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Young AM, Van Buren S, Rashid NU. Differential transcript usage analysis incorporating quantification uncertainty via compositional measurement error regression modeling. Biostatistics 2024; 25:559-576. [PMID: 37040757 PMCID: PMC11017126 DOI: 10.1093/biostatistics/kxad008] [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: 07/01/2021] [Revised: 12/22/2022] [Accepted: 02/06/2023] [Indexed: 04/13/2023] Open
Abstract
Differential transcript usage (DTU) occurs when the relative expression of multiple transcripts arising from the same gene changes between different conditions. Existing approaches to detect DTU often rely on computational procedures that can have speed and scalability issues as the number of samples increases. Here we propose a new method, CompDTU, that uses compositional regression to model the relative abundance proportions of each transcript that are of interest in DTU analyses. This procedure leverages fast matrix-based computations that make it ideally suited for DTU analysis with larger sample sizes. This method also allows for the testing of and adjustment for multiple categorical or continuous covariates. Additionally, many existing approaches for DTU ignore quantification uncertainty in the expression estimates for each transcript in RNA-seq data. We extend our CompDTU method to incorporate quantification uncertainty leveraging common output from RNA-seq expression quantification tool in a novel method CompDTUme. Through several power analyses, we show that CompDTU has excellent sensitivity and reduces false positive results relative to existing methods. Additionally, CompDTUme results in further improvements in performance over CompDTU with sufficient sample size for genes with high levels of quantification uncertainty, while also maintaining favorable speed and scalability. We motivate our methods using data from the Cancer Genome Atlas Breast Invasive Carcinoma data set, specifically using RNA-seq data from primary tumors for 740 patients with breast cancer. We show greatly reduced computation time from our new methods as well as the ability to detect several novel genes with significant DTU across different breast cancer subtypes.
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Affiliation(s)
- Amber M Young
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC, 27599, USA
| | - Scott Van Buren
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC, 27599, USA
| | - Naim U Rashid
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC, 27599, USA and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC, 27599, USA
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Innocenti F, Yazdani A, Rashid N, Qu X, Ou FS, Van Buren S, Bertagnolli M, Kabbarah O, Blanke CD, Venook AP, Lenz HJ, Vincent BG. Tumor Immunogenomic Features Determine Outcomes in Patients with Metastatic Colorectal Cancer Treated with Standard-of-Care Combinations of Bevacizumab and Cetuximab. Clin Cancer Res 2022; 28:1690-1700. [PMID: 35176136 PMCID: PMC9093780 DOI: 10.1158/1078-0432.ccr-21-3202] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/22/2021] [Accepted: 02/11/2022] [Indexed: 12/16/2022]
Abstract
PURPOSE CALGB/SWOG 80405 was a randomized phase III trial in first-line patients with metastatic colorectal cancer treated with bevacizumab, cetuximab, or both, plus chemotherapy. We tested the effect of tumor immune features on overall survival (OS). EXPERIMENTAL DESIGN Primary tumors (N = 554) were profiled by RNA sequencing. Immune signatures of macrophages, lymphocytes, TGFβ, IFNγ, wound healing, and cytotoxicity were measured. CIBERSORTx scores of naive and memory B cells, plasma cells, CD8+ T cells, resting and activated memory CD4+ T cells, M0 and M2 macrophages, and activated mast cells were measured. RESULTS Increased M2 macrophage score [HR, 6.30; 95% confidence interval (CI), 3.0-12.15] and TGFβ signature expression (HR, 1.35; 95% CI, 1.05-1.77) were associated with shorter OS. Increased scores of plasma cells (HR, 0.55; 95% CI, 0.38-0.87) and activated memory CD4+ T cells (HR, 0.34; 95% CI, 0.16-0.65) were associated with longer OS. Using optimal cutoffs from these four features, patients were categorized as having either 4, 3, 2, or 0-1 beneficial features associated with longer OS, and the median (95% CI) OS decreased from 42.5 (35.8-47.8) to 31.0 (28.8-34.4), 25.2 (20.6-27.9), and 17.7 (13.5-20.4) months respectively (P = 3.48e-11). CONCLUSIONS New immune features can be further evaluated to improve patient response. They provide the rationale for more effective immunotherapy strategies.
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Affiliation(s)
| | - Akram Yazdani
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Naim Rashid
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | - Scott Van Buren
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Alan P. Venook
- University of California at San Francisco, San Francisco, CA
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Innocenti F, Yazdani A, Qu X, Ou FS, Van Buren S, Kabbarah O, Blanke CD, Venook AP, Lenz HJ, Vincent BG. Immune signatures to affect overall survival (OS) and response to bevacizumab (Bev) or cetuximab (Cet) in patients (pts) with metastatic colorectal cancer (mCRC) of CALGB/SWOG 80405 (Alliance). J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.3515] [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
3515 Background: CALGB/SWOG 80405 was a randomized phase III trial in first-line mCRC patients treated with Bev, Cet, or both, plus chemotherapy. No difference in OS was found between Bev and Cet. We tested the effect of immune signatures on OS in all the three arms of the study and analyzed differences in OS between the Cet and Bev arms. Methods: 578 primary tumors were profiled by RNAseq. Immune signatures of TGF-β, cytotoxic T cells, wound healing, macrophages, lymphocytes, and INF-γ, as well as relative frequencies of CD8+ T-cells, memory resting CD4+ T cells, memory activated CD4+ T cells, macrophages M1 and M2, and activated mast cells were measured. Multivariate Cox proportional hazard models were applied using elastic-net penalization with covariates (age, race, gender, all RAS and BRAF V600E mutations). For relevant signatures, optimal cut-offs for OS were calculated. Results: In all the three arms of the study, high expression of macrophages M2 (HR 6.81, 95% CI 3.56-30.16) and TGF-β (HR 1.37, 95% CI 1.03-2.10) conferred reduced OS compared to low expression; high expression of plasma cells (HR 0.52, 95% CI 0.27-0.83) and memory-activated CD4+ T cells (HR 0.34, 95% CI 0.10-0.65) conferred increased OS compared to low expression. Using optimal cut-offs from these 4 signatures, pts have been categorized as to whether they had either 4, 3, 2, 1, or 0 beneficial signatures associated with increased OS. In all arms of the study (N = 469, after accounting for covariates), the median (95% CI) OS decreased from 42.5 (35.8-47.8; N = 79), to 31.0 (28.8-34.4; N = 177), 25.2 (20.6-27.9; N = 144), and 17.0 (13.5-20.4; N = 69) months when the number of beneficial signatures decreased from 4, to 3, 2, and 0-1 (combined due to a low number of pts), respectively (p = 3.48e-11). In the Bev arm (N = 205), high expression of macrophages M2 conferred reduced OS compared to low expression (HR 6.6, 95% CI 2.7-67.1). In the Cet arm (N = 165), high expression of macrophages M2 conferred reduced OS compared to low expression (HR 4.3, 95% CI 2.1-79.8); high expression of plasma cells (HR 0.36, 95% CI 0.06-0.55) and memory activated CD4+ T cells (HR 0.37, 95% CI 0.03-0.98) conferred increased OS compared to low expression of either signatures. The plasma cell signature interacted with Bev and Cet on the OS of pts (interaction p = 0.009). Conclusions: Tumor immune signatures in mCRC pts are determinants of survival. In pts treated with Bev- and Cet-combination therapies that are standard of care, immune signatures affect response to therapy. These results, provide new markers for treatment selection and for the development of novel active combinations including immune checkpoint inhibitors. Support: U10CA180821, U10CA180882, U24CA196171; https://acknowledgments.alliancefound.org
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Affiliation(s)
| | - Akram Yazdani
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Scott Van Buren
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Alan P. Venook
- University of California San Francisco, San Francisco, CA
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Van Buren S, Sarkar H, Srivastava A, Rashid NU, Patro R, Love MI. Compression of quantification uncertainty for scRNA-seq counts. Bioinformatics 2021; 37:1699-1707. [PMID: 33471073 PMCID: PMC8289386 DOI: 10.1093/bioinformatics/btab001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/16/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Motivation Quantification estimates of gene expression from single-cell RNA-seq (scRNA-seq) data have inherent uncertainty due to reads that map to multiple genes. Many existing scRNA-seq quantification pipelines ignore multi-mapping reads and therefore underestimate expected read counts for many genes. alevin accounts for multi-mapping reads and allows for the generation of ‘inferential replicates’, which reflect quantification uncertainty. Previous methods have shown improved performance when incorporating these replicates into statistical analyses, but storage and use of these replicates increases computation time and memory requirements. Results We demonstrate that storing only the mean and variance from a set of inferential replicates (‘compression’) is sufficient to capture gene-level quantification uncertainty, while reducing disk storage to as low as 9% of original storage, and memory usage when loading data to as low as 6%. Using these values, we generate ‘pseudo-inferential’ replicates from a negative binomial distribution and propose a general procedure for incorporating these replicates into a proposed statistical testing framework. When applying this procedure to trajectory-based differential expression analyses, we show false positives are reduced by more than a third for genes with high levels of quantification uncertainty. We additionally extend the Swish method to incorporate pseudo-inferential replicates and demonstrate improvements in computation time and memory usage without any loss in performance. Lastly, we show that discarding multi-mapping reads can result in significant underestimation of counts for functionally important genes in a real dataset. Availability and implementation makeInfReps and splitSwish are implemented in the R/Bioconductor fishpond package available at https://bioconductor.org/packages/fishpond. Analyses and simulated datasets can be found in the paper’s GitHub repo at https://github.com/skvanburen/scUncertaintyPaperCode. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Scott Van Buren
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Hirak Sarkar
