1
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Johnson ND, Cutler DJ, Conneely KN. Investigating the potential of single-cell DNA methylation data to detect allele-specific methylation and imprinting. Am J Hum Genet 2024; 111:654-667. [PMID: 38471507 PMCID: PMC11023823 DOI: 10.1016/j.ajhg.2024.02.009] [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: 06/22/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Allele-specific methylation (ASM) is an epigenetic modification whereby one parental allele becomes methylated and the other unmethylated at a specific locus. ASM is most often driven by the presence of nearby heterozygous variants that influence methylation, but also occurs somatically in the context of genomic imprinting. In this study, we investigate ASM using publicly available single-cell reduced representation bisulfite sequencing (scRRBS) data on 608 B cells sampled from six healthy B cell samples and 1,230 cells from 11 chronic lymphocytic leukemia (CLL) samples. We developed a likelihood-based criterion to test whether a CpG exhibited ASM, based on the distributions of methylated and unmethylated reads both within and across cells. Applying our likelihood ratio test, 65,998 CpG sites exhibited ASM in healthy B cell samples according to a Bonferroni criterion (p < 8.4 × 10-9), and 32,862 CpG sites exhibited ASM in CLL samples (p < 8.5 × 10-9). We also called ASM at the sample level. To evaluate the accuracy of our method, we called heterozygous variants from the scRRBS data, which enabled variant-based calls of ASM within each cell. Comparing sample-level ASM calls to the variant-based measures of ASM, we observed a positive predictive value of 76%-100% across samples. We observed high concordance of ASM across samples and an overrepresentation of ASM in previously reported imprinted genes and genes with imprinting binding motifs. Our study demonstrates that single-cell bisulfite sequencing is a potentially powerful tool to investigate ASM, especially as studies expand to increase the number of samples and cells sequenced.
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Affiliation(s)
- Nicholas D Johnson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA; Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA; Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA.
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2
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Li YE, Preissl S, Miller M, Johnson ND, Wang Z, Jiao H, Zhu C, Wang Z, Xie Y, Poirion O, Kern C, Pinto-Duarte A, Tian W, Siletti K, Emerson N, Osteen J, Lucero J, Lin L, Yang Q, Zhu Q, Zemke N, Espinoza S, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Hodge RD, Linnarsson S, Bakken T, Levi B, Keene CD, Shang J, Lein E, Wang A, Behrens MM, Ecker JR, Ren B. A comparative atlas of single-cell chromatin accessibility in the human brain. Science 2023; 382:eadf7044. [PMID: 37824643 PMCID: PMC10852054 DOI: 10.1126/science.adf7044] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 11/09/2022] [Accepted: 09/14/2023] [Indexed: 10/14/2023]
Abstract
Recent advances in single-cell transcriptomics have illuminated the diverse neuronal and glial cell types within the human brain. However, the regulatory programs governing cell identity and function remain unclear. Using a single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq), we explored open chromatin landscapes across 1.1 million cells in 42 brain regions from three adults. Integrating this data unveiled 107 distinct cell types and their specific utilization of 544,735 candidate cis-regulatory DNA elements (cCREs) in the human genome. Nearly a third of the cCREs demonstrated conservation and chromatin accessibility in the mouse brain cells. We reveal strong links between specific brain cell types and neuropsychiatric disorders including schizophrenia, bipolar disorder, Alzheimer's disease (AD), and major depression, and have developed deep learning models to predict the regulatory roles of noncoding risk variants in these disorders.
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Affiliation(s)
- Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Michael Miller
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Zihan Wang
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Henry Jiao
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Chenxu Zhu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhaoning Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olivier Poirion
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Colin Kern
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Wei Tian
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kimberly Siletti
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Nora Emerson
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julia Osteen
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jacinta Lucero
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Qian Yang
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Quan Zhu
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Nathan Zemke
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Sarah Espinoza
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Trygve Bakken
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98104, USA
| | - Jingbo Shang
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Joseph R Ecker
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 92093, USA
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3
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Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li Y, Siletti K, Liem M, Claffey N, O’Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding SL, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR. Single-cell DNA methylation and 3D genome architecture in the human brain. Science 2023; 382:eadf5357. [PMID: 37824674 PMCID: PMC10572106 DOI: 10.1126/science.adf5357] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 11/07/2022] [Accepted: 09/05/2023] [Indexed: 10/14/2023]
Abstract
Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in 517 thousand cells (399 thousand neurons and 118 thousand non-neurons) from 46 regions of three adult male brains. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. We further developed single-cell methylation barcodes that reliably predict brain cell types using the methylation status of select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell-type-specific gene regulation in adult human brains.
