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- Creator:
- Grosh, Karl and Li, Yizeng
- Description:
- In a sensitive cochlea, the basilar membrane response to transient excitation of any kind--normal acoustic or artificial intracochlear excitation--consists of not only a primary impulse but also a coda of delayed secondary responses with varying amplitudes but similar spectral content around the characteristic frequency of the measurement location. The coda, sometimes referred to as echoes or ringing, has been described as a form of local, short term memory which may influence the ability of the auditory system to detect gaps in an acoustic stimulus such as speech. Depending on the individual cochlea, the temporal gap between the primary impulse and the following coda ranges from once to thrice the group delay of the primary impulse (the group delay of the primary impulse is on the order of a few hundred microseconds). The coda is physiologically vulnerable, disappearing when the cochlea is compromised even slightly. The multicomponent sensitive response is not yet completely understood. We use a physiologically-based, mathematical model to investigate (i) the generation of the primary impulse response and the dependence of the group delay on the various stimulation methods, (ii) the effect of spatial perturbations in the properties of mechanically sensitive ion channels on the generation and separation of delayed secondary responses. The model suggests that the presence of the secondary responses depends on the wavenumber content of a perturbation and the activity level of the cochlea. In addition, the model shows that the varying temporal gaps between adjacent coda seen in experiments depend on the individual profiles of perturbations. Implications for non-invasive cochlear diagnosis are also discussed.
- Discipline:
- Engineering and 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
-
- Creator:
- Meurer, William J., Meka, Arjun, and Porath, Jon
- Description:
- Introduction: Diagnostic testing is common in the emergency department. The value of some testing is questionable. The purpose of this study was to assess how varying levels of benefit, risk, and costs influenced an individual’s desire to have diagnostic testing. Methods: A survey through Amazon Mechanical Turk presented hypothetical clinical situations: low risk chest pain and minor traumatic brain injury. Each scenario included three given variables (benefit, risk, and cost), that was independently randomly varied over four possible values (0.1%, 1%, 5%, 10% for benefit and risk and $0, $100, $500, and $1000 for the individual’s personal cost for receiving the test). Benefit was defined as the probability of finding the target disease (traumatic intracranial hemorrhage or acute coronary syndrome). Results: A total of 1000 unique respondents completed the survey. Increasing benefit from 0.1% to 10%, the percent of respondents who accepted a diagnostic test went from 28.4% to 53.1%. [OR: 3.42 (2.57-4.54)] As risk increased from 0.1% to 10%, this number decreased from 52.5% to 28.5%. [OR: 0.33 (0.25-0.44)] Increasing cost from $0 to $1000 had the greatest change of those accepting the test from 61.1% to 21.4%, respectively. [OR: 0.15 (0.11-0.2)] Conclusions: The desire for testing was strongly sensitive to the benefits, risks and costs. Many participants wanted a test when there was no added cost, regardless of benefit or risk levels, but far fewer elected to receive the test as cost increased incrementally. This suggests that out of pocket costs may deter patients from undergoing diagnostic testing with low potential benefit.
- Discipline:
- Health Sciences
-
- Creator:
- Carson, William F. IV
- Description:
- Data files pertaining to the manuscript entitled: "THE STAT4/MLL1 EPIGENETIC AXIS REGULATES THE ANTIMICROBIAL FUNCTIONS OF MURINE MACROPHAGES"
- Discipline:
- Health Sciences
-
- Creator:
- Meurer, William
- Description:
- Dataset for analysis in SPSS
- Discipline:
- Health Sciences
-
- Creator:
- Data-Driven Detroit, Goodspeed, Robert, Reference U.S.A., Veinot, Tiffany C., Yan, Xiang, State of Michigan Department of Elections, and Okullo, Dolorence
- Description:
- The Social Environment refers to characteristics of the people and institutions in a census tract, including: 1) Religious organizations (churches and places of worship); and 2) Voter turnout for the 2012 Presidential Election. Coverage for all data: 10-county Detroit-Warren-Ann Arbor Combined Statistical Area.
- Keyword:
- Voter Turnout, Religious Institutions, Spatial Measures, and Census Tract Level
- Discipline:
- Health Sciences and Social Sciences
-
- Creator:
- Reference USA, City of Detroit, ESRI, Data Driven Detroit, and Veinot, Tiffany C.
- Description:
- Active living resources include spaces and organizations that facilitate physical activity, including 1) park land, 2) recreation areas (including parks, golf courses, amusement parks, beaches and other recreational landmarks); and 3) recreation centers (including gyms, dancing instruction, martial arts instruction, bowling centers, yoga instruction, sports clubs, fitness programs, golf course, pilates instruction, personal trainers, swimming pools, skating rinks, etc.) Coverage for all data: 10-county Detroit-Warren-Ann Arbor Combined Statistical Area.
- Keyword:
- Recreation Areas, Park Land, Census tract level, Metropolitan Detroit, Spatial Measures, Recreation Centers, and Michigan
- Discipline:
- Health Sciences, Social Sciences, and Other
-
- 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:
- Meurer, William
- Description:
- Full analytical dataset with labels in SPSS
- Keyword:
- Diagnostic testing
- Discipline:
- Health Sciences
-
- Creator:
- Okullo, Dolorence, Yan, Xiang (Jacob), Data Driven Detroit, Veinot, Tiffany C., Gomez-Lopez, Iris N., and Goodspeed, Robert
- Description:
- The food environment is: 1) The physical presence of food that affects a person’s diet; 2) A person’s proximity to food store locations; 3) The distribution of food stores, food service, and any physical entity by which food may be obtained; or 4) A connected system that allows access to food. (Source: https://www.cdc.gov/healthyplaces/healthtopics/healthyfood/general.htm) Data included here concern: 1) Food access; and 2) Liquor access. Spatial Coverage for most data: 10-county Detroit-Warren-Ann Arbor Combined Statistical Area, Michigan, USA. See exception for grocery store data below.
- Keyword:
- Food Deserts, Census tract level, Full-Line Grocery Stores, Modified Retail Food Environment Index (MRFEI), Farmer’s Markets, Spatial Measures, and Fast Food Establishments
- Discipline:
- Social Sciences, Health Sciences, and Other
-
- Creator:
- Yoshida, Sei and Swanson, Joel A
- Description:
- The rapid activation of the mechanistic target of rapamycin complex-1 (mTORC1) by growth factors is increased by extracellular amino acids through yet-undefined mechanisms of amino acid transfer into endolysosomes. Because the endocytic process of macropinocytosis concentrates extracellular solutes into endolysosomes and is increased in cells stimulated by growth factors or tumor-promoting phorbol esters, we analyzed its role in amino acid–dependent activation of mTORC1. Here, we show that growth factor-dependent activation of mTORC1 by amino acids, but not glucose, requires macropinocytosis. In murine bone marrow–derived macrophages and murine embryonic fibroblasts stimulated with their cognate growth factors or with phorbol myristate acetate, activation of mTORC1 required an Akt-independent vesicular pathway of amino acid delivery into endolysosomes, mediated by the actin cytoskeleton. Macropinocytosis delivered small, fluorescent fluid-phase solutes into endolysosomes sufficiently fast to explain growth factor–mediated signaling by amino acids. Therefore, the amino acid–laden macropinosome is an essential and discrete unit of growth factor receptor signaling to mTORC1
- Keyword:
- growth factor signaling, Macropinosomes, and mTORC1
- Discipline:
- Health Sciences
-
- Creator:
- Okullo, Dolorence, Gomez-Lopez, Iris N., Goodspeed, Robert, Reddy, Shruthi, Veinot, Tiffany C, Clarke, Phillipa J., and Data Driven Detroit
- Description:
- The information and education environment refers to: 1) the presence of information infrastructures such as broadband Internet access and public libraries in a location; 2) a person’s proximity to information infrastructures and sources; 3) the distribution of information infrastructures, sources and in a specific location; and 4) exposure to specific messages (information content) within a specific location. Coverage for all data: 10-county Detroit-Warren-Ann Arbor Combined Statistical Area.
