TY - JOUR A1 - Agarwal, Ankit A1 - Caesar, Levke A1 - Marwan, Norbert A1 - Maheswaran, Rathinasamy A1 - Merz, Bruno T1 - Network-based identification and characterization of teleconnections on different scales JF - Scientific Reports N2 - Sea surface temperature (SST) patterns can – as surface climate forcing – affect weather and climate at large distances. One example is El Niño-Southern Oscillation (ENSO) that causes climate anomalies around the globe via teleconnections. Although several studies identified and characterized these teleconnections, our understanding of climate processes remains incomplete, since interactions and feedbacks are typically exhibited at unique or multiple temporal and spatial scales. This study characterizes the interactions between the cells of a global SST data set at different temporal and spatial scales using climate networks. These networks are constructed using wavelet multi-scale correlation that investigate the correlation between the SST time series at a range of scales allowing instantaneously deeper insights into the correlation patterns compared to traditional methods like empirical orthogonal functions or classical correlation analysis. This allows us to identify and visualise regions of – at a certain timescale – similarly evolving SSTs and distinguish them from those with long-range teleconnections to other ocean regions. Our findings re-confirm accepted knowledge about known highly linked SST patterns like ENSO and the Pacific Decadal Oscillation, but also suggest new insights into the characteristics and origins of long-range teleconnections like the connection between ENSO and Indian Ocean Dipole. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-45423-5 SN - 2045-2322 VL - 9 PB - Macmillan Publishers Limited CY - London ER - TY - GEN A1 - Weber, Edzard A1 - Tiefenbacher, Anselm A1 - Gronau, Norbert T1 - Need for standardization and systematization of test data for job-shop scheduling T2 - Postprints der Universität Potsdam Wirtschafts- und Sozialwissenschaftliche Reihe N2 - The development of new and better optimization and approximation methods for Job Shop Scheduling Problems (JSP) uses simulations to compare their performance. The test data required for this has an uncertain influence on the simulation results, because the feasable search space can be changed drastically by small variations of the initial problem model. Methods could benefit from this to varying degrees. This speaks in favor of defining standardized and reusable test data for JSP problem classes, which in turn requires a systematic describability of the test data in order to be able to compile problem adequate data sets. This article looks at the test data used for comparing methods by literature review. It also shows how and why the differences in test data have to be taken into account. From this, corresponding challenges are derived which the management of test data must face in the context of JSP research. Keywords T3 - Zweitveröffentlichungen der Universität Potsdam : Wirtschafts- und Sozialwissenschaftliche Reihe - 134 KW - job shop scheduling KW - JSP KW - social network analysis KW - method comparision Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472229 SN - 1867-5808 IS - 134 ER - TY - JOUR A1 - Weber, Edzard A1 - Tiefenbacher, Anselm A1 - Gronau, Norbert T1 - Need for Standardization and Systematization of Test Data for Job-Shop Scheduling JF - Data N2 - The development of new and better optimization and approximation methods for Job Shop Scheduling Problems (JSP) uses simulations to compare their performance. The test data required for this has an uncertain influence on the simulation results, because the feasable search space can be changed drastically by small variations of the initial problem model. Methods could benefit from this to varying degrees. This speaks in favor of defining standardized and reusable test data for JSP problem classes, which in turn requires a systematic describability of the test data in order to be able to compile problem adequate data sets. This article looks at the test data used for comparing methods by literature review. It also shows how and why the differences in test data have to be taken into account. From this, corresponding challenges are derived which the management of test data must face in the context of JSP research. KW - job shop scheduling KW - JSP KW - social network analysis KW - method comparision Y1 - 2019 U6 - https://doi.org/10.3390/data4010032 SN - 2306-5729 VL - 4 IS - 1 PB - MDPI CY - Basel ER - TY - GEN A1 - Büchele, Dominique A1 - Chao, Madlen A1 - Ostermann, