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- Creator:
- Stringer, Kathleen A.
- Description:
- These data were produced from the survival analysis of the pre-treatment metabolomics data generated from the Phase II clinical trial of L-carnitine treatment for septic shock (the RACE trial - see https://clinicaltrials.gov/ct2/show/NCT01665092). The results based on respective acetylcarnitine or valine concentration are presented (pdf). The csv files contain the at risk numbers from the Kaplan-Meier survival analysis. These findings described in our manuscript: Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. and All of the metabolomics data are available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org which is supported by NIH grant U2C-DK119886 and where it has been assigned Project ID (accession number ST001319). The data can be accessed directly via its Project DOIs: (DOI: http://dx.doi.org/10.21228/M8VX0Z).
- Keyword:
- sepsis, septic shock, survival, mortality, metabolomics, and pharmacometabolomics
- Citation to related publication:
- Puskarich, M. A., Jennaro, T. S., Gillies, C. E., Evans, C. R., Karnovsky, A., McHugh, C. E., Flott, T. L., Jones, A. E., Stringer, K. A., & Investigators, O. behalf of the R. T. (2021). Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. (Preprint) https://doi.org/10.1101/2021.01.28.21250687 and Puskarich MA, Jennaro TS, Gillies CE, et al; the RACE Trial Investigators. Pharmacometabolomics identifies candidate predictor metabolites of an L-carnitine treatment mortality benefit in septic shock. Clin Transl Sci. 2021; 14: 2288–2299. https://doi.org/10.1111/cts.13088
- Discipline:
- Health Sciences
-
- Creator:
- Ludlow, Andrew
- Description:
- Single molecule long read RNA/cDNA sequencing of TERT revealed 45 TERT mRNA variants including 13 known and 32 novel variants. Among the variants, TERT Delta 2-4, which lacks exons 2-4 but retains the original open reading frame, was selected for further study. Induced pluripotent stem cells and cancer cells express higher levels of TERT Delta 2-4 compared to primary human bronchial epithelial cells. Overexpression of TERT Delta 2-4 enhanced clonogenicity and resistance to cisplatin-induced apoptosis. Knockdown of endogenous TERT Delta 2-4 in Calu-6 cells reduced clonogenicity and resistance to cisplatin. Our results suggest that TERT Delta 2-4 enhances cancer cells’ resistance to intrinsic apoptosis. RNA sequencing following knockdown of Delta 2-4 TERT indicates that translation is downregulated and that mitochondrial related proteins are upregulated compared to controls.
- Keyword:
- TERT, Alternative splicing, Telomere, and Telomerase
- Citation to related publication:
- Kim, J.J., Ahn, A., Ying, J.Y. et al. Discovery and characterization of a novel telomerase alternative splicing isoform that protects lung cancer cells from chemotherapy induced cell death. Sci Rep 15, 6787 (2025). https://doi.org/10.1038/s41598-025-90639-3
- Discipline:
- Science
-
- Creator:
- Ludlow, Andrew and Kim, Jeongjin
- Description:
- Part of the regulation of telomerase activity includes the alternative splicing (AS) of the catalytic subunit telomerase reverse transcriptase (TERT). Although a therapeutic window for telomerase/TERT inhibition exists between cancer cells and somatic cells, stem cells express TERT and rely on telomerase activity for physiological replacement of cells. Therefore, identifying differences in TERT regulation between stem cells and cancer cells is essential for developing telomerase inhibition-based cancer therapies that reduce damage to stem cells. In this study, we measured TERT splice variant expression and telomerase activity in induced pluripotent stem cells (iPSCs), neural progenitor cells (NPCs), and non-small cell lung cancer cells (NSCLC, Calu-6 cells). We observed that a NOVA1-PTBP1-PTBP2 axis regulates TERT alternative splicing (AS) in iPSCs and their differentiation into NPCs. We also found that splice-switching of TERT, which regulates telomerase activity, is induced by different cell densities in stem cells but not cancer cells. Lastly, we identified cell type-specific splicing factors that regulate TERT AS. Overall, our findings represent an important step forward in understanding the regulation of TERT AS in stem cells and cancer cells. These data and subsequent studies may reveal a splicing factor(s) or their binding site(s) that could be targeted with small molecule drugs or antisense oligonucleotides, respectively, to reduce telomerase activity in cancer cells and promote durable cancer remissions.
