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- Creator:
- Anahita, Amiri Farahani
- Description:
- this dataset is the output of WRF-Chem model for several simulations.
- Keyword:
- Lake spray aerosol
- Citation to related publication:
- https://www.overleaf.com/project/5eb6b9a5c184ea00018c67f7
- Discipline:
- Science
- Title:
- Lake spray aerosol emissions dataset
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- Creator:
- McCuen, Brett A.
- Description:
- This data are TIC events identified in MACCS magnetometer data throughout 2015. These events are short-timescale (< 60 s), large -amplitude (> 6 nT/s) magnetic disturbances measured at Earth's surface that are analyzed for space weather research purposes. and The events were identified in a year's worth of magnetic field data using an algorithm developed in the MATLAB platform. The algorithm dBdt_main.m can be run using the associated scripts (clean_maccs.m, simple_dbdt.m, extremes1.m, newdbdt.m) to return the events in the 2015_AllEvents.csv file. The substorm onset delays of each event are determined with the onset_delays.m script and the substorm event list 20191127-15-56-substorms.csv (both included).
- Keyword:
- space weather impacts, geomagnetically induced currents, GIC, transient induced currents, TIC, and dB/dt search algorithm
- Discipline:
- Science
- Title:
- 2015 Transient Induced Current (TIC) Events
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- 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
- Discipline:
- Health Sciences and Engineering
- Title:
- CRIMSON open source project - Flow Solver Source Code for PLOS Computational Biology
-
- 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 well as three applications examples 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/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
- Discipline:
- Health Sciences and Engineering
- Title:
- CRIMSON open source project - Graphical User Interface (GUI) Source Code and Application Examples for PLOS Computational Biology
-
- Creator:
- Shane, Alexander
- Description:
- This data set was created with the purpose to study the electron pitch angle distributions on dayside closed crustal fields at Mars and to compare with theoretical predictions made by numerical modeling. Analyzing the plasma environment of the crustal fields was another point of study to determine if whistler waves can interact with high energy superthermal electrons.
- Keyword:
- Mars, superthermal electron, pitch angle distribution, and crustal magnetic field
- Discipline:
- Science
- Title:
- Mars Dayside Closed Crustal Field Electron Pitch Angle Distributions Data and Ephemeris Info
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Tengou-Togo (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Tengou-Togo, and Mali
- Citation to related publication:
- www.dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Tengou-Togo-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Documentary-style videos about villages and social relations in Dogon country. Documentaries are given in two or three video formats each.
- Keyword:
- Mali, Dogon, and villages
- Citation to related publication:
- www.dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Central Mali villages and people documentaries
-
- 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:
- Science and Health Sciences
- Title:
- Performance Summary Display Descriptions: Describing Visualization Content
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- Creator:
- Jeffrey Heath
- Description:
- fieldwork in Bonosso village, Côte d’Ivoire, chiefly 2016-19. See "readme" file for description of the materials.
- Keyword:
- Pere language
- Citation to related publication:
- Heath, Jeffrey, & Tioté, Brahima. (2019). A grammar of Pere (Bere, Mbre) of Côte d'Ivoire. Zenodo. http://doi.org/10.5281/zenodo.3346581
- Discipline:
- Humanities
- Title:
- Pere language lexical datasheets and audio files
-
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) Baseline Scans. 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 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) Time Integrated Activity (TIA) Image. 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, 5) 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, and 6) SPECT Projections and CT Mumaps. 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
0Works -
- 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
- Title:
- Analyzing Reviewer Responses to Systematic Review Search Methodology through Open Peer Review
-
- Creator:
- van Velden, Grace and Reddy, Raghav
- Description:
- A household survey was developed to capture household perceptions and behaviors around drinking water use. It consisted of several modules: key informant and household demographics, household assets and consumption, water use behaviors in the dry season, water use behaviors during the rest of the year, and water supply maintenance and repair. Intervention and safe water device surveys were also developed; the household and intervention surveys were administered via Qualtrics. and This record consists of several survey instruments, exported where appropriate from Qualtrics into PDF and .qsf.
- Keyword:
- Bangladesh, arsenic, sustainability, survey
- Citation to related publication:
- Reddy, R. (2020). Arsenic in Bangladesh's Drinking Water: Evaluating Factors That Have Hindered Two Decades of Mitigation Efforts, and the Opportunities to Address Them. [Doctoral thesis, University of Michigan]. University of Michigan - Deep Blue. http://hdl.handle.net/2027.42/155203
- Discipline:
- Engineering
- Title:
- Household survey about water use perceptions and behaviors for use in Bangladesh
-
- Creator:
- Gainsburg, Izzy and Earl, Allison
- Description:
- This research explores trigger warnings as an interpersonal emotion-regulation strategy, introducing a temporal dimension to interpersonal emotion-regulation by regulating others' future, anticipated emotions. Across studies, believing that trigger warnings are protective (versus coddling) increased their effect on anticipated negative affect, but weakened their effect on experienced negative affect. Study 1 demonstrated that anticipated anxiety for warned-of content predicts intentions to avoid information. Furthermore, beliefs about trigger warnings as protective (versus coddling) best predicted anticipated anxiety for warned-of content and subsequent intentions to avoid. In Study 2, participants had higher anticipated negative affect for videos with trigger warnings, compared to those without, and this mediated increased avoidance for warned-of videos. In Study 3, trigger warnings preceding essays increased anticipated negative affect and attentional-regulation strategies, but reduced experiences of negative affect. For more information, please see the article Gainsburg, I., & Earl, A. (2018). Trigger warnings as an interpersonal emotion-regulation tool: Avoidance, attention, and affect depend on beliefs. Journal of Experimental Social Psychology, 79, 252–263. https://doi.org/10.1016/j.jesp.2018.08.006
- Citation to related publication:
- Gainsburg, I., & Earl, A. (2018). Trigger warnings as an interpersonal emotion-regulation tool: Avoidance, attention, and affect depend on beliefs. Journal of Experimental Social Psychology, 79, 252–263. https://doi.org/10.1016/j.jesp.2018.08.006
- Discipline:
- Social Sciences
- Title:
- Data and Syntax for 'Trigger warnings as an interpersonal emotion-regulation tool'
-
Profiles of near-surface rock mass strength across gradients in erosion, burial, and time [Data set]
- Creator:
- Townsend, Kirk F, Clark, Marin K, and Zekkos, Dimitrios
- Description:
- These datasets support the findings of Townsend et al. (2020). In this article, we project profiles of rock mass shear strength into the shallow subsurface (~30 m depth) using the Hoek and Brown criterion with Geological Strength Index (GSI) observations of outcrop structure and surface conditions, and Schmidt hammer rebound values of intact (unfractured) rock hardness. We compare these projected rock mass shear strength profiles to shear-wave velocity profiles collected using shallow geophysical arrays. We evaluate our methods in the Western Transverse Ranges of southern California, which exhibit strong gradients in the depth of latest-Mesozoic through Cenozoic sedimentary rocks exposed at the surface today, and in erosion rates quantified from catchment-average cosmogenic radionuclide concentrations and low-temperature apatite and zircon (U-Th)/He thermochronometry. We find that stratigraphic age and burial depth exerts the strongest apparent control on rock strength and S-wave velocities, likely due to diagenetic changes associated with burial. For rocks of the same age and inferred burial history, we observe that shear strength and S-wave velocities are positively correlated with erosion rate. We suggest that increasing erosion rates cause decreased residence time of rock masses within the critical zone, resulting in less weathered rocks.
- Keyword:
- rock strength, seismic, and erosion rate
- Discipline:
- Science
- Title:
- Profiles of near-surface rock mass strength across gradients in erosion, burial, and time [Data set]
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset is composed of eight flat-mounted (dissected and fixed) retinae from juvenile and adult zebrafish. Rows of UV cones have been traced in each retina; additionally, we have identified locations of Y-junctions (row insertions). Also included is MATLAB code for calculating which Y-junctions belong to grain boundaries. Please see the readme file for a description of included codes and image files.
- Keyword:
- zebrafish cone mosaic, topological defects, tissue patterning, and grain boundaries
- Citation to related publication:
- Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. PLoS Comput Biol. 2020 (under review)
- Discipline:
- Science
- Title:
- Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae
-
- Creator:
- Agnit Mukhopadhyay
- Description:
- Conducting quantitative metrics-based performance analysis of first-principles-based global magnetosphere models is an essential step in understanding their capabilities and limitations, and providing scope for improvements in order to enhance their space weather prediction capabilities for a range of solar conditions. In this study, a detailed comparison of the performance of three global magnetohydrodynamic (MHD) models in predicting the Earth’s magnetopause location and ionospheric cross polar cap potential (CPCP) has been presented. Using the Community Coordinated Modeling Center’s Run-on-Request system and extensive database on results from various magnetospheric scenarios simulated for a variety of solar wind conditions, the aforementioned model predictions have been compared for magnetopause standoff distance estimations obtained from six empirical models, and with cross polar cap potential estimations obtained from the Assimmilative Mapping of Ionospheric Electrodynamics (AMIE) Model and the Super Dual Auroral Radar Network (SuperDARN) observations. We have considered a range of events spanning different space weather activity to analyze the performance of these models. Using a fit performance metric analysis for each event, we have quantified the models’ reproducibility of magnetopause standoff distances and CPCP against empirically-predicted observations, and identified salient features that govern the performance characteristics of the modeled magnetospheric and ionospheric quantities.
