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- Creator:
- Figueroa, C. Alberto
- Description:
- This information provides the data and commands to manually setup the computational simulations used in the PLOS ONE paper 'Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome' using CRIMSON (CARDIOVASCULAR INTEGRATED MODELLING & SIMULATION) a prototype simulation environment developed under the support of the European Research Council (( http://www.crimson.software/)., Note that a Windows version of the CRIMSON flowsolver is provided as part of the CRIMSON Windows installer, but you will need a very powerful Windows computer to run these simulations, as the models used in the present work are extremely computationally-demanding. It is recommended that you use a Linux version of the CRIMSON flowsolver on a high-performance computer., Option 1 (ready-to-use files to immediately start the simulation): 1. Please unzip the Ready-to-use files. 2. Copy the folders of each of the three conditions to the high performance computer. 3. In addition to different codes used, each folder provides the boundary conditions applied in the simulations described in the manuscript (e.g. LPN parameters). To run the 3D simulations for each condition simply launch the it using the CRIMSON flowsolver. In addition, the solver.inp file can be modified to run a 0D "real-time simulation" (please open solver.inp with a text editor and modify line 4 "Simulate in Purely Zero Dimensions:" to "True")., Option 2 (using the MITK files): 1. Please download and install Crimson software ( http://www.crimson.software/). 2. Please unzip the MITK files and the Ready-to-use files. 3. From amongst the provided MITK files, load the MITK file of interest to CRIMSON (using the MITK files, additional changes can be made to the computational model in case the user wants to explore different settings/boundary conditions e.g. change the vascular wall properties, introducing a change in the geometry to create a virtual stenosis). 3. Navigate to the tree in the "Data Manager" panel and select the "Pulmonaries", "CRIMSON SOLVER" and then "Solver study 3D" items, in the described order. 4. In the right hand panel select the "CRIMSON Solver setup" tab and scroll down the right hand bar until to find the "Setup Solver" box; click to output the simulation files (faceInfo.dat, geombc.dat.1, multidomain.dat, netlist_surface.dat,numstart.dat, presolver folder, solver.inp, restart.0.1). 5. Copy and replace the geombc.dat.1 and restart.0.1 generated by CRIMSON for each individual condition to the respective unziped folder in the Ready-to-use file (discard the remaining files that were output by CRIMSON). Note that if you have not changed anything about the model (e.g. vascular wall properties), then doing this will produce restart.0.1 and geombc.dat.1 files which are identical to the ready-to-use versions. 6. Finally copy each Condition folder to the high performance computer and simply launch the simulation using the CRIMSON flowsolver., and For technical queries please contact crimson-users@googlegroups.com. --October 2018.
- Citation to related publication:
- Silva Vieira M, Arthurs CJ, Hussain T, Razavi R, Figueroa CA (2018) Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome. PLOS ONE 13(11): e0205829. https://doi.org/10.1371/journal.pone.0205829
- Discipline:
- Engineering and Health Sciences
-
- Creator:
- Lee, Dahee, Panicker, Veena, and Landis-Lewis, Zach
- Description:
- We use the term “performance summary display” (PSD) to mean a kind of visualization that relates performance levels to other types of information. In the context of healthcare organizations, PSDs are intended to be communicated to a healthcare professional, team, or organization. and Displays were identified, classified, and elements counted and coded. The performance summary display ontology provides a set of descriptions of components of displays that have been used to annotate performance feedback visualizations.
- Keyword:
- Performance
- Citation to related publication:
- Lee, D., Panicker, V., Gross, C., Zhang, J., & Landis-Lewis, Z. (2020). What was visualized? A method for describing content of performance summary displays in feedback interventions. BMC medical research methodology, 20(1), 90. https://doi.org/10.1186/s12874-020-00951-x
- Discipline:
- Health Sciences and Science
-
- Creator:
- Stringer, Kathleen A.
- Description:
- These data were produced from the survival analysis of the pre-treatment metabolomics data generated from the Phase II clinical trial of L-carnitine treatment for septic shock (the RACE trial - see https://clinicaltrials.gov/ct2/show/NCT01665092). The results based on respective acetylcarnitine or valine concentration are presented (pdf). The csv files contain the at risk numbers from the Kaplan-Meier survival analysis. These findings described in our manuscript: Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. and All of the metabolomics data are available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org which is supported by NIH grant U2C-DK119886 and where it has been assigned Project ID (accession number ST001319). The data can be accessed directly via its Project DOIs: (DOI: http://dx.doi.org/10.21228/M8VX0Z).
