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Le VT, Knight S, Watrous JD, Najhawan M, Dao K, McCubrey RO, Bair TL, Horne BD, May HT, Muhlestein JB, Nelson JR, Carlquist JF, Knowlton KU, Jain M, Anderson JL. Higher docosahexaenoic acid levels lower the protective impact of eicosapentaenoic acid on long-term major cardiovascular events. Front Cardiovasc Med 2023; 10:1229130. [PMID: 37680562 PMCID: PMC10482040 DOI: 10.3389/fcvm.2023.1229130] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/26/2023] [Indexed: 09/09/2023] Open
Abstract
Introduction Long-chain omega-3 polyunsaturated fatty acids (OM3 PUFA) are commonly used for cardiovascular disease prevention. High-dose eicosapentaenoic acid (EPA) is reported to reduce major adverse cardiovascular events (MACE); however, a combined EPA and docosahexaenoic acid (DHA) supplementation has not been proven to do so. This study aimed to evaluate the potential interaction between EPA and DHA levels on long-term MACE. Methods We studied a cohort of 987 randomly selected subjects enrolled in the INSPIRE biobank registry who underwent coronary angiography. We used rapid throughput liquid chromatography-mass spectrometry to quantify the EPA and DHA plasma levels and examined their impact unadjusted, adjusted for one another, and fully adjusted for comorbidities, EPA + DHA, and the EPA/DHA ratio on long-term (10-year) MACE (all-cause death, myocardial infarction, stroke, heart failure hospitalization). Results The average subject age was 61.5 ± 12.2 years, 57% were male, 41% were obese, 42% had severe coronary artery disease (CAD), and 311 (31.5%) had a MACE. The 10-year MACE unadjusted hazard ratio (HR) for the highest (fourth) vs. lowest (first) quartile (Q) of EPA was HR = 0.48 (95% CI: 0.35, 0.67). The adjustment for DHA changed the HR to 0.30 (CI: 0.19, 0.49), and an additional adjustment for baseline differences changed the HR to 0.36 (CI: 0.22, 0.58). Conversely, unadjusted DHA did not significantly predict MACE, but adjustment for EPA resulted in a 1.81-fold higher risk of MACE (CI: 1.14, 2.90) for Q4 vs. Q1. However, after the adjustment for baseline differences, the risk of MACE was not significant for DHA (HR = 1.37; CI: 0.85, 2.20). An EPA/DHA ratio ≥1 resulted in a lower rate of 10-year MACE outcomes (27% vs. 37%, adjusted p-value = 0.013). Conclusions Higher levels of EPA, but not DHA, are associated with a lower risk of MACE. When combined with EPA, higher DHA blunts the benefit of EPA and is associated with a higher risk of MACE in the presence of low EPA. These findings can help explain the discrepant results of EPA-only and EPA/DHA mixed clinical supplementation trials.
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Affiliation(s)
- Viet T. Le
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, United States
- Department of Physician Assistant Studies, Rocky Mountain University of Health Professions, Provo, UT, United States
| | - Stacey Knight
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, United States
- The University of Utah, School of Medicine, Salt Lake City, UT, United States
| | - Jeramie D. Watrous
- Department of Medicine, University of California San Diego, San Diego, CA, United States
| | - Mahan Najhawan
- Department of Medicine, University of California San Diego, San Diego, CA, United States
| | - Khoi Dao
- Department of Medicine, University of California San Diego, San Diego, CA, United States
| | - Raymond O. McCubrey
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, United States
| | - Tami L. Bair
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, United States
| | - Benjamin D. Horne
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, United States
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Heidi T. May
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, United States
| | - Joseph B. Muhlestein
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, United States
- The University of Utah, School of Medicine, Salt Lake City, UT, United States
| | - John R. Nelson
- California Cardiovascular Institute, Fresno, CA, United States
| | - John F. Carlquist
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, United States
- The University of Utah, School of Medicine, Salt Lake City, UT, United States
| | - Kirk U. Knowlton
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, United States
- The University of Utah, School of Medicine, Salt Lake City, UT, United States
- Department of Medicine, University of California San Diego, San Diego, CA, United States
| | - Mohit Jain
- Department of Medicine, University of California San Diego, San Diego, CA, United States
| | - Jeffrey L. Anderson
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, United States
- The University of Utah, School of Medicine, Salt Lake City, UT, United States
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Buckler AJ, Doros G, Kinninger A, Lakshmanan S, Le VT, Libby P, May HT, Muhlestein JB, Nelson JR, Nicolaou A, Roy SK, Shaikh K, Shekar C, Tayek JA, Zheng L, Bhatt DL, Budoff MJ. Quantitative imaging biomarkers of coronary plaque morphology: insights from EVAPORATE. Front Cardiovasc Med 2023; 10:1204071. [PMID: 37600044 PMCID: PMC10435977 DOI: 10.3389/fcvm.2023.1204071] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
Aims Residual cardiovascular risk persists despite statin therapy. In REDUCE-IT, icosapent ethyl (IPE) reduced total events, but the mechanisms of benefit are not fully understood. EVAPORATE evaluated the effects of IPE on plaque characteristics by coronary computed tomography angiography (CCTA). Given the conclusion that the IPE-treated patients demonstrate that plaque burden decreases has already been published in the primary study analysis, we aimed to demonstrate whether the use of an analytic technique defined and validated in histological terms could extend the primary study in terms of whether such changes could be reliably seen in less time on drug, at the individual (rather than only at the cohort) level, or both, as neither of these were established by the primary study result. Methods and Results EVAPORATE randomized the patients to IPE 4 g/day or placebo. Plaque morphology, including lipid-rich necrotic core (LRNC), fibrous cap thickness, and intraplaque hemorrhage (IPH), was assessed using the ElucidVivo® (Elucid Bioimaging Inc.) on CCTA. The changes in plaque morphology between the treatment groups were analyzed. A neural network to predict treatment assignment was used to infer patient representation that encodes significant morphological changes. Fifty-five patients completed the 18-month visit in EVAPORATE with interpretable images at each of the three time points. The decrease of LRNC between the patients on IPE vs. placebo at 9 months (reduction of 2 mm3 vs. an increase of 41 mm3, p = 0.008), widening at 18 months (6 mm3 vs. 58 mm3 increase, p = 0.015) were observed. While not statistically significant on a univariable basis, reductions in wall thickness and increases in cap thickness motivated multivariable modeling on an individual patient basis. The per-patient response assessment was possible using a multivariable model of lipid-rich phenotype at the 9-month follow-up, p < 0.01 (sustained at 18 months), generalizing well to a validation cohort. Conclusion Plaques in the IPE-treated patients acquired more characteristics of stability. Reliable assessment using histologically validated analysis of individual response is possible at 9 months, with sustained stabilization at 18 months, providing a quantitative basis to elucidate drug mechanism and assess individual patient response.
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Affiliation(s)
- Andrew J. Buckler
- Department of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Elucid Bioimaging Inc., Boston, MA, United States
| | | | - April Kinninger
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Suvasini Lakshmanan
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Viet T. Le
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, United States
- Rocky Mountain University of Health Profession, Provo, UT, United States
| | - Peter Libby
- Brigham and Women’s Hospital Heart & Vascular Center and Harvard Medical School, Boston, MA, United States
| | - Heidi T. May
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, United States
| | - Joseph B. Muhlestein
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, United States
| | - John R. Nelson
- California Cardiovascular Institute, Fresno, CA, United States
| | | | - Sion K. Roy
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Kashif Shaikh
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Chandana Shekar
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - John A. Tayek
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Luke Zheng
- BAIM Institute, Boston, MA, United States
| | - Deepak L. Bhatt
- Brigham and Women’s Hospital Heart & Vascular Center and Harvard Medical School, Boston, MA, United States
| | - Matthew J. Budoff
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, United States
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Sheppard JP, Lakshmanan S, Roy S, Bhatt DL, Budoff MJ, Nelson JR. SERUM LEVELS OF EICOSAPENTAENOIC ACID BUT NOT DOCOSAHEXAENOIC ACID CORRELATE WITH REDUCTION IN CORONARY LIPID PLAQUE VOLUME IN PATIENTS ON STATIN OR STATIN PLUS OMEGA-3 FATTY ACID THERAPY. J Am Coll Cardiol 2023. [DOI: 10.1016/s0735-1097(23)02074-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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Lakshmanan S, Budoff MJ, Nelson JR. Letter by Lakshmanan et al Regarding Article "Effects of Randomized Treatment With Icosapent Ethyl and a Mineral Oil Comparator on Interleukin-1β, Interleukin-6, C-Reactive Protein, Oxidized Low-Density Lipoprotein Cholesterol, Homocysteine, Lipoprotein(a), and Lipoprotein-Associated Phospholipase A2: A REDUCE-IT Biomarker Substudy". Circulation 2022; 146:e284-e285. [PMID: 36374969 DOI: 10.1161/circulationaha.122.061986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Suvasini Lakshmanan
- Lundquist Institute at Harbor-University of California Los Angeles Medical Center, Torrance
| | - Matthew J Budoff
- Lundquist Institute at Harbor-University of California Los Angeles Medical Center, Torrance
| | - John R Nelson
- Lundquist Institute at Harbor-University of California Los Angeles Medical Center, Torrance
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Sheppard JP, Lakshmanan S, Dahal S, Roy SK, Bhatt DL, Budoff MJ, Nelson JR. EPA Versus Mixed EPA/DHA Plus Statin for Coronary Atherosclerosis. JACC Cardiovasc Imaging 2022; 15:1825-1828. [DOI: 10.1016/j.jcmg.2022.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/30/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022]
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Toth PP, Chapman MJ, Parhofer KG, Nelson JR. Differentiating EPA from EPA/DHA in cardiovascular risk reduction. Am Heart J Plus 2022; 17:100148. [PMID: 38559888 PMCID: PMC10978325 DOI: 10.1016/j.ahjo.2022.100148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 04/04/2024]
Abstract
None of the clinical trials of omega-3 fatty acids using combinations of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were able to show any effect on cardiovascular outcomes, despite reductions in triglyceride levels. In contrast, the Reduction of Cardiovascular Events With Icosapent Ethyl-Intervention Trial (REDUCE-IT), which employed high-dose (4 g) purified EPA, demonstrated a 25% reduction in atherosclerotic cardiovascular disease-related events compared with placebo (hazard ratio 0.75; 95% confidence interval 0.68-0.83; P < 0.001). Moreover, REDUCE-IT is the first clinical trial using a lipid-lowering agent as adjuvant therapy to a statin to show a significant reduction in cardiovascular mortality. Significant reductions in stroke, need for revascularization, and myocardial infarction were also observed. The pharmacology of EPA is distinct from that of DHA, with a differential effect on membrane structure, lipoprotein oxidation, and the production of downstream metabolites that promote the resolution of inflammation. Attained plasma levels of EPA may be an important determinant of efficacy, with a substudy of REDUCE-IT suggesting that the threshold for clinical benefit of EPA is approximately 100 μg/mL, a level achieved in only a minority of patients in other studies. No similar clinical trials of DHA monotherapy have been conducted, so no such threshold has been established. The results of the REDUCE-IT and the Japan EPA Lipid Intervention Study (JELIS) together affirm the efficacy of EPA therapy for cardiovascular disease risk reduction in certain patient populations.
