for Reduced-Dose Fluoroscopic Fiducial Tracking. Med Phys 2013. [DOI: 10.1118/1.4815655] [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: 11/07/2022] Open
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36
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Colhoun HM, Livingstone SJ, Looker HC, Morris AD, Wild SH, Lindsay RS, Reed C, Donnan PT, Guthrie B, Leese GP, McKnight J, Pearson DWM, Pearson E, Petrie JR, Philip S, Sattar N, Sullivan FM, McKeigue P. Hospitalised hip fracture risk with rosiglitazone and pioglitazone use compared with other glucose-lowering drugs. Diabetologia 2012; 55:2929-37. [PMID: 22945303 PMCID: PMC3464390 DOI: 10.1007/s00125-012-2668-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 06/25/2012] [Indexed: 01/12/2023]
Abstract
AIMS/HYPOTHESIS Current drug labels for thiazolidinediones (TZDs) warn of increased fractures, predominantly for distal fractures in women. We examined whether exposure to TZDs affects hip fracture in women and men and compared the risk to that found with other drugs used in diabetes. METHODS Using a nationwide database of prescriptions, hospital admissions and deaths in those with type 2 diabetes in Scotland we calculated TZD exposure among 206,672 individuals. Discrete-time failure analysis was used to model the effect of cumulative drug exposure on hip fracture during 1999-2008. RESULTS There were 176 hip fractures among 37,479 exposed individuals. Hip fracture risk increased with cumulative exposure to TZD: OR per year of exposure 1.18 (95% CI 1.09, 1.28; p = 3 × 10(-5)), adjusted for age, sex and calendar month. Hip fracture increased with cumulative exposure in both men (OR 1.20; 95% CI 1.03, 1.41) and women (OR 1.18; 95% CI 1.07, 1.29) and risks were similar for pioglitazone (OR 1.18) and rosiglitazone (OR 1.16). The association was similar when adjusted for exposure to other drugs for diabetes and for other potential confounders. There was no association of hip fracture with cumulative exposure to sulfonylureas, metformin or insulin in this analysis. The 90-day mortality associated with hip fractures was similar in ever-users of TZD (15%) and in never-users (13%). CONCLUSIONS/INTERPRETATION Hip fracture is a severe adverse effect with TZDs, affecting both sexes; labels should be changed to warn of this. The excess mortality is at least as much as expected from the reported association of pioglitazone with bladder cancer.
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Affiliation(s)
- H M Colhoun
- Medical Research Institute, University of Dundee, Ninewells Hospital & Medical School, Dundee, Scotland DD1 9SY, UK.
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Elder DHJ, Donnelly L, Wong A, Szwejkowski BR, Pauriah M, Lim TK, Pringle SD, Choy A, Pearson E, Morris A, George J, Struthers A, Palmer C, Doney A, Lang CC. 011 HbA1c and mortality in diabetic individuals with heart failure: an observational cohort study. Heart 2012. [DOI: 10.1136/heartjnl-2012-301877b.11] [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] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Basnett I, Shrestha MK, Shah M, Pearson E, Thapa K, Andersen KL. Evaluation of nurse providers of comprehensive abortion care using MVA in Nepal. J Nepal Health Res Counc 2012; 10:5-9. [PMID: 22929628] [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] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND Although Nepal's maternal mortality ratio has fallen over the past decade, unsafe abortion remains a leading cause of maternal morbidity and mortality. A key strategy for improving access to safe abortion services is to train mid-level providers such as nurses in comprehensive abortion care (CAC). The Family Health Division of the Nepal Ministry of Health trained an initial cohort of 96 nurses to provide first trimester CAC services using manual vacuum aspiration (MVA) between September 2006 and July 2009. This study evaluates the acceptability and quality of CAC services provided by trained nurses in Nepal. METHODS Five assessments were used to evaluate post-training service provision on CAC: facility logbooks registry, nurse provider interviews, facility assessments, facility manager interviews and procedure observation checklists. Ninety-two nurses from 50 facilities participated in the evaluation. Descriptive statistics are reported. RESULTS Overall, 5,600 women received CAC services from 42 facilities where nurses were providing services between June 2009 and April 2010. Complications were experienced by 68 surgical abortion clients (1.6%) and 12 medical abortion clients (1.2%). All nurses reported that clients were happy to receive care from them, and 67% of facility managers reported that clients preferred nurse providers over physicians or had no preference. Facility managers and nurses reported a need for additional support, including further training and improved drug and equipment supply. CONCLUSIONS Trained nurses provide high quality CAC services in Nepal. Additional support in the form of facilitative supervision and training should be considered to strengthen CAC service provision.
