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Huang K, Zhang Y, Cheng HD, Xing P. MSF-GAN: Multi-Scale Fuzzy Generative Adversarial Network for Breast Ultrasound Image Segmentation. Annu Int Conf IEEE Eng Med Biol Soc 2021; 2021:3193-3196. [PMID: 34891920 DOI: 10.1109/embc46164.2021.9630108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Automatic breast ultrasound image (BUS) segmentation is still a challenging task due to poor image quality and inherent speckle noise. In this paper, we propose a novel multi-scale fuzzy generative adversarial network (MSF-GAN) for breast ultrasound image segmentation. The proposed MSF-GAN consists of two networks: a generative network to generate segmentation maps for input BUS images, and a discriminative network that employs a multi-scale fuzzy (MSF) entropy module for discrimination. The major contribution of this paper is applying fuzzy logic and fuzzy entropy in the discriminative network which can distinguish the uncertainty of segmentation maps and groundtruth maps and forces the generative network to achieve better segmentation performance. We evaluate the performance of MSF-GAN on three BUS datasets and compare it with six state-of-the-art deep neural network-based methods in terms of five metrics. MSF-GAN achieves the highest mean IoU of 78.75%, 73.30%, and 71.12% on three datasets, respectively.
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Yan X, Ding J, Cheng HD. A Novel Adaptive Fuzzy Deep Learning Approach for Histopathologic Cancer Detection. Annu Int Conf IEEE Eng Med Biol Soc 2021; 2021:3518-3521. [PMID: 34891998 DOI: 10.1109/embc46164.2021.9630824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We proposed a novel model that integrates the fuzzy theory and group equivariant convolutional neural network for histopathologic cancer detection. The proposed fuzzy group equivariant convolutional neural network consists of the convolutional network, a novel fuzzy global pooling layer, and a fully connected network. In the fuzzy global pooling layer, the generated feature maps are transferred into the fuzzy domain by two different fuzzification methods. One of the fuzzy feature maps exploits the uncertainty information of histopathologic images, and the other keeps the original information. Furthermore, the fuzzy feature maps are processed by using Min-max operations. The experiments verified that the proposed method could always find the maximum fuzzy entropy and exploit and present the uncertainty of histopathologic images well. The experiments using the benchmark dataset demonstrate that the proposed model becomes more accurate and outperforms the existing models including the benchmark models. Compared to the benchmark model with 89.8% of accuracy, 96.3% of AUC, and 0.260 of negative log-likelihood loss, the proposed model obtained 91.7% of accuracy, 97.2% of AUC, and 0.214 of negative log-likelihood loss.
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Cheng HD, Dowell KG, Bailey-Kellogg C, Goods BA, Love JC, Ferrari G, Alter G, Gach J, Forthal DN, Lewis GK, Greene K, Gao H, Montefiori DC, Ackerman ME. Diverse antiviral IgG effector activities are predicted by unique biophysical antibody features. Retrovirology 2021; 18:35. [PMID: 34717659 PMCID: PMC8557579 DOI: 10.1186/s12977-021-00579-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/20/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The critical role of antibody Fc-mediated effector functions in immune defense has been widely reported in various viral infections. These effector functions confer cellular responses through engagement with innate immune cells. The precise mechanism(s) by which immunoglobulin G (IgG) Fc domain and cognate receptors may afford protection are poorly understood, however, in the context of HIV/SHIV infections. Many different in vitro assays have been developed and utilized to measure effector functions, but the extent to which these assays capture distinct antibody activities has not been fully elucidated. RESULTS In this study, six Fc-mediated effector function assays and two biophysical antibody profiling assays were performed on a common set of samples from HIV-1 infected and vaccinated subjects. Biophysical antibody profiles supported robust prediction of diverse IgG effector functions across distinct Fc-mediated effector function assays. While a number of assays showed correlated activities, supervised machine learning models indicated unique antibody features as primary contributing factors to the associated effector functions. Additional experiments established the mechanistic relevance of relationships discovered using this unbiased approach. CONCLUSIONS In sum, this study provides better resolution on the diversity and complexity of effector function assays, offering a clearer perspective into this family of antibody mechanisms of action to inform future HIV-1 treatment and vaccination strategies.
