CRIO and Scientific Computing

Chest CT scans and chest x-rays now added to COVID-19 datasets

Scientific Computing continues to enhance and update the de-identified COVID-19 datasets, which currently consist of over 250 distinct data elements.

A radiology file has now been added to the daily updated COVID-19 data sets hosted on the Mount Sinai Data Warehouse website. This file contains the impressions for all chest CT scans and chest x-rays associated with the COVID-19 patient encounter, and has been extracted from the radiology report and de-identified.

These COVID-19 data sets have been downloaded over 4,000 times. If you have any questions please feel free to reach out to us here.

De-identified Patient COVID-19 Data Now Available

Message from the CRIO Office and Scientific Computing

De-identified Patient COVID-19 Data Now Available

A deidentified cohort of patients under investigation for or diagnosed with COVID-19 is now available. The cohort includes all patients with an encounter at a Mount Sinai facility (either in person or virtual) who have been diagnosed with Covid-19, who are under investigation for Covid-19, or who have screened negative for Covid-19. The data set will be updated regularly.

This is an evolving data set. New data elements will be added over the coming days and weeks, including imaging, historical diagnoses, medications and more.

The data set, along with a list of projects for potential collaboration, is available at: https://msdw.mountsinai.org at the top of the page in yellow, under Covid-19 Research.

Research Informatics Support for COVID-19 Related Projects

Per the Dean’s Office, we are establishing a comprehensive registry of patients with respiratory distress and other serious Covid-19 symptoms as a sharable resource available to the entire Mount Sinai community. To anticipate and meet the needs of our researchers, we need you to submit information about planned and ongoing projects related to the COVID-19 pandemic at the following site https://redcap.mountsinai.org/redcap/surveys/?s=T4CCLYNL39. Researchers can view all existing projects to identify collaborators and similar efforts.

Information on ongoing projects approved by IRB is available at the following site: http://digitalcommons.us/index.

For any further assistance with digital resources, please feel free to use the Digital Concierge service which provides weekly virtual clinics and 1:1 consultations via ticketing requests. The Digital Concierge will assist projects to ensure that they are consistent with regulatory requirements.

Feel free to open a ticket with our Digital Concierge Service any time: http://osticket.mssm.edu/support/.

How to submit to ticketing system:

Please submit tickets online at: http://osticket.mssm.edu/support/
Directions: Open a new ticket – Select Digital Concierge – Enter your contact information – Select the requested service – Include any additional details:

E-Consent Electronic Consenting Platform

Message from the CRIO Office

The Office of the Chief Research Informatics Officer is pleased to announce widespread availability of electronic consenting platform that supports interactive multimedia engagement into clinical trials, administration of informed research consents, and survey data collection.

The E-Consent Electronic Consenting Platform is now available for free, at no cost for all clinical research projects.

E-Consent is a multipurpose, scalable, electronic informed consent system that can be used in a multitude of settings. The platform allows research staff to easily upload multimedia information about a research protocol together with an approved informed consent. These materials are then delivered to potential study participants electronically, in an easy-to-understand and user-friendly way. The system is compatible with a wide range of devices and display sizes, including tablets, mobile devices, laptops, desktops, and others. Further details are available at https://www.ncbi.nlm.nih.gov/pubmed/31349301.

E-Consent has been developed in collaboration with the Mount Sinai IRB to ensure regulatory compliance: IRB-19-02049 Assessment of Multipurpose Scalable Electronic Informed Consent Platform.

If you would like to explore and/or use this offering for your research projects, please contact Daniel Robins, MD <daniel.robins@mountsinai.org> or open a ticket with the Digital Concierge service at http://osticket.mssm.edu/support/.

Registry of COVID-19 Projects

To submit information about planned and ongoing projects related to the COVID-19 pandemic visit:
https://redcap.mountsinai.org/redcap/surveys/?s=T4CCLYNL39

A self-reported list of COVID-related projects is available at:
https://msdw.mountsinai.org

Information on ongoing projects approved by IRB is available at the following site:
http://digitalcommons.us/index

Research Informatics Support for COVID-19 Related Projects

Message from the CRIO Office and Scientific Computing

Research Informatics Support for COVID-19 Related Projects

Per the Dean’s Office, we are establishing a comprehensive registry of patients with respiratory distress and other serious Covid-19 symptoms as a sharable resource available to the entire Mount Sinai community. To anticipate and meet the needs of our researchers, we need you to submit information about planned and ongoing projects related to the COVID-19 pandemic at the following site https://redcap.mountsinai.org/redcap/surveys/?s=T4CCLYNL39. Researchers can view all existing projects to identify collaborators and similar efforts.

