231 results on '"Kim, Grace Hyun J."'
Search Results
2. Automated abdominal adipose tissue segmentation and volume quantification on longitudinal MRI using 3D convolutional neural networks with multi-contrast inputs
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Kafali, Sevgi Gokce, Shih, Shu-Fu, Li, Xinzhou, Kim, Grace Hyun J., Kelly, Tristan, Chowdhury, Shilpy, Loong, Spencer, Moretz, Jeremy, Barnes, Samuel R., Li, Zhaoping, and Wu, Holden H.
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- 2024
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3. Multi‐scale, domain knowledge‐guided attention + random forest: a two‐stage deep learning‐based multi‐scale guided attention models to diagnose idiopathic pulmonary fibrosis from computed tomography images
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Yu, Wenxi, Zhou, Hua, Choi, Youngwon, Goldin, Jonathan G, Teng, Pangyu, Wong, Weng Kee, McNitt‐Gray, Michael F, Brown, Matthew S, and Kim, Grace Hyun J
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Medical and Biological Physics ,Engineering ,Physical Sciences ,Biomedical Engineering ,Bioengineering ,Lung ,Rare Diseases ,Biomedical Imaging ,Machine Learning and Artificial Intelligence ,Networking and Information Technology R&D (NITRD) ,Autoimmune Disease ,4.1 Discovery and preclinical testing of markers and technologies ,4.2 Evaluation of markers and technologies ,Humans ,Aged ,Random Forest ,Deep Learning ,Idiopathic Pulmonary Fibrosis ,Lung Diseases ,Interstitial ,Tomography ,X-Ray Computed ,Retrospective Studies ,attention models ,computed tomography ,deep learning ,domain knowledge ,idiopathic pulmonary fibrosis ,machine learning ,medical imaging ,Other Physical Sciences ,Oncology and Carcinogenesis ,Nuclear Medicine & Medical Imaging ,Biomedical engineering ,Medical and biological physics - Abstract
BackgroundIdiopathic pulmonary fibrosis (IPF) is a progressive, irreversible, and usually fatal lung disease of unknown reasons, generally affecting the elderly population. Early diagnosis of IPF is crucial for triaging patients' treatment planning into anti-fibrotic treatment or treatments for other causes of pulmonary fibrosis. However, current IPF diagnosis workflow is complicated and time-consuming, which involves collaborative efforts from radiologists, pathologists, and clinicians and it is largely subject to inter-observer variability.PurposeThe purpose of this work is to develop a deep learning-based automated system that can diagnose subjects with IPF among subjects with interstitial lung disease (ILD) using an axial chest computed tomography (CT) scan. This work can potentially enable timely diagnosis decisions and reduce inter-observer variability.MethodsOur dataset contains CT scans from 349 IPF patients and 529 non-IPF ILD patients. We used 80% of the dataset for training and validation purposes and 20% as the holdout test set. We proposed a two-stage model: at stage one, we built a multi-scale, domain knowledge-guided attention model (MSGA) that encouraged the model to focus on specific areas of interest to enhance model explainability, including both high- and medium-resolution attentions; at stage two, we collected the output from MSGA and constructed a random forest (RF) classifier for patient-level diagnosis, to further boost model accuracy. RF classifier is utilized as a final decision stage since it is interpretable, computationally fast, and can handle correlated variables. Model utility was examined by (1) accuracy, represented by the area under the receiver operating characteristic curve (AUC) with standard deviation (SD), and (2) explainability, illustrated by the visual examination of the estimated attention maps which showed the important areas for model diagnostics.ResultsDuring the training and validation stage, we observe that when we provide no guidance from domain knowledge, the IPF diagnosis model reaches acceptable performance (AUC±SD = 0.93±0.07), but lacks explainability; when including only guided high- or medium-resolution attention, the learned attention maps are not satisfactory; when including both high- and medium-resolution attention, under certain hyperparameter settings, the model reaches the highest AUC among all experiments (AUC±SD = 0.99±0.01) and the estimated attention maps concentrate on the regions of interests for this task. Three best-performing hyperparameter selections according to MSGA were applied to the holdout test set and reached comparable model performance to that of the validation set.ConclusionsOur results suggest that, for a task with only scan-level labels available, MSGA+RF can utilize the population-level domain knowledge to guide the training of the network, which increases both model accuracy and explainability.
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- 2023
4. Quantitative Image Analysis at Chronic Lung Allograft Dysfunction Onset Predicts Mortality
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Weigt, S Samuel, Kim, Grace-Hyun J, Jones, Heather D, Ramsey, Allison L, Amubieya, Olawale, Abtin, Fereidoun, Pourzand, Lila, Lee, Jihey, Shino, Michael Y, DerHovanessian, Ariss, Stripp, Barry, Noble, Paul W, Sayah, David M, Saggar, Rajan, Britton, Ian, Lynch, Joseph P, Belperio, John A, and Goldin, Jonathan
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Biomedical and Clinical Sciences ,Clinical Sciences ,Lung ,Clinical Research ,Rare Diseases ,Good Health and Well Being ,Allografts ,Bronchiolitis Obliterans ,Chronic Disease ,Follow-Up Studies ,Humans ,Lung Transplantation ,Primary Graft Dysfunction ,Retrospective Studies ,Risk Factors ,Syndrome ,Medical and Health Sciences ,Surgery ,Clinical sciences ,Immunology - Abstract
BackgroundChronic lung allograft dysfunction (CLAD) phenotype determines prognosis and may have therapeutic implications. Despite the clarity achieved by recent consensus statement definitions, their reliance on radiologic interpretation introduces subjectivity. The Center for Computer Vision and Imaging Biomarkers at the University of California, Los Angeles (UCLA) has established protocols for chest high-resolution computed tomography (HRCT)-based computer-aided quantification of both interstitial disease and air-trapping. We applied quantitative image analysis (QIA) at CLAD onset to demonstrate radiographic phenotypes with clinical implications.MethodsWe studied 47 first bilateral lung transplant recipients at UCLA with chest HRCT performed within 90 d of CLAD onset and 47 no-CLAD control HRCTs. QIA determined the proportion of lung volume affected by interstitial disease and air-trapping in total lung capacity and residual volume images, respectively. We compared QIA scores between no-CLAD and CLAD, and between phenotypes. We also assigned radiographic phenotypes based solely on QIA, and compared their survival outcomes.ResultsCLAD onset HRCTs had more lung affected by the interstitial disease (P = 0.003) than no-CLAD controls. Bronchiolitis obliterans syndrome (BOS) cases had lower scores for interstitial disease as compared with probable restrictive allograft syndrome (RAS) (P < 0.0001) and mixed CLAD (P = 0.02) phenotypes. BOS cases had more air-trapping than probable RAS (P < 0.0001). Among phenotypes assigned by QIA, the relative risk of death was greatest for mixed (relative risk [RR] 11.81), followed by RAS (RR 6.27) and BOS (RR 3.15).ConclusionsChest HRCT QIA at CLAD onset appears promising as a method for precise determination of CLAD phenotypes with survival implications.
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- 2022
5. Volumetric measurements are preferred in the evaluation of mutant IDH inhibition in non-enhancing diffuse gliomas: Evidence from a phase I trial of ivosidenib
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Ellingson, Benjamin M, Kim, Grace Hyun J, Brown, Matt, Lee, Jihey, Salamon, Noriko, Steelman, Lori, Hassan, Islam, Pandya, Shuchi S, Chun, Saewon, Linetsky, Michael, Yoo, Bryan, Wen, Patrick Y, Mellinghoff, Ingo K, Goldin, Jonathan, and Cloughesy, Timothy F
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Cancer ,Rare Diseases ,Neurosciences ,Bioengineering ,Detection ,screening and diagnosis ,4.2 Evaluation of markers and technologies ,Brain Neoplasms ,Glioma ,Glycine ,Humans ,Isocitrate Dehydrogenase ,Magnetic Resonance Imaging ,Pyridines ,IDH-mutant gliomas ,ivosidenib ,LGG RANO ,low-grade gliomas ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
BackgroundSince IDH-mutant (mIDH) low-grade gliomas (LGGs) progress slowly and have a relatively long survival, there is a significant need for earlier measurements of clinical benefit. Guidance using the LGG RANO criteria recommends serial bidirectional (2D) measurements on a single slice; however, questions remain as to whether volumetric (3D) measurements are better, since they would allow for more accurate measurements in irregular shaped lesions and allow readers to better assess areas of subtle change.MethodsTwenty-one (out of 24) non-enhancing, recurrent mIDH1 LGGs were enrolled in a phase I, multicenter, open-label study of oral ivosidenib (NCT02073994), and with imaging pre- and post-treatment as part of this exploratory ad hoc analysis. 2D and 3D measurements on T2-weighted FLAIR images were centrally evaluated at an imaging contract research organization using a paired read and forced adjudication paradigm. The effects of 2D vs 3D measurements on progression-free survival (PFS), growth rate measurement variability, and reader concordance and adjudication rates were quantified.Results3D volumetric measurements showed significantly longer estimated PFS (P = .0181), more stable (P = .0063) and considerably slower measures of tumor growth rate (P = .0037), the highest inter-reader agreement (weighted kappa = 0.7057), and significantly lower reader discordance rates (P = .0002) with 2D LGG RANO.Conclusion3D volumetric measurements are better for determining response assessment in LGGs due to more stable measures of tumor growth rates (ie, less "yo-yo-ing" of measurements over time), highest inter-reader agreement, and lowest reader discordance rates. Continued evaluation in future studies is warranted to determine whether these measurements reflect clinical benefit.
