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1.
Bioengineering (Basel) ; 11(6)2024 Jun 19.
Article in English | MEDLINE | ID: mdl-38927862

ABSTRACT

The decision to extubate patients on invasive mechanical ventilation is critical; however, clinician performance in identifying patients to liberate from the ventilator is poor. Machine Learning-based predictors using tabular data have been developed; however, these fail to capture the wide spectrum of data available. Here, we develop and validate a deep learning-based model using routinely collected chest X-rays to predict the outcome of attempted extubation. We included 2288 serial patients admitted to the Medical ICU at an urban academic medical center, who underwent invasive mechanical ventilation, with at least one intubated CXR, and a documented extubation attempt. The last CXR before extubation for each patient was taken and split 79/21 for training/testing sets, then transfer learning with k-fold cross-validation was used on a pre-trained ResNet50 deep learning architecture. The top three models were ensembled to form a final classifier. The Grad-CAM technique was used to visualize image regions driving predictions. The model achieved an AUC of 0.66, AUPRC of 0.94, sensitivity of 0.62, and specificity of 0.60. The model performance was improved compared to the Rapid Shallow Breathing Index (AUC 0.61) and the only identified previous study in this domain (AUC 0.55), but significant room for improvement and experimentation remains.

2.
Crit Care Med ; 52(7): 1007-1020, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38380992

ABSTRACT

OBJECTIVES: Machine learning algorithms can outperform older methods in predicting clinical deterioration, but rigorous prospective data on their real-world efficacy are limited. We hypothesized that real-time machine learning generated alerts sent directly to front-line providers would reduce escalations. DESIGN: Single-center prospective pragmatic nonrandomized clustered clinical trial. SETTING: Academic tertiary care medical center. PATIENTS: Adult patients admitted to four medical-surgical units. Assignment to intervention or control arms was determined by initial unit admission. INTERVENTIONS: Real-time alerts stratified according to predicted likelihood of deterioration sent either to the primary team or directly to the rapid response team (RRT). Clinical care and interventions were at the providers' discretion. For the control units, alerts were generated but not sent, and standard RRT activation criteria were used. MEASUREMENTS AND MAIN RESULTS: The primary outcome was the rate of escalation per 1000 patient bed days. Secondary outcomes included the frequency of orders for fluids, medications, and diagnostic tests, and combined in-hospital and 30-day mortality. Propensity score modeling with stabilized inverse probability of treatment weight (IPTW) was used to account for differences between groups. Data from 2740 patients enrolled between July 2019 and March 2020 were analyzed (1488 intervention, 1252 control). Average age was 66.3 years and 1428 participants (52%) were female. The rate of escalation was 12.3 vs. 11.3 per 1000 patient bed days (difference, 1.0; 95% CI, -2.8 to 4.7) and IPTW adjusted incidence rate ratio 1.43 (95% CI, 1.16-1.78; p < 0.001). Patients in the intervention group were more likely to receive cardiovascular medication orders (16.1% vs. 11.3%; 4.7%; 95% CI, 2.1-7.4%) and IPTW adjusted relative risk (RR) (1.74; 95% CI, 1.39-2.18; p < 0.001). Combined in-hospital and 30-day-mortality was lower in the intervention group (7% vs. 9.3%; -2.4%; 95% CI, -4.5% to -0.2%) and IPTW adjusted RR (0.76; 95% CI, 0.58-0.99; p = 0.045). CONCLUSIONS: Real-time machine learning alerts do not reduce the rate of escalation but may reduce mortality.


