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- Creator:
- Derstine, Brian A., Holcombe, Sven A., Ross, Brian E., Sullivan, June A., Wang, Stewart C., and Su, Grace L.
- Description:
- Sarcopenia is the age-related loss of skeletal muscle mass and function. Computed tomography (CT) assessments of sarcopenia utilize measurements of skeletal muscle cross-sectional area (SMA), radiation attenuation (SMRA), intramuscular adipose tissue (IMAT), and skeletal muscle gauge (SMG). Unadjusted SMA is strongly correlated with both height and body mass index (BMI); therefore, SMA must be adjusted for body size to assess sarcopenic low muscle mass fairly in individuals of different heights and BMI. SMA/height (rather than SMA/height^2) provides optimal height adjustment for skeletal muscle index (SMI), and vertebra-specific relative muscle index (RMI) equations optimally adjust for both height and BMI. Since L3 measurement is not available in all CT scans, sarcopenic low muscle mass may be assessed using other levels. Both a mid-vertebral slice and an inferior slice have been used to define `L3 SMA', but the effect of vertebral slice location on SMA measurements is unexplored. Healthy reference values for skeletal muscle measures at mid- and inferior vertebra slices between T10 and L5, have not yet been reported.
- Keyword:
- sarcopenia, skeletal muscle, reference population, Morphomics, Analytic Morphomics, and body composition
- Citation to related publication:
- Derstine, B.A., Holcombe, S.A., Wang, N.C. et al. Relative muscle indices and healthy reference values for sarcopenia assessment using T10 through L5 computed tomography skeletal muscle area. Scientific Reports 14, 21799 (2024). https://doi.org/10.1038/s41598-024-71613-x
- Discipline:
- Health Sciences
-
- Creator:
- Kimbrough, Erik, Murray, Jennifer, Sarmiento, Olga, Krupka, Erin, Ramalingam, Abhijit , Kee, Frank, Kumar, Rajnish, Sánchez-Franco, Sharon , and Hunter, Ruth
- Description:
- THE DATA: Unfortunately, we are unable to share our data for this project. Since we were working with a vulnerable population (children), we were asked by Queens University Belfast’s IRB-equivalent to include language in the consent documents indicating that the data would not be shared outside of the research team. Thus, the datasets generated during and/or analyzed during the current study are not publicly available as participants were informed that no-one outside of the research team would have access to the research data when they signed their consent forms. Thus, we provide Stata, R and Mplus scripts used to generate all tables and figures reported in the paper. Since we cannot share the raw study data, most of these files cannot be run, but in the interest of transparency we include the scripts so that our code can be checked. Since a major portion of the paper is the LTA modeling, we took an additional step there and generated simulated data that allows the R+Mplus scripts to be run. These runnable scripts and the simulated data are contained in the subfolder LTA_code_EXEC. For further information about the study datasets, please contact the authors (Emails: Jennifer.Murray@qub.ac.uk; ruth.hunter@qub.ac.uk)
- Keyword:
- norms heterogeneity, experimental economics, and RCT
- Citation to related publication:
- Kimbrough, E., Krupka, E., Kumar, R., Murray, J., and Ramalingam, A. (conditional accept). On the Stability of Norms and Norm-Following Propensity: A Cross Cultural Panel Study with Adolescents. Experimental Economics
- Discipline:
- Health Sciences and Social Sciences
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- Creator:
- Bitzer, Markus
- Description:
- Kidney tissue was analyzed for spatial localization of features and associations with clinical parameters.
- Keyword:
- Kidney, Pathology, Human, and Image analysis
- Discipline:
- Health Sciences
-
- Creator:
- Herzog, Joshua M, Verkade, Angela, and Sick, Volker
- Description:
- Data deposited here includes 60 image sets (30 individual participants, and 2 eyes per individual) consisting of raw fluorescence images, diffuse reflection images using ambient lighting, images used for correction, and calibration, and metadata. Images are split into two wavelength bands as described in the methodology. Raw images are stored in Hierarchical Data Format 5 (HDF5) file nodes (one file per eye) and each image node contains a tag for frame rate, exposure duration, and timestamp (stored in ImageData.zip). Summary statistics including demographic data, participant-reported diseases (e.g., diabetes, keratoconus), and pupil size are also stored in a text-based comma-separated table and as an Excel spreadsheet. Finally, 2-channel pseudocolor images and ratiometric grayscale images combining the two fully-processed image bands are stored as portable network graphics (PNG) files (stored in PseudocolorImages.zip).
