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Article ; Online: Predicting Progression to Septic Shock in the Emergency Department Using an Externally Generalizable Machine-Learning Algorithm.

Wardi, Gabriel / Carlile, Morgan / Holder, Andre / Shashikumar, Supreeth / Hayden, Stephen R / Nemati, Shamim

2021 Volume 77, Issue 4, Page(s) 395–406

Abstract: Study objective: Machine-learning algorithms allow improved prediction of sepsis syndromes in the emergency department (ED), using data from electronic medical records. Transfer learning, a new subfield of machine learning, allows generalizability of an ...

Abstract	Study objective: Machine-learning algorithms allow improved prediction of sepsis syndromes in the emergency department (ED), using data from electronic medical records. Transfer learning, a new subfield of machine learning, allows generalizability of an algorithm across clinical sites. We aim to validate the Artificial Intelligence Sepsis Expert for the prediction of delayed septic shock in a cohort of patients treated in the ED and demonstrate the feasibility of transfer learning to improve external validity at a second site. Methods: This was an observational cohort study using data from greater than 180,000 patients from 2 academic medical centers between 2014 and 2019, using multiple definitions of sepsis. The Artificial Intelligence Sepsis Expert algorithm was trained with 40 input variables at the development site to predict delayed septic shock (occurring greater than 4 hours after ED triage) at various prediction windows. We then validated the algorithm at a second site, using transfer learning to demonstrate generalizability of the algorithm. Results: We identified 9,354 patients with severe sepsis, of whom 723 developed septic shock at least 4 hours after triage. The Artificial Intelligence Sepsis Expert algorithm demonstrated excellent area under the receiver operating characteristic curve (>0.8) at 8 and 12 hours for the prediction of delayed septic shock. Transfer learning significantly improved the test characteristics of the Artificial Intelligence Sepsis Expert algorithm and yielded comparable performance at the validation site. Conclusion: The Artificial Intelligence Sepsis Expert algorithm accurately predicted the development of delayed septic shock. The use of transfer learning allowed significantly improved external validity and generalizability at a second site. Future prospective studies are indicated to evaluate the clinical utility of this model.
MeSH term(s)	Aged ; Artificial Intelligence ; Cohort Studies ; Emergency Service, Hospital ; Female ; Humans ; Male ; Middle Aged ; Retrospective Studies ; Risk Factors ; Shock, Septic/diagnosis
Language	English
Publishing date	2021-01-15
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Observational Study ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Validation Study
ZDB-ID	603080-4
ISSN	1097-6760 ; 0196-0644
ISSN (online)	1097-6760
ISSN	0196-0644
DOI	10.1016/j.annemergmed.2020.11.007
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Article: Hypoxia signatures in closed-circuit rebreather divers.

Popa, Daniel / Kutz, Craig / Carlile, Morgan / Brett, Kaighley / Moya, Esteban A / Powell, Frank / Witucki, Peter / Sadler, Richard / Sadler, Charlotte

Diving and hyperbaric medicine

2022 Volume 52, Issue 4, Page(s) 237–244

Abstract: Introduction: Faults or errors during use of closed-circuit rebreathers (CCRs) can cause hypoxia. Military aviators face a similar risk of hypoxia and undergo awareness training to determine their 'hypoxia signature', a personalised, reproducible set of ...

Abstract	Introduction: Faults or errors during use of closed-circuit rebreathers (CCRs) can cause hypoxia. Military aviators face a similar risk of hypoxia and undergo awareness training to determine their 'hypoxia signature', a personalised, reproducible set of symptoms. We aimed to establish a hypoxia signature among divers, and to investigate their ability to detect hypoxia and self-rescue while cognitively overloaded. Methods: Eight CCR divers and 12 scuba divers underwent an initial unblinded hypoxia exposure followed by three trials; a second hypoxic trial and two normoxic trials in randomised order. Hypoxia was induced by breathing on a CCR with no oxygen supply. Subjects pedalled on a cycle ergometer while playing a neurocognitive computer game to simulate real world task loading. Subjects identified hypoxia symptoms by pointing to a board listing common hypoxia symptoms, and were instructed to perform a 'bailout' procedure to mimic self-rescue if they perceived hypoxia. Divers were prompted to bailout if peripheral oxygen saturation fell to 75%, or after six minutes during normoxic trials. Subsequently we interviewed subjects to determine their ability to distinguish hypoxia from normoxia. Results: Ninety-five percent of subjects (19/20) showed agreement between unblinded and blinded hypoxia symptoms. Subjects correctly identified the gas mixture in 85% of the trials. During unblinded hypoxia, only 25% (5/20) of subjects performed unprompted bailout. Fifty-five percent of subjects (11/20) correctly performed the bailout but only when prompted, while 15% (3/20) were unable to bailout despite prompting. During blinded hypoxia 45% of subjects (9/20) performed the bailout unprompted while 15% (3/20) remained unable to bailout despite prompting. Conclusions: Although our data support a normobaric hypoxia signature among both CCR and scuba divers under experimental conditions, most subjects were unable to recognise hypoxia in real time and perform a self-rescue unprompted, although this improved in the second hypoxia trial. These results do not support hypoxia exposure training for CCR divers.
Language	English
Publishing date	2022-12-16
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2237920-4
ISSN	1833-3516
ISSN	1833-3516
DOI	10.28920/dhm52.4.237-244
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Article ; Online: Paternal low protein diet perturbs inter-generational metabolic homeostasis in a tissue-specific manner in mice.