Subject(s)
Clinical Deterioration , Machine Learning , Humans , Female , Male , Prospective Studies , Middle Aged , Aged , Hospital Rapid Response Team/organization & administration , Hospital Rapid Response Team/statistics & numerical data , Hospital Mortality
4.
Obes Sci Pract ; 8(4): 474-482, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35949284

ABSTRACT

Objectives: Hospitalized patients with severe obesity require adapted hospital management. The aim of this study was to evaluate a machine learning model to predict in-hospital mortality among this population. Methods: Data of unselected consecutive emergency department admissions of hospitalized patients with severe obesity (BMI ≥ 40 kg/m2) was analyzed. Data was retrieved from five hospitals from the Mount Sinai health system, New York. The study time frame was between January 2011 and December 2019. Data was used to train a gradient-boosting machine learning model to identify in-hospital mortality. The model was trained and evaluated based on the data from four hospitals and externally validated on held-out data from the fifth hospital. Results: A total of 14,078 hospital admissions of inpatients with severe obesity were included. The in-hospital mortality rate was 297/14,078 (2.1%). In univariate analysis, albumin (area under the curve [AUC] = 0.77), blood urea nitrogen (AUC = 0.76), acuity level (AUC = 0.73), lactate (AUC = 0.72), and chief complaint (AUC = 0.72) were the best single predictors. For Youden's index, the model had a sensitivity of 0.77 (95% CI: 0.67-0.86) with a false positive rate of 1:9. Conclusion: A machine learning model trained on clinical measures provides proof of concept performance in predicting mortality in patients with severe obesity. This implies that such models may help to adopt specific decision support tools for this population.

6.
BMC Endocr Disord ; 22(1): 13, 2022 Jan 06.
Article in English | MEDLINE | ID: mdl-34991575

ABSTRACT

BACKGROUND: Research regarding the association between severe obesity and in-hospital mortality is inconsistent. We evaluated the impact of body mass index (BMI) levels on mortality in the medical wards. The analysis was performed separately before and during the COVID-19 pandemic. METHODS: We retrospectively retrieved data of adult patients admitted to the medical wards at the Mount Sinai Health System in New York City. The study was conducted between January 1, 2011, to March 23, 2021. Patients were divided into two sub-cohorts: pre-COVID-19 and during-COVID-19. Patients were then clustered into groups based on BMI ranges. A multivariate logistic regression analysis compared the mortality rate among the BMI groups, before and during the pandemic. RESULTS: Overall, 179,288 patients were admitted to the medical wards and had a recorded BMI measurement. 149,098 were admitted before the COVID-19 pandemic and 30,190 during the pandemic. Pre-pandemic, multivariate analysis showed a "J curve" between BMI and mortality. Severe obesity (BMI > 40) had an aOR of 0.8 (95% CI:0.7-1.0, p = 0.018) compared to the normal BMI group. In contrast, during the pandemic, the analysis showed a "U curve" between BMI and mortality. Severe obesity had an aOR of 1.7 (95% CI:1.3-2.4, p < 0.001) compared to the normal BMI group. CONCLUSIONS: Medical ward patients with severe obesity have a lower risk for mortality compared to patients with normal BMI. However, this does not apply during COVID-19, where obesity was a leading risk factor for mortality in the medical wards. It is important for the internal medicine physician to understand the intricacies of the association between obesity and medical ward mortality.


Subject(s)
Body Mass Index , COVID-19/mortality , Hospital Mortality/trends , Hospitalization/statistics & numerical data , Obesity/physiopathology , SARS-CoV-2/isolation & purification , Aged , COVID-19/epidemiology , COVID-19/pathology , COVID-19/virology , Case-Control Studies , Female , Humans , Male , Middle Aged , New York City/epidemiology , Prognosis , Retrospective Studies , Risk Factors , Survival Rate
7.
BMJ Open ; 11(10): e050216, 2021 10 27.
Article in English | MEDLINE | ID: mdl-34706952

