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Lopes DM, Wells JA, Ma D, Wallis L, Park D, Llewellyn SK, Ahmed Z, Lythgoe MF, Harrison IF. Glymphatic inhibition exacerbates tau propagation in an Alzheimer's disease model. Alzheimers Res Ther 2024; 16:71. [PMID: 38576025 PMCID: PMC10996277 DOI: 10.1186/s13195-024-01439-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND The aggregation and spread of misfolded amyloid structured proteins, such as tau and α-synuclein, are key pathological features associated with neurodegenerative disorders, including Alzheimer's and Parkinson's disease. These proteins possess a prion-like property, enabling their transmission from cell to cell leading to propagation throughout the central and peripheral nervous systems. While the mechanisms underlying their intracellular spread are still being elucidated, targeting the extracellular space has emerged as a potential therapeutic approach. The glymphatic system, a brain-wide pathway responsible for clearing extracellular metabolic waste from the central nervous system, has gained attention as a promising target for removing these toxic proteins. METHODS In this study, we investigated the impact of long-term modulation of glymphatic function on tau aggregation and spread by chronically treating a mouse model of tau propagation with a pharmacological inhibitor of AQP4, TGN-020. Thy1-hTau.P301S mice were intracerebrally inoculated with tau into the hippocampus and overlying cortex, and subsequently treated with TGN-020 (3 doses/week, 50 mg/kg TGN-020, i.p.) for 10-weeks. During this time, animal memory was studied using cognitive behavioural tasks, and structural MR images were acquired of the brain in vivo prior to brain extraction for immunohistochemical characterisation. RESULTS Our findings demonstrate increased tau aggregation in the brain and transhemispheric propagation in the hippocampus following the inhibition of glymphatic clearance. Moreover, disruption of the glymphatic system aggravated recognition memory in tau inoculated mice and exacerbated regional changes in brain volume detected in the model. When initiation of drug treatment was delayed for several weeks post-inoculation, the alterations were attenuated. CONCLUSIONS These results indicate that by modulating AQP4 function and, consequently, glymphatic clearance, it is possible to modify the propagation and pathological impact of tau in the brain, particularly during the initial stages of the disease. These findings highlight the critical role of the glymphatic system in preserving healthy brain homeostasis and offer valuable insights into the therapeutic implications of targeting this system for managing neurodegenerative diseases characterized by protein aggregation and spread.
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Affiliation(s)
- Douglas M Lopes
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Jack A Wells
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Da Ma
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Lauren Wallis
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Daniel Park
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Sophie K Llewellyn
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Zeshan Ahmed
- Neuroscience Next Generation Therapeutics (NGTx), Eli Lilly and Company, Cambridge, MA, USA
| | - Mark F Lythgoe
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Ian F Harrison
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK.
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Morgan S, Reid I, Bendon C, Ishaq M, Shayan R, Pope B, Park D, Karnezis T. A Family-Based Study of Inherited Genetic Risk in Lipedema. Lymphat Res Biol 2024; 22:106-111. [PMID: 38407896 PMCID: PMC11044871 DOI: 10.1089/lrb.2023.0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Background: Lipedema is a progressive condition involving excessive deposition of subcutaneous adipose tissue, predominantly in the lower limbs, which severely compromises quality of life. Despite the impact of lipedema, its molecular and genetic bases are poorly understood, making diagnosis and treatment difficult. Historical evaluation of individuals with lipedema indicates a positive family history in 60%-80% of cases; however, genetic investigation of larger family cohorts is required. Here, we report the largest family-based sequencing study to date, aimed at identifying genetic changes that contribute to lipedema. Methods and Results: DNA samples from 31 individuals from 9 lipedema families were analyzed to reveal genetic variants predicted to alter protein function, yielding candidate variants in 469 genes. We did not identify any individual genes that contained likely disease-causing variants across all participating families. However, gene ontology analysis highlighted vasopressin receptor activity, microfibril binding, and patched binding as statistically significantly overrepresented categories for the set of candidate variants. Conclusions: Our study suggests that lipedema is not caused by a single exomic genetic factor, providing support for the hypothesis of genetic heterogeneity in the etiology of lipedema. As the largest study of its kind in the lipedema field, the results advance our understanding of the disease and provide a roadmap for future research aimed at improving the lives of those affected by lipedema.
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Affiliation(s)
- Steven Morgan
- Lymphatic, Adipose and Regenerative Medicine Group, Department of O'Brien Institute, St Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Isabella Reid
- Lymphatic, Adipose and Regenerative Medicine Group, Department of O'Brien Institute, St Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Charlotte Bendon
- Department of Plastic and Reconstructive Surgery, West Wing, John Radcliffe Hospital, Headley Way, Oxford, United Kingdom
| | - Musarat Ishaq
- Lymphatic, Adipose and Regenerative Medicine Group, Department of O'Brien Institute, St Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Ramin Shayan
- Lymphatic, Adipose and Regenerative Medicine Group, Department of O'Brien Institute, St Vincent's Institute of Medical Research, Fitzroy, Australia
- Department of Medicine, St Vincent's Hospital, Fitzroy, Australia
| | - Bernard Pope
- Melbourne Bioinformatics, The University of Melbourne, Parkville, Australia
- Department of Surgery (Royal Melbourne Hospital), The University of Melbourne, Parkville, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia
| | - Daniel Park
- Melbourne Bioinformatics, The University of Melbourne, Parkville, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Australia
| | - Tara Karnezis
- Lymphatic, Adipose and Regenerative Medicine Group, Department of O'Brien Institute, St Vincent's Institute of Medical Research, Fitzroy, Australia
- Department of Medicine, St Vincent's Hospital, Fitzroy, Australia
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Smith JC, Williamson BD, Cronkite DJ, Park D, Whitaker JM, McLemore MF, Osmanski JT, Winter R, Ramaprasan A, Kelley A, Shea M, Wittayanukorn S, Stojanovic D, Zhao Y, Toh S, Johnson KB, Aronoff DM, Carrell DS. Data-driven automated classification algorithms for acute health conditions: applying PheNorm to COVID-19 disease. J Am Med Inform Assoc 2024; 31:574-582. [PMID: 38109888 PMCID: PMC10873852 DOI: 10.1093/jamia/ocad241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/19/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
OBJECTIVES Automated phenotyping algorithms can reduce development time and operator dependence compared to manually developed algorithms. One such approach, PheNorm, has performed well for identifying chronic health conditions, but its performance for acute conditions is largely unknown. Herein, we implement and evaluate PheNorm applied to symptomatic COVID-19 disease to investigate its potential feasibility for rapid phenotyping of acute health conditions. MATERIALS AND METHODS PheNorm is a general-purpose automated approach to creating computable phenotype algorithms based on natural language processing, machine learning, and (low cost) silver-standard training labels. We applied PheNorm to cohorts of potential COVID-19 patients from 2 institutions and used gold-standard manual chart review data to investigate the impact on performance of alternative feature engineering options and implementing externally trained models without local retraining. RESULTS Models at each institution achieved AUC, sensitivity, and positive predictive value of 0.853, 0.879, 0.851 and 0.804, 0.976, and 0.885, respectively, at quantiles of model-predicted risk that maximize F1. We report performance metrics for all combinations of silver labels, feature engineering options, and models trained internally versus externally. DISCUSSION Phenotyping algorithms developed using PheNorm performed well at both institutions. Performance varied with different silver-standard labels and feature engineering options. Models developed locally at one site also worked well when implemented externally at the other site. CONCLUSION PheNorm models successfully identified an acute health condition, symptomatic COVID-19. The simplicity of the PheNorm approach allows it to be applied at multiple study sites with substantially reduced overhead compared to traditional approaches.
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Affiliation(s)
- Joshua C Smith
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Brian D Williamson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, United States
| | - David J Cronkite
- Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, United States
| | - Daniel Park
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Jill M Whitaker
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Michael F McLemore
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Joshua T Osmanski
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Robert Winter
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, United States
| | - Arvind Ramaprasan
- Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, United States
| | - Ann Kelley
- Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, United States
| | - Mary Shea
- Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, United States
| | - Saranrat Wittayanukorn
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, United States
| | - Danijela Stojanovic
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, United States
| | - Yueqin Zhao
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, United States
| | - Sengwee Toh
- Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Kevin B Johnson
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - David M Aronoff
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, United States
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Buddle VP, Lee M, Feng J, Khurana E, Park A, Park D. The Effect of Marijuana on Postoperative Spine Patients' Emergency Department Visits, Readmission Rates, and Opioid Consumption. J Am Acad Orthop Surg Glob Res Rev 2024; 8:01979360-202402000-00006. [PMID: 38323931 PMCID: PMC10849310 DOI: 10.5435/jaaosglobal-d-23-00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/21/2023] [Indexed: 02/08/2024]
Abstract
OBJECTIVE To compare postoperative opioid consumption with patients who tested negative for tetrahydrocannabinol (THC) preoperatively with those who were THC-positive and patients who were positive for THC and any other drug and to compare 90-day rates of postoperative emergency department (ED) visits and 90-day readmission rates, using morphine milligram equivalents (MMEs), for those three patient populations. METHODS Three patient groups were confirmed with preoperative urine drug screens. Chart reviews were conducted to determine whether there was an ED visit or hospital readmission 90 days from the index procedure. MMEs were calculated for all patients. RESULTS There were a total of 252 patients in the THC-negative control group, 54 in the THC-positive group, and 47 in the THC-and-opioid-positive group. The 90-day ED visit and 90-day readmission rates were not statistically significant among the groups. Both the multidrug and THC-only-positive patients showed a higher 90-day MME compared with the control patients. DISCUSSION Our study demonstrates that THC used may increase opioid consumption. The THC patients to be cautious toward are the multidrug user. Although not statistically significant, multidrug patients were noted for a trend toward increased ED visits and readmissions.
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Affiliation(s)
- Vincent Patrick Buddle
- From the William Beaumont Hospital, Royal Oak, MI (Dr. Buddle, Dr. Feng, and Dr. Daniel Park); the The Ohio State University Medical College (Mr. Lee); and Michigan Orthopaedic Surgeons (Mr. Khurana, Dr. Ahyoung Park, and Dr. Daniel Park)
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Park D, Jeon WJ, Yang C, Castillo DR. Advancing Esophageal Cancer Treatment: Immunotherapy in Neoadjuvant and Adjuvant Settings. Cancers (Basel) 2024; 16:318. [PMID: 38254805 PMCID: PMC10813716 DOI: 10.3390/cancers16020318] [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: 11/27/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Locally advanced esophageal cancer (LAEC) poses a significant and persistent challenge in terms of effective treatment. Traditionally, the primary strategy for managing LAEC has involved concurrent neoadjuvant chemoradiation followed by surgery. However, achieving a pathologic complete response (pCR) has proven to be inconsistent, and despite treatment, roughly half of patients experience locoregional recurrence or metastasis. Consequently, there has been a paradigm shift towards exploring the potential of immunotherapy in reshaping the landscape of LAEC management. Recent research has particularly focused on immune checkpoint inhibitors, investigating their application in both neoadjuvant and adjuvant settings. These inhibitors, designed to block specific proteins in immune cells, are meant to enhance the immune system's ability to target and combat cancer cells. Emerging evidence from these studies suggests the possibility of a mortality benefit, indicating that immunotherapy may contribute to improved overall survival rates for individuals grappling with esophageal cancer. This manuscript aims to meticulously review the existing literature surrounding neoadjuvant and adjuvant immunotherapy in the context of LAEC management. The intention is to thoroughly examine the methodologies and findings of relevant studies, providing a comprehensive synthesis of the current understanding of the impact of immunotherapy on esophageal cancer.
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Affiliation(s)
- Daniel Park
- University of California, San Francisco-Fresno Branch Campus, Fresno, CA 93701, USA;
| | - Won Jin Jeon
- Loma Linda University Medical Center, Loma Linda, CA 92354, USA;
| | - Chieh Yang
- Department of Internal Medicine for UCSF, University of California, and UC Riverside, Riverside, CA 92521, USA;
| | - Dani Ran Castillo
- City of Hope-Duarte, Department of Hematology & Oncology, Duarte, CA 91010, USA
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6
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Feng X, Patel EU, White JL, Li S, Zhu X, Zhao N, Shi J, Park D, Liu CM, Kaul R, Prodger JL, Quinn TC, Grabowski MK, Tobian AAR. Association of oral microbiome with oral human papillomavirus infection: a population study of the National Health and Nutrition Examination Survey, 2009-2012. J Infect Dis 2024:jiae004. [PMID: 38181070 DOI: 10.1093/infdis/jiae004] [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: 10/20/2023] [Revised: 12/19/2023] [Accepted: 01/03/2024] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Oral human papillomavirus(HPV) infection and the oral microbiome are associated with oropharyngeal cancer. However, population-based data on the association of oral microbiome with oral HPV infection are limited. METHOD We performed a cross-sectional analysis of 5,496 participants aged 20-59 in National Health and Nutrition Examination Surveys(NHANES):2009-2012. The association between either oral microbiome alpha diversity or beta diversity and oral HPV infection was assessed using multivariable logistic regression or principal coordinate analyses(PCoA) and multivariate analysis of variance(PERMANOVA). RESULTS For alpha diversity, we found a lower number of observed Amplicon sequence variants(ASVs) (adjusted odds ratio[aOR] = 0.996; 95%CI = 0.992-0.999) and reduced Faith's Phylogenetic Diversity(aOR = 0.95; 95%CI = 0.90-0.99) associated with high-risk oral HPV infection in the overall population. This trend was observed in males for both high-risk and any oral HPV infection. Beta diversity showed differentiation of oral microbiome community by high-risk oral HPV infection as measured by Bray-Curtis dissimilarity (R2 = 0.054%; P = .029) and unweighted UniFrac distance (R2 = 0.046%; P = .045) among the overall population, and associations were driven by males. CONCLUSIONS Both oral microbiome alpha diversity(within-sample richness and phylogenetic diversity) and beta diversity(heterogeneous dispersion of oral microbiome community) are associated with HPV infection. Longitudinal studies are needed to characterize the role of the microbiome in the natural history of oral HPV infection.
