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Ganglberger W, Krishnamurthy PV, Quadri SA, Tesh RA, Bucklin AA, Adra N, Da Silva Cardoso M, Leone MJ, Hemmige A, Rajan S, Panneerselvam E, Paixao L, Higgins J, Ayub MA, Shao YP, Coughlin B, Sun H, Ye EM, Cash SS, Thompson BT, Akeju O, Kuller D, Thomas RJ, Westover MB. Sleep staging in the ICU with heart rate variability and breathing signals. An exploratory cross-sectional study using deep neural networks. Front Netw Physiol 2023; 3:1120390. [PMID: 36926545 PMCID: PMC10013021 DOI: 10.3389/fnetp.2023.1120390] [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] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023]
Abstract
Introduction: To measure sleep in the intensive care unit (ICU), full polysomnography is impractical, while activity monitoring and subjective assessments are severely confounded. However, sleep is an intensely networked state, and reflected in numerous signals. Here, we explore the feasibility of estimating conventional sleep indices in the ICU with heart rate variability (HRV) and respiration signals using artificial intelligence methods Methods: We used deep learning models to stage sleep with HRV (through electrocardiogram) and respiratory effort (through a wearable belt) signals in critically ill adult patients admitted to surgical and medical ICUs, and in age and sex-matched sleep laboratory patients Results: We studied 102 adult patients in the ICU across multiple days and nights, and 220 patients in a clinical sleep laboratory. We found that sleep stages predicted by HRV- and breathing-based models showed agreement in 60% of the ICU data and in 81% of the sleep laboratory data. In the ICU, deep NREM (N2 + N3) proportion of total sleep duration was reduced (ICU 39%, sleep laboratory 57%, p < 0.01), REM proportion showed heavy-tailed distribution, and the number of wake transitions per hour of sleep (median 3.6) was comparable to sleep laboratory patients with sleep-disordered breathing (median 3.9). Sleep in the ICU was also fragmented, with 38% of sleep occurring during daytime hours. Finally, patients in the ICU showed faster and less variable breathing patterns compared to sleep laboratory patients Conclusion: The cardiovascular and respiratory networks encode sleep state information, which, together with artificial intelligence methods, can be utilized to measure sleep state in the ICU.
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Affiliation(s)
- Wolfgang Ganglberger
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States.,Sleep and Health Zurich, University of Zurich, Zurich, Switzerland.,Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, United States
| | - Parimala Velpula Krishnamurthy
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Syed A Quadri
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Ryan A Tesh
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Abigail A Bucklin
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Noor Adra
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Madalena Da Silva Cardoso
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Michael J Leone
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Aashritha Hemmige
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Subapriya Rajan
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Ezhil Panneerselvam
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Luis Paixao
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Jasmine Higgins
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Muhammad Abubakar Ayub
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Yu-Ping Shao
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Brian Coughlin
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States
| | - Haoqi Sun
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States.,Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, United States
| | - Elissa M Ye
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States
| | - Sydney S Cash
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - B Taylor Thompson
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Oluwaseun Akeju
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, United States.,Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, United States
| | | | - Robert J Thomas
- Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States.,Beth Israel Deaconess Medical Center, Department of Medicine, Division of Pulmonary, Critical Care and Sleep, Boston, MA, United States
| | - M Brandon Westover
- Department of Neurology, Massachusetts General Hospital, MGH, Boston, MA, United States.,Clinical Data Animation Center (CDAC), Massachusetts General Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States.,Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, United States
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9
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Bonmatí LM, Miguel A, Suárez A, Aznar M, Beregi JP, Fournier L, Neri E, Laghi A, França M, Sardanelli F, Penzkofer T, Lambin P, Blanquer I, Menzel M, Seymour K, Figueiras S, Krischak K, Martínez R, Mirsky Y, Yang G, Alberich-Bayarri Á. CHAIMELEON Project: Creation of a Pan-European Repository of Health Imaging Data for the Development of AI-Powered Cancer Management Tools. Front Oncol 2022; 12:742701. [PMID: 35280732 PMCID: PMC8913333 DOI: 10.3389/fonc.2022.742701] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 07/16/2021] [Accepted: 01/28/2022] [Indexed: 12/13/2022] Open
Abstract
The CHAIMELEON project aims to set up a pan-European repository of health imaging data, tools and methodologies, with the ambition to set a standard and provide resources for future AI experimentation for cancer management. The project is a 4 year long, EU-funded project tackling some of the most ambitious research in the fields of biomedical imaging, artificial intelligence and cancer treatment, addressing the four types of cancer that currently have the highest prevalence worldwide: lung, breast, prostate and colorectal. To allow this, clinical partners and external collaborators will populate the repository with multimodality (MR, CT, PET/CT) imaging and related clinical data. Subsequently, AI developers will enable a multimodal analytical data engine facilitating the interpretation, extraction and exploitation of the information stored at the repository. The development and implementation of AI-powered pipelines will enable advancement towards automating data deidentification, curation, annotation, integrity securing and image harmonization. By the end of the project, the usability and performance of the repository as a tool fostering AI experimentation will be technically validated, including a validation subphase by world-class European AI developers, participating in Open Challenges to the AI Community. Upon successful validation of the repository, a set of selected AI tools will undergo early in-silico validation in observational clinical studies coordinated by leading experts in the partner hospitals. Tool performance will be assessed, including external independent validation on hallmark clinical decisions in response to some of the currently most important clinical end points in cancer. The project brings together a consortium of 18 European partners including hospitals, universities, R&D centers and private research companies, constituting an ecosystem of infrastructures, biobanks, AI/in-silico experimentation and cloud computing technologies in oncology.
