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Jiang VS, Kartik D, Thirumalaraju P, Kandula H, Kanakasabapathy MK, Souter I, Dimitriadis I, Bormann CL, Shafiee H. Advancements in the future of automating micromanipulation techniques in the IVF laboratory using deep convolutional neural networks. J Assist Reprod Genet 2023; 40:251-257. [PMID: 36586006 PMCID: PMC9935764 DOI: 10.1007/s10815-022-02685-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/06/2022] [Indexed: 01/01/2023] Open
Abstract
PURPOSE To determine if deep learning artificial intelligence algorithms can be used to accurately identify key morphologic landmarks on oocytes and cleavage stage embryo images for micromanipulation procedures such as intracytoplasmic sperm injection (ICSI) or assisted hatching (AH). METHODS Two convolutional neural network (CNN) models were trained, validated, and tested over three replicates to identify key morphologic landmarks used to guide embryologists when performing micromanipulation procedures. The first model (CNN-ICSI) was trained (n = 13,992), validated (n = 1920), and tested (n = 3900) to identify the optimal location for ICSI through polar body identification. The second model (CNN-AH) was trained (n = 13,908), validated (n = 1908), and tested (n = 3888) to identify the optimal location for AH on the zona pellucida that maximizes distance from healthy blastomeres. RESULTS The CNN-ICSI model accurately identified the polar body and corresponding optimal ICSI location with 98.9% accuracy (95% CI 98.5-99.2%) with a receiver operator characteristic (ROC) with micro and macro area under the curves (AUC) of 1. The CNN-AH model accurately identified the optimal AH location with 99.41% accuracy (95% CI 99.11-99.62%) with a ROC with micro and macro AUCs of 1. CONCLUSION Deep CNN models demonstrate powerful potential in accurately identifying key landmarks on oocytes and cleavage stage embryos for micromanipulation. These findings are novel, essential stepping stones in the automation of micromanipulation procedures.
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Affiliation(s)
- Victoria S Jiang
- Division of Reproductive Endocrinology and Infertility, Vincent Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Suite 10A, Boston, MA, 02114, USA
| | - Deeksha Kartik
- Division of Engineering in Medicine, Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA, 02139, USA
| | - Prudhvi Thirumalaraju
- Division of Engineering in Medicine, Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA, 02139, USA
| | - Hemanth Kandula
- Division of Engineering in Medicine, Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA, 02139, USA
| | - Manoj Kumar Kanakasabapathy
- Division of Engineering in Medicine, Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA, 02139, USA
| | - Irene Souter
- Division of Reproductive Endocrinology and Infertility, Vincent Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Suite 10A, Boston, MA, 02114, USA
| | - Irene Dimitriadis
- Division of Reproductive Endocrinology and Infertility, Vincent Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Suite 10A, Boston, MA, 02114, USA
| | - Charles L Bormann
- Division of Reproductive Endocrinology and Infertility, Vincent Obstetrics and Gynecology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Suite 10A, Boston, MA, 02114, USA.
| | - Hadi Shafiee
- Division of Engineering in Medicine, Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Cambridge, MA, 02139, USA.
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Jones JM, Stone M, Sulaeman H, Fink RV, Dave H, Levy ME, Di Germanio C, Green V, Notari E, Saa P, Biggerstaff BJ, Strauss D, Kessler D, Vassallo R, Reik R, Rossmann S, Destree M, Nguyen KA, Sayers M, Lough C, Bougie DW, Ritter M, Latoni G, Weales B, Sime S, Gorlin J, Brown NE, Gould CV, Berney K, Benoit TJ, Miller MJ, Freeman D, Kartik D, Fry AM, Azziz-Baumgartner E, Hall AJ, MacNeil A, Gundlapalli AV, Basavaraju SV, Gerber SI, Patton ME, Custer B, Williamson P, Simmons G, Thornburg NJ, Kleinman S, Stramer SL, Opsomer J, Busch MP. Estimated US Infection- and Vaccine-Induced SARS-CoV-2 Seroprevalence Based on Blood Donations, July 2020-May 2021. JAMA 2021; 326:1400-1409. [PMID: 34473201 PMCID: PMC8414359 DOI: 10.1001/jama.2021.15161] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
IMPORTANCE People who have been infected with or vaccinated against SARS-CoV-2 have reduced risk of subsequent infection, but the proportion of people in the US with SARS-CoV-2 antibodies from infection or vaccination is uncertain. OBJECTIVE To estimate trends in SARS-CoV-2 seroprevalence related to infection and vaccination in the US population. DESIGN, SETTING, AND PARTICIPANTS In a repeated cross-sectional study conducted each month during July 2020 through May 2021, 17 blood collection organizations with blood donations from all 50 US states; Washington, DC; and Puerto Rico were organized into 66 study-specific regions, representing a catchment of 74% of the US population. For each study region, specimens from a median of approximately 2000 blood donors were selected and tested each month; a total of 1 594 363 specimens were initially selected and tested. The final date of blood donation collection was May 31, 2021. EXPOSURE Calendar time. MAIN OUTCOMES AND MEASURES Proportion of persons with detectable SARS-CoV-2 spike and nucleocapsid antibodies. Seroprevalence was weighted for demographic differences between the blood donor sample and general population. Infection-induced seroprevalence was defined as the prevalence of the population with both spike and nucleocapsid antibodies. Combined infection- and vaccination-induced seroprevalence was defined as the prevalence of the population with spike antibodies. The seroprevalence estimates were compared with cumulative COVID-19 case report incidence rates. RESULTS Among 1 443 519 specimens included, 733 052 (50.8%) were from women, 174 842 (12.1%) were from persons aged 16 to 29 years, 292 258 (20.2%) were from persons aged 65 years and older, 36 654 (2.5%) were from non-Hispanic Black persons, and 88 773 (6.1%) were from Hispanic persons. The overall infection-induced SARS-CoV-2 seroprevalence estimate increased from 3.5% (95% CI, 3.2%-3.8%) in July 2020 to 20.2% (95% CI, 19.9%-20.6%) in May 2021; the combined infection- and vaccination-induced seroprevalence estimate in May 2021 was 83.3% (95% CI, 82.9%-83.7%). By May 2021, 2.1 SARS-CoV-2 infections (95% CI, 2.0-2.1) per reported COVID-19 case were estimated to have occurred. CONCLUSIONS AND RELEVANCE Based on a sample of blood donations in the US from July 2020 through May 2021, vaccine- and infection-induced SARS-CoV-2 seroprevalence increased over time and varied by age, race and ethnicity, and geographic region. Despite weighting to adjust for demographic differences, these findings from a national sample of blood donors may not be representative of the entire US population.
