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Donev K, Sundararajan V, Johnson D, Balan J, Chambers M, Paulson VA, Scherpelz KP, Abdullaev Z, Quezado M, Cimino PJ, Pratt D, Valerio E, Alves de Castro JV, Carraro DM, Torrezan GT, Wolff BM, Kulikowski LD, Costa FD, Aldape K, Ida CM. Diffuse hemispheric glioma with H3 p.K28M (K27M) mutation: Unusual non-midline presentation of diffuse midline glioma, H3 K27M-altered? J Neuropathol Exp Neurol 2024; 83:357-364. [PMID: 38447592 PMCID: PMC11029465 DOI: 10.1093/jnen/nlae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
Diffuse midline glioma, H3 K27-altered (DMG-H3 K27) is an aggressive group of diffuse gliomas that predominantly occurs in pediatric patients, involves midline structures, and displays loss of H3 p.K28me3 (K27me3) expression by immunohistochemistry and characteristic genetic/epigenetic profile. Rare examples of a diffuse glioma with an H3 p.K28M (K27M) mutation and without involvement of the midline structures, so-called "diffuse hemispheric glioma with H3 p.K28M (K27M) mutation" (DHG-H3 K27), have been reported. Herein, we describe 2 additional cases of radiologically confirmed DHG-H3 K27 and summarize previously reported cases. We performed histological, immunohistochemical, molecular, and DNA methylation analysis and provided clinical follow-up in both cases. Overall, DHG-H3 K27 is an unusual group of diffuse gliomas that shows similar clinical, histopathological, genomic, and epigenetic features to DMG-H3 K27 as well as enrichment for activating alterations in MAPK pathway genes. These findings suggest that DHG-H3 K27 is closely related to DMG-H3 K27 and may represent an unusual presentation of DMG-H3 K27 without apparent midline involvement and with frequent MAPK pathway activation. Detailed reports of additional cases with clinical follow-up will be important to expand our understanding of this unusual group of diffuse gliomas and to better define the clinical outcome and how to classify DHG-H3 K27.
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Affiliation(s)
- Kliment Donev
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Vanitha Sundararajan
- OhioHealth Riverside Methodist Hospital, Columbus, Ohio, USA
- CORPath Pathology Services, Columbus, Ohio, USA
| | - Derek Johnson
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jagadheshwar Balan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Meagan Chambers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Vera A Paulson
- Department of Laboratory Medicine and Pathology, Genetics and Solid Tumor Laboratory, University of Washington, Seattle, Washington, USA
| | - Kathryn P Scherpelz
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Patrick J Cimino
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Ediel Valerio
- Department of Pathology, A.C. Camargo Cancer Center, Sao Paulo, Brazil
| | | | - Dirce Maria Carraro
- Genomics and Molecular Biology Group, International Center of Research CIPE, A.C. Camargo Cancer Center, Sao Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics (INCITO), Sao Paulo, Brazil
| | - Giovana Tardin Torrezan
- Genomics and Molecular Biology Group, International Center of Research CIPE, A.C. Camargo Cancer Center, Sao Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics (INCITO), Sao Paulo, Brazil
| | - Beatriz Martins Wolff
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Leslie Domenici Kulikowski
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Felipe D’Almeida Costa
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
- Dasa Laboratories, Sao Paulo, Brazil
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Cristiane M Ida
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Artymiuk CJ, Basu S, Koganti T, Tandale P, Balan J, Dina MA, Barr Fritcher EG, Wu X, Ashworth T, He R, Viswanatha DS. Clinical Validation of a Targeted Next-Generation Sequencing Panel for Lymphoid Malignancies. J Mol Diagn 2024:S1525-1578(24)00077-1. [PMID: 38582399 DOI: 10.1016/j.jmoldx.2024.03.008] [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] [Received: 12/01/2023] [Revised: 02/16/2024] [Accepted: 03/22/2024] [Indexed: 04/08/2024] Open
Abstract
Lymphoid malignancies are a heterogeneous group of hematological disorders characterized by a diverse range of morphologic, immunophenotypic, and clinical features. Next-generation sequencing (NGS) is increasingly being applied to delineate the complex nature of these malignancies and identify high-value biomarkers with diagnostic, prognostic, or therapeutic benefit. However, there are various challenges in using NGS routinely to characterize lymphoid malignancies, including pre-analytic issues, such as sequencing DNA from formalin-fixed, paraffin-embedded tissue, and optimizing the bioinformatic workflow for accurate variant calling and filtering. This study reports the clinical validation of a custom capture-based NGS panel to test for molecular markers in a range of lymphoproliferative diseases and histiocytic neoplasms. The fully validated clinical assay represents an accurate and sensitive tool for detection of single-nucleotide variants and small insertion/deletion events to facilitate the characterization and management of patients with hematologic cancers specifically of lymphoid origin.