- Citation to related publication:
- Mukhopadhyay, A., et al. (2020). Global Magnetohydrodynamic Simulations: Performance Quantification of Magnetopause Distances and Convection Potential Predictions. Forthcoming.
- Discipline:
- Engineering and Science
- Title:
- Dataset Containing Global Modeling Results Comparing Magnetopause Distances and CPCP
-
- Creator:
- Zhang, Kaihua and Collette, Matthew D.
- Description:
- This Ph.D. research focuses on two subject areas: experimental and numerical model, which serves as two essential parts of a digital twin. A digital twin contains models of real-world structures and fuses data from observations of the structures and scale experiment to pull the models into better agreement with the real world. Digital twin models have the promise of representing complex marine structures and providing enhanced lifecycle performance and risk forecasts. Experimentally verifying the updating approaches is necessary but rarely performed. Thus, the proposed work is designing an experiment and developing a numerical model updated by the experimental data. The dataset contains all the data collected in the experiment of a four-crack hexagon- shaped specimen is presented, designed to mimic many of the properties of complex degrading marine structural systems, such as crack interaction, component inter- dependence, redundant load path, and non-binary failure.
- Keyword:
- System Reliability, Dynamic Bayesian Networks, Fatigue Experiment, Crack Length Measurement, Experimental Validation, Reliability Prediction
- Citation to related publication:
- Kaihua, Zhang (2020) "Development and Experimental Validation of Dynamic Bayesian Networks for System Reliability Prediction" Doctoral Dissertation, University of Michigan. Deep Blue. http://hdl.handle.net/2027.42/155231, "Evaluating Crack Growth Prediction in Structural Systems with Dynamic Bayesian Networks", submitted to Computers and Structure, and "Experimental Investigation of Structural System Capacity with Multiple Fatigue Cracks", submitted to Marine Structures
- Discipline:
- Engineering
- Title:
- Dataset for thesis "Development and Experimental Validation of Dynamic Bayesian Networks for System Reliability Prediction"
-
- Creator:
- Johnson, JE and Molnar, PH
- Description:
- This IF compilation was assembled from the existing literature to understand if preservation biases affected the record of iron formations.
- Keyword:
- Archean ocean chemistry, temporal record of iron formations, and early Earth iron cycle
- Citation to related publication:
- Johnson, J. E., & Molnar, P. H. ( 2019). Widespread and persistent deposition of iron formations for two billion years. Geophysical Research Letters, 46, 3327– 3339. https://doi.org/10.1029/2019GL081970
- Discipline:
- Science
- Title:
- Widespread and persistent deposition of iron formations for two billion years: Compilation Dataset
-
- 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
- Title:
- Data for "Comparison of Anorectal Function Measured using Wearable Digital Manometry and a High Resolution Manometry System." article (PLOS ONE) PONE-D-20-01826R1
-
- Creator:
- Zhang, Yizhen
- Description:
- We collected hours of functional magnetic resonance imaging data from human subjects listening to natural stories. We developed a predictive model of the voxel-wise response and further applied it to thousands of new words to understand how the brain stores and connects different concepts. and This is a dataset for the paper: Zhang, Y., Han, K., Worth, R., & Liu, Z. (2020). Connecting concepts in the brain by mapping cortical representations of semantic relations. Nature communications, 11(1), 1-13. https://doi.org/10.1038/s41467-020-15804-w. This project is also documented at https://osf.io/eq2ba/.
- Keyword:
- fMRI, natural story comprehension, neural encoding, semantic processing, word relations, and naturalistic stimuli
- Citation to related publication:
- Zhang, Y., Han, K., Worth, R., & Liu, Z. (2020). Connecting concepts in the brain by mapping cortical representations of semantic relations. Nature communications, 11(1), 1-13. https://doi.org/10.1038/s41467-020-15804-w
- Discipline:
- Science
- Title:
- Connecting Concepts in the Brain by Mapping Cortical Representations of Semantic Relations
-
- Creator:
- Huang, Cheng MI
- Description:
- A 2D planar representation of a generic laboratory-scale combustor is established to assess the capabilities of ROMs for representing realistic combustion flowfields. The purpose of this dataset is to provide a testbed to build reduced model for relevant challenging reacting flow problems using different methods. The dataset was generated under the Air Force Center of Excellence on Multi-Fidelity Modeling of Rocket Combustion Dynamics and the goal of the center is to advance the state-of-the-art in Reduced Order Models (ROMs) and enable efficient prediction of instabilities in liquid fueled rocket combustion systems. Instrument and/or Software specifications: - recommendation: Matlab and Tecplot 1. Data_150000to159999.tar: the unsteady flow field data from time step 150000 to 159999 (time increment, dt, between each time step is 1E-7 sec). 2. Data_160000to169999.tar: the unsteady flow field data from time step 160000 to 169999 (time increment, dt, between each time step is 1E-7 sec). 3. Data_170000to179999.tar: the unsteady flow field data from time step 170000 to 179999 (time increment, dt, between each time step is 1E-7 sec). 4. Data_180000to189999.tar: the unsteady flow field data from time step 180000 to 189999 (time increment, dt, between each time step is 1E-7 sec). 5. Data_190000to199999.tar: the unsteady flow field data from time step 190000 to 199999 (time increment, dt, between each time step is 1E-7 sec). 6. Data_200000to209999.tar: the unsteady flow field data from time step 200000 to 209999 (time increment, dt, between each time step is 1E-7 sec). 7. Data_210000to219999.tar: the unsteady flow field data from time step 210000 to 219999 (time increment, dt, between each time step is 1E-7 sec). 8. Data_220000to229999.tar: the unsteady flow field data from time step 220000 to 229999 (time increment, dt, between each time step is 1E-7 sec). 9. grid.dat: the topology of the CFD mesh used to generate this data (can be directly loaded in Tecplot). 10. the file "sample_code.zip" contains the sample Matlab scripts to load and output the .dat files to help the researchers to get started. To run the script, the software Matlab is required and the researchers can simply run sampleIO.m script in Matlab to test the code. Detailed documentation of how the data is generated can be found in: https://afcoe.engin.umich.edu/benchmark-data
- Citation to related publication:
- Huang, C., Duraisamy, K., and Merkle, C.L., Investigations and Improvement of Robustness of Reduced-Order Models of Reacting Flow, AIAA Journal, 2019., Swischuk, R., Kramer, B., Huang, C., and Willcox, K., Learning Physics-Based Reduced-Order Models for a Single-Injector Combustion Process , AIAA Journal, 2020., and Harvazinski, M.E., Huang, C., Sankaran, V., Feldman, T.W., Anderson, W.E., Merkle, C.L., and Talley, D.G., Coupling between hydrodynamics, acoustics, and heat release in a self-excited unstable combustor, Physics of Fluids, 2015.
- Discipline:
- Engineering
- Title:
- [Updated] 2D Benchmark Reacting Flow Dataset for Reduced Order Modeling Exploration
-
- Creator:
- Huang, Cheng MI
- Description:
- This collection contains a hierarchy of test problems for turbulent reacting flow simulations. It is meant to provide a testbed to build reduced model for relevant challenging reacting flow problems using different methods. In addition, this collection also serves to engage a broad community of experts in computational science and the field of engineering to address certain challenges in constructing reduced models for reacting flow simulations. All the datasets in this collection were generated under the Air Force Center of Excellence on Multi-Fidelity Modeling of Rocket Combustion Dynamics and the goal of the center is to advance the state-of-the-art in Reduced Order Models (ROMs) and enable efficient and accurate prediction of instabilities in liquid fueled rocket combustion systems.
- Discipline:
- Engineering
2Works -
- Creator:
- Valeriy Tenishev
- Description:
- This data represents examples of some applications of AMPS and illustrates the potential of the code for modeling various physical phenomena.
- Keyword:
- Monte Carlo, DSMC
- Discipline:
- Science
- Title:
- Application of the Monte Carlo method in modeling dusty gas, dust in plasma, and energetic ions in planetary and magnetospheric applications
-
- Creator:
- Bougher, S. W. (University of Michigan) and Brecht, A. S. (NASA Ames Research Center)
- Description:
- This work examines the planetary wave-induced variability within the upper mesosphere/lower thermosphere of Venus by utilizing the Venus Thermospheric General Circulation Model (VTGCM). Rossby and Kelvin wave perturbations are driven by variations in the geopotential height of the VTGCM lower boundary (~70 km). A suite of simulations was conducted to examine the impact of the individual and combined waves propagating from two different lower boundary conditions (uniform and varying). The Kelvin wave is the more dominant wave which produces the most variability, as was shown in Hoshino et al., 2012. The combination of the Kelvin and Rossby waves provides a maximum temperature amplitude of 13 K at 92 km and maximum zonal wind amplitude of 23 m/s at 102 km. The combined waves overall are able to propagate up to 125 km. Most of the variation within the temperature, winds, and composition occurs between 70 km and 110 km. The varying lower boundary increases the magnitude of the wave deposition but weakly changes the propagation altitude. The thermal variation due to the planetary waves does not reproduce most observed variations. The simulated O2 IR nightglow emission is sensitive to the waves with respect to intensity and local time, but lacks latitudinal variation. The integrated intensity ranges from 1.2 MR to 1.65 MR and the local time ranges from 0.33 local time to 23.6 local time. Overall, planetary waves do affect the atmospheric structure, but there are still observed large variations that planetary waves alone cannot explain (i.e. thermal structure).
