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- Creator:
- Yu, Chi-Lin, Eggleston, Rachel, Zhang, Kehui, Nickerson, Nia, Sun, Xin, Marks, Rebecca A., Hu, Xiaosu, Brennan, Jonathan R. , Wellman, Henry M. , and Kovelman, Ioulia
- Description:
- The dataset includes 51 children (age range = 6-12 years) who listened to the first chapter of Alice’s Adventures in Wonderland during fNIRS neuroimaging. We also provide the text of the story with several word-by-word predictors motivated by research in Theory of Mind development and language. These annotated, naturalistic datasets can be used to replicate prior work and test new hypotheses about everyday social cognition and natural language comprehension in the developing brain.
- Keyword:
- neuroimaging, fNIRS, Children, Theory of Mind, Language, Naturalistic Neuroscience, and Story Listening
- Discipline:
- Science
-
- Creator:
- Khabiri, Morteza and Freddolino, Peter L.
- Description:
- Genome-wide predictions of all transcription factor binding sites on the D. melanogaster genome were developed for use in predicting the locations of Polycomb response elements, as described in https://doi.org/10.1101/516500
- Keyword:
- Systems Biology and Drosophila
- Citation to related publication:
- Khabiri, M., & Freddolino, P. L. (2019). Genome-wide Prediction of Potential Polycomb Response Elements and their Functions. Preprint. BioRxiv, 516500. https://doi.org/10.1101/516500
- Discipline:
- Science
-
- Creator:
- Hero, Alfred O, Zhai, Yaya, Burke, Thomas, Doraiswamy, Murali, Ginsburg, Geoffrey S, Henao, Ricardo, Turner, Ronald B, and Woods, Christopher W
- Description:
- The data deposited here is as follows: The clinical shedding/symptom data, RNAseq, steroid, and wearable E4 data was partially presented in publications [1]-[3] and the cognitive lumos and VAFS data is presented in the paper [4], which is under review and embargoed. The data files are: subject.json, sample.json, and genematrix_TPM.csv. In addition, a copy of the blank consent form used to enroll volunteers in the study is included (17964_Adult Consent_2015Mar17-Mod 1_clean.pdf)., Clinical symptom and viral shedding data (in subject.json): reports each subject's accumulated and maximum self-reported symptom score (modified Jackson score) and shedding titrations from nasal-pharyngeal washes after inoculation. , RNAseq data (genematrix_TMP.csv): Whole blood was collected in PAXgene™ Blood RNA tubes (PreAnalytiX), and total RNA extracted using the PAXgene™ Blood miRNA Kit (QIAGEN) using the manufacturer’s recommended protocol. RNA quantity and quality were assessed using Nanodrop 2000 spectrophotometer (Thermo-Fisher) and Bioanalyzer 2100 with RNA 6000 Nano Chips (Agilent). RNA sequencing libraries were prepared using Illumina TruSeq mRNA Library Kit with RiboZero Globin depletion, and sequenced on an Illumina NextSeq sequencer with 50bp paired-end reads (target 40M reads per sample). After demultiplexing to FASTQ paired-end read counts files, the 396 samples were TPM transformed using HISAT2 software with the reference genome Homo_sapiens.GRCh38.84. Each sample corresponds to one of the 18 subjects at one of 22 time points. One of these samples was of insufficient quality to be mapped to read counts. In addition to the TPM normalized RNAseq data contained in this repository, the raw FASTQ data for the 395 samples are deposited in the GEO repository ( https://www.ncbi.nlm.nih.gov/geo), Accession # GSE215087. , Cognitive data (sample.json): Outcomes from a NeuroCognitive Performance Test (NCPT) that was taken approximately 3 time daily by all volunteers. The NCPT is a repeatable, web-based, computerized, cognitive assessment platform designed to measure subtle changes in performance across multiple cognitive domains. Subject scores along 18 cognitive variables data were collected at approximated 22 time points during the challenge study. The data structure sample.json contains the raw cognitive data and the extracted 18 cognitive scores over time for each subject. , The Visual Analog Fatigue Scale (sample.json): the VAFS is a measure of cognitive fatigue that was measured approximately 3 times per day at the same time as the NCPT and blood draw. , Wearable device data (sample.json): participants wore an Empatica E4 device for the duration of the challenge study. Summarized features are provided for each subject that include sleep duration (mean and std), sleep offset (mean and std), and temperature (mean and std). , Steroid data was also collected and is included in the sample.json. This steroid data was collected from the whole blood samples and consists of cortisol, melatonin, and DHEAS. , and See README.txt for more specific details on the data structures contained in the sample.json, subject.json, and genematrix_TPM.csv files.
- Keyword:
- human challenge study and cognitive health and immunity
- Citation to related publication:
- X She, Y Zhai, R Henao, CW Woods, C Chiu, Geoffrey S. Ginsburg, Peter X.K. Song, AO. Hero, “Adaptive multi-channel event segmentation and feature extraction for monitoring health outcomes,” IEEE Transactions on Biomedical Engineering, vol. 68, no. 8, pp. 2377-2388, Aug. 2021, doi: 10.1109/TBME.2020.3038652. Available on arxiv:2008.09215 , Emilia Grzesiak, Brinnae Bent, Micah T. McClain, Christopher W. Woods, Ephraim L. Tsalik, Bradly P. Nicholson, Timothy Veldman, Thomas W. Burke, Zoe Gardener, Emma Bergstrom, Ronald B. Turner, Christopher Chiu, P. Murali Doraiswamy, Alfred Hero, Ricardo Henao, Geoffrey S. Ginsburg, Jessilyn Dunn Assessment of the Feasibility of Using Noninvasive Wearable Biometric Monitoring Sensors to Detect Influenza and the Common Cold Before Symptom Onset. JAMA Netw Open. 2021;4(9):e2128534. doi:10.1001/jamanetworkopen.2021.28534 , E Sabeti, S Oh, PX Song, A Hero. “A Pattern Dictionary Method for Anomaly Detection,” Entropy, vol 24, pp. 1095 Aug 2022. doi: 10.3390/e24081095, and Yaya Zhai, P. Murali Doraiswamy, Christopher W. Woods, Ronald B. Turner, Thomas W. Burke, Geoffrey S. Ginsburg, Alfred O. Hero, "Pre-exposure cognitive performance variability is associated with severity of respiratory infection," manuscript under review.
- Discipline:
- Health Sciences and Social Sciences
-
Bangime language (Mali) audio files
User Collection- Creator:
- Heath, Jeffrey
- Description:
- Audio files for Bangime language (genetic isolate, eastern Mali)
5Works -
Appendices for "Regulation of Müller Stem Cell Properties: Insights From a Zebrafish Model"
User Collection- Creator:
- Sifuentes, Christopher J
- Description:
- Appendix1: Differential expression data for zebrafish regeneration and mouse degeneration models. Appendix2: Gene ontology data for zebrafish regeneration and mouse degeneration models. Appendix3: Pathway data for zebrafish regeneration and mouse degeneration models. Appendix4: Differential expression data and genes within linked peaks for mi2004 mutants. Appendix5: Gene ontology data for mi2004 mutants. Appendix6: Pathway data for mi2004 mutants. Appendix7: Linkage plots for mi2004 mutants. Appendix8: Inverse PCR and genome-walking data.