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Affiliation(s)
- Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jingtian Zhou
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Qiurui Zeng
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rosa G. Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mia Kenworthy
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jordan Altshul
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Cynthia Valadon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Andrew Aldridge
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R. Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jiaying Xu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nicholas D. Johnson
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jacinta Lucero
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Julia K. Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nora Emerson
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jon Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jasper Lee
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yang Li
- Ludwig Institute for Cancer Research, La Jolla, CA 92037, USA
| | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet; 171 77 Stockholm, Sweden
| | - Michelle Liem
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Naomi Claffey
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Caz O’Connor
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | | | | | - Song-Lin Ding
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Rebecca Hodge
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Boaz P. Levi
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet; 171 77 Stockholm, Sweden
| | - Ed Lein
- Allen Institute for Brain Science; Seattle, WA 98109, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA 92037, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - M. Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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4
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Johnson ND, Wu X, Still CD, Chu X, Petrick AT, Gerhard GS, Conneely KN, DiStefano JK. Differential DNA methylation and changing cell-type proportions as fibrotic stage progresses in NAFLD. Clin Epigenetics 2021; 13:152. [PMID: 34353365 PMCID: PMC8340447 DOI: 10.1186/s13148-021-01129-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is characterized by changes in cell composition that occur throughout disease pathogenesis, which includes the development of fibrosis in a subset of patients. DNA methylation (DNAm) is a plausible mechanism underlying these shifts, considering that DNAm profiles differ across tissues and cell types, and DNAm may play a role in cell-type differentiation. Previous work investigating the relationship between DNAm and fibrosis in NAFLD has been limited by sample size and the number of CpG sites interrogated. RESULTS Here, we performed an epigenome-wide analysis using Infinium MethylationEPIC array data from 325 individuals with NAFLD, including 119 with severe fibrosis and 206 with no histological evidence of fibrosis. After adjustment for latent confounders, we identified 7 CpG sites whose DNAm associated with fibrosis (p < 5.96 × 10-8). Analysis of RNA-seq data collected from a subset of individuals (N = 56) revealed that gene expression at 288 genes associated with DNAm at one or more of the 7 fibrosis-related CpGs. DNAm-based estimates of cell-type proportions showed that estimated proportions of natural killer cells increased, while epithelial cell proportions decreased with disease stage. Finally, we used an elastic net regression model to assess DNAm as a biomarker of fibrotic stage and found that our model predicted fibrosis with a sensitivity of 0.93 and provided information beyond a model based solely on cell-type proportions. CONCLUSION These findings are consistent with DNAm as a mechanism underpinning or marking fibrosis-related shifts in cell composition and demonstrate the potential of DNAm as a possible biomarker of NAFLD fibrosis.
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Affiliation(s)
- Nicholas D Johnson
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - Xiumei Wu
- Diabetes and Fibrotic Disease Unit, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Xin Chu
- Geisinger Obesity Institute, Danville, PA, USA
| | | | - Glenn S Gerhard
- Lewis Katz School of Medicine, Temple University School of Medicine, Philadelphia, PA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - Johanna K DiStefano
- Diabetes and Fibrotic Disease Unit, Translational Genomics Research Institute, Phoenix, AZ, USA.
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5
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Kim H, Kang Y, Li Y, Chen L, Lin L, Johnson ND, Zhu D, Robinson MH, McSwain L, Barwick BG, Yuan X, Liao X, Zhao J, Zhang Z, Shu Q, Chen J, Allen EG, Kenney AM, Castellino RC, Van Meir EG, Conneely KN, Vertino PM, Jin P, Li J. Ten-eleven translocation protein 1 modulates medulloblastoma progression. Genome Biol 2021; 22:125. [PMID: 33926529 PMCID: PMC8082834 DOI: 10.1186/s13059-021-02352-9] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 04/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Medulloblastoma (MB) is the most common malignant pediatric brain tumor that originates in the cerebellum and brainstem. Frequent somatic mutations and deregulated expression of epigenetic regulators in MB highlight the substantial role of epigenetic alterations. 5-hydroxymethylcytosine (5hmC) is a highly abundant cytosine modification in the developing cerebellum and is regulated by ten-eleven translocation (TET) enzymes. RESULTS We investigate the alterations of 5hmC and TET enzymes in MB and their significance to cerebellar cancer formation. We show total abundance of 5hmC is reduced in MB, but identify significant enrichment of MB-specific 5hmC marks at regulatory regions of genes implicated in stem-like properties and Nanog-binding motifs. While TET1 and TET2 levels are high in MBs, only knockout of Tet1 in the smoothened (SmoA1) mouse model attenuates uncontrolled proliferation, leading to a favorable prognosis. The pharmacological Tet1 inhibition reduces cell viability and platelet-derived growth factor signaling pathway-associated genes. CONCLUSIONS These results together suggest a potential key role of 5hmC and indicate an oncogenic nature for TET1 in MB tumorigenesis, suggesting it as a potential therapeutic target for MBs.
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Affiliation(s)
- Hyerim Kim
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yunhee Kang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Li Chen
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Li Lin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicholas D Johnson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Dan Zhu
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - M Hope Robinson
- Department of Pediatric Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Leon McSwain
- Department of Pediatric Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| | - Xianrui Yuan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xinbin Liao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hydrocephalus Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jie Zhao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hydrocephalus Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhiping Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hydrocephalus Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qiang Shu
- The Children's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianjun Chen
- Department of Systems Biology and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, 91010, USA
| | - Emily G Allen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Anna M Kenney
- Department of Pediatric Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| | - Robert C Castellino
- Department of Pediatric Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Erwin G Van Meir
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Paula M Vertino
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Jian Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Hydrocephalus Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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6
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Johnson ND, Huang L, Li R, Li Y, Yang Y, Kim HR, Grant C, Wu H, Whitsel EA, Kiel DP, Baccarelli AA, Jin P, Murabito JM, Conneely KN. Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood. Epigenetics 2019; 15:294-306. [PMID: 31506003 DOI: 10.1080/15592294.2019.1666651] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 01/10/2023] Open
Abstract
DNA methylation (DNAm) has a well-established association with age in many tissues, including peripheral blood mononuclear cells (PBMCs). Compared to DNAm, the closely related epigenetic modification known as DNA hydroxymethylation (DNAhm) was much more recently discovered in mammals. Preliminary investigations have observed a positive correlation between gene body DNAhm and cis-gene expression. While some of these studies have observed an association between age and global DNAhm, none have investigated region-specific age-related DNAhm in human blood samples. In this study, we investigated DNAhm and gene expression in PBMCs of 10 young and 10 old, healthy female volunteers. Thousands of regions were differentially hydroxymethylated in the old vs. young individuals in gene bodies, exonic regions, enhancers, and promoters. Consistent with previous work, we observed directional consistency between age-related differences in DNAhm and gene expression. Further, age-related DNAhm and genes with high levels of DNAhm were enriched for immune system processes which may support a role of age-related DNAhm in immunosenescence.
