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Net community production (NCP) and gross oxygen production (GOP), based on oxygen-argon ratios and triple oxygen isotopes, from seasonal NES-LTER Transect cruises in 2018
This data package provides net community production (NCP) and gross oxygen production (GOP, a measure of gross primary production) for the winter, spring, summer, and fall Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) Transect cruises in 2018. Two tables are provided: a high-frequency table with NCP rates calculated from measurements of O2/Ar made continuously by an at-sea equilibrator inlet mass spectrometer (EIMS), and a low-frequency table with both NCP and GOP rates calculated for discrete samples measured post-cruise. The GOP rates were calculated from triple O2 isotopic (TOI) ratios. These data are derived from the EIMS and TOI data for the NES-LTER Transect cruises in EDI data package knb-lter-nes.6.3.
Net community production (NCP) and gross oxygen production (GOP), based on oxygen-argon ratios and triple oxygen isotopes, from seasonal NES-LTER Transect cruises in 2019
This data package provides net community production (NCP) and gross oxygen production (GOP, a measure of gross primary production) for the winter, spring, summer, and fall Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) Transect cruises in 2019. Two tables are provided: a high-frequency table with NCP rates calculated from measurements of O2/Ar made continuously by an at-sea equilibrator inlet mass spectrometer (EIMS), and a low-frequency table with both NCP and GOP rates calculated for discrete samples measured post-cruise. The GOP rates were calculated from triple O2 isotopic (TOI) ratios. These data are derived from the EIMS and TOI data for the NES-LTER Transect cruises in EDI data package knb-lter-nes.6.3.
Oxygen-argon dissolved gas ratios using Equilibrator Inlet Mass Spectrometry (EIMS) and triple oxygen isotopes (TOI) from NES-LTER Transect cruises, ongoing since 2018
In order to calculate net community production (NCP) rates on Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) transect cruises, gas tracer data were collected with a continuous at-sea mass spectrometer. The ratio of O2/Ar, measured continuously from underway water, yields 8,000-15,000 rates of NCP per cruise. Discrete water samples (50 to 150 per cruise) were collected for triple oxygen isotope (TOI) analysis to estimate gross primary production (GPP) rates and ratios of NCP/GPP. Along-shelf (upstream-downstream) transects were conducted in addition to the main across-shelf transect. This data package provides two types of data tables for NES-LTER transect cruises beginning in 2018: a high-frequency continuous Equilibration Inlet Mass Spectrometer (EIMS) table, provided by year, and a low-frequency discrete triple oxygen isotope (TOI) table with all years combined. Rates calculated from these measurements are provided as separate packages, per year, in the EDI repository.
Net community production (NCP) and gross oxygen production (GOP), based on oxygen-argon ratios and triple oxygen isotopes, from seasonal NES-LTER Transect cruises in 2020
This data package provides net community production (NCP) and gross oxygen production (GOP, a measure of gross primary production) for the winter, spring, and summer Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) Transect cruises in 2020. Two tables are provided: a high-frequency table with NCP rates calculated from measurements of O2/Ar made continuously by an at-sea equilibrator inlet mass spectrometer (EIMS), and a low-frequency table with both NCP and GOP rates calculated for discrete samples measured post-cruise. The GOP rates were calculated from triple O2 isotopic (TOI) ratios. These data are derived from the EIMS and TOI data for the NES-LTER Transect cruises in EDI data package knb-lter-nes.6.3.
Net community production (NCP) and gross oxygen production (GOP), based on oxygen-argon ratios and triple oxygen isotopes, from seasonal NES-LTER Transect cruises in 2021
This data package provides net community production (NCP) and gross oxygen production (GOP, a measure of gross primary production) for the winter and summer Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) Transect cruises in 2021. Two tables are provided: a high-frequency table with NCP rates calculated from measurements of O2/Ar made continuously by an at-sea equilibrator inlet mass spectrometer (EIMS), and a low-frequency table with both NCP and GOP rates calculated for discrete samples measured post-cruise. The GOP rates were calculated from triple O2 isotopic (TOI) ratios. These data are derived from the EIMS and TOI data for the NES-LTER Transect cruises in EDI data package knb-lter-nes.6.3.
Net community production (NCP) and gross oxygen production (GOP), based on oxygen-argon ratios and triple oxygen isotopes, from seasonal NES-LTER Transect cruises in 2022
This data package provides net community production (NCP) and gross oxygen production (GOP, a measure of gross primary production) for the winter and summer Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) Transect cruises in 2022. Two tables are provided: a high-frequency table with NCP rates calculated from measurements of O2/Ar made continuously by an at-sea equilibrator inlet mass spectrometer (EIMS), and a low-frequency table with both NCP and GOP rates calculated for discrete samples measured post-cruise. The GOP rates were calculated from triple O2 isotopic (TOI) ratios. These data are derived from the EIMS and TOI data for the NES-LTER Transect cruises in EDI data package knb-lter-nes.6.3.
