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Article: An infodemiological framework for tracking the spread of SARS-CoV-2 using integrated public data.

Liu, Zhimin / Jiang, Zuodong / Kip, Geoffrey / Snigdha, Kirti / Xu, Jennings / Wu, Xiaoying / Khan, Najat / Schultz, Timothy

Pattern recognition letters

2022 Volume 158, Page(s) 133–140

Abstract: The outbreak of the SARS-CoV-2 novel coronavirus has caused a health crisis of immeasurable magnitude. Signals from heterogeneous public data sources could serve as early predictors for infection waves of the pandemic, particularly in its early phases, ... ...

Abstract	The outbreak of the SARS-CoV-2 novel coronavirus has caused a health crisis of immeasurable magnitude. Signals from heterogeneous public data sources could serve as early predictors for infection waves of the pandemic, particularly in its early phases, when infection data was scarce. In this article, we characterize temporal pandemic indicators by leveraging an integrated set of public data and apply them to a Prophet model to predict COVID-19 trends. An effective natural language processing pipeline was first built to extract time-series signals of specific articles from a news corpus. Bursts of these temporal signals were further identified with Kleinberg's burst detection algorithm. Across different US states, correlations for Google Trends of COVID-19 related terms, COVID-19 news volume, and publicly available wastewater SARS-CoV-2 measurements with weekly COVID-19 case numbers were generally high with lags ranging from 0 to 3 weeks, indicating them as strong predictors of viral spread. Incorporating time-series signals of these effective predictors significantly improved the performance of the Prophet model, which was able to predict the COVID-19 case numbers between one and two weeks with average mean absolute error rates of 0.38 and 0.46 respectively across different states.
Language	English
Publishing date	2022-04-26
Publishing country	Netherlands
Document type	Journal Article
ISSN	0167-8655
ISSN	0167-8655
DOI	10.1016/j.patrec.2022.04.030
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Article ; Online: Identifying signs and symptoms of AL amyloidosis in electronic health records using natural language processing, diagnosis codes, and manually abstracted registry data.

Silvert, Eli / Hester, Laura / Ramudu, Eshwan / Pawlowski, Colin / Kranenburg, Britte / Buadi, Francis / Muchtar, Eli / Khaled, Samer / Tran, Namphuong / Soundararajan, Venky / Khan, Najat / Gertz, Morie / Dispenzieri, Angela

American journal of hematology

2023 Volume 98, Issue 9, Page(s) E255–E258

MeSH term(s)	Humans ; Electronic Health Records ; Natural Language Processing ; Immunoglobulin Light-chain Amyloidosis/diagnosis ; Routinely Collected Health Data ; Algorithms
Language	English
Publishing date	2023-07-04
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	196767-8
ISSN	1096-8652 ; 0361-8609
ISSN (online)	1096-8652
ISSN	0361-8609
DOI	10.1002/ajh.27019
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Article ; Online: Using Computer Vision to Improve Endoscopic Disease Quantification in Therapeutic Clinical Trials of Ulcerative Colitis.

Stidham, Ryan W / Cai, Lingrui / Cheng, Shuyang / Rajaei, Flora / Hiatt, Tadd / Wittrup, Emily / Rice, Michael D / Bishu, Shrinivas / Wehkamp, Jan / Schultz, Weiwei / Khan, Najat / Stojmirovic, Aleksandar / Ghanem, Louis R / Najarian, Kayvan

Gastroenterology

2023 Volume 166, Issue 1, Page(s) 155–167.e2

Abstract: Background & aims: Endoscopic assessment of ulcerative colitis (UC) typically reports only the maximum severity observed. Computer vision methods may better quantify mucosal injury detail, which varies among patients.: Methods: Endoscopic video from ... ...