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Affiliation(s)
- Peter P. Toth
- CGH Medical Center, Sterling, IL, USA
- Cicarrone Center for the Prevention of Cardiovascular Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Klaus G. Parhofer
- Medical Clinic IV – Grosshadern Hospital of the University of Munich, Munich, Germany
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Diffenderfer MR, Rajapakse N, Pham E, He L, Dansinger ML, Nelson JR, Schaefer EJ. Plasma fatty acid profiles: Relationships with sex, age, and state-reported heart disease mortality rates in the United States. J Clin Lipidol 2022; 16:184-197. [DOI: 10.1016/j.jacl.2021.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022]
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Abstract
Treatment with icosapent ethyl 4 g/day, a highly purified and stable ethyl ester of eicosapentaenoic acid (EPA), demonstrated a significant reduction in atherosclerotic cardiovascular disease (ASCVD) events and death in REDUCE-IT. However, analyses of REDUCE-IT and meta-analyses have suggested that this clinical benefit is greater than can be achieved by triglyceride reduction alone. EPA therefore may have additional pleiotropic effects, including anti-inflammatory and anti-aggregatory mechanisms. EPA competes with arachidonic acid for cyclooxygenase and lipoxygenase, producing anti-inflammatory and anti-aggregatory metabolites rather than the more deleterious metabolites associated with arachidonic acid. Changing the EPA:arachidonic acid ratio may shift metabolic status from pro-inflammatory/pro-aggregatory to anti-inflammatory/anti-aggregatory. EPA also has antioxidant effects and increases synthesis of nitric oxide. Incorporation of EPA into phospholipid bilayers influences membrane structure and may help to prevent cardiac arrhythmias. Clinically, this may translate into improved vascular health, including regression of atherosclerotic plaque. Overall, EPA has a range of pleiotropic effects that contribute to a reduction in ASCVD.
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Affiliation(s)
- John R Nelson
- California Cardiovascular Institute, Fresno, California, USA
| | - Matthew J Budoff
- Department of Medicine, Lundquist Institute, Torrance, California, USA
| | - Omar R Wani
- Northern Arizona Healthcare Medical Group - Flagstaff, Flagstaff, AZ, USA
| | - Viet Le
- Cardiovascular Research, Intermountain Heart Institute/CV Research, Intermountain Healthcare, Murray, Utah, and Rocky Mountain University of Health Professions, Provo, USA
| | - Dhiren K Patel
- Department of Pharmacy Practice, MCPHS University, Boston, MA, USA
| | - Ashley Nelson
- Department of Internal Medicine, Saint Agnes Medical Center, Fresno, California, USA
| | - Richard L Nemiroff
- Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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Budoff MJ, Bhatt DL, Kinninger A, Lakshmanan S, Muhlestein JB, Le VT, May HT, Shaikh K, Shekar C, Roy SK, Tayek J, Nelson JR. Effect of icosapent ethyl on progression of coronary atherosclerosis in patients with elevated triglycerides on statin therapy: final results of the EVAPORATE trial. Eur Heart J 2021; 41:3925-3932. [PMID: 32860032 PMCID: PMC7654934 DOI: 10.1093/eurheartj/ehaa652] [Citation(s) in RCA: 228] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/10/2020] [Accepted: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
Aims Despite the effects of statins in reducing cardiovascular events and slowing progression of coronary atherosclerosis, significant cardiovascular (CV) risk remains. Icosapent ethyl (IPE), a highly purified eicosapentaenoic acid ethyl ester, added to a statin was shown to reduce initial CV events by 25% and total CV events by 32% in the REDUCE-IT trial, with the mechanisms of benefit not yet fully explained. The EVAPORATE trial sought to determine whether IPE 4 g/day, as an adjunct to diet and statin therapy, would result in a greater change from baseline in plaque volume, measured by serial multidetector computed tomography (MDCT), than placebo in statin-treated patients. Methods and results A total of 80 patients were enrolled in this randomized, double-blind, placebo-controlled trial. Patients had to have coronary atherosclerosis as documented by MDCT (one or more angiographic stenoses with ≥20% narrowing), be on statin therapy, and have persistently elevated triglyceride (TG) levels. Patients underwent an interim scan at 9 months and a final scan at 18 months with coronary computed tomographic angiography. The pre-specified primary endpoint was change in low-attenuation plaque (LAP) volume at 18 months between IPE and placebo groups. Baseline demographics, vitals, and laboratory results were not significantly different between the IPE and placebo groups; the median TG level was 259.1 ± 78.1 mg/dL. There was a significant reduction in the primary endpoint as IPE reduced LAP plaque volume by 17%, while in the placebo group LAP plaque volume more than doubled (+109%) (P = 0.0061). There were significant differences in rates of progression between IPE and placebo at study end involving other plaque volumes including fibrous, and fibrofatty (FF) plaque volumes which regressed in the IPE group and progressed in the placebo group (P < 0.01 for all). When further adjusted for age, sex, diabetes status, hypertension, and baseline TG, plaque volume changes between groups remained significantly different, P < 0.01. Only dense calcium did not show a significant difference between groups in multivariable modelling (P = 0.053). Conclusions Icosapent ethyl demonstrated significant regression of LAP volume on MDCT compared with placebo over 18 months. EVAPORATE provides important mechanistic data on plaque characteristics that may have relevance to the REDUCE-IT results and clinical use of IPE.
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Affiliation(s)
- Matthew J Budoff
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, Torrance, CA 90502, USA
| | - Deepak L Bhatt
- Department of Medicine, Brigham and Women's Hospital Heart & Vascular Center and Harvard Medical School, Boston, MA, USA
| | - April Kinninger
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, Torrance, CA 90502, USA
| | - Suvasini Lakshmanan
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, Torrance, CA 90502, USA
| | - Joseph B Muhlestein
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Viet T Le
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA.,Department of Medicine, Rocky Mountain University of Health Profession, Provo, UT, USA
| | - Heidi T May
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Kashif Shaikh
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, Torrance, CA 90502, USA
| | - Chandana Shekar
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, Torrance, CA 90502, USA
| | - Sion K Roy
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, Torrance, CA 90502, USA
| | - John Tayek
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, Torrance, CA 90502, USA
| | - John R Nelson
- California Cardiovascular Institute, Fresno, CA, USA
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House GM, Sobotik EB, Nelson JR, Archer GS. A comparison of white/red and white/blue LED light fixtures on Pekin duck production, stress and behaviour. Br Poult Sci 2021; 62:467-473. [PMID: 33624574 DOI: 10.1080/00071668.2021.1891524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
1. The objective of this study was to determine the effects of two mixed LED light spectra on duck production, stress and fear responses. Pekin ducks were reared under either white/red (WR) or white/blue (WB) LED light.2. No differences were observed in feed conversion ratio (P = 0.690) or d 35 body weight (P = 0.919). Furthermore, no differences were observed in plasma interleukin-12 concentrations (P = 0.449), anti-keyhole limpet haemocyanin IgG titre (P = 0.503) or composite physical asymmetry score (P = 0.839). WR caused lower heterophil to lymphocyte ratios (0.40 ± 0.03, P = 0.029) and plasma corticosterone concentrations (4498 ± 534 pg/ml, P = 0.038) than WB (0.58 ± 0.08; 6518 ± 795 pg/ml, respectively). No differences were found in the number of attempts to induce tonic immobility (TI) or in inversion intensity. A shorter latency to first head movement during TI (9.44 ± 1.22 s, P = 0.06) and an overall shorter latency to right from TI (25.66 ± 2.99 s, P < 0.001) was observed for birds under WR compared to WB (20.91 ± 6.01 s; 58.76 ± 8.86 s). The duration of time spent in the second stage of TI, where birds observed their environment using head movements while still remaining immobile on their backs, was shorter in WR (16.23 ± 1.73 s, P = 0.001) compared to WB (37.85 ± 6.38 s).3. The results indicated that rearing ducks under WR caused less stress susceptibility and fear responses compared to ducks under WB. Pekin duck welfare may be compromised by blue LED light exposure, even at supplemental levels utilised in commercial poultry lighting.
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Affiliation(s)
- G M House
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
| | - E B Sobotik
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
| | - J R Nelson
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
| | - G S Archer
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
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Scherer B, Surrette C, Li H, Torab P, Kvam E, Galligan C, Go S, Grossmann G, Hammond T, Johnson T, St-Pierre R, Nelson JR, Potyrailo RA, Khire T, Hsieh K, Wang TH, Wong PK, Puleo CM. Digital electrical impedance analysis for single bacterium sensing and antimicrobial susceptibility testing. Lab Chip 2021; 21:1073-1083. [PMID: 33529300 DOI: 10.1039/d0lc00937g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Single-molecule and single-cell analysis techniques have opened new opportunities for characterizing and analyzing heterogeneity within biological samples. These detection methods are often referred to as digital assays because the biological sample is partitioned into many small compartments and each compartment contains a discrete number of targets (e.g. cells). Using digital assays, researchers can precisely detect and quantify individual targets, and this capability has made digital techniques the basis for many modern bioanalytical tools (including digital PCR, single cell RNA sequencing, and digital ELISA). However, digital assays are dominated by optical analysis systems that typically utilize microscopy to analyze partitioned samples. The utility of digital assays may be dramatically enhanced by implementing cost-efficient and portable electrical detection capabilities. Herein, we describe a digital electrical impedance sensing platform that enables direct multiplexed measurement of single cell bacterial cells. We outline our solutions to the challenge of multiplexing impedance sensing across many culture compartments and demonstrate the potential for rapidly differentiating antimicrobial resistant versus susceptible strains of bacteria.