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- 2022
6. ChatGPT in radiology: A systematic review of performance, pitfalls, and future perspectives
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Keshavarz, Pedram, Bagherieh, Sara, Nabipoorashrafi, Seyed Ali, Chalian, Hamid, Rahsepar, Amir Ali, Kim, Grace Hyun J., Hassani, Cameron, Raman, Steven S., and Bedayat, Arash
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- 2024
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7. Procedural outcomes associated with use of the AngioVac System for right heart thrombi: A safety report from RAPID registry data.
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Moriarty, John M, Liao, Millie, Kim, Grace Hyun J, Yang, Eric, Desai, Kush, Ranade, Mona, and Plotnik, Adam N
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Background: Right heart thrombi can be a source of considerable morbidity and mortality, especially when associated with pulmonary embolism. Methods: To understand the safety and procedural efficacy associated with vacuum-assisted thrombectomy using the AngioVac System (AngioDynamics, Latham, NY, USA) to remove right heart thrombi, we conducted a subanalysis of the Registry of AngioVac Procedures in Detail (RAPID) multicenter registry representing 47 (20.1%) of 234 participants in the registry. Forty-two (89.4%) patients had thrombi located in the right atrium alone, three (6.4%) in the right ventricle alone, and two (4.3%) in both the right atrium and ventricle. Four (8.5%) patients had concomitant caval thrombi, three (6.4%) also had catheter-related thrombi, and one (2.1%) patient had both caval and catheter-related thrombi with their right heart thrombi. Results: Extracorporeal bypass time was less than 1 hour for 39 (83.0%) procedures. Seventy to 100% removal of thrombus was achieved in 59.6% of patients. Estimated blood loss was less than 250 cc for 43 procedures (91.6%). Mean hemoglobin decreased from 10.7 ± 2.2 g/dL preoperatively to 9.6 ± 1.6 g/dL postoperatively. Transfusions were administered for eight procedures (17.0%), with only one (2.1%) patient receiving more than 2 units of blood. Six patients (12.8%) experienced procedure-related adverse events, including three (6.4%) patients who experienced distal emboli and three (6.4%) patients who developed bleeding-related complications. All adverse events resolved prior to discharge. There was one death (2.1%) reported that was not procedure related. Conclusion: Vacuum-assisted thrombectomy can be performed safely in patients with right heart thrombi. ClinicalTrials.gov Identifier: NCT04414332.
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- 2022
8. Genicular Artery Embolization for the Treatment of Symptomatic Knee Osteoarthritis.
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Padia, Siddharth A, Genshaft, Scott, Blumstein, Gideon, Plotnik, Adam, Kim, Grace Hyun J, Gilbert, Stephanie J, Lauko, Kara, and Stavrakis, Alexandra I
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Neurosciences ,Clinical Research ,Osteoarthritis ,Pain Research ,Arthritis ,Patient Safety ,Prevention ,Clinical Trials and Supportive Activities ,Chronic Pain ,6.1 Pharmaceuticals ,Musculoskeletal - Abstract
Genicular artery embolization (GAE) is a novel therapy to treat patients with symptomatic knee osteoarthritis (OA) by reducing synovial arterial hypervascularity. This study evaluates the safety and efficacy of GAE for the treatment of symptomatic knee OA. A prospective, single-center, open-label U.S. Food and Drug Administration-approved investigational device exemption study was conducted. Patients enrolled in the study were 40 to 80 years old, with moderate or severe knee OA (Kellgren-Lawrence grade 2, 3, or 4), who previously had failure of conservative therapy. Baseline pain (visual analog scale [VAS]) and symptom scores (Western Ontario and McMaster Universities Osteoarthritis Index [WOMAC]) were assessed. After femoral arterial access was achieved, GAE of 1, 2, or 3 genicular arteries supplying the location of the subject's pain, as determined by digital subtraction angiography and cone-beam computed tomography, was performed using 100-μm particles. Adverse events and symptoms scores were assessed at 1 week, 1 month, 3 months, 6 months, and 1 year after GAE. Over a 10-month period, 40 subjects were enrolled. The median age was 69 years (range, 49 to 80 years). The median body mass index was 29 kg/m2 (range, 19 to 44 kg/m2). Knee OA severity was grade 2 in 18% of the patients, grade 3 in 43%, and grade 4 in 40%. Technical success was achieved in 100% of the subjects. Transient skin discoloration and transient mild knee pain after the procedure were common and expected. Treatment-related adverse events included a groin hematoma requiring overnight observation in 1 subject, self-resolving focal skin ulceration in 7 subjects, and an asymptomatic small bone infarct on magnetic resonance imaging at 3 months in 2 subjects. The WOMAC total and VAS pain scores decreased by 61% and 67% at 12 months from a median baseline of 52 (of 96) and 8 (of 10), respectively. Twenty-seven patients (68%) had a reduction of ≥50% in both WOMAC total and VAS pain scores. This prospective trial demonstrates that GAE is effective and durable in reducing pain symptoms from moderate or severe knee OA that is refractory to other conservative therapy, with an acceptable safety profile. Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
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- 2021
9. The Extent and Diverse Trajectories of Longitudinal Changes in Rheumatoid Arthritis Interstitial Lung Diseases Using Quantitative HRCT Scores.
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Lee, Jeong Seok, Kim, Grace-Hyun J, Ha, You-Jung, Kang, Eun Ha, Lee, Yun Jong, Goldin, Jonathan G, and Lee, Eun Young
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interstitial lung disease ,quantitative score ,rheumatoid arthritis ,Clinical Sciences - Abstract
We aimed to validate quantitative high-resolution computed tomography (HRCT) imaging analyses of interstitial lung disease (ILD) in rheumatoid arthritis (RA) patients, and to delineate a broad spectrum of annual longitudinal changes of ILD severity in the RA-ILD cohorts. Retrospective cohort 1 (n = 26) had matched PFT results and prospective cohort 2 (n = 34) were followed for over two years with baseline serum specimen. Automated quantitative analysis of HRCT was expressed as the extent of ground-glass opacity, lung fibrosis, honeycombing, and their summation-the total extent of quantitative ILD (QILD). Higher QILD score was associated with lower pulmonary function especially for DLCO% (ρ = -0.433, p = 0.027). Higher serum level of Krebs von den Lungen 6 were significantly associated with high QILD scores (ρ = 0.400, p = 0.026). Regarding QILD score changes in whole lung, even a single point increase was significantly associated with interval progression detected by the radiologist. Four distinct patterns (improvement, worsening, convex-like, and concave-like) during the 24 months were described by QILD scores. Prolonged disease duration of ILD at baseline was significantly associated with worsening of QILD scores. QILD has the potential to reliably evaluate the dynamic severity changes in patients with RA-ILD.