- Keyword:
- Venus, planetary waves, upper mesophere, lower thermosphere, and O2 nightglow
- Citation to related publication:
- Brecht, A. S., S. W. Bougher, D. Shields, and H. Liu, Planetary-scale Wave Impacts on the Venusian Upper Mesosphere and Lower Thermosphere, Icarus, in review, (2020). doi:...
- Discipline:
- Science
- Title:
- Planetary-scale Wave Impacts on the Venusian Upper Mesosphere and Lower Thermosphere: Supporting Datasets for VTGCM Numerical Simulations
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- The most important part of this deposit is the code necessary for simulating the anisotropic phase-field crystal on a cone geometry. The second most important is the code for analyzing the simulation results, including the spatial distribution of Y-junctions in the simulated retinae. Included are simulation results in which we systematically scan both the undercooling parameters and the strength of noise in the initial conditions. Finally, we include an additional simulation example (as in Figure 7D). Please see readme file for description of main (MATLAB) functions used for simulating and analyzing simulations.
- Keyword:
- zebrafish cone mosaic, topological defects, grain boundaries, and phase-field crystal model
- Citation to related publication:
- Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky bioRxiv 806679; doi: https://doi.org/10.1101/806679 and Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky PLoS Comput Biol. 2020 (under review)
- Discipline:
- Science
- Title:
- Code and example simulations of phase-field crystal model (for cone mosaic formation)
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset includes an example cell packing (containing ~20,000 cells). This example cell packing is the same cell packing in Supplementary Figure 11. The Corson_PBC_Square_Sweep_func.m is the main function for simulating lateral inhibition on this (and other) example packings. Please see readme for which simulation parameters may be tuned within this lateral inhibition function.
- Keyword:
- tissue patterning, lateral inhibition, and topological defect
- Citation to related publication:
- Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. PLoS Comput Biol. 2020 (under review), Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679, and Corson F, Couturier L, Rouault H, Mazouni K, Schweisguth F. Self-organized Notch dynamics generate stereotyped sensory organ patterns in Drosophila. Science. 2017 May 5;356(6337):eaai7407. doi: 10.1126/science.aai7407. Epub 2017 Apr 6. PMID: 28386027.
- Discipline:
- Science
- Title:
- Code and accompanying input data for simulating lateral inhibition on motionless cell packing
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of UV cone nuclei near the retinal margin in live fish. These UV cones express a transgenic fluorescent reporter (that is nuclear-localized and photoconvertible). The most important images in this dataset are: Zoomed-out (1X magnification) images immediately after photoconversion Zoomed-out (1X magnification) images two to four days after photoconversion In the images immediately after photoconversion, we check if the row orientation rotates by more than a certain amount (10 degrees, 12 degrees, 14 degrees, etc.) at the retinal margin. If so, we call the region coinciding with this domain rotation an existing grain boundary. We, then, check where new Y-junctions are incorporated (by the time of later imaging) to see if they are preferentially incorporated near existing grain boundaries.
- Keyword:
- zebrafish cone mosaic, topological defects, tissue patterning, grain boundaries, and photoconversion
- Citation to related publication:
- Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. PLoS Comput Biol. 2020 (under review) and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
- Title:
- Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of UV cone nuclei (labelled by transgenic expression of a photoconvertible fluorescent protein) near the retinal margin in live fish. The most important images in the dataset are the following: 1. Images (at 4X magnification) of UV cones immediately after photoconversion of a patch near the retinal margin 2. Images (at 4X magnification) of UV cones 2-4 days after photoconversion of a patch near the retinal margin Also, included is code for calculating triangulations (which connect UV cone nuclei which are nearest neighbors). This code allows us to check for motion of UV cones relative to each other between the time of photoconversion and subsequent imaging.
- Keyword:
- zebrafish cone mosaic, topological defects, tissue patterning, grain boundaries, photoconversion, and defect motion
- Citation to related publication:
- Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. PLoS Comput Biol. 2020 (under review) and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
- Title:
- Dataset for analyzing Y-junction motion in live fish retinae
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of UV cone nuclei near the retinal margin in live zebrafish. These UV cone nuclei are labelled by transgenic expression of a fluorescent reporter (that is photoconvertible). The most important data are: 1. The zoomed-in (4X magnification) images of UV cone nuclei immediately after photoconversion 2. The zoomed-in (4X magnification) images of UV cone nuclei 2-4 days after photoconversion Also included is code for segmenting UV cone nuclei (both in image from immediately after photoconversion and in image from days later) and for shifting and rotating the two images to maximally align corresponding UV cone nuclei. After aligning corresponding UV cones, we compute triangulations over UV cone nuclei positions (for both images) and identify bonds that are common to both images. We use these common bonds to calculate the lattice vectors for the UV cone lattice.
- Keyword:
- zebrafish cone mosaic, tissue patterning, lattice vectors, and photoconversion
- Citation to related publication:
- Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. PLoS Comput Biol. 2020 (under review) and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679
- Discipline:
- Science
- Title:
- Dataset for calculating lattice vectors (and anisotropy) of zebrafish cone mosaic
-
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- This dataset contains images of dissected and fixed retinae in which cones of specific subtypes are labeled either by transgenic expression of a fluorescent reporter or by antibody staining (Figures 1 and 2 and 6A and Supplementary Figure 7A). This dataset also contains images of dissected and fixed retinae in ZO1 is immunostained (Figure 6C-E and Supplementary Figure 7B). Please see the readme file for which files correspond to which figures.
- Keyword:
- zebrafish cone mosaic, topological defects, and tissue patterning
- Citation to related publication:
- Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. bioRxiv 806679; doi: https://doi.org/10.1101/806679 and Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky. Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation. PLoS Comput Biol. 2020 (under review)
- Discipline:
- Science
- Title:
- Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7
-
Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation
User Collection
- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- The outer epithelial layer of zebrafish retinae contains a crystalline array of cone photoreceptors, called the cone mosaic. As this mosaic grows by mitotic addition of new photoreceptors at the rim of the hemispheric retina, topological defects, called “Y-Junctions”, form to maintain approximately constant cell spacing. The generation of topological defects due to growth on a curved surface is a distinct feature of the cone mosaic not seen in other well-studied biological patterns like the R8 photoreceptor array in the _ Drosophila compound eye. Since defects can provide insight into cell-cell interactions responsible for pattern formation, here we characterize the arrangement of cones in individual Y-Junction cores (see Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7) as well as the spatial distribution of Y-junctions across entire retinae (see Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae). We find that for individual Y-junctions, the distribution of cones near the core corresponds closely to structures observed in physical crystals (see Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7). In addition, Y-Junctions are organized into lines, called grain boundaries, from the retinal center to the periphery (see Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae and Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae). In physical crystals, regardless of the initial distribution of defects, defects can coalesce into grain boundaries via the mobility of individual particles. By imaging in live fish, we demonstrate that grain boundaries in the cone mosaic instead appear during initial mosaic formation, without requiring defect motion (see Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae and Dataset for analyzing Y-junction motion in live fish retinae). Motivated by this observation, we show that a computational model of repulsive cell-cell interactions generates a mosaic with grain boundaries (see Code and example simulations of phase-field crystal model (for cone mosaic formation)). In contrast to paradigmatic models of fate specification in mostly motionless cell packings (see Code and accompanying input data for simulating lateral inhibition on motionless cell packing), this finding emphasizes the role of cell motion, guided by cell-cell interactions during differentiation, in forming biological crystals. Such a route to the formation of regular patterns may be especially valuable in situations, like growth on a curved surface, where the resulting long-ranged, elastic, effective interactions between defects can help to group them into grain boundaries.
- Keyword:
- zebrafish cone mosaic, lattice vectors, topological defects, tissue patterning, grain boundaries, lateral inhibition, photoconversion, phase-field crystal model, and defect motion
- Discipline:
- Science
7Works -
- Creator:
- Zhang, Yan, Fujian Normal University, Yang, Ping, Fujian Normal University, Tong, Chuan, Fujian Normal University, Zhang, Xinyan, Chinese Academy of Sciences, Changchun, Liu, Xingtu, Chinese Academy of Sciences, Changchun, Zhang, Shaoqing, Chinese Academy of Sciences, Changchun, Meyers, Philip. University of Michigan, and Gao, Chuanyu , Chinese Academy of Sciences, Changchun
- Description:
- A high-resolution study of bulk properties in a peat sequence from the Xinjiang Altai Mountains of northwestern China, has allowed reconstruction of local variations in peat properties and peat C and N accumulation rates (CAR and NAR) during the Holocene. Analyses of peat bulk density, loss on ignition, and concentrations of TOC and TN and their elemental ratios and stable isotopic values suggest that changes in peat-forming vegetation types during different parts of this epoch are the major factors responsible for the variations of peat properties in this sequence.
