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  1. Article: Open Development and Clinical Validation Of Multiple 3D-Printed Sample-Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing Bottleneck.

    Callahan, Cody J / Lee, Rose / Zulauf, Katelyn E / Tamburello, Lauren / Smith, Kenneth P / Previtera, Joe / Cheng, Annie / Green, Alex / Azim, Ahmed Abdul / Yano, Amanda / Doraiswami, Nancy / Kirby, James E / Arnaout, Ramy A

    medRxiv : the preprint server for health sciences

    2020  

    Abstract: The SARS-CoV-2 pandemic has caused a severe international shortage of the nasopharyngeal swabs that are required for collection of optimal specimens, creating a critical bottleneck in the way of high-sensitivity virological testing for COVID-19. To ... ...

    Abstract The SARS-CoV-2 pandemic has caused a severe international shortage of the nasopharyngeal swabs that are required for collection of optimal specimens, creating a critical bottleneck in the way of high-sensitivity virological testing for COVID-19. To address this crisis, we designed and executed an innovative, radically cooperative, rapid-response translational-research program that brought together healthcare workers, manufacturers, and scientists to emergently develop and clinically validate new swabs for immediate mass production by 3D printing. We performed a rigorous multi-step preclinical evaluation on 160 swab designs and 48 materials from 24 companies, laboratories, and individuals, and shared results and other feedback via a public data repository (http://github.com/rarnaout/Covidswab/). We validated four prototypes through an institutional review board (IRB)-approved clinical trial that involved 276 outpatient volunteers who presented to our hospital's drive-through testing center with symptoms suspicious for COVID-19. Each participant was swabbed with a reference swab (the control) and a prototype, and SARS-CoV-2 reverse-transcriptase polymerase chain reaction (RT-PCR) results were compared. All prototypes displayed excellent concordance with the control (κ=0.85-0.89). Cycle-threshold (Ct) values were not significantly different between each prototype and the control, supporting the new swabs' non-inferiority (Mann-Whitney U [MWU] p>0.05). Study staff preferred one of the prototypes over the others and the control swab overall. The total time elapsed between identification of the problem and validation of the first prototype was 22 days. Contact information for ordering can be found at http://printedswabs.org. Our experience holds lessons for the rapid development, validation, and deployment of new technology for this pandemic and beyond.
    Keywords covid19
    Language English
    Publishing date 2020-05-07
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.04.14.20065094
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Guidelines for Diagnosis and Management of Infective Endocarditis in Adults: A WikiGuidelines Group Consensus Statement.

    McDonald, Emily G / Aggrey, Gloria / Tarik Aslan, Abdullah / Casias, Michael / Cortes-Penfield, Nicolas / Dong, Mei Qin Denise / Egbert, Susan / Footer, Brent / Isler, Burcu / King, Madeline / Maximos, Mira / Wuerz, Terence C / Azim, Ahmed Abdul / Alza-Arcila, Jhongert / Bai, Anthony D / Blyth, Michelle / Boyles, Tom / Caceres, Juan / Clark, Devin /
    Davar, Kusha / Denholm, Justin T / Forrest, Graeme / Ghanem, Bassam / Hagel, Stefan / Hanretty, Alexandra / Hamilton, Fergus / Jent, Philipp / Kang, Minji / Kludjian, Geena / Lahey, Tim / Lapin, Jonathan / Lee, Rachael / Li, Timothy / Mehta, Dhara / Moore, Jessica / Mowrer, Clayton / Ouellet, Georges / Reece, Rebecca / Ryder, Jonathan H / Sanctuaire, Alexandre / Sanders, James M / Stoner, Bobbi Jo / So, Jessica M / Tessier, Jean-François / Tirupathi, Raghavendra / Tong, Steven Y C / Wald-Dickler, Noah / Yassin, Arsheena / Yen, Christina / Spellberg, Brad / Lee, Todd C

    JAMA network open

    2023  Volume 6, Issue 7, Page(s) e2326366

    Abstract: Importance: Practice guidelines often provide recommendations in which the strength of the recommendation is dissociated from the quality of the evidence.: Objective: To create a clinical guideline for the diagnosis and management of adult bacterial ... ...