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- 2021
10. Reproducibility of lung nodule radiomic features: Multivariable and univariable investigations that account for interactions between CT acquisition and reconstruction parameters
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Emaminejad, Nastaran, Wahi‐Anwar, Muhammad Wasil, Kim, Grace Hyun J, Hsu, William, Brown, Matthew, and McNitt‐Gray, Michael
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Medical and Biological Physics ,Physical Sciences ,Bioengineering ,Lung Cancer ,Lung ,Biomedical Imaging ,Clinical Research ,Cancer ,Algorithms ,Early Detection of Cancer ,Humans ,Lung Neoplasms ,Reproducibility of Results ,Tomography ,X-Ray Computed ,biomarkers ,CT acquisition and reconstruction conditions ,lung nodules ,multivariable analysis ,quantitative imaging/analysis ,radiomics ,reproducibility ,univariable analysis ,Other Physical Sciences ,Biomedical Engineering ,Oncology and Carcinogenesis ,Nuclear Medicine & Medical Imaging ,Biomedical engineering ,Medical and biological physics - Abstract
PurposeRecent studies have demonstrated a lack of reproducibility of radiomic features in response to variations in CT parameters. In addition, reproducibility of radiomic features has not been well established in clinical datasets. We aimed to investigate the effects of a wide range of CT acquisition and reconstruction parameters on radiomic features in a realistic setting using clinical low dose lung cancer screening cases. We performed univariable and multivariable explorations to consider the effects of individual parameters and the simultaneous interactions between three different acquisition/reconstruction parameters of radiation dose level, reconstructed slice thickness, and kernel.MethodA cohort of 89 lung cancer screening patients were collected that each had a solid lung nodule >4mm diameter. A computational pipeline was used to perform a simulation of dose reduction of the raw projection data, collected from patient scans. This was followed by reconstruction of raw data with weighted filter back projection (wFBP) algorithm and automatic lung nodule detection and segmentation using a computer-aided detection tool. For each patient, 36 different image datasets were created corresponding to dose levels of 100%, 50%, 25%, and 10% of the original dose level, three slice thicknesses of 0.6 mm, 1 mm, and 2 mm, as well as three reconstruction kernels of smooth, medium, and sharp. For each nodule, 226 well-known radiomic features were calculated at each image condition. The reproducibility of radiomic features was first evaluated by measuring the intercondition agreement of the feature values among the 36 image conditions. Then in a series of univariable analyses, the impact of individual CT parameters was assessed by selecting subsets of conditions with one varying and two constant CT parameters. In each subset, intraparameter agreements were assessed. Overall concordance correlation coefficient (OCCC) served as the measure of agreement. An OCCC ≥ 0.9 implied strong agreement and reproducibility of radiomic features in intercondition or intraparameter comparisons. Furthermore, the interaction of CT parameters in impacting radiomic feature values was investigated via ANOVA.ResultsAll included radiomic features lacked intercondition reproducibility (OCCC 50% of radiomic features.ConclusionWe systematically explored the multidimensional space of CT parameters in affecting lung nodule radiomic features. Univariable and multivariable analyses of this study not only showed the lack of reproducibility of the majority of radiomic features but also revealed existing interactions among CT parameters, meaning that the effect of individual CT parameters on radiomic features can be conditional upon other CT acquisition and reconstruction parameters. Our findings advise on careful radiomic feature selection and attention to the inclusion criteria for CT image acquisition protocols within the datasets of radiomic studies.
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- 2021
11. A study design for statistical learning technique to predict radiological progression with an application of idiopathic pulmonary fibrosis using chest CT images
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Kim, Grace Hyun J, Shi, Yu, Yu, Wenxi, and Wong, Weng Kee
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Biomedical and Clinical Sciences ,Clinical Sciences ,Bioengineering ,Lung ,Rare Diseases ,Biomedical Imaging ,Autoimmune Disease ,Respiratory ,Humans ,Idiopathic Pulmonary Fibrosis ,Retrospective Studies ,Tomography ,X-Ray Computed ,Vital Capacity ,Particle swap optimization ,Quantitative lung fibrosis ,Machine learning ,Random forest ,Medical image ,Medical and Health Sciences ,General Clinical Medicine ,Public Health ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundIdiopathic pulmonary fibrosis (IPF) is a fatal interstitial lung disease characterized by an unpredictable decline in lung function. Predicting IPF progression from the early changes in lung function tests have known to be a challenge due to acute exacerbation. Although it is unpredictable, the neighboring regions of fibrotic reticulation increase during IPF's progression. With this clinical information, quantitative characteristics of high-resolution computed tomography (HRCT) and a statistical learning paradigm, the aim is to build a model to predict IPF progression.DesignA paired set of anonymized 193 HRCT images from IPF subjects with 6-12 month intervals were collected retrospectively. The study was conducted in two parts: (1) Part A collects the ground truth in small regions of interest (ROIs) with labels of "expected to progress" or "expected to be stable" at baseline HRCT and develop a statistical learning model to classify voxels in the ROIs. (2) Part B uses the voxel-level classifier from Part A to produce whole-lung level scores of a single-scan total probability's (STP) baseline.MethodsUsing annotated ROIs from 71 subjects' HRCT scans in Part A, we applied Quantum Particle Swarm Optimization-Random Forest (QPSO-RF) to build the classifier. Then, 122 subjects' HRCT scans were used to test the prediction. Using Spearman rank correlations and survival analyses, we ascertained STP associations with 6-12 month changes in quantitative lung fibrosis and forced vital capacity.ConclusionThis study can serve as a reference for collecting ground truth, and developing statistical learning techniques to predict progression in medical imaging.
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- 2021
12. End‐to‐end domain knowledge‐assisted automatic diagnosis of idiopathic pulmonary fibrosis (IPF) using computed tomography (CT)
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Yu, Wenxi, Zhou, Hua, Goldin, Jonathan G, Wong, Weng Kee, and Kim, Grace Hyun J
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Medical and Biological Physics ,Engineering ,Physical Sciences ,Biomedical Engineering ,Bioengineering ,Rare Diseases ,Autoimmune Disease ,Clinical Research ,Biomedical Imaging ,Lung ,Respiratory ,Humans ,Idiopathic Pulmonary Fibrosis ,Lung Diseases ,Interstitial ,Prospective Studies ,Retrospective Studies ,Tomography ,X-Ray Computed ,computed tomography ,deep learning ,idiopathic pulmonary fibrosis ,optimal design ,Other Physical Sciences ,Oncology and Carcinogenesis ,Nuclear Medicine & Medical Imaging ,Biomedical engineering ,Medical and biological physics - Abstract
PurposeDomain knowledge (DK) acquired from prior studies is important for medical diagnosis. This paper leverages the population-level DK using an optimality design criterion to train a deep learning model in an end-to-end manner. In this study, the problem of interest is at the patient level to diagnose a subject with idiopathic pulmonary fibrosis (IPF) among subjects with interstitial lung disease (ILD) using a computed tomography (CT). IPF diagnosis is a complicated process with multidisciplinary discussion with experts and is subject to interobserver variability, even for experienced radiologists. To this end, we propose a new statistical method to construct a time/memory-efficient IPF diagnosis model using axial chest CT and DK, along with an optimality design criterion via a DK-enhanced loss function of deep learning.MethodsFour state-of-the-art two-dimensional convolutional neural network (2D-CNN) architectures (MobileNet, VGG16, ResNet-50, and DenseNet-121) and one baseline 2D-CNN are implemented to automatically diagnose IPF among ILD patients. Axial lung CT images are retrospectively acquired from 389 IPF patients and 700 non-IPF ILD patients in five multicenter clinical trials. To enrich the sample size and boost model performance, we sample 20 three-slice samples (triplets) from each CT scan, where these three slices are randomly selected from the top, middle, and bottom of both lungs respectively. Model performance is evaluated using a fivefold cross-validation, where each fold was stratified using a fixed proportion of IPF vs non-IPF.ResultsUsing DK-enhanced loss function increases the model performance of the baseline CNN model from 0.77 to 0.89 in terms of study-wise accuracy. Four other well-developed models reach satisfactory model performance with an overall accuracy >0.95 but the benefits brought on by the DK-enhanced loss function is not noticeable.ConclusionsWe believe this is the first attempt that (a) uses population-level DK with an optimal design criterion to train deep learning-based diagnostic models in an end-to-end manner and (b) focuses on patient-level IPF diagnosis. Further evaluation of using population-level DK on prospective studies is warranted and is underway.
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- 2021
13. Using Transitional Changes on High-Resolution Computed Tomography to Monitor the Impact of Cyclophosphamide or Mycophenolate Mofetil on Systemic Sclerosis-Related Interstitial Lung Disease.
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Kim, Grace Hyun J, Tashkin, Donald P, Lo, Pechin, Brown, Matthew S, Volkmann, Elizabeth R, Gjertson, David W, Khanna, Dinesh, Elashoff, Robert M, Tseng, Chi-Hong, Roth, Michael D, and Goldin, Jonathan G
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Humans ,Lung Diseases ,Interstitial ,Scleroderma ,Systemic ,Mycophenolic Acid ,Cyclophosphamide ,Immunosuppressive Agents ,Tomography ,X-Ray Computed ,Treatment Outcome ,Adult ,Middle Aged ,Female ,Male ,Rare Diseases ,Clinical Research ,Scleroderma ,Biomedical Imaging ,Autoimmune Disease ,Lung ,Respiratory ,Clinical Sciences ,Immunology ,Public Health and Health Services ,Arthritis & Rheumatology - Abstract
ObjectiveTo examine changes in the extent of specific patterns of interstitial lung disease (ILD) as they transition from one pattern to another in response to immunosuppressive therapy in systemic sclerosis-related ILD (SSc-ILD).MethodsWe evaluated changes in the quantitative extent of specific lung patterns of ILD using volumetric high-resolution computed tomography (HRCT) scans obtained at baseline and after 2 years of therapy in patients treated with either cyclophosphamide (CYC) for 1 year or mycophenolate mofetil (MMF) for 2 years in Scleroderma Lung Study II. ILD patterns included lung fibrosis, ground glass, honeycombing, and normal lung. Net change was calculated as the difference in the probability of change from one ILD pattern to another. Wilcoxon's signed rank test was used to compare the changes.ResultsForty-seven and 50 patients had baseline and follow-up scans in the CYC and MMF groups, respectively. Mean net improvements reflecting favorable changes from one ILD pattern to another in the whole lung in the CYC and MMF groups, respectively, were as follows: from lung fibrosis to a normal lung pattern, 21% and 19%; from a ground-glass pattern to a normal lung pattern, 30% and 28%; and from lung fibrosis to a ground-glass pattern, 5% and 0.5%. The mean overall improvement in transitioning from a ground-glass pattern or lung fibrosis to a normal lung pattern was significant for both treatments (all P < 0.001).ConclusionSignificantly favorable transitions from both ground-glass and lung fibrosis ILD patterns to a normal lung pattern were observed in patients undergoing immunosuppressive treatment for SSc-ILD, suggesting the usefulness of examining these transitions for insights into the underlying pathobiology of treatment response.
