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Abstract and Applied Analysis     Open Access   (Followers: 3, SJR: 0.512, h-index: 32)
Active and Passive Electronic Components     Open Access   (Followers: 7, SJR: 0.157, h-index: 15)
Advances in Acoustics and Vibration     Open Access   (Followers: 33, SJR: 0.259, h-index: 6)
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Bone Marrow Research     Open Access   (Followers: 2)
Canadian J. of Gastroenterology & Hepatology     Open Access   (Followers: 5, SJR: 0.856, h-index: 53)
Canadian J. of Infectious Diseases and Medical Microbiology     Open Access   (Followers: 5, SJR: 0.409, h-index: 25)
Canadian Respiratory J.     Open Access   (Followers: 1, SJR: 0.503, h-index: 42)
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Case Reports in Anesthesiology     Open Access   (Followers: 10)
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Case Reports in Vascular Medicine     Open Access  
Case Reports in Veterinary Medicine     Open Access   (Followers: 7)
Child Development Research     Open Access   (Followers: 17)
Chinese J. of Engineering     Open Access   (Followers: 2)
Chinese J. of Mathematics     Open Access  
Cholesterol     Open Access   (Followers: 1, SJR: 0.906, h-index: 12)
Complexity     Hybrid Journal   (Followers: 6, SJR: 0.526, h-index: 27)
Computational and Mathematical Methods in Medicine     Open Access   (Followers: 2, SJR: 0.415, h-index: 22)
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Critical Care Research and Practice     Open Access   (Followers: 10, SJR: 0.916, h-index: 14)
Current Gerontology and Geriatrics Research     Open Access   (Followers: 9, SJR: 0.8, h-index: 12)
Depression Research and Treatment     Open Access   (Followers: 15, SJR: 0.77, h-index: 11)
Dermatology Research and Practice     Open Access   (Followers: 3, SJR: 0.576, h-index: 15)
Diagnostic and Therapeutic Endoscopy     Open Access   (SJR: 0.651, h-index: 18)
Discrete Dynamics in Nature and Society     Open Access   (Followers: 5, SJR: 0.323, h-index: 24)
Disease Markers     Open Access   (Followers: 1, SJR: 0.774, h-index: 49)
Education Research Intl.     Open Access   (Followers: 21)
Emergency Medicine Intl.     Open Access   (Followers: 7)
Enzyme Research     Open Access   (Followers: 4, SJR: 0.457, h-index: 18)
Evidence-based Complementary and Alternative Medicine     Open Access   (Followers: 20, SJR: 0.615, h-index: 50)
Experimental Diabetes Research     Open Access   (Followers: 13, SJR: 1.591, h-index: 30)
Gastroenterology Research and Practice     Open Access   (Followers: 3, SJR: 0.664, h-index: 21)
Genetics Research Intl.     Open Access   (Followers: 1)
Geofluids     Open Access   (Followers: 5, SJR: 0.693, h-index: 38)
HPB Surgery     Open Access   (Followers: 5, SJR: 0.798, h-index: 22)
Infectious Diseases in Obstetrics and Gynecology     Open Access   (Followers: 6, SJR: 0.976, h-index: 34)
Interdisciplinary Perspectives on Infectious Diseases     Open Access   (Followers: 2, SJR: 0.763, h-index: 15)
Intl. J. of Aerospace Engineering     Open Access   (Followers: 72, SJR: 0.241, h-index: 6)
Intl. J. of Agronomy     Open Access   (Followers: 8, SJR: 0.223, h-index: 2)
Intl. J. of Alzheimer's Disease     Open Access   (Followers: 12, SJR: 1.193, h-index: 25)
