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  1. Article ; Online: Severe Tick-Borne Encephalitis (TBE) in a Patient with X-Linked Agammaglobulinemia; Treatment with TBE Virus IgG Positive Plasma, Clinical Outcome and T Cell Responses.

    Hedin, Wilhelm / Bergman, Peter / Akhirunessa, Mily / Söderholm, Sandra / Buggert, Marcus / Granberg, Tobias / Gredmark-Russ, Sara / Smith, C I Edvard / Pettke, Aleksandra / Wahren Borgström, Emilie

    Journal of clinical immunology

    2024  Volume 44, Issue 5, Page(s) 116

    Abstract: Purpose: A patient with X-linked agammaglobulinemia (XLA) and severe tick-borne encephalitis (TBE) was treated with TBE virus (TBEV) IgG positive plasma. The patient's clinical response, humoral and cellular immune responses were characterized pre- and ... ...

    Abstract Purpose: A patient with X-linked agammaglobulinemia (XLA) and severe tick-borne encephalitis (TBE) was treated with TBE virus (TBEV) IgG positive plasma. The patient's clinical response, humoral and cellular immune responses were characterized pre- and post-infection.
    Methods: ELISA and neutralisation assays were performed on sera and TBEV PCR assay on sera and cerebrospinal fluid. T cell assays were conducted on peripheral blood the patient and five healthy vaccinated controls.
    Results: The patient was admitted to the hospital with headache and fever. He was not vaccinated against TBE but receiving subcutaneous IgG-replacement therapy (IGRT). TBEV IgG antibodies were low-level positive (due to scIGRT), but the TBEV IgM and TBEV neutralisation tests were negative. During hospitalisation his clinical condition deteriorated (Glasgow coma scale 3/15) and he was treated in the ICU with corticosteroids and external ventricular drainage. He was then treated with plasma containing TBEV IgG without apparent side effects. His symptoms improved within a few days and the TBEV neutralisation test converted to positive. Robust CD8
    Conclusion: TBEV IgG-positive plasma given to an XLA patient with TBE without evident adverse reactions may have contributed to a positive clinical outcome. Similar approaches could offer a promising foundation for researching therapeutic options for patients with humoral immunodeficiencies. Importantly, a robust CD8
    MeSH term(s) Humans ; Encephalitis, Tick-Borne/immunology ; Encephalitis, Tick-Borne/diagnosis ; Encephalitis, Tick-Borne/therapy ; Male ; Agammaglobulinemia/immunology ; Agammaglobulinemia/therapy ; Encephalitis Viruses, Tick-Borne/immunology ; Genetic Diseases, X-Linked/immunology ; Genetic Diseases, X-Linked/therapy ; Immunoglobulin G/blood ; Immunoglobulin G/immunology ; Antibodies, Viral/blood ; T-Lymphocytes/immunology ; Treatment Outcome ; Adult ; Immunization, Passive/methods
    Chemical Substances Immunoglobulin G ; Antibodies, Viral
    Language English
    Publishing date 2024-04-27
    Publishing country Netherlands
    Document type Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 779361-3
    ISSN 1573-2592 ; 0271-9142
    ISSN (online) 1573-2592
    ISSN 0271-9142
    DOI 10.1007/s10875-024-01718-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Acquisition of ionic copper by the bacterial outer membrane protein OprC through a novel binding site.

    Bhamidimarri, Satya Prathyusha / Young, Tessa R / Shanmugam, Muralidharan / Soderholm, Sandra / Baslé, Arnaud / Bumann, Dirk / van den Berg, Bert

    PLoS biology

    2021  Volume 19, Issue 11, Page(s) e3001446

    Abstract: Copper, while toxic in excess, is an essential micronutrient in all kingdoms of life due to its essential role in the structure and function of many proteins. Proteins mediating ionic copper import have been characterised in detail for eukaryotes, but ... ...

