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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
-
- 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
-
- 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
-
- 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:
- 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:
- 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:
- 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:
- 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:
- 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
-
- 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
-
- 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:
- 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
-
- Creator:
- Lockhart, Nancy
- 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. and 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. Facilities were then matched based on facility type, district, and number of monthly ANC registrants.
- Keyword:
- Antenatal care, Ghana, and Maternal health
- Discipline:
- Health Sciences and International Studies
2Works -
- 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
-
- 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:
- 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
-
- 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:
- Lee, HaEun, Lori, Jody R, Sieka, Joseph, Reynolds, Christopher W, and Lockhart, Nancy
- Description:
- Mobile obstetric emergency system (MORES) is a promising intervention to enhance communication between rural health facilities and hospitals and to improve maternal and newborn outcomes.
- Keyword:
- Obstetric referral, WhatsApp, Mobile health, Referral system, and International Heath
- Citation to related publication:
- Lee, H., Dahn B., Sieka, J., Nyanplu, A., Reynolds, C., Edson, C., Lockhart, N., & Lori, J. The use of a mobile obstetric emergency system (MORES) to improve obstetric referrals in Bong County, Liberia: A pre/post study. International Journal of Gynecology & Obstetrics. (2023) http://doi.org/10.1002/ijgo.15175
- Discipline:
- Health Sciences and International Studies
-
- Creator:
- Heath, Jeffrey
- Description:
- Documentary videos of pottery making, notably a four-part documentary of one potter's work. Credits are at the end of videos. Additional documentaries from Mali may be added later.
- Keyword:
- pottery
- 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
-
- Creator:
- Lumeng, Julie C
- Description:
- Healthy full-term infants were enrolled in a longitudinal study designed to examine the development of infant eating behavior. Infant weight and length was measured, mothers completed questionnaires regarding infant eating behaviors, and infants were weighed and length measured at ages 1, 2, 4, 6 and 10 months. Trajectories of eating behaviors were identified using latent class growth modeling and bivariate analyses examined associations of infant eating behavior trajectory membership with infant and maternal characteristics. Cross-lagged analyses examined associations between BEBQ subscales and infant weight-for-length z-score.
- Keyword:
- infant, eating, weight gain, and feeding
- Citation to related publication:
- Harlan McCaffery, Julie Zaituna, Sophie Busch, Niko Kaciroti, Alison L. Miller, Julie C. Lumeng, Katherine L. Rosenblum, Ashley Gearhardt, Megan H. Pesch, Developmental trajectories of eating behaviors and cross-lagged associations with weight across infancy, Appetite, 2023, 106978
- Discipline:
- Health Sciences
-
- Creator:
- Turner, Cortney, Khalil, Huzefa, Murphy-Weinberg, Virginia, Hagenauer, Megan, Gates, Linda, Tang, Yu, Weinberg, Lauren, Grysko, Robert, Floran-Garduno, Leonor, Dokas, Thomas, Samaniego, Catherine, Zhao, Zhuo, Fang, Yu, Sen, Srijan, Lopez, Juan, Watson Jr., Stanley, and Akil, Huda
- Description:
- This research was conducted on freshmen at the University of Michigan. Activity and sleep data from Fitbit is included along with a data dictionary.
- Keyword:
- Mood Disorder, Polygenic Risk Score, College Freshmen, Resilience, and Susceptibility
- Citation to related publication:
- Turner, C., Khalil, H., Murphy-Weinberg, V., Hagenauer, M., Gates, L., Tang, Y., Weinberg, L., Grysko, R., Floran, L., Dokas, T., Samaniego, C., Zhao, J., Fang, Y., Sen, S., Lopez, J., Watson Jr, S., Akil, H.: Stress, Genetics and Mood: Impact of COVID-19 on a College Freshman Sample, submitted to PNAS.
- Discipline:
- Health Sciences
-
- Creator:
- Lumeng, Julie C
- Description:
- Healthy full-term infants were enrolled in a longitudinal study designed to examine the development of infant eating behavior. Infant weight and length was measured, mothers completed questionnaires regarding infant eating behaviors, and infant capacity for regulation of energy intake was evaluated by comparing intake between two days: one with feedings given on demand and one with feedings offered hourly. The infant's ability to downregulate intake in response to more frequent feedings was calculated.