- Keyword:
- sepsis, septic shock, survival, mortality, metabolomics, and pharmacometabolomics
- Citation to related publication:
- Puskarich, M. A., Jennaro, T. S., Gillies, C. E., Evans, C. R., Karnovsky, A., McHugh, C. E., Flott, T. L., Jones, A. E., Stringer, K. A., & Investigators, O. behalf of the R. T. (2021). Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. (Preprint) https://doi.org/10.1101/2021.01.28.21250687
- Discipline:
- Health Sciences
-
- Creator:
- Bhaumik, Deesha
- Description:
- This cross-sectional analysis included 584 participants in the Center for Oral Health Research in Appalachia cohort 1 (COHRA1). We sequenced the V4 region of the 16S rRNA of supragingival plaque from 185 caries-active and 565 caries-free teeth using the Illumina MiSeq platform. Sequences were filtered using the R DADA2 package and assigned taxonomy using the Human Oral Microbiome Database ( http://www.homd.org/).
- Keyword:
- Amplicon Sequence Variant
- Citation to related publication:
- In press
- Discipline:
- Health Sciences
-
- 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:
- Shtull-Leber, Eytan
- Description:
- We present the SAS code used to conduct the data manipulation and analysis for our research on pre-hospital midazolam use before and after RAMPART.
- Keyword:
- emergency medical services, knowledge translation, status epilepticus, benzodiazepines, midazolam, EMS, and Seizure
- Discipline:
- Health Sciences
-
- Creator:
- Liu, Y , Ettinger, AS, Téllez-Rojo, M, Sánchez, BN, Zhang, ZZ, Cantoral, A, and Hu, H
- Description:
- We used data 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 mothers and informed assent from children prior to enrollment.
- Citation to related publication:
- Liu, Y., Ettinger, A. S., Téllez-Rojo, M., Sánchez, B. N., Zhang, Z., Cantoral, A., Hu, H., & Peterson, K. E. (2020). Prenatal Lead Exposure, Type 2 Diabetes, and Cardiometabolic Risk Factors in Mexican Children at Age 10–18 Years. The Journal of Clinical Endocrinology & Metabolism, 105(1), 210–218. https://doi.org/10.1210/clinem/dgz038
- Discipline:
- Health Sciences
-
- Creator:
- Wen, Ai, Foxman. Betsy, Srinivasan, Usha , Goldberg, Deborah , Marrs, Carl F , Owen, John, Wing, Deborah A., Misra, Dawn , Cronenwett, Anna , Ponnaluri, Sreelatha, Miles-Jay, Arianna, Bucholz, Brigette, and Abbas, Khadija
- Description:
- This is the bacterial DNA data extracted from the gram stain slides. The targeted bacteria genera and species include: Atopobium spp., bacterial vaginosis-associated bacterium (BVAB) types 1, 2 and 3 in the order Clostridiales, Escherichia coli, Gardnerella vaginalis, Group B Streptococcus, Lactobacillus spp., Mobiluncus spp., Mycoplasma spp., and Ureaplasma spp. We also used a primer set for Lactic Acid Bacteria (LAB) that includes lactic acid producing bacteria of the genera Lactobacillus, Pediococcus, Leuconostoc, and Weissella. We calculated the relative proportion of each bacterial taxon using the bacterial copies measured by each specific bacteria primer divided by the total bacterial copies. The limit of detection was 100 copies and readings lower than the limit were considered negative
- Citation to related publication:
- Wen A, Srinivasan U, Goldberg D, Owen J, Marrs CF, Misra D, Wing DA, Ponnaluri S, Miles-Jay A, Bucholz B, Abbas K, Foxman B. Selected vaginal bacteria and risk of preterm birth: an ecological perspective. J Infect Dis. 2014 Apr 1;209(7):1087-94. https://doi.org/10.1093/infdis/jit632. Epub 2013 Nov 22. PMID: 24273044; PMCID: PMC3952673. and Foxman B, Wen A, Srinivasan U, Goldberg D, Marrs CF, Owen J, Wing DA, Misra D. Mycoplasma, bacterial vaginosis-associated bacteria BVAB3, race, and risk of preterm birth in a high-risk cohort. Am J Obstet Gynecol. 2014 Mar;210(3):226.e1-7. https://doi.org/10.1016/j.ajog.2013.10.003. Epub 2013 Oct 4. PMID: 24096128; PMCID: PMC3943817.
- Discipline:
- Health Sciences
-
Preterm Birth
User Collection- Creator:
- Betsy Foxman
- Description:
- This collection has been retired as of Sept 28. 2020 and replaced with the "Preterm Birth" work listed below.
- Discipline:
- Health Sciences
1Works -
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:
- 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
-
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:
- Almazroa, Ahmed
- Description:
- The dataset includes 3 different files: 1) MESSIDOR dataset file contains 460 original images and 460 images for every single ophthalmologist manual marking in total of 3220 images for the entire file. 2) Bin Rushed Ophthalmic center file and contains 195 original images and 195 images for every single ophthalmologist manual marking in total of 1365 images for the entire file. 3) Magrabi Eye center file and contains 95 original images and 95 images for every single ophthalmologist manual marking in total of 665 images for the entire file. The total of all the dataset images are 750 original images and 4500 manual marked images. The images are saved in JPG and TIFF format., NOTE ON THE DATA: Depositor accidentally left out 50 images from the BinRushed folder from the original deposit. A corrected BinRushed folder that includes these 50 images was added to this data set on May 21, 2018., and NOTE ON DOWNLOADING: The file "MESSIDOR.zip" is too large to be downloaded through Deep Blue Data. Please use Globus to download this file.
- Keyword:
- Medical imaging, Optic cup, Image processing, Optic disc, Glaucoma, Optic nerve head, Image segmentation, Fundus images, and Automated glaucoma screening system
- Citation to related publication:
- Ahmed Almazroa, Sami Alodhayb, Essameldin Osman, Eslam Ramadan, Mohammed Hummadi, Mohammed Dlaim, Muhannad Alkatee, Kaamran Raahemifar, Vasudevan Lakshminarayanan, "Retinal fundus images for glaucoma analysis: the RIGA dataset", Proc. SPIE 10579, Medical Imaging 2018: Imaging Informatics for Healthcare, Research, and Applications, 105790B (6 March 2018); doi: 10.1117/12.2293584; https://doi.org/10.1117/12.2293584
- Discipline:
- Health Sciences
-
- Creator:
- Chun-Seok Cho, Jingyue Xi, Hyun Min Kang, and Jun Hee Lee
- 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=GSE169706). (3) is deposited here. In addition, this deposit includes the processed RDS (single R object) data files.
- Keyword:
- Seq-Scope, scRNA-seq, and spatial transcriptomics
- Citation to related publication:
- Chun-Seok Cho, Jingyue Xi, Sung-Rye Park, Jer-En Hsu, Myungjin Kim, Goo Jun, Hyun-Min Kang, Jun Hee Lee “Seq-Scope: Submicrometer-resolution spatial transcriptomics for single cell and subcellular studies” (preprint) bioRxiv https://doi.org/10.1101/2021.01.25.427807 and Related data sets in NCBI’s Gene Expression Omnibus (GEO) repository: Cho C, Xi J, Si Y, Lee JH, Kang HM, Park S, Hsu J, Kim M, Jun G “Seq-Scope: Submicrometer-resolution spatial barcoding technology that enables microscopic examination of tissue transcriptome at single cell and subcellular levels” https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169706
- Discipline:
- Health 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:
- Adler, Jeremy
- Description:
- Data comparing the Simplified Endoscopic Mucosal Assessment for Crohn's Disease (SEMA-CD) from video recordings of colonoscopies to SEMA-CD scoring of their corresponding colonoscopy reports from pediatric patients with Crohn's disease.
- Keyword:
- Crohn's disease and colonoscopy
- Discipline:
- Health Sciences
-
- Creator:
- Payam Mirshams Shahshahani
- Description:
- The two R codes are related to the feasible balance region calculations for Figures 2, 3, and 4 in the paper. The MATLAB codes are related to the simulations of the recoverable initial quasi-static states, the results of which are shown in Figure 5 of the paper.
