Biochemical, biophysical, and immunological characterization of respiratory secretions in severe SARS-CoV-2 infections
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
No abstract available
Article activity feed
-
-
SciScore for 10.1101/2022.03.28.22272848: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Study Approval: All secretion samples were obtained under the auspices of research protocols approved the Stanford Institutional Review Board (IRB) (Stanford IRB approval #28205, #53685, #55650, #37232, and #43805).
Consent: Samples were collected after written informed consent from patients or their surrogates prior to inclusion in the study.Sex as a biological variable not detected. Randomization Histology quantification: 150 500 pixel x 500 pixel regions of interest (ROIs) were randomly sampled from each tissue section imaged with the Aperio (Leica) AT2 Digital Pathology whole slide scanner. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: …
SciScore for 10.1101/2022.03.28.22272848: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Study Approval: All secretion samples were obtained under the auspices of research protocols approved the Stanford Institutional Review Board (IRB) (Stanford IRB approval #28205, #53685, #55650, #37232, and #43805).
Consent: Samples were collected after written informed consent from patients or their surrogates prior to inclusion in the study.Sex as a biological variable not detected. Randomization Histology quantification: 150 500 pixel x 500 pixel regions of interest (ROIs) were randomly sampled from each tissue section imaged with the Aperio (Leica) AT2 Digital Pathology whole slide scanner. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Rabbit anti-versican antibody, clone EPR12277 (ab177480; Abcam) and rabbit anti-TSG-6 antibody (ab204049; Abcam) were used at 1:50 dilution. anti-versicansuggested: (Abcam Cat# ab177480, RRID:AB_2827732)anti-TSG-6suggested: NoneExperimental Models: Cell Lines Sentences Resources For figure 3 and supplemental figures, most of the lung tissue samples from healthy, COVID-19 ARDS, and non-COVID-19 ARDS groups were obtained in collaboration with clinical partners at University of Texas Health Science Center at Houston (HSC-MS-15-1049 and HSC-MS-08-0354) and Houston Methodist Hospital (Pro00003392). HSC-MS-15-1049suggested: NoneHSC-MS-08-0354suggested: NoneSoftware and Algorithms Sentences Resources Slides were scanned in bright-field at a 20× objective and the digital images imported for analysis using the Aperio Imagescope v12.4.3.5008 viewing software. Imagescopesuggested: (ImageScope, RRID:SCR_014311)The RGB image was deconvolved into its hematoxylin and DAB components using the algorithm from (77), implemented in the rgb2hed function in the scikit-image Python package. Pythonsuggested: (IPython, RRID:SCR_001658)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:These studies have several limitations. Most notable is the small numbers of cases and samples of secretions involved. These findings need to be confirmed in larger, multi-center studies involving individuals with diverse backgrounds and case presentations. The underlying mechanisms that lead to increased HA would also benefit from further research to identify the causative cell types and signalling pathways. In addition, data in SARS-CoV-2 animal models would enable improved understanding of the contribution of HA to pathogenesis in this disease. Finally, to safely acquire the rheology data, the COVID-19 samples were heat treated to render the samples non-infectious. In control CF samples, this same heat treatment was found to decrease the modulus (Supplemental Figure 4A), presumably due to the denaturation of biopolymers in the sample. Since we observed that higher modulus samples had larger responses to enzymatic treatment, the true effect of enzymatic treatment on COVID-19 lung secretion may be larger than that reported here using heat-treated samples. Future studies should further evaluate a range of enzymatic treatment dosages and durations to assess the rheological effects on non-heat-treated COVID-19 lung secretions. Additionally, the necessity of using induction to collect healthy sputum is a limitation. These studies may inform the development of much needed therapeutics for patients with COVID-19. Indeed, a study of oral hymecromone as a potential tool for HA inhib...
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04359654 Completed Nebulised Dornase Alfa for Treatment of COVID-19 NCT04541979 Recruiting Aerosoliserat DNase for Treatment of Respiratory Failure in … NCT02780752 Completed A Study of Oral Hymecromone and Hyaluronan Synthesis Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-
-
-
SciScore for 10.1101/2020.09.11.20191692: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Written informed consent was obtained from patients or their surrogates.
IRB: The cells were isolated as described previously in accordance with approval from the institution’s human subjects review committee.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Five were male, three were female. Table 2: Resources
Software and Algorithms Sentences Resources Image analysis was performed using Image J (NIH), as described previously34. Image Jsuggested: (ImageJ, RRID:SCR_003070)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when …
SciScore for 10.1101/2020.09.11.20191692: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Written informed consent was obtained from patients or their surrogates.
IRB: The cells were isolated as described previously in accordance with approval from the institution’s human subjects review committee.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Five were male, three were female. Table 2: Resources
Software and Algorithms Sentences Resources Image analysis was performed using Image J (NIH), as described previously34. Image Jsuggested: (ImageJ, RRID:SCR_003070)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:These studies have several limitations. Most notable is the small numbers of cases and samples of sputum involved. These findings need to be confirmed in larger, multi-center studies involving individuals with diverse backgrounds and case presentations. The underlying mechanism of the increased HA we found would also benefit from further research of the cell types and signalling pathways that produce HA in the lung. In addition, data in SARS-CoV-2 animal models would enable improved understanding of the contribution of HA to pathogenesis in this disease. That stated, given the evidence supporting low molecule weight HA’s role in respiratory inflammation, including COVID-19-associated respiratory distress and mortality, further investigation of the utility of agents known to reduce HA content, such as hymecromone, is recommended. In summary, these data reveal a novel role for HA in COVID-19 respiratory secretions that have important implications for the development of much needed therapeutics for patients with COVID-19.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
-