Index Catalog // Deep Blue Data

The Össur Power Knee with Phase-Based Control Provides Clinical Benefits over Passive Microprocessor Knees

Creator:: Best, T. Kevin, Seelhoff, C. Andrew, Wensman, Jeffrey, and Gregg, Robert D.
Description:: The dataset was collected to assess the clinical benefits of the latest generation Össur Power Knee with and without phase-based control compared to traditional passive microprocessor-controlled knees. The study included seven above-knee amputee participants and examined performance across a series of sit/stand and walking experiments. Data captured includes event logs, processed inverse kinematics and dynamics data, scaled OpenSim skeletons for each session, and raw motion capture and force plate data for various test conditions (HKIC, OSSR, PRES). All data is text-based and can be viewed in any compatible text editor. Data can be visualized in OpenSim. The dataset is organized by subject and test condition. Each folder includes a scaled subject OpenSim skeleton (*_skeleton.osim), a marker file for a range of motion trial (*_range_of_motion.trc), and three test folders each containing: Event Logs (*.event_log.csv): Time-stamped records of experimental events. Inverse Kinematics Data (*_IK.mot): Joint angle trajectories. Inverse Dynamics Data (*_ID.mot): Joint moment trajectories. Raw Marker Data (*_markers.csv): 3D coordinates of motion capture markers. Ground Reaction Force Data (*_GRF.mot): Force plate measurements of ground reactions during movement tasks.
Keyword:: Robotic Prostheses, Transfemoral Amputees, and Prosthesis Control
Citation to related publication:: T. Kevin Best, C. Andrew Seelhoff, Jeffrey Wensman, Robert D. Gregg, "The Össur Power Knee with Phase-Based Control Provides Clinical Benefits over Passive Microprocessor Knees," Submitted to the Journal of NeuroEngineering and Rehabilitation, 2025.
Discipline:: Engineering and Health Sciences

Raw data for gene expression data in SH-SY5Y cells exposed to lead (Pb) during neural differentiation

Creator:: Morgan, Rachel K, Tapaswi, Anagha, and Colacino, Justin
Description:: SH-SY5Y cells were differentiated into neuron-like cells in the presence of continuous and environmentally relevant levels of lead (Pb). Cells were collected every three days (beginning on day 6 of the 18 day protocol) for the purposes of RNA extraction and subsequent sequencing.
Keyword:: Neurotoxicology, Chemical Exposure, Benchmark Dose, Transcriptomics
Citation to related publication:: Rachel K. Morgan, Anagha Tapaswi, Katelyn M. Polemi, Elizabeth C. Tolrud, Kelly M. Bakulski, Laurie K. Svoboda, Dana C. Dolinoy, Justin A. Colacino bioRxiv 2024.10.29.620844; doi: https://doi.org/10.1101/2024.10.29.620844
Discipline:: Health Sciences

National Perspectives of Youth (SoMe) Dataset and Key

Creator:: Rager, Theresa, Mmeje, Okeoma, and Parker, Jayelin
Description:: Our final sample included 445 participants. Most identified as White (65.0%), non-Hispanic (82.8%), and heterosexual (60.0%). The study revealed disparities in comfort levels regarding receiving home-based STI-test kits at home and other household members seeing them; responses varied by education level, gender identity, and U.S. region. Individuals with less than a high school education were less likely to feel comfortable self-collecting for STI testing.
Keyword:: sexually transmitted infection
Citation to related publication:: Parker JN, Rager TL, Burns J, Mmeje O. Data Verification and Respondent Validity for an Internet-Based Sexual Health Survey: Tutorial. JMIR Form Res. 2024;8. doi:10.2196/56788
Discipline:: Health Sciences

Sec61A2 Translocon Insulin Biosynthesis Data

Creator:: Arvan, Peter
Description:: Beta cells with knockdown (or KO) of Sec61A2. Mouse, rat, human cell types. Also knockdown in mouse islets or dispersed mouse islet cells. Most experiments analyzed by Western blotting of proinsulin (and other).
Keyword:: Sec61A2
Citation to related publication:: Xiaoxi Xu, Thomas W. Bell, Truc Le, Ivy Zhao, Emily Walker, Yiqing Wang, Ning Xu, Scott A. Soleimanpour, Holger A. Russ, Ling Qi, Billy Tsai, Ming Liu*, Peter Arvan*: Role of Sec61α2 translocon in insulin biosynthesis. Diabetes, 2024 Sep 26:db240115. Online ahead of print.
Discipline:: Health Sciences

Linking single-cell dynamics to cell fate in differentiating hPSCs - example data

Creator:: Teague, Seth, Yu, Zhiyuan, and Heemskerk, Idse
Description:: Images were collected as part of a project investigating the interpretation of BMP signaling dynamics by differentiating human pluripotent stem cells. Image files are in the proprietary Imaris (.ims) file format. MATLAB and Python code for image processing and quantification is provided with the data and at https://github.com/seth414/HeemskerkLabMethods. Processed data originally published in Teague et al., 2024 (see below).
Keyword:: cell tracking, human pluripotent stem cells, immunofluorescence, and signaling dynamics
Citation to related publication:: Teague, S., Primavera, G., Chen, B. et al. Time-integrated BMP signaling determines fate in a stem cell model for early human development. Nat Commun 15, 1471 (2024). https://doi.org/10.1038/s41467-024-45719-9
Discipline:: Health Sciences and Engineering

Dataset and Associated Code for Assessment of the national Health, Education, and Air Quality Benefits of the US EPA's School Bus Rebate Program