- Keyword:
- Residential Broadband Data Adoption Rates, Census tract level, Broadband Internet Access and Speed, Colleges and Universities, Public Libraries, Spatial Measures, and Schools
- Discipline:
- Science, Social Sciences, and Health Sciences
-
- Creator:
- Piette, John and Abbott, Patricia A
- Description:
- Contained within is a subset of the larger dataset collected in La Paz, Bolivia in 2014. This data contains the analytic dataset (cross-sectional/descriptive) that includs the PACIC, Morisky, PHQ8, AUDIT, and a subset of socidemographic characteristics for NCD patients in La Paz.
- Keyword:
- Global Health, Bolivia, and Non-communicable disease
- Discipline:
- Health Sciences
-
- Creator:
- Kerber, Kevin A and Meurer, William J
- Description:
- Data set
- Keyword:
- dizziness
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark P
- Description:
- The dataset represents the complete search strategies for all literature databases searched during the systematic review. The Endnote and Excel files of all citations considered for inclusion in the review are also included.
- Keyword:
- systematic review, pharmacy, education, addiction, and substance abuse
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark P
- Description:
- The dataset represents the complete search strategies for all literature databases searched during the systematic review. The Endnote library that contains all citations is also included.
- Keyword:
- Systematic review, Anti-osteoporotic drugs, Fractures, Surgery, and Meta-analysis
- Discipline:
- Health Sciences
-
- Creator:
- Saini, Sameer D
- Description:
- See attached survey and codebook
- 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
- Description:
- The dataset represents the complete, reproducible search strategies for all literature databases searched during the systematic review. The Endnote file and the Endnote import files contain all citations considered for inclusion in the review.
- Keyword:
- addiction, nursing, systematic review, education, and substance use
- Citation to related publication:
- Smothers, Zachary MBS; Reynolds, Victoria PharmD; McEachern, Mark MLIS; Derouin, Anne L. DNP, RN, CPNP, FAANP; Carter, Brigit M. PhD, RN, CCRN; Muzyk, Andrew PharmD Substance Use Education in Schools of Nursing, Nurse Educator: May/June 2018 - Volume 43 - Issue 3 - p 136-139. https://doi.org/10.1097/NNE.0000000000000449 and https://www.ncbi.nlm.nih.gov/pubmed/28858952
- Discipline:
- Health Sciences
-
- Creator:
- Detroit Residential Parcel Survey, United States Postal Service, Wayne County Register of Deeds, US Census, Yu, Deehan, Public and Affordable Housing Research Corporation (PAHRC), Veinot, Tiffany, RealtyTRAC, National Low Income Housing Coalition (NLIHC), Okullo, Dolorence, Wayne County Treasurer, Health Resource and Services Administration (HRSA), and Data Driven Detroit
- Description:
- This dataset includes census tract-level data concerning housing in Metropolitan Detroit. The data includes: 1) Total housing units and total mortgages in the tract; 2) Land use; 3) Real estate information (foreclosures, sales transactions, and home values); 4) Vacant housing; 5) Housing age and available facilities; 6) Housing condition; and 7) Spatial measures of subsidized housing in the tract. Data coverage should say 2006 to 2015.
- Keyword:
- Housing Conditions, Community Health, Subsidized Housing Locations, Availability of Kitchen and Plumbing Facilities, Vacant Properties, Census tract level, Age of Housing, Spatial Measures, Home Sale Transactions, Land Use by Category, Housing Units and Ownership, Housing Values, and Foreclosed Properties
- Discipline:
- Social Sciences and Health Sciences
-
- Creator:
- Veinot,Tiffany,C., Michigan Department of Health & Human Services, U.S. Census Bureau, American Community Survey, Data Driven Detroit, Okullo, Dolorence, and Michigan Department of Vital Statistics
- Description:
- Health status data includes data about the health of persons within a census tract in Metropolitan Detroit, measured at the census tract level. This includes data about 1) mortality by condition; 2) exposures to toxic substances; and 3) disability. Coverage for all data: 10-county Detroit-Warren-Ann Arbor Combined Statistical Area.
- Keyword:
- Community Health, Mortality Rates by Condition , Disability, Elevated Blood Lead Levels, Census Tract level, All-Cause Mortality Rates, and Spatial Measures
- Discipline:
- Health Sciences and Social 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:
- Berlin, Nicholas and MacEachern, Mark
- Description:
- This systematic review and meta-analysis assesses decision aids in the context of patients considering post-mastectomy breast reconstruction. and NOTE: An updated Read Me file was added to this data set on May 24, 2018 replacing the original.
- Keyword:
- Post-mastectomy, Decision-making, Systematic review, Decision aids, Meta-analysis, and Breast reconstruction
- Citation to related publication:
- Berlin NL, Tandon VJ, Hawley ST, et al. Feasibility and Efficacy of Decision Aids to Improve Decision Making for Postmastectomy Breast Reconstruction: A Systematic Review and Meta-analysis. Med Decis Making. 2019;39(1):5–20. https://doi.org/10.1177/0272989X18803879
- 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:
- Moyer, Cheryl A
- Description:
- Data reflect the knowledge, attitudes, and beliefs of health care providers regarding neonatal near-misses in Neonatal Intensive Care Units (NICUs) in southern Ghana.
- Keyword:
- qualitative methods, neonatal mortality, neonatal near-misses, and developing country
- Discipline:
- 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:
- MacEachern, Mark and Muzyk, Andrew
- Description:
- The systematic review explores the role of the emergency department in naloxone distribution and harm reduction strategies associated with opioid use.
- Keyword:
- Opioid use, Systematic review, Emergency department, Literature searches, and Naloxone
- Citation to related publication:
- Gunn AH, Smothers ZPW, Schramm-Sapyta N, Freiermuth CE, MacEachern M, Muzyk AJ. (2018). The emergency department as an opportunity for naloxone distribution. Western Journal of Emergency Medicine, 19(6), 1036-42. doi: 10.5811/westjem.2018.8.38829 https://doi.org/10.5811/westjem.2018.8.38829
- Discipline:
- Health Sciences
-
- Creator:
- Mirshams Shahshahani, Payam
- Description:
- Investigating minimum human reaction times is often confounded by the motivation, training, and state of arousal of the subjects. We used the reaction times of athletes competing in the shorter sprint events in the Athletics competitions in recent Olympics (2004-2016) to determine minimum human reaction times because there's little question as to their motivation, training, or state of arousal. The reaction times of sprinters however are only available on the IAAF web page for each individual heat, in each event, at each Olympic. Therefore we compiled all these data into two separate excel sheets which can be used for further analyses.
- Keyword:
- minimum reaction time, sprinter, Olympics, Athletics, sex difference, starting block, and false start
- Citation to related publication:
- Mirshams Shahshahani P, Lipps DB, Galecki AT, Ashton-Miller JA (2018) On the apparent decrease in Olympic sprinter reaction times. PLoS ONE 13(6): e0198633. https://doi.org/10.1371/journal.pone.0198633
- Discipline:
- Engineering, Health Sciences, Science, Other, and General Information Sources
-
- 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:
- 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
-
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 -
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 -
- Creator:
- Gharzai, Laila A, Green, Michael D, Griffith, Kent A, and Jolly, Shruti
- Description:
- Three sensitivity analyses were performed. First, a second matching step was performed in which two controls were selected for each case, where possible using a nearest neighbor and caliper metric. Controls needed to have propensity scores within 0.1 of the case to be selected. Thirty-eight of the 39 cases had at least one control using this method and for 36 cases two controls could be selected. The average difference between case and control propensity adjuvant RT was 0.008 (range 0.00003-0.095). A second sensitivity analysis was performed to guard against immortal time bias. In order to mitigate the possibility of this effect, cases known not to have undergone adjuvant RT have been screened for suitable follow-up without a recurrence (local or regional recurrence, metastatic failure, and/or death) to ensure that if adjuvant RT had been prescribed as part of the multi-modality treatment regimen, that it would have been initiated. Three months was selected as the mandatory follow-up time. One to one matching was carried out and all 39 cases were matched to a control. A third sensitivity analysis was performed to account for stage migration seen in control patients that presented to the University of Michigan with more advanced disease. Patients that underwent adjuvant radiation were matched one to one with control group patients who did not receive adjuvant radiation, and who had the same stage at diagnosis as compared to stage at University of Michigan presentation.
