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  • 1
    In: Magnetic Resonance in Medicine, Wiley, Vol. 91, No. 5 ( 2024-05), p. 1803-1821
    Abstract: has often been proposed as a quantitative imaging biomarker for diagnosis, prognosis, and treatment response assessment for various tumors. None of the many software tools for quantification are standardized. The ISMRM Open Science Initiative for Perfusion Imaging–Dynamic Contrast‐Enhanced (OSIPI‐DCE) challenge was designed to benchmark methods to better help the efforts to standardize measurement. Methods A framework was created to evaluate values produced by DCE‐MRI analysis pipelines to enable benchmarking. The perfusion MRI community was invited to apply their pipelines for quantification in glioblastoma from clinical and synthetic patients. Submissions were required to include the entrants' values, the applied software, and a standard operating procedure. These were evaluated using the proposed score defined with accuracy, repeatability, and reproducibility components. Results Across the 10 received submissions, the score ranged from 28% to 78% with a 59% median. The accuracy, repeatability, and reproducibility scores ranged from 0.54 to 0.92, 0.64 to 0.86, and 0.65 to 1.00, respectively (0–1 = lowest–highest). Manual arterial input function selection markedly affected the reproducibility and showed greater variability in analysis than automated methods. Furthermore, provision of a detailed standard operating procedure was critical for higher reproducibility. Conclusions This study reports results from the OSIPI‐DCE challenge and highlights the high inter‐software variability within estimation, providing a framework for ongoing benchmarking against the scores presented. Through this challenge, the participating teams were ranked based on the performance of their software tools in the particular setting of this challenge. In a real‐world clinical setting, many of these tools may perform differently with different benchmarking methodology.
    Type of Medium: Online Resource
    ISSN: 0740-3194 , 1522-2594
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2024
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  • 2
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2012
    In:  Arthritis Research & Therapy Vol. 14, No. 3 ( 2012), p. R131-
    In: Arthritis Research & Therapy, Springer Science and Business Media LLC, Vol. 14, No. 3 ( 2012), p. R131-
    Type of Medium: Online Resource
    ISSN: 1478-6354
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2012
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  • 3
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 81, No. 4_Supplement ( 2021-02-15), p. PS13-18-PS13-18
    Abstract: Background: This study evaluates the ability to predict the response of locally advanced breast cancers to neoadjuvant therapy (NAT) using patient-specific magnetic resonance imaging (MRI) data and a biophysical mathematical model. The 3D mathematical model consists of three parts: tumor cell proliferation, tumor spread (diffusion), and treatment. In particular, the tumor cells proliferate according to logistic growth, and the diffusion term is coupled to the mechanical properties of the surrounding fibroglandular and adipose tissues to inform individual tumor growth patterns (specific to each patient’s anatomy). The model’s treatment term accounts for tumor cell reduction according to approximate local drug delivery for each patient. Methods: Patients (N = 21) with intermediate to high grade invasive breast cancers with varying receptor status, who were eligible for NAT as a component of their clinical care, were recruited. Each patient was treated with standard-of-care consisting of one or two NAT regimens in sequence followed by surgical resection of any residual tumor. MRI data are acquired at four time points: 1) prior to initiation of NAT, 2) after 1 cycle of NAT, 3) after 2-4 cycles of NAT, and 4) 1 cycle after scan 3. The MRI data is processed and evaluated using our semi-automated pipeline. Specifically, diffusion-weighted MRI data is utilized to characterize the cellularity throughout the tumor tissue, and dynamic contrast-enhanced (DCE-) MRI data is used to segment the breast tissue and analyze the local drug delivery using pharmacokinetic analysis and population-derived plasma curves of drug concentrations. The model’s predictive ability is assessed using three different strategies. First, the model is calibrated using each patient’s first two scans to enable predictions of the total tumor cellularity, volume, and longest axis that are directly compared to the values measured from their third scan. Second, the model’s predictions for tumor response are compared to the corresponding response evaluation criteria in solid tumors (RECIST) results. Third, the model is re-calibrated using scans 3 and 4 and simulated to the time of surgery