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Trivedi K, Le V, Nelson JR. The case for adding eicosapentaenoic acid (icosapent ethyl) to the ABCs of cardiovascular disease prevention. Postgrad Med 2021; 133:28-41. [PMID: 32762268 DOI: 10.1080/00325481.2020.1783937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 01/10/2020] [Accepted: 06/15/2020] [Indexed: 01/10/2023]
Abstract
The high-purity eicosapentaenoic acid (EPA) prescription fish oil-derived omega-3 fatty acid (omega-3), icosapent ethyl (IPE), was recently approved by the United States Food and Drug Administration (FDA) for cardiovascular disease (CVD) prevention in high-risk patients. This approval is based on the 25% CVD event risk reduction observed with IPE in the pre-specified primary composite endpoint (cardiovascular [CV] death, nonfatal myocardial infarction, nonfatal stroke, coronary revascularization, or hospitalization for unstable angina) in the landmark Reduction of Cardiovascular Events with Icosapent Ethyl-Intervention Trial (REDUCE-IT). Notably, this reduction in CVD event risk with IPE was an incremental benefit to well-controlled low-density lipoprotein cholesterol; patients in REDUCE-IT had elevated triglyceride (TG) levels (135-499 mg/dL) and either had a history of atherosclerotic CVD or diabetes with additional CV risk factors. Given the CVD event risk reduction in REDUCE-IT, within a year following trial results, several global medical societies added IPE to their clinical guidelines. IPE is a stable, highly purified, FDA-approved prescription EPA ethyl ester. In contrast, mixed omega-3 products (docosahexaenoic acid + EPA combinations) have limited or no evidence for CVD event risk reduction, and nonprescription fish oil dietary supplements are not regulated as medicine by the FDA. We offer our perspective and rationale for why this evidence-based EPA-only formulation, IPE, should be added to the 'E' in the ABCDEF methodology for CV prevention. We provide multiple lines of evidence regarding an unmet need for CVD prevention beyond statin therapy, IPE clinical trials, IPE cost-effectiveness analyses, and proposed pleiotropic (non-lipid) mechanisms of action of EPA, as well as other relevant clinical considerations. See Figure 1 for the graphical abstract.[Figure: see text].
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Affiliation(s)
| | - Viet Le
- Intermountain Medical Center , Murray, UT, USA
- Principle PA Faculty, Rocky Mountain University of Health Professions , Provo, UT, USA
| | - John R Nelson
- California Cardiovascular Institute , Fresno, CA, USA
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13
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Lakshmanan S, Shekar C, Kinninger A, Dahal S, Onuegbu A, Cai AN, Hamal S, Birudaraju D, Roy SK, Nelson JR, Budoff MJ, Bhatt DL. Comparison of mineral oil and non-mineral oil placebo on coronary plaque progression by coronary computed tomography angiography. Cardiovasc Res 2020; 116:479-482. [PMID: 31825484 PMCID: PMC7031703 DOI: 10.1093/cvr/cvz329] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023] Open
Affiliation(s)
- Suvasini Lakshmanan
- Department of Cardiology, Lundquist Institute for Biomedical Innovation and Research at Harbor UCLA Medical Center, 1124 West Carson Street Torrance, CA 90502, USA
| | - Chandana Shekar
- Department of Cardiology, University of Arizona College of Medicine, Phoenix, AZ, USA
| | - April Kinninger
- Department of Cardiology, Lundquist Institute for Biomedical Innovation and Research at Harbor UCLA Medical Center, 1124 West Carson Street Torrance, CA 90502, USA
| | - Suraj Dahal
- Department of Cardiology, Lundquist Institute for Biomedical Innovation and Research at Harbor UCLA Medical Center, 1124 West Carson Street Torrance, CA 90502, USA
| | - Afiachukwu Onuegbu
- Department of Cardiology, Lundquist Institute for Biomedical Innovation and Research at Harbor UCLA Medical Center, 1124 West Carson Street Torrance, CA 90502, USA
| | - Andrew N Cai
- Department of Cardiology, Lundquist Institute for Biomedical Innovation and Research at Harbor UCLA Medical Center, 1124 West Carson Street Torrance, CA 90502, USA
| | - Sajad Hamal
- Department of Cardiology, Lundquist Institute for Biomedical Innovation and Research at Harbor UCLA Medical Center, 1124 West Carson Street Torrance, CA 90502, USA
| | - Divya Birudaraju
- Department of Cardiology, Lundquist Institute for Biomedical Innovation and Research at Harbor UCLA Medical Center, 1124 West Carson Street Torrance, CA 90502, USA
| | - Sion K Roy
- Department of Cardiology, Lundquist Institute for Biomedical Innovation and Research at Harbor UCLA Medical Center, 1124 West Carson Street Torrance, CA 90502, USA
| | - John R Nelson
- Department of Cardiology, California Cardiovascular Institute, Fresno, CA, USA
| | - Matthew J Budoff
- Department of Cardiology, Lundquist Institute for Biomedical Innovation and Research at Harbor UCLA Medical Center, 1124 West Carson Street Torrance, CA 90502, USA
| | - Deepak L Bhatt
- Department of Medicine, Brigham and Women's Hospital Heart & Vascular Center, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
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Budoff MJ, Muhlestein JB, Bhatt DL, Le Pa VT, May HT, Shaikh K, Shekar C, Kinninger A, Lakshmanan S, Roy SK, Tayek J, Nelson JR. Effect of icosapent ethyl on progression of coronary atherosclerosis in patients with elevated triglycerides on statin therapy: a prospective, placebo-controlled randomized trial (EVAPORATE): interim results. Cardiovasc Res 2020; 117:1070-1077. [PMID: 32609331 DOI: 10.1093/cvr/cvaa184] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 12/30/2022] Open
Abstract
AIMS Though statin therapy is known to slow coronary atherosclerosis progression and reduce cardiovascular (CV) events, significant CV risk still remains. In the REDUCE-IT study, icosapent ethyl (IPE) added to statin therapy reduced initial CV events by 25% and total CV events by 30%, but its effects on coronary atherosclerosis progression have not yet been fully investigated. Therefore, this study is to determine whether IPE 4 g/day will result in a greater change from baseline in plaque volume measured by serial multidetector computed tomography than placebo in statin-treated patients. METHODS AND RESULTS EVAPORATE is a randomized, double-blind, placebo-controlled trial. Patients had to have coronary atherosclerosis by coronary computed tomographic angiography (CCTA) (≥1 angiographic stenoses with ≥20% narrowing), on stable statin therapy with low-density lipoprotein cholesterol levels 40-115 mg/dL, and persistently high triglyceride levels (135-499 mg/dL). Patients underwent an interim scan at 9 months and were followed for an additional 9 months with CCTA at 0, 9, and 18 months. Here, we present the protocol-specified interim efficacy results. A total of 80 patients were enrolled, with 67 completing the 9-month visit and having interpretable CCTA at baseline and at 9 months (age = 57 ± 6 years, male = 36, 63%). At the 9-month interim analysis, there was no significant change in low attenuation plaque (LAP) between active and placebo groups (74% vs. 94%, P = 0.469). However, there was slowing of total non-calcified plaque (sum of LAP, fibrofatty, and fibrous plaque) (35% vs. 43%, P = 0.010), total plaque (non-calcified + calcified plaque) (15% vs. 26%, P = 0.0004), fibrous plaque (17% vs. 40%, P = 0.011), and calcified plaque (-1% vs. 9%, P = 0.001), after adjustment by baseline plaque, age, sex, diabetes, baseline triglyceride levels, and statin use. CONCLUSION EVAPORATE is the first study using CCTA to evaluate the effects of IPE as an adjunct to statin therapy on atherosclerotic plaque characteristics in a high-risk CV population with persistently high triglyceride levels. It provides important mechanistic data in regards to the reduction in CV events in the REDUCE-IT clinical trial. CLINICALTRIALS. GOVIDENTIFIER NCT029226027.
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Affiliation(s)
- Matthew J Budoff
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, CDCRC, Torrance, CA 90502, USA
| | - Joseph B Muhlestein
- Department of Internal Medicine, Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Deepak L Bhatt
- Department of Internal Medicine, Brigham and Women's Hospital Heart & Vascular Center and Harvard Medical School, Boston, MA, USA
| | - Viet T Le Pa
- Department of Internal Medicine, Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA.,Department of Internal Medicine, Rocky Mountain University of Health Profession, Provo, UT, USA
| | - Heidi T May
- Department of Internal Medicine, Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Kashif Shaikh
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, CDCRC, Torrance, CA 90502, USA
| | - Chandana Shekar
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, CDCRC, Torrance, CA 90502, USA
| | - April Kinninger
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, CDCRC, Torrance, CA 90502, USA
| | - Suvasini Lakshmanan
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, CDCRC, Torrance, CA 90502, USA
| | - Sion K Roy
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, CDCRC, Torrance, CA 90502, USA
| | - John Tayek
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, 1124 W Carson Street, CDCRC, Torrance, CA 90502, USA
| | - John R Nelson
- Department of Internal Medicine, California Cardiovascular Institute, Fresno, CA, USA
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Lakshmanan S, Shekar C, Kinninger A, Dahal S, Onuegbu A, Cai AN, Hamal S, Birudaraju D, Cherukuri L, Flores F, Dailing C, Roy SK, Bhatt DL, Nelson JR, Budoff MJ. Association of high-density lipoprotein levels with baseline coronary plaque volumes by coronary CTA in the EVAPORATE trial. Atherosclerosis 2020; 305:34-41. [PMID: 32615321 DOI: 10.1016/j.atherosclerosis.2020.05.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/24/2020] [Accepted: 05/20/2020] [Indexed: 01/18/2023]
Abstract
BACKGROUND AND AIMS Dyslipidemia with elevated triglycerides (TGL) and low high-density lipoprotein cholesterol (HDL-C) predicts residual cardiovascular risk, despite goal LDL-C levels and optimal statin therapy. Coronary plaque characterization by CCTA can provide mechanistic understanding of coronary artery disease and associated prognosis. The role of HDL-C in the pathogenesis of atherosclerosis is not well understood in statin-treated patients with elevated TGL. We sought to examine the association of HDL-C levels with baseline coronary plaque volumes, namely total plaque (TP) and total non-calcified plaque (TNCP) volumes by CCTA in participants enrolled in the EVAPORATE trial. METHODS We analyzed 80 participants who were enrolled in the trial. Linear regression analysis as a univariate and multivariate model adjusted for significant cardiovascular risk factors was performed to evaluate independent association of HDL-C and baseline coronary plaque volumes. In an exploratory analysis, stratified by sex, we compared the association of serum HDL-C levels with baseline coronary plaque volumes in males and females. RESULTS Mean (SD) age of participants (n = 80) was 57.1 (8.6) years and 43% were male. Median (Inter Quartile Range/IQR) log-TNCP volume was 83.0 (0.1-7.3) mm3 and median (IQR) log-TP volume was 144.8 (0.1-7.1) mm3. After adjustment for relevant clinical covariates including age, gender, BMI, hypertension, diabetes, past smoking and baseline TGL levels, increasing levels of HDL-C remain independently associated with lower baseline log-TNCP volumes (β: 0.043 ± 0.021, p = 0.042) and baseline log-TP volumes (β: 0.046 ± 0.022, p = 0.035) on CCTA. On stratifying by sex in a multivariable regression analysis, HDL-C levels were inversely associated with baseline log-TNCP volumes (β: 0.066 ± 0.026, p = 0.018) and log-TP volumes (β: 0.077 ± 0.025, p = 0.004) in females, but not in males (log-TNCP volumes β: 0.038 ± 0.034, p = 0.282) and log-TP volumes (β: -0.033 ± 0.036, p = 0.364). CONCLUSIONS In a cohort of statin treated patients with known atherosclerosis and residually elevated TGL, there was a significant inverse relationship between HDL-C levels and baseline coronary plaque, TP and TNCP volumes on CCTA. Our findings provide more detailed mechanistic evidence regarding the protective role of HDL-C in coronary atherosclerosis in a high-risk cohort. Further investigation to evaluate the interaction of HDL-C levels and coronary plaque volumes on differential CVD risk in statin-treated patients with elevated TGL levels is warranted.
