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Jeong JJ, Vey BL, Bhimireddy A, Kim T, Santos T, Correa R, Dutt R, Mosunjac M, Oprea-Ilies G, Smith G, Woo M, McAdams CR, Newell MS, Banerjee I, Gichoya J, Trivedi H. The EMory BrEast imaging Dataset (EMBED): A Racially Diverse, Granular Dataset of 3.4 Million Screening and Diagnostic Mammographic Images. Radiol Artif Intell 2023; 5:e220047. [PMID: 36721407 PMCID: PMC9885379 DOI: 10.1148/ryai.220047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/04/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023]
Abstract
Supplemental material is available for this article. Keywords: Mammography, Breast, Machine Learning © RSNA, 2023.
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Lei Y, Wang T, Jeong JJ, Janopaul-Naylor J, Kesarwala AH, Roper J, Tian S, Bradley JD, Liu T, Higgins K, Yang X. Automated lung tumor delineation on positron emission tomography/computed tomography via a hybrid regional network. Med Phys 2023; 50:274-283. [PMID: 36203393 PMCID: PMC9868056 DOI: 10.1002/mp.16001] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Multimodality positron emission tomography/computed tomography (PET/CT) imaging combines the anatomical information of CT with the functional information of PET. In the diagnosis and treatment of many cancers, such as non-small cell lung cancer (NSCLC), PET/CT imaging allows more accurate delineation of tumor or involved lymph nodes for radiation planning. PURPOSE In this paper, we propose a hybrid regional network method of automatically segmenting lung tumors from PET/CT images. METHODS The hybrid regional network architecture synthesizes the functional and anatomical information from the two image modalities, whereas the mask regional convolutional neural network (R-CNN) and scoring fine-tune the regional location and quality of the output segmentation. This model consists of five major subnetworks, that is, a dual feature representation network (DFRN), a regional proposal network (RPN), a specific tumor-wise R-CNN, a mask-Net, and a score head. Given a PET/CT image as inputs, the DFRN extracts feature maps from the PET and CT images. Then, the RPN and R-CNN work together to localize lung tumors and reduce the image size and feature map size by removing irrelevant regions. The mask-Net is used to segment tumor within a volume-of-interest (VOI) with a score head evaluating the segmentation performed by the mask-Net. Finally, the segmented tumor within the VOI was mapped back to the volumetric coordinate system based on the location information derived via the RPN and R-CNN. We trained, validated, and tested the proposed neural network using 100 PET/CT images of patients with NSCLC. A fivefold cross-validation study was performed. The segmentation was evaluated with two indicators: (1) multiple metrics, including the Dice similarity coefficient, Jacard, 95th percentile Hausdorff distance, mean surface distance (MSD), residual mean square distance, and center-of-mass distance; (2) Bland-Altman analysis and volumetric Pearson correlation analysis. RESULTS In fivefold cross-validation, this method achieved Dice and MSD of 0.84 ± 0.15 and 1.38 ± 2.2 mm, respectively. A new PET/CT can be segmented in 1 s by this model. External validation on The Cancer Imaging Archive dataset (63 PET/CT images) indicates that the proposed model has superior performance compared to other methods. CONCLUSION The proposed method shows great promise to automatically delineate NSCLC tumors on PET/CT images, thereby allowing for a more streamlined clinical workflow that is faster and reduces physician effort.
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Affiliation(s)
- Yang Lei
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Tonghe Wang
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Jiwoong J Jeong
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - James Janopaul-Naylor
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Aparna H Kesarwala
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Justin Roper
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Sibo Tian
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Jeffrey D Bradley
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Tian Liu
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Kristin Higgins
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
| | - Xiaofeng Yang
- Department of Radiation Oncology and Winship Cancer Institute, Emory University, School of Medicine, Atlanta, Georgia, USA
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Jeong JJ, Tariq A, Adejumo T, Trivedi H, Gichoya JW, Banerjee I. Systematic Review of Generative Adversarial Networks (GANs) for Medical Image Classification and Segmentation. J Digit Imaging 2022; 35:137-152. [PMID: 35022924 PMCID: PMC8921387 DOI: 10.1007/s10278-021-00556-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/05/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 11/28/2022] Open
Abstract
In recent years, generative adversarial networks (GANs) have gained tremendous popularity for various imaging related tasks such as artificial image generation to support AI training. GANs are especially useful for medical imaging-related tasks where training datasets are usually limited in size and heavily imbalanced against the diseased class. We present a systematic review, following the PRISMA guidelines, of recent GAN architectures used for medical image analysis to help the readers in making an informed decision before employing GANs in developing medical image classification and segmentation models. We have extracted 54 papers that highlight the capabilities and application of GANs in medical imaging from January 2015 to August 2020 and inclusion criteria for meta-analysis. Our results show four main architectures of GAN that are used for segmentation or classification in medical imaging. We provide a comprehensive overview of recent trends in the application of GANs in clinical diagnosis through medical image segmentation and classification and ultimately share experiences for task-based GAN implementations.