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- 2020
14. Bexotegrast in Patients with Idiopathic Pulmonary Fibrosis: The INTEGRIS-IPF Study
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Lancaster, Lisa, primary, Cottin, Vincent, additional, Ramaswamy, Murali, additional, Wuyts, Wim A., additional, Jenkins, R. Gisli, additional, Scholand, Mary Beth, additional, Kreuter, Michael, additional, Valenzuela, Claudia, additional, Ryerson, Christopher J, additional, Goldin, Jonathan, additional, Kim, Grace Hyun J, additional, Jurek, Marzena, additional, Decaris, Martin, additional, Clark, Annie, additional, Turner, Scott, additional, Barnes, Chris N., additional, Achneck, Hardean E, additional, Cosgrove, Gregory, additional, Lefebvre, Éric A, additional, and Flaherty, Kevin R., additional
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- 2024
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15. Long-term survival of single and multifocal stage 1 lung carcinoma using image-guided thermal ablation.
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Jahanshahi, Noor J., primary, Kooraki, Soheil, additional, Villegas, Bianca, additional, Kim, Grace Hyun J., additional, Goldman, Jonathan W., additional, Genshaft, Scott J., additional, Suh, Robert D., additional, and Abtin, Fereidoun, additional
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- 2024
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16. Quantifying lung fissure integrity using a three-dimensional patch-based convolutional neural network on CT images for emphysema treatment planning
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Tada, Dallas K., primary, Teng, Pangyu, additional, Vyapari, Kalyani, additional, Banola, Ashley, additional, Foster, George, additional, Diaz, Esteban, additional, Kim, Grace Hyun J., additional, Goldin, Jonathan G., additional, Abtin, Fereidoun, additional, McNitt-Gray, Michael, additional, and Brown, Matthew S., additional
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- 2024
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17. Prediction of progression in idiopathic pulmonary fibrosis using CT scans atbaseline: A quantum particle swarm optimization - Random forest approach
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Shi, Yu, Wong, Weng Kee, Goldin, Jonathan G., Brown, Matthew S., and Kim, Grace Hyun J.
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Biomedical imaging ,Texture features ,Wrapper methods - Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease characterized by an unpredictable progressive declinein lung function. Natural history of IPF is unknown and the prediction of disease progression at the time ofdiagnosis is notoriously difficult. High resolution computed tomography (HRCT) has been used for the diagnosisof IPF, but not generally for monitoring purpose. The objective of this work is to develop a novel predictivemodel for the radiological progression pattern at voxel-wise level using only baseline HRCT scans. Mainly, thereare two challenges: (a) obtaining a data set of features for region of interest (ROI) on baseline HRCT scans andtheir follow-up status; and (b) simultaneously selecting important features from high-dimensional space, andoptimizing the prediction performance. We resolved the first challenge by implementing a study design andhaving an expert radiologist contour ROIs at baseline scans, depending on its progression status in follow-upvisits. For the second challenge, we integrated the feature selection with prediction by developing an algorithmusing a wrapper method that combines quantum particle swarm optimization to select a small number of featureswith random forest to classify early patterns of progression. We applied our proposed algorithm to analyzeanonymized HRCT images from 50 IPF subjects from a multi-center clinical trial. We showed that it yields aparsimonious model with 81.8% sensitivity, 82.2% specificity and an overall accuracy rate of 82.1% at the ROIlevel. These results are superior to other popular feature selections and classification methods, in that ourmethod produces higher accuracy in prediction of progression and more balanced sensitivity and specificity witha smaller number of selected features. Our work is the first approach to show that it is possible to use onlybaseline HRCT scans to predict progressive ROIs at 6 months to 1year follow-ups using artificial intelligence.
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- 2019
18. Longitudinal Changes in Quantitative Interstitial Lung Disease on CT after Immunosuppression in the Scleroderma Lung Study II
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Goldin, Jonathan G, Kim, Grace Hyun J, Tseng, Chi-Hong, Volkmann, Elizabeth, Furst, Daniel, Clements, Philip, Brown, Matt, Roth, Michael, Khanna, Dinesh, and Tashkin, Donald P
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Biomedical and Clinical Sciences ,Clinical Sciences ,Lung ,Clinical Research ,Clinical Trials and Supportive Activities ,Scleroderma ,Biomedical Imaging ,Rare Diseases ,Evaluation of treatments and therapeutic interventions ,6.1 Pharmaceuticals ,Respiratory ,Adult ,Cyclophosphamide ,Double-Blind Method ,Female ,Humans ,Immunosuppression Therapy ,Immunosuppressive Agents ,Longitudinal Studies ,Lung Diseases ,Interstitial ,Male ,Middle Aged ,Mycophenolic Acid ,Scleroderma ,Systemic ,Tomography ,X-Ray Computed ,Scleroderma Lung Study II ,mycophenolate mofetil ,cyclophosphamide ,Cardiovascular medicine and haematology ,Clinical sciences - Abstract
RationaleThe Scleroderma Lung Study II (SLS II) demonstrated significant improvements in pulmonary function and dyspnea at 24 months compared with baseline when patients with symptomatic scleroderma-related interstitial lung disease (SSc-ILD) were treated with either cyclophosphamide for 1 year (followed for another year on placebo) or mycophenolate mofetil for 2 years in a randomized, double-blind clinical trial. Physiologic and clinical outcomes of SLS II have been published previously.ObjectivesThe aim of the study was to assess changes from baseline in the extent of SSc-ILD on high-resolution computed tomography (HRCT) measured in the SLS II participants using quantitative image analysis after 2 years and to determine whether these HRCT changes were correlated with the changes in physiologic and clinical measures over the same time interval.MethodsNinety-seven of the 142 randomized subjects (cyclophosphamide group, 47 subjects; mycophenolate mofetil group, 50 subjects) participating in SLS II underwent thoracic volumetric thin-section HRCT at both baseline and 24 months. Quantitative computer-aided diagnosis scores using volumetric HRCT scans were obtained using a previously developed computer-aided system. The scores were quantitative lung fibrosis, quantitative ground glass, quantitative honeycomb, and quantitative interstitial lung disease (QILD), the latter representing the sum of quantitative lung fibrosis, quantitative ground glass, and quantitative honeycomb. These scores were obtained both for the whole lung and for individual lobes. Paired t tests were used for the combined (pooled) cyclophosphamide and mycophenolate mofetil groups to compare 24-month changes from baseline in both the whole lung and the lobe of maximal involvement as determined at baseline (worst lobe).ResultsAt the end of the 24-month trial, QILD in the whole lung was significantly reduced by a mean of 2.51% in the pooled groups (adjusted 95% confidence interval, -4.00 to -1.03%; P = 0.001). There was no significant difference in the QILD score improvement between the cyclophosphamide (-2.66%) and mycophenolate (-2.38%) groups when assessed separately (P = 0.88). For the pooled group, the 24-month changes in QILD scores in the whole lung correlated significantly with other outcomes, including 24-month changes in forced vital capacity (ρ = -0.37), single-breath diffusing capacity of the lung for carbon monoxide (ρ = -0.22), and breathlessness as measured by the Transition Dyspnea Index (ρ = -0.26).ConclusionsTreatment of SSc-ILD with either cyclophosphamide for 1 year, followed by placebo for a second year, or mycophenolate for 2 years was associated with a significant reduction (improvement) in the extent of HRCT SSc-ILD assessed by computer-aided diagnosis scores, which correlated well with one or more other measures of treatment response. These findings demonstrate that actual changes in lung structure accompany improvements in physiologic and/or symptomatic measures in SSc-ILD.
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- 2018
19. Bexotegrast in Patients with Idiopathic Pulmonary Fibrosis: The INTEGRIS-IPF Clinical Trial.
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Lancaster, Lisa, Cottin, Vincent, Ramaswamy, Murali, Wuyts, Wim A., Jenkins, R. Gisli, Scholand, Mary Beth, Kreuter, Michael, Valenzuela, Claudia, Ryerson, Christopher J., Goldin, Jonathan, Kim, Grace Hyun J., Jurek, Marzena, Decaris, Martin, Clark, Annie, Turner, Scott, Barnes, Chris N., Achneck, Hardean E., Cosgrove, Gregory P., Lefebvre, Éric A., and Flaherty, Kevin R.