Tumor growth kinetics of human LM2-4LUC+ triple negative breast carcinoma cells
<p><strong>Cell culture and data set</strong></p> <p>Tumor growth data used in this study were obtained from experiments involving the use of a LM2-4<sup>LUC+</sup> cells (or LM2-4), a metastatic variant of the human triple-negative breast carcinoma MDA-MB-231 cells. Animal studies were performed as described previously under Roswell Park Comprehensive Cancer Center (RPCCC) Institutional Animal Care and Use Committee (IACUC) protocol number 1227M [1-7]. Tumor growth data were pooled from eight separate experiments conducted with a total of 581 observations, and represent control (vehicle-treated) animals from published studies [1-7]. Vehicle formulation was carboxymethylcellulose sodium (USP, 0.5% w/v), NaCl (USP, 1.8% w/v), Tween-80 (NF, 0.4% w/v), benzyl alcohol (NF, 0.9% w/v), and reverse osmosis deionized water (added to final volume) and adjusted to pH 6 (see [3]) and was given at 10ml/kg/day for 7-14 days prior after tumor implantation and before tumor resection [1-7].</p> <ul> </ul> <p><strong>Tumor injections</strong></p> <p>LM2-4<sup>LUC+</sup> cells were orthotopically implanted (10<sup>6</sup> cells per injection) into the right inguinal mammary fat pads of 6- to 8-week-old female severe combined immunodeficient (SCID) mice.</p> <p><strong>Tumor measurements</strong></p> <p>Tumor size was measured regularly with calipers to a maximum volume of 2 cm<sup>3</sup>, calculated by the formula </p> <p><span class="math-tex">\(V = \frac{\pi}{6} w^2 L\)</span></p> <p>(ellipsoid) where <em>L</em> is the largest and <em>w</em> is the smallest tumor diameter.</p> <p><strong>Please cite: </strong>Vaghi C, Rodallec A, Fanciullino R, Ciccolini J, Mochel JP, et al. (2020) Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors, PLoS Comput Biol, 16, p. e1007178. <a href="https://doi.org/10.1371/journal.pcbi.1007178">https://doi.org/10.1371/journal.pcbi.1007178</a></p> <p> </p> <p>In the file, the columns correspond to:</p> <ul> <li>ID: identifier of the animal</li> <li>Time: day of the tumor measurement after implantation</li> <li>Observation: tumor measurement (in mm<sup>3</sup>)</li> </ul> <p> </p> <p><strong>References</strong></p> <p>[1] Benzekry, S., Lamont, C., Beheshti, A., Tracz, A., Ebos, J. M. L., Hlatky, L., & Hahnfeldt, P. (2014). Classical mathematical models for description and prediction of experimental tumor growth. PLoS Comput Biol, <em>10</em>(8), e1003800. http://doi.org/10.1371/journal.pcbi.1003800</p> <p>[2] Benzekry S, Tracz A, Mastri M, Corbelli R, Barbolosi D, Ebos JML. (2016) Modeling Spontaneous Metastasis Following Surgery: An In Vivo-In Silico Approach. Cancer Res.;76(3):535–547. doi:10.1158/0008-5472.CAN-15-1389.</p> <p>[3] Ebos JML, Lee CR, Bogdanovic E, Alami J, Van Slyke P, Francia G, et al. (2008) Vascular Endothelial Growth Factor-Mediated Decrease in Plasma Soluble Vascular Endothelial Growth Factor Receptor-2 Levels as a Surrogate Biomarker for Tumor Growth. Cancer Res.;68(2):521–529. doi:10.1158/0008-5472.CAN-07-3217.</p> <p>[4] Ebos JML, Mastri M, Lee CR, Tracz A, Hudson JM, Attwood K, et al. (2014) Neoadjuvant antiangiogenic therapy reveals contrasts in primary and metastatic tumor efficacy. EMBO Mol Med;6:1561–76. https://doi.org/10.15252/emmm.201403989</p> <p>[5] Ebos JML, Lee CR, Cruz-Munoz W, Bjarnason GA, Christensen JG, Kerbel RS. (2009) Accelerated metastasis after short-term treatment with a potent inhibitor of tumor angiogenesis. Cancer Cell;15:232–9. https://doi.org/10.1016/j.ccr.2009.01.021</p> <p>[6] Mastri M, Tracz A, Lee CR, Dolan M, Attwood K, Christensen JG, et al. (2018) A Transient Pseudosenescent Secretome Promotes Tumor Growth after Antiangiogenic Therapy Withdrawal. Cell Rep.; 25 (13):3706–20 e8. Epub 2018/12/28. https://doi.org/10.1016/j.celrep.2018.12.017</p> <p>[7] Vaghi C, Rodallec A, Fanciullino R, Ciccolini J, Mochel JP, et al. (2020) Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors, PLoS Comput Biol, 16, p. e1007178. <a href="https://doi.org/10.1371/journal.pcbi.1007178">https://doi.org/10.1371/journal.pcbi.1007178</a></p>
all-uf-triples: v0.0.1 August 2015 version of All UF triples from vivo.ufl.edu
<p>v0.0.1 August 2015 version of All UF triples from vivo.ufl.edu</p> <p>2015-08-06 release 0.0.1</p> <p>File: all-uf-triples-august-2015.tar.gz (178M) MD5: (all-uf-triples-august-2015.tar.gz) = 262c4e82be87cc24b04ccad188e75487 Download: http://vivo.ufl.edu/all-uf-triples-august-2015.tar.gz</p> <p>Unzips to all-uf-triples-august-2015.nt (~2.5GB)</p> <p>File Contains about 18.7 million lines $ wc -l all-uf-triples-august-2015.nt 18785880 all-uf-triples-august-2015.nt</p>