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Affiliation(s)
- Xinyi Feng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eshan U Patel
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jodie L White
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shilan Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xianming Zhu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ni Zhao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Park
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Cindy M Liu
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Rupert Kaul
- Departments of Medicine and Immunology, University of Toronto, Toronto, ON, Canada
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Thomas C Quinn
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infection Diseases, Baltimore, MD, USA
| | - M Kate Grabowski
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Aaron A R Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Day E, Galiwango RM, Park D, Huibner S, Aziz M, Anok A, Nnamutete J, Isabirye Y, Wasswa JB, Male D, Kigozi G, Tobian AA, Prodger JL, Liu CM, Kaul R. Insertive vaginal sex is associated with altered penile immunology and enrichment of Gardnerella vaginalis in uncircumcised Ugandan men. Am J Reprod Immunol 2024; 91:e13801. [PMID: 38282609 PMCID: PMC10825315 DOI: 10.1111/aji.13801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/13/2023] [Accepted: 11/17/2023] [Indexed: 01/30/2024] Open
Abstract
PROBLEM HIV susceptibility is linked to the penile immune milieu (particularly IL-8 levels) and microbiome. The effects of insertive vaginal sex itself on penile immunology and microbiota are not well described. METHOD OF STUDY We compared the immune milieu and microbiology of the coronal sulcus (CS) and distal urethra in 47 uncircumcised Ugandan men reporting ever (n = 42) or never (n = 5) having had vaginal intercourse. Soluble immune factors were assayed by multiplex ELISA, and penile bacteria abundance by 16S rRNA qPCR and sequencing. Co-primary endpoints were penile levels of IL-8 and soluble E-cadherin. RESULTS Independent of classical STIs, men reporting prior vaginal sex demonstrated elevated IL-8 levels in both the coronal sulcus (1.78 vs. 0.81 log10 pg/mL, p = .021) and urethra (2.93 vs. 2.30 log10 pg/mL; p = .003), with a strong inverse relationship between urethral IL-8 levels and the time from last vaginal sex (r = -0.436; p = .004). Vaginal sex was also associated with elevated penile IL-1α/β and soluble E-cadherin (sEcad), a marker of epithelial disruption. Gardnerella vaginalis (Gv) was only present in the penile microbiome of men reporting prior vaginal sex, and urethral Gv absolute abundance was strongly associated with urethral inflammation (r = 0.556; p < .001); corynebacteria were enriched in the CS of men reporting no prior vaginal sex and were associated with reduced CS inflammation. CONCLUSIONS Sexual intercourse was associated with sustained changes in penile immunology, potentially mediated through microbial alterations, in particular the urethral abundance of G. vaginalis. Future studies should further characterize the effects of sexual debut on penile bacteria and immunology.
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Affiliation(s)
- Erin Day
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Ronald M. Galiwango
- Departments of Immunology and Medicine, University of Toronto, Ontario, Canada
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Daniel Park
- George Washington Milken Institute School of Public Health, Washington DC, USA
| | - Sanja Huibner
- Departments of Immunology and Medicine, University of Toronto, Ontario, Canada
| | - Maliha Aziz
- George Washington Milken Institute School of Public Health, Washington DC, USA
| | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | | | | | - Deo Male
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Aaron A.R. Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jessica L. Prodger
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Cindy M. Liu
- George Washington Milken Institute School of Public Health, Washington DC, USA
| | - Rupert Kaul
- Departments of Immunology and Medicine, University of Toronto, Ontario, Canada
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Zakko P, Blankenship A, Jawad A, Kasir R, Lee M, Park D. Anterior Cervical Discectomy and Fusions Supplemented With Cellular or Noncellular Allografts Have Similar Radiographic Fusion and Clinical Outcomes. Clin Spine Surg 2023; 36:426-430. [PMID: 37381143 DOI: 10.1097/bsd.0000000000001475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 05/17/2023] [Indexed: 06/30/2023]
Abstract
STUDY DESIGN A retrospective, single-center study. OBJECTIVE The aim of this study was to assess radiographic fusion after anterior cervical discectomy and fusion (ACDF) supplemented with either demineralized bone matrix or ViviGen in a polyetheretherketone biomechanical interbody cage. SUMMARY OF BACKGROUND DATA Cellular and noncellular allografts are utilized as adjuncts in attempts to improve fusion after ACDF. The purpose of this study was to assess radiographic fusion and clinical outcomes after ACDF supplemented with cellular or noncellular allografts. MATERIALS AND METHODS A single surgeon's clinical practice database was interrogated for consecutive patients who underwent a primary ACDF using cellular or noncellular allograft from 2017 to 2019. These subjects were matched by age, sex, body mass index, smoking status, and levels operated. Patient demographic and preoperative and postoperative patient-reported outcome measures (PROMs) including Visual Analog Scale Pain, Neck Disability Index, EuroQol-5 Dimension (EQ-5D), Patient-Reported Outcomes Measurement Information System (PROMIS), and Eating Assessment Tool 10 were collected preoperatively and at 3, 6, and 12 months postoperatively. Radiographic evidence of fusion was determined by <2 mm motion between spinous processes on flexion and extension radiographs and assessing bony bridging at 3, 6, and 12 months postoperatively. RESULTS There were 68 total patients, with 34 patients in each group, and 69 and 67 operative levels in the cellular and noncellular allograft groups, respectively. There was no difference in age, sex, body mass index, or smoking status between groups ( P >0.05). There was no difference in number of 1-level, 2-level, 3-level, or 4-level ACDFs between cellular and noncellular groups ( P >0.05). At 3, 6, and 12 months postoperatively, there was no difference in the percent of operated levels with <2 mm motion between spinous processes, complete bony bridging, or both <2 mm motion and complete bony bridging in the cellular and noncellular groups ( P >0.05). There was no difference in the number of patients fused at all operated levels at 3, 6, or 12 months postoperatively ( P >0.05). No patient required revision ACDF for symptomatic pseudarthrosis. There was no significant difference in PROMs between the cellular and noncellular groups at 12 months postoperatively except for improved EQ-5D and PROMIS-physical in the cellular compared with noncellular group ( P =0.03). CONCLUSIONS Similar radiographic fusion rates were achieved with cellular and noncellular allografts at all operated levels with similar PROMs in the cellular and noncellular groups at 3, 6, and 12 months postoperatively. Thus, ACDFs supplemented with cellular allograft demonstrate adequate radiographic fusion rates when compared with noncellular allografts with similar patient outcomes. LEVEL OF EVIDENCE Level III.
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Affiliation(s)
- Philip Zakko
- Department of Orthopaedic Surgery, Beaumont Health, Royal Oak, MI
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9
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Jeon WJ, Joung B, Moon JH, Hino C, Park D, Pham B, Castillo DR, Chong E, Kaur S, Grismore C, Cao H. An innovative intervention for the prevention of vaso-occlusive episodes in sickle cell disease. Hematology 2023; 28:2215575. [PMID: 37227254 DOI: 10.1080/16078454.2023.2215575] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
OBJECTIVES Sickle cell disease (SCD) is characterized by a mutation in the beta-globin gene resulting in abnormal hemoglobin S (HgbS). The significant sequela of SCD include anemia and recurrent vaso-occlusive episodes (VOEs) which may effectuate patients to receive chronic blood transfusions. Current pharmacotherapy options for SCD include hydroxyurea, voxelotor, Lglutamine, and crizanlizumab. Simple and exchange transfusions are often utilized as prophylaxis to prevent emergency department (ED)/urgent care (UC) visits or hospitalizations from VOEs by reducing the level of sickled red blood cells (RBCs). In addition, the treatment of VOEs involves intravenous (IV) hydration and pain management. Studies have demonstrated that sickle cell infusion centers (SCIC) decrease hospital admissions for VOEs, and IV hydration and pain medications are the key components of management employed. Thus, we hypothesized that implementing a structured infusion protocol in the outpatient setting would reduce the incidence of VOEs. METHODS Here, we discuss two patients with SCD who were trialed on scheduled outpatient IV hydration and opioids with the goal of decreasing the frequency of VOEs in the setting of the current blood product shortage and the patients' refusal to receive exchange transfusions. RESULTS Overall, the two patients had opposing outcomes- one demonstrated reduced frequency of VOEs, whereas the other had mixed results due to noncompliance to scheduled outpatient sessions. DISCUSSION/CONCLUSION The use of outpatient SCICs may be an effective intervention for prevention of VOEs in patients with SCD, and further patient-centered research and quality improvement initiatives are needed to further quantify and understand the factors contributing to their efficacy.
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Affiliation(s)
- Won Jin Jeon
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Bowon Joung
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Jin Hyun Moon
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Christopher Hino
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Daniel Park
- Department of Internal Medicine, School of Medicine, University of California San Francisco-Fresno, Fresno, CA, USA
| | - Bryan Pham
- Department of Internal Medicine, School of Medicine, University of California San Francisco-Fresno, Fresno, CA, USA
| | - Dan Ran Castillo
- Division of Medical Oncology/ Hematology, Department of Internal Medicine, Loma Linda University Medical Center, Loma Linda, CA, USA
| | - Esther Chong
- Division of Medical Oncology/ Hematology, Department of Internal Medicine, Loma Linda University Medical Center, Loma Linda, CA, USA
| | - Simmer Kaur
- Division of Medical Oncology/ Hematology, Department of Internal Medicine, Loma Linda University Medical Center, Loma Linda, CA, USA
| | - Chanell Grismore
- Director of Sickle Cell Servies, Loma Linda University Medical Center, Loma Linda, CA, USA
| | - Huynh Cao
- Division of Medical Oncology/ Hematology, Department of Internal Medicine, Loma Linda University Medical Center, Loma Linda, CA, USA
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Sorensen SA, Gouwens NW, Wang Y, Mallory M, Budzillo A, Dalley R, Lee B, Gliko O, Kuo HC, Kuang X, Mann R, Ahmadinia L, Alfiler L, Baftizadeh F, Baker K, Bannick S, Bertagnolli D, Bickley K, Bohn P, Brown D, Bomben J, Brouner K, Chen C, Chen K, Chvilicek M, Collman F, Daigle T, Dawes T, de Frates R, Dee N, DePartee M, Egdorf T, El-Hifnawi L, Enstrom R, Esposito L, Farrell C, Gala R, Glomb A, Gamlin C, Gary A, Goldy J, Gu H, Hadley K, Hawrylycz M, Henry A, Hill D, Hirokawa KE, Huang Z, Johnson K, Juneau Z, Kebede S, Kim L, Lee C, Lesnar P, Li A, Glomb A, Li Y, Liang E, Link K, Maxwell M, McGraw M, McMillen DA, Mukora A, Ng L, Ochoa T, Oldre A, Park D, Pom CA, Popovich Z, Potekhina L, Rajanbabu R, Ransford S, Reding M, Ruiz A, Sandman D, Siverts L, Smith KA, Stoecklin M, Sulc J, Tieu M, Ting J, Trinh J, Vargas S, Vumbaco D, Walker M, Wang M, Wanner A, Waters J, Williams G, Wilson J, Xiong W, Lein E, Berg J, Kalmbach B, Yao S, Gong H, Luo Q, Ng L, Sümbül U, Jarsky T, Yao Z, Tasic B, Zeng H. Connecting single-cell transcriptomes to projectomes in mouse visual cortex. bioRxiv 2023:2023.11.25.568393. [PMID: 38168270 PMCID: PMC10760188 DOI: 10.1101/2023.11.25.568393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neuron's role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morpho-electric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.
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Affiliation(s)
| | | | - Yun Wang
- Allen Institute for Brain Science
| | | | | | | | | | | | | | - Xiuli Kuang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | | | | | | | | | | | | | | | - Chao Chen
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Kai Chen
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science
| | | | | | | | | | | | | | | | | | | | | | | | - Hong Gu
- Allen Institute for Brain Science
| | | | | | | | | | | | - Zili Huang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | - Lisa Kim
- Allen Institute for Brain Science
| | | | | | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | | | - Yaoyao Li
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | | | | | | | | | | | | | - Zoran Popovich
- University of Washington, Dept. of Computer Science and Engineering
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wei Xiong
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Ed Lein
- Allen Institute for Brain Science
| | - Jim Berg
- Allen Institute for Brain Science
| | | | | | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Qingming Luo
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Lydia Ng
- Allen Institute for Brain Science
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11
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Kasir R, Zakko P, Hasan S, Aleem I, Park D, Nerenz D, Abdulhak M, Perez-Cruz M, Schwalb J, Saleh ES, Easton R, Khalil JG. The Duration of Symptoms Influences Outcomes After Lumbar Microdiscectomies: A Michigan Spine Surgery Improvement Collaborative. Global Spine J 2023:21925682231210469. [PMID: 37918421 DOI: 10.1177/21925682231210469] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
STUDY DESIGN Retrospective Cohort. OBJECTIVE We investigate whether duration of symptoms a patient experiences prior to lumbar microdiscectomy affects pain, lifestyle, and return to work metrics after surgery. METHODS A retrospective review of patients with a diagnosis of lumbar radiculopathy undergoing microdiscectomy was conducted using a statewide registry. Patients were grouped based on self-reported duration of symptoms prior to surgical intervention (Group 1: symptoms less than 3 months; Group 2: symptoms between 3 months and 1 year; and Group 3: symptoms greater than 1 year). Radicular pain scores, PROMIS PF Physical Function measure (PROMIS PF), EQ-5D scores, and return to work rates at 90 days, 1 year, and 2 years after surgery were compared using univariate and multivariate analysis. RESULTS There were 2408 patients who underwent microdiscectomy for lumbar disc herniation for radiculopathy with 532, 910, and 955 in Groups 1, 2, and 3, respectively. Postoperative leg pain was lower for Group 1 at 90 days, 1 year, and 2 years compared to Groups 2 and 3 (P < .05). Postoperative PROMIS PF and EQ-5D scores were higher for Group 1 at 90 days, 1 year, and 2 years compared to Groups 2 and 3 (P < .05). CONCLUSION Patients with prolonged symptoms prior to surgical intervention experience smaller improvements in postoperative leg pain, PROMIS PF, and EQ-5D than those who undergo surgery earlier. Patients undergoing surgery within 3 months of symptom onset have the highest rates of return to work at 1 year after surgery.