- Keyword:
- peat properties, stable carbon and nitrogen isotopes, carbon and nitrogen accumulation rates, and Altai Mountains of northwestern China
- Citation to related publication:
- Peat properties and Holocene carbon and nitrogen accumulation rates in a peatland in the Xinjiang Altai Mountains, northwestern China
- Discipline:
- Science
- Title:
- Dataset from analysis of a peat core from the Tielishahan peatland in the Xinjiang Altai Mountains, northwestern China
-
- Creator:
- Light, Charles X, Arbic, Brian K, Martin, Paige E, Brodeau, Laurent, Farrar, J Thomas, Griffies, Stephen M, Kirtman, Ben P, Laurindo, Lucas, Menemenlis, Dimitris, Molod, Andrea, Nelson, Arin D, Nyadjiro, Ebenezer, O'Rourke, Amanda K, Shriver, Jay, Siqueira, Leo, Small, R Justin, and Strobach, Udi
- Description:
- The precipitation data itself is the output of the models/datasets that we analyze in our paper. Most of it is in .nc or .nc4 format, although we provide code to extract the data into time series .mat files. We used MATLAB to perform our analysis.
- Keyword:
- precipitation and power spectra
- Discipline:
- Science
- Title:
- High-frequency precipitation variance in high-resolution global coupled ocean-atmosphere models: Precipitation data and analysis code
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right medial cuneiform (entocuneiform) of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81820), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
- Title:
- CT Data of UMMP VP 81820, Cantius mckennai right medial cuneiform (entocuneiform)
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right navicular of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81831), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
- Title:
- CT Data of UMMP VP 81831, Cantius mckennai right navicular
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right astragalar [astragalus] body of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81827), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
- Title:
- CT Data of UMMP VP 81827, Cantius mckennai right astragalar body
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right calcaneum of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81821), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
- Title:
- CT Data of UMMP VP 81825, Cantius mckennai right calcaneum
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right cuboid of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81823), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
- Title:
- CT Data of UMMP VP 81823, Cantius mckennai right cuboid
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right proximal metatarsal 1 of the Cantius trigonodus (University of Michigan Museum of Paleontology catalog number UMMP VP 81822), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
- Title:
- CT Data of UMMP VP 81822, Cantius trigonodus right proximal metatarsal 1
-
- Creator:
- University of Michigan Museum of Paleontology and CTEES
- Description:
- Reconstructed CT slices for a right distal tibia of Cantius mckennai (University of Michigan Museum of Paleontology catalog number UMMP VP 81821), as a series of TIFF images. Raw projections are not included in this dataset.
- Keyword:
- Paleontology, Fossil, CT, Primates, Notharctidae, UMMP, University of Michigan Museum of Paleontology, Eocene, and CTEES
- Discipline:
- Science
- Title:
- CT Data of UMMP VP 81821, Cantius mckennai right distal tibia
-
- 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
- Title:
- .stl file of Circle of Willis Benchmark geometric model for hemodynamic simulation software
-
- 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
- Title:
- Literature search files for review on lifestyle therapy for the management of atrial fibrillation
-
- Creator:
- Moniri, Saman and Shahani, Ashwin J.
- Description:
- The data is comprised of 20 .hdf files of the X-ray projections recorded during isothermal annealing of Zn-Mg samples, at discrete time-steps shown below for files names ending in ‘...30141’ to ‘…30161’: 30141: prior to annealing; 30142: 1 min annealing; 30143: 3 min; 30144: 5 min; 30145: 7 min; 30146: 10 min; 30147: 15 min; 30148: 20 min; 30150: 31 min; 30151: 1 hr; 30152: 2 hr; 30153: 3 hr; 30154: 4 hr; 30155: 5 hr; 30156: 6 hr; 30157:7 hr; 30158: 8 hr; 30159:9 hr; 30160: 9 hr, 10 min; 30161: 10 hr The raw data file is in .hdf format and can be reconstructed into .tiff, e.g., by using the TomoPy toolbox in Python.
- Keyword:
- Spiral eutectics
- Discipline:
- Engineering
- Title:
- Topological transitions of spiral eutectics
-
- Creator:
- Forrest, Stephen R., Panda, Anurag, Qu, Yue, Che, Xiaozhou, Coburn, Caleb, and Burlingame, Quinn
- Description:
- Mathematica Diffusion Simulation: Programmed by Coburn, Caleb. Simulation of diffusion in organic heterostructures, including least square fits and statistical goodness of fit analysis. Used to calculate fits to transient data in Fig 1, 3 and Extended Data Fig.2. Example data file included for download Matlab Montecarlo simulation: Programmed by Coburn, Caleb. Montecarlo simulation of charge diffusion on a cubic lattice to determine lateral diffusion length as a function of barrier height, assuming thermionic emission over the barrier. Matlab 2D Diffusion Simulation:Programmed by Coburn, Caleb. Modified from BYU Physics 430 Course Manual. Simulates diffusion around a film discontinuity, such a cut. Used to generate fits to Extended Data Fig. 1
- Keyword:
- Organic semiconductors and Charge diffusion
- Citation to related publication:
- Burlingame, Q., Coburn, C., Che, X., Panda, A., Qu, Y., & Forrest, S. R. (2018). Centimetre-scale electron diffusion in photoactive organic heterostructures. Nature, 554(7690), 77-80. https://doi.org/10.1038/nature25148
- Discipline:
- Science
- Title:
- Centimeter-Scale Electron Diffusion in Photoactive Organic Heterostructures
-
- Creator:
- Flanner, Mark
- Description:
- Greenhouse gas (GHG) additions to Earth’s atmosphere initially reduce global outgoing longwave radiation (OLR), thereby warming the planet. In select environments with temperature inversions, however, increased GHG concentrations can actually increase local OLR. Negative top-of-atmosphere and effective radiative forcing (ERF) from this situation give the impression that local surface temperatures could cool in response to GHG increases. Here we consider an extreme scenario in which GHG concentrations are increased only within the warmest layers of winter near-surface inversions of the Arctic and Antarctic. We find, using a fully coupled Earth system model, that the underlying surface warms despite the GHG addition exerting negative ERF and cooling the troposphere in the vicinity of the GHG increase. This unique radiative forcing and thermal response is facilitated by the high stability of the polar winter atmosphere, which inhibits thermal mixing and amplifies the impact of surface radiative forcing on surface temperature. These findings also suggest that strategies to exploit negative ERF via injections of short-lived GHGs into inversion layers would likely be unsuccessful in cooling the planetary surface. and Note: A revised data description file was added to this work on April 11, 2018 containing additional information about the data set than was provided in the original description. Additional keywords and a full citation to the related article were added as well.
- Keyword:
- climate, greenhouse gas, polar inversion layers, radiative forcing (and/or effective radiative forcing), and MODTRAN simulation
- Citation to related publication:
- Flanner, M. G., Huang, X., Chen, X.,& Krinner, G. (2018). Climate response to negative greenhouse gas radiative forcing in polar winter. Geophysical Research Letters, 45, 1997–2004. https://doi.org/10.1002/2017GL076668
- Discipline:
- Science
- Title:
- Data in support of the study "Climate response to negative greenhouse gas radiative forcing in polar winter"
-
- 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
- Title:
- Literature search files for systematic review on naloxone distribution in emergency departments
-
- Creator:
- University of Michigan Transportation Research Institute, Rupp, Jonathan D., Klein, Katelyn F., and Reed, Matthew P.
- Description:
- The files include an Excel file with the x-, y-, and z- coordinates that make up the nodal coordinates for a surface model of small (5th percentle) female pelvis geometry, the finite element model (.k file) that represents the nodal coordinates, and two surface files that represent the geometry (.obj and .ply).
- Citation to related publication:
- Katelyn F. Klein, Matthew P. Reed, and Jonathan D. Rupp. "Development of Geometric Specifications for the Pelvis of a Small Female Anthropomorphic Test Device." IRCOBI Conference 2016, IRC-16-79. http://www.ircobi.org/wordpress/downloads/irc16/pdf-files/79.pdf
- Discipline:
- Engineering
- Title:
- Small Female Pelvis Geometry Model
-
- 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
- Title:
- The ethical and professional use of social media in surgery - A review of the literature
-
- Creator:
- Li, Jieming, Zhang, Leyou, Johnson-Buck, Alexander, and Walter, Nils G.
- Description:
- Traces from single-molecule fluorescence microscopy (SMFM) experiments exhibit photophysical artifacts that typically necessitate human expert screening, which is time-consuming and introduces potential for user-dependent expectation bias. Here, we have used deep learning to develop a rapid, automatic SMFM trace selector, termed AutoSiM, that improves the sensitivity and specificity of an assay for a DNA point mutation based on single-molecule recognition through equilibrium Poisson sampling (SiMREPS). The improved performance of AutoSiM is based on accepting both more true positives and fewer false positives than the conventional approach of hidden Markov modeling (HMM) followed by thresholding. As a second application, the selector was used for automated screening of single-molecule Förster resonance energy transfer (smFRET) data to identify high-quality traces for further analysis, and achieves ~90% concordance with manual selection while requiring less processing time. AutoSiM can be adapted readily to novel datasets, requiring only modest Transfer Learning.