    Abstract Importance: Practice guidelines often provide recommendations in which the strength of the recommendation is dissociated from the quality of the evidence.
    Objective: To create a clinical guideline for the diagnosis and management of adult bacterial infective endocarditis (IE) that addresses the gap between the evidence and recommendation strength.
    Evidence review: This consensus statement and systematic review applied an approach previously established by the WikiGuidelines Group to construct collaborative clinical guidelines. In April 2022 a call to new and existing members was released electronically (social media and email) for the next WikiGuidelines topic, and subsequently, topics and questions related to the diagnosis and management of adult bacterial IE were crowdsourced and prioritized by vote. For each topic, PubMed literature searches were conducted including all years and languages. Evidence was reported according to the WikiGuidelines charter: clear recommendations were established only when reproducible, prospective, controlled studies provided hypothesis-confirming evidence. In the absence of such data, clinical reviews were crafted discussing the risks and benefits of different approaches.
    Findings: A total of 51 members from 10 countries reviewed 587 articles and submitted information relevant to 4 sections: establishing the diagnosis of IE (9 questions); multidisciplinary IE teams (1 question); prophylaxis (2 questions); and treatment (5 questions). Of 17 unique questions, a clear recommendation could only be provided for 1 question: 3 randomized clinical trials have established that oral transitional therapy is at least as effective as intravenous (IV)-only therapy for the treatment of IE. Clinical reviews were generated for the remaining questions.
    Conclusions and relevance: In this consensus statement that applied the WikiGuideline method for clinical guideline development, oral transitional therapy was at least as effective as IV-only therapy for the treatment of IE. Several randomized clinical trials are underway to inform other areas of practice, and further research is needed.
    MeSH term(s) Adult ; Humans ; Consensus ; Endocarditis/diagnosis ; Endocarditis/therapy ; Endocarditis, Bacterial/prevention & control ; Prospective Studies ; Practice Guidelines as Topic
    Language English
    Publishing date 2023-07-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2574-3805
    ISSN (online) 2574-3805
    DOI 10.1001/jamanetworkopen.2023.26366
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The basophil surface marker CD203c identifies Aspergillus species sensitization in patients with cystic fibrosis.

    Mirković, Bojana / Lavelle, Gillian M / Azim, Ahmed Abdul / Helma, Kristine / Gargoum, Fatma S / Molloy, Kevin / Gernez, Yael / Dunne, Katie / Renwick, Julie / Murphy, Philip / Moss, Richard B / Greene, Catherine M / Gunaratnam, Cedric / Chotirmall, Sanjay H / McElvaney, Noel G

    The Journal of allergy and clinical immunology

    2016  Volume 137, Issue 2, Page(s) 436–443.e9

    Abstract: Background: Colonization by Aspergillus fumigatus in patients with cystic fibrosis (CF) can cause A fumigatus sensitization and/or allergic bronchopulmonary aspergillosis (ABPA), which affects pulmonary function and clinical outcomes. Recent studies ... ...

    Abstract Background: Colonization by Aspergillus fumigatus in patients with cystic fibrosis (CF) can cause A fumigatus sensitization and/or allergic bronchopulmonary aspergillosis (ABPA), which affects pulmonary function and clinical outcomes. Recent studies show that specific allergens upregulate the surface-expressed basophil marker CD203c in sensitized subjects, a response that can be readily measured by using flow cytometry.
    Objective: We sought to identify A fumigatus sensitization in patients with CF by using the basophil activation test (BAT).
    Methods: Patients with CF attending Beaumont Hospital were screened for study inclusion. BAT was used to identify A fumigatus sensitization. Serologic (total and A fumigatus-specific IgE), pulmonary function, and body mass index measurements were performed.
    Results: The BAT discriminates A fumigatus-sensitized from nonsensitized patients with CF. Persistent isolation of A fumigatus in sputum is a significant risk factor for A fumigatus sensitization. Levels of the A fumigatus-stimulated basophil activation marker CD203c inversely correlated with pulmonary function and body mass index in A fumigatus-sensitized but not nonsensitized patients with CF. Total and A fumigatus-specific IgE, but not IgG, levels are increased in A fumigatus-sensitized patients with CF and ABPA when compared with those in A fumigatus-sensitized and nonsensitized patients with CF without ABPA. Itraconazole treatment did not affect A fumigatus sensitization.
    Conclusion: Combining the BAT with routine serologic testing allows classification of patients with CF into 3 groups: nonsensitized, A fumigatus-sensitized, and ABPA. Accurate and prompt identification of A fumigatus-associated clinical status might allow early and targeted therapeutic intervention, potentially improving clinical outcomes.
    MeSH term(s) Antibody Specificity/immunology ; Antifungal Agents/pharmacology ; Antifungal Agents/therapeutic use ; Antigens, Fungal/immunology ; Antigens, Surface/metabolism ; Aspergillosis/diagnosis ; Aspergillosis/drug therapy ; Aspergillosis/etiology ; Aspergillosis/metabolism ; Aspergillus/immunology ; Basophils/immunology ; Basophils/metabolism ; Biomarkers ; Body Mass Index ; Cystic Fibrosis/complications ; Cystic Fibrosis/physiopathology ; Female ; Forced Expiratory Volume ; Humans ; Immunoglobulin E/blood ; Immunoglobulin E/immunology ; Immunoglobulin G/blood ; Immunoglobulin G/immunology ; Immunophenotyping ; Leukocyte Count ; Male ; Phosphoric Diester Hydrolases/metabolism ; Prospective Studies ; Pyrophosphatases/metabolism ; Sputum/immunology ; Sputum/microbiology
    Chemical Substances Antifungal Agents ; Antigens, Fungal ; Antigens, Surface ; Biomarkers ; ENPP3 protein, human ; Immunoglobulin G ; Immunoglobulin E (37341-29-0) ; Phosphoric Diester Hydrolases (EC 3.1.4.-) ; Pyrophosphatases (EC 3.6.1.-)
    Language English
    Publishing date 2016-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 121011-7
    ISSN 1097-6825 ; 1085-8725 ; 0091-6749
    ISSN (online) 1097-6825 ; 1085-8725
    ISSN 0091-6749
    DOI 10.1016/j.jaci.2015.07.045
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The Role of Short-Chain Fatty Acids, Produced by Anaerobic Bacteria, in the Cystic Fibrosis Airway.