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Affiliation(s)
- Suvasini Lakshmanan
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | | | - April Kinninger
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Suraj Dahal
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Afiachukwu Onuegbu
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Andrew N Cai
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Sajad Hamal
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Divya Birudaraju
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Lavanya Cherukuri
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Ferdinand Flores
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Christopher Dailing
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Sion K Roy
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Deepak L Bhatt
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - John R Nelson
- Department of Cardiology, California Cardiovascular Institute, Fresno, CA, USA
| | - Matthew J Budoff
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA.
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17
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Farukhi ZM, Demler OV, Caulfield MP, Kulkarni K, Wohlgemuth J, Cobble M, Luttmann-Gibson H, Li C, Nelson JR, Cook NR, Buring JE, Krauss RM, Manson JE, Mora S. Comparison of nonfasting and fasting lipoprotein subfractions and size in 15,397 apparently healthy individuals: An analysis from the VITamin D and OmegA-3 TriaL. J Clin Lipidol 2020; 14:241-251. [PMID: 32205068 DOI: 10.1016/j.jacl.2020.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Elevated postprandial triglycerides reflect a proatherogenic milieu, but underlying mechanisms are unclear. OBJECTIVE We examined differences between fasting and nonfasting profiles of directly measured lipoprotein size and subfractions to assess if postprandial triglycerides reflected increases in very low density lipoprotein (VLDL), intermediate density lipoprotein (IDL) and remnants, or small dense lipid depleted LDL (sdLDL) particles. METHODS We conducted a cross-sectional analysis of 15,397 participants (10,135 fasting; 5262 nonfasting [<8 hours since last meal]) from the VITamin D and OmegA-3 TriaL. Baseline cholesterol subfractions were measured by the vertical auto profile method and particle subfractions by ion mobility. We performed multivariable linear regression adjusting for cardiovascular and lipoprotein-modifying risk factors. RESULTS Mean age (SD) was 68.0 years (±7.0), with 50.9% women. Adjusted mean triglyceride concentrations were higher nonfasting by 17.8 ± 1.3%, with higher nonfasting levels of directly measured VLDL cholesterol (by 3.5 ± 0.6%) and total VLDL particles (by 2.0 ± 0.7%), specifically large VLDL (by 12.3 ± 1.3%) and medium VLDL particles (by 5.3 ± 0.8%), all P < .001. By contrast, lower concentrations of low density lipoprotein (LDL) and IDL cholesterol and particles were noted for nonfasting participants. sdLDL cholesterol levels and particle concentrations showed no statistically significant difference by fasting status (-1.3 ± 2.1% and 0.07 ± 0.6%, respectively, P > .05). CONCLUSIONS Directly measured particle and cholesterol concentrations of VLDL, not sdLDL, were higher nonfasting and may partly contribute to the proatherogenicity of postprandial hypertriglyceridemia. These differences, although statistically significant, were small and may not fully explain the increased risk of postprandial hypertriglyceridemia.
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Affiliation(s)
- Zareen M Farukhi
- Center for Lipid Metabolomics, Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Olga V Demler
- Center for Lipid Metabolomics, Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | | | - Heike Luttmann-Gibson
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Chunying Li
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John R Nelson
- California Cardiovascular Institute, Fresno, CA, USA
| | - Nancy R Cook
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ronald M Krauss
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - JoAnn E Manson
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Samia Mora
- Center for Lipid Metabolomics, Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Cardiovascular Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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18
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Abstract
Eicosapentaenoic acid (EPA) is a key anti-inflammatory/anti-aggregatory long-chain polyunsaturated omega-3 fatty acid. Conversely, the omega-6 fatty acid, arachidonic acid (AA) is a precursor to a number of pro-inflammatory/pro-aggregatory mediators. EPA acts competitively with AA for the key cyclooxygenase and lipoxygenase enzymes to form less inflammatory products. As a result, the EPA:AA ratio may be a marker of chronic inflammation, with a lower ratio corresponding to higher levels of inflammation. It is now well established that inflammation plays an important role in cardiovascular disease. This review examines the role of the EPA:AA ratio as a marker of cardiovascular disease and the relationship between changes in the ratio (mediated by EPA intake) and changes in cardiovascular risk. Epidemiological studies have shown that a lower EPA:AA ratio is associated with an increased risk of coronary artery disease, acute coronary syndrome, myocardial infarction, stroke, chronic heart failure, peripheral artery disease, and vascular disease. Increasing the EPA:AA ratio through treatment with purified EPA has been shown in clinical studies to be effective in primary and secondary prevention of coronary artery disease and reduces the risk of cardiovascular events following percutaneous coronary intervention. The EPA:AA ratio is a valuable predictor of cardiovascular risk. Results from ongoing clinical trials will help to define thresholds for EPA treatment associated with better clinical outcomes.
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Affiliation(s)
- J R Nelson
- a California Cardiovascular Institute , Fresno , CA , USA
| | - S Raskin
- b Lipid Clinic , Sutter East Bay Medical Foundation , Oakland , CA , USA
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19
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Nelson JR, He L, Dansinger M. Prevalence of Diabetes Mellitus with REDUCE-IT-Like Indications: Ramifications for Residual Risk and Potential Risk Reduction. J Clin Lipidol 2019. [DOI: 10.1016/j.jacl.2019.04.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Gyanchandani R, Kvam E, Heller R, Finehout E, Smith N, Kota K, Nelson JR, Griffin W, Puhalla S, Brufsky AM, Davidson NE, Lee AV. Whole genome amplification of cell-free DNA enables detection of circulating tumor DNA mutations from fingerstick capillary blood. Sci Rep 2018; 8:17313. [PMID: 30470782 PMCID: PMC6251935 DOI: 10.1038/s41598-018-35470-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/01/2018] [Indexed: 12/25/2022] Open
Abstract
The ability to measure mutations in plasma cell-free DNA (cfDNA) has the potential to revolutionize cancer surveillance and treatment by enabling longitudinal monitoring not possible with solid tumor biopsies. However, obtaining sufficient quantities of cfDNA remains a challenge for assay development and clinical translation; consequently, large volumes of venous blood are typically required. Here, we test proof-of-concept for using smaller volumes via fingerstick collection. Matched venous and fingerstick blood were obtained from seven patients with metastatic breast cancer. Fingerstick blood was separated at point-of-care using a novel paper-based concept to isolate plasma centrifuge-free. Patient cfDNA was then analyzed with or without a new method for whole genome amplification via rolling-circle amplification (WG-RCA). We identified somatic mutations by targeted sequencing and compared the concordance of mutation detection from venous and amplified capillary samples by droplet-digital PCR. Patient mutations were detected with 100% concordance after WG-RCA, although in some samples, allele frequencies showed greater variation likely due to differential amplification or primer inaccessibility. These pilot findings provide physiological evidence that circulating tumor DNA is accessible by fingerstick and sustains presence/absence of mutation detection after whole-genome amplification. Further refinement may enable simpler and less-invasive methods for longitudinal or theranostic surveillance of metastatic cancer.
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Affiliation(s)
- Rekha Gyanchandani
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA.,Western Oncolytics, 265 William Pitt Way, Pittsburgh, PA, 15238, USA
| | - Erik Kvam
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA.
| | - Ryan Heller
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA.,QIAGEN, 100 Cummings Center, Beverly, MA, 01915, USA
| | - Erin Finehout
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA.,Terumo BCT, 10811 Collins Ave, Lakewood, CO, 80215, USA
| | - Nicholas Smith
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Karthik Kota
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - John R Nelson
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA
| | - Weston Griffin
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA
| | - Shannon Puhalla
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Adam M Brufsky
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Nancy E Davidson
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA.,Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA, 98109, USA
| | - Adrian V Lee
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA.
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21
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Budoff M, Brent Muhlestein J, Le VT, May HT, Roy S, Nelson JR. Effect of Vascepa (icosapent ethyl) on progression of coronary atherosclerosis in patients with elevated triglycerides (200-499 mg/dL) on statin therapy: Rationale and design of the EVAPORATE study. Clin Cardiol 2018; 41:13-19. [PMID: 29365351 PMCID: PMC5838559 DOI: 10.1002/clc.22856] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/17/2017] [Accepted: 11/21/2017] [Indexed: 02/02/2023] Open
Abstract
Despite reducing progression and promoting regression of coronary atherosclerosis, statin therapy does not fully address residual cardiovascular (CV) risk. High‐purity eicosapentaenoic acid (EPA) added to a statin has been shown to reduce CV events and induce regression of coronary atherosclerosis in imaging studies; however, data are from Japanese populations without high triglyceride (TG) levels and baseline EPA serum levels greater than those in North American populations. Icosapent ethyl is a high‐purity prescription EPA ethyl ester approved at 4 g/d as an adjunct to diet to reduce TG levels in adults with TG levels >499 mg/dL. The objective of the randomized, double‐blind, placebo‐controlled EVAPORATE study is to evaluate the effects of icosapent ethyl 4 g/d on atherosclerotic plaque in a North American population of statin‐treated patients with coronary atherosclerosis, TG levels of 200 to 499 mg/dL, and low‐density lipoprotein cholesterol levels of 40 to 115 mg/dL. The primary endpoint is change in low‐attenuation plaque volume measured by multidetector computed tomography angiography. Secondary endpoints include incident plaque rates; quantitative changes in different plaque types and morphology; changes in markers of inflammation, lipids, and lipoproteins; and the relationship between these changes and plaque burden and/or plaque vulnerability. Approximately 80 patients will be followed for 9 to 18 months. The clinical implications of icosapent ethyl 4 g/d treatment added to statin therapy on CV endpoints are being evaluated in the large CV outcomes study REDUCE‐IT. EVAPORATE will provide important imaging‐derived data that may add relevance to the clinically derived outcomes from REDUCE‐IT.
