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Bedwell D, Sharma J, Du M, Wong E, Mutyam V, Li Y, Chen J, Wangen J, Thrasher K, Fu L, Peng N, Tang L, Liu K, Mathew B, Bostwick B, Augelli-Szafran C, Bihler H, Liang F, Mahiou J, Saltz J, Rab A, Hong J, Sorscher E, Mendenhall E, Coppola C, Keeling K, Green R, Mense M, Suto M, Rowe S. 531: Identification of a compound that mediates readthrough of CFTR nonsense mutations by reducing eRF1 levels. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)01955-x] [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: 10/20/2022]
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Mallipattu SK, Jawa R, Moffitt R, Hajagos J, Fries B, Nachman S, Gan TJ, Saltz M, Saltz J, Kaushansky K, Skopicki H, Abell-Hart K, Chaudhri I, Deng J, Garcia V, Gayen S, Kurc T, Bolotova O, Yoo J, Dhaliwal S, Nataraj N, Sun S, Tsai C, Wang Y, Abbasi S, Abdullah R, Ahmad S, Bai K, Bennett-Guerrero E, Chua A, Gomes C, Griffel M, Kalogeropoulos A, Kiamanesh D, Kim N, Koraishy F, Lingham V, Mansour M, Marcos L, Miller J, Poovathor S, Rubano J, Rutigliano D, Sands M, Santora C, Schwartz J, Shroyer K, Spitzer S, Stopeck A, Talamini M, Tharakan M, Vosswinkel J, Wertheim W, Mallipattu SK, Jawa R, Moffitt R, Hajagos J, Fries B, Nachman S, Gan TJ, Saltz M, Saltz J, Kaushansky K, Skopicki H, Abell-Hart K, Chaudhri I, Deng J, Garcia V, Gayen S, Kurc T, Bolotova O, Yoo J, Dhaliwal S, Nataraj N, Sun S, Tsai C, Wang Y, Abbasi S, Abdullah R, Ahmad S, Bai K, Bennett-Guerrero E, Chua A, Gomes C, Griffel M, Kalogeropoulos A, Kiamanesh D, Kim N, Koraishy F, Lingham V, Mansour M, Marcos L, Miller J, Poovathor S, Rubano J, Rutigliano D, Sands M, Santora C, Schwartz J, Shroyer K, Spitzer S, Stopeck A, Talamini M, Tharakan M, Vosswinkel J, Wertheim W. Geospatial Distribution and Predictors of Mortality in Hospitalized Patients With COVID-19: A Cohort Study. Open Forum Infect Dis 2020; 7:ofaa436. [PMID: 33117852 PMCID: PMC7543608 DOI: 10.1093/ofid/ofaa436] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 08/14/2020] [Accepted: 09/09/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The global coronavirus disease 2019 (COVID-19) pandemic offers the opportunity to assess how hospitals manage the care of hospitalized patients with varying demographics and clinical presentations. The goal of this study was to demonstrate the impact of densely populated residential areas on hospitalization and to identify predictors of length of stay and mortality in hospitalized patients with COVID-19 in one of the hardest hit counties internationally. METHODS This was a single-center cohort study of 1325 sequentially hospitalized patients with COVID-19 in New York between March 2, 2020, to May 11, 2020. Geospatial distribution of study patients' residences relative to population density in the region were mapped, and data analysis included hospital length of stay, need and duration of invasive mechanical ventilation (IMV), and mortality. Logistic regression models were constructed to predict discharge dispositions in the remaining active study patients. RESULTS The median age of the study cohort (interquartile range [IQR]) was 62 (49-75) years, and more than half were male (57%) with history of hypertension (60%), obesity (41%), and diabetes (42%). Geographic residence of the study patients was disproportionately associated with areas of higher population density (r s = 0.235; P = .004), with noted "hot spots" in the region. Study patients were predominantly hypertensive (MAP > 90 mmHg; 670, 51%) on presentation with lymphopenia (590, 55%), hyponatremia (411, 31%), and kidney dysfunction (estimated glomerular filtration rate < 60 mL/min/1.73 m2; 381, 29%). Of the patients with a disposition (1188/1325), 15% (182/1188) required IMV and 21% (250/1188) developed acute kidney injury. In patients on IMV, the median (IQR) hospital length of stay in survivors (22 [16.5-29.5] days) was significantly longer than that of nonsurvivors (15 [10-23.75] days), but this was not due to prolonged time on the ventilator. The overall mortality in all hospitalized patients was 15%, and in patients receiving IMV it was 48%, which is predicted to minimally rise from 48% to 49% based on logistic regression models constructed to project disposition in the remaining patients on ventilators. Acute kidney injury during hospitalization (odds ratioE, 3.23) was the strongest predictor of mortality in patients requiring IMV. CONCLUSIONS This is the first study to collectively utilize the demographics, clinical characteristics, and hospital course of COVID-19 patients to identify predictors of poor outcomes that can be used for resource allocation in future waves of the pandemic.