ABSTRACT

OBJECTIVE: Hypoalbuminaemia is an important prognostic factor. It may be associated with poor nutritional states, chronic heart and kidney disease, long-standing infection and cancer. Hypotension is a hallmark of circulatory failure. We evaluated hypoalbuminaemia and hypotension synergism as predictor of in-hospital mortality and intensive care unit (ICU) admission. DESIGN: We retrospectively analysed emergency department (ED) visits from January 2011 to December 2019. SETTING: Data were retrieved from five Mount Sinai health system hospitals, New York. PARTICIPANTS: We included consecutive ED patients ≥18 years with albumin measurements. PRIMARY AND SECONDARY OUTCOME MEASURES: Clinical outcomes were in-hospital mortality and ICU admission. The rates of these outcomes were stratified by systolic blood pressure (SBP) (<90 vs ≥90 mm Hg) and albumin levels. Variables included demographics, presenting vital signs, comorbidities (measured as ICD codes) and other common blood tests. Multivariable logistic regression models analysed the adjusted OR of different levels of albumin and SBP for predicting ICU admission and in-hospital mortality. The models were adjusted for demographics, vital signs, comorbidities and common laboratory results. Patients with albumin 3.5-4.5 g/dL and SBP ≥90 mm Hg were used as reference. RESULTS: The cohort included 402 123 ED arrivals (27.9% of total adult ED visits). The rates of in-hospital mortality, ICU admission and overall admission were 1.7%, 8.4% and 47.1%, respectively. For SBP <90 mm Hg and albumin <2.5 g/dL, mortality and ICU admission rates were 34.0% and 40.6%, respectively; for SBP <90 mm Hg and albumin ≥2.5 g/dL 8.2% and 24.1%, respectively; for SBP ≥90 mm Hg and albumin <2.5 g/dL 11.4% and 18.6%, respectively; for SBP ≥90 mm Hg and albumin 3.5-4.5 g/dL 0.5% and 6.4%, respectively. Multivariable analysis showed that in patients with hypotension and albumin <2.5 g/dL the adjusted OR for in-hospital mortality was 37.1 (95% CI 32.3 to 42.6), and for ICU admission was 5.4 (95% CI 4.8 to 6.1). CONCLUSION: Co-occurrence of hypotension and hypoalbuminaemia is associated with poor hospital outcomes.


Subject(s)
Hypoalbuminemia , Hypotension , Adult , Cohort Studies , Critical Care , Emergency Service, Hospital , Hospital Mortality , Humans , Intensive Care Units , Retrospective Studies
8.
Obesity (Silver Spring) ; 29(9): 1547-1553, 2021 09.
Article in English | MEDLINE | ID: mdl-33945220

ABSTRACT

OBJECTIVE: Obesity is associated with severe coronavirus disease 2019 (COVID-19) infection. Disease severity is associated with a higher COVID-19 antibody titer. The COVID-19 antibody titer response of patients with obesity versus patients without obesity was compared. METHODS: The data of individuals tested for COVID-19 serology at the Mount Sinai Health System in New York City between March 1, 2020, and December 14, 2021, were retrospectively retrieved. The primary outcome was peak antibody titer, assessed as a binary variable (1:2,880, which was the highest detected titer, versus lower than 1:2,880). In patients with a positive serology test, peak titer rates were compared between BMI groups (<18.5, 18.5 to 25, 25 to 30, 30 to 40, and ≥40 kg/m2 ). A multivariable logistic regression model was used to analyze the independent association between different BMI groups and peak titer. RESULTS: Overall, 39,342 individuals underwent serology testing and had BMI measurements. A positive serology test was present in 12,314 patients. Peak titer rates were associated with obesity (BMI < 18.5 [34.5%], 18.5 to 25 [29.2%], 25 to 30 [37.7%], 30 to 40 [44.7%], ≥40 [52.0%]; p < 0.001). In a multivariable analysis, severe obesity had the highest adjusted odds ratio for peak titer (95% CI: 2.1-3.0). CONCLUSION: COVID-19 neutralizing antibody titer is associated with obesity. This has implications on the understanding of the role of obesity in COVID-19 severity.


Subject(s)
Antibodies, Viral/blood , COVID-19 , Obesity , Antibodies, Neutralizing/blood , COVID-19/immunology , Humans , Logistic Models , Obesity/complications , Retrospective Studies
9.
J Med Virol ; 93(9): 5481-5486, 2021 Sep.
Article in English | MEDLINE | ID: mdl-33963565

ABSTRACT

As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections continue, there is a substantial need for cost-effective and large-scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS-CoV-2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT-PCR/MALDI-TOF mass spectrometry-based assay (Agena MassARRAY®) to detect SARS-CoV-2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS-CoV-2 RNA in saliva by the cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS-CoV-2 detection on the novel Agena system as well as on a conventional real-time RT-PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS-CoV-2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.