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Affiliation(s)
- Rafid Kasir
- Department of Orthopedic Surgery, Beaumont Hospital, Royal Oak, MI, USA
| | - Philip Zakko
- Department of Orthopedic Surgery, Beaumont Hospital, Royal Oak, MI, USA
| | - Sazid Hasan
- Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Ilyas Aleem
- Department of Orthopedic Surgery, University of Michigan Ann Arbor, MI, USA
| | - Daniel Park
- Department of Orthopedic Surgery, Beaumont Hospital, Royal Oak, MI, USA
| | - David Nerenz
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, USA
| | - Muwaffak Abdulhak
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, USA
| | - Mick Perez-Cruz
- Department of Neurosurgery, Beaumont Health, Royal Oak, MI, USA
| | - Jason Schwalb
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, USA
| | - Ehab S Saleh
- Department of Orthopedic Surgery, Beaumont Hospital, Royal Oak, MI, USA
| | - Richard Easton
- Department of Orthopedic Surgery, Beaumont Hospital, Royal Oak, MI, USA
| | - Jad G Khalil
- Department of Orthopedic Surgery, Beaumont Hospital, Royal Oak, MI, USA
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12
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Lewis JA, Samuels LR, Weems J, Park D, Winter R, Lindsell CJ, Callaway-Lane C, Audet C, Slatore CG, Wiener RS, Dittus RS, Kripalani S, Yankelevitz DF, Henschke CI, Moghanaki D, Matheny ME, Vogus TJ, Roumie CL, Spalluto LB. The Association of Organizational Readiness With Lung Cancer Screening Utilization. Am J Prev Med 2023; 65:844-853. [PMID: 37224985 PMCID: PMC10592591 DOI: 10.1016/j.amepre.2023.05.018] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023]
Abstract
INTRODUCTION Lung cancer screening is widely underutilized. Organizational factors, such as readiness for change and belief in the value of change (change valence), may contribute to underutilization. The aim of this study was to evaluate the association between healthcare organizations' preparedness and lung cancer screening utilization. METHODS Investigators cross-sectionally surveyed clinicians, staff, and leaders at10 Veterans Affairs from November 2018 to February 2021 to assess organizational readiness to implement change. In 2022, investigators used simple and multivariable linear regression to evaluate the associations between facility-level organizational readiness to implement change and change valence with lung cancer screening utilization. Organizational readiness to implement change and change valence were calculated from individual surveys. The primary outcome was the proportion of eligible Veterans screened using low-dose computed tomography. Secondary analyses assessed scores by healthcare role. RESULTS The overall response rate was 27.4% (n=1,049), with 956 complete surveys analyzed: median age of 49 years, 70.3% female, 67.6% White, 34.6% clinicians, 61.1% staff, and 4.3% leaders. For each 1-point increase in median organizational readiness to implement change and change valence, there was an associated 8.4-percentage point (95% CI=0.2, 16.6) and a 6.3-percentage point increase in utilization (95% CI= -3.9, 16.5), respectively. Higher clinician and staff median scores were associated with increased utilization, whereas leader scores were associated with decreased utilization after adjusting for other roles. CONCLUSIONS Healthcare organizations with higher readiness and change valence utilized more lung cancer screening. These results are hypothesis generating. Future interventions to increase organizations' preparedness, especially among clinicians and staff, may increase lung cancer screening utilization.
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Affiliation(s)
- Jennifer A Lewis
- VA Tennessee Valley Health Care System Geriatric Research Education and Clinical Center (GRECC), Veterans Health Administration, Nashville, Tennessee; Medical Service, VA Tennessee Valley Healthcare System, Veterans Health Administration, Nashville, Tennessee; Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee.
| | - Lauren R Samuels
- VA Tennessee Valley Health Care System Geriatric Research Education and Clinical Center (GRECC), Veterans Health Administration, Nashville, Tennessee; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jacy Weems
- Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Daniel Park
- VA Tennessee Valley Health Care System Geriatric Research Education and Clinical Center (GRECC), Veterans Health Administration, Nashville, Tennessee; Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Robert Winter
- VA Tennessee Valley Health Care System Geriatric Research Education and Clinical Center (GRECC), Veterans Health Administration, Nashville, Tennessee; Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christopher J Lindsell
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Carol Callaway-Lane
- VA Tennessee Valley Health Care System Geriatric Research Education and Clinical Center (GRECC), Veterans Health Administration, Nashville, Tennessee; Medical Service, VA Tennessee Valley Healthcare System, Veterans Health Administration, Nashville, Tennessee; Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Carolyn Audet
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Health Policy, Vanderbilt University, Nashville, Tennessee
| | - Christopher G Slatore
- Center to Improve Veteran Involvement in Care (CIVIC), Health Services Research and Development, Veterans Affairs Portland Health Care System, Portland, Oregon; Section of Pulmonary and Critical Care Medicine, Veterans Affairs Portland Health Care System, Portland, Oregon; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Oregon Health & Science University, Portland, Oregon; VA National Center for Lung Cancer Screening (NCLCS), Veterans Health Administration, Washington, District of Columbia
| | - Renda Soylemez Wiener
- VA National Center for Lung Cancer Screening (NCLCS), Veterans Health Administration, Washington, District of Columbia; Center for Healthcare Organization & Implementation Research, VA Boston Healthcare System, Boston, Massachusetts; The Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts
| | - Robert S Dittus
- VA Tennessee Valley Health Care System Geriatric Research Education and Clinical Center (GRECC), Veterans Health Administration, Nashville, Tennessee; Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sunil Kripalani
- Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, Tennessee; Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David F Yankelevitz
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Claudia I Henschke
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, New York; VA Phoenix Health Care System, Phoenix, Arizona
| | - Drew Moghanaki
- Radiation Oncology Service, Veteran Affairs Greater Los Angeles Healthcare System, Los Angeles, California; Department of Radiation Oncology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Michael E Matheny
- VA Tennessee Valley Health Care System Geriatric Research Education and Clinical Center (GRECC), Veterans Health Administration, Nashville, Tennessee; Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Timothy J Vogus
- Owen Graduate School of Management, Vanderbilt University, Nashville, Tennessee
| | - Christianne L Roumie
- VA Tennessee Valley Health Care System Geriatric Research Education and Clinical Center (GRECC), Veterans Health Administration, Nashville, Tennessee; Division of General Internal Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Health Policy, Vanderbilt University, Nashville, Tennessee
| | - Lucy B Spalluto
- VA Tennessee Valley Health Care System Geriatric Research Education and Clinical Center (GRECC), Veterans Health Administration, Nashville, Tennessee; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee; Center for Clinical Quality and Implementation Research, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Radiology, Vanderbilt University Medical Center, Nashville, Tennessee
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Yang Z, Zamarud A, Marianayagam N, Park D, Yener U, Soltys SG, Chang SD, Meola A, Lu W, Gu X. Overall Survival Prediction in Stereotactic Radiosurgery Patients with Glioblastoma Via a Deep-Learning Approach. Int J Radiat Oncol Biol Phys 2023; 117:e159. [PMID: 37784752 DOI: 10.1016/j.ijrobp.2023.06.988] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Accurate and automated early survival prediction is critical for glioblastoma (GBM) patients as their poor prognosis requires timely treatment decision-making. We have developed a deep learning (DL)-based GBM overall survival (OS) prediction model based on a multi-institutional public dataset using only pre-operative basic structural multi-parametric magnetic resonance images (MRIs). The purpose of this study is to evaluate this DL-based OS prediction model with an institutional stereotactic radiosurgery (SRS) clinical trial dataset. MATERIALS/METHODS The task of this study is to classify GBM patients into 3 OS classes: long-survivors (>15 months), mid-survivors (between 10 and 15 months) and short-survivors (< 10 months). The proposed OS prediction model is an ensemble of a ResNet-based classifier and a K-NN classifier. The ResNet-based classifier is trained in a Siamese fashion to explore inter-class differences. During testing, training sample features are implemented with a K-NN classifier to ensemble with the ResNet-based classifier. A public dataset from Medical Image Computing and Computer Assisted Intervention (MICCAI) Brain Tumor Segmentation (BraTS) challenge 2020 (235 patients) were used for model establishing and initial validation. Then the validated model was evaluated on 19 GBM patients from an institutional SRS clinical trial. Each data entry consists of pre-operative basic structural multi-parametric MRIs and survival days, as well as patient ages for BraTS data and basic clinical characteristics for institutional data. GBM sub-regions, including contrast-enhancing tumor, peri-tumoral edema, and necrotic/non-enhancing tumor core, were segmented in the multi-parametric MRIs by an in-house DL model for both datasets. The OS prediction model was trained on 90% of the segmented BraTS data and validated on the rest 10%, then further evaluated on the institutional data. The model performance was assessed by prediction accuracy (ACC) and the area under the curve (AUC). RESULTS For this 3-class OS classification task, our DL-based prediction model achieved an ACC of 65.22% and an AUC of 0.81 on the BraTS dataset compared with the top-ranked result from the BraTS challenge 2020 (Rank 1st: ACC 61.7%), and an ACC of 52.63% and an AUC of 0.69 on the institutional dataset. Further analysis of the institutional dataset found that the predicted OS class had a statistically significant correlation with treatment volume (p = 0.012) and age (p = 0.006), which matches the analysis that the patients' ground truth OS class is statistical significantly correlated with treatment volume (p = 0.045). CONCLUSION Our DL-based OS prediction model for GBM using basic structural multi-parametric pre-operative MRIs has demonstrated promising performance in both public and institutional dataset with minimal manual processing requirements. This OS prediction model can be potentially applied to assist timely clinical decision-making.
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Affiliation(s)
- Z Yang
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX
| | - A Zamarud
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA
| | - N Marianayagam
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA
| | - D Park
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA
| | - U Yener
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA
| | - S G Soltys
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - S D Chang
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA
| | - A Meola
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA
| | - W Lu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX
| | - X Gu
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX; Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
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14
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Vogt LC, Reske KA, Park D, Habrock Bach T, Stewart HB, Arter OG, Stoeckel D, Steinkamp HM, Liang SY, Durkin MJ, Kwon JH. Personal protective equipment use among dental healthcare personnel during the coronavirus disease 2019 (COVID-19) pandemic and the impact of an educational video in clinical practice. Infect Control Hosp Epidemiol 2023; 44:1472-1480. [PMID: 36924218 PMCID: PMC10507497 DOI: 10.1017/ice.2023.6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 03/18/2023]
Abstract
OBJECTIVE Dental healthcare personnel (DHCP) are at high risk of exposure to coronavirus disease 2019 (COVID-19). We sought to identify how DHCP changed their use of personal protective equipment (PPE) as a result of the COVID-19 pandemic, and to pilot an educational video designed to improve knowledge of proper PPE use. DESIGN The study comprised 2 sets of semistructured qualitative interviews. SETTING The study was conducted in 8 dental clinics in a Midwestern metropolitan area. PARTICIPANTS In total, 70 DHCP participated in the first set of interviews; 63 DHCP participated in the second set of interviews. METHODS In September-November 2020 and March-October 2021, we conducted 2 sets of semistructured interviews: (1) PPE use in the dental community during COVID-19, and (2) feedback on the utility of an educational donning and doffing video. RESULTS Overall, 86% of DHCP reported having prior training. DHCP increased the use of PPE during COVID-19, specifically N95 respirators and face shields. DHCP reported real-world challenges to applying infection control methods, often resulting in PPE modification and reuse. DHCP reported double masking and sterilization methods to extend N95 respirator use. Additional challenges to PPE included shortages, comfort or discomfort, and compatibility with specialty dental equipment. DHCP found the educational video helpful and relevant to clinical practice. Fewer than half of DHCP reported exposure to a similar video. CONCLUSIONS DHCP experienced significant challenges related to PPE access and routine use in dental clinics during the COVID-19 pandemic. An educational video improved awareness and uptake of appropriate PPE use among DHCP.