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Affiliation(s)
- Nicholas D Johnson
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - Luoxiu Huang
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Ronghua Li
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Yuchen Yang
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Hye Rim Kim
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Cancer Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Crystal Grant
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Douglas P Kiel
- Hebrew SeniorLife, Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Joanne M Murabito
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA.,Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
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7
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Johnson ND, Wiener HW, Smith AK, Nishitani S, Absher DM, Arnett DK, Aslibekyan S, Conneely KN. Non-linear patterns in age-related DNA methylation may reflect CD4 + T cell differentiation. Epigenetics 2017; 12:492-503. [PMID: 28387568 DOI: 10.1080/15592294.2017.1314419] [Citation(s) in RCA: 11] [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: 01/08/2023] Open
Abstract
DNA methylation (DNAm) is an important epigenetic process involved in the regulation of gene expression. While many studies have identified thousands of loci associated with age, few have differentiated between linear and non-linear DNAm trends with age. Non-linear trends could indicate early- or late-life gene regulatory processes. Using data from the Illumina 450K array on 336 human peripheral blood samples, we identified 21 CpG sites that associated with age (P<1.03E-7) and exhibited changing rates of DNAm change with age (P<1.94E-6). For 2 of these CpG sites (cg07955995 and cg22285878), DNAm increased with age at an increasing rate, indicating that differential DNAm was greatest among elderly individuals. We observed significant replication for both CpG sites (P<5.0E-8) in a second set of peripheral blood samples. In 8 of 9 additional data sets comprising samples of monocytes, T cell subtypes, and brain tissue, we observed a pattern directionally consistent with DNAm increasing with age at an increasing rate, which was nominally significant in the 3 largest data sets (4.3E-15<P<0.039). cg07955995 and cg22285878 reside in the promoter region of KLF14, which encodes a protein involved in immune cell differentiation via the repression of FOXP3. These findings may suggest a possible role for cg07955995 and cg22285878 in immunosenescence.
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Affiliation(s)
| | - Howard W Wiener
- b Department of Epidemiology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Alicia K Smith
- c Department of Gynecology and Obstetrics , Emory University , Atlanta , GA , USA.,d Department of Psychiatry and Behavioral Sciences , Emory University , Atlanta , GA , USA
| | - Shota Nishitani
- c Department of Gynecology and Obstetrics , Emory University , Atlanta , GA , USA.,d Department of Psychiatry and Behavioral Sciences , Emory University , Atlanta , GA , USA
| | - Devin M Absher
- e HudsonAlpha Institute for Biotechnology , Huntsville , AL , USA
| | - Donna K Arnett
- f College of Public Health , University of Kentucky , Lexington , KY , USA
| | - Stella Aslibekyan
- b Department of Epidemiology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Karen N Conneely
- a Department of Human Genetics , Emory University , Atlanta , GA , USA
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Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM, Ecker JR. Global epigenomic reconfiguration during mammalian brain development. Science 2013; 341:1237905. [PMID: 23828890 PMCID: PMC3785061 DOI: 10.1126/science.1237905] [Citation(s) in RCA: 1296] [Impact Index Per Article: 117.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA methylation is implicated in mammalian brain development and plasticity underlying learning and memory. We report the genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis. During this period, highly conserved non-CG methylation (mCH) accumulates in neurons, but not glia, to become the dominant form of methylation in the human neuronal genome. Moreover, we found an mCH signature that identifies genes escaping X-chromosome inactivation. Last, whole-genome single-base resolution 5-hydroxymethylcytosine (hmC) maps revealed that hmC marks fetal brain cell genomes at putative regulatory regions that are CG-demethylated and activated in the adult brain and that CG demethylation at these hmC-poised loci depends on Tet2 activity.
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Affiliation(s)
- Ryan Lister
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Plant Energy Biology [Australian Research Council Center of Excellence (CoE)] and Computational Systems Biology (Western Australia CoE), School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Eran A Mukamel
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mark Urich
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Clare A Puddifoot
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nicholas D Johnson
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jacinta Lucero
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yun Huang
- La Jolla Institute for Allergy and Immunology and Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, NY 10032, USA.,Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Matthew D Schultz
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Bioinformatics Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Julian Tonti-Filippini
- Plant Energy Biology [Australian Research Council Center of Excellence (CoE)] and Computational Systems Biology (Western Australia CoE), School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Holger Heyn
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Shijun Hu
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology and Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08907, Spain.,InstitucióCatalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Fatemeh G Haghighi
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, NY 10032, USA
| | - Terrence J Sejnowski
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92037, USA.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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9
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DeCook LJ, Thoma M, Huneke T, Johnson ND, Wiegand RA, Patnaik MM, Litzow MR, Hogan WJ, Porrata LF, Holtan SG. Impact of lymphocyte and monocyte recovery on the outcomes of allogeneic hematopoietic SCT with fludarabine and melphalan conditioning. Bone Marrow Transplant 2012; 48:708-14. [PMID: 23103674 DOI: 10.1038/bmt.2012.211] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have recently shown that lymphocyte and monocyte recovery by day +100 are associated with survival post myeloablative allogeneic hematopoietic transplant for acute leukemia. We hypothesized that lymphocyte and monocyte recovery would have a similar impact on survival in the reduced intensity setting. To test this hypothesis, we analyzed clinical data from 118 consecutive fludarabine/melphalan-conditioned patients by correlating peripheral blood absolute lymphocyte counts and monocyte counts (ALC and AMC, respectively) at days +15, +30, +60 and +100 with the outcomes. Multivariate analysis revealed that day +100 AMC (risk ratio (RR) 0.22, 95% confidence interval (CI) 0.07-0.73, P=0.01) and mild chronic GVHD (RR 0.09, 95% CI 0.005-0.43, P=0.008) were independently associated with survival. To explore whether the patterns of lymphocyte and monocyte recovery had a prognostic value, we performed unsupervised hierarchical clustering on the studied hematopoietic parameters and identified three patient clusters, A-C. Patient clusters A and B both had improved OS compared with cluster C (77.8 months vs not reached vs 22.3 months, respectively, P<0.001). No patient in cluster C had a day +100 AMC >300. Both severe acute GVHD and relapse occurred more frequently in cluster C. Our data suggest that patients with low AMC by day +100 post fludarabine/melphalan-conditioned allogeneic hematopoietic SCT may be at risk for poor outcomes.
