1
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Hu Y, Narayan A, Xu Y, Wolfe J, Vu D, Trinh T, Kantak C, Ivy SP, Eder JP, Deng Y, LoRusso P, Kim JW, Patel AA. Circulating Tumor DNA Dynamics Fail to Predict Efficacy of Poly(ADP-ribose) Polymerase/VEGFR Inhibition in Patients With Heavily Pretreated Advanced Solid Tumors. JCO Precis Oncol 2024; 8:e2300289. [PMID: 38412387 PMCID: PMC10914240 DOI: 10.1200/po.23.00289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/19/2023] [Accepted: 12/06/2023] [Indexed: 02/29/2024] Open
Abstract
PURPOSE Cell-free circulating tumor DNA (ctDNA) has shown its potential as a quantitative biomarker for longitudinal monitoring of response to anticancer therapies. However, ctDNA dynamics have not been studied in patients with heavily pretreated, advanced solid tumors, for whom therapeutic responses can be weak. We investigated whether changes in ctDNA could predict clinical outcomes in such a cohort treated with combined poly(ADP-ribose) polymerase/vascular endothelial growth factor receptor inhibitor therapy. MATERIALS AND METHODS Patients with metastatic pancreatic ductal adenocarcinoma (PDAC), triple-negative breast cancer (TNBC), small-cell lung cancer (SCLC), or non-small-cell lung cancer (NSCLC) received up to 7 days of cediranib 30 mg orally once daily monotherapy lead-in followed by addition of olaparib 200 mg orally twice daily. Patients had progressed on a median of three previous lines of therapy. Plasma samples were collected before and after cediranib monotherapy lead-in and on combination therapy at 7 days, 28 days, and every 28 days thereafter. ctDNA was quantified from plasma samples using a multigene mutation-based assay. Radiographic assessment was performed every 8 weeks. RESULTS ctDNA measurements were evaluable in 63 patients. The median baseline ctDNA variant allele fractions (VAFs) were 20%, 28%, 27%, and 34% for PDAC, TNBC, SCLC, and NSCLC, respectively. No association was observed between baseline VAF and radiographic response, progression-free survival, or overall survival (OS). Similarly, no association was found between ctDNA decline and radiographic response or survival. However, an increase in ctDNA at 56 days of combination therapy was associated with disease progression and inferior OS in a landmark analysis. CONCLUSION ctDNA levels or dynamics did not correlate with radiographic response or survival outcomes in patients with advanced metastatic malignancies treated with olaparib and cediranib.
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Affiliation(s)
- Yiduo Hu
- Department of Internal Medicine, Section of Medical Oncology, Yale University School of Medicine, New Haven, CT
| | - Azeet Narayan
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT
| | - Yunshan Xu
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT
| | - Julia Wolfe
- Department of Internal Medicine, Section of Medical Oncology, Yale University School of Medicine, New Haven, CT
| | - Dennis Vu
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT
| | - Thi Trinh
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT
| | - Chaitanya Kantak
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT
| | - S. Percy Ivy
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joseph Paul Eder
- Department of Internal Medicine, Section of Medical Oncology, Yale University School of Medicine, New Haven, CT
- Parthenon Therapeutics, Cambridge, MA
| | - Yanhong Deng
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT
| | - Patricia LoRusso
- Department of Internal Medicine, Section of Medical Oncology, Yale University School of Medicine, New Haven, CT
| | - Joseph W. Kim
- Department of Internal Medicine, Section of Medical Oncology, Yale University School of Medicine, New Haven, CT
| | - Abhijit A. Patel
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT
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2
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Batool SM, Hsia T, Beecroft A, Lewis B, Ekanayake E, Rosenfeld Y, Escobedo AK, Gamblin AS, Rawal S, Cote RJ, Watson M, Wong DTW, Patel AA, Skog J, Papadopoulos N, Bettegowda C, Castro CM, Lee H, Srivastava S, Carter BS, Balaj L. Extrinsic and intrinsic preanalytical variables affecting liquid biopsy in cancer. Cell Rep Med 2023; 4:101196. [PMID: 37725979 PMCID: PMC10591035 DOI: 10.1016/j.xcrm.2023.101196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 12/01/2022] [Accepted: 08/22/2023] [Indexed: 09/21/2023]
Abstract
Liquid biopsy, through isolation and analysis of disease-specific analytes, has evolved as a promising tool for safe and minimally invasive diagnosis and monitoring of tumors. It also has tremendous utility as a companion diagnostic allowing detection of biomarkers in a range of cancers (lung, breast, colon, ovarian, brain). However, clinical implementation and validation remains a challenge. Among other stages of development, preanalytical variables are critical in influencing the downstream cellular and molecular analysis of different analytes. Although considerable progress has been made to address these challenges, a comprehensive assessment of the impact on diagnostic parameters and consensus on standardized and optimized protocols is still lacking. Here, we summarize and critically evaluate key variables in the preanalytical stage, including study population selection, choice of biofluid, sample handling and collection, processing, and storage. There is an unmet need to develop and implement comprehensive preanalytical guidelines on the optimal practices and methodologies.
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Affiliation(s)
| | - Tiffaney Hsia
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexandra Beecroft
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Brian Lewis
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Emil Ekanayake
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yulia Rosenfeld
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ana K Escobedo
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Austin S Gamblin
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Siddarth Rawal
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | - Richard J Cote
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | - Mark Watson
- Washington University School of Medicine, St. Louis, MO, USA
| | - David T W Wong
- University of California Los Angeles, Los Angeles, CA, USA
| | | | - Johan Skog
- Exosome Diagnostics, Waltham, MA 02451, USA
| | | | | | - Cesar M Castro
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hakho Lee
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Bob S Carter
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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3
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Batool SM, Yekula A, Khanna P, Hsia T, Gamblin AS, Ekanayake E, Escobedo AK, You DG, Castro CM, Im H, Kilic T, Garlin MA, Skog J, Dinulescu DM, Dudley J, Agrawal N, Cheng J, Abtin F, Aberle DR, Chia D, Elashoff D, Grognan T, Krysan K, Oh SS, Strom C, Tu M, Wei F, Xian RR, Skates SJ, Zhang DY, Trinh T, Watson M, Aft R, Rawal S, Agarwal A, Kesmodel SB, Yang C, Shen C, Hochberg FH, Wong DTW, Patel AA, Papadopoulos N, Bettegowda C, Cote RJ, Srivastava S, Lee H, Carter BS, Balaj L. The Liquid Biopsy Consortium: Challenges and opportunities for early cancer detection and monitoring. Cell Rep Med 2023; 4:101198. [PMID: 37716353 PMCID: PMC10591039 DOI: 10.1016/j.xcrm.2023.101198] [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: 02/09/2022] [Revised: 12/01/2022] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The emerging field of liquid biopsy stands at the forefront of novel diagnostic strategies for cancer and other diseases. Liquid biopsy allows minimally invasive molecular characterization of cancers for diagnosis, patient stratification to therapy, and longitudinal monitoring. Liquid biopsy strategies include detection and monitoring of circulating tumor cells, cell-free DNA, and extracellular vesicles. In this review, we address the current understanding and the role of existing liquid-biopsy-based modalities in cancer diagnostics and monitoring. We specifically focus on the technical and clinical challenges associated with liquid biopsy and biomarker development being addressed by the Liquid Biopsy Consortium, established through the National Cancer Institute. The Liquid Biopsy Consortium has developed new methods/assays and validated existing methods/technologies to capture and characterize tumor-derived circulating cargo, as well as addressed existing challenges and provided recommendations for advancing biomarker assays.
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Affiliation(s)
| | - Anudeep Yekula
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Prerna Khanna
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tiffaney Hsia
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin S Gamblin
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emil Ekanayake
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana K Escobedo
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dong Gil You
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cesar M Castro
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hyungsoon Im
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tugba Kilic
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Johan Skog
- Exosome Diagnostics Inc., Waltham, MA, USA
| | | | - Jonathan Dudley
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Jordan Cheng
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - David Chia
- University of California Los Angeles, Los Angeles, CA, USA
| | - David Elashoff
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - Scott S Oh
- University of California Los Angeles, Los Angeles, CA, USA
| | - Charles Strom
- University of California Los Angeles, Los Angeles, CA, USA
| | - Michael Tu
- Liquid Diagnostics LLC., Los Angeles, CA, USA
| | - Fang Wei
- University of California Los Angeles, Los Angeles, CA, USA
| | - Rena R Xian
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven J Skates
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Thi Trinh
- Yale University School of Medicine, New Haven, CT, USA
| | - Mark Watson
- Washington University School of Medicine, St. Louis, MO, USA
| | - Rebecca Aft
- Washington University School of Medicine, St. Louis, MO, USA
| | - Siddarth Rawal
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | | | | | | | - Cheng Shen
- California Institute of Technology, Pasadena, CA, USA
| | | | - David T W Wong
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | - Richard J Cote
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Hakho Lee
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bob S Carter
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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4
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Tyagi T, Jain K, Yarovinsky TO, Chiorazzi M, Du J, Castro C, Griffin J, Korde A, Martin KA, Takyar SS, Flavell RA, Patel AA, Hwa J. Platelet-derived TLT-1 promotes tumor progression by suppressing CD8+ T cells. J Exp Med 2023; 220:213620. [PMID: 36305874 DOI: 10.1084/jem.20212218] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/25/2022] [Accepted: 10/05/2022] [Indexed: 01/19/2023] Open
Abstract
Current understanding of tumor immunosuppressive mechanisms forms the basis for modern day immunotherapies. Immunoregulatory role of platelets in cancer remains largely elusive. Platelets from non-small cell lung cancer (NSCLC) patients revealed a distinct activation phenotype. TREM-like transcript 1 (TLT-1), a platelet protein, was increased along with enhanced extracellular release from NSCLC platelets. The increased platelet TLT-1 was also evident in humanized mice with patient-derived tumors. In immunocompetent mice with syngeneic tumors, TLT-1 binding to T cells, in vivo, led to suppression of CD8 T cells, promoting tumor growth. We identified direct interaction between TLT-1 and CD3ε on T cells, implicating the NF-κB pathway in CD8 T cell suppression. Anti-TLT-1 antibody rescued patients' T cells from platelet-induced suppression ex vivo and reduced tumors in mice in vivo. Clinically, higher TLT-1 correlated with reduced survival of NSCLC patients. Our findings thus identify TLT-1 as a platelet-derived immunosuppressor that suppresses CD8 T cells and demonstrate its therapeutic and prognostic significance in cancer.