to compare the model’s predictions to each patient’s response status determined by surgical pathology. Results: Calibrating the model with MRI data for one cycle of therapy yields predictions strongly correlated with tumor response measured from each patient’s third scan, concordance correlation coefficients of 0.91, 0.90, and 0.86 for total cellularity, volume, and longest axis, respectively (p & lt; 0.01, N = 18). The model’s predictions are significantly (p & lt; 0.01) correlated with tumor response as designated by RECIST for the cohort. Specifically, the model predicts greater percent reduction in the longest axis for the RECIST designated responder group (i.e., complete response and partial response) compared to non-responders. At the time of surgery, the model predicts changes in total tumor cellularity from baseline that are significantly (p & lt; 0.01) correlated with pathological response status—an area under the receiver operator characteristic curve of 0.92 and a sensitivity and specificity of 1.0 and 0.74, respectively. Discussion: These preliminary results suggest that this clinical-mathematical approach can be predictive of tumor response very early in the course of NAT on a patient-specific basis. Moreover, the study was performed in the community-care setting across a heterogenous group of patients, indicating the approach may be practical for wide-spread application. NCI U01 CA174706, NCI U01 CA154602, CPRIT RR160005, ACS-RSG-18-006-01-CCE, R01CA240589, NCI-U24CA226110, CPRIT RR160093 Citation Format: Angela M Jarrett, David A. Hormuth, II, Anum K Syed, Chengyue Wu, John Virostko, Anna G Sorace, Julie C DiCarlo, Jeanne Kowalski, Debra Patt, Boone Goodgame, Sarah Avery, Thomas E Yankeelov. Predicting breast cancer response to neoadjuvant therapies using a mathematical model individualized with patient-specific magnetic resonance imaging data: Preliminary Results [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS13-18.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
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  • 4
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    Online Resource
    American Association for Cancer Research (AACR) ; 2021
    In:  Cancer Research Vol. 81, No. 4_Supplement ( 2021-02-15), p. PS3-26-PS3-26
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 81, No. 4_Supplement ( 2021-02-15), p. PS3-26-PS3-26
    Abstract: Introduction. X-ray mammography is the standard-of-care screening protocol for breast cancer due to its low cost, widespread availability, and greater specificity. While magnetic resonance imaging (MRI) has lower specificity, it has superior tissue contrast, and dynamic contrast-enhanced (DCE) MRI has been shown to increase MRI specificity due to its ability to estimate tissue vascular properties. Because of the increased expense and scan time for MRI, there is an ongoing effort to develop abbreviated breast MRI scans for screening high-risk patients at a lower cost without compromising quantitative information. Here we investigate the effects of the limited dynamic time course afforded by an abbreviated breast MRI exam on the quantitative tissue information computed from retrospectively abbreviated DCE-MRI data. Methods. Data acquisition. We evaluate the error in perfusion model parameters computed using DCE-MRI time courses sourced from three datasets acquired with very different temporal resolutions (dt). These datasets are the ACRIN 6883 multi-site breast trial (dt = 15 s), The University of Texas at Austin (UTA) neoadjuvant therapy study (dt = 7.3 s), and The University of Chicago (UC) ultra-fast breast DCE-MRI study (dt = 3.4 s). Ten representative patients are chosen from each of these datasets for a total of 30 DCE-MRI patient datasets. All 30 full-time courses (FTCs) are retrospectively truncated into a series of abbreviated-time courses (ATCs). An ATC containing the first n post-contrast injection time points of a DCE-MRI time course is referred to as “ATC n.” For the ACRIN dataset, n is the inclusive set of integers from 7 to 18; and, similarly, for the UC data, n is the inclusive set of integers from 12 to 23. For the UTA dataset, n is the inclusive set ranging from 13 through 53, incrementing by eight. Data Analysis. The groups of FTCs and ATCs are analyzed by one of three models, determined by the specifics of the acquisition details of each dataset. The standard Kety-Tofts (SKT) model is fit to the UTA time courses, the reference-region (RR) model is fit to the ACRIN time courses, and the Patlak model is fit to the UC time courses. The volume transfer constant (Ktrans) characterizes tissue enhancement in all three models; whereas, the extravascular/extracellular volume fraction (ve) is specific to the SKT and RR models, and the plasma volume fraction (vp) is specific to the Patlak model. Due to the absence of an arterial input function (AIF) for the ACRIN