- Keyword:
- infant, eating, weight gain, feeding, and energy regulation
- Citation to related publication:
- Reynolds, L. A., McCaffery, H., Appugliese, D., Kaciroti, N. A., Miller, A. L., Rosenblum, K. L., ... & Lumeng, J. C. (2023). Capacity for Regulation of Energy Intake in Infancy. JAMA pediatrics, 177(6), 590-598.
- Discipline:
- Health Sciences
-
ABC Baby Study
User Collection- Creator:
- Lumeng, Julie C
- Description:
- The primary goal of this project was to identify domains of infant eating behavior and their trajectories over the first year of life. A convenience sample of 284 mother-infant dyads was recruited and enrolled from communities within a 1-hour driving distance of Ann Arbor, Michigan, via social media; flyers in outpatient pediatric clinics and community settings; and targeted outreach by telephone, email, and mail to pregnant women and mothers of newborn infants receiving care within the University of Michigan health system between October 2015 and February 2019. The planned sample size was based on a priori power calculations anticipating 3-5 eating behavior factors, each with 3 different trajectories, providing 81% power to detect a 10% or more change in the likelihood of exhibiting one of an anticipated 3 trajectory patterns of infant growth; the ultimate sample size of 284 was based on feasibility related to recruitment and retention. , The study included a repeated-measures, within-participant experimental design embedded within a longitudinal observational cohort study. The goal was to examine the development of infant eating behavior longitudinally at ages 0.5, 2, 4, 6, 9 and 12 months based on data collected from questionnaires, eating behavior experiments, and anthropometry via home visits by trained research staff. The study was described to participants as seeking to understand infant eating behavior and interactions between mothers and babies in the first year after birth. Inclusion criteria were gestational age of 37.0 to 42.0 weeks, weight appropriate for gestational age, no significant perinatal or neonatal complications, biological mother was the legal and custodial guardian, and infant’s having had consumed 2 oz or more in 1 feeding from an artificial nipple at least once per week. Exclusion criteria were mother not fluent in English; mother younger than 18 years; infant medical problems or diagnosis affecting current or future eating, growth, or development; or child protective services involvement. Mothers provided written informed consent for themselves and their infants. The study was approved by the University of Michigan institutional review board. To facilitate recruitment, dyads could be enrolled at 1 of 3 age points up to and including age 4 months; data collected at enrollment are referred to as baseline. , and Mothers responded to questionnaires on demographics, psychosocial stress, perinatal history, feeding behaviors and practices, sleep, their own eating behaviors, infant temperament, their own and the infant’s diet, and infant eating behaviors. Maternal and infant anthropometry was measured by trained research assistants. Mother-infant dyads participated in protocols designed to measure infant response to sucrose, infant ability to delay gratification, infant response to a challenging feeding, the relative reinforcing value of food, eating in the absence of hunger, capacity for regulation of energy intake in response to more frequent feedings and in response to increased caloric density, and response to novel and familiar foods. Maternal feeding behaviors were also coded from video. Biological samples included infant stool and maternal breastmilk.
- Keyword:
- infant, eating, weight gain, and sucking
- Discipline:
- Health Sciences
4Works -
- Creator:
- Diaz-Espinosa, Jennifer, Stringer, Kathleen, and Rosania, Gus
- Description:
- These data were produced from a study that assessed mitochondrial metabolic function by measuring two metabolites, l-carnitine and acetylcarnitine, to determine their effectiveness as candidate clinical biomarkers for age-related, drug-induced alterations in mitochondrial metabolism. To study age and medication-related changes in mitochondrial metabolism, we administered the FDA-approved mitochondriotropic drug, clofazimine (CFZ), or vehicle for to young and old mice. These findings are described in our manuscript: Clofazimine-Mediated, Age-Related Changes in Skeletal Muscle Mitochondrial Metabolites. Data reported was supported by funding from the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health (NIH) under award numbers R01GM127787 (GRR), R35GM136312 (KAS), P30AR069620 (K Jepsen), and T32GM140223 (L Isom).