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Affiliation(s)
- Cody J Artymiuk
- Molecular Hematopathology Laboratory, Mayo Clinic, Rochester, Minnesota.
| | - Shubham Basu
- Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Tejaswi Koganti
- Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | | | | | - Michelle A Dina
- Molecular Hematopathology Laboratory, Mayo Clinic, Rochester, Minnesota
| | | | - Xianglin Wu
- Clinical Genomics Sequencing Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Taylor Ashworth
- Clinical Genomics Sequencing Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Rong He
- Hematopathology, Mayo Clinic, Rochester, Minnesota
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3
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Walsh JR, Sun G, Balan J, Hardcastle J, Vollenweider J, Jerde C, Rumilla K, Koellner C, Koleilat A, Hasadsri L, Kipp B, Jenkinson G, Klee E. A supervised learning method for classifying methylation disorders. BMC Bioinformatics 2024; 25:66. [PMID: 38347515 PMCID: PMC10863277 DOI: 10.1186/s12859-024-05673-1] [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: 09/20/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND DNA methylation is one of the most stable and well-characterized epigenetic alterations in humans. Accordingly, it has already found clinical utility as a molecular biomarker in a variety of disease contexts. Existing methods for clinical diagnosis of methylation-related disorders focus on outlier detection in a small number of CpG sites using standardized cutoffs which differentiate healthy from abnormal methylation levels. The standardized cutoff values used in these methods do not take into account methylation patterns which are known to differ between the sexes and with age. RESULTS Here we profile genome-wide DNA methylation from blood samples drawn from within a cohort composed of healthy controls of different age and sex alongside patients with Prader-Willi syndrome (PWS), Beckwith-Wiedemann syndrome, Fragile-X syndrome, Angelman syndrome, and Silver-Russell syndrome. We propose a Generalized Additive Model to perform age and sex adjusted outlier analysis of around 700,000 CpG sites throughout the human genome. Utilizing z-scores among the cohort for each site, we deployed an ensemble based machine learning pipeline and achieved a combined prediction accuracy of 0.96 (Binomial 95% Confidence Interval 0.868[Formula: see text]0.995). CONCLUSION We demonstrate a method for age and sex adjusted outlier detection of differentially methylated loci based on a large cohort of healthy individuals. We present a custom machine learning pipeline utilizing this outlier analysis to classify samples for potential methylation associated congenital disorders. These methods are able to achieve high accuracy when used with machine learning methods to classify abnormal methylation patterns.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alaa Koleilat
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
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Balan J, Koganti T, Basu S, Dina MA, Artymiuk CJ, Barr Fritcher EG, Halverson KE, Wu X, Jenkinson G, Viswanatha DS. MICon - A Contamination Detection Workflow for NGS Laboratories using Microhaplotype Locus and Supervised Learning. J Mol Diagn 2023:S1525-1578(23)00105-8. [PMID: 37236547 DOI: 10.1016/j.jmoldx.2023.05.001] [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] [Received: 07/18/2022] [Revised: 11/09/2022] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Innovation in sequencing instrumentation is increasing the per-batch data volumes and decreasing the per-base costs. Multiplexed chemistry protocols after the addition of index tags have further contributed to efficient and cost-effective sequencer utilization. With these pooled processing strategies, however, comes an increased risk of sample contamination. Sample contamination poses a risk of missing critical variants in a patient sample or wrongly reporting variants derived from the contaminant, which are particularly relevant issues in oncology specimen testing where low variant allele frequencies have clinical relevance. Small custom targeted Next Generation Sequencing (NGS) panels yield limited variants and pose challenges in delineating true somatic variants versus contamination calls. A number of popular contamination identification tools have the ability to perform well in whole genome/exome sequencing data, but in smaller gene panels there are fewer variant candidates for the tools to perform accurately. To prevent clinical reporting of potentially contaminated samples in small NGS panels, we have developed MICon (Microhaplotype Contamination detection) - a novel contamination detection model that utilizes microhaplotype site variant allele frequencies. In a heterogeneous hold-out test cohort of 210 samples, the model demonstrated state-of-the-art performance with an AUROC of 0.995.
