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  1. Article ; Online: Host response signature trends in bacteraemia.

    Brandon, Richard B / Yager, Thomas D / Cermelli, Silvia / Davis, Roy F / Navalkar, Krupa

    Infectious diseases (London, England)

    2024  Volume 56, Issue 5, Page(s) 416–417

    MeSH term(s) Humans ; Bacteremia
    Language English
    Publishing date 2024-02-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2839775-7
    ISSN 2374-4243 ; 2374-4235
    ISSN (online) 2374-4243
    ISSN 2374-4235
    DOI 10.1080/23744235.2024.2324072
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Thesis ; Online: Antibody Based Strategies For Multiplexed Diagnostics

    Navalkar, Krupa Arun

    2014  

    Abstract: Peptide microarrays are to proteomics as sequencing is to genomics. As microarrays become more content-rich, higher resolution proteomic studies will parallel deep sequencing of nucleic acids. Antigen-antibody interactions can be studied at a much higher ...

    Abstract Peptide microarrays are to proteomics as sequencing is to genomics. As microarrays become more content-rich, higher resolution proteomic studies will parallel deep sequencing of nucleic acids. Antigen-antibody interactions can be studied at a much higher resolution using microarrays than was possible only a decade ago. My dissertation focuses on testing the feasibility of using either the Immunosignature platform, based on non-natural peptide sequences, or a pathogen peptide microarray, which uses bioinformatically-selected peptides from pathogens for creating sensitive diagnostics. Both diagnostic applications use relatively little serum from infected individuals, but each approaches diagnosis of disease differently. The first project compares pathogen epitope peptide (life-space) and non-natural (random-space) peptide microarrays while using them for the early detection of Coccidioidomycosis (Valley Fever). The second project uses NIAID category A, B and C priority pathogen epitope peptides in a multiplexed microarray platform to assess the feasibility of using epitope peptides to simultaneously diagnose multiple exposures using a single assay. Cross-reactivity is a consistent feature of several antigen-antibody based immunodiagnostics. This work utilizes microarray optimization and bioinformatic approaches to distill the underlying disease specific antibody signature pattern. Circumventing inherent cross-reactivity observed in antibody binding to peptides was crucial to achieve the goal of this work to accurately distinguishing multiple exposures simultaneously.
    Keywords Medicine|Bioinformatics|Immunology
    Subject code 540
    Language ENG
    Publishing date 2014-01-01 00:00:01.0
    Publisher Arizona State University
    Publishing country us
    Document type Thesis ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Stratification of COVID-19 Severity Using SeptiCyte RAPID, a Novel Host Immune Response Test.

    Gravrand, Victor / Mellot, François / Ackermann, Felix / Ballester, Marie-Christine / Zuber, Benjamin / Kirk, James T / Navalkar, Krupa / Yager, Thomas D / Petit, Fabien / Pascreau, Tiffany / Farfour, Eric / Vasse, Marc

    Viruses

    2023  Volume 15, Issue 2

    Abstract: ... ...

    Abstract SeptiCyte
    MeSH term(s) Humans ; COVID-19 Testing ; COVID-19/diagnosis ; SARS-CoV-2/genetics ; Sepsis/diagnosis ; Area Under Curve ; Lung Injury ; Proteins
    Chemical Substances PLAC8 protein, human ; Proteins
    Language English
    Publishing date 2023-02-02
    Publishing country Switzerland
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15020419
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Peptide based diagnostics: are random-sequence peptides more useful than tiling proteome sequences?

    Navalkar, Krupa Arun / Johnston, Stephan Albert / Stafford, Phillip

    Journal of immunological methods

    2015  Volume 417, Page(s) 10–21

    Abstract: Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based ... ...

