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165 results for “nucleosides”
Supplementary Information for "Nucleoside Phosphorylases Make N7-Xanthosine, a "Non native" Regioisomer of Xanthosine"
<p>This is the external Supplementary Information for our publication "Nucleoside Phosphorylases Make N7-Xanthosine, a "Non native" Regioisomer of Xanthosine".</p> <p>The .pdf file contains the Supplementary Information: author contributions, accessibility statement, experimental procedures, and supplementary items, among others.</p> <p>The .zip file contains the raw data and metadata for all items (supplementary and main text) as well as the calculation results. This includes UV, HPLC, NMR, HRMS, and DFT results. The full set of raw HPLC chromatograms is - unfortunately - only available to us in a proprietary file format but we are happy to share these data upon request. This revised version contains additional UV data on experiments excluding oxidation of xanthine to uric acid as well as additional NMR data on purified N7-xanthosine and reference data for N9-xanthosine and xanthine in D2O.</p> <p>To some extent, this work builds on and borrows from our previous publications on spectral unmixing (https://doi.org/10.3390/mps2030060, https://doi.org/10.1002/cbic.202000204), continuous reaction monitoring (https://doi.org/10.1021/acs.analchem.1c05356), and thermodynamic reaction control (https://doi.org/10.1002/adsc.201901230, https://doi.org/10.5281/zenodo.3568858, https://doi.org/10.1002/cphc.202000901, https://doi.org/10.1021/acscatal.1c02589).</p>
Supplementary Material for "General Principles for Yield Optimization of Nucleoside Phosphorylase-Catalyzed Transglycosylations"
<p>This is the supplementary material for our publication "General Principles for Yield Optimization of Nucleoside Phosphorylase-Catalyzed Transglycosylations".</p> <p>The .pdf file contains the supplementary information: Author Contributions, Conflict of Interest, Sample analysis by HPLC, Table S1 and S1, Figure S1 and a suggested workflow for NPase-catalyzed nucleoside synthesis.</p> <p>The .xlsx file contains an implementation of the simplified formula for yield prediction (equation (4) ), using previously reported thermodynamic data (10.5281/zenodo.3459298).</p> <p>The Python code and all data calculated from numerical solutions of the system of equilibrium constraints is available elsewhere (10.5281/zenodo.3522588).</p>
Supplementary Material for "Thermodynamic Reaction Control of Nucleoside Phosphorolysis"
<p>This is the supplementary material for our publication "Thermodynamic Reaction Control of Nucleoside Phosphorolysis".</p> <p>The .pdf file contains the supplementary information: Author Contributions, Figure S1 and Tables S1-S3.</p> <p>The .zip file contains the raw data, metadata and results from Figure 1, 2, 4 and 5.</p> <p>The .xlsx file contains</p> <ol> <li>the apparent transformed values of the reaction enthalpy and entropy of nucleosides <strong>1</strong>-<strong>24</strong></li> <li>the calculated apparent Gibbs free energies of nucleosides <strong>1</strong>-<strong>24</strong> and</li> <li>the implementation of these values for the calculation of equilibrium conversions of nucleosides <strong>1</strong>-<strong>24</strong> with variable (adjustable) reaction conditions (concentrations of the nucleoside, phosphate and reaction temperature).</li> </ol> <p>For the software employed for spectra unmixing, please see doi: 10.5281/zenodo.3243376 and our previous work (doi: 10.3390/mps2030060) as well as its supporting material (doi: 10.5281/zenodo.3333469) for clarification.</p>
Supplementary Material for "Route Efficiency Assessment and Review of the Synthesis of β-Nucleosides via N-Glycosylation of Nucleobases"
<p>This is the external Supplementary Material for our publication "Route Efficiency Assessment and Review of the Synthesis of β-Nucleosides via <em>N</em>-Glycosylation of Nucleobases", which has been released as a preprint on <em>ChemRxiv </em>(https://doi.org/10.26434/chemrxiv.12753413.v1). The files in this record are additionally available from <em>ChemRxiv</em>.</p>