- Keyword:
- Müller glia, zebrafish, regeneration, stem cell, and photoreceptor
- Citation to related publication:
- Sifuentes, C. J. (2016). Regulation of Müller glial stem cell properties: Insights from a zebrafish model (Doctoral dissertation). Retrieved from http://hdl.handle.net/2027.42/135939
8Works -
- Creator:
- Yan, Xiang (Jacob), Clarke, Phillipa J., Okullo, Dolorence, Goodspeed, Robert, Data Driven Detroit, Gomez-Lopez, Iris N., and Veinot, Tiffany C
- Description:
- This collection was produced as part of the project, “A ‘Big Data’ Approach to Understanding Neighborhood Effects in Chronic Illness Disparities.” The Investigators for the project are Tiffany Veinot, Veronica Berrocal, Phillipa Clarke, Robert Goodspeed, Daniel Romero, and VG Vinod Vydiswaran from the University of Michigan. The study took place from 2015-2016, with funding from the University of Michigan’s Social Sciences Annual Institute, MCubed, and the Sloan and Moore Foundations. Contact: Tiffany Veinot, MLS, PhD Office: 3443 North Quad Phone: 734/615-8281 Email: tveinot@umich.edu MCubed project page: https://mcubed.umich.edu/projects/%E2%80%9Cbig-data%E2%80%9D-approach-understanding-neighborhood-effects-chronic-illness-disparities
- Keyword:
- Food Environment, Health Status, Employment, Health Care Resources, Neighborhood Safety, Healthcare Utilization, Transportation, Census tract level, Information and Education Environment, Spatial Measures, Detroit, Active Living Resources, Social Environment, Demographics, Community Health, Housing, and student-friendly
- Discipline:
- Social Sciences
6Works -
Transmission of Oral microbiome and Sequencing
User Collection- Creator:
- Lee, Kyu Han
- Description:
- De-identified participant data from household transmission study of influenza in Nicaragua Oligotype count table and taxonomic classifications
- Keyword:
- Influenza and Microbiome
- Discipline:
- Health Sciences
2Works -
Preterm Birth
User Collection- Creator:
- Betsy Foxman
- Description:
- This collection has been retired as of Sept 28. 2020 and replaced with the "Preterm Birth" work listed below.
- Discipline:
- Health Sciences
1Works -
- Creator:
- Gonzales, Wilkinson Daniel Wong
- Description:
- The Lannang Corpus (LanCorp) is a sociolinguistic POS-tagged 375,000-word speech-and-text corpus of Lannang languages based on audio recordings collected in metropolitan Manila between 2016 and 2020. It hopes to furnish scholars interested in Sino-Philippine (socio)linguistics with a contemporary, multilingual corpus (i.e., Hokkien, Tagalog, English, Lánnang-uè, Mandarin) compiled using recorded oral data primarily collected from a Sino-Philippine community in metropolitan Manila by the community: the Manila Lannangs. The publicly available corpus contains manual transcriptions (time-aligned to the audio), source language and part-of-speech tags derived using a mix of manual and computational methods, and a wide range of social metadata; it is also organized and stored systematically for easy data retrieval and (socio)linguistic analysis. Although there are existing sociolinguistic corpora, they are small in scale and were not released publicly due to lack of informant consent – LanCorp readily fills the gap.
- Keyword:
- Lannang, Chinese Filipino, Filipino-Chinese, Hokkien, diaspora, mixed language, recordings, oral variety, multilingual, corpus, data, dataset, databank, LanCorp, Lannang Corpus, sociolinguistics, and ELAN
- Citation to related publication:
- [1] Gonzales, Wilkinson Daniel Wong. 2021. Interactions of Sinitic languages in the Philippines: Sinicization, Filipinization, and Sino-Philippine language creation. The Palgrave handbook of Chinese language studies, ed. by Zhengdao Ye. London: Palgrave-MacMillan., [2] Gonzales, Wilkinson Daniel Wong. 2021. Filipino, Chinese, neither, or both? The Lannang identity and its relationship with language. Language & Communication 77., [3] Gonzales, Wilkinson Daniel Wong. 2022. “Truly a Language of Our Own” A Corpus-Based, Experimental, and Variationist Account of Lánnang-uè in Manila. Ann Arbor: University of Michigan Ph.D. dissertation., [4] Gonzales, Wilkinson Daniel Wong. 2022. Hybridization. Philippine English: Development, Structure, and Sociology of English in the Philippines, ed. by Ariane Macalinga Borlongan. London: Routledge., and [5] Gonzales, Wilkinson Daniel Wong. in preparation. Advancing Sino-Philippine (socio)linguistics using the Lannang Corpus (LanCorp) – a multilingual, POS-tagged, and audio-textual databank.
- Discipline:
- Social Sciences
-
- Creator:
- Cuyler, Antonio, Carruthers, Matthew, and Imbesi, Jason
- Description:
- we conducted an emergent qualitative systematic content analysis of scholarship published in Cultural Trends, the International Journal of Cultural Policy, and the Journal of Arts Management, Law, and Society since the peer-reviewed journals’ inceptions.
- Keyword:
- content analysis, cultural policy, and oppression
- Discipline:
- Humanities and Arts
-
- Creator:
- Bacon, Elizabeth, Hanson, Erika N., Austin, Sarah, Delacroix, Emerson, Uhlmann, Wendy, Roberts, Scott, and Resnicow, Ken
- Description:
- Survey respondents were cancer-affected patients seen at an academic medical center, and self-reported experiences with genetic testing and counseling. This is raw dataset is saved in comma separated value (.csv) format.
- Keyword:
- Genetic Testing, Clinician Recommandation , NCCN Guidelines, Hereditary Genetic Testing, and Disparities in Genetic Counseling
- Citation to related publication:
- American Association of Kidney Patients: A List of Support Groups in Michigan. https://aakp.org/wp-content/uploads/2020/06/Support-Groups-Michigan.pdf
- Discipline:
- Science and Health Sciences
-
- Creator:
- George De la Rosa, Mery Vet, Patel, Dipali, McCann, Marc R., Stringer, Kathleen A., and Rosania, Gus R.
- Description:
- These data were produced from a study that employed a database strategy to identify candidate mitochondrial metabolites that could be clinically useful to identify individuals at increased risk of mitochondrial-related ADRs. The main candidate metabolite identified by the database strategy was evaluated using a mouse model of mitochondrial drug toxicity. These findings are described in our manuscript: Database Screening as a Strategy to Identify Endogenous Candidate Metabolites to Probe and Assess Mitochondrial Drug Toxicity. Data reported was supported by funding from the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health (NIH) under award numbers R01GM127787 (GRR) & R35GM136312 (KAS).
- Keyword:
- mitochondrial-realted metabolites, adverse drug reactions, and mitochondrial drug toxicity
- Discipline:
- Health Sciences
-
- Creator:
- Bougher, Stephen W. and Roeten, Kali J.