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Affiliation(s)
- L J DeCook
- Department of Medicine, Division of Hematology, Mayo Clinic Graduate School of Medicine, Rochester, MN, USA
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11
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Gylys-Morin VM, Graham TB, Blebea JS, Dardzinski BJ, Laor T, Johnson ND, Oestreich AE, Passo MH. Knee in early juvenile rheumatoid arthritis: MR imaging findings. Radiology 2001; 220:696-706. [PMID: 11526269 DOI: 10.1148/radiol.2203000461] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [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] [Indexed: 11/11/2022]
Abstract
PURPOSE To determine the magnetic resonance (MR) imaging findings in the knee in early juvenile rheumatoid arthritis. MATERIALS AND METHODS MR imaging (1.5 T) was performed in the more symptomatic knee in 30 children with juvenile rheumatoid arthritis with a symptom duration 1 year or less. Conventional, fast spin-echo, three-dimensional gradient-echo, and gadolinium-enhanced T1-weighted images were assessed. Two radiologists independently read the images, and a third resolved disagreements. These images were compared with knee radiographs in 27 children. RESULTS Mean maximal synovial thickness was 4.8 mm +/- 2.4 (SD). Mean synovial volume was 15.4 mL +/- 10.8. Suprapatellar joint effusions were seen in 26 (87%) of 30 knees, meniscal hypoplasia in 11 (37%) of 30 knees, and abnormal epiphyseal marrow in eight (27%) of 30 knees. Three knees had articular cartilage contour irregularity, fissures, and/or thinning. One knee had a bone erosion. Knee radiographs showed suprapatellar fullness in 78% of the knees, joint space narrowing in one knee, and no bone abnormalities. CONCLUSION Synovial hypertrophy and joint effusions are the most frequent MR imaging findings of knees in early juvenile rheumatoid arthritis. Early in the disease, radiographically occult cartilage and bone erosions are uncommonly seen at MR imaging. The potential relationship of synovitis to cartilage abnormalities deserves further study.
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Affiliation(s)
- V M Gylys-Morin
- Department of Radiology, Children's Hospital Medical Center, 3333 Burnet Ave, Cincinnati, OH 45229-3039, USA.
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12
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Emery KH, McAneney CM, Racadio JM, Johnson ND, Evora DK, Garcia VF. Absent peritoneal fluid on screening trauma ultrasonography in children: a prospective comparison with computed tomography. J Pediatr Surg 2001; 36:565-9. [PMID: 11283878 DOI: 10.1053/jpsu.2001.22283] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [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] [Indexed: 11/11/2022]
Abstract
BACKGROUND Although the accuracy of focused abdominal sonography for trauma (FAST) in adults has been demonstrated, results of this technique in children have been conflicting with few comparisons against computed tomography (CT), the imaging gold standard. METHODS A total of 160 hemodynamically stable pediatric trauma victims referred for abdominal CT initially underwent rapid screening sonography looking for free fluid. Both studies were interpreted in blinded fashion. RESULTS Forty-four of the 160 patients had an intraabdominal injury on CT, 24 (55%) of which had normal screening sonography. Fifteen of the 44 (34%) had no free fluid on either modality. Accuracy of sonography compared with CT was 76% with a negative predictive value 81%. CONCLUSIONS Sonography for free fluid alone is not reliable to exclude blunt intraabdominal injury in hemodynamically stable children given the considerable percentage of injured patients without free fluid. J Pediatr Surg 36:565-569.
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Affiliation(s)
- K H Emery
- Department of Radiology, Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH 45229-3039, USA
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Abstract
OBJECTIVE To compare complication rates between central venous catheter tip location and noncentral tip location after peripherally inserted central catheter (PICC) placement in children. METHODS Between 1994 and 1998, data from all children who underwent PICC placement were analyzed. Patient demographics, catheter characteristics, catheter duration, infusate composition, and catheter complications were entered prospectively into a computerized database. Catheter tip locations were determined by fluoroscopy and were defined as central if they resided in the superior vena cava, right atrium, or high inferior vena cava at or above the level of the diaphragm, and as noncentral if located elsewhere. Differences in complication rates between the central and noncentral groups were analyzed. RESULTS Data from a total of 1266 PICCs were analyzed from 1053 patients with a mean age of 6.49 +/-.2 years (range: 0-45.0 years). Of the 1266 PICCs, 1096 (87%) were central in tip location, and 170 (13%) were noncentral in tip location. The central group had 42 complications of 1096 catheters (3.8%), while the noncentral group had 49 complications of 170 catheters (28.8%). Controlling for patient age, catheter size, gender, and catheter duration with a logistic regression model, there remained a statistically significant increased likelihood of complication in the noncentral group versus the central group (adjusted odds ratio: 8.28; 95% confidence interval: 5.11-13.43). CONCLUSIONS Centrally placed catheter tips are associated with fewer complications than are noncentrally placed catheter tips. Clinicians should ensure that catheter tips reside centrally after PICC placement in infants and children.