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Affiliation(s)
- Matthew Budoff
- Department of Internal Medicine, Los Angeles Biomedical Research Institute, Torrance, California
| | - J Brent Muhlestein
- Department of Internal Medicine, Intermountain Heart Institute, Intermountain Medical Center, Murray, Utah.,Department of Internal Medicine, University of Utah, Salt Lake City
| | - Viet T Le
- Department of Internal Medicine, Intermountain Heart Institute, Intermountain Medical Center, Murray, Utah
| | - Heidi T May
- Department of Internal Medicine, Intermountain Heart Institute, Intermountain Medical Center, Murray, Utah
| | - Sion Roy
- Department of Internal Medicine, Los Angeles Biomedical Research Institute, Torrance, California
| | - John R Nelson
- Department of Cardiology, California Cardiovascular Institute, Fresno, California
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22
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Affiliation(s)
| | | | - Viet Le
- Intermountain Medical Center, Murray, UT, USA
| | - R. Preston Mason
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Elucida Research, Beverly, MA, USA
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23
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Surrette C, Shoudy D, Corwin A, Gao W, Zavodszky MI, Karsten SL, Miller T, Gerdes MJ, Wood N, Nelson JR, Puleo CM. Microfluidic Tissue Mesodissection in Molecular Cancer Diagnostics. SLAS Technol 2016; 22:425-430. [PMID: 27864340 DOI: 10.1177/2211068216680208] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We present a mesodissection platform that retains the advantages of laser-based dissection instrumentation with the speed and ease of manual dissection. Tissue dissection in clinical laboratories is often performed by manually scraping a physician-selected region from standard glass slide mounts. In this manner, costs associated with dissection remain low, but spatial resolution is compromised. In contrast, laser microdissection methods maintain spatial resolution that matches the requirements for analysis of important tissue heterogeneity but remains costly and labor intensive. We demonstrate a microfluidic tool for rapid extraction of histological regions of interest from formalin-fixed paraffin-embedded tissue, which uses a simple and automated method that is compatible with most downstream enzymatic reactions, including protocols used for next-generation DNA sequencing.
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Affiliation(s)
- Christine Surrette
- 1 Electronics Organization, GE Global Research Center, Niskayuna, NY, USA
| | - David Shoudy
- 2 Diagnostics and Biomedical Technologies, GE Global Research Center, Niskayuna, NY, USA
| | - Alex Corwin
- 1 Electronics Organization, GE Global Research Center, Niskayuna, NY, USA
| | - Wei Gao
- 2 Diagnostics and Biomedical Technologies, GE Global Research Center, Niskayuna, NY, USA
| | - Maria I Zavodszky
- 2 Diagnostics and Biomedical Technologies, GE Global Research Center, Niskayuna, NY, USA
| | | | - Todd Miller
- 1 Electronics Organization, GE Global Research Center, Niskayuna, NY, USA
| | - Michael J Gerdes
- 2 Diagnostics and Biomedical Technologies, GE Global Research Center, Niskayuna, NY, USA
| | - Nichole Wood
- 2 Diagnostics and Biomedical Technologies, GE Global Research Center, Niskayuna, NY, USA
| | - John R Nelson
- 2 Diagnostics and Biomedical Technologies, GE Global Research Center, Niskayuna, NY, USA
| | - Chris M Puleo
- 1 Electronics Organization, GE Global Research Center, Niskayuna, NY, USA
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24
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Philip S, Chowdhury S, Nelson JR, Benjamin Everett P, Hulme-Lowe CK, Schmier JK. A novel cost-effectiveness model of prescription eicosapentaenoic acid extrapolated to secondary prevention of cardiovascular diseases in the United States. J Med Econ 2016; 19:1003-10. [PMID: 27352086 DOI: 10.1080/13696998.2016.1207652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVE Given the substantial economic and health burden of cardiovascular disease and the residual cardiovascular risk that remains despite statin therapy, adjunctive therapies are needed. The purpose of this model was to estimate the cost-effectiveness of high-purity prescription eicosapentaenoic acid (EPA) omega-3 fatty acid intervention in secondary prevention of cardiovascular diseases in statin-treated patient populations extrapolated to the US. METHODS The deterministic model utilized inputs for cardiovascular events, costs, and utilities from published sources. Expert opinion was used when assumptions were required. The model takes the perspective of a US commercial, third-party payer with costs presented in 2014 US dollars. The model extends to 5 years and applies a 3% discount rate to costs and benefits. Sensitivity analyses were conducted to explore the influence of various input parameters on costs and outcomes. RESULTS Using base case parameters, EPA-plus-statin therapy compared with statin monotherapy resulted in cost savings (total 5-year costs $29,393 vs $30,587 per person, respectively) and improved utilities (average 3.627 vs 3.575, respectively). The results were not sensitive to multiple variations in model inputs and consistently identified EPA-plus-statin therapy to be the economically dominant strategy, with both lower costs and better patient utilities over the modeled 5-year period. LIMITATIONS The model is only an approximation of reality and does not capture all complexities of a real-world scenario without further inputs from ongoing trials. The model may under-estimate the cost-effectiveness of EPA-plus-statin therapy because it allows only a single event per patient. CONCLUSION This novel model suggests that combining EPA with statin therapy for secondary prevention of cardiovascular disease in the US may be a cost-saving and more compelling intervention than statin monotherapy.
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Affiliation(s)
| | | | - John R Nelson
- c California Cardiovascular Institute , Fresno , CA , USA
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L'Italien GJ, Nelson JR, Mathur VS, Mason RP, Chowdhury PR, Philip S, Kulkarni K, Murthy V, Vemuri D, Shah U, Valencia R, Nanda N, Deedwania PC, Chowdhury S. Abstract 410: Link Between Hypertension and Insulin Resistance in South Asians: Implications for Prevention of Cardiovascular Complications. Arterioscler Thromb Vasc Biol 2016. [DOI: 10.1161/atvb.36.suppl_1.410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background:
The coexistence of hypertension (HTN) and insulin resistance (IR) substantially increases cardiovascular risk (CVR) and diabetes (DM) perhaps by endothelial dysfunction from low-grade chronic inflammation and oxidative stress. South Asian immigrants in United States (SA-USA) have a high salt consumption, IR, and salt sensitivity. The triglyceride (TG)/ HDL ratio is a known correlate of IR with ratios ≥3.5 associated with high risk. It is unknown whether SA-USA have a coexistence of HTN, IR, and DM resulting in high CVR.
Methods:
We reviewed the clinical history and Vertical Auto Profile technology (VAP) + lipid panel utilizing ultracentrifugation to directly measure lipid sub-fractions, for 348 participants (42% women) of the South Asian Cardiovascular Registry. Prevalent DM and Pre-DM were defined as HbA1c ≥ 6.5 and 5.7-6.4, respectively.
Results:
Of the 348 participants, mean age 55.3 years, 128 had HTN and were stratified into clinical risk groups based on fasting TG (mg/dL) levels: TG<150 (n=69), TG 150-199 (n=24), TG 200-499 (n=32), TG>500 (n=3). The corresponding TG/HDL ratios were: 1.7, 3.5, 6.2, and 20.4, respectively; the median TG (mg/dL) levels were: 100, 182, 268, and 572, respectively; the median LDL (mg/dL) levels were: 113, 144, 133, 102, respectively; the rates of DM were: 13%, 17%, 38%, and 67%; and the rates of Pre-DM/DM were: 62%, 63%, 78%, and 67%, respectively. Relative Risk for DM with TG/HDL≥ 3.5 was 3.6 (46 % had TG/HDL ≥ 3.5).
Conclusions:
South Asian immigrants participating in a community registry have: 1) A high rate of coexistence of HTN and IR portending a very high relative risk of diabetes. 2) A discordance of LDL levels and IR in patients with HTN. As IR gets higher, the relative risk of diabetes goes up but LDL levels decline.
Clinical Implications:
South Asian immigrants in the United States have a diet that is very high in salt, simple carbohydrates, and saturated fat. Many are vegetarian with no consumption of fish. Public health efforts to help reduce risk of CVD in South Asian immigrants should focus on low salt diet, with consumption of multigrain complex carbohydrates, poly-unsaturated fatty acids, omega-3 fatty acids, and lifestyle changes to reduce metabolic syndrome, diabetes, and hypertension.
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Affiliation(s)
- Gilbert J L'Italien
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - John R Nelson
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - Virendra S Mathur
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - R. Preston Mason
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - Palash R Chowdhury
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - Sephy Philip
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - Kris Kulkarni
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - Vemuri Murthy
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - Dwarka Vemuri
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - Uday Shah
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - Robert Valencia
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - Navin Nanda
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
| | - Prakash C Deedwania
- South Asian Healthcare Foundation, South Asian Healthcare Foundation, Sugar Land, TX
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Abstract
BACKGROUND/OBJECTIVES Epidemiological, diet-based, and some interventional outcomes studies suggest that polyunsaturated omega-3 fatty acids (OM3FAs), specifically eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), confer cardiovascular protection in some patient populations. This review examines the historical context of OM3FAs in cardiovascular disease and future perspectives on the place of OM3FA products in reducing cardiovascular risk. METHODS Relevant articles were identified via PubMed/Medline and Google Scholar searches through 2015 and through reference lists of selected publications. Articles determined by the authors to be relevant to the topic of this review were included. RESULTS Review of the identified articles indicated that inconsistent results among interventional outcomes studies have been attributed to use of low doses of OM3FAs, patient cohorts with non-elevated triglyceride (TG) levels, differential use of concomitant statin therapy, and study designs with insufficient statistical power. Several prescription OM3FA products are now approved as an adjunct to diet to reduce TG levels in adults with severe (≥500 mg/dL) hypertriglyceridemia. Most formulations contain both EPA and DHA; one formulation contains purified EPA. In randomized controlled trials, these products significantly reduced TG levels in patients with very high TG levels (≥500 mg/dL [≥13.0 mmol/L]) and in statin-treated patients with high TG levels (200-499 mg/dL [5.2-12.9 mmol/L]). The DHA-containing products raised LDL-C levels in these studies, whereas the EPA-only product had no effect on LDL-C, suggesting that all OM3FA prescription products are not therapeutically equivalent. Besides lowering TG levels, OM3FAs (particularly EPA) exert anti-inflammatory effects and may slow multiple atherogenic processes. Two well designed interventional outcomes studies (REDUCE-IT and STRENGTH) are evaluating prescription-strength, high-dose OM3FAs (4 g/day) in statin-treated patients with persistently high TG levels. CONCLUSIONS The results of the ongoing prescription-strength, high-dose OM3FA interventional trials will help define the potential role of OM3FAs in addressing residual cardiovascular risk despite statin therapy.