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IDIOPATHIC pulmonary fibrosis ,COUGH ,CLINICAL trials ,PULMONARY fibrosis ,INVESTIGATIONAL drugs ,DRUG development - Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is a rare and progressive disease that causes progressive cough, exertional dyspnea, impaired quality of life, and death. Objectives: Bexotegrast (PLN-74809) is an oral, once-daily, investigational drug in development for the treatment of IPF. Methods: This Phase-2a multicenter, clinical trial randomized participants with IPF to receive, orally and once daily, bexotegrast at 40 mg, 80 mg, 160 mg, or 320 mg, or placebo, with or without background IPF therapy (pirfenidone or nintedanib), in an approximately 3:1 ratio in each bexotegrast dose cohort, for at least 12 weeks. The primary endpoint was incidence of treatment-emergent adverse events (TEAEs). Exploratory efficacy endpoints included change from baseline in FVC, quantitative lung fibrosis (QLF) extent (%), and changes from baseline in fibrosis-related biomarkers. Measurements and Main Results: Bexotegrast was well tolerated, with similar rates of TEAEs in the pooled bexotegrast and placebo groups (62/89 [69.7%] and 21/31 [67.7%], respectively). Diarrhea was the most common TEAE; most participants with diarrhea also received nintedanib. Participants who were treated with bexotegrast experienced a reduction in FVC decline over 12 weeks compared with those who received placebo, with or without background therapy. A dose-dependent antifibrotic effect of bexotegrast was observed with QLF imaging, and a decrease in fibrosis-associated biomarkers was observed with bexotegrast versus placebo. Conclusions: Bexotegrast demonstrated a favorable safety and tolerability profile, up to 12 weeks for the doses studied. Exploratory analyses suggest an antifibrotic effect according to FVC, QLF imaging, and circulating levels of fibrosis biomarkers. Clinical trial registered with (NCT04396756). [ABSTRACT FROM AUTHOR]
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- 2024
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20. Quantitative bone scan lesion area as an early surrogate outcome measure indicative of overall survival in metastatic prostate cancer
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Brown, Matthew S, Kim, Grace Hyun J, Chu, Gregory H, Ramakrishna, Bharath, Allen-Auerbach, Martin, Fischer, Cheryce P, Levine, Benjamin, Gupta, Pawan K, Schiepers, Christiaan W, and Goldin, Jonathan G
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Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Aging ,Clinical Research ,Prostate Cancer ,Urologic Diseases ,Cancer ,Clinical Trials and Supportive Activities ,4.1 Discovery and preclinical testing of markers and technologies ,Evaluation of treatments and therapeutic interventions ,Detection ,screening and diagnosis ,6.1 Pharmaceuticals ,prostate cancer ,bone scan ,computer-aided diagnosis ,Clinical sciences ,Biomedical engineering - Abstract
A clinical validation of the bone scan lesion area (BSLA) as a quantitative imaging biomarker was performed in metastatic castration-resistant prostate cancer (mCRPC). BSLA was computed from whole-body bone scintigraphy at baseline and week 12 posttreatment in a cohort of 198 mCRPC subjects (127 treated and 71 placebo) from a clinical trial involving a different drug from the initial biomarker development. BSLA computation involved automated image normalization, lesion segmentation, and summation of the total area of segmented lesions on bone scan AP and PA views as a measure of tumor burden. As a predictive biomarker, treated subjects with baseline BSLA [Formula: see text] had longer survival than those with higher BSLA ([Formula: see text] and [Formula: see text]). As a surrogate outcome biomarker, subjects were categorized as progressive disease (PD) if the BSLA increased by a prespecified 30% or more from baseline to week 12 and non-PD otherwise. Overall survival rates between PD and non-PD groups were statistically different ([Formula: see text] and [Formula: see text]). Subjects without PD at week 12 had longer survival than subjects with PD: median 398 days versus 280 days. BSLA has now been demonstrated to be an early surrogate outcome for overall survival in different prostate cancer drug treatments.
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- 2018
21. Endovascular Removal of Thrombus and Right Heart Masses Using the AngioVac System: Results of 234 Patients from the Prospective, Multicenter Registry of AngioVac Procedures in Detail (RAPID)
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Moriarty, John M., Rueda, Victoria, Liao, Millie, Kim, Grace Hyun J., Rochon, Paul J., Zayed, Mohamed A., Lasorda, David, Golowa, Yosef S., Shavelle, David M., and Dexter, David J.
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- 2021
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22. Estimating organ doses from tube current modulated CT examinations using a generalized linear model
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Bostani, Maryam, McMillan, Kyle, Lu, Peiyun, Kim, Grace Hyun J, Cody, Dianna, Arbique, Gary, Greenberg, S Bruce, DeMarco, John J, Cagnon, Chris H, and McNitt‐Gray, Michael F
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Medical and Biological Physics ,Physical Sciences ,Biomedical Imaging ,Bioengineering ,Adult ,Child ,Female ,Humans ,Linear Models ,Male ,Monte Carlo Method ,Radiometry ,Reference Standards ,Tomography ,X-Ray Computed ,CT ,generalized linear model ,Monte Carlo simulations ,organ dose estimation ,tube current modulation ,CT ,Other Physical Sciences ,Biomedical Engineering ,Oncology and Carcinogenesis ,Nuclear Medicine & Medical Imaging ,Biomedical engineering ,Medical and biological physics - Abstract
PurposeCurrently, available Computed Tomography dose metrics are mostly based on fixed tube current Monte Carlo (MC) simulations and/or physical measurements such as the size specific dose estimate (SSDE). In addition to not being able to account for Tube Current Modulation (TCM), these dose metrics do not represent actual patient dose. The purpose of this study was to generate and evaluate a dose estimation model based on the Generalized Linear Model (GLM), which extends the ability to estimate organ dose from tube current modulated examinations by incorporating regional descriptors of patient size, scanner output, and other scan-specific variables as needed.MethodsThe collection of a total of 332 patient CT scans at four different institutions was approved by each institution's IRB and used to generate and test organ dose estimation models. The patient population consisted of pediatric and adult patients and included thoracic and abdomen/pelvis scans. The scans were performed on three different CT scanner systems. Manual segmentation of organs, depending on the examined anatomy, was performed on each patient's image series. In addition to the collected images, detailed TCM data were collected for all patients scanned on Siemens CT scanners, while for all GE and Toshiba patients, data representing z-axis-only TCM, extracted from the DICOM header of the images, were used for TCM simulations. A validated MC dosimetry package was used to perform detailed simulation of CT examinations on all 332 patient models to estimate dose to each segmented organ (lungs, breasts, liver, spleen, and kidneys), denoted as reference organ dose values. Approximately 60% of the data were used to train a dose estimation model, while the remaining 40% was used to evaluate performance. Two different methodologies were explored using GLM to generate a dose estimation model: (a) using the conventional exponential relationship between normalized organ dose and size with regional water equivalent diameter (WED) and regional CTDIvol as variables and (b) using the same exponential relationship with the addition of categorical variables such as scanner model and organ to provide a more complete estimate of factors that may affect organ dose. Finally, estimates from generated models were compared to those obtained from SSDE and ImPACT.ResultsThe Generalized Linear Model yielded organ dose estimates that were significantly closer to the MC reference organ dose values than were organ doses estimated via SSDE or ImPACT. Moreover, the GLM estimates were better than those of SSDE or ImPACT irrespective of whether or not categorical variables were used in the model. While the improvement associated with a categorical variable was substantial in estimating breast dose, the improvement was minor for other organs.ConclusionsThe GLM approach extends the current CT dose estimation methods by allowing the use of additional variables to more accurately estimate organ dose from TCM scans. Thus, this approach may be able to overcome the limitations of current CT dose metrics to provide more accurate estimates of patient dose, in particular, dose to organs with considerable variability across the population.
