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Makepeace KA, Rookyard AW, Das L, Vardarajan BN, Chakrabarty JK, Jain A, Kang MS, Werth EG, Reyes-Dumeyer D, Zerlin-Esteves M, Honig LS, Mayeux R, Brown LM. Data-Independent Acquisition and Label-Free Quantification for Quantitative Proteomics Analysis of Human Cerebrospinal Fluid. Curr Protoc 2024; 4:e1014. [PMID: 38506436 PMCID: PMC11032743 DOI: 10.1002/cpz1.1014] [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] [Indexed: 03/21/2024]
Abstract
This article presents a practical guide to mass spectrometry-based data-independent acquisition and label-free quantification for proteomics analysis applied to cerebrospinal fluid, offering a robust and scalable approach to probing the proteomic composition of the central nervous system. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Cerebrospinal fluid sample collection and preparation for mass spectrometry analysis Basic Protocol 2: Mass spectrometry sample analysis with data-independent acquisition Support Protocol: Data-dependent mass spectrometry and spectral library construction Basic Protocol 3: Analysis of mass spectrometry data.
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Affiliation(s)
- Karl A.T. Makepeace
- Department of Biological Sciences, Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY, USA
| | - Alexander W. Rookyard
- Department of Biological Sciences, Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY, USA
| | - Lipi Das
- Department of Biological Sciences, Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY, USA
| | - Badri N. Vardarajan
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jayanta K. Chakrabarty
- Department of Biological Sciences, Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY, USA
| | - Anu Jain
- Department of Biological Sciences, Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY, USA
| | - Min Suk Kang
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Emily G. Werth
- Department of Biological Sciences, Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY, USA
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Marielba Zerlin-Esteves
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lawrence S. Honig
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lewis M. Brown
- Department of Biological Sciences, Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY, USA
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Leung JM, Rojas JC, Sands LP, Chan B, Rajbanshi B, Du Z, Du P. Plasma SOMAmer proteomics of postoperative delirium. Brain Behav 2024; 14:e3422. [PMID: 38346717 PMCID: PMC10861352 DOI: 10.1002/brb3.3422] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Postoperative delirium is prevalent in older adults and has been shown to increase the risk of long-term cognitive decline. Plasma biomarkers to identify the risk for postoperative delirium and the risk of Alzheimer's disease and related dementias are needed. METHODS This biomarker discovery case-control study aimed to identify plasma biomarkers associated with postoperative delirium. Patients aged ≥65 years undergoing major elective noncardiac surgery were recruited. The preoperative plasma proteome was interrogated with SOMAmer-based technology targeting 1433 biomarkers. RESULTS In 40 patients (20 with vs. 20 without postoperative delirium), a preoperative panel of 12 biomarkers discriminated patients with postoperative delirium with an accuracy of 97.5%. The final model of five biomarkers delivered a leave-one-out cross-validation accuracy of 80%. Represented biological pathways included lysosomal and immune response functions. CONCLUSION In older patients who have undergone major surgery, plasma SOMAmer proteomics may provide a relatively non-invasive benchmark to identify biomarkers associated with postoperative delirium.