dataset, the RR model was most appropriate with the pectoral muscle serving as the reference region. The UTA dataset has a population AIF and is thus able to be modeled by the SKT. Lastly, the UC dataset does not capture the tissue washout necessary for ve estimation, so the Patlak model was chosen for analyzing tissue enhancement. Results and Conclusion. The longest ATCs of 4.5, 6.4, and 1.3 min. yielded average errors of 9.1%, 7%, and 3.6% in Ktrans for the ACRIN, UTA, and UC datasets, respectively; and the shortest ATCs of 2, 1.6, and 0.6 min. yielded higher average errors of 24.2%, 22.8%, and 65% in Ktrans, respectively. This is expected from simulations as even the most aggressive ATCs did not substantially exclude the tissue enhancement, characterized by Ktrans. Errors in ve were higher overall since shorter ATCs exclude much of the washout phase. As Ktrans has been shown to discriminate between malignant and benign lesions in full length DCE-MRI scans, it is promising that tolerable errors are observed in the abbreviated MRI setting. There is potential for implementing quantitative abbreviated DCE-MRI scans in the clinic for enhanced diagnostic specificity while freeing up scan time for additional imaging sequences without interfering with standard-of-care image acquisition. Citation Format: Kalina P Slavkova, Julie C DiCarlo, Anum K Syed, Chengyue Wu, John Virostko, Anna G Sorace, Thomas E Yankeelov. Characterizing errors in perfusion model parameters derived from retrospectively abbreviated quantitative DCE-MRI data [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS3-26.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 16_Supplement ( 2020-08-15), p. 5485-5485
    Abstract: Introduction: We show that the combination of quantitative magnetic resonance imaging (MRI) and mathematical modeling can accurately predict tumor response for individual patients, and we demonstrate the selection of personalized therapeutic regimens using our mathematical model to vary, in silico, a range of clinically feasible treatment plans to achieve the greatest tumor control. Methods: Breast cancer patients (N = 18) were scanned by MRI at three time points during neoadjuvant therapy (NAT): 1) prior to NAT, 2) after one cycle of their initial NAT regimen, and 3) after the completion of their initial NAT regimen. Specifically, diffusion-weighted MRI data characterizing tumor cellularity was collected to estimate tumor cell burden, and dynamic contrast-enhanced MRI data was collected to estimate the local drug delivery using pharmacokinetic analysis and population-derived plasma curves of the administered chemotherapies. To predict tumor response, we calibrated our tissue scale, 3D, biophysical mathematical model to each patient's MRI data set using their first two scans. Using the calibrated, patient-specific parameters, the model was projected forward to the third scan time. The predicted total tumor cellularity, volume, and longest axis were compared to the actual values measured from the patient's third scan. Following evaluation of the model's predictive ability, we then employed the model to identify potentially superior, clinically relevant, alternative dosing regimens for each patient. The alternative regimens were defined using the same total amount of drug each patient received during their standard regimen, while varying dosages and frequency between their second and third scans. Statistical analysis was completed with Pearson correlation and Wilcoxon signed rank test. Results: The model's predictions of tumor response are significantly correlated to the measured tumor burden at the time of scan 3 (r2 & gt; 0.88, p & lt; 0.01) for total cellularity, total volume, and longest axis. For the alternative dosing regimens assessed, the model predicted that individual patients could have achieved, on average, an additional 21% (0-46%) reduction in total cellularity. The optimal dosing regimens chosen by the model were predicted to significantly outperform standard regimens for tumor control (p & lt; 0.001). Conclusions: These results suggest that the mathematical model can be predictive of tumor response by MRI in the clinical setting using data at the earliest times of therapy. With in silico studies, we illustrate how therapeutic regimens can be selected for individual patients for better tumor control, revealing that standard regimens may not be the most effective for every patient. These results represent a first step towards mathematically-based, personalized patient regimens. Future work aims to optimize therapy regimens via established optimal control theory methods. Citation Format: Angela M. Jarrett, Ernesto A. Lima, David A. Hormuth, Chengyue Wu, John Virostko, Anna G. Sorace, Julie C. DiCarlo, Debra Patt, Boone Goodgame, Sarah Avery, Thomas E. Yankeelov. Patient-specific neoadjuvant regimens for breast cancer identified via image-driven mathematical modeling [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5485.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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  • 6