- Keyword:
- Telomere, telomerase, TERT, alternative RNA splicing
- Citation to related publication:
- Kim JJ, Sayed ME, Ahn A, Slusher AL, Ying JY, et al. (2023) Dynamics of TERT regulation via alternative splicing in stem cells and cancer cells. PLOS ONE 18(8): e0289327. https://doi.org/10.1371/journal.pone.0289327
- Discipline:
- Science
-
Great Lakes Historical Ice Dynamics
User Collection
- Creator:
- King, Katelyn B., Fujisaki-Manome, Ayumi, Brant, Cory, and Alofs, Karen
- Description:
- This collection includes raster layers (as a geodatabase) with ice metrics for each of the Great Lakes representing the historical time period of 1898-1960. One metric is spatial mean ice duration (the number of days per year when the lake was frozen) and the other is coefficient of variation of ice duration (variability across years).
- Keyword:
- Great Lakes, Ice , Ice duration, Ice variability, Historical , Huron, Ontario, Erie, Michigan, and Superior
- Discipline:
- Science
1Works -
- Creator:
- Bu, Xiangyun, Geng, Yihao, Yin, Siyuan, Luo, Liyan, Aubin, Cameron A., and Moore, Talia Y.
- Description:
- Suction is a useful strategy to grasp objects or anchor a body, especially when prolonged contact is desired. For passive suction cups, detachment requires manual delamination, which cannot occur autonomously. Active suction cups detach via equalizing pressure in the suction cavity with the surrounding environment, either by adding fluid (e.g., from a compressed air source) or reducing the cavity volume. While this detachment mechanism can be autonomous, it is inefficient, resulting in a net zero or loss of fluid. A more efficient detachment mechanism would enable multiple iterations of attachment and detachment without requiring additional fluid. To address this need, we designed a suction cup with a secondary release chamber embedded in the contact ring. The release chamber triggers delamination by deforming the shape of the contact ring. Through empirical testing, we found the optimal location and geometry of the release chamber. Our design allows for reliable detachment with a 5~mL decrease in release chamber volume, regardless of the adhesive suction force. Because the release chamber is a closed system, attachment and detachment results in net gain of fluid. Therefore, we propose a novel secondary benefit of adhesion via suction: harvesting fluid to power other pressure-driven soft robotic systems. and This ZIP archive includes CAD models for: The exploded view of the suction cup assembly and the molds of all suction cup configurations shown in Figure 4 of the paper: (b) Different release chamber locations (c) Different membrane thicknesses (d) Constant volume with varying release chamber areas (e) Constant area with varying release chamber heights (f) Constant height with varying release chamber areas
- Keyword:
- suction, adhesion, energy harvesting, and soft robotics
- Citation to related publication:
- Xiangyun Bu, Yihao Geng, Siyuan Yin, Liyan Luo, Cameron A. Aubin, Talia Y. Moore (2025) "Release Chamber Enables Suction Cup to Delaminate and Harvest Fluid" IEEE RoboSoft.
- Discipline:
- Engineering
-
- Creator:
- Howard, Cecilia M. and Sheldon, Nathan D.