- Keyword:
- One-legged balance, Biomechanics, Hip Abductor, and Unipedal Stance
- Citation to related publication:
- Shahshahani, P. M., & Ashton-Miller, J. A. (2020). On the importance of the hip abductors during a clinical one legged balance test: A theoretical study. PLOS ONE, 15(11), e0242454. https://doi.org/10.1371/journal.pone.0242454
- Discipline:
- Health Sciences and Engineering
-
- 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:
- Tan, Meng H, Iyengar, Ravi, Mizokami-Stout, Kara, Yentz, Sarah, MacEachern, Mark P, Shen, Li Yan, Redman, Bruce, and Gianchandani, Roma
- Description:
- The dataset includes most citations considered for inclusion in the scoping review. The citations are accessible in the Endnote file, as well as the primary citation export files from each database. The literature search strategies are included for reproducibility and transparency purposes.
- Keyword:
- Literature search, Scoping review, and Endocrinopathies
- Citation to related publication:
- Tan MH, Iyengar R, Mizokami-Stout K, et al. Spectrum of immune checkpoint inhibitors-induced endocrinopathies in cancer patients: a scoping review of case reports. Clin Diabetes Endocrinol. 2019;5:1. Published 2019 Jan 22. https://doi.org/10.1186/s40842-018-0073-4
- Discipline:
- Health Sciences
-
- Creator:
- Muzyk, Andrew, Smothers, Zachary, Akrobetu, Dennis, Ruiz Veve, Jennifer, MacEachern, Mark P, Tetrault, Jeanette M, and Gruppen, Larry
- Description:
- The dataset includes all citations considered for inclusion in the scoping review. The citations are accessible in Endnote (enlx) and Microsoft Excel (xlsx), as well as the primary citation export files from each database. The literature search strategies are included for reproducibility and transparency purposes. See the published methods for more information.
- Keyword:
- Medical Education, Substance Use Disorders, and Scoping Review
- Citation to related publication:
- Muzyk A, Smothers ZPW, Akrobetu D, Ruiz Veve J, MacEachern M, Tetrault JM, Grupen L. (2019). Substance use disorder education in medical schools: A scoping review of the literature. Academic Medicine. PMID: 31348067. and https://doi.org/10.1097/ACM.0000000000002883
- Discipline:
- Health Sciences
-
- Creator:
- Tronson, Natalie C and Tchessalova, Daria
- Description:
- The main goal of this research was to identify potential molecular pathways that contribute to memory dysregulation and decline that persists long after illness or inflammation. We have previously established a subchronic immune challenge model that results in memory impairments months after the inflammatory challenge. This project aimed to determine whether memory impairments were accompanied by transcriptional dysregulation in memory related brain region (the hippocampus). These data show the differential gene expression as log2fold change (and p-value) in males and females 3 months after immune challenge (Supp Tables 1 and 2); after a subsequent immune challenge (Supp Tables 3 and 4); the differential regulation of genes in males and females (Supp Table 5); genes differentially expressed in the hippocampus of males and females at baseline (Supp Table 6) and the differential regulation of those genes in males and females after immune challenge (Supp Tables 7,8).
- Keyword:
- hippocampus, lipopolysaccharide, differential gene expression, RNA sequencing, neuroimmune, sex differences, learning and memory, and inflammation
- Citation to related publication:
- Tchessalova, D., & Tronson, N. C. (2019). Enduring and sex-specific changes in hippocampal gene expression after a subchronic immune challenge. BioRxiv, 566570. https://doi.org/10.1101/566570
- Discipline:
- Science 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:
- Gliske, Stephen V and Stacey, William C
- Description:
- This data repository includes the quantitative features of high frequency, intracranial EEG along with all necessary scripts to reproduce the figures of the accompanying manuscript.
- Keyword:
- high frequency oscillation, HFO, high frequency activity, and epilepsy
- Citation to related publication:
- (under review)
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- Gliske, Stephen V and Stacey, William C
- Description:
- This data is part of a large program to translate detection and interpretation of HFOs into clinical use. A zip file is included which contains hfo detections, metadata, and Matlab scripts. The matlab scripts analyze this input data and produce figures as in the referenced paper (note: the blind source separation method is stochastic, and so the figures may not be exactly the same). A file "README.txt" provides more detail about each individual file within the zip file.
- Keyword:
- hfo, high frequency oscillation, ripple, fast ripple, blind source separation, non-negative matrix factorization, and temporal variability
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- Saini, Sameer D
- Description:
- See attached survey and codebook
- Discipline:
- Health Sciences
-
- Creator:
- DeLong, Michael R, Tandon, Vickram J, Farajzadeh, Matthew, Berlin, Nicholas L, MacEachern, Mark P, Rudkin, George H, Da Lio, Andrew L, and Cederna, Paul S
- Description:
- The dataset includes all citations considered for inclusion in the systematic review. The citations are accessible in Endnote (enlx), as well as through the primary citation export files from each database. The literature search strategies are included for reproducibility and transparency purposes. See the published methods for more information.