Intl. J. of Analysis     Open Access  
Intl. J. of Analytical Chemistry     Open Access   (Followers: 22, SJR: 0.157, h-index: 2)
Intl. J. of Antennas and Propagation     Open Access   (Followers: 11, SJR: 0.385, h-index: 15)
Intl. J. of Biodiversity     Open Access   (Followers: 4)
Intl. J. of Biomaterials     Open Access   (Followers: 5, SJR: 0.485, h-index: 10)
Intl. J. of Biomedical Imaging     Open Access   (Followers: 4, SJR: 0.581, h-index: 23)
Intl. J. of Breast Cancer     Open Access   (Followers: 13)
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Intl. J. of Chronic Diseases     Open Access   (Followers: 1)
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Intl. J. of Corrosion     Open Access   (Followers: 11, SJR: 0.19, h-index: 7)
Intl. J. of Dentistry     Open Access   (Followers: 6, SJR: 0.558, h-index: 11)
Intl. J. of Differential Equations     Open Access   (Followers: 8, SJR: 0.363, h-index: 11)
Intl. J. of Digital Multimedia Broadcasting     Open Access   (Followers: 5, SJR: 0.144, h-index: 10)
Intl. J. of Electrochemistry     Open Access   (Followers: 8)
Intl. J. of Endocrinology     Open Access   (Followers: 3, SJR: 0.961, h-index: 24)
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Intl. J. of Hepatology     Open Access   (Followers: 4)
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Intl. J. of Navigation and Observation     Open Access   (Followers: 20, SJR: 0.411, h-index: 7)
Intl. J. of Nephrology     Open Access   (Followers: 1, SJR: 0.926, h-index: 14)
Intl. J. of Optics     Open Access   (Followers: 7, SJR: 0.262, h-index: 7)
Intl. J. of Otolaryngology     Open Access   (Followers: 3)
Intl. J. of Pediatrics     Open Access   (Followers: 5)
Intl. J. of Peptides     Open Access   (Followers: 4, SJR: 0.73, h-index: 16)
Intl. J. of Photoenergy     Open Access   (Followers: 2, SJR: 0.348, h-index: 28)
Intl. J. of Plant Genomics     Open Access   (Followers: 4, SJR: 1.578, h-index: 20)
Intl. J. of Polymer Science     Open Access   (Followers: 24, SJR: 0.265, h-index: 11)
Intl. J. of Population Research     Open Access   (Followers: 2)
Intl. J. of Reconfigurable Computing     Open Access   (SJR: 0.182, h-index: 8)
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Intl. J. of Rheumatology     Open Access   (Followers: 5, SJR: 1.015, h-index: 18)
Intl. J. of Rotating Machinery     Open Access   (Followers: 2, SJR: 0.402, h-index: 19)
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Intl. J. of Stochastic Analysis     Open Access   (Followers: 4, SJR: 0.234, h-index: 19)
Intl. J. of Surgical Oncology     Open Access   (Followers: 1, SJR: 0.753, h-index: 11)
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Intl. Scholarly Research Notices     Open Access   (Followers: 210)
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Journal Cover International Journal of Proteomics
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  This is an Open Access Journal Open Access journal
   ISSN (Print) 2090-2116 - ISSN (Online) 2090-2174
   This journal is no longer being updated because:
    The journal ceased publication
  • Miniaturized Digestion and Extraction of Surface Proteins from Candida
           albicans following Treatment with Histatin 5 for Mass Spectrometry