- Keyword:
- adenocortical carcinoma and English
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark
- Description:
- The search data supports a literature review project on lifestyle therapies for the management of atrial fibrillation. The data included in the dataset are the reproducible search strategies (in docx) and the exported results of all citations from all databases (txt and ris files). These searches and exported result files contain all citations originating from the database searches that were considered for inclusion.
- Keyword:
- literature searches, atrial fibrillation, lifestyle therapy, and lifestyle therapies
- Citation to related publication:
- Abdul-Aziz AA, Altawil M, Lyon A, MacEachern M, Richardson CR, Rubenfire M, Pelosi F Jr, Jackson EA. Lifestyle Therapy for the Management of Atrial Fibrillation. Am J Cardiol. 2018 May 1;121(9):1112-1117. doi: 10.1016/j.amjcard.2018.01.023. PubMed PMID: 29650239., https://www.ncbi.nlm.nih.gov/pubmed/29650239, and https://doi.org/10.1016/j.amjcard.2018.01.023
- Discipline:
- Health Sciences
-
- Creator:
- Haydar, Bishr and MacEachern, Mark
- Description:
- The research adheres to PRISMA-HARM recommendations for systematic reviews. The reproducible search strategies for all databases, the citation export files from all databases, and the eligibility screening decisions are included in the dataset.
- Keyword:
- Systematic review, Patient transportation, intrahospital, intra-hospital, and Critically ill patients
- Citation to related publication:
- Haydar B, Baetzel A, Elliott A, MacEachern M, Kamal A, Christensen R. Adverse Events During Intrahospital Transport of Critically Ill Children: A Systematic Review. Anesth Analg. 2019. http://dx.doi.org/doi:10.1213/ANE.0000000000004585
- Discipline:
- Health Sciences
-
- Creator:
- Hatch, Nan E.
- Description:
- Crouzon FGFR2-C342Y/+ and wild type littermate pups on a BALB/c congenic background were injected with lentivirus expressing TNAP enzyme or phosphate buffered saline shortly after birth. Mice were euthanized 4 weeks after birth for analyses.
- Keyword:
- craniofacial, bone, craniosynostosis, FGFR2, TNAP, mouse model, and development
- Citation to related publication:
- Nam, H. K., Vesela, I., Schutte, S. D., & Hatch, N. E. (2020). Viral delivery of tissue nonspecific alkaline phosphatase diminishes craniosynostosis in one of two FGFR2C342Y/+ mouse models of Crouzon syndrome. PLOS ONE, 15(5), e0234073. https://doi.org/10.1371/journal.pone.0234073
- Discipline:
- Health Sciences
-
- Creator:
- Crisp, Dakota N., Saggio, Maria L., Scott, Jared, Stacey, William C., Nakatani, Mitsuyoshi, Gliske, Stephen V., and Lin, Jack
- Description:
- This data and scripts are meant to test and show seizure differentiation based on bifurcation theory. A zip file is included which contains real and simulated seizure waveforms, Matlab scripts, and metadata. The matlab scripts allow for visual review validation and objective feature analysis. The file “README.txt” provides more detail about each individual file within the zip file. and Data citation: Crisp, D.N., Saggio, M.L., Scott, J., Stacey, W.C., Nakatani, M., Gliske, S.F., Lin, J. (2019). Epidynamics: Navigating the map of seizure dynamics - Code & Data [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/ejhy-5h41
- Keyword:
- Bifurcation, Epilepsy, Seizure, and Divergence
- Citation to related publication:
- Saggio, M.L., Crisp, D., Scott, J., Karoly, P.J., Kuhlmann, L., Nakatani, M., Murai, T., Dümpelmann, M., Schulze-Bonhage, A., Ikeda, A., Cook, M., Gliske, S.V., Lin, J., Bernard, C., Jirsa, V., Stacey, W., 2020. In pre-print. Epidynamics characterize and navigate the map of seizure dynamics. bioRxiv 2020.02.08.940072. https://doi.org/10.1101/2020.02.08.940072
- Discipline:
- Engineering, Science, and Health Sciences
-
- Creator:
- Crisp, Dakota N., Cheung, Warwick, Gliske, Stephen V., Lai, Alan, Freestone, Dean R., Grayden, David B., Cook, Mark J., and Stacey, William C.
- Description:
- The data and the scripts are to show that seizure onset dynamics and evoked responses change over the progression of epileptogenesis defined in this intrahippocampal tetanus toxin rat model. All tests explored in this study can be repeated with the data and scripts included in this repository. and Dataset citation: Crisp, D.N., Cheung, W., Gliske, S.V., Lai, A., Freestone, D.R., Grayden, D.B., Cook, MJ., Stacey, W.C. (2019). Epileptogenesis modulates spontaneous and responsive brain state dynamics [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/r6vg-9658
- Keyword:
- evoked response, stimulation, bifurcation, epilepsy, seizure, divergence, and dynamics
- Citation to related publication:
- Crisp, D. N., Cheung, W., Gliske, S. V., Lai, A., Freestone, D. R., Grayden, D. B., Cook, M. J., & Stacey, W. C. (2020). Quantifying epileptogenesis in rats with spontaneous and responsive brain state dynamics. Brain Communications, 2(1). https://doi.org/10.1093/braincomms/fcaa048
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- Meurer, William
- Description:
- SPSS is required to access processed dataset in .sav format. Model output is provided as a word document, and Qualtrics survey instrument is included as PDF and .docx, where .docx version contains survey logic and question numbers.
- Keyword:
- Diagnostic Testing, Emergency Medicine, and Financial Incentives
- Citation to related publication:
- Iyengar, R., Winkels, J., Smith, C. M., Meka, A. P., MD, Porath, J. D., MD, & Meurer, W. J., MD, MS. (2019, January 21). The Effect of Financial Incentives on Patient Decisions to Undergo Low-Value Head CT Scans. https://doi.org/10.31219/osf.io/4mdfw
- Discipline:
- Health Sciences
-
- Creator:
- Lim, Hongki and Dewaraja, Yuni K.
- Description:
- Internally administered targeted radionuclide therapy (TRT) with radio-labelled targeting molecules that deliver cytotoxic radiation to tumor has been used successfully to treat multiple cancers. Lu-177, used increasingly in TRT, emits both beta particles that deliver the therapeutic effect. FDA recently approved a fixed activity (4 cycles of 7.4 GBq/cycle as in NETTER -1) administered every 8 weeks. With the patient studies under this treatment, we collected CT images and corresponding volume of interest (organs, lesions) contours.
- Keyword:
- Lu-177, CT, Segmentation, Organ, Tumor, Label
- 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:
- 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:
- Dulka, Eden A
- Description:
- This data is a subset of that originally produced as part of an effort to characterize GnRH neuron activity during prepubertal development in control and PNA mice and investigate the potential influences of sex and PNA treatment on this process (1). It was later used in (2) to further investigate the firing patterns of GnRH neurons in these categories of mice and determine how these patterns might differ based on age and treatment condition. The data files can be opened and examined using Wavemetric's Igor Pro software. Code used to further examine and visualize the data can be found at https://gitlab.com/um-mip/mc-project-code. This research was supported by National Institute of Health/Eunice Kennedy Shriver National Institute of Child Health and Human Development R01 HD34860 and P50 HD28934. (1) Dulka EA, Moenter SM. Prepubertal development of gonadotropin-releasing hormone (GnRH) neuron activity is altered by sex, age and prenatal androgen exposure. Endocrinology 2017; 158:3941-3953 (2) Penix JJ, DeFazio RA, Dulka EA, Schnell S, Moenter SM. Firing patterns of gonadotropin-releasing hormone (GnRH) neurons are sculpted by their biology. Pending.
- Keyword:
- action potential, Monte Carlo, polycystic ovary syndrome, puberty, and androgen
- Citation to related publication:
- Dulka EA, Moenter SM. Prepubertal development of gonadotropin-releasing hormone neuron activity is altered by sex, age and prenatal androgen exposure. Endocrinology 2017; 158:3943-3953. https://dx.doi.org/10.1210%2Fen.2017-00768 and Penix JJ, DeFazio RA, Dulka EA, Schnell S, Moenter SM. Firing patterns of gonadotropin-releasing hormone (GnRH) neurons are sculpted by their biology. Pending.