Morgan, Hannah L / Furse, Samuel / Dias, Irundika H K / Shabir, Kiran / Castellanos, Marcos / Khan, Iqbal / May, Sean T / Holmes, Nadine / Carlile, Matthew / Sang, Fei / Wright, Victoria / Koulman, Albert / Watkins, Adam J

Communications biology

2022 Volume 5, Issue 1, Page(s) 929

Abstract: The underlying mechanisms driving paternally-programmed metabolic disease in offspring remain poorly defined. We fed male C57BL/6 mice either a control normal protein diet (NPD; 18% protein) or an isocaloric low protein diet (LPD; 9% protein) for a ... ...

Abstract	The underlying mechanisms driving paternally-programmed metabolic disease in offspring remain poorly defined. We fed male C57BL/6 mice either a control normal protein diet (NPD; 18% protein) or an isocaloric low protein diet (LPD; 9% protein) for a minimum of 8 weeks. Using artificial insemination, in combination with vasectomised male mating, we generated offspring using either NPD or LPD sperm but in the presence of NPD or LPD seminal plasma. Offspring from either LPD sperm or seminal fluid display elevated body weight and tissue dyslipidaemia from just 3 weeks of age. These changes become more pronounced in adulthood, occurring in conjunction with altered hepatic metabolic and inflammatory pathway gene expression. Second generation offspring also display differential tissue lipid abundance, with profiles similar to those of first generation adults. These findings demonstrate that offspring metabolic homeostasis is perturbed in response to a suboptimal paternal diet with the effects still evident within a second generation.
MeSH term(s)	Animals ; Diet, Protein-Restricted ; Fathers ; Homeostasis ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Semen
Language	English
Publishing date	2022-09-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-03914-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Leveraging Remote Research Associates During a Pandemic.

Cronin, Alexandrea O / Carlile, Morgan A / Dameff, Christian J / Coyne, Christopher J / Castillo, Edward M

The western journal of emergency medicine

2020 Volume 21, Issue 5, Page(s) 1114–1117

Abstract: Introduction: The coronavirus disease 2019 (COVID-19) pandemic has seriously impacted clinical research operations in academic medical centers due to social distancing measures and stay-at-home orders. The purpose of this paper is to describe the ... ...

Abstract	Introduction: The coronavirus disease 2019 (COVID-19) pandemic has seriously impacted clinical research operations in academic medical centers due to social distancing measures and stay-at-home orders. The purpose of this paper is to describe the implementation of a program to continue clinical research based out of an emergency department (ED) using remote research associates (RA). Methods: Remote RAs were trained and granted remote access to the electronic health record (EHR) by the health system's core information technology team. Upon gaining access, remote RAs used a dual-authentication process to gain access to a host-based, firewall-protected virtual network where the EHR could be accessed to continue screening and enrollment for ongoing studies. Study training for screening and enrollment was also provided to ensure study continuity. Results: With constant support and guidance available to establish this EHR access pathway, the remote RAs were able to gain access relatively independently and without major technical troubleshooting. Each remote RA was granted access and trained on studies within one week and self-reported a high degree of program satisfaction, EHR access ease, and study protocol comfort through informal evaluation surveys. Conclusions: In response to the COVID-19 pandemic, we virtualized a clinical research program to continue important ED-based studies.
MeSH term(s)	Academic Medical Centers/organization & administration ; Betacoronavirus ; Biomedical Research/organization & administration ; COVID-19 ; California ; Coronavirus Infections/prevention & control ; Electronic Health Records ; Emergency Service, Hospital/organization & administration ; Humans ; Medical Informatics ; Pandemics/prevention & control ; Pneumonia, Viral/prevention & control ; Program Development ; Research Personnel/organization & administration ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-07-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2375700-0
ISSN	1936-9018 ; 1936-900X
ISSN (online)	1936-9018
ISSN	1936-900X
DOI	10.5811/westjem.2020.6.48043
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Predicting progression to septic shock in the emergency department using an externally generalizable machine learning algorithm.