    • Abstract: A common approach to isolate surface proteins from fungal and bacterial cells is to perform a proteolytic cleavage of proteins on the surface of intact cells suspended in solution. This paper describes miniaturization of this technique, in which cells are adhered on glass surfaces, and all sample treatments are conducted at μL volumes. Specifically, Candida albicans cells were attached onto HSA-coated glass slides. By depositing the appropriate reagent solutions on the adhered cells, we successfully performed cell washing, treatment with antifugal peptide, Histatin 5, and a proteolysis on intact cells with trypsin. The resulting peptides were subsequently analysed by mass spectrometry. In general, the data obtained was similar to that collected with suspended cells in much larger sample volumes. However, our miniaturized workflow offers the benefit of greatly reducing the consumption of cells and reagents.
      PubDate: Thu, 01 Dec 2016 12:21:59 +000
  • Comparative Proteomic Analysis of Differential Proteins in Response to
           Aqueous Extract of Quercus infectoria Gall in Methicillin-Resistant
           Staphylococcus aureus

    • Abstract: The aim of this study is to analyze the differential proteins in MRSA ATCC 33591 treated with aqueous extract from Q. infectoria gall. Protein extracts were obtained from MRSA cells by sonication and were separated by 2D polyacrylamide gels. Protein spots of interest were extracted from the gels and identified using LC-ESI-QTOF MS. The concentration of Q. infectoria extract used for 2D-gel electrophoresis was subinhibitory concentration. Minimum inhibitory concentration (MIC) value of the extract against MRSA was 19.50 μg/mL with bacteriostatic action at 1x MIC from time-kill assay. However, the extract exhibited dose-dependent manner and was bactericidal at 4x MIC with more than 3 log10 CFU/mL reduction at 4 h. 2D-GE map showed that 18 protein spots were upregulated and another six were downregulated more than twofold () after treatment with subinhibitory concentration. Out of six proteins being downregulated, four proteins were identified as ferritin and catalase, branched-chain alpha-keto acid dehydrogenase subunit E2, and succinyl-CoA ligase [ADP-forming] subunit beta. Seven upregulated proteins which have been successfully identified were 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein, formate C-acetyltransferase, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ, NAD dependent epimerase/dehydratase family protein, and phosphopantothenoyl cysteine decarboxylase. It is postulated that the main mechanism of aqueous extract from gall of Q. infectoria was most likely involved in energy metabolism and protein stress.
      PubDate: Mon, 05 Sep 2016 13:55:42 +000
  • Optimization of Urea Based Protein Extraction from Formalin-Fixed
           Paraffin-Embedded Tissue for Shotgun Proteomics

    • Abstract: Urea based protein extraction of formalin-fixed paraffin-embedded (FFPE) tissue provides the most efficient workflow for proteomics due to its compatibility with liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). This study optimizes the use of urea for proteomic analysis of clinical FFPE tissue. A series of protein extraction conditions manipulating temperature and buffer composition were compared to reduce carbamylation introduced by urea and increase protein detection. Each extraction was performed on a randomized pair of serial sections of homogenous FFPE tissue and analyzed with LC-ESI-MS/MS. Results were compared in terms of yield, missed cleavages, and peptide carbamylation. Lowering extraction temperature to 60°C decreased carbamylation at the cost of decreased protein detection and yield. Protein extraction for at least 20 minutes at 95°C followed by 60°C for 2 hours maximized total protein yield while maintaining protein detection and reducing carbamylation by 7.9%. When accounting for carbamylation during analysis, this modified extraction temperature provides equivalent peptide and protein detection relative to the commercially available Qproteome® FFPE Tissue Kit. No changes to buffer composition containing 7 M urea, 2 M thiourea, and 1 M ammonium bicarbonate resulted in improvements to control conditions. Optimized urea in-solution digestion provides an efficient workflow with maximized yields for proteomic analysis of clinically relevant FFPE tissue.
      PubDate: Wed, 31 Aug 2016 11:04:39 +000
  • S-Nitrosylation Proteome Profile of Peripheral Blood Mononuclear Cells in
           Human Heart Failure

    • Abstract: Nitric oxide (NO) protects the heart against ischemic injury; however, NO- and superoxide-dependent S-nitrosylation (S-NO) of cysteines can affect function of target proteins and play a role in disease outcome. We employed 2D-GE with thiol-labeling FL-maleimide dye and MALDI-TOF MS/MS to capture the quantitative changes in abundance and S-NO proteome of HF patients (versus healthy controls, /group). We identified 93 differentially abundant (59-increased/34-decreased) and 111 S-NO-modified (63-increased/48-decreased) protein spots, respectively, in HF subjects (versus controls, fold-change ≥1.5, ). Ingenuity pathway analysis of proteome datasets suggested that the pathways involved in phagocytes’ migration, free radical production, and cell death were activated and fatty acid metabolism was decreased in HF subjects. Multivariate adaptive regression splines modeling of datasets identified a panel of proteins that will provide >90% prediction success in classifying HF subjects. Proteomic profiling identified ATP-synthase, thrombospondin-1 (THBS1), and vinculin (VCL) as top differentially abundant and S-NO-modified proteins, and these proteins were verified by Western blotting and ELISA in different set of HF subjects. We conclude that differential abundance and S-NO modification of proteins serve as a mechanism in regulating cell viability and free radical production, and THBS1 and VCL evaluation will potentially be useful in the prediction of heart failure.
      PubDate: Thu, 18 Aug 2016 16:28:42 +000
  • Label-Free Proteomic Analysis of Flavohemoglobin Deleted Strain of
           Saccharomyces cerevisiae