    Mirković, Bojana / Murray, Michelle A / Lavelle, Gillian M / Molloy, Kevin / Azim, Ahmed Abdul / Gunaratnam, Cedric / Healy, Fiona / Slattery, Dubhfeasa / McNally, Paul / Hatch, Joe / Wolfgang, Matthew / Tunney, Michael M / Muhlebach, Marianne S / Devery, Rosaleen / Greene, Catherine M / McElvaney, Noel G

    American journal of respiratory and critical care medicine

    2015  Volume 192, Issue 11, Page(s) 1314–1324

    Abstract: Rationale: Anaerobic bacteria are present in large numbers in the airways of people with cystic fibrosis (PWCF). In the gut, anaerobes produce short-chain fatty acids (SCFAs) that modulate immune and inflammatory processes.: Objectives: To ... ...

    Abstract Rationale: Anaerobic bacteria are present in large numbers in the airways of people with cystic fibrosis (PWCF). In the gut, anaerobes produce short-chain fatty acids (SCFAs) that modulate immune and inflammatory processes.
    Objectives: To investigate the capacity of anaerobes to contribute to cystic fibrosis (CF) airway pathogenesis via SCFAs.
    Methods: Samples of 109 PWCF were processed using anaerobic microbiological culture with bacteria present identified by 16S RNA sequencing. SCFA levels in anaerobic supernatants and bronchoalveolar lavage (BAL) were determined by gas chromatography. The mRNA and/or protein expression of two SCFA receptors, GPR41 and GPR43, in CF and non-CF bronchial brushings and 16HBE14o(-) and CFBE41o(-) cells were evaluated using reverse transcription polymerase chain reaction, Western blot analysis, laser scanning cytometry, and confocal microscopy. SCFA-induced IL-8 secretion was monitored by ELISA.
    Measurements and main results: Fifty-seven (52.3%) of 109 PWCF were anaerobe positive. Prevalence increased with age, from 33.3% to 57.7% in PWCF younger (n = 24) and older (n = 85) than 6 years of age. All evaluated anaerobes produced millimolar concentrations of SCFAs, including acetic, propionic, and butyric acids. SCFA levels were higher in BAL samples of adults than in those of children. GPR41 levels were elevated in CFBE41o(-) versus 16HBE14o(-) cells; CF versus non-CF bronchial brushings; and 16HBE14o(-) cells after treatment with cystic fibrosis transmembrane conductance regulator inhibitor CFTR(inh)-172, CF BAL, or inducers of endoplasmic reticulum stress. SCFAs induced a dose-dependent and pertussis toxin-sensitive IL-8 response in bronchial epithelial cells, with a higher production of IL-8 in CFBE41o(-) than in 16HBE14o(-) cells.
    Conclusions: This study illustrates that SCFAs contribute to excessive production of IL-8 in CF airways colonized with anaerobes via up-regulated GPR41.
    MeSH term(s) Adolescent ; Adult ; Age Factors ; Bacteria, Anaerobic ; Blotting, Western ; Bronchoalveolar Lavage Fluid/microbiology ; Child ; Child, Preschool ; Chromatography, Gas ; Cystic Fibrosis/microbiology ; Cystic Fibrosis Transmembrane Conductance Regulator/analysis ; Enzyme-Linked Immunosorbent Assay ; Epithelial Cells/microbiology ; Fatty Acids/biosynthesis ; Female ; Humans ; Infant ; Male ; Middle Aged ; Polymerase Chain Reaction ; Respiratory Mucosa/microbiology ; Up-Regulation ; Young Adult
    Chemical Substances Fatty Acids ; Cystic Fibrosis Transmembrane Conductance Regulator (126880-72-6)
    Language English
    Publishing date 2015-08-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.201505-0943OC
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  5. Article ; Online: Immunogenicity of the Ad26.COV2.S Vaccine for COVID-19.