VHP4Safety Compound Wikidata Triples
<p>Export as a CSV file with triples from the VHP4Safety Compound Wiki.</p>
Double-Versus Triple-Potential Well Energy Harvesters: Dynamics and Power Output
<div>The present datasets and figures focus on the analysis of BEH and TEH systems where the corresponding depth of the potential well and the width of their characteristics are the same. The efficiency of energy harvesting for TEH and BEH systems assuming similar potential parameters is provided. The basic types of multistable energy harvesters are bistable energy harvesting systems (BEH) and tristable energy harvesting systems (TEH). Providing such parameters allows for reliable formulation of conclusions about the efficiency in both types of systems. These energy harvesting systems are based on permanent magnets and a cantilever beam designed to obtain energy from vibrations. Starting from the bond graphs, we derived the nonlinear equations of motion. Then we followed the bifurcations along the increasing frequency for both configurations. To identify the character of particular solutions, we estimated their corresponding phase portraits, Poincare sections, and Lyapunov exponents. The selected solutions are associated with their voltage output. The results in this numerical study show clearly that the bistable potential is more efficient for energy harvesting provided the corresponding excitation amplitude is large enough. However, the tristable one could work better in the limits of low-level and low-frequency excitations. </div> <div> <h2>Series information</h2> <p>Potential characteristics of energy harvesting systems caused by magnetic field of distributed permanent magnets:</p> <ul> <li>Fig4a_b_V_y1.txt</li> <li>Fig4a_r_V_y1.txt</li> </ul> <p>Potential characteristics of energy harvesting systems caused by magnetic field effect as in the previous case and an additional change in the stiffness of the flexible cantilever beam:</p> <ul> <li>Fig4b_b_V_y1.txt</li> <li>Fig4b_r_V_y1.txt</li> </ul> <p>Series of steady states of the system against frequency for two potential wells. </p> <ul> <li>Fig6a_p005.txt</li> <li>Fig6c_p025.txt</li> <li>Fig6e_p05.txt</li> <li>Fig6g_p085.txt</li> </ul> <p>Series of steady states of the system against frequency for three potential wells</p> <ul> <li>Fig6b_p005.txt</li> <li>Fig6d_p025.txt</li> <li>Fig6f_p05.txt</li> <li>Fig6h_p085.txt</li> </ul> <p>The excitation amplitude increases downwards from 0.05 to 0.85 and its values are listed in the corresponding description. The results were obtained for zero initial conditions. ω and x are dimensionless.</p> </div> <div><strong>Figures:</strong></div> <div> <p><a href="https://zenodo.org/api/records/14176152/draft/files/Fig%202.jpg/content" target="_blank" rel="noopener"><br>ig 2.jpg</a> - A graph of bonds representing the dynamics of the tested design solutions of energy harvesting systems.</p> <p><a href="https://zenodo.org/api/records/14176152/draft/files/Fig%203.jpg/content" target="_blank" rel="noopener">Fig 3.jpg</a> - A Lagrangian bond graph, with causality conflicts intentionally introduced.</p> <p><a href="https://zenodo.org/api/records/14176152/draft/files/Fig%204.jpg/content" target="_blank" rel="noopener">Fig 4.jpg</a> - Potential characteristics of energy harvesting systems caused by: (<strong>a</strong>) magnetic field of distributed permanent magnets (Fig. 1); (<strong>b</strong>) magnetic field effect as in previous case and an additional change in stiffness of the flexible cantilever beam (to satisfy equal potential barriers <em>V</em><sub>2</sub> = <em>V</em><sub>3</sub> ) used in further calculations.</p> <p><a href="https://zenodo.org/api/records/14176152/draft/files/Fig%206.jpg/content" target="_blank" rel="noopener">Fig 6.jpg</a> - Bifurcation diagrams (stroboscopic) of steady states of the system against frequency for: (<strong>a</strong>) Two potential wells; (<strong>b</strong>) three potential wells. The excitation amplitude increases downwards from 0.05 to 0.85 and its values are listed in the corresponding sub-figures. The results were obtained for zero initial conditions. <em>ω</em> and <em>x</em> are dimensionless.</p> <p><a href="https://zenodo.org/api/records/14176152/draft/files/Fig%207.jpg/content" target="_blank" rel="noopener">Fig 7.jpg</a> - Exemplary solutions showing the geometrical structures of chaotic phase flows and the corresponding Poincaré cross-sections of a BEH. <em>Dc</em> denotes the corresponding correlation dimension. <em>ω</em>, <em>p</em>, <em>x, </em>and x' are dimensionless.