Universität Innsbruck - Data Repository
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Data for Neuner and Buchner 2023: The dose makes the poison: The longer the heat lasts, the lower the temperature for functional impairment and damage. Environmental and Experimental Botany
No full text<h2>A primer on your dataset's description (to be edited)</h2><p>The influence of proper documentation on the reusability for research data should not be underestimated!<br>In order to help others understand how to interpret and reuse your data, we provide you with a few questions to help you structure your dataset's description (though please don't feel obligated to stick to them):</p><h3>Context and methodology</h3><ul><li>What is the research domain or project in which this dataset was created?</li><li>Which purpose does this dataset serve?</li><li>How was this dataset created?</li></ul><h3>Technical details</h3><ul><li>What is the structure of this dataset? Do the folders and files follow a certain naming convention?</li><li>Is any specific software required to open and work with this dataset?</li><li>Are there any additional resources available regarding the dataset, e.g. documentation, source code, etc.?</li></ul><h3>Further details</h3><ul><li>Is there anything else that other people may need to know when they want to reuse the dataset?</li></ul>
Volatilomic profiles of gastric juice in gastric cancer patients - Raw data
No full text<p>Raw data for the publication "Volatilomic profiles of gastric juice in gastric cancer patients". Measured with Agilent 8890/7079B GC-MS (Agilent, USA).</p>
Survival strategies of artificial active agents
No full text<p>Artificial cells can be engineered to display dynamics sharing remarkable features in common with the survival behavior of living organisms. In particular, such active systems can respond to stimuli provided by the environment and undertake specific displacements to remain out of equilibrium, e.g. by moving towards regions with higher fuel concentration. In spite of the intense experimental activity aiming at investigating this fascinating behavior, a rigorous definition and characterization of such "survival strategies" from a statistical physics perspective is still missing. In this work, we take a first step in this direction by adapting and applying to active systems the theoretical framework of Transition Path Theory, which was originally introduced to investigate rare thermally activated transitions in passive systems. We perform experiments on camphor disks navigating Petri dishes and perform simulations in the paradigmatic active Brownian particle model to show how the notions of transition probability density and committor function provide the pivotal concepts to identify survival strategies, improve modeling, and obtain and validate experimentally testable predictions. The definition of survival in these artificial systems paves the way to move beyond simple observation and to formally characterize, design and predict complex life-like behaviors.</p>
Concentration of α-amplexichromanol (27a) in lung and plasma of mice with ovalbumin induced asthma
No full text<p>Neukirch, K. et al. Exploration of Long-Chain Vitamin E Metabolites for the Discovery of a Highly Potent, Orally Effective, and Metabolically Stable 5-LOX Inhibitor that Limits Inflammation. J Med Chem 64, 11496-11526 (2021). https://doi.org/10.1021/acs.jmedchem.1c00806</p><p>BALB/c mice received <strong>27a</strong> (p.o.) or vehicle (0.5% carboxymethylcellulose in 10% Tween 20; 0.5 mL) on days 0 and 7, 1 h (p.o) before being sensitized to ovalbumin (100 μg adsorbed to 3.3 mg of aluminum hydroxide gel, s.c., Sigma-Aldrich). Mice were sacrificed on days 1, 3, 8, 10, or 21 to collect lung and plasma. Compound <strong>27a</strong> was analyzed in plasma and lung homogenates by UPLC-MS/MS as described in Neukirch et al., 2021. Lung tissue (100 mg/mL) was homogenized in PBS pH 7.4 at 4°C for 1−2 min using an Omni tissue homogenizer (Omni, Kennesaw, GA).</p>
Research data from the article "Media as Cookie Cutters. Exploring the Digital Mediality of News on Instagram."