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Affiliation(s)
- Hao D. Cheng
- grid.254880.30000 0001 2179 2404Thayer School of Engineering, Dartmouth College, Hanover, NH USA ,grid.254880.30000 0001 2179 2404Molecular and Cellular Biology Program, Dartmouth College, 14 Engineering Dr., Hanover, NH 03755 USA
| | - Karen G. Dowell
- grid.254880.30000 0001 2179 2404Department of Computer Science, Dartmouth College, Hanover, 03755 USA
| | - Chris Bailey-Kellogg
- grid.254880.30000 0001 2179 2404Department of Computer Science, Dartmouth College, Hanover, 03755 USA
| | - Brittany A. Goods
- grid.116068.80000 0001 2341 2786Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ,grid.116068.80000 0001 2341 2786Department of Biological Engineering, Koch Institute at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - J. Christopher Love
- grid.116068.80000 0001 2341 2786Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ,grid.116068.80000 0001 2341 2786Department of Biological Engineering, Koch Institute at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Guido Ferrari
- grid.189509.c0000000100241216Department of Surgery, Duke University Medical Center, Durham, NC 27710 USA ,grid.189509.c0000000100241216Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27719 USA
| | - Galit Alter
- grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | - Johannes Gach
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, Irvine School of Medicine, University California, Irvine, CA 92697 USA
| | - Donald N. Forthal
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, Irvine School of Medicine, University California, Irvine, CA 92697 USA
| | - George K. Lewis
- grid.411024.20000 0001 2175 4264Division of Vaccine Research, Institute of Human Virology, University Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Kelli Greene
- grid.189509.c0000000100241216Department of Surgery, Duke University Medical Center, Durham, NC 27710 USA
| | - Hongmei Gao
- grid.189509.c0000000100241216Department of Surgery, Duke University Medical Center, Durham, NC 27710 USA
| | - David C. Montefiori
- grid.189509.c0000000100241216Department of Surgery, Duke University Medical Center, Durham, NC 27710 USA ,grid.189509.c0000000100241216Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27719 USA
| | - Margaret E. Ackerman
- grid.254880.30000 0001 2179 2404Thayer School of Engineering, Dartmouth College, Hanover, NH USA ,grid.254880.30000 0001 2179 2404Molecular and Cellular Biology Program, Dartmouth College, 14 Engineering Dr., Hanover, NH 03755 USA
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Xu F, Zhang Y, Cheng HD, Zhang B, Ding J, Ning C, Wang Y. Tumor saliency estimation for breast ultrasound images via breast anatomy modeling. Artif Intell Med 2021; 119:102155. [PMID: 34531014 DOI: 10.1016/j.artmed.2021.102155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 06/19/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022]
Abstract
Tumor saliency estimation aims to localize tumors by modeling the visual stimuli in medical images. However, it is a challenging task for breast ultrasound (BUS) image due to the complicated anatomic structure of the breast and poor image quality; and existing saliency estimation approaches only model the generic visual stimuli, e.g., local and global contrast, location, and feature correlation, and achieve poor performance for tumor saliency estimation. In this paper, we propose a novel optimization model to estimate tumor saliency by utilizing breast anatomy. First, we model breast anatomy and decompose breast ultrasound image into layers using Neutro-Connectedness; then utilize the layers to generate the foreground and background maps; and finally propose a novel objective function to estimate the tumor saliency by integrating the foreground map, background map, adaptive center bias, and region-based correlation cues. The extensive experiments demonstrate that the proposed approach obtains more accurate foreground and background maps with breast anatomy; especially, for the images having large or small tumors. Meanwhile, the new objective function can handle the images without tumors. The newly proposed method achieves state-of-the-art performance comparing to eight tumor saliency estimation approaches using two BUS datasets.
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Affiliation(s)
- Fei Xu
- Department of Computer Science, Utah State University, Logan, USA
| | - Yingtao Zhang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - H D Cheng
- Department of Computer Science, Utah State University, Logan, USA.
| | - Boyu Zhang
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, USA
| | - Jianrui Ding
- School of Computer Science and Technology, Harbin Institute of Technology, Weihai, China
| | - Chunping Ning
- Department of Ultrasound, Affiliated Hospital of Medical College Qingdao University, Qingdao, China
| | - Ying Wang
- Department of General Surgery, Second Hospital of Hebei Medical University, Shijiazhuang, China
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Cheng HD, Tirosh I, de Haan N, Stöckmann H, Adamczyk B, McManus CA, O'Flaherty R, Greville G, Saldova R, Bonilla FA, Notarangelo LD, Driessen GJ, Holm IA, Rudd PM, Wuhrer M, Ackerman ME, Nigrovic PA. IgG Fc glycosylation as an axis of humoral immunity in childhood. J Allergy Clin Immunol 2019; 145:710-713.e9. [PMID: 31669096 DOI: 10.1016/j.jaci.2019.10.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Hao D Cheng
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH
| | - Irit Tirosh
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Rheumatology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Israel
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Henning Stöckmann
- Glycoscience Group, National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Barbara Adamczyk
- Glycoscience Group, National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Ciara A McManus
- Glycoscience Group, National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Róisín O'Flaherty
- Glycoscience Group, National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Gordon Greville
- Glycoscience Group, National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Radka Saldova
- Glycoscience Group, National Institute for Bioprocessing Research and Training, Dublin, Ireland; College of Health and Agricultural Science, UCD School of Medicine, University College Dublin, Dublin, Ireland
| | | | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Gertjan J Driessen
- Department of Pediatrics, Juliana Children's Hospital, Haga Teaching Hospital, The Hague, The Netherlands; Department of Pediatrics, Erasmus Medical Center, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Ingrid A Holm
- Division of Endocrinology, Boston Children's Hospital, Boston, Mass
| | - Pauline M Rudd
- Glycoscience Group, National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Margaret E Ackerman
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH; Thayer School of Engineering, Dartmouth College, Hanover, NH.
| | - Peter A Nigrovic
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, Mass.
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Cheng HD, Grimm SK, Gilman MS, Gwom LC, Sok D, Sundling C, Donofrio G, Karlsson Hedestam GB, Bonsignori M, Haynes BF, Lahey TP, Maro I, von Reyn CF, Gorny MK, Zolla-Pazner S, Walker BD, Alter G, Burton DR, Robb ML, Krebs SJ, Seaman MS, Bailey-Kellogg C, Ackerman ME. Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site. JCI Insight 2018. [PMID: 29515029 PMCID: PMC5922287 DOI: 10.1172/jci.insight.97018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Major advances in donor identification, antigen probe design, and experimental methods to clone pathogen-specific antibodies have led to an exponential growth in the number of newly characterized broadly neutralizing antibodies (bnAbs) that recognize the HIV-1 envelope glycoprotein. Characterization of these bnAbs has defined new epitopes and novel modes of recognition that can result in potent neutralization of HIV-1. However, the translation of envelope recognition profiles in biophysical assays into an understanding of in vivo activity has lagged behind, and identification of subjects and mAbs with potent antiviral activity has remained reliant on empirical evaluation of neutralization potency and breadth. To begin to address this discrepancy between recombinant protein recognition and virus neutralization, we studied the fine epitope specificity of a panel of CD4-binding site (CD4bs) antibodies to define the molecular recognition features of functionally potent humoral responses targeting the HIV-1 envelope site bound by CD4. Whereas previous studies have used neutralization data and machine-learning methods to provide epitope maps, here, this approach was reversed, demonstrating that simple binding assays of fine epitope specificity can prospectively identify broadly neutralizing CD4bs-specific mAbs. Building on this result, we show that epitope mapping and prediction of neutralization breadth can also be accomplished in the assessment of polyclonal serum responses. Thus, this study identifies a set of CD4bs bnAb signature amino acid residues and demonstrates that sensitivity to mutations at signature positions is sufficient to predict neutralization breadth of polyclonal sera with a high degree of accuracy across cohorts and across clades.