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Affiliation(s)
- Tarun Tyagi
- Yale Cardiovascular Research Center, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Kanika Jain
- Yale Cardiovascular Research Center, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Timur O Yarovinsky
- Yale Cardiovascular Research Center, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Michael Chiorazzi
- Department of Immunobiology, Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT.,Yale Cancer Center, New Haven, CT
| | - Jing Du
- Yale Cardiovascular Research Center, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Cecilia Castro
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Jules Griffin
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Asawari Korde
- Pulmonary Critical Care, Yale Internal Medicine, New Haven, CT
| | - Kathleen A Martin
- Yale Cardiovascular Research Center, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Shervin S Takyar
- Pulmonary Critical Care, Yale Internal Medicine, New Haven, CT.,Yale Cancer Center, New Haven, CT
| | - Richard A Flavell
- Department of Immunobiology, Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT.,Yale Cancer Center, New Haven, CT
| | - Abhijit A Patel
- Yale Therapeutic Radiology, Yale Cancer Center, New Haven, CT.,Yale Cancer Center, New Haven, CT
| | - John Hwa
- Yale Cardiovascular Research Center, Department of Internal Medicine, Yale School of Medicine, New Haven, CT.,Yale Cancer Center, New Haven, CT
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5
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Cheng LY, Dai P, Wu LR, Patel AA, Zhang DY. Direct capture and sequencing reveal ultra-short single-stranded DNA in biofluids. iScience 2022; 25:105046. [PMID: 36147958 PMCID: PMC9486625 DOI: 10.1016/j.isci.2022.105046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 06/20/2022] [Accepted: 08/26/2022] [Indexed: 11/29/2022] Open
Abstract
Cell-free DNA (cfDNA) has become the predominant analyte of liquid biopsy; however, recent studies suggest the presence of subnucleosomal-sized DNA fragments in circulation that are likely single-stranded. Here, we report a method called direct capture and sequencing (DCS) tailored to recover such fragments from biofluids by directly capturing them using short degenerate probes followed by single strand-based library preparation and next-generation sequencing. DCS revealed a new DNA population in biofluids, named ultrashort single-stranded DNA (ussDNA). Evaluation of the size distribution and abundance of ussDNA manifested generality of its presence in humans, animal species, and plants. In humans, red blood cells were found to contain abundant ussDNA; plasma-derived ussDNA exhibited modal size at 50 nt. This work reports the presence of an understudied DNA population in circulation, and yet more work is awaiting to study its generation mechanism, tissue of origin, disease implications, etc.
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Affiliation(s)
- Lauren Y Cheng
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Peng Dai
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia R Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA.,Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
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6
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Song P, Wu LR, Yan YH, Zhang JX, Chu T, Kwong LN, Patel AA, Zhang DY. Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics. Nat Biomed Eng 2022; 6:232-245. [PMID: 35102279 PMCID: PMC9336539 DOI: 10.1038/s41551-021-00837-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [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: 05/02/2019] [Accepted: 05/27/2021] [Indexed: 12/15/2022]
Abstract
Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the monitoring of drug resistance, and for the early detection of cancers. However, the analysis of cfDNA for clinical diagnostic applications remains challenging because of the low concentrations of cfDNA, and because cfDNA is fragmented into short lengths and is susceptible to chemical damage. Barcodes of unique molecular identifiers have been implemented to overcome the intrinsic errors of next-generation sequencing, which is the prevailing method for highly multiplexed cfDNA analysis. However, a number of methodological and pre-analytical factors limit the clinical sensitivity of the cfDNA-based detection of cancers from liquid biopsies. In this Review, we describe the state-of-the-art technologies for cfDNA analysis, with emphasis on multiplexing strategies, and discuss outstanding biological and technical challenges that, if addressed, would substantially improve cancer diagnostics and patient care.
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Affiliation(s)
- Ping Song
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia Ruojia Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Tianqing Chu
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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7
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Popat A, Patel AA, Warnes G. Cell Cycle Analysis of ER Stress and Autophagy. Methods Mol Biol 2022; 2543:155-166. [PMID: 36087266 DOI: 10.1007/978-1-0716-2553-8_13] [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: 06/15/2023]
Abstract
Autophagy and ER stress are most often studied employing a Western blotting approach to the measurement of autophagy by LC3B upregulation and the ER stress sensor signaling proteins PERK (protein kinase R-like endoplasmic reticulum kinase), IRE1, and ATF6 which initiate protein refolding and elongation of the ER until ER homeostasis is returned. If the misfolding of proteins is increased, then ER stress is maintained, and microautophagy of the ER or specifically reticulophagy occurs. However, LC3B, PERK, protein misfolding, and changes in ER mass (reticulophagy) can also be measured in a cell cycle-dependent manner by flow cytometry and the use of antibodies, protein misfolding, and ER tracking fluorescent probes.
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Affiliation(s)
- A Popat
- Flow Cytometry Core Facility, The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary London University, London, UK
| | - A A Patel
- Flow Cytometry Core Facility, The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary London University, London, UK
| | - Gary Warnes
- Flow Cytometry Core Facility, The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary London University, London, UK.
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8
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Song P, Chen SX, Yan YH, Pinto A, Cheng LY, Dai P, Patel AA, Zhang DY. Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing. Nat Biomed Eng 2021; 5:690-701. [PMID: 33941896 PMCID: PMC9631981 DOI: 10.1038/s41551-021-00713-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/09/2021] [Indexed: 02/02/2023]
Abstract
DNA sequence variants with allele fractions below 1% are difficult to detect and quantify by sequencing owing to intrinsic errors in sequencing-by-synthesis methods. Although molecular-identifier barcodes can detect mutations with a variant-allele frequency (VAF) as low as 0.1% using next-generation sequencing (NGS), sequencing depths of over 25,000× are required, thus hampering the detection of mutations at high sensitivity in patient samples and in most samples used in research. Here we show that low-frequency DNA variants can be detected via low-depth multiplexed NGS after their amplification, by a median of 300-fold, using polymerase chain reaction and rationally designed 'blocker' oligonucleotides that bind to the variants. Using an 80-plex NGS panel and a sequencing depth of 250×, we detected single nucleotide polymorphisms with a VAF of 0.019% and contamination in human cell lines at a VAF as low as 0.07%. With a 16-plex NGS panel covering 145 mutations across 9 genes involved in melanoma, we detected low-VAF mutations (0.2-5%) in 7 out of the 19 samples of freshly frozen tumour biopsies, suggesting that tumour heterogeneity could be notably higher than previously recognized.
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Affiliation(s)
- Ping Song
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Sherry X Chen
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Yan Helen Yan
- Department of Bioengineering, Rice University, Houston, TX, USA.,Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | | | - Lauren Y Cheng
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Peng Dai
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA. .,Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA.
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9
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Ichkhanian Y, Vosoughi K, Aghaie Meybodi M, Jacques J, Sethi A, Patel AA, Aadam AA, Triggs JR, Bapaye A, Dorwat S, Benias P, Chaves DM, Barret M, Law RJ, Browers N, Pioche M, Draganov PV, Kotzev A, Estremera F, Albeniz E, Ujiki MB, Callahan ZM, Itani MI, Brewer OG, Khashab MA. Correction to: Comprehensive analysis of adverse events associated with gastric peroral endoscopic myotomy: an international multicenter study. Surg Endosc 2020; 35:1765. [PMID: 32424623 DOI: 10.1007/s00464-020-07651-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Y Ichkhanian
- Division of Gastroenterology and Hepatology, Johns Hopkins Medical Institution, Baltimore, MD, USA
| | - K Vosoughi
- Division of Gastroenterology and Hepatology, Johns Hopkins Medical Institution, Baltimore, MD, USA
| | - M Aghaie Meybodi
- Division of Gastroenterology and Hepatology, Johns Hopkins Medical Institution, Baltimore, MD, USA
| | - J Jacques
- Gastroenterology Department, Limoges University Hospital, 2 Avenue Martin Luther King, 87042, Rouen, France
| | - A Sethi
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, USA
| | - A A Patel
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, USA
| | - A A Aadam
- Division of Gastroenterology and Hepatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - J R Triggs
- Division of Gastroenterology and Hepatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - A Bapaye
- Department of Digestive Diseases & Endoscopy, Deenanath Mangeshkar Hospital and Research Center, Pune, Maharashtra, India
| | - S Dorwat
- Department of Digestive Diseases & Endoscopy, Deenanath Mangeshkar Hospital and Research Center, Pune, Maharashtra, India
| | - P Benias
- Division of Gastroenterology, Zucker School of Medicine at Hofstra/Northwell, Long Island Jewish Medical Center, Northwell Health System, New Hyde Park, NY, USA
| | - D M Chaves
- Gastroenterologia, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - M Barret
- Gastroenterology Unit, Cochin University Hospital, Université Paris Descartes, Paris, France.,Unité INSERM U1016, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - R J Law
- University of Michigan Health Care System, Ann Arbor, USA
| | - N Browers
- University of Michigan Health Care System, Ann Arbor, USA
| | - M Pioche
- Service d'Hépato-gastro-entérologie, Hôpital Edouard Herriot, CHU Lyon, Lyon, France
| | - P V Draganov
- Division of Gastroenterology, Hepatology and Nutrition, University of Florida, Gainesville, FL, USA
| | - A Kotzev
- Clinic of Gastroenterology, University Hospital "Alexandrovska", Sofia, Bulgaria
| | - F Estremera
- Clinic of Gastroenterology, University Hospital "Alexandrovska", Sofia, Bulgaria
| | - E Albeniz
- Division of Gastroenterology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - M B Ujiki
- Section of Minimally Invasive Surgery, Department of Surgery, NorthShore University Health System, Evanston, IL, USA
| | - Z M Callahan
- Section of Minimally Invasive Surgery, Department of Surgery, NorthShore University Health System, Evanston, IL, USA
| | - M I Itani
- Division of Gastroenterology and Hepatology, Johns Hopkins Medical Institution, Baltimore, MD, USA
| | - O G Brewer
- Division of Gastroenterology and Hepatology, Johns Hopkins Medical Institution, Baltimore, MD, USA
| | - M A Khashab
- Division of Gastroenterology and Hepatology, Johns Hopkins Medical Institution, Baltimore, MD, USA. .,Division of Gastroenterology and Hepatology, Johns Hopkins Hospital, Sheikh Zayed Bldg, 1800 Orleans Street, Suite 7125G, Baltimore, MD, 21287, USA.
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10
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Patel AA, Nicholson K, Goldman T. Ultrasound Guided Robotic Assisted Myomectomy. J Minim Invasive Gynecol 2019. [DOI: 10.1016/j.jmig.2019.09.726] [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: 10/25/2022]
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11
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Patel AA, Nimaroff ML. 2920 A Retrospective Look at Gynecological Surgical Complications. J Minim Invasive Gynecol 2019. [DOI: 10.1016/j.jmig.2019.09.498] [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: 10/25/2022]
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12
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Heywood I, Camilo F, Cotton WD, Yusef-Zadeh F, Abbott TD, Adam RM, Aldera MA, Bauermeister EF, Booth RS, Botha AG, Botha DH, Brederode LRS, Brits ZB, Buchner SJ, Burger JP, Chalmers JM, Cheetham T, de Villiers D, Dikgale-Mahlakoana MA, du Toit LJ, Esterhuyse SWP, Fanaroff BL, Foley AR, Fourie DJ, Gamatham RRG, Goedhart S, Gounden S, Hlakola MJ, Hoek CJ, Hokwana A, Horn DM, Horrell JMG, Hugo B, Isaacson AR, Jonas JL, Jordaan JDBL, Joubert AF, Józsa GIG, Julie RPM, Kapp FB, Kenyon JS, Kotzé PPA, Kriel H, Kusel TW, Lehmensiek R, Liebenberg D, Loots A, Lord RT, Lunsky BM, Macfarlane PS, Magnus LG, Magozore CM, Mahgoub O, Main JPL, Malan JA, Malgas RD, Manley JR, Maree MDJ, Merry B, Millenaar R, Mnyandu N, Moeng IPT, Monama TE, Mphego MC, New WS, Ngcebetsha B, Oozeer N, Otto AJ, Passmoor SS, Patel AA, Peens-Hough A, Perkins SJ, Ratcliffe SM, Renil R, Rust A, Salie S, Schwardt LC, Serylak M, Siebrits R, Sirothia SK, Smirnov OM, Sofeya L, Swart PS, Tasse C, Taylor DT, Theron IP, Thorat K, Tiplady AJ, Tshongweni S, van Balla TJ, van der Byl A, van der Merwe C, van Dyk CL, Van Rooyen R, Van Tonder V, Van Wyk R, Wallace BH, Welz MG, Williams LP. Inflation of 430-parsec bipolar radio bubbles in the Galactic Centre by an energetic event. Nature 2019; 573:235-237. [PMID: 31511683 DOI: 10.1038/s41586-019-1532-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/28/2019] [Indexed: 11/09/2022]
Abstract
The Galactic Centre contains a supermassive black hole with a mass of four million Suns1 within an environment that differs markedly from that of the Galactic disk. Although the black hole is essentially quiescent in the broader context of active galactic nuclei, X-ray observations have provided evidence for energetic outbursts from its surroundings2. Also, although the levels of star formation in the Galactic Centre have been approximately constant over the past few hundred million years, there is evidence of increased short-duration bursts3, strongly influenced by the interaction of the black hole with the enhanced gas density present within the ring-like central molecular zone4 at Galactic longitude |l| < 0.7 degrees and latitude |b| < 0.2 degrees. The inner 200-parsec region is characterized by large amounts of warm molecular gas5, a high cosmic-ray ionization rate6, unusual gas chemistry, enhanced synchrotron emission7,8, and a multitude of radio-emitting magnetized filaments9, the origin of which has not been established. Here we report radio imaging that reveals a bipolar bubble structure, with an overall span of 1 degree by 3 degrees (140 parsecs × 430 parsecs), extending above and below the Galactic plane and apparently associated with the Galactic Centre. The structure is edge-brightened and bounded, with symmetry implying creation by an energetic event in the Galactic Centre. We estimate the age of the bubbles to be a few million years, with a total energy of 7 × 1052 ergs. We postulate that the progenitor event was a major contributor to the increased cosmic-ray density in the Galactic Centre, and is in turn the principal source of the relativistic particles required to power the synchrotron emission of the radio filaments within and in the vicinity of the bubble cavities.
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Affiliation(s)
- I Heywood
- Department of Physics, University of Oxford, Oxford, UK. .,Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa. .,South African Radio Astronomy Observatory, Cape Town, South Africa.
| | - F Camilo
- South African Radio Astronomy Observatory, Cape Town, South Africa.
| | - W D Cotton
- South African Radio Astronomy Observatory, Cape Town, South Africa.,National Radio Astronomy Observatory, Charlottesville, VA, USA
| | - F Yusef-Zadeh
- CIERA and Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA
| | - T D Abbott
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R M Adam
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M A Aldera
- Tellumat (Pty) Ltd, Retreat, South Africa
| | - E F Bauermeister
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R S Booth
- Chalmers University of Technology, Gothenburg, Sweden
| | - A G Botha
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - D H Botha
- EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa
| | - L R S Brederode
- South African Radio Astronomy Observatory, Cape Town, South Africa.,SKA Organisation, Jodrell Bank, Macclesfield, UK
| | - Z B Brits
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S J Buchner
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J P Burger
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J M Chalmers
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - T Cheetham
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - D de Villiers
- Department of Electrical and Electronic Engineering, Stellenbosch University, Stellenbosch, South Africa
| | | | - L J du Toit
- EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa
| | - S W P Esterhuyse
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - B L Fanaroff
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A R Foley
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - D J Fourie
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R R G Gamatham
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S Goedhart
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S Gounden
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M J Hlakola
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - C J Hoek
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A Hokwana
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - D M Horn
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J M G Horrell
- IDIA, University of Cape Town, Rondebosch, South Africa
| | - B Hugo
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A R Isaacson
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J L Jonas
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J D B L Jordaan
- South African Radio Astronomy Observatory, Cape Town, South Africa.,EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa
| | - A F Joubert
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - G I G Józsa
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R P M Julie
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - F B Kapp
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J S Kenyon
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa
| | - P P A Kotzé
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - H Kriel
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - T W Kusel
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R Lehmensiek
- EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa.,Department of Electrical Engineering, Cape Peninsula University of Technology, Bellville, South Africa
| | - D Liebenberg
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A Loots
- Presidential Infrastructure Coordinating Commission, Pretoria, South Africa
| | - R T Lord
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - B M Lunsky
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - P S Macfarlane
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - L G Magnus
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - C M Magozore
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - O Mahgoub
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J P L Main
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J A Malan
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R D Malgas
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J R Manley
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M D J Maree
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - B Merry
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R Millenaar
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - N Mnyandu
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - I P T Moeng
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - T E Monama
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M C Mphego
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - W S New
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - B Ngcebetsha
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - N Oozeer
- South African Radio Astronomy Observatory, Cape Town, South Africa.,African Institute for Mathematical Sciences, Muizenberg, South Africa
| | - A J Otto
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S S Passmoor
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A A Patel
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A Peens-Hough
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S J Perkins
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S M Ratcliffe
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R Renil
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A Rust
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S Salie
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - L C Schwardt
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M Serylak
- South African Radio Astronomy Observatory, Cape Town, South Africa.,Department of Physics and Astronomy, University of the Western Cape, Bellville, South Africa
| | - R Siebrits
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S K Sirothia
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - O M Smirnov
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - L Sofeya
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - P S Swart
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - C Tasse
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,GEPI, CNRS, PSL Research University, Meudon, France
| | - D T Taylor
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - I P Theron
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa
| | - K Thorat
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A J Tiplady
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S Tshongweni
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - T J van Balla
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A van der Byl
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - C van der Merwe
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - C L van Dyk
- Peralex Electronics (Pty) Ltd, Bergvliet, South Africa
| | - R Van Rooyen
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - V Van Tonder
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R Van Wyk
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - B H Wallace
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M G Welz
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - L P Williams
- South African Radio Astronomy Observatory, Cape Town, South Africa
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Collard MD, Xi Y, Patel AA, Scott KM, Jones S, Chhabra A. Initial experience of CT-guided pulsed radiofrequency ablation of the pudendal nerve for chronic recalcitrant pelvic pain. Clin Radiol 2019; 74:897.e17-897.e23. [PMID: 31447049 DOI: 10.1016/j.crad.2019.06.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 06/28/2019] [Indexed: 11/27/2022]
Abstract
AIM To evaluate initial experience with computed tomography (CT)-guided pulsed radiofrequency ablation (pRFA) of the pudendal nerve in cases of recalcitrant neuropathic pelvic pain. Endpoints include technical feasibility, safety, and efficacy of therapy. MATERIALS AND METHODS Ten patients who underwent pRFA ablation for neuropathic pudendal nerve pain during the trial period were followed for response to treatment for 6 months. Each patient was treated with pRFA under CT-guidance with concurrent perineural injection of anaesthetic and/or corticosteroid. Pain scores were then measured using a numeric rating scale at fixed intervals up to 6 months. RESULTS All procedures were considered technically successful with no immediate complications. pRFA demonstrated improved duration of pain improvement compared to the most recent perineural injection (p=0.0195), but not compared to the initial injection (p=0.64). Reported pain scores were lower with pRFA than with both the first and most recent injection but this did not reach statistical significance (p=0.1094 and p=0.7539, respectively). CONCLUSION Overall, pRFA of the pudendal nerve using CT-guidance can be a safe and effective therapy. This technique provides direct visualisation of the nerve to maximise safety and efficacy while offering a novel form of therapy for patients with chronic, recalcitrant pelvic pain.
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Affiliation(s)
- M D Collard
- Radiology Department, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Y Xi
- Radiology Department, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - A A Patel
- Radiology Department, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - K M Scott
- Physical Medicine and Rehabilitation Department, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - S Jones
- Anesthesia and Pain Management Department, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - A Chhabra
- Radiology Department, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA; Orthopedic Surgery Department, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.
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14
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Affiliation(s)
- Sarah B Goldberg
- Department of Medicine (Medical Oncology), Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, CT, USA
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15
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Narayan A, Johnkennedy R, Zakaria M, Lee V, Patel AA. META RNA profiling: Multiplexed quantitation of targeted RNAs across large numbers of samples. Methods 2019; 152:41-47. [PMID: 30308315 DOI: 10.1016/j.ymeth.2018.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/06/2018] [Accepted: 09/30/2018] [Indexed: 01/18/2023] Open
Abstract
META RNA profiling is a simple and inexpensive method to measure the expression of multiple targeted RNAs across many samples. By assigning sample-specific tags up-front during reverse-transcription, cDNAs from multiple samples can be pooled prior to amplification and deep sequencing. Such early parallelization of samples simplifies the workflow, minimizes cross-sample experimental variability, and reduces reagent and sequencing costs. Herein we describe the theoretical framework of the method and provide a detailed protocol to facilitate its implementation.
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Affiliation(s)
- Azeet Narayan
- Department of Therapeutic Radiology, Yale University, New Haven, CT, United States
| | - Rofina Johnkennedy
- Department of Therapeutic Radiology, Yale University, New Haven, CT, United States
| | - Maheen Zakaria
- Department of Therapeutic Radiology, Yale University, New Haven, CT, United States
| | - Victor Lee
- Department of Therapeutic Radiology, Yale University, New Haven, CT, United States
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale University, New Haven, CT, United States.
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16
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Popat A, Patel AA, Warnes G. A Flow Cytometric Study of ER Stress and Autophagy. Cytometry A 2018; 95:672-682. [PMID: 30451364 DOI: 10.1002/cyto.a.23665] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/09/2018] [Accepted: 10/08/2018] [Indexed: 01/18/2023]
Abstract
The mechanistic link between ER stress, autophagy, and resultant cell death was investigated by the use of drugs Thapsigargin (Tg) and Chloroquine (CQ) with prior induction and or blockade of autophagy and apoptosis which modulated the ER stress response and resultant form of cell death. All these biological processes can be measured flow cytometrically allowing the determination of the type of cell death, G1 cell cycle arrest, cell cycle dependent measurement of ER stress transducer PERK, misfolded proteins, reticulophagy, and autophagy marker LC3B. Jurkat cells after Tg or CQ treatment became necrotic and apoptotic, showed G1 cell cycle arrest, autophagy, and ER stress. Prior induction of autophagy before ER stress increased levels of necrotic and apoptotic cell death. Autophagy was further up-regulated, while PERK was reduced or abrogated. CQ showed reduced levels of misfolded proteins and reticulophagy, while Tg showed no change in misfolded protein levels but increased reticulophagy and thus displayed more ER stress. Prior blockade of apoptosis before induction of ER stress resulted in cell survival except with high Tg levels which induced necrosis. Autophagy was up-regulated with modulation of PERK and reticulophagy levels with an abrogation of the misfolded protein response. Blockade of apoptosis with induction of autophagy before ER stress showed death by necrosis with high dose drugs and cell survival with low doses of drugs. CQ induced reduced levels G1 cell cycle arrest while it was maintained with Tg. Autophagy was also maintained with reduced levels of ER stress. These data demonstrates a profound link between the processes of ER stress, autophagy, and the resultant form of cell death all of which can be modulated depending upon the sequence and concentration of drugs employed. © 2018 International Society for Advancement of Cytometry.
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Affiliation(s)
- A Popat
- Flow Cytometry Core Facility, The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary London University, London, England
| | - A A Patel
- Flow Cytometry Core Facility, The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary London University, London, England
| | - G Warnes
- Flow Cytometry Core Facility, The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary London University, London, England
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Abstract
Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer worldwide and in the United States. OSCC remains a major cause of morbidity and mortality in patients with head and neck cancers. Tobacco and alcohol consumption alone or with chewing betel nut are potential risk factors contributing to the high prevalence of OSCC. Multimodality therapies, including surgery, chemotherapy, biologic therapy, and radiotherapy, particularly intensity-modulated radiotherapy (IMRT), are the current treatments for OSCC patients. Despite recent advances in these treatment modalities, the overall survival remains poor over the past years. Recent data from whole-exome sequencing reveal that TP53 is commonly mutated in human papillomavirus-negative OSCC patients. Furthermore, these data stressed the importance of the TP53 gene in suppressing the development and progression of OSCC. Clinically, TP53 mutations are largely associated with poor survival and tumor resistance to radiotherapy and chemotherapy in OSCC patients, which makes the TP53 mutation status a potentially useful molecular marker prognostic and predictive of clinical response in these patients. Several forms of DNA damage have been shown to activate p53, including those generated by ionizing radiation and chemotherapy. The DNA damage stabilizes p53 in part via the DNA damage signaling pathway that involves sensor kinases, including ATM and ATR and effector kinases, such as Chk1/2 and Wee1, which leads to posttranscriptional regulation of a variety of genes involved in DNA repair, cell cycle control, apoptosis, and senescence. Here, we discuss the link of TP53 mutations with treatment outcome and survival in OSCC patients. We also provide evidence that small-molecule inhibitors of critical proteins that regulate DNA damage repair and replication stress during the cell cycle progression, as well as other molecules that restore wild-type p53 activity to mutant p53, can be exploited as novel therapeutic approaches for the treatment of OSCC patients bearing p53 mutant tumors.
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Affiliation(s)
- A Lindemann
- 1 Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Takahashi
- 1 Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - A A Patel
- 1 Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - A A Osman
- 1 Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J N Myers
- 1 Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Goldberg SB, Narayan A, Kole AJ, Decker RH, Teysir J, Carriero NJ, Lee A, Nemati R, Nath SK, Mane SM, Deng Y, Sukumar N, Zelterman D, Boffa DJ, Politi K, Gettinger SN, Wilson LD, Herbst RS, Patel AA. Early Assessment of Lung Cancer Immunotherapy Response via Circulating Tumor DNA. Clin Cancer Res 2018; 24:1872-1880. [PMID: 29330207 DOI: 10.1158/1078-0432.ccr-17-1341] [Citation(s) in RCA: 285] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/05/2017] [Accepted: 01/08/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Decisions to continue or suspend therapy with immune checkpoint inhibitors are commonly guided by tumor dynamics seen on serial imaging. However, immunotherapy responses are uniquely challenging to interpret because tumors often shrink slowly or can appear transiently enlarged due to inflammation. We hypothesized that monitoring tumor cell death in real time by quantifying changes in circulating tumor DNA (ctDNA) levels could enable early assessment of immunotherapy efficacy.Experimental Design: We compared longitudinal changes in ctDNA levels with changes in radiographic tumor size and with survival outcomes in 28 patients with metastatic non-small cell lung cancer (NSCLC) receiving immune checkpoint inhibitor therapy. CtDNA was quantified by determining the allele fraction of cancer-associated somatic mutations in plasma using a multigene next-generation sequencing assay. We defined a ctDNA response as a >50% decrease in mutant allele fraction from baseline, with a second confirmatory measurement.Results: Strong agreement was observed between ctDNA response and radiographic response (Cohen's kappa, 0.753). Median time to initial response among patients who achieved responses in both categories was 24.5 days by ctDNA versus 72.5 days by imaging. Time on treatment was significantly longer for ctDNA responders versus nonresponders (median, 205.5 vs. 69 days; P < 0.001). A ctDNA response was associated with superior progression-free survival [hazard ratio (HR), 0.29; 95% CI, 0.09-0.89; P = 0.03], and superior overall survival (HR, 0.17; 95% CI, 0.05-0.62; P = 0.007).Conclusions: A drop in ctDNA level is an early marker of therapeutic efficacy and predicts prolonged survival in patients treated with immune checkpoint inhibitors for NSCLC. Clin Cancer Res; 24(8); 1872-80. ©2018 AACR.
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Affiliation(s)
- Sarah B Goldberg
- Department of Medicine (Medical Oncology), Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Azeet Narayan
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Adam J Kole
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Roy H Decker
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Jimmitti Teysir
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | | | - Angela Lee
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Roxanne Nemati
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Sameer K Nath
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Shrikant M Mane
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Yanhong Deng
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, Connecticut
| | - Nitin Sukumar
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, Connecticut
| | - Daniel Zelterman
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Daniel J Boffa
- Department of Thoracic Surgery, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Scott N Gettinger
- Department of Medicine (Medical Oncology), Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Lynn D Wilson
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Roy S Herbst
- Department of Medicine (Medical Oncology), Yale School of Medicine, Yale University, New Haven, Connecticut
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, Yale University, New Haven, Connecticut.
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19
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Wu LR, Chen SX, Wu Y, Patel AA, Zhang DY. Publisher Correction: Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification. Nat Biomed Eng 2017; 1:1005. [DOI: 10.1038/s41551-017-0156-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Wu LR, Chen SX, Wu Y, Patel AA, Zhang DY. Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification. Nat Biomed Eng 2017; 1:714-723. [PMID: 29805844 DOI: 10.1038/s41551-017-0126-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Rare DNA-sequence variants hold important clinical and biological information, but existing detection techniques are expensive, complex, allele-specific, or don't allow for significant multiplexing. Here, we report a temperature-robust polymerase-chain-reaction method, which we term blocker displacement amplification (BDA), that selectively amplifies all sequence variants, including single-nucleotide variants (SNVs), within a roughly 20-nucleotide window by 1,000-fold over wild-type sequences. This allows for easy detection and quantitation of hundreds of potential variants originally at ≤0.1% in allele frequency. BDA is compatible with inexpensive thermocycler instrumentation and employs a rationally designed competitive hybridization reaction to achieve comparable enrichment performance across annealing temperatures ranging from 56 °C to 64 °C. To show the sequence generality of BDA, we demonstrate enrichment of 156 SNVs and the reliable detection of single-digit copies. We also show that the BDA detection of rare driver mutations in cell-free DNA samples extracted from the blood plasma of lung-cancer patients is highly consistent with deep sequencing using molecular lineage tags, with a receiver operator characteristic accuracy of 95%.
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Affiliation(s)
- Lucia R Wu
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Sherry X Chen
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Yalei Wu
- Thermo Fisher, San Francisco, CA, 94080, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA.
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21
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Arora SK, Patel AA. Effect of fiber blends, total solids, heat treatment, whey protein concentrate and stage of sugar incorporation on dietary fiber-fortified Kheer. J Food Sci Technol 2017; 54:3512-3520. [PMID: 29051646 DOI: 10.1007/s13197-017-2808-0] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Revised: 08/04/2017] [Accepted: 08/10/2017] [Indexed: 11/30/2022]
Abstract
Owing to the proven beneficial role of dietary fiber (DF) on human health, feasibility of incorporating commercially available soluble and insoluble DF preparations into rice-milk-pudding (kheer, a popular Indian delicacy) was studied through process modification. The novel approach of preparing reduced fat DF-fortified-kheer (DFFK) by developing liquid/cream phase and particulate/rice phase separately, and subsequently blending the two was developed. The major processing variables studied were total solids (TS) in the liquid phase, type of fiber blend, flavor-simulation through heat treatment or added whey protein, and the presence of sugar in water for pre-cooking of rice. Reduced fat DFFK made from three different pre-standardized fiber blends was quite acceptable to the sensory panel (overall rating 7.5). With increasing TS in milk up to 16.5%, sensory acceptability of DFFK increased. There was a small but perceivable improvement in the flavour of DFFK when precooking of rice was carried out in sweetened water. Reduced fat DFFK from different fiber blends was found to be reasonably close to conventional kheer. DFFK prepared from Blend-I provided 3.31 g dietary fiber/100 kcal (suitable for the claim "High-in-Fiber") with 38.71% Reduced-Fat. With the developed process of fortification of kheer with DF, it is possible to reduce fat (and thus calories) to cater to the needs of consumers seeking good health.
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Affiliation(s)
- Simran Kaur Arora
- Depatment of Food Science & Technology, G.B.P.U.A. & T., Pantnagar, US Nagar, India
| | - A A Patel
- National Dairy Research Institute, Karnal, India
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22
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Arora SK, Patel AA, Kumar N, Chauhan OP. Determination of relationship between sensory viscosity rating and instrumental flow behaviour of soluble dietary fibers. J Food Sci Technol 2016; 53:2067-76. [PMID: 27413236 DOI: 10.1007/s13197-016-2193-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/25/2022]
Abstract
The shear-thinning low, medium and high-viscosity fiber preparations (0.15-1.05 % psyllium husk, 0.07-0.6 % guar gum, 0.15-1.20 % gum tragacanth, 0.1-0.8 % gum karaya, 0.15-1.05 % high-viscosity Carboxy Methyl Cellulose and 0.1-0.7 % xanthan gum) showed that the consistency coefficient (k) was a function of concentration, the relationship being exponential (R(2), 0.87-0.96; P < 0.01). The flow behaviour index (n) (except for gum karaya and CMC) was exponentially related to concentration (R(2), 0.61-0.98). The relationship between k and sensory viscosity rating (SVR) was essentially linear in nearly all cases. The SVR could be predicted from the consistency coefficient using the regression equations developed. Also, the relationship of k with fiber concentration would make it possible to identify the concentration of a particular gum required to have desired consistency in terms of SVR.
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Affiliation(s)
| | - A A Patel
- National Dairy Research Institute, Karnal, India
| | | | - O P Chauhan
- Defence Food Research Laboratories, Mysore, India
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23
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Maka VV, Pancha H, Shukla SN, Talati SS, Shah PM, Patel KM, Anand AS, Shah SA, Patel AA, Parikh S. Clinical Characteristics and prognostic analysis of Triple-negative Breast Cancer: Single institute experience. Gulf J Oncolog 2016; 1:38-44. [PMID: 27050178] [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] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a poor prognostic subset of breast cancer that lacks the benefit of specific targeted therapy. MATERIALS AND METHODS A prospective study of the clinical profile of triple negative breast cancer cases at a tertiary referral centre. The duration of the study period was 26 months and the median follow up period was ten months. A total of 111 invasive breast cancer patients were evaluated from 1st August 2009 to 31st October 2011. We examined TNBC patients with respect to clinicopathological parameters, adjuvant chemotherapy regimens and relapse free survival. RESULTS In our study, patients were young (median age at presentation, 47yrs), premenopausal (54%), tumour size was discordant with lymph node positivity, the histology was predominantly intraductal carcinoma (90%), histological grade higher than two (90%). Relapses were early and preferential visceral (32%) and CNS metastasises (11.7%). 91% of patients were eligible for adjuvant therapy but only 80% of the patients could complete full course of adjuvant chemotherapy. Anthracycline-based regimens (43%), sequential anthracycline and taxane-based regimen (24%) and other regimes like CMF (13%) were used as adjuvant chemotherapy in eligible TNBC patients. Median relapse free survival in patients following adjuvant chemotherapy was around 10 months at last follow-up. CONCLUSIONS Patients with TNBC have aggressive clinicopathological characteristics with early and higher rate of disease relapse and therefore derive inadequate benefit from current adjuvant chemotherapy. So, new treatment strategies in adjuvant chemotherapy for TNBC are needed.
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Affiliation(s)
- V V Maka
- Department of Medical Oncology, Gujarat Cancer and Research Institute, Ahmedabad, Gujarat, India
| | - H Pancha
- Department of Medical Oncology, Gujarat Cancer and Research Institute, Ahmedabad, Gujarat, India
| | - S N Shukla
- Department of Medical Oncology, Gujarat Cancer and Research Institute, Ahmedabad, Gujarat, India
| | - S S Talati
- Department of Medical Oncology, Gujarat Cancer and Research Institute, Ahmedabad, Gujarat, India
| | - P M Shah
- Department of Medical Oncology, Gujarat Cancer and Research Institute, Ahmedabad, Gujarat, India
| | - K M Patel
- Department of Medical Oncology, Gujarat Cancer and Research Institute, Ahmedabad, Gujarat, India
| | - A S Anand
- Department of Medical Oncology, Gujarat Cancer and Research Institute, Ahmedabad, Gujarat, India
| | - S A Shah
- Department of Medical Oncology, Gujarat Cancer and Research Institute, Ahmedabad, Gujarat, India
| | - A A Patel
- Department of Medical Oncology, Gujarat Cancer and Research Institute, Ahmedabad, Gujarat, India
| | - S Parikh
- Department of Medical Oncology, Gujarat Cancer and Research Institute, Ahmedabad, Gujarat, India
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24
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Jha A, Patel AA, Gopal TKS, Ravishankar CN. Heat penetration characteristics and physico-chemical properties of in-pouch processed dairy dessert (kheer). J Food Sci Technol 2014; 51:2560-7. [PMID: 25328196 DOI: 10.1007/s13197-012-0750-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 05/25/2012] [Accepted: 05/29/2012] [Indexed: 11/25/2022]
Abstract
Kheer, a traditional milk product of South East Asia, containing cooked rice grains in a creamy sweetened concentrated milk, has no large-scale production due to its poor shelf life. Shelf-life was improved by development of a process based on in-pouch thermal processing employing a rotary retort. Product development included optimization of rice-to-milk solids ratio (0.18-0.52) and total milk solids levels (16-26 %) to simulate the conventional product in taste, appearance and textural attributes. Various Fo values (12.4-14.8) were examined with regard to product quality. While the TBA value tended to increase (0.073-0.081) the reflectance value (35.3-43.4) declined with increasing Fo. The pH of the product (6.04-6.10) showed a slight tendency to increase with Fo. Sensorily, the product was found to be acceptable for a period of 150 days at 37 °C.
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Affiliation(s)
- Alok Jha
- Department of A. H. & Dairying, Banaras Hindu University, Varanasi, 221 005 India
| | - A A Patel
- Dairy Technology Division, National Dairy Research Institute, Karnal, 132 001 India
| | | | - C N Ravishankar
- Central Institute of Fisheries Technology, Kochi, 682 029 India
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25
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Ponomarenko LA, Gorbachev RV, Yu GL, Elias DC, Jalil R, Patel AA, Mishchenko A, Mayorov AS, Woods CR, Wallbank JR, Mucha-Kruczynski M, Piot BA, Potemski M, Grigorieva IV, Novoselov KS, Guinea F, Fal'ko VI, Geim AK. Cloning of Dirac fermions in graphene superlattices. Nature 2013; 497:594-7. [PMID: 23676678 DOI: 10.1038/nature12187] [Citation(s) in RCA: 429] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 04/03/2013] [Indexed: 11/09/2022]
Abstract
Superlattices have attracted great interest because their use may make it possible to modify the spectra of two-dimensional electron systems and, ultimately, create materials with tailored electronic properties. In previous studies (see, for example, refs 1-8), it proved difficult to realize superlattices with short periodicities and weak disorder, and most of their observed features could be explained in terms of cyclotron orbits commensurate with the superlattice. Evidence for the formation of superlattice minibands (forming a fractal spectrum known as Hofstadter's butterfly) has been limited to the observation of new low-field oscillations and an internal structure within Landau levels. Here we report transport properties of graphene placed on a boron nitride substrate and accurately aligned along its crystallographic directions. The substrate's moiré potential acts as a superlattice and leads to profound changes in the graphene's electronic spectrum. Second-generation Dirac points appear as pronounced peaks in resistivity, accompanied by reversal of the Hall effect. The latter indicates that the effective sign of the charge carriers changes within graphene's conduction and valence bands. Strong magnetic fields lead to Zak-type cloning of the third generation of Dirac points, which are observed as numerous neutrality points in fields where a unit fraction of the flux quantum pierces the superlattice unit cell. Graphene superlattices such as this one provide a way of studying the rich physics expected in incommensurable quantum systems and illustrate the possibility of controllably modifying the electronic spectra of two-dimensional atomic crystals by varying their crystallographic alignment within van der Waals heterostuctures.
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Affiliation(s)
- L A Ponomarenko
- School of Physics and Astronomy, University of Manchester, Manchester M13 9PL, UK
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26
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Webster TJ, Patel AA, Rahaman MN, Sonny Bal B. Anti-infective and osteointegration properties of silicon nitride, poly(ether ether ketone), and titanium implants. Acta Biomater 2012; 8:4447-54. [PMID: 22863905 DOI: 10.1016/j.actbio.2012.07.038] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/19/2012] [Accepted: 07/25/2012] [Indexed: 11/17/2022]
Abstract
Silicon nitride (Si(3)N(4)) is an industrial ceramic used in spinal fusion and maxillofacial reconstruction. Maximizing bone formation and minimizing bacterial infection are desirable attributes in orthopedic implants designed to adhere to living bone. This study has compared these attributes of Si(3)N(4) implants with implants made from two other orthopedic biomaterials, i.e. poly(ether ether ketone) (PEEK) and titanium (Ti). Dense implants made of Si(3)N(4), PEEK, or Ti were surgically implanted into matching rat calvarial defects. Bacterial infection was induced with an injection of 1×10(4)Staphylococcus epidermidis. Control animals received saline only. On 3, 7, and 14days, and 3months post-surgery four rats per time period and material were killed, and calvariae were examined to quantify new bone formation and the presence or absence of bacteria. Quantitative evaluation of osteointegration to adjacent bone was done by measuring the resistance to implant push-out (n=8 rats each for Ti and PEEK, and n=16 rats for Si(3)N(4)). Three months after surgery in the absence of bacterial injection new bone formation around Si(3)N(4) was ∼69%, compared with 24% and 36% for PEEK and Ti, respectively. In the presence of bacteria new bone formation for Si(3)N(4), Ti, and PEEK was 41%, 26%, and 21%, respectively. Live bacteria were identified around PEEK (88%) and Ti (21%) implants, whereas none were present adjacent to Si(3)N(4). Push-out strength testing demonstrated statistically superior bone growth onto Si(3)N(4) compared with Ti and PEEK. Si(3)N(4) bioceramic implants demonstrated superior new bone formation and resistance to bacterial infection compared with Ti and PEEK.
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Affiliation(s)
- T J Webster
- School of Engineering and Department of Orthopaedics, Brown University, Providence, RI 02917, USA
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27
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Abstract
Study design: Retrospective clinical study of patients treated for subaxial cervical spine trauma (SCST) at a tertiary medical center. Purpose: Evaluate the validity of the Subaxial Injury Classification (SLIC) system in surgical versus non-surgical decision making for SCST. Inclusion criteria: Age >12 years, presence of SCST with complete clinical and radiological (CT and MRI) data. Exclusion criteria: Patients with incomplete radiographic or clinical data, pathological fractures, isolated upper cervical trauma (occiput to C2), isolated transverse process or spinous process fractures, chronic or age indeterminate fractures, isolate MRI findings, and severe systemic trauma with death prior to either surgical or non-surgical treatment. Results: Fourteen patients were treated non-surgically (C), whereas 24 were treated surgically (S). In the C group, the SLIC score ranged from 0 to 5 points (standard deviation [SD] = 1.20 points; mean 1.07; median 1). Just 1 patient had an SLIC score greater than 2 (7.1% of the patients). In the S group, the SLIC score ranged from 1 to 10 points (standard deviation [SD] = 2.03 points; mean 5.6; median 6). Just 2 patients had an SLIC score smaller than 4 (both with 1 point each, 8.3% of the total group). All the other 22 (accounting for 91.6%) patients had an SLIC of 4 or more points. Conclusions: Our study suggests that the SLIC classification looks to be a promising system to aid spinal surgeons in the decision-making process of subaxial cervical trauma, but a large prospective cohort study is required.