- 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:
- MacEachern, Mark P, Marti, Kyriaki C, Mylonas, Anastassios I, and Gruppen, Larry
- Description:
- The dataset includes most citations considered for inclusion in the scoping review. The citations are accessible in the Endnote (enlx) file, as well as the primary citation export files from each database. The literature search strategies are included for reproducibility and transparency purposes. See the methods of the article for more information.
- Keyword:
- Dental Education, Dentistry, Education, Humanities, and Scoping Review
- Citation to related publication:
- Marti KC, Mylonas AI, MacEachern M, Gruppen L. (2019). Humanities in predoctoral dental education: A scoping review. Journal of Dental Education, 83(10), 1174-1198. DOI: 10.21815/JDE.019.126, http://www.jdentaled.org/content/83/10/1174.long, and https://doi.org/10.21815/JDE.019.126
- 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:
- Lee, Joyce Y, Knauer, Heather A, Lee, Shawna J, MacEachern, Mark P, and Garfield, Craig F
- 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, Fathers, Education, and Perinatal
- Citation to related publication:
- Lee JY, Knauer HA, Lee SJ, MacEachern MP, Garfield CF. (2018). Father-inclusive perinatal parent education programs: A systematic review. Pediatrics, 142(1). PMID: 29903835. and https://doi.org/10.1542/peds.2018-0437
- 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:
- 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:
- Hatch, Nan E.
- Description:
- Crouzon FGFR2-C342Y/+ and wild type littermate pups on a C57BL/6 congenic background were injected with lentivirus expressing recombinant TNAP enzyme or phosphate buffered saline shortly after birth. Mice were euthanized 3 weeks after birth for analyses.
- Keyword:
- craniofacial, bone, craniosynotosis, FGFR2, TNAP tissue nonspecific alkaline phosphatase, mouse model, and development
- Citation to related publication:
- Nam, H. K., Vesela, I., Schutte, S. D., & Hatch, N. E. (2020). Viral delivery of tissue nonspecific alkaline phosphatase diminishes craniosynostosis in one of two FGFR2C342Y/+ mouse models of Crouzon syndrome. PLOS ONE, 15(5), e0234073. https://doi.org/10.1371/journal.pone.0234073
- 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:
- Whitaker, Steven T., Nataraj, Gopal, Nielsen, Jon-Fredrik, and Fessler, Jeffrey A.
- Description:
- File: P,jf06Sep2019,mese.7 The multi-echo spin echo (MESE) data was acquired using a 3D acquisition with an initial 90 degree excitation pulse followed by 32 refocusing (180 degree) pulses, resulting in 32 echoes with echo spacing of 10 ms. The repetition time of the sequence was 1200 ms. Each refocusing pulse was flanked by crusher gradients to impart 14 cycles of phase across the imaging volume. The initial excitation pulse had time-bandwidth product of 6, duration of 3 ms, and slab thickness of 0.9 cm, and each refocusing pulse had time-bandwidth product of 2, duration of 2 ms, and slab thickness of 2.1 cm. The scan took 36 min 11 s and covered a field of view (FOV) of 22 x 22 x 0.99 cm^3 with matrix size 200 x 200 x 9., File: P,jf06Sep2019,b1.7 The Bloch-Siegert (BS) scans were acquired using a 3D acquisition. The excitation pulse of these scans had time-bandwidth product of 8 and duration of 1 ms. The pair of scans used +/-4 kHz off-resonant Fermi pulses between excitation and readout. The BS scans took 2 min 40 s in total and covered a FOV of 22 x 22 x 0.99 cm^3 with matrix size 200 x 50 x 9., File: P,jf06Sep2019,mwf.7 The small-tip fast recovery (STFR) scans were acquired using a 3D acquisition. The first two and last two scans were pairs of spoiled gradient-recalled echo (SPGR) scans with echo time difference of 2.3 ms. (In the related paper, only the first set was used, i.e., only 11 of the 13 scans were used.) The remaining scans used scan parameters that were optimized to minimize the Cramer-Rao Lower Bound (CRLB) of estimates of myelin water fraction (MWF). The RF pulses had time-bandwidth product of 8 and duration of 1 ms. Each pair of SPGR scans took 58 s and the nine STFR scans took 3 min 36 s for a total scan time of 5 min 32 s (4 min 34 s if one pair of SPGR scans is ignored). The scans covered a field of view (FOV) of 22 x 22 x 0.99 cm^3 with matrix size 200 x 200 x 9., File: meseslice5.mat Contains the 32 echoes of the MESE image data for the middle slice of the imaging volume. Saved using Mathworks MATLAB R2019a., File: b1slice5.mat Contains the transmit field inhomogeneity map for the middle slice of the imaging volume., File: recon.jld Key "img" contains the 11 STFR images for the middle slice of the imaging volume. Key "b0map" contains a field map estimated from the two SPGR scans. Key "mask" contains a mask of the voxels for which to estimate MWF. Key "T1img" contains a T1-weighted image for anatomical reference., File: headmask.mat Contains a mask for visualizing just the brain (ignores the skull) for the middle slice of the imaging volume., File: rois.mat Contains masks for various regions of interest (ROIs), used for computing statistics. Keys "mtopleft", "mtopright", "mbottomleft", and "mbottomright" refer to the corresponding locations on the anatomical reference image (see related paper). Key "mic" refers to the internal capsules, and key "mgm" refers to a gray matter ROI., The raw data files (P-files) can be read into the Julia programming language using the Julia version of the Michigan Image Reconstruction Toolbox ( https://github.com/JeffFessler/MIRT.jl) or into MATLAB using TOPPE ( https://github.com/toppeMRI/toppe). The reconstructed slices used in the related paper are provided for convenience, and are stored in .mat files that can be loaded into Julia (using the package MAT.jl) or MATLAB, and a .jld file that can be loaded into Julia (using the package JLD.jl). The Julia code for processing the data to create MWF maps is hosted publicly on GitHub at https://github.com/StevenWhitaker/STFR-MWF., and Files: toppe-master.zip and MIRT.jl-master.zip are archived versions of the TOPPE and Michigan Image Reconstruction Toolbox code sets from GitHub as of 2/28/2020.
- Keyword:
- myelin, machine learning, kernel learning, magnetic resonance imaging, and scan design
- Citation to related publication:
- Whitaker, S. T., Nataraj, G., Nielsen, J.-F., & Fessler, J. A. (2020). Myelin water fraction estimation using small-tip fast recovery MRI. Magnetic Resonance in Medicine, 84(4), 1977–1990. https://doi.org/10.1002/mrm.28259
- Discipline:
- Health Sciences and Engineering
-
- 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:
- LaBarre, Jennifer L., Peterson, Karen E., Kachman, Maureen T., Perng, Wei., Tang, Lu., Hao, Wei., Zhou, Ling., Karnovsky, Alla., Cantoral, Alejandra., Téllez-Rojo, Martha María., Song, Peter XK., and Burant, Charles F.
- Description:
- Participants were enrolled in the Early Life Exposure in Mexico to ENvironmental Toxicants (ELEMENT) project which was started in 1994 and consists of three sequentially-enrolled birth cohorts from Mexico City Maternity Hospitals (20). A subset of these children, age 8-14 years, were contacted through their primary caregiver to provide urine samples, serum samples, anthropometry and complete an interview-based questionnaire (n=250). Subjects for this analysis have baseline and follow data on anthropometry, metabolic biomarkers and adequate serum volume for metabolomics analyses (n=206).
- Citation to related publication:
- LaBarre, J. L., Peterson, K. E., Kachman, M. T., Perng, W., Tang, L., Hao, W., Zhou, L., Karnovsky, A., Cantoral, A., Téllez-Rojo, M. M., Song, P. X. K., & Burant, C. F. (2020). Mitochondrial Nutrient Utilization Underlying the Association Between Metabolites and Insulin Resistance in Adolescents. The Journal of Clinical Endocrinology & Metabolism, 105(7), 2442–2455. https://doi.org/10.1210/clinem/dgaa260
- Discipline:
- Health Sciences
-
- Creator:
- Kue, Jessie and Meurer, William
- Description:
- NHAMCS is an annual survey of emergency department visits. and SAS programs are required to read this data.
