README for "Gene Expression Biomarkers of the Response To Sleep Loss With and Without Modafinil [supporting datasets]" dataset.
Bureau of Transportation Statistics (BTS), U.S. Department of Transportation (USDOT)
2023-11-27

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LINKS TO DATASET
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A. Dataset archive link: https://doi.org/10.21949/1529859
      


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SUMMARY OF DATASET
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Sleep disruption presents a substantial risk to health and safety, particularly due to the risks of performance degradation in safety-critical operations that can result in catastrophic injuries or mortality. Federal regulations exist to minimize the risks of fatigue with limitations on hours worked and requirements for fatigue risk management plans. Yet, even with workload controls and scheduled opportunities for rest, fatigue may be caused by factors such as personal and lifestyle choices, illness, and circadian disruption from travel across multiple time zones. Complicating risk mitigation is the challenge of identifying and measuring fatigue. Here, we report on gene expression biomarkers (biological indicators) for cognitive impairment during sleep loss. We observe hundreds of genes whose expression is associated with attention changes during one night of sleep loss. Several genes are identified that we previously associated with attention impairment in a separate study of sleep loss. The reproducibility of findings may indicate the robustness of these candidate fatigue impairment biomarkers. However, some biomarker genes only associate with certain tests of impairment (e.g., attention lapses but not self-reported fatigue), suggesting that different biomarker panels may be developed to assess the particular cognitive domains that need monitoring for a given safety critical operation. We also find that using a drug countermeasure (modafinil) not only helps mitigate impairment on tests of attention lapses, but also disrupts gene expression associations with attention lapses. Further research is needed to confirm whether this represents a unique effect of modafinil administration, or emphasizes the need to ensure biomarker validation occurs both in the presence and absence of countermeasures.


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TABLE OF CONTENTS
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A. General Information
B. Sharing/Access & Policies Information
C. Data and Related File Overview
D. Methodological Information
E. Data-Specific Information for: Gene Expression Biomarkers of the Response To Sleep Loss With and Without Modafinil [supporting datasets]
F. Update Log



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A. GENERAL INFORMATION
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0. Title of Dataset: Gene Expression Biomarkers of the Response To Sleep Loss With and Without Modafinil [supporting datasets]
   


1. Description of Dataset: Sleep disruption presents a substantial risk to health and safety, particularly due to the risks of performance degradation in safety-critical operations that can result in catastrophic injuries or mortality. Federal regulations exist to minimize the risks of fatigue with limitations on hours worked and requirements for fatigue risk management plans. Yet, even with workload controls and scheduled opportunities for rest, fatigue may be caused by factors such as personal and lifestyle choices, illness, and circadian disruption from travel across multiple time zones. Complicating risk mitigation is the challenge of identifying and measuring fatigue. Here, we report on gene expression biomarkers (biological indicators) for cognitive impairment during sleep loss. We observe hundreds of genes whose expression is associated with attention changes during one night of sleep loss. Several genes are identified that we previously associated with attention impairment in a separate study of sleep loss. The reproducibility of findings may indicate the robustness of these candidate fatigue impairment biomarkers. However, some biomarker genes only associate with certain tests of impairment (e.g., attention lapses but not self-reported fatigue), suggesting that different biomarker panels may be developed to assess the particular cognitive domains that need monitoring for a given safety critical operation. We also find that using a drug countermeasure (modafinil) not only helps mitigate impairment on tests of attention lapses, but also disrupts gene expression associations with attention lapses. Further research is needed to confirm whether this represents a unique effect of modafinil administration, or emphasizes the need to ensure biomarker validation occurs both in the presence and absence of countermeasures.
   