Information on ongoing projects approved by IRB is available at the following site: http://digitalcommons.us/index.

For any further assistance with digital resources, please feel free to use the Digital Concierge service which provides weekly virtual clinics and 1:1 consultations via ticketing requests. The Digital Concierge will assist projects to ensure that they are consistent with regulatory requirements.

Feel free to open a ticket with our Digital Concierge Service any time: http://osticket.mssm.edu/support/.

How to submit to ticketing system:

Please submit tickets online at: http://osticket.mssm.edu/support/

Directions: Open a new ticket – Select Digital Concierge – Enter your contact information – Select the requested service – Include any additional details:

Digital Concierge Service: Informatics and Data Science Walk-in Clinics - UPDATE (03/18/2020)

The Digital Concierge Service: Informatics and Data Science Walk-in Clinics will be all digital and not meeting in person until further notice.

Digital Concierge walk-in clinic hours are every Wednesday from 4-5pm: join virtual room at https://zoom.us/my/digitalconcierge

For help with Informatics and Data Science, open at Support Ticket: http://osticket.mssm.edu/support/
or write Daniel.Robins@mountsinai.org

For help with the Mount Sinai Data Warehouse (MSDW) or Cohort Selection Tools, open a Support Ticket: https://scicomp.mssm.edu/jira/servicedesk/customer/portal/4
or write Oketha.Petty@mssm.edu

For help with REDCap open at Support Ticket by writing REDCap-Support@mssm.edu
or write Scott.Robertson@mssm.edu

Employee Health

Update on COVID-19 Testing, PPE and Communication Assistance (05/11/2020)

MSHS Employee Antibody Testing Asymptomatic Employee Testing Information Sheet (05/07/2020)

Employee Health Services (EHS) is offering Mount Sinai Health System employees who have not developed COVID-19 symptoms a blood test to assess if you have developed COVID-19 antibodies. Antibodies are proteins your body forms when it fights a COVID-19 infection. Testing for antibodies can show whether you had COVID-19 in the past, even if you had no symptoms. This test does not show whether you have current COVID-19 infection and it does not test for any other virus or pathogen.

This testing process does not apply to you if:

  • You have already received a COVID-19 antibody test at a Mount Sinai testing site
  • You have registered with EHS and you are already scheduled for a testing appointment
  • You currently have or had COVID-19 symptoms in the last 14 days. Please contact EHS through this link (https://is.gd/employee_covid_registry) and a member of the EHS will to arrange for you to be tested.

Your taking this test is voluntary. You do not need to take this test in order for you to be at work and perform your work duties. Whether you take it or not, and what the result is, will not affect your work duties.

You will receive your test results through MyChart. If you do not already have a MyChart account, please log into https://mychart.mountsinai.org/mychart/accesscheck.asp to set it up. Your test result may be shared with the New York State Department of Health and the Centers for Medicare and Medicaid Services if they ask for it. The results will also become part of your EHS record. Your test results will not be shared with your supervisor.

The antibody test that we offer is called the “COVID-19 ELISA IgG Antibody Test.” It has received emergency use authorization from the Food and Drug Administration. The test is designed to detect antibodies in a blood sample. The lab will first check your blood specimen for a type of antibody called IgG. If the test result is positive, the lab runs a second test on the same specimen to assess for the level of antibodies in your blood, called a titer.

The results of the first part of the test are typically available in 24-48 hours. All employees tested will receive a positive (pending confirmation) or negative result in MyChart. Only specimens that are pending confirmation for IgG antibodies are tested for titers. Those results are typically available in MyChart 2-3 days after the initial results. They will provide a numeric value with your titer. The “titer” listed indicates the strength of your antibody response. We do not yet know whether a high titer means you are more protected from reinfection.