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Affiliation(s)
- Hao D Cheng
- Thayer School of Engineering and.,Molecular and Cellular Biology Program, Dartmouth College, Hanover, New Hampshire, USA
| | | | - Morgan Sa Gilman
- Thayer School of Engineering and.,Molecular and Cellular Biology Program, Dartmouth College, Hanover, New Hampshire, USA
| | - Luc Christian Gwom
- Thayer School of Engineering and.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Christopher Sundling
- Unit of Infectious Diseases, Department of Medicine, Solna, Karolinska Institute, Stockholm, Sweden
| | - Gina Donofrio
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | | | | | | | - Timothy P Lahey
- Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Isaac Maro
- Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.,DarDar Health Programs, Dar es salaam, Tanzania.,Tokyo Medical and Dental University, Tokyo, Japan
| | - C Fordham von Reyn
- Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Miroslaw K Gorny
- Department of Pathology, NYU School of Medicine, New York, New York, USA
| | - Susan Zolla-Pazner
- Departments of Medicine and Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, Massachusetts, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA.,Ragon Institute of MGH, MIT, and Harvard University, Cambridge, Massachusetts, USA
| | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Shelly J Krebs
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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Wang FW, Fu SM, Jin YC, Gong XH, Cheng HD, Wu KJ. [Retrospective analysis of diagnosis and treatment of breast cancer in pregnancy]. Zhonghua Wai Ke Za Zhi 2018; 56:114-118. [PMID: 29397624 DOI: 10.3760/cma.j.issn.0529-5815.2018.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the principles of diagnosis and treatment of breast cancer during pregnancy. Methods: Clinical data of patients with breast cancer during pregnancy admitted to Obstetrics and Gynecology Hospital of Fudan University between January 2012 to July 2017 were analyzed retrospectively. A total of 17 patients were diagnosed with breast cancer in pregnancy, the median age was 32 years (range from 25 to 45 years old), pathological staging revealed 2 patient with stage 0, 1 with stage Ⅱa, 7 with stage Ⅱb, 1 with stage Ⅲa, 2 with stage Ⅲc, 4 with stage Ⅳ. Results: Thirteen patients received surgical treatment in pregnancy, the gestational age at surgery was (27.7±4.6) weeks; 2 patients with ductal carcinoma in situ received mastectomy, 11 patients with breast cancer underwent modified radical mastectomy. In patients undergoing surgery during pregnancy, no prophylactic contractions were used in 4 patients who had been treated earlier, there were 2 patients with frequent contractions within 24 hours after operation in these patients. Follow-up 9 patients were given oral nifedipine to prevent contractions, no obvious contractions occurred after the operation. Seven patients received chemotherapy during pregnancy; the chemotherapy of 4 cases of triple negative breast cancer was weekly paclitaxel sequential epirubicin and cyclophosphamide, the chemotherapy of the other three patients was docetaxel sequential epirubicin and cyclophosphamide. Fifteen patients underwent cesarean section to terminate pregnancy, 2 patients underwent spontaneous labor. The gestational age of birth was (36.9 ±1.3) weeks. Less than 35 weeks of termination of pregnancy occurred in one patient, the fetus was delivered to the neonatal intensive care unit due to neonatal respiratory distress syndrome, and suffered from congenital dysaudia. The prognosis of the other 16 survived infants was good. The median follow-up time was 10 months (range from 4 to 27) months, in 13 patients of stage 0 to Ⅲc, one patient were diagnosed with bone metastasis at 12 months after surgery, the remaining 12 patients had no disease progression, the progression free survival rate was 12/13, the overall survival rate was 13/13. Among the 4 patients with stage Ⅳ, one died in 7 months after delivery, one had new liver metastasis in 8 months after delivery. The remaining 2 patients were in stable condition. Conclusions: Breast cancer in pregnancy can be treated effectively, multidisciplinary cooperation and detailed assessment of maternal-fetal risks and benefits are necessary. Chemotherapy during pregnancy is safe for maternal-fetal, but it needed a large sample of clinical studies and long-term follow-up. The neonatal outcome was associated with gestational age, and therefore premature delivery was avoided as much as possible during treatment.
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Affiliation(s)
- F W Wang
- Department of Breast Surgery, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China
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Cheng HD, Stöckmann H, Adamczyk B, McManus CA, Ercan A, Holm IA, Rudd PM, Ackerman ME, Nigrovic PA. High-throughput characterization of the functional impact of IgG Fc glycan aberrancy in juvenile idiopathic arthritis. Glycobiology 2017; 27:1099-1108. [PMID: 28973482 PMCID: PMC5881781 DOI: 10.1093/glycob/cwx082] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/30/2017] [Accepted: 09/09/2017] [Indexed: 12/19/2022] Open
Abstract
Juvenile idiopathic arthritis (JIA) encompasses all forms of chronic idiopathic arthritis that arise before age 16. Previous studies have found JIA to be associated with lower Fc galactosylation of circulating IgG, but the overall spectrum of glycan changes and the net impact on IgG function are unknown. Using ultra performance liquid chromatography (UPLC), we compared IgG glycosylation in 54 subjects with recent-onset untreated JIA with 98 healthy pediatric controls, paired to biophysical profiling of affinity for 20 IgG receptors using a high-throughput multiplexed microsphere assay. Patients with JIA exhibited an increase in hypogalactosylated and hyposialylated IgG glycans, but no change in fucosylation or bisection, together with alteration in the spectrum of IgG ligand binding. Supervised machine learning demonstrated a robust capacity to discriminate JIA subjects from controls using either glycosylation or binding data. The binding signature was driven predominantly by enhanced affinity for Fc receptor like protein 5 (FcRL5), a noncanonical Fc receptor expressed on B cells. Affinity for FcRL5 correlated inversely with galactosylation and sialylation, a relationship confirmed through enzymatic manipulation. These results demonstrate the capacity of combined structural and biophysical IgG phenotyping to define the overall functional impact of IgG glycan changes and implicate FcRL5 as a potential cellular sensor of IgG glycosylation.