- Description:
- The NASA MAVEN (Mars Atmosphere and Volatile Evolution) spacecraft, which is currently in orbit around Mars, has been taking systematic measurements of the densities and deriving temperatures in the upper atmosphere of Mars between about 140 to 240 km above the surface since late 2014. Wind measurement campaigns are also conducted once per month for 5-10 orbits. These densities, temperatures and winds change with time (e.g. solar cycle, season, local time) and location, and sometimes fluctuate quickly. Global dust storm events are also known to significantly impact these density, temperature and wind fields in the Mars thermosphere. For the current project, the derived temperatures and O plus CO2 densities are used to characterize the upper atmosphere dayside thermal and density structure. Presently, more than 6 years of Neutral Gas and Ion Mass Spectrometer (NGIMS) measurements of neutral densities have been obtained by the MAVEN team (e.g. Mahaffy et al. 2015; Bougher et al 2015; Elrod et al., 2017; 2021; Stone et al. 2018; Gupta et al., 2021). Measured neutral density distributions are compared to simulations from a computer model of the Mars atmosphere called M-GITM (Mars Global Ionosphere-Thermosphere Model), developed at U. of Michigan. Since the global circulation plays a role in the structure, variability, and evolution of the atmosphere, understanding the processes that drive the winds in the upper atmosphere of Mars also provides the needed context for understanding density and temperature distributions and how the atmosphere behaves as a whole system. Three dimensional M-GITM simulations for extreme Mars seasonal and solar cycle conditions were conducted for detailed comparisons with NGIMS derived temperatures and O/CO2 ratio distributions (Bougher et al. 2022). Extracted model densities and temperatures along the MAVEN inbound trajectory of each orbit path (between ~300 km and periapsis) are provided in this Deep Blue Data archive. Corresponding M-GITM heat balance terms are also provided in vertical 1-D tabulated formats. README files are included for each suite of 1-D "flythru" tables, detailing the contents of each file. In addition, a general README file is provided that summarizes the inputs and outputs of the M-GITM code simulations for this study. Finally, a basic version of the M-GITM code can be found on Github at https:/github.com/dpawlows/MGITM.
- Keyword:
- Mars, NASA MAVEN Mission, NGIMS instrument , and M-GITM numerical simulations
- Citation to related publication:
- Bougher, S. W., Benna, M., Elrod, M., Roeten, K., & Thiemann, E. (2023). MAVEN/NGIMS dayside exospheric temperatures over solar cycle and seasons: Role of dayside thermal balances in regulating temperatures. Journal of Geophysical Research: Planets, 128, e2022JE007475. https://doi.org/10.1029/2022JE007475
- Discipline:
- Science
-
- Creator:
- Walsh, Lisa L
- Description:
- Stable isotope values of carbon (δ13C) and nitrogen (δ15N) from Virginia opossum (Didelphis virginiana) guard hairs were analyzed to evaluate the ecology and winter adaptations in opossums by Dr. Lisa L. Walsh as part of her Ph.D. thesis in the Ecology and Evolutionary Biology Department. The collection of stable isotope data took place from 2017 to 2019. Guard hair was processed at the University of Michigan and analyzed by the University of New Mexico Center for Stable Isotopes (UNM-CSI, USA). Captive and wild opossums were evaluated for evidence of biannual or incomplete biannual molting, a mammalian adaptation to harsh winters. Results suggest opossums do not exhibit either winter molting strategy and that guard hairs capture the opossum’s lifetime diet (Walsh and Tucker 2021). The stable isotope values were used to test the hypothesis that a Type A generalist’s niche is positively correlated with habitat heterogeneity and to evaluate which climate variables best explained isotope values. There was a positive correlation between isotopic niche size and habitat-diversity indexes (Walsh and Tucker 2020). The δ13C values from opossums in the Midwest and Northeast to test whether opossums rely on anthropogenic trash to survive extreme winters. There was no significant relationship between δ13C and winter variables, but there was a significant increase in variance of Midwest opossums’ δ13C after the 1970 corn agricultural boom (Walsh and Tucker 2023).
- Keyword:
- stable isotope, Virginia opossum, mesopredator, ecology, and mammal
- Citation to related publication:
- Walsh, L.L. and P.K. Tucker. 2020. Habitat heterogeneity is correlated with isotopic niche breadth across the range of a mammalian generalist mesopredator. Ecosphere, 11(12): e03314. https://doi.org/10.1002/ecs2.3314, Walsh, L.L. and P.K. Tucker. 2021. Stable isotope values suggest opossums (Didelphis virginiana) at their northern edge do not seasonally molt. Northeastern Naturalist, 28(1): 1-8. https://doi.org/10.1656/045.028.0101, and Walsh, L.L., and P.K. Tucker. 2023. Evaluating anthropogenic influence on a mesopredator: Opossum (Didelphis virginiana) isotope values influenced by corn agriculture more than urbanization. Canadian Journal of Zoology, 101: https://doi.org/10.1139/cjz-2021-0172.
- Discipline:
- Science
-
- Creator:
- Jenkins, G. J. and Bougher, S. W.
- Description:
- In early 2019, the Mars Atmosphere and Volatile Evolution (MAVEN) mission underwent an ~2-month aerobraking campaign, during which time the spacecraft periapsis altitude was lowered from its nominal altitude range of 140-160 km to as low as ~123 km. Excluding spacecraft walk-in/out maneuvers, accelerometer measurements were made along 272 orbits with coverage spanning Ls 340-3°, latitudes ~5-54°S, longitudes 0-360°, and Local Solar Time (LST) ~22-17 hours. In this study, we perform a diagnostic analysis of the full aerobraking data set by fitting 4-harmonic waves to mass densities. We then study the variations of these waves as a function of latitude with an emphasis on those observed previously in Mars’ thermosphere by MAVEN and other missions. Additionally, we utilize data collected during the same time period from the Mars Reconnaissance Orbiter’s Mars Climate Sounder to study the vertical propagation of waves originating from the middle atmosphere. Key results indicate that normalized wave amplitudes decrease with latitude, and this is consistent with the latitudinal structure of a diurnal Kelvin mode. We also observe that waves imprinted from the middle atmosphere show normalized amplitude growth with increasing altitude. A complete summary of data sets, analysis methodology, and scientific results is given. The purpose of this study is to add to the body of knowledge surrounding Martian atmospheric wave features and to provide further constraints for future numerical modeling and subsequent tidal mode identification.
- Keyword:
- MAVEN, Mars Thermosphere, Accelerometer Data Set, Global Data Set, and Wave Analysis of Tides
- Citation to related publication:
- Jenkins, G. A., Bougher, S. W., Lugo, R., Tolson, R. H., Zurek, R. W., Baird, D., Steele, L., Kass, D., Withers, P. (2023), MAVEN Accelerometer Observations of Thermospheric Densities during Aerobraking and Deep Dip 2: Wave Features and Connections to Upward Propagating Thermal Tides, Journal of Geophysical Research: Planets, xx, xx.
- Discipline:
- Science
-
Mound survey
User Collection- Creator:
- Galaty, Michael
- Description:
- TBD
- Keyword:
- archaeology
- Discipline:
- Humanities and Social Sciences
0Works -
- Creator:
- Title, Pascal O. and Bemmels, Jordan B.
- Description:
- The ENVIREM dataset v1.0 is a set of 16 climatic and 2 topographic variables that can be used in modeling species' distributions. The strengths of this dataset include their close ties to ecological processes, and their availability at a global scale, at several spatial resolutions, and for several time periods. The underlying temperature and precipitation data that went into their construction comes from the WorldClim dataset ( www.worldclim.org), and the solar radiation data comes from the Consortium for Spatial Information ( www.cgiar-csi.org). The data are compatible with and expand the set of variables from WorldClim v1.4 ( www.worldclim.org). For more information, please visit the project website: envirem.github.io
- Keyword:
- raster, species distribution modeling, and bioclimatic
- Citation to related publication:
- Title, P. O. and Bemmels, J. B. (2018), ENVIREM: an expanded set of bioclimatic and topographic variables increases flexibility and improves performance of ecological niche modeling. Ecography, 41: 291-307. http://doi.org/10.1111/ecog.02880
- Discipline:
- Science
-
- Creator:
- Lee, Kyu Han
- Description:
- Data include variables used to run accelerated failure time models examining the association between the nose/throat microbiome and 1) symptom duration, 2) shedding duration, and 3) time to infection. Certain individual participant data have been excluded due to identifiability concerns. Data also include the oligotype count table and taxonomic classifications.