    • Abstract: Yeast flavohemoglobin, YHb, encoded by the nuclear gene YHB1, has been implicated in the nitrosative stress responses in Saccharomyces cerevisiae. It is still unclear how S. cerevisiae can withstand this NO level in the absence of flavohemoglobin. To better understand the physiological function of flavohemoglobin in yeast, in the present study a label-free differential proteomics study has been carried out in wild-type and YHB1 deleted strains of S. cerevisiae grown under fermentative conditions. From the analysis, 417 proteins in Y190 and 392 proteins in ΔYHB1 were identified with high confidence. Interestingly, among the differentially expressed identified proteins, 40 proteins were found to be downregulated whereas 41 were found to be upregulated in ΔYHB1 strain of S. cerevisiae ( value < 0.05). The differentially expressed proteins were also classified according to gene ontology (GO) terms. The most enriched and significant GO terms included nitrogen compound biosynthesis, amino acid biosynthesis, translational regulation, and protein folding. Interactions of differentially expressed proteins were generated using Search Tool for the Retrieval of Interacting Genes (STRING) database. This is the first report which offers a more complete view of the proteome changes in S. cerevisiae in the absence of flavohemoglobin.
      PubDate: Mon, 11 Jan 2016 08:35:39 +000
  • Molecular Integrity of Mitochondria Alters by Potassium Chloride

    • Abstract: Potassium chloride (KCl) has been commonly used in homogenization buffer and procedures of protein extraction. It is known to facilitate release of membrane-associated molecules but the higher concentration of KCl may affect the integrity of mitochondria by breaching the electrostatic force between the lipids and proteins. Therefore, it has been intended to explore the effect of KCl on mitochondrial proteome. The mitochondria were isolated from the mice liver and sub-fractionated into mitochondrial matrix and outer mitochondrial membrane fraction. The fractions were analysed by denaturing polyacrylamide gel electrophoresis (PAGE) and 2D-PAGE. The analysis of ultrastructure and protein profiles by MALDI-MS and data-mining reveals KCl-associated alterations in the integrity of mitochondria and its proteome. The mitochondrial membrane, cristae, and the matrix proteins appear altered under the influence of KCl.
      PubDate: Thu, 10 Dec 2015 12:35:42 +000
  • Human Urine Proteomics: Analytical Techniques and Clinical Applications in
           Renal Diseases

    • Abstract: Urine has been in the center of attention among scientists of clinical proteomics in the past decade, because it is valuable source of proteins and peptides with a relative stable composition and easy to collect in large and repeated quantities with a noninvasive procedure. In this review, we discuss technical aspects of urinary proteomics in detail, including sample preparation, proteomic technologies, and their advantage and disadvantages. Several recent experiments are presented which applied urinary proteome for biomarker discovery in renal diseases including diabetic nephropathy, immunoglobulin A (IgA) nephropathy, focal segmental glomerulosclerosis, lupus nephritis, membranous nephropathy, and acute kidney injury. In addition, several available databases in urinary proteomics are also briefly introduced.
      PubDate: Sun, 29 Nov 2015 11:34:56 +000
  • A Multicenter Trial Defining a Serum Protein Signature Associated with
           Pancreatic Ductal Adenocarcinoma

