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Ohnishi C, Ohnishi T, Ibrahim K, Ntiamoah P, Ross D, Yamaguchi M, Yagi Y. Color Standardization and Stain Intensity Calibration for Whole Slide Image-Based Immunohistochemistry Assessment. Microsc Microanal 2024; 30:118-132. [PMID: 38156737 DOI: 10.1093/micmic/ozad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/26/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
Automated quantification of human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) using whole slide imaging (WSI) is expected to eliminate subjectivity in visual assessment. However, the color intensity in WSI varies depending on the staining process and scanner device. Such variations affect the image analysis results. This paper presents methods to diminish the influence of color variation produced in the staining process using a calibrator slide consisting of peptide-coated microbeads. The calibrator slide is stained along with tissue sample slides, and the 3,3'-diaminobenzidine (DAB) color intensities of the microbeads are used for calibrating the color variation of the sample slides. An off-the-shelf image analysis tool is employed for the automated assessment, in which cells are classified by the thresholds for the membrane staining. We have adopted two methods for calibrating the color variation based on the DAB color intensities obtained from the calibrator slide: (1) thresholds for classifying the DAB membranous intensity are adjusted, and (2) the color intensity of WSI is corrected. In the experiment, the calibrator slides and tissue of breast cancer slides were stained together on different days and used to test our protocol. With the proposed protocol, the discordance in the HER2 evaluation was reduced to one slide out of 120 slides.
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Affiliation(s)
- Chie Ohnishi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1133 York Avenue, New York, NY 10065, USA
- School of Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Takashi Ohnishi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1133 York Avenue, New York, NY 10065, USA
| | - Kareem Ibrahim
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1133 York Avenue, New York, NY 10065, USA
| | - Peter Ntiamoah
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1133 York Avenue, New York, NY 10065, USA
| | - Dara Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1133 York Avenue, New York, NY 10065, USA
| | - Masahiro Yamaguchi
- School of Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Yukako Yagi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1133 York Avenue, New York, NY 10065, USA
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Farris AB, Alexander MP, Balis UGJ, Barisoni L, Boor P, Bülow RD, Cornell LD, Demetris AJ, Farkash E, Hermsen M, Hogan J, Kain R, Kers J, Kong J, Levenson RM, Loupy A, Naesens M, Sarder P, Tomaszewski JE, van der Laak J, van Midden D, Yagi Y, Solez K. Banff Digital Pathology Working Group: Image Bank, Artificial Intelligence Algorithm, and Challenge Trial Developments. Transpl Int 2023; 36:11783. [PMID: 37908675 PMCID: PMC10614670 DOI: 10.3389/ti.2023.11783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/22/2023] [Indexed: 11/02/2023]
Abstract
The Banff Digital Pathology Working Group (DPWG) was established with the goal to establish a digital pathology repository; develop, validate, and share models for image analysis; and foster collaborations using regular videoconferencing. During the calls, a variety of artificial intelligence (AI)-based support systems for transplantation pathology were presented. Potential collaborations in a competition/trial on AI applied to kidney transplant specimens, including the DIAGGRAFT challenge (staining of biopsies at multiple institutions, pathologists' visual assessment, and development and validation of new and pre-existing Banff scoring algorithms), were also discussed. To determine the next steps, a survey was conducted, primarily focusing on the feasibility of establishing a digital pathology repository and identifying potential hosts. Sixteen of the 35 respondents (46%) had access to a server hosting a digital pathology repository, with 2 respondents that could serve as a potential host at no cost to the DPWG. The 16 digital pathology repositories collected specimens from various organs, with the largest constituent being kidney (n = 12,870 specimens). A DPWG pilot digital pathology repository was established, and there are plans for a competition/trial with the DIAGGRAFT project. Utilizing existing resources and previously established models, the Banff DPWG is establishing new resources for the Banff community.
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Affiliation(s)
- Alton B. Farris
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GE, United States
| | - Mariam P. Alexander
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Ulysses G. J. Balis
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Laura Barisoni
- Department of Pathology and Medicine, Duke University, Durham, NC, United States
| | - Peter Boor
- Institute of Pathology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University Clinic, Aachen, Germany
- Department of Nephrology and Immunology, RWTH Aachen University Clinic, Aachen, Germany
| | - Roman D. Bülow
- Institute of Pathology, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University Clinic, Aachen, Germany
| | - Lynn D. Cornell
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Anthony J. Demetris
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Evan Farkash
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Meyke Hermsen
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Julien Hogan
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GE, United States
- Nephrology Service, Robert Debré Hospital, University of Paris, Paris, France
| | - Renate Kain
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Jesper Kers
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - Jun Kong
- Georgia State University, Atlanta, GA, United States
- Emory University, Atlanta, GA, United States
| | - Richard M. Levenson
- Department of Pathology, University of California Davis Health System, Sacramento, CA, United States
| | - Alexandre Loupy
- Institut National de la Santé et de la Recherche Médicale, UMR 970, Paris Translational Research Centre for Organ Transplantation, and Kidney Transplant Department, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, University of Paris, Paris, France
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Pinaki Sarder
- Division of Nephrology, Hypertension, and Renal Transplantation, Department of Medicine, Intelligent Critical Care Center, College of Medicine, University of Florida at Gainesville, Gainesville, FL, United States
| | - John E. Tomaszewski
- Department of Pathology, The State University of New York at Buffalo, Buffalo, NY, United States
| | - Jeroen van der Laak
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
- Center for Medical Image Science and Visualization, Linköping University, Linköping, Sweden
| | - Dominique van Midden
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yukako Yagi
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Kim Solez
- Department of Pathology, University of Alberta, Edmonton, AB, Canada
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Ohnishi C, Ohnishi T, Ntiamoah P, Ross DS, Yamaguchi M, Yagi Y. Standardizing HER2 immunohistochemistry assessment: calibration of color and intensity variation in whole slide imaging caused by staining and scanning. Appl Microsc 2023; 53:8. [PMID: 37704877 PMCID: PMC10499734 DOI: 10.1186/s42649-023-00091-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/05/2023] [Indexed: 09/15/2023] Open
Abstract
In the evaluation of human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) - one of the standard biomarkers for breast cancer- visual assessment is laborious and subjective. Image analysis using whole slide image (WSI) could produce more consistent results; however, color variability in WSIs due to the choice of stain and scanning processes may impact image analysis. We therefore developed a calibration protocol to diminish the staining and scanning variations of WSI using two calibrator slides. The IHC calibrator slide (IHC-CS) contains peptide-coated microbeads with different concentrations. The color distribution obtained from the WSI of stained IHC-CS reflects the staining process and scanner characteristics. A color chart slide (CCS) is also useful for calibrating the color variation due to the scanner. The results of the automated HER2 assessment were compared to confirm the effectiveness of two calibration slides. The IHC-CS and HER2 breast cancer cases were stained on different days. All stained slides and CCS were digitized by two different WSI scanners. Results revealed 100% concordance between automated evaluation and the pathologist's assessment with both the scanner and staining calibration. The proposed method may enable consistent evaluation of HER2.
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Affiliation(s)
- Chie Ohnishi
- School of Engineering, Tokyo Institute of Technology, Kanagawa, 226-8503, Japan.
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, USA.
| | - Takashi Ohnishi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Peter Ntiamoah
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Dara S Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
| | - Masahiro Yamaguchi
- School of Engineering, Tokyo Institute of Technology, Kanagawa, 226-8503, Japan
| | - Yukako Yagi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, USA
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Naydenov N, Teplov A, Zirakchian MZ, Ruan S, Chu BP, Serencsits B, Iraca M, Talarico O, Miller B, Kunin H, Schwartz J, Kesner A, Furenlid LR, Dauer L, Yagi Y, Humm JL, Zanzonico P, Sofocleous CT, Kirov AS. Yttrium-90 Activity Quantification in PET/CT-Guided Biopsy Specimens from Colorectal Hepatic Metastases Immediately after Transarterial Radioembolization Using Micro-CT and Autoradiography. J Vasc Interv Radiol 2023; 34:1556-1564.e4. [PMID: 37201655 DOI: 10.1016/j.jvir.2023.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 04/13/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023] Open
Abstract
PURPOSE To evaluate the yttrium-90 (90Y) activity distribution in biopsy tissue samples of the treated liver to quantify the dose with higher spatial resolution than positron emission tomography (PET) for accurate investigation of correlations with microscopic biological effects and to evaluate the radiation safety of this procedure. MATERIALS AND METHODS Eighty-six core biopsy specimens were obtained from 18 colorectal liver metastases (CLMs) immediately after 90Y transarterial radioembolization (TARE) with either resin or glass microspheres using real-time 90Y PET/CT guidance in 17 patients. A high-resolution micro-computed tomography (micro-CT) scanner was used to image the microspheres in part of the specimens and allow quantification of 90Y activity directly or by calibrating autoradiography (ARG) images. The mean doses to the specimens were derived from the measured specimens' activity concentrations and from the PET/CT scan at the location of the biopsy needle tip for all cases. Staff exposures were monitored. RESULTS The mean measured 90Y activity concentration in the CLM specimens at time of infusion was 2.4 ± 4.0 MBq/mL. The biopsies revealed higher activity heterogeneity than PET. Radiation exposure to the interventional radiologists during post-TARE biopsy procedures was minimal. CONCLUSIONS Counting the microspheres and measuring the activity in biopsy specimens obtained after TARE are safe and feasible and can be used to determine the administered activity and its distribution in the treated and biopsied liver tissue with high spatial resolution. Complementing 90Y PET/CT imaging with this approach promises to yield more accurate direct correlation of histopathological changes and absorbed dose in the examined specimens.
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Affiliation(s)
- Nicola Naydenov
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexei Teplov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Shutian Ruan
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bae P Chu
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian Serencsits
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marisa Iraca
- University of Rhode Island, Kingston, Rhode Island
| | - Olga Talarico
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Henry Kunin
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jazmin Schwartz
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam Kesner
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Larry Dauer
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John L Humm
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pat Zanzonico
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Assen S Kirov
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York.
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Toyoda T, Thomae B, Kandula V, Manerikar A, Kaiho T, Yagi Y, Cerier E, Bharat A, Kurihara C. Association of Acute Kidney Injury Grade with Primary Graft Dysfunction Grade after Lung Transplantation: A Cohort Study. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Yagi Y, Cerier E, Toyoda T, Manerikar A, Thomae B, Kandula V, Bharat A, Kurihara C. Pre-Transplantation Recipient Blood Transfusions Increase the Risk of Primary Graft Dysfunction Following Lung Transplantation. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Yagi Y, Cerier E, Toyoda T, Dhaliwal B, Tomic R, Bharat A, Kurihara C. Lung Transplantation in a Patient with End-Stage Lung Disease and Suspected Early-Stage Lung Cancer: A Case Report. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Toyoda T, Thomae B, Kandula V, Manerikar A, Kaiho T, Yagi Y, Cerier E, Bharat A, Kurihara C. Association of Acute Kidney Injury Grade with Chronic Kidney Disease after Lung Transplantation: A Cohort Study. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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9
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Toyoda T, Lysne J, Thomae B, Kandula V, Manerikar A, Kaiho T, Yagi Y, Cerier E, Tomic R, Budinger G, Bharat A, Kurihara C. Cytomegalovirus Serologic Mismatch Impact Long-Term Outcomes after Lung Transplantation. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Sakamoto H, Nishimura M, Teplov A, Cesmecioglu E, Kawata N, Shia J, Yagi Y. Pathological evaluation of a rectal endoscopic submucosal dissection specimen using micro-computed tomography. Endoscopy 2022; 54:E254-E255. [PMID: 34102679 DOI: 10.1055/a-1506-2683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Affiliation(s)
- Hirotsugu Sakamoto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Division of Gastroenterology, Jichi Medical University, Shimotsuke, Japan
| | - Makoto Nishimura
- Gastroenterology, Hepatology and Nutrition Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexei Teplov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Emine Cesmecioglu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Noboru Kawata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Division of Endoscopy, Shizuoka Cancer Center, Shizuoka, Japan
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Yoshida M, Cesmecioglu E, Firat C, Sakamoto H, Teplov A, Kawata N, Ntiamoah P, Ohnishi T, Ibrahim K, Vakiani E, Garcia-Aguilar J, Hameed M, Shia J, Yagi Y. Pathological Evaluation of Rectal Cancer Specimens Using Micro-Computed Tomography. Diagnostics (Basel) 2022; 12:diagnostics12040984. [PMID: 35454033 PMCID: PMC9044748 DOI: 10.3390/diagnostics12040984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/12/2022] [Indexed: 12/10/2022] Open
Abstract
Whole-block imaging (WBI) using micro-computed tomography (micro-CT) allows the nondestructive reconstruction of a three-dimensional view of tissues, implying that WBI may be used for accurate pathological evaluation of patients with rectal cancer. HOWEVER, the clinical impact of this approach is unclear. We aimed to clarify the efficacy of WBI in the whole-mount specimens of locally advanced rectal cancer. A total of 237 whole-mount formalin-fixed paraffin-embedded blocks from 13 patients with rectal cancer who underwent surgical treatment were enrolled and scanned with micro-CT to generate three-dimensional images. WBI was evaluated following the conventional pathological review of the corresponding whole-slide imaging (WSI). WBI identified all tumor sites detected using WSI. Furthermore, WBI revealed one additional tumor site, which was not detected using WSI. Tumor resection margin was significantly closer to the soft-tissue edge when measured using WBI (7.7 mm vs. 6.6 mm, p < 0.01). Seventy-six percent of tumor deposits on WSI were changed according to the evidence of tumor interaction with the surrounding tissues confirmed using WBI. Furthermore, WBI revealed 25 additional lymph nodes, six of which were metastatic. The combination of conventional hematoxylin and eosin-stained imaging and WBI may contribute to an accurate pathological assessment.
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Affiliation(s)
- Masao Yoshida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
- Division of Endoscopy, Shizuoka Cancer Center, Shizuoka 411-8777, Japan;
- Correspondence: ; Tel.: +1-646-888-7617; Fax: +1-929-321-7025
| | - Emine Cesmecioglu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
- Department of Pathology, Marmara University Research and Education Hospital, Istanbul 34899, Turkey
| | - Canan Firat
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
| | - Hirotsugu Sakamoto
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, Tochigi 329-0498, Japan;
| | - Alexei Teplov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
| | - Noboru Kawata
- Division of Endoscopy, Shizuoka Cancer Center, Shizuoka 411-8777, Japan;
| | - Peter Ntiamoah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
| | - Takashi Ohnishi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
| | - Kareem Ibrahim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
| | - Julio Garcia-Aguilar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (E.C.); (C.F.); (A.T.); (P.N.); (T.O.); (K.I.); (E.V.); (M.H.); (J.S.); (Y.Y.)
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12
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Kawata N, Teplov A, Ntiamoah P, Shia J, Hameed M, Yagi Y. Micro-computed tomography: A novel diagnostic technique for the evaluation of gastrointestinal specimens. Endosc Int Open 2021; 9:E1886-E1889. [PMID: 34917457 PMCID: PMC8670991 DOI: 10.1055/a-1546-8063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/23/2021] [Indexed: 11/29/2022] Open
Abstract
Micro-computed tomography (micro-CT) is a non-destructive modality that can be used to obtain high-resolution three-dimensional (3 D) images of the whole sample tissue; the usefulness of micro-CT has been reported for evaluation of breast cancer and lung cancer. However, this novel diagnostic technique has never been used for evaluating endoscopically resected gastrointestinal specimens. In the present study, we scanned 13 formalin-fixed paraffin-embedded (FFPE) tissue blocks of a normal human colon and gastric tissue samples using micro-CT. The evaluation comprised a comparison of the acquired whole block images with the images of the corresponding cross-sectional slice of the hematoxylin and eosin-stained slide. Micro-CT was able to produce images of the whole sample and clearly depict tissues such as glandular structures, muscularis mucosae, and blood vessels in the FFPE tissue blocks of normal gastrointestinal samples. Furthermore, the 3 D reconstructed could be used to create a cross-sectional image and reflected the surface structure of samples obtained from any site. Micro-CT has the potential to become a highly promising pathological diagnostic assistance tool for endoscopically resected gastrointestinal specimens in combination with conventional microscopic examination.
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Affiliation(s)
- Noboru Kawata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States,Division of Endoscopy, Shizuoka Cancer Center, Shizuoka, Japan
| | - Alexei Teplov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Peter Ntiamoah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States
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Kuzume K, Koizumi M, Kagata Y, Nishimura K, Kuwabara Y, Okamoto M, Asami T, Murakami Y, Yagi Y, Midoro-Horiuti T. A056 HOW TO DRINK MILK - ASSESSMENT OF AN INTERMITTENT ORAL IMMUNOTHERAPY FOR SEVERE MILK ALLERGY. Ann Allergy Asthma Immunol 2021. [DOI: 10.1016/j.anai.2021.08.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Cree IA, Tan PH, Travis WD, Wesseling P, Yagi Y, White VA, Lokuhetty D, Scolyer RA. Counting mitoses: SI(ze) matters! Mod Pathol 2021; 34:1651-1657. [PMID: 34079071 PMCID: PMC8376633 DOI: 10.1038/s41379-021-00825-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 11/08/2022]
Abstract
Mitoses are often assessed by pathologists to assist the diagnosis of cancer, and to grade malignancy, informing prognosis. Historically, this has been done by expressing the number of mitoses per n high power fields (HPFs), ignoring the fact that microscope fields may differ substantially, even at the same high power (×400) magnification. Despite a requirement to define HPF size in scientific papers, many authors fail to address this issue adequately. The problem is compounded by the switch to digital pathology systems, where ×400 equivalent fields are rectangular and also vary in the area displayed. The potential for error is considerable, and at times this may affect patient care. This is easily solved by the use of standardized international (SI) units. We, therefore, recommend that features such as mitoses are always counted per mm2, with an indication of the area to be counted and the method used (usually "hotspot" or "average") to obtain the results.
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Affiliation(s)
- Ian A Cree
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France.
| | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pieter Wesseling
- Department of Pathology, Amsterdam University Medical Centers/VUmc, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Valerie A White
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Dilani Lokuhetty
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
- Department of Pathology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Richard A Scolyer
- Melanoma Institute Australia and Faculty of Medicine and Health, The University of Sydney, Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, and NSW Health Pathology, Sydney, NSW, Australia
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15
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Schüffler PJ, Geneslaw L, Yarlagadda DVK, Hanna MG, Samboy J, Stamelos E, Vanderbilt C, Philip J, Jean MH, Corsale L, Manzo A, Paramasivam NHG, Ziegler JS, Gao J, Perin JC, Kim YS, Bhanot UK, Roehrl MHA, Ardon O, Chiang S, Giri DD, Sigel CS, Tan LK, Murray M, Virgo C, England C, Yagi Y, Sirintrapun SJ, Klimstra D, Hameed M, Reuter VE, Fuchs TJ. Integrated digital pathology at scale: A solution for clinical diagnostics and cancer research at a large academic medical center. J Am Med Inform Assoc 2021; 28:1874-1884. [PMID: 34260720 PMCID: PMC8344580 DOI: 10.1093/jamia/ocab085] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Broad adoption of digital pathology (DP) is still lacking, and examples for DP connecting diagnostic, research, and educational use cases are missing. We blueprint a holistic DP solution at a large academic medical center ubiquitously integrated into clinical workflows; researchapplications including molecular, genetic, and tissue databases; and educational processes. MATERIALS AND METHODS We built a vendor-agnostic, integrated viewer for reviewing, annotating, sharing, and quality assurance of digital slides in a clinical or research context. It is the first homegrown viewer cleared by New York State provisional approval in 2020 for primary diagnosis and remote sign-out during the COVID-19 (coronavirus disease 2019) pandemic. We further introduce an interconnected Honest Broker for BioInformatics Technology (HoBBIT) to systematically compile and share large-scale DP research datasets including anonymized images, redacted pathology reports, and clinical data of patients with consent. RESULTS The solution has been operationally used over 3 years by 926 pathologists and researchers evaluating 288 903 digital slides. A total of 51% of these were reviewed within 1 month after scanning. Seamless integration of the viewer into 4 hospital systems clearly increases the adoption of DP. HoBBIT directly impacts the translation of knowledge in pathology into effective new health measures, including artificial intelligence-driven detection models for prostate cancer, basal cell carcinoma, and breast cancer metastases, developed and validated on thousands of cases. CONCLUSIONS We highlight major challenges and lessons learned when going digital to provide orientation for other pathologists. Building interconnected solutions will not only increase adoption of DP, but also facilitate next-generation computational pathology at scale for enhanced cancer research.