No full text<p>This repository houses the research data for the article "Media as Cookie Cutters: Exploring the Digital Mediality of News on Instagram," providing a comprehensive set of files that underpin the study's examination of how Instagram's design and user experience shape the presentation and construction of news narratives. The dataset includes:</p><ul><li>A selection of Instagram posts from public news accounts, represented through images and corresponding textual descriptions, to illustrate the multimodal analysis of news presentation.</li><li>A videographic scroll-through capturing the UX of interacting with Instagram news feeds.</li><li>Tweets from Gary Lineker as examples of news-related content shared on social media platforms outside Instagram.</li></ul><p>This repository is intended for academic and research purposes, facilitating further study into the evolving landscape of digital news dissemination. For further information or inquiries regarding this dataset, please do not hesitate to <a href="mailto:[email protected] ">contact the author</a> directly.</p><p>Gary Lineker (@GaryLineker). "Ah, just do it anyway. Sod 'em." Twitter, June 22, 2021. <a href="https://twitter.com/GaryLineker/status/1407258630316036098">https://twitter.com/GaryLineker/status/1407258630316036098</a>.</p><p>Gary Lineker (@GaryLineker). "Do it Munich. Do it. Light it up for the world to see. @UEFA." Twitter, June 22, 2021. <a href="https://twitter.com/GaryLineker/status/1407273525409370114">https://twitter.com/GaryLineker/status/1407273525409370114</a>.</p><p>SRF News (@srfnews). "Uefa verbiete Regenbogen-Beleuchtung in München." Instagram. June 22, 2021. <a href="https://www.instagram.com/p/CQa46etLMqW">https://www.instagram.com/p/CQa46etLMqW</a>.</p><p>Tagesschau (@tagesschau). "Beleuchtung in Regenbogenfarben abgelehnt." Instagram. June 22, 2021. <a href="https://www.instagram.com/p/CQao0tjKk6a">https://www.instagram.com/p/CQao0tjKk6a</a>. </p><p>Zeit im Bild (@zeitimbild). "UEFA verbietet Regenbogen-Beleuchtung des Stadions in München." Instagram. June 22, 2021. <a href="https://www.instagram.com/p/CQa8WIGCwPf">https://www.instagram.com/p/CQa8WIGCwPf</a></p>
Effects of orally administered chromanols on pulmonary levels of lipid mediators in ovalbumine sensitized mice
No full text<p>Female mice were pretreated per os with α-T-13'-COOH (α-13′-carboxychromanol) and α-AC (α-amplexichromanol) (10 mg kg-1) or vehicle (DMSO 2% in CMC 0.5%, 0.5 ml) 60 min before each OVA (ovalbumine) challenge. Animals were sacrificed at day 21 and 14 to valuate pulmonary levels of COX products and 12/15-LOX-derived metabolites.</p><p>The methods and results were published in Cerqua et al., Pharmacol. Res., 2022 Jul;181:106250.doi: 10.1016/j.phrs.2022.106250 </p><p>Raw analyst files (.wiff and .wiff.scan) of the UPLC-MS/MS results were uploaded, together with an excel file for the sample list.</p><p>Non-esterified fatty acids and lipid mediators (LM) were extracted from plasma or lung homogenates using reversed phase cartridges (Sep-Pak® Vac 6cc 500 mg/6 ml C18; Waters). Internal standards added: d4-LTB4, d4-prostaglandin (PG)E2, d8–5S-hydroxyeicosatetraenoic acid (HETE), d5-lipoxin A4, d5-resolvin D2, (200 nM, each, Cayman Chemicals), and d8-arachidonic acid (AA, 10 μM, Cayman Chemicals). Lipid mediators were separated on an Acquity UPLC BEH C18 column (2.1 × 100 mm, Waters) using an Acquity UPLC system (Waters) and detected using a QTRAP 5500 mass spectrometer (SCIEX), equipped with an electrospray ionization source. Diagnostic ion fragments were determined by scheduled multiple reaction monitoring in the negative ion mode for peak identification.</p>
Analysis of the phosphatidylglycerol fatty acid composition in α-T-13′-COOH-treated macrophages
No full text<p>RAW264.7 cells were incubated with vehicle (DMSO, 'w/o') or 0.5 or 5.0 µM α-T-13′-COOH for 24 h. The fatty acid distribution of phosphatidylglycerol was then analyzed by UPLC-MS/MS.</p><p>Raw analyst files (.wiff and .wiff.scan) of the UPLC-MS/MS results were uploaded, together with an Excel file for the sample list.</p><p>The methods and results were published in Liao et al., Int J Mol Sci, 2023 May 25;24(11):9229. doi: 10.3390/ijms24119229 </p><p>Lipids were extracted from RAW264.7 cell pellets by the successive addition of methanol, PBS (pH 7.4), chloroform, and saline (final ratio: 34:14:35:17). After the evaporation of the organic solvent, the remaining lipid fraction was dissolved in methanol, stored at −20 °C, and analyzed by UPLC-MS/MS. Internal standards: 1,2-dimyristoyl-<i>sn</i>-glycero-3-phosphatidylcholine (DMPC), 1,2-dimyristoyl-<i>sn</i>-glycero-3-phosphatidyl-ethanolamine (DMPE).