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Affiliation(s)
- Lucy C. Vogt
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Kimberly A. Reske
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel Park
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Tracey Habrock Bach
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Henry B. Stewart
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Olivia G. Arter
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel Stoeckel
- St. Louis University Center for Advanced Dental Education, St. Louis, Missouri
- St. Louis Children’s Hospital, St. Louis, Missouri
| | - Heidi M. Steinkamp
- St. Louis University Center for Advanced Dental Education, St. Louis, Missouri
| | - Stephen Y. Liang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
- Department of Emergency Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J. Durkin
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jennie H. Kwon
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
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15
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Bosserman RE, Farnsworth CW, O’Neil CA, Cass C, Park D, Ballman C, Wallace MA, Struttmann E, Stewart H, Arter O, Peacock K, Fraser VJ, Budge PJ, Olsen MA, Burnham CAD, Babcock HM, Kwon JH. Seroprevalence of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) antibodies among healthcare personnel in the Midwestern United States, September 2020-April 2021. Antimicrob Steward Healthc Epidemiol 2023; 3:e133. [PMID: 37592963 PMCID: PMC10428156 DOI: 10.1017/ash.2022.375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 08/19/2023]
Abstract
Objective To determine the prevalence of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) IgG nucleocapsid (N) antibodies among healthcare personnel (HCP) with no prior history of COVID-19 and to identify factors associated with seropositivity. Design Prospective cohort study. Setting An academic, tertiary-care hospital in St. Louis, Missouri. Participants The study included 400 HCP aged ≥18 years who potentially worked with coronavirus disease 2019 (COVID-19) patients and had no known history of COVID-19; 309 of these HCP also completed a follow-up visit 70-160 days after enrollment. Enrollment visits took place between September and December 2020. Follow-up visits took place between December 2020 and April 2021. Methods At each study visit, participants underwent SARS-CoV-2 IgG N-antibody testing using the Abbott SARS-CoV-2 IgG assay and completed a survey providing information about demographics, job characteristics, comorbidities, symptoms, and potential SARS-CoV-2 exposures. Results Participants were predominately women (64%) and white (79%), with median age of 34.5 years (interquartile range [IQR], 30-45). Among the 400 HCP, 18 (4.5%) were seropositive for IgG N-antibodies at enrollment. Also, 34 (11.0%) of 309 were seropositive at follow-up. HCP who reported having a household contact with COVID-19 had greater likelihood of seropositivity at both enrollment and at follow-up. Conclusions In this cohort of HCP during the first wave of the COVID-19 pandemic, ∼1 in 20 had serological evidence of prior, undocumented SARS-CoV-2 infection at enrollment. Having a household contact with COVID-19 was associated with seropositivity.
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Affiliation(s)
- Rachel E. Bosserman
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Christopher W. Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Caroline A. O’Neil
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Candice Cass
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel Park
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Claire Ballman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Emily Struttmann
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Henry Stewart
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Olivia Arter
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Kate Peacock
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Victoria J. Fraser
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Philip J. Budge
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Margaret A. Olsen
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Hilary M. Babcock
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jennie H. Kwon
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
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Scott JW, Nguyen MD, Park D, Halperin WP. Magnetic Susceptibility of Andreev Bound States in Superfluid ^{3}He-B. Phys Rev Lett 2023; 131:046001. [PMID: 37566829 DOI: 10.1103/physrevlett.131.046001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/23/2023] [Accepted: 06/12/2023] [Indexed: 08/13/2023]
Abstract
Nuclear magnetic resonance measurements of the magnetic susceptibility of superfluid ^{3}He imbibed in anisotropic aerogel reveal anomalous behavior at low temperatures. Although the frequency shift clearly identifies a low-temperature phase as the B phase, the magnetic susceptibility does not display the expected decrease associated with the formation of the opposite-spin Cooper pairs. This susceptibility anomaly appears to be the predicted high-field behavior corresponding to the Ising-like magnetic character of surface Andreev bound states within the planar aerogel structures.
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Affiliation(s)
- J W Scott
- Northwestern University, Evanston, Illinois 60208, USA
| | - M D Nguyen
- Northwestern University, Evanston, Illinois 60208, USA
| | - D Park
- Northwestern University, Evanston, Illinois 60208, USA
| | - W P Halperin
- Northwestern University, Evanston, Illinois 60208, USA
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Castillo DR, Jeon WJ, Park D, Pham B, Yang C, Joung B, Moon JH, Lee J, Chong EG, Park K, Reeves ME, Duerksen-Hughes P, Mirshahidi HR, Mirshahidi S. Comprehensive Review: Unveiling the Pro-Oncogenic Roles of IL-1ß and PD-1/PD-L1 in NSCLC Development and Targeting Their Pathways for Clinical Management. Int J Mol Sci 2023; 24:11547. [PMID: 37511306 PMCID: PMC10380530 DOI: 10.3390/ijms241411547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
In the past decade, targeted therapies for solid tumors, including non-small cell lung cancer (NSCLC), have advanced significantly, offering tailored treatment options for patients. However, individuals without targetable mutations pose a clinical challenge, as they may not respond to standard treatments like immune-checkpoint inhibitors (ICIs) and novel targeted therapies. While the mechanism of action of ICIs seems promising, the lack of a robust response limits their widespread use. Although the expression levels of programmed death ligand 1 (PD-L1) on tumor cells are used to predict ICI response, identifying new biomarkers, particularly those associated with the tumor microenvironment (TME), is crucial to address this unmet need. Recently, inflammatory cytokines such as interleukin-1 beta (IL-1β) have emerged as a key area of focus and hold significant potential implications for future clinical practice. Combinatorial approaches of IL-1β inhibitors and ICIs may provide a potential therapeutic modality for NSCLC patients without targetable mutations. Recent advancements in our understanding of the intricate relationship between inflammation and oncogenesis, particularly involving the IL-1β/PD-1/PD-L1 pathway, have shed light on their application in lung cancer development and clinical outcomes of patients. Targeting these pathways in cancers like NSCLC holds immense potential to revolutionize cancer treatment, particularly for patients lacking targetable genetic mutations. However, despite these promising prospects, there remain certain aspects of this pathway that require further investigation, particularly regarding treatment resistance. Therefore, the objective of this review is to delve into the role of IL-1β in NSCLC, its participation in inflammatory pathways, and its intricate crosstalk with the PD-1/PD-L1 pathway. Additionally, we aim to explore the potential of IL-1β as a therapeutic target for NSCLC treatment.
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Affiliation(s)
- Dani Ran Castillo
- Division of Hematology and Oncology, Loma Linda University Cancer Center, Loma Linda, CA 92354, USA; (D.R.C.); (E.G.C.); (M.E.R.); (H.R.M.)
| | - Won Jin Jeon
- Department of Internal Medicine, Loma Linda University, Loma Linda, CA 92350, USA; (W.J.J.); (B.P.); (B.J.); (J.H.M.)
| | - Daniel Park
- Department of Internal Medicine, University of San Francisco-Fresno, Fresno, CA 93701, USA;
| | - Bryan Pham
- Department of Internal Medicine, Loma Linda University, Loma Linda, CA 92350, USA; (W.J.J.); (B.P.); (B.J.); (J.H.M.)
| | - Chieh Yang
- Department of Internal Medicine, School of Medicine, University of California Riverside, Riverside, CA 92521, USA;
| | - Bowon Joung
- Department of Internal Medicine, Loma Linda University, Loma Linda, CA 92350, USA; (W.J.J.); (B.P.); (B.J.); (J.H.M.)
| | - Jin Hyun Moon
- Department of Internal Medicine, Loma Linda University, Loma Linda, CA 92350, USA; (W.J.J.); (B.P.); (B.J.); (J.H.M.)
| | - Jae Lee
- School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA;
| | - Esther G. Chong
- Division of Hematology and Oncology, Loma Linda University Cancer Center, Loma Linda, CA 92354, USA; (D.R.C.); (E.G.C.); (M.E.R.); (H.R.M.)
| | - Kiwon Park
- Department of Pharmacy, Loma Linda University, Loma Linda, CA 92350, USA;
| | - Mark E. Reeves
- Division of Hematology and Oncology, Loma Linda University Cancer Center, Loma Linda, CA 92354, USA; (D.R.C.); (E.G.C.); (M.E.R.); (H.R.M.)
| | - Penelope Duerksen-Hughes
- Division of Biochemistry, Department of Medicine & Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA;
| | - Hamid R. Mirshahidi
- Division of Hematology and Oncology, Loma Linda University Cancer Center, Loma Linda, CA 92354, USA; (D.R.C.); (E.G.C.); (M.E.R.); (H.R.M.)
| | - Saied Mirshahidi
- Biospecimen Laboratory, Loma Linda University Cancer Center, Loma Linda, CA 92354, USA
- Division of Microbiology and Molecular Genetics, Department of Medicine & Basic Sciences, Loma Linda University, Loma Linda 92350, CA, USA
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Chaudhary V, Sarohia GS, Phillips MR, Park D, Xie J, Zeraatkar D, Fung M, Thabane L, Loewenstein A, Holz FG, Garg SJ, Kaiser PK, Bhandari M, Guymer RH, Fraser-Bell S, Sivaprasad S, Wykoff CC. Role of anti-vascular endothelial growth factor in the management of non-proliferative diabetic retinopathy without centre-involving diabetic macular oedema: a meta-analysis of trials. Eye (Lond) 2023; 37:1966-1974. [PMID: 36369263 PMCID: PMC10333362 DOI: 10.1038/s41433-022-02269-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 08/23/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
This systematic review and meta-analysis investigated the impact of anti-vascular endothelial growth factor (VEGF) treatment in management of eyes with non-proliferative diabetic retinopathy (NPDR) without centre involving diabetic macular oedema (CI-DMO). We searched multiple databases for all randomised clinical trials (RCTs) that evaluated anti-VEGF treatment versus observation in eyes with NPDR without CI-DMO. Data was collected for six outcomes (best corrected visual acuity (BCVA) improvement, diabetic retinopathy severity score (DRSS), central subfield thickness, progression to vision threatening complications (VTCs), ocular adverse events and quality of life measures). Risk of bias was assessed using Cochrane risk-of-bias tool for randomised trials (RoB 2) and certainty of evidence was assessed using Grade of Recommendations, Assessment, Development and Evaluation (GRADE). We identified a total of 2 unique RCTs that compared aflibercept and sham to treat a total of 811 eyes. For BCVA change, there was a small, clinically insignificant benefit for aflibercept treatment at year 2 (MD 0.70, 95% CI 0.02-1.38, GRADE rating: MODERATE). DRSS demonstrated a statistically significant improvement with aflibercept use at year 2 (RR 3.76, 95% CI 2.75-5.13, GRADE rating: MODERATE). VTCs were significantly less in aflibercept arm at year 2 (RR 0.30, 95% CI 0.23-0.40, GRADE rating: MODERATE). In conclusion, aflibercept treatment versus observation in eyes with NPDR without CI-DMO can result in reduced risk of development of VTCs and regression of DRSS score over 2 years. Future trials are needed to increase the precision of the treatment effect and to provide data on quality-of-life metrics.PROSPERO Registration: CRD42021288608.
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Affiliation(s)
- Varun Chaudhary
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.
- Department of Surgery, McMaster University, Hamilton, ON, Canada.
| | - Gurkaran S Sarohia
- Department of Ophthalmology and Visual Sciences, University of Alberta, Edmonton, AB, Canada
| | - Mark R Phillips
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Daniel Park
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jim Xie
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Dena Zeraatkar
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Matthew Fung
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | - Lehana Thabane
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
- Biostatistics Unit, St. Joseph's Healthcare-Hamilton, Hamilton, ON, Canada
| | - Anat Loewenstein
- Division of Ophthalmology, Tel Aviv Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Frank G Holz
- Division of Ophthalmology, University of Bonn, Bonn, Germany
| | - Sunir J Garg
- Mid Atlantic Retina, The Retina Service of Wills Eye Hospital, Philadelphia, PA, USA
| | - Peter K Kaiser
- Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mohit Bhandari
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
- Division of Orthopaedic Surgery, Department of Surgery, McMaster University, St. Joseph's Hospital, Hamilton, ON, Canada
| | - Robyn H Guymer
- Centre for Eye Research Australia Royal, Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Department of Surgery, (Ophthalmology), The University of Melbourne, Melbourne, VIC, Australia
| | - Samantha Fraser-Bell
- Macular Research Group, Save Sight Institute, University of Sydney, Sydney, NSW, Australia
- Sydney Eye Hospital, Sydney, NSW, Australia
| | - Sobha Sivaprasad
- NIHR Moorfields Biomedical Research Centre, Moorfields Eye Hospital, London, UK
| | - Charles C Wykoff
- Retina Consultants of Texas, Retina Consultants of America, Houston, TX, USA
- Blanton Eye Institute, Houston Methodist Hospital, Houston, TX, USA
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19
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Castillo DR, Park D, Jeon WJ, Joung B, Lee J, Yang C, Pham B, Hino C, Chong E, Shields A, Nguyen A, Brothers J, Liu Y, Zhang KK, Cao H. Unveiling the Prognostic Significance of BCL6+/CD10+ Mantle Cell Lymphoma: Meta-Analysis of Individual Patients and Systematic Review. Int J Mol Sci 2023; 24:10207. [PMID: 37373354 DOI: 10.3390/ijms241210207] [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: 05/18/2023] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma (NHL) characterized by a hallmark translocation of t (11; 14). CD10 negativity has been used to differentiate MCL from other NHL types; however, recently, there has been an increase in the number of reported cases of CD10-positive MCL. This warrants further investigation into this rarer immunophenotype and its clinical significance. BCL6, which is a master transcription factor for the regulation of cell proliferation and key oncogene in B cell lymphomagenesis, has been reported to have co-expression with CD10 in MCL. The clinical significance of this aberrant antigen expression remains unknown. We conducted a systematic review by searching four databases and selected five retrospective analyses and five case series. Two survival analyses were conducted to determine if BCL6 positivity conferred a survival difference: 1. BCL6+ vs. BCL6- MCL. 2. BCL6+/CD10+ vs. BCL6-/CD10+ MCL. Correlation analysis was conducted to determine if BCL6 positivity correlated with the Ki67 proliferation index (PI). Overall survival (OS) rates were performed by the Kaplan-Meier method and log-rank test. Our analyses revealed that BCL6+ MCL had significantly shorter overall survival (median OS: 14 months vs. 43 months; p = 0.01), BCL6+/CD10+ MCL had an inferior outcome vs. BCL6+/CD10- MCL (median OS: 20 months vs. 55 months p = 0.1828), BCL6+ MCL had significantly higher percentages of Ki67% (Ki67% difference: 24.29; p = 0.0094), and BCL6 positivity had a positive correlation with CD10+ status with an odds ratio 5.11 (2.49, 10.46; p = 0.0000286). Our analysis showed that BCL6 expression is correlated with CD10 positivity in MCL, and BCL6 expression demonstrated an inferior overall survival. The higher Ki67 PI in BCL6+ MCL compared to BCL6- MCL further supports the idea that the BCL6+ immunophenotype may have prognostic value in MCL. MCL management should consider incorporating prognostic scoring systems adjusted for BCL6 expression. Targeted therapies against BCL6 may offer potential therapeutic options for managing MCL with aberrant immunophenotypes.
