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- Creator:
- Malyarenko, Dariya, Chenevert, Thomas L, Heist, Kevin, Bonham, Christopher, and Ross, Brian
- Description:
- The imaging data was used to measure repeatability and temporal trends of quantitative imaging biomarkers of myelofibrosis in bone marrow based on apparent diffusion coefficient, fat fraction and magnetization transfer ratio. The dataset consists of time series of the MRI Meta-image-header (MHD) images of wild type and diseased mice combined by the imaging time point. The MHD images are an ITK compatible format that can be viewed in standard image viewer, like 3D Slicer. Each time point image archive is structured with a directory tree that contains ./././"mouseID"/"scan-date"/"acquisition type"/
- Keyword:
- murine tibia MRI, bone marrow imaging, apparent diffusion coefficient (ADC), proton density fat fraction (PDFF), magnetization transfer ratio (MTR), and pre-clinical model of myelofibrosis
- Citation to related publication:
- Ross BD, Malyarenko D, Heist K, Amouzandeh G, Jang Y, Bonham CA, Amirfazli C, Luker GD, Chenevert TL. Repeatability of Quantitative Magnetic Resonance Imaging Biomarkers in the Tibia Bone Marrow of a Murine Myelofibrosis Model. Tomography. 2023 Feb 28;9(2):552-566. doi: 10.3390/tomography9020045. PMID: 36961004; PMCID: PMC10037563.
- Discipline:
- Health Sciences
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- Creator:
- Samuel, Sara M, Wilson, Diane L, and Fleming, Emily K
- Description:
- The International Committee of Medical Journal Editors (ICMJE) requires researchers to post individual participant data (IPD) plans for interventional clinical trials with registration in order to be eligible for publication in its member journals. This study looked at how researchers interpret the ICMJE requirements and the related prompts for information used by ClinicalTrials.gov. This data consists of the analyzed contents of the IPD plans that researchers at the University of Michigan (U-M) submitted with trial registrations for the first 27 months that the 2019 requirement was in effect.
- Keyword:
- research data sharing, research data policy, research data, clinical trials, ClinicalTrials.gov, individual participant data, IPD, data sharing plan, and compliance
- Citation to related publication:
- Samuel, S. M. & Wilson, D. L. & Fleming, E., (2023) “Evaluating individual participant data plans for ICMJE compliance: A case study at University of Michigan”, Journal of the Society for Clinical Data Management 3(4). doi: https://doi.org/10.47912/jscdm.257
- Discipline:
- Health Sciences, Social Sciences, and General Information Sources
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- Creator:
- Lumeng, Julie C
- Description:
- Infant eating behavior is likely driven not only by hunger and satiety reflective of caloric need, but also by the reward value of food. The reward value of food can be understood in terms of wanting, liking, and salience. Little is understood about infant response to the reward value of food, or its predictors, particularly prenatally. This project sought to understand whether prenatal factors during pregnancy predict infant reward response to food, as measured by questionnaires in early infancy.