- Keyword:
- adverse drug reactions, mitochondrial metabolism, l-carnitine, acetylcarnitine, and cardiac muscle
- Citation to related publication:
- Metabolites 2023
- Discipline:
- Health Sciences
-
- Creator:
- Chenevert, Thomas L., Malyarenko, Dariya, Amouzandeh, Ghoncheh, Pickup, Stephen, Zhou, Rong, Manning, Henry Charles, Gamon, Seth T., Shoghi, Kooresh I., Quirk, James D., Sriram, Renuka, Larson, Peder, Lewis, Mickael T., Pautler, Robia G., Kinahan, Paul E., and Muzi, Mark
- Description:
- Goals of this work quantify repeatability and reproducibility across multiple NIH/NCI Co-Clinical Imaging Research Resources Program (CIRP) preclinical MRI systems in performing diffusion measurement using a standardized acquisition protocol on a shared phantom containing temperature-controlled medium of known diffusivity. To achieve these goals, the CIRP Image Acquisition Data Processing (IADP) working group (WG) performed a round-robin study of an ice water-based DWI phantom using a detailed phantom preparation procedure and standardized DWI acquisition protocol, with both site- and core-lab generated ADC measurements derived from shared datasets.
- Keyword:
- diffusion MRI, pre-clinical MRI, apparent diffusion coefficient (ADC), repeatability, reproducibility, and accuracy
- Citation to related publication:
- Tomography 2023, 9, 375–386. https://doi.org/10.3390/tomography9010030
- Discipline:
- Health Sciences
-
- 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:
- 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:
- Healthy full-term infants were enrolled in a longitudinal study designed to examine the development of infant eating behavior. Infant weight and length was measured, mothers completed questionnaires regarding infant eating behaviors, and infant sucking behavior was quantified using the NFANT device during a typical feeding. The predictive value of the NFANT-generated sucking metrics for infant weight gain was evaluated.
- Keyword:
- infant, eating, weight gain, and sucking
- Citation to related publication:
- Feldman, Keith, Katharine Asta, Ashley N. Gearhardt, Julie M. Sturza, Danielle Appugliese, Alison L. Miller, Katherine Rosenblum, Kai Ling Kong, Amanda K. Crandall, and Julie C. Lumeng. "Characterization of a Vigorous sucking style in early infancy and its predictive value for weight gain and eating behaviors at 12 months." Appetite (2023): 106525.
- Discipline:
- Health Sciences
-
- Creator:
- Bellile, Emily L, Taylor, Jeremy MG, and Wolf, Gregory T
- Description:
- The University of Michigan’s Head and Neck Specialized Program of Research Excellence (SPORE) included an epidemiology project that approached every previously untreated adult head and neck squamous carcinoma (HNSCC) patient evaluated in the multidisciplinary Head and Neck Oncology Program of the University of Michigan (UM; Ann Arbor, MI) Comprehensive Cancer Center for participation in our longitudinal epidemiology study. This analytic dataset includes the most commonly requested covariates and outcome variables for survival analysis of this cohort of HNSCC patients. Data cleaning and creation of this analysis dataset was performed with SAS software v 9.3 (Carey,NC) by a biostatistician supporting multiple projects in the University of Michigan’s Head and Neck Specialized Program of Research Excellence (SPORE) and is available in RedCap for UM investigators to join with discipline specific data collected on the same cohort through a de-identified ID link.
