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1,028 results for “Protons”
Source data file for "Vibrational signature of hydrated protons confined in MXene interlayers"
<p>Source data file for the manuscript entitled: "Vibrational signature of hydrated protons confined in MXene interlayers"</p>
Dataset for Quantum anomaly detection in the latent space of proton collision events at the LHC
<p>Dataset used for https://arxiv.org/abs/2301.10780. The initial dataset is compressed to a low-dimensional latent space using a deep autoencoder. Files with compressed data are provided here in HDF5 format. Different sets of files are given, for different choices of dimensionality for the latent space. A description of the dataset is provided in https://arxiv.org/abs/2301.10780</p>
EMIC-driven precipitation events observed by ELFIN, using proton precipitation as a proxy for EMIC waves
<p>This dataset lists the time intervals of the precipitation events observed by ELFIN nearby proton precipitation (a proxy for EMIC waves). This dataset is analyzed in the paper "Electron Precipitation Observed by ELFIN Using Proton Precipitation as a Proxy for Electromagnetic Ion Cyclotron (EMIC) Waves", currently under review in Geophysical Research Letters.</p>
Data release for "Measurements of neutrino oscillation parameters from the T2K experiment using 3.6E21 protons on target"
<p>This archive contains the electronic version in ROOT format of the measurements of oscillation parameters in the paper "Measurements of neutrino oscillation parameters using 3.6 \times 10^{21} protons on target with the T2K experiment". Its arxiv identifier is <a href="https://arxiv.org/abs/2303.03222">arXiv:2303.03222 [hep-ex]</a>, and Published in <a href="https://doi.org/10.1140/epjc/s10052-023-11819-x"><em>Eur. Phys. J. C</em> <strong>83</strong>, 782 (2023)</a>.</p> <p>**************************************<br>***** Results included in this release<br>**************************************<br>Both Bayesian and frequentist results are provided, with details of each analysis provided in the paper. All published oscillation parameters are provided, with 2D confidence/credible regions and 1D DeltaChi^2 and posterior probability density distributions. The Bayesian and frequentist results are separated in two different files ("Bayesian_DataRelase.root" and "Frequentist_DataRelease.root"), and an a tag in the TGraph and histogram names also allow to differentiate them: "cred" for credible interval from the Bayesian analysis, "conf" for confidence interval from the frequentist analysis. For the 1D distributions, the posteriors are Bayeisan results and the DeltaChi^2 are frequentist results.</p> <p>Results for each mass hierarchy hypothesis are provided, denoted "NH" for normal hierarchy and "IH" for inverted hierarchy. The Bayesian file also includes the results marginalised over the mass hierarchy, denoted by the tag "both" in the object names.<br>The Bayesian and frequentist results use different conventions for the mass splitting in the inverted hierarchy: the Bayesian results are in term of #Deltam^{2}_{32} for both normal (NH) and inverted (IH) hierarchies, whereas the frequentist results are plotted versus #Deltam^{2}_{32} for the NH, and |#Deltam^{2}_{31}| for the IH.</p> <p>When employed, the constraint on theta13 from reactor experiment results corresponds to the value in the PDG 2019 summary table: sin^2(theta_13)=(2.18+-0.07) x 10^{-2}. This is commonly referred to as "the reactor constraint".<br>Results marked "woRC" are without this reactor constraint, and "wRC" are with the reactor constraint.</p> <p>A glossary is provided at the end of this readme.</p> <p>Two example ROOT macros ("Bayesian_example.cpp" and "Frequentist_example.cpp") showcase how to extract information from the data release. These produce pdf files of the results that can be directly compared to the "*ref.pdf" files for validation.