Creator:: Pedde, Meredith
Description:: In this study, we took advantage of the randomized allocation of the US EPA's funding for school bus replacements and retrofits to causally assess the impacts of upgrading buses through the EPA’s national School Bus Rebate Program on attendance, educational performance, and community air quality (PM2.5). Specifically, we used classical intent-to-treat analyses for randomized controlled trials to compare the changes in school district average attendance, test scorers (reading language arts and math), and PM2.5 levels after vs before the 2012 through 2017 lotteries by funding selection status.
Keyword:: School Bus Emissions, Diesel Air Pollution, Attendance, Test scores, Educational performance, PM2.5, Air pollution, and Air quality
Citation to related publication:: Adar SD, Pedde M, Hirth R, Szpiro A. 2024. Assessing the National Health, Education, and Air Quality Benefits of the United States Environmental Protection Agency’s School Bus Rebate Program: A Randomized Controlled Trial Design. Research Report 221. Boston, MA: Health Effects Institute. https://www.healtheffects.org/publication/assessing-national-health-education-and-air-quality-benefits-united-states-environmental
Discipline:: Health Sciences

Supplement to "Long non-coding RNAs expressed in mouse pituitary development and mature hormone-producing cells"

Creator:: Camper, SA, Brinkmeier, ML, George, AS, Cheung, LYM, Mills, RE, and Melamed, P
Description:: We used FastQC to trim poor quality reads and Tuxedo Suite, TopHat, and Bowtie for alignment. Read counts are expressed in transcripts per kilobase million (TPM). and Bulk RNA seq data has been deposited in Geo (GSE277389). Embryonic pituitary cDNA clone end sequences are deposited at https://fantom.gsc.riken.jp/data/.
Keyword:: pituitary gland gene expression
Discipline:: Health Sciences

Dataset and Associated Code to Assess the Attendance Benefits of the US EPA School Bus Rebate Program

Creator:: Pedde, Meredith
Description:: In this study, we took advantage of the randomized allocation of the US EPA's funding for school bus replacements and retrofits to causally assess the impacts of upgrading buses on student attendance through the EPA’s national School Bus Rebate Program. Specifically, we used classical intent-to-treat analyses for randomized controlled trials to compare the change in school district level attendance rates after vs before the 2012 through 2017 lotteries by funding selection status . We used overall district attendance rates since rates were not available for only school-bus riders.
Keyword:: School Bus Emissions, Diesel Air Pollution, and School Attendance
Citation to related publication:: Pedde, M., Szpiro, A., Hirth, R. et al. Randomized design evidence of the attendance benefits of the EPA School Bus Rebate Program. Nat Sustain (2023). https://doi.org/10.1038/s41893-023-01088-7
Discipline:: Health Sciences

Dataset and Associated Code to Assess the Educational Benefits of the US EPA School Bus Rebate Program

Creator:: Pedde, Meredith
Description:: In this study, we took advantage of the randomized allocation of the US EPA's funding for school bus replacements and retrofits to causally assess the impacts of upgrading buses on students' educational performance through the EPA’s national School Bus Rebate Program. Specifically, we used classical intent-to-treat analyses for randomized controlled trials to compare the change in school district level reading and language arts and math standardized test scores after vs before the 2012 through 2016 lotteries by funding selection status . We used overall district average standardized test scores since rates were not available for only school-bus riders.
Keyword:: School Bus Emissions, Diesel Air Pollution, and Student standardized testing
Citation to related publication:: Pedde, M., Szpiro, A., Hirth, R., Adar, S. School Bus Rebate Program and Student Educational Performance Test Scores. JAMA Network Open (2024). https://doi.org/10.1001/jamanetworkopen.2024.3121
Discipline:: Health Sciences

Literature search files for review on lifestyle therapy for the management of atrial fibrillation

Creator:: MacEachern, Mark
Description:: The search data supports a literature review project on lifestyle therapies for the management of atrial fibrillation. The data included in the dataset are the reproducible search strategies (in docx) and the exported results of all citations from all databases (txt and ris files). These searches and exported result files contain all citations originating from the database searches that were considered for inclusion.
Keyword:: literature searches, atrial fibrillation, lifestyle therapy, and lifestyle therapies
Citation to related publication:: Abdul-Aziz AA, Altawil M, Lyon A, MacEachern M, Richardson CR, Rubenfire M, Pelosi F Jr, Jackson EA. Lifestyle Therapy for the Management of Atrial Fibrillation. Am J Cardiol. 2018 May 1;121(9):1112-1117. doi: 10.1016/j.amjcard.2018.01.023. PubMed PMID: 29650239., https://www.ncbi.nlm.nih.gov/pubmed/29650239, and https://doi.org/10.1016/j.amjcard.2018.01.023
Discipline:: Health Sciences

The Össur Power Knee with Phase-Based Control Provides Clinical Benefits over Passive Microprocessor Knees

Raw data for gene expression data in SH-SY5Y cells exposed to lead (Pb) during neural differentiation

National Perspectives of Youth (SoMe) Dataset and Key

Sec61A2 Translocon Insulin Biosynthesis Data

Linking single-cell dynamics to cell fate in differentiating hPSCs - example data

Dataset and Associated Code for Assessment of the national Health, Education, and Air Quality Benefits of the US EPA's School Bus Rebate Program

Supplement to "Long non-coding RNAs expressed in mouse pituitary development and mature hormone-producing cells"

Dataset and Associated Code to Assess the Attendance Benefits of the US EPA School Bus Rebate Program

Dataset and Associated Code to Assess the Educational Benefits of the US EPA School Bus Rebate Program

Literature search files for review on lifestyle therapy for the management of atrial fibrillation

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