- Keyword:
- Head and Neck Cancer, HNSCC, Squamous Cell Cancer, Epidemiology, Head and Neck Specialized Program of Research Excellence (SPORE). , Cancer, Prognosis, and Survival Analysis
- Citation to related publication:
- Cigarette use, comorbidities, and prognosis in a prospective head and neck squamous cell carcinoma population. Peterson LA, Bellile EL, Wolf GT, Virani S, Shuman AG, Taylor JM, Rozek LS; University of Michigan Head and Neck Specialized Program of Research Excellence Program. Head Neck. 2016 Dec;38(12):1810-1820. doi: 10.1002/hed.24515. Epub 2016 Jul 19. PMID: 27432208. , Development and Assessment of a Model for Predicting Individualized Outcomes in Patients With Oropharyngeal Cancer. Beesley LJ, Shuman AG, Mierzwa ML, Bellile EL, Rosen BS, Casper KA, Ibrahim M, Dermody SM, Wolf GT, Chinn SB, Spector ME, Baatenburg de Jong RJ, Dronkers EAC, Taylor JMG. JAMA Netw Open. 2021 Aug 2;4(8):e2120055. doi: 10.1001/jamanetworkopen.2021.20055. PMID: 34369988., Amlani, L; Bellile, E; Spector, M; Smith, J; Brenner, C; Rozek, L; Nguyen, A; Zarins, K; Thomas, D; McHugh, J; Taylor, J; Wolf, GT. Expression of p53 and prognosis in patients with head and neck squamous cell carcinoma (HNSCC); Int J Cancer Clin Res 2019, 6:122. DOI: 10.23937/2378-3419/1410122., and Spector ME, Bellile E, Amlani L, Zarins K, Smith J, Brenner JC, Rozek L, Nguyen A, Thomas D, McHugh JB, Taylor JMG, Wolf GT; University of Michigan Head and Neck SPORE Program. Prognostic Value of Tumor-Infiltrating Lymphocytes in Head and Neck Squamous Cell Carcinoma. JAMA Otolaryngol Head Neck Surg. 2019 Nov 1;145(11):1012-1019. doi: 10.1001/jamaoto.2019.2427. PMID: 31486841; PMCID: PMC6735419.
- Discipline:
- Science and Health Sciences
-
- Creator:
- Raghani, Ravi M, Urie, Russell R, and Shea, Lonnie D
- Description:
- The IN were sampled during and after ICB and sequenced to identify gene expression signatures that correlated with sensitivity or resistance. We also analyzed gene expression at the IN prior to ICB treatment to identify markers predicting therapeutic response. Longitudinally interrogating an IN, to monitor changes associated with ICB response, presents a new opportunity to personalize care and investigate mechanisms underlying treatment resistance.
- Keyword:
- Immunotherapy resistance, Biomaterials, Metastasis, Checkpoint blockade, and Therapy monitoring
- Discipline:
- Engineering and 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 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
-
- Creator:
- George De la Rosa, Mery Vet, Patel, Dipali, McCann, Marc R., Stringer, Kathleen A., and Rosania, Gus R.
- Description:
- These data were produced from a study that employed a database strategy to identify candidate mitochondrial metabolites that could be clinically useful to identify individuals at increased risk of mitochondrial-related ADRs. The main candidate metabolite identified by the database strategy was evaluated using a mouse model of mitochondrial drug toxicity. These findings are described in our manuscript: Database Screening as a Strategy to Identify Endogenous Candidate Metabolites to Probe and Assess Mitochondrial Drug Toxicity. Data reported was supported by funding from the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health (NIH) under award numbers R01GM127787 (GRR) & R35GM136312 (KAS).
- Keyword:
- mitochondrial-realted metabolites, adverse drug reactions, and mitochondrial drug toxicity
- Discipline:
- Health Sciences
-
- Creator:
- Reynolds, Mack B., Hong, Hanna S., Zhang, Li, Lyssiotis, Costas A., and O'Riordan, Mary X.
- Description:
- Untargeted lipidomics (Data S1) and targeted metabolomics (Data S2) analysis from in vitro culture of a murine macrophage cell line expressing shRNA targeted to Cardiolipin synthase (CRLS1), referred to as CRLS1 knockdown (KD), or a paired non-target shRNA-expressing (NT-Control). CRLS1 KD and NT-Control macrophages were either directly analyzed (untargeted lipidomics) or stimulated with lipopolysaccharide for a variety of timepoints and then analyzed (targeted metabolomics). Datasets are available as .csv files.
- Keyword:
- Lipidomics, Metabolomics, Cardiolipin, Macrophage, CRLS1, lipopolysaccharide, and LPS
- Citation to related publication:
- Reynolds M.B. et al. (2023). Cardiolipin coordinates inflammatory metabolic reprogramming through regulation of Complex II disassembly and degradation. Science Advances, 9(5). DOI: 10.1126/sciadv.ade8701
- Discipline:
- Health Sciences
-
- Creator:
- Szuromi, Matthew P. and Stacey, William C.