- Keyword:
- wanting, liking, salience, infancy, eating, growth, and prenatal
- Discipline:
- Health Sciences
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- Creator:
- Cevidanes, Lucia
- Description:
- Image Pre-Processing To allow reliable detection and comparison of changes between several individuals or within the same individual at different time points, before extracting the quantitative bone texture/morphometry features, all hr-CBCT scans were pre-processed using validated protocols. Extraction of Trabecular Bone Texture-based and Morphometry Imaging Features Using the “crop-volume” tool in 3D Slicer, a rectangular shaped volume of interest (VOI) was cropped from the trabecular bone in the mandibular condyles and the articular fossa. Then, using the average minimum and maximum intensity values of all VOIs, we standardized the grey level intensities of the VOIs to eliminate inaccuracies of textural features calculation and possible dependency on the global characteristics of the images. Lastly, imaging markers were extracted from the standardized VOIs using “BoneTexture” module in 3D-slicer. Measurement of the 3D Articular Joint Space To assess the progression/improvement of osteoarthritic changes in the affected individuals, we measured the 3D superior joint space. We pre-labelled two landmarks in the sagittal view of the oriented CBCT scans: on the most superior point of the condyle and on the opposing surface of the articular fossa. To avoid biasing the landmarks’ placements, pre-labelling was performed simultaneously on T1 and T2 scans, using two independent windows in ITK-SNAP. After the volumetric reconstruction of the identified landmarks, linear measurements were obtained in millimeters using the Q3DC tool in 3D Slicer. Three-dimensional Shape Analyses and Quantification of Remodeling in the Condyles SPHARM-PDM software was used to compute the correspondence across 4002 surface points among all condyles. The output point-based models displayed color-coded maps that enabled visual evaluation of consistent parametrization of all condyles. An average condyle shape for the TMJ OA and control groups was calculated through propagation of original surface point correspondences across all stages of deformations and averaging the condyle surface meshes. For visualization of the 3D qualitative changes of the average models within the same group at different time points or among different groups, semi-transparent overlays were created using 3D Slicer software. The vector differences were presented on the condyle surfaces, scaled according to the magnitude of difference, and pointing towards the direction of bone change. For quantification of remodeling in the condyles, calculation of signed distances across condyles surface meshes reflected the quantitative bone changes in the TMJ OA and control samples. To quantify regional bone changes across the lateral and anterior surfaces of the condyles, we used the Pick ‘n Paint tool in 3D Slicer to propagate regional surface points to the corresponding regions of shapes across all subjects and time points.
- Keyword:
- Degenerative joint disease, Temporomandibular joint osteoarthritis, TMJ OA, Machine learning, Prognosis
- Discipline:
- Health Sciences
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- Creator:
- Lori, Jody R., Moyer, Cheryl, Lockhart, Nancy, Zielinski, Ruth E., Kukula, Vida, Apetorgbor, Veronica, Awini, Elizabeth, Badu-Gyan, Georgina, and Williams, John
- Description:
- GRAND is a five-year, cluster randomized controlled trial. The study is registered on ClinicalTrials.gov, [ID#: NCT04033003] and is a collaboration between University of Michigan in the United States and the Dodowa Health Research Center in Ghana. , The study setting for GRAND is four districts (Akwapim North, Yilo Krobo, Nsawam-Adoagyiri, and Lower Manya Krobo) within the Eastern Region of Ghana. Health facilities were selected based the number ANC registrants per month and average gestational age of women at registration in each facility., and Facilities were then matched based on facility type, district, and number of monthly ANC registrants. A cluster randomized controlled trial was conducted in 14 facilities in four districts of the Eastern Region of Ghana. Health facilities were randomized using a matched pairs design; each pair was similar in the number of deliveries and average gestational age of the women at enrollment in antenatal care. The locations of the facilities were far enough apart to avoid cross-group contamination. In each pair of facilities, one was randomly assigned to the intervention (G-ANC) and the other to the control (I-ANC). Recruitment began July 2019 and ended when enrollment targets were met. Data collection ended July 2023 when data collection was complete.
- Keyword:
- Antenatal care, Ghana, and Maternal health
- Citation to related publication:
- Lori, J., Kukula, V., Liu, L. et al. Improving health literacy through group antenatal care: results from a cluster randomized controlled trial in Ghana. BMC Pregnancy Childbirth 24, 37 (2024). https://doi.org/10.1186/s12884-023-06224-x
- Discipline:
- International Studies and Health Sciences
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- Creator:
- Rana, Gurpreet K., Reynolds, Christopher W., Rha, Jennifer Y., Lenselink, Allison M., Asokumar, Dhanya, Zebib, Laura, Giacona, Francesca L. , Islam, Nowshin N., Kannikeswaran, Sanjana, Manuel, Kara, Cheung, Allison, Marzoughi, Maedeh , and Heisler, Michele
- Description:
- The search data supports a literature review project on "Innovative strategies and implementation science approaches for health delivery among migrants in humanitarian settings". The data included in the dataset are the complete search strategies (rtf file) and the exported results of all citations from all databases (ris file) after removal of duplicate citations.