    Abstract Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based rather than peptide-based disease detection is more specific. We examined two different approaches to peptide-based diagnostics using Coccidioides (aka Valley Fever) as the disease model. Although the pathogen was discovered more than a century ago, a highly sensitive diagnostic remains unavailable. We present a case study where two different approaches to diagnosing Valley Fever were used: first, overlapping Valley Fever epitopes representing immunodominant Coccidioides antigens were tiled using a microarray format of presynthesized peptides. Second, a set of random sequence peptides identified using a 10,000 peptide immunosignaturing microarray was compared for sensitivity and specificity. The scientific hypothesis tested was that actual epitope peptides from Coccidioides would provide sufficient sensitivity and specificity as a diagnostic. Results demonstrated that random sequence peptides exhibited higher accuracy when classifying different stages of Valley Fever infection vs. epitope peptides. The epitope peptide array did provide better performance than the existing immunodiffusion array, but when directly compared to the random sequence peptides, reported lower overall accuracy. This study suggests that there are competing aspects of antibody recognition that involve conservation of pathogen sequence and aspects of mimotope recognition and amino acid substitutions. These factors may prove critical when developing the next generation of high-performance immunodiagnostics.
    MeSH term(s) Amino Acid Sequence ; Antigens, Fungal/immunology ; Coccidioides/immunology ; Coccidioidomycosis/diagnosis ; Epitopes/immunology ; High-Throughput Screening Assays/methods ; Humans ; Peptides ; Protein Array Analysis/methods ; Proteome/immunology
    Chemical Substances Antigens, Fungal ; Epitopes ; Peptides ; Proteome
    Language English
    Publishing date 2015-02
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 120142-6
    ISSN 1872-7905 ; 0022-1759
    ISSN (online) 1872-7905
    ISSN 0022-1759
    DOI 10.1016/j.jim.2014.12.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Peptide based diagnostics: Are random-sequence peptides more useful than tiling proteome sequences?

    Navalkar, Krupa Arun / Phillip Stafford / Stephan Albert Johnston

    Journal of Immunological Methods. 2015 Feb., v. 417

    2015  

    Abstract: Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based ... ...

    Abstract Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based rather than peptide-based disease detection is more specific. We examined two different approaches to peptide-based diagnostics using Coccidioides (aka Valley Fever) as the disease model. Although the pathogen was discovered more than a century ago, a highly sensitive diagnostic remains unavailable. We present a case study where two different approaches to diagnosing Valley Fever were used: first, overlapping Valley Fever epitopes representing immunodominant Coccidioides antigens were tiled using a microarray format of presynthesized peptides. Second, a set of random sequence peptides identified using a 10,000 peptide immunosignaturing microarray was compared for sensitivity and specificity. The scientific hypothesis tested was that actual epitope peptides from Coccidioides would provide sufficient sensitivity and specificity as a diagnostic. Results demonstrated that random sequence peptides exhibited higher accuracy when classifying different stages of Valley Fever infection vs. epitope peptides. The epitope peptide array did provide better performance than the existing immunodiffusion array, but when directly compared to the random sequence peptides, reported lower overall accuracy. This study suggests that there are competing aspects of antibody recognition that involve conservation of pathogen sequence and aspects of mimotope recognition and amino acid substitutions. These factors may prove critical when developing the next generation of high-performance immunodiagnostics.
    Keywords amino acid substitution ; antibodies ; case studies ; Coccidioides ; coccidioidomycosis ; diagnostic techniques ; disease detection ; disease models ; epitopes ; ligands ; microarray technology ; pathogens ; peptides ; proteome ; reports
    Language English
    Dates of publication 2015-02
    Size p. 10-21.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 120142-6
    ISSN 1872-7905 ; 0022-1759
    ISSN (online) 1872-7905
    ISSN 0022-1759
    DOI 10.1016/j.jim.2014.12.002
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Validation of SeptiCyte RAPID to Discriminate Sepsis from Non-Infectious Systemic Inflammation.

    Balk, Robert / Esper, Annette M / Martin, Greg S / Miller, Russell R / Lopansri, Bert K / Burke, John P / Levy, Mitchell / Opal, Steven / Rothman, Richard E / D'Alessio, Franco R / Sidhaye, Venkataramana K / Aggarwal, Neil R / Greenberg, Jared A / Yoder, Mark / Patel, Gourang / Gilbert, Emily / Parada, Jorge P / Afshar, Majid / Kempker, Jordan A /
    van der Poll, Tom / Schultz, Marcus J / Scicluna, Brendon P / Klein Klouwenberg, Peter M C / Liebler, Janice / Blodget, Emily / Kumar, Santhi / Navalkar, Krupa / Yager, Thomas D / Sampson, Dayle / Kirk, James T / Cermelli, Silvia / Davis, Roy F / Brandon, Richard B

    Journal of clinical medicine

    2024  Volume 13, Issue 5

    Abstract: 1) ...

    Abstract (1)
    Language English
    Publishing date 2024-02-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662592-1
    ISSN 2077-0383
    ISSN 2077-0383
    DOI 10.3390/jcm13051194
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Stratification of COVID-19 severity using SeptiCyte RAPID, a novel host immune response test

    Gravrand, Victor / Mellot, François / Ackermann, Felix / Ballester, Marie-Christine / Zuber, Benjamin / Kirk, James T. / Navalkar, Krupa / Yager, Thomas D. / Petit, Fabien / Pascreau, Tiffany / Farfour, Eric / Vasse, Marc

    medRxiv

    Abstract: SeptiCyte RAPID is a gene expression assay measuring the relative expression levels of host response genes PLA2G7 and PLAC8, indicative of a dysregulated immune response during sepsis. As severe forms of COVID-19 may be considered viral sepsis, we ... ...