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Pavone M, Dyson M, Pearson E, Kakinuma T, Bulun S. Alterations in retinoid signaling in endometriosis may lead to differences in decidualization. Fertil Steril 2011. [DOI: 10.1016/j.fertnstert.2011.07.379] [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: 10/17/2022]
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Zhang Z, Han X, Pearson E, Bian J, Sidky E, Pelizzari C, Pan X. SU-E-J-07: A Preliminary Study on Optimal Dose-Allocation Parameters for Low-Dose Cone-Beam CT. Med Phys 2011. [DOI: 10.1118/1.3611775] [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: 11/07/2022] Open
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41
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Grelewicz Z, Pearson E, Alaei P, Pelizzari C, Wiersma R. Investigation of a Dynamical kV Aperture together with Combined MV-kV Dose Planning for Implementing Real-time 3D MV-kV Prostate Motion Tracking. Int J Radiat Oncol Biol Phys 2010. [DOI: 10.1016/j.ijrobp.2010.07.1564] [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]
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Grelewicz Z, Pearson E, Alaei P, Pelizzari C, Wiersma R. SU-GG-J-78: Investigation of Combined MV-KV Prostate Treatment Dose Planning for Real-Time MV-KV IGRT. Med Phys 2010. [DOI: 10.1118/1.3468302] [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: 11/07/2022] Open
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43
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Han X, Pearson E, Bian J, Cho S, Sidky E, Pelizzari C, Pan X. SU-GG-I-32: Preliminary Performance Evaluation of CBCT Image Reconstruction from Reduced Projection Data by TV-Minimization. Med Phys 2010. [DOI: 10.1118/1.3468065] [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: 11/07/2022] Open
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44
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Pearson E. What are the practical implications of developments in genetics? J R Coll Physicians Edinb 2010. [DOI: 10.4997/jrcpe.2010.s02] [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: 11/19/2022] Open
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Wiersma R, Pearson E, Pellizarri C. Development of a Dynamic kV Collimator for Low Diagnostic Dose Real-time 3D Motion Tracking during Radiation Therapy by Combined MV-kV Imaging. Int J Radiat Oncol Biol Phys 2009. [DOI: 10.1016/j.ijrobp.2009.07.1330] [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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46
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Pavone M, Pearson E, Milad M, Cheng Y, Bulun S. Endometriotic stromal cells express a molecular pattern consistent with decreased retinoid uptake, metabolism and action. Fertil Steril 2009. [DOI: 10.1016/j.fertnstert.2009.07.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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47
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Tong Z, Yang Z, Meyer JJ, McInnes AW, Xue L, Azimi AM, Baird J, Zhao Y, Pearson E, Wang C, Chen Y, Zhang K. A Novel Locus for X-linked Retinitis Pigmentosa. Ann Acad Med Singap 2009. [DOI: 10.47102/annals-acadmedsg.v35n7p476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Introduction: Retinitis pigmentosa (RP) is the most prevalent group of inherited retinopathies and demonstrates considerable clinical and genetic heterogeneity, with wide variations in disease severity, progression, and gene involvement. We studied a large family with RP to determine the pattern of inheritance and to identify the disease-causing gene/locus.
Materials and Methods: Ophthalmic examination was performed on 35 family members to identify affected individuals and carriers and to characterise the disease phenotype. Genetic linkage analysis was performed using short tandem repeat (STR) polymorphic markers encompassing the known loci for X-linked RP (xlRP) including RP2, RP3, RP6, RP23, and RP24. Mutation screening was performed by direct sequencing of PCR-amplified genomic DNA of the RP2 and RPGR genes of the affected individuals.
Results: A highly penetrant, X-linked form of RP was observed in this family. Age of onset was from 5 to 8 years and visual acuity ranged from 20/25 in children to light perception in older adults. Linkage analysis and direct sequencing showed that no known loci/genes were associated with the phenotype in this kindred.
Conclusion: A novel disease gene locus/loci is responsible for the xlRP phenotype in this family.
Key words: Genetic linkage, Mutation screening, Retinopathy
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Affiliation(s)
- Zongzhong Tong
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Zhenglin Yang
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Jay J Meyer
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Allen W McInnes
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Lai Xue
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Asif M Azimi
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Jenn Baird
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Yu Zhao
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Erik Pearson
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | | | - Yali Chen
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Kang Zhang
- University of Utah Health Sciences Center, Salt Lake City, Utah, USA
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Cho S, Pearson E, Pelizzari CA, Pan X. Region-of-interest image reconstruction with intensity weighting in circular cone-beam CT for image-guided radiation therapy. Med Phys 2009; 36:1184-92. [PMID: 19472624 DOI: 10.1118/1.3085825] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Imaging plays a vital role in radiation therapy and with recent advances in technology considerable emphasis has been placed on cone-beam CT (CBCT). Attaching a kV x-ray source and a flat panel detector directly to the linear accelerator gantry has enabled progress in target localization techniques, which can include daily CBCT setup scans for some treatments. However, with an increasing number of CT scans there is also an increasing concern for patient exposure. An intensity-weighted region-of-interest (IWROI) technique, which has the potential to greatly reduce CBCT dose, in conjunction with the chord-based backprojection-filtration (BPF) reconstruction algorithm, has been developed and its feasibility in clinical use is demonstrated in this article. A nonuniform filter is placed in the x-ray beam to create regions of two different beam intensities. In this manner, regions outside the target area can be given a reduced dose but still visualized with a lower contrast to noise ratio. Image artifacts due to transverse data truncation, which would have occurred in conventional reconstruction algorithms, are avoided and image noise levels of the low- and high-intensity regions are well controlled by use of the chord-based BPF reconstruction algorithm. The proposed IWROI technique can play an important role in image-guided radiation therapy.
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Affiliation(s)
- Seungryong Cho
- Department of Radiology, University of Chicago, Chicago, Illinois 60637, USA
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49
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Wiersma R, Pearson E, Pelizzari C. TH-C-303A-05: Development of a Dynamic KV Collimator for Low Diagnostic Dose Real-Time 3D Motion Tracking During Radiation Therapy by Combined MV-KV Imaging. Med Phys 2009. [DOI: 10.1118/1.3182630] [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: 11/07/2022] Open
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50
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Han X, Bian J, Cho S, Sidky E, Pearson E, Pelizzari C, Pan X. SU-FF-I-46: Accurate Image Reconstruction From Incomplete Kilovoltage Cone-Beam CT Data in Radiation Therapy. Med Phys 2009. [DOI: 10.1118/1.3181165] [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: 11/07/2022] Open
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