- Description:
- This study uses a compilation of microbialite occurrences in the Archean and Paleoproterozoic from the literature to investigate how depositional environment changed across environmental shifts such as the Great Oxidation Event and the Huronian Glaciations. Key Points: - We compiled microbialite occurrences from the Archean and Paleoproterozoic with broad depositional environment information, which has not previously been incorporated in larger compilations of occurrences. - Tidal and other terrestrially-influenced settings comprise the majority of the early microbialite record, even across major environmental shifts and Abstract: Changes in microbialite abundance during the Archean and Paleoproterozoic have been attributed to a variety of environmental and biological factors. Past work looking at large-scale patterns of microbialite abundance generally assumes shallow marine deposition rather than incorporating specific settings, however, there is significant variance in conditions that might impact microbialite formation and preservation between marine, tidal, and terrestrial environments. We compiled microbialite occurrences from the Archean and Paleoproterozoic with integrated depositional environment information in order to assess how microbialite development and preservation changed across different settings. Microbially induced sedimentary structures formed a significant part of the record, but their identification primarily in conjunction with stromatolites rather than independently suggests that they may be undercounted. Broad trends in abundance were similar to previous compilations, but critically, we found that the majority of microbialites from this period formed in tidal environments. The proportion of terrestrially-influenced (including tidal) microbialites increased during periods of craton development in the Neoarchean and mid-Paleoproterozoic, with increases in marine microbialite abundance trailing. Tidal microbialite abundance also recovered more quickly than marine abundance following the Great Oxidation Event and Huronian Glaciations.
- Keyword:
- Microbialite, Stromatolite, Archean, Paleoproterozoic, Geosciences, and Tidal
- Citation to related publication:
- Howard, C.M. (2025). Unraveling Records of Time and Environment in Microbial Ecosystems from the Archean to Today (Ph.D. Dissertation). University of Michigan. and Howard, C.M. and Sheldon, N.D. (in prep). Chapter 2 Microbialite Niches across the Archean and Paleoproterozoic.
- Discipline:
- Science
-
- Creator:
- King, Katelyn, Schell, Justin, Alofs, Karen, Thomer, Andrea, Wehrly, Kevin, Lenard, Michael , and Lopez-Fernandez, Hernan
- Description:
- Michigan lakes are an important resource, however, their ecosystems are declining and projected to continue to face further impacts under future land use and climate change. Understanding how lake ecosystems respond to environmental stressors and management actions is critical for identifying resilient lakes and developing adaptation strategies. However, the ability to manage lakes is hampered by a lack of historical information. Historical lake data in Michigan were originally archived as index cards at the Michigan Department of Natural Resources. All of the images of these cards are stored in this collection, Collections, Heterogeneous data, and Next Generation Ecological Studies (CHANGES) - Michigan Lake Surveys, and the images for this specific dataset are stored in the CHANGES Project- Fish Growth Analysis (GROW) dataset. The CHANGES project used a crowd sourcing platform called Zooniverse to transcribe at least basic information (i.e. dates, collected by) from all of these cards. Some of the card types, such as the one in this dataset, were prioritized to transcribe to produce a usable (i.e. machine-readable, uniform, and standardized) historical dataset. and Fish growth cards document fish that were aged and measured during fish surveys. The data that were transcribed from these cards and included in this dataset (grow_data.csv) are for each fish species: the number of fish measured in each age group, and the minimum, maximum, and average length of the fish for each age group. The final growth dataset includes length-at-age information for 36 different species (grow_species_table). For a description of all fields of this data table see grow_datadictionary.