- Department of Computer Science, University of Maryland College Park, MD 20742, USA.,Center for Bioinformatics and Computational Biology, University of Maryland College Park, MD 20742, USA
| | - Avi Srivastava
- New York Genome Center, New York, NY 10013, USA.,Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Naim U Rashid
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.,Lineberger Comprehensive Cancer Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rob Patro
- Department of Computer Science, University of Maryland College Park, MD 20742, USA.,Center for Bioinformatics and Computational Biology, University of Maryland College Park, MD 20742, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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Lee EY, Flynn MR, Du G, Lewis MM, Herring AH, Van Buren E, Van Buren S, Kong L, Mailman RB, Huang X. Editor's Highlight: Lower Fractional Anisotropy in the Globus Pallidus of Asymptomatic Welders, a Marker for Long-Term Welding Exposure. Toxicol Sci 2016; 153:165-73. [PMID: 27466214 DOI: 10.1093/toxsci/kfw116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
INTRODUCTION Welding fumes contain several metals including manganese (Mn), iron (Fe), and copper (Cu) that at high exposure may co-influence welding-related neurotoxicity. The relationship between brain accumulation of these metals and neuropathology, especially in welders with subclinical exposure levels, is unclear. This study examined the microstructural integrity of basal ganglia (BG) regions in asymptomatic welders using diffusion tensor imaging (DTI). METHODS Subjects with (n = 43) and without (age- and gender-matched controls; n = 31) history of welding were studied. Occupational questionnaires estimated short-term (HrsW; welding hours and E90; cumulative exposure, past 90 days) and long-term (YrsW; total years welding and ELT; cumulative exposure, lifetime) exposure. Whole blood metal levels (Mn, Fe, and Cu) were obtained. Brain MRI pallidal index (PI), R1 (1/T1), and R2* (1/T2*) were measured to estimate Mn and Fe accumulation in BG [caudate, putamen, and globus pallidus (GP)]. DTI was used to assess BG microstructural differences, and related with exposure measurements. RESULTS When compared with controls, welders had significantly lower fractional anisotropy (FA) in the GP. In welders, GP FA values showed non-linear relationships to YrsW, blood Mn, and PI. GP FA decreased after a critical level of YrsW or Mn was reached, whereas it decreased with increasing PI values until plateauing at the highest PI values. GP FA, however, did not show any relationship with short-term exposure measurements (HrsW, E90), blood Cu and Fe, or R(2)* values. CONCLUSION GP FA captured microstructural changes associated with chronic low-level Mn exposure, and may serve as a biomarker for neurotoxicity in asymptomatic welders.
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Affiliation(s)
- Eun-Young Lee
- *Department of Neurology, Pennsylvania State University-Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033
| | - Michael R Flynn
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Guangwei Du
- *Department of Neurology, Pennsylvania State University-Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033
| | - Mechelle M Lewis
- *Department of Neurology, Pennsylvania State University-Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033; Department of Pharmacology, Pennsylvania State University-Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033
| | - Amy H Herring
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Eric Van Buren
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Scott Van Buren
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lan Kong
- Department of Public Health Sciences
| | - Richard B Mailman
- *Department of Neurology, Pennsylvania State University-Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033; Department of Pharmacology, Pennsylvania State University-Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033
| | - Xuemei Huang
- *Department of Neurology, Pennsylvania State University-Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033; Department of Pharmacology, Pennsylvania State University-Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033; Department of Radiology; Department of Neurosurgery; Department of Kinesiology, Pennsylvania State University-Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033
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Lee EY, Flynn MR, Du G, Li Y, Lewis MM, Herring AH, Van Buren E, Van Buren S, Kong L, Fry RC, Snyder AM, Connor JR, Yang QX, Mailman RB, Huang X. Increased R2* in the Caudate Nucleus of Asymptomatic Welders. Toxicol Sci 2016; 150:369-77. [PMID: 26769335 DOI: 10.1093/toxsci/kfw003] [Citation(s) in RCA: 16] [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] [Indexed: 12/21/2022] Open
Abstract
Welding has been associated with neurobehavioral disorders. Welding fumes contain several metals including copper (Cu), manganese (Mn), and iron (Fe) that may interact to influence welding-related neurotoxicity. Although welding-related airborne Fe levels are about 10-fold higher than Mn, previous studies have focused on Mn and its accumulation in the basal ganglia. This study examined differences in the apparent transverse relaxation rates [R2* (1/T2*), estimate of Fe accumulation] in the basal ganglia (caudate nucleus, putamen, and globus pallidus) between welders and controls, and the dose-response relationship between estimated Fe exposure and R2* values. Occupational questionnaires estimated recent and lifetime Fe exposure, and blood Fe levels and brain magnetic resonance imaging (MRI) were obtained. Complete exposure and MRI R2* and R1 (1/T1: measure to estimate Mn accumulation) data from 42 subjects with welding exposure and 29 controls were analyzed. Welders had significantly greater exposure metrics and higher whole-blood Fe levels compared with controls. R2* in the caudate nucleus was significantly higher in welders after controlling for age, body mass index, respirator use, caudate R1, and blood metals of Cu and Mn, whereas there was no difference in R1 values in the basal ganglia between groups. The R2* in the caudate nucleus was positively correlated with whole-blood Fe concentration. This study provides the first evidence of higher R2* in the caudate nucleus of welders, which is suggestive of increased Fe accumulation in this area. Further studies are needed to replicate the findings and determine the neurobehavioral relevance.