- Keyword:
- Influenza and Microbiome
- Citation to related publication:
- Lee KH, Gordon A, Shedden K, Kuan G, Ng S, Balmaseda A, Foxman B. The respiratory microbiome and susceptibility to influenza virus infection. PloS One. 2019;14:e0207898. https://doi.org/10.1371/journal.pone.0207898
- Discipline:
- Health Sciences
-
- Creator:
- Figueroa, C. Alberto
- Description:
- This information provides the data and commands to manually setup the computational simulations used in the PLOS ONE paper 'Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome' using CRIMSON (CARDIOVASCULAR INTEGRATED MODELLING & SIMULATION) a prototype simulation environment developed under the support of the European Research Council (( http://www.crimson.software/)., Note that a Windows version of the CRIMSON flowsolver is provided as part of the CRIMSON Windows installer, but you will need a very powerful Windows computer to run these simulations, as the models used in the present work are extremely computationally-demanding. It is recommended that you use a Linux version of the CRIMSON flowsolver on a high-performance computer., Option 1 (ready-to-use files to immediately start the simulation): 1. Please unzip the Ready-to-use files. 2. Copy the folders of each of the three conditions to the high performance computer. 3. In addition to different codes used, each folder provides the boundary conditions applied in the simulations described in the manuscript (e.g. LPN parameters). To run the 3D simulations for each condition simply launch the it using the CRIMSON flowsolver. In addition, the solver.inp file can be modified to run a 0D "real-time simulation" (please open solver.inp with a text editor and modify line 4 "Simulate in Purely Zero Dimensions:" to "True")., Option 2 (using the MITK files): 1. Please download and install Crimson software ( http://www.crimson.software/). 2. Please unzip the MITK files and the Ready-to-use files. 3. From amongst the provided MITK files, load the MITK file of interest to CRIMSON (using the MITK files, additional changes can be made to the computational model in case the user wants to explore different settings/boundary conditions e.g. change the vascular wall properties, introducing a change in the geometry to create a virtual stenosis). 3. Navigate to the tree in the "Data Manager" panel and select the "Pulmonaries", "CRIMSON SOLVER" and then "Solver study 3D" items, in the described order. 4. In the right hand panel select the "CRIMSON Solver setup" tab and scroll down the right hand bar until to find the "Setup Solver" box; click to output the simulation files (faceInfo.dat, geombc.dat.1, multidomain.dat, netlist_surface.dat,numstart.dat, presolver folder, solver.inp, restart.0.1). 5. Copy and replace the geombc.dat.1 and restart.0.1 generated by CRIMSON for each individual condition to the respective unziped folder in the Ready-to-use file (discard the remaining files that were output by CRIMSON). Note that if you have not changed anything about the model (e.g. vascular wall properties), then doing this will produce restart.0.1 and geombc.dat.1 files which are identical to the ready-to-use versions. 6. Finally copy each Condition folder to the high performance computer and simply launch the simulation using the CRIMSON flowsolver., and For technical queries please contact crimson-users@googlegroups.com. --October 2018.
- Citation to related publication:
- Silva Vieira M, Arthurs CJ, Hussain T, Razavi R, Figueroa CA (2018) Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome. PLOS ONE 13(11): e0205829. https://doi.org/10.1371/journal.pone.0205829
- Discipline:
- Engineering and Health Sciences
-
- Creator:
- Zhu, Jialei, Penner, Joyce E., Yu, Fangqun, Sillman, Sanford, Andreae, Meinrat O., and Coe, Hugh
- Description:
- The dataset contains the Fortran programs applied in the latest CESM/IMPACT model as well as the data created from this model, which are used in the referenced paper.
- Keyword:
- Organic nucleation and Radiative forcing
- Citation to related publication:
- Zhu, J. et al. Decrease in radiative forcing by organic aerosol nucleation, climate, and land use change. Nature Communications 10, 423 (24 January 2019). https://doi.org/10.1038/s41467-019-08407-7
- Discipline:
- Science
-
- Creator:
- Yan, Haoyang MI and Yates, J Frank
- Description:
- The research aims to demonstrate judgment accuracy about other individuals' socio-political opinions produced by prototype matching and base/shift heuristics or people's own strategies (control).
- Keyword:
- judgment accuracy and socio-political opinions
- Discipline:
- Social Sciences
-
- Creator:
- Haydar, Bishr and MacEachern, Mark
- Description:
- The research adheres to PRISMA-HARM recommendations for systematic reviews. The reproducible search strategies for all databases, the citation export files from all databases, and the eligibility screening decisions are included in the dataset.
- Keyword:
- Systematic review, Patient transportation, intrahospital, intra-hospital, and Critically ill patients
- Citation to related publication:
- Haydar B, Baetzel A, Elliott A, MacEachern M, Kamal A, Christensen R. Adverse Events During Intrahospital Transport of Critically Ill Children: A Systematic Review. Anesth Analg. 2019. http://dx.doi.org/doi:10.1213/ANE.0000000000004585
- Discipline:
- Health Sciences
-
- Creator:
- Heath, Jeffrey
- Description:
- Jalkunan is an endangered language of the Mande family, spoken in the village cluster of Blédougou in southwestern Burkina Faso. The lexical work complements a published grammar with texts. See the readme for further information.
- Keyword:
- Jalkunan, Burkina Faso, Mande languages, and Lexicon
- Citation to related publication:
- Heath, Jeffrey. A grammar of Jalkunan (Mande, Burkina Faso). 2017. http://hdl.handle.net/2027.42/139025
- Discipline:
- Humanities
-
- Creator:
- Heath, Jeffrey, Hantgan, Abbie , and Elders, Stefan
- Description:
- The work on the Bangime language, spoken by the Bangande people, was carried out as part of a larger linguistic fieldwork project focused on Dogon languages. Bangime is confirmed as a language isolate with no demonstrable linguistic relatives—possibly the only such isolate in West Africa.
- Keyword:
- Bangime, Mali, and Lexicon
- Citation to related publication:
- Heath & Hantgan. A grammar of Bangime. Berlin: de Gruyter, 2018. ISBN 978-3-11-055749-7
- Discipline:
- Humanities
-
- Creator:
- Heath, Jeffrey , Ouattara, Aminata , and Hantgan, Abbie
- Description:
- Our project, mainly on Dogon languages of Mali, has branched out to Burkina Faso with emphasis on documentation of the most endangered languages. Tiefo-N was studied on an emergency basis since it was down to two aging competent speakers. For additional comments and links to a reference grammar, see the readme file.
- Keyword:
- Gur languages, Tiefo, Tiefo-N language, and Lexicon
- Citation to related publication:
- Jeffrey Heath, Aminata Ouattara & Abbie Hantgan. Short grammar of Tiefo-N of Nyafogo (Gur, Burkina Faso). Language Description Heritage Library (MPI). http://ldh.clld.org/2017/01/01/escidoc2378140/ and A copy of this publication is also available in Deep Blue: http://dx.doi.org/10.17617/2.2378140
- Discipline:
- Humanities
-
- 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
-
- Creator:
- Crisp, Dakota N., Cheung, Warwick, Gliske, Stephen V., Lai, Alan, Freestone, Dean R., Grayden, David B., Cook, Mark J., and Stacey, William C.