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Affiliation(s)
- Hao D Cheng
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, 03755 NH, USA
| | - Henning Stöckmann
- NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin A94 X099, Ireland
| | - Barbara Adamczyk
- NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin A94 X099, Ireland
| | - Ciara A McManus
- NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin A94 X099, Ireland
| | - Altan Ercan
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ingrid A Holm
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA, USA
| | - Pauline M Rudd
- NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin A94 X099, Ireland
| | - Margaret E Ackerman
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, 03755 NH, USA
- Thayer School of Engineering, Dartmouth College, Hanover, 03755 NH, USA
| | - Peter A Nigrovic
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
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Wang Y, Guo ZX, Tan NW, Cheng HD, Song YL. [Analysis and discussion of risk factors related to dental implant failure]. Zhonghua Kou Qiang Yi Xue Za Zhi 2017; 52:510-512. [PMID: 28835034 DOI: 10.3760/cma.j.issn.1002-0098.2017.08.012] [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] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The implant prosthesis has been extensively used in clinic recently, and implant failure is appearing. Many factors may cause the failure, and they work together generally. This paper summarizes and analyzes the failure cases related to implant treatment and relevant risk factors of oral implants in Department of Implantation, School of Stomatology, The Fourth Military Medical University during the past six years, in order to improve the success rate of implant prosthesis and provide guidance for clinical application.
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Affiliation(s)
- Y Wang
- Department of Implantation, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Xi'an 710032, China
| | - Z X Guo
- Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, Xi'an 710032, China
| | - N W Tan
- Department of Implantation, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Xi'an 710032, China
| | - H D Cheng
- Department of Implantation, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Xi'an 710032, China
| | - Y L Song
- Department of Implantation, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Xi'an 710032, China
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Huang Y, Ferrari G, Alter G, Forthal DN, Kappes JC, Lewis GK, Love JC, Borate B, Harris L, Greene K, Gao H, Phan TB, Landucci G, Goods BA, Dowell KG, Cheng HD, Bailey-Kellogg C, Montefiori DC, Ackerman ME. Diversity of Antiviral IgG Effector Activities Observed in HIV-Infected and Vaccinated Subjects. J Immunol 2016; 197:4603-4612. [PMID: 27913647 PMCID: PMC5137799 DOI: 10.4049/jimmunol.1601197] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/18/2016] [Indexed: 01/14/2023]
Abstract
Diverse Ab effector functions mediated by the Fc domain have been commonly associated with reduced risk of infection in a growing number of nonhuman primate and human clinical studies. This study evaluated the anti-HIV Ab effector activities in polyclonal serum samples from HIV-infected donors, VAX004 vaccine recipients, and healthy HIV-negative subjects using a variety of primary and cell line-based assays, including Ab-dependent cellular cytotoxicity (ADCC), Ab-dependent cell-mediated viral inhibition, and Ab-dependent cellular phagocytosis. Additional assay characterization was performed with a panel of Fc-engineered variants of mAb b12. The goal of this study was to characterize different effector functions in the study samples and identify assays that might most comprehensively and dependably capture Fc-mediated Ab functions mediated by different effector cell types and against different viral targets. Deployment of such assays may facilitate assessment of functionally unique humoral responses and contribute to identification of correlates of protection with potential mechanistic significance in future HIV vaccine studies. Multivariate and correlative comparisons identified a set of Ab-dependent cell-mediated viral inhibition and phagocytosis assays that captured different Ab activities and were distinct from a group of ADCC assays that showed a more similar response profile across polyclonal serum samples. The activities of a panel of b12 monoclonal Fc variants further identified distinctions among the ADCC assays. These results reveal the natural diversity of Fc-mediated Ab effector responses among vaccine recipients in the VAX004 trial and in HIV-infected subjects, and they point to the potential importance of polyfunctional Ab responses.