Wardi, Gabriel / Carlile, Morgan / Holder, Andre / Shashikumar, Supreeth / Hayden, Stephen R / Nemati, Shamim

medRxiv : the preprint server for health sciences

2020

Abstract: Objective: Machine-learning (ML) algorithms allow for improved prediction of sepsis syndromes in the ED using data from electronic medical records. Transfer learning, a new subfield of ML, allows for generalizability of an algorithm across clinical ... ...

Abstract	Objective: Machine-learning (ML) algorithms allow for improved prediction of sepsis syndromes in the ED using data from electronic medical records. Transfer learning, a new subfield of ML, allows for generalizability of an algorithm across clinical sites. We aimed to validate the Artificial Intelligence Sepsis Expert (AISE) for the prediction of delayed septic shock in a cohort of patients treated in the ED and demonstrate the feasibility of transfer learning to improve external validity at a second site. Methods: Observational cohort study utilizing data from over 180,000 patients from two academic medical centers between 2014 and 2019 using multiple definitions of sepsis. The AISE algorithm was trained using 40 input variables at the development site to predict delayed septic shock (occurring greater than 4 hours after ED triage) at varying prediction windows. We then validated the AISE algorithm at a second site using transfer learning to demonstrate generalizability of the algorithm. Results: We identified 9354 patients with severe sepsis of which 723 developed septic shock at least 4 hours after triage. The AISE algorithm demonstrated excellent area under the receiver operating curve (>0.8) at 8 and 12 hours for the prediction of delayed septic shock. Transfer learning significantly improved the test characteristics of the AISE algorithm and yielded comparable performance at the validation site. Conclusions: The AISE algorithm accurately predicted the development of delayed septic shock. The use of transfer learning allowed for significantly improved external validity and generalizability at a second site. Future prospective studies are indicated to evaluate the clinical utility of this model.
Language	English
Publishing date	2020-11-04
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.11.02.20224931
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Deployment of artificial intelligence for radiographic diagnosis of COVID-19 pneumonia in the emergency department.

Carlile, Morgan / Hurt, Brian / Hsiao, Albert / Hogarth, Michael / Longhurst, Christopher A / Dameff, Christian

Journal of the American College of Emergency Physicians open

2020 Volume 1, Issue 6, Page(s) 1459–1464

Abstract: Objective: The coronavirus disease 2019 pandemic has inspired new innovations in diagnosing, treating, and dispositioning patients during high census conditions with constrained resources. Our objective is to describe first experiences of physician ... ...

Abstract	Objective: The coronavirus disease 2019 pandemic has inspired new innovations in diagnosing, treating, and dispositioning patients during high census conditions with constrained resources. Our objective is to describe first experiences of physician interaction with a novel artificial intelligence (AI) algorithm designed to enhance physician abilities to identify ground-glass opacities and consolidation on chest radiographs. Methods: During the first wave of the pandemic, we deployed a previously developed and validated deep-learning AI algorithm for assisted interpretation of chest radiographs for use by physicians at an academic health system in Southern California. The algorithm overlays radiographs with "heat" maps that indicate pneumonia probability alongside standard chest radiographs at the point of care. Physicians were surveyed in real time regarding ease of use and impact on clinical decisionmaking. Results: Of the 5125 total visits and 1960 chest radiographs obtained in the emergency department (ED) during the study period, 1855 were analyzed by the algorithm. Among these, emergency physicians were surveyed for their experiences on 202 radiographs. Overall, 86% either strongly agreed or somewhat agreed that the intervention was easy to use in their workflow. Of the respondents, 20% reported that the algorithm impacted clinical decisionmaking. Conclusions: To our knowledge, this is the first published literature evaluating the impact of medical imaging AI on clinical decisionmaking in the emergency department setting. Urgent deployment of a previously validated AI algorithm clinically was easy to use and was found to have an impact on clinical decision making during the predicted surge period of a global pandemic.
Language	English
Publishing date	2020-11-05
Publishing country	United States
Document type	Journal Article
ISSN	2688-1152
ISSN (online)	2688-1152
DOI	10.1002/emp2.12297
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Leveraging Remote Research Associates During a Pandemic

Cronin, Alexandrea O. / Carlile, Morgan A. / Dameff, Christian J. / Coyne, Christopher J. / Castillo, Edward M.