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Affiliation(s)
- J M Racadio
- Department of Radiology, Children's Hospital Medical Center, Cincinnati, Ohio 45229-3039, USA.
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14
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Abstract
Most organizations planning to implement picture archiving and communications systems (PACS) are aware of the need to integrate the hospital information system (HIS) and radiology information system (RIS) with the PACS, yet few are acutely aware of the challenges associated with this requirement. This report highlights the results of collaborative efforts between Children's Hospital Medical Center-Cincinnati (CHMC) applications specialists with expertise in the HIS and CHMC information system, radiology staff familiar with the enterprise and radiology workflow and data flow requirements; and General Electric integration engineers familiar with the SMS HIS and RIS, and GE PACS. CHMC received Board approval, including full funding of the entire PACS project, in October 1998. An aggressive time frame for installation was established, as CHMC's PACS leadership committed to the selection, design, and implementation of PACS and computed radiography (CR) within 18 to 20 months. CHMC selected GE (Milwaukee, WI) as its PACS vendor in July 1999, and began its implementation in November 1999. We will present the four-stage integration process undertaken at CHMC: (1) planning the integration effort, (2) designing the Interface, (3) building the interface, and (4) testing the Interface.
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Affiliation(s)
- N D Johnson
- Department of Radiology, Children's Hospital Medical Center, Cincinnati, OH 45243, USA.
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15
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Sudan DL, Radio SJ, Matamoros A, Johnson ND, Shearon CC, Glogowski KR, Hill AC, Goertzen TC, Fox IJ, Langnas AN, Beschorner WE. Effect of surrogate tolerogenesis on the vascular rejection of pig heart xenografts. Transplantation 2000; 69:232-5. [PMID: 10670632 DOI: 10.1097/00007890-200001270-00007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Organ xenografts are fulminantly rejected by antibody-mediated vascular rejection. Surrogate tolerogenesis (ST), the induction of tolerance within the donor, is effective with aorta xenografts. This preliminary study assesses the effect of ST on preformed antibodies and rejection of porcine heart xenografts. METHODS Tolerance to the donor pig was induced by infusing recipient marrow into fetal pigs. Later, pig splenocytes were transfused and heterotopic pig hearts transplanted using chimeric or nonchimeric pigs. Anti-pig antibodies were assessed. RESULTS With ST alone, xenografts developed cellular rejection at 4-6 days, whereas control grafts developed vascular rejection at 3-4 days (cellular vs. vascular, P<0.03). There was a reduction in preformed antibodies (P<0.03). ST combined with moderate cyclosporine prevented rejection at 9+ and 25 days in sensitized recipients compared with vascular rejection at 0.5-2 days for controls (P<0.07). CONCLUSIONS ST seems to provide protection against vascular rejection. The cellular rejection seems sensitive to cyclosporine.
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Affiliation(s)
- D L Sudan
- Department of Surgery, University of Nebraska Medical Center, Omaha 68198, USA
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16
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Abstract
Causes of pediatric gastrointestinal (GI) bleeding in children are numerous. The role of radiology in defining associated pathology, pinpointing the bleeding site, and intervening to control hemorrhage is discussed here. Barium studies, computed tomography (CT), and magnetic resonance imaging (MRI) each may play a role in identifying the underlying pathology associated with the bleeding. The exact source of bleeding may be localized by means of nuclear scintigraphy as well as selective angiography. In cases of life-threatening or persistent hemorrhage, once a bleeding source is identified, the interventional radiologist may offer percutaneous transcatheter therapy with selective intraarterial vasopressin infusion or embolotherapy.
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Affiliation(s)
- J M Racadio
- Department of Radiology, Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
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17
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Abstract
The authors assessed the feasibility of placing peripherally inserted central venous catheters via scalp veins in infants and newborns. In 60 newborns and infants, aged 3 days to 10 months, placement of 62 2-F peripherally inserted central venous catheters was attempted with scalpvein access. The tip location was central in 30 of the 62 catheters (48%) and long peripheral intravenous in 17 (27%); access failed in 15 (24%). Scalp-vein access for peripherally inserted central venous catheters offers a safe and effective alternative route for gaining central venous access in infants and newborns.
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Affiliation(s)
- J M Racadio
- Department of Radiology, Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
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Abstract
OBJECTIVE To determine how well MRI can detect tarsal coalition compared with CT, the current imaging standard. MATERIALS AND METHODS Coronal and axial CT and MRI were performed within 3 weeks of each other on 40 feet in 20 consecutive patients referred with symptoms of possible tarsal coalition. Scans were read independently in blinded fashion by different imagers. Coalitions were either complete (osseous) or incomplete (non-osseous). Results were compared with available surgical data and clinical follow-up. RESULTS Both modalities prospectively identified 15 coalitions (9 patients) and each missed 1 calcaneonavicular coalition. Twenty-three of the remaining 24 feet were negative for coalition on both CT and MRI. An atypical incomplete talocalcaneal coalition seen on CT was not identified prospectively on MRI. CONCLUSION MRI is very good for detecting tarsal coalition and has a high rate of agreement with CT, the imaging "gold standard." When clinical suspicion for coalition is high, CT remains a more cost-effective diagnostic modality. If other causes for ankle pain are also entertained, MRI can be performed and provide nearly equivalent diagnostic accuracy for detecting tarsal coalition.
