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  1. Article ; Online: Author Correction: Training the trainable cells of the immune system and beyond.

    Kar, Upendra K / Joosten, Leo A B

    Nature immunology

    2020  Volume 21, Issue 5, Page(s) 588

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Language English
    Publishing date 2020-03-11
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ZDB-ID 2016987-5
    ISSN 1529-2916 ; 1529-2908
    ISSN (online) 1529-2916
    ISSN 1529-2908
    DOI 10.1038/s41590-020-0647-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Training the trainable cells of the immune system and beyond.

    Kar, Upendra K / Joosten, Leo A B

    Nature immunology

    2020  Volume 21, Issue 2, Page(s) 115–119

    MeSH term(s) Animals ; Humans ; Immunity, Innate/immunology ; Immunologic Memory/immunology
    Language English
    Publishing date 2020-01-07
    Publishing country United States
    Document type Congress
    ZDB-ID 2016987-5
    ISSN 1529-2916 ; 1529-2908
    ISSN (online) 1529-2916
    ISSN 1529-2908
    DOI 10.1038/s41590-019-0583-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Transcriptomic and Proteomic Characterization of the Immune Response to Elective Spinal Reconstructive Surgery: Impact of Aging and Comparison with Traumatic Injury Response.

    Bonaroti, Jillian W / Ozel, Mehves / Chen, Tianmeng / Darby, Jennifer L / Sun, Xuejing / Moheimani, Hamed / Reitz, Katherine M / Kar, Upendra K / Zuckerbraun, Brian S / Das, Jishnu / Okonkwo, David O / Billiar, Timothy R

    Journal of the American College of Surgeons

    2023  Volume 238, Issue 5, Page(s) 924–941

    Abstract: Background: Major surgery triggers trauma-like stress responses linked to age, surgery duration, and blood loss, resembling polytrauma. This similarity suggests elective surgery as a surrogate model for studying polytrauma immune responses. We ... ...

    Abstract Background: Major surgery triggers trauma-like stress responses linked to age, surgery duration, and blood loss, resembling polytrauma. This similarity suggests elective surgery as a surrogate model for studying polytrauma immune responses. We investigated stress responses across age groups and compared them with those of polytrauma patients.
    Study design: Patients undergoing major spinal reconstruction surgery were divided into older (age >65 years, n = 5) and young (age 18 to 39 years, n = 6) groups. A comparison group consisted of matched trauma patients (n = 8). Blood samples were collected before, during, and after surgery. Bone marrow mononuclear cells and peripheral blood mononuclear cells were analyzed using cellular indexing of transcriptomes and epitopes sequencing or single-cell RNA sequencing. Plasma was subjected to dual-platform proteomic analysis (SomaLogic and O-link).
    Results: Response to polytrauma was highest within 4 hours. By comparison, the response to surgery was highest at 24 hours. Both insults triggered significant changes in cluster of differentiation 14 monocytes, with increased inflammation and lower major histocompatibility complex-class 2 expression. Older patient's cluster of differentiation 14 monocytes displayed higher inflammation and less major histocompatibility complex-class 2 suppression; a trend was also seen in bone marrow mononuclear cells. Although natural killer cells were markedly activated after polytrauma, they were suppressed after surgery, especially in older patients. In plasma, innate immunity proteins dominated at 24 hours, shifting to adaptive immunity proteins by 6 weeks with heightened inflammation in older patients. Senescence-associated secretory phenotype proteins were higher in older patients at baseline and further elevated during and after surgery.
    Conclusions: Although both major surgery and polytrauma initiate immune and stress responses, substantial differences exist in timing and cellular profiles, suggesting major elective surgery is not a suitable surrogate for the polytrauma response. Nonetheless, distinct responses in young vs older patients highlight the utility of elective spinal in studying patient-specific factors affecting outcomes after major elective surgery.
    MeSH term(s) Humans ; Aged ; Adolescent ; Young Adult ; Adult ; Transcriptome ; Leukocytes, Mononuclear ; Proteomics ; Surgery, Plastic ; Aging ; Multiple Trauma/surgery ; Gene Expression Profiling ; Immunity ; Inflammation
    Language English
    Publishing date 2023-12-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1181115-8
    ISSN 1879-1190 ; 1072-7515
    ISSN (online) 1879-1190
    ISSN 1072-7515
    DOI 10.1097/XCS.0000000000000922
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  4. Article ; Online: Integral membrane proteins: bottom-up, top-down and structural proteomics.