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC 27710
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Donald N Forthal
- Division of Infectious Diseases, University of California School of Medicine, Irvine, CA 92697
| | - John C Kappes
- Division of Infectious Diseases, University of California School of Medicine, Irvine, CA 92697
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - George K Lewis
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - J Christopher Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Bhavesh Borate
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Linda Harris
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Kelli Greene
- Department of Surgery, Duke University Medical Center, Durham, NC 27710
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, NC 27710
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710
| | - Tran B Phan
- Division of Infectious Diseases, University of California School of Medicine, Irvine, CA 92697
| | - Gary Landucci
- Division of Infectious Diseases, University of California School of Medicine, Irvine, CA 92697
| | - Brittany A Goods
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Karen G Dowell
- Department of Computer Science, Dartmouth College, Hanover, NH 03755; and
| | - Hao D Cheng
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | | | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710
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11
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Boesch AW, Brown EP, Cheng HD, Ofori MO, Normandin E, Nigrovic PA, Alter G, Ackerman ME. Highly parallel characterization of IgG Fc binding interactions. MAbs 2015; 6:915-27. [PMID: 24927273 DOI: 10.4161/mabs.28808] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Because the variable ability of the antibody constant (Fc) domain to recruit innate immune effector cells and complement is a major factor in antibody activity in vivo, convenient means of assessing these binding interactions is of high relevance to the development of enhanced antibody therapeutics, and to understanding the protective or pathogenic antibody response to infection, vaccination, and self. Here, we describe a highly parallel microsphere assay to rapidly assess the ability of antibodies to bind to a suite of antibody receptors. Fc and glycan binding proteins such as FcγR and lectins were conjugated to coded microspheres and the ability of antibodies to interact with these receptors was quantified. We demonstrate qualitative and quantitative assessment of binding preferences and affinities across IgG subclasses, Fc domain point mutants, and antibodies with variant glycosylation. This method can serve as a rapid proxy for biophysical methods that require substantial sample quantities, high-end instrumentation, and serial analysis across multiple binding interactions, thereby offering a useful means to characterize monoclonal antibodies, clinical antibody samples, and antibody mimics, or alternatively, to investigate the binding preferences of candidate Fc receptors.
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Affiliation(s)
- Austin W Boesch
- Thayer School of Engineering, Dartmouth College, Hanover, NH USA
| | - Eric P Brown
- Thayer School of Engineering, Dartmouth College, Hanover, NH USA
| | - Hao D Cheng
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH USA
| | - Maame Ofua Ofori
- Thayer School of Engineering, Dartmouth College, Hanover, NH USA
| | - Erica Normandin
- Thayer School of Engineering, Dartmouth College, Hanover, NH USA
| | - Peter A Nigrovic
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA USA
| | - Galit Alter
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA USA
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH USA; Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH USA; Department of Microbiology and Immunology, Geisel School of Medicine, Lebanon, NH USA
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12
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Mahan AE, Tedesco J, Dionne K, Baruah K, Cheng HD, De Jager PL, Barouch DH, Suscovich T, Ackerman M, Crispin M, Alter G. A method for high-throughput, sensitive analysis of IgG Fc and Fab glycosylation by capillary electrophoresis. J Immunol Methods 2014; 417:34-44. [PMID: 25523925 DOI: 10.1016/j.jim.2014.12.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 02/02/2023]
Abstract
The N-glycan of the IgG constant region (Fc) plays a central role in tuning and directing multiple antibody functions in vivo, including antibody-dependent cellular cytotoxicity, complement deposition, and the regulation of inflammation, among others. However, traditional methods of N-glycan analysis, including HPLC and mass spectrometry, are technically challenging and ill suited to handle the large numbers of low concentration samples analyzed in clinical or animal studies of the N-glycosylation of polyclonal IgG. Here we describe a capillary electrophoresis-based technique to analyze plasma-derived polyclonal IgG-glycosylation quickly and accurately in a cost-effective, sensitive manner that is well suited for high-throughput analyses. Additionally, because a significant fraction of polyclonal IgG is glycosylated on both Fc and Fab domains, we developed an approach to separate and analyze domain-specific glycosylation in polyclonal human, rhesus and mouse IgGs. Overall, this protocol allows for the rapid, accurate, and sensitive analysis of Fc-specific IgG glycosylation, which is critical for population-level studies of how antibody glycosylation may vary in response to vaccination or infection, and across disease states ranging from autoimmunity to cancer in both clinical and animal studies.
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Affiliation(s)
- Alison E Mahan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
| | | | - Kendall Dionne
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
| | - Kavitha Baruah
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Hao D Cheng
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
| | - Philip L De Jager
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, United States
| | - Dan H Barouch
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Todd Suscovich
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
| | - Margaret Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
| | - Max Crispin
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States.
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13
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Liu Y, Cheng HD, Huang J, Zhang Y, Tang X, Tian J. An effective non-rigid registration approach for ultrasound image based on "demons" algorithm. J Digit Imaging 2014; 26:521-9. [PMID: 23053907 DOI: 10.1007/s10278-012-9532-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Medical image registration is an important component of computer-aided diagnosis system in diagnostics, therapy planning, and guidance of surgery. Because of its low signal/noise ratio (SNR), ultrasound (US) image registration is a difficult task. In this paper, a fully automatic non-rigid image registration algorithm based on demons algorithm is proposed for registration of ultrasound images. In the proposed method, an "inertia force" derived from the local motion trend of pixels in a Moore neighborhood system is produced and integrated into optical flow equation to estimate the demons force, which is helpful to handle the speckle noise and preserve the geometric continuity of US images. In the experiment, a series of US images and several similarity measure metrics are utilized for evaluating the performance. The experimental results demonstrate that the proposed method can register ultrasound images efficiently, robust to noise, quickly and automatically.
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Affiliation(s)
- Yan Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, No. 92, Xidazhi Street, Harbin, 150001, People's Republic of China
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14
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Liu Y, Cheng HD, Huang J, Zhang Y, Tang X. An effective approach of lesion segmentation within the breast ultrasound image based on the cellular automata principle. J Digit Imaging 2013; 25:580-90. [PMID: 22237810 DOI: 10.1007/s10278-011-9450-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In this paper, a novel lesion segmentation within breast ultrasound (BUS) image based on the cellular automata principle is proposed. Its energy transition function is formulated based on global image information difference and local image information difference using different energy transfer strategies. First, an energy decrease strategy is used for modeling the spatial relation information of pixels. For modeling global image information difference, a seed information comparison function is developed using an energy preserve strategy. Then, a texture information comparison function is proposed for considering local image difference in different regions, which is helpful for handling blurry boundaries. Moreover, two neighborhood systems (von Neumann and Moore neighborhood systems) are integrated as the evolution environment, and a similarity-based criterion is used for suppressing noise and reducing computation complexity. The proposed method was applied to 205 clinical BUS images for studying its characteristic and functionality, and several overlapping area error metrics and statistical evaluation methods are utilized for evaluating its performance. The experimental results demonstrate that the proposed method can handle BUS images with blurry boundaries and low contrast well and can segment breast lesions accurately and effectively.