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Affiliation(s)
- K H Emery
- Department of Radiology, Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-8145, USA
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Affiliation(s)
- L F Donnelly
- Department of Radiology, Duke University Medical Center, Durham, NC 27710, USA
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Wong JA, Mendelson AM, Johnson ND, Schwartz DC. Reopening of the ductal ampulla during balloon angioplasty of native aortic coarctation. AJR Am J Roentgenol 1997; 169:316-7. [PMID: 9207571 DOI: 10.2214/ajr.169.1.9207571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Abstract
The MRI findings of two patients with fibrolipoma of median nerve are presented. A characteristic 'cable-like' appearance of the tumour was present on T1-weighted images. Unique imaging features of these cases included extension of the lesion into the radial digital nerve of the index finger in case 1 and extraneuronal extension of a exophytic fatty mass from the median nerve into the thenar eminence in case 2.
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Affiliation(s)
- H A Evans
- Department of Radiology and Pediatrics, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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Donnelly LF, Johnson ND, Taylor CN. Increased efficiency of radiology information management with a radiology support system. AJR Am J Roentgenol 1997; 168:611-2. [PMID: 9057498 DOI: 10.2214/ajr.168.3.9057498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- L F Donnelly
- Department of Radiology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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Affiliation(s)
- M J Nowicki
- Division of Gastroenterology and Nutrition, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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Samarawickrama DY, Lynch E, Seymour K, Burke FM, Johnson ND, Yegenah S, Morris-Clapp C, Grootveld MC. Professional bleaching of teeth in dental practice techniques. J Ir Dent Assoc 1996; 42:74-6. [PMID: 9242120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- D Y Samarawickrama
- Department of Conservative Dentistry, London Hospital Medical College Dental School, UK
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Betz BW, Bisset GS, Johnson ND, Daugherty CC, Balistreri WF. MR imaging of biliary cysts in children with biliary atresia: clinical associations and pathologic correlation. AJR Am J Roentgenol 1994; 162:167-71. [PMID: 8273658 DOI: 10.2214/ajr.162.1.8273658] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
OBJECTIVE We used MR imaging to determine the prevalence of biliary cysts in children with end-stage biliary atresia and evaluated the association of cysts with cholangitis, choleretic therapy, portoenterostomy, biochemical abnormalities, and MR findings of end-stage liver disease. The MR features of these cysts were correlated with their gross and histopathologic appearances. MATERIALS AND METHODS We retrospectively reviewed 48 MR studies, clinical history, and laboratory data of 44 consecutive children with biliary atresia. RESULTS MR images showed cysts in eight patients (18%). Cysts were statistically (p < .04) more common in patients who had a history of cholangitis, but were not associated with choleretic therapy or portoenterostomy surgery. Cysts were not statistically correlated with abnormalities in hepatic biochemical function or MR features of end-stage liver disease. Four livers with cysts were available for histopathologic study. Cysts were filled with bile, and most had an epithelial lining, consistent with a biliary origin. The epithelium was frequently ulcerated, accompanied by periportal extravasation of bile and inflammation. These findings suggest chronic obstruction with microscopic perforation. CONCLUSION Biliary cysts are common in biliary atresia and may be related to previous episodes of cholangitis with attendant obstruction of biliary radicles. The presence of these cysts did not correlate with hepatic function, portoenterostomy surgery, or the extent of liver disease.
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Affiliation(s)
- B W Betz
- Department of Radiology, Children's Hospital Medical Center, Cincinnati, OH
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Abstract
Four neonates suffered caval thrombosis secondary to indwelling central catheters. Dissolution of thrombus with recombinant tissue plasminogen activator (rt-PA) as a low-dose infusion (0.05 mg/kg/hr) directly into thrombus was successful in three patients. rt-PA was ceased after three days in the fourth patient because of catheter malposition. Thrombolysis was achieved between four and ten days. Rethrombosis occurred in one patient despite heparin prophylaxis. Plasminogen activator infusions were titrated to maintain fibrinogen levels above 100 mg/dl. One neonate suffered an intracranial haemorrhage. Regional rt-PA is an alternative to thrombectomy in critically ill neonates.
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Affiliation(s)
- B J Anderson
- Department of Intensive Care, Royal Children's Hospital, Melbourne, Victoria, Australia
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29
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Abstract
Fulminant hepatic failure causes a bleeding diathesis as a result of impaired synthesis of hepatic clotting factors, thrombocytopenia, fibrinolysis and disseminated intravascular coagulation. Administration of clotting factor concentrates can cause thrombosis in patients with acute hepatic failure. Regional infusion of recombinant tissue-type plasminogen activator may be used to induce local thrombolysis. A case report of a five-year-old child is presented and the literature is reviewed.
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Abstract
Unlike gray-scale sonography, color Doppler ultrasonography allows reliable visualization of the ureteric jet phenomenon. A study was undertaken to determine whether any measurable parameter predicts the presence of vesicoureteric reflux. Measurements of mean urine jet velocity, longitudinal angle, transverse angle, and distance of the origin of the jet from the midline of the bladder were obtained on 31 infants and children (62 ureters) with a proved urinary tract infection. Of these measurements, only the distance of the ureteric orifice from the midline of the bladder was found to correlate with vesicoureteric reflux (mean distance in the reflux group, 10.25 mm +/- 2.40 (standard deviation [SD]); in the nonreflux group, 7.98 mm +/- 2.40 [P = .004]). The authors conclude that the more laterally positioned the ureteric orifice, the more likely it is to reflux. Color Doppler ultrasound measurement of the laterality of the ureteric orifice may be useful for predicting which children with a urinary tract infection would benefit from voiding cystourethrography.
