Faculty Bibliography

As COVID-19 pandemic public health measures are easing globally, the emergence of new SARS-CoV-2 strains continue to present high risk for vulnerable populations. The antibody-mediated protection acquired from vaccination and/or infection is seen to wane over time and the immunocompromised populations can no longer expect benefit from monoclonal antibody prophylaxis. Hence, there is a need to monitor new variants and its effect on vaccine performance. In this context, surveillance of new SARS-CoV-2 infections and serology testing are gaining consensus for use as screening methods, especially for at-risk groups. Here, we described an improved COVID-19 screening strategy, comprising predictive algorithms and concurrent, rapid, accurate, and quantitative SARS-CoV-2 antigen and host antibody testing strategy, at point of care (POC). We conducted a retrospective analysis of 2553 pre- and asymptomatic patients who were tested for SARS-CoV-2 by RT-PCR. The pre-screening model had an AUC (CI) of 0.76 (0.73-0.78). Despite being the default method for screening, body temperature had lower AUC (0.52 [0.49-0.55]) compared to case incidence rate (0.65 [0.62-0.68]). POC assays for SARS-CoV-2 nucleocapsid protein (NP) and spike (S) receptor binding domain (RBD) IgG antibody showed promising preliminary results, demonstrating a convenient, rapid (<20 min), quantitative, and sensitive (ng/mL) antigen/antibody assay. This integrated pre-screening model and simultaneous antigen/antibody approach may significantly improve accuracy of COVID-19 infection and host immunity screening, helping address unmet needs for monitoring vaccine effectiveness and severe disease surveillance.

We are beginning a new era of Smart Diagnostics-integrated biosensors powered by recent innovations in embedded electronics, cloud computing, and artificial intelligence (AI). Universal and AI-based in vitro diagnostics (IVDs) have the potential to exponentially improve healthcare decision making in the coming years. This perspective covers current trends and challenges in translating Smart Diagnostics. We identify essential elements of Smart Diagnostics platforms through the lens of a clinically validated platform for digitizing biology and its ability to learn disease signatures. This platform for biochemical analyses uses a compact instrument to perform multiclass and multiplex measurements using fully integrated microfluidic cartridges compatible with the point of care. Image analysis digitizes biology by transforming fluorescence signals into inputs for learning disease/health signatures. The result is an intuitive Score reported to the patients and/or providers. This AI-linked universal diagnostic system has been validated through a series of large clinical studies and used to identify signatures for early disease detection and disease severity in several applications, including cardiovascular diseases, COVID-19, and oral cancer. The utility of this Smart Diagnostics platform may extend to multiple cell-based oncology tests via cross-reactive biomarkers spanning oral, colorectal, lung, bladder, esophageal, and cervical cancers, and is well-positioned to improve patient care, management, and outcomes through deployment of this resilient and scalable technology. Lastly, we provide a future perspective on the direction and trajectory of Smart Diagnostics and the transformative effects they will have on health care.

As of 8 August 2022, SARS-CoV-2, the causative agent of COVID-19, has infected over 585 million people and resulted in more than 6.42 million deaths worldwide. While approved SARS-CoV-2 spike (S) protein-based vaccines induce robust seroconversion in most individuals, dramatically reducing disease severity and the risk of hospitalization, poorer responses are observed in aged, immunocompromised individuals and patients with certain pre-existing health conditions. Further, it is difficult to predict the protection conferred through vaccination or previous infection against new viral variants of concern (VoC) as they emerge. In this context, a rapid quantitative point-of-care (POC) serological assay able to quantify circulating anti-SARS-CoV-2 antibodies would allow clinicians to make informed decisions on the timing of booster shots, permit researchers to measure the level of cross-reactive antibody against new VoC in a previously immunized and/or infected individual, and help assess appropriate convalescent plasma donors, among other applications. Utilizing a lab-on-a-chip ecosystem, we present proof of concept, optimization, and validation of a POC strategy to quantitate COVID-19 humoral protection. This platform covers the entire diagnostic timeline of the disease, seroconversion, and vaccination response spanning multiple doses of immunization in a single POC test. Our results demonstrate that this platform is rapid (~15 min) and quantitative for SARS-CoV-2-specific IgG detection.

BACKGROUND:Centralisation of rectal cancer surgery to designated centres was a key objective of the Irish national cancer control program. A national audit of rectal cancer surgery indicated centralisation was associated with improved early surgical outcomes. This study aimed to determine the impact of implementation of the national cancer strategy on survival from rectal cancer. MATERIALS AND METHODS:Data were collected from the National Cancer Registry of Ireland to include all patients with Stage I-III rectal cancer undergoing rectal cancer surgery with curative intent between 2003 and 2012. Five-year overall survival and cancer-specific survival was compared between patients in the pre-centralisation (2003-2007) and post-centralisation period (2008-2012) and between patients receiving surgery in designated cancer centres and non-cancer centres. RESULTS:The proportion of rectal cancer surgery performed in a designated cancer centre increased from 42% during 2003-2007 to 58% during 2008-2012. Five-year overall survival increased from 66.1% in 2003-2007 to 73.5% in 2008-2012 (p < 0.001). Five-year cancer-specific survival increased from 75.3% in 2003-2007 to 81.9% in 2008-2012 (p < 0.001). Surgery in a cancer centre and surgery post-centralisation were significantly associated with overall and cancer specific survival using Cox proportional hazards regression. CONCLUSION:Survival following resection of rectal cancer was significantly improved following implementation of a national cancer strategy incorporating centralisation of rectal cancer surgery.