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- 2017
23. Accelerated ferumoxytol‐enhanced 4D multiphase, steady‐state imaging with contrast enhancement (MUSIC) cardiovascular MRI: validation in pediatric congenital heart disease
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Zhou, Ziwu, Han, Fei, Rapacchi, Stanislas, Nguyen, Kim‐Lien, Brunengraber, Daniel Z, Kim, Grace‐Hyun J, Finn, J Paul, and Hu, Peng
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Biomedical and Clinical Sciences ,Cardiovascular Medicine and Haematology ,Clinical Sciences ,Pediatric ,Heart Disease ,Clinical Research ,Bioengineering ,Biomedical Imaging ,Cardiovascular ,4.2 Evaluation of markers and technologies ,Detection ,screening and diagnosis ,Adolescent ,Algorithms ,Artifacts ,Cardiac-Gated Imaging Techniques ,Child ,Contrast Media ,Female ,Ferrosoferric Oxide ,Heart Defects ,Congenital ,Humans ,Image Enhancement ,Image Interpretation ,Computer-Assisted ,Imaging ,Three-Dimensional ,Infant ,Infant ,Newborn ,Magnetic Resonance Imaging ,Cine ,Male ,Reproducibility of Results ,Respiratory-Gated Imaging Techniques ,Sensitivity and Specificity ,cardiac cine ,compressed sensing ,ferumoxytol ,magnetic resonance angiography ,parallel imaging ,pediatric MRI ,Medicinal and Biomolecular Chemistry ,Biomedical Engineering ,Nuclear Medicine & Medical Imaging ,Clinical sciences ,Biomedical engineering - Abstract
The purpose of this work was to validate a parallel imaging (PI) and compressed sensing (CS) combined reconstruction method for a recently proposed 4D non-breath-held, multiphase, steady-state imaging technique (MUSIC) cardiovascular MRI in a cohort of pediatric congenital heart disease patients. We implemented a graphics processing unit accelerated CS-PI combined reconstruction method and applied it in 13 pediatric patients who underwent cardiovascular MRI after ferumoxytol administration. Conventional breath-held contrast-enhanced magnetic resonance angiography (CE-MRA) was first performed during the first pass of ferumoxytol injection, followed by the original MUSIC and the proposed CS-PI MUSIC during the steady-state distribution phase of ferumoxytol. Qualities of acquired images were then evaluated using a four-point scale. Left ventricular volumes and ejection fractions calculated from the original MUSIC and the CS-PI MUSIC were also compared with conventional multi-slice 2D cardiac cine MRI. The proposed CS-PI MUSIC reduced the imaging time of the MUSIC acquisition to 4.6 ± 0.4 min from 8.9 ± 1.2 min. Computationally intensive image reconstruction was completed within 5 min without interruption of sequential clinical scans. The proposed method (mean 3.3-4.0) provided image quality comparable to that of the original MUSIC (3.2-4.0) (all P ≥ 0.42), and better than conventional breath-held first-pass CE-MRA (1.1-3.3) for 13 anatomical structures (all P ≤ 0.0014) with good inter-observer agreement (κ > 0.46). The calculated ventricular volumes and ejection fractions from both original MUSIC (r > 0.90) and CS-PI MUSIC (r > 0.85) correlated well with 2D cine imaging. In conclusion, PI and CS were successfully incorporated into the 4D MUSIC acquisition to further reduce scan time by approximately 50% while maintaining highly comparable image quality in a clinically practical reconstruction time.
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- 2017
24. Novel lung imaging biomarkers and skin gene expression subsetting in dasatinib treatment of systemic sclerosis-associated interstitial lung disease
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Martyanov, Viktor, Kim, Grace-Hyun J, Hayes, Wendy, Du, Shuyan, Ganguly, Bishu J, Sy, Oumar, Lee, Sun Ku, Bogatkevich, Galina S, Schieven, Gary L, Schiopu, Elena, Marangoni, Roberta Gonçalves, Goldin, Jonathan, Whitfield, Michael L, and Varga, John
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Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Lung ,Rare Diseases ,Clinical Research ,Autoimmune Disease ,Biotechnology ,Scleroderma ,Detection ,screening and diagnosis ,4.2 Evaluation of markers and technologies ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Inflammatory and immune system ,Respiratory ,Adult ,Aged ,Biomarkers ,Dasatinib ,Female ,Gene Expression Regulation ,Humans ,Lung Diseases ,Interstitial ,Male ,Middle Aged ,Scleroderma ,Systemic ,Skin ,Tomography ,X-Ray Computed ,General Science & Technology - Abstract
BackgroundThere are no effective treatments or validated clinical response markers in systemic sclerosis (SSc). We assessed imaging biomarkers and performed gene expression profiling in a single-arm open-label clinical trial of tyrosine kinase inhibitor dasatinib in patients with SSc-associated interstitial lung disease (SSc-ILD).MethodsPrimary objectives were safety and pharmacokinetics. Secondary outcomes included clinical assessments, quantitative high-resolution computed tomography (HRCT) of the chest, serum biomarker assays and skin biopsy-based gene expression subset assignments. Clinical response was defined as decrease of >5 or >20% from baseline in the modified Rodnan Skin Score (MRSS). Pulmonary function was assessed at baseline and day 169.ResultsDasatinib was well-tolerated in 31 patients receiving drug for a median of nine months. No significant changes in clinical assessments or serum biomarkers were seen at six months. By quantitative HRCT, 65% of patients showed no progression of lung fibrosis, and 39% showed no progression of total ILD. Among 12 subjects with available baseline and post-treatment skin biopsies, three were improvers and nine were non-improvers. Improvers mapped to the fibroproliferative or normal-like subsets, while seven out of nine non-improvers were in the inflammatory subset (p = 0.0455). Improvers showed stability in forced vital capacity (FVC) and diffusing capacity for carbon monoxide (DLCO), while both measures showed a decline in non-improvers (p = 0.1289 and p = 0.0195, respectively). Inflammatory gene expression subset was associated with higher baseline HRCT score (p = 0.0556). Non-improvers showed significant increase in lung fibrosis (p = 0.0313).ConclusionsIn patients with SSc-ILD dasatinib treatment was associated with acceptable safety profile but no significant clinical efficacy. Patients in the inflammatory gene expression subset showed increase in skin fibrosis, decreasing pulmonary function and worsening lung fibrosis during the study. These findings suggest that target tissue-specific gene expression analyses can help match patients and therapeutic interventions in heterogeneous diseases such as SSc, and quantitative HRCT is useful for assessing clinical outcomes.Trial registrationClinicaltrials.gov NCT00764309.
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- 2017
25. Quantitative Computed Tomography Lung COVID Scores with Laboratory Markers: Utilization to Predict Rapid Progression and Monitor Longitudinal Changes in Patients with Coronavirus 2019 (COVID-19) Pneumonia
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Kang, Da Hyun, primary, Kim, Grace Hyun J., additional, Park, Sa-Beom, additional, Lee, Song-I, additional, Koh, Jeong Suk, additional, Brown, Matthew S., additional, Abtin, Fereidoun, additional, McNitt-Gray, Michael F., additional, Goldin, Jonathan G., additional, and Lee, Jeong Seok, additional
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- 2024
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26. Pulmonary Fibrosis Stakeholder Summit: A Joint National Heart, Lung, and Blood Institute, Three Lakes Foundation, and Pulmonary Fibrosis Foundation Workshop Report
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Montesi, Sydney B, primary, Gomez, Christian R, additional, Beers, Michael, additional, Brown, Robert, additional, Chattopadhyay, Ishanu, additional, Flaherty, Kevin R., additional, Garcia, Christine Kim, additional, Gomperts, Brigitte, additional, Hariri, Lida P, additional, Hogaboam, Cory M, additional, Jenkins, R. Gisli, additional, Kaminski, Naftali, additional, Kim, Grace Hyun J., additional, Königshoff, Melanie, additional, Kolb, Martin, additional, Kotton, Darrell N, additional, Kropski, Jonathan A., additional, Lasky, Joseph, additional, Magin, Chelsea M., additional, Maher, Toby M., additional, McCormick, Mark, additional, Moore, Bethany B, additional, Nickerson-Nutter, Cheryl, additional, Oldham, Justin, additional, Podolanczuk, Anna J., additional, Raghu, Ganesh, additional, Rosas, Ivan, additional, Rowe, Steven M, additional, Schmidt, William T., additional, Schwartz, David, additional, Shore, Jessica E, additional, Spino, Cathie, additional, Craig, Matthew, additional, and Martinez, Fernando J., additional
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- 2023
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27. Genicular Artery Embolization for the Treatment of Symptomatic Knee Osteoarthritis
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Padia, Siddharth A., Genshaft, Scott, Blumstein, Gideon, Plotnik, Adam, Kim, Grace Hyun J., Gilbert, Stephanie J., Lauko, Kara, and Stavrakis, Alexandra I.
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- 2021
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28. Prediction of idiopathic pulmonary fibrosis progression using early quantitative changes on CT imaging for a short term of clinical 18–24-month follow-ups
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Kim, Grace Hyun J., Weigt, Stephan S., Belperio, John A., Brown, Matthew S., Shi, Yu, Lai, Joshua H., and Goldin, Jonathan G.
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- 2020
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29. Toward clinically usable CAD for lung cancer screening with computed tomography.