- Keyword:
- emergency department and hypertension
- Citation to related publication:
- Kue, J., & Meurer, W. (2020). Association between blood pressure, race, ethnicity and likelihood of admission to the hospital from United States emergency departments – A cross sectional study. F1000Research, 9, 1116. https://doi.org/10.12688/f1000research.24757.1
- Discipline:
- Health Sciences
-
- Creator:
- Batterman, Stuart; University of Michigan
- Description:
- We evaluated PM levels at the Agbogbloshie e-waste and scrap yard site in Accra, Ghana, and at upwind and downwind locations. This monitoring forms part of the West Africa-Michigan Charter II for GEOHealth cohort study, which is analyzing occupational exposures and health risks at this site.
- Keyword:
- Air pollution, particulate matter, e-waste, Fires, and monitoring
- Citation to related publication:
- Kwarteng, L., Baiden, E. A., Fobil, J., Arko-Mensah, J., Robins, T., & Batterman, S. (2020). Air Quality Impacts at an E-Waste Site in Ghana Using Flexible, Moderate-Cost and Quality-Assured Measurements. GeoHealth, 4(8), e2020GH000247. https://doi.org/10.1029/2020GH000247
- Discipline:
- Health Sciences and Engineering
-
- Creator:
- Crisp, Dakota N., Parent, Rachel, Nakatani, Mitsuyoshi, Murphy, Geoffrey G. , and Stacey, William C.
- Description:
- This data and scripts are meant to test and show that seizure onset dynamics can be modulated using anti-epileptic drugs. A zip file is included that contains all waveform data, MATLAB processing scripts, and metadata. The MATLAB scripts allow for visual review validation and objective feature analysis. The file includes various README files explaining the scripts and their relationships in greater detail.
- Keyword:
- Bifurcation, Epilepsy, Seizure, and Electrophysiology
- Discipline:
- Health Sciences, Engineering, and Science
-
- 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
-
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:
- 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
-
- Creator:
- Attari, Ali
- Description:
- Please refer to the "README.txt" for more details., MATLAB R2018a (Mathworks, Natick, MA, USA) was used to process this data., and Excel (Microsoft Office) was used to store survey data on the comfort of both systems and also to provide absolute and relative intraobserver variablities for the DM device.
- Keyword:
- Digital Manometry
- Citation to related publication:
- Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system Attari A, Chey WD, Baker JR, Ashton-Miller JA (2020) Comparison of anorectal function measured using wearable digital manometry and a high resolution manometry system. PLOS ONE 15(9): e0228761. https://doi.org/10.1371/journal.pone.0228761
- Discipline:
- Engineering, Science, and Health Sciences
-
- Creator:
- Figueroa, C. Alberto
- Description:
- This .stl file represents the largest vessels of the cerebral circulation, specifically around the Circle of Willis. The file was created from a Computed Tomography Angiography (CTA) of a relatively healthy patient. It consisted of a 512 x 512 x 709 voxel image with a resolution of 0:35 mm x 0:35 mm x 0:5 mm. The model includes the basilar artery (1), left and right internal carotid arteries (2, and 3), left and right anterior cerebral arteries (4, and 5), left and right middle cerebral arteries (6, and 7), left and right posterior cerebral arteries (8, and 9), and various communicating arteries (10, 11, and 12).
- Keyword:
- Circle of Willis, Blood flow simulation, Hemodynamics, and Benchmarking blood flow
- Citation to related publication:
- N. Wilson, K. Wang, R. Dutton, C.A. Taylor, "A software framework for creating patient specific geometric models from medical imaging data for simulation based medical planning of vascular surgery", Medical Image Computing and Computer-Assisted Intervention MICCAI 2001, Springer, 2001, pp. 449–456. doi: 10.1007/3-540-45468-3_54 and N. Xiao, J.D. Humphrey, C.A. Figueroa, "Multi-Scale Computational Model of Three-Dimensional Hemodynamics within a Deformable Full-Body Arterial Network”, Journal of Computational Physics, 2013, Vol 244, pp. 22-40. doi: 10.1016/j.jcp.2012.09.016
- Discipline:
- Engineering and Health Sciences
-
- Creator:
- Townsend, Whitney A, MacEachern, Mark P, and Song, Jean
- Description:
- We conducted a search through BioMed Central's 54 medicine and public health journals that provide OPR documentation in order to identify systematic review papers published in 2017. For each article we determined if OPR data, reviewer and author comments, were accessible. If so, we assessed the search methodology and reporting quality of the search process with a grading rubric based on PRISMA and PRESS standards, and then mined peer reviewer comments for references to the search methodology.
- Keyword:
- Systematic Reviews, Peer Review, Open Peer Review, Methodology, Research Methods, and Reporting
- Discipline:
- Health Sciences
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized diagnostic imaging scans of two patients. The images provided are pre-therapy scans used by clinicians for diagnosis and for selecting patients for treatment with Lu-177 DOTATATE. Multiple imaging modalities are present including diagnostic CT, MRI, and Ga68 PET, depending on the selected patient. All images are in DICOM format.
- Keyword:
- Lu-177, Lutathera, Dosimetry, Radionuclide, CT, MRI, and PET
- Discipline:
- Health Sciences
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized planar whole body images of two patients. Patient scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE. Both anterior and posterior views are provided. All images are in DICOM format.
- Keyword:
- Lu-177, Lutathera, Dosimetry, Radionuclide, and Planar
- Discipline:
- Health Sciences
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized SPECT/CT scans of two patients. Patient scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE. Both the SPECT and the co-registered CT are provided. All images are in DICOM format.
- Keyword:
- Lu-177, Dosimetry, Radionuclide, SPECT, and CT
- Discipline:
- Health Sciences
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized time integrated activity maps for two patients. SPECT/CT scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE and combined into a single activity map for each patient. All images are in DICOM format.
- Keyword:
- Lu-177, Dosimetry, Radionuclide, SPECT, and CT
- Discipline:
- Health Sciences
-
- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This publication contains anonymized DICOM structure files that were outlined on SPECT/CT scans for two patients. Organ contours include the liver, right and left kidneys, and spleen when present. Two to four lesions were outlined for each patient.