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Affiliation(s)
| | - Tejaswi Koganti
- Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Shubham Basu
- Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Michelle A Dina
- Molecular Hematopathology Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Cody J Artymiuk
- Molecular Hematopathology Laboratory, Mayo Clinic, Rochester, Minnesota
| | | | - Katie E Halverson
- Biospecimen Accessioning and Processing, Mayo Clinic, Rochester, Minnesota
| | - Xianglin Wu
- Clinical Genomics Sequencing Laboratory, Mayo Clinic, Rochester, Minnesota
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Zimmerman Zuckerman E, Thompson JA, Schneider AR, Campion MB, Johns JJ, Stier TJ, Peterson LM, Ward AM, Blommel JH, Gnanaolivu RD, Lauer KP, Sivasankaran G, Balan J, Dasari S, Sakai Y, Marcou CA, Zheng G, Halling KC, Shen W, Viswanatha DS, Niu Z. Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperatures. SLAS Technol 2022; 27:214-218. [DOI: 10.1016/j.slast.2021.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Balan J, Jenkinson G, Nair A, Saha N, Koganti T, Voss J, Zysk C, Barr Fritcher EG, Ross CA, Giannini C, Raghunathan A, Kipp BR, Jenkins R, Ida C, Halling KC, Blackburn PR, Dasari S, Oliver GR, Klee EW. SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA. Front Genet 2021; 12:739054. [PMID: 34745213 PMCID: PMC8569241 DOI: 10.3389/fgene.2021.739054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Detecting gene fusions involving driver oncogenes is pivotal in clinical diagnosis and treatment of cancer patients. Recent developments in next-generation sequencing (NGS) technologies have enabled improved assays for bioinformatics-based gene fusions detection. In clinical applications, where a small number of fusions are clinically actionable, targeted polymerase chain reaction (PCR)-based NGS chemistries, such as the QIAseq RNAscan assay, aim to improve accuracy compared to standard RNA sequencing. Existing informatics methods for gene fusion detection in NGS-based RNA sequencing assays traditionally use a transcriptome-based spliced alignment approach or a de-novo assembly approach. Transcriptome-based spliced alignment methods face challenges with short read mapping yielding low quality alignments. De-novo assembly-based methods yield longer contigs from short reads that can be more sensitive for genomic rearrangements, but face performance and scalability challenges. Consequently, there exists a need for a method to efficiently and accurately detect fusions in targeted PCR-based NGS chemistries. We describe SeekFusion, a highly accurate and computationally efficient pipeline enabling identification of gene fusions from PCR-based NGS chemistries. Utilizing biological samples processed with the QIAseq RNAscan assay and in-silico simulated data we demonstrate that SeekFusion gene fusion detection accuracy outperforms popular existing methods such as STAR-Fusion, TOPHAT-Fusion and JAFFA-hybrid. We also present results from 4,484 patient samples tested for neurological tumors and sarcoma, encompassing details on some novel fusions identified.