Subject(s)
COVID-19 Nucleic Acid Testing/standards , COVID-19/diagnosis , Diagnostic Tests, Routine/standards , RNA, Viral/genetics , SARS-CoV-2/genetics , Saliva/virology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/standards , Benchmarking , COVID-19/virology , COVID-19 Nucleic Acid Testing/instrumentation , COVID-19 Nucleic Acid Testing/methods , Diagnostic Tests, Routine/instrumentation , Diagnostic Tests, Routine/methods , Humans , Limit of Detection , Nasopharynx/virology , Specimen Handling/standards , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
10.
Health Care Manag Sci ; 24(1): 234-243, 2021 Mar.
Article in English | MEDLINE | ID: mdl-33161511

ABSTRACT

Medical knowledge is increasing at an exponential rate. At the same time, unexplained variations in practice and patient outcomes and unacceptable rates of medical errors and inefficiencies in health care delivery have emerged. Our Institute for Health Care Delivery Science (I-HDS) began in 2014 as a novel platform to conduct multidisciplinary healthcare delivery research. We followed ten strategies to develop a successful institute with excellence in methodology and strong understanding of the value of team science. Our work was organized around five hubs: 1) Quality/Process Improvement and Systematic Review, 2) Comparative Effectiveness Research, Pragmatic Clinical Trials, and Predictive Analytics, 3) Health Economics and Decision Modeling, 4) Qualitative, Survey, and Mixed Methods, and 5) Training and Mentoring. In the first 5 years of the I-HDS, we have identified opportunities for change in clinical practice through research using our health system's electronic health record (EHR) data, and designed programs to educate clinicians in the value of research to improve patient care and recognize efficiencies in processes. Testing the value of several model interventions has guided prioritization of evidence-based quality improvements. Some of the changes in practice have already been embedded in the EHR workflow successfully. Development and sustainability of the I-HDS has been fostered by a mix of internal and external funding, including philanthropic foundations. Challenges remain due to the highly competitive funding environment and changes needed to adapt the EHR to healthcare delivery research. Further stakeholder engagement and culture change working with hospital leadership and I-HDS core and affiliate members continues.


Subject(s)
Delivery of Health Care , Electronic Health Records , Health Services Research , Comparative Effectiveness Research , Decision Support Techniques , Humans , Patient Care
11.
J Am Soc Nephrol ; 32(1): 151-160, 2021 01.
Article in English | MEDLINE | ID: mdl-32883700

ABSTRACT

BACKGROUND: Early reports indicate that AKI is common among patients with coronavirus disease 2019 (COVID-19) and associated with worse outcomes. However, AKI among hospitalized patients with COVID-19 in the United States is not well described. METHODS: This retrospective, observational study involved a review of data from electronic health records of patients aged ≥18 years with laboratory-confirmed COVID-19 admitted to the Mount Sinai Health System from February 27 to May 30, 2020. We describe the frequency of AKI and dialysis requirement, AKI recovery, and adjusted odds ratios (aORs) with mortality. RESULTS: Of 3993 hospitalized patients with COVID-19, AKI occurred in 1835 (46%) patients; 347 (19%) of the patients with AKI required dialysis. The proportions with stages 1, 2, or 3 AKI were 39%, 19%, and 42%, respectively. A total of 976 (24%) patients were admitted to intensive care, and 745 (76%) experienced AKI. Of the 435 patients with AKI and urine studies, 84% had proteinuria, 81% had hematuria, and 60% had leukocyturia. Independent predictors of severe AKI were CKD, men, and higher serum potassium at admission. In-hospital mortality was 50% among patients with AKI versus 8% among those without AKI (aOR, 9.2; 95% confidence interval, 7.5 to 11.3). Of survivors with AKI who were discharged, 35% had not recovered to baseline kidney function by the time of discharge. An additional 28 of 77 (36%) patients who had not recovered kidney function at discharge did so on posthospital follow-up. CONCLUSIONS: AKI is common among patients hospitalized with COVID-19 and is associated with high mortality. Of all patients with AKI, only 30% survived with recovery of kidney function by the time of discharge.