- Description:
- The data and the scripts are to show that seizure onset dynamics and evoked responses change over the progression of epileptogenesis defined in this intrahippocampal tetanus toxin rat model. All tests explored in this study can be repeated with the data and scripts included in this repository. and Dataset citation: Crisp, D.N., Cheung, W., Gliske, S.V., Lai, A., Freestone, D.R., Grayden, D.B., Cook, MJ., Stacey, W.C. (2019). Epileptogenesis modulates spontaneous and responsive brain state dynamics [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/r6vg-9658
- Keyword:
- evoked response, stimulation, bifurcation, epilepsy, seizure, divergence, and dynamics
- Citation to related publication:
- Crisp, D. N., Cheung, W., Gliske, S. V., Lai, A., Freestone, D. R., Grayden, D. B., Cook, M. J., & Stacey, W. C. (2020). Quantifying epileptogenesis in rats with spontaneous and responsive brain state dynamics. Brain Communications, 2(1). https://doi.org/10.1093/braincomms/fcaa048
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- Nasser, Ahmad and Gumise, Wonder
- Description:
- The work on accelerating authenticated boot for embedded system resulted in designing an algorithm in python to perform the random address generation and cryptographic MAC calculation. The Sampled Boot schemes implemented in this package allow a significant reduction of the time needed to authenticate firmware images during startup, while still retaining a high degree of trust. This is particularly useful for automotive applications in which startup time constraints make secure boot a time prohibitive process. and Citation for this dataset: Nasser, A., Gumise, W. (2019). Authenticated Boot Acceleration Algorithm [Code and data]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/yeh1-1x17
- Keyword:
- Trusted Computing, IOT security, Embedded Security, and Cyber Physical Systems
- Citation to related publication:
- Nasser, A., Gumise, W., and Ma, D., "Accelerated Secure Boot for Real-Time Embedded Safety Systems," SAE Int. J. Transp. Cyber. & Privacy 2(1) : 35-48, 2019, https://doi.org/10.4271/11-02-01-0003
- Discipline:
- Science
-
- Creator:
- Siegel, Jason B. , Stefanopoulou, Anna G., and McKahn, Denise (McKay)
- Description:
- This section contains work related to the modeling of voltage degradation in a 24 cell PEM fuel cell stack with 300 cm2 cross-sectional area. The experimental hardware used to validate the model consists of a computer controlled system that coordinates air, hydrogen, cooling, and electrical subsystems to operate the stack. Dry hydrogen is pressure regulated for full utilization in the dead-ended anode. Using a solenoid valve, the anode is periodically purged to recover the gradual degradation in voltage. A membrane based humidifier controls the vapor content of the cathode gas stream while a mass flow controller is used to regulate the flow to the desired stoichiometry.
- Citation to related publication:
- Denise A. McKay, Jason B. Siegel, William Ott, and Anna G. Stefanopoulou. Parameterization and prediction of temporal fuel cell voltage behavior during flooding and drying conditions. Journal of Power Sources, 178(1):207 - 222, 2008. https://doi.org/10.1016/j.jpowsour.2007.12.031
- Discipline:
- Engineering
-
- Creator:
- Bowen Li, Yiling Zhang, Siqian Shen, and Johanna Mathieu
- Description:
- The project outputs summarize all the publications, talks, and codes we accomplished under this NSF funding. In the project, we develop methodologies to manage uncertainty in future electric power systems and quantify how uncertainty affects power system sustainability. and Talks, papers, and poster in Deep Blue: http://hdl.handle.net/2027.42/149653
- Keyword:
- chance constraint, distributionally robust optimization, optimal power flow, demand response, and unimodality
- Citation to related publication:
- B. Li and J. L. Mathieu, "Analytical reformulation of chance-constrained optimal power flow with uncertain load control," 2015 IEEE Eindhoven PowerTech, Eindhoven, 2015, pp. 1-6. https://doi.org/10.1109/PTC.2015.7232803, B. Li, J. L. Mathieu and R. Jiang, "Distributionally Robust Chance Constrained Optimal Power Flow Assuming Log-Concave Distributions," 2018 Power Systems Computation Conference (PSCC), Dublin, 2018, pp. 1-7. https://doi.org/10.23919/PSCC.2018.8442927, B. Li, M. Vrakopoulou and J. L. Mathieu, "Chance Constrained Reserve Scheduling Using Uncertain Controllable Loads Part II: Analytical Reformulation," in IEEE Transactions on Smart Grid, vol. 10, no. 2, pp. 1618-1625, March 2019. https://doi.org/10.1109/TSG.2017.2773603, B. Li, R. Jiang and J. L. Mathieu, "Distributionally Robust Chance-Constrained Optimal Power Flow Assuming Unimodal Distributions With Misspecified Modes," in IEEE Transactions on Control of Network Systems, vol. 6, no. 3, pp. 1223-1234, Sept. 2019. https://doi.org/10.1109/TCNS.2019.2930872, B. Li, R. Jiang and J. L. Mathieu, "Distributionally robust risk-constrained optimal power flow using moment and unimodality information," 2016 IEEE 55th Conference on Decision and Control (CDC), Las Vegas, NV, 2016, pp. 2425-2430. https://doi.org/10.1109/CDC.2016.7798625, B. Li, S. D. Maroukis, Y. Lin and J. L. Mathieu, "Impact of uncertainty from load-based reserves and renewables on dispatch costs and emissions," 2016 North American Power Symposium (NAPS), Denver, CO, 2016, pp. 1-6. https://doi.org/10.1109/NAPS.2016.7747830, G. Martínez, J. Liu, B. Li, J. L. Mathieu and C. L. Anderson, "Enabling renewable resource integration: The balance between robustness and flexibility," 2015 53rd Annual Allerton Conference on Communication, Control, and Computing (Allerton), Monticello, IL, 2015, pp. 195-202. https://doi.org/10.1109/ALLERTON.2015.7447004, J. Liu, M. G. Martinez, B. Li, J. Mathieu and C. L. Anderson, "A Comparison of Robust and Probabilistic Reliability for Systems with Renewables and Responsive Demand," 2016 49th Hawaii International Conference on System Sciences (HICSS), Koloa, HI, 2016, pp. 2373-2380. https://doi.org/10.1109/HICSS.2016.297, Li, B., Jiang, R. & Mathieu, J.L. "Ambiguous risk constraints with moment and unimodality information." Math. Program. 173, 151–192 (2019). https://doi.org/10.1007/s10107-017-1212-x, M. Vrakopoulou, B. Li and J. L. Mathieu, "Chance Constrained Reserve Scheduling Using Uncertain Controllable Loads Part I: Formulation and Scenario-Based Analysis," in IEEE Transactions on Smart Grid, vol. 10, no. 2, pp. 1608-1617, March 2019. https://doi.org/10.1109/TSG.2017.2773627, Y. Zhang, S. Shen and J. L. Mathieu, "Data-driven optimization approaches for optimal power flow with uncertain reserves from load control," 2015 American Control Conference (ACC), Chicago, IL, 2015, pp. 3013-3018. https://doi.org/10.1109/ACC.2015.7171795, Y. Zhang, S. Shen and J. L. Mathieu, "Distributionally Robust Chance-Constrained Optimal Power Flow With Uncertain Renewables and Uncertain Reserves Provided by Loads," in IEEE Transactions on Power Systems, vol. 32, no. 2, pp. 1378-1388, March , and Y. Zhang, S. Shen, B. Li and J. L. Mathieu, "Two-stage distributionally robust optimal power flow with flexible loads," 2017 IEEE Manchester PowerTech, Manchester, 2017, pp. 1-6. https://doi.org/10.1109/PTC.2017.7981202
- Discipline:
- Engineering
-
- Creator:
- Linyan, Xiang and Oleg, Zikanov
- Description:
- The Liquid Metal Battery (LMB), a promising energy-storage device that contains liquid-metal interior, is studied numerically in the paper. The metal pad roll instability was modeled based on the open-source CFD software, OpenFOAM. It's based on the solver for simulations of incompressible multiphase flows multiphaseInterFoam modified to include the electromagnetic fields and account for the sharp variations of the electrical conductivity.