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Affiliation(s)
- Dani Ran Castillo
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Daniel Park
- Department of Internal Medicine, School of Medicine, University of California San Francisco-Fresno, Fresno, CA 93701, USA
| | - Won Jin Jeon
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Bowon Joung
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Jae Lee
- School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Chieh Yang
- Department of Internal Medicine, School of Medicine, University of California Riverside, Riverside, CA 92521, USA
| | - Bryan Pham
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Christopher Hino
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Esther Chong
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Andrea Shields
- Department of Pathology, Loma Linda University, Loma Linda, CA 92354, USA
| | - Anthony Nguyen
- Department of Nutrition, Texas A&M University, College Station, TX 77030, USA
| | - Joel Brothers
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
| | - Yan Liu
- Department of Pathology, Loma Linda University, Loma Linda, CA 92354, USA
| | - Ke K Zhang
- Department of Nutrition, Texas A&M University, College Station, TX 77030, USA
- Center for Epigenetics & Disease Prevention, Institute of Biosciences & Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Huynh Cao
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA
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Park D, Arveschoug A, Wahlmeier S, Petersen-Fitts G, Zakko P. The Effect of Plate Thickness on Fusion, Complications, and Outcomes in Anterior Cervical Spine Surgery. Cureus 2023; 15:e41048. [PMID: 37519557 PMCID: PMC10374268 DOI: 10.7759/cureus.41048] [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] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
Background and objective Anterior cervical discectomy and fusion (ACDF) is a common surgery involving the cervical spine. The goals of ACDF include obtaining a solid fusion and minimizing complications such as dysphagia. The effect of plate thickness on fusion, dysphagia, and patient outcomes is not well established. In light of this, this study aimed to evaluate the effect of plate thickness on fusion rates, complications, and outcomes in ACDF. Methods A case-control study involving ACDF performed by a single surgeon was conducted with the aim of comparing two commercially available plating systems: the Medtronic plate (Atlantis Vision Elite, Medtronic, Memphis, TN) and Aegis plate (CastleLoc-P, Aegis, Englewood, CO). The patients treated with the Medtronic plate served as the control group (Std) as the plate is widely utilized, while those treated with the Aegis plate, which is touted as one of the thinnest plates on the market, constituted the case low-profile group (LP). Demographic variables, fusion status, and patient-reported outcome measures (PROM) were compared between the two systems. Results Baseline demographic data were not significantly different between groups. The LP plate group had a significantly lower rate of fusion per patient as well as per level at 12 months. PROM did not significantly differ at any time point between the groups. Dysphagia scores could be correlated with radiographic measures reported in the Prevertebral Soft Tissue Swelling - Index (PVSTS-I). Conclusion Based on our findings, the plate thickness was not associated with dysphagia rates; however, the use of a thinner plate correlated with a lower rate of radiographic fusion at 12 months. The PVSTS-I may be useful for identifying patients with abnormal and severely abnormal dysphagia scores.
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Affiliation(s)
- Daniel Park
- Orthopaedic Surgery, Beaumont Health, Royal Oak, USA
| | | | | | | | - Phil Zakko
- Orthopaedic Surgery, Beaumont Health, Royal Oak, USA
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Ghoreifi A, Kaneko M, Peretsman S, Iwata A, Brooks J, Shakir A, Sugano D, Cai J, Cacciamani G, Park D, Lebastchi AH, Ukimura O, Bahn D, Gill I, Abreu AL. Patient-reported Satisfaction and Regret Following Focal Therapy for Prostate Cancer: A Prospective Multicenter Evaluation. EUR UROL SUPPL 2023; 50:10-16. [PMID: 37101771 PMCID: PMC10123415 DOI: 10.1016/j.euros.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2023] [Indexed: 02/22/2023] Open
Abstract
Background Several reports are available regarding the treatment decision regret of patients receiving conventional treatments for localized prostate cancer (PCa); yet data on patients undergoing focal therapy (FT) are sparse. Objective To evaluate the treatment decision satisfaction and regret among patients who underwent FT for PCa with high-intensity focused ultrasound (HIFU) or cryoablation (CRYO). Design setting and participants We identified consecutive patients who underwent HIFU or CRYO FT as the primary treatment for localized PCa at three US institutions. A survey with validated questionnaires, including the five-question Decision Regret Scale (DRS), International Prostate Symptom Score (IPSS), and International Index of Erectile Function (IIEF-5), was mailed to the patients. The regret score was calculated based on the five items of the DRS, and regret was defined as a DRS score of >25. Outcome measurements and statistical analysis Multivariable logistic regression models were applied to assess the predictors of treatment decision regret. Results and limitations Of 236 patients, 143 (61%) responded to the survey. Baseline characteristics were similar between responders and nonresponders. During a median (interquartile range) follow-up of 43 (26-68) mo, the treatment decision regret rate was 19.6%. On a multivariable analysis, higher prostate-specific antigen (PSA) at nadir after FT (odds ratio [OR] 1.48, 95% confidence interval [CI] 1.1-2, p = 0.009), presence of PCa on follow-up biopsy (OR 3.98, 95% CI 1.5-10.6, p = 0.006), higher post-FT IPSS (OR 1.18, 95% CI 1.01-1.37, p = 0.03), and newly diagnosed impotence (OR 6.67, 95% CI 1.57-27, p = 0.03) were independent predictors of treatment regret. The type of energy treatment (HIFU/CRYO) was not a predictor of regret/satisfaction. Limitations include retrospective abstraction. Conclusions FT for localized PCa is well accepted by the patients, with a low regret rate. Higher PSA at nadir, presence of cancer on follow-up biopsy, bothersome postoperative urinary symptoms, and impotence after FT were independent predictors of treatment decision regret. Patient summary In this report, we looked at the factors affecting satisfaction and regret in patients with prostate cancer undergoing focal therapy. We found that focal therapy is well accepted by the patients, while presence of cancer on follow-up biopsy as well as bothersome urinary symptoms and sexual dysfunction can predict treatment decision regret.
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Hamilton TM, Mansour TR, Hadi M, Deshpande N, Shultz L, Springer K, Hu J, Nerenz D, Zakko P, Khalil J, Park D, Easton R, Perez-Cruet MJ, Taliaferro K, Abdulhak M, Schwalb JM, Park P, Chang VW. 669 Is Outpatient Spine Surgery at an Ambulatory Surgical Center Better Than at a Hospital? A MSSIC Study. Neurosurgery 2023. [DOI: 10.1227/neu.0000000000002375_669] [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: 03/17/2023] Open
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Yeh YC, Park D, Yang SY, Kuo CC. Developing and validating the Taiwan version of the meaningful activity participation assessment (T-MAPA) with Rasch analysis. BMC Geriatr 2023; 23:159. [PMID: 36949379 PMCID: PMC10032021 DOI: 10.1186/s12877-023-03839-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/22/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Meaningful activity participation has shown good predictability for healthy ageing in older adults, and their participation can be assessed using the Meaningful Activity Participation Assessment (MAPA). However, the MAPA has never been validated in any Taiwanese population. Moreover, different cultures may interpret meaningful activity participation differently. This study thus aimed to cross-culturally adapt the MAPA into a Taiwan version (i.e., the T-MAPA) and to investigate the psychometric properties of the T-MAPA in older adults in Taiwan. METHODS This study consisted of 3 phases. First, the original MAPA was cross-culturally adapted in 6 stages, including forward, synthesis of, and back translations, cognitive debriefing, expert review, and pilot testing on 18 older adults. Second, a Rasch-Andrich rating scale model was applied to evaluate the psychometric properties (including category function, unidimensionality, item functioning and targeting, and reliability) of the adapted version in a sample of 146 older adults. Lastly, the convergent validity and test-retest reliability were examined on 120 and 49 older adults, respectively. RESULTS After cross-cultural adaptation, the first version of the T-MAPA contained 29 items. Optimal category function was obtained by reducing the response categories of the frequency subscale to 4 and retaining a 5-point rating for the meaningfulness subscale. After the removal of 1 misfit item, a 28-item T-MAPA was generated. This version demonstrated unidimensionality, measurement invariance among different subgroups (regarding sex and education), acceptable item targeting (< 1 logit) and negligible floor and ceiling effects (1.37%; 0.68%), high reliability (person reliability coefficient = 0.86; small standard error < 0.5 with large test information > 4), confirmed convergent validity (absolute r = .49-0.54 with psychological well-being, depressive symptoms, and mental and physical health), and excellent test-retest reliability (intraclass correlation coefficient = 0.94). CONCLUSION The cross-culturally adapted 28-item T-MAPA is suitable for application to the older population in Taiwan to measure meaningful activity participation. Future examinations of the T-MAPA in other populations with specific clinical features are warranted to extend its utility in practice.
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Affiliation(s)
- Ya-Chin Yeh
- Department of Occupational Therapy, Shu-Zen Junior College of Medicine and Management, 452, Huanqiu Rd., Luzhu Dist, Kaohsiung, Taiwan
| | - Daniel Park
- Chan Division of Occupational Science and Occupational Therapy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA, 90089-9003, USA
| | - Shang-Yu Yang
- Department of Healthcare Administration, College of Medical and Health Science, Asia University, 500, Lioufeng Rd, Wufeng, Taichung, Taiwan
| | - Chang-Chih Kuo
- Department of Occupational Therapy, Kaohsiung Medical University, 100, Shyh-Chung 1st Rd, Kaohsiung, Taiwan.
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Chiu L, Park D, Gupta DK, Matheny ME. UTILIZATION OF SGLT2 INHIBITORS IN UNITED STATES VETERANS WITH HEART FAILURE WITH REDUCED EJECTION FRACTION. J Am Coll Cardiol 2023. [DOI: 10.1016/s0735-1097(23)00730-1] [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: 03/07/2023]
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Yap T, Gainor J, McKean M, Bockorny B, Barve M, Sweis R, Vaishampayan U, Tarhini A, Kilari D, Chand A, Abdul-Karim R, Park D, Babu S, Ju Y, Dewall S, Liu L, Kennedy A, Marantz J, Gan L. 1O Safety, pharmacokinetics, efficacy, and biomarker results of SRK-181 (a latent TGFβ1 inhibitor) from a phase I trial (DRAGON trial). ESMO Open 2023. [DOI: 10.1016/j.esmoop.2023.100967] [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: 04/05/2023] Open
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Ramos-Llordén G, Park D, Kirsch JE, Scholz A, Keil B, Maffei C, Lee HH, Bilgiç B, Edlow BL, Mekkaoui C, Yendiki A, Witzel T, Huang SY. Eddy current-induced artifacts correction in high gradient strength diffusion MRI with dynamic field monitoring: demonstration in ex vivo human brain imaging. bioRxiv 2023:2023.02.15.528684. [PMID: 36824894 PMCID: PMC9948962 DOI: 10.1101/2023.02.15.528684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Purpose To demonstrate the advantages of spatiotemporal magnetic field monitoring to correct eddy current-induced artifacts (ghosting and geometric distortions) in high gradient strength diffusion MRI (dMRI). Methods A dynamic field camera with 16 NMR field probes was used to characterize eddy current fields induced from diffusion gradients for different gradients strengths (up to 300 mT/m), diffusion directions, and shots in a 3D multi-shot EPI sequence on a 3T Connectom scanner. The efficacy of dynamic field monitoring-based image reconstruction was demonstrated on high-resolution whole brain ex vivo dMRI. A 3D multi-shot image reconstruction framework was informed with the actual nonlinear phase evolution measured with the dynamic field camera, thereby accounting for high-order eddy currents fields on top of the image encoding gradients in the image formation model. Results Eddy current fields from diffusion gradients at high gradient strength in a 3T Connectom scanner are highly nonlinear in space and time, inducing high-order spatial phase modulations between odd/even echoes and shots that are not static during the readout. Superior reduction of ghosting and geometric distortion was achieved with dynamic field monitoring compared to ghosting approaches such as navigator- and structured low-rank-based methods or MUSE, followed by image-based distortion correction with eddy. Improved dMRI analysis is demonstrated with diffusion tensor imaging and high-angular resolution diffusion imaging. Conclusion Strong eddy current artifacts characteristic of high gradient strength dMRI can be well corrected with dynamic field monitoring-based image reconstruction, unlike the two-step approach consisting of ghosting correction followed by geometric distortion reduction with eddy.