Subject(s)
Acute Kidney Injury/etiology , COVID-19/complications , SARS-CoV-2 , Acute Kidney Injury/epidemiology , Acute Kidney Injury/therapy , Acute Kidney Injury/urine , Aged , Aged, 80 and over , COVID-19/mortality , Female , Hematuria/etiology , Hospital Mortality , Hospitals, Private/statistics & numerical data , Hospitals, Urban/statistics & numerical data , Humans , Incidence , Inpatients , Leukocytes , Male , Middle Aged , New York City/epidemiology , Proteinuria/etiology , Renal Dialysis , Retrospective Studies , Treatment Outcome , Urine/cytology
13.
Am J Public Health ; 111(2): 247-252, 2021 02.
Article in English | MEDLINE | ID: mdl-33211588

ABSTRACT

In April 2020, in light of COVID-19-related blood shortages, the US Food and Drug Administration (FDA) reduced the deferral period for men who have sex with men (MSM) from its previous duration of 1 year to 3 months.Although originally born out of necessity, the decades-old restrictions on MSM donors have been mitigated by significant advancements in HIV screening, treatment, and public education. The severity of the ongoing COVID-19 pandemic-and the urgent need for safe blood products to respond to such crises-demands an immediate reconsideration of the 3-month deferral policy for MSM.We review historical HIV testing and transmission evidence, discuss the ethical ramifications of the current deferral period, and examine the issue of noncompliance with donor deferral rules. We also propose an eligibility screening format that involves an individual risk-based screening protocol and, unlike current FDA guidelines, does not effectively exclude donors on the basis of gender identity or sexual orientation. Our policy proposal would allow historically marginalized community members to participate with dignity in the blood donation process without compromising blood donation and transfusion safety outcomes.


Subject(s)
Blood Donors/ethics , Blood Safety/standards , Blood Transfusion/standards , COVID-19/epidemiology , Donor Selection/standards , Sexual and Gender Minorities/statistics & numerical data , COVID-19/therapy , COVID-19/transmission , HIV Infections/transmission , Health Policy , Homosexuality, Male/statistics & numerical data , Humans , Male , Transgender Persons/statistics & numerical data , United States
14.
J Am Coll Nutr ; 40(1): 3-12, 2021 01.
Article in English | MEDLINE | ID: mdl-32701397

ABSTRACT

OBJECTIVE: Malnutrition among hospital patients, a frequent, yet under-diagnosed problem is associated with adverse impact on patient outcome and health care costs. Development of highly accurate malnutrition screening tools is, therefore, essential for its timely detection, for providing nutritional care, and for addressing the concerns related to the suboptimal predictive value of the conventional screening tools, such as the Malnutrition Universal Screening Tool (MUST). We aimed to develop a machine learning (ML) based classifier (MUST-Plus) for more accurate prediction of malnutrition. METHOD: A retrospective cohort with inpatient data consisting of anthropometric, lab biochemistry, clinical data, and demographics from adult (≥ 18 years) admissions at a large tertiary health care system between January 2017 and July 2018 was used. The registered dietitian (RD) nutritional assessments were used as the gold standard outcome label. The cohort was randomly split (70:30) into training and test sets. A random forest model was trained using 10-fold cross-validation on training set, and its predictive performance on test set was compared to MUST. RESULTS: In all, 13.3% of admissions were associated with malnutrition in the test cohort. MUST-Plus provided 73.07% (95% confidence interval [CI]: 69.61%-76.33%) sensitivity, 76.89% (95% CI: 75.64%-78.11%) specificity, and 83.5% (95% CI: 82.0%-85.0%) area under the receiver operating curve (AUC). Compared to classic MUST, MUST-Plus demonstrated 30% higher sensitivity, 6% higher specificity, and 17% increased AUC. CONCLUSIONS: ML-based MUST-Plus provided superior performance in identifying malnutrition compared to the classic MUST. The tool can be used for improving the operational efficiency of RDs by timely referrals of high-risk patients.