- Keyword:
- fish, lake, growth, length, and Michigan
- Citation to related publication:
- King, K.B.S., Schell, J, Wehrly, K.E., Lenard, M., Singer, R., López-Fernández, H., Thomer, A.K., & Alofs, K.M. Community science helps digitize 78 years of fish and habitat data for thousands of lakes in Michigan, USA. under review and Grabda, E.E., Flood, P.J., King, K.B.S., Breck, J.E., Wehrly, K.E., and Alofs, K.M. 2025. Mismatch between climate-based bioenergetics model of fish growth and long-term and regional-scale empirical data. Canadian Journal of Fisheries and Aquatic Sciences. 82: 1-15. https://doi.org/10.1139/cjfas-2024-0266
- Discipline:
- Science
-
- Creator:
- King, Katelyn , Schell, Justin, Alofs, Karen, Thomer, Andrea, Wehrly, Kevin, Lenard, Michael , and Lopez-Fernandez, Hernan
- Description:
- Michigan lakes are an important resource, however, their ecosystems are declining and projected to continue to face further impacts under future land use and climate change. Understanding how lake ecosystems respond to environmental stressors and management actions is critical for identifying resilient lakes and developing adaptation strategies. However, the ability to manage lakes is hampered by a lack of historical information. Historical lake data in Michigan were originally archived as index cards at the Michigan Department of Natural Resources. All of the images of these cards are stored in this collection, Collections, Heterogeneous data, and Next Generation Ecological Studies (CHANGES) - Michigan Lake Surveys, and the images for this specific dataset are stored in the CHANGES Project- Lake Summary (SUMM) dataset. The CHANGES project used a crowd sourcing platform called Zooniverse to transcribe at least basic information (i.e. dates, collected by) from all of these cards. Some of the card types, such as the one in this dataset, were prioritized to transcribe to produce a usable (i.e. machine-readable, uniform, and standardized) historical dataset. and Lake summary cards that we transcribed and curated include habitat information for a lake as well as observed fish species (summ_data.csv). These variables include anthropogenic lake characteristics such as fishing intensity, shoreline structures, and dams; lake morphometric characteristics like depth and area; as well as in situ measures of temperature, dissolved oxygen, and Secchi depth. Many of the characteristics were listed as a range, and therefore, have a column for minimum and maximum in the data file (e.g. temp_surface_min_c and temp_surface_max_c). In addition, the lake summary cards listed the fish species present, so the csv file includes columns with the fish species common name (summ_species_table) and corresponding values are either a ‘1’ representing presence of a species or ‘0’ representing absence. For a full description of all the fields of this data table see summ_datadictionary.
- Keyword:
- lake, fish, Secchi, temperature, nutrients, oxygen, shoreline, habitat, dams, lake depth, lake area, and fishing intensity
- Citation to related publication:
- King, K.B.S., Schell, J, Wehrly, K.E., Lenard, M., Singer, R., López-Fernández, H., Thomer, A.K., & Alofs, K.M. Community science helps digitize 78 years of fish and habitat data for thousands of lakes in Michigan, USA. under review
- Discipline:
- Science
-
- Creator:
- King, Katelyn, Schell, Justin, Alofs, Karen, Thomer, Andrea, Wehrly, Kevin, Lenard, Michael, and Lopez-Fernandez, Hernan
- Description:
- Michigan lakes are an important resource, however, their ecosystems are declining and projected to continue to face further impacts under future land use and climate change. Understanding how lake ecosystems respond to environmental stressors and management actions is critical for identifying resilient lakes and developing adaptation strategies. However, the ability to manage lakes is hampered by a lack of historical information. Historical lake data in Michigan were originally archived as index cards at the Michigan Department of Natural Resources. All of the images of these cards are stored in this collection, Collections, Heterogeneous data, and Next Generation Ecological Studies (CHANGES) - Michigan Lake Surveys, and the images for this specific dataset are stored in the CHANGES Project- Fish Collection (FISHc) dataset. The CHANGES project used a crowd sourcing platform called Zooniverse to transcribe at least basic information (i.e. dates, collected by) from all of these cards. Some of the card types, such as the one in this dataset, were prioritized to transcribe to produce a usable (i.e. machine-readable, uniform, and standardized) historical dataset. and Fish collection card types include targeted and non-targeted fisheries surveys by the Department of Natural Resources and this information was transcribed and curated into a csv file (fishc_data.csv). These records include information on the gear types used, the area surveyed and the length and mesh size of nets fished. The number and common name of fish species caught were recorded as well and included in a species table (fishc_species_table). A description of all data fields can be found in the fishc_datadictionary.