</p> <p><a href="https://zenodo.org/api/records/14176152/draft/files/Fig%208.jpg/content" target="_blank" rel="noopener">Fig 8.jpg</a> - Examples of periodic responses of a BEH system identified for dimensionless mechanical vibration amplitudes: (<strong>a</strong>) <em>p</em> = 0.05; (<strong>b</strong>) <em>p</em> = 0.25; (<strong>c</strong>) <em>p</em> = 0.5; (<strong>d</strong>) <em>p</em> = 0.85. <em>ω</em>, <em>p</em>, <em>x, </em>and<em> x'</em> are dimensionless.</p> <p><a href="https://zenodo.org/api/records/14176152/draft/files/Fig%209.jpg/content" target="_blank" rel="noopener">Fig 9.jpg</a> - Example solutions showing geometric structures of chaotic phase flows and corresponding Poincaré cross-sections, which were identified for a system with three potential wells (TEH). <em>Dc</em> denotes the corresponding correlation dimension. <em>ω</em>, <em>p</em>, <em>x, </em>and<em> x'</em> are dimensionless.</p> <p>Fig 10.jpg – Influence of external load characteristics on periodic induced solutions in a TEH. Trajectory shapes are plotted for selected frequencies ω. <em>ω</em>, <em>p</em>, <em>x, </em>and<em> x'</em> are dimensionless.</p> <p><a href="https://zenodo.org/api/records/14176152/draft/files/Fig%2011.jpg/content" target="_blank" rel="noopener">Fig 11.jpg</a> - Multicolored maps of the values of effective energy harvesting systems (RMS voltage outputs) with the potential: (<strong>a</strong>) two-well (BEH); (<strong>b</strong>) three-well (TEH) for zero initial conditions. <em>ω</em> and <em>p</em> are dimensionless, while <em>U<sub>RMS</sub></em> is expressed in Volts.</p> <p><a href="https://zenodo.org/api/records/14176152/draft/files/Fig%2012.jpg/content" target="_blank" rel="noopener">Fig 12.jpg</a> - Comparison of RMS<strong> </strong>voltage outputs for two and three wells potential systems versus amplitude and frequency. ω is dimensionless while <em>U<sub>RMS</sub></em> is expressed in Volts.</p> </div>
Raw data for the manuscript "Experimental Higher-Order Interference in a Nonlinear Triple Slit"
<p>This folder contains the raw data and analysis coded need to reproduce all of the major results in the manuscript "Experimental Higher-Order Interference in a Nonlinear Triple Slit". </p> <p>The folder "matlab" contains the data and code used to produce all of the main data figures in the paper. The various script load the data, and plots the final results used in the paper. </p> <p>The folder "mathematica" contains the scripts to implement our 4-th order perturbative quantum solution. There is one script to fit to experimental data to find the effective nonlinearity, and another to generate the dependence of the different terms if kappa as a function of Z. The result is plotted in the matlab script found in the directory "matlab\quantum"</p>
Evaluation of transcription factor knockout impact on paclitaxel response for Triple Negative Breast Cancer
<div>Data and code related to Zenodo repository: 10.5281/zenodo.11238552</div> <div> </div> <div>Two experimental formats included:</div> <div>'fixed' prefix: data from terminal time point of siRNA screen applied to HCC1143, HCC1806, and MDA-MB-468 Triple Negative Breast Cancer cell lines.</div> <div>'live' prefix: data from live-cell imaging of cell cycle reporter (HDHB-mClover/NLS-mCherry) HCC1143 Triple Negative Breast Cancer cell line.</div> <div>Note: 'live' level 1 data is available upon request (heiserl@ohsu.edu, calistri@ohsu.edu).</div> <div> </div> <div>Experimental goal:</div> <div>Evaluate whether siRNA knockdown of transcription factors elevated during paclitaxel response impact cell count, cell morphology or cycling dynamics.</div> <div> </div> <div>Methods:</div> <div>siRNA Knockdown: Cells were plated in 90ul of serum free media per well of a 96 well plate. 24 hours later, siRNA knockdown mixture was prepared using a cell-line optimized concentration of Lipofectamine RNAiMAX (cat 13778075-075, Invitrogen) and siRNA (Horizon Discovery ON-TARGETplus) following RNAiMAX recommended protocol. The final concentration of siRNA per well was 1pmol and the final volume of RNAiMAX per well was 75nL for HCC1143, and 37.5nL for HCC1806 or MDA-MB-468 in 100uL of cell containing volume. 