Subject(s)
Malnutrition , Nutrition Assessment , Adult , Humans , Machine Learning , Malnutrition/diagnosis , Mass Screening , Retrospective Studies
15.
Am J Emerg Med ; 46: 520-524, 2021 Aug.
Article in English | MEDLINE | ID: mdl-33191048

ABSTRACT

BACKGROUND AND AIM: New York City (NYC) is an epicenter of the COVID-19 pandemic in the United States. Proper triage of patients with possible COVID-19 via chief complaint is critical but not fully optimized. This study aimed to investigate the association between presentation by chief complaints and COVID-19 status. METHODS: We retrospectively analyzed adult emergency department (ED) patient visits from five different NYC hospital campuses from March 1, 2020 to May 13, 2020 of patients who underwent nasopharyngeal COVID-19 RT-PCR testing. The positive and negative COVID-19 cohorts were then assessed for different chief complaints obtained from structured triage data. Sub-analysis was performed for patients older than 65 and within chief complaints with high mortality. RESULTS: Of 11,992 ED patient visits who received COVID-19 testing, 6524/11992 (54.4%) were COVID-19 positive. 73.5% of fever, 67.7% of shortness of breath, and 65% of cough had COVID-19, but others included 57.5% of weakness/fall/altered mental status, 55.5% of glycemic control, and 51.4% of gastrointestinal symptoms. In patients over 65, 76.7% of diarrhea, 73.7% of fatigue, and 69.3% of weakness had COVID-19. 45.5% of dehydration, 40.5% of altered mental status, 27% of fall, and 24.6% of hyperglycemia patients experienced mortality. CONCLUSION: A novel high risk COVID-19 patient population was identified from chief complaint data, which is different from current suggested CDC guidelines, and may help triage systems to better isolate COVID-19 patients. Older patients with COVID-19 infection presented with more atypical complaints warranting special consideration. COVID-19 was associated with higher mortality in a unique group of complaints also warranting special consideration.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Emergency Service, Hospital/statistics & numerical data , Pandemics , Triage/methods , Adult , Aged , COVID-19/epidemiology , Female , Follow-Up Studies , Humans , Male , Middle Aged , New York City/epidemiology , Retrospective Studies
16.
BMJ Open ; 10(11): e040736, 2020 11 27.
Article in English | MEDLINE | ID: mdl-33247020

ABSTRACT

OBJECTIVE: The COVID-19 pandemic is a global public health crisis, with over 33 million cases and 999 000 deaths worldwide. Data are needed regarding the clinical course of hospitalised patients, particularly in the USA. We aimed to compare clinical characteristic of patients with COVID-19 who had in-hospital mortality with those who were discharged alive. DESIGN: Demographic, clinical and outcomes data for patients admitted to five Mount Sinai Health System hospitals with confirmed COVID-19 between 27 February and 2 April 2020 were identified through institutional electronic health records. We performed a retrospective comparative analysis of patients who had in-hospital mortality or were discharged alive. SETTING: All patients were admitted to the Mount Sinai Health System, a large quaternary care urban hospital system. PARTICIPANTS: Participants over the age of 18 years were included. PRIMARY OUTCOMES: We investigated in-hospital mortality during the study period. RESULTS: A total of 2199 patients with COVID-19 were hospitalised during the study period. As of 2 April, 1121 (51%) patients remained hospitalised, and 1078 (49%) completed their hospital course. Of the latter, the overall mortality was 29%, and 36% required intensive care. The median age was 65 years overall and 75 years in those who died. Pre-existing conditions were present in 65% of those who died and 46% of those discharged. In those who died, the admission median lymphocyte percentage was 11.7%, D-dimer was 2.4 µg/mL, C reactive protein was 162 mg/L and procalcitonin was 0.44 ng/mL. In those discharged, the admission median lymphocyte percentage was 16.6%, D-dimer was 0.93 µg/mL, C reactive protein was 79 mg/L and procalcitonin was 0.09 ng/mL. CONCLUSIONS: In our cohort of hospitalised patients, requirement of intensive care and mortality were high. Patients who died typically had more pre-existing conditions and greater perturbations in inflammatory markers as compared with those who were discharged.