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Affiliation(s)
- Peter J Schüffler
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Luke Geneslaw
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - D Vijay K Yarlagadda
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew G Hanna
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jennifer Samboy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Evangelos Stamelos
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Chad Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - John Philip
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Health Informatics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc-Henri Jean
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lorraine Corsale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Allyne Manzo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Neeraj H G Paramasivam
- Department of Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - John S Ziegler
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jianjiong Gao
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Juan C Perin
- Department of Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Young Suk Kim
- School of Medicine, Stanford University, Stanford, California, USA
| | - Umeshkumar K Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael H A Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Orly Ardon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sarah Chiang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dilip D Giri
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Carlie S Sigel
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lee K Tan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Melissa Murray
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christina Virgo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christine England
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - S Joseph Sirintrapun
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Thomas J Fuchs
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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16
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Kizawa Y, Yamaguchi T, Yagi Y, Miyashita M, Shima Y, Ogawa A. Conditions, possibility and priority for admission into inpatient hospice/palliative care units in Japan: a nationwide survey. Jpn J Clin Oncol 2021; 51:1437-1443. [PMID: 34184056 DOI: 10.1093/jjco/hyab098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/12/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Known barriers to admission into inpatient hospice/palliative care units (PCUs) include poor accessibility and stringent conditions for admission. However, the exact criteria are unclear. The aim of this study was to clarify the actual conditions, possibilities and priorities for admission to PCU in Japan. METHODS We conducted a nationwide, anonymous, self-administered questionnaire survey to the responsible physicians of all 251 PCUs in 2014. RESULTS Responses were received from 190 institutions (response rate 76%). The most frequent condition for admission was 'either the patient or the family knows the diagnosis' [86%, 95% confidence interval (CI): 80-90]. For the conditions for admission to PCU, 10-40% fewer facilities answered that the patient's consent or understanding was required compared with those that answered the patient or family's consent was sufficient. Seventy-one percent (95% CI: 64-77) of PCUs answered that either the patient or a family member needed to agree to a do-not-resuscitate (DNR) policy. The factors most likely to result in refusal of admission to a PCU varied greatly. Ninety-four percent (95% CI: 90-97) of PCUs answered that patients who had undergone a long waiting time after applying for admission would be given higher priority, and approximately 50% of PCUs answered they gave priority to their outpatients and inpatients. CONCLUSIONS The findings of this study should be used to modify the system so that appropriate palliative care can be provided to patients who wish to be admitted to PCU.
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Affiliation(s)
- Yoshiyuki Kizawa
- Department of Palliative Medicine, Kobe University School of Medicine, Kobe, Japan
| | - Takashi Yamaguchi
- Department of Palliative Medicine, Konan Medical Center, Kobe, Japan
| | - Yukako Yagi
- Department of Palliative Medicine, Konan Medical Center, Kobe, Japan
| | - Mitsunori Miyashita
- Department of Palliative Nursing, Health Sciences, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasuo Shima
- Department of Palliative Medicine, Tsukuba Medical Center Hospital, Ibaraki, Japan
| | - Asao Ogawa
- Department of Psycho-Oncology Service, National Cancer Center Hospital East, Kashiwa, Japan
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17
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Asai M, Koike Y, Kuwatsuka Y, Yagi Y, Kashiyama K, Tanaka K, Mishima H, Yoshiura K, Utani A, Murota H. Multifaceted array-based keloidal gene expression profiling reveals specific MDFI upregulation in keloid lesions. Clin Exp Dermatol 2021; 46:1255-1261. [PMID: 33899950 DOI: 10.1111/ced.14698] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Keloid lesions are characterized by mesenchymal cell proliferation and excessive extracellular matrix deposition. Previous microarray analyses have been performed to investigate the mechanism of keloid development. However, the molecular pathology that contributes to keloid development remains obscure. AIM To explore the underlying essential molecules of keloids using microarrays. METHODS We performed microarray analyses of keloid and nonlesional skin tissues both in vivo and in vitro. Gene expression levels were compared between tissues and cells. Quantitative reverse transcription (qRT)-PCR and immunohistochemical staining were used to determine the expression levels of molecules of interest in keloid tissues. RESULTS Several common molecules were upregulated in both keloid tissues and keloid-lesional fibroblasts. PTPRD and NTM were upregulated both in vivo and in vitro. The genes MDFI and ITGA4 were located at the centre of the gene coexpression network analysis using keloid tissues. qRT-PCR revealed significant expression levels of PTPRD and MDFI in keloid tissues. Immunopathological staining revealed that MDFI-positive cells, which have fibroblast characteristics, were located in the keloid-associated lymphoid tissue (KALT) portion of the keloid tissue. CONCLUSION Our gene expression profiles of keloids could distinguish the difference between lesional tissue and cultured lesional fibroblasts, and MDFI was found to be commonly expressed in both tissues and cells. Thus, MDFI-positive cells, which were located in the KALT, may play an important role in keloid pathogenesis and thus might be useful for in vitro keloid studies.
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Affiliation(s)
- M Asai
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Y Koike
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Y Kuwatsuka
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Y Yagi
- Department of Dermatology, Osaka Red Cross Hospital, Osaka, Japan
| | - K Kashiyama
- Department of Plastic and Reconstructive Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - K Tanaka
- Department of Plastic and Reconstructive Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - H Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - K Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - A Utani
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - H Murota
- Department of Dermatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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18
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Frankenstein Z, Uraoka N, Aypar U, Aryeequaye R, Rao M, Hameed M, Zhang Y, Yagi Y. Automated 3D scoring of fluorescence in situ hybridization (FISH) using a confocal whole slide imaging scanner. Appl Microsc 2021; 51:4. [PMID: 33835321 PMCID: PMC8035347 DOI: 10.1186/s42649-021-00053-y] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/29/2021] [Indexed: 11/10/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner technology has superior depth resolution compared to wide-field fluorescence imaging. Confocal WSI has the ability to perform serial optical sections with specimen imaging, which is critical for 3D tissue reconstruction for volumetric spatial analysis. The standard clinical manual scoring for FISH is labor-intensive, time-consuming and subjective. Application of multi-gene FISH analysis alongside 3D imaging, significantly increase the level of complexity required for an accurate 3D analysis. Therefore, the purpose of this study is to establish automated 3D FISH scoring for z-stack images from confocal WSI scanner. The algorithm and the application we developed, SHIMARIS PAFQ, successfully employs 3D calculations for clear individual cell nuclei segmentation, gene signals detection and distribution of break-apart probes signal patterns, including standard break-apart, and variant patterns due to truncation, and deletion, etc. The analysis was accurate and precise when compared with ground truth clinical manual counting and scoring reported in ten lymphoma and solid tumors cases. The algorithm and the application we developed, SHIMARIS PAFQ, is objective and more efficient than the conventional procedure. It enables the automated counting of more nuclei, precisely detecting additional abnormal signal variations in nuclei patterns and analyzes gigabyte multi-layer stacking imaging data of tissue samples from patients. Currently, we are developing a deep learning algorithm for automated tumor area detection to be integrated with SHIMARIS PAFQ.
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Affiliation(s)
- Ziv Frankenstein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Naohiro Uraoka
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Umut Aypar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ruth Aryeequaye
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Mamta Rao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
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19
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Yagi Y, Kojima K, Sakurai T, Sakamoto T, In K, Tamiya A, Atagi S, Momozane T, Kimura Y, Kishima H, Kodama K. P78.14 The Efficacy and Safety of ICIs in Treating Postoperative Recurrence of NSCLC: Results of Two Hospitals in Japan. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.1177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Ikemura K, Bellin E, Yagi Y, Billett H, Saada M, Simone K, Stahl L, Szymanski J, Goldstein DY, Reyes Gil M. Using Automated Machine Learning to Predict the Mortality of Patients With COVID-19: Prediction Model Development Study. J Med Internet Res 2021; 23:e23458. [PMID: 33539308 PMCID: PMC7919846 DOI: 10.2196/23458] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/23/2020] [Accepted: 02/03/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND During a pandemic, it is important for clinicians to stratify patients and decide who receives limited medical resources. Machine learning models have been proposed to accurately predict COVID-19 disease severity. Previous studies have typically tested only one machine learning algorithm and limited performance evaluation to area under the curve analysis. To obtain the best results possible, it may be important to test different machine learning algorithms to find the best prediction model. OBJECTIVE In this study, we aimed to use automated machine learning (autoML) to train various machine learning algorithms. We selected the model that best predicted patients' chances of surviving a SARS-CoV-2 infection. In addition, we identified which variables (ie, vital signs, biomarkers, comorbidities, etc) were the most influential in generating an accurate model. METHODS Data were retrospectively collected from all patients who tested positive for COVID-19 at our institution between March 1 and July 3, 2020. We collected 48 variables from each patient within 36 hours before or after the index time (ie, real-time polymerase chain reaction positivity). Patients were followed for 30 days or until death. Patients' data were used to build 20 machine learning models with various algorithms via autoML. The performance of machine learning models was measured by analyzing the area under the precision-recall curve (AUPCR). Subsequently, we established model interpretability via Shapley additive explanation and partial dependence plots to identify and rank variables that drove model predictions. Afterward, we conducted dimensionality reduction to extract the 10 most influential variables. AutoML models were retrained by only using these 10 variables, and the output models were evaluated against the model that used 48 variables. RESULTS Data from 4313 patients were used to develop the models. The best model that was generated by using autoML and 48 variables was the stacked ensemble model (AUPRC=0.807). The two best independent models were the gradient boost machine and extreme gradient boost models, which had an AUPRC of 0.803 and 0.793, respectively. The deep learning model (AUPRC=0.73) was substantially inferior to the other models. The 10 most influential variables for generating high-performing models were systolic and diastolic blood pressure, age, pulse oximetry level, blood urea nitrogen level, lactate dehydrogenase level, D-dimer level, troponin level, respiratory rate, and Charlson comorbidity score. After the autoML models were retrained with these 10 variables, the stacked ensemble model still had the best performance (AUPRC=0.791). CONCLUSIONS We used autoML to develop high-performing models that predicted the survival of patients with COVID-19. In addition, we identified important variables that correlated with mortality. This is proof of concept that autoML is an efficient, effective, and informative method for generating machine learning-based clinical decision support tools.