- Keyword:
- Systematic Review, Acellular Dermal Matrix, Breast Reconstructions, and Tissue Expanders
- Citation to related publication:
- DeLong MR, Tandon VJ, Farajzadeh M, Berlin NL, MacEachern MP, Rudkin GH, Da Lio AL, Cederna PS. (2019). Systematic review of the impact of acellular dermal matrix on aesthetics and patient satisfaction in tissue expander-to-implant breast reconstructions. Plastic and Reconstructive Surgery. and https://doi.org/10.1097/PRS.0000000000006212
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark P MLIS, Bennett, Katelyn G MD, Preminger, Aviva MD, Berlin, Nicolas MD, and Vercler, Christian J MD
- Description:
- The dataset includes the reproducible search strategies for all literature databases searched during the review, the key articles used to generate relevant search terms and test the effectiveness of the searches, the Endnote library that has all citations considered for inclusion, a flow chart describing the screening process, and the screening forms used for inclusion and exclusion.
- Keyword:
- Plastic surgery, Professionalism, Surgery, and Social media
- Citation to related publication:
- Bennett K, Berlin N, MacEachern MP, Buchman S, Vercler C. (2018). The ethical and professional use of social media in surgery - A systematic review of the literature. Plastic and Reconstructive Surgery, 142(3), 388e-398e. PMID: 30148789. https://doi.org/10.1097/prs.0000000000004692
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark P and Criss, Cory N
- Description:
- While collaboration with industry is paramount to innovation, the recent emphasis on industrial relationship transparency has sparked new guidelines, research studies, and standardizations focused on re-defining conflict of interest. There is limited data on defining the specific financial amount wherein a conflict of interest is relevant. This study is the first to assess the potential financial effects on high-quality clinical data, or the “indirect sponsorship”.
- Keyword:
- Sponsorship, Indirect sponsorship, Surgery, Robotic surgery, and DaVinci
- Citation to related publication:
- Criss CN, MacEachern MP, Matusko N, Dimick JB, Maggard-Gibbons M, Gadepalli SK. The Impact of Corporate Payments on Robotic Surgery Research: A Systematic Review. Ann Surg. 2019 Mar; 269 (3): 389-396. doi: 10.1097/SLA.0000000000003000. PMID: 30067545. https://doi.org/10.1097/SLA.0000000000003000
- 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
-
Transmission of Oral microbiome and Sequencing
User Collection- Creator:
- Lee, Kyu Han
- Description:
- De-identified participant data from household transmission study of influenza in Nicaragua Oligotype count table and taxonomic classifications
- Keyword:
- Influenza and Microbiome
- Discipline:
- Health Sciences
2Works -
- Creator:
- Lee, Kyu Han, Foxman, Betsy, and Gordon, Aubree
- Description:
- Data include variables used to run mixed effects models examining the association between the nose/throat microbiome and influenza virus infection. Certain individual participant data have been excluded due to identifiability concerns. Data also include the oligotype count table and taxonomic classifications. and Curation Notes: Readme updated Nov. 29, 2018 with context for oligotype and taxonomy files, and citation to associated article.
- Keyword:
- Influenza and Microbiome
- Citation to related publication:
- Lee KH, Gordon A, Shedden K, Kuan G, Ng S, Balmaseda A, Foxman B. The respiratory microbiome and susceptibility to influenza virus infection. PloS One. 2019;14:e0207898. https://doi.org/10.1371/journal.pone.0207898
- Discipline:
- Health Sciences
-
- Creator:
- Lee, Kyu Han
- Description:
- Data include variables used to run accelerated failure time models examining the association between the nose/throat microbiome and 1) symptom duration, 2) shedding duration, and 3) time to infection. Certain individual participant data have been excluded due to identifiability concerns. Data also include the oligotype count table and taxonomic classifications.
