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09/29/2021
Angelyn Thornton
No Subjects

 

Each month Levy Library showcases the achievements of Mount Sinai faculty and researchers by highlighting an article and its altmetrics. Altmetrics are alternative measures of impact that capture non-traditional data like abstract views, article downloads, and social media activity. Our altmetrics data is provided by the PlumX platform.

 

This month we highlight Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. This article was written in part by Ruben Mylvaganam MD.

 

ABSTRACT

Some patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop severe pneumonia and acute respiratory distress syndrome1 (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from that in other types of pneumonia2. Here we investigate SARS-CoV-2 pathobiology by characterizing the immune response in the alveoli of patients infected with the virus. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens, and analysed them using flow cytometry and bulk transcriptomic profiling. We performed single-cell RNA sequencing on 10 bronchoalveolar lavage fluid samples collected from patients with severe coronavirus disease 2019 (COVID-19) within 48 h of intubation. In the majority of patients with SARS-CoV-2 infection, the alveolar space was persistently enriched in T cells and monocytes. Bulk and single-cell transcriptomic profiling suggested that SARS-CoV-2 infects alveolar macrophages, which in turn respond by producing T cell chemoattractants. These T cells produce interferon-γ to induce inflammatory cytokine release from alveolar macrophages and further promote T cell activation. Collectively, our results suggest that SARS-CoV-2 causes a slowly unfolding, spatially limited alveolitis in which alveolar macrophages containing SARS-CoV-2 and T cells form a positive feedback loop that drives persistent alveolar inflammation.

 

Fig. 1: Schematic and demographics of the SCRIPT cohort.
a, Our model of the alveolus during infection with SARS-CoV-2, based on the main findings. (1) The normal alveolus contains ACE2-expressing alveolar type 1 and type 2 cells (AT1 and AT2, respectively) and TRAMs. (2) SARS-CoV-2 infects AT1 and AT2 cells and TRAMs. Infected TRAMs express T cell chemokines. (3) Cross-reactive or de novo-generated effector-memory T cells recognize SARS-CoV-2 antigens presented by TRAMs and produce IFNγ, further activating TRAM to produce cytokines and chemokines. (4) Activated T cells proliferate and continue to produce IFNγ, eventually leading to death of infected TRAMs and recruitment of monocytes, which rapidly differentiate into MoAMs. (5) Recruited MoAMs become infected with SARS-CoV-2, continuing to present antigens to T cells and maintaining the feedback loop until viral clearance is achieved. b, Timing of hospital admission, BAL fluid collection, duration of mechanical ventilation and duration of hospital stay (thin grey line) in patients with severe COVID-19, grouped by outcomes. Day 0 is defined as the day of the first intubation. c, Distribution of patient age. Differences not significant by pairwise t-test with false discovery rate (FDR) correction. d, Proportions of women (red) and men (blue) (pairwise χ2-tests of proportions with continuity and FDR correction). e, Self-reported ethnicity (pairwise χ2-tests of proportions with continuity and FDR correction). f, Body mass index (BMI) (t-test with FDR correction). g, SOFA score (pairwise Wilcoxon rank-sum tests with FDR correction). h, APS (pairwise Wilcoxon rank-sum tests with FDR correction). i, Length of stay in ICU (pairwise t-tests with FDR correction). j, Duration of mechanical ventilation (pairwise t-tests with FDR correction). k, Mortality in patients with COVID-19 was similar to patients in other groups (25% versus 35%, P = 0.10, χ2 = 2.63, χ2-tests of proportions).

 

View this article profile here!

09/22/2021
Angelyn Thornton

 

Samantha Walsh, MLS, MA (She/her/hers)

Manager of Information & Education Services

 

Did you know that many of the educational sessions offered by your Levy Librarians are recorded and available on our YouTube channel? Whether you can’t make the live session or just need a quick refresh on a topic, these videos are available on-demand to help you navigate library resources & further your research!