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Affiliation(s)
- Jacqueline M. Leung
- Department of Anesthesia and Perioperative CareUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Julio C. Rojas
- Memory and Aging Center, Department of Neurology, Weill Institute for NeurosciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Laura P. Sands
- Virginia Tech, Center for GerontologyBlacksburgVirginiaUSA
| | - Brandon Chan
- Memory and Aging Center, Department of Neurology, Weill Institute for NeurosciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Binita Rajbanshi
- Memory and Aging Center, Department of Neurology, Weill Institute for NeurosciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Zhiyuan Du
- Virginia Tech, Department of StatisticsBlacksburgVirginiaUSA
| | - Pang Du
- Virginia Tech, Department of StatisticsBlacksburgVirginiaUSA
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Behera RN, Bisht VS, Giri K, Ambatipudi K. Realm of proteomics in breast cancer management and drug repurposing to alleviate intricacies of treatment. Proteomics Clin Appl 2023; 17:e2300016. [PMID: 37259687 DOI: 10.1002/prca.202300016] [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: 02/16/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
Breast cancer, a multi-networking heterogeneous disease, has emerged as a serious impediment to progress in clinical oncology. Although technological advancements and emerging cancer research studies have mitigated breast cancer lethality, a precision cancer-oriented solution has not been achieved. Thus, this review will persuade the acquiescence of proteomics-based diagnostic and therapeutic options in breast cancer management. Recently, the evidence of breast cancer health surveillance through imaging proteomics, single-cell proteomics, interactomics, and post-translational modification (PTM) tracking, to construct proteome maps and proteotyping for stage-specific and sample-specific cancer subtyping have outperformed conventional ways of dealing with breast cancer by increasing diagnostic efficiency, prognostic value, and predictive response. Additionally, the paradigm shift in applied proteomics for designing a chemotherapy regimen to identify novel drug targets with minor adverse effects has been elaborated. Finally, the potential of proteomics in alleviating the occurrence of chemoresistance and enhancing reprofiled drugs' effectiveness to combat therapeutic obstacles has been discussed. Owing to the enormous potential of proteomics techniques, the clinical recognition of proteomics in breast cancer management can be achievable and therapeutic intricacies can be surmountable.
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Affiliation(s)
- Rama N Behera
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Vinod S Bisht
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kuldeep Giri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kiran Ambatipudi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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Domingo G, Vannini C, Bracale M, Bonfante P. Proteomics as a tool to decipher plant responses in arbuscular mycorrhizal interactions: a meta-analysis. Proteomics 2023; 23:e2200108. [PMID: 36571480 DOI: 10.1002/pmic.202200108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/09/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
The beneficial symbiosis between plants and arbuscular mycorrhizal (AM) fungi leads to a deep reprogramming of plant metabolism, involving the regulation of several molecular mechanisms, many of which are poorly characterized. In this regard, proteomics is a powerful tool to explore changes related to plant-microbe interactions. This study provides a comprehensive proteomic meta-analysis conducted on AM-modulated proteins at local (roots) and systemic (shoots/leaves) level. The analysis was implemented by an in-depth study of root membrane-associated proteins and by a comparison with a transcriptome meta-analysis. A total of 4262 differentially abundant proteins were retrieved and, to identify the most relevant AM-regulated processes, a range of bioinformatic studies were conducted, including functional enrichment and protein-protein interaction network analysis. In addition to several protein transporters which are present in higher amounts in AM plants, and which are expected due to the well-known enhancement of AM-induced mineral uptake, our analysis revealed some novel traits. We detected a massive systemic reprogramming of translation with a central role played by the ribosomal translational apparatus. On one hand, these new protein-synthesis efforts well support the root cellular re-organization required by the fungal penetration, and on the other they have a systemic impact on primary metabolism.
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Affiliation(s)
- Guido Domingo
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | - Candida Vannini
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | - Marcella Bracale
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
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Ning T, Ning C, Li S, Mo C, Liu Z, Wang H. Integrative proteomics and phosphoproteomics profiling on osteogenic differentiation of periodontal ligament stem cell. Proteomics 2022; 22:e2200067. [PMID: 36044325 DOI: 10.1002/pmic.202200067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 12/29/2022]
Abstract
This study aims to elucidate the phosphorylated profile of periodontal ligament stem cells (PDLSCs) osteogenic differentiation, which contributes to the promotion of periodontium regeneration. PDLSCs cultured in the osteogenic induction medium for 14 days were analyzed by proteomics and phosphoproteomics. Potential functions of phosphorylated differentially expressed proteins (DEPs) were annotated and enriched based on Gene Ontology (GO). Furtherly, overlapped DEPs were identified and conducted protein-protein interaction (PPI) network united with the top 20 up/downregulated phosphorylated DEPs. Hub phosphorylated DEPs were analyzed by Cytoscape, and the protein kinase phosphorylation network was predicted by iGPS. Proteomics identified 87 upregulated and 227 downregulated DEPs. Phosphoproteomics identified 460 upregulated and 393 downregulated phosphorylated DEPs, and they were primarily enriched in mitochondrial function and ion-channel related terms. Furthermore, 63 overlapped DEPs were recognized for more accurate predictions. Among the top 10 hub phosphorylated DEPs, only Integrin alpha-5 (ITGA5) expressed upregulated phosphorylation, and half of them belonged to extracellular matrix (ECM) proteins. In addition, numerous kinases corresponding to four interactive hub phosphorylated DEPs were predicted, including Collagen alpha-2(I) (COL1A2), Syndecan-1 (SDC1), Fibrillin-1 (FBN1), and ITGA5. Our findings established a basis for further elucidation of the phosphorylation of PDLSCs osteogenic differentiation, and COL1A2/SDC1/ITGA5/FBN1 phosphorylated network may dominate this process.