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Affiliation(s)
| | - S K Mallipattu
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - R Jawa
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - R Moffitt
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Hajagos
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - B Fries
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Nachman
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - T J Gan
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Saltz
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Saltz
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - K Kaushansky
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - H Skopicki
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - K Abell-Hart
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - I Chaudhri
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Deng
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - V Garcia
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Gayen
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - T Kurc
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - O Bolotova
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Yoo
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Dhaliwal
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - N Nataraj
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Sun
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - C Tsai
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - Y Wang
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Abbasi
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - R Abdullah
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Ahmad
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - K Bai
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - E Bennett-Guerrero
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - A Chua
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - C Gomes
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Griffel
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - A Kalogeropoulos
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - D Kiamanesh
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - N Kim
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - F Koraishy
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - V Lingham
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Mansour
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - L Marcos
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Miller
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Poovathor
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Rubano
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - D Rutigliano
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Sands
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - C Santora
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Schwartz
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - K Shroyer
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Spitzer
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - A Stopeck
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Talamini
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Tharakan
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Vosswinkel
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - W Wertheim
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S K Mallipattu
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - R Jawa
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - R Moffitt
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Hajagos
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - B Fries
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Nachman
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - T J Gan
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Saltz
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Saltz
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - K Kaushansky
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - H Skopicki
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - K Abell-Hart
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - I Chaudhri
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Deng
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - V Garcia
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Gayen
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - T Kurc
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - O Bolotova
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Yoo
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Dhaliwal
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - N Nataraj
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Sun
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - C Tsai
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - Y Wang
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Abbasi
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - R Abdullah
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Ahmad
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - K Bai
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - E Bennett-Guerrero
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - A Chua
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - C Gomes
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Griffel
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - A Kalogeropoulos
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - D Kiamanesh
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - N Kim
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - F Koraishy
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - V Lingham
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Mansour
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - L Marcos
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Miller
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Poovathor
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Rubano
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - D Rutigliano
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Sands
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - C Santora
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Schwartz
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - K Shroyer
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - S Spitzer
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - A Stopeck
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Talamini
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - M Tharakan
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - J Vosswinkel
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
| | - W Wertheim
- Renaissance School of Medicine at Stony Brook University, Stony Brook University, Stony Brook, New York, USA
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Prior F, Almeida J, Kathiravelu P, Kurc T, Smith K, Fitzgerald TJ, Saltz J. Open access image repositories: high-quality data to enable machine learning research. Clin Radiol 2020; 75:7-12. [PMID: 31040006 PMCID: PMC6815686 DOI: 10.1016/j.crad.2019.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/01/2019] [Indexed: 02/07/2023]
Abstract
Originally motivated by the need for research reproducibility and data reuse, large-scale, open access information repositories have become key resources for training and testing of advanced machine learning applications in biomedical and clinical research. To be of value, such repositories must provide large, high-quality data sets, where quality is defined as minimising variance due to data collection protocols and data misrepresentations. Curation is the key to quality. We have constructed a large public access image repository, The Cancer Imaging Archive, dedicated to the promotion of open science to advance the global effort to diagnose and treat cancer. Drawing on this experience and our experience in applying machine learning techniques to the analysis of radiology and pathology image data, we will review the requirements placed on such information repositories by state-of-the-art machine learning applications and how these requirements can be met.