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Affiliation(s)
| | - Garrett Jenkinson
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Asha Nair
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Neiladri Saha
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Tejaswi Koganti
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Jesse Voss
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, United States
| | - Christopher Zysk
- Applied Genomics Division, Perkin Elmer, Waltham, MA, United States
| | | | - Christian A Ross
- Information Technology, Mayo Clinic, Rochester, MN, United States
| | - Caterina Giannini
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, United States
| | - Aditya Raghunathan
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, United States
| | - Benjamin R Kipp
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, United States
| | - Robert Jenkins
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, United States
| | - Cris Ida
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, United States
| | - Kevin C Halling
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, United States
| | - Patrick R Blackburn
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Surendra Dasari
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Gavin R Oliver
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Eric W Klee
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
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Sankaranarayanan S, Balan J, Walsh JR, Wu Y, Minnich S, Piazza A, Osborne C, Oliver GR, Lesko J, Bates KL, Khezeli K, Block DR, DiGuardo M, Kreuter J, O'Horo JC, Kalantari J, Klee EW, Salama ME, Kipp B, Morice WG, Jenkinson G. COVID-19 Mortality Prediction From Deep Learning in a Large Multistate Electronic Health Record and Laboratory Information System Data Set: Algorithm Development and Validation. J Med Internet Res 2021; 23:e30157. [PMID: 34449401 PMCID: PMC8480399 DOI: 10.2196/30157] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/18/2021] [Accepted: 08/11/2021] [Indexed: 12/16/2022] Open
Abstract
Background COVID-19 is caused by the SARS-CoV-2 virus and has strikingly heterogeneous clinical manifestations, with most individuals contracting mild disease but a substantial minority experiencing fulminant cardiopulmonary symptoms or death. The clinical covariates and the laboratory tests performed on a patient provide robust statistics to guide clinical treatment. Deep learning approaches on a data set of this nature enable patient stratification and provide methods to guide clinical treatment. Objective Here, we report on the development and prospective validation of a state-of-the-art machine learning model to provide mortality prediction shortly after confirmation of SARS-CoV-2 infection in the Mayo Clinic patient population. Methods We retrospectively constructed one of the largest reported and most geographically diverse laboratory information system and electronic health record of COVID-19 data sets in the published literature, which included 11,807 patients residing in 41 states of the United States of America and treated at medical sites across 5 states in 3 time zones. Traditional machine learning models were evaluated independently as well as in a stacked learner approach by using AutoGluon, and various recurrent neural network architectures were considered. The traditional machine learning models were implemented using the AutoGluon-Tabular framework, whereas the recurrent neural networks utilized the TensorFlow Keras framework. We trained these models to operate solely using routine laboratory measurements and clinical covariates available within 72 hours of a patient’s first positive COVID-19 nucleic acid test result. Results The GRU-D recurrent neural network achieved peak cross-validation performance with 0.938 (SE 0.004) as the area under the receiver operating characteristic (AUROC) curve. This model retained strong performance by reducing the follow-up time to 12 hours (0.916 [SE 0.005] AUROC), and the leave-one-out feature importance analysis indicated that the most independently valuable features were age, Charlson comorbidity index, minimum oxygen saturation, fibrinogen level, and serum iron level. In the prospective testing cohort, this model provided an AUROC of 0.901 and a statistically significant difference in survival (P<.001, hazard ratio for those predicted to survive, 95% CI 0.043-0.106). Conclusions Our deep learning approach using GRU-D provides an alert system to flag mortality for COVID-19–positive patients by using clinical covariates and laboratory values within a 72-hour window after the first positive nucleic acid test result.
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Affiliation(s)
| | | | | | - Yanhong Wu
- Mayo Clinic, Rochester, MN, United States
| | | | - Amy Piazza
- Mayo Clinic, Rochester, MN, United States
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Ida C, Barr Fritcher E, Zysk C, Voss J, Wu X, Balan J, Kollmeyer T, Raghunathan A, Giannini C, Klee E, Kipp B, Jenkins R. PATH-26. NEURO-ONCOLOGY NEXT-GENERATION SEQUENCING 219-GENE PANEL FOR COMPREHENSIVE CLINICAL TESTING. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Mayampurath A, Yu CY, Song E, Balan J, Mechref Y, Tang H. Computational framework for identification of intact glycopeptides in complex samples. Anal Chem 2013; 86:453-63. [PMID: 24279413 DOI: 10.1021/ac402338u] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Glycosylation is an important protein modification that involves enzymatic attachment of sugars to amino acid residues. Understanding the structure of these sugars and the effects of glycosylation are vital for developing indicators of disease development and progression. Although computational methods based on mass spectrometric data have proven to be effective in monitoring changes in the glycome, developing such methods for the glycoproteome are challenging, largely due to the inherent complexity in simultaneously studying glycan structures with their corresponding glycosylation sites. This paper introduces a computational framework for identifying intact N-linked glycopeptides, i.e. glycopeptides with N-linked glycans attached to their glycosylation sites, in complex proteome samples. Scoring algorithms are presented for tandem mass spectra of glycopeptides resulting from collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD) fragmentation modes. An empirical false-discovery rate estimation method, based on a target-decoy search approach, is derived for assigning confidence. The power of our method is further enhanced when multiple data sets are pooled together to increase identification confidence. Using this framework, 103 highly confident N-linked glycopeptides from 53 sites across 33 glycoproteins were identified in complex human serum proteome samples using conventional proteomic platforms with standard depletion of the 7-most abundant proteins. These results indicate that our method is ready to be used for characterizing site-specific protein glycosylation in complex samples.