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Affiliation(s)
- A F Joaquim
- Department of Neurology, Neurosurgery Division, State University of Campinas, Campinas-SP, Brazil
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28
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Narayan A, Carriero NJ, Gettinger SN, Kluytenaar J, Kozak KR, Yock TI, Muscato NE, Ugarelli P, Decker RH, Patel AA. Ultrasensitive measurement of hotspot mutations in tumor DNA in blood using error-suppressed multiplexed deep sequencing. Cancer Res 2012; 72:3492-8. [PMID: 22581825 DOI: 10.1158/0008-5472.can-11-4037] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Detection of cell-free tumor DNA in the blood has offered promise as a cancer biomarker, but practical clinical implementations have been impeded by the lack of a sensitive and accurate method for quantitation that is also simple, inexpensive, and readily scalable. Here we present an approach that uses next-generation sequencing to quantify the small fraction of DNA molecules that contain tumor-specific mutations within a background of normal DNA in plasma. Using layers of sequence redundancy designed to distinguish true mutations from sequencer misreads and PCR misincorporations, we achieved a detection sensitivity of approximately 1 variant in 5,000 molecules. In addition, the attachment of modular barcode tags to the DNA fragments to be sequenced facilitated the simultaneous analysis of more than 100 patient samples. As proof-of-principle, we showed the successful use of this method to follow treatment-associated changes in circulating tumor DNA levels in patients with non-small cell lung cancer. Our findings suggest that the deep sequencing approach described here may be applied to the development of a practical diagnostic test that measures tumor-derived DNA levels in blood.
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Affiliation(s)
- Azeet Narayan
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut, USA
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29
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Sandrasegaran K, Patel AA, Ramaswamy R, Samuel VP, Northcutt BG, Frank MS, Francis IR. Characterization of adrenal masses with diffusion-weighted imaging. Int Braz J Urol 2011. [DOI: 10.1590/s1677-55382011000600020] [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: 11/21/2022] Open
Affiliation(s)
| | - AA Patel
- Indiana University School of Medicine
| | | | - VP Samuel
- Indiana University School of Medicine
| | | | - MS Frank
- Indiana University School of Medicine
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30
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Sandrasegaran K, Akisik FM, Patel AA, Rydberg M, Cramer HM, Agaram NP, Schmidt CM. Diffusion-weighted imaging in characterization of cystic pancreatic lesions. Clin Radiol 2011; 66:808-14. [PMID: 21601184 DOI: 10.1016/j.crad.2011.01.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 01/10/2011] [Indexed: 12/19/2022]
Abstract
AIM To evaluate whether apparent diffusion coefficient (ADC) measurements from diffusion-weighted imaging (DWI) can characterize or predict the malignant potential of cystic pancreatic lesions. MATERIALS AND METHODS Retrospective review of the magnetic resonance imaging (MRI) database over a 2-year period revealed 136 patients with cystic pancreatic lesions. Patients with DWI studies and histological confirmation of cystic mass were included. In patients with known pancreatitis, lesions with amylase content of >1000 IU/l that resolved on subsequent scans were included as pseudocysts. ADC of cystic lesions was measured by two independent reviewers. These values were then compared to categorize these lesions as benign or malignant using conventional MRI sequences. RESULTS Seventy lesions were analysed: adenocarcinoma (n=4), intraductal papillary mucinous neoplasm (IPMN; n=28), mucinous cystic neoplasm (MCN; n=9), serous cystadenoma (n=16), and pseudocysts (n=13). There was no difference between ADC values of malignant and non-malignant lesions (p=0.06), between mucinous and serous tumours (p=0.12), or between IPMN and MCN (p=0.42). ADC values for low-grade IPMN were significantly higher than those for high-grade or invasive IPMN (p=0.03). CONCLUSION ADC values may be helpful in deciding the malignant potential of IPMN. However, they are not useful in differentiating malignant from benign lesions or for characterizing cystic pancreatic lesions.
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Affiliation(s)
- K Sandrasegaran
- Department of Radiology, Indiana University School of Medicine, Indianapolis, IN, USA.
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31
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Sureshkumar KK, Patel AA, Arora S, Marcus RJ. When is it reasonable to split pediatric en bloc kidneys for transplantation into two adults? Transplant Proc 2011; 42:3521-3. [PMID: 21094808 DOI: 10.1016/j.transproceed.2010.08.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 07/09/2010] [Accepted: 08/19/2010] [Indexed: 12/14/2022]
Abstract
BACKGROUND Traditionally, kidneys from donors ≥60 years old and pediatric kidneys are considered marginal organs for transplantation. Pediatric donor kidneys are underutilized for transplantation into adult recipients due to concern for poor outcomes. METHODS Using data from the Organ Procurement and Transplant Network, we analyzed patterns of pediatric kidney use (single vs en bloc) in the United States from 1987 to 2007. Using the Cox proportional hazards model, graft outcomes of pediatric donor kidneys transplanted as single vs en bloc grafts from different donor weight groups were compared with renal transplantation from donors ≥60 years old in an attempt to define a pediatric donor weight at which kidneys can be justifiably split to expand the donor pool. RESULTS Compared with older donor kidneys, graft failure risk of pediatric single kidneys was consistently lower when the donor weight exceeded 10 kg. On the other hand, graft survival benefit for pediatric en bloc kidneys was evident starting at donor weight ≤10 kg in comparison to older donor kidneys. Pediatric en bloc kidneys performed consistently better than pediatric single kidneys for all donor weight groups. CONCLUSIONS Splitting of pediatric donor en bloc kidneys for transplantation into 2 adults when the donor weight exceeds 10 kg was associated with acceptable graft outcomes. This practice, along with increased use of small pediatric donor kidneys, may help to alleviate the waiting list burden in renal transplantation.
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Affiliation(s)
- K K Sureshkumar
- Division of Nephrology and Hypertension, Allegheny General Hospital, Pittsburgh PA 15212, USA.
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Kim TH, Zollinger L, Shi XF, Kim SE, Rose J, Patel AA, Jeong EK. Quantification of diffusivities of the human cervical spinal cord using a 2D single-shot interleaved multisection inner volume diffusion-weighted echo-planar imaging technique. AJNR Am J Neuroradiol 2010; 31:682-7. [PMID: 20019109 DOI: 10.3174/ajnr.a1881] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [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: 12/29/2022]
Abstract
BACKGROUND AND PURPOSE DTI is a highly sensitive technique, which can detect pathology not otherwise noted with conventional imaging methods. This paper provides the atlas of reliable normative in vivo DTI parameters in the cervical spinal cord and its potential applications toward quantifying pathology. MATERIALS AND METHODS In our study, we created a reference of normal diffusivities of the cervical spinal cord by using a 2D ss-IMIV-DWEPI technique from 14 healthy volunteers and compared parameters with those in 8 patients with CSM. The 2D ss-IMIV-DWEPI technique was applied in each subject to acquire diffusion-weighted images. FA, lambda( parallel), and lambda( perpendicular) were calculated. A reference of normal DTI indices from 12 regions of interest was created and compared with DTI indices of 8 patients. RESULTS A map of reference diffusivity values was obtained from healthy controls. We found statistically significant differences in diffusivities between healthy volunteers and patients with CSM with different severities of disease, by using FA, lambda( parallel), and lambda( perpendicular) values. CONCLUSIONS DTI using 2D ss-IMIV-DWPEI is sensitive to spinal cord pathology. This technique can be used to detect and quantify the degree of pathology within the cervical spinal cord from multiple disease states.
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Affiliation(s)
- T H Kim
- Department of Radiology, Utah Center for Advanced Imaging Research, University of Utah, Salt Lake City, 84108-1218, USA
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Turnbull FM, Abraira C, Anderson RJ, Byington RP, Chalmers JP, Duckworth WC, Evans GW, Gerstein HC, Holman RR, Moritz TE, Neal BC, Ninomiya T, Patel AA, Paul SK, Travert F, Woodward M. Intensive glucose control and macrovascular outcomes in type 2 diabetes. Diabetologia 2009; 52:2288-98. [PMID: 19655124 DOI: 10.1007/s00125-009-1470-0] [Citation(s) in RCA: 864] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 06/19/2009] [Indexed: 01/12/2023]
Abstract
AIMS/HYPOTHESIS Improved glucose control in type 2 diabetes is known to reduce the risk of microvascular events. There is, however, continuing uncertainty about its impact on macrovascular disease. The aim of these analyses was to generate more precise estimates of the effects of more-intensive, compared with less-intensive, glucose control on the risk of major cardiovascular events amongst patients with type 2 diabetes. METHODS A prospectively planned group-level meta-analysis in which characteristics of trials to be included, outcomes of interest, analyses and subgroup definitions were all pre-specified. RESULTS A total of 27,049 participants and 2,370 major vascular events contributed to the meta-analyses. Allocation to more-intensive, compared with less-intensive, glucose control reduced the risk of major cardiovascular events by 9% (HR 0.91, 95% CI 0.84-0.99), primarily because of a 15% reduced risk of myocardial infarction (HR 0.85, 95% CI 0.76-0.94). Mortality was not decreased, with non-significant HRs of 1.04 for all-cause mortality (95% CI 0.90-1.20) and 1.10 for cardiovascular death (95% CI 0.84-1.42). Intensively treated participants had significantly more major hypoglycaemic events (HR 2.48, 95% CI 1.91-3.21). Exploratory subgroup analyses suggested the possibility of a differential effect for major cardiovascular events in participants with and without macrovascular disease (HR 1.00, 95% CI 0.89-1.13, vs HR 0.84, 95% CI 0.74-0.94, respectively; interaction p = 0.04). CONCLUSIONS/INTERPRETATION Targeting more-intensive glucose lowering modestly reduced major macrovascular events and increased major hypoglycaemia over 4.4 years in persons with type 2 diabetes. The analyses suggest that glucose-lowering regimens should be tailored to the individual.
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Affiliation(s)
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- The George Institute for International Health, University of Sydney, Sydney, NSW 2050, Australia.