Supplementary Information for "The Peculiar Case of the Hyperthermostable Pyrimidine Nucleoside Phosphorylase from Thermus thermophilus"
<p>This is the external Supplementary Information for our publication "The Peculiar Case of the Hyperthermostable Pyrimidine Nucleoside Phosphorylase from <em>Thermus thermophilus</em>".</p> <p>The .pdf file contains the Supplementary Information: author contributions, experimental procedures and supplementary items.</p> <p>The .zip file contains the raw data and metadata for all items (supplementary and main text) and the calculations.</p> <p>The Python code used for spectral unmixing is available on this platform (10.5281/zenodo.3243376) and has been described in our previous publications (10.3390/mps2030060, 10.5281/zenodo.3333469, 10.1002/cbic.202000204, 10.5281/zenodo.3723806 ). Further applications of this method can be found in our recent article in <em>Adv. Synth. Catal.</em> (10.1002/adsc.201901230) and its supporting material (10.5281/zenodo.3568858).</p>
Source data for the publication "Tracking excited state decay mechanisms of pyrimidine nucleosides in real time", Nature Communications, 2021
<p>The archives contain the raw data used to generate the transient absorption spectra for uridine (Figure 1) and 5-methyluridine (Figure 2) presented in the main paper, as well as the trajectory plots and auxiliary spectra presented in the Supplementary Information of the paper "Tracking excited state decay mechanisms of pyrimidine nucleosides in real time" authored by R. Borrego-Varillas et al. published in Nature Communications, 2021. Specifically:</p> <p><strong>URD</strong>: folder with raw data from the uridine trajectories (56 trajectories) performed at the SS-CASPT2/SA-2-CASSCF(10,8) and SS-CASPT2/SA-2-CASSCF(10,10) level of theory</p> <p><strong>5mURD</strong>: folder with raw data from the 5-methyluridine trajectories (57 trajectories) performed at the SS-CASPT2/SA-2-CASSCF(10,8) and SS-CASPT2/SA-2-CASSCF(10,10) level of theory</p> <p>The raw data of each trajectory is inside a folder named <em>geom_XXX</em> where <em>XXX</em> stands for a 3-digit label of the trajectory. The trajectories have been selected out of a pool of 500 trajectories according to the S0-S1 vertical gap so that only trajectories whose energy gap falls under the envelope of the pulse are selected</p> <p><strong>URD</strong>: 003 005 006 011 015 023 039 040 054 056 060 083 098 104 112 114 116 121 122 147 152 158 161 171 173 175 177 186 189 200 204 211 219 223 225 232 234 235 236 246 251 252 257 259 265 268 271 272 279 286 287 289 305 313 318 336</p> <p><strong>5mURD</strong>: 010 044 045 048 052 057 065 074 085 094 097 099 100 105 110 112 113 121 131 137 138 140 144 145 159 164 170 179 182 183 184 186 189 199 203 205 209 214 219 220 221 239 243 250 251 273 284 290 295 301 302 320 325 327 328 333 334</p> <p>In each geom_XXX folder there are following files:</p> <p><strong>S1-S<em>Y</em>.dat</strong>: ASCII files () in which the individual columns correspond to </p> <p>col1: time [fs] </p> <p>col2: transition energy of state S<em>Y</em> with respect to S1 [cm-1] where S0 is the ground state</p> <p>col3-5: X, Y and Z components of the transition dipole moment between S1 and S<em>Y</em> [a.u.]</p> <p>col6: magnitude of the transition dipole moment between S1 and S<em>Y</em> [a.u.] </p> <p>col7: angle between transition dipole moment at time t and t=0 [deg]</p> <p>Note that in URD S1-S0.dat contains in most cases about 500 data points (0-500 fs), in 5mURD S1-S0.dat contains 1000 data points (0-1000 fs) except for a few cases in which the trajectories were interrupted earlier. This data has been used to simulate the stimulated emission before the hopping event and the hot ground state photoinduced absorption after hopping. S1-S<em>Y</em>.dat () contain only data points until the hopping event which have been used to simulate the excited state photoinduced absorption.</p> <p>The spectra reported in the main article (Figs 1 & 2) as well as in the SI can be reproduced following eq. 13-18 in the Supplementary Information.