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Affiliation(s)
- Tingting Ning
- Department of Endodontics and Operative Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Caiyu Ning
- Forestry and Landscape Architecture College, South China Agricultural University, Guangzhou, Guangdong, China
| | - Siwei Li
- Department of Endodontics and Operative Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Chuzi Mo
- Department of Endodontics and Operative Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Zhao Liu
- Department of Endodontics and Operative Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - He Wang
- Department of Endodontics and Operative Dentistry, Stomatological Hospital, Southern Medical University, Guangzhou, China
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Li YJ, Ma JN, Wang ZQ, Yang EP, Wang MJ, Ming J, Wang DH, Niu JC, Liu WY, Hu XM. [Analysis of Differential Proteins Related to Platelet Activation in Patients with Essential Thrombocythemia Based on Label-Free Quantitative Technology]. Zhongguo Shi Yan Xue Ye Xue Za Zhi 2022; 30:836-843. [PMID: 35680814 DOI: 10.19746/j.cnki.issn.1009-2137.2022.03.028] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To analysis the specific protein markers of essential thrombocythemia (ET) based on proteomics technology, to explore and verify the differential protein related to platelet activation. METHODS Blood samples were obtained from ET patients and healthy people and a certain protein mass spectrometry was detected using label-free quantitative technology. The proteins relative abundance increased or down-regulated by 1.3 times in the disease group compared with the control group, and the protein abundance in the two groups t test P<0.05 were defined as differential proteins. Bioinformatics analysis of the differential proteins was performed using GO and KEGG. The difference in the average protein abundance between the two groups was analyzed by t test and P<0.05 was considered statistically significant. Differential proteins were selected for verification by parallel reaction monitoring (PRM) technology. RESULTS A total of 140 differential proteins were found, of which 72 were up-regulated and 68 were down-regulated. KEGG enrichment showed that the differential protein expression was related to the platelet activation pathway. The differential proteins related to platelet activation were GPV, COL1A2, GP1bα, COL1A1 and GPVI. Among them, the expressions of GPV, GP1bα and GPVI were up-regulated, and the expressions of COL1A2 and COL1A1 were down-regulated. PRM verification of COL1A1, GP1bα, GPVI and GPV was consistent with LFP proteomics testing. CONCLUSION Differential proteins in ET patients are related to platelet activation pathway activation.Differential proteins such as GPV, GPVI, COL1A1 and GP1bα can be used as new targets related to ET platelet activation.