</p><p>Phospholipids (PC, PE, PI, PS, PG) were separated on an Acquity UPLC BEH C8 column (130 Å, 1.7 μm, 2.1 × 100 mm; Waters, Milford, MA, USA) using an Acquity UPLC system (Waters), which was coupled to a QTRAP 5500 mass spectrometer (Sciex, Framingham, MA, USA) equipped with a Turbo V Ion Source and an electrospray ionization probe. Chromatographic separation was performed at a flow rate of 0.75 mL/min and at a column temperature of 45 °C. The mobile phase was composed of eluent A (acetonitrile/water, 95/5, with 2 mM ammonium acetate) and eluent B (water/acetonitrile, 90/10, with 2 mM ammonium acetate). The gradient was ramped from 70% to 80% A within 5 min and to 100% A within 2 min, followed by isocratic elution for another 2 min. Eluted phospholipids were detected upon the fragmentation of parental ions (PC: [M+OAc]−, all other phospholipids: [M-H]−) to fatty acid anions derived from <i>sn</i>-1 and <i>sn</i>-2 positions by multiple reaction monitoring using a QTRAP 5500 mass spectrometer. The ion spray voltage was set to −4500 V, the curtain gas to 30 psi, the collision gas to medium, and the heated capillary temperature to either 350 °C (PC), 500 °C (PI), 550 °C (PS, PG), or 650 °C (PE). The sheath gas pressure was set to 45 (PS) or 55 psi (PC, PE, PI, PG) and the auxiliary gas pressure was set to either to 75 psi (PC, PE, PI, PG) or 80 psi (PS). The declustering potential was set to −40 V (PS), −44 V (PC), −45 V (PG), or −50 V (PE, PI), the entrance potential to −10 eV (PC; PE, PI, PS, PG), the collision energy to −38 eV (PE), −46 eV (PC), −52 eV (PG), −56 eV (PS), or −62 eV (PI), and the collision cell exit potential to −11 V (PC, PI), −12 V (PE), −18 V (PG), or −20 V (PS).</p><p>The instruments were either operated with Analyst 1.6.2 (QTRAP 5500, Sciex) or Analyst 1.7.1 (QTRAP 6500+, Sciex).</p>
Analysis of the phosphatidylinositol fatty acid composition in α-T-13′-COOH-treated macrophages
No full text<p>RAW264.7 cells were incubated with vehicle (DMSO, 'w/o') or 0.5 or 5.0 µM α-T-13′-COOH for 24 h. The fatty acid distribution of phosphatidylinositol was then analyzed by UPLC-MS/MS.</p><p>Raw analyst files (.wiff and .wiff.scan) of the UPLC-MS/MS results were uploaded, together with an Excel file for the sample list.</p><p>The methods and results were published in Liao et al., Int J Mol Sci, 2023 May 25;24(11):9229. doi: 10.3390/ijms24119229.</p><p>Lipids were extracted from RAW264.7 cell pellets by the successive addition of methanol, PBS (pH 7.4), chloroform, and saline (final ratio: 34:14:35:17). After the evaporation of the organic solvent, the remaining lipid fraction was dissolved in methanol, stored at −20 °C, and analyzed by UPLC-MS/MS. Internal standards: 1,2-dimyristoyl-<i>sn</i>-glycero-3-phosphatidylcholine (DMPC), 1,2-dimyristoyl-<i>sn</i>-glycero-3-phosphatidyl-ethanolamine (DMPE).</p><p>Phospholipids (PC, PE, PI, PS, PG) were separated on an Acquity UPLC BEH C8 column (130 Å, 1.7 μm, 2.1 × 100 mm; Waters, Milford, MA, USA) using an Acquity UPLC system (Waters), which was coupled to a QTRAP 5500 mass spectrometer (Sciex, Framingham, MA, USA) equipped with a Turbo V Ion Source and an electrospray ionization probe. Chromatographic separation was performed at a flow rate of 0.75 mL/min and at a column temperature of 45 °C. The mobile phase was composed of eluent A (acetonitrile/water, 95/5, with 2 mM ammonium acetate) and eluent B (water/acetonitrile, 90/10, with 2 mM ammonium acetate). The gradient was ramped from 70% to 80% A within 5 min and to 100% A within 2 min, followed by isocratic elution for another 2 min. Eluted phospholipids were detected upon the fragmentation of parental ions (PC: [M+OAc]−, all other phospholipids: [M-H]−) to fatty acid anions derived from <i>sn</i>-1 and <i>sn</i>-2 positions by multiple reaction monitoring using a QTRAP 5500 mass spectrometer. The ion spray voltage was set to −4500 V, the curtain gas to 30 psi, the collision gas to medium, and the heated capillary temperature to either 350 °C (PC), 500 °C (PI), 550 °C (PS, PG), or 650 °C (PE). The sheath gas pressure was set to 45 (PS) or 55 psi (PC, PE, PI, PG) and the auxiliary gas pressure was set to either to 75 psi (PC, PE, PI, PG) or 80 psi (PS). The declustering potential was set to −40 V (PS), −44 V (PC), −45 V (PG), or −50 V (PE, PI), the entrance potential to −10 eV (PC; PE, PI, PS, PG), the collision energy to −38 eV (PE), −46 eV (PC), −52 eV (PG), −56 eV (PS), or −62 eV (PI), and the collision cell exit potential to −11 V (PC, PI), −12 V (PE), −18 V (PG), or −20 V (PS).</p><p>The instruments were either operated with Analyst 1.6.2 (QTRAP 5500, Sciex) or Analyst 1.7.1 (QTRAP 6500+, Sciex). </p>