- Keyword:
- Fluorescence, Imaging, Ocular lens, Corneal disease, Cataract, and Diabetes
- Citation to related publication:
- Herzog, Joshua M., Verkade, Angela, and Sick, Volker. "Corneal shadowgraphy: a simple, low-cost, rapid, and quantitative tool with potential clinical utility." Manuscript in review. 2024. and Herzog, Joshua M., Verkade, Angela, and Sick, Volker. "Quantitative and rapid in vivo imaging of human lenticular fluorescence." Manuscript in review. 2024.
- Discipline:
- Health Sciences and Engineering
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- Creator:
- A. Tapaswi, N. Cemalovic, K. Polemi, J. Sexton, and J. Colacino
- Description:
- MCF10A non-tumorigenic breast cells were dosed with environmental toxicants and stained with multiple cellular stains to study morphological perturbations. Following up on feature results, MCF10A cells were stained with an anti-beta catenin antibody to study beta catenin nuclear translocation. Cell profiler software was used to measure and export per cell data .CSV formats to be further analyze din BMDExpress2 and R studio
- Keyword:
- Breast cancer , Cell Painting, Chemical exposure, Benchmark dose, and Cell Profiler
- Discipline:
- Health Sciences
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- Creator:
- Fahim, Abigail T
- Description:
- The purpose of this research is to compare levels of unprenylated Rab proteins in CHM-/- iPSC-RPE cells with and without compactin. Compactin is a statin that inhibits prenyl synthesis and thereby reduces prenylation overall and has an unbiased inhibitory effect on all protein prenylation. So we expect that for Rabs that are already poorly prenylated at baseline in choroideremia RPE cells, compactin will have minimal effect. However, for Rabs that are efficiently prenylated at baseline, compactin should have a much greater effect. And then we used tandem mass tag spectrometry to compare the ratio of each unprenylated Rab in compactin-treated choroideremia cells vs untreated choroideremia cells. In the spreadsheet, "F8" refers to the CHM-/- iPSC-RPE cells and "WT" refers to the isogenic control iPSC-RPE cells. In the "Proteins only" tab, column M shows the ratio of each protein in "DMSO" (untreated) choroideremia cells compared to Compactin-treated choroideremia cells. Compactin-treated control cells are also included in other columns. Untreated control cells could not be used because prenylation is so efficient in these cells, there is almost no material available after doing the in vitro prenylation assay (i.e. almost no unprenylated proteins to biotinylate). The column descriptions can be found in the sheet titled "Explanations." In addition, AAs= number of amino acids in the protein, MW= molecular weight of the protein, and pI= isoelectric point. The software is set to report abundance values only when certain criteria are met (S/N of 6, unique peptide etc). A value is NOT reported when the data for a protein fall below these criteria and the cell is instead left blank.
- Keyword:
- choroideremia, retinal pigment epithelium, prenylation, and Rab protein
- Citation to related publication:
- Raeker, M.O., Perera, N.D., Karoukis, A.J., Chen, L., Feathers, K.L., Ali, R.R., Thompson, D.A., Fahim, A.T. Reduced retinal pigment epithelial autophagy due to loss of Rab12 prenylation in a human iPSC-RPE model of choroideremia. Cells, manuscript accepted, in press.