</p> <p>**************************************<br>***** Objects inside the ROOT files<br>**************************************<br>The ROOT objects contained inside the files are named first with an identifier of which parameter(s) are being shown, followed by the reactor constraint tag, followed by the mass hierarchy tag.<br>For the frequentist results, there's an additional "FC" tag, marking if critical DeltaChi^2 values have been computed with Feldman-Cousins ("FC") or using Wilks' theorem (constant DeltaChi^2).</p> <p>**************************************<br>*** 2D regions<br>**************************************<br>Objects of the form<br>gr2D_varX_varY_<wRC,woRC>_<NH,IH,both>_<conf,cred><68,90,955,997>(_N)<br>are TGraphs corresponding to the 2D confidence ("conf") or credible ("cred") regions for the 2 variables (varX, varY). N is the iterator for different TGraphs corresponding to the same region; these occur when confidence regions are discontinuous (for example when deltaCP loops over from +pi to -pi).<br>68, 90, 955, 997 are the percentage credible/confidence levels.</p> <p>The best fit markers are also provided for the 2D results:<br>gr2D_varX_varY_<wRC,woRC>_<NH,IH,both>_bestfit</p> <p>The best fit markers and contour lines are computed for each MH *separately*, i.e. assuming DeltaChi^2 is 0 at the minimum or that the total posterior probability integrates to 1 in the mass hierarchy considered. There is only one exception, some 2D regions for (sin^2(theta_23), dcp) are also provided using a best fit over both MH to allow for comparisons with other experiments using this convention. This special set of contours has an extra tag "globalMH" in its name to distinguish it from the others.</p> <p>For larger confidence/credible exclusion regions (e.g. 99.7%) and when the Bayesian analysis shows the result for dm2 for both hierarchies, the regions may be split in to discontinuous regions. They are named "_0" and "_1", and the value on the y-axis denotes dm^{2}_{23}, from which the hierarchy can be deduced. The examples show examples of how this can be acheived.</p> <p>**************************************<br>*** 1D plots<br>**************************************<br>Objects of the form<br>h1D_var<chi2,posterior>_<wRC,woRC>_<NH,IH><br>are TH1D of the DeltaChi^2 ("chi2") or posterior probability ("posterior") for oscillation parameter "var".</p> <p>The Bayesian and frequentist results use different conventions with respect to the mass hierarchy:<br>- 1D DeltaChi^2 plots use a global minimum over both hierarchies<br>- Each 1D posterior probability plot integrates to unity *individually*</p> <p>**************************************<br>***** Additional notes for frequentist results<br>**************************************<br>Most of the 2D frequentist regions were computed using the standard DeltaChi^2 values (from the Gaussian case), and not the Feldman-Cousins method. They therefore have only approximate coverage.<br>For the 2D distributions, only {sin^2(theta_23), deltaCP} with reactor constraint were computed using the Feldman-Cousins method, and are expected to have proper coverage. To distinguish them from other confidence regions, a tag "FC" is included in the name of the corresponding TGraph.<br>Additionally, those extra regions using Feldman-Cousins method are provided with two conventions regarding the best fit used to evaluate them. The TGraphs with an extra tag "globalMH" use a best fit over both MH hypothesis. The ones without this extra tag use the best fit obtained in each MH to compute the confidence regions for this MH.</p> <p>For the 1D plots, critical delta chi2 values obtained with the Feldman-Cousins method are provided for theta23 and deltaCP (with reactor constraint "wRC" case only):<br>grCritical_{variable}chi2_wRC_{MH}_conf{CL}<br> variable: th23, dCP<br> MH: NH, IH<br> CL: 68, 90, 955, 997</p> <p>To obtain the FC-corrected confidence interval in those 2 cases for a given confidence level, take the intersection of grCritical with the corresponding 1D histogram. This is shown in the example macros.