Abstract	Background & aims: Endoscopic assessment of ulcerative colitis (UC) typically reports only the maximum severity observed. Computer vision methods may better quantify mucosal injury detail, which varies among patients. Methods: Endoscopic video from the UNIFI clinical trial (A Study to Evaluate the Safety and Efficacy of Ustekinumab Induction and Maintenance Therapy in Participants With Moderately to Severely Active Ulcerative Colitis) comparing ustekinumab and placebo for UC were processed in a computer vision analysis that spatially mapped Mayo Endoscopic Score (MES) to generate the Cumulative Disease Score (CDS). CDS was compared with the MES for differentiating ustekinumab vs placebo treatment response and agreement with symptomatic remission at week 44. Statistical power, effect, and estimated sample sizes for detecting endoscopic differences between treatments were calculated using both CDS and MES measures. Endoscopic video from a separate phase 2 clinical trial replication cohort was performed for validation of CDS performance. Results: Among 748 induction and 348 maintenance patients, CDS was lower in ustekinumab vs placebo users at week 8 (141.9 vs 184.3; P < .0001) and week 44 (78.2 vs 151.5; P < .0001). CDS was correlated with the MES (P < .0001) and all clinical components of the partial Mayo score (P < .0001). Stratification by pretreatment CDS revealed ustekinumab was more effective than placebo (P < .0001) with increasing effect in severe vs mild disease (-85.0 vs -55.4; P < .0001). Compared with the MES, CDS was more sensitive to change, requiring 50% fewer participants to demonstrate endoscopic differences between ustekinumab and placebo (Hedges' g = 0.743 vs 0.460). CDS performance in the JAK-UC replication cohort was similar to UNIFI. Conclusions: As an automated and quantitative measure of global endoscopic disease severity, the CDS offers artificial intelligence enhancement of traditional MES capability to better evaluate UC in clinical trials and potentially practice.
MeSH term(s)	Humans ; Artificial Intelligence ; Colitis, Ulcerative/diagnosis ; Colitis, Ulcerative/drug therapy ; Colonoscopy/methods ; Computers ; Remission Induction ; Severity of Illness Index ; Ustekinumab/adverse effects
Chemical Substances	Ustekinumab (FU77B4U5Z0)
Language	English
Publishing date	2023-10-11
Publishing country	United States
Document type	Clinical Trial ; Clinical Trial, Phase II ; Journal Article
ZDB-ID	80112-4
ISSN	1528-0012 ; 0016-5085
ISSN (online)	1528-0012
ISSN	0016-5085
DOI	10.1053/j.gastro.2023.09.049
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Article ; Online: Durability of the Single-Dose Ad26.COV2.S Vaccine in the Prevention of COVID-19 Infections and Hospitalizations in the US Before and During the Delta Variant Surge.

Polinski, Jennifer M / Weckstein, Andrew R / Batech, Michael / Kabelac, Carly / Kamath, Tripthi / Harvey, Raymond / Jain, Sid / Rassen, Jeremy A / Khan, Najat / Schneeweiss, Sebastian

JAMA network open

2022 Volume 5, Issue 3, Page(s) e222959

Abstract: Importance: Vaccination against the SARS-CoV-2 virus is critical to control the pandemic. Randomized clinical trials demonstrated efficacy of the single-dose Ad26.COV2.S COVID-19 vaccine, but data on longer-term protection in clinical practice and ... ...

Abstract	Importance: Vaccination against the SARS-CoV-2 virus is critical to control the pandemic. Randomized clinical trials demonstrated efficacy of the single-dose Ad26.COV2.S COVID-19 vaccine, but data on longer-term protection in clinical practice and effectiveness against variants are needed. Objective: To assess the association between receiving the Ad26.COV2.S vaccine and COVID-19-related infections and hospitalizations before and during the Delta variant surge. Design, setting, and participants: This cohort study included adults aged 18 years and older who were newly Ad26.COV2.S-vaccinated matched to as many as 10 unvaccinated individuals by date, location, age, sex, and comorbidity index. This was followed by 1:4 propensity score matching on COVID-19 risk factors. Data were collected from US insurance claims data from March 1, 2020, through August 31, 2021. Exposures: Vaccination with Ad26.COV2.S vs no vaccination. Main outcomes and measures: Vaccine effectiveness (VE) was estimated for recorded COVID-19 infection and COVID-19-related hospitalization, nationwide and in subgroups by age, high-risk factors, calendar time, and states with high incidences of the Delta variant. VE estimates were corrected for underrecording of vaccinations in insurance data. Results: Among 422 034 vaccinated individuals (mean [SD] age, 54.7 [17.4] years; 236 437 [56.0%] women) and 1 645 397 matched unvaccinated individuals (mean [SD] age, 54.5 [17.5] years; 922 937 [56.1%] women), VE was 76% (95% CI, 75%-77%) for COVID-19 infections and 81% (95% CI, 78%-82%) for COVID-19-related hospitalizations. VE was stable for at least 180 days after vaccination and over calendar time. Among states with high Delta variant incidence, VE during June to August 2021 was 74% (95% CI, 71%-77%) for infections and 81% (95% CI, 75%-86%) for hospitalizations. VE for COVID-19 was higher in individuals younger than 65 years (78%; 95% CI, 77%-79%) and lower in immunocompromised patients (64%; 95% CI, 59%-68%). All estimates were corrected for vaccination underrecording; uncorrected VE, which served as a lower bound, was 66% (95% CI, 64%-67%) for any recorded COVID-19 infection and 72% (95% CI, 69%-74%) for COVID-19-related hospitalization. Conclusions and relevance: This cohort study in US clinical practice showed stable VE of Ad26.COV2.S for at least 6 months before as well as during the time the Delta variant emerged and became dominant.
MeSH term(s)	Ad26COVS1 ; Adolescent ; Adult ; Aged ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/prevention & control ; Cohort Studies ; Female ; Hospitalization/statistics & numerical data ; Humans ; Incidence ; Male ; Middle Aged ; Propensity Score ; SARS-CoV-2 ; United States ; Vaccine Efficacy ; Young Adult
Chemical Substances	Ad26COVS1
Language	English
Publishing date	2022-03-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2022.2959
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Article: Durability of Protection Post-Primary COVID-19 Vaccination in the United States.