    Abstract Copper, while toxic in excess, is an essential micronutrient in all kingdoms of life due to its essential role in the structure and function of many proteins. Proteins mediating ionic copper import have been characterised in detail for eukaryotes, but much less so for prokaryotes. In particular, it is still unclear whether and how gram-negative bacteria acquire ionic copper. Here, we show that Pseudomonas aeruginosa OprC is an outer membrane, TonB-dependent transporter that is conserved in many Proteobacteria and which mediates acquisition of both reduced and oxidised ionic copper via an unprecedented CxxxM-HxM metal binding site. Crystal structures of wild-type and mutant OprC variants with silver and copper suggest that acquisition of Cu(I) occurs via a surface-exposed "methionine track" leading towards the principal metal binding site. Together with whole-cell copper quantitation and quantitative proteomics in a murine lung infection model, our data identify OprC as an abundant component of bacterial copper biology that may enable copper acquisition under a wide range of conditions.
    MeSH term(s) Animals ; Bacterial Outer Membrane Proteins/chemistry ; Bacterial Outer Membrane Proteins/metabolism ; Binding Sites ; Copper/metabolism ; Ions ; Male ; Methionine/metabolism ; Mice ; Models, Molecular ; Protein Conformation ; Pseudomonas Infections/metabolism ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/metabolism
    Chemical Substances Bacterial Outer Membrane Proteins ; Ions ; Copper (789U1901C5) ; Methionine (AE28F7PNPL)
    Language English
    Publishing date 2021-11-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.3001446
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: High Prevalence of SARS-CoV-2 Omicron Infection Despite High Seroprevalence, Sweden, 2022.

    Groenheit, Ramona / Bacchus, Philip / Galanis, Ilias / Sondén, Klara / Bujila, Ioana / Efimova, Tatiana / Garli, Fredrik / Lindsjö, Oskar Karlsson / Mansjö, Mikael / Movert, Elin / Pettke, Aleksandra / Rapp, Marie / Sperk, Maike / Söderholm, Sandra / Asin, Karin Valentin / Zanetti, Sarah / Karlberg, Maria Lind / Bråve, Andreas / Blom, Kim /
    Klingström, Jonas

    Emerging infectious diseases

    2023  Volume 29, Issue 6, Page(s) 1240–1243

    Abstract: We performed 2 surveys during 2022 to estimate point prevalences of SARS-CoV-2 infection compared with overall seroprevalence in Sweden. Point prevalence was 1.4% in March and 1.5% in September. Estimated seroprevalence was >80%, including among ... ...

    Abstract We performed 2 surveys during 2022 to estimate point prevalences of SARS-CoV-2 infection compared with overall seroprevalence in Sweden. Point prevalence was 1.4% in March and 1.5% in September. Estimated seroprevalence was >80%, including among unvaccinated children. Continued SARS-CoV-2 surveillance is necessary for detecting emerging, possibly more pathogenic variants.
    MeSH term(s) Child ; Humans ; COVID-19/epidemiology ; Prevalence ; SARS-CoV-2 ; Sweden/epidemiology ; Seroepidemiologic Studies
    Language English
    Publishing date 2023-05-04
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1380686-5
    ISSN 1080-6059 ; 1080-6040
    ISSN (online) 1080-6059
    ISSN 1080-6040
    DOI 10.3201/eid2906.221862
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Point prevalence of SARS-CoV-2 infection in Sweden at six time points during 2020.

    Groenheit, Ramona / Beser, Jessica / Kühlmann Berenzon, Sharon / Galanis, Ilias / van Straten, Edward / Duracz, Jan / Rapp, Marie / Hansson, Disa / Mansjö, Mikael / Söderholm, Sandra / Muradrasoli, Shaman / Risberg, Anna / Ölund, Richard / Wiklund, Andreas / Metzkes, Kristoffer / Lundberg, Matilda / Bacchus, Philip / Tegmark Wisell, Karin / Bråve, Andreas

    BMC infectious diseases

    2022  Volume 22, Issue 1, Page(s) 861

    Abstract: Background: In order to estimate the prevalence and understand the spread of SARS-CoV-2 in Sweden, the Public Health Agency of Sweden, with support from the Swedish Armed Forces, conducted a series of point prevalence surveys between March and December ... ...