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Affiliation(s)
- Jiwoong J Jeong
- Department of Biomedical Informatics, Emory School of Medicine, Atlanta, USA.
| | - Amara Tariq
- Department of Biomedical Informatics, Emory School of Medicine, Atlanta, USA
| | | | - Hari Trivedi
- Department of Radiology, Emory School of Medicine, Atlanta, USA
| | - Judy W Gichoya
- Department of Radiology, Emory School of Medicine, Atlanta, USA
| | - Imon Banerjee
- Department of Biomedical Informatics, Emory School of Medicine, Atlanta, USA.,Department of Radiology, Emory School of Medicine, Atlanta, USA
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Shin JU, Park JH, Oh SH, Jeong JJ, Kang S, Nam K, Chung WY, Lee JH. Early intervention in thyroidectomy scars: demographics, symptoms, and prevention. J Wound Care 2015; 24:163-4, 166-8, 170-1. [PMID: 25853473 DOI: 10.12968/jowc.2015.24.4.163] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Although hypertrophic scars are cosmetically problematic for patients following thyroidectomy, the associated risk factors are not well defined. Our objective was to determine the factors associated with hypertrophic scar development following thyroidectomy. METHOD A retrospective chart review was performed collecting data on sex, age, body mass index (BMI), operation site, skin characteristics (pigmentation, erythema, elasticity, and hydration), and clinical scar characteristics (itching, tightening, induration, adhesion, and oedema). It was also noted if the patient had early scar intervention with intralesional steroid injection or non-ablative fractional laser irradiation, and preventive topical treatment agents. The effects of these factors were analysed using univariate and multivariate analyses. RESULTS Data from 1141 patients showed the incidence of hypertrophic scars was 13.9%. Significant variables in univariate analysis were combined for multivariate analysis. Young age, high BMI, itching, tightening, induration, and adhesion were associated with hypertrophic scar formation. Early scar intervention, as well as the use of preventive topical agents, were associated with decreased hypertrophic scar formation. CONCLUSION Based on our results, we suggest that dermatologists consider using non-ablative fractional laser, intralesional steroid injection, and topical preventive agents to lower the incidence of hypertrophic scars, especially in young patients or those with high BMI and/or clinical symptoms such as itching, tightening, induration, and adhesion.
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Affiliation(s)
- J U Shin
- Department of Dermatology and Cutaneous Biology Research Institute
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Ranjan R, Lee YG, Karpurapu M, Syed MA, Chung S, Deng J, Jeong JJ, Zhao G, Xiao L, Sadikot RT, Weiss MJ, Christman JW, Park GY. p47phox and reactive oxygen species production modulate expression of microRNA-451 in macrophages. Free Radic Res 2014; 49:25-34. [PMID: 25287330 DOI: 10.3109/10715762.2014.974037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The production of microRNAs (miRNA) is influenced by various stimuli, including environmental stresses. We hypothesized that reactive oxygen species (ROS)-associated stress could regulate macrophage miRNA synthesis. miRNAs undergo unique steps of maturation processing through either one of two pathways of cytoplasmic processing. Unlike the canonical pathway, the regulation of alternative cytoplasmic processing of miRNA has not been fully elucidated yet. We cultured bone marrow derived macrophages (BMDM) from wild type (WT) and p47(phox-/-) mice and profiled miRNA expression using microarrays. We analyzed 375 miRNAs including four endogenous controls to normalize the data. At resting state, p47(phox-/-) BMDM has the markedly reduced expression of miR-451 compared to WT BMDM, without other significant differences. Unlike majority of miRNAs, miR-451 goes through the unique alternative processing pathway, in which Ago2 plays a key role. In spite of significant reduction of mature miR-451, however, its precursor form, pre-mir-451, was similar in both BMDMs, suggesting that the processing of pre-mir-451 is impaired in p47(phox-/-) BMDM. Moreover, p47(phox-/-) BMDM expressed significantly reduced level of Ago2. In contrast, Ago2 mRNA levels were similar in WT and p47(phox-/-) BMDM, suggesting a post-transcriptional defect of Ago2 production in p47(phox-/-) macrophages, which resulted in impaired processing of pre-miR-451. In order to examine the functional significance of miR-451 in macrophages, we cultured BMDMs from miR-451 knock-out mice. Of interest, miR-451-deficient BMDM exhibited reduced ROS generation upon zymosan stimulation, compared to WT BMDM. Our studies suggest functional crosstalk between ROS and miR-451 in the regulation of macrophage oxidant stress.
