Universität Innsbruck - Data Repository
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Learning how to find targets in the micro-world: The case of intermittent active Brownian particles
No full text<p>Finding the best strategy to minimize the time needed to find a given target is a crucial task both in nature and in reaching decisive technological advances. By considering learning agents able to switch their dynamics between standard and active Brownian motion, here we focus on developing effective target-search behavioral policies for microswimmers navigating a homogeneous environment and searching for targets of unknown position. We exploit \textit{Projective Simulation}, a reinforcement learning algorithm, to acquire an efficient stochastic policy represented by the probability of switching the phase, i.e. the navigation mode, in response to the type and the duration of the current phase. Our findings reveal that the target-search efficiency increases with the particle's self-propulsion during the active phase and that, while the optimal duration of the passive case decreases monotonically with the activity, the optimal duration of the active phase displays a non-monotonic behavior.</p>
Noise-cancellation algorithm for simulations of Brownian particles
No full text<p>We investigate the usage of a recently introduced noise-cancellation algorithm for Brownian simulations to enhance the precision of measuring transport properties such as the mean-square displacement or the velocityautocorrelation function. The algorithm is based on explicitly storing the pseudorandom numbers used to create the randomized displacements in computer simulations and subtracting them from the simulated trajectories. The resulting correlation function of the reduced motion is connected to the target correlation function up to a crosscorrelation term. Using analytical theory and computer simulations, we demonstrate that the cross-correlation term can be neglected in all three systems studied in this paper. We further expand the algorithm to Monte Carlo simulations and analyze the performance of the algorithm and rationalize that it works particularly well for unbounded, weakly interacting systems in which the precision of the mean-square displacement can be improved by orders of magnitude.</p><p> </p>
Intermediate scattering function of a gravitactic circle swimmer
No full text<p>We analyze gravitaxis of a Brownian circle swimmer by deriving and analytically characterizing the experimentally measurable intermediate scattering function (ISF). To solve the associated Fokker-Planck equation, we use a spectral-theory approach, finding formal expressions in terms of eigenfunctions and eigenvalues of the overdamped-noisy-driven pendulum problem. We further perform a Taylor series of the ISF in the wavevector to extract the cumulants up to the fourth order. We focus on the skewness and kurtosis analyzed for four observation directions in the 2D plane. Validating our findings involves conducting Langevin-dynamics simulations and interpreting the results using a harmonic approximation. The skewness and kurtosis are amplified as the orienting torque approaches the intrinsic angular drift of the circle swimmer from above, highlighting deviations from Gaussian behavior. Transforming the ISF to the comoving frame, a measurable quantity, reveals gravitactic effects and diverse behaviors spanning from diffusive motion at low wavenumbers to circular motion at intermediate wavenumbers and directed motion at higher wavenumbers.</p>
MS_Lumos_2019_November
No full text<p>MS Raw Data collected at Obitrap Fusion Lumos in November 2019 at the Institute of Biochemistry, University of Innsbruck</p><p>This record contains Proteomics of Alienke van Pijkeren (UIBK) & Yang Zhang (UIBK), and Metabolite measurements (M. Hotze, UIBK) and for Sara (UMCG, NL), Alienke van Pijkeren (UIBK) and Alex (UIBK).</p>
NMR data - publication: Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA
No full textDatasets supporting the journal article "Imaging Dihydrogen Bond-Driven Assembly of Borazine on Au(111)"
No full text<p>STM folder: Scanning tunneling microscopy data</p><p>IETS folder: Inelastic electron tunneling spectroscopy data (Figure S3)</p>
Analysis of the phosphatidylserine 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 phosphatidylserine 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>
Effects of intraperitoneally administered chromanols on pulmonary levels of lipid mediators in ovalbumine sensitized mice
No full text<p>Female mice were pretreated i.p. with α-T-13'-COOH (α-13′-carboxychromanol) and α-AC (α-amplexichromanol) (10 mg kg-1) or vehicle (DMSO 2%, 0.5 ml) 30 min before each OVA (ovalbumine) challenge. Animals were sacrificed at day 14 to evaluate in the lung homogenate COX products and 12/15-LOX-derived products formed from arachidonic acid (12-HETE and 15-HETE), eicosapentaenoic acid (12-HEPE and 15-HEPE) and docosahexaenoic acid (17-HDHA, 14-HDHA) 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 Cerqua et al., Pharmacol. Res., 2022 Jul;181:106250.doi: 10.1016/j.phrs.2022.106250 </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><p> </p>
Concentration of leukotrienes 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 (OVA) (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. LTB4, and LTB4 isomers were 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>