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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:
- 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