- Keyword:
- deep learning, single-molecule fluorescence, total internal reflection microscopy, SiMREPS, smFRET, and Forster resonance energy transfer
- Citation to related publication:
- Jieming Li, Leyou Zhang, Alexander Johnson-Buck, Nils G. Walter. (2020) Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning. Nature Communications, In Press. and Hayward, S., Lund, P., Kang, Q., Johnson-Buck, A., Tewari, M., Walter, N. (2018). Single-molecule microscopy image data and analysis files for "Ultra-specific and Amplification-free Quantification of Mutant DNA by Single-molecule Kinetic Fingerprinting" [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/Z2CZ35DF
- Discipline:
- Science
- Title:
- AutoSiM software and sample single-molecule trace data accompanying "Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning"
-
- Creator:
- Sean Sharp
- Description:
- Coastal wetlands intercept significant amounts of nitrogen (N) from watersheds, especially when surrounding land cover is dominated by agriculture and urban development. Through plant uptake, soil immobilization, and denitrification wetlands can remove excess N from flow through water sources and mitigate eutrophication of connected aquatic ecosystems. Excess N can also change plant community composition in wetlands, including communities threatened by invasive species. Understanding how variable hydrology and N loading impact wetland N removal and community composition can help attain desired management outcomes, including optimizing N removal and/or preventing invasion by non-natives. By using a dynamic, process-based ecosystem simulation model, we are able to simulate various levels of hydrology and N loading that would otherwise be difficult to manipulate. We investigate the effects of hydroperiod, hydrologic residence time, N loading, and the NH4+:NO3- ratio on both N removal and the invasion success of two non-native species (Typha x glauca or Phragmites australis) in temperate freshwater coastal wetlands using Mondrian, a process-based, wetland ecosystem simulation model. We found that when residence time increased, annual N removal increased up to 10-fold while longer hydroperiods also increased N removal, but only when residence time was >10 days and N loading was >30 g N m-2 y-1. N removal efficiency also increased with increasing residence time and hydroperiod, but was less affected by N loading. However, longer hydrologic residence time increased vulnerability of wetlands to invasion by both invasive plants at low to medium N loading rates where native communities are typically more resistant to invasion. This suggests a potential tradeoff between ecosystem services related to nitrogen removal and wetland invasibility. These results help elucidate complex interactions of community composition, N loading and hydrology on N removal, helping managers to prioritize N removal when N loading is high or controlling plant invasion in more vulnerable wetlands.
- Keyword:
- Mondrian, Simulation model, Coastal wetlands, Invasive species, and Ecosystem modeling
- Citation to related publication:
- http://dx.doi.org/10.1016/j.ecolmodel.2014.01.010
- Discipline:
- Science
- Title:
- Hydrologic flushing rates drive nitrogen cycling and plant invasion in a freshwater coastal wetland model Ecological Applications EAP20-0253 Reproducable Data Archive
-
- 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
- Discipline:
- Health Sciences
- Title:
- FGFR2-C342Y/+ and FGFR2+/+ Treated with/without Tissue Nonspecific AlkalinePhosphatase (TNAP) Mouse Skulls: BalbC strain 4 weeks postnatal
-
- Creator:
- Fries, Kevin J
- Description:
- This data is in support of the publication in review "Using sensor data to dynamically map large-scale models to site-scale forecasts: A case study using the National Water Model". It is all the raw data extracted from the NWM flow forecasts for Iowa and the IFIS stage readings. For the NWM data, each date has it's own tab-delimited file with columns being the time (hrs) and rows being the NHD site. For the IFIS gages, each tab delimited file is for a single site for the period of record.
- Citation to related publication:
- Fries, K. J., & Kerkez, B. (2018). Using sensor data to dynamically map large-scale models to site-scale forecasts: A case study using the national water model. Water Resources Research, 54, 5636-5653. https://doi.org/10.1029/2017WR022498
- Discipline:
- Engineering
- Title:
- Data for "Using sensor data to dynamically map large-scale models to site-scale forecasts: A case study using the National Water Model"
-
- 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
- Citation to related publication:
- Andrew J. Muzyk, Emily Peedin, Juliana Lipetzky, Haley Parker, Mark P. McEachern & Kelan Thomas (2017) Substance use education in US schools of pharmacy: A systematic review of the literature, Substance Abuse, 38:4, 455-463, https://doi.org/10.1080/08897077.2017.1341448 and https://www.ncbi.nlm.nih.gov/pubmed/28605276
- Discipline:
- Health Sciences
- Title:
- Literature Search Strategies for "Substance Use Education in United States Schools of Pharmacy: A Systematic Review of the Literature"
-
- Creator:
- Horsley, Timothy J. and Sampson, Christina P.
- Description:
- The data (raw data, composite files [processed], and some images) can be read by the program TerraSurveyor. Version 3.0.34.10 of the software was used to create the composite files in this deposit. and The magnetometer data was the second step in a geophysical survey program that began with magnetic susceptibility survey of a portion of the Weedon Island Preserve in St. Petersburg, Florida. Geophysical survey was used to map human occupation of the study area and to guide subsequent archaeological excavations.
- Keyword:
- magnetometry, geophysical survey, remote sensing, Florida archaeology, and coastal archaeology
- Citation to related publication:
- Sampson, C. P. (2019) Safety Harbor at the Weeden Island Site: Late Pre-Columbian Craft, Community, and Complexity on Florida's Gulf Coast. PhD Dissertation, University of Michigan. and Sampson, Christina Perry and Timothy J. Horsley. Using Multi-Staged Magnetic Survey and Excavation to Assess Community Settlement Organization: A Case Study from the Central Peninsular Gulf Coast of Florida. Advances in Archaeological Practice. Cambridge University Press: 18 December 2019. https://doi.org/10.1017/aap.2019.45
- Discipline:
- Science and Social Sciences
- Title:
- Magnetometer Survey Data from the Weeden Island Site (8Pi1), Florida (2013-2014)
-
- Creator:
- Moldwin, Mark B
- Description:
- Tab delimited file containing the records of all papers published in JGR-Space Physics in 2012. The records were pulled from Thomsen-Reuters ISI-Web-of-Science on June 3, 2016 including citations. Gender was identified independently by the creator of the file.
- Keyword:
- Gender and Nationality Bias, Space Physics, and Bibliometrics
- Citation to related publication:
- Moldwin, M. B., & Liemohn, M. W. (2018). High‐citation papers in space physics: examination of gender, country, and paper characteristics. Journal of Geophysical Research: Space Physics, 123. https://doi.org/10.1002/2018JA025291
- Discipline:
- Science
- Title:
- JGR-Space-2012-Data
-
- Creator:
- Geng, Yina, Van Anders, Greg, and Glotzer, Sharon C.
- Description:
- The data are the 13 target structures used in developing our model for predicting colloidal crystal structures from the geometries of particular shapes. The target structures are: simple cubic (SC), body-centered cubic (BCC), face-centered cubic (FCC), simple chiral cubic (SCC), hexagonal (HEX-1-0.6), diamond (D), graphite (G), honeycomb (H), body-centered tetragonal (BCT-1-1-2.4), high-pressure Lithium (Li), Manganese (beta-Mn), Uranium (beta-U), Tungsten (beta-W). At least nine simulations were run on each of the target structures. All of the data are formatted as .pos files.
- Keyword:
- Inverse Design and Machine Learning
- Citation to related publication:
- " Yina Geng, Greg van Anders, Sharon C. Glotzer, ""Predicting colloidal crystals from shapes via inverse design and machine learning [pre-print]"" https://arxiv.org/pdf/1801.06219.pdf"
- Discipline:
- Science
- Title:
- Predicting Crystal Structures using Digital Alchemy Inverse Materials Design and the Random Forest Technique of Machine Learning
-
- Creator:
- Zurbuchen, Thomas H.
- Description:
- Audification Routines in MATLAB and IDL
- Citation to related publication:
- Alexander, Robert L., Sile O’Modhrain, D. Aaron Roberts, Jason A. Gilbert, and Thomas H. Zurbuchen. “The Bird’s Ear View of Space Physics: Audification as a Tool for the Spectral Analysis of Time Series Data.” Journal of Geophysical Research: Space Physics 119, no. 7 (2014): 5259–71. https://doi.org/10.1002/2014JA020025
- Discipline:
- Science
- Title:
- The Bird's Ear View of Space Physics: Audification as a Tool for the Spectral Analysis of Time Series Data
-
- 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
- Title:
- Systematic review of the impact of acellular dermal matrix on aesthetics and patient satisfaction in tissue expander-to-implant breast reconstructions [Literature Search Files]
-
- Creator:
- Chen, Yuxi
- Description:
- We use the MHD with embedded particle-in-cell model (MHD-EPIC) to study the Geospace Environment Modeling (GEM) dayside kinetic processes challenge event at 01:50-03:00 UT on 2015-11-18, when the magnetosphere was driven by a steady southward IMF. In the MHD-EPIC simulation, the dayside magnetopause is covered by a PIC code so that the dayside reconnection is properly handled. We compare the magnetic fields and the plasma profiles of the magnetopause crossing with the MMS3 spacecraft observations. Most variables match the observations well in the magnetosphere, in the magnetosheath, and also during the current sheet crossing. The MHD-EPIC simulation produces flux ropes, and we demonstrate that some magnetic field and plasma features observed by the MMS3 spacecraft can be reproduced by a flux rope crossing event. We use an algorithm to automatically identify the reconnection sites from the simulation results. It turns out that there are usually multiple X-lines at the magnetopause. By tracing the locations of the X-lines, we find the typical moving speed of the X-line endpoints is about 70~km/s, which is higher than but still comparable with the ground-based observations.