- Keyword:
- Liquid metal battery, Interfacial waves, Instability, and OpenFOAM
- Citation to related publication:
- Linyan Xiang (相林言) and Oleg Zikanov, “Numerical simulation of rolling pad instability in cuboid liquid metal batteries,” Physics of Fluids, vol. 31, no. 12, p. 124104, 2019, https://doi.org/10.1063/1.5123170 and Oleg Zikanov, "Shallow water modeling of rolling pad instability in liquid metal batteries." Theoretical and Computational Fluid Dynamics, 32, 325–347, 2018, https://doi.org/10.1007/s00162-018-0456-2
- Discipline:
- Science
-
- 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 and Jiao, Z., Chen, Y., Manchester, W. (2020). Data for Solar Flare Intensity Prediction with Machine Learning Models [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/b07j-bj08
- Discipline:
- Engineering and Science
-
- Creator:
- Tronson, Natalie C and Tchessalova, Daria
- Description:
- The main goal of this research was to identify potential molecular pathways that contribute to memory dysregulation and decline that persists long after illness or inflammation. We have previously established a subchronic immune challenge model that results in memory impairments months after the inflammatory challenge. This project aimed to determine whether memory impairments were accompanied by transcriptional dysregulation in memory related brain region (the hippocampus). These data show the differential gene expression as log2fold change (and p-value) in males and females 3 months after immune challenge (Supp Tables 1 and 2); after a subsequent immune challenge (Supp Tables 3 and 4); the differential regulation of genes in males and females (Supp Table 5); genes differentially expressed in the hippocampus of males and females at baseline (Supp Table 6) and the differential regulation of those genes in males and females after immune challenge (Supp Tables 7,8).
- Keyword:
- hippocampus, lipopolysaccharide, differential gene expression, RNA sequencing, neuroimmune, sex differences, learning and memory, and inflammation
- Citation to related publication:
- Tchessalova, D., & Tronson, N. C. (2019). Enduring and sex-specific changes in hippocampal gene expression after a subchronic immune challenge. BioRxiv, 566570. https://doi.org/10.1101/566570
- Discipline:
- Science and Health Sciences
-
- Creator:
- Gebarski, Benjamin B. and Becker, Udo
- Description:
- Files are uploaded as crystallographic information files (.cif), the standard text file format for representing crystallographic information. These files contain the optimized molecular models for pentavalent plutonium incorporation reactions into/onto barite, anglesite, celestine, anhydrite, aragonite, and calcite host minerals.
- Keyword:
- actinide, quantum mechanics, molecular model, plutonium, incorporation, surface, radioactive, contamination, and nuclear waste
- Citation to related publication:
- Gebarski, B. B. and Becker, U. Quantum-Mechanical Determination of the Incorporation of Pentavalent Plutonium into Carbonate and Sulfate Minerals. (2019) Geochimica et Cosmochimica Acta. https://doi.org/10.1016/j.gca.2019.10.015
- Discipline:
- Science
-
- 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
-
- Creator:
- Holmes, Patrick
- Description:
- This work was collected to evaluate Stability Basins for characterizing the limits of human stability during Sit-to-Stand. and MATLAB code was used to process the data into individual trials. Trials are labeled by Sit-to-Stand type (Natural, Momentum-Transfer, or Quasi-Static) and experimental condition. MATLAB code for analyzing the data and computing Stability Basins is provided. A GUI is provided to animate a subject's movement and display projections of the Stability Basins in the horizontal and vertical planes.
- Keyword:
- biomechanics, mathematical model, locomotion, fall risk, reachability, and feedback control
- Citation to related publication:
- https://arxiv.org/abs/1908.01876 and Holmes, P. D., Danforth, S. M., Fu, X.-Y., Moore, T. Y., & Vasudevan, R. (n.d.). Characterizing the limits of human stability during motion: Perturbative experiment validates a model-based approach for the Sit-to-Stand task. Royal Society Open Science, 7(1), 191410. https://doi.org/10.1098/rsos.191410
- Discipline:
- Engineering
-
- Creator:
- Hatch, Nan E.
- Description:
- Crouzon FGFR2-C342Y/+ and wild type littermate pups on a C57BL/6 congenic background were injected with lentivirus expressing recombinant TNAP enzyme or phosphate buffered saline shortly after birth. Mice were euthanized 3 weeks after birth for analyses.
- Keyword:
- craniofacial, bone, craniosynotosis, FGFR2, TNAP tissue nonspecific alkaline phosphatase, mouse model, and development
- Citation to related publication:
- Nam, H. K., Vesela, I., Schutte, S. D., & Hatch, N. E. (2020). Viral delivery of tissue nonspecific alkaline phosphatase diminishes craniosynostosis in one of two FGFR2C342Y/+ mouse models of Crouzon syndrome. PLOS ONE, 15(5), e0234073. https://doi.org/10.1371/journal.pone.0234073
- Discipline:
- Health Sciences
-
- Creator:
- Ahluwalia, Vinayak S., Steimle, Lauren N., and Denton, Brian T.
- Description:
- This repository includes test instances of infinite-horizon Markov decision processes with multiple models of parameters (i.e., "Multi-model Markov decision processes"). We generated each test instance in the dataset using a Python script. The test instances can be read in using the provided C++ and Python script. See the README for details.
- Keyword:
- Markov decision processes, mixed-integer programming, stochastic programming, and dynamic programming
- Citation to related publication:
- Ahluwalia, Steimle, and Denton. "Policy-based branch-and-bound for infinite-horizon Multi-model Markov decision processes". 2020.
- Discipline:
- Engineering
-
- Creator:
- Whitaker, Steven T., Nataraj, Gopal, Nielsen, Jon-Fredrik, and Fessler, Jeffrey A.