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Lim S, Schultz L, Zakko P, Macki M, Hamilton T, Pawloski J, Fadel H, Mansour T, Yeh HH, Preston G, Nerenz D, Schwalb JM, Abdulhak M, Park P, Aleem I, Easton R, Khalil J, Perez-Cruet M, Park D, Chang V. The Potential Negative Effects of Smoking on Cervical and Lumbar Surgery Beyond Pseudarthrosis: A Michigan Spine Surgery Improvement Collaborative Study. World Neurosurg 2023; 173:e241-e249. [PMID: 36791883 DOI: 10.1016/j.wneu.2023.02.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 09/23/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023]
Abstract
OBJECTIVE To review the Michigan Spine Surgery Improvement Collaborative registry to investigate the long-term associations between current smoking status and outcomes after elective cervical and lumbar spine surgery. METHODS Using the Michigan Spine Surgery Improvement Collaborative, we captured all cases from January 1, 2017, to November 21, 2020, with outcomes data available; 19,251 lumbar cases and 7936 cervical cases were included. Multivariate regression analyses were performed to assess the relationship of smoking with the clinical outcomes. RESULTS Current smoking status was associated with lower urinary retention and satisfaction for patients after lumbar surgery and was associated with less likelihood of achieving minimal clinically important difference in primary outcome measures including Patient-Reported Outcomes Measurement Information System, back pain, leg pain, and EuroQol-5D at 90 days and 1 year after surgery. Current smokers were also less likely to return to work at 90 days and 1 year after surgery. Among patients who underwent cervical surgery, current smokers were less likely to have urinary retention and dysphagia postoperatively. They were less likely to be satisfied with the surgery outcome at 1 year. Current smoking was associated with lower likelihood of achieving minimal clinically important difference in Patient-Reported Outcomes Measurement Information System, neck pain, arm pain, and EuroQol-5D at various time points. There was no difference in return-to-work status. CONCLUSIONS Our analysis suggests that smoking is negatively associated with functional improvement, patient satisfaction, and return-to-work after elective spine surgery.
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Affiliation(s)
- Seokchun Lim
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA
| | - Lonni Schultz
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA; Department of Public Health Sciences, Henry Ford Hospital, Detroit, Michigan, USA
| | - Philip Zakko
- Department of Orthopedics, William Beaumont Hospital, Royal Oak, Michigan, USA
| | - Mohamed Macki
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA
| | - Travis Hamilton
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA
| | - Jacob Pawloski
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA
| | - Hassan Fadel
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA
| | - Tarek Mansour
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA
| | - Hsueh-Han Yeh
- Center for Health Services Research, Henry Ford Hospital, Detroit, Michigan, USA
| | - Gordon Preston
- Department of Orthopedics, William Beaumont Hospital, Royal Oak, Michigan, USA
| | - David Nerenz
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA; Center for Health Services Research, Henry Ford Hospital, Detroit, Michigan, USA
| | - Jason M Schwalb
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA
| | - Muwaffak Abdulhak
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA
| | - Paul Park
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Ilyas Aleem
- Department of Orthopedics, University of Michigan, Ann Arbor, Michigan, USA
| | - Richard Easton
- Department of Orthopedics, William Beaumont Hospital, Troy, Michigan, USA
| | - Jad Khalil
- Department of Orthopedics, William Beaumont Hospital, Royal Oak, Michigan, USA
| | | | - Daniel Park
- Department of Orthopedics, William Beaumont Hospital, Royal Oak, Michigan, USA
| | - Victor Chang
- Department of Neurological Surgery, Henry Ford Hospital, Detroit, Michigan, USA.
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Adams G, Moreno GK, Petros BA, Uddin R, Levine Z, Kotzen B, Messer K, Dobbins ST, DeRuff KC, Loreth C, Brock-Fisher T, Schaffner SF, Chaluvadi S, Kanjilal S, Luban J, Ozonoff A, Park D, Turbett S, Siddle KJ, MacInnis BL, Sabeti P, Lemieux J. The 2022 RSV surge was driven by multiple viral lineages. medRxiv 2023:2023.01.04.23284195. [PMID: 36656774 PMCID: PMC9844019 DOI: 10.1101/2023.01.04.23284195] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The US experienced an early and severe respiratory syncytial virus (RSV) surge in autumn 2022. Despite the pressure this has put on hospitals and care centers, the factors promoting the surge in cases are unknown. To investigate whether viral characteristics contributed to the extent or severity of the surge, we sequenced 105 RSV-positive specimens from symptomatic patients diagnosed with RSV who presented to the Massachusetts General Hospital (MGH) and its outpatient practices in the Greater Boston Area. Genomic analysis of the resulting 77 genomes (54 with >80% coverage, and 23 with >5% coverage) demonstrated that the surge was driven by multiple lineages of RSV-A (91%; 70/77) and RSV-B (9%; 7/77). Phylogenetic analysis of all US RSV-A revealed 12 clades, 4 of which contained Massachusetts and Washington genomes. These clades individually had times to most recent common ancestor (tMRCA) between 2014 and 2017, and together had a tMRCA of 2009, suggesting that they emerged well before the COVID-19 pandemic. Similarly, the RSV-B genomes had a tMRCA between 2016 and 2019. We found that the RSV-A and RSV-B genomes in our sample did not differ statistically from the estimated clock rate of the larger phylogenetic tree (10.6 and 12.4 substitutions per year, respectively). In summary, the polyphyletic nature of viral genomes sequenced in the US during the autumn 2022 surge is inconsistent with the emergence of a single, highly transmissible causal RSV lineage.
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Affiliation(s)
- Gordon Adams
- Massachusetts General Hospital, Boston, MA, 02142.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Gage K. Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Brittany A. Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard/Massachusetts Institute of Technology, MD-PhD Program, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Rockib Uddin
- Massachusetts General Hospital, Boston, MA, 02142.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Zoe Levine
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Harvard/Massachusetts Institute of Technology, MD-PhD Program, Boston, MA, USA.,Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Ben Kotzen
- Massachusetts General Hospital, Boston, MA, 02142.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Katelyn Messer
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | | | | | | | - Stephen F. Schaffner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,Brigham and Women’s Hospital, Boston, MA, 02115
| | | | | | - Jeremy Luban
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Al Ozonoff
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Park
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sarah Turbett
- Massachusetts General Hospital, Boston, MA, 02142.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | | | - Pardis Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,Brigham and Women’s Hospital, Boston, MA, 02115.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Jacob Lemieux
- Massachusetts General Hospital, Boston, MA, 02142.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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Rizvi S, Khakwani M, Pancham S, Tsitsikas D, Rudzki Z, Hassan‐Smith G, Bowen M, Wright C, Park D. Bone marrow necrosis and fat embolism syndrome in sickle cell disease during COVID-19 infection treated successfully with sequential red cell and plasma exchange. EJHaem 2022; 4:JHA2621. [PMID: 36718354 PMCID: PMC9877825 DOI: 10.1002/jha2.621] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022]
Abstract
Fat embolism syndrome (FES) is a rare life-threatening condition that is particularly seen in milder forms of sickle cell disease (SCD). Widespread systemic fat emboli are generated in the context of extensive bone marrow necrosis. Multi-organ failure with a high morbidity and mortality may quickly develop. Infection with Parvovirus B19 is a common precipitant. Here, the authors report the case of a 35-year-old Afro-Caribbean man with HbSC disease who presented with FES having tested positive for SARS-COV-2. He rapidly became critically ill and required admission to the intensive care unit for organ support. He was treated with red cell exchange and plasma exchange and made a good recovery to leave hospital at week 7.
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Affiliation(s)
- Syed Rizvi
- Department of Acute Internal MedicineUniversity Hospitals Birmingham (UHB) NHS Foundation TrustBirminghamUK
| | - Muhammad Khakwani
- Department of HaematologyUniversity Hospitals Birmingham (UHB) NHS Foundation TrustBirminghamUK
| | - Shivan Pancham
- Department of HaematologySandwell and West Birmingham Hospitals (SWBH) NHS TrustBirminghamUK
| | - Dimitris Tsitsikas
- Department of HaematologyHomerton University Hospital (HUH) NHS Foundation TrustLondonUK
| | - Zbigniew Rudzki
- Department of HistopathologyUniversity Hospitals Birmingham (UHB) NHS Foundation TrustBirminghamUK
| | - Ghaniah Hassan‐Smith
- Department of NeurologyUniversity Hospitals Birmingham (UHB) NHS Foundation TrustBirminghamUK
| | - Michael Bowen
- Department of Neuro-radiologyUniversity Hospitals Birmingham (UHB) NHS Foundation TrustBirminghamUK
| | - Christine Wright
- Department of HaematologySandwell and West Birmingham Hospitals (SWBH) NHS TrustBirminghamUK
| | - Daniel Park
- Department of Respiratory and Critical Care MedicineUniversity Hospitals Birmingham (UHB) NHS Foundation TrustBirminghamUK
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Sinz NJ, Hwang RW, Lee GH, Baker KC, Arnold P, Sasso R, Park D, Fischgrund J, Niu R, Kim DH. Pedicle Screw-Associated Violation of the Adjacent Unfused Facet Joint: Clinical Outcomes and Fusion Rates. Global Spine J 2022:21925682221145651. [PMID: 36510742 DOI: 10.1177/21925682221145651] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
STUDY DESIGN Retrospective review of a prospective randomized trial. OBJECTIVES To compare outcome scores and fusion rates in patients with and without pedicle screw-associated facet joint violation (FJV) after a single-level lumbar fusion. METHODS Clinical outcomes data and computed tomography (CT) imaging were reviewed for 157 patients participating in a multicenter prospective trial. Post-operative CT scans at 12-months follow-up were examined for fusion status and FJV. Patient-reported outcomes (PROs) included Oswestry Disability Index (ODI) and Visual Analog Scale (VAS) for leg and low back pain. Chi-square test of independence was used to compare proportions between groups on categorical measures. Two-sample t-test was used to identify differences in mean patient outcome scores. Logistic regression models were performed to determine association between FJV and fusion rates. RESULTS Of the 157 patients included, there were 18 (11.5%) with FJV (Group A) and 139 (88.5%) without FJV (Group B). Patients with FJV experienced less improvement in ODI (P = .004) and VAS back pain scores (P = .04) vs patients without FJV. There was no difference in mean VAS leg pain (P = .4997). The rate of fusion at 12-months for patients with FJV (27.8%) was lower compared to those without FJV (71.2%) (P = .0002). Patients with FJV were 76% less likely to have a successful fusion at 12-months. CONCLUSION Pedicle screw-associated violation of the adjacent unfused facet joint during single-level lumbar fusion is associated with less improvement in back pain, back pain-associated disability, and a lower fusion rate at 1-year after surgery.
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Affiliation(s)
- Nathan J Sinz
- Department of Orthopaedic Surgery, Tufts Medical Center, Boston, MA, USA
| | - Raymond W Hwang
- Department of Orthopaedic Surgery, Tufts Medical Center, Boston, MA, USA
- Department of Orthopaedic Surgery, New England Baptist Hospital, Boston, MA, USA
| | - Gyu-Ho Lee
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin C Baker
- Bone & Joint Center, Dept. of Orthopaedic Surgery, Henry Ford Health System, Detroit, MI, USA
| | - Paul Arnold
- Carle Neuroscience Institute, Urbana, IL, USA
| | - Rick Sasso
- Department of Orthopaedic Surgery, Indiana University School of Medicine, Indianapolis, IL, USA
| | - Daniel Park
- Department of Orthopaedic Surgery, William Beaumont Hospital, Royal Oak, MI, USA
| | - Jeffrey Fischgrund
- Department of Orthopaedic Surgery, William Beaumont Hospital, Royal Oak, MI, USA
| | - Ruijia Niu
- Department of Orthopaedic Surgery, New England Baptist Hospital, Boston, MA, USA
| | - David H Kim
- Department of Orthopaedic Surgery, Tufts Medical Center, Boston, MA, USA
- Department of Orthopaedic Surgery, New England Baptist Hospital, Boston, MA, USA
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Abstract
PURPOSE OF REVIEW Voluntary medical male circumcision (VMMC) is a surgical procedure that reduces HIV acquisition risk by almost two-thirds. However, global implementation is lagging, in part due to VMMC hesitancy. A better understanding of the mechanism(s) by which this procedure protects against HIV may increase acceptance of VMMC as an HIV risk reduction approach among health care providers and their clients. RECENT FINDINGS HIV acquisition in the uncircumcised penis occurs preferentially across the inner foreskin tissues, due to increased susceptibility that is linked to elevated inflammatory cytokine levels in the sub-preputial space and an increased tissue density of HIV-susceptible CD4 + T cells. Inflammation can be caused by sexually transmitted infections, but is more commonly induced by specific anaerobic components of the penile microbiome. Circumcision protects by both directly removing the susceptible tissues of the inner foreskin, and by inducing a less inflammatory residual penile microbiome. VMMC reduces HIV susceptibility by removing susceptible penile tissues, and also through impacts on the penile immune and microbial milieu. Understanding these mechanisms may not only increase VMMC acceptability and reinvigorate global VMMC programs, but may also lead to non-surgical HIV prevention approaches focused on penile immunology and/or microbiota.
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Affiliation(s)
- Jessica L Prodger
- Departments of Microbiology and Immunology and Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | | | - Aaron A R Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Daniel Park
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Cindy M Liu
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Rupert Kaul
- Departments of Medicine and Immunology, University of Toronto, Medical Sciences Building Rm. 6356, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- University Health Network, Toronto, ON, Canada.