What does it mean if I have a negative test result?

A negative test result means that the IgG antibody was not found in your blood sample. This does not mean you have not been exposed to COVID-19. A negative result may occur if you are tested early in your illness and your body has not had time to produce antibodies to the infection. At this time, we are not offering repeat antibody testing for employees who had no symptoms and who tested negative or were positive with low titers. If you later become symptomatic with COVID-19-like illness, please register with EHS by completing an EHS REDcap form and someone will contact you to arrange for a different test called nasopharyngeal swab or PCR testing, which tests for active COVID-19 illness.

What does it mean if I have a positive test result?

If you have a positive test result, it is likely that you have previously had COVID-19 and that you have developed an antibody response to the virus. Unfortunately, we do not know how long the antibodies remain in your blood. So we cannot say whether or for how long you are immune. There is also the chance that a positive result could be wrong. This is called a “false positive” result. At this time, we do not know if a positive antibody test means you cannot be infected with the virus again. But it likely reduces your risk of being sick again. If you have additional questions about your test results, please contact your primary care doctor.

No matter what your test results are, please continue to follow social distancing rules, wash your hands often with soap and water for at least 20 seconds, and avoid touching your face.

If you test positive, you may be a candidate for the Mount Sinai plasma donation program. Plasma is the liquid part of the blood. Plasma with high levels of COVID-19 antibodies is being tried as a possible treatment for patients who are seriously ill with COVID-19. If you are interested in donating plasma, please contact the New York Blood Center at nybloodcenter.org.

At this time, we are not offering repeat antibody testing for employees who had no symptoms and who tested negative or were positive with low titers. If in the future you become symptomatic with an illness like COVID-19, please contact EHS by completing an EHS REDcap form and a member of the EHS team will contact you to arrange for nasopharyngeal swab (PCR) testing, which tests for active infection.
This testing protocol is subject to change based on local, state, and federal health authority guidelines.

COVID-19 ELISA IgG Antibody Fact Sheet For Patients

You are being given this fact sheet because your blood sample(s) was tested for the antibodies related to SARS-CoV-2 infection using the COVID-19 ELISA IgG Antibody Test.

This fact sheet contains information to help you understand the risks and benefits of using this test for the presence of these antibodies in your blood. After reading this fact sheet, if you have questions or would like to discuss the information provided, please talk to your health care provider.

For the most up to date information on COVID-19 please visit the CDC Coronavirus Disease 2019 (COVID-19) webpage: https://www.cdc.gov/COVID19

What is COVID-19?

COVID-19 is caused by the SARS-CoV-2 virus. The virus, which can cause mild to severe respiratory illness, was first identified in Wuhan, China, and has now spread globally. There is limited information available to characterize the spectrum of clinical illness associated with COVID-19 but it likely spreads to others when a person shows signs or symptoms of being sick (e.g., fever, coughing, difficulty breathing, etc.).

What is the COVID-19 ELISA IgG antibody test?

The test is designed to detect antibodies in a blood sample that would indicate you may have been exposed to or are recovering from the COVID-19 virus.

Why was my sample tested?

You were tested because your health care provider believes that you may have been exposed to the virus that causes COVID-19 for one of the following reasons:

  • Based on your signs and symptoms
  • You are recovered from COVID-19
  • You have been in close contact with an individual suspected of or confirmed to have COVID-19.

Testing of the samples will help find out if you may possess antibodies consistent with COVID-19.
What are the known and potential risks and benefits of the test?

Potential risks include:

  • Possible discomfort or other complications that can happen during sample collection.
  • Possible incorrect test result (see below for more information).

Potential benefits include:
The results, along with other information, can help your health care provider make informed recommendations about your care.

  • The test may identify whether you have a high titer of antibodies to the virus, which your health care provider may wish to discuss with you regarding possible blood donation.

What does it mean if I have a positive test result?

If you have a positive test result, it is likely that you have previously had COVID-19 and that you have developed an antibody response to the virus. Your health care provider will work with you to determine how best to care for you based on the test results along with other factors of your medical history, including any previous symptoms, possible exposure to COVID-19, and the location of places you have recently traveled. There is also the chance that this test can give a positive result that is wrong (a false positive result).
Your health care provider will work with you to determine how best to care for you based on the test results along with medical history, and your symptoms.