    Kar, Upendra K / Simonian, Margaret / Whitelegge, Julian P

    Expert review of proteomics

    2017  Volume 14, Issue 8, Page(s) 715–723

    Abstract: Introduction: Integral membrane proteins and lipids constitute the bilayer membranes that surround cells and sub-cellular compartments, and modulate movements of molecules and information between them. Since membrane protein drug targets represent a ... ...

    Abstract Introduction: Integral membrane proteins and lipids constitute the bilayer membranes that surround cells and sub-cellular compartments, and modulate movements of molecules and information between them. Since membrane protein drug targets represent a disproportionately large segment of the proteome, technical developments need timely review. Areas covered: Publically available resources such as Pubmed were surveyed. Bottom-up proteomics analyses now allow efficient extraction and digestion such that membrane protein coverage is essentially complete, making up around one third of the proteome. However, this coverage relies upon hydrophilic loop regions while transmembrane domains are generally poorly covered in peptide-based strategies. Top-down mass spectrometry where the intact membrane protein is fragmented in the gas phase gives good coverage in transmembrane regions, and membrane fractions are yielding to high-throughput top-down proteomics. Exciting progress in native mass spectrometry of membrane protein complexes is providing insights into subunit stoichiometry and lipid binding, and cross-linking strategies are contributing critical in-vivo information. Expert commentary: It is clear from the literature that integral membrane proteins have yielded to advanced techniques in protein chemistry and mass spectrometry, with applications limited only by the imagination of investigators. Key advances toward translation to the clinic are emphasized.
    MeSH term(s) Glycosylation ; Humans ; Mass Spectrometry ; Membrane Proteins/chemistry ; Membrane Proteins/metabolism ; Organelles/metabolism ; Proteomics/methods
    Chemical Substances Membrane Proteins
    Language English
    Publishing date 2017-07-31
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 2299100-1
    ISSN 1744-8387 ; 1478-9450
    ISSN (online) 1744-8387
    ISSN 1478-9450
    DOI 10.1080/14789450.2017.1359545
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Plasma proteomics reveals early, broad release of chemokine, cytokine, TNF, and interferon mediators following trauma with delayed increases in a subset of chemokines and cytokines in patients that remain critically ill.

    Bonaroti, Jillian / Billiar, Isabel / Moheimani, Hamed / Wu, Junru / Namas, Rami / Li, Shimena / Kar, Upendra K / Vodovotz, Yoram / Neal, Matthew D / Sperry, Jason L / Billiar, Timothy R

    Frontiers in immunology

    2022  Volume 13, Page(s) 1038086

    Abstract: Severe injury is known to cause a systemic cytokine storm that is associated with adverse outcomes. However, a comprehensive assessment of the time-dependent changes in circulating levels of a broad spectrum of protein immune mediators and soluble immune ...

    Abstract Severe injury is known to cause a systemic cytokine storm that is associated with adverse outcomes. However, a comprehensive assessment of the time-dependent changes in circulating levels of a broad spectrum of protein immune mediators and soluble immune mediator receptors in severely injured trauma patients remains uncharacterized. To address this knowledge gap, we defined the temporal and outcome-based patterns of 184 known immune mediators and soluble cytokine receptors in the circulation of severely injured patients. Proteomics (aptamer-based assay, SomaLogic, Inc) was performed on plasma samples drawn at 0, 24, and 72 hours (h) from time of admission from 150 trauma patients, a representative subset from the Prehospital Plasma during Air Medical Transport in Trauma Patients at Risk for Hemorrhagic Shock (PAMPer) trial. Patients were categorized into outcome groups including Early Non-Survivors (died within 72 h; ENS; n=38), Non-Resolvers (died after 72 h or required ≥7 days of intensive care; NR; n=78), and Resolvers (survivors that required < 7 days of intensive care; R; n=34), with low Injury Severity Score (ISS) patients from the Tranexamic Acid During Prehospital Transport in Patients at Risk for Hemorrhage After Injury (STAAMP) trial as controls. The major findings include an extensive release of immune mediators and cytokine receptors at time 0h that is more pronounced in ENS and NR patients. There was a selective subset of mediators elevated at 24 and 72 h to a greater degree in NR patients, including multiple cytokines and chemokines not previously described in trauma patients. These findings were validated in a quantitative fashion using mesoscale discovery immunoassays (MSD) from an external validation cohort (VC) of samples from 58 trauma patients matched for R and NR status. This comprehensive longitudinal description of immune mediator patterns associated with trauma outcomes provides a new level of characterization of the immune response that follows severe injury.
    MeSH term(s) Humans ; Cytokines ; Interferons ; Critical Illness ; Proteomics ; Chemokines ; Receptors, Cytokine
    Chemical Substances Cytokines ; Interferons (9008-11-1) ; Chemokines ; Receptors, Cytokine
    Language English
    Publishing date 2022-11-30
    Publishing country Switzerland
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2022.1038086
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  6. Article: Multi-Omic Admission-Based Prognostic Biomarkers Identified by Machine Learning Algorithms Predict Patient Recovery and 30-Day Survival in Trauma Patients.