Introduction: Tracheostomy in COVID-19 patients is a controversial and difficult clinical decision. A recent COVID-19 Severity Score (CSS) was validated to identify high-risk patients requiring hospitalization. We hypothesized that the CSS would be associated with survival in patients considered for tracheostomy.
Method(s): We reviewed 77 mechanically ventilated COVID-19 patients evaluated for percutaneous dilational tracheostomy (PDT) from March-June 2020 at a public tertiary care center. Decision for PDT was based on clinical judgment of the screening surgeons. The CSS was retrospectively calculated using mean biomarker values from admission to time of PDT consult. Primary end point was survival to discharge. The Youden index identified an optimal CSS cut point for survival.
Result(s): Mean CSS for 42 survivors vs 35 nonsurvivors was significantly different (CSS 52 vs 66; p = 0.003). The Youden index returned an optimal CSS of 55 (area under the curve 0.7; 95% CI, 43 to 72). Median CSS was 40 (interquartile range 27 to 49) in the Low CSS (<55 group) and 72 (interquartile range 66 to 93) in the high CSS (>= 55) group (Fig. 1a). Eighty-seven percent of low CSS patients underwent PDT, with 74% survival, and 61% of high CSS patients underwent PDT with only 41% surviving (Fig. 1b). Patients with high CSS had 77% lower odds of survival (odds ratio 0.2; 95% CI, 0.1 to 0.7).
Conclusion(s): Higher CSS was associated with decreased survival to discharge in patients evaluated for PDT, with a score > 55 predictive of mortality. The novel CSS can be a useful adjunct in determining which COVID-19 patients will benefit from tracheostomy. Further prospective validation of this tool is warranted. [Formula presented]
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BACKGROUND:Retrospective study of COVID-19 positive patients treated at NYU Langone Health (NYULH). OBJECTIVE:Identify clinical markers predictive of disease severity to assist in clinical decision triage and provide additional biological insights into disease progression. METHODS:Clinical activity of 3740 de-identified patients at NYULH between January and August 2020. Models were trained on clinical data during different parts of their hospital stay to predict three clinical outcomes: deceased, ventilated, or admitted to ICU. RESULTS:XGBoost model trained on clinical data from the final 24 hours excelled at predicting mortality (AUC=0.92, specificity=86% and sensitivity=85%). Respiration rate was the most important feature, followed by SpO2 and age 75+. Performance of this model to predict the deceased outcome extended 5 days prior with AUC=0.81, specificity=70%, sensitivity=75%. When only using clinical data from the first 24 hours, AUCs of 0.79, 0.80, and 0.77 were obtained for deceased, ventilated, or ICU admitted, respectively. Although respiration rate and SpO2 levels offered the highest feature importance, other canonical markers including diabetic history, age and temperature offered minimal gain. When lab values were incorporated, prediction of mortality benefited the most from blood urea nitrogen (BUN) and lactate dehydrogenase (LDH). Features predictive of morbidity included LDH, calcium, glucose, and C-reactive protein (CRP). CONCLUSIONS:Together this work summarizes efforts to systematically examine the importance of a wide range of features across different endpoint outcomes and at different hospitalization time points.

Objective/UNASSIGNED:Retrospective study of COVID-19 positive patients treated at NYU Langone Health (NYULH) to identify clinical markers predictive of disease severity to assist in clinical decision triage and provide additional biological insights into disease progression. Materials and Methods/UNASSIGNED:Clinical activity of 3740 de-identified patients at NYULH between January and August 2020. Models were trained on clinical data during different parts of their hospital stay to predict three clinical outcomes: deceased, ventilated, or admitted to ICU. Results/UNASSIGNED:XGBoost model trained on clinical data from the final 24 hours excelled at predicting mortality (AUC=0.92, specificity=86% and sensitivity=85%). Respiration rate was the most important feature, followed by SpO2 and age 75+. Performance of this model to predict the deceased outcome extended 5 days prior with AUC=0.81, specificity=70%, sensitivity=75%. When only using clinical data from the first 24 hours, AUCs of 0.79, 0.80, and 0.77 were obtained for deceased, ventilated, or ICU admitted, respectively. Although respiration rate and SpO2 levels offered the highest feature importance, other canonical markers including diabetic history, age and temperature offered minimal gain. When lab values were incorporated, prediction of mortality benefited the most from blood urea nitrogen (BUN) and lactate dehydrogenase (LDH). Features predictive of morbidity included LDH, calcium, glucose, and C-reactive protein (CRP). Conclusion/UNASSIGNED:Together this work summarizes efforts to systematically examine the importance of a wide range of features across different endpoint outcomes and at different hospitalization time points.