    Abstract Background: In order to estimate the prevalence and understand the spread of SARS-CoV-2 in Sweden, the Public Health Agency of Sweden, with support from the Swedish Armed Forces, conducted a series of point prevalence surveys between March and December 2020.
    Methods: Sampling material and instructions on how to perform self-sampling of the upper respiratory tract were delivered to the homes of the participants. Samples were analysed by real-time PCR, and the participants completed questionnaires regarding symptoms.
    Findings: The first survey in the Stockholm region in March 2020 included 707 participants and showed a SARS-CoV-2 prevalence of 2.5%. The following five surveys, performed on a national level, with between 2461 and 2983 participants, showed SARS-CoV-2 prevalences of 0.9% (April), 0.3% (May), 0.0% (August), 0.0% (September), and 0.7% (December). All positive cases who responded to questionnaires reported experiencing symptoms that occurred from 2 weeks before the date of sampling up to and including the date of sampling.
    Interpretation: None of the individuals shown to be PCR-positive were asymptomatic at the time of sampling or in the 14 days prior to sampling. This is in contrast to many other surveys in which a substantial proportion of positive cases have been reported to be asymptomatic. Our surveys demonstrate a decreasing ratio between notified cases and the observed prevalence throughout the year, in line with increasing testing capacity and the consecutive inclusion of all symptomatic individuals in the case definition for testing.
    MeSH term(s) Humans ; COVID-19/epidemiology ; Prevalence ; SARS-CoV-2 ; Sweden/epidemiology ; Public Health
    Language English
    Publishing date 2022-11-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041550-3
    ISSN 1471-2334 ; 1471-2334
    ISSN (online) 1471-2334
    ISSN 1471-2334
    DOI 10.1186/s12879-022-07858-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Outer membrane permeability: Antimicrobials and diverse nutrients bypass porins in

    Ude, Johanna / Tripathi, Vishwachi / Buyck, Julien M / Söderholm, Sandra / Cunrath, Olivier / Fanous, Joseph / Claudi, Beatrice / Egli, Adrian / Schleberger, Christian / Hiller, Sebastian / Bumann, Dirk

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Volume 118, Issue 31

    Abstract: Gram-negative bacterial pathogens have an outer membrane that restricts entry of molecules into the cell. Water-filled protein channels in the outer membrane, so-called porins, facilitate nutrient uptake and are thought to enable antibiotic entry. Here, ... ...

    Abstract Gram-negative bacterial pathogens have an outer membrane that restricts entry of molecules into the cell. Water-filled protein channels in the outer membrane, so-called porins, facilitate nutrient uptake and are thought to enable antibiotic entry. Here, we determined the role of porins in a major pathogen,
    MeSH term(s) Anti-Bacterial Agents/metabolism ; Bacterial Outer Membrane Proteins/metabolism ; Biological Transport/physiology ; Cell Membrane/physiology ; Cell Membrane Permeability ; Nutrients/metabolism ; Porins/metabolism ; Pseudomonas aeruginosa/physiology
    Chemical Substances Anti-Bacterial Agents ; Bacterial Outer Membrane Proteins ; Porins
    Language English
    Publishing date 2021-07-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2107644118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Molecular reprogramming and phenotype switching in

    Huemer, Markus / Mairpady Shambat, Srikanth / Bergada-Pijuan, Judith / Söderholm, Sandra / Boumasmoud, Mathilde / Vulin, Clément / Gómez-Mejia, Alejandro / Antelo Varela, Minia / Tripathi, Vishwachi / Götschi, Sandra / Marques Maggio, Ewerton / Hasse, Barbara / Brugger, Silvio D / Bumann, Dirk / Schuepbach, Reto A / Zinkernagel, Annelies S

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Volume 118, Issue 7

    Abstract: Staphylococcus ... ...

    Abstract Staphylococcus aureus
    MeSH term(s) Aconitate Hydratase/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Cells, Cultured ; Drug Resistance, Bacterial ; Humans ; Metabolome ; Mice ; Mice, Inbred C57BL ; Phenotype ; Ribosomal Proteins/genetics ; Ribosomal Proteins/metabolism ; Staphylococcal Infections/drug therapy ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/drug effects ; Staphylococcus aureus/genetics ; Staphylococcus aureus/metabolism ; Staphylococcus aureus/pathogenicity
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Ribosomal Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; Aconitate Hydratase (EC 4.2.1.3)
    Language English
    Publishing date 2021-02-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2014920118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Microwave-assisted derivatization procedures for gas chromatography/mass spectrometry analysis

    Söderholm, Sandra L / Damm, Markus / Kappe, C. Oliver

    Molecular diversity. 2010 Nov., v. 14, no. 4

    2010  

    Abstract: In this review, published applications of microwave-assisted derivatization procedures for gas chromatography/mass spectrometry (GC/MS) are summarized. Among the broad range of analytical techniques available, GC/MS is still the method of choice for most ...