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Affiliation(s)
- Yan Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, No. 92, Xidazhi Street, Harbin, 150001, People's Republic of China
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15
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Abstract
Breast ultrasound (BUS) image segmentation is a very difficult task due to poor image quality and speckle noise. In this paper, local features extracted from roughly segmented regions of interest (ROIs) are used to describe breast tumors. The roughly segmented ROI is viewed as a bag. And subregions of the ROI are considered as the instances of the bag. Multiple-instance learning (MIL) method is more suitable for classifying breast tumors using BUS images. However, due to the complexity of BUS images, traditional MIL method is not applicable. In this paper, a novel MIL method is proposed for solving such task. First, a self-organizing map is used to map the instance space to the concept space. Then, we use the distribution of the instances of each bag in the concept space to construct the bag feature vector. Finally, a support vector machine is employed for classifying the tumors. The experimental results show that the proposed method can achieve better performance: the accuracy is 0.9107 and the area under receiver operator characteristic curve is 0.96 (p < 0.005).
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Affiliation(s)
- Jianrui Ding
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, No. 92, Xidazhi Street, Harbin, 150001, People's Republic of China
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16
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Liu Y, Cheng HD, Huang JH, Zhang YT, Tang XL, Tian JW, Wang Y. Computer aided diagnosis system for breast cancer based on color Doppler flow imaging. J Med Syst 2012; 36:3975-82. [PMID: 22791011 DOI: 10.1007/s10916-012-9869-4] [Citation(s) in RCA: 18] [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] [Received: 05/18/2012] [Accepted: 06/26/2012] [Indexed: 11/24/2022]
Abstract
Color Doppler flow imaging takes a great value in diagnosing and classifying benign and malignant breast lesions. However, scanning of color Doppler sonography is operator-dependent and ineffective. In this paper, a novel breast classification system based on B-Mode ultrasound and color Doppler flow imaging is proposed. First, different feature extraction methods were used to obtain the texture and geometric features from B-Mode ultrasound images. In color Doppler feature extraction stage, several spectrum features are extracted by applying blood flow velocity analysis to Doppler signals. Moreover, a velocity coherent vector method is proposed based on color coherence vector, which is helpful for designing to the optimize detection of flow indices from different blood flow velocity fields automatically. Finally, a support vector machine classifier with selected feature vectors is used to classify breast tumors into benign and malignant. The experimental results demonstrate that the proposed computer-aided diagnosis system is useful for reducing the unnecessary biopsy and death rate.
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Affiliation(s)
- Yan Liu
- School of Computer Science and Technology, Harbin Institute of Technology, People's Republic of China.
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17
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Shan J, Cheng HD, Wang Y. Completely automated segmentation approach for breast ultrasound images using multiple-domain features. Ultrasound Med Biol 2012; 38:262-275. [PMID: 22230134 DOI: 10.1016/j.ultrasmedbio.2011.10.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 09/29/2011] [Accepted: 10/26/2011] [Indexed: 05/31/2023]
Abstract
Lesion segmentation is a challenging task for computer aided diagnosis systems. In this article, we propose a novel and fully automated segmentation approach for breast ultrasound (BUS) images. The major contributions of this work are: an efficient region-of-interest (ROI) generation method is developed and new features to characterize lesion boundaries are proposed. After a ROI is located automatically, two newly proposed lesion features (phase in max-energy orientation and radial distance), combined with a traditional intensity-and-texture feature, are utilized to detect the lesion by a trained artificial neural network. The proposed features are tested on a database of 120 images and the experimental results prove their strong distinguishing ability. Compared with other breast ultrasound segmentation methods, the proposed method improves the TP rate from 84.9% to 92.8%, similarity rate from 79.0% to 83.1% and reduces the FP rate from 14.1% to 12.0%, using the same database. In addition, sensitivity analysis demonstrates the robustness of the proposed method.
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Affiliation(s)
- Juan Shan
- Department of Computer Science, Utah State University, Logan, UT 84322, USA
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18
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Wang Y, Wang H, Guo Y, Ning C, Liu B, Cheng HD, Tian J. Novel computer-aided diagnosis algorithms on ultrasound image: effects on solid breast masses discrimination. J Digit Imaging 2009; 23:581-91. [PMID: 19902300 DOI: 10.1007/s10278-009-9245-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 08/12/2009] [Accepted: 09/12/2009] [Indexed: 10/20/2022] Open
Abstract
The objective of this study is to retrospectively investigate whether using the newly developed algorithms would improve radiologists' accuracy for discriminating malignant masses from benign ones on ultrasonographic (US) images. Five radiologists blinded to the histological results and clinical history independently interpreted 226 cases according to the sonographic lexicon of the fourth edition of the Breast Imaging Reporting and Data System and assigned a final assessment category to indicate the probability of malignancy. For each case, each radiologist provided three diagnoses: first with the original images, subsequently with the assistant of the resulting images processed by the proposed CAD algorithms which are called as processed images, and another using the processed images only. Observers' malignancy rating data were analyzed with the receiver operating characteristic (ROC) curve. For reading only with the processed images, areas under the ROC curve (A(z)) of each reader (0.863, 0.867, 0.859, 0.868, 0.878) were better than that with the original images (0.772, 0.807, 0.796, 0.828, 0.846), difference of the average A(z) between the twice reading was significant (p < 0.001). Compared with the results single used processed images, A(z) of utilizing the combined images were increased (0.866, 0.885, 0.872, 0.894, 0.903), but the difference is not statistically significant (p = 0.081). The proposed CAD method has potential to be a good aid to radiologists in distinguishing malignant breast solid masses from benign ones.