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Affiliation(s)
- F Prior
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham St, Little Rock, AR 72205, USA.
| | - J Almeida
- National Institutes of Health, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - P Kathiravelu
- Department of Biomedical Informatics, Emory University, 101 Woodruff Circle, #4104, Atlanta, GA 30322, USA
| | - T Kurc
- Department of Biomedical Informatics, Stoney Brook University, Health Science Center Level 3, Room 043, Stony Brook, NY 11794, USA
| | - K Smith
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham St, Little Rock, AR 72205, USA
| | - T J Fitzgerald
- Department of Radiation Oncology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - J Saltz
- Department of Biomedical Informatics, Stoney Brook University, Health Science Center Level 3, Room 043, Stony Brook, NY 11794, USA
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Konen J, Summerbell E, Dwivedi B, Galior K, Hou Y, Rusnak L, Chen A, Saltz J, Zhou W, Boise LH, Vertino P, Cooper L, Salaita K, Kowalski J, Marcus AI. Image-guided genomics of phenotypically heterogeneous populations reveals vascular signalling during symbiotic collective cancer invasion. Nat Commun 2017; 8:15078. [PMID: 28497793 PMCID: PMC5437311 DOI: 10.1038/ncomms15078] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/27/2017] [Indexed: 02/06/2023] Open
Abstract
Phenotypic heterogeneity is widely observed in cancer cell populations. Here, to probe this heterogeneity, we developed an image-guided genomics technique termed spatiotemporal genomic and cellular analysis (SaGA) that allows for precise selection and amplification of living and rare cells. SaGA was used on collectively invading 3D cancer cell packs to create purified leader and follower cell lines. The leader cell cultures are phenotypically stable and highly invasive in contrast to follower cultures, which show phenotypic plasticity over time and minimally invade in a sheet-like pattern. Genomic and molecular interrogation reveals an atypical VEGF-based vasculogenesis signalling that facilitates recruitment of follower cells but not for leader cell motility itself, which instead utilizes focal adhesion kinase-fibronectin signalling. While leader cells provide an escape mechanism for followers, follower cells in turn provide leaders with increased growth and survival. These data support a symbiotic model of collective invasion where phenotypically distinct cell types cooperate to promote their escape. The mechanisms linking phenotypic heterogeneity to collective cancer invasion are unclear. Here the authors develop an image-guided genomic technique to select and amplify leader and follower cells from in vitro invading cell packs and find a cooperative symbiotic relationship between these two cell populations.
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Affiliation(s)
- J Konen
- Graduate Program in Cancer Biology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - E Summerbell
- Graduate Program in Cancer Biology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - B Dwivedi
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - K Galior
- Department of Chemistry, Emory University, 506 Atwood Drive, Atlanta, Georgia 30322, USA
| | - Y Hou
- Department of Biomedical Informatics, Emory University, 36 Eagle Row, Atlanta, Georgia 30322, USA
| | - L Rusnak
- Graduate Program in Cancer Biology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - A Chen
- Graduate Program in Cancer Biology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - J Saltz
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York 11794, USA
| | - W Zhou
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA.,Department of Hematology and Medical Oncology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - L H Boise
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA.,Department of Hematology and Medical Oncology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - P Vertino