    In: Magnetic Resonance in Medicine, Wiley, Vol. 89, No. 3 ( 2023-03), p. 1134-1150
    Abstract: Click here for author‐reader discussions
    Type of Medium: Online Resource
    ISSN: 0740-3194 , 1522-2594
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 1493786-4
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  • 7
    In: Magnetic Resonance in Medicine, Wiley, Vol. 89, No. 4 ( 2023-04), p. 1617-1633
    Abstract: Click here for author‐reader discussions
    Type of Medium: Online Resource
    ISSN: 0740-3194 , 1522-2594
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2023
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  • 8
    In: International Journal of Clinical Rheumatology, OMICS Publishing Group, Vol. 6, No. 1 ( 2011-02), p. 15-24
    Type of Medium: Online Resource
    ISSN: 1758-4272
    Language: English
    Publisher: OMICS Publishing Group
    Publication Date: 2011
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  • 9
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 4_Supplement ( 2022-02-15), p. P3-03-03-P3-03-03
    Abstract: Background: Early and accurate prediction of response to neoadjuvant therapy (NAT) would empower personalization of breast cancer treatment regimens based on expected response. Noninvasive, quantitative dynamic contrast-enhanced (DCE-MRI) and diffusion-weighted magnetic resonance imaging (DW-MRI), when performed during the course of NAT, can accurately predict the ultimate pathological response. While these techniques have been incorporated into clinical trials in the academic setting, they have not yet been translated to the community setting, where most cancer patients receive their care. Implementation of quantitative MRI in the community setting widely expands the potential impact it can provide by 1) allowing community settings to participate in clinical trials that require quantitative MRI, and 2) advancing quantitative MRI towards standard-of-care for prediction of response in breast cancer. Methods: Women with locally advanced breast cancer (N = 28) were imaged four times during the course of NAT: 1) prior to the start of NAT, 2) after 1 cycle of NAT, 3) after 2-4 cycles of NAT, and 4) 1 cycle after MRI #3. Imaging data was acquired on 3T Siemens Skyra scanners equipped with breast coils and sited in a community hospital and radiology clinic, respectively. DW-MRI and DCE-MRI were acquired over 10 slices of 5 mm thickness. DW-MRI was acquired with diagonal monopolar diffusion-encoding gradients with b-values of 0, 200, and 800 s/mm2 in a total scan time of 1 minute 39 seconds. Voxel wise tumor cellularity was quantified using the apparent diffusion coefficient (ADC). For DCE-MRI, a gadolinium-based contrast agent was administered intravenously at 2 mL/sec after the acquisition of baseline scans. DCE-MRI data was acquired dynamically with a temporal resolution of 7.27 seconds for a total acquisition time of 8 minutes. The volume transfer constant Ktrans was calculated using Patlak analysis of DCE-MRI data to characterize the tumor vasculature. The tumor was semi-automatically segmented using a manually drawn region of interest followed by fuzzy c-means clustering of DCE-MRI data to identify a functional tumor volume. Measurements of tumor volume were combined with both ADC and Ktrans to yield metrics of tumor cellularity and bulk tumor flow, respectively. Results: Women who achieved pathological complete response at the time of surgery (pCR; n=8) displayed significantly different treatment-induced changes in MRI-derived tumor parameters versus women who did not achieve pCR (non-pCR, n=20). After 1 cycle of NAT, women who achieved pCR had smaller functional tumor volume and lower cellularity (p & lt; 0.05) than non-pCR study participants. At the third and fourth MRI, tumor volume, ADC, Ktrans, cellularity, and bulk tumor flow were all significantly different between the pCR and non-pCR cohorts (p & lt; 0.05). Of note, longest tumor diameter was not predictive of pCR at any time point in this study. Conclusions: This study demonstrates that quantitative DCE- and DW-MRI can be implemented successfully in community care facilities within standard-of-care settings for imaging locally advanced breast cancer. Metrics extracted from the change in DW-MRI (ADC) and DCE-MRI (Ktrans) can accurately predict pathological complete response to neoadjuvant therapy and may be more sensitive to tumor response than the RECIST criteria. Furthermore, incorporating quantitative metrics with tumor volume further increases the ability to predict pathological response to NAT in locally advanced breast cancer. While there are still challenges to address to effectively implement these quantitative metrics into the clinical workflow, this study is first in its kind to transition a decade’s worth of quantitative MRI advancements from academic settings into standard-of-care. Citation Format: John Virostko, Anna G Sorace, Kalina P Slavkova, Anum S Kazerouni, Angela M Jarrett, Julie C DiCarlo, Stefanie Woodard, Sarah Avery, Boone W Goodgame, Debra Patt, Thomas E Yankeelov. Quantitative multiparametric MRI predicts response to neoadjuvant therapy in the community setting [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-03-03.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 10