24 hours after siRNA transfection cells were treated with an addition of 100uL complete media containing either DMSO vehicle control or paclitaxel. </div> <div> </div> <div>Fixed-cell assays: Cells were plated at 3000 cells in 100ul of complete media per well in a 96 well plate (#08-772-225, FisherScientific). After 24 hours, an additional 100ul of either vehicle (0.1% DMSO) or paclitaxel containing complete media was added. After 72 hours cells were fixed with 4% Formaldehyde (#28908, ThermoFisher Scientific) for 15 minutes at room temperature, then permeabilized with 0.3% Triton X-100 (#X100-100ML, Sigma Aldrich) for 10 minutes at room temperature, then washed twice with PBS. Fixed cells were then stained with 0.5ug/mL DAPI (4083S, Cell Signaling Technology) in PBS for 15 minutes at room temperature. Following DAPI staining, wells were washed once with PBS, then stained with 1:20,000 HCS CellMask Green in PBS (H32714, Invitrogen) for 15 minutes at room temperature. Wells were washed twice with room temperature PBS and then 4 fields of view per well imaged on an InCell 6000 (GE Healthcare). Images were segmented with two custom Cellpose models to segment the nucleus (using parameters: diameter = 50, chan = DAPI, chan2 = Cellmask Orange) and cytoplasm (using parameters: diameter = 90, chan = Cellmask Orange, chan2 = DAPI). Image quantification was performed in R (v4.3.1) using EBImage (v4.42.0), and cells were annotated based on the number of distinct nuclei segmented within each cytoplasmic mask. </div> <div> </div> <div>HDHB reporter live-cell assays: siRNA knockdown and drug treatment was performed as described above, and then the plate was loaded on an Incucyte S3 (Sartorious) and cells imaged every 15 minutes for 72 hours post drug treatment. At each timepoint 4 fields of view were captured at 20x magnificantion in each well using the phase, red and green channels. A cytoplasmic mask was computed from the mean of normalized red/green channel (cellpose parameters: diameter = 57, chan = mean(normalized(red), normalized(green)), and a nuclear mask was computed from the red channel (cellpose parameters: diameter = 30, chan = DAPI) using custom trained Cellpose models. Image quantification was performed in R (v4.3.1) using EBImage (v4.42.0). An additional perinuclear ring mask was computed as the 11 pixel dilation from the nuclear mask, but still bound by the cytoplasmic mask. To determine mClover localization thresholds for cell cycle assignment, 250 cell images were randomly selected and manually assigned to the G1, S/G2 or M cell cycle state based on mClover localization. The mClover intensity ratios were then used to determine thresholds for automated cell cycle phase calling which was applied to the rest of the data set (Supplemental Figure 5A). Mononuclear cells with a Perinuclear:Nuclear mean intensity ratio greater than 0.8 and Nuclear:Cytoplasmic total intensity less than 0.5 were assigned to the S/G2 phase. Mononuclear and Multinuclear cells with a Nuclear:Cytoplasmic total intensity ratio greater than 0.8 and Perinuclear:Nuclear mean intensity ratio less than 0.8 were assigned to the ‘M’ phase. The remainder of mononuclear cells were assigned ‘G1’, and the remainder of multinucleated cells were assigned ‘Multinucleated’. </div> <div> </div> <div>Included files:</div> <div>fixed_level_1-plate_#.zip : Six .zip archives containing the raw images (DAPI/CellMask/Brightfield) from fixed-cell experiments.</div> <div>plate 1: HCC1143 cells treated with plate A schema</div> <div>plate 2: HCC1143 cells treated with plate B schema</div> <div>plate 3: HCC1806 cells treated with plate A schema</div> <div>plate 4: HCC1806 cells treated with plate B schema</div> <div>plate 5: MDA-MB-468 cells treated with plate A schema</div> <div>plate 6: MDA-MB-468 cells treated with plate B schema</div> <div>fixed_level_2: Data quantified from cellpose masks at the single-nuclei level (redundant cytoplasm information)</div> <div>fixed_level_3: Data from 'fixed_level_2.csv' collapsed to the single cell level, including staining intensity and aggregate nuclear information</div> <div>fixed_incell_to_cellpose.rmd: R markdown code for converting original incell files (fixed_level_1) to RGB images for cellpose segmentation</div> <div>fixed_image_quantification.rmd: R markdown code for quantifying images using cellpose segmentation masks and original images (fixed_level_1)</div> <div>fixed_cellpose_models.zip: Archive including cellpose models used for fixed experiment</div> <div>live_level_2: Data quantified from cellpose masks at the single-nuclei level (redundant cytoplasm information)</div> <div>live_level_3: Data from 'live_level_2.csv' collapsed to the single cell level, including staining intensity and aggregate nuclear information</div> <div>live_level_4: Data from 'live_level_3.csv' collapsed to the single condition level summarizing the number, multinucleation status and phase of cells at each time point.</div> <div>live_image_quantification.rmd: R markdown code for quantifying images using cellpose segmentation masks and original images (live_level_1).</div> <div>l ive_incu_archive2rgb.rmd: R markdown code for converting incucyte archive formatted data into RGB images, where the blue channel is the arithmetic mean of the min-max (0-1) normalized red and green channels.</div> <div>live_cellpose_models.zip: Archive including cellpose models used for live experiment.</div> <div> </div> <div> </div>