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Brown, Matthew S, Lo, Pechin, Goldin, Jonathan G, Barnoy, Eran, Kim, Grace Hyun J, McNitt-Gray, Michael F, and Aberle, Denise R
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Lung ,Humans ,Lung Neoplasms ,Diagnosis ,Differential ,Tomography ,X-Ray Computed ,Reproducibility of Results ,ROC Curve ,Female ,Male ,Early Detection of Cancer ,Lung Cancer ,Clinical Trials and Supportive Activities ,Bioengineering ,Cancer ,Clinical Research ,Biomedical Imaging ,4.2 Evaluation of markers and technologies ,Detection ,screening and diagnosis ,Lung cancer ,Multiple pulmonary nodules ,Computer-assisted diagnosis ,Early detection of cancer ,X-ray computerized axial tomography ,Clinical Sciences ,Nuclear Medicine & Medical Imaging - Abstract
ObjectivesThe purpose of this study was to define clinically appropriate, computer-aided lung nodule detection (CAD) requirements and protocols based on recent screening trials. In the following paper, we describe a CAD evaluation methodology based on a publically available, annotated computed tomography (CT) image data set, and demonstrate the evaluation of a new CAD system with the functionality and performance required for adoption in clinical practice.MethodsA new automated lung nodule detection and measurement system was developed that incorporates intensity thresholding, a Euclidean Distance Transformation, and segmentation based on watersheds. System performance was evaluated against the Lung Imaging Database Consortium (LIDC) CT reference data set.ResultsThe test set comprised thin-section CT scans from 108 LIDC subjects. The median (±IQR) sensitivity per subject was 100 (±37.5) for nodules ≥ 4 mm and 100 (±8.33) for nodules ≥ 8 mm. The corresponding false positive rates were 0 (±2.0) and 0 (±1.0), respectively. The concordance correlation coefficient between the CAD nodule diameter and the LIDC reference was 0.91, and for volume it was 0.90.ConclusionsThe new CAD system shows high nodule sensitivity with a low false positive rate. Automated volume measurements have strong agreement with the reference standard. Thus, it provides comprehensive, clinically-usable lung nodule detection and assessment functionality.Key points• CAD requirements can be based on lung cancer screening trial results. • CAD systems can be evaluated using publically available annotated CT image databases. • A new CAD system was developed with a low false positive rate. • The CAD system has reliable measurement tools needed for clinical use.
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- 2014
30. Prediction of progression in idiopathic pulmonary fibrosis using CT scans at baseline: A quantum particle swarm optimization - Random forest approach
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Shi, Yu, Wong, Weng Kee, Goldin, Jonathan G., Brown, Matthew S., and Kim, Grace Hyun J.
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- 2019
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31. Pulmonary Fibrosis Stakeholder Summit: A Joint NHLBI, Three Lakes Foundation, and Pulmonary Fibrosis Foundation Workshop Report.
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Montesi, Sydney B., Gomez, Christian R., Beers, Michael, Brown, Robert, Chattopadhyay, Ishanu, Flaherty, Kevin R., Garcia, Christine Kim, Gomperts, Brigitte, Hariri, Lida P., Hogaboam, Cory M., Jenkins, R. Gisli, Kaminski, Naftali, Kim, Grace Hyun J., Königshoff, Melanie, Kolb, Martin, Kotton, Darrell N., Kropski, Jonathan A., Lasky, Joseph, Magin, Chelsea M., and Maher, Toby M.
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PULMONARY fibrosis ,IDIOPATHIC pulmonary fibrosis ,DISEASE risk factors ,INTERSTITIAL lung diseases ,EXPERIMENTAL design ,LAKES - Abstract
Despite progress in elucidation of disease mechanisms, identification of risk factors, biomarker discovery, and the approval of two medications to slow lung function decline in idiopathic pulmonary fibrosis and one medication to slow lung function decline in progressive pulmonary fibrosis, pulmonary fibrosis remains a disease with a high morbidity and mortality. In recognition of the need to catalyze ongoing advances and collaboration in the field of pulmonary fibrosis, the NHLBI, the Three Lakes Foundation, and the Pulmonary Fibrosis Foundation hosted the Pulmonary Fibrosis Stakeholder Summit on November 8–9, 2022. This workshop was held virtually and was organized into three topic areas: 1) novel models and research tools to better study pulmonary fibrosis and uncover new therapies, 2) early disease risk factors and methods to improve diagnosis, and 3) innovative approaches toward clinical trial design for pulmonary fibrosis. In this workshop report, we summarize the content of the presentations and discussions, enumerating research opportunities for advancing our understanding of the pathogenesis, treatment, and outcomes of pulmonary fibrosis. [ABSTRACT FROM AUTHOR]
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- 2024
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32. Late Breaking Abstract - Safety, tolerability and antifibrotic activity of bexotegrast: Phase 2a INTEGRIS-IPF study (NCT04396756)
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Wuyts, Wim A, primary, Valenzuela, Claudia, additional, Jenkins, Gisli, additional, Goldin, Jonathan G, additional, Kim, Grace Hyun J, additional, Jurek, Marzena, additional, Turner, Scott, additional, Decaris, Martin, additional, Barnes, Chris N, additional, Lefebvre, Éric, additional, Cosgrove, Gregory, additional, and Cottin, Vincent, additional
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- 2023
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33. Two CT image-based Biomarkers for Predicting Progression in fibrosing interstitial lung diseases
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Oh, Ju hyun, primary, Kim, Grace Hyun J., additional, Weigt, S. Samuel, additional, Wilkinson, Jared D, additional, Abtin, Fereidoun, additional, Pourzand, Lila, additional, Villegas, Bianca, additional, Lee, Jihey, additional, Lee, Kyungjong, additional, Goldin, Jonathan, additional, and Song, Jin Woo, additional
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- 2023
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34. Derivation of a high-resolution CT-based, semi-automated radiographic score in tuberculosis and its relationship to bacillary load and antitubercular therapy
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Riou, Catherine, primary, du Bruyn, Elsa, additional, Kim, Grace Hyun J., additional, da Costa, Irene, additional, Lee, Jihey, additional, Sher, Alan, additional, Wilkinson, Robert J., additional, Allwood, Brian W., additional, and Goldin, Jonathan, additional
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- 2023
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35. Combining Clinical and Biological Data to Predict Progressive Pulmonary Fibrosis in Patients With Systemic Sclerosis Despite Immunomodulatory Therapy
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Volkmann, Elizabeth R., primary, Wilhalme, Holly, additional, Assassi, Shervin, additional, Kim, Grace Hyun J., additional, Goldin, Jonathan, additional, Kuwana, Masataka, additional, Tashkin, Donald P., additional, and Roth, Michael D., additional
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- 2023
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36. Translating AI to Clinical Practice: Overcoming Data Shift with Explainability
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Choi, Youngwon, primary, Yu, Wenxi, additional, Nagarajan, Mahesh B., additional, Teng, Pangyu, additional, Goldin, Jonathan G., additional, Raman, Steven S., additional, Enzmann, Dieter R., additional, Kim, Grace Hyun J., additional, and Brown, Matthew S., additional
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- 2023
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37. Percutaneous Cryoablation for the Treatment of Recurrent Malignant Pleural Mesothelioma: Safety, Early-Term Efficacy, and Predictors of Local Recurrence
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Abtin, Fereidoun, Quirk, Matthew T., Suh, Robert D., Hsu, William, Han, Simon X., Kim, Grace-Hyun J., Genshaft, Scott, Sandberg, Jesse K., Olevsky, Olga, and Cameron, Robert B.
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- 2017
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38. Quantitative interstitial lung disease scores in idiopathic inflammatory myopathies: longitudinal changes and clinical implications.
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Yeo, Jina, Yoon, Soon Ho, Kim, Ju Yeon, Lee, Jeong Seok, Lee, Eun Young, Goo, Jin Mo, Pourzand, Lila, Goldin, Jonathan G, Kim, Grace‐Hyun J, and Ha, You‐Jung
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BIOMARKERS ,DISEASE progression ,MUSCLE diseases ,INFLAMMATION ,LUNG transplantation ,MULTIVARIATE analysis ,INTERSTITIAL lung diseases ,QUANTITATIVE research ,RETROSPECTIVE studies ,VITAL capacity (Respiration) ,DESCRIPTIVE statistics ,RESEARCH funding ,MYOSITIS ,COMPUTER-aided diagnosis ,COMPUTED tomography ,LOGISTIC regression analysis ,DATA analysis software ,PROGRESSION-free survival ,LONGITUDINAL method ,DISEASE complications - Abstract
Objectives To investigate computer-aided quantitative scores from high‐resolution CT (HRCT) images and determine their longitudinal changes and clinical significance in patients with idiopathic inflammatory myopathies (IIMs)-related interstitial lung disease (IIMs-ILD). Methods The clinical data and HRCT images of 80 patients with IIMs who underwent serial HRCT scans at least twice were retrospectively analysed. Quantitative ILD (QILD) scores (%) were calculated as the sum of the extent of lung fibrosis, ground-glass opacity, and honeycombing. The individual time-estimated ΔQILD between two consecutive scans was derived using a linear approximation of yearly changes. Results The baseline median QILD (interquartile range) scores in the whole lung were 28.1% (19.1–43.8). The QILD was significantly correlated with forced vital capacity (r = −0.349, P = 0.002) and diffusing capacity for carbon monoxide (r = −0.381, P = 0.001). For ΔQILD between the first two scans, according to the visual ILD subtype, QILD aggravation was more frequent in patients with usual interstitial pneumonia (UIP) than non-UIP (80.0% vs 44.4%, P = 0.013). Multivariable logistic regression analyses identified UIP was significantly related to radiographic ILD progression (ΔQILD >2%, P = 0.015). Patients with higher baseline QILD scores (>28.1%) had a higher risk of lung transplantation or death (P = 0.015). In the analysis of three serial HRCT scans (n = 41), dynamic ΔQILD with four distinct patterns (improving, worsening, convex and concave) was observed. Conclusion QILD changes in IIMs-ILD were dynamic, and baseline UIP patterns seemed to be related to a longitudinal progression in QILD. These may be potential imaging biomarkers for lung function, changes in ILD severity and prognosis in IIMs-ILD. [ABSTRACT FROM AUTHOR]
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- 2023
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39. Free-breathing quantification of hepatic fat in healthy children and children with nonalcoholic fatty liver disease using a multi-echo 3-D stack-of-radial MRI technique
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Armstrong, Tess, Ly, Karrie V., Murthy, Smruthi, Ghahremani, Shahnaz, Kim, Grace Hyun J., Calkins, Kara L., and Wu, Holden H.