- Keyword:
- humanitarian setting, migrant, forced displacement , health delivery, implementation science, and scoping review
- Discipline:
- Health Sciences
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- Creator:
- Zielinski, Ruth E, Kukula, Vida, Apetorgbor, Veronica, Awini, Elizabeth, Moyer, Cheryl, Badu-Gyan, Georgina, Williams, John, Lockhart, Nancy, and Lori, Jody R
- Description:
- This is a process evaluation of the RCT, Group Antenatal Care and Delivery project (GRAND) to identify and document patient, provider, and system barriers and facilitators to program implementation. Using both quantitative and qualitative methods, potential and actual influences on the quality and conduct of the program's operations, implementation, and service delivery were identified. Only the seven (7) sites randomized to the Group ANC (G-ANC) intervention were included for collection of process evaluation data since the evaluation was of G-ANC implementation. Data were collected from August 2019 to November 2020 and included both quantitative and qualitative data sources.
- Keyword:
- Group Antenatal Care, Ghana, and Process Evaluation
- Citation to related publication:
- Zielinski R, Kukula V, Apetorgbor V, Awini E, Moyer C, Badu-Gyan G, et al. (2023) “With group antenatal care, pregnant women know they are not alone”: The process evaluation of a group antenatal care intervention in Ghana. PLoS ONE 18(11): e0291855. https://doi.org/10.1371/journal.pone.0291855
- Discipline:
- International Studies and Health Sciences
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- Creator:
- Chen, Kevin S, Noureldein, Mohamed H, McGinley, Lisa M, Hayes, John M, Rigan, Diana M, Kwentus, Jaquelin F, Mason, Shayna N, Mendelson, Faye E, Savelieff, Masha G, and Feldman, Eva L
- Description:
- Therapeutic mechanisms of human neural stem cells (hNSCs) were studied in an Alzheimer's disease mouse model (5XFAD). hNSCs restored spatial memory abilities in 5XFAD animals; however, amyloid beta levels were unchanged. Spatial transcriptomics was used to probe mechanisms of hNSCs. Focusing on a subset of plaque-induced genes, gene normalization was seen particularly in microglia, confirmed by PROGENy and Cell Chat analyses. and The spatial transcriptomics data from this publication have been deposited in NCBI Gene Expression Omnibus (16) and are accessible through GEO Series accession number GSE209583 ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209583 and enter token gzglogqkvjqrhmt). Additional supporting data are available from the corresponding author upon reasonable request.
- Citation to related publication:
- Chen KS, Noureldein MH, McGinley LM, Hayes JM, Rigan DM, Kwentus JF, Mason SN, Mendelson FE, Savelieffd MG, Feldman EL. Human neural stem cells restore spatial memory in a transgenic Alzheimer's disease mouse model by an immunomodulating mechanism. bioRxiv [Preprint]. 2023 Nov 4:2023.11.01.565161. doi: 10.1101/2023.11.01.565161. PMID: 37961246; PMCID: PMC10635057.