Impact of paclitaxel treatment on the Triple Negative Breast Cancer Cell line HCC1143
<div>Data and code related to Zenodo repository: 10.5281/zenodo.11237850</div> <div> </div> <div>Experimental goal:</div> <div>Evaluate the impact of escalating paclitaxel dose on cell count, nuclear morphology and cellular outcome.</div> <div> </div> <div>Methods:</div> <div>Cells were plated at 3000 cells in 100ul of complete media per well in a 96 well plate (#08-772-225, FisherScientific). After 24 hours, an additional 100ul of either vehicle (0.1% DMSO) or paclitaxel containing complete media was added. After 72 hours cells were fixed with 4% Formaldehyde (#28908, ThermoFisher Scientific) for 15 minutes at room temperature, then permeabilized with 0.3% Triton X-100 (#X100-100ML, Sigma Aldrich) for 10 minutes at room temperature, then washed twice with PBS. Fixed cells were blocked with 1% BSA (A7906-100G, Millipore Sigma) in PBS for 1 hour at room temperature and then stained overnight with 1:100 anti-CDKN2A/p16INK4A+CDKN2B/p15INK4B-AF644 (#ab199756, Abcam), and 1:100 anti-cPARP-AF647 (#6987S, Cell Signaling Technology) or 1:500 anti-TUBB3-AF647 (#ab190575, Abcam) overnight at 4C. Each well was washed twice with room temp PBS then stained with 0.5ug/mL DAPI (4083S, Cell Signaling Technology) in PBS for 15 minutes at room temperature. Following DAPI staining, wells were washed once with PBS, then stained with 1:20,000 HCS CellMask in PBS (Orange: #H32713, Green: #H32714, Invitrogen) for 15 minutes at room temperature. Wells were washed twice with room temperature PBS and then 4 fields of view per well imaged on an InCell 6000 (GE Healthcare). Images were segmented with two custom Cellpose models to segment the nucleus (using parameters: diameter = 45, chan = DAPI, chan2 = Cellmask Orange) and cytoplasm (using parameters: diameter = 90, chan = Cellmask Orange, chan2 = DAPI). Image quantification was performed in R (v4.3.1) using EBImage (v4.42.0), and cells were annotated based on the number of distinct nuclei segmented within each cytoplasmic mask. </div> <div> </div> <div>Included files:</div> <div>row_#_level_1.zip : 6 zip file containing original images from InCell 6000, one zip per row</div> <div>level_2.csv : Data quantified to the nuclear level (cytoplasmic quantification is duplicates across multiplet nuclei)</div> <div>level_3.csv: Data quantified at the cellular level including number of nuclei and stain intensities for segmented compartments</div> <div>platemap.csv: Description of each well from the stained plate</div> <div>cellpose_modelz.zip: Zip file containing the two CellPose models used for segmentation</div> <div>image_quantification.rmd : R markdown file containing code for extracting and quantifying image intensities using the raw images (level_1) and segmentation masks created from cellpose.</div>
Dataset for Algorithms and Complexity for Counting Configurations in Steiner Triple Systems
<p>This dataset contains the classification of full n-line configurations (for all n <= 13, filename: "full_line_config_<n>.txt.gz") and w_3 configurations (for all w <= 16, filename: "w_3_config_<w>.txt.gz") together with the sizes of minimum generating sets. Each file lists "m<s>" so that s is the size of the minimum generating set of the subsequent configuration, which is denoted by writing the points of each of its lines row-wise. For example</p> <p>m3<br> 0 1 4<br> 0 2 6<br> 0 3 5<br> 1 2 5<br> 1 3 6<br> 2 3 4<br> 4 5 6</p> <p>is the Fano plane and its minimum generating set has size 3.</p> <p>Additionally, the file "fulllineconjecture.txt.gz" contains the 623 Steiner triple systems of order 25 (i.e., all rows which contain curly brackets) used in Theorem 7 in the paper below, followed by a row starting with 1 and then describing the number of occurrences of all 179 full n-line configurations for n <= 8, i.e., first the number of occurrences of Pasch configurations, then mitre configurations, then the 5 full 6-line configurations, the 19 full 7-line configurations, and finally the 153 full 8-line configurations contained in the STS(25) in the preceding row. The ordering follows the ordering within the files "full_line_config_<n>.txt.gz". This file is built so that omitting all lines with curly brackets is a valid gap code and results in a prove of said theorem (i.e., zgrep -v "{" fulllineconjecture.txt.gz | gap yields 180).</p> <p><br> Further details can be found in the corresponding publication</p> <p>"Algorithms and Complexity for Counting Configurations in Steiner Triple Systems"</p> <p>by Daniel Heinlein and Patric R. J. Östergård.</p> <p>All files are compressed with gzip.</p>