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Affiliation(s)
- Laurence S Sperling
- a a Emory University School of Medicine and Rollins School of Public Health at Emory University , Atlanta , GA , USA
| | - John R Nelson
- b b UCSF School of Medicine, Fresno-Medicine Residency Program-Volunteer , Fresno , CA , USA
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May HT, Nelson JR, Lirette ST, Kulkarni KR, Anderson JL, Griswold ME, Horne BD, Correa A, Muhlestein JB. The utility of the apolipoprotein A1 remnant ratio in predicting incidence coronary heart disease in a primary prevention cohort: The Jackson Heart Study. Eur J Prev Cardiol 2015; 23:769-76. [PMID: 26481445 DOI: 10.1177/2047487315612733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/29/2015] [Indexed: 01/14/2023]
Abstract
BACKGROUND Dyslipidemia plays a significant role in the progression of cardiovascular disease. The apolipoprotein (apo) A1 remnant ratio (apo A1/VLDL3-C + IDL-C) has recently been shown to be a strong predictor of death/myocardial infarction risk among women >50 years undergoing angiography. However, whether this ratio is associated with coronary heart disease risk among other populations is unknown. We evaluated the apo A1 remnant ratio and its components for coronary heart disease incidence. DESIGN Observational. METHODS Participants (N = 4722) of the Jackson Heart Study were evaluated. Baseline clinical characteristics and lipoprotein subfractions (Vertical Auto Profile method) were collected. Cox hazard regression analysis, adjusted by standard cardiovascular risk factors, was utilized to determine associations of lipoproteins with coronary heart disease. RESULTS Those with new-onset coronary heart disease were older, diabetic, smokers, had less education, used more lipid-lowering medication, and had a more atherogenic lipoprotein profile. After adjustment, the apo A1 remnant ratio (hazard ratio = 0.67 per 1-SD, p = 0.002) was strongly associated with coronary heart disease incidence. This association appears to be driven by the IDL-C denominator (hazard ratio = 1.23 per 1-SD, p = 0.007). Remnants (hazard ratio = 1.21 per 1-SD, p = 0.017), but not apo A1 (hazard ratio = 0.85 per 1-SD, p = 0.121) or VLDL3-C (hazard ratio = 1.13 per 1-SD, p = 0.120) were associated with coronary heart disease. Standard lipids were not associated with coronary heart disease incidence. CONCLUSION We found the apo A1 remnant ratio to be strongly associated with coronary heart disease. This ratio appears to better stratify risk than standard lipids, apo A1, and remnants among a primary prevention cohort of African Americans. Its utility requires further study as a lipoprotein management target for risk reduction.
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Affiliation(s)
| | | | | | | | - Jeffrey L Anderson
- Intermountain Medical Center, Murray, USA University of Utah, Salt Lake City, USA
| | | | - Benjamin D Horne
- Intermountain Medical Center, Murray, USA University of Utah, Salt Lake City, USA
| | - Adolfo Correa
- University of Mississippi Medical Center, Jackson, USA
| | - Joseph B Muhlestein
- Intermountain Medical Center, Murray, USA University of Utah, Salt Lake City, USA
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Borow KM, Nelson JR, Mason RP. Biologic plausibility, cellular effects, and molecular mechanisms of eicosapentaenoic acid (EPA) in atherosclerosis. Atherosclerosis 2015; 242:357-66. [DOI: 10.1016/j.atherosclerosis.2015.07.035] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/06/2015] [Accepted: 07/20/2015] [Indexed: 01/08/2023]
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Nelson JR. Hospital medicine viewed through practice management dictums. J Hosp Med 2015; 10:637-8. [PMID: 26126721 DOI: 10.1002/jhm.2413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/22/2015] [Accepted: 05/27/2015] [Indexed: 11/12/2022]
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Abstract
Whole-genome amplification by multiple displacement amplification (MDA) is a patented method to generate potentially unlimited genomic material when researchers are challenged with trace samples, or the amount of genomic DNA required for analysis exceeds the amount on hand. It is an isothermal reaction, using Phi29 DNA polymerase and random hexamer primers for unbiased amplification of linear DNA molecules, such as genomic DNA. The random-primed MDA reaction provides extensive amplification coverage of the genome, generates extremely long DNA products, and provides high DNA yields. This unit explains the reaction, and describes use of the commercial kits available.
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May HT, Nelson JR, Kulkarni KR, Anderson JL, Horne BD, Bair TL, Muhlestein JB. A new ratio for better predicting future death/myocardial infarction than standard lipid measurements in women >50 years undergoing coronary angiography: the apolipoprotein A1 remnant ratio (Apo A1/ [VLDL₃+IDL]). Lipids Health Dis 2013; 12:55. [PMID: 23621905 PMCID: PMC3653758 DOI: 10.1186/1476-511x-12-55] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Women often lag behind men in their risk of cardiovascular events. However, with age and the onset of menopause, women's cardiovascular risk eventually becomes similar to that of men. This change in risk may, in part, be attributable to a shift to a more atherogenic lipid profile. Our objective was to evaluate standard- and sub-lipid parameters and the apo A1 remnant ratio: (apo A1/[VLDL₃-C+IDL-C]) for their associations with death/myocardial infarction among peri- and post-menopausal women. METHODS Women (N=711) >50 years of age undergoing coronary angiography were evaluated. Baseline clinical and angiographic characteristics, lipids, and sub-lipid levels (Vertical Auto Profile method) were collected. Cox regression analysis, adjusted by standard cardiovascular risk factors, was utilized to determine associations of lipid and sub-lipid tertiles(T) with death/myocardial infarction at 1 and 3 years. RESULTS Patients averaged 67.7±9.4 years and 53.6% had underlying severe (≥70% stenosis) coronary artery disease. The apo A1 remnant ratio was found to have stronger associations for 1 year (T1 vs. T3: HR=2.13, p=0.03, T2 vs. T3: HR=1.57, p=0.21) and 3 year (T1 vs. T3: HR=2.32, p=0.002, T2 vs. T3: HR=1.97, p=0.01) death/myocardial infarction than any individual lipid (LDL-C, HDL-C, triglycerides, non-HDL-C) or sub-lipid (apo A1, apo B, VLDL₃-C+IDL-C) measure, or any other well-known ratio (triglyercies/HDL-C, apo B/A1, TChol/HDL-C, HDL-C/[VLDL₃-C+IDL-C]). CONCLUSIONS The apo A1 remnant ratio was a significant predictor of short and intermediate-term death/myocardial infarction risk among women >50 years of age. Furthermore, this ratio was found to have greater predictive ability than traditional lipid and sub-lipid parameters and represents a potential new risk marker.
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Affiliation(s)
- Heidi T May
- Intermountain Medical Center, Cardiovascular Department, 5121 S. Cottonwood Street, Murray, UT 84157, USA.
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Affiliation(s)
- John R Nelson
- Overlake Hospital Medical Center, 1034 NE 116th Ave, Bellevue, WA 98004, USA.
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Glenzer SH, MacGowan BJ, Meezan NB, Adams PA, Alfonso JB, Alger ET, Alherz Z, Alvarez LF, Alvarez SS, Amick PV, Andersson KS, Andrews SD, Antonini GJ, Arnold PA, Atkinson DP, Auyang L, Azevedo SG, Balaoing BNM, Baltz JA, Barbosa F, Bardsley GW, Barker DA, Barnes AI, Baron A, Beeler RG, Beeman BV, Belk LR, Bell JC, Bell PM, Berger RL, Bergonia MA, Bernardez LJ, Berzins LV, Bettenhausen RC, Bezerides L, Bhandarkar SD, Bishop CL, Bond EJ, Bopp DR, Borgman JA, Bower JR, Bowers GA, Bowers MW, Boyle DT, Bradley DK, Bragg JL, Braucht J, Brinkerhoff DL, Browning DF, Brunton GK, Burkhart SC, Burns SR, Burns KE, Burr B, Burrows LM, Butlin RK, Cahayag NJ, Callahan DA, Cardinale PS, Carey RW, Carlson JW, Casey AD, Castro C, Celeste JR, Chakicherla AY, Chambers FW, Chan C, Chandrasekaran H, Chang C, Chapman RF, Charron K, Chen Y, Christensen MJ, Churby AJ, Clancy TJ, Cline BD, Clowdus LC, Cocherell DG, Coffield FE, Cohen SJ, Costa RL, Cox JR, Curnow GM, Dailey MJ, Danforth PM, Darbee R, Datte PS, Davis JA, Deis GA, Demaret RD, Dewald EL, Di Nicola P, Di Nicola JM, Divol L, Dixit S, Dobson DB, Doppner T, Driscoll JD, Dugorepec J, Duncan JJ, Dupuy PC, Dzenitis EG, Eckart MJ, Edson SL, Edwards GJ, Edwards MJ, Edwards OD, Edwards PW, Ellefson JC, Ellerbee CH, Erbert GV, Estes CM, Fabyan WJ, Fallejo RN, Fedorov M, Felker B, Fink JT, Finney MD, Finnie LF, Fischer MJ, Fisher JM, Fishler BT, Florio JW, Forsman A, Foxworthy CB, Franks RM, Frazier T, Frieder G, Fung T, Gawinski GN, Gibson CR, Giraldez E, Glenn SM, Golick BP, Gonzales H, Gonzales SA, Gonzalez MJ, Griffin KL, Grippen J, Gross SM, Gschweng PH, Gururangan G, Gu K, Haan SW, Hahn SR, Haid BJ, Hamblen JE, Hammel BA, Hamza AV, Hardy DL, Hart DR, Hartley RG, Haynam CA, Heestand GM, Hermann MR, Hermes GL, Hey DS, Hibbard RL, Hicks DG, Hinkel DE, Hipple DL, Hitchcock JD, Hodtwalker DL, Holder JP, Hollis JD, Holtmeier GM, Huber SR, Huey AW, Hulsey DN, Hunter SL, Huppler TR, Hutton MS, Izumi N, Jackson JL, Jackson MA, Jancaitis KS, Jedlovec DR, Johnson B, Johnson MC, Johnson T, Johnston MP, Jones OS, Kalantar DH, Kamperschroer JH, Kauffman RL, Keating GA, Kegelmeyer LM, Kenitzer SL, Kimbrough JR, King K, Kirkwood RK, Klingmann JL, Knittel KM, Kohut TR, Koka KG, Kramer SW, Krammen JE, Krauter KG, Krauter GW, Krieger EK, Kroll JJ, La Fortune KN, Lagin LJ, Lakamsani VK, Landen OL, Lane SW, Langdon AB, Langer SH, Lao N, Larson DW, Latray D, Lau GT, Le Pape S, Lechleiter BL, Lee Y, Lee TL, Li J, Liebman JA, Lindl JD, Locke SF, Loey HK, London RA, Lopez FJ, Lord DM, Lowe-Webb RR, Lown JG, Ludwigsen AP, Lum NW, Lyons RR, Ma T, MacKinnon AJ, Magat MD, Maloy DT, Malsbury TN, Markham G, Marquez RM, Marsh AA, Marshall CD, Marshall SR, Maslennikov IL, Mathisen DG, Mauger GJ, Mauvais MY, McBride JA, McCarville T, McCloud JB, McGrew A, McHale B, MacPhee AG, Meeker JF, Merill JS, Mertens EP, Michel PA, Miller MG, Mills T, Milovich JL, Miramontes R, Montesanti RC, Montoya MM, Moody J, Moody JD, Moreno KA, Morris J, Morriston KM, Nelson JR, Neto M, Neumann JD, Ng E, Ngo QM, Olejniczak BL, Olson RE, Orsi NL, Owens MW, Padilla EH, Pannell TM, Parham TG, Patterson RW, Pavel G, Prasad RR, Pendlton D, Penko FA, Pepmeier BL, Petersen DE, Phillips TW, Pigg D, Piston KW, Pletcher KD, Powell CL, Radousky HB, Raimondi BS, Ralph JE, Rampke RL, Reed RK, Reid WA, Rekow VV, Reynolds JL, Rhodes JJ, Richardson MJ, Rinnert RJ, Riordan BP, Rivenes AS, Rivera AT, Roberts CJ, Robinson JA, Robinson RB, Robison SR, Rodriguez OR, Rogers SP, Rosen MD, Ross GF, Runkel M, Runtal AS, Sacks RA, Sailors SF, Salmon JT, Salmonson JD, Saunders RL, Schaffer JR, Schindler TM, Schmitt MJ, Schneider MB, Segraves KS, Shaw MJ, Sheldrick ME, Shelton RT, Shiflett MK, Shiromizu SJ, Shor M, Silva LL, Silva SA, Skulina KM, Smauley DA, Smith BE, Smith LK, Solomon AL, Sommer S, Soto JG, Spafford NI, Speck DE, Springer PT, Stadermann M, Stanley F, Stone TG, Stout EA, Stratton PL, Strausser RJ, Suter LJ, Sweet W, Swisher MF, Tappero JD, Tassano JB, Taylor JS, Tekle EA, Thai C, Thomas CA, Thomas A, Throop AL, Tietbohl GL, Tillman JM, Town RPJ, Townsend SL, Tribbey KL, Trummer D, Truong J, Vaher J, Valadez M, Van Arsdall P, Van Prooyen AJ, Vergel de Dios EO, Vergino MD, Vernon SP, Vickers JL, Villanueva GT, Vitalich MA, Vonhof SA, Wade FE, Wallace RJ, Warren CT, Warrick AL, Watkins J, Weaver S, Wegner PJ, Weingart MA, Wen J, White KS, Whitman PK, Widmann K, Widmayer CC, Wilhelmsen K, Williams EA, Williams WH, Willis L, Wilson EF, Wilson BA, Witte MC, Work K, Yang PS, Young BK, Youngblood KP, Zacharias RA, Zaleski T, Zapata PG, Zhang H, Zielinski JS, Kline JL, Kyrala GA, Niemann C, Kilkenny JD, Nikroo A, Van Wonterghem BM, Atherton LJ, Moses EI. Demonstration of ignition radiation temperatures in indirect-drive inertial confinement fusion hohlraums. Phys Rev Lett 2011; 106:085004. [PMID: 21405580 DOI: 10.1103/physrevlett.106.085004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Indexed: 05/30/2023]
