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Xu S, Sy LS, Hong V, Farrington P, Glenn SC, Ryan DS, Shirley AM, Lewin BJ, Tseng HF, Vazquez-Benitez G, Glanz JM, Fireman B, McClure DL, Hurley LP, Yu O, Wernecke M, Smith N, Weintraub ES, Qian L. Mortality risk after COVID-19 vaccination: A self-controlled case series study. Vaccine 2024; 42:1731-1737. [PMID: 38388239 DOI: 10.1016/j.vaccine.2024.02.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND Although previous studies found no-increased mortality risk after COVID-19 vaccination, residual confounding bias might have impacted the findings. Using a modified self-controlled case series (SCCS) design, we assessed the risk of non-COVID-19 mortality, all-cause mortality, and four cardiac-related death outcomes after primary series COVID-19 vaccination. METHODS We analyzed all deaths between December 14, 2020, and August 11, 2021, among individuals from eight Vaccine Safety Datalink sites. Demographic characteristics of deaths in recipients of COVID-19 vaccines and unvaccinated individuals were reported. We conducted SCCS analyses by vaccine type and death outcomes and reported relative incidences (RI). The observation period for death spanned from the dates of emergency use authorization to the end of the study period (August 11, 2021) without censoring the observation period upon death. We pre-specified a primary risk interval of 28-day and a secondary risk interval of 14-day after each vaccination dose. Adjusting for seasonality in mortality analyses is crucial because death rates vary over time. Deaths among unvaccinated individuals were included in SCCS analyses to account for seasonality by incorporating calendar month in the models. RESULTS For Pfizer-BioNTech (BNT162b2), RIs of non-COVID-19 mortality, all-cause mortality, and four cardiac-related death outcomes were below 1 and 95 % confidence intervals (CIs) excluded 1 across both doses and both risk intervals. For Moderna (mRNA-1273), RI point estimates of all outcomes were below 1, although the 95 % CIs of two RI estimates included 1: cardiac-related (RI = 0.78, 95 % CI, 0.58-1.04) and non-COVID-19 cardiac-related mortality (RI = 0.80, 95 % CI, 0.60-1.08) 14 days after the second dose in individuals without pre-existing cancer and heart disease. For Janssen (Ad26.COV2.S), RIs of four cardiac-related death outcomes ranged from 0.94 to 0.98 for the 14-day risk interval, and 0.68 to 0.72 for the 28-day risk interval and 95 % CIs included 1. CONCLUSION Using a modified SCCS design and adjusting for temporal trends, no-increased risk was found for non-COVID-19 mortality, all-cause mortality, and four cardiac-related death outcomes among recipients of the three COVID-19 vaccines used in the US.
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Affiliation(s)
- Stanley Xu
- Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States; Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, United States.
| | - Lina S Sy
- Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Vennis Hong
- Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Paddy Farrington
- School of Mathematics and Statistics, The Open University, Milton Keynes, UK
| | - Sungching C Glenn
- Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Denison S Ryan
- Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Abraelle M Shirley
- Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Bruno J Lewin
- Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | - Hung-Fu Tseng
- Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
| | | | - Jason M Glanz
- Institute for Health Research, Kaiser Permanente Colorado, Denver, CO, United States; Department of Epidemiology, University of Colorado School of Public Health, Aurora, CO, United States
| | - Bruce Fireman
- Kaiser Permanente Vaccine Study Center, Kaiser Permanente Northern California, Oakland, CA, United States
| | - David L McClure
- Marshfield Clinic Research Institute, Marshfield, WI, United States
| | | | - Onchee Yu
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, United States
| | | | - Ning Smith
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, United States
| | - Eric S Weintraub
- Immunization Safety Office, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lei Qian
- Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, United States
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Shirley AM, Morrisette KL, Choi SK, Reynolds K, Zhou H, Zhou MM, Wei R, Zhang Y, Cheng P, Wong E, Sangha N, An J. Validation of ICD-10 hospital discharge diagnosis codes to identify incident and recurrent ischemic stroke from a US integrated healthcare system. Pharmacoepidemiol Drug Saf 2023; 32:1439-1445. [PMID: 37528669 PMCID: PMC10830879 DOI: 10.1002/pds.5675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023]
Abstract
PURPOSE This study validated incident and recurrent ischemic stroke identified by International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10) hospital discharge diagnosis codes. METHODS Using electronic health records (EHR) of adults (≥18 years) receiving care from Kaiser Permanente Southern California with ICD-10 hospital discharge diagnosis codes of ischemic stroke (I63.x, G46.3, and G46.4) between October 2015 and September 2020, we identified 75 patients with both incident and recurrent stroke events (total 150 cases). Two neurologists independently evaluated validity of ICD-10 codes through chart reviews. RESULTS The positive predictive value (PPV, 95% CI) for incident stroke was 93% (95% CI: 88%, 99%) and the PPV for recurrent stroke was 72% (95% CI: 62%, 82%). The PPV for recurrent stroke improved after applying a gap of 20 days (PPV of 75%; 95% CI: 63%, 87%) or removing hospital admissions related to stroke-related procedures (PPV of 78%; 95% CI: 68%, 88%). CONCLUSION The ICD-10 hospital discharge diagnosis codes for ischemic stroke showed a high PPV for incident cases, while the PPV for recurrent cases were less optimal. Algorithms to improve the accuracy of ICD-10 codes for recurrent ischemic stroke may be necessary.