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Affiliation(s)
- Luis Martí Bonmatí
- Medical Imaging Department, La Fe University and Polytechnic Hospital & Biomedical Imaging Research Group Grupo de Investigación Biomédica en Imagen (GIBI2) at La Fe University and Polytechnic Hospital and Health Research Institute, Valencia, Spain,*Correspondence: Luis Martí Bonmatí,
| | - Ana Miguel
- Medical Imaging Department, La Fe University and Polytechnic Hospital & Biomedical Imaging Research Group Grupo de Investigación Biomédica en Imagen (GIBI2) at La Fe University and Polytechnic Hospital and Health Research Institute, Valencia, Spain
| | | | | | | | - Laure Fournier
- Collège des enseignants en radiologie de France, Paris, France
| | - Emanuele Neri
- Diagnostic Radiology 3, Department of Translational Research, University of Pisa, Pisa, Italy
| | - Andrea Laghi
- Medicina Traslazionale e Oncologia, Sant Andrea Sapienza Rome, Rome, Italy
| | - Manuela França
- Department of Radiology, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Francesco Sardanelli
- Servizio di Diagnostica per Immagini, “Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Donato, Milanese, Italy
| | - Tobias Penzkofer
- Department of Radiology, CHARITÉ-Universitätsmedizin Berlin, Berlin, Germany
| | - Phillipe Lambin
- Department of Precision Medicine, Maastricht University, Maastricht, Netherlands
| | - Ignacio Blanquer
- Computing Science Department, Universitat Politècnica de València, València, Spain
| | - Marion I. Menzel
- GE Healthcare, München, Germany,Department of Physics, Technical University of Munich, Garching, Germany
| | | | | | - Katharina Krischak
- European Institute for Biomedical Imaging Research, EIBIR gemeinnützige GmbH, Vienna, Austria
| | - Ricard Martínez
- Departamento de Derecho Constitucional, Ciencia Política y Administración, Universitat de València, València, Spain
| | - Yisroel Mirsky
- Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Guang Yang
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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10
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Ensenyat-Mendez M, Llinàs-Arias P, Orozco JIJ, Íñiguez-Muñoz S, Salomon MP, Sesé B, DiNome ML, Marzese DM. Current Triple-Negative Breast Cancer Subtypes: Dissecting the Most Aggressive Form of Breast Cancer. Front Oncol 2021; 11:681476. [PMID: 34221999 PMCID: PMC8242253 DOI: 10.3389/fonc.2021.681476] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly heterogeneous disease defined by the absence of estrogen receptor (ER) and progesterone receptor (PR) expression, and human epidermal growth factor receptor 2 (HER2) overexpression that lacks targeted treatments, leading to dismal clinical outcomes. Thus, better stratification systems that reflect intrinsic and clinically useful differences between TNBC tumors will sharpen the treatment approaches and improve clinical outcomes. The lack of a rational classification system for TNBC also impacts current and emerging therapeutic alternatives. In the past years, several new methodologies to stratify TNBC have arisen thanks to the implementation of microarray technology, high-throughput sequencing, and bioinformatic methods, exponentially increasing the amount of genomic, epigenomic, transcriptomic, and proteomic information available. Thus, new TNBC subtypes are being characterized with the promise to advance the treatment of this challenging disease. However, the diverse nature of the molecular data, the poor integration between the various methods, and the lack of cost-effective methods for systematic classification have hampered the widespread implementation of these promising developments. However, the advent of artificial intelligence applied to translational oncology promises to bring light into definitive TNBC subtypes. This review provides a comprehensive summary of the available classification strategies. It includes evaluating the overlap between the molecular, immunohistochemical, and clinical characteristics between these approaches and a perspective about the increasing applications of artificial intelligence to identify definitive and clinically relevant TNBC subtypes.