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Affiliation(s)
- Kenji Ikemura
- Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States.,Tsubomi Technology, The Bronx, NY, United States
| | - Eran Bellin
- Department of Epidemiology and Population Health and Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Henny Billett
- Department of Oncology and Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
| | | | | | - Lindsay Stahl
- Department of Epidemiology and Population Health and Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
| | - James Szymanski
- Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
| | - D Y Goldstein
- Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
| | - Morayma Reyes Gil
- Department of Pathology, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY, United States
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21
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Xu B, Teplov A, Ibrahim K, Inoue T, Stueben B, Katabi N, Hameed M, Yagi Y, Ghossein R. Detection and assessment of capsular invasion, vascular invasion and lymph node metastasis volume in thyroid carcinoma using microCT scanning of paraffin tissue blocks (3D whole block imaging): a proof of concept. Mod Pathol 2020; 33:2449-2457. [PMID: 32616872 PMCID: PMC7688566 DOI: 10.1038/s41379-020-0605-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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] [Received: 04/29/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 11/24/2022]
Abstract
In the modern era, detailed pathologic characteristics of a thyroid tumor are crucial to achieve accurate diagnosis and guide treatment. The presence of capsular invasion (CI) is diagnostic for carcinoma, whereas vascular invasion (VI) and nodal metastasis (NM) are included in risk stratification. However, the very definition of CI and VI is surrounded by controversies and an accurate assessment of NM is lacking. Whole Block Imaging (WBI) by microCT is a new imaging modality to create 3D reconstruction of whole tissue block with microscopic level resolution without the need for tissue sectioning. In this study, we aimed to define CI, VI, and NM volume using WBI by microCT. Twenty-eight paraffin blocks (PBs) from 26 thyroid tumors were scanned. Ten PBs contained CI, whereas 7 had VI. 3D microCT images were compared with whole slide images (WSI) of corresponding H&E slides. In 2 cases with VI and/or CI, WSI of serial H&E slides were obtained and underwent 3D-reconstruction to be compared with the WBI. Satellite tumor nodules beyond tumor capsule were shown to be CI by demonstrating the point of penetration using microCT and 3D reconstruction. Additional foci of CI were detected using microCT. VI was seen using microCT. Fibrin associated with tumor thrombus was not always present on serially sectioned H&E slides. WBI by microCT scanner was able to assess the volume of NM. In conclusion, WBI is able to detect CI, VI, and assess the volume of NM in thyroid carcinoma without tissue sectioning. It is the ultimate method for the complete sampling of the tumor capsule. It has the potential to increase the detection rate of CI, better define criteria for CI and VI, and provide an accurate assessment of the volume of nodal disease. This technology may impact the future practice of surgical pathology.
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Affiliation(s)
| | | | | | | | | | | | | | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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22
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Muranishi H, Zushi R, Yagi Y, Kawasaki S, Tanaka S, Fukuda M, Kobata H. Impact of door-to-deployment time of venoarterial extracorporeal membrane oxygenation for out-of-hospital refractory cardiac arrest patients secondary to cardiovascular causes. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.1828] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Door-to-balloon time in patients with ST-elevation myocardial infarction is reported to be an independent predictor of the prognostic implication. However, the effect of door-to-deployment time (DTDT) of venoarterial extracorporeal membrane oxygenation (VA-ECMO) on patients with out-of-hospital cardiac arrest (OHCA) is unclear.
Purpose
This single-center, retrospective, observational study aimed to evaluate the effect of DTDT of VA-ECMO for mortality or neurological outcome of extracorporeal cardiopulmonary resuscitation (ECPR) in patients with cardiogenic OHCA.
Method
This single-center, retrospective, observational study was conducted from January 2008 to April 2019. The primary endpoint was 1-month overall survival measured after ECMO initiation. Moreover, the secondary endpoint was 1-month survival with favorable neurological functions defined as having a cerebral performance category score of 1 or 2.
Result
A total of 3082 patients with OHCA were brought to our institution and 84 received ECPR. Of these, 51 consecutive adult patients with cardiogenic OHCA without sustained return of spontaneous circulation during transport were included in this analysis. Approximately 18 patients (18/51, 35.3%) survived after 1 month and were discharged. Among the survivors, 15 (15/18, 83.3%) were discharged with a favorable neurological outcome. The baseline characteristics between the survivors and non-survivors were not significantly different, except for the initial shockable rhythm [18/18 (100%) versus 28/33 (84.9%), P=0.03]. There were no significant differences between the median time from collapse to hospital arrival [31.0 min (IQR 25.0–31.0) versus 29.0 min (IQR 25.0–39.5), P=0.53] and from call to hospital arrival [28.0 min (IQR 22.0–32.5) versus 27.0 min (IQR 23.3–34.5), P=0.56]. The median DTDT of VA-ECMO was significantly shorter in survivors [13.0 min (IQR 11.5–18.3) versus 21.0 minutes (IQR 15.5–32.0), P=0.01]. The Kaplan–Meier survival analysis showed that the group with a DTDT ≤20 min had a significantly higher 1-month overall survival rate (P<0.01) and survival rate with a favorable neurological outcome (P=0.01) than that with a DTDT >20 minutes. Using the Cox proportional hazards analysis, DTDT ≤20 minutes and bystander-witnessed significantly affected the overall survival rate at 1 month [adjusted hazard ratio (HR), 0.44; 95% confidence interval (CI), 0.20–0.95; P=0.03 and adjusted HR, 0.31; 95% CI, 0.13–0.74; P<0.01, respectively]. Regarding survival rate with a favorable neurological outcome, the result was relatively similar [adjusted HR, 0.46; 95% CI, 0.22–0.96; P=0.04 and adjusted HR, 0.37; 95% CI, 0.16–0.85; P=0.02, respectively].
Conclusion
This study revealed that the DTDT of VA-ECMO is significantly associated with the 1-month mortality and neurological prognosis of patients with cardiogenic OHCA. However, further studies will be required to confirm these findings.
Kaplan-Meier survival curve
Funding Acknowledgement
Type of funding source: None
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Affiliation(s)
- H Muranishi
- Osaka Mishima Emergency Critical Care Center, Takatsuki, Japan
| | - R Zushi
- Osaka Mishima Emergency Critical Care Center, Takatsuki, Japan
| | - Y Yagi
- Osaka Mishima Emergency Critical Care Center, Takatsuki, Japan
| | - S Kawasaki
- Osaka Mishima Emergency Critical Care Center, Takatsuki, Japan
| | - S Tanaka
- Osaka Mishima Emergency Critical Care Center, Takatsuki, Japan
| | - M Fukuda
- Osaka Mishima Emergency Critical Care Center, Takatsuki, Japan
| | - H Kobata
- Osaka Mishima Emergency Critical Care Center, Takatsuki, Japan
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Abstract
Whole slide imaging (WSI) has various uses, including the development of decision support systems, image analysis, education, conferences, and remote diagnostics. It is also used to develop artificial intelligence using machine learning methods. In the clinical setting, however, many issues have hindered the implementation of WSI. These issues are becoming more important as WSI is gaining wider use in clinical practice, particularly with the implementation of artificial intelligence in pathological diagnosis. One of the most important issues is the standardization of color for WSI, which is an important component of digital pathology. In this paper, we review the major factors of color variation and how to evaluate and modify color variation to establish color standardization. There are five major reasons for color variation, which include specimen thickness, staining, scanner, viewer, and display. Recognizing that the color is not standardized is the first step towards standardization, and it is difficult to ascertain whether the appropriate color of the WSI is displayed at the reviewers' end.
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Affiliation(s)
- Takashi Inoue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.,Department of General Thoracic Surgery, Dokkyo Medical University, 880 Kitakobayashi, Mibu, Shimotuga-gun, Tochigi 3210293, Japan
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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Farris AB, Moghe I, Wu S, Hogan J, Cornell LD, Alexander MP, Kers J, Demetris AJ, Levenson RM, Tomaszewski J, Barisoni L, Yagi Y, Solez K. Banff Digital Pathology Working Group: Going digital in transplant pathology. Am J Transplant 2020; 20:2392-2399. [PMID: 32185875 PMCID: PMC7496838 DOI: 10.1111/ajt.15850] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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] [Received: 01/31/2020] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 01/25/2023]
Abstract
The Banff Digital Pathology Working Group (DPWG) was formed in the time leading up to and during the joint American Society for Histocompatibility and Immunogenetics/Banff Meeting, September 23-27, 2019, held in Pittsburgh, Pennsylvania. At the meeting, the 14th Banff Conference, presentations directly and peripherally related to the topic of "digital pathology" were presented; and discussions before, during, and after the meeting have resulted in a list of issues to address for the DPWG. Included are practice standardization, integrative approaches for study classification, scoring of histologic parameters (eg, interstitial fibrosis and tubular atrophy and inflammation), algorithm classification, and precision diagnosis (eg, molecular pathways and therapeutics). Since the meeting, a survey with international participation of mostly pathologists (81%) was conducted, showing that whole slide imaging is available at the majority of centers (71%) but that artificial intelligence (AI)/machine learning was only used in ≈12% of centers, with a wide variety of programs/algorithms employed. Digitalization is not just an end in itself. It also is a necessary precondition for AI and other approaches. Discussions at the meeting and the survey highlight the unmet need for a Banff DPWG and point the way toward future contributions that can be made.