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Affiliation(s)
- R Ranjan
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois , Chicago, IL , USA
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Choi KJ, Lee HS, Yoon YS, Park SS, Kim JS, Jeong JJ, Choi YR. Distal metatarsal osteotomy for hallux varus following surgery for hallux valgus. ACTA ACUST UNITED AC 2011; 93:1079-83. [PMID: 21768632 DOI: 10.1302/0301-620x.93b8.26430] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We reviewed the outcome of distal chevron metatarsal osteotomy without tendon transfer in 19 consecutive patients (19 feet) with a hallux varus deformity following surgery for hallux valgus. All patients underwent distal chevron metatarsal osteotomy with medial displacement and a medial closing wedge osteotomy along with a medial capsular release. The mean hallux valgus angle improved from -11.6° pre-operatively to 4.7° postoperatively, the mean first-second intermetatarsal angle improved from -0.3° to 3.3° and the distal metatarsal articular angle from 9.5° to 2.3° and the first metatarsophalangeal joints became congruent post-operatively in all 19 feet. The mean relative length ratio of the metatarsus decreased from 1.01 to 0.99 and the mean American Orthopaedic Foot and Ankle Society score improved from 77 to 95 points. In two patients the hallux varus recurred. One was symptom-free but the other remained symptomatic after a repeat distal chevron osteotomy. There were no other complications. We consider that distal chevron metatarsal osteotomy with a medial wedge osteotomy and medial capsular release is a useful procedure for the correction of hallux varus after surgery for hallux valgus.
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Affiliation(s)
- K J Choi
- Choi Kyung Jin Orthopaedic Hospital, 369-26 Woobong Building 3F, Shindang-dong, Jung-gu, Seoul, Korea
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Lee J, Jeong JJ, Lee YS, Nam KH, Chang HS, Chung WY, Soh EY, Kim YS, Park CS. Incidence and clinical behavior of papillary thyroid carcinoma in renal allograft recipients: a single center experience. Transplant Proc 2009; 40:3751-4. [PMID: 19100481 DOI: 10.1016/j.transproceed.2008.07.127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2008] [Accepted: 07/10/2008] [Indexed: 10/21/2022]
Abstract
The chronic use of immunosuppressive therapy in transplant recipients increases the long-term risk for carcinoma. However, there is insufficient knowledge regarding the incidence and biological behavior of papillary thyroid carcinomas (PTC) in renal allograft recipients. In the present study we examined the incidence and biological behavior of PTCs among 1739 patients transplanted between January 1986 and December 1999 who had been followed for a mean period of 137 months (range, 84-238 months). During the follow-up, 129 (7.4%) recipients were identified to display posttransplantation malignancies, including 12 (0.7%) with PTCs. The 6 male and 6 female patients had a mean age of 41 years (range, 23-57 years). Nine cases (incidentalomas) were diagnosed based on ultrasonographic (US) screening. Eight of those 9 were TNM stage I, 2 of the 3 clinical carcinomas were TNM stage IVa. During a mean follow-up of 94 months (range, 18-159 months), 2 (16.7%) PTC patients developed locoregional recurrence, but no patients showed distant metastases. These data showed that recipients had a higher incidence of PTC compared with the general Korean population (0.7% vs 0.02%). Posttransplantation PTC tended to show no difference in gender distribution, and was often associated with aggressive lymphatic metastasis. However, most incidentalomas showed favorable treatment outcomes. In conclusion, routine surveillance of the thyroid gland using US screening is recommended to ensure early detection, treatment, and favorable prognosis of PTC.
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Affiliation(s)
- J Lee
- Department of Endocrine Surgery, Ajou University Medical Center, Seoul, Korea
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