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- 2018
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40. Quantitative image analysis in COVID-19 acute respiratory distress syndrome: a cohort observational study.
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Dolinay, Tamas, primary, Jun, Dale, additional, Maller, Abigail, additional, Chung, Augustine, additional, Grimes, Brandon, additional, Hsu, Lillian, additional, Nelson, David, additional, Villagas, Bianca, additional, Kim, Grace Hyun J, additional, and Goldin, Jonathan, additional
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- 2023
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41. Association of Symptoms of Gastroesophageal Reflux, Esophageal Dilation, and Progression of Systemic Sclerosis–Related Interstitial Lung Disease
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Volkmann, Elizabeth R., primary, Tashkin, Donald P., additional, Leng, Mei, additional, Kim, Grace Hyun J., additional, Goldin, Jonathan, additional, and Roth, Michael D., additional
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- 2023
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42. Mycophenolate mofetil versus oral cyclophosphamide in scleroderma-related interstitial lung disease (SLS II): a randomised controlled, double-blind, parallel group trial
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Tashkin, Donald P, Roth, Michael D, Clements, Philip J, Furst, Daniel E, Khanna, Dinesh, Kleerup, Eric C, Goldin, Jonathan, Arriola, Edgar, Volkmann, Elizabeth R, Kafaja, Suzanne, Silver, Richard, Steen, Virginia, Strange, Charlie, Wise, Robert, Wigley, Fredrick, Mayes, Maureen, Riley, David J, Hussain, Sabiha, Assassi, Shervin, Hsu, Vivien M, Patel, Bela, Phillips, Kristine, Martinez, Fernando, Golden, Jeffrey, Connolly, M Kari, Varga, John, Dematte, Jane, Hinchcliff, Monique E, Fischer, Aryeh, Swigris, Jeffrey, Meehan, Richard, Theodore, Arthur, Simms, Robert, Volkov, Suncica, Schraufnagel, Dean E, Scholand, Mary Beth, Frech, Tracy, Molitor, Jerry A, Highland, Kristin, Read, Charles A, Fritzler, Marvin J, Kim, Grace Hyun J, Tseng, Chi-Hong, and Elashoff, Robert M
- Published
- 2016
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43. Multi‐scale, domain knowledge‐guided attention + random forest: a two‐stage deep learning‐based multi‐scale guided attention models to diagnose idiopathic pulmonary fibrosis from computed tomography images
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Yu, Wenxi, primary, Zhou, Hua, additional, Choi, Youngwon, additional, Goldin, Jonathan G., additional, Teng, Pangyu, additional, Wong, Weng Kee, additional, McNitt‐Gray, Michael F., additional, Brown, Matthew S., additional, and Kim, Grace Hyun J., additional
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- 2022
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44. Correction to: Toward clinically usable CAD for lung cancer screening with computed tomography
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Brown, Matthew S., Lo, Pechin, Goldin, Jonathan G., Barnoy, Eran, Kim, Grace Hyun J., McNitt-Gray, Michael F., and Aberle, Denise R.
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- 2020
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45. Quantitative CT lung COVID scores: Prediction of rapid progression and monitoring longitudinal changes in COVID-19 pneumonia patients
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Kang, Da Hyun, primary, Kim, Grace Hyun J., additional, Park, Sa-Beom, additional, Lee, Song-I, additional, Koh, Jeong Suk, additional, Brown, Matthew S., additional, Abtin, Fereidoun, additional, McNitt-Gray, Michael F., additional, Lee, Jeong Seok, additional, and Goldin, Jonathan G., additional
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- 2022
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46. Quantitative image analysis in COVID-19 acute respiratory distress syndrome: a cohort observational study.
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Dolinay, Tamas, primary, Jun, Dale, additional, Maller, Abigail, additional, Chung, Augustine, additional, Grimes, Brandon, additional, Hsu, Lillian, additional, Nelson, David, additional, Villagas, Bianca, additional, Kim, Grace Hyun J, additional, and Goldin, Jonathan, additional
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- 2022
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47. Multi-scale, domain knowledge-guided attention + random forest: a two-stage deep learning-based multi-scale guided attention models to diagnose idiopathic pulmonary fibrosis from computed tomography images.
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Wenxi Yu, Hua Zhou, Youngwon Choi, Goldin, Jonathan G., Pangyu Teng, Weng Kee Wong, McNitt-Gray, Michael F., Brown, Matthew S., and Kim, Grace Hyun J.
- Subjects
IDIOPATHIC pulmonary fibrosis ,DEEP learning ,COMPUTED tomography ,RANDOM forest algorithms ,RECEIVER operating characteristic curves ,INTERSTITIAL lung diseases - Abstract
Background: Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible, and usually fatal lung disease of unknown reasons, generally affecting the elderly population. Early diagnosis of IPF is crucial for triaging patients' treatment planning into anti-fibrotic treatment or treatments for other causes of pulmonary fibrosis. However, current IPF diagnosis workflow is complicated and time-consuming, which involves collaborative efforts from radiologists, pathologists, and clinicians and it is largely subject to inter-observer variability. Purpose: The purpose of this work is to develop a deep learning-based automated system that can diagnose subjects with IPF among subjects with interstitial lung disease (ILD) using an axial chest computed tomography (CT) scan. This work can potentially enable timely diagnosis decisions and reduce inter-observer variability. Methods: Our dataset contains CT scans from 349 IPF patients and 529 non-IPF ILD patients. We used 80% of the dataset for training and validation purposes and 20% as the holdout test set. We proposed a two-stage model:at stage one, we built a multi-scale, domain knowledge-guided attention model (MSGA) that encouraged the model to focus on specific areas of interest to enhance model explainability, including both high- and medium-resolution attentions; at stage two, we collected the output from MSGA and constructed a random forest (RF) classifier for patient-level diagnosis, to further boost model accuracy. RF classifier is utilized as a final decision stage since it is interpretable, computationally fast, and can handle correlated variables. Model utility was examined by (1) accuracy, represented by the area under the receiver operating characteristic curve (AUC) with standard deviation (SD), and (2) explainability, illustrated by the visual examination of the estimated attention maps which showed the important areas for model diagnostics. Results: During the training and validation stage, we observe that when we provide no guidance from domain knowledge, the IPF diagnosis model reaches acceptable performance (AUC±SD = 0.93±0.07), but lacks explainability; when including only guided high- or medium-resolution attention, the learned attentionmaps are not satisfactory;when including both high- and medium-resolution attention, under certain hyperparameter settings, the model reaches the highest AUC among all experiments (AUC±SD = 0.99±0.01) and the estimated attention maps concentrate on the regions of interests for this task. Three bestperforming hyperparameter selections according to MSGA were applied to the holdout test set and reached comparable model performance to that of the validation set. Conclusions: Our results suggest that, for a task with only scan-level labels available, MSGA+RF can utilize the population-level domain knowledge to guide the training of the network, which increases both model accuracy and explainability. [ABSTRACT FROM AUTHOR]
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- 2023
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48. Automated quantification system predicts survival in rheumatoid arthritis-associated interstitial lung disease
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Oh, Ju Hyun, primary, Kim, Grace Hyun J, additional, Cross, Gary, additional, Barnett, Joseph, additional, Jacob, Joseph, additional, Hong, Seokchan, additional, and Song, Jin Woo, additional
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- 2022
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49. Procedural outcomes associated with use of the AngioVac System for right heart thrombi: A safety report from RAPID registry data
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Moriarty, John M, primary, Liao, Millie, additional, Kim, Grace Hyun J, additional, Yang, Eric, additional, Desai, Kush, additional, Ranade, Mona, additional, and Plotnik, Adam N, additional
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- 2022
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50. Quantitative image analysis in COVID-19 acute respiratory distress syndrome: a cohort observational study.
- Author
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Dolinay, Tamas, primary, Jun, Dale, additional, Maller, Abigail, additional, Chung, Augustine, additional, Grimes, Brandon, additional, Hsu, Lillian, additional, Nelson, David, additional, Villagas, Bianca, additional, Kim, Grace Hyun J, additional, and Goldin, Jonathan, additional
- Published
- 2021
- Full Text
- View/download PDF
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