- Discipline:
- Health Sciences and Science
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Lu-177 DOTATATE Anonymized Patient Datasets
User Collection- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This collection is comprised of a number of works that collectively represent the imaging studies and information necessary for dosimetric analysis of a patient treated with Lutathera. All works may be used as standalone datasets or in conjunction with the others in this collection depending on the analysis performed. Files are stored using the DICOM standard widely accepted for storage and transmission of medical images and related information. All patient private information has been anonymized using MIM commercial software (MIM Software Inc.). Data from 2 patients, referred to as patient 4 and patient 6, has been provided in this collection and is divided among 6 works as outlined below:, 1) Pre-Therapy Diagnostic Images. Description: Patient diagnostic scans performed prior to Lutathera treatment. Used for identifying lesions and measuring progression. Note that the date of the baseline scan may be several months before the Lutathera treatment and changes in the anatomy are possible. Files: (1) Ga68 Dotatate PET/CT, Either: (1) MRI, (1) standalone diagnostic CT, 2) Planar Whole Body Scans. Description: Planar whole body Lu-177 scans taken at 4 time points within a week after treatment. Two views (Anterior and Posterior) and 3 energy windows (one main window at 208 keV and 2 adjacent scatter windows) are available for each time point. The units of this image is counts. Energy window information, acquisition data/time and duration can be found in DICOM header. Files: (6) individual images at each time point (24 total images per patient) , 3) SPECT/CT Scans. Description: Lu-177 SPECT/CT scans at 4 time points within a week after treatment (same time points as the planar scans). Images were acquired on a Siemens Intevo system and reconstructed using xSPECT Quant. The units of this image is Bq/mL. Information on the reconstruction, acquisition date/time, duration, Lu-177 administration time and activity can be found in the DICOM header. Files: (1) Folder with reconstructed SPECT slices per time point (4 folders total per patient), (1) Folder containing co-registered CT slices per time point (4 folders total per patient), 4) Lesion and Organ Volumes of Interest. Description: DICOM RT structure files containing organ and lesion volumes of interest (VOI) that were defined on the CT of the scan1 SPECT/CT in 3). Organs were defined using semi-automatic tools (atlas based and CNN-based) while lesions were defined manually by a radiologist guided by baseline scans. Only lesions >2 cc were defined. Files: (1) File containing organ contours, (1) File containing lesion contours, 5) Time Integrated Activity Maps. Description: A DICOM file containing the time-integrated activity map over all 4 time points within a week after treatment. This combines the SPECT/CT scans provided in 3) into a single integrated activity map. This map was generated via the MIM MRT Dosimetry package: The 4 time points were registered to the reference SPECT scan (time point 1) using a contour intensity based SPECT alignment and the voxel-level time-activity data was fit using exponential functions. Voxel-level integration was performed to generate the TIA map. The units of this image is Bq/mL * sec. Files: (1) Folder with Time-integrated activity image per patient, and 6) Projection Data and CT based Attenuation Coefficient Maps. Description: SPECT projection data for each of the 4 Lutathera scans taken within a week after treatment is provided in 3 forms: unaltered, Siemens [Reformatted], and Siemens [Advanced]. The difference between the Projections and the [Advanced] Projections is that the [Advanced] consists of uncorrected raw projection data and the other the corrected projection data (e.g. camera uniformity corrections). The [Advanced] projections are used in xSPECT reconstruction (where all corrections are done during the reconstruction), while the other is used in Flash 3D reconstruction. CT-based attenuation coefficient maps (mumaps) are provided for each of the 4 scans taken within a week after treatment. Two methods are provided for each mumap: xSPECT and F3D as the matrix size is different for the 2 cases (256 x 256 for xSPECT and 128 x 128 for Flash3D). Files: (3) Folders containing raw SPECT projections, (2) Folders containing CT attenuation coefficient maps (mumaps)
- Keyword:
- Lu-177, Lutathera, Dosimetry, Radionuclide, and CTMRIPET
- Discipline:
- Health Sciences
6Works -
- Creator:
- Figueroa, Carlos A., Computational Vascular Biomechanics Lab, University of Michigan, and et al.