- Keyword:
- MHD, PIC, and simulation
- Citation to related publication:
- Chen, Yuxi, et al. "Magnetohydrodynamic with embedded particle-in-cell simulation of the Geospace Environment Modeling dayside kinetic processes challenge event." arXiv preprint arXiv:2001.04563 (2020). https://arxiv.org/abs/2001.04563
- Discipline:
- Science
- Title:
- MHD-EPIC simulation data of the GEM dayside kinetic processes challenge event
-
- 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
- Title:
- Father-inclusive perinatal parent education programs: A systematic review [Literature Search Files]
-
- 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
- Citation to related publication:
- Shtull-Leber E, Silbergleit R, Meurer WJ (2017) Pre-hospital midazolam for benzodiazepine-treated seizures before and after the Rapid Anticonvulsant Medication Prior to Arrival Trial: A national observational cohort study. PLoS ONE 12(3): e0173539. https://doi.org/10.1371/journal.pone.0173539
- Discipline:
- Health Sciences
- Title:
- Pre-Hospital Midazolam for Treatment of Status Epilepticus Before and After the Rapid Anticonvulsant Medication Prior to Arrival Trial (RAMPART): A National Observational Cohort Study
-
- Creator:
- Bustamante, Angela C., Opron, Kristopher, Ehlenbach, William J., Crane, Paul K., Keene, Dirk, Standiford, Theodore J., and Singer, Benjamin H.
- Description:
- This study was conducted to detect and analyze modules, or clusters of genes, associated with sepsis, using RNAseq data obtained from 12 participants who died of sepsis and 12 participants who died of non-infectious critical illness while hospitalized. This deposit contains the input data and parameters needed to reproduce the weighted gene co-expression network analysis (WGCNA) and gene enrichment analysis performed on this data. This analysis requires the R packages "WGCNA" version 1.68 and "DESeq2" version 1.22.2 available for download from bioconductor ( http://bioconductor.org). The external bioinformatics tool DAVID version 6.8 ( https://david.ncifcrf.gov/) was used as an additional gene enrichment analysis. Please see the supplemental methods document within this deposit and published research letter for more detailed information.
- Keyword:
- Sepsis, RNAseq, Transcriptomics, Human, and Brain
- Citation to related publication:
- Bustamante, A.C., Opron, K., Ehlenbach, W.J., Larson, E.B., Crane, P.K., Keene, C.D., Standiford, T.J., Singer, B.H., 2020. Transcriptomic Profiles of Sepsis in the Human Brain. Am J Respir Crit Care Med. https://doi.org/10.1164/rccm.201909-1713LE
- Discipline:
- Science
- Title:
- Transcriptomic Profiles of Sepsis in the Human Brain
-
- Creator:
- Brandt, Daniel, A., Bussy-Virat, Charles, D., and Ridley, Aaron, J.
- Description:
- The Multifaceted Optimization Algorithm (MOA) is a tool for generating corrected empirical model thermospheric densities during geomagnetic storms. It consists of a suite of Python functions that operate around the Spacecraft Orbit Characterization Kit (SpOCK), an orbital propagator developed by Charles D. Bussy-Virat, PhD, Joel Getchius, and Aaron J. Ridley, PhD at the University of Michigan, and it estimates new densities for the NRLMSISE-00 atmospheric model. MOA generates new model densities by estimating modifications to inputs to the NLRMSISE-00 model that minimize the orbit error between modeled spacecraft in SpOCK, and their actual altitudes as described in publicly-available Two-Line Element Sets (TLEs), made available online via Space-track.org. MOA consists of three sub-process: (1) The Area Optimization Algorithm (AROPT), (2) the F10.7 Optimization Algorithm (FOPT), and (3) the Ap Optimization Algorithm (APOPT). AROPT computes the contribution to the drag of the modeled spacecraft due to their varying projected area. FOPT estimates modifications to the 10.7 cm solar radio flux in NRLMSISE-00, and APOPT estimates modifications to the Earth's magnetic activity in NRLMSISE-00. MOA finds these modifications across many spacecraft, and the medians of those modifications are then applied in NLRMSISE-00 along the orbit of another satellite to generate new densities for verification. In this instance, modifications are applied along the orbits of the Swarm spacecraft and compared to Swarm GPS-derived densities.
- Keyword:
- Orbit, Satellite, Two-line Element Set, Thermosphere, and Drag
- Discipline:
- Engineering
- Title:
- A Simple Method for Correcting Empirical Model Densities during Geomagnetic Storms Using Satellite Orbit Data
-
- 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
- Title:
- Spectrum of immune checkpoint inhibitors-induced endocrinopathies in cancer patients [Literature Search Files]
-
- Creator:
- Ward, Jamie L ., Flanner, Mark G., Bergin, Mike, Dibb, Jack E., Polashenski, Chris M., Soja, Amber J., and Thomas, Jennie L.
- Description:
- Biomass burning produces smoke aerosols that are emitted into the atmosphere. Some smoke constituents, notably black carbon (BC), are highly effective light-absorbing aerosols (LAA). Emitted LAA can be transported to high albedo regions like the Greenland Ice Sheet (GrIS) and affect local snowmelt. In the summer, the effects of LAA in Greenland are uncertain. To explore how LAA affect GrIS snowmelt and surface energy flux in the summer, we conduct idealized global climate model simulations with perturbed aerosol amounts and properties in the GrIS snow and overlying atmosphere. The in-snow and atmospheric aerosol burdens we select range from background values measured on the GrIS to unrealistically high values. This helps us explore the linearity of snowmelt response and to achieve high signal-to-noise ratios. With LAA operating only in the atmosphere, we find no significant change in snowmelt due to the competing effects of surface dimming and tropospheric warming. Regardless of atmospheric LAA presence, in-snow BC-equivalent mixing ratios greater than ~60 ng/g produce statistically significant snowmelt increases over much of the GrIS. We find that net surface energy flux changes correspond well to snowmelt changes for all cases. The dominant component of surface energy flux change is solar energy flux, but sensible and longwave energy fluxes respond to temperature changes. Atmospheric LAA dampen the magnitude of solar radiation absorbed by in-snow LAA when both varieties are simulated. In general, the significant melt and surface energy flux changes we simulate occur with LAA quantities that have never been recorded in Greenland.
- Keyword:
- climate, Greenland Ice Sheet, black carbon, biomass burning, snowmelt, and surface energy balance
- Citation to related publication:
- Ward, J.L., et al. (2018). Modeled Response of Greenland Snowmelt to the Presence of Biomass Burning-Based Absorbing Aerosols in the Atmosphere and Snow. Journal of Geophysical Research: Atmospheres. 123, 6122– 6141. https://doi.org/10.1029/2017JD027878
- Discipline:
- Science
- Title:
- Data in support of the study "Modeled Response of Greenland Snowmelt to the Presence of Biomass Burning-Based Absorbing Aerosols in the Atmosphere and Snow"
-
- Creator:
- Moniri, Saman, Bale, Hrishikesh , Volkenandt, Tobias, Wang, Yeqing, Gao, Jianrong, Lu, Tianxian, Sun, Kai, and Shahani, Ashwin J.
- Description:
- The data file contains (1) the grayscale images of the nano-tomography experiments that can be segmented into binary images and visualized to show the 3D morphology of spiral eutectics; and (2) crystallographic orientation maps of serial-sectioned sample, which can be processed in a variety of EBSD software packages.
- Keyword:
- crystallization, chirality, self-organization, and spiral eutectics
- Citation to related publication:
- Moniri, S., Bale, H., Volkenandt, T., Wang, Y., Gao, J., Lu, T., Sun, K., Ritchie, R.O., & Shahani, A.J. (23 January 2020). Multi‐Step Crystallization of Self‐Organized Spiral Eutectics. Small (1906146). https://doi.org/10.1002/smll.201906146
- Discipline:
- Engineering
- Title:
- Dataset for 'Multi‑Step Crystallization of Self‑Organized Spiral Eutectics'
-
- 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
- Title:
- Literature search strategies for "Substance Use Education in Schools of Nursing: A Systematic Review of the Literature"
-
- 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
- Title:
- Humanities in predoctoral dental education: A scoping review [Literature Search Files]
-
- Creator:
- Burger, Laura L , Wagenmaker, Elizabeth R., Phumsatitpong, Chayarndorn , Olson, David P., and Moenter, Suzanne M.
- Description:
- Polycystic ovary syndrome (PCOS) is the most common form of infertility in women. The causes of PCOS are not yet understood and both genetics and early-life exposure have been considered as candidates. With regard to the latter, circulating androgens are elevated in mid-late gestation in women with PCOS, potentially exposing offspring to elevated androgens in utero; daughters of women with PCOS are at increased risk for developing this disorder. Consistent with these clinical observations, prenatal androgenization (PNA) of several species recapitulates many phenotypes observed in PCOS. There is increasing evidence that symptoms associated with PCOS, including elevated luteinizing hormone (LH) (and presumably gonadotropin-releasing hormone (GnRH)) pulse frequency emerge during the pubertal transition. We utilized translating ribosomal affinity purification coupled with RNA sequencing to examine GnRH neuron mRNAs from prepubertal (3wk) and adult female control and PNA mice. Prominent in GnRH neurons were transcripts associated with protein synthesis and cellular energetics, in particular oxidative phosphorylation. The GnRH neuron transcript profile was affected more by the transition from prepuberty to adulthood than by PNA treatment, however PNA did change the developmental trajectory of GnRH neurons. This included families of transcripts related to both protein synthesis and oxidative phosphorylation, which were more prevalent in adults than in prepubertal mice but were blunted in PNA adults. These findings suggest that prenatal androgen exposure can program alterations in the translatome of GnRH neurons, providing a mechanism independent of changes in the genetic code for altered expression. These are Microsoft Excel Files
- Keyword:
- GnRH Neuron TRAP Seq
- Citation to related publication:
- Unprocessed RNASeq data is available at Gene Expression Omnibus ( https://www.ncbi.nlm.nih.gov/gds) accession GSE155314.