- Keyword:
- Lu-177, Dosimetry, Radionuclide, SPECT, and Contour
- Discipline:
- Health Sciences
-
Lu-177 DOTATATE Anonymized Patient Datasets
User Collection- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This collection is comprised of a number of works that collectively represent the imaging studies and information necessary for dosimetric analysis of a patient treated with Lutathera. All works may be used as standalone datasets or in conjunction with the others in this collection depending on the analysis performed. Files are stored using the DICOM standard widely accepted for storage and transmission of medical images and related information. All patient private information has been anonymized using MIM commercial software (MIM Software Inc.). Data from 2 patients, referred to as patient 4 and patient 6, has been provided in this collection and is divided among 6 works as outlined below:, 1) Pre-Therapy Diagnostic Images. Description: Patient diagnostic scans performed prior to Lutathera treatment. Used for identifying lesions and measuring progression. Note that the date of the baseline scan may be several months before the Lutathera treatment and changes in the anatomy are possible. Files: (1) Ga68 Dotatate PET/CT, Either: (1) MRI, (1) standalone diagnostic CT, 2) Planar Whole Body Scans. Description: Planar whole body Lu-177 scans taken at 4 time points within a week after treatment. Two views (Anterior and Posterior) and 3 energy windows (one main window at 208 keV and 2 adjacent scatter windows) are available for each time point. The units of this image is counts. Energy window information, acquisition data/time and duration can be found in DICOM header. Files: (6) individual images at each time point (24 total images per patient) , 3) SPECT/CT Scans. Description: Lu-177 SPECT/CT scans at 4 time points within a week after treatment (same time points as the planar scans). Images were acquired on a Siemens Intevo system and reconstructed using xSPECT Quant. The units of this image is Bq/mL. Information on the reconstruction, acquisition date/time, duration, Lu-177 administration time and activity can be found in the DICOM header. Files: (1) Folder with reconstructed SPECT slices per time point (4 folders total per patient), (1) Folder containing co-registered CT slices per time point (4 folders total per patient), 4) Lesion and Organ Volumes of Interest. Description: DICOM RT structure files containing organ and lesion volumes of interest (VOI) that were defined on the CT of the scan1 SPECT/CT in 3). Organs were defined using semi-automatic tools (atlas based and CNN-based) while lesions were defined manually by a radiologist guided by baseline scans. Only lesions >2 cc were defined. Files: (1) File containing organ contours, (1) File containing lesion contours, 5) Time Integrated Activity Maps. Description: A DICOM file containing the time-integrated activity map over all 4 time points within a week after treatment. This combines the SPECT/CT scans provided in 3) into a single integrated activity map. This map was generated via the MIM MRT Dosimetry package: The 4 time points were registered to the reference SPECT scan (time point 1) using a contour intensity based SPECT alignment and the voxel-level time-activity data was fit using exponential functions. Voxel-level integration was performed to generate the TIA map. The units of this image is Bq/mL * sec. Files: (1) Folder with Time-integrated activity image per patient, and 6) Projection Data and CT based Attenuation Coefficient Maps. Description: SPECT projection data for each of the 4 Lutathera scans taken within a week after treatment is provided in 3 forms: unaltered, Siemens [Reformatted], and Siemens [Advanced]. The difference between the Projections and the [Advanced] Projections is that the [Advanced] consists of uncorrected raw projection data and the other the corrected projection data (e.g. camera uniformity corrections). The [Advanced] projections are used in xSPECT reconstruction (where all corrections are done during the reconstruction), while the other is used in Flash 3D reconstruction. CT-based attenuation coefficient maps (mumaps) are provided for each of the 4 scans taken within a week after treatment. Two methods are provided for each mumap: xSPECT and F3D as the matrix size is different for the 2 cases (256 x 256 for xSPECT and 128 x 128 for Flash3D). Files: (3) Folders containing raw SPECT projections, (2) Folders containing CT attenuation coefficient maps (mumaps)
- Keyword:
- Lu-177, Lutathera, Dosimetry, Radionuclide, and CTMRIPET
- Discipline:
- Health Sciences
6Works -
- Creator:
- Arthurs, Christopher J., Khlebnikov, Rostislav, Melville, Alexander, Marčan, Marija, Gomez, Alberto, Dillon-Murphy, Desmond, Cuomo, Federica, Vieira, Miguel, Schollenberger, Jonas, Lynch, Sabrina, Tossas-Betancourt, Christopher, Iyer, Kritika, Hopper, Sara, Livingston, Elizabeth, Youssefi, Pouya, Noorani, Alia, Ben Ahmed, Sabrina, Nauta, Foeke J.N., van Bakel, Theodorus M.J., Ahmed, Yunus, van Bakel, Petrus A.J., Mynard, Jonathan, Di Achille, Paolo, Gharahi, Hamid, Lau, Kevin D., Filonova, Vasilina, Aguirre, Miquel, Nama, Nitesh, Xiao, Nan, Baek, Seungik, Garikipati, Krishna, Sahni, Onkar, Nordsletten, David, and Figueroa, Carlos A.
- Description:
- This repository contains the source code for the CRIMSON GUI, as required in the PLOS Computational Biology publication: CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation by the same authors., This is a snapshot of the software; build dependencies can be found at https://doi.org/10.7302/ssj9-n788. Please visit https://github.com/carthurs/CRIMSONGUI/releases/tag/PLOS_Comp_Bio & www.crimson.software for more general information and the most up to date version of the software., and Software can be compiled in Windows.
- Keyword:
- Blood Flow Simulation, Patient-specific, Open-source Software, Image-based simulation, Cardiovascular Medical Image, Segmentation, and Finite Element Simulation
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, M. Marčan, A. Gomez, D. Dillon-Murphy, F. Cuomo, M.S. Vieira, J. Schollenberger, S.R. Lynch, C. Tossas-Betancourt, K. Iyer, S. Hopper, E. Livingston, P. Youssefi, A. Noorani, S. Ben Ahmed, F.J.H. Nauta, T.M.J. van Bakel, Y. Ahmed, P.A.J. van Bakel, J. Mynard, P. Di Achille, H. Gharahi, K. D. Lau, V. Filonova, M. Aguirre, N. Nama, N. Xiao, S. Baek, K. Garikipati, O. Sahni, D. Nordsletten, C.A. Figueroa bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960 and Computational Vascular Biomechanics Lab @ the University of Michigan and other collaborators, The Qt Company, NSIS Team and contributors, PostgreSQL Global Development Group, Oracle Corporation, Kitware. CRIMSON open source project - Build Dependencies [Data set], (2021). University of Michigan - Deep Blue. https://doi.org/10.7302/ssj9-n788
- Discipline:
- Health Sciences and Engineering
-
- Creator:
- Arthurs, Christopher J., Khlebnikov, Rostislav, Melville, Alexander, Marčan, Marija, Gomez, Alberto, Dillon-Murphy, Desmond, Cuomo, Federica, Vieira, Miguel, Schollenberger, Jonas, Lynch, Sabrina, Tossas-Betancourt, Christopher, Iyer, Kritika, Hopper, Sara, Livingston, Elizabeth, Youssefi, Pouya, Noorani, Alia, Ben Ahmed, Sabrina, Nauta, Foeke J.N., van Bakel, Theodorus M.J., Ahmed, Yunus, van Bakel, Petrus A.J., Mynard, Jonathan, Di Achille, Paolo, Gharahi, Hamid, Lau, Kevin D., Filonova, Vasilina, Aguirre, Miquel, Nama, Nitesh, Xiao, Nan, Baek, Seungik, Garikipati, Krishna, Sahni, Onkar, Nordsletten, David, and Figueroa, Carlos A.
- Description:
- This repository contains the source code for the CRIMSON Flow Solver as required in the PLOS Computational Biology publication: CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation by the same authors., This is a snapshot of the software. Please visit https://github.com/carthurs/CRIMSONFlowsolver/releases/tag/PLOS_Comp_Bio & www.crimson.software for more general information and the most up to date version of the software. , and Software can be compiled in Cygwin and Linux.
- Keyword:
- Blood Flow Simulation, Patient-specific, Open-source Software, Image-based simulation, Cardiovascular Medical Image, Segmentation, and Finite Element Simulation
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, M. Marčan, A. Gomez, D. Dillon-Murphy, F. Cuomo, M.S. Vieira, J. Schollenberger, S.R. Lynch, C. Tossas-Betancourt, K. Iyer, S. Hopper, E. Livingston, P. Youssefi, A. Noorani, S. Ben Ahmed, F.J.H. Nauta, T.M.J. van Bakel, Y. Ahmed, P.A.J. van Bakel, J. Mynard, P. Di Achille, H. Gharahi, K. D. Lau, V. Filonova, M. Aguirre, N. Nama, N. Xiao, S. Baek, K. Garikipati, O. Sahni, D. Nordsletten, C.A. Figueroa bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960 and Arthurs, C., Khlebnikov, R., Melville, A., Marčan, M., Gomez, A., Dillon-Murphy, D., Cuomo, F., Vieira, M., Schollenberger, J., Lynch, S., Tossas-Betancourt, C., Iyer, K., Hopper, S., Livingston, E., Youssefi, P., Noorani, A., Ben Ahmed, S., Nauta, F., van Bakel, T., Ahmed, Y., van Bakel, P., Mynard, J., Di Achille, P., Gharahi, H., Lau, K., Filonova, V., Aguirre, M., Nama, N., Xiao, N., Baek, S., Garikipati, K., Sahni, O., Nordsletten, D., Figueroa, C. (2021). CRIMSON open source project - Graphical User Interface (GUI) Source Code for PLOS Computational Biology [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/679b-dw96
- Discipline:
- Engineering and Health Sciences
-
- 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:
- Dewaraja, Yuni, K and Van, Benjamin J
- Description:
- This publication contains the anonymized SPECT/CT scans of two patients. Patient scans were taken at 4 different time points in the week following a therapeutic dose of Lu-177 DOTATATE. Each of the scans contains 5 subfolders, 3 of which contain SPECT projection data used for reconstructing SPECT images, and 2 contain the linear attenuation coefficient maps for the CT scans that correspond to each patients SPECT projections. All images are in DICOM format.