Abstract
We demonstrate the hohlraum radiation temperature and symmetry required for ignition-scale inertial confinement fusion capsule implosions. Cryogenic gas-filled hohlraums with 2.2 mm-diameter capsules are heated with unprecedented laser energies of 1.2 MJ delivered by 192 ultraviolet laser beams on the National Ignition Facility. Laser backscatter measurements show that these hohlraums absorb 87% to 91% of the incident laser power resulting in peak radiation temperatures of T(RAD)=300 eV and a symmetric implosion to a 100 μm diameter hot core.
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Affiliation(s)
- S H Glenzer
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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Shelton RT, Kamperschroer JH, Lagin LJ, Nelson JR, O'Brien DW. Target diagnostic control system implementation for the National Ignition Facility (invited). Rev Sci Instrum 2010; 81:10E101. [PMID: 21033966 DOI: 10.1063/1.3464576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The extreme physics of targets shocked by NIF's 192-beam laser is observed by a diverse suite of diagnostics. Many diagnostics are being developed by collaborators at other sites, but ad hoc controls could lead to unreliable and costly operations. A diagnostic control system (DCS) framework for both hardware and software facilitates development and eases integration. Each complex diagnostic typically uses an ensemble of electronic instruments attached to sensors, digitizers, cameras, and other devices. In the DCS architecture each instrument is interfaced to a low-cost WINDOWS XP processor and JAVA application. Each instrument is aggregated with others as needed in the supervisory system to form an integrated diagnostic. The JAVA framework provides data management, control services, and operator graphical user interface generation. DCS instruments are reusable by replication with reconfiguration for specific diagnostics in extensible markup language. Advantages include minimal application code, easy testing, and high reliability. Collaborators save costs by assembling diagnostics with existing DCS instruments. This talk discusses target diagnostic instrumentation used on NIF and presents the DCS architecture and framework.
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Affiliation(s)
- R T Shelton
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA.
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Archambault P, Snelgrove PVR, Fisher JAD, Gagnon JM, Garbary DJ, Harvey M, Kenchington EL, Lesage V, Levesque M, Lovejoy C, Mackas DL, McKindsey CW, Nelson JR, Pepin P, Piché L, Poulin M. From sea to sea: Canada's three oceans of biodiversity. PLoS One 2010; 5:e12182. [PMID: 20824204 PMCID: PMC2930843 DOI: 10.1371/journal.pone.0012182] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 07/23/2010] [Indexed: 11/19/2022] Open
Abstract
Evaluating and understanding biodiversity in marine ecosystems are both necessary and challenging for conservation. This paper compiles and summarizes current knowledge of the diversity of marine taxa in Canada's three oceans while recognizing that this compilation is incomplete and will change in the future. That Canada has the longest coastline in the world and incorporates distinctly different biogeographic provinces and ecoregions (e.g., temperate through ice-covered areas) constrains this analysis. The taxonomic groups presented here include microbes, phytoplankton, macroalgae, zooplankton, benthic infauna, fishes, and marine mammals. The minimum number of species or taxa compiled here is 15,988 for the three Canadian oceans. However, this number clearly underestimates in several ways the total number of taxa present. First, there are significant gaps in the published literature. Second, the diversity of many habitats has not been compiled for all taxonomic groups (e.g., intertidal rocky shores, deep sea), and data compilations are based on short-term, directed research programs or longer-term monitoring activities with limited spatial resolution. Third, the biodiversity of large organisms is well known, but this is not true of smaller organisms. Finally, the greatest constraint on this summary is the willingness and capacity of those who collected the data to make it available to those interested in biodiversity meta-analyses. Confirmation of identities and intercomparison of studies are also constrained by the disturbing rate of decline in the number of taxonomists and systematists specializing on marine taxa in Canada. This decline is mostly the result of retirements of current specialists and to a lack of training and employment opportunities for new ones. Considering the difficulties encountered in compiling an overview of biogeographic data and the diversity of species or taxa in Canada's three oceans, this synthesis is intended to serve as a biodiversity baseline for a new program on marine biodiversity, the Canadian Healthy Ocean Network. A major effort needs to be undertaken to establish a complete baseline of Canadian marine biodiversity of all taxonomic groups, especially if we are to understand and conserve this part of Canada's natural heritage.
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Affiliation(s)
- Philippe Archambault
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Rimouski, Province de Quebec, Canada.
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Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, Vezenov DV. The challenges of sequencing by synthesis. Nat Biotechnol 2009; 27:1013-23. [PMID: 19898456 DOI: 10.1038/nbt.1585] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA sequencing-by-synthesis (SBS) technology, using a polymerase or ligase enzyme as its core biochemistry, has already been incorporated in several second-generation DNA sequencing systems with significant performance. Notwithstanding the substantial success of these SBS platforms, challenges continue to limit the ability to reduce the cost of sequencing a human genome to $100,000 or less. Achieving dramatically reduced cost with enhanced throughput and quality will require the seamless integration of scientific and technological effort across disciplines within biochemistry, chemistry, physics and engineering. The challenges include sample preparation, surface chemistry, fluorescent labels, optimizing the enzyme-substrate system, optics, instrumentation, understanding tradeoffs of throughput versus accuracy, and read-length/phasing limitations. By framing these challenges in a manner accessible to a broad community of scientists and engineers, we hope to solicit input from the broader research community on means of accelerating the advancement of genome sequencing technology.
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Affiliation(s)
- Carl W Fuller
- GE Healthcare Life Sciences, Piscataway, New Jersey, USA.
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Glasheen JJ, Goldenberg J, Nelson JR. Achieving hospital medicine's promise through internal medicine residency redesign. Mt Sinai J Med 2008; 75:436-441. [PMID: 18828165 DOI: 10.1002/msj.20077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The promise of the hospital medicine movement is that the hospitalist model of care will provide better outcomes than the system it replaced. This means improving the quality and processes of care, reducing inefficiencies and lowering costs. Despite some documented improvements in these areas hospitalists have yet to achieve their pinnacle. These shortfalls likely result from training providers in residencies that have yet to evolve to address the specific needs of hospitalists. While most internal medicine residency training programs stress inpatient care they underemphasize key components of a successful hospitalist career. This paper overviews the state of the hospitalist movement, the current educational training deficiencies and the methods to deliver hospitalist-focused training.
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Affiliation(s)
- Jeffrey J Glasheen
- Department of Medicine, Division of General Internal Medicine, Hospital Medicine Section, University of Colorado at Denver Health Sciences Center, Denver, CO, USA.
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Kumar S, Sood A, Wegener J, Finn PJ, Nampalli S, Nelson JR, Sekher A, Mitsis P, Macklin J, Fuller CW. Terminal phosphate labeled nucleotides: synthesis, applications, and linker effect on incorporation by DNA polymerases. Nucleosides Nucleotides Nucleic Acids 2005; 24:401-8. [PMID: 16247959 DOI: 10.1081/ncn-200059823] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A number of terminal phosphate-labeled nucleotides with three or more phosphates and with varied length linkers attached between the terminal phosphate and the dye have been synthesized. These nucleotides have been tested as substrates for different DNA and RNA polymerases. We have also explored their utility in DNA sequencing, SNP analysis, nucleic acid amplification, quantitative PCR, and other biochemical assays.