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Affiliation(s)
| | | | - Simon Wu
- University of AlbertaEdmontonCanada
| | | | | | | | - Jesper Kers
- Amsterdam University Medical CentersAmsterdamthe Netherlands,Leiden University Medical CenterLeidenthe Netherlands
| | | | | | - John Tomaszewski
- University at BuffaloState University of New YorkBuffaloNew York
| | | | - Yukako Yagi
- Memorial Sloan Kettering Cancer CenterNew YorkNew York
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25
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Ozawa Y, Santo N, Yagi Y, Nishiyama T, Yokoi T, Koike S, Nakamura K, Ishioka K, Ozu C, Toya K, Yorozu A, Saito S. Response of leukocyte to iodine-125 permanent prostate seed implantation predict PSA failure in patients with localized prostate cancer. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)32717-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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26
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Ozawa Y, Santo N, Yagi Y, Nishiyama T, Yokoi T, Koike S, Nakamura K, Ishioka K, Ozu C, Toya K, Yorozu A, Saito S. Secondary bladder cancer arising after iodine-125 permanent seed implantation for localized prostate cancer. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)34033-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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27
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Yagi Y, Aly RG, Tabata K, Barlas A, Rekhtman N, Eguchi T, Montecalvo J, Hameed M, Manova-Todorova K, Adusumilli PS, Travis WD. Three-Dimensional Histologic, Immunohistochemical, and Multiplex Immunofluorescence Analyses of Dynamic Vessel Co-Option of Spread Through Air Spaces in Lung Adenocarcinoma. J Thorac Oncol 2020; 15:589-600. [PMID: 31887430 PMCID: PMC7288352 DOI: 10.1016/j.jtho.2019.12.112] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [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: 09/12/2019] [Revised: 12/09/2019] [Accepted: 12/13/2019] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Spread through air spaces (STAS) is a method of invasion in lung adenocarcinoma and is associated with tumor recurrence and poor survival. The spatial orientation of STAS cells in the lung alveolar parenchyma is not known. The aim of this study was to use high-resolution and high-quality three-dimensional (3D) reconstruction of images from immunohistochemical (IHC) and multiplex immunofluorescence (IF) experiments to understand the spatial architecture of tumor cell clusters by STAS in the lung parenchyma. METHODS Four lung adenocarcinomas, three micropapillary-predominant and one solid predominant adenocarcinoma subtypes, were investigated. A 3D reconstruction image was created from formalin-fixed, paraffin-embedded blocks. A total of 350 serial sections were obtained and subjected to hematoxylin and eosin (100 slides), IHC (200 slides), and multiplex IF staining (50 slides) with the following antibodies: cluster of differentiation 31, collagen type IV, thyroid transcription factor-1, and E-cadherin. Whole slide images were reconstructed into 3D images for evaluation. RESULTS Serial 3D image analysis by hematoxylin and eosin, IHC, and IF staining revealed that the micropapillary clusters and solid nests of STAS are focally attached to the alveolar walls, away from the main tumor. CONCLUSIONS Our 3D reconstructions found that STAS tumor cells can attach to the alveolar walls rather than appearing free floating, as seen on the two-dimensional sections. This suggests that the tumor cells detach from the main tumor, migrate through air spaces, and reattach to the alveolar walls through vessel co-option, allowing them to survive and grow. This may explain the higher recurrence rate and worse survival of patients with STAS-positive tumors who undergo limited resection than those who undergo lobectomy.
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Affiliation(s)
- Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rania G Aly
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Alexandria University, Alexandria, Egypt
| | - Kazuhiro Tabata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Nagasaki University Hospital, Nagasaki, Japan
| | - Afsar Barlas
- Molecular Cytology, Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Takashi Eguchi
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center, New York, New York; Division of Thoracic Surgery, Department of Surgery, Shinshu University, Matsumoto, Japan
| | - Joeseph Montecalvo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Henry Ford Hospital System, Detroit, Michigan
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katia Manova-Todorova
- Molecular Cytology, Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prasad S Adusumilli
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center, New York, New York; Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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29
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Kajiura S, Chikaoka S, Yokota T, Kadota A, Fukai S, Matsushita T, Hayashi N, Yagi Y, Ryu N, Horikawa H, Takemura K, Furuichi A, Nakajima K, Moto I, Nanjyo S, Mihara H, Ando T, Murakami N, Yasuda I, Hayashi R. The relationship between naldemedine administration and the maximum dose of oral opioids. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz261.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Hossain MS, Hanna MG, Uraoka N, Nakamura T, Edelweiss M, Brogi E, Hameed MR, Yamaguchi M, Ross DS, Yagi Y. Automatic quantification of HER2 gene amplification in invasive breast cancer from chromogenic in situ hybridization whole slide images. J Med Imaging (Bellingham) 2019; 6:047501. [PMID: 31763355 PMCID: PMC6868351 DOI: 10.1117/1.jmi.6.4.047501] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/28/2019] [Indexed: 12/28/2022] Open
Abstract
Human epidermal growth factor receptor 2 (HER2), a transmembrane tyrosine kinase receptor encoded by the ERBB2 gene on chromosome 17q12, is a predictive and prognostic biomarker in invasive breast cancer (BC). Approximately 20% of BC are HER2-positive as a result of ERBB2 gene amplification and overexpression of the HER2 protein. Quantification of HER2 is performed routinely on all invasive BCs, to assist in clinical decision making for prognosis and treatment for HER2-positive BC patients by manually counting gene signals. We propose an automated system to quantify the HER2 gene status from chromogenic in situ hybridization (CISH) whole slide images (WSI) in invasive BC. The proposed method selects untruncated and nonoverlapped singular nuclei from the cancer regions using color unmixing and machine learning techniques. Then, HER2 and chromosome enumeration probe 17 (CEP17) signals are detected based on the RGB intensity and counted per nucleus. Finally, the HER2-to-CEP17 signal ratio is calculated to determine the HER2 amplification status following the ASCO/CAP 2018 guidelines. The proposed method reduced the labor and time for the quantification. In the experiment, the correlation coefficient between the proposed automatic CISH quantification method and pathologist manual enumeration was 0.98. The p -values larger than 0.05 from the one-sided paired t -test ensured that the proposed method yields statistically indifferent results to the reference method. The method was established on WSI scanned by two different scanners. Through the experiments, the capability of the proposed system has been demonstrated.
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Affiliation(s)
- Md. Shakhawat Hossain
- Tokyo Institute of Technology, School of Engineering, Department of Information and Communications Engineering, Yokohama, Japan
- Memorial Sloan Kettering Cancer Center, Department of Pathology, New York, New York, United States
- Address all correspondence to Md. Shakhawat Hossain, E-mail:
| | - Matthew G. Hanna
- Memorial Sloan Kettering Cancer Center, Department of Pathology, New York, New York, United States
| | - Naohiro Uraoka
- Memorial Sloan Kettering Cancer Center, Department of Pathology, New York, New York, United States
| | - Tomoya Nakamura
- Tokyo Institute of Technology, School of Engineering, Department of Information and Communications Engineering, Yokohama, Japan
- Japan Science and Technology Agency, PRESTO, Saitama, Japan
| | - Marcia Edelweiss
- Memorial Sloan Kettering Cancer Center, Department of Pathology, New York, New York, United States
| | - Edi Brogi
- Memorial Sloan Kettering Cancer Center, Department of Pathology, New York, New York, United States
| | - Meera R. Hameed
- Memorial Sloan Kettering Cancer Center, Department of Pathology, New York, New York, United States
| | - Masahiro Yamaguchi
- Tokyo Institute of Technology, School of Engineering, Department of Information and Communications Engineering, Yokohama, Japan
| | - Dara S. Ross
- Memorial Sloan Kettering Cancer Center, Department of Pathology, New York, New York, United States
| | - Yukako Yagi
- Memorial Sloan Kettering Cancer Center, Department of Pathology, New York, New York, United States
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31
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Tabata K, Uraoka N, Benhamida J, Hanna MG, Sirintrapun SJ, Gallas BD, Gong Q, Aly RG, Emoto K, Matsuda KM, Hameed MR, Klimstra DS, Yagi Y. Validation of mitotic cell quantification via microscopy and multiple whole-slide scanners. Diagn Pathol 2019; 14:65. [PMID: 31238983 PMCID: PMC6593538 DOI: 10.1186/s13000-019-0839-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/11/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The establishment of whole-slide imaging (WSI) as a medical diagnostic device allows that pathologists may evaluate mitotic activity with this new technology. Furthermore, the image digitalization provides an opportunity to develop algorithms for automatic quantifications, ideally leading to improved reproducibility as compared to the naked eye examination by pathologists. In order to implement them effectively, accuracy of mitotic figure detection using WSI should be investigated. In this study, we aimed to measure pathologist performance in detecting mitotic figures (MFs) using multiple platforms (multiple scanners) and compare the results with those obtained using a brightfield microscope. METHODS Four slides of canine oral melanoma were prepared and digitized using 4 WSI scanners. In these slides, 40 regions of interest (ROIs) were demarcated, and five observers identified the MFs using different viewing modes: microscopy and WSI. We evaluated the inter- and intra-observer agreements between modes with Cohen's Kappa and determined "true" MFs with a consensus panel. We then assessed the accuracy (agreement with truth) using the average of sensitivity and specificity. RESULTS In the 40 ROIs, 155 candidate MFs were detected by five pathologists; 74 of them were determined to be true MFs. Inter- and intra-observer agreement was mostly "substantial" or greater (Kappa = 0.594-0.939). Accuracy was between 0.632 and 0.843 across all readers and modes. After averaging over readers for each modality, we found that mitosis detection accuracy for 3 of the 4 WSI scanners was significantly less than that of the microscope (p = 0.002, 0.012, and 0.001). CONCLUSIONS This study is the first to compare WSIs and microscopy in detecting MFs at the level of individual cells. Our results suggest that WSI can be used for mitotic cell detection and offers similar reproducibility to the microscope, with slightly less accuracy.