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Affiliation(s)
- Ying Wang
- Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, Heilongjiang 150086, People's Republic of China
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19
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Liu B, Cheng HD, Huang J, Tian J, Liu J, Tang X. Automated segmentation of ultrasonic breast lesions using statistical texture classification and active contour based on probability distance. Ultrasound Med Biol 2009; 35:1309-1324. [PMID: 19481332 DOI: 10.1016/j.ultrasmedbio.2008.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2008] [Revised: 11/28/2008] [Accepted: 12/10/2008] [Indexed: 05/27/2023]
Abstract
Because of its complicated structure, low signal/noise ratio, low contrast and blurry boundaries, fully automated segmentation of a breast ultrasound (BUS) image is a difficult task. In this paper, a novel segmentation method for BUS images without human intervention is proposed. Unlike most published approaches, the proposed method handles the segmentation problem by using a two-step strategy: ROI generation and ROI segmentation. First, a well-trained texture classifier categorizes the tissues into different classes, and the background knowledge rules are used for selecting the regions of interest (ROIs) from them. Second, a novel probability distance-based active contour model is applied for segmenting the ROIs and finding the accurate positions of the breast tumors. The active contour model combines both global statistical information and local edge information, using a level set approach. The proposed segmentation method was performed on 103 BUS images (48 benign and 55 malignant). To validate the performance, the results were compared with the corresponding tumor regions marked by an experienced radiologist. Three error metrics, true-positive ratio (TP), false-negative ratio (FN) and false-positive ratio (FP) were used for measuring the performance of the proposed method. The final results (TP = 91.31%, FN = 8.69% and FP = 7.26%) demonstrate that the proposed method can segment BUS images efficiently, quickly and automatically.
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Affiliation(s)
- Bo Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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20
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Guo Y, Cheng HD, Tian J, Zhang Y. A novel approach to speckle reduction in ultrasound imaging. Ultrasound Med Biol 2009; 35:628-40. [PMID: 19243880 DOI: 10.1016/j.ultrasmedbio.2008.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 07/01/2008] [Accepted: 09/08/2008] [Indexed: 05/15/2023]
Abstract
Speckle noise is inherent in ultrasound images, and it generally tends to reduce the resolution and contrast, thereby degrading the diagnostic accuracy of this modality. Speckle reduction is very important and critical for ultrasound imaging. In this paper, we propose a novel approach for speckle reduction using 2-D homogeneity and directional average filters. We have conducted experiments on numerous artificial images, clinic breast ultrasound images and vascular images. The experimental results are compared with that of other methods and the performance is evaluated using several merits, and they demonstrate that the proposed approach can reduce the speckle noise effectively without blurring the edges and damaging the textual information. It will be very useful for computer-aided diagnosis systems using ultrasound images.
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Affiliation(s)
- Yanhui Guo
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang Province, China
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21
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Abstract
This paper presents a comparative study of the diagnostic results of the ultrasologists with/without using a novel enhancement algorithm for breast ultrasonic images based on fuzzy entropy principle and textural information. Totally, 350 ultrasound images of 115 cases were analyzed including 59 benign and 56 malignant lesions. The original breast images were fuzzified, the edge and textural information were extracted, and the images were enhanced. The original and enhanced images were assessed and evaluated by ultrasologists using double blind method before and after enhancement. The diagnostic sensitivity and specificity were calculated by the areas (Az) under the receiver operating characteristic (ROC) curves. And the two diagnostic results before and after enhancement were compared by Chi-square test in a 2 x 2 table. The results demonstrated that the discrimination rate of breast masses had been highly improved after employing the novel enhancement algorithm. The result indicates the sensitivity could be raised from 74.3% to 89.3% with the false-positive rate 14.3%, and the area (Az) under the ROC curve of diagnosis also increased from 0.84 to 0.93. The novel enhancement algorithm can increase the classification accuracy and decrease the rate of missing and misdiagnosis, and it is useful for breast cancer control.
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Affiliation(s)
- Jia-Wei Tian
- Department of Ultrasound, Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, People's Republic of China
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22
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Guo Y, Cheng HD, Huang J, Tian J, Zhao W, Sun L, Su Y. Breast ultrasound image enhancement using fuzzy logic. Ultrasound Med Biol 2006; 32:237-47. [PMID: 16464669 DOI: 10.1016/j.ultrasmedbio.2005.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 10/05/2005] [Accepted: 10/13/2005] [Indexed: 05/06/2023]
Abstract
Breast cancer is still a serious disease in the world. Early detection is very essential for breast cancer prevention and diagnosis. Breast ultrasound (US) imaging has been proven to be a valuable adjunct to mammography in the detection and classification of breast lesions. Because of the fuzzy and noisy nature of the US images and the low contrast between the breast cancer and tissue, it is difficult to provide an accurate and effective diagnosis. This paper presents a novel algorithm based on fuzzy logic that uses both the global and local information and has the ability to enhance the fine details of the US images while avoiding noise amplification and overenhancement. We normalize the images and then fuzzify the normalized images based on the maximum entropy principle. Edge and textural information are extracted to describe the lesion features and the scattering phenomenon of US images and the contrast ratio measuring the degree of enhancement is computed and modified. The defuzzification process is used to obtain the enhanced US images. To demonstrate the performance of the proposed approach, the algorithm was tested on 86 breast US images. Experimental results confirm that the proposed method can effectively enhance the details of the breast lesions without overenhancement or underenhancement.