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Patel AA, Wolfgang JA, Niemierko A, Hong TS, Yock T, Choi NC. Implications of Respiratory Motion as Measured by Four-Dimensional Computed Tomography for Radiation Treatment Planning of Esophageal Cancer. Int J Radiat Oncol Biol Phys 2009; 74:290-6. [DOI: 10.1016/j.ijrobp.2008.12.060] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 12/14/2008] [Accepted: 12/15/2008] [Indexed: 11/29/2022]
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35
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Talati R, Baker WL, Patel AA, Reinhart K, Coleman CI. Adding a dopamine agonist to preexisting levodopa therapy vs. levodopa therapy alone in advanced Parkinson's disease: a meta analysis. Int J Clin Pract 2009; 63:613-23. [PMID: 19222614 DOI: 10.1111/j.1742-1241.2009.02027.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [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: 11/29/2022] Open
Abstract
BACKGROUND To perform a meta analysis of randomised placebo-controlled trials evaluating the use of dopamine agonist (DA) or placebo to preexisting levodopa therapy for the treatment of advanced Parkinson's disease (PD). We focused on clinically important efficacy [Unified Parkinson's Disease Rating Scale (UPDRS) activities of daily living (ADL) and motor scores as well as change in 'off' time and levodopa dose] and safety outcomes (withdrawal because of adverse drug events (ADEs), dyskinesias, hallucinations and mortality). METHODS A systematic literature search was performed between January 1990 and July 2007. The primary outcome measures assessed were the reduction in scores of Unified Parkinson's Disease Rating Scale (UPDRS) activities of daily living (ADL) and motor scores as well as reduction in 'off' time and reductions in levodopa dose from baseline. Safety end-points were also evaluated. RESULTS A total of 15 trials (n = 4380 subjects) were included in the meta analysis. Adjunctive DA use resulted in greater improvement as measured by the UPDRS ADL [weighted mean difference (WMD) -2.20, 95% confidence interval (CI) -2.64 to -1.76; p < 0.0001] and motor score reduction (WMD -5.56, 95% CI -6.82 to -4.31; p < 0.0001) as well as reduction in 'off' time measured in hours/day (WMD -1.20, 95% CI -1.78 to -0.62; p < 0.0001) and reduction in levodopa dose (WMD -128.5 mg, 95% CI -175.0 to -82.1; p < 0.0001) vs. placebo. Incidence of dyskinesia and hallucinations was higher with DAs [odds ratio (OR) 3.27, 95% CI 2.65-4.03; p < 0.0001] and (OR 3.34, 95% CI 2.44-4.58; p < 0.0001). Non-ergot DAs were qualitatively better, although both ergot and non-ergot DAs showed statistically significant improvements in all UPDRS scores. CONCLUSION Adjunctive DA use to levodopa is superior to levodopa alone in reducing PD symptoms in patients not controlled with monotherapy. DAs seem especially useful amongst PD patients with wearing-off phenomenon from levodopa therapy, but can cause some adverse events.
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Affiliation(s)
- R Talati
- University of Connecticut School of Pharmacy, Storrs, CT, USA
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Torres K, Patel AA, Styliński K, Błoński M, Torres A, Staśkiewicz G, Maciejewski R, Wojtaszek M. The body constitution of patients and intubation scales as predictors of difficult intubation considered in relation to the experience of the intubator. Folia Morphol (Warsz) 2008; 67:171-174. [PMID: 18828097] [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: 05/26/2023]
Abstract
The aims of the study were to identify factors that may result in difficulties in intubation, and to compare the results obtained when an experienced and when a less experienced anaesthesiologist was involved. The 96 patients included in the study were evaluated for difficult intubation according to the following scales: Mallampati, upper lip bite test (ULBT) and Patil. The mobility of the cervical segments of the vertebral column, the distance between the jugular notch of the sternum and the chin and the anatomical constitution of the body were other factors that were taken into consideration. Statistical analysis was performed in order to identify factors that may result in difficulties in intubation for an experienced and for a less experienced anaesthesiologist.
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Affiliation(s)
- K Torres
- Department of Human Anatomy, Medical University, Lublin, Poland.
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Perkovic V, Cass A, Patel AA, Suriyawongpaisal P, Barzi F, Chadban S, Macmahon S, Neal B. High prevalence of chronic kidney disease in Thailand. Kidney Int 2007; 73:473-9. [PMID: 18059458 DOI: 10.1038/sj.ki.5002701] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe the prevalence of stage III and IV chronic kidney disease in Thailand from a representative sample of individuals aged 35 years and above using a stratified, multistage, cluster-sampling method. Population estimates were calculated by applying sampling weights from the 2000 Thai census. Glomerular filtration rates were estimated from serum creatinine using the Cockroft-Gault and the simplified Modification of Diet in Renal Disease (MDRD) formulae. The prevalence of stage III disease among individuals aged 35 years and above was estimated to be about 20% using the Cockroft-Gault formula and about 13% from the MDRD formula. Stage IV disease was present in about 0.9 and 0.6% of this population using the respective formulae. The highest prevalence rates were observed in less well-developed rural areas and the lowest in developed urban areas. The prevalence of chronic kidney disease was significantly higher than that reported in individuals over 40 years old from the United States for both stage III and IV disease and higher than the reported incidence in Taiwan and Australia. This high prevalence of chronic kidney disease in Thailand has obvious implications for the health of its citizens and for the allocation of health-care resources.
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Affiliation(s)
- V Perkovic
- George Institute for International Health, University of Sydney, Sydney, New South Wales, Australia.
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Abstract
CONTEXT In 2005, the International Society of Urologic Pathology consensus conference recommended that men with biopsy Gleason score 3 + 4 or 4 + 3 prostate cancer and tertiary pattern 5 should have their cancer classified as Gleason score 8 or 9, respectively. Yet, the management of men with Gleason score 7 vs 8 or 9 prostate cancer differs. OBJECTIVE To compare the prognostic significance of Gleason score 7 with tertiary grade 5 vs other Gleason scores with respect to time to prostate-specific antigen (PSA) failure in men with prostate cancer. DESIGN, SETTING, AND PATIENTS From 1989 to 2005, 2370 men with clinical tumor category 1c to 3b, node-negative, and nonmetastatic prostate cancer underwent definitive therapy with surgery or radiation therapy with or without hormonal therapy. A pathologist with expertise in genitourinary cancers assigned Gleason scores to the prostate needle biopsy specimens. Cox regression was used to assess whether a significant association existed between the presence of tertiary grade 5 in men with Gleason score 7 disease and time to recurrence compared with men with Gleason score 7 without tertiary grade 5, Gleason score 5 to 6, or 8 to 10 disease, adjusting for known prognostic factors and treatment. MAIN OUTCOME MEASURE Time to PSA failure. RESULTS Men with Gleason score 7 and tertiary grade 5 disease had a significantly shorter time to PSA failure than men with 7 without tertiary grade 5 (median time, 5.0 vs 6.7 years, respectively; adjusted hazard ratio (HR), 0.56; 95% confidence interval [CI], 0.32-0.97; P = .04) or score of 6 or less (median time, 15.4 years; adjusted HR, 0.24; 95% CI, 0.13-0.43; P < .001). However, a significant difference was not observed when these men were compared with men with Gleason score 8 to 10 disease (median time, 5.1 years; adjusted HR, 0.96; 95% CI, 0.54-1.71; P = .90). CONCLUSION In this study population, men with prostate cancer having biopsy Gleason score 7 and tertiary grade 5 had a higher risk of PSA-failure when compared with men with Gleason score 7 without tertiary grade 5 and had a comparable risk with men with Gleason score 8 to 10.
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Affiliation(s)
- Abhijit A Patel
- Department of Radiation Oncology, Brigham and Women's Hospital and Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA.
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Abstract
OBJECTIVE Family and personal history of colorectal cancer and associated tumours are crucial in identifying families with hereditary nonpolyposis colorectal cancer (HNPCC). The aim of this study was to determine the adequacy of these aspects of history-taking in the management of colorectal cancer patients. PATIENTS AND METHODS Colorectal cancer patients attending outpatient follow-up were interviewed to obtain a detailed family and personal history of cancers. The medical notes were then reviewed to identify whether these had been documented previously. RESULTS One hundred and one patients took part. In seven, no family history had been recorded; none of these actually had a significant pedigree. In 88, the family history was not significant, a finding correctly documented in the records. Three had a high-risk family history and another three had a personal history of other possible HNPCC-related cancers. In each of these patients, the relevant findings had been documented, but no further action had been taken. CONCLUSIONS Family history was taken in the majority of patients, but in the only three with a pedigree indicative of HNPCC, its significance was not appreciated. The potential relevance of multiple HNPCC-related cancers in the same individual was also overlooked. Improved education and referral pathways are needed to ensure that families with HNPCC have access to appropriate surveillance and genetic testing.
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Affiliation(s)
- V O Alberto
- Centre for Academic Surgery, Barts and the London, Queen Mary's School of Medicine and Dentistry, London University, London, UK
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Flampouri S, Jiang SB, Sharp GC, Wolfgang J, Patel AA, Choi NC. Estimation of the delivered patient dose in lung IMRT treatment based on deformable registration of 4D-CT data and Monte Carlo simulations. Phys Med Biol 2006; 51:2763-79. [PMID: 16723765 DOI: 10.1088/0031-9155/51/11/006] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [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: 11/11/2022]
Abstract
The purpose of this study is to accurately estimate the difference between the planned and the delivered dose due to respiratory motion and free breathing helical CT artefacts for lung IMRT treatments, and to estimate the impact of this difference on clinical outcome. Six patients with representative tumour motion, size and position were selected for this retrospective study. For each patient, we had acquired both a free breathing helical CT and a ten-phase 4D-CT scan. A commercial treatment planning system was used to create four IMRT plans for each patient. The first two plans were based on the GTV as contoured on the free breathing helical CT set, with a GTV to PTV expansion of 1.5 cm and 2.0 cm, respectively. The third plan was based on the ITV, a composite volume formed by the union of the CTV volumes contoured on free breathing helical CT, end-of-inhale (EOI) and end-of-exhale (EOE) 4D-CT. The fourth plan was based on GTV contoured on the EOE 4D-CT. The prescribed dose was 60 Gy for all four plans. Fluence maps and beam setup parameters of the IMRT plans were used by the Monte Carlo dose calculation engine MCSIM for absolute dose calculation on both the free breathing CT and 4D-CT data. CT deformable registration between the breathing phases was performed to estimate the motion trajectory for both the tumour and healthy tissue. Then, a composite dose distribution over the whole breathing cycle was calculated as a final estimate of the delivered dose. EUD values were computed on the basis of the composite dose for all four plans. For the patient with the largest motion effect, the difference in the EUD of CTV between the planed and the delivered doses was 33, 11, 1 and 0 Gy for the first, second, third and fourth plan, respectively. The number of breathing phases required for accurate dose prediction was also investigated. With the advent of 4D-CT, deformable registration and Monte Carlo simulations, it is feasible to perform an accurate calculation of the delivered dose, and compare our delivered dose with doses estimated using prior techniques.
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Affiliation(s)
- Stella Flampouri
- Department of Radiation Oncology, Massachusetts General Hospital, and Harvard Medical School, Boston, MA 02114, USA.