    Abdelhamid, Sultan S / Scioscia, Jacob / Vodovotz, Yoram / Wu, Junru / Rosengart, Anna / Sung, Eunseo / Rahman, Syed / Voinchet, Robert / Bonaroti, Jillian / Li, Shimena / Darby, Jennifer L / Kar, Upendra K / Neal, Matthew D / Sperry, Jason / Das, Jishnu / Billiar, Timothy R

    Metabolites

    2022  Volume 12, Issue 9

    Abstract: Admission-based circulating biomarkers for the prediction of outcomes in trauma patients could be useful for clinical decision support. It is unknown which molecular classes of biomolecules can contribute biomarkers to predictive modeling. Here, we ... ...

    Abstract Admission-based circulating biomarkers for the prediction of outcomes in trauma patients could be useful for clinical decision support. It is unknown which molecular classes of biomolecules can contribute biomarkers to predictive modeling. Here, we analyzed a large multi-omic database of over 8500 markers (proteomics, metabolomics, and lipidomics) to identify prognostic biomarkers in the circulating compartment for adverse outcomes, including mortality and slow recovery, in severely injured trauma patients. Admission plasma samples from patients (
    Language English
    Publishing date 2022-08-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662251-8
    ISSN 2218-1989
    ISSN 2218-1989
    DOI 10.3390/metabo12090774
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  7. Article ; Online: High Dimensional Multiomics Reveals Unique Characteristics of Early Plasma Administration in Polytrauma Patients With TBI.

    Wu, Junru / Moheimani, Hamed / Li, Shimena / Kar, Upendra K / Bonaroti, Jillian / Miller, Richard S / Daley, Brian J / Harbrecht, Brian G / Claridge, Jeffrey A / Gruen, Danielle S / Phelan, Herbert A / Guyette, Francis X / Neal, Matthew D / Das, Jishnu / Sperry, Jason L / Billiar, Timothy R

    Annals of surgery

    2022  Volume 276, Issue 4, Page(s) 673–683

    Abstract: Objectives: The authors sought to identify causal factors that explain the selective benefit of prehospital administration of thawed plasma (TP) in traumatic brain injury (TBI) patients using mediation analysis of a multiomic database.: Background: ... ...