Subject(s)
COVID-19/blood , Critical Care , Hospital Mortality , Hospitalization , Pandemics , Adolescent , Adult , Aged , Aged, 80 and over , C-Reactive Protein/metabolism , COVID-19/epidemiology , COVID-19/mortality , Comorbidity , Critical Care/statistics & numerical data , Female , Fibrin Fibrinogen Degradation Products/metabolism , Hospitals , Humans , Lymphocytes/metabolism , Male , Middle Aged , New York City/epidemiology , Procalcitonin/blood , Retrospective Studies , Risk Factors , SARS-CoV-2 , Young Adult
17.
J Med Internet Res ; 22(11): e24018, 2020 11 06.
Article in English | MEDLINE | ID: mdl-33027032

ABSTRACT

BACKGROUND: COVID-19 has infected millions of people worldwide and is responsible for several hundred thousand fatalities. The COVID-19 pandemic has necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods to meet these needs are lacking. OBJECTIVE: The aims of this study were to analyze the electronic health records (EHRs) of patients who tested positive for COVID-19 and were admitted to hospitals in the Mount Sinai Health System in New York City; to develop machine learning models for making predictions about the hospital course of the patients over clinically meaningful time horizons based on patient characteristics at admission; and to assess the performance of these models at multiple hospitals and time points. METHODS: We used Extreme Gradient Boosting (XGBoost) and baseline comparator models to predict in-hospital mortality and critical events at time windows of 3, 5, 7, and 10 days from admission. Our study population included harmonized EHR data from five hospitals in New York City for 4098 COVID-19-positive patients admitted from March 15 to May 22, 2020. The models were first trained on patients from a single hospital (n=1514) before or on May 1, externally validated on patients from four other hospitals (n=2201) before or on May 1, and prospectively validated on all patients after May 1 (n=383). Finally, we established model interpretability to identify and rank variables that drive model predictions. RESULTS: Upon cross-validation, the XGBoost classifier outperformed baseline models, with an area under the receiver operating characteristic curve (AUC-ROC) for mortality of 0.89 at 3 days, 0.85 at 5 and 7 days, and 0.84 at 10 days. XGBoost also performed well for critical event prediction, with an AUC-ROC of 0.80 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. In external validation, XGBoost achieved an AUC-ROC of 0.88 at 3 days, 0.86 at 5 days, 0.86 at 7 days, and 0.84 at 10 days for mortality prediction. Similarly, the unimputed XGBoost model achieved an AUC-ROC of 0.78 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. Trends in performance on prospective validation sets were similar. At 7 days, acute kidney injury on admission, elevated LDH, tachypnea, and hyperglycemia were the strongest drivers of critical event prediction, while higher age, anion gap, and C-reactive protein were the strongest drivers of mortality prediction. CONCLUSIONS: We externally and prospectively trained and validated machine learning models for mortality and critical events for patients with COVID-19 at different time horizons. These models identified at-risk patients and uncovered underlying relationships that predicted outcomes.


Subject(s)
Coronavirus Infections/diagnosis , Coronavirus Infections/mortality , Machine Learning/standards , Pneumonia, Viral/diagnosis , Pneumonia, Viral/mortality , Acute Kidney Injury/epidemiology , Adolescent , Adult , Aged , Aged, 80 and over , Betacoronavirus , COVID-19 , Cohort Studies , Electronic Health Records , Female , Hospital Mortality , Hospitalization/statistics & numerical data , Hospitals , Humans , Male , Middle Aged , New York City/epidemiology , Pandemics , Prognosis , ROC Curve , Risk Assessment/methods , Risk Assessment/standards , SARS-CoV-2 , Young Adult
18.
Science ; 370(6521): 1227-1230, 2020 12 04.
Article in English | MEDLINE | ID: mdl-33115920