- Description:
- The data and scripts are meant to show how burster dynamics determine response to a single biphasic stimulus. The files include data which show trends in the propensity of termination for different burster types and the MATLAB scripts used to generate this data. The MATLAB scripts also allow the user to generate their own data sets for alternative bursting paths and stimulus parameter combinations. Furthermore, they allow the user to visually examine the effects of single stimuli in the voltage timeseries and in state space. How the user can access these features of the script is described in the file "ReadMe.pdf."
- Keyword:
- Epilepsy, Stimulation, Modelling, Dynamics, Seizure, and Dynamotype
- Citation to related publication:
- (PROVISIONAL) Optimization of Ictal Aborting Stimulation Using the Dynamotype Taxonomy
- Discipline:
- Health Sciences, Engineering, and Science
-
- Creator:
- Lin, Jack and Stacey, William C.
- Description:
- The characterization of HFO networks through functional connectivity analysis and network centrality. Details of the code repository can be found in the README.txt file.
- Keyword:
- Epilepsy, High Frequency Oscillation, HFO, Network, and EEG
- Citation to related publication:
- Pending
- Discipline:
- Health Sciences
-
- Creator:
- Walker, Logan A, Li, Ye, McGlothlin, Maggie, and Cai, Dawen
- Description:
- These are datasets released from our manuscript "A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications". Included in this data release are: `noise16.tif`: a file containing background noise collected from a 1000-frame acquisition of a ORCA-Fusion camera; `noise8.tif`: a file containing the 16-bit data collective above converted into a 8-bit form; `brainbow.tif`: This is a mouse Brainbow image originally published and described in Roossien, et al. Bioinformatics 2019; `bead.tif`: This is a 3D image of 100nm Invitrogen TetraSpeck fluorescent microspheres imaged in a blue channel using a custom microscope; `fly.tif`: This is a 3D image of a fly Bitbow brain collected as described in Li, et al. Front. Neural Circuits 2021; and `neurite.tif`: This is a 3D image of DiD-labeled mouse V1 tissue, collected using a custom microscope.
- Keyword:
- neuroscience, microscopy, and Bitbow
- Discipline:
- Health Sciences
-
Real-time, volumetric imaging of radiation dose delivery deep into the liver during cancer treatment
- Creator:
- Wei Zhang
- Description:
- Ionizing radiation acoustic imaging (iRAI) allows online monitoring of radiation’s interactions with tissues during radiation therapy, providing real-time, adaptive feedback for cancer treatments. Using the data set presented here, this study demonstrated iRAI can image the temporal dose accumulation of a radiaiton treatment plan. Clincial standard treatment plan with both rabbit and patient in vivo were first real-time volumetric visulized by iRAI. This data set is the rawdata for our paper published in Nature Biotechnology entitled "Real-time, volumetric imaging of radiation dose delivery deep into the liver during cancer treatment ".
- Discipline:
- Health Sciences
-
- Creator:
- Hero, Alfred O, Zhai, Yaya, Burke, Thomas, Doraiswamy, Murali, Ginsburg, Geoffrey S, Henao, Ricardo, Turner, Ronald B, and Woods, Christopher W
- Description:
- The data deposited here is as follows: The clinical shedding/symptom data, RNAseq, steroid, and wearable E4 data was partially presented in publications [1]-[3] and the cognitive lumos and VAFS data is presented in the paper [4], which is under review and embargoed. The data files are: subject.json, sample.json, and genematrix_TPM.csv. In addition, a copy of the blank consent form used to enroll volunteers in the study is included (17964_Adult Consent_2015Mar17-Mod 1_clean.pdf)., Clinical symptom and viral shedding data (in subject.json): reports each subject's accumulated and maximum self-reported symptom score (modified Jackson score) and shedding titrations from nasal-pharyngeal washes after inoculation. , RNAseq data (genematrix_TMP.csv): Whole blood was collected in PAXgene™ Blood RNA tubes (PreAnalytiX), and total RNA extracted using the PAXgene™ Blood miRNA Kit (QIAGEN) using the manufacturer’s recommended protocol. RNA quantity and quality were assessed