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Affiliation(s)
- Kazuhiro Tabata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
- Department of Pathology, Nagasaki University Hospital, 1-7-1 Sakamoto, Nagasaki, Nagasaki 8528501 Japan
| | - Naohiro Uraoka
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
| | - Jamal Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
| | - Matthew G. Hanna
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
| | | | - Brandon D. Gallas
- Center For Devices and Radiological Health, Office of Science and Engineering Laboratories, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993 USA
| | - Qi Gong
- Center For Devices and Radiological Health, Office of Science and Engineering Laboratories, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993 USA
| | - Rania G. Aly
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
- Department of Pathology, Faculty of Medicine, Alexandria university, 22 El-Guish Road, El-Shatby, Alexandria, 21526 Egypt
| | - Katsura Emoto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, 10065 NY USA
| | - Kant M. Matsuda
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
| | - Meera R. Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
| | - David S. Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
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Hanna MG, Reuter VE, Samboy J, England C, Corsale L, Fine SW, Agaram NP, Stamelos E, Yagi Y, Hameed M, Klimstra DS, Sirintrapun SJ. Implementation of Digital Pathology Offers Clinical and Operational Increase in Efficiency and Cost Savings. Arch Pathol Lab Med 2019; 143:1545-1555. [PMID: 31173528 DOI: 10.5858/arpa.2018-0514-oa] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Digital pathology (DP) implementations vary in scale, based on aims of intended operation. Few laboratories have completed a full-scale DP implementation, which may be due to high overhead costs that disrupt the traditional pathology workflow. Neither standardized criteria nor benchmark data have yet been published showing practical return on investment after implementing a DP platform. OBJECTIVE.— To provide benchmark data and practical metrics to support operational efficiency and cost savings in a large academic center. DESIGN.— Metrics reviewed include archived pathology asset retrieval; ancillary test request for recurrent/metastatic disease; cost analysis and turnaround time (TAT); and DP experience survey. RESULTS.— Glass slide requests from the department slide archive and an off-site surgery center showed a 93% and 97% decrease, respectively. Ancillary immunohistochemical orders, compared in 2014 (52%)-before whole slide images (WSIs) were available in the laboratory information system-and 2017 (21%) showed $114 000/y in anticipated savings. Comprehensive comparative cost analysis showed a 5-year $1.3 million savings. Surgical resection cases with prior WSIs showed a 1-day decrease in TAT. A DP experience survey showed 80% of respondents agreed WSIs improved their clinical sign-out experience. CONCLUSIONS.— Implementing a DP operation showed a noteworthy increase in efficiency and operational utility. Digital pathology deployments and operations may be gauged by the following metrics: number of glass slide requests as WSIs become available, decrease in confirmatory testing for patients with metastatic/recurrent disease, long-term decrease in off-site pathology asset costs, and faster TAT. Other departments may use our benchmark data and metrics to enhance patient care and demonstrate return on investment to justify adoption of DP.
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Affiliation(s)
- Matthew G Hanna
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Victor E Reuter
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jennifer Samboy
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine England
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lorraine Corsale
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samson W Fine
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Narasimhan P Agaram
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Evangelos Stamelos
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yukako Yagi
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera Hameed
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David S Klimstra
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - S Joseph Sirintrapun
- From the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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Sawa Y, Matsumiya G, Matsuda K, Tatsumi E, Abe T, Fukunaga K, Ichiba S, Taguchi T, Kokubo K, Masuzawa T, Myoui A, Nishimura M, Nishimura T, Nishinaka T, Okamoto E, Tokunaga S, Tomo T, Tsukiya T, Yagi Y, Yamaoka T. Journal of Artificial Organs 2018: the year in review : Journal of Artificial Organs Editorial Committee. J Artif Organs 2019; 22:1-5. [PMID: 30796540 DOI: 10.1007/s10047-019-01094-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Y Sawa
- Division of Cardiovascular Surgery, Department of Surgery, Osaka University Graduate School of Medicine, Osaka, Japan.
| | - G Matsumiya
- Department of Cardiovascular Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - K Matsuda
- Emergency and Critical Care Medicine, University of Yamanashi Hospital, Yamanashi, Japan
| | - E Tatsumi
- Department of Artificial Organs, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - T Abe
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - K Fukunaga
- Faculty of Health Sciences, Kyorin University, Tokyo, Japan
| | - S Ichiba
- Department of Surgical Intensive Care Medicine, Nippon Medical School Hospital, Tokyo, Japan
| | - T Taguchi
- Biomaterial Unit, National Institute of Material Science, Ibaraki, Japan
| | - K Kokubo
- Department of Medical Engineering and Technology, Kitasato University School of Allied Health Science, Kanagawa, Japan
| | - T Masuzawa
- Department of Mechanical Engineering, Ibaraki University, Ibaraki, Japan
| | - A Myoui
- Medical Center for Translational Research, Osaka University Hospital, Osaka, Japan
| | - M Nishimura
- Division of Organ Regeneration Surgery, Tottori University Faculty of Medicine, Tottori, Japan
| | - T Nishimura
- Department of Therapeutic Strategy for Heart Failure, The University of Tokyo, Tokyo, Japan
| | - T Nishinaka
- Department of Cardiovascular Surgery, Tokyo Women's Medical University, Tokyo, Japan
| | - E Okamoto
- Department of Human Science and Informatics, School of Bioscience and Engineering, Tokai University, Sapporo, Japan
| | - S Tokunaga
- The Department of Cardiovascular Surgery, JCHO Kyushu Hospital, Fukuoka, Japan
| | - T Tomo
- Second Department of Internal Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - T Tsukiya
- Department of Artificial Organs, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Y Yagi
- Department of Clinical Engineering, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - T Yamaoka
- Department of Biomedical Engineering, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
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Yoshida H, Yokota H, Singh R, Kiyuna T, Yamaguchi M, Kikuchi S, Yagi Y, Ochiai A. Meeting Report: The International Workshop on Harmonization and Standardization of Digital Pathology Image, Held on April 4, 2019 in Tokyo. Pathobiology 2019; 86:322-324. [PMID: 31707388 DOI: 10.1159/000502718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/11/2019] [Indexed: 12/19/2022] Open
Affiliation(s)
- Hiroshi Yoshida
- Department of Diagnostic Pathology, National Cancer Center, Tokyo, Japan
| | - Hideo Yokota
- Image Processing Research Team, RIKEN Center for Advanced Photonics, RIKEN, Wako, Japan
| | - Rajendra Singh
- Department of Pathology and Dermatology, Icahn School of Medicine Mount Sinai, New York, New York, USA
| | - Tomoharu Kiyuna
- Digital Healthcare Business Development Office, NEC Corporation, Tokyo, Japan
| | | | - Susumu Kikuchi
- Technology Innovation Global, Office of CTO, Olympus Optical Co. Ltd, Tokyo, Japan
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Atsushi Ochiai
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan,
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Fraggetta F, Yagi Y, Garcia-Rojo M, Evans AJ, Tuthill JM, Baidoshvili A, Hartman DJ, Fukuoka J, Pantanowitz L. The Importance of eSlide Macro Images for Primary Diagnosis with Whole Slide Imaging. J Pathol Inform 2018; 9:46. [PMID: 30662792 PMCID: PMC6319037 DOI: 10.4103/jpi.jpi_70_18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 09/26/2018] [Accepted: 10/31/2018] [Indexed: 11/25/2022] Open
Abstract
Introduction: A whole slide image (WSI) is typically comprised of a macro image (low-power snapshot of the entire glass slide) and stacked tiles in a pyramid structure (with the lowest resolution thumbnail at the top). The macro image shows the label and all pieces of tissue on the slide. Many whole slide scanner vendors do not readily show the macro overview to pathologists. We demonstrate that failure to do so may result in a serious misdiagnosis. Materials and Methods: Various examples of errors were accumulated that occurred during the digitization of glass slides where the virtual slide differed from the macro image of the original glass slide. Such examples were retrieved from pathology laboratories using different types of scanners in the USA, Canada, Europe, and Asia. Results: The reasons for image errors were categorized into technical problems (e.g., automatic tissue finder failure, image mismatches, and poor scan coverage) and human operator mistakes (e.g., improper manual region of interest selection). These errors were all detected because they were highlighted in the macro image. Conclusion: Our experience indicates that WSI can be subject to inadvertent errors related to glitches in scanning slides, corrupt images, or mistakes made by humans when scanning slides. Displaying the macro image that accompanies WSIs is critical from a quality control perspective in digital pathology practice as this can help detect these serious image-related problems and avoid compromised diagnoses.
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Affiliation(s)
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Marcial Garcia-Rojo
- Department of Pathology, Hospital Universitario Puerta del Mar, Cádiz, Spain
| | - Andrew J Evans
- Department of Pathology, University Health Network, Toronto, Canada
| | - J Mark Tuthill
- Department of Pathology, Henry Ford Health System, Detroit, Michigan, USA
| | | | - Douglas J Hartman
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Hospital, Nagasaki, Japan
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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Iizuka M, Morita Y, Ishida T, Shiraishi H, Morisawa S, Ishida N, Fujita H, Yagi Y, Jobu K, Miyamura M. Quality control of hospital preparations: Establishment of a simple and rapid method for quantifying ulinastatin in vaginal suppositories. Pharmazie 2018; 73:683-687. [PMID: 30522549 DOI: 10.1691/ph.2018.8069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ulinastatin vaginal suppositories, used to prevent threatened premature delivery, are frequently used in hospitals. However, there is no established method for quantifying ulinastatin contained in suppositories. Therefore, we investigated a simple and efficient method for quantifying ulinastatin contained in suppositories. Our analytical method involved removal of the base; optimising the enzyme inhibition reaction time and enzyme reaction time; and measuring the absorbance. The modified method was reproducible, operation time was significantly shortened, and cost was reduced to approximately 1/17 of that of the previously reported method. This simple and rapid quantitative method could contribute to the improvement of quality control of ulinastatin vaginal suppositories as an extemporaneous hospital preparation.