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Affiliation(s)
- J L Marshall
- Department of Radiology, Royal Children's Hospital, Melbourne, Victoria, Australia
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Affiliation(s)
- N D Johnson
- Department of Radiology, University of Rochester Medical Center, Rochester NY 14642
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Lane DA, Johnson ND, Barton SC, Thomas GH, Schroeder WH. Development and evaluation of a novel gas and particle sampler for semivolatile chlorinated organic compounds in ambient air. Environ Sci Technol 1988; 22:941-947. [PMID: 22195716 DOI: 10.1021/es00173a012] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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Abstract
Twenty-five magnetic resonance hip studies were performed on 19 infants with congenital hip dislocation. These patients had a poor initial treatment response, a teratologic dislocation, or a late presentation. Detailed images of single hips obtained with small surface coils resulted in excellent visualization of all the clinically important soft-tissue and cartilaginous structures of the hip. No other imaging modality demonstrates all of these structures simultaneously.
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Affiliation(s)
- N D Johnson
- Department of Radiology, University of Rochester Medical Center, NY 14642
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Kanal E, Burk DL, Brunberg JA, Johnson ND, Wood BP, Flom L. Pediatric musculoskeletal magnetic resonance imaging. Radiol Clin North Am 1988; 26:211-39. [PMID: 3277221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
MRI has demonstrated clinical applicability and improved diagnostic capability in the musculoskeletal system to a degree rivaling its success in the neurologic system. For certain regions such as the joints, the superficial nature of these structures is ideal for the application of localized radiofrequency coils, enabling considerably improved signal, spatial resolution, and detectable contrast. The multiplanar capability is often invaluable in assessing such regions as the weight-bearing surfaces of the hips. It has been shown to be the most sensitive single test for diagnosing avascular necrosis, and has yielded very high resolution images of the internal architecture of the joints and soft tissues in an entirely noninvasive manner and without the need for the administration of exogenous contrast agents. Short TE images are quite useful in evaluating fatty background regions of interest, such as the bone marrow and subcutaneous tissue, whereas long TR and TE studies are frequently more suitable for soft tissue pathology. The lack of ionizing radiation and the continued failure of intensive research to disclose any deleterious effects at the levels used for clinical diagnostic imaging make this tool especially appealing for application to the pediatric population. With the continual development of new pulsing sequences, contrast agents, and further advances in imaging/spectroscopic correlation, magnetic resonance imaging of the musculoskeletal system is ensured of a solid role in the clinical diagnostic evaluation of the pediatric population.
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Affiliation(s)
- E Kanal
- Pittsburgh NMR Institute, PA
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Thompson JS, Thorson AG, Edney JA, Johnson ND, Bryson BL, Hodgson PE. Experience with cholecystectomy at the University of Nebraska Hospital. Nebr Med J 1984; 69:389-94. [PMID: 6521778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Johnson ND, Chu CC, Ehrlich PR, Mooney HA. The seasonal dynamics of leaf resin, nitrogen, and herbivore damage in Eriodictyon californicum and their parallels in Diplacus aurantiacus. Oecologia 1984; 61:398-402. [PMID: 28311070 DOI: 10.1007/bf00379642] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/1983] [Indexed: 10/26/2022]
Abstract
The chaparral shrub Eriodictyon californicum produces a flavonoid leaf resin with a chemically similar composition to that previously reported for the sympatric shrub Diplacus aurantiacus. We determined the phenology, resin content, and nitrogen content of Eriodictyon leaves and the leaf area lost to herbivores. Nitrogen content and resin content were both negatively correlated with leaf age at each sampling date, but nitrogen decreased during the growing season while resin increased. The fraction of leaf area lost during the growing season averaged less than 7% and was highest on the oldest leaves. The seasonal pattern of resin production in Eriodictyon corresponds to that in Diplacus, indicating that the similar environments of Eriodyctyon and Diplacus have led to convergent leaf resins. This convergence in these two plants has implications for chemicals of similar function in other chaparral shrubs.
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Affiliation(s)
- N D Johnson
- Department of Biology, Stanford University, 94305, Stanford, CA, USA
| | - C C Chu
- Department of Biology, Stanford University, 94305, Stanford, CA, USA
| | - P R Ehrlich
- Department of Biology, Stanford University, 94305, Stanford, CA, USA
| | - H A Mooney
- Department of Biology, Stanford University, 94305, Stanford, CA, USA
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Abstract
Chitosan is a deacetylated derivative of arthropod chitin. We found that it formed a coagulum in contact with defibrinated blood, heparinized blood, and washed red cells. When knitted DeBakey grafts were treated with chitosan, they were impermeable to blood. Examination of these grafts at 24 hours revealed no rebleeding. Examination at one, two, three, and four months showed the grafts to be encased in smooth muscle with a living endothelial lining and an abundant vasa vasorum. Control grafts showed the usual fibrous healing.
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Abstract
To evaluate the contribution of an isolated femoral venous value to venous hemodynamics, ten patients (12 limbs) who had undergone femoral valve transposition without saphenous vein stripping or ligation of perforators were followed up for 12 to 18 months after surgery. Ascending and descending venography were performed to document anatomic patency. Dynamic venous pressures and venous refilling times were recorded to evaluate muscle pump function and cutaneous congestion, respectively. Signs of venous hypertension and the need for elastic support were noted. No patient attained normal venous pressure at any time after surgery. Normalization of venous refilling time was transient: nine of 12 limbs had reverted to preoperative abnormal levels at 12 to 18 months and all required elastic support. Femoral value reconstruction performed alone for venous stasis is not sufficient. In postthrombotic venous ulcer, incompetent calf perforators remain a central problem.