</p> <p>**************************************<br>***** Additional notes for Bayesian results<br>**************************************<br>For plots involving the mass splitting, the choice of hierarchy is given by the sign:<br> dm32>0 is normal hierarchy (Delta m^2_{32} > 0)<br> dm32<0 is inverted hierarchy (Delta m^2_{32} < 0)</p> <p>For the Jarlskog invariant, the prior on deltaCP is either flat in deltaCP, or flat in sindeltaCP ("flatsindcp")</p> <p>Note that the posteriors have not been smoothed, and may contain small discontinuities due to MCMC statistical uncertainties, e.g. in "h1D_dCPposterior_wRC_IH" around delta CP=-1.47.</p> <p>Plots with "_bestfit" appended signify the point in the space with the highest posterior density, and is not necessarily the global minimum of the test-statistic.</p> <p>For the 1D posterior distributions, the user can freely calculate credible intervals from the distributions. It is recommended to start at the point of the highest posterior density, and moving down in posterior density to produce asymmetric credible intervals. The root macro "Bayesian_example.cpp" shows a method to do this.</p> <p>**************************************<br>***** Glossary<br>**************************************</p> <p>"RC" - Reaction Constraint from PDG 2019 sin^2(theta_13)=(2.18+-0.07) x 10^{-2}.<br>"wRC" - With Reactor Constraint<br>"woRC" - Without Reactor Constraint<br>"FC" - Feldman-Cousins<br>"NH" - Normal Hierarchy<br>"IH" - Inverted Hierarchy<br>"both" - Marginalised over normal and inverted hierarchy<br>"cred" - Credible interval<br>"conf" - Confidence interval<br> "68" - 68% (1 sigma)<br> "90" - 90%<br> "955" - 95.5% (2 sigma)<br> "997" - 99.7% (3 sigma)<br>"chi2" - DeltaChi^2 (-2lnL) for parameter<br>"Critical" - Critical DeltaChi^2 computed with Feldman-Cousins</p> <p>"th13" - sin^2(theta_13)<br>"th23" - sin^2(theta_23)<br>"dCP" - delta CP<br>"dm2" - Delta m^2_{23} (NH), |Delta m^2_{13} (IH)| for confidence intervals; used in frequentist analysis.<br>"dm32" - Delta m^{2_{23} regardless of hierarchy; in the Bayesian analysis Delta m^2_{23} is always plotted.<br>"jarlskog" - Jarlskog invariant, only in Bayesian analysis<br>"flatsindcp" - Flat in sin delta CP</p>
La and Mn-doped cobalt spinel oxygen evolution catalyst for proton exchange membrane electrolysis
<p>Finding electrocatalysts using earth-abundant materials as a replacement to iridium for oxygen-evolution reaction (OER) in proton exchange membrane water electrolyzer (PEMWE) represents a critical step in reducing the cost for green hydrogen production. We report here a nanofibrous cobalt spinel catalyst co-doped with lanthanum and manganese prepared from zeolitic imidazolate framework embedded in electrospun polymer fiber. The catalyst demonstrated a low overpotential of 353 millivolts at 10 milliamperes per square centimeter and a low degradation for OER over 360 hours in acidic electrolyte. PEMWE containing this catalyst at anode demonstrated a current density of 2000 milliamperes per square centimeter at 2.47 volts (Nafion® 115 membrane) or 4000 milliamperes per square centimeter at 3.00 volt (Nafion® 212 membrane), and low degradation in accelerated-stress-test. High-resolution electronic microscopy and operando X-ray absorption spectroscopy, combined with computational modeling, revealed the different functions of lanthanum, manganese, and cobalt in enabling enhanced activity, conductivity and acidic tolerance within the OER operating window.</p>
Data release for "Updated T2K measurements of muon neutrino and antineutrino disappearance using 3.6E21 protons on target"
