Johns Hopkins Research Data Repository
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Data associated with the publication: Internal states as a source of subject-dependent movement variability are represented by large-scale brain networks.
No full textThis repository contains the data and scripts used to generate the plots for the publication “Internal states as a source of subject-dependent movement variability and their representation by large-scale networks in the human brain.” It contains 6 folders. _data contains neural and behavioral data at various stages of processing as .mat files. _figures is where the figures will be saved after running the scripts saved as a .pdf. _library contains scripts downloaded from MATLAB’s File Exchange used for generating the figures. _scripts contains custom MATLAB scripts .m files used to generate the figures. Run MAIN.m to generate figures. Scripts and functions were created using MATLAB_R2021b. _table contains tables used for generating figures. It contains excel files and .txt files. _toolboxes contains the version of the open-source software used to generate the figures. The intended use of this code is to generate the figures for the publication from the processed data
Data associated with the publication: Designing n-type all-ionic thermoelectric polymers with improved air stability via a solution-processing anion exchange technique.
No full textThis dataset contains original instrument data for material conductivities, Seebeck coefficients, and electron microscopy of ionic polymer films used in a thermoelectric effect study
Data associated with the publication: Temporal interference current stimulation in peripheral nerves is not driven by envelope extraction
No full textMost data consists of electromyogram data from the rat biceps femoris and plantar muscles following electrical stimulation of the sciatic nerve. We used a variety of stimulation parameters, which are shared in the accompanying article. We created COMSOL models of the fields that these stimulation parameters created, which are also shared. We include the signals processing steps to reproduce our figures, for transparency
Data associated with the publication: Iapetan subduction initiation recorded in the Leka Ophiolite Complex, Norway.
No full textContents of this dataset includes whole rock major and trace element analyses by XRF and LA-ICP-MS, U-Pb isotope ratios and calculated dates from LA-ICP-MS analyses of zircon, and U-Pb isotope ratios and calculated dates from CA-ID-TIMS analyses of zircon
Data associated with the publication: Co-transcriptional folding of the glmS ribozyme enables a rapid response to metabolite
No full textThis dataset is related to a manuscript submitted to Nucleic Acids Research, describing co-transcriptional folding of the Bacillus subtilis glmS ribozyme, using single molecule total internal reflection fluorescence microscopy.
The glmS ribozyme riboswitch, located in the 5’ UTR of the Bacillus subtilis glmS mRNA, regulates cell wall biosynthesis through ligand-induced self-cleavage and decay of the glmS mRNA. Although self-cleavage of the refolded glmS ribozyme has been studied extensively, the kinetics of ribozyme folding and ligand binding during transcription is not understood. Here, we combine TIRF single-molecule assays with kinetic modeling to show that self-cleavage can occur during transcription before the ribozyme is fully synthesized. Moreover, co-transcriptional folding of the RNA at a physiological elongation rate allows the ribozyme core itself to become reactive. DMS footprinting further revealed how slow sequential folding favors formation of the native core structure through fraying of misfolded helices and nucleation of a native pseudoknot. Ribozyme self-cleavage at an early stage of transcription may benefit glmS regulation in B. subtilis, as it exposes the mRNA to exoribonuclease before translation starts. Our results emphasize the importance of co-transcriptional folding of RNA tertiary structure for cis-regulation of mRNA stability
Data associated with the publication: Sedimentary pyrite formation in a seasonally oxygen-stressed estuary: potential imprints of microbial ecology and position-specific isotope fractionation
No full textThis study focuses on geochemical analyses of shallow sediments from two sites in Chesapeake Bay. We used these analyses to study the effects of seasonal oxygen decline and biological turnover on pyrite burial rates and pyrite sulfur isotope compositions. Pyrite burial in marine and estuarine sediments is a key process that impacts oxygen levels in the ocean-atmosphere system over geological timescales. Pyrite’s sulfur isotope composition can also be used to study ancient environmental conditions. We found that at both studied sites, pyrite primarily forms in the summer and dissolves in the winter. The more frequently ventilated site had higher pyrite concentrations because of higher rates of formation in the summer, which may be influenced by sulfur oxidizing microbial communities. Despite differences in rates of pyrite formation between sites, sulfur isotope ratios (34S/32S) of pyrite are similar between the sites and are lower than the 34S/32S ratios of coexisting pyrite precursors. This offset between pyrite sulfur isotopes and pyrite precursors may be due to position-specific isotope effects. Here, we include the following data that support these results: 1) Solid phase sulfur and carbon isotope geochemistry for sediment samples from Chesapeake Bay Sites CB4.3C and CB4.3W, 2) Radiogenic isotope data (Pb-210, Ra-226, Cs-137, Be-7) for sediment samples from Chesapeake Bay Sites CB4.3C and CB4.3W, 3) Matlab code for the position-specific isotope effect model
Data associated with the publication: Trends in estuarine pyrite formation point to an alternative model for Paleozoic pyrite burial
No full textThis data set contains three components. Component 1 is a set of geochemical data from sediment cores collected from the Chesapeake Bay (Maryland and Virginia, USA). Component 2 is a spreadsheet containing a modified copy of a geochemical dataset downloaded from Phase 1 of the Sedimentary Geochemistry and Paleoenvironments repository (Farrell et al., 2021; doi.org/10.1111/gbi.12462) in August 2023. A text file associated with Component 2 describes how the data in the spreadsheet have been filtered from the original SGP download. Component 3 contains a modified section of code from the COPSE biogeochemical model (Lenton et al., 2018; doi.org/10.1016/j.earscirev.2017.12.004) as well a Matlab file (.mat format) that contains vectors for use in the modified section of code
Data associated with the publication: Stable high-conductivity ethylenedioxythiophene polymers via borane-adduct doping
No full textDevice current-voltage data, microscopy and diffraction morphology data, spectral data, thermoelectric dat
Data associated with the publication: Ion channel selectivity through ion modulated changes of selectivity filter pKa values
No full textThis dataset contains simulations and parameter files associated with the publication "Ion channel selectivity through ion modulated changes of selectivity filter pKa values." Simulation files are in NetCDF format and parameter files are in parm7 format. See README document for more details
Data associated with the publication: Blended conjugated host and unconjugated dopant polymers towards N-type all-polymer conductors and high-ZT thermoelectrics
No full textDevice current-voltage data, microscopy and diffraction morphology data, spectral data, thermoelectric data