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic with millions infected and more than 1 million fatalities. Questions regarding the robustness, functionality, and longevity of the antibody response to the virus remain unanswered. Here, on the basis of a dataset of 30,082 individuals screened at Mount Sinai Health System in New York City, we report that the vast majority of infected individuals with mild-to-moderate COVID-19 experience robust immunoglobulin G antibody responses against the viral spike protein. We also show that titers are relatively stable for at least a period of about 5 months and that anti-spike binding titers significantly correlate with neutralization of authentic SARS-CoV-2. Our data suggest that more than 90% of seroconverters make detectable neutralizing antibody responses. These titers remain relatively stable for several months after infection.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , SARS-CoV-2/immunology , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , COVID-19/blood , Enzyme-Linked Immunosorbent Assay , Humans , Immunoglobulin G/blood , Immunoglobulin G/immunology , Neutralization Tests
19.
Cancer Cell ; 38(5): 594-597, 2020 11 09.
Article in English | MEDLINE | ID: mdl-33086031

ABSTRACT

Coronavirus disease 2019 (COVID-19), like cancer, is a complex disease with clinical phases of progression. Initially conceptualized as a respiratory disease, COVID-19 is increasingly recognized as a multi-organ and heterogeneous illness. Disease staging is a method for measuring the progression and severity of an illness using objective clinical and molecular criteria. Integral to cancer staging is "metastasis," defined as the spread of a disease-producing agent, including neoplastic cells and pathogens such as certain viruses, from the primary site to distinct anatomic locations. Staging provides valuable frameworks and benchmarks for clinical decision-making in patient management, improved prognostication, and evidence-based treatment selection.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/complications , Inflammation/etiology , Multiple Organ Failure/etiology , Pneumonia, Viral/complications , Severity of Illness Index , Virus Internalization , Virus Replication , COVID-19 , Coronavirus Infections/epidemiology , Coronavirus Infections/pathology , Coronavirus Infections/virology , Humans , Inflammation/pathology , Multiple Organ Failure/pathology , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , SARS-CoV-2
20.
Nat Med ; 26(11): 1708-1713, 2020 11.
Article in English | MEDLINE | ID: mdl-32934372

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a new human disease with few effective treatments1. Convalescent plasma, donated by persons who have recovered from COVID-19, is the acellular component of blood that contains antibodies, including those that specifically recognize SARS-CoV-2. These antibodies, when transfused into patients infected with SARS-CoV-2, are thought to exert an antiviral effect, suppressing virus replication before patients have mounted their own humoral immune responses2,3. Virus-specific antibodies from recovered persons are often the first available therapy for an emerging infectious disease, a stopgap treatment while new antivirals and vaccines are being developed1,2. This retrospective, propensity score-matched case-control study assessed the effectiveness of convalescent plasma therapy in 39 patients with severe or life-threatening COVID-19 at The Mount Sinai Hospital in New York City. Oxygen requirements on day 14 after transfusion worsened in 17.9% of plasma recipients versus 28.2% of propensity score-matched controls who were hospitalized with COVID-19 (adjusted odds ratio (OR), 0.86; 95% confidence interval (CI), 0.75-0.98; chi-square test P value = 0.025). Survival also improved in plasma recipients (adjusted hazard ratio (HR), 0.34; 95% CI, 0.13-0.89; chi-square test P = 0.027). Convalescent plasma is potentially effective against COVID-19, but adequately powered, randomized controlled trials are needed.


Subject(s)
COVID-19/pathology , COVID-19/therapy , Adult , Aged , Antibodies, Viral/blood , COVID-19/epidemiology , Case-Control Studies , Female , Humans , Immunization, Passive , Male , Middle Aged , Pandemics , Propensity Score , Retrospective Studies , SARS-CoV-2/immunology , Severity of Illness Index , Treatment Outcome , COVID-19 Serotherapy
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