- Description:
- This collection concerns the CRIMSON (CardiovasculaR Integrated Modelling and SimulatiON) software environment. CRIMSON provides a powerful, customizable and user-friendly system for performing three-dimensional and reduced-order computational haemodynamics studies via a pipeline which involves: 1) segmenting vascular structures from medical images; 2) constructing analytic arterial and venous geometric models; 3) performing finite element mesh generation; 4) designing, and 5) applying boundary conditions; 6) running incompressible Navier-Stokes simulations of blood flow with fluid-structure interaction capabilities; and 7) post-processing and visualizing the results, including velocity, pressure and wall shear stress fields. , The minimum specifications to run CRIMSON are: Any AMD64 CPU (note: Intel Core i series are AMD64), Windows (only tested on Windows 10 but might work on Windows 7), 8 GB of RAM , If you are running non-trivial models you will want to have: Quad core CPU or higher, Solid state drive for storing data, Windows, 16 GB of RAM, Dedicated discrete GPU for rendering models. , and Software in this collection is a snapshot; please visit https://github.com/carthurs/CRIMSONGUI & www.crimson.software for more general information and the most up to date version of the software.
- Keyword:
- Blood Flow Simulation, Patient-specific, Open-source Software, Image-based simulation, Cardiovascular Medical Image, Segmentation, and Finite Element Simulation
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, et al. bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960
- Discipline:
- Health Sciences and Engineering
4Works -
- Creator:
- Hatch, Nan E.
- Description:
- Craniosynostosis is the premature fusion of cranial bones. The goal of this study was to determine if delivery of recombinant tissue nonspecific alkaline phosphatase (TNAP) could prevent or diminish the severity of craniosynostosis in a C57BL/6 FGFR2C342Y/+ model of neonatal onset craniosynostosis or a BALB/c FGFR2C342Y/+ model of postnatal onset craniosynostosis. Mice were injected with a lentivirus encoding a mineral targeted form of TNAP immediately after birth. Cranial bone fusion as well as cranial bone volume, mineral content and density were assessed by micro computed tomography. Craniofacial shape was measured with calipers., Alkaline phosphatase, alanine amino transferase (ALT) and aspartate amino transferase (AST) activity levels were measured in serum. Neonatal delivery of TNAP diminished craniosynostosis severity from 94% suture obliteration in vehicle treated mice to 67% suture obliteration in treated mice, p<0.02) and the incidence of malocclusion from 82.4% to 34.7% (p<0.03), with no effect on cranial bone in C57BL/6 FGFR2C342Y/+ mice. In contrast, treatment with TNAP improved cranial bone volume (p< 0.01), density (p< 0.01) and mineral content (p< 0.01) but had no effect on craniosynostosis or malocclusion in BALB/c FGFR2C342Y/+ mice. , These results indicate that post-natal recombinant TNAP enzyme therapy diminishes craniosynostosis severity in the C57BL/6 FGFR2C342Y/+ neonatal onset mouse model of Crouzon syndrome, and that effects of exogenous TNAP are genetic background dependent., and Included in this collection is one set of images representing the C57BL/6 FGFR2C342Y/+ model of neonatal onset craniosynostosis, and one for the BALB/c FGFR2C342Y/+ model of postnatal onset craniosynostosis
- Keyword:
- craniofacial, bone, craniosynostosis, FGFR2, TNAP, mouse model, and development
- Discipline:
- Health Sciences
2Works -
Radionuclide PET/CT, SPECT/CT, and Contours Collection
User Collection- Creator:
- Van, Benjamin and Dewaraja, Yuni
- Description:
- Interest in quantitative imaging of Y-90 and Lu-177 is growing due to their increased use as minimally invasive treatments for primary and metastatic tumors such as HCC and NETs. Accurate quantification of the 3D activity distribution for voxel-level dosimetry requires SPECT/CT and PET/CT imaging. This collection provides research access to anonymized PET/CT and SPECT/CT scans along with the relevant lesion/organ contours taken from University of Michigan clinical research studies of selected patients undergoing radionuclide treatments. All patients signed an informed consent to participate in the research studies. See the readme in each dataset for information on use and citation of this data.