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Affiliation(s)
- Yanhui Guo
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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23
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Cheng HD, Chen YH, Jiang XH. Thresholding using two-dimensional histogram and fuzzy entropy principle. IEEE Trans Image Process 2000; 9:732-735. [PMID: 18255445 DOI: 10.1109/83.841949] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This paper presents a thresholding approach by performing fuzzy partition on a two-dimensional (2-D) histogram based on fuzzy relation and maximum fuzzy entropy principle. The experiments with various gray level and color images have demonstrated that the proposed approach outperforms the 2-D nonfuzzy approach and the one dimensional (1-D) fuzzy partition approach.
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24
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Abstract
In this paper, a novel hierarchical approach to color image segmentation is studied. We extend the general idea of a histogram to the homogeneity domain. In the first phase of the segmentation, uniform regions are identified via multilevel thresholding on a homogeneity histogram. While we process the homogeneity histogram, both local and global information is taken into consideration. This is particularly helpful in taking care of small objects and local variation of color images. An efficient peak-finding algorithm is employed to identify the most significant peaks of the histogram. In the second phase, we perform histogram analysis on the color feature hue for each uniform region obtained in the first phase. We successfully remove about 99.7% singularity off the original images by redefining the hue values for the unstable points according to the local information. After the hierarchical segmentation is performed, a region merging process is employed to avoid over-segmentation. CIE(L*a*b*) color space is used to measure the color difference. Experimental results have demonstrated the effectiveness and superiority of the proposed method after an extensive set of color images was tested.
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Affiliation(s)
- H D Cheng
- Department of Computer Science, Utah State University, Logan, UT 84322-4205, USA.
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25
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Abstract
Breast cancer continues to be a significant public health problem in the United States. Approximately, 182,000 new cases of breast cancer are diagnosed and 46,000 women die of breast cancer each year. Even more disturbing is the fact that one out of eight women in the United States will develop breast cancer at some point during her lifetime. Since the cause of breast cancer remains unknown, primary prevention becomes impossible. Computer-aided mammography is an important and challenging task in automated diagnosis. It has great potential over traditional interpretation of film-screen mammography in terms of efficiency and accuracy. Microcalcifications are the earliest sign of breast carcinomas and their detection is one of the key issues for breast cancer control. In this study, a novel approach to microcalcification detection based on fuzzy logic technique is presented. Microcalcifications are first enhanced based on their brightness and nonuniformity. Then, the irrelevant breast structures are excluded by a curve detector. Finally, microcalcifications are located using an iterative threshold selection method. The shapes of microcalcifications are reconstructed and the isolated pixels are removed by employing the mathematical morphology technique. The essential idea of the proposed approach is to apply a fuzzified image of a mammogram to locate the suspicious regions and to interact the fuzzified image with the original image to preserve fidelity. The major advantage of the proposed method is its ability to detect microcalcifications even in very dense breast mammograms. A series of clinical mammograms are employed to test the proposed algorithm and the performance is evaluated by the free-response receiver operating characteristic curve. The experiments aptly show that the microcalcifications can be accurately detected even in very dense mammograms using the proposed approach.
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Affiliation(s)
- H D Cheng
- Department of Computer Science, Utah State University, Logan 84322, USA.
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26
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Abstract
The spatial ambiguity among pixels has inherent vagueness rather than randomness, therefore, the conventional methods might not work well. We propose fuzzy homogeneity vectors to handle the greyness and spatial uncertainties among pixels, and to perform multilevel thresholding. The experimental results prove that the proposed approach works better than the histogram-based algorithms.
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27
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Abstract
In this paper, we apply a quasi-one-dimensional unsteady nonlinear fluid model to study human pulmonary circulation. Eighteen generations of blood vessels composed of the branching arterial, capillary and venous distensible vessel segments make up the complete pulmonary circulation. The numerical result gives satisfactory agreement with the physiological experimental data: a dramatic pressure drop occurs in the arterioles and postcapillaries, a negative transmural pressure is shown in the postcapillary and small venous segments, a large reverse flow occurs in the main pulmonary artery during the diastolic period, and the reverse flow decreases gradually along the pulmonary tree. In the microgravity case where g = 180 cm s-2, the computation illustrated the effect of gravity force on the blood distribution in the different parts of the pulmonary circulation. The effect of gravity on the total output is not obvious. The effect of local factors which initiate the variations of the geometrical or pulmonary circulation can be stimulated quantitatively by this model. The proposal model can be very useful for clinical practice and for studying the extreme cases which are very difficult to investigate by experiments.
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Affiliation(s)
- C W Li
- Systems Design Engineering Dept, University of Waterloo, Ontario, Canada
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28
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Cheng HD, Lin WC, Fu KS. Space-Time Domain Expansion Approach to VLSI and Its Application to Hierarchical Scene Matching. IEEE Trans Pattern Anal Mach Intell 1985; 7:306-319. [PMID: 21869265 DOI: 10.1109/tpami.1985.4767659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
VLSI technology has recently received increasing attention due to its high performance and high reliability. Designing a VLSI structure systematically for a given task becomes a very important problem to many computer engineers. In this paper, we present a method to transform a recursive computation task into a VLSI structure systematically. The main advantages of this approach are its simplicity and completeness. Several examples, such as vector inner product, matrix multiplication, convolution, comparison operations in relational database and fast Fourier transformation (FFT), are given to demonstrate the transformation procedure. Finally, we apply the proposed method to hierarchical scene matching. Scene matching refers to the process of locating or matching a region of an image with a corresponding region of another view of the same image taken from a different viewing angle or at a different time. We first present a constant threshold estimation for hierarchical scene matching. The VLSI implementation of the hierarchical scene matching is then described in detail.
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Affiliation(s)
- H D Cheng
- School of Electrical Engineering, Purdue University, West Lafayette, IN 47907
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