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Yagi Y, Tomita A, Nittono H. Approach-avoidance responses to curved vs. angular objects: A facial EMG study. Int J Psychophysiol 2018. [DOI: 10.1016/j.ijpsycho.2018.07.463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Yagi Y, Aly R, Tabata K, Rekhtman N, Eguchi T, Montecalvo J, Manova K, Adusumilli P, Hameed M, Travis W. OA03.07 Three-Dimensional Immunofluorescence Analysis of Dynamic Vessel Co-Option of Spread Through Air Spaces (STAS) in Lung Cancer. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Tsunoda A, Takahashi T, Hayashi K, Yagi Y, Kusanagi H. Laparoscopic ventral rectopexy in patients with fecal incontinence associated with rectoanal intussusception: prospective evaluation of clinical, physiological and morphological changes. Tech Coloproctol 2018; 22:425-431. [PMID: 29956002 DOI: 10.1007/s10151-018-1811-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 06/14/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Physiological changes after laparoscopic ventral rectopexy (LVR) in patients with rectoanal intussusception (RAI) remain unclear. This study was undertaken to evaluate physiological and morphological changes after LVR for RAI, and to study clinical outcomes following LVR with special reference to fecal incontinence (FI). METHODS The study was conducted on patients who had LVR for RAI between February 2012 and December 2016 at our institution Patients with RAI and FI were included in the study. Patients with RAI and obstructed defecation and those with RAI and neurologic FI were not included. The patients had anorectal manometry preoperatively, and 3, 6, and 12 months postoperatively. Defecography was performed before and 6 months after the procedure. FI was evaluated using the Fecal Incontinence Severity Index (FISI). RESULTS There were 34 patients (median age 77 years (range 60-93) years). Thirty-two patients (94%) were female and the median number of vaginal deliveries was 2 (range 0-5). Neither maximum resting pressure nor maximum squeeze pressure increased postoperatively. There was an overall increase in both defecatory desire volume (median preoperative 75 ml vs. 90 ml at 12 months; p = 0.002) and maximum tolerated volume (median preoperative 145 ml vs.175 ml at 12 months; p = 0.002). Postoperatively, RAI was eliminated in all patients but one, although 13 had residual rectorectal intussusception found at defecography. There was an overall reduction in both rectocele size (median preop 29 mm vs. postop 10 mm; p = 0.008) and pelvic floor descent (median preop 26 mm vs. postop 20 mm; p = 0.005). Twelve months after surgery, a reduction of at least 50% was observed in the FISI score for 31 incontinent patients (91%). CONCLUSIONS LVR for RAI produced adequate improvement of FI, and successful anatomical correction of RAI was confirmed by postoperative proctography. Postoperative increase in the rectal volume may have a positive effect on continence.
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Affiliation(s)
- A Tsunoda
- Department of Gastroenterological Surgery, Kameda Medical Center, Kamogawa, Japan.
| | - T Takahashi
- Department of Gastroenterological Surgery, Kameda Medical Center, Kamogawa, Japan
| | - K Hayashi
- Department of Gastroenterological Surgery, Kameda Medical Center, Kamogawa, Japan
| | - Y Yagi
- Department of Gastroenterological Surgery, Kameda Medical Center, Kamogawa, Japan
| | - H Kusanagi
- Department of Gastroenterological Surgery, Kameda Medical Center, Kamogawa, Japan
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Yagi Y, Kosugi K, Tanimoto T. Treatment Approaches for Malignant Pleural Effusion. JAMA 2018; 319:1506-1507. [PMID: 29634824 DOI: 10.1001/jama.2018.1319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Yukako Yagi
- Department of Palliative Medicine, National Cancer Center Hospital East, Chiba, Japan
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Yagi Y, Kosugi K, Tanimoto T. Randomized Phase III and Extension Studies of Naldemedine in Patients With Opioid-Induced Constipation and Cancer. J Clin Oncol 2018; 36:1049-1050. [PMID: 29406801 DOI: 10.1200/jco.2017.76.9349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Yukako Yagi
- Yukako Yagi and Kazuhiro Kosugi, National Cancer Center Hospital East, Chiba, Japan; and Tetsuya Tanimoto, Jyoban Hospital of Tokiwa Foundation, Fukushima, Japan
| | - Kazuhiro Kosugi
- Yukako Yagi and Kazuhiro Kosugi, National Cancer Center Hospital East, Chiba, Japan; and Tetsuya Tanimoto, Jyoban Hospital of Tokiwa Foundation, Fukushima, Japan
| | - Tetsuya Tanimoto
- Yukako Yagi and Kazuhiro Kosugi, National Cancer Center Hospital East, Chiba, Japan; and Tetsuya Tanimoto, Jyoban Hospital of Tokiwa Foundation, Fukushima, Japan
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Inoue M, Shirotani Y, Yamashita S, Takata H, Kofuji H, Ambe D, Honda N, Yagi Y, Nagao S. Temporal and spatial variations of 134Cs and 137Cs levels in the Sea of Japan and Pacific coastal region: Implications for dispersion of FDNPP-derived radiocesium. J Environ Radioact 2018; 182:142-150. [PMID: 29227876 DOI: 10.1016/j.jenvrad.2017.11.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/15/2017] [Accepted: 11/24/2017] [Indexed: 06/07/2023]
Abstract
To investigate the dispersion of Fukushima Dai-ichi Nuclear Power Plant (FDNPP)-derived radiocesium in the Sea of Japan and western Pacific coastal region and determine the sources of radiocesium in these areas, we examined the temporal and spatial variations of 134Cs and 137Cs concentrations (activities) during 2011-2016 in seawaters around the western Japanese Archipelago, particularly in the Sea of Japan. In May 2013, the surface concentration of 134Cs was ∼0.5 mBq/L (decay-corrected to March 11, 2011), and that of 137Cs exceeded the pre-accident level in this study area, where the effects of radiocesium depositions just after the FDNPP accident disappeared in surface waters in October 2011. Subsequently, radiocesium concentrations gradually increased during 2013-2016 (∼0.5-1 mBq/L for 134Cs), exhibiting approximately homogeneous distributions in each year. The temporal and spatial variations of 134Cs and 137Cs concentrations indicated that FDNPP-derived radiocesium around the western Japanese Archipelago, including the Sea of Japan, has been supported by the Kuroshio Current and its branch, Tsushima Warm Current, during 2013-2016. However, in the Sea of Japan, the penetration of 134Cs was limited to depths of less than ∼200 m during three years following the re-delivery of FDNPP-derived radiocesium.
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Affiliation(s)
- M Inoue
- Low Level Radioactivity Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Nomi, Ishikawa 923-1224, Japan.
| | - Y Shirotani
- Low Level Radioactivity Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Nomi, Ishikawa 923-1224, Japan
| | - S Yamashita
- Low Level Radioactivity Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Nomi, Ishikawa 923-1224, Japan
| | - H Takata
- Marine Ecology Research Institute, Isumi, Onjuku Chiba 299-5105, Japan
| | - H Kofuji
- Low Level Radioactivity Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Nomi, Ishikawa 923-1224, Japan
| | - D Ambe
- National Research Institute of Fisheries Science, Fisheries Research Agency, Fukuura, Kanazawa, Yokohama 236-8648, Japan
| | - N Honda
- Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Suido-cho, Chuou-ku, Niigata, 951-8121, Japan
| | - Y Yagi
- Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Suido-cho, Chuou-ku, Niigata, 951-8121, Japan
| | - S Nagao
- Low Level Radioactivity Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Nomi, Ishikawa 923-1224, Japan
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Yagi Y, Tabata K, Rekhtman N, Eguchi T, Fu X, Montecalvo J, Adusumilli P, Hameed M, Travis W. OA 18.06 Three-Dimensional Assessment of Spread Through Air Spaces in Lung Adenocarcinoma: Insights and Implications. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Farahani N, Braun A, Jutt D, Huffman T, Reder N, Liu Z, Yagi Y, Pantanowitz L. Three-dimensional Imaging and Scanning: Current and Future Applications for Pathology. J Pathol Inform 2017; 8:36. [PMID: 28966836 PMCID: PMC5609355 DOI: 10.4103/jpi.jpi_32_17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 04/14/2017] [Accepted: 07/03/2017] [Indexed: 11/04/2022] Open
Abstract
Imaging is vital for the assessment of physiologic and phenotypic details. In the past, biomedical imaging was heavily reliant on analog, low-throughput methods, which would produce two-dimensional images. However, newer, digital, and high-throughput three-dimensional (3D) imaging methods, which rely on computer vision and computer graphics, are transforming the way biomedical professionals practice. 3D imaging has been useful in diagnostic, prognostic, and therapeutic decision-making for the medical and biomedical professions. Herein, we summarize current imaging methods that enable optimal 3D histopathologic reconstruction: Scanning, 3D scanning, and whole slide imaging. Briefly mentioned are emerging platforms, which combine robotics, sectioning, and imaging in their pursuit to digitize and automate the entire microscopy workflow. Finally, both current and emerging 3D imaging methods are discussed in relation to current and future applications within the context of pathology.
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Affiliation(s)
| | - Alex Braun
- 3Scan, Inc., San Francisco, California, USA
| | - Dylan Jutt
- 3Scan, Inc., San Francisco, California, USA
| | | | - Nick Reder
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Zheng Liu
- Department of Pathology, Saint Barnabas Medical Center, Livingston, New Jersey, USA
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Merrill AL, Buckley J, Tang R, Brachtel E, Rai U, Michaelson J, Ly A, Specht MC, Yagi Y, Smith BL. A Study of the Growth Patterns of Breast Carcinoma Using 3D Reconstruction: A Pilot Study. Breast J 2016; 23:83-89. [PMID: 27860134 DOI: 10.1111/tbj.12688] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 11/29/2022]
Abstract
Lumpectomy with microscopically clear margins is a safe and effective approach for surgical management of breast carcinoma. Margins are positive for tumor in 18-50% of lumpectomies, as it is not possible to accurately determine the shape or microscopic borders of a tumor preoperatively or intraoperatively. We examined the 3D microanatomy and growth patterns of common breast carcinoma subtypes to provide guidance for lumpectomy surgery. Prospective consent was obtained for the use of excess tissue from patients undergoing lumpectomy or mastectomy for breast carcinoma. Tissue blocks from nine breast carcinomas were serially sectioned. Hematoxylin and eosin-stained slides at 100 μm intervals were scanned using a Nanozoomer (Hamamatsu, Japan) microscopic-resolution scanner. Three-dimensional reconstructions of tumors were created from scanned images using Reconstruct, open-access software. Breast carcinoma subtypes demonstrated characteristic growth patterns within breast tissue, which may have implications for lumpectomy surgery. Invasive ductal carcinomas showed a spherical shape, with a spiculated surface representing tumor cells infiltrating into surrounding parenchyma. Ductal carcinoma in situ appeared to spread along the duct system, creating dilated, tortuous, tumor-filled ducts. The invasive lobular carcinomas examined had a haphazard, linear, infiltrative growth pattern, different from the shape seen in ductal carcinomas. Our preliminary work suggests that invasive ductal and invasive lobular carcinomas appear to have distinct growth patterns in three dimensions and ductal carcinoma in situ appears to grow in a linear fashion along the duct network. The microanatomy studies described have the potential to guide refinements in breast lumpectomy technique.