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Affiliation(s)
- Jefferson M. Jones
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Mars Stone
- Vitalant Research Institute, San Francisco, California
| | | | | | - Honey Dave
- Vitalant Research Institute, San Francisco, California
| | | | | | | | - Edward Notari
- Scientific Affairs, American Red Cross, Rockville, Maryland
| | - Paula Saa
- Scientific Affairs, American Red Cross, Gaithersburg, Maryland
| | - Brad J. Biggerstaff
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | | | | | | | | | | | | | - Chris Lough
- LifeSouth Community Blood Centers, Gainesville, Florida
| | | | | | - Gerardo Latoni
- Banco de Sangre de Servicios Mutuos, San Juan, Puerto Rico
| | | | | | - Jed Gorlin
- Innovative Blood Resources, St Paul, Minnesota
| | - Nicole E. Brown
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Carolyn V. Gould
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kevin Berney
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Tina J. Benoit
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Maureen J. Miller
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Alicia M. Fry
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Aron J. Hall
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Adam MacNeil
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Adi V. Gundlapalli
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sridhar V. Basavaraju
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Susan I. Gerber
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Monica E. Patton
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Brian Custer
- Vitalant Research Institute, San Francisco, California
| | | | | | - Natalie J. Thornburg
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Steven Kleinman
- University of British Columbia, Vancouver, British Columbia, Canada
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Shokr A, Pacheco LGC, Thirumalaraju P, Kanakasabapathy MK, Gandhi J, Kartik D, Silva FSR, Erdogmus E, Kandula H, Luo S, Yu XG, Chung RT, Li JZ, Kuritzkes DR, Shafiee H. Mobile Health (mHealth) Viral Diagnostics Enabled with Adaptive Adversarial Learning. ACS Nano 2021; 15:665-673. [PMID: 33226787 PMCID: PMC8299938 DOI: 10.1021/acsnano.0c06807] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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] [Indexed: 05/04/2023]
Abstract
Deep-learning (DL)-based image processing has potential to revolutionize the use of smartphones in mobile health (mHealth) diagnostics of infectious diseases. However, the high variability in cellphone image data acquisition and the common need for large amounts of specialist-annotated images for traditional DL model training may preclude generalizability of smartphone-based diagnostics. Here, we employed adversarial neural networks with conditioning to develop an easily reconfigurable virus diagnostic platform that leverages a dataset of smartphone-taken microfluidic chip photos to rapidly generate image classifiers for different target pathogens on-demand. Adversarial learning was also used to augment this real image dataset by generating 16,000 realistic synthetic microchip images, through style generative adversarial networks (StyleGAN). We used this platform, termed smartphone-based pathogen detection resource multiplier using adversarial networks (SPyDERMAN), to accurately detect different intact viruses in clinical samples and to detect viral nucleic acids through integration with CRISPR diagnostics. We evaluated the performance of the system in detecting five different virus targets using 179 patient samples. The generalizability of the system was confirmed by rapid reconfiguration to detect SARS-CoV-2 antigens in nasal swab samples (n = 62) with 100% accuracy. Overall, the SPyDERMAN system may contribute to epidemic preparedness strategies by providing a platform for smartphone-based diagnostics that can be adapted to a given emerging viral agent within days of work.
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Affiliation(s)
- Ahmed Shokr
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Luis G C Pacheco
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Department of Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA 40110-100, Brazil
| | - Prudhvi Thirumalaraju
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Manoj Kumar Kanakasabapathy
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Jahnavi Gandhi
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Deeksha Kartik
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Filipe S R Silva
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Department of Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA 40110-100, Brazil
| | - Eda Erdogmus
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Hemanth Kandula
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Shenglin Luo
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Xu G Yu
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts 02129, United States
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Raymond T Chung
- Liver Center, Gastrointestinal Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
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