<p>This data release accompanies the results of T2K's analysis of muon neutrino and antineutrino oscillation data collected between 2010 and 2020. The file format is ROOT and contains the best-fit point and the 68% and 90% confidence level contours in the oscillation parameters space investigated by the analysis. The results for both mass ordering are included. Each entry in the file is a TGraph described in DataReleaseNuMuAntiNuMuDis.pdf.</p> <p>This is in <a href="https://doi.org/10.1103/PhysRevD.108.072011">Physical Review D </a>and available on the <a href="https://arxiv.org/abs/2305.09916">arXiv:2305.09916 [hep-ex]</a>.</p>
Human STING is a proton channel (Live-cell MGAT Super-Resolution Experiment)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) expressing SEP-mRuby3 targeted to cis/medial Golgi (MGAT) were transduced with pXPR023 (lentiCRISPRv2) expressing an sgRNA targeting STING and selected with 0.1 µg/mL puromycin for 5 days. Cells were then transduced with blasticidin-STING-miRFP680 and selected using 10 µg/mL blasticidin HCl for 5 days. Cells were plated in 96-well glass-bottom plates (Greiner Bio-One) at 6,000 cells/well. After 48 hours, cells were incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061) and stimulated with 1 µM diABZI (Invivogen, #tlrl-diabzi). All images were acquired using an LSM980 with Airyscan2 (Zeiss) with 37°C with 5% CO2 incubation. 8 z-stacks were acquired with 0.15 µm z-step. Images were acquired using a 63X 1.40 NA DIC M27 objective with Immersol 518F 37°C oil. Acquired images were Airyscan processed and then analyzed as described in the image analysis section.</p> <p>Each frame represens one timepoint imaged every 5 minutes post diABZI treatment. Channels are: SEP (super-ecliptic pHluorin), mRuby3, and STING-miRFP680.</p> <p> </p>
Human STING is a proton channel (Live-cell GALT pH Measurement upon STING agonist treatment with or without C53)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to GALT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM Bafilomycin A1 (Santa Cruz Biotechnology cat. #sc-201550),<strong> </strong>1 µM diABZI (Invivogen, #tlrl-diabzi), 20 µg/mL cGAMP (Invivogen, #tlrl-nacga23-1) with 5 ng/µL digitonin (Promega, #G9441) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (Live-cell MGAT pH Measurement upon STING agonist treatment with or without C53)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to MGAT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM Bafilomycin A1 (Santa Cruz Biotechnology cat. #sc-201550),<strong> </strong>1 µM diABZI (Invivogen, #tlrl-diabzi), 20 µg/mL cGAMP (Invivogen, #tlrl-nacga23-1) with 5 ng/µL digitonin (Promega, #G9441) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (Live-cell MGAT STING WT or S53L pH Measurement upon STING agonist treatment with or without C53)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to MGAT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. Cells then were transduced with pXPR023 (lentiCRISPRv2) expressing an sgRNA targeting STING and selected with 0.1 µg/mL puromycin for 5 days. Finally, cells were transduced with blasticidin-STING-HA (WT or S53L) and selected using 10 µg/mL blasticidin HCl for 5 days.<strong> </strong> BJ1 SEP-mRuby3 STING-HA (WT or S53L) cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM diABZI (Invivogen, #tlrl-diabzi) for 1 hr with or without the addition of 10 µM C53 (Cayman, #37354). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment. Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (HEK293T Autophagy Experiment)
<p>RFP-LC3 and STING-HA-expressing FIP200 KO 293T cells were seeded on Fibronectin bovine plasma coated 24-well glass-bottom plates (Greiner Bio-One) the night before stimulation. Cells were then stimulated with 20 µg/ml cGAMP (Invivogen, #tlrl-nacga23-1) with 5ug/ml digitonin (Promega, #G9441) or 1 µM DIABZI (Invivogen, #tlrl-diabzi) with or without the addition of 10 µM C53 (Cayman, #37354) for 1 hour. Cells were then fixed with 2% Paraformaldehyde (Electron Microscopy Sciences) in PHEM buffer (Electron Microscopy Sciences) for 30 minutes at 37°C, washed three times with PBS and quenched with freshly prepared 0.1M Glycine for 10 minutes. Cells were permeabilized in 100% methanol for 30 minutes and stained with