- Discipline:
- Science
- Title:
- Prenatal androgen exposure alters the developmental trajectory of both GnRH neuron and preoptic area RNA transcripts in female mice.
-
- Creator:
- Gosner, Linda R., Nowlin, Jessica, and Smith, Alexander J.
- Description:
- Included here are 1) a detailed description of each of the dataset’s components, 2) a database of finds from the survey, 3) databases of the faunal bone studied by specialist Damià Ramis, 4) notes and documentation made in the field, 5) excavation photographs 6) artifact photographs.
- Keyword:
- Sardinia, Mediterranean archaeology, archaeological survey, excavation, and Classical archaeology
- Citation to related publication:
- Dommelen, Peter van, Enrique Díes Cusí, Linda R. Gosner, Jeremy Hayne, Guillem Pérez-Jordà, Damià Ramis, Andrea Roppa, and Alfonso Stiglitz. 2018. “Un millennio di storie: nuove notizie preliminari sul Progetto S’Urachi (San Vero Milis, OR), 2016-2018.” Quaderni. Rivista di Archeologia 29: 141–65., Gosner, Linda R., and Alexander J. Smith. 2018. “Landscape Use and Local Settlement at the Nuraghe S’Urachi (West-Central Sardinia): Results from the First Two Seasons of Site Survey.” Fasti Online Documents & Research: Survey Series, no. 7: 1–27. www.fastionline.org/docs/FOLDER-sur-2018-7.pdf., Gosner, Linda R., Jeremy Hayne, Emanuele Madrigali, Jessica Nowlin. 2020. New Evidence for Local Continuity and Phoenician Influence in the Ceramic Assemblage from Iron Age Su Padrigheddu (West-Central Sardinia). Proceedings of the IX Congreso de Estudios Fenicios y Púnicos. Myrta 5: 1649-1657., Madrigali, Emanuele, Linda R. Gosner, Jeremy Hayne, Jessica Nowlin, and Damià Ramis. 2019. “Tradizioni e interazioni nella quotidianità dell’età del ferro. nuove evidenze da Su Padrigheddu (San Vero Milis, OR).” Quaderni. Rivista di Archeologia 30: 107–26., Stiglitz, Alfonso, Enrique Díes Cusí, Damià Ramis, Andrea Roppa, and Peter van Dommelen. 2015. “Intorno al nuraghe: notizie preliminari sul Progetto S’Urachi (San Vero Milis, OR).” Quaderni. Rivista di Archeologia 26: 191–218., and Gosner, Linda R., Jessica Nowlin, and Alexander J. Smith. in preparation. Ground-truthing the Site-based Survey at S’Urachi and Su Padrigheddu (West-Central Sardinia): Results of the 2016 and 2017 Seasons.
- Discipline:
- Social Sciences
- Title:
- S’Urachi Site-Based Archaeological Survey 2016-2017
-
- Creator:
- Jiao, Zhenbang, Chen, Yang, and Manchester, Ward
- Description:
- GOES_flare_list: contains a list of more than 12,013 flare events. The list has 6 columns, flare classification, active region number, date, start time end time, emission peak time. SHARP_data.hdf5 files contain time series of 20 physical variables derived from the SDO/HMI SHARP data files. These data are saved at a 12 minute cadence and are used to train the LSTM model.
- Keyword:
- Solar Flare Prediction and Machine Learning
- Citation to related publication:
- Jiao, Z., Sun, H., Wang, X., Manchester, W., Gombosi, T., Hero, A., Chen, Y., Solar Flare Intensity Prediction with Machine Learning Models, 2020, Space Weather Journal, in press
- Discipline:
- Science and Engineering
- Title:
- Data for Solar Flare Intensity Prediction with Machine Learning Models
-
- Creator:
- Baskar, Deepika and Gorodetsky, Alex
- Description:
- Studying the effect of wind on urban air mobility typically requires comprehensive fluid dynamics simulations in a realistic urban geometry. Motivated to enable wide-spread autonomous drone activity in urban centers, such studies have indeed been considered by several authors in the recent literature. However, the accessibility of these approaches to those with less fluid dynamics experience and/or without access to purpose built simulation tools has limited validation and application of the resulting path planning strategies. and The .dat files contain the flow variables for each of the 402240 points sampled from the region under study. For flow visualization purposes, the .dat files are readable using Tecplot Software.
- Keyword:
- UAM, Energy efficient path planning , CFD, and City of Boston
- Citation to related publication:
- D. Baskar, A.A. Gorodetsky (2019). A Simulated Wind-field Dataset for Testing Energy Efficient Path-Planning Algorithms for UAVs in Urban Environment. Forthcoming.
- Discipline:
- Engineering and Other
- Title:
- A Simulated Wind-field Dataset for Testing Energy Efficient Path-Planning Algorithms for UAVs in Urban Environment
-
- 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
- Title:
- Action current data for investigating the development and organization of GnRH neuron activity in mice.
-
- Creator:
- Chen, Yang and Manchester, Ward IV
- Description:
- GOES_flare_list: contains a list of more than 10,000 flare events. The list has 6 columns, flare classification, active region number, date, start time end time, emission peak time, GOES_B_flare_list: contains time series data of SDO/HMI SHARP parameters for B class solar flares , GOES_MX_flare_list: contains time series data of SDO/HMI SHARP parameters for M and X class solar flares, SHARP_B_flare_data_300.hdf5 and SHARP_MX_flare_data_300.hdf5 files contain time series more than 20 physical variables derived from the SDO/HMI SHARP data files. These data are saved at a 12 minute cadence and are used to train the LSTM model., and B_HARPs_CNNencoded_part_xxx.hdf5 and M_X HARPs_CNNencoded_part_xxx.hdf5 include neural network encoded features derived from vector magnetogram images derived from the Solar Dynamics Observatory (SDO) Helioseismic and Magnetic Imager (HMI). These data files typically contains one or two sequences of magnetograms covering an active region for a period of 24h with a 1 hour cadence. We encode each magnetogram with frames of a fixed size of 8x16 with 512 channels.
- Keyword:
- machine learning, data science, and solar flare prediction
- Citation to related publication:
- Chen, Y., Manchester, W., Hero, A., Toth, G., DuFumier, B. Zhou, T., Wang, X., Zhu, H., Sun, Zeyu, Gombosi, T., Identifying Solar Flare Precursors Using Time Series of SDO/HMI Images and SHARP Parameters, Space Weather, 17, 1404–1426. https://doi.org/10.1029/2019SW002214
- Discipline:
- Science and Engineering
- Title:
- Data and Data products for machine learning applied to solar flares
-
- 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
- Title:
- Retinal fundus images for glaucoma analysis: the RIGA dataset
-
- Creator:
- Malik, Hafiz and Khan, Muhammad Khurran, King Saud University
- Description:
- Details of the microphone used for data collection, acoustic environment in which data was collected, and naming convention used are provided here. 1 - Microphones Used: The microphones used to collect this dataset belong to 7 different trademarks. Table (1) illustrates the number of used Mics of different trademarks and models. Table 1: Trademarks and models of Mics Mic Trademark Mic Model # of Mics Shure SM-58 3 Electro-Voice RE-20 2 Sennheiser MD-421 3 AKG C 451 2 AKG C 3000 B 2 Neumann KM184 2 Coles 4038 2 The t.bone MB88U 6 Total 22 2- Environment Description: A brief description of the 6 environments in which the dataset was collected is presented here: (i) Soundproof room: a small room (nearly 1.5m × 1.5m × 2m), which is closed and completely isolated. With an exception of a small window in the front side of the room which is made of glass, all the walls of the room are made of wood and covered by a layer of sponge from the inner side, and the floor is covered by carpet. (ii) Class room: standard class room (6m × 5m × 3m). (iii) Lab: small lab (4m × 4m × 3m). All the walls are made of glasses and the floor is covered by carpet. The lab contains 9 computers. (iv) Stairs: is in the second floor. The place of recording is 3m × 5m (v) Parking: is the college parking. (vi) Garden: is an open space outside the buildings. 3- Naming Convention: This set of rules were followed as a naming convention to give each file in the dataset a unique name: (i) The file name is 19 characters long, and consists of 5 sections separated by underscores. (ii) The first section is of 3 characters indicates the Microphone trademark. (iii) The second section of 4 characters indicates the microphone model as in table (2). (iv) The third section of 2 characters indicates a specific microphone within a set of microphones of the same trademark and model, since we have more than one microphone of the same trademark and model. (v) The fourth section of 2 characters indicates the environment, where Soundproof room --> 01 Class room --> 02 Lab --> 03 Stairs --> 04 Parking --> 05 Garden --> 06 (vi) The fifth section of 2 characters indicates the language, where Arabic --> 01 English --> 02 Chinese --> 03 Indonesian --> 04 (vii) The sixth section of 2 characters indicates the speaker. Table 2: Microphones Naming Criteria Original Mic Trademark and model --> Naming Convenient Shure SM-58 --> SHU_0058 Electro-Voice RE-20 --> ELE_0020 Sennheiser MD-421 --> SEN_0421 AKG C 451 --> AKG_0451 AKG C 3000 B --> AKG_3000 Neumann KM184 --> NEU_0184 Coles 4038 --> COL_4038 The t.bone MB88U --> TBO_0088 For example: SEN_0421_02_01_02_03 is an English file recorded by speaker number 3 in the soundproof room using microphone number 2 of Sennheiser MD-421
- Keyword:
- audio forensic, multimedia forensics, microphone identification, tamper detection, splicing detection, and codec identification
- Citation to related publication:
- Muhammad Khurram Khan, Mohammed Zakariah, Hafiz Malik & Kim-Kwang Raymond Choo (2018). A novel audio forensic data-set for digital multimedia forensics, Australian Journal of Forensic Sciences, 50:5, 525-542, http://dx.doi.org/10.1080/00450618.2017.1296186
- Discipline:
- Government, Politics and Law, Science, and Engineering
- Title:
- The KSU-UMD Dataset for Benchmarking for Audio Forensic Algorithms
-
- 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:
- To be published in F1000, DOI pending
- Discipline:
- Health Sciences
- Title:
- Dataset derived from 2014 National Hospital Ambulatory Care Survey - Emergency Department
-
- 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
- Discipline:
- Health Sciences
- Title:
- FGFR2-C342Y/+ and FGFR2+/+ Treated with/without Tissue Nonspecific Alkaline Phosphatase (TNAP) Mouse Skulls: C57B:6 strain 3 weeks postnatal
-
- Creator:
- Heath, Jeffrey
- Description:
- Yorno So is the variety of the Toro So subgroup of the Dogon language family. It is spoken in the Yendouma village cluster along the base of cliffs on the eastern side of the Dogon (Bandiagara) plateau in east-central Mali. It is not yet completely clear whether it is best described as a dialect of Toro So (which also includes Sangha So, Ibi So, and other varieties), or as a separate language. As of May 2018 my opinion is that it is a dialect. A grammar of Yorno So was published electronically at Language Description Heritage Library in 2017. http://ldh.clld.org/2017/09/01/escidoc2326768-2/ This is backed up at Deep Blue documents. http://hdl.handle.net/2027.42/139021. An excerpt of this document that includes a transcription and an English translation of audio files texts 1-6 is included in this dataset. Texts 07, 08, and 09 have not yet been transcribed. I give permission to other linguists to transcribe, translate, and/or analyze those texts.