 

Check out these three videos: 

 

Review Types: Selecting the Right Review Methodology for Your Research Question

--> https://youtu.be/tjC_7PWVDcY 

Are you overwhelmed with the sheer amount of review types out there in the research literature? Don't understand the difference between systematic and scoping reviews? Recently heard of integrative reviews but are clueless as to what they entail? Join Librarian Carrie Levinson for a 60-minute session on the most popular review types, including literature/narrative, systematic, scoping, integrative, and rapid reviews. Each review type is defined and differentiated from the rest so that you can determine which review is most appropriate for your topic.

 

Searching the New PubMed

--> https://youtu.be/Wx8xqhzop8Q 

Launched in 2020, the redesigned PubMed has many features that even experienced PubMed searches may benefit from exploring! Join Librarian Lily Martin as she introduces the new display, navigation, and output features now available. The session then goes beyond new features to provide a refresher on PubMed best practices, including searching and working with search results.

 

How to Build a Search

--> https://youtu.be/5KW5Zd8DDso 

Beginning with an information need and concluding with a comprehensive search query, this quick 30-minute session will give you the tools you need to create an effective search strategy. While we focus on PubMed, the session is designed so that the skills learned may be used on any bibliographic database or search engine. Librarian Samantha Walsh goes over Boolean search operators (AND, OR, NOT), parentheses, asterisks, quotation marks, and using the Search Builder on PubMed's advanced search page to build a robust search strategy.

 

Browse our YouTube channel

09/15/2021
Angelyn Thornton
No Subjects

Lily Martin, MLIS (She/her/hers)

Reference & Instruction Librarian

 

This Fall we have a new batch of open classes designed to help you confidently navigate the research literature and realize your publishing goals. Learn best practices for using the library catalog and searching across multiple databases, get organized with a reference management tool, understand the ins-and-outs of conducting a systematic review, and more!

Plus, a few new offerings will include:

  • Inside Scopus & Web of Science, covering how and when to use two popular citation databases, Scopus and Web of Science.
  • Maximizing Article Discoverability, offering tips on how to boost your scholarly visibility.
  • The Peer Review Process, a primer on navigating peer review for new authors.

 

Open classes are available to the entire Mount Sinai community via Zoom. Register now on libcal.mssm.edu!

 

09/08/2021
Angelyn Thornton
No Subjects

October will soon be upon us and the month will bring with it two exciting opportunities for researchers of any experience level to explore the world of Open Access publishing.

Open Access is the free, immediate, online availability of research articles coupled with the rights to use these articles fully in the digital environment.1 Open Access publishing helps authors reach broader audiences and allows anyone to read, share, and reuse research without the restrictions of traditional models. With the power to transform how medical and scientific research is conducted, Open Access has direct and widespread implications for academia, medicine, science, and society as a whole. In the wake of the COVID-19 pandemic, scientific research is being published at record turnaround speeds. Even journals that had previously not offered any open access options have sped up their processes and are now making their content available to all. 

Keep reading to learn about upcoming opportunities to learn more about the world of Open Access:

 

Levy Library Research Insider Seminar

Join us on Tuesday, October 5th, 2021 for our next Research Insider event - Free or Fee: How Open Access Publishing Impacts Your Choices as an Author. The Open Access publishing model has ushered numerous pressing questions for academics:

  • Why are some journals offering or requiring a fee to publish an article?
  • How does paying to publish impact the prestige and accessibility of your work?
  • What is a Creative Commons license and how does it impact the dissemination of your work?

Learn how Open Access is changing how you publish your research, what requirements funding agencies impose on researchers, and who owns the copyright of published works.

 

Open Access Week

Open Access Week 2021 will take place October 25-31. This yearly celebration is an opportunity for academic and research communities to broaden their knowledge of Open Access publishing, to teach others of its benefits, and to continue efforts to bring Open Access to the forefront by inspiring wider participation and awareness.

 

Want to learn more about upcoming events or scholarly communications? Ask A Librarian!


1. Scholarly Publishing and Academic Resources Coalition, sparcopen.org/open-access

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