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA.,Department of Radiation Oncology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - L Cooper
- Department of Biomedical Informatics, Emory University, 36 Eagle Row, Atlanta, Georgia 30322, USA
| | - K Salaita
- Department of Chemistry, Emory University, 506 Atwood Drive, Atlanta, Georgia 30322, USA
| | - J Kowalski
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA.,Department of Biostatistics and Bioinformatics, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
| | - A I Marcus
- Winship Cancer Institute, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA.,Department of Hematology and Medical Oncology, Emory University, 1365C Clifton Road, Atlanta, Georgia 30322, USA
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Adachi JI, Totake K, Shirahata M, Mishima K, Suzuki T, Yanagisawa T, Fukuoka K, Nishikawa R, Arimappamagan A, Manoj N, Mahadevan A, Bhat D, Arvinda H, Indiradevi B, Somanna S, Chandramouli B, Petterson SA, Hermansen SK, Dahlrot RH, Hansen S, Kristensen BW, Carvalho F, Jalali S, Singh S, Croul S, Aldape K, Zadeh G, Choi J, Park SH, Khang SK, Suh YL, Kim SP, Lee YS, Kim SH, Coberly S, Samayoa K, Liu Y, Kiaei P, Hill J, Patterson S, Damore M, Dahiya S, Emnett R, Phillips J, Haydon D, Leonard J, Perry A, Gutmann D, Epari S, Ahmed S, Gurav M, Raikar S, Moiyadi A, Shetty P, Gupta T, Jalali R, Georges J, Zehri A, Carlson E, Martirosyan N, Elhadi A, Nichols J, Ighaffari L, Eschbacher J, Feuerstein B, Anderson T, Preul M, Jensen K, Nakaji P, Girardi H, Monville F, Carpentier S, Giry M, Voss J, Jenkins R, Boisselier B, Frayssinet V, Poggionovo C, Catteau A, Mokhtari K, Sanson M, Peyro-Saint-Paul H, Giannini C, Hide T, Nakamura H, Makino K, Yano S, Anai S, Shinojima N, Kuroda JI, Takezaki T, Kuratsu JI, Higuchi F, Matsuda H, Iwata K, Ueki K, Kim P, Kong J, Cooper L, Wang F, Gao J, Teodoro G, Scarpace L, Mikkelsen T, Schniederjan M, Moreno C, Saltz J, Brat D, Cho U, Hong YK, Lee YS, Lober R, Lu L, Gephart MH, Fisher P, Miyazaki M, Nishihara H, Itoh T, Kato M, Fujimoto S, Kimura T, Tanino M, Tanaka S, Nguyen N, Moes G, Villano JL, Nishihara H, Kanno H, Kato Y, Tanaka S, Ohnishi T, Harada H, Ohue S, Kouno S, Inoue A, Yamashita D, Okamoto S, Nitta M, Muragaki Y, Maruyama T, Sawada T, Komori T, Saito T, Okada Y, Omay SB, Gunel JM, Clark VE, Li J, Omay EZE, Serin A, Kolb LE, Hebert RM, Bilguvar K, Ozduman K, Pamir MN, Kilic T, Baehring J, Piepmeier JM, Brennan CW, Huse J, Gutin PH, Yasuno K, Vortmeyer A, Gunel M, Perry A, Pugh S, Rogers CL, Brachman D, McMillan W, Jenrette J, Barani I, Shrieve D, Sloan A, Mehta M, Prabowo A, Iyer A, Veersema T, Anink J, Meeteren ASV, Spliet W, van Rijen P, Ferrier T, Capper D, Thom M, Aronica E, Chharchhodawala T, Sable M, Sharma MC, Sarkar C, Suri V, Singh M, Santosh V, Thota B, Srividya M, Sravani K, Shwetha S, Arivazhagan A, Thennarasu K, Chandramouli B, Hegde A, Kondaiah P, Somasundaram K, Rao M, Santosh V, Kumar VP, Thota B, Shastry A, Arivazhagan A, Thennarasu K, Kondaiah P, Shastry A, Narayan R, Thota B, Somanna S, Thennarasu K, Arivazhagan A, Santosh V, Shastry A, Naz S, Thota B, Thennarasu K, Arivazhagan A, Somanna S, Santosh V, Kondaiah P, Venneti S, Garimella M, Sullivan L, Martinez D, Huse J, Heguy A, Santi M, Thompson C, Judkins A, Voronovich Z, Chen L, Clark K, Walsh M, Mannas J, Horbinski C, Wiestler B, Capper D, Holland-Letz T, Korshunov A, von Deimling A, Pfister SM, Platten M, Weller M, Wick W, Zieman G, Dardis C, Ashby L, Eschbacher J. PATHOLOGY. Neuro Oncol 2013. [DOI: 10.1093/neuonc/not184] [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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Bluml S, Panigrahy A, Laskov M, Dhall G, Nelson MD, Finlay JL, Gilles FH, Arita H, Kinoshita M, Kagawa N, Fujimoto Y, Hashimoto N, Yoshimine T, Kinoshita M, Arita H, Kagawa N, Fujimoto Y, Hashimoto N, Yoshimine T, Hamilton JD, Wang J, Levin VA, Hou P, Loghin ME, Gilbert MR, Leeds NE, deGroot JF, Puduvalli V, Jackson EF, Yung WKA, Kumar AJ, Ellingson BM, Cloughesy TF, Pope WB, Zaw T, Phillips H, Lalezari S, Nghiemphu PL, Ibrahim H, Motevalibashinaeini