- Keyword:
- lake , fish, gear, abundance, and Michigan
- Citation to related publication:
- King, K.B.S., Schell, J, Wehrly, K.E., Lenard, M., Singer, R., López-Fernández, H., Thomer, A.K., & Alofs, K.M. Community science helps digitize 78 years of fish and habitat data for thousands of lakes in Michigan, USA. under review and King, K.B.S, Giacomini, H.C., Wehrly, K., López-Fernández, H., Thomer, A.K., & Alofs, K.M. (2023). Using historical fish catch data to evaluate predicted changes in relative abundance in response to a warming climate. Ecography. 2023:8. https://doi.org/10.1111/ecog.06798
- Discipline:
- Science
-
- Creator:
- Sutton, Etienne, Snapp, Sieglinde, Morrone, Vicki, and Blesh, Jennifer
- Description:
- Cover crops support ecosystem services in agroecosystems, but their performance can be highly variable. Functional trait ecology provides a useful framework for understanding variation in cover crop performance across different growing conditions. However, trait variation within species remains understudied compared to variation between species. In a two-year experiment, we measured nine functional traits for three cover crop species across 13 fields on working farms that spanned a gradient of soil health. Each field contained three cover crop treatments: a functionally diverse mixture of cereal rye (Secale cereale), crimson clover (Trifolium incarnatum), and dwarf-essex rapeseed (Brassica napus), and rye and clover monocrops. We evaluated i) the magnitude and relative importance of intraspecific and interspecific trait variation; ii) which soil health indicators best explained trait variation; and iii) whether interspecific interactions in mixture induced trait plasticity. Despite strong trait contrasts between species, intraspecific trait variation comprised 50% of total trait variation, on average. Trait variation was best explained by particulate organic matter nitrogen (POM N), soil phosphorus, pH, and permanganate oxidizable carbon for clover; by POM N and soil phosphorus for rye; and by POM N for dwarf essex. Rye and clover also showed significant trait plasticity in mixture relative to monocrop treatments. Our study demonstrates that intraspecific and interspecific trait variation are equally important, and that examining trait variation within species can improve the ability to predict cover crop outcomes. This information can inform cropping system design in distinct contexts to promote success of component species and complementary ecosystem functions.
- Keyword:
- cover crop, functional trait, soil health, mixture, species interactions, and intraspecific trait variation
- Citation to related publication:
- Sutton, E., Snapp, S., Morrone, V., & Blesh, J. (2025). Cover crop functional trait plasticity in response to soil conditions and interspecific interactions. Plant and Soil. https://doi.org/10.1007/s11104-025-07471-x
- Discipline:
- Science
-
- Creator:
- Quartey, Nii-Boi A and Liemohn, Michael W
- Description:
- This dataset contains results from the BATS-R-US multispecies MHD code simulating the solar wind interaction at Mars at the following orbital and solar cycle locations: solar maximum at perihelion, solar maximum at aphelion, solar minimum at perihelion, solar minimum at aphelion. These simulations contain results with and without the crustal magnetic fields and includes variables such as the magnetic field and ion density., 2025-02-25: The metadata in this dataset has been updated in response to reviewer comments during the journal review process. Additional Tecplot 360 EX file containing MAVEN multifluid MHD simulation data added. The multifluid MHD simulation result from this result is from the MAVEN simulation library. The simulation result is run for 25,000 iterations., and 2025-04-28: The following files have been replaced with the following as these files contain the nominal solar wind conditions: z_0_mhd_permax.plt -> permax_3d.plt z_0_mhd_aphmax.plt -> aphmax_3d.plt z_0_mhd_permin.plt -> permin_3d.plt z_0_mhd_aphmin.plt -> aphmin_3d.plt The following file has been removed as the slice can be extracted from permax_3d.plt: x_0_mhd_permax.plt
- Keyword:
- mars, magnetosphere, magnetotail, current sheet, asymmetry, multispecies, multifluid, MHD, and MAVEN
- Citation to related publication:
- https://doi.org/10.1029/2024JA033445
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Lubensky, David K, Studer, Lorenz, and Fu, Jianping
- Description:
- Studies of fate patterning during development typically emphasize cell-cell communication via diffusible chemical signals. Recent experiments on stem cell colonies (see Xue et al. Nature Materials 2018), however, suggest that in some cases mechanical stresses, rather than secreted chemicals, enable long-ranged cell-cell interactions that specify positional information and pattern cell fates. The authors of this earlier publication reported a set of in vitro experiments in which uniformly supplied chemical media induced spatially patterned fates in cell colony in a disc geometry. They provided significant evidence that inter-cellular mechanical interactions, as well as mechanical interactions between cells and the substrate, play an important role in this in vitro differentiation process. As part of these experiments, they showed that the concentric width of the outer fate domain is approximately constant as the colony diameter is increased from 300 um to 800 um. In this subsequent publication, we propose a mathematical model for this fate patterning process and explore how the fate pattern depends on substrate stiffness. The experimental images of cell colonies, both for varying cell colony diameter (from Xue et al. Nature Materials 2018) and for varying substrate stiffness (data generated for the publication linked to these data), are provided here. Each example has an image for PAX3 signal (marker for outer fate domain; Paired box gene 3) and an image for DAPI signal (staining nuclei; 4′,6-diamidino-2-phenylindole).
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force sensing, and Vertebrate development
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Science and Engineering
-
- Creator:
- Nunley, Hayden and Lubensky, David K
- Description:
- In a previous study (Xue et al. Nature Materials 2018), the authors showed that a key fate patterning event in vertebrate development can be reproduced in an in vitro stem cell culture. They further showed that this in vitro fate pattern seems to depend on mechanical signals rather than secreted chemical signals. In this follow-up study, a mathematical model of this process is proposed. The code in this deposit is for the simulation of this mathematical model in various cell layer geometries and substrate geometries. These geometries include a 1D cell layer, quasi-1D stripe geometry, disc geometry (all on a very thin substrate or a substrate composed of microposts) as well as a 1D cell layer on a finite-thickness substrate. Our model implies that the width of the outer fate domain varies non-monotonically with substrate stiffness, a prediction that we confirm experimentally.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, and Force sensing
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205, Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9, Banerjee S, Marchetti MC. Substrate rigidity deforms and polarizes active gels. EPL (Europhysics Letters) 96, 28003 (2011). https://doi.org/10.1209/0295-5075/96/28003, Edwards CM, Schwarz US. Force Localization in Contracting Cell Layers, Physical Review Letters 107, 128101 (2011). https://doi.org/10.1103/PhysRevLett.107.128101, and Banerjee S, Marchetti MC. Contractile Stresses in Cohesive Cell Layers on Finite-Thickness Substrates, Physical Review Letters 109, 108101 (2012). https://doi.org/10.1103/PhysRevLett.109.108101
- Discipline:
- Engineering and Science
-
- Creator:
- Heath, Jeffrey
- Description:
- Five short videos, three about food preparation, one about agriculture, and one about catching and cooking a giant pouched rat (Cricetomys)., The videos were incidental byproducts of Heath's linguistic fieldwork on the endangered Pere language spoken in Bonosso village on the outskirts of Tiéningboué city in north central Côte d'Ivoire. The footage was shot by project manager Minkailou Djiguiba as indicated in the credits at the end of each video. , and A much larger number of videos have been made from Mali and Burkina Faso and are deposited in other collections in Deep Blue Data. Many of the videos from all of these countries are also disseminated in a youtube channel that is managed by Djiguiba: https://www.youtube.com/@PratiquesCulturellesMaliBF. For more on Pere language see the Deep Blue Dataset "Pere language lexical datasheets and audio files" ( https://doi.org/10.7302/k6r9-r160) and the grammar cited as “A grammar of Pere (Bere, Mbre) of Côte d'Ivoire“ Under Related items in Deep Blue Documents, below ( https://hdl.handle.net/2027.42/163773) (copy at Zenodo, https://zenodo.org/records/3354193).