    Abstract Objectives: The authors sought to identify causal factors that explain the selective benefit of prehospital administration of thawed plasma (TP) in traumatic brain injury (TBI) patients using mediation analysis of a multiomic database.
    Background: The Prehospital Air Medical Plasma (PAMPer) Trial showed that patients with TBI and a pronounced systemic response to injury [defined as endotype 2 (E2)], have a survival benefit from prehospital administration of TP. An interrogation of high dimensional proteomics, lipidomics and metabolomics previously demonstrated unique patterns in circulating biomarkers in patients receiving prehospital TP, suggesting that a deeper analysis could reveal causal features specific to TBI patients.
    Methods: A novel proteomic database (SomaLogic Inc., aptamer-based assay, 7K platform) was generated using admission blood samples from a subset of patients (n=149) from the PAMPer Trial. This proteomic dataset was combined with previously reported metabolomic and lipidomic datasets from these same patients. A 2-step analysis was performed to identify factors that promote survival in E2-TBI patients who had received early TP. First, features were selected using both linear and multivariate-latent-factor regression analyses. Then, the selected features were entered into the causal mediation analysis.
    Results: Causal mediation analysis of observable features identified 16 proteins and 41 lipids with a high proportion of mediated effect (>50%) to explain the survival benefit of early TP in E2-TBI patients. The multivariate latent-factor regression analyses also uncovered 5 latent clusters of features with a proportion effect >30%, many in common with the observable features. Among the observable and latent features were protease inhibitors known to inhibit activated protein C and block fibrinolysis (SERPINA5 and CPB2), a clotting factor (factor XI), as well as proteins involved in lipid transport and metabolism (APOE3 and sPLA(2)-XIIA).
    Conclusions: These findings suggest that severely injured patients with TBI process exogenous plasma differently than those without TBI. The beneficial effects of early TP in E2-TBI patients may be the result of improved blood clotting and the effect of brain protective factors independent of coagulation.
    MeSH term(s) Brain Injuries, Traumatic/therapy ; Emergency Medical Services/methods ; Humans ; Multiple Trauma/therapy ; Plasma ; Proteomics
    Language English
    Publishing date 2022-07-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 340-2
    ISSN 1528-1140 ; 0003-4932
    ISSN (online) 1528-1140
    ISSN 0003-4932
    DOI 10.1097/SLA.0000000000005610
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  8. Article ; Online: Lipidomic signatures align with inflammatory patterns and outcomes in critical illness.

    Wu, Junru / Cyr, Anthony / Gruen, Danielle S / Lovelace, Tyler C / Benos, Panayiotis V / Das, Jishnu / Kar, Upendra K / Chen, Tianmeng / Guyette, Francis X / Yazer, Mark H / Daley, Brian J / Miller, Richard S / Harbrecht, Brian G / Claridge, Jeffrey A / Phelan, Herb A / Zuckerbraun, Brian S / Neal, Matthew D / Johansson, Pär I / Stensballe, Jakob /
    Namas, Rami A / Vodovotz, Yoram / Sperry, Jason L / Billiar, Timothy R

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 6789

    Abstract: Alterations in lipid metabolism have the potential to be markers as well as drivers of pathobiology of acute critical illness. Here, we took advantage of the temporal precision offered by trauma as a common cause of critical illness to identify the ... ...

    Abstract Alterations in lipid metabolism have the potential to be markers as well as drivers of pathobiology of acute critical illness. Here, we took advantage of the temporal precision offered by trauma as a common cause of critical illness to identify the dynamic patterns in the circulating lipidome in critically ill humans. The major findings include an early loss of all classes of circulating lipids followed by a delayed and selective lipogenesis in patients destined to remain critically ill. The previously reported survival benefit of early thawed plasma administration was associated with preserved lipid levels that related to favorable changes in coagulation and inflammation biomarkers in causal modelling. Phosphatidylethanolamines (PE) were elevated in patients with persistent critical illness and PE levels were prognostic for worse outcomes not only in trauma but also severe COVID-19 patients. Here we show selective rise in systemic PE as a common prognostic feature of critical illness.
    MeSH term(s) Humans ; Critical Illness ; Lipidomics ; COVID-19 ; Biomarkers ; Inflammation
    Chemical Substances Biomarkers
    Language English
    Publishing date 2022-11-10
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-34420-4
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  9. Article: Characterization of Streptococcus pneumoniae ophthalmic, systemic & commensal isolates by pulsed-field gel electrophoresis & ribotyping.

    Kar, Upendra K / Satpathy, Gita / Das, B K / Panda, S K

    The Indian journal of medical research

    2008  Volume 127, Issue 2, Page(s) 171–177

    Abstract: Background & objective: Streptococcus pneumoniae is common in ocular and systemic infections and is a part of normal nasopharyngeal flora. Very few studies regarding genetic analysis of S. pneumoniae isolates causing eye infections are available. This ... ...