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Affiliation(s)
- Miquel Ensenyat-Mendez
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Pere Llinàs-Arias
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, United States
| | - Sandra Íñiguez-Muñoz
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Matthew P Salomon
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Borja Sesé
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Maggie L DiNome
- Department of Surgery, David Geffen School of Medicine, University California Los Angeles (UCLA), Los Angeles, CA, United States
| | - Diego M Marzese
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
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11
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Pinochet P, Eude F, Becker S, Shah V, Sibille L, Toledano MN, Modzelewski R, Vera P, Decazes P. Evaluation of an Automatic Classification Algorithm Using Convolutional Neural Networks in Oncological Positron Emission Tomography. Front Med (Lausanne) 2021; 8:628179. [PMID: 33718406 PMCID: PMC7953145 DOI: 10.3389/fmed.2021.628179] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/25/2021] [Indexed: 12/11/2022] Open
Abstract
Introduction: Our aim was to evaluate the performance in clinical research and in clinical routine of a research prototype, called positron emission tomography (PET) Assisted Reporting System (PARS) (Siemens Healthineers) and based on a convolutional neural network (CNN), which is designed to detect suspected cancer sites in fluorine-18 fluorodeoxyglucose (18F-FDG) PET/computed tomography (CT). Method: We retrospectively studied two cohorts of patients. The first cohort consisted of research-based patients who underwent PET scans as part of the initial workup for diffuse large B-cell lymphoma (DLBCL). The second cohort consisted of patients who underwent PET scans as part of the evaluation of miscellaneous cancers in clinical routine. In both cohorts, we assessed the correlation between manually and automatically segmented total metabolic tumor volumes (TMTVs), and the overlap between both segmentations (Dice score). For the research cohort, we also compared the prognostic value for progression-free survival (PFS) and overall survival (OS) of manually and automatically obtained TMTVs. Results: For the first cohort (research cohort), data from 119 patients were retrospectively analyzed. The median Dice score between automatic and manual segmentations was 0.65. The intraclass correlation coefficient between automatically and manually obtained TMTVs was 0.68. Both TMTV results were predictive of PFS (hazard ratio: 2.1 and 3.3 for automatically based and manually based TMTVs, respectively) and OS (hazard ratio: 2.4 and 3.1 for automatically based and manually based TMTVs, respectively). For the second cohort (routine cohort), data from 430 patients were retrospectively analyzed. The median Dice score between automatic and manual segmentations was 0.48. The intraclass correlation coefficient between automatically and manually obtained TMTVs was 0.61. Conclusion: The TMTVs determined for the research cohort remain predictive of total and PFS for DLBCL. However, the segmentations and TMTVs determined automatically by the algorithm need to be verified and, sometimes, corrected to be similar to the manual segmentation.
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Affiliation(s)
- Pierre Pinochet
- Department of Nuclear Medicine, Henri Becquerel Cancer Center, Rouen, France
| | - Florian Eude
- Department of Nuclear Medicine, Henri Becquerel Cancer Center, Rouen, France
| | - Stéphanie Becker
- Department of Nuclear Medicine, Henri Becquerel Cancer Center, Rouen, France.,LITIS Quantif-EA 4108, University of Rouen, Rouen, France
| | - Vijay Shah
- Siemens Medical Solutions USA, Inc., Knoxville, TN, United States
| | - Ludovic Sibille
- Siemens Medical Solutions USA, Inc., Knoxville, TN, United States
| | | | - Romain Modzelewski
- Department of Nuclear Medicine, Henri Becquerel Cancer Center, Rouen, France.,LITIS Quantif-EA 4108, University of Rouen, Rouen, France
| | - Pierre Vera
- Department of Nuclear Medicine, Henri Becquerel Cancer Center, Rouen, France.,LITIS Quantif-EA 4108, University of Rouen, Rouen, France
| | - Pierre Decazes
- Department of Nuclear Medicine, Henri Becquerel Cancer Center, Rouen, France.,LITIS Quantif-EA 4108, University of Rouen, Rouen, France
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