- Description:
- File: P,jf06Sep2019,mese.7 The multi-echo spin echo (MESE) data was acquired using a 3D acquisition with an initial 90 degree excitation pulse followed by 32 refocusing (180 degree) pulses, resulting in 32 echoes with echo spacing of 10 ms. The repetition time of the sequence was 1200 ms. Each refocusing pulse was flanked by crusher gradients to impart 14 cycles of phase across the imaging volume. The initial excitation pulse had time-bandwidth product of 6, duration of 3 ms, and slab thickness of 0.9 cm, and each refocusing pulse had time-bandwidth product of 2, duration of 2 ms, and slab thickness of 2.1 cm. The scan took 36 min 11 s and covered a field of view (FOV) of 22 x 22 x 0.99 cm^3 with matrix size 200 x 200 x 9., File: P,jf06Sep2019,b1.7 The Bloch-Siegert (BS) scans were acquired using a 3D acquisition. The excitation pulse of these scans had time-bandwidth product of 8 and duration of 1 ms. The pair of scans used +/-4 kHz off-resonant Fermi pulses between excitation and readout. The BS scans took 2 min 40 s in total and covered a FOV of 22 x 22 x 0.99 cm^3 with matrix size 200 x 50 x 9., File: P,jf06Sep2019,mwf.7 The small-tip fast recovery (STFR) scans were acquired using a 3D acquisition. The first two and last two scans were pairs of spoiled gradient-recalled echo (SPGR) scans with echo time difference of 2.3 ms. (In the related paper, only the first set was used, i.e., only 11 of the 13 scans were used.) The remaining scans used scan parameters that were optimized to minimize the Cramer-Rao Lower Bound (CRLB) of estimates of myelin water fraction (MWF). The RF pulses had time-bandwidth product of 8 and duration of 1 ms. Each pair of SPGR scans took 58 s and the nine STFR scans took 3 min 36 s for a total scan time of 5 min 32 s (4 min 34 s if one pair of SPGR scans is ignored). The scans covered a field of view (FOV) of 22 x 22 x 0.99 cm^3 with matrix size 200 x 200 x 9., File: meseslice5.mat Contains the 32 echoes of the MESE image data for the middle slice of the imaging volume. Saved using Mathworks MATLAB R2019a., File: b1slice5.mat Contains the transmit field inhomogeneity map for the middle slice of the imaging volume., File: recon.jld Key "img" contains the 11 STFR images for the middle slice of the imaging volume. Key "b0map" contains a field map estimated from the two SPGR scans. Key "mask" contains a mask of the voxels for which to estimate MWF. Key "T1img" contains a T1-weighted image for anatomical reference., File: headmask.mat Contains a mask for visualizing just the brain (ignores the skull) for the middle slice of the imaging volume., File: rois.mat Contains masks for various regions of interest (ROIs), used for computing statistics. Keys "mtopleft", "mtopright", "mbottomleft", and "mbottomright" refer to the corresponding locations on the anatomical reference image (see related paper). Key "mic" refers to the internal capsules, and key "mgm" refers to a gray matter ROI., The raw data files (P-files) can be read into the Julia programming language using the Julia version of the Michigan Image Reconstruction Toolbox ( https://github.com/JeffFessler/MIRT.jl) or into MATLAB using TOPPE ( https://github.com/toppeMRI/toppe). The reconstructed slices used in the related paper are provided for convenience, and are stored in .mat files that can be loaded into Julia (using the package MAT.jl) or MATLAB, and a .jld file that can be loaded into Julia (using the package JLD.jl). The Julia code for processing the data to create MWF maps is hosted publicly on GitHub at https://github.com/StevenWhitaker/STFR-MWF., and Files: toppe-master.zip and MIRT.jl-master.zip are archived versions of the TOPPE and Michigan Image Reconstruction Toolbox code sets from GitHub as of 2/28/2020.
- Keyword:
- myelin, machine learning, kernel learning, magnetic resonance imaging, and scan design
- Citation to related publication:
- Whitaker, S. T., Nataraj, G., Nielsen, J.-F., & Fessler, J. A. (2020). Myelin water fraction estimation using small-tip fast recovery MRI. Magnetic Resonance in Medicine, 84(4), 1977–1990. https://doi.org/10.1002/mrm.28259
- Discipline:
- Health Sciences and Engineering
-
- Creator:
- Liemohn, Michael W
- Description:
- The editorial decision process for the Journal of Geophysics Research Space Physics is assisted by over 1,000 scientists every year, providing over 3,000 reviews per year. These statistics are presented for the years 2013 through 2018, showing some fluctuations but, overall, consistency in the response of the space physics research community to requests to serve as manuscript reviewers. Over half of these reviews are submitted on time, and the average time to review actually dropped as the load increased. This is greatly appreciated and the community is to be commended and thanked for their willingness to help make this journal thrive and remain a premiere publication in the field.
- Keyword:
- Editorial and reviewer statistics
- Citation to related publication:
- Liemohn, M. W. (2020). Editorial: Multiyear analysis of JGR Space Physics reviewing statistics. Journal of Geophysical Research Space Physics, 125, e2019JA027719. https://doi.org/10.1029/2019JA027719
- Discipline:
- Science
-
- Creator:
- Moniri, Saman, Xiao, Xianghui, and Shahani, Ashwin J.
- Description:
- The data is comprised of 22 directories, each housing a .hdf file of the X-ray projections recorded during solidification of Al-Si-Cu-Sr. The flat and dark projections are also included as two separate .hdf files (total file count: 24). The raw data file is in .hdf format and can be reconstructed into .tiff, e.g., by using the TomoPy toolbox in Python.
- Keyword:
- Crystallization, growth modifiers, silicon, in situ, X-ray tomography
- Citation to related publication:
- Wang, Y., Gao, J., Ren, Y., De Andrade, V., & Shahani, A. J. (2020). Formation of a Three-Phase Spiral Structure Due to Competitive Growth of a Peritectic Phase with a Metastable Eutectic. JOM, 72(8), 2965–2973. https://doi.org/10.1007/s11837-020-04237-x
- Discipline:
- Engineering
-
- Creator:
- Moser, Carol, Schoenebeck, Sarita , and Resnick, Paul
- Description:
- These data, survey instruments (including informed consent) and analysis scripts come from Carol Moser's dissertation titled, Impulse Buying: Designing for Self-Control with E-commerce.
- Keyword:
- Impulse Buying, Self-control, and Experimental Design
- Discipline:
- Social Sciences
-
- Creator:
- Arbic, Brian K. and Luecke, Conrad A.
- Description:
- The locations ("locs") files in this directory contain indices pointing to the locations in the CMA superset datafiles that were used in the Luecke et al. 2020 comparison of HYCOM and MITgcm model output to CMA observations.
- Keyword:
- Physical oceanography, Numerical modeling, Ocean modeling, Model/data comparisons, and Internal gravity waves
- Citation to related publication:
- Luecke, C. A., Arbic, B. K., Richman, J. G., Shriver, J. F., Alford, M. H., Ansong, J. K., Bassette, S. L., Buijsman, M. C., Menemenlis, D., Scott, R. B., Timko, P. G., Voet, G., Wallcraft, A. J., & Zamudio, L. (2020). Statistical Comparisons of Temperature Variance and Kinetic Energy in Global Ocean Models and Observations: Results From Mesoscale to Internal Wave Frequencies. Journal of Geophysical Research: Oceans, 125(5), e2019JC015306. https://doi.org/10.1029/2019JC015306
- Discipline:
- Science
-
- Creator:
- Agrawal, Mayank and Glotzer, Sharon C
- Description:
- Micron-scale robots require systems that can morph into arbitrary target configurations controlled by external agents such as heat, light, electricity, and chemical environment. Achieving this behavior using conventional approaches is challenging because the available materials at these scales are not programmable like their macroscopic counterparts. To overcome this challenge, we propose a design strategy to make a robotic machine that is both programmable and compatible with colloidal-scale physics. Our strategy uses motors in the form of active colloidal particles that constantly propel forward. We sequence these motors end-to-end in a closed chain forming a two-dimensional loop that folds under its mechanical constraints. We encode the target loop shape and its motion by regulating six design parameters, each scale-invariant and achievable at the colloidal scale. The research dataset includes simulation, visualization, and analysis scripts and results generated for the 2D chain loops of self-propelling particles. File Description:, -- arrows_folding - Contains the data for the folded chain loop shapes resembling an arrowhead., -- bending_vs_variation - Contains the data to study the stability of a particular shape in simulations as one of the segments of the shape bends and/or the distribution of propulsion on it varies., -- curved_triangle - Contains the data to study motion and bending of a triangle shape made using chain loop., -- example_shapes - Contains data for various examples of shapes that can be generated by designing the chain loops., -- nskT_vs_fakT - Contains the data for a specific shape to study the effect of scaling up the number of particles (governed by ns) and the propulsion (governed by fa) in its chain., -- stability - Contains the data and theoretical model (stability.py) to study the stability of the six different shapes., -- tuning_design_forM - Contains the data for sequential tuning the design parameters to fold the shape "M" as described in the corresponding publication., and -- two_neighboring_cds_segments_ - Contains the data to study a system of two neighboring chain segments with respect to different parameters discussed in the publication.