What does it mean if I have a negative test result?

A negative test result means that the antibodies to the virus that causes COVID-19 were not found in your blood sample. However, it is possible for this test to give a negative result that is incorrect (false negative) in some people with previous COVID-19 infection. A negative result may occur if you are tested early in your illness and your body hasn’t had time to produce antibodies to infection. If this is the case, your health care provider will consider the test result together with all other aspects of your medical history (such as symptoms, possible exposures, and location of places to which you have recently traveled) in deciding how to care for you.
It is important that you work with your health care provider to help you understand the next steps you should take.

Is this test FDA-approved or cleared?

No. This test is not yet approved or cleared by the United States Food and Drug Administration (FDA). When there are no FDA-approved or cleared tests available, and other criteria are met, FDA can make tests available under an emergency access mechanism called an Emergency Use Authorization (EUA). The EUA for this test is supported by the Secretary of Health and Human Service’s (HHS’s) declaration that circumstances exist to justify the emergency use of in vitro diagnostics (IVDs) for the detection and/or diagnosis of the virus that causes COVID-19. This EUA will remain in effect (meaning this test can be used) for the duration of the COVID-19 declaration justifying emergency of IVDs, unless it is terminated or revoked by FDA (after which the test may no longer be used).

Research Resources

COVID-19 Autopsy Tissue Utilization (04/2020)

Please download the form below to request autopsy tissue from COVID-19 cases for research projects

COVID-19 Autopsy Tissue Utilization Committee Form_April 2020 (Word Doc Form)

Cryopreservation Support (Freezers, C02, Liquid Nitrogen – LN2) During COVID-19 Lab Disruptions

To: Basic Sciences Research Personnel

From:
Reginald W. Miller, DVM, DACLAM
Dean for Research Operations & Infrastructur

Re: Cryopreservation Support (Freezers, C02, Liquid Nitrogen – LN2) During COVID-19 Lab Disruptions

Thank you for participating on the recent Basic Sciences Town Hall Webinar on March 18th. This document addresses several concerns related to cryopreservation support that came up during the call:

Liquid Nitrogen (LN2) and Carbon Dioxide (C02):

The primary vendor for LN2 and C02 in the Metropolitan NY Area is TW Smith. This vendor delivers large, 50 gallon, tanks to campus 2-3 times per week. As a critical care vendor to hospitals and other essential services, TW Smith has received approval to continue operations during emergencies as an Essential Service. Furthermore, healthcare facilities/research institutions receive priority delivery during any shortages in supply. Deliveries of LN2 will continue, without interruption. Labs should plan to have someone on site to receive scheduled deliveries. Note: By design, LN2 tanks continuously evaporate during use or storage to prevent dangerous pressure build-up. Thus, it is impractical to store extra tanks on campus to prevent shortages. Regular deliveries are the best option.

Cryogenic Storage Facility

Although deliveries are expected to continue, best practices suggest establishing back-up plans for unanticipated emergencies (natural disasters, work stoppages, etc). The use of small, Dewer LN2 units, is a common practice within many labs using cell lines. These units, due to their small size, require frequent refilling. The ISSMS has established a Cryogenic Storage Facility outfitted with several large, stainless steel, LN2 tanks, each with a capacity for 700 boxes. These units have an LN2 tank duration of four (4) weeks. Each tank is temperature monitored 24/7 with remote call-out features. It is highly recommended that researchers consider establishing a back up supply of critical cell lines in this facility. Please see below the information for the Cryogenic Storage Facility:

Cryogenic Facility

We maintain a state-of-the-art cryogenics facility for long-term storage of cell lines by ISMMS investigators. We can accommodate deposit and delivery of cells as well as viable freezing of cells on a regularly scheduled basis. You can rent a safety deposit box, which contains space for 81 individual vials for $60 per year. We can provide back-up to investigators who have their own freezers or serve as the primary means of viable cell storage. A cost estimate can be obtained by filling out a Cryogenic Facility Rental Request Form. Contact Shen Yao at shen.yao@mssm.edu for additional information.