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Affiliation(s)
- Abhijit A Patel
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, Connecticut 06536, USA
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Abstract
Some protein-coding genes in metazoan genomes contain a minor class of introns that are excised by a distinct, low-abundance spliceosome. We have developed a quantitative RT-PCR assay that allows comparison of the relative rates of intron removal from the transcripts present in a pre-mRNA population. We show that the U12-type introns are more slowly spliced than the major-class (U2-type) introns from three endogenous pre-mRNAs in human tissue culture cells. In Drosophila melanogaster S2 cells, using minigene constructs designed to produce nearly identical mRNAs, we observe increased expression of fluorescent protein and mature mRNA upon mutation of a U12-type to a U2-type intron. These results provide evidence that the level of gene expression in vivo is lowered by the presence of a U12-type intron and implicate the U12-type spliceosome as a target in the post-transcriptional regulation of gene expression.
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Affiliation(s)
| | | | - Joan A. Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
Corresponding author e-mail:
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Abstract
A hybrid cellular automaton model is described and used to simulate early tumor growth and examine the roles of host tissue vascular density and tumor metabolism in the ability of a small number of monoclonal transformed cells to develop into an invasive tumor. The model incorporates normal cells, tumor cells, necrotic or empty space, and a random network of native microvessels as components of a cellular automaton state vector. Diffusion of glucose and H(+)ions (the latter largely resulting from the tumor's excessive reliance on anaerobic metabolism) to and from the microvessels, and their utilization or production by cells, is modeled through the solution of differential equations. In this way, the cells and microvessels affect the extracellular concentrations of glucose and H(+)which, in turn, affect the evolution of the automaton. Simulations of the model demonstrate that: (i) high tumor H(+)ion production is favorable for tumor growth and invasion; however for every H(+)ion production rate, there exists a range of optimal microvessel densities (leading to a local pH favorable to tumor but not to normal cells) for which growth and invasion is most effective, (ii) at vascular densities below this range, both tumor and normal cells die due to excessively low pH, (iii) for vascular densities above the optimal range the microvessel network is highly efficient at removing acid and therefore the tumor cells lose their advantage over normal cells gained by high local H(+)concentration. While significant spatial gradients of glucose formed, no regions of detrimentally poor glucose perfusion (for either cell type) were observed, regardless of microvessel density. Depending on metabolic phenotype, a variety of tumor morphologies similar to those clinically observed were realized in the simulations. Lastly, a sharp transition (analogous to that of the adenoma-carcinoma sequence) between states of initial tumor confinement and efficient invasiveness was observed when H(+)production reached a critical value.
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Affiliation(s)
- A A Patel
- Department of Interventional Radiology, M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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Nathan JD, Patel AA, McVey DC, Thomas JE, Prpic V, Vigna SR, Liddle RA. Capsaicin vanilloid receptor-1 mediates substance P release in experimental pancreatitis. Am J Physiol Gastrointest Liver Physiol 2001; 281:G1322-8. [PMID: 11668042 DOI: 10.1152/ajpgi.2001.281.5.g1322] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [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: 01/31/2023]
Abstract
We examined whether the capsaicin vanilloid receptor-1 (VR1) mediates substance P (SP) release from primary sensory neurons in experimental pancreatitis. Pancreatitis was achieved by 12 hourly injections of caerulein (50 microg/kg ip) in mice. One group received capsazepine (100 micromol/kg sc), a competitive VR1 antagonist, at 4-h intervals. Neurokinin-1 receptor (NK1R) internalization in acinar cells, used as an index of endogenous SP release, was assessed by immunocytochemical quantification of NK1R endocytosis. The severity of pancreatitis was assessed by measurements of serum amylase, pancreatic myeloperoxidase (MPO) activity, and histological grading. Caerulein administration caused significant elevations in serum amylase and pancreatic MPO activity, produced histological evidence of pancreatitis, and caused a dramatic increase in NK1R endocytosis. Capsazepine treatment significantly reduced the level of NK1R endocytosis, and this was associated with similar reductions in pancreatic MPO activity and histological severity of pancreatitis. These results demonstrate that repeated caerulein stimulation causes experimental pancreatitis that is mediated in part by stimulation of VR1 on primary sensory neurons, resulting in endogenous SP release.
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Affiliation(s)
- J D Nathan
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
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Patel AA, Hatle L, Mimish L. Pulmonary stenosis and severe biventricular dysfunction: improvement following percutaneous valvuloplasty. J Heart Valve Dis 1999; 8:307-11. [PMID: 10399667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
A 15-year-old boy with severe pulmonary stenosis associated with severe right and left ventricular systolic dysfunction is reported. After successful percutaneous pulmonary valvuloplasty, there was an initial and early improvement in right ventricular (RV) function, followed by a delayed and more gradual improvement in left ventricular (LV) function. At long-term follow up, both RV and LV systolic functions were nearly normalized. Several mechanisms may be implicated, including ventricular interdependence, geometric factors, altered compliance and intrinsic alteration in the LV muscle. A delayed, but sustained, improvement in LV systolic function following relief of RV pressure overload suggests that the latter mechanism must have played an important role in the genesis of the LV dysfunction. Pulmonary stenosis associated with severe biventricular dysfunction may be treated primarily by percutaneous pulmonary balloon valvuloplasty with near-total recovery of the ventricular function.
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Affiliation(s)
- A A Patel
- King Faisal Specialist Hospital and Research Center, Department of Cardiovascular Diseases, Riyadh, Saudi Arabia
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Abstract
Infection with the human immunodeficiency virus (HIV) is increasing in prevalence, and disease patterns are changing as patient survival lengthens. The purpose of this cross-sectional epidemiological study was to assess the prevalence and severity of self-reported symptoms of otolaryngologic disease in a group of patients attending a general HIV outpatient clinic (n = 203), and to compare the prevalence of self-reported symptoms with a sample of patients without HIV infection (n = 100). Of the HIV-infected patients, 65% of patients had AIDS, 35% were HIV-positive, and the median CD4 count was 135. Although only 11% of patients had seen an otolaryngologist in the prior 6 months, the majority of patients (66%) reported the presence of sinonasal disease during that time. Allergic rhinitis (80%) and sinusitis (54%) were the most commonly reported sinonasal symptoms, and 44% regularly used nasal or sinus medications. Sinonasal disease severity was significantly higher than the self-reported severity of mouth/throat disease (p = 0.01), ear disease (p = 0.03), and neck/salivary disease (p = 0.01). Although patients' self-reported overall health status was associated (p = 0.02) with CD4 count, the severity of sinonasal symptoms was not associated (p = 0.93) with CD4 count. Similarly, sinonasal symptom severity did not differ between HIV-positive and AIDS patients (p = 0.45). In other words, sinonasal disease severity did not improve as general health status improved.
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Affiliation(s)
- J P Porter
- Bobby R. Alford Department of Otorhinolaryngology and Communicative Sciences, Baylor College of Medicine, Houston, Texas 77030, USA
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Oghalai JS, Patel AA, Nakagawa T, Brownell WE. Fluorescence-imaged microdeformation of the outer hair cell lateral wall. J Neurosci 1998; 18:48-58. [PMID: 9412485 PMCID: PMC6793406] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Outer hair cell (OHC) electromotility appears to be central to mammalian hearing and originates within its lateral wall. The OHC lateral wall is a unique trilaminate structure consisting of the plasma membrane (PM), the cortical lattice (CL), and the subsurface cisternae (SSC). We selectively labeled and imaged the lateral wall components in the isolated guinea pig OHC under confocal microscopy. The PM was labeled with a voltage-sensitive dye, di-8-ANEPPS; the SSC was labeled with the sphingomyelin precursor, NBD-C6-ceramide; and F-actin in the CL was labeled with conjugates of phalloidin. Interactions among the three layers were evaluated with the micropipette aspiration technique. The PM was tethered to the CL and SSC until, at a critical deformation pressure, the PM separated, allowing visualization of the extracisternal space, and ultimately formed a vesicle. After detaching, the stiffness parameter of the PM was 22% of that of the intact lateral wall. We conclude that the lateral wall PM is more compliant than the CL/SSC complex. The data clarify the structural basis for electromotile force coupling in the OHC lateral wall.
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Affiliation(s)
- J S Oghalai
- Bobby R. Alford Department of Otorhinolaryngology and Communicative Sciences, Baylor College of Medicine, Houston, Texas 77030, USA
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Ross CN, Gaskin G, Gregor-Macgregor S, Patel AA, Davey NJ, Lechler RI, Williams G, Rees AJ, Pusey CD. Renal transplantation following immunoadsorption in highly sensitized recipients. Transplantation 1993; 55:785-9. [PMID: 8475552 DOI: 10.1097/00007890-199304000-00019] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.9] [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: 01/31/2023]
Abstract
Five highly sensitized patients, with panel reactivity greater than 80% for 1.75-5 years, were treated by extracorporeal staphylococcal protein-A immunoadsorption, prednisolone, and cyclophosphamide. The five patients underwent treatment of 18-40 (mean 31) liters of plasma, respectively in 4-7 (mean 5.6) sessions. This reduced the titer of cytotoxic antibodies to sensitizing antigens to < 1/8 in all cases and abolished reactivity to crossreacting antigens. Two patients required retreatment following resynthesis of cytotoxic antibodies. All five patients have been transplanted, and four of these now have stable serum creatinines of 168 mumol/L at 34 months, 208 mumol/L at 29 months, 96 mumol/L at 5 months, and 125 mumol/L at 3 months posttransplantation. One patient had primary graft dysfunction due to acute tubular necrosis; the kidney was removed after eight weeks and showed cortical necrosis without evidence of acute rejection.
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Affiliation(s)
- C N Ross
- Department of Medicine, Royal Postgraduate Medical School, Hammersmith Hospital, London, England
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Abstract
The Chernobyl nuclear reactor accident in Russia in 1986 has further revealed the susceptibility of the environment to radioactive contamination. This can have serious implications for the safety of milk as well as other foods. Global fallout and other isotope releases can threaten to increase the radionuclide levels in milk alarmingly, and thus make it unfit for human consumption. Perception of such fears in the past resulted in considerable research efforts being directed towards radioactive decontamination of milk by different means. The holding of milk and milk products long enough to deactivate certain radioisotopes prior to consumption, conversion of milk into butter, and manufacturing cheese by using modified processes are some of the approaches in minimizing the radioactivity risk to consumers. Extensive studies carried out in the USA have shown that though somewhat expensive, ion-exchange treatment of milk in large-scale, automated plants can eliminate 90% or more of the radionuclides of concern, i.e. strontium-90, and iodine-131, and much of caesium-137. Various factors affecting the efficiency of the ion exchange process and properties of the treated milk are reviewed. Other processing techniques such as electrodialysis are also briefly discussed in relation to removal of radionuclides from milk.
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Affiliation(s)
- A A Patel
- Institut für Lebensmittelverfahrenstechnik, Technische Universität München, Germany
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