- Keyword:
- Côte d'Ivoire, documentary video, and Pere language
- Discipline:
- Humanities
-
- Creator:
- Jalin, Aditya MI, Swatthong, Nawat MI, Rozwadowski, Michelle MI, Kumar, Rajnish MI, Braun, Tom MI, Carlozzi, Noelle MI, Hanauer, David MI, Hassett, Afton MI, Tewari, Muneesh MI, and Choi, Sung MI
- Description:
- Research Overview: This dataset captures the longitudinal experience of both patients undergoing hematopoietic cell transplantation (HCT) and their caregivers through continuous physiological monitoring, daily mood reporting, and periodic health assessments. The data provides unprecedented insight into the dynamic relationship between caregiver well-being and patient outcomes during the critical post-transplant period. and Key Points: Digital biomarker data collected from 166 HCT caregiver-patient dyads over 120 days post-transplant Comprehensive physiological monitoring through wearable devices (Fitbit® Charge 3) Integration of daily mood reports, PROMIS® health measures, and clinical outcomes Unique paired data structure allowing analysis of caregiver-patient dynamics
- Keyword:
- Hematopoietic Stem Cell Transplantation, Caregiver-patient dyads, Physiological monitoring, Wearable Devices, Digital Biomarkers, and Health-related Quality of Life
- Citation to related publication:
- Jalin A, Swatthong N, Rozwadowski M, Kumar R, Barton D, Braun T, Carlozzi N, Hanauer DA, Hassett A, Choi SW. A Digital Biomarker Dataset in Hematopoietic Cell Transplantation: A Longitudinal Study of Caregiver-Patient Dyads (dHCT). medRxiv [Preprint]. 2024 Nov 22:2024.11.21.24317641. doi: 10.1101/2024.11.21.24317641. PMID: 39606379; PMCID: PMC11601742. and Rozwadowski M, Dittakavi M, Mazzoli A, Hassett AL, Braun T, Barton DL, Carlozzi N, Sen S, Tewari M, Hanauer DA, Choi SW. Promoting Health and Well-Being Through Mobile Health Technology (Roadmap 2.0) in Family Caregivers and Patients Undergoing Hematopoietic Stem Cell Transplantation: Protocol for the Development of a Mobile Randomized Controlled Trial. JMIR Res Protoc. 2020 Sep 18;9(9):e19288. doi: 10.2196/19288. PMID: 32945777; PMCID: PMC7532463.
- Discipline:
- Health Sciences
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Lubensky, David K, Studer, Lorenz, and Fu, Jianping
- Description:
- In an earlier study (Xue et al. Nature Materials 2018), stem cells differentiated into one of two cell types, neural plate border (NPB) or neural plate (NP), in vitro. This previous study demonstrated that this differentiation is likely mechanics-guided. Part of this demonstration was measurements of the displacement of microposts under the cell layer as the cells differentiate. These measurements suggested that the NPB cells are more contractile than NP cells. In a follow-up study (linked to this dataset), we quantitatively analyzed these data to demonstrate even further that the NPB cells are mechanically different than the NP cells and that the post displacement profile is not explained by a model of a cell layer with uniform mechanical properties. This analysis motivated the mathematical model -- for this cell colony system -- that we proposed and analyzed.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force sensing, and Vertebrate development
- Citation to related publication:
- Hayden Nunley, Xufeng Xue, Jianping Fu, David K. Lubensky bioRxiv 2021.04.30.442205; doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Engineering and Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Fu, Jianping, and Lubensky, David K
- Description:
- In an earlier publication (Xue et al. Nature Materials 2018), the authors reported a set of in vitro experiments in which uniformly supplied chemical media induced spatially patterned fates in cell colony in a disc geometry. They provided significant evidence that inter-cellular mechanical interactions, as well as mechanical interactions between cells and the substrate, play an important role in this in vitro differentiation process. In this subsequent publication, we propose a mathematical model for this fate patterning process and explore how the fate pattern depends on substrate stiffness. One ingredient of this mathematical model is that the cells at the very edge of the colony (lacking adherens junctions on one side) are geometrically different than the rest (by occupying a larger area on the micropattern). These images of DAPI (staining nuclei) and ECad (at adherens junctions) for colonies during early cell differentiation demonstrate this difference. Corresponding code for analysis is included.