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Affiliation(s)
- Shiv Kumar
- GE Healthcare, 800 Centennial Ave., Piscataway, NJ 08855-1327, USA
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40
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Jouvencel P, Tourneux P, Pérez T, Sauret A, Nelson JR, Brissaud O, Demarquez JL. Cathéters centraux et épanchements péricardiques en période néonatale : étude rétrospective multicentrique. Arch Pediatr 2005; 12:1456-61. [PMID: 16084702 DOI: 10.1016/j.arcped.2005.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2004] [Accepted: 06/04/2005] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To evaluate the use of neonatal central venous catheters (CVC) in 38 french neonatal units and occurrence of pericardial effusion (PCE) over the past 5 years. MATERIALS AND METHODS We surveyed 38 units with a questionnaire and studied the cases of PCE in five units. RESULTS Response rate was 89% (34/38). Accepted CVC tip positions were: junction of right atrium (RA) and vena cava (VC) 76%, VC 58%, RA 11%. Fifty percent of the centers had been exposed to PCE. 16 cases of PCE were studied. Median gestational age was 31 weeks (range: 26.1 to 40 weeks). Median time from insertion: 3.2 days (range: 0.4-13.5). In all cases CVC tip was intracardiac at insertion with inadequate withdrawing in 13 cases. Sudden cardiac collapse was reported in eight cases, and unexplained cardiorespiratory instability in six cases. Echography showed PCE in 14 cases. One diagnosis was post-mortem. CVC was withdrawn in 12 patients and 13 underwent pericardiocentesis. Four patients died and two had neurological sequelae. CONCLUSION PCE was associated with intracardiac CVC tip. The CVC tip should be controlled with radiography or echography outside the cardiac silhouette. PCE diagnosis must be considered in face of unexplained cardiovascular decompensation of neonate with CVC.
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Affiliation(s)
- P Jouvencel
- Service de pédiatrie et néonatologie, 13, avenue Interne J.-Loëb, centre hospitalier de la Côte Basque, 64100 Bayonne, France.
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Sood A, Kumar S, Nampalli S, Nelson JR, Macklin J, Fuller CW. Terminal phosphate-labeled nucleotides with improved substrate properties for homogeneous nucleic acid assays. J Am Chem Soc 2005; 127:2394-5. [PMID: 15724985 DOI: 10.1021/ja043595x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleotides with a dye attached to the terminal phosphate with four or more phosphates (tetra- or pentaphosphates) are superior substrates than the corresponding triphosphates for DNA and RNA polymerases. When fluorogenic dyes are directly attached to the terminal phosphate, they can be released by the action of polymerase and alkaline phosphatase. The released dye changes color and fluorescence properties. The fluorescent signal can also be amplified by using multiple labeled nucleotides to detect small amounts of template. We have explored the utility of these nucleotides in a variety of applications including homogeneous SNP detection methods, DNA sequencing, and quantitation of PCR and RCA.
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Affiliation(s)
- Anup Sood
- GE Healthcare, 800 Centennial Avenue, Piscataway, New Jersey 08855, USA
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42
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Nampalli S, Finn PJ, Sun L, Xiao H, Nelson JR, Grossmann G, Flick PK, Fuller CW, Kumar S. Negatively charged, dye labeled-dideoxynucleotides for "direct-load" DNA sequencing. Nucleosides Nucleotides Nucleic Acids 2003; 22:1471-4. [PMID: 14565445 DOI: 10.1081/ncn-120023013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A four-color set of negatively charged, single dye as well as energy transfer dye labeled-ddNTPs were synthesized and evaluated in combination with a novel polymerase in a "direct-load" DNA sequencing, obviating the laborious and time consuming post-reaction work-up.
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Affiliation(s)
- Satyam Nampalli
- Amersham Biosciences, Piscataway, New Jersey 08855-1327, USA
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43
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Finn PJ, Bull MG, Xiao H, Phillips PD, Nelson JR, Grossmann G, Nampalli S, McArdle BF, Mamone JA, Flick PK, Fuller CW, Kumar S. Efficient incorporation of positively charged 2', 3'-dideoxynucleoside-5'-triphosphates by DNA polymerases and their application in 'direct-load' DNA sequencing. Nucleic Acids Res 2003; 31:4769-78. [PMID: 12907718 PMCID: PMC169923 DOI: 10.1093/nar/gkg669] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A series of charge-modified, dye-labeled 2', 3'-dideoxynucleoside-5'-triphosphates have been synthesized and evaluated as reagents for dye-terminator DNA sequencing. Unlike the commonly used dye-labeled terminators, these terminators possess a net positive charge and migrate in the opposite direction to dye-labeled Sanger fragments during electrophoresis. Post-sequencing reaction purification is not required to remove unreacted nucleotide or associated breakdown products prior to electrophoresis. Thus, DNA sequencing reaction mixtures can be loaded directly onto a separating medium such as a sequencing gel. The charge-modified nucleotides have also been shown to be more efficiently incorporated by a number of DNA polymerases than regular dye-labeled dideoxynucleotide terminators or indeed normal dideoxynucleoside-5'-triphosphates.
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Affiliation(s)
- Patrick J Finn
- Amersham Biosciences, 800 Centennial Avenue, Piscataway, NJ 08855-1327, USA
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Lawrence CW, Gibbs PE, Murante RS, Wang XD, Li Z, McManus TP, McGregor WG, Nelson JR, Hinkle DC, Maher VM. Roles of DNA polymerase zeta and Rev1 protein in eukaryotic mutagenesis and translesion replication. Cold Spring Harb Symp Quant Biol 2003; 65:61-9. [PMID: 12760021 DOI: 10.1101/sqb.2000.65.61] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- C W Lawrence
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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Detter JC, Jett JM, Lucas SM, Dalin E, Arellano AR, Wang M, Nelson JR, Chapman J, Lou Y, Rokhsar D, Hawkins TL, Richardson PM. Isothermal strand-displacement amplification applications for high-throughput genomics. Genomics 2002; 80:691-8. [PMID: 12523365 DOI: 10.1006/geno.2002.7020] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Amplification of source DNA is a nearly universal requirement for molecular biology applications. The primary methods currently available to researchers are limited to in vivo amplification in Escherichia coli hosts and the polymerase chain reaction. Rolling-circle DNA replication is a well-known method for synthesis of phage genomes and recently has been applied as rolling circle amplification (RCA) of specific target sequences as well as circular vectors used in cloning. Here, we demonstrate that RCA using random hexamer primers with 29 DNA polymerase can be used for strand-displacement amplification of different vector constructs containing a variety of insert sizes to produce consistently uniform template for end-sequencing reactions. We show this procedure to be especially effective in a high-throughput plasmid production sequencing process. In addition, we demonstrate that whole bacterial genomes can be effectively amplified from cells or small amounts of purified genomic DNA without apparent bias for use in downstream applications, including whole genome shotgun sequencing.
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Affiliation(s)
- John C Detter
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
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46
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Geehr EC, Nelson JR. Hospitalists: who they are and what they do. Physician Exec 2002; 28:26-31. [PMID: 12448139] [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] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
The hospitalist movement is spreading like wildfire. Find out the latest statistics on hospitalists.
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Abstract
This article has discussed several fundamental concepts in the development and implementation of a hospitalist program. Perhaps the two most important barriers to the success of hospitalist practices are lack of buy-in from PCPs and other physicians (which is becoming much less common) and the inability to gain durable financial support from the hospital or other sponsoring entity. These issues always should be addressed before starting a program. Systems for adequate communication between hospitalists and community physicians will ensure buy-in is maintained. Unique challenges for those administering a hospitalist group include physician scheduling that balances continuity with a sustainable career track. Finally, providing leadership with a medical director increases the likelihood that operational problems are quickly managed, and that strategic planning takes place to ensure the future success of the program.
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Affiliation(s)
- John R Nelson
- Overlake Hospital Medical Center, 1035 N.E. 116th Avenue, Bellevue, WA 98004, USA.
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Finn PJ, Sun L, Nampalli S, Xiao H, Nelson JR, Mamone JA, Grossmann G, Flick PK, Fuller CW, Kumar S. Synthesis and application of charge-modified dye-labeled dideoxynucleoside-5'-triphosphates to 'direct-load' DNA sequencing. Nucleic Acids Res 2002; 30:2877-85. [PMID: 12087172 PMCID: PMC117042 DOI: 10.1093/nar/gkf387] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A novel series of charge-modified, dye-labeled 2',3'-dideoxynucleoside-triphosphate terminators were synthesized and evaluated as reagents for DNA sequencing. These terminators possess an advantage over existing reagents in that no purification is required to remove unreacted nucleotide or associated breakdown products prior to electrophoretic separation of the sequencing fragments. This obviates the need for a time consuming post-reaction work up, allowing direct loading of DNA sequencing reaction mixtures onto a slab gel. Thermo Sequenase II DNA polymerase poorly incorporates the charge-modified terminators compared with regular dye-labeled terminators. However, extending the linker arm between dye and nucleotide and using a mutant form of a related DNA polymerase can in part mitigate the decrease in substrate efficiency. We also present evidence that these charge-modified terminators can relieve gel compression artefacts when used with dGTP in sequencing reactions.
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Affiliation(s)
- Patrick J Finn
- Amersham Biosciences, 800 Centennial Avenue, Piscataway, NJ 08855-1327, USA
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Nelson JR, Cai YC, Giesler TL, Farchaus JW, Sundaram ST, Ortiz-Rivera M, Hosta LP, Hewitt PL, Mamone JA, Palaniappan C, Fuller CW. TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. Biotechniques 2002; Suppl:44-7. [PMID: 12083397] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
We have developed a novel, isothermal DNA amplification strategy that employs phi29 DNA polymerase and rolling circle amplification to generate high-quality templates for DNA sequencing reactions. The TempliPhi DNA amplification kits take advantage of the fact that cloned DNA is typically obtained in circular vectors, which are readily replicated in vitro using phi29 DNA polymerase by a rolling circle mechanism. This single subunit, proofreading DNA polymerase has excellent processivity and strand displacement properties for generation of multiple, tandem double-stranded copies of the circular DNA, generating as much as 10(7)-fold amplification. Large amounts of product (1-3 microg) can be obtained in as little as 4 hours. Input DNA can be as little as 0.01 ng of purified plasmid DNA, a single bacterial colony, or a 1 microL of a saturated overnight culture. Additionally, the presence of an associated proof reading function within the phi29 DNA polymerase ensures high-fidelity amplification. Once completed, the product DNA can be used directly in sequencing reactions. Additionally, the properties of phi29 DNA polymerase and its use in applications such as amplification ofhuman genomic DNA for genotyping studies is discussed.
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Affiliation(s)
- John R Nelson
- Genomics Reagents Department, Amersham Biosciences, Piscataway, NJ 08855, USA
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Abstract
Hospitalist practice highlights the need for effective communication between doctors that share the care of a patient, and between doctors and patients. Telephone contact with patients after hospital discharge can enhance adherence, inform the hospitalist about the results of treatment or of adverse outcomes, and allow the hospitalist to receive feedback from the patient and family.
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