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 4_Supplement ( 2022-02-15), p. P3-02-09-P3-02-09
    Abstract: Background: Standard of care (SOC) breast MRI exams typically acquire 4-7 frames of dynamic contrast-enhanced MRI (DCE-MRI) for cancer screening and staging. Post-contrast images depict lesion spiculations and boundaries to identify and characterize tumors. Pharmacokinetic (PK) analysis of DCE-MRI involves modeling blood flow to the lesion and surrounding tissue and has shown promise in diagnosis and prediction of therapeutic response. Currently, SOC DCE-MRI requires ~60-90 seconds per volume for images with sufficient quality and spatial resolution. However, PK analysis of DCE-MRI requires faster time course sampling. For this reason, PK modeling is limited to research scans with lower spatial resolution and higher temporal resolution. PK modeling would improve feedback of treatment response, and implementation in the SOC exam would increase imaging trial participation. In this study, we tested the estimation of Ktrans, a mixed perfusion and permeability PK parameter, from three images at optimal time points after contrast agent (CA) injection, and compared it to the Ktrans estimation from analysis of the full-length time course.. Methods: Women (N=23) with newly diagnosed invasive breast cancers who were eligible for neoadjuvant therapy (NAT) were scanned with a research MRI protocol as part of a treatment-monitoring study. Images acquired prior to the start of NAT were used. MRI was performed on 3.0T Siemens Skyra scanners at two sites with bilateral breast coils. The research protocol included ten sagittal slices centered about the primary tumor. The DCE-MRI images came from a fast sequence with 1.3 × 1.3 × 5.0 mm resolution acquired at 7.3 seconds per frame (66 frames total,) with a gadolinium-based CA injected one minute into the scan. A population arterial input function was used to implement a mathematical graph-based search of possible tissue CA concentration curves from the expected range of PK parameters. The search results gave a set of three optimized sub-sampled timepoints, Topt, from the full set of sample times, Tfull, at which to best sample the CA concentration curves to optimally estimate PK values. The imaging data was analyzed to find one parameter map from image times Tfull, and another from the subset of images at times Topt. The difference in Ktrans was computed at each parameter map voxel, and the concordance correlation coefficient (CCC) was computed per patient to determine agreement. The median Ktrans values were also compared for each patient. Results: The graph-based search of CA concentration curves found optimal times Topt of 37, 66, and 153 seconds after injection. The averaged values over all patients for median and maximum Ktrans from the original Tfull image set were 0.07 and 0.5 (min)-1. The average difference in Ktrans values between the Topt and Tfull sets was 0.02 (min)-1. When the median Ktrans values for each patient were compared, the average difference in median Ktrans values was 15% +/- 9%. The concordance correlation coefficients comparing the Topt and Tfull -sampled parameter maps for each patient were 0.89 +/- 0.12, showing high agreement. Discussion: This retrospective analysis suggests that it is possible to estimate PK parameters from a few properly selected post-contrast images inserted into a SOC DCE-MRI exam. The combination of optimal timing with fast acquisition techniques for high-resolution imaging could be used to provide quantitative data while preserving post-contrast images with the necessary spatial resolution for clinical reading. Importantly, the test images were acquired in the community setting with widely available MRI hardware, further indicating the potential for integration with SOC exams. Funding: NCI U24 CA226110, NCI U01 CA174706, NCI U01 CA142565, CPRIT RR160005 Citation Format: Julie C DiCarlo, Angela M Jarrett, Anum S Kazerouni, John Virostko, Anna G Sorace, Kalina P Slavkova, Debra Patt, Boone W Goodgame, Sarah Avery, Thomas E Yankeelov. Three timepoint pharmacokinetic modeling to incorporate within standard of care MRI breast exams [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-02-09.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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