</p> <p> </p> <p><strong>HighMediumLayer_traj.xyz.zip</strong>: archived Cartesian coordinates of the High Layer (nucleobase) and Medium Layer (sugar and waters within 5 Å distance from nucleobase) along the dynamics</p> <p>Note that due to the different number of waters in each trajectory the size of the Medium layer (and thus the size of the system) may vary from trajectory to trajectory.</p> <p>Note that due to the different duration of each trajectory the number of geometries may vary from trajectory to trajectory.</p> <p><strong>LowLayer.xyz:</strong> Cartesian coordinates of the Low Layer (waters > 5 Å from the nucleobase); the coordinates of these waters are kept fixed along the trajectory.</p> <p>The coordinates of High, Medium and Low layers can be used to reproduce the QMMM calculations (energies, gradients and transition dipole moments along each trajectory) with the official COBRAMM release (<a href="https://gitlab.com/cobrammgroup/cobramm.git">https://gitlab.com/cobrammgroup/cobramm.git</a>) following the parameters provided in Supplementary Note 2 of the Supplementary Information.</p>
Supplementary Information for "Semi-automated high-throughput substrate screening assay for nucleoside kinases
<p>This is the external Supplementary Information for our publication "Semi-automated high-throughput substrate screening assay for nucleoside kinases". Files are to follow soon. We apologize for the delay. Thank you for your patience.</p> <p> </p> <p>The preprint and the Supporting Information are available at ChemRxiv (https://doi.org/10.33774/chemrxiv-2021-k0w7q).</p>
Cheese community and virome nucleoside mass spec from Arome
<p>These are files from LC-MS/MS analysis of nucleosides from cheese microbial communities and their viromes. For each run, we have uploaded the .mgf, .raw, and .ms1 files. We have also uploaded run descriptions, a first pass analysis from Arome, and the LC-MS/MS methods and exclusions lists. If you want to know more about the specific details of the cheeses that we sampled, please check out our pub "<a href="https://research.arcadiascience.com/pub/data-set-metagenomics-timecourse-cheese/release/1">Paired long- and short-read metagenomics of cheese rind microbial communities at multiple time points</a>". </p> <p>File list:</p> <p>Run data files: .raw, .mgf, .ms1 file types </p> <p>Run descriptions: arome_run_descriptions.csv</p> <p>First pass analysis from Arome: 20221209_Arcadia_Nucleo_HILIC_POS_quant_ALL_IDs.csv</p> <p>Exclusion lists: exclusionmasstable_1.csv, exclusionmasstable_2.csv</p> <p>Methods file: MethodSummary_POS1.txt</p>
TOTEM: Switch From Other Nucleoside Reverse Transcriptase Inhibitors (NRTIs) to Once Daily Truvada
ClinicalTrials.gov study NCT00323492. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study Comparing Lopinavir/Ritonavir (LPV/r) + Emtricitabine/Tenofovir Disoproxil Fumarate (FTC/TDF) With a Nucleoside Sparing Regimen Consisting of Lopinavir/Ritonavir + Raltegravir (RAL)
ClinicalTrials.gov study NCT00711009. IPD Sharing: Not stated. Countries: 7. Publications: 2.
Effectiveness of Nucleoside Supplementation or Switch to Tenofovir in Reversing Fat Loss in HIV Infected Adults
ClinicalTrials.gov study NCT00119379. IPD Sharing: NO. Countries: 1. Publications: 2.
Dolutegravir Compared to Darunavir/Ritonavir , Each in Combination With Dual Nucleoside Reverse Transcriptase Inhibitors (NRTIs) in ART-naive Subjects
ClinicalTrials.gov study NCT01449929. IPD Sharing: Not stated. Countries: 9. Publications: 2.
A Study of Early Immunologic Response in Asian Patients With Chronic Hepatitis B, Treated With Pegasys (Peginterferon Alfa-2a (40KD)), Nucleoside Analogues, or Both
ClinicalTrials.gov study NCT00962871. IPD Sharing: Not stated. Countries: 4. Publications: 2.
A Trial of 2 Options for Second Line Combination Antiretroviral Therapy Following Virological Failure of a Standard Non-nucleoside Reverse Transcriptase Inhibitor (NNRTI)+2N(t)RTI First Line Regimen
ClinicalTrials.gov study NCT00931463. IPD Sharing: Not stated. Countries: 17. Publications: 4.