    Abstract In this review, published applications of microwave-assisted derivatization procedures for gas chromatography/mass spectrometry (GC/MS) are summarized. Among the broad range of analytical techniques available, GC/MS is still the method of choice for most high-throughput screening procedures in forensic/clinical toxicology, doping control and food and environmental analysis. Despite the many advantages of the GC/MS method, time-consuming derivatization steps are often required in order to obtain desirable chromatographic characteristics or to improve the stability and detectability of the target analytes. These derivatization processes typically require reaction times from 30 min up to several hours at elevated temperature. In contrast, microwave protocols have demonstrated to be able to reduce the time required for derivatization to a few minutes, and can thus very effectively shorten the overall analysis time, in particular when carried out in a high-throughput format. Herein, the literature in this field is summarized and recent experimental techniques for performing parallel GC/MS derivatization protocols are discussed.
    Keywords gas chromatography ; mass spectrometry
    Language English
    Dates of publication 2010-11
    Size p. 869-888.
    Publisher Springer Netherlands
    Publishing place Dordrecht
    Document type Article
    ZDB-ID 1376507-3
    ISSN 1573-501X ; 1381-1991
    ISSN (online) 1573-501X
    ISSN 1381-1991
    DOI 10.1007/s11030-010-9242-9
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Phosphoproteome characterization reveals that Sendai virus infection activates mTOR signaling in human epithelial cells.

    Öhman, Tiina / Söderholm, Sandra / Paidikondala, Maruthibabu / Lietzén, Niina / Matikainen, Sampsa / Nyman, Tuula A

    Proteomics

    2015  Volume 15, Issue 12, Page(s) 2087–2097

    Abstract: Sendai virus (SeV) is a common respiratory pathogen in mice, rats, and hamsters. Host cell recognition of SeV is mediated by pathogen recognition receptors, which recognize viral components and induce intracellular signal transduction pathways that ... ...

    Abstract Sendai virus (SeV) is a common respiratory pathogen in mice, rats, and hamsters. Host cell recognition of SeV is mediated by pathogen recognition receptors, which recognize viral components and induce intracellular signal transduction pathways that activate the antiviral innate immune response. Viruses use host proteins to control the activities of signaling proteins and their downstream targets, and one of the most important host protein modifications regulated by viral infection is phosphorylation. In this study, we used phosphoproteomics combined with bioinformatics to get a global view of the signaling pathways activated during SeV infection in human lung epithelial cells. We identified altogether 1347 phosphoproteins, and our data shows that SeV infection induces major changes in protein phosphorylation affecting the phosphorylation of almost one thousand host proteins. Bioinformatics analysis showed that SeV infection activates known pathways including MAPK signaling, as well as signaling pathways previously not linked to SeV infection including Rho family of GTPases, HIPPO signaling, and mammalian target of rapamycin (mTOR)-signaling pathway. Further, we performed functional studies with mTOR inhibitors and siRNA approach, which revealed that mTOR signaling is needed for both the host IFN response as well as viral protein synthesis in SeV-infected human lung epithelial cells.
    MeSH term(s) Animals ; Blotting, Western ; Computational Biology ; Cricetinae ; Epithelial Cells/cytology ; Epithelial Cells/metabolism ; Humans ; Interferons/metabolism ; Lung Neoplasms/metabolism ; Lung Neoplasms/pathology ; Lung Neoplasms/virology ; Mice ; Phosphoproteins/genetics ; Phosphoproteins/metabolism ; Phosphorylation ; Protein Array Analysis ; Proteomics/methods ; RNA, Messenger/genetics ; Rats ; Real-Time Polymerase Chain Reaction ; Respirovirus Infections/metabolism ; Respirovirus Infections/virology ; Reverse Transcriptase Polymerase Chain Reaction ; Sendai virus/physiology ; Signal Transduction ; TOR Serine-Threonine Kinases/genetics ; TOR Serine-Threonine Kinases/metabolism ; Tumor Cells, Cultured
    Chemical Substances Phosphoproteins ; RNA, Messenger ; Interferons (9008-11-1) ; MTOR protein, human (EC 2.7.1.1) ; TOR Serine-Threonine Kinases (EC 2.7.1.1)
    Language English
    Publishing date 2015-06
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2032093-0
    ISSN 1615-9861 ; 1615-9853
    ISSN (online) 1615-9861
    ISSN 1615-9853
    DOI 10.1002/pmic.201400586
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Microwave-assisted derivatization procedures for gas chromatography/mass spectrometry analysis.