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Affiliation(s)
- Andrea L Merrill
- Division of Surgical Oncology, Center for Breast Cancers, Massachusetts General Hospital, Boston, Massachusetts
| | - Julliette Buckley
- Division of Surgical Oncology, Center for Breast Cancers, Massachusetts General Hospital, Boston, Massachusetts
| | - Rong Tang
- Division of Surgical Oncology, Center for Breast Cancers, Massachusetts General Hospital, Boston, Massachusetts
| | - Elena Brachtel
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Upahvan Rai
- Division of Surgical Oncology, Center for Breast Cancers, Massachusetts General Hospital, Boston, Massachusetts
| | - James Michaelson
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Michelle C Specht
- Division of Surgical Oncology, Center for Breast Cancers, Massachusetts General Hospital, Boston, Massachusetts
| | - Yukako Yagi
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Barbara L Smith
- Division of Surgical Oncology, Center for Breast Cancers, Massachusetts General Hospital, Boston, Massachusetts
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Ajimizu H, Ozasa H, Sato S, Sakamori Y, Funazo T, Yasuda Y, Nomizo T, Tsuji T, Yoshida H, Yagi Y, Nagai H, Sato A, Tsuchiya M, Muro S, Nagasaka Y, Mishima M, Kim Y. Survival impact of treatment for chronic obstructive pulmonary disease in patients with advanced non-small cell lung cancer. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw384.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Ohnishi T, Nakamura Y, Tanaka T, Tanaka T, Hashimoto N, Haneishi H, Batchelor TT, Gerstner ER, Taylor JW, Snuderl M, Yagi Y. Deformable image registration between pathological images and MR image via an optical macro image. Pathol Res Pract 2016; 212:927-936. [PMID: 27613662 PMCID: PMC5097673 DOI: 10.1016/j.prp.2016.07.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 07/02/2016] [Accepted: 07/31/2016] [Indexed: 02/05/2023]
Abstract
Computed tomography (CT) and magnetic resonance (MR) imaging have been widely used for visualizing the inside of the human body. However, in many cases, pathological diagnosis is conducted through a biopsy or resection of an organ to evaluate the condition of tissues as definitive diagnosis. To provide more advanced information onto CT or MR image, it is necessary to reveal the relationship between tissue information and image signals. We propose a registration scheme for a set of PT images of divided specimens and a 3D-MR image by reference to an optical macro image (OM image) captured by an optical camera. We conducted a fundamental study using a resected human brain after the death of a brain cancer patient. We constructed two kinds of registration processes using the OM image as the base for both registrations to make conversion parameters between the PT and MR images. The aligned PT images had shapes similar to the OM image. On the other hand, the extracted cross-sectional MR image was similar to the OM image. From these resultant conversion parameters, the corresponding region on the PT image could be searched and displayed when an arbitrary pixel on the MR image was selected. The relationship between the PT and MR images of the whole brain can be analyzed using the proposed method. We confirmed that same regions between the PT and MR images could be searched and displayed using resultant information obtained by the proposed method. In terms of the accuracy of proposed method, the TREs were 0.56±0.39mm and 0.87±0.42mm. We can analyze the relationship between tissue information and MR signals using the proposed method.
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Affiliation(s)
- Takashi Ohnishi
- Center for Frontier Medical Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan.
| | - Yuka Nakamura
- Graduate School of Engineering, Chiba University, Japan
| | - Toru Tanaka
- Graduate School of Engineering, Chiba University, Japan
| | - Takuya Tanaka
- Graduate School of Engineering, Chiba University, Japan
| | - Noriaki Hashimoto
- Center for Frontier Medical Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Hideaki Haneishi
- Center for Frontier Medical Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Tracy T Batchelor
- Massachusetts General Hospital Cancer Center, Boston, MA 02144, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Elizabeth R Gerstner
- Massachusetts General Hospital Cancer Center, Boston, MA 02144, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Jennie W Taylor
- Massachusetts General Hospital Cancer Center, Boston, MA 02144, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Matija Snuderl
- New York University Langone Medical Center, New York, NY 10016, USA
| | - Yukako Yagi
- Harvard Medical School, Boston, MA 02215, USA; Massachusetts General Hospital Pathology Imaging and Communication Technology (PICT) Center, Boston, MA 02214, USA
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Gainor JF, Shaw AT, Sequist LV, Fu X, Azzoli CG, Piotrowska Z, Huynh TG, Zhao L, Fulton L, Schultz KR, Howe E, Farago AF, Sullivan RJ, Stone JR, Digumarthy S, Moran T, Hata AN, Yagi Y, Yeap BY, Engelman JA, Mino-Kenudson M. EGFR Mutations and ALK Rearrangements Are Associated with Low Response Rates to PD-1 Pathway Blockade in Non-Small Cell Lung Cancer: A Retrospective Analysis. Clin Cancer Res 2016; 22:4585-93. [PMID: 27225694 DOI: 10.1158/1078-0432.ccr-15-3101] [Citation(s) in RCA: 885] [Impact Index Per Article: 110.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/08/2016] [Indexed: 12/26/2022]
Abstract
PURPOSE PD-1 inhibitors are established agents in the management of non-small cell lung cancer (NSCLC); however, only a subset of patients derives clinical benefit. To determine the activity of PD-1/PD-L1 inhibitors within clinically relevant molecular subgroups, we retrospectively evaluated response patterns among EGFR-mutant, anaplastic lymphoma kinase (ALK)-positive, and EGFR wild-type/ALK-negative patients. EXPERIMENTAL DESIGN We identified 58 patients treated with PD-1/PD-L1 inhibitors. Objective response rates (ORR) were assessed using RECIST v1.1. PD-L1 expression and CD8(+) tumor-infiltrating lymphocytes (TIL) were evaluated by IHC. RESULTS Objective responses were observed in 1 of 28 (3.6%) EGFR-mutant or ALK-positive patients versus 7 of 30 (23.3%) EGFR wild-type and ALK-negative/unknown patients (P = 0.053). The ORR among never- or light- (≤10 pack years) smokers was 4.2% versus 20.6% among heavy smokers (P = 0.123). In an independent cohort of advanced EGFR-mutant (N = 68) and ALK-positive (N = 27) patients, PD-L1 expression was observed in 24%/16%/11% and 63%/47%/26% of pre-tyrosine kinase inhibitor (TKI) biopsies using cutoffs of ≥1%, ≥5%, and ≥50% tumor cell staining, respectively. Among EGFR-mutant patients with paired, pre- and post-TKI-resistant biopsies (N = 57), PD-L1 expression levels changed after resistance in 16 (28%) patients. Concurrent PD-L1 expression (≥5%) and high levels of CD8(+) TILs (grade ≥2) were observed in only 1 pretreatment (2.1%) and 5 resistant (11.6%) EGFR-mutant specimens and was not observed in any ALK-positive, pre- or post-TKI specimens. CONCLUSIONS NSCLCs harboring EGFR mutations or ALK rearrangements are associated with low ORRs to PD-1/PD-L1 inhibitors. Low rates of concurrent PD-L1 expression and CD8(+) TILs within the tumor microenvironment may underlie these clinical observations. Clin Cancer Res; 22(18); 4585-93. ©2016 AACRSee related commentary by Gettinger and Politi, p. 4539.
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Affiliation(s)
- Justin F Gainor
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.
| | - Alice T Shaw
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Lecia V Sequist
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Xiujun Fu
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Zofia Piotrowska
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Tiffany G Huynh
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Ling Zhao
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Linnea Fulton
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Katherine R Schultz
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Emily Howe
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Anna F Farago
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Ryan J Sullivan
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Subba Digumarthy
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Aaron N Hata
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Yukako Yagi
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Beow Y Yeap
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jeffrey A Engelman
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
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Hashimoto N, Bautista PA, Haneishi H, Snuderl M, Yagi Y. Development of a 2D Image Reconstruction and Viewing System for Histological Images from Multiple Tissue Blocks: Towards High-Resolution Whole-Organ 3D Histological Images. Pathobiology 2016; 83:127-39. [PMID: 27100217 DOI: 10.1159/000443278] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
High-resolution 3D histology image reconstruction of the whole brain organ starts from reconstructing the high-resolution 2D histology images of a brain slice. In this paper, we introduced a method to automatically align the histology images of thin tissue sections cut from the multiple paraffin-embedded tissue blocks of a brain slice. For this method, we employed template matching and incorporated an optimization technique to further improve the accuracy of the 2D reconstructed image. In the template matching, we used the gross image of the brain slice as a reference to the reconstructed 2D histology image of the slice, while in the optimization procedure, we utilized the Jaccard index as the metric of the reconstruction accuracy. The results of our experiment on the initial 3 different whole-brain tissue slices showed that while the method works, it is also constrained by tissue deformations introduced during the tissue processing and slicing. The size of the reconstructed high-resolution 2D histology image of a brain slice is huge, and designing an image viewer that makes particularly efficient use of the computing power of a standard computer used in our laboratories is of interest. We also present the initial implementation of our 2D image viewer system in this paper.
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