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Park D, Izaguirre J, Coffey R, Xu H. Modeling the Effect of Cooperativity in Ternary Complex Formation and Targeted Protein Degradation Mediated by Heterobifunctional Degraders. ACS Bio Med Chem Au 2022; 3:74-86. [PMID: 37101604 PMCID: PMC10125322 DOI: 10.1021/acsbiomedchemau.2c00037] [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] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022]
Abstract
Chemically induced proximity between certain endogenous enzymes and a protein of interest (POI) inside cells may cause post-translational modifications to the POI with biological consequences and potential therapeutic effects. Heterobifunctional (HBF) molecules that bind with one functional part to a target POI and with the other to an E3 ligase induce the formation of a target-HBF-E3 ternary complex, which can lead to ubiquitination and proteasomal degradation of the POI. Targeted protein degradation (TPD) by HBFs offers a promising approach to modulate disease-associated proteins, especially those that are intractable using other therapeutic approaches, such as enzymatic inhibition. The three-way interactions among the HBF, the target POI, and the ligase-including the protein-protein interaction between the POI and the ligase-contribute to the stability of the ternary complex, manifested as positive or negative binding cooperativity in its formation. How such cooperativity affects HBF-mediated degradation is an open question. In this work, we develop a pharmacodynamic model that describes the kinetics of the key reactions in the TPD process, and we use this model to investigate the role of cooperativity in the ternary complex formation and in the target POI degradation. Our model establishes the quantitative connection between the ternary complex stability and the degradation efficiency through the former's effect on the rate of catalytic turnover. We also develop a statistical inference model for determining cooperativity in intracellular ternary complex formation from cellular assay data and demonstrate it by quantifying the change in cooperativity due to site-directed mutagenesis at the POI-ligase interface of the SMARCA2-ACBI1-VHL ternary complex. Our pharmacodynamic model provides a quantitative framework to dissect the complex HBF-mediated TPD process and may inform the rational design of effective HBF degraders.
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Affiliation(s)
- Daniel Park
- Roivant Discovery, New York, New York10036, United States
| | | | - Rory Coffey
- Roivant Discovery, New York, New York10036, United States
| | - Huafeng Xu
- Roivant Discovery, New York, New York10036, United States
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Harris E, Thacker L, Takayesu J, Jolly S, Park D, Russo A, Kidd E, Shah A, Damast S, Fields E. Multi-Institutional Evaluation of Health Disparities in Rural Cervical Cancer Patients. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1238] [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: 11/30/2022]
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Park D, Sawin Y, Niemierko A, Foote C, Irwin K, Russo A. Understanding Anxiety in Patients Receiving Vaginal Brachytherapy for Endometrial Cancer. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1282] [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: 12/01/2022]
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35
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Pena B, Knight W, Cavasin M, Ferrari I, Abdel-Hafiz M, Vagnozzi R, Bosi S, Park D, Shandas R, Song K, McKinsey T, Sbaizero O, Taylor M, Prato M, Mestroni L. Injectable carbon nanotube-functionalized hydrogel as a tool for cardiac tissue engineering. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.3016] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background/Introduction
Heart failure (HF) is an expensive major public health problem in the United States and around the world (1). The current treatments for HF are aimed at reducing symptoms, slowing disease progression, and reducing mortality and not aimed at repairing heart muscle or restoring function. Furthermore, even with these treatments, approximately half of patients with HF will die within 5 years of diagnosis (2). Cardiac transplantation remains the only definitive treatment for those affected with end-stage HF, but availability of donor hearts remains a major limitation (3).
Purpose
The ability of the adult heart to regenerate cardiomyocytes (CMs) lost after injury is limited, generating interest in developing tissue engineering therapies to avoid progression towards HF. Rigid carbon nanotubes (CNTs) scaffolds have been used to improve CMs viability, proliferation, and maturation (4), but require undesirable invasive surgeries for implantation. To overcome this limitation, we engineered an injectable reverse thermal gel (RTG) functionalized with CNTs (RTG-CNT) that transitions from a liquid-solution to a gel-based matrix shortly after reaching body temperature allowing for a liquid-based delivery rapidly followed by a stable-gel localization (5).
Methods and results
Here we show experimental evidences the RTG-CNT hydrogel, used as a three-dimensional (3D) niche to culture human induced pluripotent stem cells (hiPSC)-CMs, promotes hiPSC-CMs alignment and elongation with increased Cx43 localization and improved contraction function when compared with traditional two-dimensional (2D) fibronectin controls and plain 3D RTG system without CNTs. Moreover, the short-term (4-week) biocompatibility of the RTG-CNT hydrogel was also assessed in a mouse model (intracardial injection). The results confirmed that the RTG-CNT hydrogel is well tolerated by the cardiac tissue.
Conclusion
Our results indicated that the injectable RTG-CNT hydrogel has the potential to be used as a minimally invasive tool for cardiac tissue engineering efforts.
Funding Acknowledgement
Type of funding sources: Other. Main funding source(s): NATIONAL HEART, LUNG, AND BLOOD (NHLBI) INSTITUTE
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Affiliation(s)
- B Pena
- University of Colorado , Aurora , United States of America
| | - W Knight
- University of Colorado , Aurora , United States of America
| | - M Cavasin
- University of Colorado , Aurora , United States of America
| | - I Ferrari
- University of Colorado , Aurora , United States of America
| | - M Abdel-Hafiz
- University of Colorado , Aurora , United States of America
| | - R Vagnozzi
- University of Colorado , Aurora , United States of America
| | - S Bosi
- University of Trieste, Chemical and Pharmaceutical Sciences , Trieste , Italy
| | - D Park
- University of Colorado , Aurora , United States of America
| | - R Shandas
- University of Colorado , Aurora , United States of America
| | - K Song
- University of Colorado , Aurora , United States of America
| | - T McKinsey
- University of Colorado , Aurora , United States of America
| | - O Sbaizero
- University of Trieste, Engineering and Architecture , Trieste , Italy
| | - M Taylor
- University of Colorado , Aurora , United States of America
| | - M Prato
- University of Trieste, Chemical and Pharmaceutical Sciences , Trieste , Italy
| | - L Mestroni
- University of Colorado , Aurora , United States of America
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Kim M, Park D, Kim D, Lee M, Jeon D, Jang S, Kim J, Kim E, Yoon K, Lim S, Lee K, Choi S. Discovery of an allosteric small molecule inhibitor that can potently target SHP2 in vitro and in vivo. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)00894-2] [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: 11/03/2022]
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37
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Reske KA, Park D, Bach TH, Stewart HB, Vogt LC, Arter OG, Stoeckel D, Steinkamp HM, Liang SY, Durkin MJ, Kwon JH. Assessment of dental health care personnel protocol deviations and self-contamination during personal protective equipment donning and doffing. J Am Dent Assoc 2022; 153:1070-1077.e1. [PMID: 36175202 PMCID: PMC9511115 DOI: 10.1016/j.adaj.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/24/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022]
Abstract
Background Dental health care personnel (DHCP) may be at increased risk of exposure to severe acute respiratory syndrome coronavirus 2, the virus that causes COVID-19, as well as other clinically important pathogens. Proper use of personal protective equipment (PPE) reduces occupational exposure to pathogens. The authors performed an assessment of PPE donning and doffing practices among DHCP, using a fluorescent marker as a surrogate for pathogen transmission. Methods Participants donned PPE (that is, disposable gown, gloves, face mask, and eye protection) and the fluorescent marker was applied to their palms and abdomen. DHCP then doffed PPE according to their usual practices. The donning and doffing processes were video recorded, areas of fluorescence were noted, and protocol deviations were assessed. Statistical analyses included frequency, type, and descriptions of protocol deviations and factors associated with fluorescence. Results Seventy DHCP were enrolled. The donning and doffing steps with the highest frequency of protocol deviations were hand hygiene (66% of donning and 78% of doffing observations involved a deviation) and disposable gown use (63% of donning and 60% of doffing observations involved a deviation). Fluorescence was detected on 69% of DHCP after doffing, most frequently on hands. An increasing number of protocol deviations was significantly associated with increased risk of fluorescence. DHCP with a gown doffing deviation, excluding doffing out of order, were more likely to have fluorescence detected. Conclusions DHCP self-contamination was common with both donning and doffing PPE. Practical Implications Proper use of PPE is an important component of occupational health.
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Savage JA, Kiecker T, McMann N, Park D, Rothendler M, Mosher K. Leaf out time correlates with wood anatomy across large geographic scales and within local communities. New Phytol 2022; 235:953-964. [PMID: 35179794 PMCID: PMC9313884 DOI: 10.1111/nph.18041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
There is a long-standing idea that the timing of leaf production in seasonally cold climates is linked to xylem anatomy, specifically vessel diameter because of the hydraulic requirements of expanding leaves. We tested for a relationship between the timing of leaf out and vessel diameter in 220 plants in three common gardens accounting for species' phylogenetic relationships. We investigated how vessel diameter related to wood porosity, plant height and leaf length. We also used dye perfusion tests to determine whether plants relied on xylem produced during the previous growing season at the time of leaf out. In all three gardens, there was later leaf out in species with wider vessels. Ring-porous species had the widest vessels, exhibited latest leaf out and relied less on xylem made during the previous growing season than diffuse-porous species. Wood anatomy and leaf phenology did not exhibit a phylogenetic signal. The timing of leaf out is correlated with wood anatomy across species regardless of species' geographic origin and phylogenetic relationships. This correlation could be a result of developmental and physiological links between leaves and wood or tied to a larger safety efficiency trade-off.
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Affiliation(s)
| | - Thomas Kiecker
- Department of BiologyUniversity of MinnesotaDuluthMN55812USA
| | - Natalie McMann
- Department of BiologyUniversity of MinnesotaDuluthMN55812USA
| | - Daniel Park
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47907USA
| | | | - Kennedy Mosher
- Department of BiologyUniversity of MinnesotaDuluthMN55812USA
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39
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature 2022; 609:101-108. [PMID: 35798029 PMCID: PMC9433318 DOI: 10.1038/s41586-022-05049-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 70.0] [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: 12/21/2021] [Accepted: 06/29/2022] [Indexed: 11/23/2022]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission. Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.,Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.,Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.,Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego, USA
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Pradeep K Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. .,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. .,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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40
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Abstract
The National Academies of Sciences, Engineering, and Medicine (NASEM) has identified food allergies as a critical public health issue that significantly affects quality of life for patients and their families. Despite the crisis-level status of food allergies, especially in children, there are currently no curative treatments. As a result, impacted families must learn how to carry the burden of disease management. Using an expanded application of the concept of communication work, this study features data from interviews with 26 parents of food allergic children and explores how parents navigate the nuances of food allergy maintenance while negotiating and preserving valued relationships and identities through everyday talk. Results revealed that parents used communication to legitimate food allergy, balance potential face-threats with identity and relational goals, and coordinate care with spouses. Due to the lack of therapeutic treatment options, we found that parents utilize communication work, which is both demanding and effortful, as a form of disease management.
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Affiliation(s)
- Jennifer J Bute
- Department of Communication Studies, Indiana University-Purdue University Indianapolis
| | - Clarissa Bowers
- Department of Communication Studies, Indiana University-Purdue University Indianapolis
| | - Daniel Park
- Department of Communication Studies, Indiana University-Purdue University Indianapolis
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41
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Vaidyanathan S, Gamage S, Dathathreya K, Kryk R, Manoharan A, Zhao Z, Zhang L, Choi J, Park D, Park S, Soper SA. Fluidic operation of a polymer-based nanosensor chip for analysing single molecules. Flow (Camb) 2022; 2:E14. [PMID: 35936867 PMCID: PMC9356744 DOI: 10.1017/flo.2022.8] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Most medical diagnostic tests are expensive, involve slow turnaround times from centralized laboratories and require highly specialized equipment with seasoned technicians to carry out the assay. To facilitate realization of precision medicine at the point of care, we have developed a mixed-scale nanosensor chip featuring high surface area pillar arrays where solid-phase reactions can be performed to detect and identify nucleic acid targets found in diseased patients. Products formed can be identified and detected using a polymer nanofluidic channel. To guide delivery of this platform, we discuss the operation of various components of the device and simulations (COMSOL) used to guide the design by investigating parameters such as pillar array loading, and hydrodynamic and electrokinetic flows. The fabrication of the nanosensor is discussed, which was performed using a silicon (Si) master patterned with a combination of focused ion beam milling and photolithography with deep reactive ion etching. The mixed-scale patterns were transferred into a thermoplastic via thermal nanoimprint lithography, which facilitated fabrication of the nanosensor chip making it appropriate for in vitro diagnostics. The results from COMSOL were experimentally verified for hydrodynamic flow using Rhodamine B as a fluorescent tracer and electrokinetic flow using single fluorescently labelled oligonucleotides (single-stranded DNAs, ssDNAs).
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Affiliation(s)
- Swarnagowri Vaidyanathan
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
| | - Sachindra Gamage
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
| | - Kavya Dathathreya
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
| | - Renee Kryk
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
| | - Anishkumar Manoharan
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
| | - Zheng Zhao
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
| | - Lulu Zhang
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
- Mechanical & Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Daniel Park
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
- Mechanical & Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
- Mechanical & Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Steven A. Soper
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
- Department of Cancer Biology and KU Cancer Center, The University of Kansas Medical Center, Kansas City, KS 66106, USA
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42
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Bosserman RE, Farnsworth CW, O’Neil CA, Cass C, Park D, Ballman C, Wallace MA, Struttmann E, Stewart H, Arter O, Peacock K, Fraser VJ, Budge PJ, Olsen MA, Burnham CAD, Babcock HM, Kwon JH. Antibodies in healthcare personnel following severe acute respiratory syndrome coronavirus virus 2 (SARS-CoV-2) infection. Antimicrob Steward Healthc Epidemiol 2022; 2:e93. [PMID: 36483363 PMCID: PMC9726486 DOI: 10.1017/ash.2022.231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 05/27/2023]
Abstract
In a prospective cohort of healthcare personnel (HCP), we measured severe acute respiratory syndrome coronavirus virus 2 (SARS-CoV-2) nucleocapsid IgG antibodies after SARS-CoV-2 infection. Among 79 HCP, 68 (86%) were seropositive 14-28 days after their positive PCR test, and 54 (77%) of 70 were seropositive at the 70-180-day follow-up. Many seropositive HCP (95%) experienced an antibody decline by the second visit.