Dose Ranging Study of GSK1265744 Plus Nucleoside Reverse Transcriptase Inhibitors for Induction of Human Immunodeficiency Virus-1 (HIV-1) Virologic Suppression Followed by Virologic Suppression Mainte
ClinicalTrials.gov study NCT01641809. IPD Sharing: Not stated. Countries: 2. Publications: 3.
Host-derived Lactobacillus plantarum alleviates hyperuricemia by improving gut microbial community and hydrolase-mediated degradation of purine nucleosides
Open the record for dataset details and reuse information.
Adipocyte release of nucleosides contributes to obesity-associated inflammation
Open the record for dataset details and reuse information.
Supplementary Material for "Efficient biocatalytic synthesis of dihalogenated purine nucleoside analogues applying thermodynamic calculations"
<p>This is the supplementary material for our publication "Efficient biocatalytic synthesis of dihalogenated purine nucleoside analogues applying thermodynamic calculations". We wish to thank all authors for their contribution and have uploaded this dataset in their name.</p> <p>We apologize that these files are not publicly available. Please contact Dr. Anke Kurreck for access to raw and analyzed data.</p> <p>Naturally, this work builds on previous publications. Specifically, we have borrowed data from our recent work on the thermodynamic control of nucleoside phosphorolysis (10.1002/adsc.201901230; the full dataset can be found at 10.5281/zenodo.3568858) and employed equations and methodology described in our piece on yield optimization of nucleoside transgylcosylations (10.1002/cbic.201900740; the external supplementary information can be accessed at 10.5281/zenodo.3565561 and 10.5281/zenodo.3522588).</p>
Supplementary Material for "Updating and Extending an UV/Vis Spectroscopy-Based Assay for Monitoring of Transformations Between Nucleosides and Nucleobases"
<p>This is the supplementary material for our publication "Updating and Extending an UV/Vis Spectroscopy-Based Assay for Monitoring of Transformations Between Nucleosides and Nucleobases".</p> <p> </p> <p><strong>For a detailed description of this material, please see the "Notes on the Supporting Material".</strong></p> <p> </p> <p>Naturally, this publication builds on previous work. The Python code used for spectral unmixing is available on this platform (10.5281/zenodo.3243376) and has been described in our previous publication (10.3390/mps2030060, 10.5281/zenodo.3333469). Applications of this methodology are described in our recent article in <em>Adv. Synth. Catal.</em> (10.1002/adsc.201901230) and its supporting material (10.5281/zenodo.3568858).</p> <p>I wish to thank all authors of this publication for their contribution, using the method and generously sharing your experience and your data with me. This helped us develop robust protocols, learn about the potential and limits of the method and ultimately made this update article possible. While I have been the primary user of the method, your applications, questions and problems have spurred us to think outside of the box and find solutions that helped us expand our repertoire of "unmixable" reactions. This Supplementary Information contains some of our shared data and I thank each of you for contributing to this work.</p> <p> </p>
Supplementary Material for "Kinetic Analysis of the Hydrolysis of Pentose-1-phosphates through Apparent Nucleoside Phosphorolysis Equilibrium Shifts"
<p>This is the external Supplementary Information for our publication "Kinetic Analysis of the Hydrolysis of Pentose-1-phosphates through Apparent Nucleoside Phosphorolysis Equilibrium Shifts".</p> <p>The .pdf file contains the Supplementary Information: author contributions, experimental procedures, derivation of equations and supplementary items.</p> <p>The .zip file contains the raw data and metadata for all items (supplementary and main text) and the calculations.</p> <p>Like most publications, this one builds on previous work. The Python code used for spectral unmixing is available on this platform (10.5281/zenodo.3243376) and has been described in our previous publications (10.3390/mps2030060, 10.5281/zenodo.3333469, 10.1002/cbic.202000204, 10.5281/zenodo.3723806 ). Further applications of this method can be found in our recent article in <em>Adv. Synth. Catal.</em> (10.1002/adsc.201901230) and its supporting material (10.5281/zenodo.3568858), as well as a preprint (10.26434/chemrxiv.12993416.v1) and its supporting material (10.5281/zenodo.4043929).</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.