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Affiliation(s)
- Anoop Mayampurath
- School of Informatics & Computing, Indiana University , Bloomington, Indiana 47408, United States
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10
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Balan J. Measuring minimal concentrations of attractants detected by the nematodePanagrellus redivivus. J Chem Ecol 2013; 11:105-11. [PMID: 24311102 DOI: 10.1007/bf00987609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/1983] [Revised: 06/01/1984] [Indexed: 11/30/2022]
Abstract
A simple method for the experimental determination of minimal concentrations of attractants detected by the nematodePanagrellus redivivus is described. The lowest concentrations of methyl, ethyl, propyl, butyl, and amyl acetate as well as the minimal differences in concentrations of these attractants detectable byPanagrellus redivivus are presented.
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Affiliation(s)
- J Balan
- Institute of Molecular Biology, Slovak Academy of Sciences Dúbravská cesta, 842 51, Bratislava, Czechoslovakia
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11
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Cugy D, Balan J, Cugy S, Leger B, Giordanella JP. Évolution de la prévalence des scores d’Epworth supérieurs à 14 observée au sein des centres d’examen de la Gironde sur la période 2004–2011. Neurophysiol Clin 2013. [DOI: 10.1016/j.neucli.2013.01.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Yang C, Hillas P, Tang J, Balan J, Notbohm H, Polarek J. Development of a recombinant human collagen-type III based hemostat. J Biomed Mater Res B Appl Biomater 2004; 69:18-24. [PMID: 15015205 DOI: 10.1002/jbm.b.20030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [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] [Indexed: 11/10/2022]
Abstract
Animal-tissue-derived collagen, containing mostly type I collagen with a minor amount of type III collagen, has been widely used in the production of hemostats for many decades, although it has been known for a long time that type III collagen is more likely to induce platelet aggregation in vitro. Because it is hard to purify type III from animal tissue, it has not been possible to correlate this finding with in vivo data. In this report, it is demonstrated that recombinant human collagen III fibrils are more capable of inducing platelet aggregation in vitro than those comprised of bovine collagen I, in agreement with previously published data on tissue-derived type III collagen. When formed into three-dimensional matrices, the use of type III collagen results in formulations with better mechanical integrity, larger surface area, and higher hemostatic activity in a rabbit spleen injury model as compared with commercially available hemostats formed from bovine type I collagen.
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Affiliation(s)
- C Yang
- Fibrogen, Inc., South San Francisco, California 94080, USA
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13
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Cugy D, Penide D, Paty J, Balan J, Vinclair J, Cugy S, Lenain JL, Giordanella JP. Prévalence de la plainte relative aux troubles du sommeil : Suivi de 205 347 sujets de 1988 à 1998. Encephale 2004; 30:228-35. [PMID: 15235520 DOI: 10.1016/s0013-7006(04)95434-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Primary healthcare checkups are regularly performed by French healthcare centers. We report analysis of sleep disorders complaint registered from 1988 to 1998 in Bordeaux-Cauderan and Cenon CPAM welfare centers. The prevalence of sleep disorders is estimated from a total of 205 347 checkups. The population is segmented by age (18-24: 19 332, 25-34:46 694, 35-44:51 072, 45-54:46 886, 55-64:32 658, 65 +:7 705), gender (male: 101 801; female: 103 546) and population category (general: 147 188, underprivileged: 22 785, prioritized: 35 374). Datas shows a relationship between sex and age. Surprisingly we found a relation between Buying Power for Net Wages and Prevalence of Sleep Complaint. There is a significant correlation (R(2)=0,718, p<0,0079). These data are in relationship with M. Ohayon findings relatively to low income and sleep complaint.