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Affiliation(s)
- Rachel E. Bosserman
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Christopher W. Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Caroline A. O’Neil
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Candice Cass
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel Park
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Claire Ballman
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Emily Struttmann
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Henry Stewart
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Olivia Arter
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Kate Peacock
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Victoria J. Fraser
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Philip J. Budge
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Margaret A. Olsen
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Hilary M. Babcock
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jennie H. Kwon
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
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43
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Hino C, Pham B, Park D, Yang C, Nguyen MH, Kaur S, Reeves ME, Xu Y, Nishino K, Pu L, Kwon SM, Zhong JF, Zhang KK, Xie L, Chong EG, Chen CS, Nguyen V, Castillo DR, Cao H. Targeting the Tumor Microenvironment in Acute Myeloid Leukemia: The Future of Immunotherapy and Natural Products. Biomedicines 2022; 10:biomedicines10061410. [PMID: 35740430 PMCID: PMC9219790 DOI: 10.3390/biomedicines10061410] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 05/18/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022] Open
Abstract
The tumor microenvironment (TME) plays an essential role in the development, proliferation, and survival of leukemic blasts in acute myeloid leukemia (AML). Within the bone marrow and peripheral blood, various phenotypically and functionally altered cells in the TME provide critical signals to suppress the anti-tumor immune response, allowing tumor cells to evade elimination. Thus, unraveling the complex interplay between AML and its microenvironment may have important clinical implications and are essential to directing the development of novel targeted therapies. This review summarizes recent advancements in our understanding of the AML TME and its ramifications on current immunotherapeutic strategies. We further review the role of natural products in modulating the TME to enhance response to immunotherapy.
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Affiliation(s)
- Christopher Hino
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.H.); (B.P.); (K.N.); (L.P.); (S.M.K.)
| | - Bryan Pham
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.H.); (B.P.); (K.N.); (L.P.); (S.M.K.)
| | - Daniel Park
- Department of Internal Medicine, School of Medicine, University of California San Francisco–Fresno, Fresno, CA 93701, USA;
| | - Chieh Yang
- Department of Internal Medicine, School of Medicine, University of California Riverside, Riverside, CA 92521, USA;
| | - Michael H.K. Nguyen
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Simmer Kaur
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Mark E. Reeves
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Yi Xu
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Kevin Nishino
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.H.); (B.P.); (K.N.); (L.P.); (S.M.K.)
| | - Lu Pu
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.H.); (B.P.); (K.N.); (L.P.); (S.M.K.)
| | - Sue Min Kwon
- Department of Internal Medicine, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (C.H.); (B.P.); (K.N.); (L.P.); (S.M.K.)
| | - Jiang F. Zhong
- Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA;
| | - Ke K. Zhang
- Department of Nutrition, Texas A&M University, College Station, TX 77030, USA; (K.K.Z.); (L.X.)
- Center for Epigenetics & Disease Prevention, Institute of Biosciences & Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Linglin Xie
- Department of Nutrition, Texas A&M University, College Station, TX 77030, USA; (K.K.Z.); (L.X.)
- Center for Epigenetics & Disease Prevention, Institute of Biosciences & Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Esther G. Chong
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Chien-Shing Chen
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
| | - Vinh Nguyen
- Department of Biology, University of California Riverside, Riverside, CA 92521, USA;
| | - Dan Ran Castillo
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
- Correspondence: (D.R.C.); (H.C.)
| | - Huynh Cao
- Department of Oncology/Hematology, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA; (M.H.K.N.); (S.K.); (M.E.R.); (Y.X.); (E.G.C.); (C.-S.C.)
- Correspondence: (D.R.C.); (H.C.)
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Hwang A, Doornenbal J, Park D, Bal I, Bukari MSANI, Yan Y, Abdulhaq H. Clinicopathological characteristics of high-risk multiple myeloma in Hispanic versus non-Hispanic patients in central California. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.8056] [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: 11/20/2022] Open
Abstract
8056 Background: Roughly 37% of Multiple Myeloma (MM) patients in the U.S. are non-white minorities. Advanced stage at diagnosis and specific cytogenetic abnormalities are associated with high-risk disease and poor prognosis. Few studies evaluated these risk factors in ethnic minorities. To further investigate, we analyzed ethnic variations in characteristics and outcomes of high-risk MM patients who were treated at our institution in Fresno, CA (49.6% Hispanic population). Methods: Patients diagnosed with high-risk MM at Community Medical Centers from 1-1-2011 to 12-31-2020 were included. High risk was defined by Mayo Clinic mSMART 3.0 classification. Demographic and disease-relevant information were collected. Cytogenetics, R ISS stage, 1st line treatment (doublet vs triplet), and treatment response (IMWG response criteria) were evaluated. Hispanic and non Hispanic comparisons were made by Fisher’s exact test where appropriate. Progression Free Survival (PFS) and Overall Survival (OS) were evaluated by Kaplan-Meier estimates and compared via log-rank test. Univariate cox proportional hazard model for survival was used to examine the association of variables with mortality risk after 1st line therapy. Results: 147 MM patients were screened. 42 high risk patients were identified: 11 (26%) Hispanic, 31 (74%) non Hispanic (22 white, 8 African American, 1 East Indian). Median age at diagnosis was 65. 26 (61%) were females. 25 (59%) were R ISS stage 3. Hispanic vs non Hispanic median income was $46119 vs $65080 (p=0.035). 6 Hispanics had Medi-Cal insurance vs 2 non-Hispanics (54.6% vs 6.5%, p=0.003). More Hispanics had Lambda light chain disease (73% vs 26%; p=0.01). 13 non Hispanics had del 17p vs 0 Hispanics (p=0.009). 40/42 patients (95%) received triplet therapy. 4 Hispanics received ASCT vs 9 non Hispanics (40% vs 33.3%, p=0.716). Hispanics and non Hispanics did not have significantly different treatment responses per IMWG criteria (p=0.799). No significant difference in PFS was seen between Hispanics and non Hispanics (805 vs 793 days; p=0.089); OS was better in Hispanics (1062 days vs 453 days; p=0.008). Per univariate cox proportional Hazard model, female sex (HR 4.34) and age (HR 1.05) were associated with higher mortality while Hispanic ethnicity was associated with lower mortality (HR 0.19). Conclusions: Hispanic and non Hispanic high risk MM patients differed significantly in median income, insurance, and del 17p incidence. These did not translate to a difference in 1st line therapy or treatment response. OS in our study is higher in Hispanic high-risk MM patients compared to other ethnicities and warrants further investigation. [Table: see text]
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Affiliation(s)
- Andrew Hwang
- University of California-San Francisco, Fresno, CA
| | | | | | - Inderpreet Bal
- University of California San Francisco, San Francisco, CA
| | | | - Yueqi Yan
- UC Merced Biostatistics and Data Support Center, Merced, CA
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45
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv 2022:2021.12.21.21268143. [PMID: 35411350 PMCID: PMC8996633 DOI: 10.1101/2021.12.21.21268143] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M. Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M. Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B. Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C. Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L. Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Nicholson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian H Mchardy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David P Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S. Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K. Martin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R. MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T. Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA
| | - Pradeep K. Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C. Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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46
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv 2022. [PMID: 35411350 DOI: 10.1101/2022.01.27.22269965] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Nicholson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian H Mchardy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA
| | - Pradeep K Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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47
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Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. Gigascience 2022; 11:6529104. [PMID: 35169842 PMCID: PMC8847733 DOI: 10.1093/gigascience/giac003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Background The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. Results As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories. Conclusions Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.
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Affiliation(s)
| | - Ruth E Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA
| | - Catarina Inês Mendes
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Andrew J Page
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK
| | - Nabil-Fareed Alikhan
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK
| | - Dan Fornika
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 1W5, Canada
| | - Josefina Campos
- INEI-ANLIS “Dr Carlos G. Malbrán,” Buenos Aires C1282AFF, Argentina
| | - Daniel Park
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Idowu B Olawoye
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria
| | - Paul E Oluniyi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria
| | - Dominique Anderson
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Rhiannon Cameron
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
| | - Damion Dooley
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
| | - Lee S Katz
- Center for Food Safety, University of Georgia, Atlanta, GA 30333, USA
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA
| | - Allison Black
- Department of Epidemiology, University of Washington, WA 98109, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tanya Barrett
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anjanette Johnston
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | | | - Adam A Witney
- Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, UK
| | - Gregory H Tyson
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin 12277, Germany
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Brian Alcock
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- The Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Emma Hodcroft
- Biozentrum, University of Basel, Basel 3012, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - William W L Hsiao
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7 V6T 1Z7, Canada
| | - Ana Tereza R Vasconcelos
- Bioinformatics Laboratory National Laboratory of Scientific Computation LNCC/MCTI, Petrópolis 25651-075, Brazil
| | - Duncan R MacCannell
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA
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48
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Yeung SC, Park JY, Park D, You Y, Yan P. The effect of systemic and topical ophthalmic medications on choroidal thickness: a review. Br J Clin Pharmacol 2022; 88:2673-2685. [DOI: 10.1111/bcp.15237] [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] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/02/2022] [Accepted: 01/10/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Shanna C. Yeung
- Faculty of Medicine The University of British Columbia Vancouver Canada
| | | | - Daniel Park
- Faculty of Medicine University of Toronto Toronto Canada
| | - Yuyi You
- Department of Clinical Medicine Macquarie University Sydney Australia
- Save Sight Institute The University of Sydney Sydney Australia
| | - Peng Yan
- Department of Ophthalmology and Vision Sciences, Toronto Western Hospital, University Health Network University of Toronto Toronto Canada
- Kensington Vision and Research Center Toronto Canada
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49
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Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES. Author Correction: Human neocortical expansion involves glutamatergic neuron diversification. Nature 2022; 601:E12. [PMID: 34992294 PMCID: PMC8770134 DOI: 10.1038/s41586-021-04322-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Szabina Furdan
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Desiree Marshall
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica Melief
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Leona Mezei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Norbert Mihut
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gaspar Olah
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Attila Ozsvar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Viktor Szemenyei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Philip C de Witt Hamer
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander Idema
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Idan Segev
- Edmond and Lily Safra Center for Brain Sciences and Department of Neurobiology, The Hebrew University Jerusalem, Jerusalem, Israel
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
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50
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Chee L, Ritchie D, Ludford-Menting M, Ripley J, Chung J, Park D, Norton S, Kenealy M, Koldej R. Dysregulation of immune cell and cytokine signaling correlates with clinical outcomes in myelodysplastic syndrome (MDS). Eur J Haematol 2021; 108:342-353. [PMID: 34963023 DOI: 10.1111/ejh.13742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Myelodysplastic syndromes (MDS) are characterized by ineffective hematopoiesis. Although hypomethylating agents (HMA) have improved survival in higher-risk MDS, most patients eventually succumb to progressive disease. Utilizing samples collected prospectively from three MDS clinical trials, we analyzed genetic and immunological biomarkers and correlated them with clinical outcomes. METHODS 154 samples were analyzed from 133 de novo MDS patients for T-cell and myeloid cell immunophenotyping and gene expression analysis. Treatments were with HMA or immunomodulatory drug (IMiD) alone or in combination. RESULTS We observed differences in immune cell subsets between lower and higher risk IPSS groups with NKT cells, MDSCs, intermediate-proinflammatory and non-classical monocytes being higher in the latter group while naïve CD4+ T-cells were reduced. Intermediate-proinflammatory monocytes were increased in non-responders and those failing to achieve at least a hematological improvement. Pro-inflammatory NKT cells were increased at diagnosis for patients failing to derive clinical benefit after 12 months of treatment. Gene expression analysis of paired bone marrow (BM) colony-forming units (CFUs) from diagnosis and 4 cycles post-treatment confirmed that genes involved in cytokine signaling were downregulated in C4 normal colonies. CONCLUSIONS These findings support the central roles of dysregulation in innate immunity and inflammatory signaling in the pathogenesis of MDS which correlated with clinical outcomes post-treatment.
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Affiliation(s)
- L Chee
- Australian Cancer Research Foundation (ACRF) Translational Laboratory, The Royal Melbourne Hospital, Melbourne, VIC, 3000, Australia.,Department of Clinical Haematology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC, 3050, Australia.,Department of Medicine, The University of Melbourne, Parkville, VIC, 3050, Australia.,The Australasian Leukaemia and Lymphoma Group, Richmond, VIC, 3121, Australia
| | - D Ritchie
- Australian Cancer Research Foundation (ACRF) Translational Laboratory, The Royal Melbourne Hospital, Melbourne, VIC, 3000, Australia.,Department of Clinical Haematology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC, 3050, Australia.,Department of Medicine, The University of Melbourne, Parkville, VIC, 3050, Australia.,The Australasian Leukaemia and Lymphoma Group, Richmond, VIC, 3121, Australia
| | - M Ludford-Menting
- Australian Cancer Research Foundation (ACRF) Translational Laboratory, The Royal Melbourne Hospital, Melbourne, VIC, 3000, Australia
| | - J Ripley
- Australian Cancer Research Foundation (ACRF) Translational Laboratory, The Royal Melbourne Hospital, Melbourne, VIC, 3000, Australia.,Liverpool Hospital, Liverpool, NSW, 2170, Australia
| | - J Chung
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - D Park
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - S Norton
- Nanix Limited, Dunedin, New Zealand
| | - M Kenealy
- The Australasian Leukaemia and Lymphoma Group, Richmond, VIC, 3121, Australia.,Cabrini Hospital, Malvern, VIC, 3144, Australia.,Monash University, Clayton, VIC, 3800, Australia
| | - R Koldej
- Australian Cancer Research Foundation (ACRF) Translational Laboratory, The Royal Melbourne Hospital, Melbourne, VIC, 3000, Australia.,Department of Medicine, The University of Melbourne, Parkville, VIC, 3050, Australia
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