using Nanodrop 2000 spectrophotometer (Thermo-Fisher) and Bioanalyzer 2100 with RNA 6000 Nano Chips (Agilent). RNA sequencing libraries were prepared using Illumina TruSeq mRNA Library Kit with RiboZero Globin depletion, and sequenced on an Illumina NextSeq sequencer with 50bp paired-end reads (target 40M reads per sample). After demultiplexing to FASTQ paired-end read counts files, the 396 samples were TPM transformed using HISAT2 software with the reference genome Homo_sapiens.GRCh38.84. Each sample corresponds to one of the 18 subjects at one of 22 time points. One of these samples was of insufficient quality to be mapped to read counts. In addition to the TPM normalized RNAseq data contained in this repository, the raw FASTQ data for the 395 samples are deposited in the GEO repository ( https://www.ncbi.nlm.nih.gov/geo), Accession # GSE215087. , Cognitive data (sample.json): Outcomes from a NeuroCognitive Performance Test (NCPT) that was taken approximately 3 time daily by all volunteers. The NCPT is a repeatable, web-based, computerized, cognitive assessment platform designed to measure subtle changes in performance across multiple cognitive domains. Subject scores along 18 cognitive variables data were collected at approximated 22 time points during the challenge study. The data structure sample.json contains the raw cognitive data and the extracted 18 cognitive scores over time for each subject. , The Visual Analog Fatigue Scale (sample.json): the VAFS is a measure of cognitive fatigue that was measured approximately 3 times per day at the same time as the NCPT and blood draw. , Wearable device data (sample.json): participants wore an Empatica E4 device for the duration of the challenge study. Summarized features are provided for each subject that include sleep duration (mean and std), sleep offset (mean and std), and temperature (mean and std). , Steroid data was also collected and is included in the sample.json. This steroid data was collected from the whole blood samples and consists of cortisol, melatonin, and DHEAS. , and See README.txt for more specific details on the data structures contained in the sample.json, subject.json, and genematrix_TPM.csv files.
- Keyword:
- human challenge study and cognitive health and immunity
- Citation to related publication:
- X She, Y Zhai, R Henao, CW Woods, C Chiu, Geoffrey S. Ginsburg, Peter X.K. Song, AO. Hero, “Adaptive multi-channel event segmentation and feature extraction for monitoring health outcomes,” IEEE Transactions on Biomedical Engineering, vol. 68, no. 8, pp. 2377-2388, Aug. 2021, doi: 10.1109/TBME.2020.3038652. Available on arxiv:2008.09215 , Emilia Grzesiak, Brinnae Bent, Micah T. McClain, Christopher W. Woods, Ephraim L. Tsalik, Bradly P. Nicholson, Timothy Veldman, Thomas W. Burke, Zoe Gardener, Emma Bergstrom, Ronald B. Turner, Christopher Chiu, P. Murali Doraiswamy, Alfred Hero, Ricardo Henao, Geoffrey S. Ginsburg, Jessilyn Dunn Assessment of the Feasibility of Using Noninvasive Wearable Biometric Monitoring Sensors to Detect Influenza and the Common Cold Before Symptom Onset. JAMA Netw Open. 2021;4(9):e2128534. doi:10.1001/jamanetworkopen.2021.28534 , E Sabeti, S Oh, PX Song, A Hero. “A Pattern Dictionary Method for Anomaly Detection,” Entropy, vol 24, pp. 1095 Aug 2022. doi: 10.3390/e24081095, and Yaya Zhai, P. Murali Doraiswamy, Christopher W. Woods, Ronald B. Turner, Thomas W. Burke, Geoffrey S. Ginsburg, Alfred O. Hero, "Pre-exposure cognitive performance variability is associated with severity of respiratory infection," manuscript under review.
- Discipline:
- Health Sciences and Social Sciences
-
- Creator:
- Hsu, Jer-En, Cho, Chun-Seok, Kim, Myungjin, Xi, Jingyue, and Lee, Jun Hee
- Description:
- There are three experimental outputs from Seq-Scope. (1) High definition map coordinate identifier (HDMI) sequence, tile and spatial coordinate information from 1st-Seq, (2) HDMI sequence, coupled with cDNA sequence from 2nd-Seq, and (3) Histological image obtained from Hematoxylin and Eosin (H&E) staining of the tissue slice. (1) and (2) were uploaded to GEO ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186601). (3) is deposited here. In addition, this deposit includes the processed RDS (single R object) data files.