    Stephenson, Kathryn E / Le Gars, Mathieu / Sadoff, Jerald / de Groot, Anne Marit / Heerwegh, Dirk / Truyers, Carla / Atyeo, Caroline / Loos, Carolin / Chandrashekar, Abishek / McMahan, Katherine / Tostanoski, Lisa H / Yu, Jingyou / Gebre, Makda S / Jacob-Dolan, Catherine / Li, Zhenfeng / Patel, Shivani / Peter, Lauren / Liu, Jinyan / Borducchi, Erica N /
    Nkolola, Joseph P / Souza, Morgana / Tan, Chen Sabrina / Zash, Rebecca / Julg, Boris / Nathavitharana, Ruvandhi R / Shapiro, Roger L / Azim, Ahmed Abdul / Alonso, Carolyn D / Jaegle, Kate / Ansel, Jessica L / Kanjilal, Diane G / Guiney, Caitlin J / Bradshaw, Connor / Tyler, Anna / Makoni, Tatenda / Yanosick, Katherine E / Seaman, Michael S / Lauffenburger, Douglas A / Alter, Galit / Struyf, Frank / Douoguih, Macaya / Van Hoof, Johan / Schuitemaker, Hanneke / Barouch, Dan H

    JAMA

    2021  Volume 325, Issue 15, Page(s) 1535–1544

    Abstract: Importance: Control of the global COVID-19 pandemic will require the development and deployment of safe and effective vaccines.: Objective: To evaluate the immunogenicity of the Ad26.COV2.S vaccine (Janssen/Johnson & Johnson) in humans, including the ...

    Abstract Importance: Control of the global COVID-19 pandemic will require the development and deployment of safe and effective vaccines.
    Objective: To evaluate the immunogenicity of the Ad26.COV2.S vaccine (Janssen/Johnson & Johnson) in humans, including the kinetics, magnitude, and phenotype of SARS-CoV-2 spike-specific humoral and cellular immune responses.
    Design, setting, and participants: Twenty-five participants were enrolled from July 29, 2020, to August 7, 2020, and the follow-up for this day 71 interim analysis was completed on October 3, 2020; follow-up to assess durability will continue for 2 years. This study was conducted at a single clinical site in Boston, Massachusetts, as part of a randomized, double-blind, placebo-controlled phase 1 clinical trial of Ad26.COV2.S.
    Interventions: Participants were randomized to receive 1 or 2 intramuscular injections with 5 × 1010 viral particles or 1 × 1011 viral particles of Ad26.COV2.S vaccine or placebo administered on day 1 and day 57 (5 participants in each group).
    Main outcomes and measures: Humoral immune responses included binding and neutralizing antibody responses at multiple time points following immunization. Cellular immune responses included immunospot-based and intracellular cytokine staining assays to measure T-cell responses.
    Results: Twenty-five participants were randomized (median age, 42; age range, 22-52; 52% women, 44% male, 4% undifferentiated), and all completed the trial through the day 71 interim end point. Binding and neutralizing antibodies emerged rapidly by day 8 after initial immunization in 90% and 25% of vaccine recipients, respectively. By day 57, binding and neutralizing antibodies were detected in 100% of vaccine recipients after a single immunization. On day 71, the geometric mean titers of spike-specific binding antibodies were 2432 to 5729 and the geometric mean titers of neutralizing antibodies were 242 to 449 in the vaccinated groups. A variety of antibody subclasses, Fc receptor binding properties, and antiviral functions were induced. CD4+ and CD8+ T-cell responses were induced.
    Conclusion and relevance: In this phase 1 study, a single immunization with Ad26.COV2.S induced rapid binding and neutralization antibody responses as well as cellular immune responses. Two phase 3 clinical trials are currently underway to determine the efficacy of the Ad26.COV2.S vaccine.
    Trial registration: ClinicalTrials.gov Identifier: NCT04436276.
    MeSH term(s) Adult ; Antibodies, Neutralizing/blood ; Antibodies, Viral/blood ; COVID-19/immunology ; COVID-19/prevention & control ; COVID-19 Vaccines/administration & dosage ; COVID-19 Vaccines/immunology ; Double-Blind Method ; Female ; Humans ; Immunity, Cellular ; Immunity, Humoral ; Immunogenicity, Vaccine ; Male ; Middle Aged ; Vaccine Potency ; Young Adult
    Chemical Substances Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines
    Language English
    Publishing date 2021-03-11
    Publishing country United States
    Document type Clinical Trial, Phase I ; Comparative Study ; Journal Article ; Randomized Controlled Trial ; Research Support, N.I.H., Extramural
    ZDB-ID 2958-0
    ISSN 1538-3598 ; 0254-9077 ; 0002-9955 ; 0098-7484
    ISSN (online) 1538-3598
    ISSN 0254-9077 ; 0002-9955 ; 0098-7484
    DOI 10.1001/jama.2021.3645
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