anti-HA (Millipore, #11867423001) for 1 hour at room temperature in 3% BSA, washed 5 times, and then stained with Alexa 647 anti-rat IgG (H+L) (Thermo, A-21247) in 3% BSA for 1 hour. After five washes, cells were incubated in 2X SSC with 200 ng/mL DAPI (Thermo Fisher) and imaged using the Nikon microscope used for organelle pH images. Images were acquired using a 60X 1.40 NA Plan Apo λ oil immersion objective (Nikon MRD01605) with Nikon type F immersion oil with the following lasers and filters: DAPI (405 nm laser, Chroma <a href="https://www.chroma.com/products/parts/et455-50m">ET455/50</a>), RFP-LC3B (561 nm laser, Chroma ET605/52), and STING-HA (640 nm laser, Chroma ET705/72), assaying five z planes per field of view with 0.625 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks. Channels are: DAPI, LC3B-RFP, and STING.</p>
Human STING is a proton channel (Live-cell pH Calibration Meaurements)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to GALT constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For pH calibration experiments, cells were treated with buffers at defined pH values supplemented with nigericin and valinomycin following manufacturer’s instructions (Thermo Fisher Scientific cat. # P35379). Additional buffers at pH 7, 6, and 5 were created by titration with acid. All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one pH value: 7.5, 7, 6.5, 6, 5.5, 5, and 4.5 (except for replicate 1, which omitted pH 7). Channels are: Hoechst 34580, SEP (super-ecliptic GFP), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (Live-cell MGAT, GALT, and LAMP1 pH Measurements Upon BafA1 and diABZI treatment)
<p>hTERT-immortalized BJ1 cells (ATCC CRL-2522) were transduced with lentiviral ratiometric reporters targeted to MGAT, GALT, or LAMP1 constructed based on designs reported in Linders et al. <em>ACS Chem. Biol. </em>2022, with superecliptic pHluorin and mRuby3. Transduced cells were sorted based on mRuby3 expression using a Sony MA900 sorter. BJ1 SEP-mRuby3 cells were plated in 24-well glass-bottom plates (Greiner Bio-One) at 40,000 cells/well. After 48 hours, cells were stained for 45 minutes at 37°C with 0.5 µg/ml Hoechst 34580 (Thermo Fisher Scientific, cat. #H21486). Cells were then washed and incubated in Fluorobrite DMEM (Thermo Fisher Scientific, cat. #A1896701) medium supplemented with 10% FBS, 1% Pen-strep, and 1x GlutaMAX (Thermo Fisher Scientific, cat. #35050061). For time-course experiments, cells were stimulated with 1 µM Bafilomycin A1 (Santa Cruz Biotechnology cat. #sc-201550), or 1 µM diABZI (Invivogen, #tlrl-diabzi). All images were acquired using a Ti2-E inverted epifluorescence microscope (Nikon) with automated XYZ stage control, hardware autofocus, and a Yokogawa CSU-W1 confocal spinning disk unit with Zyla 4.2 PLUS sCMOS camera. An Okolab cage incubator was set to 37°C with 5% CO2. 405, 488, 561, and 640 nm laser lines were used for fluorescence illumination and all hardware was controlled using NIS elements software. Images were acquired using a 40X 0.95 NA CFI Plan Apo λ objective (Nikon MRD70470) with the following lasers and filters: Hoechst (405 nm laser, Chroma Multi LED set #89401), superecliptic pHluorin (488 nm laser, Chroma Multi LED set #89401), and mRuby3 (561 nm laser, Chroma Multi LED set #89401), assaying three z planes per field of view with 1.25 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks with each frame representing one timepoint: 0, 10, 20, 30, 40, 50, 60 minutes post treatment (except for replicate 1, which omitted the final timepoint). Channels are: Hoechst 34580, SEP (super-ecliptic pHluorin), mRuby3, and SEP/mRuby3 (ratio). Crops indicate cropped fields of view presented in the manuscript.</p>
Human STING is a proton channel (HEK293T Inflammasome Experiment)