Western Journal of Emergency Medicine: Integrating Emergency Care with Population Health, vol 21, iss 5

2020

Abstract	Introduction: The coronavirus disease 2019 (COVID-19) pandemic has seriously impacted clinical research operations in academic medical centers due to social distancing measures and stay-at-home orders. The purpose of this paper is to describe the implementation of a program to continue clinical research based out of an emergency department (ED) using remote research associates (RA).Methods: Remote RAs were trained and granted remote access to the electronic health record (EHR) by the health system’s core information technology team. Upon gaining access, remote RAs used a dual-authentication process to gain access to a host-based, firewall-protected virtual network where the EHR could be accessed to continue screening and enrollment for ongoing studies. Study training for screening and enrollment was also provided to ensure study continuity.Results: With constant support and guidance available to establish this EHR access pathway, the remote RAs were able to gain access relatively independently and without major technical troubleshooting. Each remote RA was granted access and trained on studies within one week and self-reported a high degree of program satisfaction, EHR access ease, and study protocol comfort through informal evaluation surveys.Conclusions: In response to the COVID-19 pandemic, we virtualized a clinical research program to continue important ED-based studies.
Keywords	Virtual research associates ; electronic health record ; clinical research ; COVID-19 ; corona virus ; covid19
Publishing date	2020-01-01
Publisher	eScholarship, University of California
Publishing country	us
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Leveraging Remote Research Associates During a Pandemic

Alexandrea O. Cronin / Morgan A. Carlile / Christian J. Dameff / Christopher J. Coyne / Edward M. Castillo

Western Journal of Emergency Medicine, Vol 21, Iss

2020 Volume 5

Abstract	Introduction: The coronavirus disease 2019 (COVID-19) pandemic has seriously impacted clinical research operations in academic medical centers due to social distancing measures and stay-at-home orders. The purpose of this paper is to describe the implementation of a program to continue clinical research based out of an emergency department (ED) using remote research associates (RA). Methods: Remote RAs were trained and granted remote access to the electronic health record (EHR) by the health system’s core information technology team. Upon gaining access, remote RAs used a dual-authentication process to gain access to a host-based, firewall-protected virtual network where the EHR could be accessed to continue screening and enrollment for ongoing studies. Study training for screening and enrollment was also provided to ensure study continuity. Results: With constant support and guidance available to establish this EHR access pathway, the remote RAs were able to gain access relatively independently and without major technical troubleshooting. Each remote RA was granted access and trained on studies within one week and self-reported a high degree of program satisfaction, EHR access ease, and study protocol comfort through informal evaluation surveys. Conclusions: In response to the COVID-19 pandemic, we virtualized a clinical research program to continue important ED-based studies.
Keywords	Medicine ; R ; Medical emergencies. Critical care. Intensive care. First aid ; RC86-88.9
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	eScholarship Publishing, University of California
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Development and Prospective Validation of a Deep Learning Algorithm for Predicting Need for Mechanical Ventilation.

Shashikumar, Supreeth P / Wardi, Gabriel / Paul, Paulina / Carlile, Morgan / Brenner, Laura N / Hibbert, Kathryn A / North, Crystal M / Mukerji, Shibani S / Robbins, Gregory K / Shao, Yu-Ping / Westover, M Brandon / Nemati, Shamim / Malhotra, Atul

Chest

2020 Volume 159, Issue 6, Page(s) 2264–2273

Abstract: Background: Objective and early identification of hospitalized patients, and particularly those with novel coronavirus disease 2019 (COVID-19), who may require mechanical ventilation (MV) may aid in delivering timely treatment.: Research question: ... ...