- Keyword:
- Biomechanics, Cell mechanics, and Developmental pattern formation
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Engineering and Science
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- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Studer, Lorenz, Fu, Jianping, and Lubensky, David K
- Description:
- In an earlier study (Xue et al. Nature Materials 2018), stem cells differentiated into one of two cell types, neural plate border (NPB) or neural plate (NP), in vitro with the NP forming a central circular domain. This previous study demonstrated that this differentiation is likely mechanics-guided. Part of this demonstration was measurements of the displacement of microposts under the cell layer as the cells differentiate. These measurements suggested that the NPB cells are more contractile than NP cells (see Dataset of cell layers on micro-patterned substrates compost of posts). The authors of the 2018 study and of a follow-up study further explored how the size of the NPB domain depends on experimental conditions (see Dataset of stem cell colonies differentiating in neural induction medium and code for analysis of resulting fate pattern). To further understand what factors could be driving NPB formation, we estimated cell area at the colony edge (see Dataset on cell areas and nuclear densities in differentiating stem cell colonies). This analysis inspired a mathematical model of mechanical patterning: fate affects cell contractility, and pressure in the cell layer biases fate. Cells at the colony edge, more contractile than cells at the center, seed a pattern that propagates via force transmission. We simulated the model in various cell geometries and for different substrates (see Code for simulating NP/NPB fate patterning in stem cell colonies). Strikingly, our model implies that the width of the outer fate domain varies non-monotonically with substrate stiffness, a prediction that we confirm experimentally. Our findings thus support the idea that mechanical stress can mediate patterning in the complete absence of chemical morphogens, even in non-motile cell layers, thus expanding the repertoire of possible roles for mechanical signals in development and morphogenesis.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force Sensing, and Vertebrate development
- Discipline:
- Science
4Works -
- Creator:
- Heath, Jeffrey
- Description:
- Seven short audio files and one pdf document with transcriptions for all of them: and 1) noun stems; 2) noun stems in different clausal positions; 3) verb stems including perfective/imperfective morphology; 4) H-toned first plural and second plural pronouns in various positions; 5) third singular and third plural pronouns, in contrast to logophoric-reflexive singular and plural pronouns; 6) tonal effect of first singular pronominal on the following stem; 7) tones of postpositions.
- Keyword:
- Tigemaxo
- Discipline:
- Humanities
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- Creator:
- Frydendall, Elyse K and Scott, Emily E
- Description:
- This table contains the names, molecular mass (g/mol), and SMILES structure for all compounds tested for CYP2W1 inhibition in the high throughput screen described in this chapter in the tab titled “Compound Library”. Compounds that were identified as CYP2W1 inhibitors are listed in the tab titled “CYP2W1 inhibitors.” This tab contains compound names, molecular mass (g/mol), average standard deviation, number of experiments in which a compound was classified as a hit, number of experimental replicates, hit rate, and SMILES structure.
- Keyword:
- cytochrome P450 enzyme and high throughput inhibition assay
- Discipline:
- Health Sciences