Oral cavity cancer has a low 5-y survival rate, but outcomes improve when the disease is detected early. Cytology is a less invasive method to assess oral potentially malignant disorders relative to the gold-standard scalpel biopsy and histopathology. In this report, we aimed to determine the utility of cytological signatures, including nuclear F-actin cell phenotypes, for classifying the entire spectrum of oral epithelial dysplasia and oral squamous cell carcinoma. We enrolled subjects with oral potentially malignant disorders, subjects with previously diagnosed malignant lesions, and healthy volunteers without lesions and obtained brush cytology specimens and matched scalpel biopsies from 486 subjects. Histopathological assessment of the scalpel biopsy specimens classified lesions into 6 categories. Brush cytology specimens were analyzed by machine learning classifiers trained to identify relevant cytological features. Multimodal diagnostic models were developed using cytology results, lesion characteristics, and risk factors. Squamous cells with nuclear F-actin staining were associated with early disease (i.e., lower proportions in benign lesions than in more severe lesions), whereas small round parabasal-like cells and leukocytes were associated with late disease (i.e., higher proportions in severe dysplasia and carcinoma than in less severe lesions). Lesions with the impression of oral lichen planus were unlikely to be either dysplastic or malignant. Cytological features substantially improved upon lesion appearance and risk factors in predicting squamous cell carcinoma. Diagnostic models accurately discriminated early and late disease with AUCs (95% CI) of 0.82 (0.77 to 0.87) and 0.93 (0.88 to 0.97), respectively. The cytological features identified here have the potential to improve screening and surveillance of the entire spectrum of oral potentially malignant disorders in multiple care settings.

BACKGROUND:The COVID-19 pandemic has resulted in significant morbidity and mortality, with large numbers of patients requiring intensive care threatening to overwhelm healthcare systems globally. There is an urgent need for a COVID-19 disease severity assessment that can assist in patient triage and resource allocation for patients at risk for severe disease. OBJECTIVE:The goal of this study was to develop, validate, and scale a clinical decision support system and mobile app to assist in COVID-19 severity assessment, management, and care. METHODS:Model training data from 701 patients with COVID-19 were collected across practices within the Family Health Centers network at New York University Langone Health. A two-tiered model was developed. Tier 1 uses easily available, non-laboratory data to help determine whether biomarker-based testing and/or hospitalization is necessary. Tier 2 predicts probability of mortality using biomarker measurements (CRP, PCT, D-dimer) and age. Both Tier 1 and Tier 2 models were validated using two external datasets from hospitals in Wuhan, China comprising 160 and 375 patients, respectively. RESULTS:All biomarkers were measured at significantly higher levels in patients that died vs. those that were not hospitalized or discharged (P < .001). The Tier 1 and Tier 2 internal validation had AUC (95% confidence interval) of 0.79 (0.74-0.84) and 0.95 (0.92-0.98), respectively. The Tier 1 and Tier 2 external validation had AUCs of 0.79 (0.74-0.84) and 0.97 (0.95-0.99), respectively. CONCLUSIONS:Our results demonstrate validity of the clinical decision support system and mobile app, which are now ready to assist healthcare providers in making evidence-based decisions in managing COVID-19 patient care. The deployment of these new capabilities has potential for immediate impact in community clinics, sites whereby application of such tools could lead to improvements in patient outcomes and cost containment. CLINICALTRIAL/UNASSIGNED/:

SARS-CoV-2 is the virus that causes coronavirus disease (COVID-19) which has reached pandemic levels resulting in significant morbidity and mortality affecting every inhabited continent. The large number of patients requiring intensive care threatens to overwhelm healthcare systems globally. Likewise, there is a compelling need for a COVID-19 disease severity test to prioritize care and resources for patients at elevated risk of mortality. Here, an integrated point-of-care COVID-19 Severity Score and clinical decision support system is presented using biomarker measurements of C-reactive protein (CRP), N-terminus pro B type natriuretic peptide (NT-proBNP), myoglobin (MYO), D-dimer, procalcitonin (PCT), creatine kinase-myocardial band (CK-MB), and cardiac troponin I (cTnI). The COVID-19 Severity Score combines multiplex biomarker measurements and risk factors in a statistical learning algorithm to predict mortality. The COVID-19 Severity Score was trained and evaluated using data from 160 hospitalized COVID-19 patients from Wuhan, China. Our analysis finds that COVID-19 Severity Scores were significantly higher for the group that died versus the group that was discharged with median (interquartile range) scores of 59 (40-83) and 9 (6-17), respectively, and area under the curve of 0.94 (95% CI 0.89-0.99). Although this analysis represents patients with cardiac comorbidities (hypertension), the inclusion of biomarkers from other pathophysiologies implicated in COVID-19 (e.g., D-dimer for thrombotic events, CRP for infection or inflammation, and PCT for bacterial co-infection and sepsis) may improve future predictions for a more general population. These promising initial models pave the way for a point-of-care COVID-19 Severity Score system to impact patient care after further validation with externally collected clinical data. Clinical decision support tools for COVID-19 have strong potential to empower healthcare providers to save lives by prioritizing critical care in patients at high risk for adverse outcomes.