- Keyword:
- Lu-177, Dosimetry, Radionuclide, SPECT, and CT
- Discipline:
- Health Sciences
-
- Creator:
- Computational Vascular Biomechanics Lab @ the University of Michigan and other collaborators, The Qt Company, NSIS Team and contributors, PostgreSQL Global Development Group, Oracle Corporation, and Kitware
- Description:
- This repository contains several open-source components as well as software developed by our own lab that are required to build the GUI of the open source CRIMSON software from scratch using Visual Studio 2013 update 5:, cmake-3.13.5-win64-x64.zip: build tool; nsis-3.05-setup.exe: packaging tool; postgresql-9.5.21-1-windows-x64-binaries.zip: Qt dependency; presolver_win.zip: windows binary for CRIMSON Presolver built using MinGW; qt-opensource-windows-x86-msvc2013_64-5.7.0.exe: Qt GUI library; mysql-5.7.29-winx64.zip: Qt dependencies, Software in this repository is a snapshot; please visit https://github.com/carthurs/CRIMSONGUI & www.crimson.software for more general information and the most up to date version of the software., and This repository completes the following Deep Blue repository: GUI repository: https://doi.org/10.7302/679b-dw96
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, M. Marčan, A. Gomez, D. Dillon-Murphy, F. Cuomo, M.S. Vieira, J. Schollenberger, S.R. Lynch, C. Tossas-Betancourt, K. Iyer, S. Hopper, E. Livingston, P. Youssefi, A. Noorani, S. Ben Ahmed, F.J.H. Nauta, T.M.J. van Bakel, Y. Ahmed, P.A.J. van Bakel, J. Mynard, P. Di Achille, H. Gharahi, K. D. Lau, V. Filonova, M. Aguirre, N. Nama, N. Xiao, S. Baek, K. Garikipati, O. Sahni, D. Nordsletten, C.A. Figueroa bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960 and Arthurs, C., Khlebnikov, R., Melville, A., Marčan, M., Gomez, A., Dillon-Murphy, D., Cuomo, F., Vieira, M., Schollenberger, J., Lynch, S., Tossas-Betancourt, C., Iyer, K., Hopper, S., Livingston, E., Youssefi, P., Noorani, A., Ben Ahmed, S., Nauta, F., van Bakel, T., Ahmed, Y., van Bakel, P., Mynard, J., Di Achille, P., Gharahi, H., Lau, K., Filonova, V., Aguirre, M., Nama, N., Xiao, N., Baek, S., Garikipati, K., Sahni, O., Nordsletten, D., Figueroa, C. (2021). CRIMSON open source project - Graphical User Interface (GUI) Source Code for PLOS Computational Biology [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/679b-dw96
- Discipline:
- Health Sciences and Engineering
-
- Creator:
- Figueroa, Carlos A., Computational Vascular Biomechanics Lab, University of Michigan, and et al.
- Description:
- This collection concerns the CRIMSON (CardiovasculaR Integrated Modelling and SimulatiON) software environment. CRIMSON provides a powerful, customizable and user-friendly system for performing three-dimensional and reduced-order computational haemodynamics studies via a pipeline which involves: 1) segmenting vascular structures from medical images; 2) constructing analytic arterial and venous geometric models; 3) performing finite element mesh generation; 4) designing, and 5) applying boundary conditions; 6) running incompressible Navier-Stokes simulations of blood flow with fluid-structure interaction capabilities; and 7) post-processing and visualizing the results, including velocity, pressure and wall shear stress fields. , The minimum specifications to run CRIMSON are: Any AMD64 CPU (note: Intel Core i series are AMD64), Windows (only tested on Windows 10 but might work on Windows 7), 8 GB of RAM , If you are running non-trivial models you will want to have: Quad core CPU or higher, Solid state drive for storing data, Windows, 16 GB of RAM, Dedicated discrete GPU for rendering models. , and Software in this collection is a snapshot; please visit https://github.com/carthurs/CRIMSONGUI & www.crimson.software for more general information and the most up to date version of the software.
- Keyword:
- Blood Flow Simulation, Patient-specific, Open-source Software, Image-based simulation, Cardiovascular Medical Image, Segmentation, and Finite Element Simulation
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, et al. bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960
- Discipline:
- Health Sciences and Engineering
4Works -
- Creator:
- Umberfield, Elizabeth, Ford, Kathleen, Stansbury, Cooper, and Harris, Marcelline R.
- Description:
- Research Overview: This dataset is clinical consent forms, collected as part of Dr. Elizabeth Umberfield's dissertation research of at the University of Michigan. 134 consent forms are used in the analysis, 102 of which are shared here (not all are shared due to data protection agreements with participating sites). The research aimed to enable representation of clinical consent forms and their permissions within the Informed Consent Ontology. These efforts were supported by the Rackham Graduate Student Research Grant, and Dr. Umberfield's doctoral training was supported by the Robert Wood Johnson Foundation Future of Nursing Scholars Program.
- Keyword:
- Consent, Consent Form, Informed Consent, Health Care, and Healthcare
- Citation to related publication:
- Umberfield, E., Jiang, Y., Fenton, S., Stansbury, C., Ford, K., Crist, K., Kardia, S., Thomer, A., & Harris, M. R. (In Press). Lessons Learned for Identifying and Annotating Permissions in Clinical Consents. Applied Clinical Informatics. and Umberfield, E., Stansbury, C., Ford, K., Jiang, Y., Kardia, S. L. R., Thomer, A., & Harris, M. R. (Under Review). Evaluating and Extending the Informed Consent Ontology for Representing Permissions from the Clinical Domain.
- 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:
- Saylor, Kate M., Sirihorachai, Rattima , and Manojlovich, Milisa
- Description:
- The search data supports a literature review project on counting interventions to reduce the incidence of retained surgical instruments. The data included in the dataset are the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). These searches and exported result files contain all citations originating from the database searches that were considered for inclusion.
- Keyword:
- literature search , retained surgical instruments, counting, and nursing
- Discipline:
- Health Sciences
-
- Creator:
- Saylor, Kate M., King, Wesley M., and Gamarel, Kristi E.
- Description:
- The search data supports a literature review project on Firearm violence among LGBTQ+ communities. The data included in the dataset are the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). These searches and exported result files contain all citations originating from the database searches that were considered for inclusion.
- Keyword:
- LGBTQ, Transgender, Firearms
- Discipline:
- Health Sciences
-
- Creator:
- Arthurs, Christopher J., Khlebnikov, Rostislav, Melville, Alexander, Marčan, Marija, Gomez, Alberto, Dillon-Murphy, Desmond, Cuomo, Federica, Vieira, Miguel, Schollenberger, Jonas, Lynch, Sabrina, Tossas-Betancourt, Christopher, Iyer, Kritika, Hopper, Sara, Livingston, Elizabeth, Youssefi, Pouya, Noorani, Alia, Ben Ahmed, Sabrina, Nauta, Foeke J.N., van Bakel, Theodorus M.J., Ahmed, Yunus, van Bakel, Petrus A.J., Mynard, Jonathan, Di Achille, Paolo, Gharahi, Hamid, Lau, Kevin D., Filonova, Vasilina, Aguirre, Miquel, Nama, Nitesh, Xiao, Nan, Baek, Seungik, Garikipati, Krishna, Sahni, Onkar, Nordsletten, David, and Figueroa, Carlos A.