    Abstract SeptiCyte RAPID is a gene expression assay measuring the relative expression levels of host response genes PLA2G7 and PLAC8, indicative of a dysregulated immune response during sepsis. As severe forms of COVID-19 may be considered viral sepsis, we evaluated SeptiCyte RAPID in a series of 94 patients admitted to Foch Hospital (Suresnes, France) with proven SARS-CoV-2 infection. EDTA blood was collected in the emergency department (ED) in 67 cases, in the intensive care unit (ICU) in 23 cases and in conventional units in 4 cases. SeptiScore (0-15 scale) increased with COVID-19 severity. Patients in ICU had the highest SeptiScores, producing values comparable to 8 patients with culture-confirmed bacterial sepsis. Receiver operating characteristic (ROC) curve analysis had an area under the curve (AUC) of 0.81 for discriminating patients requiring ICU admission from patients who were immediately discharged or from patients requiring hospitalization in conventional units. SeptiScores increased with the extent of the lung injury. For 68 patients, a chest computed tomography (CT) scan was performed within 24 hours of COVID-19 diagnosis. SeptiScore > 7 suggested lung injury ≥ 50 % (AUC = 0.86). SeptiCyte RAPID was compared to other biomarkers for discriminating Critical + Severe COVID-19 in ICU, versus Moderate + Mild COVID-19 not in ICU. The mean AUC for SeptiCyte RAPID was superior to that of any individual biomarker or combination thereof. In contrast to C-reactive protein (CRP), correlation of SeptiScore with lung injury was not impacted by treatment with anti-inflammatory agents. SeptiCyte RAPID can be a useful tool to identify patients with severe forms of COVID-19 in ED, as well as during follow-up.
    Keywords covid19
    Language English
    Publishing date 2022-09-18
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2022.09.15.22279735
    Database COVID19

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  8. Article ; Online: Evaluation of the host immune response assay SeptiCyte RAPID for potential triage of COVID-19 patients.

    Montero, Maria Milagro / Hardy-Werbin, Max / Gonzalez-Gallardo, Soledad / Torres, Erica / Rueda, Rebeca / Hannet, Irene / Kirk, James T / Yager, Thomas D / Navalkar, Krupa / Arenas, Maria Del Mar / Arietta-Aldea, Itziar / Castañeda, Silvia / Gómez-Junyent, Joan / Gómez-Zorrilla, Silvia / Guerri-Fernandez, Roberto / Sanchez-Martinez, Francisca / López-Montesinos, Immaculada / Pelegrín, Ivan / Sendra, Elena /
    Sorlí, Luisa / Villar-García, Judith / Bellosillo, Beatriz / Horcajada, Juan Pablo

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 944

    Abstract: Tools for the evaluation of COVID-19 severity would help clinicians with triage decisions, especially the decision whether to admit to ICU. The aim of this study was to evaluate SeptiCyte RAPID, a host immune response assay (Immunexpress, Seattle USA) as ...

    Abstract Tools for the evaluation of COVID-19 severity would help clinicians with triage decisions, especially the decision whether to admit to ICU. The aim of this study was to evaluate SeptiCyte RAPID, a host immune response assay (Immunexpress, Seattle USA) as a triaging tool for COVID-19 patients requiring hospitalization and potentially ICU care. SeptiCyte RAPID employs a host gene expression signature consisting of the ratio of expression levels of two immune related mRNAs, PLA2G7 and PLAC8, measured from whole blood samples. Blood samples from 146 adult SARS-CoV-2 (+) patients were collected within 48 h of hospital admission in PAXgene blood RNA tubes at Hospital del Mar, Barcelona, Spain, between July 28th and December 1st, 2020. Data on demographics, vital signs, clinical chemistry parameters, radiology, interventions, and SeptiCyte RAPID were collected and analyzed with bioinformatics methods. The performance of SeptiCyte RAPID for COVID-19 severity assessment and ICU admission was evaluated, relative to the comparator of retrospective clinical assessment by the Hospital del Mar clinical care team. In conclusion, SeptiCyte RAPID was able to stratify COVID-19 cases according to clinical severity: critical vs. mild (AUC = 0.93, p < 0.0001), critical vs. moderate (AUC = 0.77, p = 0.002), severe vs. mild (AUC = 0.85, p = 0.0003), severe vs. moderate (AUC = 0.63, p = 0.05). This discrimination was significantly better (by AUC or p-value) than could be achieved by CRP, lactate, creatine, IL-6, or D-dimer. Some of the critical or severe cases had "early" blood draws (before ICU admission; n = 33). For these cases, when compared to moderate and mild cases not in ICU (n = 37), SeptiCyte RAPID had AUC = 0.78 (p = 0.00012). In conclusion, SeptiCyte RAPID was able to stratify COVID-19 cases according to clinical severity as defined by the WHO COVID-19 Clinical Management Living Guidance of January 25th, 2021. Measurements taken early (before a patient is considered for ICU admission) suggest that high SeptiScores could aid in predicting the need for later ICU admission.
    MeSH term(s) Adult ; Humans ; COVID-19/diagnosis ; SARS-CoV-2/genetics ; Retrospective Studies ; Triage ; Spain ; Intensive Care Units ; Proteins
    Chemical Substances PLAC8 protein, human ; Proteins
    Language English
    Publishing date 2023-01-18
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-28178-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Serum Protein Changes in Pediatric Sepsis Patients Identified With an Aptamer-Based Multiplexed Proteomic Approach.

