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- Creator:
- Banerjee, Pavel , Ray, Sujay, Dai, Liuhan, Sandford, Erin, Chatterjee, Tanmay, Mandal, Shankar, Siddiqui, Javed, Tewari, Muneesh, and Walter, Nils G
- Description:
- Early and personalized intervention in complex diseases requires robust molecular diagnostics, yet the simultaneous detection of diverse biomarkers—microRNAs (miRNAs), mutant DNAs, and proteins—remains challenging due to low abundance and preprocessing incompatibilities. We present Biomarker Single-molecule Chromato-kinetic multi-Omics Profiling and Enumeration (Bio-SCOPE), a next-generation, triple-modality, multiplexed detection platform that integrates both chromatic and kinetic fingerprinting for nanoscale molecular profiling through digital encoding. Bio-SCOPE achieves femtomolar sensitivity, single-base mismatch specificity, and minimal matrix interference, enabling precise, parallel quantification of up to six biomarkers in a single sample with single-molecule resolution. We demonstrate its versatility in accurately detecting low-abundance miRNA signatures from human tissues, identifying upregulated miRNAs in the plasma of prostate cancer patients, and measuring elevated interleukin-6 (IL-6) and hsa-miR-21 levels in cytokine release syndrome patients (the studies that collected these samples were approved by University of Michigan's Medical School Institutional Review Board HUM00043354, HUM00115179 and HUM00037879). By seamlessly integrating multiomic biomarker panels on a unified, high-precision platform, Bio-SCOPE provides a transformative tool for molecular diagnostics and precision medicine.
- Keyword:
- biomarker, fingerprinting, multiplexed detection, digital encoding, single molecule, multiomic, precision medicine
- Citation to related publication:
- Banerjee, Ray, Dai et al. Chromato-Kinetic Fingerprinting Enables Multiomic Digital Counting of Single Disease Biomarker Molecules. ACS Nano. Submitted.
- Discipline:
- Science
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- Creator:
- Bai, Bobo and Zhang, Youxue
- Description:
- This dataset is referenced in the manuscript “Multicomponent diffusion in basaltic melts: A temperature-independent eigenvector matrix, and a multicomponent diffusion calculator”. This manuscript explores the temperature independence of diffusion eigenvectors in an 8-component basaltic melt and provides an open-access calculator for the community to compute multicomponent diffusion profiles.
- Keyword:
- Eigen-components, Multicomponent diffusion, Uphill diffusion, and Multicomponent diffusion calculator
- Discipline:
- Science
-
- Creator:
- Faulkner, Alexa
- Description:
- This study uses in vivo two-photon calcium imaging in the visual cortex of mice to demonstrate that encoding of learned environmental visual cues is flexibly represented across different task contexts. This dataset is comprised of in vivo two-photon calcium imaging from visual cortex of mice during learning and performance of a visual discrimination task. data was acquired suing Scanbox and analysis performed in Matlab and Python.
- Keyword:
- neuroscience, two photon calcium imaging, visual cortex, and mouse
- Discipline:
- Science
-
- Creator:
- Heath, Jeffrey
- Description:
- Documentary fieldwork on Tebul Ure and other Dogon languages (grammars, lexicons, texts, audio, video). This deposit contains only audio recordings but links out to other pieces of the work.
- Keyword:
- Tebul Ure, Dogon, and Audio
- Discipline:
- Humanities
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- Creator:
- Weeks, Brian C
- Description:
- Each folder contains all of the data for a specific specimen; the folder names correspond to the University of Michigan Museum of Zoology catalog number for the specimen. The photographs have been used to measure skeletal traits using the Skelevision model, which is a computer vision approach to identifying and measuring elements of the skeleton (length of the tibiotarsus, tarsometatarsus, femur, humerus, ulna, radius, carpometacarpus, 2nd digit 1st phalanx, skull, and keel; the outer diameter of the sclerotic ring at its widest point; and the distance from the back of the skull to the tip of the bill). The dataset includes images of 12,421 specimens from 1,881 species of passerine birds.
- Keyword:
- Songbird skeletons, Functional traits, Comparative morphometrics, and Computer vision
- Citation to related publication:
- Weeks, B.C., Z. Zhou, C.M. Probst, J.S. Berv, B. O’Brien, B.W. Benz, H.R. Skeen, M. Ziebell, L. Bodt, and D.F. Fouhey. 2024. Skeletal trait measurements for thousands of bird species. bioRxiv. https://doi.org/10.1101/2024.12.19.629481 and Weeks, B.C., Z. Zhou, C.M. Probst, J.S. Berv, B. O’Brien, B.W. Benz, H.R. Skeen, M. Ziebell, L. Bodt, and D.F. Fouhey. 2024. Skeletal trait measurements for thousands of bird species. Scientific Data. https://doi.org/10.1038/s41597-025-05234-y
- Discipline:
- Science
-
- Creator:
- Craven, Nicholas C, Singh, Ramanish, Quach, Co D, Gilmer, Justin B, Crawford, Brad, Marin-Rimoldi, Eliseo, Smith, Ryan, DeFever, Ryan, Dyukov, Maxim, Fothergill, Jenny, Jones, Chris, Moore, Timothy, Butler, Brandon L, Anderson, Joshua A, Iacovella, Christopher, Jankowski, Eric, Maginn, Eric, Potoff, Jeffrey, Glotzer, Sharon C, McCabe, Clare, Cummings, Peter T, and Siepmann, Ilja J
- Description:
- Data are collected in 5 separate workspace, one for the main density data calculations across the space and 4 for the subproject simulations that were performed to validate and dive deeper into specific engine implementations. In order to copy the simulation trajectory and calculated averages used to generate figures, these workspace folders must be downloaded and pointed to the correct place in the GitHub Project Structure, which can be found at https://github.com/mosdef-hub/reproducibility_study and Each compressed file contains the data for a single workspace.