K, Lai A, Ellingson BM, Cloughesy TF, Zaw T, Harris R, Lalezari S, Nghiemphu PL, Motevalibashinaeini K, Lai A, Pope WB, Douw L, Van de Nieuwenhuijzen ME, Heimans JJ, Baayen JC, Stam CJ, Reijneveld JC, Juhasz C, Mittal S, Altinok D, Robinette NL, Muzik O, Chakraborty PK, Barger GR, Ellingson BM, Cloughesy TF, Zaw TM, Lalezari S, Nghiemphu PL, Motevalibashinaeini K, Lai A, Goldin J, Pope WB, Ellingson BM, Cloughesy TF, Harris R, Pope WB, Nghiemphu PL, Lai A, Zaw T, Chen W, Ahlman MA, Giglio P, Kaufmann TJ, Anderson SK, Jaeckle KA, Uhm JH, Northfelt DW, Flynn PJ, Buckner JC, Galanis E, Zalatimo O, Weston C, Allison D, Bota D, Kesari S, Glantz M, Sheehan J, Harbaugh RE, Chiba Y, Kinoshita M, Kagawa N, Fujimoto Y, Tsuboi A, Hatazawa J, Sugiyama H, Hashimoto N, Yoshimine T, Nariai T, Toyohara J, Tanaka Y, Inaji M, Aoyagi M, Yamamoto M, Ishiwara K, Ohno K, Jalilian L, Essock-Burns E, Cha S, Chang S, Prados M, Butowski N, Nelson S, Kawahara Y, Nakada M, Hayashi Y, Kai Y, Hayashi Y, Uchiyama N, Kuratsu JI, Hamada JI, Yeom K, Rosenberg J, Andre JB, Fisher PG, Edwards MS, Barnes PD, Partap S, Essock-Burns E, Jalilian L, Lupo JM, Crane JC, Cha S, Chang SM, Nelson SJ, Romanowski CA, Hoggard N, Jellinek DA, Clenton S, McKevitt F, Wharton S, Craven I, Buller A, Waddle C, Bigley J, Wilkinson ID, Metherall P, Eckel LJ, Keating GF, Wetjen NM, Giannini C, Wetmore C, Jain R, Narang J, Arbab AS, Schultz L, Scarpace L, Mikkelsen T, Babajni-Feremi A, Jain R, Poisson L, Narang J, Scarpace L, Gutman D, Jaffe C, Saltz J, Flanders A, Daniel B, Mikkelsen T, Zach L, Guez D, Last D, Daniels D, Hoffman C, Mardor Y, Guha-Thakurta N, Debnam JM, Kotsarini C, Wilkinson ID, Jellinek D, Griffiths PD, Khandanpour N, Hoggard N, Kotsarini C, Wilkinson ID, Jellinek D, Griffiths PD, Bambrough P, Hoggard N, Hamilton JD, Levin VA, Hou P, Prabhu S, Loghin ME, Gilbert MR, Bassett RL, Wang J, Yung WA, Jackson EF, Kumar AJ, Campen CJ, Soman S, Fisher PG, Edwards MS, Yeom KW, Vos MJ, Berkhof J, Postma TJ, Sanchez E, Sizoo EM, Heimans JJ, Lagerwaard FJ, Buter J, Noske DP, Reijneveld JC, Colen RR, Mahajan B, Jolesz FA, Zinn PO, Lupo JM, Molinaro A, Chang S, Lawton K, Cha S, Nelson SJ, Alexandru D, Bota D, Linskey ME, Chaumeil MM, Gini B, Yang H, Iwanami A, Subramanian S, Ozawa T, Read EJ, Pieper RO, Mischel P, James CD, Ronen SM, LaViolette PS, Cochran E, Al-Gizawiy M, Connelly JM, Malkin MG, Rand SD, Mueller WM, Schmainda KM, LaViolette PS, Cohen AD, Cochran E, Prah M, Hartman CJ, Connelly JM, Rand SD, Malkin MG, Mueller WM, Schmainda KM, Qiao XJ, He R, Brown M, Goldin J, Cloughesy T, Pope WB. RADIOLOGY. Neuro Oncol 2011; 13:iii136-iii144. [PMCID: PMC3222969 DOI: 10.1093/neuonc/nor162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
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Abstract
Point-of-care testing (POCT) is an increasingly popular method of delivering laboratory testing. Management of POCT is challenging given the variety of devices, locations, and staff that need to be coordinated to ensure quality results and meet regulatory guidelines. Electronic capture and transfer of data are preferred for managing POCT, but there is currently no standard method of connecting different devices. Johns Hopkins Medical Institutions (JHMI) developed a common data management system with interfaces to all of its POCT devices. All POCT data are collected in one database and analyzed in a similar fashion. Where data were once collected by carrying laptops to each nursing unit, the POCT devices can now connect directly to the database over the Internet. Algorithms have been created to automate the data analysis and review process. Over the several years that this software has been used, JHMI has experienced improved quality, accuracy, and management of its POCT program. The labor saved by increased automation of data review is refocused on enhancing the performance and scope of the program. Current connectivity and analysis algorithms have future application to remote consultation, management of home self-monitoring patients, and examination of real-time data.