- Discipline:
- Health Sciences
1Works -
- Creator:
- Asthana, Vishwaratn, Monovoukas, Demetri, Kucharski, Kevin, Chopra, Zoey, Perkins, Sidney, and Bugga, Pallavi
- Description:
- It is difficult to model outcomes in patients post-ST Elevation Myocardial Infarction (STEMI), particularly onset of heart failure. The acute insult following a myocardial infarction and chronic degeneration seen in HF involve a similar process where a loss of cardiomyocytes and abnormal remodeling lead to pump failure. This process may alter the strength and direction of the heart’s net depolarization signal. The investigators hypothesized that changes over time in unique parameters extracted using vectorcardiography (VCG) have the potential to predict clinical outcomes in patients post-STEMI and could eventually be used as a non-invasive and cost-effective surveillance tool for characterizing the severity and progression of HF to guide evidence-based therapies.
- Keyword:
- Cardiology, ECG, VCG, STEMI, and Heart Failure
- Discipline:
- Health Sciences
-
- 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
-
- Creator:
- Irani, Sanaya , Tolia, Sangini, Finks, Jonathan, and Sandhu, Gurjit
- Description:
- Program Description DoT was founded in 2012 with a mission to increase diversity amongst medical professionals by preparing students from underrepresented communities in Detroit to successfully pursue careers in healthcare. Our program builds on a partnership between Cass Technical High School (CTHS) and the University of Michigan Medical School (UMMS). The CTHS student body is reflective of the Detroit population with more than 80% of students identifying with racial and ethnic minority backgrounds. Students with an interest in healthcare apply for the program as ninth graders. In recent years, the program has received over 60 applications for approximately 30 positions in each grade. DoT’s unique strength lies in its longitudinal structure. There are three branches of the program – Foundations (ninth and tenth grade), Rising (eleventh and twelfth grade) and Succeed (undergraduate). Ninth graders start out in DoT Foundations. Each student is paired with a first-year medical student mentor at UMMS for the entire academic year. DoT students travel to UMMS every month for a visit day, with activities designed to give students hands-on experiences in healthcare, such as suturing and ultrasound skills in the simulation center, and clinical shadowing. Students then meet with their medical student mentor over lunch. The latter part of the day is dedicated to working on their capstone projects. For the capstone projects, students work in small teams led by medical student leaders to identify a community health issue, partner with a local organization, and present their proposed solutions at a formal symposium at the end of the year. , Transition to Virtual Programming In light of the recent COVID-19 pandemic, a growing number of universities cancelled all campus events including those of pipeline programs. We felt that our programming offered an important service to our students that would be greatly missed, so our team worked to quickly create and implement a virtual program. We ensured that each of our students had access to technology at home and those who did not were offered scholarships. During our introductory student session and new parent meeting, our leadership team discussed how to set up a Gmail email address for weekly communications and taught the students how to use Zoom, Google Drive, Google Docs and Google Sheets for online learning collaboration. For the virtual Foundations program, we offered 1-hour seminars each month, where a physician was invited to give a 30-minute presentation about different organ systems, followed by a 30-minute case-based session where students worked with medical student mentors to apply their new knowledge. We also created novel sessions such as “The Path to College and Medical School” and collaborated with members of the Black Medical Association (BMA) and Latin American and Native American Medical Association (LANAMA) to host a panel session where students could learn from medical students who identified as URiM. For the mentorship aspect, we created “pods” of Foundations, Rising, and Succeed students along with medical student and physician mentors. The Foundations students and mentors met every month for an hour on Zoom, a virtual communication platform, to work on their Capstone project. Rising and Succeed students joined the group for three full-pod meetings. The goal was to increase near-peer mentorship and connections between DoT students at all levels. , and Study Population Due to the virtual nature of the 2020-2021 program, we accepted 100% of 9th grade applicants from CTHS. We also expanded our reach to a new school, The School at Marygrove (TSM), which is also located in Detroit, Michigan. TSM is involved in the Detroit-20 Partnership with the University of Michigan College of Education and includes a novel three-year residency program for novice teachers. During the 2020-2021 school year, 108 students participated in the Foundations programming with 72 of them being 9th graders and 36 being 10th graders. The students were mostly from CTHS with 12 students out of the 108 total being from TSM. Students were predominantly from an African American/Black racial background (68.4% from N=98 respondents). The students were representative of their respective schools. The majority of students at CTHS identify as black, come from low-income homes, and have variable levels of parental education.