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Affiliation(s)
- D Cugy
- Association pour la Prévention du Handicap dû aux troubles du sommeil et de la vigilance, 33000 Bordeaux
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14
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Balan J. [Household economy and gender differences in international migration: a case study of Bolivians in Argentina]. Estud Migr Latinoam 1990; 5:269-94. [PMID: 12342978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The author analyzes household economy and sex differentials among Bolivian immigrants in Argentina. "While male Bolivian (mainly from Cochabamba) immigrants come to Argentina in search of better job opportunities, female immigration does not result generally from an individual decision, but from the adjustment to family, implying a loss in status and independence as compared to their place of origin. Job opportunities for Bolivian female workers are reduced mainly on account of their poor literacy levels; thus they often work for very low wages, deprived of any social benefits." (SUMMARY IN ENG)
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Dandler J, Balan J. Marriage process and household formation in Bolivia and Argentina: the impact of migration in a peasant society. Fertil Determ Res Notes 1988:10-2. [PMID: 12315485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
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16
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C. D, Balan J. Why People Move. Population (French Edition) 1983. [DOI: 10.2307/1532540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Balan J. [Agricultural structures and internal migration in a historical perspective: Latin American case studies]. Rev Mex Sociol 1981; 43:141-92. [PMID: 12338904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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Krizková L, Balan J, Nemec P, Kolozsváry A. Predactious fungi Dactylaria pyriformis and Dactylaria thaumasia: production of attractants and nematicides. Folia Microbiol (Praha) 1976; 21:493-4. [PMID: 1033116 DOI: 10.1007/bf02876942] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Dactylaria pyriformis Juniper and Dactylaria thaumasia Drechsler are predacious fung forming three-edimensional sticky reticula in which nematodes are captured. It was shown by methods developed in our laboratory that in submerged cultivations both of these fungi produce substances attracting nematodes and compounds having nematicidal activity.
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Krizkova L, Nemec P, Kolozsvary A, Balan J. A Qualitative Method for Detection of Nematode Attracting Substances and Proof of Production of Three Different Attractants By the Fungus Monacrosporium Rutgeriensis. ACTA ACUST UNITED AC 1976. [DOI: 10.1163/187529276x00580] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Abstract
Oomycetes and predacious Fungi imperfecti were preserved viable for four years by storage at 22 degrees C under paraffin oil. This method of culture preservation was checked on 52 species belonging to 4 orders and 13 genera.
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Balan J, Krizková L, Nemec P, Vollek V. Production of nematode-attracting and nematicidal substances by predacious fungi. Folia Microbiol (Praha) 1974; 19:512-9. [PMID: 4474116 DOI: 10.1007/bf02872918] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Krizková L, Balan J, Balanová J, Nemec P. Incidence of antiprotozoal and antivermal antibiotics in fungi. IV. Fungi imperfecti, order Moniliales, collected in China. J Antibiot (Tokyo) 1974; 27:234-9. [PMID: 4212080 DOI: 10.7164/antibiotics.27.234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Balan J, Lechevalier HA. The predaceous fungus Arthrobotrys dactyloides: induction of trap formation. Mycologia 1972; 64:919-22. [PMID: 5065014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Balan J, Gerber NN. Attraction and Killing of the Nematode Panagrellus Redivivus By the Predaceous Fungus Arthrobotrys Dactyloides. ACTA ACUST UNITED AC 1972. [DOI: 10.1163/187529272x00403] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Balan J, Fuska J, Kuhr I, Kuhrová V. Bikaverin, an antibiotic from ibberella fujikoi, effective against Leishmania brasiliensis. Folia Microbiol (Praha) 1970; 15:479-84. [PMID: 5497222 DOI: 10.1007/bf02880192] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Balan J, Balanová J, Nemec P, Baráthová H, Ulicná V. Incidence of antiprotozoal and antivermal antibiotics in fungi. 3. Genus Penicillium. J Antibiot (Tokyo) 1969; 22:355-7. [PMID: 4981263 DOI: 10.7164/antibiotics.22.355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Nemec P, Krizková L, Balan J, Balanová J, Kutková M. Incidence of antiprotozoal and antivermal antibiotics in fungi. I. Class Fungi imperfecti. J Antibiot (Tokyo) 1969; 22:345-50. [PMID: 4981261 DOI: 10.7164/antibiotics.22.345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Nemec P, Krizková L, Balan J, Balanová J, Kutková M. Incidence of antiprotozoal and antivermal antibiotics in fungi. II. Class Oomycetes. J Antibiot (Tokyo) 1969; 22:351-4. [PMID: 4981262 DOI: 10.7164/antibiotics.22.351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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