    Shubin, Nicholas J / Navalkar, Krupa / Sampson, Dayle / Yager, Thomas D / Cermelli, Silvia / Seldon, Therese / Sullivan, Erin / Zimmerman, Jerry J / Permut, Lester C / Piliponsky, Adrian M

    Critical care medicine

    2019  Volume 48, Issue 1, Page(s) e48–e57

    Abstract: Objectives: Sepsis, a life-threatening organ dysfunction caused by a dysregulated host response to infection, is a leading cause of death and disability among children worldwide. Identifying sepsis in pediatric patients is difficult and can lead to ... ...

    Abstract Objectives: Sepsis, a life-threatening organ dysfunction caused by a dysregulated host response to infection, is a leading cause of death and disability among children worldwide. Identifying sepsis in pediatric patients is difficult and can lead to treatment delay. Our objective was to assess the host proteomic response to infection utilizing an aptamer-based multiplexed proteomics approach to identify novel serum protein changes that might help distinguish between pediatric sepsis and infection-negative systemic inflammation and hence can potentially improve sensitivity and specificity of the diagnosis of sepsis over current clinical criteria approaches.
    Design: Retrospective, observational cohort study.
    Setting: PICU and cardiac ICU, Seattle Children's Hospital, Seattle, WA.
    Patients: A cohort of 40 children with clinically overt sepsis and 30 children immediately postcardiopulmonary bypass surgery (infection-negative systemic inflammation control subjects) was recruited. Children with sepsis had a confirmed or suspected infection, two or more systemic inflammatory response syndrome criteria, and at least cardiovascular and/or pulmonary organ dysfunction.
    Interventions: None.
    Measurements and main results: Serum samples from 35 of the sepsis and 28 of the bypass surgery subjects were available for screening with an aptamer-based proteomic platform that measures 1,305 proteins to search for large-scale serum protein expression pattern changes in sepsis. A total of 111 proteins were significantly differentially expressed between the sepsis and control groups, using the linear models for microarray data (linear modeling) and Boruta (decision trees) R packages, with 55 being previously identified in sepsis patients. Weighted gene correlation network analysis helped identify 76 proteins that correlated highly with clinical sepsis traits, 27 of which had not been previously reported in sepsis.
    Conclusions: The serum protein changes identified with the aptamer-based multiplexed proteomics approach used in this study can be useful to distinguish between sepsis and noninfectious systemic inflammation.
    MeSH term(s) Aptamers, Peptide ; Blood Proteins/analysis ; Child ; Cohort Studies ; Humans ; Proteomics/methods ; Retrospective Studies ; Sepsis/blood ; Sepsis/diagnosis ; Sepsis/genetics
    Chemical Substances Aptamers, Peptide ; Blood Proteins
    Language English
    Publishing date 2019-12-02
    Publishing country United States
    Document type Journal Article ; Observational Study
    ZDB-ID 197890-1
    ISSN 1530-0293 ; 0090-3493
    ISSN (online) 1530-0293
    ISSN 0090-3493
    DOI 10.1097/CCM.0000000000004083
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: GuiTope

    Halperin Rebecca F / Stafford Phillip / Emery Jack S / Navalkar Krupa / Johnston Stephen

    BMC Bioinformatics, Vol 13, Iss 1, p

    an application for mapping random-sequence peptides to protein sequences

    2012  Volume 1

    Abstract: Abstract Background Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein ...

    Abstract Abstract Background Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. Results GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. Conclusions GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC) at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.
    Keywords Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Subject code 004
    Language English
    Publishing date 2012-01-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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