2. Dataset archive link: https://doi.org/10.21949/1529859
       


3. Authorship Information: 
   Principal Data Creator or Data Manager Contact Information
        Name: Hilary A. Uyhelji
           Institution: Civil Aerospace Medical Institute
           Address: 6500 S. MacArthur Blvd. Oklahoma City, OK 73169
           Email: hilary.uyhelji@faa.gov

   Data Distributor Contact Information
        Name: Hilary A. Uyhelji
           Institution: Civil Aerospace Medical Institute
           Address: 6500 S. MacArthur Blvd. Oklahoma City, OK 73169
           Email: hilary.uyhelji@faa.gov

   Organizational Contact Information
        Name: Hilary A. Uyhelji
           Institution: Civil Aerospace Medical Institute
           Address: 6500 S. MacArthur Blvd. Oklahoma City, OK 73169
           Email: hilary.uyhelji@faa.gov
	   

4. Date of data collection and update interval: 2023
   


5. Geographic location of data collection: United States
   


6. Information about funding sources that supported the collection of the data: This research was funded by the Federal Aviation Administration, including the award of DTFAAC-17-X-00001 to the Naval Medical Research Unit – Dayton supporting blood collections.
   




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B. SHARING/ACCESS & POLICIES INFORMATION 
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0. Recommended citation for the data: 


United States. Department of Transportation. Federal Aviation Administration. Office of Aviation. Civil Aerospace Medical Institute (2023). 
Gene Expression Biomarkers of the Response To Sleep Loss With and Without Modafinil [supporting datasets]. https://doi.org/10.21949/1529859
   


1. Licenses/restrictions placed on the data: This document is disseminated under the sponsorship of the U.S. Department of Transportation in the interest of information exchange. The United States Government assumes no liability for the contents thereof. To protect the privacy of subject participants and conform to the restrictions of the Institutional Review Board, raw and individual-level data will not be made available.

   

2. Was data derived from another source?: No
   
   
   
3. This document was created to meet the requirements enumerated in the U.S. Department of Transportation's 'Plan to Increase Public Access to the Results of Federally-Funded Scientific Research' Version 1.1 << https://doi.org/10.21949/1520559 >> and guidelines suggested by the DOT Public Access website << https://doi.org/10.21949/1503647  >>, in effect and current as of December 03, 2020.
 



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C. DATA & RELATED FILE OVERVIEW
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1. File List for the 95447_DATASET_20231127_1800.zip collection      
        
   A. Filename: SupplTables1to9_DEGs_2023.10.20.xlsx 
          
        Short description: Contains tables 1 through 9
         

   B. Filename: SupplTables10to16_DEGs_2023.10.20.xlsx
           
        Short description: Contains tables 10 through 16
      

   C. Filename: README.txt
      
	Short description: This file that you are reading. Describes dataset content.
	

   D. Filename: 95447.json
         
        Short description: The DCAT US v1.1 metadata file. 
         
 
   E. Filename: SupplTables1to9_DEGs_2023.10.20_SupplTable1.csv
          
        Short description: Table 1 in csv form.

   F. Filename: SupplTables1to9_DEGs_2023.10.20_SupplTable2.csv
          
        Short description: Table 2 in csv form.

   G. Filename: SupplTables1to9_DEGs_2023.10.20_SupplTable3.csv
          
        Short description: Table 3 in csv form.

   H. Filename: SupplTables1to9_DEGs_2023.10.20_SupplTable4.csv
          
        Short description: Table 4 in csv form.

   I. Filename: SupplTables1to9_DEGs_2023.10.20_SupplTable5.csv
          
        Short description: Table 5 in csv form.

   J. Filename: SupplTables1to9_DEGs_2023.10.20_SupplTable6.csv
          
        Short description: Table 6 in csv form.

   K. Filename: SupplTables1to9_DEGs_2023.10.20_SupplTable7.csv
          
        Short description: Table 7 in csv form.

   L. Filename: SupplTables1to9_DEGs_2023.10.20_SupplTable8.csv
          
        Short description: Table 8 in csv form.

   M. Filename: SupplTables1to9_DEGs_2023.10.20_SupplTable9.csv
          
        Short description: Table 9 in csv form.