Zheutlin, Amanda / Ott, Miles / Sun, Ran / Zemlianskaia, Natalia / Meyer, Craig S / Rubel, Meagan / Hayden, Jennifer / Neri, Breno / Kamath, Tripthi / Khan, Najat / Schneeweiss, Sebastian / Sarsour, Khaled

Vaccines

2022 Volume 10, Issue 9

Abstract: The durability of immune responses after COVID-19 vaccination will drive long-term vaccine effectiveness across settings and may differ by vaccine type. To determine durability of protection of COVID-19 vaccines (BNT162b2, mRNA-1273, and Ad26.COV2.S) ... ...

Abstract	The durability of immune responses after COVID-19 vaccination will drive long-term vaccine effectiveness across settings and may differ by vaccine type. To determine durability of protection of COVID-19 vaccines (BNT162b2, mRNA-1273, and Ad26.COV2.S) following primary vaccination in the United States, a matched case-control study was conducted in three cohorts between 1 January and 7 September 2021 using de-identified data from a database covering 168 million lives. Odds ratios (ORs) for developing outcomes of interest (breakthrough SARS-CoV-2 infection, hospitalization, or intensive care unit admission) were determined for each vaccine (no direct comparisons). In total, 17,017,435 individuals were identified. Relative to the baseline, stable protection was observed for Ad26.COV2.S against infections (OR [95% confidence interval (CI)], 1.31 [1.18-1.47]) and hospitalizations (OR [95% CI], 1.25 [0.86-1.80]). Relative to the baseline, protection waned over time against infections for BNT162b2 (OR [95% CI], 2.20 [2.01-2.40]) and mRNA-1273 (OR [95% CI], 2.07 [1.87-2.29]) and against hospitalizations for BNT162b2 (OR [95% CI], 2.38 [1.79-3.17]). Baseline protection remained stable for intensive care unit admissions for all three vaccines. Calculated baseline VE was consistent with published literature. This study suggests that the three vaccines in three separate populations may have different durability profiles.
Language	English
Publishing date	2022-09-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines10091458
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Article ; Online: Creation of an ustekinumab external control arm for Crohn's disease using electronic health records data: A pilot study.

PloS one

2023 Volume 18, Issue 3, Page(s) e0282267

Abstract: Background: Randomized trials are the gold-standard for clinical evidence generation, but they can sometimes be limited by infeasibility and unclear generalizability to real-world practice. External control arm (ECA) studies may help address this ... ...