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Rudo ND, Johnson ND, Harris JP, Flinn WR, Reiman G, Yao JS, Bergan JJ. Assessment of a modified technique of distal splenorenal shunting. Surgery 1981; 90:602-9. [PMID: 6974411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Warren's distal splenorenal shunt has been effective in treatment of recurrent variceal hemorrhage. To simplify the operative procedure, two alterations in the technique were used in this study. The first was to approach the splenic and renal veins simultaneously through a single inframesocolonic retroperitoneal incision in the plane of the pancreatic fusion fossa. The second was abandonment of the portoazygos disconnection. Since 1974, twenty-nine patients have undergone this modified operation. The patients ranged in age from 21 to 76 years. Fourteen patients had alcoholic cirrhosis, 13 had nonalcoholic cirrhosis, and the etiology was unknown in two. There were 14 Child's class A patients, 12 class B, and three class C. Significant ascites was present at operation in seven patients. Hepatofugal flow was demonstrated angiographically in four patients. The follow-up period ranged from 6 months to 6 years; 19 patients were followed up for 1 year or longer. There were three early postoperative deaths (10.3%), and one patient died 2 months postoperatively. Recurrent variceal bleeding was seen early in one patient and late (2 months) in another. Only one of the surviving patients developed encephalopathy. Technical modification to simplify performance of the distal splenorenal shunt did not compromise the results of the operation. However, four of seven patients with ascites died either immediately or early after the procedure, and two of these four patients also had hepatofugal flow. Ascites and hepatofugal flow may adversely influence the results of the operation.
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Abstract
A review of infants with respiratory distress born at the Mercy Maternity Hospital, Melbourne, during the years from 1975 to 1977 showed that live-born infants totalled 13304; 288 (2.2%) had respiratory distress. Of the 13304 infants, 197 died; 75 (38.1%) were infants with respiratory distress. Hyaline membrane disease was the cause of the respiratory distress in 153 (53.1%) infants; 58 (37.9%) infants with that problem died. Hyaline membrane disease accounted for 58 (77.3%) of the 75 deaths in infants with respiratory distress. Assisted ventilation was required in 147 (51.0%) infants with respiratory distress and chronic complications of its use acceptable as bronchopulmonary dysplasia occurred in only 8.2% and retrolental fibroplasia in only 3.4%; it is suggested that assisted ventilation was commenced too late in 23 (34.0%) infants. Twenty-eight (42.0%) infants with respiratory distress died despite correct usage of assisted ventilation. This number attests to the dangers of prematurity; hence the decision to deliver an infant prematurely should not be taken lightly.
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Abstract
An amino acid sequence analysis of the N-terminal immunoglobulin heavy and light chain variable regions (VH and VL) from 16 hybridoma proteins which bind phosphorylcholine as well as the complete sequence analysis of 9 of these VH regions is presented. There seem to be more VH regions participating in the phosphorylcholine response than can be encoded directly by germ-line VH gene segments. Moreover, the V regions from IgG antibodies are considerably more variable than those from their IgM counterparts. These observations raise the possibility that a somatic mechanism for V region diversification produces greater diversity in IgG than in IgM antibodies.
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Abstract
During a five-year period, 34 patients had persistence or recurrence of abnormal hemodynamic measurements in limbs after arterial reconstruction depsite graft patency documented by arteriography. Initial operations included aortofemoral (four), femorofemoral (ten), femoropopliteal (18), and femorotibial (two) bypass. Immediate postoperative hemodynamic failure was documented in seven patients by a mean ankle/brachial systolic pressure index increase of only 0.05 +/- 0.04 following the initial reconstruction. The remaining 27 patients had delayed hemodynamic failure; mean increase in ankle pressure was only 0.06 +/- 0.05 from the preoperative period until time of detection of failure (average duration 2.5 years). In all 34 patients, arteriography demonstrated patency of the initial graft. In conjunction with the vascular laboratory examination, arteriography identified the cause of hemodynamic failure to be inadequate inflow in 10 patients, poor outflow in 16, combined inflow and outflow obstruction in one, and graft stenosis in seven. Unrecognized stenosis in areas proximal (two patients) and distal (three patients) to the bypass emphasized the importance of complete biplanar arteriography before initial operation. Reoperation was successful in correcting hemodynamic failure in 26 patients (76.5%) with a mean increase in ankle index of 0.41 +/- 0.15. Operation was technically not feasible in four patients and was not performed in another four patients because of concomitant medical problems. In two of these patients, progression to graft thrombosis was documented. The results of this study suggest that early objective recognition of an anatomically patent but hemodynamically failed graft is possible by frequent noninvasive testing. Prompt investigation by arteriography defines the cause and location of failure, and reoperation restores normal limb hemodynamics. Most important, reoperation permits salvage of the majority of these patent grafts prior to ultimate failure from thrombosis.
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Johnson ND, Hunkapiller MW, Hood LE. Analysis of phenylthiohydantoin amino acids by high-performance liquid chromatography on DuPont Zobax cyanopropylsilane columns. Anal Biochem 1979; 100:335-8. [PMID: 525782 DOI: 10.1016/0003-2697(79)90237-9] [Citation(s) in RCA: 130] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Nicolson IC, Ashby PA, Johnson ND, Versey J, Slater L. Boomslang bite with haemorrhage and activation of complement by the alternate pathway. Clin Exp Immunol 1974; 16:295-300. [PMID: 4469217 PMCID: PMC1553922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
A case of Boomslang poisoning is reported for the first time in North West Europe. The treatment is described and activation of complement by the alternate pathway in vivo was shown.
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