Freezers (-150, -80, -40) and Refrigerators (4C).

Each laboratory should ensure current contact information is attached to each freezer on campus. Contact information must include one external number for after-hours emergencies. Ideally, each unit would also be attached to a temperature monitoring system with a remote call out feature. Finally, where feasible, emergency power should be prioritized for (-80) freezers or other critical storage units (expensive reagents, valuable specimens). Freezers should be checked daily to ensure proper operation.

Freezer Failures:

Failures are an unfortunate reality for all mechanical equipment and freezers are no exception. These failures often occur after-hours or on weekends resulting in catastrophic losses. The ISMMS has engaged with a commercial entity, LabVendor, for after-hours responses to freezer emergencies. The company provides specimen relocation into one of the Hess Freezer Farm back-up units.

To access this service see the Hess Freezer Farm under https://icahn.mssm.edu/research/portal/resources/deans-cores/freezer-farm.

Contact: Tamjeed Sikder- Manager, Hess Freezer Farm to make arrangements for specimen transfers. Please contact the Hess Freezer Farm if you have specific questions on this program.

Offsite Housing for Freezers:

The ISMMS has maintained an offsite freezer farm in the Bronx, NY, for many years. Storage is free to all Mount Sinai researchers. Due to the limited space on campus for freezers, shortage of emergency power, and best practice of back up storage, investigators are encouraged to explore the off-site freezer storage option. All archival samples should be maintained off-site rather than using valuable on-campus space. Please contact Shekhar Patil, PhD- Core Admin Director (shekhar.patil@mssm.edu), to discuss off-site freezer storage at Brooks, Inc.

Dry Ice

The campus vendor for dry ice is Dry Ice Corporation. While there are other smaller vendors, most are subcontractors with Dry Ice, Corp. This vendor is recognized as an Essential Service and thus operates during emergencies. Deliveries of dry ice will continue uninterrupted. However, during the decrease in lab activity, the amount of dry ice required will decrease as well. We must use caution in reducing dry ice delivery amounts as the vendor may prioritize those facilities with the greatest perceived need. Note: Many clinical operations also require small amounts of dry ice (specimen shipping, etc) thus reductions in deliveries may affect those areas. Any reductions in dry ice ordering should be discussed with the Dean’s office before moving forward.

The preceding guidelines should be consulted during and after this COVID-19 emergency as best practices to ensure sample protection and research continuity. Please do not hesitate to contact me directly if you have any questions or suggestions.

Human Models of COVID-19 Infection

The Dean’s Stem Cell Engineering CoRE is beginning to establish models of lung and airway epithelia derived from human pluripotent stem cells for use in COVID-19 studies.

SARS-Coronavirus-2 (SARS-CoV-2) has been identified as the etiological agent causing COVID-19, the severe acute respiratory syndrome that is currently causing a pandemic of unprecedented magnitude. SARS-CoV-2 can infect mice, ferrets, hamsters, and primates. However, none of these animals develop a disease with the clinical manifestations of COVID-19. Better disease models capturing the human pathophysiology are direly needed. Lung airway epithelia provide a platform for mechanistic studies and for preclinical assessment of therapeutic interventions. This new platform is available from the Stem Cell Engineering CoRE co-directed by Drs. Eirini Papapetrou and Samuele G Marro. All ISMMS researchers interested in strengthening COVID-19-related federal grant applications are encouraged to contact the Stem Cell Engineering Core.

In an effort to gauge interest of the ISSMS community in these models, we invite all interested investigators to please contact us as soon as possible to discuss their research plans.

Samuele G Marro, PhD
samuele.marro@mssm.edu

Eirini Papapetrou, PhD
eirini.papapetrou@mssm.edu

Research PPE Request (Face Mask Form)

Face Mask Request Form:
https://mountsinai.formstack.com/forms/research_ppe_request_face_mask_form

If you have any questions, please send to researchPPErequest@mssm.edu.