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Affiliation(s)
- Abraelle M Shirley
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Kerresa L Morrisette
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Soon Kyu Choi
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Kristi Reynolds
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, California, USA
| | - Hui Zhou
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, California, USA
| | - Mengnan M Zhou
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Rong Wei
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Yiyi Zhang
- Division of General Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Pamela Cheng
- Department of Neurology, Los Angeles Medical Center, Southern California Permanente Medical Group, Los Angeles, California, USA
| | - Eric Wong
- Department of Neurology, Los Angeles Medical Center, Southern California Permanente Medical Group, Los Angeles, California, USA
| | - Navdeep Sangha
- Department of Neurology, Los Angeles Medical Center, Southern California Permanente Medical Group, Los Angeles, California, USA
- Department of Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, California, USA
| | - Jaejin An
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, California, USA
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Puttock EJ, Marquez J, Young DR, Shirley AM, Han B, McKenzie TL, Smith NJ, Manuel K, Hoelscher D, Spear S, Ruiz M, Smith C, Krytus K, Martinez I, So H, Levy M, Nolan V, Bagley E, Mehmood A, Thomas JG, Apedaile L, Ison S, Barr-Anderson DJ, Heller JG, Cohen DA. Association of masking policies with mask adherence and distancing during the SARS-COV-2 pandemic. Am J Infect Control 2022; 50:969-974. [PMID: 35545151 PMCID: PMC9080722 DOI: 10.1016/j.ajic.2022.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Quantification of the impact of local masking policies may help guide future policy interventions to reduce SARS-COV-2 disease transmission. This study's objective was to identify factors associated with adherence to masking and social distancing guidelines. METHODS Faculty from 16 U.S. colleges and universities trained 231 students in systematic direct observation. They assessed correct mask use and distancing in public settings in 126 US cities from September 2020 through August 2021. RESULTS Of 109,999 individuals observed in 126 US cities, 48% wore masks correctly with highest adherence among females, teens and seniors and lowest among non-Hispanic whites, those in vigorous physical activity, and in larger groups (P < .0001). Having a local mask mandate increased the odds of wearing a mask by nearly 3-fold (OR = 2.99, P = .0003) compared to no recommendation. People observed in non-commercial areas were least likely to wear masks. Correct mask use was greatest in December 2020 and remained high until June 2021 (P < .0001). Masking policy requirements were not associated with distancing. DISCUSSION The strong association between mask mandates and correct mask use suggests that public policy has a powerful influence on individual behavior. CONCLUSIONS Mask mandates should be considered in future pandemics to increase adherence.