    • Abstract: Background. Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with rapid tumor progression and poor prognosis. This study was motivated by the lack of sensitive and specific PDAC biomarkers and aimed to identify a diagnostic, serum protein signature for PDAC. Methods. To mimic a real life test situation, a multicenter trial comprising a serum sample cohort, including 338 patients with either PDAC or other pancreatic diseases (OPD) and controls with nonpancreatic conditions (NPC), was analyzed on 293-plex recombinant antibody microarrays targeting immunoregulatory and cancer-associated antigens. Results. Serum samples collected from different hospitals were analyzed and showed that (i) sampling from five different hospitals could not be identified as a preanalytical variable and (ii) a multiplexed biomarker signature could be identified, utilizing up to 10 serum markers that could discriminate PDAC from controls, with sensitivities and specificities in the 91–100% range. The first protein profiles associated with the location of the primary tumor in the pancreas could also be identified. Conclusions. The results demonstrate that robust enough serum signatures could be identified in a multicenter trial, potentially contributing to the development of a multiplexed biomarker immunoassay for improved PDAC diagnosis.
      PubDate: Mon, 26 Oct 2015 09:25:02 +000
  • Hypoxia Strongly Affects Mitochondrial Ribosomal Proteins and
           Translocases, as Shown by Quantitative Proteomics of HeLa Cells

    • Abstract: Hypoxia is an important and common characteristic of many human tumors. It is a challenge clinically due to the correlation with poor prognosis and resistance to radiation and chemotherapy. Understanding the biochemical response to hypoxia would facilitate the development of novel therapeutics for cancer treatment. Here, we investigate alterations in gene expression in response to hypoxia by quantitative proteome analysis using stable isotope labeling with amino acids in cell culture (SILAC) in conjunction with LCMS/MS. Human HeLa cells were kept either in a hypoxic environment or under normoxic conditions. 125 proteins were found to be regulated, with maximum alteration of 18-fold. In particular, three clusters of differentially regulated proteins were identified, showing significant upregulation of glycolysis and downregulation of mitochondrial ribosomal proteins and translocases. This interaction is likely orchestrated by HIF-1. We also investigated the effect of hypoxia on the cell cycle, which shows accumulation in G1 and a prolonged S phase under these conditions. Implications. This work not only improves our understanding of the response to hypoxia, but also reveals proteins important for malignant progression, which may be targeted in future therapies.
      PubDate: Wed, 02 Sep 2015 06:05:15 +000
  • A Proteomic Characterization of Bordetella pertussis Clinical Isolates
           Associated with a California State Pertussis Outbreak

    • Abstract: Bordetella pertussis (Bp) is the etiologic agent of pertussis (whooping cough), a highly communicable infection. Although pertussis is vaccine preventable, in recent years there has been increased incidence, despite high vaccine coverage. Possible reasons for the rise in cases include the following: Bp strain adaptation, waning vaccine immunity, increased surveillance, and improved clinical diagnostics. A pertussis outbreak impacted California (USA) in 2010; children and preadolescents were the most affected but the burden of disease fell mainly on infants. To identify protein biomarkers associated with this pertussis outbreak, we report a whole cellular protein characterization of six Bp isolates plus the pertussis acellular vaccine strain Bp Tohama I (T), utilizing gel-free proteomics-based mass spectrometry (MS). MS/MS tryptic peptide detection and protein database searching combined with western blot analysis revealed three Bp isolates in this study had markedly reduced detection of pertactin (Prn), a subunit of pertussis acellular vaccines. Additionally, antibody affinity capture technologies were implemented using anti-Bp T rabbit polyclonal antisera and whole cellular proteins to identify putative immunogens. Proteome profiling could shed light on pathogenesis and potentially lay the foundation for reduced infection transmission strategies and improved clinical diagnostics.
      PubDate: Sun, 24 May 2015 06:20:34 +000
  • SILAC-Based Quantitative Proteomic Analysis of Diffuse Large B-Cell
           Lymphoma Patients