- Discipline:
- Health Sciences
-
- Creator:
- Singer, Kanakadurga
- Description:
- Supplementary Figure 1. Example gating scheme for bone marrow mature leukocytes and hematopoietic progenitors. To stain for mature leukocytes antibodies used were against CD45, Ly6G, CD11b, CD115, CD19, and CD3e. All CD45+ cells were gated first. Neutrophils were defined as Ly6G+CD11b+, monocytes were defined as Ly6G-CD11b+CD115+ (17,18), B cells were defined as Ly6G-CD11b-CD19+, and T cells were defined as Ly6G-CD11b-CD3e+. To stain for hematopoietic stem and progenitor cells antibodies used were against lineage panel (B220, Gr1, TER119, CD11b, CD4, CD8), cKit, Sca1, CD48, CD150, CD16/32, and CD105. HSCs were defined as Lin-Sca1+cKit+CD48-CD150+, MPPs were defined as Lin-Sca1+cKit+CD48-CD150-, HPC1 were defined as Lin-Sca1+cKit+CD48+CD150-, HPC2 were defined as Lin-Sca1+cKit+CD48+CD150+, GMP were defined as Lin-Sca1-cKit+CD150-CD16/32+, PreGM were defined as Lin-Sca1+cKit+CD150-CD105-, preMegE were defined as Lin-Sca1+cKit+CD150+CD105-, and PreCFUe were defined as Lin-Sca1+cKit+CD150+CD105+. , Supplementary Figure 2. Hematopoietic stem and progenitor cell frequency by flow cytometry as a percentage of CD45 bone marrow cells in male and female Ctrl and HFD PN offspring. Hematopoietic stem cells (HSC), multipotent progenitor cells (MPP), Pre-Granulocyte Macrophage (Pre-GM), granulocyte monocyte precursors (GMP), Pre-Megakaryocyte-Erythroid Precursors (Pre-MegE) and erythroid precursors (Pre-CFUE). Analyses were Student’s t-test ang gating per Supplementary Figure 1., Supplementary Table 1. Differential gene expression between Ctrl and HFD PN male gonadal white adipose tissue (GWAT) from postnatal day 16. The significant gene expression differences were determined by the DESeq2 package for R Studio. Sequencing The RNA was extracted from adipose tissue using Trizol LS (Life Technologies) by Qiagen RNeasy Mini Kit (74106) according to the manual. The RNA was sent to the University of Michigan Advanced Genomics Core for RNA-sequencing. For RNAseq studies, gonadal white adipose tissue 3’ QuantSeq single-end poly-A mRNA libraries were generated (Lexogen). These were sequenced to a depth of 10-20M reads on Illumina NovaSeq platform. Data are available from GEO at accession number GSE227337., and Supplementary Table 2. Differentially expressed genes between Ctrl and HFD PN male gonadal white adipose tissue (GWAT) from postnatal day 16 that are significant after correction for false discovery rate were determined by the DESeq2 package for R Studio.
- Citation to related publication:
- Kim K, Varghese M, Sun H, Abrishami S, Bowers E, Bridges D, Meijer JL, Singer K* and Gregg B*. The influence of maternal high fat diet during lactation on offspring hematopoietic priming. Endocrinology. https://doi.org/10.1210/endocr/bqad182 PMID 38048597.
- Discipline:
- Health Sciences
-
- Creator:
- Wallace, Dylan M, Benyamini, Miri, Nason-Tomaszewski, Samuel R, Costello, Joseph T, Cubillos, Luis H, Mender, Matthew J, Temmar, Hisham, Willsey, Matthew S, Patil, Parag P, Chestek, Cynthia A, and Zacksenhouse, Miriam
- Description:
- This is data from Wallace, Benyamini et al., 2023, Journal of Neural Engineering. There are two sets of data included: 1. Neural features and error labels used to train error classifiers for each day used in the study 2. Trial data from an example experiment day (Monkey N, Day 6), with runs for offline calibration, online brain control, error monitoring, and error correction. The purpose of this study was to investigate the use of error signals in motor cortex to improve brain-machine interface (BMI) performance for control of two finger groups. All data is contained in .mat files, which can be opened using MATLAB or the Python SciPy library.
- Keyword:
- Brain-machine interface (BMI), Error detection, and Neural recording
- Citation to related publication:
- Wallace, D. M., Benyamini, M., Nason-Tomaszewski, S. R., Costello, J. T., Cubillos, L. H., Mender, M. J., Temmar, H., Willsey, M. S., Patil, P. G., Chestek, C. A., & Zacksenhouse, M. (2023). Error detection and correction in intracortical brain–machine interfaces controlling two finger groups. Journal of Neural Engineering, 20(4), 046037. https://doi.org/10.1088/1741-2552/acef95
- Discipline:
- Engineering, Science, and Health Sciences