Abstract	Background: Randomized trials are the gold-standard for clinical evidence generation, but they can sometimes be limited by infeasibility and unclear generalizability to real-world practice. External control arm (ECA) studies may help address this evidence gaps by constructing retrospective cohorts that closely emulate prospective ones. Experience in constructing these outside the context of rare diseases or cancer is limited. We piloted an approach for developing an ECA in Crohn's disease using electronic health records (EHR) data. Methods: We queried EHR databases and manually screened records at the University of California, San Francisco to identify patients meeting the eligibility criteria of TRIDENT, a recently completed interventional trial involving an ustekinumab reference arm. We defined timepoints to balance missing data and bias. We compared imputation models by their impacts on cohort membership and outcomes. We assessed the accuracy of algorithmic data curation against manual review. Lastly, we assessed disease activity following treatment with ustekinumab. Results: Screening identified 183 patients. 30% of the cohort had missing baseline data. Nonetheless, cohort membership and outcomes were robust to the method of imputation. Algorithms for ascertaining non-symptom-based elements of disease activity using structured data were accurate against manual review. The cohort consisted of 56 patients, exceeding planned enrollment in TRIDENT. 34% of the cohort was in steroid-free remission at week 24. Conclusion: We piloted an approach for creating an ECA in Crohn's disease from EHR data by using a combination of informatics and manual methods. However, our study reveals significant missing data when standard-of-care clinical data are repurposed. More work will be needed to improve the alignment of trial design with typical patterns of clinical practice, and thereby enable a future of more robust ECAs in chronic diseases like Crohn's disease.
MeSH term(s)	Humans ; Ustekinumab/therapeutic use ; Crohn Disease/drug therapy ; Pilot Projects ; Electronic Health Records ; Prospective Studies ; Retrospective Studies
Chemical Substances	Ustekinumab (FU77B4U5Z0)
Language	English
Publishing date	2023-03-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0282267
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Article: Cell-compatible, integrin-targeted cryptophane-

Seward, Garry K / Bai, Yubin / Khan, Najat S / Dmochowski, Ivan J

Chemical science

2014 Volume 2, Issue 6, Page(s) 1103–1110

Abstract: Peptide-modified cryptophane enables sensitive detection of protein analytes using ... ...

Abstract	Peptide-modified cryptophane enables sensitive detection of protein analytes using hyperpolarized
Language	English
Publishing date	2014-10-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/C1SC00041A
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Article ; Online: Durability of Protection against COVID-19 Breakthrough Infections and Severe Disease by Vaccines in the United States

Zheutlin, Amanda / Ott, Miles / Sun, Ran / Zemlianskaia, Natalia Zemlianskaia / Rubel, Meagan / Hayden, Jennifer / Neri, Breno / Kamath, Tripthi / Khan, Najat / Schneeweiss, Sebastian / Sarsour, Khaled

medRxiv

Abstract: Abstract Objectives: Determine durability of protection by the three currently available COVID-19 vaccines in the United States (US) following primary vaccination against breakthrough infections, hospitalizations, and intensive care unit (ICU) admissions. ...

Abstract	Abstract Objectives: Determine durability of protection by the three currently available COVID-19 vaccines in the United States (US) following primary vaccination against breakthrough infections, hospitalizations, and intensive care unit (ICU) admissions. Methods: Using claims and laboratory data covering 168 million lives, we conducted a matched case-control study with fully vaccinated individuals between January 1 and September 7, 2021. Odds ratios (OR) for developing outcomes in months two through six following full vaccination were estimated relative to the first month after full vaccination for each vaccine separately. Results: Evidence of waning protection against infections started in month 2 from vaccination for both BNT162b2 (OR [95% CI] in month 6+, 2.93 [2.72, 3.15]) and mRNA-1273 (OR [95% CI] in month 6+, 2.76 [2.51, 3.04]), and in month 4 for Ad26.COV2.S (OR [95% CI] in month 5+, 1.31 [1.18, 1.47]). Evidence of waning protection against hospitalization started in month 2 for BNT162b2 (OR [95% CI], 3.97 [3.26, 4.83] in month 6+) and in month 3 for mRNA-1273 (OR 95% CI, 1.66 [1.26, 2.19] in month 6+). There was no evidence of waning protection against hospitalization for Ad26.COV2.S (OR [95% CI], 1.25 [0.86, 1.80] in month 5+). No waning of protection was observed at any time for ICU admissions for all three vaccines. Conclusions: Following primary vaccination, all three vaccines showed strong and durable protection against ICU admissions. Ad26.COV2.S showed a more durable level of protection against breakthrough infections and hospitalizations in line with published evidence of its durable antibody and cellular immune response, although its Vaccine Effectiveness (VE) at baseline after a single-dose is lower than that for the two-dose mRNA vaccines. Additional studies are needed to understand durability following homologous or heterologous boosters.
Keywords	covid19
Language	English
Publishing date	2022-01-06
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2022.01.05.22268648
Database	COVID19

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Article ; Online: Cryptophane-folate biosensor for (129)xe NMR.

Khan, Najat S / Riggle, Brittany A / Seward, Garry K / Bai, Yubin / Dmochowski, Ivan J

Bioconjugate chemistry

2014 Volume 26, Issue 1, Page(s) 101–109

Abstract: Folate-conjugated cryptophane was developed for targeting cryptophane to membrane-bound folate receptors that are overexpressed in many human cancers. The cryptophane biosensor was synthesized in 20 nonlinear steps, which included functionalization with ... ...