    • Abstract: Diffuse large B-cell lymphoma (DLBCL), the most common lymphoma, is a heterogeneous disease where the outcome for patients with early relapse or refractory disease is very poor, even in the era of immunochemotherapy. In order to describe possible differences in global protein expression and network patterns, we performed a SILAC-based shotgun (LC-MS/MS) quantitative proteomic analysis in fresh-frozen tumor tissue from two groups of DLBCL patients with totally different clinical outcome: (i) early relapsed or refractory and (ii) long-term progression-free patients. We could identify over 3,500 proteins; more than 1,300 were quantified in all patients and 87 were significantly differentially expressed. By functional annotation analysis on the 66 proteins overexpressed in the progression-free patient group, we found an enrichment of proteins involved in the regulation and organization of the actin cytoskeleton. Also, five proteins from actin cytoskeleton regulation, applied in a supervised regression analysis, could discriminate the two patient groups. In conclusion, SILAC-based shotgun quantitative proteomic analysis appears to be a powerful tool to explore the proteome in DLBCL tumor tissue. Also, as progression-free patients had a higher expression of proteins involved in the actin cytoskeleton protein network, such a pattern indicates a functional role in the sustained response to immunochemotherapy.
      PubDate: Tue, 28 Apr 2015 07:32:52 +000
  • Quantitative Proteomics and Lipidomics Analysis of Endoplasmic Reticulum
           of Macrophage Infected with Mycobacterium tuberculosis

    • Abstract: Even though endoplasmic reticulum (ER) stress associated with mycobacterial infection has been well studied, the molecular basis of ER as a crucial organelle to determine the fate of Mtb is yet to be established. Here, we have studied the ability of Mtb to manipulate the ultrastructural architecture of macrophage ER and found that the ER-phenotypes associated with virulent (H37Rv) and avirulent (H37Ra) strains were different: a rough ER (RER) with the former against a smooth ER (SER) with the later. Further, the functional attributes of these changes were probed by MS-based quantitative proteomics (133 ER proteins) and lipidomics (8 phospholipids). Our omics approaches not only revealed the host pathogen cross-talk but also emphasized how precisely Mtb uses proteins and lipids in combination to give rise to characteristic ER-phenotypes. H37Ra-infected macrophages increased the cytosolic Ca2+ levels by attenuating the ATP2A2 protein and simultaneous induction of PC/PE expression to facilitate apoptosis. However, H37Rv inhibited apoptosis and further controlled the expression of EST-1 and AMRP proteins to disturb cholesterol homeostasis resulting in sustained infection. This approach offers the potential to decipher the specific roles of ER in understanding the cell biology of mycobacterial infection with special reference to the impact of host response.
      PubDate: Mon, 16 Feb 2015 06:18:52 +000
  • Comparative Proteomic Study Reveals the Molecular Aspects of Delayed
           Ocular Symptoms Induced by Sulfur Mustard

    • Abstract: Objective. Sulfur mustard (SM) is a highly reactive alkylating agent which produces ocular, respiratory, and skin damages. Eyes are the most sensitive organ to SM due to high intrinsic metabolic and rapid turnover rate of corneal epithelium and aqueous-mucous interfaces of the cornea and conjunctiva. Here we investigate underlying molecular mechanism of SM exposure delayed effects which is still a controversial issue after about 30 years. Materials and Methods. Following ethical approval, we have analyzed serum proteome of ten severe SM exposed male patients with delayed eye symptoms with two-dimensional electrophoresis followed by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. The western blotting was used to confirm the proteins that have been identified. Results. We have identified thirteen proteins including albumin, haptoglobin, and keratin isoforms as well as immunoglobulin kappa chain which showed upregulation while transferrin and alpha 1 antitrypsin revealed downregulation in these patients in comparison with healthy control group. Conclusions. Our results elevated participation of free iron circulatory imbalance and local matrix-metalloproteinase activity in development of delayed ocular symptoms induced by SM. It demonstrates that SM induced systemic toxicity leads to some serum protein changes that continually and gradually exacerbate the ocular surface injuries.
      PubDate: Wed, 21 Jan 2015 13:46:52 +000
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