Onboarding/Registration (TRIPLE Video Tutorial Series)
<p>In this tutorial series, researcher Agnieszka Szulińska and Research Infrastructure Coordinator Edward Gray discuss gotriple.eu. This episode explores the opportunities GoTriple offers for registered users.</p>
DATASET OF "Impact of short-acting vs. standard anaesthetic agents on obstructive sleep apnoea: a randomised, controlled, triple-blind trial"
<p>Sleep apnoea is associated with negative outcomes following general anaesthesia. Current recommendations suggest using short-acting anaesthetic agents in preference to standard agents to reduce this risk, but there is currently no evidence to support this. This randomised controlled triple-blind trial tested the hypothesis that a combination of short-acting agents (desflurane-remifentanil) would reduce the postoperative impact of general anaesthesia on sleep apnoea severity compared with standard agents (sevoflurane-fentanyl). Sixty patients undergoing hip arthroplasty under general anaesthesia were randomised to anaesthesia with desflurane-remifentanil or sevoflurane-fentanyl. Respiratory polygraphy was performed before surgery and on the first and third postoperative nights. The primary outcome was the supine apnoea-hypopnoea index on the first postoperative night. Secondary outcomes were the supine apnoea-hypopnoea index on the third postoperative night, and the oxygen desaturation index on the first and third postoperative nights. Additional outcomes included intravenous morphine equivalent consumption and pain scores on postoperative days 1, 2 and 3. Pre-operative sleep study data were similar between groups. Mean (95%CI) values for the supine apnoea-hypopnoea index on the first postoperative night were 18.9 (12.7–25.0) and 21.4 (14.2–28.7) events.h<sup>-1</sup>, respectively, in the short-acting and standard anaesthesia groups (p=0.64). Corresponding values on the third postoperative night were 28.1 (15.8–40.3) and 38.0 (18.3–57.6) events.h<sup>-1</sup> (p=0.34). Secondary sleep- and pain-related outcomes were generally similar in the two groups. In conclusion, short-acting anaesthetic agents did not reduce the impact of general anaesthesia on sleep apnoea severity compared with standard agents. These data should prompt an update of current recommendations.</p>
[RDF Triples] Courses given at the Vrije Universiteit Amsterdam 2020/2021
<p>This data set is published in Turtle format using triples. </p> <p>The dataset contains all the Courses and their information at the Vrije Universiteit Amsterdam for the university year 2020/2021. This information was gathered from the Vrije Universiteit Amsterdam online study guide </p> <p>A new vocabulary 'vu' was needed as some vocabularies did not allow full expression of the datas et.</p> <p>You can use SPARQL in order to fetch data from this dataset, the property variables one can user are:</p> <ul> <li>vu:offeredByFaculty <ul> <li>This property will return the faculty the course belongs to as a vu:<strong>FacultyName</strong>.</li> </ul> </li> <li>vu:taughtBy <ul> <li>This property will return the professors who teach that course as a vu:<strong>ProfessorName</strong>.</li> </ul> </li> <li>vu:courseContent <ul> <li>This property returns what a course is about as a string. </li> </ul> </li> <li>vu:courseLevel <ul> <li>This property returns the course level (between 100 and 600) as an integer.</li> </ul> </li> <li>vu:courseObjective <ul> <li>This property returns the objective of a course as a string.</li> </ul> </li> <li>vu:literature <ul> <li>This property returns the required literature of a course as a string.</li> </ul> </li> <li>vu:recommendedBackground <ul> <li>This poperty returns the recommended background of a course as a string.</li> </ul> </li> <li>vu:targetAudience <ul> <li>This property returns the target audience of a course as a string.</li> </ul> </li> <li>vu:teachingMethods <ul> <li>This property returns the teaching methods of a course as a string. </li> </ul> </li> </ul> <p>These are the by us created property variables. There are also some re-used variables which are:</p> <ul> <li>vuc:<strong>CourseID</strong> rdf:type teach:Course <ul> <li>This returns all courses when used in sparql.