- Citation to related publication:
- Do TH, Ma F, Andrade PR, Teles R, de Andrade Silva BJ, Hu C, Espinoza A, Hsu JE, Cho CS, Kim M, Xi J, Xing X, Plazyo O, Tsoi LC, Cheng C, Kim J, Bryson BD, O'Neill AM, Colonna M, Gudjonsson JE, Klechevsky E, Lee JH, Gallo RL, Bloom BR, Pellegrini M, Modlin RL. TREM2 macrophages induced by human lipids drive inflammation in acne lesions. Sci Immunol. 2022 Jul 22;7(73):eabo2787. doi: 10.1126/sciimmunol.abo2787. Epub 2022 Jul 22. PMID: 35867799; PMCID: PMC9400695.
- Discipline:
- Health Sciences
-
- Creator:
- Goodrich, Jaclyn M., Tang, Lu, Rodríguez-Carmona, Yanelli, Meijer, J L., Perng, Wei, Watkins, Deborah J., Meeker, John D. , Mercado-García, Adriana, Cantoral, Alejandra, Song, Peter X. , Téllez-Rojo, Martha M. , and Peterson, Karen E.
- Description:
- Phthalates are chemicals found in many products that humans are exposed to. Prenatal exposure to phthalates has been associated with adverse outcomes that are detected in childhood, adolescence, and even adulthood. In this study, we sought to identify subtle biological changes in the metabolome of children that were exposed to phthalates during gestation. We hypothesized that prenatal phthalate exposures would alter metabolic pathways related to adiposity and cardiometabolic health. The article is under review (citation to be added when paper is published). The data included here encompass all exposure, demographic, and untargeted metabolomics data needed for the analysis described in the manuscript.
- Keyword:
- Phthalates , Prenatal, and Metabolomics
- Citation to related publication:
- Goodrich J.M., Tang L.,Rodríguez-Carmona Y., Meijer J.L, Perng W., Watkins D.J., Meeker J.D., Mercado-García A., Cantoral A., Song P.X., Téllez-Rojo M.M., Peterson K.E. Trimester-specific phthalate exposures in pregnancy are associated with circulating metabolites in children. PLoS One. (Under revision – forthcoming.)
- Discipline:
- Other and Health Sciences
-
- Creator:
- Zalta, Alyson K., Vanderboll, Kathryn, Dent, Amy L., Contreras, Isaias M., Malek, Nadia, Lascano, Xrystyan N., Zellner, Kelly L., Grandhi, Jyotsna, Araujo, Precious J., Straka, Kelci, Liang, Cathy Z., Czarny, Jordyn E., Martinez, Jazmin, and Burgess, Helen J.
- Description:
- An individual participant data meta-analysis was conducted to examine 1) the degree to which bedtime, wake time, and chronotype correlate with posttraumatic stress disorder (PTSD) severity among individuals diagnosed with PTSD, 2) the standardized mean difference in bedtime, wake time, and chronotype for those with and without a PTSD diagnosis, and 3) moderators of these relationships. This deposit includes the full dataset used for data analyses. No proprietary software is required to open any of these files.
- Keyword:
- Psychology, Posttraumatic Stress Disorder, Sleep Timing, Chronotype, and Meta-Analysis
- Citation to related publication:
- Zalta, A. K., Vanderboll, K., Dent, A. L., Contreras, I. M., Malek, N., Lascano, X. N., Zellner, K. L., Grandhi, J., Araujo, P. J., Straka, K., Liang, C. Z., Czarny, J. E., Martinez, J., & Burgess, H. J. (2023). Sleep timing, chronotype, and posttraumatic stress disorder: An individual participant data meta-analysis. Psychiatry research, 321, 115061. Advance online publication. https://doi.org/10.1016/j.psychres.2023.115061
- Discipline:
- Health Sciences
-
- Creator:
- Lester, Corey A, Al Kontar, Raed, and Chen, Qiyuan
- Description:
- The dataset contains images of pills inside a medication bottle from a top down view. The dataset was used to build an image classification model for predicting the national drug code (NDC) of the medication seen in the image. There are 13,955 images of 20 distinct NDC. The image data were used to create a machine learning algorithm which could predict the NDC.