- Keyword:
- pipeline program, Underrepresented in medicine, Mentorship, Medical education, and COVID-19
- Discipline:
- Health Sciences
-
- Creator:
- Alvarado, Roman, Scheven, Ulrich M., and Meiners, Jens-Christian
- Description:
- MRI raw data Image analysis script Raw pressure and vitals data
- Keyword:
- Decompression Sickness
- Citation to related publication:
- Alvarado R, Scheven U. M, Meiners, J. C.: Real-time Imaging of Decompression Gas Bubble Growth in the Spinal Cord of Live Rats, Magnetic Resonance in Medicine, 2024, in press
- Discipline:
- Health Sciences
-
- Creator:
- Bautista-Arredondo, Luis F., Muñoz-Rocha, T. Verenice, Figueroa, José L., Téllez-Rojo, Martha M., Torres-Olascoaga, Libni A., Cantoral, Alejandra, Arboleda-Merino, Laura C., Leung, Cindy, Peterson, Karen E., and Lamadrid-Figueroa, Héctor
- Description:
- Data was collected from participants of the Early Life Exposures in Mexico to ENvironmental Toxicants (ELEMENT) study, which consists of three sequentially-enrolled birth cohorts of pregnant women. Research protocols of this study were approved by the Institutional Review Board at University of Michigan and the Mexico National Institute of Public Health. We obtained informed consent from study participants prior to enrollment.
- Keyword:
- Food Insecurity, COVID-19 Pandemic, Mexico, Cohort
- Citation to related publication:
- Bautista-Arredondo LF, Verenice Muñoz-Rocha T, Figueroa JL, Téllez-Rojo MM, Torres-Olascoaga LA, Cantoral A, Arboleda-Merino L, Leung L, Peterson KE, and Lamadrid-Figueroa H. A surge in food insecurity during the COVID-19 pandemic in a cohort in Mexico City. 2022. Article in process of publication.
- Discipline:
- Health Sciences
-
- Creator:
- Dariya, Malyarenko, Tariq, Humera, Kushwaha, Aman, Mourad, Rami, Heist, Kevin, Chenevert, Thomas L, Ross, Brian D, Chen, Heang-Ping, and Hadjiiski, Lubomir
- Description:
- The 3D GRE MRI data for murine model of myelofbifrosis with expert segmentations of mouse tibia was used to train Attention UNET model to automate bone marrow segmentation for measurements of imaging biomarkers. This dataset consists of three archives: (1) containing the source MRI images in Meta-image-header (MHD) format with resulting segmentation labels by two experts and four UNET models with different training scenarios; (2) corresponding training models; and (3) deep-learning (DL)-based segmentation tools for application to future murine tibia MRI data. and The MHD images are an ITK compatible format that can be viewed in standard image viewer, like 3D Slicer. The image archive is structured with a directory tree that contains \"mouseID"\"scan-date"\"segmentaion-scenario"\. The "training model" archive containes DL-model labeled by the data subset, and "deployment" archive containes the DL-segmentation software.
- Keyword:
- deep-learning segmentation, preclinical MRI, murine tibia, and mouse model of myelofibrosis
- Citation to related publication:
- Kushwaha A, Mourad RF, Heist K, Tariq H, Chan HP, Ross BD, Chenevert TL, Malyarenko D, Hadjiiski LM. Improved Repeatability of Mouse Tibia Volume Segmentation in Murine Myelofibrosis Model Using Deep Learning. Tomography. 2023 Mar 7;9(2):589-602. doi: 10.3390/tomography9020048. PMID: 36961007; PMCID: PMC10037585. and https://github.com/dumichgh/MFJK1_Segmentation_MHDs
- Discipline:
- Health Sciences
-
- 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
-
- 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
-
- 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
-
- 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