</li> </ul> </li> <li>dbo:language <ul> <li>This property returns the language in which a course is given as a dbr:<strong>LanguageName</strong></li> </ul> </li> <li>teach:academicTerm <ul> <li>This property is used in order to return the academic term in which a course is given as a string.</li> </ul> </li> <li>teach:courseTitle <ul> <li>This property returns the name of a course as a string.</li> </ul> </li> <li>teach:ects <ul> <li>This property returns the number of European credits one receives for a course as an integer.</li> </ul> </li> <li>teach:grading <ul> <li>This property returns the grading method of a course as a string. </li> </ul> </li> </ul> <p>This data set can be used in order to find specific information about courses without knowing the exact course name or code. For example, you can fetch all courses that have 3 credits and are in English, given at the faculty of Science. Therefore it becomes much easier for students that want to follow courses outside of their major/master, which also fit their requirements. In a normal situation, a student would need to search through all 2064 courses given at the VU to find a course that they like. </p>
Supplementary File 7 from: Rapier-Sharman N et. al., Secondary Transcriptomic Analysis of Triple-Negative Breast Cancer Reveals Reliable Universal and Subtype-Specific Mechanistic Markers, 2024
<p>Supplementary Materials File 7. Please note that though the order of the supplementary materials has changed since initial upload (File S7 was previously File S9 or S10), the contents of this zipped folder remain the same.</p>
Station Data and Earthquake Catalogs - Distinct yet adjacent earthquake sequences near the Mendocino Triple Junction: 20 December 2021 Mw 6.1 and 6.0 Petrolia, and 20 December 2022 Mw 6.4 Ferndale
<p>Supplemental Material for publication from The Seismic Record (TSR):</p> <div> <div> <div> <p>Yoon, C. E. and D. R. Shelly (2024). Distinct Yet Adjacent Earthquake Sequences near the Mendocino Triple Junction: 20 December 2021 Mw 6.1 and 6.0 Petrolia, and 20 December 2022 Mw 6.4 Ferndale, The Seismic Record. 4(1), 81–92, doi: 10.1785/0320230053.</p> <p>Data Sets S0-S4 with station data and earthquake catalogs in text format</p> <p>See README_Data_Supplement.pdf for more details about contents of each data file. Please refer to the accompanying publication and its supplement for figures, tables, and equations.</p> </div> </div> </div> <p> </p>
Dataset of The Relationship Between Postoperative Opioid Analgesia and Sleep Apnea Severity in Patients Undergoing Hip Arthroplasty: A Randomized, Controlled, Triple-Blinded Trial
<p>This the dataset related to the article entitled "he Relationship Between Postoperative Opioid Analgesia and Sleep Apnea Severity in Patients Undergoing Hip Arthroplasty: A Randomized, Controlled, Triple-Blinded Trial".</p> <p>Purpose: Residual postoperative pain after hip arthroplasty is usually treated with oral opioids. While classic opioids are associated with respiratory depression and worsening of sleep apnea, tramadol has been reported to preserve respiratory function. However, this has not been investigated in a prospective trial using respiratory polygraphy. This randomized controlled triple-blinded trial tested the hypothesis that postoperative treatment with oral opioids such as oxycodone would increase sleep apnea severity, measured with a respiratory polygraphy, compared with oral tramadol.<br> Patients and Methods: Sixty patients undergoing hip arthroplasty under spinal anesthesia with 15 mg isobaric bupivacaine 0.5% were randomized to receive postoperative pain treatment with either oral oxycodone (controlled-release 10 mg every 12 hours and immediate-release 5 mg every 4 hours as needed) or oral tramadol (controlled-release 100 mg every 8 hours and immediate-release 50 mg every 4 hours as needed). Respiratory polygraphy was performed on the first postoperative night. The primary outcome was the apnea-hypopnea index in the supine position. Secondary outcomes included the oxygen desaturation index, postoperative pain scores and intravenous morphine consumption.<br> Results: Mean supine apnea-hypopnea index on postoperative night 1 was 11.3 events.h−1 (95% confidence interval, 4.8–17.7) in the oxycodone group and 10.7 (4.6–16.8) events.h−1 in the tramadol group (p=0.89). There were no significant differences between the oxycodone and tramadol groups with respect to any secondary sleep-related or pain-related outcomes.<br> Conclusion: Oral oxycodone did not increase sleep apnea severity measured using respiratory polygraphy compared with oral tramadol on the first postoperative night after hip arthroplasty.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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