- Description:
- This repository includes the following:, - Example Case A: complete process of creating a model, running the simulation and examining the results., - Example Case B: segmenting and imposing a patient-specific aortic inflow velocity profile from a provide PC-MRI dataset., - Example Case C: simulation of a patient under rest conditions, and then of the same patient under post-liver-transplant conditions., - GUI Windows Binary Executable (version 2019.11.01), and - Flow Solver Windows Binary Executable (version 1.4.4, 2019.11.01)
- Keyword:
- Blood Flow Simulation, Patient-specific, Open-source Software, Image-based simulation, Cardiovascular Medical Image, Segmentation, and Finite Element Simulation
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, M. Marčan, A. Gomez, D. Dillon-Murphy, F. Cuomo, M.S. Vieira, J. Schollenberger, S.R. Lynch, C. Tossas-Betancourt, K. Iyer, S. Hopper, E. Livingston, P. Youssefi, A. Noorani, S. Ben Ahmed, F.J.H. Nauta, T.M.J. van Bakel, Y. Ahmed, P.A.J. van Bakel, J. Mynard, P. Di Achille, H. Gharahi, K. D. Lau, V. Filonova, M. Aguirre, N. Nama, N. Xiao, S. Baek, K. Garikipati, O. Sahni, D. Nordsletten, C.A. Figueroa bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960
- Discipline:
- Engineering and Health Sciences
-
- Creator:
- Saylor, Kate M., McCormick, Amanda D., Wilde, Megan M., Charpie, Christine E., Yu, Sunkyung, and Cousino, Melissa K.
- Description:
- The search data supports a literature review project on Psychological Functioning in Pediatric Patients with Single Ventricle Congenital Heart Disease. The data included are the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). Both the original search files and updated search files have been included in the deposit.
- Keyword:
- pediatrics, univent, Single Ventricle Congenital Heart Disease, and psychological
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark P; Sun, Gordon H; Chen, Stephanie W; Wang, Jing
- Description:
- The dataset includes all citations considered for inclusion in the systematic review. The citations are accessible in Endnote (Clarivate), 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:
- Tracheostomy, Decannulation, Spinal Cord Injury, Scoping Review, and Literature Searches
- Citation to related publication:
- Gordon H. Sun, Stephanie W. Chen, Mark P. MacEachern & Jing Wang (2020) Successful decannulation of patients with traumatic spinal cord injury: A scoping review, The Journal of Spinal Cord Medicine, DOI: 10.1080/10790268.2020.1832397
- 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:
- Saylor, Kate M., Hicks, Patrice M., Kang, Linda, Stagg, Brian C., Newman-Casey, Paula-Anne, and Woodward, Maria A.
- Description:
- The search data supports a scoping literature review project on Loss to follow-up barriers in care for Cornea Ulcers and Glaucoma. The data included are the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). Both the original search files and updated search files have been included in the deposit.
- Keyword:
- Cornea, Glaucoma, Loss to follow, and ophthalmology
- 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:
- Saylor, Kate M., Arring, Noël M., Aduse-Poku, Livingstone, Jiagge, Evelyn, Walker, Eleanor, White-Perkins, Denise, Israel, Barbara, Hinebaugh, Analise, Harb, Rayya, DeWitt, Jillian, Molnar, Maxim, Wilson-Powers, Eliza, and Brush, Barbara L.
- Description:
- The search data supports a literature review project on Strategies to Increase Black Enrollment and Retention in Cancer Clinical Trials. This dataset includes the reproducible search strategies (txt file) and the exported results of all citations from all databases (txt, ris, and.nbib files). These searches and exported result files contain all citations originating from the database searches that were considered for inclusion.
- Keyword:
- African American, Cancer, Neoplasm, clinical trials, and Minority Recruitment
- 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:
- 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:
- Saylor, Kate M
- Description:
- The dataset includes all citations considered for inclusion in the literature review. Abstracts and keywords have been removed from the citation file. The citation file was exported in an .RIS format and can be imported with any citation manger such as EndNote, Zotero, Mendeley, RefWorks, etc. The literature search strategies are included for reproducibility and transparency purposes.
- Discipline:
- Health Sciences
-
- Creator:
- Gradwohl, Kelsey M.
- Description:
- The data set includes one file: Dermatology Clerkship Chalk Talks Raw Dataset which is the raw data collected from the surveys. This raw data was then coded and scored with the following analysis. Objective knowledge questions were asked for each chalk talk which was scored by authors. A knowledge assessment score was calculated by adding the total number of points accumulated by the student, dividing it by the total number of points possible, and summarizing the score as a percentage. Pre- and post-talk knowledge assessment scores were compared for each chalk talk and for the entire curriculum using 2-tailed paired sample t-tests with statistical significance if p<0.05., Before and after each talk, students were asked how confident they felt differentiating conditions within each disease group. For the erythroderma and immunobullous talks, students were also asked how confident they felt working up the conditions. Answer choices were on a Likert scale ranging from 1 (not at all confident) to 5 (extremely confident). Pre- and post-chalk talk scores were summarized as means with standard deviations and compared using 2-tailed paired sample t-tests with statistical significance if p<0.05. , After each talk, students were asked about its efficacy in terms of enhancing their understanding of the diseases, providing a framework or approach to work-up, and facilitating interaction between student and teacher. Answer choices were on a Likert scale ranging from 1 (not at all effective) to 5 (extremely effective), and summarized as means with standard deviations. Students were asked for written feedback regarding what they liked about the talk and suggestions for improvement. Qualitative data were sorted into categories and scored by two independent raters (cohen's kappa =0.8)., and In the response Likert scale, "Not at all"=1, "Not so (much)"=2, "Somewhat"=3, "Very"=4, and "Extremely"=5.
- Keyword:
- Chalk talk, Dermatology clerkship, Dermatology education, Virtual learning, and Online learning
- Discipline:
- Health Sciences
-
- Creator:
- MacEachern, Mark
- Description:
- This collection contains literature searches for published evidence syntheses in the health sciences.
- Keyword:
- health sciences, evidence syntheses, systematic reviews, scoping reviews, and literature searches
- Discipline:
- Health Sciences
20Works -
- Creator:
- MacEachern, M. P. , Woolen, S. A., Shankar, P. R., Gagnier, J. J., Singer, L., and Davenport, M. S.
- Description:
- The intent of the project 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 2700 citations after duplicates were removed in Endnote X8.
- Keyword:
- Systematic review, Meta-analysis, Radiology, Gadolinium, Chronic kidney disease, and Literature searches
- Citation to related publication:
- Woolen, S. A., Shankar, P. R., Gagnier, J. J., MacEachern, M. P., Singer, L., & Davenport, M. S. (2020). Risk of Nephrogenic Systemic Fibrosis in Patients With Stage 4 or 5 Chronic Kidney Disease Receiving a Group II Gadolinium-Based Contrast Agent: A Systematic Review and Meta-analysis. JAMA internal medicine, 180(2), 223–230. https://doi.org/10.1001/jamainternmed.2019.5284
- Discipline:
- Health Sciences
-
- Creator:
- Bacon, Elizabeth, Hanson, Erika N., Austin, Sarah, Delacroix, Emerson, Uhlmann, Wendy, Roberts, Scott, and Resnicow, Ken
- Description:
- Survey respondents were cancer-affected patients seen at an academic medical center, and self-reported experiences with genetic testing and counseling. This is raw dataset is saved in comma separated value (.csv) format.
- Keyword:
- Genetic Testing, Clinician Recommandation , NCCN Guidelines, Hereditary Genetic Testing, and Disparities in Genetic Counseling
- Citation to related publication:
- American Association of Kidney Patients: A List of Support Groups in Michigan. https://aakp.org/wp-content/uploads/2020/06/Support-Groups-Michigan.pdf
- Discipline:
- Science and Health Sciences
-
- Creator:
- MacEachern, Mark, DeLong, M. R. , Tandon, V. J., Bertrand, A. A. , Goldberg, M. , Salibian, A. , Pusic, A. L. , Festekjian, J. H. , and Wilkins, E. G.
- 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 1168 citations after duplicates were removed in Endnote X8.
- Keyword:
- Literature searches, Breast reconstruction, Mesh, and Systematic review
- Citation to related publication:
- DeLong MR, Tandon VJ, Bertrand AA, MacEachern M, Goldberg M, Salibian A, Pusic AL, Festekjian JH, Wilkins EG. Review of Outcomes in Prepectoral Prosthetic Breast Reconstruction with and without Surgical Mesh Assistance. Plast Reconstr Surg. 2021 Feb 1;147(2):305-315. doi: 10.1097/PRS.0000000000007586. PMID: 33177453.
- 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
-
- 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 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:
- 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:
- 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