- Keyword:
- Toro So, Yorno So, Dogon, Audio, and Recording
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Dogon Toro So (Yorno So) Audio Files
-
- Creator:
- Heath, Jeffrey
- Description:
- Najamba is spoken chiefly in villages on the edges of low cliffs flanking a long valley near Douentza in central Mali. It belongs to a cluster of languages/dialects including Kindige, spoken mostly along the main Douentza-Sevare highway, and the varieties around Borko on the (very) high plateau on the northwestern edge of the Dogon (Bandiagara) plateau. These varieties are often collectively called Bondu So, but this is an exonym. A grammar of Najamba was published electronically by Language Description Heritage Library in 2017 http://ldh.clld.org/2017/02/01/escidoc2397771/ It is backed up at Deep Blue documents. http://hdl.handle.net/2027.42/139022 One cassette was recorded (on one side only) in Kubewel village in 2004. Two cassettes were recorded in Adia village in 2005 in a single long session. These have been digitized. The inventory is: Kubewel: 2004-01 side A; Adia 2005-01 side A; 2005-01 side B; 2005-02 side A; 2005-02 side B. The 2004 tape had poor sound quality and was not transcribed. A substantial part of 2005-01 side A and 2005-02 side A was transcribed and translated in unpublished keyboarded documents in 2009 (see below). The material from 2005-01 side A was further edited and appeared as a single long text at the end of the published grammar. The unpublished documents included in this work are: transcriptions: Dogon Najamba 2005_01_A Adia text transcribed 2009; Dogon Najamba 2005_02_A Adia text transcribed 2009. translations: Dogon Najamba 2005_01_A Adia text translated 2009; Dogon Najamba 2005_02_A Adia text translated 2009
- Keyword:
- Najamba, Dogon, Douenzta, Mali, Audio, and Recording
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Dogon Najamba Audio Files
-
- Creator:
- Heath, Jeffrey
- Description:
- Jalkunan is a small-population Mande language spoken in Blédougou village cluster in the Banfora plateau in SW Burkina Faso.A grammar was published electronically at Language Description Heritage Library in 2017. http://ldh.clld.org/2017/01/01/escidoc2346932/ This is backed up at Deep Blue documents. http://hdl.handle.net/2027.42/139025 http://dogonlanguages.org/other#mande Seven texts were recorded digitally in 2016 and are archived here. Three of them (texts 1, 2, and 4) were transcribed and translated at the end of the published grammar. The remaining tapes are not transcribed as of May 2018. I give permission to other linguists to transcribe, translate, and/or analyse the remaining texts.
- Keyword:
- Jalkunan, Mande, Audio, and Recording
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Mande Jalkunan Audio Files
-
- Creator:
- Heath, Jeffrey
- Description:
- Donno So is a Dogon language spoken over a wide area on the Dogon (Bandiagara) plateau, mainly between Bandiagara and the eastern edge of the plateau. It is also called Kamma So. A grammar was published electronically at Language Description Heritage Library in 2016: and https://ldh.clld.org/sources/item_2491630 This is backed up at Deep Blue documents. http://hdl.handle.net/2027.42/123062 Thirteen texts were recorded digitally in Wendekele village south of Bandiagara in approximately 2015. Because of equipment problems the texts are rather faint and difficult to transcribe. Five texts were transcribed and translated, and presented at the end of the grammar volume. The correspondences are these: Published volume: text 1, Recording: DS 02, title: hare and other animals (tale); text 2, DS 09, report on trip to Burkina; text 3, DS 10, blacksmith; text 4, DS 03, squirrel and hare (tale); text 5, DS 11, Fulbe herders. Recordings DS 01(tale of stepmother), 04 (farming), 05 (construction),06 (animals), 07 (hunting), 08 (herding), 12 (marriage), and 13 (korobasinging) are not transcribed as of May 2018. I grant permission to other linguists to transcribe, translate, and/or analyse them.
- Keyword:
- Donno So, Dogon, Audio, and Recording
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org and Heath, Jeffrey. 2016. A grammar of Donno So or Kamma So. Ann Arbor: Univ. of Michigan. Available at https://doi.org/10.17617/2.2491630 and https://ldh.clld.org/sources/item_2491630
- Discipline:
- Humanities
- Title:
- Dogon Donno So Audio Files
-
- Creator:
- Heath, Jeffrey
- Description:
- Bankan Tey is a Dogon language spoken in the village complex Walo (also spelled Oualo) near Douentza in central Mali. It is closely related to Ben Tey within Dogon. As of May 2018, Bankan Tey remains on my “to do” list in terms of grammatical description and texts. These recordings were made in Walo in 2011 and have not yet been transcribed although there is a fair chance I will be able to work on them in the next few years. If nothing materializes before 2022, I authorize other linguists to transcribe, translate, and/or analyse the texts. 2011 side A 2011 side B
- Keyword:
- Bankan Tey , Dogon, Recording, Audio, and Walo
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Dogon Bankan Tey (Walo) Audio Files
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Humburi Senni (Songhay family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Songhay, Humburi Senni, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Humburi Senni-speaking (Songhay, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Fulankiriya (Songhayfamily) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Songhay, Fulankiriya, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Fulankiriya-speaking (Songhay, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Manding Bambara (Mande family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- Villages, Mande, Manding Bambara, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Manding Bambara-speaking (Mande, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Bozo Jenama (Mande family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Mande, Bozo Jenama, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Bozo Jenama-speaking (Mande, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Moore (Gur family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Gur, Moore, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Moore-speaking (Gur, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Yanda Dom (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Yanda Dom, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Yanda Dom-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Toro Tegu (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Toro Tegu, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Toro Tegu-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Toro So (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Toro So, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Toro So-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Tomo Kan(Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Tomo Kan, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Tomo Kan-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Tommo So (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Tommo So, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Tommo So-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Tiranige (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Tiranige, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Tiranige-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Tebul Ure (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Tebul Ure, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Tebul Ure-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Penange (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Penange, Dogon, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Penange-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Nanga (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Nanga, Dogon, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Nanga-speaking (Dogon Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- images of villages in Mali in which Najamba Kindige (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Najamba, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Najamba-Kindige-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- images of villages in Mali in which Mombo (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Mombo, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Mombo-speaking (Dogon, Mali) village photos
-
- Creator:
- Heath, Jeffrey
- Description:
- Images of villages in Mali in which Donno So (Dogon family) is the primary language. Each file name contains important information about the photos, and are structured thus: LanguageFamily_Language_IdentificationNumber_GeographicCoordinate_Description_Date_InitialsOfThePhotographer
- Keyword:
- villages, Dogon, Donno So, Kamma So, and Mali
- Citation to related publication:
- Moran, Steven & Forkel, Robert & Heath, Jeffrey (eds.) 2016. Dogon and Bangime Linguistics. Jena: Max Planck Institute for the Science of Human History. http://dogonlanguages.org
- Discipline:
- Humanities
- Title:
- Donno So (Kamma So)-speaking (Dogon, Mali) village photos