Abstract	Background: Objective and early identification of hospitalized patients, and particularly those with novel coronavirus disease 2019 (COVID-19), who may require mechanical ventilation (MV) may aid in delivering timely treatment. Research question: Can a transparent deep learning (DL) model predict the need for MV in hospitalized patients and those with COVID-19 up to 24 h in advance? Study design and methods: We trained and externally validated a transparent DL algorithm to predict the future need for MV in hospitalized patients, including those with COVID-19, using commonly available data in electronic health records. Additionally, commonly used clinical criteria (heart rate, oxygen saturation, respiratory rate, Fio Results: We obtained data from more than 30,000 ICU patients (including more than 700 patients with COVID-19) from two academic medical centers. The performance of the model with a 24-h prediction horizon at the development and validation sites was comparable (AUC, 0.895 vs 0.882, respectively), providing significant improvement over traditional clinical criteria (P < .001). Prospective validation of the algorithm among patients with COVID-19 yielded AUCs in the range of 0.918 to 0.943. Interpretation: A transparent deep learning algorithm improves on traditional clinical criteria to predict the need for MV in hospitalized patients, including in those with COVID-19. Such an algorithm may help clinicians to optimize timing of tracheal intubation, to allocate resources and staff better, and to improve patient care.
MeSH term(s)	Aged ; COVID-19/complications ; COVID-19/therapy ; Critical Care ; Deep Learning ; Female ; Health Services Needs and Demand ; Hospitalization ; Humans ; Intubation, Intratracheal ; Male ; Middle Aged ; Predictive Value of Tests ; Prospective Studies ; ROC Curve ; Respiration, Artificial
Language	English
Publishing date	2020-12-17
Publishing country	United States
Document type	Journal Article ; Observational Study ; Research Support, N.I.H., Extramural
ZDB-ID	1032552-9
ISSN	1931-3543 ; 0012-3692
ISSN (online)	1931-3543
ISSN	0012-3692
DOI	10.1016/j.chest.2020.12.009
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Article: Development and Prospective Validation of a Transparent Deep Learning Algorithm for Predicting Need for Mechanical Ventilation.

Shashikumar, Supreeth P / Wardi, Gabriel / Paul, Paulina / Carlile, Morgan / Brenner, Laura N / Hibbert, Kathryn A / North, Crystal M / Mukerji, Shibani / Robbins, Gregory / Shao, Yu-Ping / Malhotra, Atul / Westover, Brandon / Nemati, Shamim

medRxiv : the preprint server for health sciences

2020

Abstract: Importance: Objective and early identification of hospitalized patients, and particularly those with novel coronavirus disease 2019 (COVID-19), who may require mechanical ventilation is of great importance and may aid in delivering timely treatment.: ... ...

Abstract	Importance: Objective and early identification of hospitalized patients, and particularly those with novel coronavirus disease 2019 (COVID-19), who may require mechanical ventilation is of great importance and may aid in delivering timely treatment. Objective: To develop, externally validate and prospectively test a transparent deep learning algorithm for predicting 24 hours in advance the need for mechanical ventilation in hospitalized patients and those with COVID-19. Design: Observational cohort study SETTING: Two academic medical centers from January 01, 2016 to December 31, 2019 (Retrospective cohorts) and February 10, 2020 to May 4, 2020 (Prospective cohorts). Participants: Over 31,000 admissions to the intensive care units (ICUs) at two hospitals. Additionally, 777 patients with COVID-19 patients were used for prospective validation. Patients who were placed on mechanical ventilation within four hours of their admission were excluded. MAIN OUTCOME(S) and MEASURE(S): Electronic health record (EHR) data were extracted on an hourly basis, and a set of 40 features were calculated and passed to an interpretable deep-learning algorithm to predict the future need for mechanical ventilation 24 hours in advance. Additionally, commonly used clinical criteria (based on heart rate, oxygen saturation, respiratory rate, FiO2 and pH) was used to assess future need for mechanical ventilation. Performance of the algorithms were evaluated using the area under receiver-operating characteristic curve (AUC), sensitivity, specificity and positive predictive value. Results: After applying exclusion criteria, the external validation cohort included 3,888 general ICU and 402 COVID-19 patients. The performance of the model (AUC) with a 24-hour prediction horizon at the validation site was 0.882 for the general ICU population and 0.918 for patients with COVID-19. In comparison, commonly used clinical criteria and the ROX score achieved AUCs in the range of 0.773 - 0.782 and 0.768 - 0.810 for the general ICU population and patients with COVID-19, respectively. Conclusions and relevance: A generalizable and transparent deep-learning algorithm improves on traditional clinical criteria to predict the need for mechanical ventilation in hospitalized patients, including those with COVID-19. Such an algorithm may help clinicians with optimizing timing of tracheal intubation, better allocation of mechanical ventilation resources and staff, and improve patient care.
Keywords	covid19
Language	English
Publishing date	2020-06-03
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.05.30.20118109
Database	MEDical Literature Analysis and Retrieval System OnLINE

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