- Keyword:
- Medication, Pills, and Image
- Discipline:
- Health Sciences
-
- Creator:
- Harper Diane M
- Description:
- Patients included in this study were all males with no prior HIV diagnosis between 18 and 45 years who had at least one primary care encounter between March 2016 and March 2019. We chose 2016 as the index year because the question of the sexual partners’ gender became coded data elements with the clinic contact. Eligible patients were grouped based on reported sexual partners at the most recent disclosure. Individuals who reported having a male sexual partner or both a male and female partner were included in the MSM group. The non-MSM group included individuals who reported only a female partner or no partner. Patients who did not answer the question were excluded from the study. The study proposal was submitted to the Institutional Review Boards of the University of Michigan Medical School and was exempted from ongoing IRB review (HUM00155091). Individual consent was waived for this study.
- Keyword:
- HIV, MSM, and annual screening
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark and Bauer, Melissa
- Description:
- The intent of the project was to identify all relevant studies and data related to the topic. There are searches for the following databases: Ovid MEDLINE, Elsevier Embase, Wiley Cochrane Central Register of Controlled Trials, and EBSCOhost CINAHL.
- Keyword:
- Health sciences, Thrombocytopenia, Literature searches, and Systematic review
- Citation to related publication:
- Bauer ME, Toledano RD, Houle T, Beilin Y, MacEachern M, McCabe M, Rector D, Cooper JP, Gernsheimer T, Landau R, Leffert L. Lumbar neuraxial procedures in thrombocytopenic patients across populations: A systematic review and meta-analysis. J Clin Anesth. 2020 May;61:109666. doi: 10.1016/j.jclinane.2019.109666. Epub 2019 Dec 4. PMID: 31810860. and Bauer ME, Arendt K, Beilin Y, Gernsheimer T, Perez Botero J, James AH, Yaghmour E, Toledano RD, Turrentine M, Houle T, MacEachern M, Madden H, Rajasekhar A, Segal S, Wu C, Cooper JP, Landau R, Leffert L. The Society for Obstetric Anesthesia and Perinatology Interdisciplinary Consensus Statement on Neuraxial Procedures in Obstetric Patients With Thrombocytopenia. Anesth Analg. 2021 Jun 1;132(6):1531-1544. doi: 10.1213/ANE.0000000000005355. PMID: 33861047.
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark, Vitous, C Ann, Dinh, Duyhoang, Jafri, Sara, Bennett, Olivia, and Suwanabol, Pasithorn
- Description:
- The intent of the project was to identify all relevant studies and data related to the topic. There are searches for the following databases: Ovid MEDLINE, Elsevier Embase, Clarivate Web of Science, and EBSCOhost CINAHL. The searches yielded 1168 citations after duplicates were removed in Endnote X8.
- Keyword:
- Health Sciences, Systematic Review, Surgeons, Well-being, and Literature Searches
- Citation to related publication:
- Vitous, C. Ann MA, MPH*; Dinh, Duyhoang Q. BS†; Jafri, Sara M. BS‡; Bennett, Olivia M. BS†; MacEachern, Mark MLIS§; Suwanabol, Pasithorn A. MD, MS* Optimizing Surgeon Well-Being, Annals of Surgery Open: March 2021 - Volume 2 - Issue 1 - p e029 doi: 10.1097/AS9.0000000000000029
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark, Khouri, Alexander, Adidharma, Widya, Haase, Steven, Waljee, Jennifer, Cederna, Paul, and Strong, Amy
- Description:
- The intent of the project was to identify all relevant studies and data related to the topic. There are searches for the following databases: Ovid MEDLINE, Elsevier Embase, Clarivate Web of Science, and Wiley Cochrane Central Register of Controlled Trials. The searches yielded 889 citations after duplicates were removed in Endnote X8.
- Keyword:
- Fat Grafting, Surgery, Hand, Systematic Review, and Health Sciences
- Citation to related publication:
- Khouri AN, Adidharma W, MacEachern M, et al. The Current State of Fat Grafting in the Hand: A Systematic Review for Hand Diseases. HAND. February 2022. doi:10.1177/15589447211066347
- Discipline:
- Health Sciences
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