Research PPE Plan

From: Reginald W. Miller, DVM, DACLAM
Dean for Research Operations & Infrastructure
Office of the Dean

To: Departmental/Designated Safety Officers (DSO)
Date: May 6, 2020
Subject: Research PPE – Face Mask Distribution Plan
Cc: Departmental Chairs, Institute Directors, Administrators, Materials Management

Hello All,
Thank you for taking on the responsibility to ensure safe laboratory practices as we begin ramping up research again. As you have heard, the target date for ramp up is May 18th, (subject to change based upon local and state government), so we want you to be prepared. A group of your colleagues, the Research PPE Working Group[1], has worked to construct a seamless process for all DSOs to provide your respective research labs with a continuous supply of face masks. As we expect the quantity of masks to vary as research increases we are asking each DSO to begin surveying the departmental needs for the weekly usage rate. The calculation rate should be based on: 1 mask/ person/ day or 5 masks/person/week. Each area should develop a method to secure PPE to conserve resources. The outline below details the process:

  • Estimation
    • Labs provide the DSOs with the weekly PPE needs based on above metrics.
  • Request PPE: Google Docs Form: Research PPE Request (Face Mask Form)
    • DSOs submit form for quantity for each department they oversee.
    • Indicate pick up time on the request form. If any changes occur, please communicate through the dedicated mailbox (below).
    • After successful submittal receive an email confirmation as receipt.
    • Data (type, amount, name, etc) will automatically export into an Excel spreadsheet, managed by Anthony Smalls.
    • Forward total requested amount to Materials Management to provide a weekly supply of face masks. Request by Wednesday for receipt on Friday.
      • DSOs must submit PPE request forms by Wednesdays to ensure replenishment for the following week.
      • Materials Management deliver PPE on Fridays to drop- off location(s).
  • Distribution Times
    • On Mondays DSO or designee pickup PPE:
      • Morning (9:30 am – 12:00 pm) or
      • Afternoon (3:00 pm – 4:30 pm).
  • Distribution Points
    • Three locations for distribution:
      • Annenberg Conference room 20-55A
      • Hess 6th Flr Conference room 6-101
      • Icahn Medical Institute (IMI): Conference room: L3-36 (3rd for)
  • Dedicated Mailbox: researchPPErequest@mssm.edu
    • This dedicated mailbox is available to the research community to ask questions, change pickup times, provide feedback, etc.
    • If you cannot make your pickup window contact Anthony Smalls at: researchPPErequest@mssm.edu or (212) 241-0640 (ext. 40640).
    • For your reference, the current list of DSO is available at: Google Doc List of DSOs

[1]Research PPE Working Group: Chris Cannistraci (HPIDH), Fanny Tang (GGS), Chen Wang (Microbiology), Bill Janssen (Neuroscience), Sandy Hatem (Precision Immunology/TCI), Josef Ehntholt (EvH&S), Anthony Smalls (Dean’s Office), and Kaware Richardson (Dean’s Office).

Tests, Imaging and other Services for Clinical Research Projects during COVID-19

BioMedical Engineering and Imaging Institute (BMEE)

Training

COVID-19: Back to Campus (Fall 2020) CITI Course now available to ISMMS Researchers

The Icahn School of Medicine has added COVID-19: Back to Campus (Fall 2020) to the available course offerings on CITI.

This complimentary course was launched to train staff, students, and faculty on COVID-19 safety, for their return to campus. The course was made possible by the contributions of several academic organizations and includes presenters from University of Maryland School of Medicine, University of North Texas Health Sciences Center, Vanderbilt University Medical Center, Yale University, and Northwestern University. Please see the COVID-19 CITI Course Instructions on how to access this course on CITI through the ISMMS subscription.

Please note that this course is being offered on a voluntary basis and is not a requirement for you to work. The course is available only through September 30, 2020.

If you have questions regarding the course, please contact your Department’s Designated Safety Officer (DSO) or Anthony Smalls, MBA.

Thank you,
ISMMS Lab Safety Committee

Translation From Research to Practice

Update on converting BiPAP machines into ventilators

Primer v2.1
Protocol v2.1
Clinical Guidelines v2.1
Alarm Protocol v2.1
Operating Checklist [VPAP ST] v2.1

Dr. Charles Powell of Mt. Sinai hospital in New York is part of a team converting BiPAP machines into much-needed ventilators: https://www.facebook.com/cnn/videos/2640448356232121/