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Shirley AM, McMichael CM, Chapple C. The sng2 mutant of Arabidopsis is defective in the gene encoding the serine carboxypeptidase-like protein sinapoylglucose:choline sinapoyltransferase. Plant J 2001; 28:83-94. [PMID: 11696189 DOI: 10.1046/j.1365-313x.2001.01123.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Serine carboxypeptidase-like (SCPL) proteins have traditionally been assigned roles in the hydrolytic processing of proteins; however, several SCPL proteins have recently been identified as catalysts in transacylation reactions of plant secondary metabolism. The novel functions of these enzymes suggest a catalytic diversity for plant SCPL proteins that extends beyond simple hydrolysis reactions. Characterization of the Arabidopsis sng2 (sinapoylglucose accumulator 2) mutant has identified another SCPL protein involved in plant secondary metabolism. The sng2 mutant was isolated by screening seed extracts for altered levels of sinapate esters, a group of phenylpropanoid compounds found in Arabidopsis and some other members of the Brassicaceae. Homozygous sng2 seeds accumulate sinapoylglucose instead of sinapoylcholine, and have increased levels of choline and decreased activity of the enzyme sinapoylglucose:choline sinapoyltransferase (SCT). Cloning of the SNG2 gene by a combination of map-based and candidate gene approaches demonstrates that SCT is another member of the growing class of SCPL acyltransferases involved in plant secondary metabolism.
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Affiliation(s)
- A M Shirley
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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Lehfeldt C, Shirley AM, Meyer K, Ruegger MO, Cusumano JC, Viitanen PV, Strack D, Chapple C. Cloning of the SNG1 gene of Arabidopsis reveals a role for a serine carboxypeptidase-like protein as an acyltransferase in secondary metabolism. Plant Cell 2000; 12:1295-306. [PMID: 10948250 PMCID: PMC149103 DOI: 10.1105/tpc.12.8.1295] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2000] [Accepted: 05/31/2000] [Indexed: 05/18/2023]
Abstract
Serine carboxypeptidases contain a conserved catalytic triad of serine, histidine, and aspartic acid active-site residues. These enzymes cleave the peptide bond between the penultimate and C-terminal amino acid residues of their protein or peptide substrates. The Arabidopsis Genome Initiative has revealed that the Arabidopsis genome encodes numerous proteins with homology to serine carboxypeptidases. Although many of these proteins may be involved in protein turnover or processing, the role of virtually all of these serine carboxypeptidase-like (SCPL) proteins in plant metabolism is unknown. We previously identified an Arabidopsis mutant, sng1 (sinapoylglucose accumulator 1), that is defective in synthesis of sinapoylmalate, one of the major phenylpropanoid secondary metabolites accumulated by Arabidopsis and some other members of the Brassicaceae. We have cloned the gene that is defective in sng1 and have found that it encodes a SCPL protein. Expression of SNG1 in Escherichia coli demonstrates that it encodes sinapoylglucose:malate sinapoyltransferase, an enzyme that catalyzes a transesterification instead of functioning like a hydrolase, as do the other carboxypeptidases. This finding suggests that SCPL proteins have acquired novel functions in plant metabolism and provides an insight into the evolution of secondary metabolic pathways in plants.
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Affiliation(s)
- C Lehfeldt
- Leibniz-Institut für Pflanzenbiochemie, Halle (Saale), Germany
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Lehfeldt C, Shirley AM, Meyer K, Ruegger MO, Cusumano JC, Viitanen PV, Strack D, Chapple C. Cloning of the SNG1 gene of Arabidopsis reveals a role for a serine carboxypeptidase-like protein as an acyltransferase in secondary metabolism. Plant Cell 2000. [PMID: 10948250 DOI: 10.2307/3871130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Serine carboxypeptidases contain a conserved catalytic triad of serine, histidine, and aspartic acid active-site residues. These enzymes cleave the peptide bond between the penultimate and C-terminal amino acid residues of their protein or peptide substrates. The Arabidopsis Genome Initiative has revealed that the Arabidopsis genome encodes numerous proteins with homology to serine carboxypeptidases. Although many of these proteins may be involved in protein turnover or processing, the role of virtually all of these serine carboxypeptidase-like (SCPL) proteins in plant metabolism is unknown. We previously identified an Arabidopsis mutant, sng1 (sinapoylglucose accumulator 1), that is defective in synthesis of sinapoylmalate, one of the major phenylpropanoid secondary metabolites accumulated by Arabidopsis and some other members of the Brassicaceae. We have cloned the gene that is defective in sng1 and have found that it encodes a SCPL protein. Expression of SNG1 in Escherichia coli demonstrates that it encodes sinapoylglucose:malate sinapoyltransferase, an enzyme that catalyzes a transesterification instead of functioning like a hydrolase, as do the other carboxypeptidases. This finding suggests that SCPL proteins have acquired novel functions in plant metabolism and provides an insight into the evolution of secondary metabolic pathways in plants.