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Affiliation(s)
- Yu-Jin Li
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Ju-Ning Ma
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Zi-Qin Wang
- Graduate School, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Er-Peng Yang
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Ming-Jing Wang
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Jing Ming
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - De-Hao Wang
- Graduate School, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ji-Cong Niu
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Wei-Yi Liu
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China,E-mail:
| | - Xiao-Mei Hu
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China,E-mail:
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Li XF, Zhang Y, Pu F, Song YW, Wang DQ. [Sequencing and Proteomic Analysis of Exosomes from Apheresis Platelets in Different Storage Periods]. Zhongguo Shi Yan Xue Ye Xue Za Zhi 2022; 30:583-592. [PMID: 35396001 DOI: 10.19746/j.cnki.issn.1009-2137.2022.02.044] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To investigate the changes of gene sequencing and proteomics of apheresis platelet (AP) exosomes in different storage periods and predict the function of AP exosomes in different storage periods. METHODS Platelets at different storage periods of 0 day (D0), 3 day (D3) and 5 day (D5) were collected, exosomes were extracted with Gradient centrifugation; gene sequencing and proteomic analysis were used to analyze the exosomes, and biological functions of platelet exosomes were analyzed and predicted by bioinformatics. Liquid mass spectrometry (LMS) was used to detect the changes and function prediction of exosomes proteins. The small RNA sequencing library was prepared, and the constructed library was sequenced and bioinformatics technology was used for data analysis. RESULTS AP exosome iTRAQ protein analysis showed that AP exosomes stored in D3 with 55 up-regulated proteins and 94 down-regulated proteins (P<0.05, FC<0.83 or FC>1.2), while AP exosomes stored in D5 with 292 up-regulated proteins and 53 down-regulated proteins (P<0.05, FC<0.83 or FC>1.2) as compared with D0. KEGG pathway analysis showed that the proteins were mainly involved in transport and metabolism, immune system, cancer, membrane transport and other processes. There were statistically significant differences between AP exosome miRNAs in different storage days (P<0.01). The number of miRNA up-regulated and down-regulated was 374 and 255 as compared with the number of platelet exosomes miRNA stored in D3 and D0, while that was 297 and 242 in D5 and D0, and 252 and 327 in D5 and D3, respectively. The target genes of differential platelet exosome miRNAs were analyzed by GO enrichment. Target genes of differential miRNA were mainly involved in membrane composition, mainly played molecular functions binding to proteins, and participated in biological processes of transcriptional regulation. CONCLUSION The exosome differential proteins and miRNAs in D5 are significantly different from those in the D0 of APs, and they are involved in various biological processes.
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Affiliation(s)
- Xiao-Fei Li
- Department of Transfusion,Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China;Department of Blood Transfusion, The Chinese PLA General Hospital First Medical Center, Beijing 100853, China
| | - Yuan Zhang
- Department of Blood Transfusion, The Chinese PLA General Hospital First Medical Center, Beijing 100853, China
| | - Fei Pu
- Department of Blood Transfusion, The Chinese PLA General Hospital First Medical Center, Beijing 100853, China
| | - Ying-Wei Song
- Department of Blood Transfusion, The Chinese PLA General Hospital First Medical Center, Beijing 100853, China
| | - De-Qing Wang
- Department of Blood Transfusion, The Chinese PLA General Hospital First Medical Center, Beijing 100853, China,E-mail:
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Singh V, Tripathi A, Dutta R. Proteomic Approaches to Decipher Mechanisms Underlying Pathogenesis in Multiple Sclerosis Patients. Proteomics 2019; 19:e1800335. [PMID: 31119864 PMCID: PMC6690771 DOI: 10.1002/pmic.201800335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 05/15/2019] [Indexed: 12/13/2022]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory demyelinating and neurodegenerative disease of the central nervous system (CNS). The cause of MS is unknown, with no effective therapies available to halt the progressive neurological disability. Development of new and improvement of existing therapeutic strategies therefore require a better understanding of MS pathogenesis, especially during the progressive phase of the disease. This can be achieved through development of biomarkers that can help to identify disease pathophysiology and monitor disease progression. Proteomics is a powerful and promising tool to accelerate biomarker detection and contribute to novel therapeutics. In this review, an overview of how proteomic technology using CNS tissues and biofluids from MS patients has provided important clues to the pathogenesis of MS is provided. Current publications, pitfalls, as well as directions of future research involving proteomic approaches to understand the pathogenesis of MS are discussed.
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Affiliation(s)
- Vaibhav Singh
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Ajai Tripathi
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Ranjan Dutta
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, 44195, USA
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