<p>HEK293T cells transduced to express NLRP3-mNeonGreen and STING-HA were plated in 24-well glass-bottom plates (Greiner Bio-One) and, after 24 hours, stimulated with 2 µM nigericin or 1 µM diABZI with or without the addition of 10 µM C53 for 1 hour. Cells were then fixed with 2% Paraformaldehyde (Electron Microscopy Sciences) in PHEM buffer (Electron Microscopy Sciences) for 30 minutes at 37°C, washed three times with PBS and quenched with freshly prepared 0.1M Glycine for 10 minutes. Cells were permeabilized in 100% methanol for 30 minutes and stained with anti-HA (Millipore, #11867423001) and anti p-STING (Cell Signaling Technology cat. #19781s) for 1 hour at room temperature in 3% BSA, washed 5 times, and then stained with Alexa 647 anti-rat IgG (H+L) (Thermo, A-21247) and Alexa 555 plus anti-rabbit (Thermo, A32732) in 3% BSA for 1 hour. After five washes, cells were incubated in 2X SSC with 200 ng/mL DAPI (Thermo Fisher) and imaged using the Nikon microscope used for organelle pH images. Images were acquired using a 60X 1.40 NA Plan Apo λ oil immersion objective (Nikon MRD01605) with Nikon type F immersion oil with the following lasers and filters: DAPI (405 nm laser, Chroma <a href="https://www.chroma.com/products/parts/et455-50m">ET455/50</a>), NLRP3 mNeonGreen (488nm laser, Chroma ET525/36) pSTING (561 nm laser, Chroma ET605/52), and STING-HA (640 nm laser, Chroma ET705/72), assaying five z planes per field of view with 0.625 µm spacing. Fields of view were selected using NIS Elements software coordinates without manual preselection.</p> <p>Images are maximum projections of multiple z-stacks. Channels are: DAPI, NLRP3 mNeonGreen, pSTING, and STING.</p>
Infrared action spectroscopy as tool for probing gas-phase dynamics: Protonated Dimethyl Ether ((CH3)2OH+) formed by the reaction of CH3OH2+ with CH3OH
<p>The series of folder contain the .log files from Gaussian(R) 16 of the different species and at different level of theories, as specified in the subfolders and filenames. The data refer to calculations that have been submitted for publication as an original research paper:</p> <p>Title: "Infrared action spectroscopy as tool for probing gas-phase dynamics: Protonated Dimethyl Ether, (CH<sub>3</sub>)<sub>2</sub>OH<sup>+</sup>, formed by the reaction of CH<sub>3</sub>OH<sub>2</sub><sup>+</sup> with CH<sub>3</sub>OH</p> <p>Journal: Molecular Physics</p> <p>Authors: V. Richardson, D.B. Rap, S. Brünken and D. Ascenzi</p>
Doping of molecular semiconductors through proton-coupled electron transfer
<p>Doping of molecular semiconductors through proton-coupled electron transfer was conducted. Doping levels, electronic properties, and thin film structures of doped polymeric semiconductors were evaluated through conductivity, UV-Vis-NIR absorption, photoelectron yield, x-ray photoelectron, and x-ray diffraction measurements, where proton-coupled electron transfer reaction enable precise control of doping levels depending on pH of doping solutions under ambient conditions.</p>
MCNP Results for Nanocomposite Shielding in High-Energy Proton Fields
<p>Monte Carlo radiation transport results for various physics schemes (neutron + proton, neutron + proton + delta ray, and neutron + proton + delta ray + light recoil ions) and nanocomposite structural models (bulk homogenous material, hollow carbon cylinders suspended in polymer matrix, and carbon spheres in nanotube structure suspended in polymer matrix) of a polymer-carbon-nanotube nanocomposite shielding material in high-energy proton beams of 63 MeV and 105 MeV. </p>
Protonated hydrogen cyanide as a tracer of pristine molecular gas
<p>The data cubes used in<a href="https://www.aanda.org/articles/aa/full_html/2023/11/aa47409-23/aa47409-23.html"> Gong et al., (2023), A&A, 679, A39 </a></p>
Study of Proton Therapy in Adjuvant Pancreatic Cancer
ClinicalTrials.gov study NCT03885284. IPD Sharing: NO. Countries: 1. Publications: 0.
A Trial of 15 Fraction vs 25 Fraction Pencil Beam Scanning Proton Radiotherapy After Mastectomy in Patients Requiring Regional Nodal Irradiation
ClinicalTrials.gov study NCT02783690. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.