   N. Filename: SupplTables10to16_DEGs_2023.10.20_SupplTable10.csv
          
        Short description: Table 10 in csv form.

   O. Filename: SupplTables10to16_DEGs_2023.10.20_SupplTable11.csv
          
        Short description: Table 11 in csv form.

   P. Filename: SupplTables10to16_DEGs_2023.10.20_SupplTable12.csv
          
        Short description: Table 12 in csv form.

   Q. Filename: SupplTables10to16_DEGs_2023.10.20_SupplTable13.csv
          
        Short description: Table 13 in csv form.

   R. Filename: SupplTables10to16_DEGs_2023.10.20_SupplTable14.csv
          
        Short description: Table 14 in csv form.

   S. Filename: SupplTables10to16_DEGs_2023.10.20_SupplTable15.csv
          
        Short description: Table 15 in csv form.

   T. Filename: SupplTables10to16_DEGs_2023.10.20_SupplTable16.csv
          
        Short description: Table 16 in csv form.
        



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D. METHODOLOGICAL INFORMATION
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1. Description of methods used for collection/generation of data: Male subjects were exposed to one night of total sleep deprivation in two separate randomized study runs by NAMRU-D, differing by administration of 200 mg modafinil or a placebo at midnight. Details of human recruitment and overall study design have been reported previously (Caldwell et al., 2020). Neurobehavioral tests comprised the number of attention lapses on the 10-minute Psychomotor Vigilance Test (PVT), the number correct in the Delayed Match to Sample (MTS), reaction time for correct responses in the Rapid Decision Making Test (RDM), and subjective self-report ratings of fatigue-inertia on a Profile of Mood States Questionnaire (POMS-F) (Caldwell et al., 2020). Although additional subjective and objective neurobehavioral measures were conducted, analyses focused on PVT, MTS, RDM, and POMS-F due to work by NAMRU-D indicating these test results changed with prolonged sleep deprivation. The current report supplements prior work with the addition of genetics analyses relative to these metrics, as described below. During the study, eight consecutive blood draws were conducted at a frequency of one draw every four hours, beginning between approximately 12:00 and 13:00 hours on the first day and ending between ~16:00 and 17:00 hours on the second study day. A sample of 2.5 mL whole blood was collected into a PAXgene RNA blood tube (BD Biosciences, 762165) at each timepoint. Immediately after collection, PAXgene RNA blood tubes were inverted 10 times, then frozen at -80 ºC until RNA extraction at the FAA CAMI. Total RNA was extracted with the PAXgene Blood miRNA kit (QIAGEN, 763134) using a QIAGEN QIAcube robotic workstation, eluted in RNAse-free water, and manually purified with Agencourt® RNAclean XP beads (Beckman Coulter, A63987).
     


2. Instrument- or software-specific information needed to interpret the data: Any spreadsheet program, such as Microsoft Excel or OpenRefine, can be used to view these tables. 
   




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E. DATA-SPECIFIC INFORMATION  
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1. SupplTables1to9_DEGs_2023.10.20.xlsx data table

A. Number of variables (columns): 9


B. Number of cases/rows: 132,899
   

C. Each row represents: each Ensembl Gene ID
  

D. Data Dictionary/Variable List: Varibles are defined in final report.


E. Missing data codes: S
        S = Appropriate Skip      
        R = Refused
	D = Don't Know


2. SupplTables10to16_DEGs_2023.10.20.xlsx data table

A. Number of variables (columns): 13


B. Number of cases/rows: 162,314
   

C. Each row represents: each Ensembl Gene ID and each GO ID
  

D. Data Dictionary/Variable List: Varibles are defined in final report.


E. Missing data codes: S
        S = Appropriate Skip      
        R = Refused
	D = Don't Know




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F. UPDATE LOG
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This README.txt file was originally created on 2023-11-27 by Peyton Tvrdy https://orcid.org/0000-0002-9720-4725 Data Management and Data Curation Fellow, peyton.tvrdy.ctr@dot.gov

2023-11-27: Original file created