- Keyword:
- molecular dynamics, monte carlo, reproducibility, and replicability
- Citation to related publication:
- https://doi.org/10.1021/acs.jced.5c00010
- Discipline:
- Science
-
- Creator:
- Heath, Jeffrey
- Description:
- lexical spreadsheets. One .xlsx spreadsheet with separate pages for nouns, numerals, adjectives, verbs, places, and "other" (including adverbs and grammatical morphemes). Each page is also copied as a .csv file, with one additional .csv containing Tiefo-D vocabulary gleaned from K. Winkelmann's German-language dissertation, Die Sprache der Cefo von Daramandugu (Burkina Faso). Previously "published" at Zenodo. , Jinejan, Flaso, Biton, and Masaso are village-like settlements, geographically apart but administratively part of Daramandougou. In sheets with a fifth column "Tiefo-D", this is a compromise form mainly useful for sorting and navigation. , and Tiefo-D is related to Tiefo-N but the two are quite different, mutually unintelligible languages. They are spoken in southwestern Burkina Faso.
- Keyword:
- Tiefo-D language
- Citation to related publication:
- Heath, J., & Ouattara, A. (2021). A Grammar of Tiefo-D of Daramandugu. Zenodo. https://doi.org/10.5281/zenodo.4715103, Heath, J., & Ouattara, A. (2021). Tiefo-D Texts from Daramandugu. Zenodo. https://doi.org/10.5281/zenodo.4715132, and Heath, J., & Ouattara, A. (2021). Tiefo-D lexicon [Data set]. Zenodo. https://doi.org/10.5281/zenodo.4715136
- Discipline:
- Humanities
-
- Creator:
- Liu, Bin , Silori, Yogita, Li, Yongxi, Forrest, Stephen R., and Ogilvie, Jennifer P.
- Description:
- We use angle-resolved reflection measurements to characterize polariton dispersion, and use ultrafast transient absorption (TA) spectroscopy to study the influence of the “open cavity” on the charge generation dynamics of the donor-acceptor bilayer and blend systems.
- Citation to related publication:
- Yogita Silori, Bin Liu, Yongxi Li, Stephen R. Forrest, and Jennifer P. Ogilvie, "Impact of Cavity Strong Coupling on the Charge Transfer Dynamics in Organic Donor-Acceptor Heterojunctions", Phys. Rev. B. Accepted April 2025, https://doi.org/10.1103/859s-sc6n
- Discipline:
- Science
-
- Creator:
- Heath, Jeffrey
- Description:
- These recordings have not been transcribed but are made available to native speakers and to linguists. Tiéyaxo is the sister dialect to Tigemaxo, which together form a language within the Bozo family. The author has completed a study of Tigemaxo but has done no work specifically on Tiéyaxo. Other works in this collection contain Tigemaxo audio files, and one such work contains a Tigemaxo and a Tieyaxo recording from 1989.
- Keyword:
- Bozo language and Tiéyaxo
- Discipline:
- Humanities
-
- Creator:
- Heath, Jeffrey
- Description:
- Recordings in Tigemaxo from 2022 in Dia village have been transcribed and the audio files are in a separate work ( https://doi.org/10.7302/hagd-xe26). The present work is a much larger set of audio recordings, also in Tigemaxo and from Dia village, but recorded in 2024. It includes ethnohistory and tales. , The ethnohistorical texts are with one main speaker (Mama Sienta), interviewed by Oumar Dienta, both male. The tales are told by a range of male and female speakers, with light backchannel accompaniment by the audience. Each tale in Tigemaxo is accompanied by a repetition or summary in French by Oumar Dienta in a separate file. The author has no plans to transcribe the 2024 recordings and is depositing this audio library for future use by native speakers and/or by linguists. The same is true of the 2019 Tigemaxo/Tiéyaxo recordings ( https://dx.doi.org/10.7302/6632), and the 2021 Tiéyaxo recordings ( https://doi.org/10.7302/2e0d-xk52), which are in two other works in this collection. , and A short catalog of the files in this work, without transcription or translation, appears in J. Heath, "Tigemaxo (Bozo) texts of 2022 in Dia village (Mali)" in Zenodo, of which a backup copy is in Deep Blue Documents (see below).
- Keyword:
- Bozo language, Tigemaxo, and Dia village Mali
- Citation to related publication:
- Heath, J. (2025). A Grammar of Tigemaxo of Dia (Bozo family, Mali). Zenodo. https://doi.org/10.5281/zenodo.15160216
- Discipline:
- Humanities