    Abstract Background & objective: Streptococcus pneumoniae is common in ocular and systemic infections and is a part of normal nasopharyngeal flora. Very few studies regarding genetic analysis of S. pneumoniae isolates causing eye infections are available. This study was undertaken to do pulse field gel electrophoresis (PFGE) analysis and ribotyping of S. pneumoniae isolates obtained from eye infections, systemic infections and nasopharyngeal flora.
    Methods: Sixty one well characterized S. pneumoniae isolates (38 from ophthalmic infections, 9 from systemic infections and 14 commensals) were characterized using PFGE of the whole genome after SmaI, restriction enzyme digestion and conventional ribotyping using Escherichia coli rRNA operon as the probe. Phylogenetic tree was drawn using unweighted pair group method analysis (UPGMA).
    Results: The 38 S. pneumoniae isolates from eye infections belonging to 15 serotypes were placed in to 11 PFGE types and 15 ribotypes. The 9 systemic isolates (7 seotypes) were distributed in 7 PFGE types and 6 ribotypes. The 14 commensal isolates were placed in 11 serotypes, 5 PFGE types and 6 ribotypes. Most of the PFGE types and ribotypes consisting of ocular isolates also contained systemic and commensal isolates.
    Interpretation & conclusion: Considerable genetic similarity was observed between the isolates from ocular and systemic infections and those colonized in nasopharynx. PFGE analysis could differentiate majority of the isolates according to site of infections. There was a considerable DNA polymorphism within the studied bacterial population.
    MeSH term(s) Bacterial Typing Techniques ; DNA/metabolism ; DNA, Bacterial/metabolism ; Electrophoresis, Gel, Pulsed-Field ; Eye Infections/microbiology ; Genes, Bacterial ; Humans ; Models, Genetic ; Molecular Weight ; Phylogeny ; Pneumococcal Infections/microbiology ; Polymorphism, Genetic ; Ribotyping/methods ; Software ; Streptococcus pneumoniae/metabolism
    Chemical Substances DNA, Bacterial ; DNA (9007-49-2)
    Language English
    Publishing date 2008-02
    Publishing country India
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 390883-5
    ISSN 0971-5916 ; 0019-5340
    ISSN 0971-5916 ; 0019-5340
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Inhibition of Hepatitis E virus replication using short hairpin RNA (shRNA).

    Kumar, Amit / Panda, Subrat Kumar / Durgapal, Hemlata / Acharya, Subrat Kumar / Rehman, Shagufta / Kar, Upendra K

    Antiviral research

    2010  Volume 85, Issue 3, Page(s) 541–550

    Abstract: Hepatitis E virus (HEV) is a non-enveloped, single-stranded, positive sense RNA virus, which is a major cause of water-borne hepatitis. RNA interference (RNAi) is a sequence-specific cellular antiviral defence mechanism, induced by double-stranded RNA, ... ...

    Abstract Hepatitis E virus (HEV) is a non-enveloped, single-stranded, positive sense RNA virus, which is a major cause of water-borne hepatitis. RNA interference (RNAi) is a sequence-specific cellular antiviral defence mechanism, induced by double-stranded RNA, which we used to investigate knockdown of several genes and the 3' cis-acting element (CAE) of HEV. In the present report, shRNAs were developed against the putative helicase and replicase domains and the 3'CAE region of HEV. Production of siRNA was confirmed by northern hybridization. The possible innate response induction due to shRNA expressions was verified by transcript analysis for interferon-beta and 2',5'-oligoadenylate synthetase genes and was found to be absent. Initially, the selected shRNAs were tested for their efficiency against the respective genes/3'CAE using inhibition of fused viral subgenomic target domain-renilla luciferase reporter constructs. The effective shRNAs were studied for their inhibitory effects on HEV replication in HepG2 cells using HEV replicon and reporter replicon. RNAi mediated silencing was demonstrated by reduction of luciferase activity in subgenomic target-reporter constructs and reporter replicon. The real time PCR was used to demonstrate inhibition of native replicon replication in transfected cells. Designed shRNAs were found to be effective in inhibiting virus replication to a variable extent (45-93%).
    MeSH term(s) Antiviral Agents/pharmacology ; Biological Products/genetics ; Biological Products/pharmacology ; Cell Line ; Gene Silencing ; Genes, Viral ; Hepatitis E virus/drug effects ; Hepatitis E virus/physiology ; Hepatocytes/virology ; Humans ; RNA, Small Interfering/genetics ; RNA, Small Interfering/pharmacology ; Virus Replication/drug effects
    Chemical Substances Antiviral Agents ; Biological Products ; RNA, Small Interfering
    Language English
    Publishing date 2010-03
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 306628-9
    ISSN 1872-9096 ; 0166-3542
    ISSN (online) 1872-9096
    ISSN 0166-3542
    DOI 10.1016/j.antiviral.2010.01.005
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