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Affiliation(s)
- C Lehfeldt
- Leibniz-Institut für Pflanzenbiochemie, Halle (Saale), Germany
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Franke R, McMichael CM, Meyer K, Shirley AM, Cusumano JC, Chapple C. Modified lignin in tobacco and poplar plants over-expressing the Arabidopsis gene encoding ferulate 5-hydroxylase. Plant J 2000; 22:223-34. [PMID: 10849340 DOI: 10.1046/j.1365-313x.2000.00727.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Ferulate 5-hydroxylase (F5H) is a cytochrome P450-dependent monooxygenase that catalyses the hydroxylation of ferulic acid, coniferaldehyde and coniferyl alcohol in the pathways leading to sinapic acid and syringyl lignin biosynthesis. Earlier studies in Arabidopsis have demonstrated that F5H over-expression increases lignin syringyl monomer content and abolishes the tissue-specificity of its deposition. To determine whether this enzyme has a similar regulatory role in plants that undergo secondary growth, we over-expressed the F5H gene in tobacco and poplar. In tobacco, over-expression of F5H under the control of the cauliflower mosaic virus 35S promoter increased lignin syringyl monomer content in petioles, but had no detectable effect on lignification in stems. By contrast, when the cinnamate 4-hydroxylase (C4H) promoter was used to drive F5H expression, there was a significant increase in stem lignin syringyl monomer content. Yields of thioglycolic acid and Klason lignin in C4H-F5H lines were lower than in the wild-type, suggesting that F5H over-expression leads to a reduced deposition or an altered extractability of lignin in the transgenic plants. Histochemical analysis suggested that the novel lignin in C4H-F5H transgenic lines was altered in its content of hydroxycinnamyl aldehydes. Transgenic poplar trees carrying the C4H-F5H transgene also displayed enhanced lignin syringyl monomer content. Taken together, these data show that hydroxylation of guaiacyl-substituted lignin precursors controls lignin monomer composition in woody plants, and that F5H over-expression is a viable metabolic engineering strategy for modifying lignin biosynthesis in forest species.
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Affiliation(s)
- R Franke
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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Meyer K, Shirley AM, Cusumano JC, Bell-Lelong DA, Chapple C. Lignin monomer composition is determined by the expression of a cytochrome P450-dependent monooxygenase in Arabidopsis. Proc Natl Acad Sci U S A 1998; 95:6619-23. [PMID: 9618461 PMCID: PMC22575 DOI: 10.1073/pnas.95.12.6619] [Citation(s) in RCA: 208] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The phenylpropanoid pathway provides precursors for the biosynthesis of soluble secondary metabolites and lignin in plants. Ferulate-5-hydroxylase (F5H) catalyzes an irreversible hydroxylation step in this pathway that diverts ferulic acid away from guaiacyl lignin biosynthesis and toward sinapic acid and syringyl lignin. This fact led us to postulate that F5H was a potential regulatory step in the determination of lignin monomer composition. To test this hypothesis, we have used Arabidopsis to examine the impact of F5H overexpression. Arabidopsis is a useful model system in which to study lignification because in wild-type plants, guaiacyl and syringyl lignins are deposited in a tissue-specific fashion, while the F5H-deficient fah1 mutant accumulates only guaiacyl lignin. Here we show that ectopic overexpression of F5H in Arabidopsis abolishes tissue-specific lignin monomer accumulation. Surprisingly, overexpression of F5H under the control of the lignification-associated cinnamate-4-hydroxylase promoter, but not the commonly employed cauliflower mosaic virus 35S promoter, generates a lignin that is almost entirely comprised of syringylpropane units. These experiments demonstrate that modification of F5H expression may enable engineering of lignin monomer composition in agronomically important plant species.
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Affiliation(s)
- K Meyer
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907-1153, USA
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