- Keyword:
- active particles, colloidal robotics, design, kilobots, and morphological control
- Citation to related publication:
- Agrawal, M, Glotzer SC. (2020). Scale-free, programmable design of morphable chain loops of kilobots and colloidal motors. PNAS. www.pnas.org/cgi/doi/10.1073/pnas.1922635117
- Discipline:
- Engineering
-
- Creator:
- Sugrue, Dennis P.
- Description:
- This data was collected and processed as part of ongoing research to characterize waterway infrastructure performance in the Great Lakes. These dataset enable researchers to evaluate both travel time and vessel carrying capacity in the waterway., I assembled AIS data from the MarineCadastre website for UTM Zones 15-18 for the years 2015-2017 available in csv format. I combined files for Navigation Seasons, defined as March to January and clipped data for a set of predefined features using a python code (AIS Data Processor.ipynb). The code writes the appended and clipped files to csv for a single Navigation Year. The written files are submitted here: Trimmed_NY2015_new.csv (n=13,228,824); Trimmed_NY2016_new.csv (n=18,782,779); Trimmed_NY2017_new.csv (n=16,816,603), Data fusion of AIS and LPMS used the following algorithm for a subset of 30 vessels on the waterway. Let A be the original AIS data and let B be the subset of records for vessel i within geographic feature j. The script for this analysis is attached (Maritime Data Fusion.ipynb), For Connecting Channels and select segments of the Great Lakes: 1. Subset A for vessel i. Let B_i⊆A | 2. Subset B_i in geographic feature, Gj. Let B_ij⊆B_i | 3. Select tmin for each unique date or any consecutive dates, record as vessel i arrival to feature j, b_ijt | 4. IF feature j is a harbor or lock, select tmax for each unique date or any consecutive dates, record as departure from feature j, b_ijt | 5. Calculate time elapsed between features for each vessel, For vessel passage through the Soo Locks: 1. Subset A for vessel i. Let B_i⊆A | 2. Subset B_i in geographic boundaries (46.5<Lat<46.6, -84.4<Lon<-84.3). Let C_(i,lock)⊆B_i | 3. Select tmin for each unique date or any consecutive dates, record as arrival to Soo Locks | 4. Select tmax for each unique date or any consecutive dates, record as departure to Soo Locks | 5. Calculate time delta between arrival and departure times, and The merged dataset is included here along with the raw LPMS data: Merged_Data_new.csv (n=42,021), LPMS obscured.csv (n=55,342). VesselNames have been obscured in these datasets to protect proprietary information for shipping companies.
- Keyword:
- Maritime Transportation Efficiency, Data Fusion, Waterway Performance
- Citation to related publication:
- Sugrue, D., Adriaens, P. (in review) Multi-dimensional Data Fusion to Evaluate Waterway Performance: Maritime Transport Efficiency of Iron Ore on the Great Lakes. Water Resources Research.
- Discipline:
- Engineering
-
- 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, Y., Tóth, G., Hietala, H., Vines, S. K., Zou, Y., Nishimura, Y., Silveira, M. V. D., Guo, Z., Lin, Y., & Markidis, S. (2020). Magnetohydrodynamic With Embedded Particle-In-Cell Simulation of the Geospace Environment Modeling Dayside Kinetic Processes Challenge Event. Earth and Space Science, 7(11), e2020EA001331. https://doi.org/10.1029/2020EA001331 and 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
-
- Creator:
- Swiger, Brian M., Liemohn, Michael W., and Ganushkina, Natalia Y.
- Description:
- We sampled the near-Earth plasma sheet using data from the NASA Time History of Events and Macroscale Interactions During Substorms mission. For the observations of the plasma sheet, we used corresponding interplanetary observations using the OMNI database. We used these data to develop a data-driven model that predicts plasma sheet electron flux from upstream solar wind variations. The model output data are included in this work, along with code for analyzing the model performance and producing figures used in the related publication. and Data files are included in hdf5 and Python pickle binary formats; scripts included are set up for use of Python 3 to access and process the pickle binary format data.
- Keyword:
- neural network, plasma sheet, solar wind, machine learning, keV electron flux, deep learning, and space weather
- Citation to related publication:
- Swiger, B. M., Liemohn, M. W., & Ganushkina, N. Y. (2020). Improvement of Plasma Sheet Neural Network Accuracy With Inclusion of Physical Information. Frontiers in Astronomy and Space Sciences, 7. https://doi.org/10.3389/fspas.2020.00042
- Discipline:
- Science and Engineering
-
- Creator:
- James, David A. and Lokam, Nikhil
- Description:
- The object of this project is to provide researchers and students with a tool to allow them to develop an intuitive understanding of singular vectors and singular values. 2x2 matrices A with real entries map circles to ellipses; in particular, unit circles centered at the origin to ellipses centered at the origin. It is known that the points on the ellipse farthest from the origin correspond to the singular vectors of A. Users can use the GUI to enter matrices of their choice and explore to visually self-determine the singular vectors/values.
- Keyword:
- SVD, Singular Value Decomposition, Singular Vector, Singular Value, and Matrix
- Discipline:
- Science and Engineering
-
Quantifying near-surface rock strength on a regional scale from hillslope stability models - dataset
- Creator:
- Townsend, Kirk F., Gallen, Sean F., and Clark, Marin K.
- Description:
- These datasets support the findings of Townsend et al. (2020). In this article, we quantify rock strength using two novel applications of hillslope stability models, resulting in estimates of cohesive and frictional strength at the spatial scale of small watersheds. We compare these results against the direct-shear test dataset here for validation of our approach. We find that cohesive strength is dependent on the original burial depth of the sedimentary rocks studied here. The low-temperature thermochronometry data was used to assess the magnitude of burial.
- Keyword:
- Thermochronology, Thermochronometry, Direct-Shear, Landslides, Rock Strength, Landscape Evolution, and Geomorphology
- Citation to related publication:
- Townsend, K.F., Gallen, S.F., & Clark, M.K., in press, Quantifying near-surface rock strength on a regional scale from hillslope stability models: Journal of Geophysical Research Earth Surface. https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JF005665
- Discipline:
- Science
-
- Creator:
- Boles, Austin H and van der Pluijm, Ben
- Description:
- This data was generated as a chapter in the dissertation of Austin Boles.
- Keyword:
- authigenic illite, hydrogen isotopes, and 40Ar/39Ar isotopic analysis
- Citation to related publication:
- Boles, A., & Pluijm, B. van der. (2020). Locally Derived, Meteoric Fluid Infiltration Was Responsible for Widespread Late Paleozoic Illite Authigenesis in the Appalachian Basin. Tectonics, 39(7), e2020TC006137. https://doi.org/10.1029/2020TC006137
- Discipline:
- Science