- Keyword:
- Influenza and Microbiome
- Citation to related publication:
- Lee KH, Gordon A, Shedden K, Kuan G, Ng S, Balmaseda A, Foxman B. The respiratory microbiome and susceptibility to influenza virus infection. PloS One. 2019;14:e0207898. https://doi.org/10.1371/journal.pone.0207898
- 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:
- 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:
- 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 -
- Creator:
- Zongyu Li, Yuni K. Dewaraja, and Jeffrey A. Fessler
- Description:
- Current methods for patient-specific voxel-level dosimetry in radionuclide therapy suffer from a trade-off between accuracy and computational efficiency. Monte Carlo (MC) radiation transport algorithms are considered the gold standard for voxel-level dosimetry but can be computationally expensive, whereas faster dose voxel kernel (DVK) convolution can be sub-optimal in the presence of tissue heterogeneities. Furthermore, the accuracies of both these methods are limited by the spatial resolution of the reconstructed emission image. To overcome these limitations, this paper considers a single deep convolutional neural network (CNN) with residual learning (named DblurDoseNet) that learns to produce dose-rate maps while compensating for the limited resolution of SPECT images. We took the novel approach of constructing a convolutional neural network with residual learning to handle the accuracy-efficiency tradeoff while compensating for the limited resolution of SPECT images. We then test our CNN on clinically relevant phantoms and patients undergoing Lu-177 DOTATATE therapy in our clinic. Our network demonstrated superior results than Monte Carlo, the current gold standard for voxel dosimetry, but only takes a fraction of time. Thus, the DblurDoseNet has the potential for real-time patient-specific dosimetry in clinical treatment planning due to its demonstrated improvement in accuracy, resolution, noise and speed over the DVK/MC approaches. Matlab is needed to access the phantoms and Python (with Numpy package installed) is needed to access the DVKs.
- Keyword:
- Deep learning, Voxel-level dosimetry, Lu-177 therapy, SPECT resolution effects
- Citation to related publication:
- "DblurDoseNet: A Deep Residual Learning Network for Voxel Radionuclide Dosimetry Compensating for SPECT Imaging Resolution" by Zongyu Li, Jeffrey A. Fessler, Justin K. Mikell, Scott J. Wilderman and Yuni K. Dewaraja. Accepted by Medical Physics, 2021. DOI: 10.1002/mp.15397
- Discipline:
- Health Sciences
-
- Creator:
- Lim, Hongki and Dewaraja, Yuni K.
- Description:
- Interest in quantitative imaging of Y-90 is growing because transarterial radioembolization (RE) with Y-90 loaded microspheres is a promising and minimally invasive treatment that is FDA approved for unresectable primary and metastatic liver tumors. These cancers are a leading cause of cancer mortality and morbidity. Radioembolization is a therapy that irradiates liver tumors with radioactive microspheres administered through a microcatheter placed in the hepatic arterial vasculature. Radioembolization is based on the principle that healthy liver and tumor are mainly vascularized by the portal vein and the hepatic artery respectively. As a result, radioactive microspheres are preferentially located in the lesions after they are administered via the hepatic artery.
- Keyword:
- Y-90, PET, SPECT, CT, Segmentation, Organ, Tumor, Label
- Citation to related publication:
- Van, B. J., Dewaraja, Y. K., Sangogo, M. L., & Mikell, J. K. (2021). Y-90 SIRT: Evaluation of TCP variation across dosimetric models. EJNMMI Physics, 8(1), 45. https://doi.org/10.1186/s40658-021-00391-6
- Discipline:
- Health Sciences
-
- Creator:
- Van, Benjamin J. and Dewaraja, Yuni K.
- Description:
- Interest in quantitative imaging of Y-90 is growing because transarterial radioembolization (RE) with Y-90 loaded microspheres is a promising and minimally invasive treatment that is FDA approved for unresectable primary and metastatic liver tumors. These cancers are a leading cause of cancer mortality and morbidity. Radioembolization is a therapy that irradiates liver tumors with radioactive microspheres administered through a microcatheter placed in the hepatic arterial vasculature. Radioembolization is based on the principle that healthy liver and tumor are mainly vascularized by the portal vein and the hepatic artery respectively. As a result, radioactive microspheres are preferentially located in the lesions after they are administered via the hepatic artery.
- Keyword:
- Y-90, PET, SPECT, CT, Segmentation, Organ, Tumor, Label, Microsphere, Radioembolization, and SIRT
- Citation to related publication:
- Van, B. J., Dewaraja, Y. K., Sangogo, M. L., & Mikell, J. K. (2021). Y-90 SIRT: Evaluation of TCP variation across dosimetric models. EJNMMI Physics, 8(1), 45. https://doi.org/10.1186/s40658-021-00391-6
- Discipline:
- Health Sciences
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