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Affiliation(s)
- Eun-Young Lee
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Michael R Flynn
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Guangwei Du
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Yunqing Li
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Mechelle M Lewis
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Amy H Herring
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Eric Van Buren
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Scott Van Buren
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Lan Kong
- Department of Public Health Sciences, Pennsylvania State University, Hershey, Pennsylvania
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Amanda M Snyder
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - James R Connor
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Qing X Yang
- Department of Radiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; and
| | - Richard B Mailman
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Xuemei Huang
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina; Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; Department of Radiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania; and Department of Kinesiology, Pennsylvania State University, University Park, Pennsylvania
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Lee EY, Flynn MR, Du G, Lewis MM, Fry R, Herring AH, Van Buren E, Van Buren S, Smeester L, Kong L, Yang Q, Mailman RB, Huang X. T1 Relaxation Rate (R1) Indicates Nonlinear Mn Accumulation in Brain Tissue of Welders With Low-Level Exposure. Toxicol Sci 2015; 146:281-9. [PMID: 25953701 PMCID: PMC4607746 DOI: 10.1093/toxsci/kfv088] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [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] [Indexed: 12/20/2022] Open
Abstract
Although the essential element manganese (Mn) is neurotoxic at high doses, the effects of lower exposure are unclear. MRI T1-weighted (TIW) imaging has been used to estimate brain Mn exposure via the pallidal index (PI), defined as the T1W intensity ratio in the globus pallidus (GP) versus frontal white matter (FWM). PI may not, however, be sensitive to Mn in GP because Mn also may accumulate in FWM. This study explored: (1) whether T1 relaxation rate (R1) could quantify brain Mn accumulation more sensitively; and (2) the dose-response relationship between estimated Mn exposure and T1 relaxation rate (R1). Thirty-five active welders and 30 controls were studied. Occupational questionnaires were used to estimate hours welding in the past 90 days (HrsW) and lifetime measures of Mn exposure. T1W imaging and T1-measurement were utilized to generate PI and R1 values in brain regions of interest (ROIs). PI did not show a significant association with any measure of Mn and/or welding-related exposure. Conversely, in several ROIs, R1 showed a nonlinear relationship to HrsW, with R1 signal increasing only after a critical exposure was reached. The GP had the greatest rate of Mn accumulation. Welders with higher exposure showed significantly higher R1 compared either with controls or with welders with lower exposure. Our data are additional evidence that Mn accumulation can be assessed more sensitively by R1 than by PI. Moreover, the nonlinear relationship between welding exposure and Mn brain accumulation should be considered in future studies and policies.
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Affiliation(s)
- Eun-Young Lee
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Michael R Flynn
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Guangwei Du
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Mechelle M Lewis
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Rebecca Fry
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Amy H Herring
- Department of Biostatistics, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Eric Van Buren
- Department of Biostatistics, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Scott Van Buren
- Department of Biostatistics, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Lisa Smeester
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Lan Kong
- Department of Public Health Sciences, Pennsylvania State University, Hershey, Pennsylvania and
| | - Qing Yang
- Departments of Radiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Richard B Mailman
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Xuemei Huang
- *Department of Neurology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, Departments of Radiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, Department of Kinesiology, Pennsylvania State University, University Park, Pennsylvania
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