Abstract	Folate-conjugated cryptophane was developed for targeting cryptophane to membrane-bound folate receptors that are overexpressed in many human cancers. The cryptophane biosensor was synthesized in 20 nonlinear steps, which included functionalization with folate recognition moiety, solubilizing peptide, and Cy3 fluorophore. Hyperpolarized (129)Xe NMR studies confirmed xenon binding to the folate-conjugated cryptophane. Cellular internalization of biosensor was monitored by confocal laser scanning microscopy and quantified by flow cytometry. Competitive blocking studies confirmed cryptophane endocytosis through a folate receptor-mediated pathway. Flow cytometry revealed 10-fold higher cellular internalization in KB cancer cells overexpressing folate receptors compared to HT-1080 cells with normal folate receptor expression. The biosensor was determined to be nontoxic in HT-1080 and KB cells by MTT assay at low micromolar concentrations typically used for hyperpolarized (129)Xe NMR experiments.
MeSH term(s)	Biological Transport ; Cell Line, Tumor ; Fluorescent Dyes/chemistry ; Folic Acid/chemistry ; Folic Acid Transporters/metabolism ; Humans ; Magnetic Resonance Spectroscopy ; Molecular Probes/chemical synthesis ; Molecular Probes/chemistry ; Molecular Probes/metabolism ; Molecular Probes/toxicity ; Polycyclic Compounds/chemical synthesis ; Polycyclic Compounds/chemistry ; Polycyclic Compounds/metabolism ; Polycyclic Compounds/toxicity
Chemical Substances	Fluorescent Dyes ; Folic Acid Transporters ; Molecular Probes ; Polycyclic Compounds ; cryptophane ; Folic Acid (935E97BOY8)
Language	English
Publishing date	2014-12-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1024041-x
ISSN	1520-4812 ; 1043-1802
ISSN (online)	1520-4812
ISSN	1043-1802
DOI	10.1021/bc5005526
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Article ; Online: Effectiveness of the Single-Dose Ad26.COV2.S COVID Vaccine

Polinski, Jennifer M. / Weckstein, Andrew R. / Batech, Michael / Kabelac, Carly / Kamath, Tripthi / Harvey, Raymond / Jain, Sid / Rassen, Jeremy A. / Khan, Najat / Schneeweiss, Sebastian

medRxiv

Abstract: Background Randomized trials demonstrated efficacy of Ad26.COV2.S, a single-dose COVID-19 vaccine. Data assessing effectiveness in clinical practice and its stability over time since vaccination and against Delta variants are needed. Methods Using U.S. ... ...

Abstract	Background Randomized trials demonstrated efficacy of Ad26.COV2.S, a single-dose COVID-19 vaccine. Data assessing effectiveness in clinical practice and its stability over time since vaccination and against Delta variants are needed. Methods Using U.S. insurance claims data through July 2021, we identified individuals newly vaccinated with Ad26.COV2.S and up to 10 unvaccinated individuals matched exactly by age, sex, date, location, comorbidity index plus 17 COVID-19 risk factors via propensity score (PS) matching. We estimated Vaccine Effectiveness (VE) with 95% confidence intervals (CI) for observed COVID-19 and COVID-19-related hospitalization, nationwide and stratified by age, immunocompromised status, calendar time, and states with high incidence of the Delta variant. We corrected VE estimates for under-recording of vaccinations in insurance data. Results Among 390,517 vaccinated and 1,524,153 matched unvaccinated individuals, VE was 79% (95% CI, 77% to 80%) for COVID-19 and 81% (79% to 84%) for COVID-19-related hospitalizations. VE was stable over calendar time. Among states with high Delta variant incidence, VE during June/July 2021 was 78% (73% to 82%) for infections and 85% (73% to 91%) for hospitalizations. VE for COVID-19 was higher in individuals <50 years (83%; 81% to 85%) and lower in immunocompromised patients (64%; 57% to 70%). All estimates were corrected for under-recording; uncorrected VE was 69% (67% to 71%) and 73% (69% to 76%), for COVID-19 and COVID-19-related hospitalization, respectively. Conclusions These non-randomized data across U.S. clinical practices show high and stable vaccine effectiveness of Ad26.COV2.S over time before the Delta variant emerged to when the Delta variant was dominant.
Keywords	covid19
Language	English
Publishing date	2021-09-12
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.09.10.21263385
Database	COVID19

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