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Affiliation(s)
- K Dyer
- Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
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Afework A, Beynon MD, Bustamante F, Cho S, Demarzo A, Ferreira R, Miller R, Silberman M, Saltz J, Sussman A, Tsang H. Digital dynamic telepathology--the Virtual Microscope. Proc AMIA Symp 1998:912-6. [PMID: 9929351 PMCID: PMC2232135] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The Virtual Microscope is being designed as an integrated computer hardware and software system that generates a highly realistic digital simulation of analog, mechanical light microscopy. We present our work over the past year in meeting the challenges in building such a system. The enhancements we made are discussed, as well as the planned future improvements. Performance results are provided showing the system scales well, so that many users can be adequately serviced by an appropriately configured data server.
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Affiliation(s)
- A Afework
- UMIACS, University of Maryland, College Park 20742, USA
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Stoffel K, Davis JD, Rottman G, Saltz J, Dick J, Merz W, Miller R. A graphical tool for ad hoc query generation. Proc AMIA Symp 1998:503-7. [PMID: 9929270 PMCID: PMC2232066] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
Medical data are characterized by complex taxonomies and evolving terminology. Questions that clinicians, medical administrators, and researchers may wish to answer using medical databases are not easily formulated as SQL queries. In this paper we describe a graphical tool that facilitates formulation of ad hoc questions as SQL queries. This tool manages multiple attribute hierarchies and creates SQL query strings by navigating through the hierarchies. This interactive tool has been optimized using indexing to improve the overall speed of the query building and the data retrieval process. Indexed queries performed 5 to 100 times faster than query strings. However, query string generation time depends on the size of the taxonomies describing the hierarchies, while the index generation time depends on the size of the data warehouse.
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Affiliation(s)
- K Stoffel
- Computer Science Department, University of Maryland, College Park 20742, USA
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Ferreira R, Moon B, Humphries J, Sussman A, Saltz J, Miller R, Demarzo A. The Virtual Microscope. Proc AMIA Annu Fall Symp 1997:449-53. [PMID: 9357666 PMCID: PMC2233368] [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] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We present the design of the Virtual Microscope, a software system employing a client/server architecture to provide a realistic emulation of a high power light microscope. We discuss several technical challenges related to providing the performance necessary to achieve rapid response time, mainly in dealing with the enormous amounts of data (tens to hundreds of gigabytes per slide) that must be retrieved from secondary storage and processed. To effectively implement the data server, the system design relies on the computational power and high I/O throughput available from an appropriately configured parallel computer.
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Sussman A, Saltz J, Das R, Gupta S, Mavriplis D, Ponnusamy R, Crowley K. PARTI primitives for unstructured and block structured problems. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0956-0521(92)90096-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
A quantitative assessment of the long-term prognostic value and clinical usefulness of recall antigen reactions in patients with malignant melanoma is not available. The authors evaluated longitudinal observations of survival made in 846 patients over a 12-year period. Each patient was initially studied with Mantoux-type recall antigen skin tests. The patients were categorized with respect to the following: high (greater than 5 mm) or low (less than or equal to 5 mm) averaged skin test reaction diameters at 48 hr; Clark level; tumor stage (I = localized tumor, II = local extension and/or region lymph node metastasis, III = systemic metastasis); ulceration; site of primary; histologic type; age; and sex. The percentage of high reactors in Stages I, II, and III were 44.3%, 37.4%, and 25%, respectively. Survival was evaluated with the Cox-Mantell hazard function model and the Cox regression model. The significant (chi-squared; probability) risk factors detected were tumor stage (94.58; less than or equal to 0.0001), Clark level (19.37; less than or equal to 0.0001), sex (16.97; less than or equal to 0.0001), and skin test reactivity (7.48; less than or equal to 0.0062). A significant relationship also was detected between skin test reactor status and the tumor stage (p less than or equal to 0.0330). When evaluated within each stage of disease, skin test reactivity predicted survival only in Stage II patients (p less than or equal to 0.0080). Five-year survival estimates among Stage II patients were 58% among high reactors and 38% among low reactors.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J Saltz
- Department of Medicine, Duke University, Durham, North Carolina
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Saltz J. The teaching of medical computation. Med Inform (Lond) 1984; 9:310-311. [PMID: 6503468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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