    Söderholm, Sandra L / Damm, Markus / Kappe, C Oliver

    Molecular diversity

    2010  Volume 14, Issue 4, Page(s) 869–888

    Abstract: In this review, published applications of microwave-assisted derivatization procedures for gas chromatography/mass spectrometry (GC/MS) are summarized. Among the broad range of analytical techniques available, GC/MS is still the method of choice for most ...

    Abstract In this review, published applications of microwave-assisted derivatization procedures for gas chromatography/mass spectrometry (GC/MS) are summarized. Among the broad range of analytical techniques available, GC/MS is still the method of choice for most high-throughput screening procedures in forensic/clinical toxicology, doping control and food and environmental analysis. Despite the many advantages of the GC/MS method, time-consuming derivatization steps are often required in order to obtain desirable chromatographic characteristics or to improve the stability and detectability of the target analytes. These derivatization processes typically require reaction times from 30 min up to several hours at elevated temperature. In contrast, microwave protocols have demonstrated to be able to reduce the time required for derivatization to a few minutes, and can thus very effectively shorten the overall analysis time, in particular when carried out in a high-throughput format. Herein, the literature in this field is summarized and recent experimental techniques for performing parallel GC/MS derivatization protocols are discussed.
    MeSH term(s) Analytic Sample Preparation Methods/methods ; Drug Stability ; Gas Chromatography-Mass Spectrometry/methods ; Gas Chromatography-Mass Spectrometry/trends ; High-Throughput Screening Assays/methods ; Inorganic Chemicals/chemistry ; Inorganic Chemicals/pharmacology ; Microwaves ; Models, Biological ; Organic Chemicals/analysis ; Organic Chemicals/chemistry ; Organic Chemicals/pharmacology
    Chemical Substances Inorganic Chemicals ; Organic Chemicals
    Language English
    Publishing date 2010-11
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1376507-3
    ISSN 1573-501X ; 1381-1991
    ISSN (online) 1573-501X
    ISSN 1381-1991
    DOI 10.1007/s11030-010-9242-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data.

    Söderholm, Sandra / Hintsanen, Petteri / Öhman, Tiina / Aittokallio, Tero / Nyman, Tuula A

    Proteome science

    2014  Volume 12, Page(s) 36

    Abstract: Background: It is possible to identify thousands of phosphopeptides and -proteins in a single experiment with mass spectrometry-based phosphoproteomics. However, a current bottleneck is the downstream data analysis which is often laborious and requires ... ...

    Abstract Background: It is possible to identify thousands of phosphopeptides and -proteins in a single experiment with mass spectrometry-based phosphoproteomics. However, a current bottleneck is the downstream data analysis which is often laborious and requires a number of manual steps.
    Results: Toward automating the analysis steps, we have developed and implemented a software, PhosFox, which enables peptide-level processing of phosphoproteomic data generated by multiple protein identification search algorithms, including Mascot, Sequest, and Paragon, as well as cross-comparison of their identification results. The software supports both qualitative and quantitative phosphoproteomics studies, as well as multiple between-group comparisons. Importantly, PhosFox detects uniquely phosphorylated peptides and proteins in one sample compared to another. It also distinguishes differences in phosphorylation sites between phosphorylated proteins in different samples. Using two case study examples, a qualitative phosphoproteome dataset from human keratinocytes and a quantitative phosphoproteome dataset from rat kidney inner medulla, we demonstrate here how PhosFox facilitates an efficient and in-depth phosphoproteome data analysis. PhosFox was implemented in the Perl programming language and it can be run on most common operating systems. Due to its flexible interface and open source distribution, the users can easily incorporate the program into their MS data analysis workflows and extend the program with new features. PhosFox source code, implementation and user instructions are freely available from https://bitbucket.org/phintsan/phosfox.
    Conclusions: PhosFox facilitates efficient and more in-depth comparisons between phosphoproteins in case-control settings. The open source implementation is easily extendable to accommodate additional features for widespread application use cases.
    Language English
    Publishing date 2014-06-26
    Publishing country England
    Document type Journal Article
    ISSN 1477-5956
    ISSN 1477-5956
    DOI 10.1186/1477-5956-12-36
    Database MEDical Literature Analysis and Retrieval System OnLINE

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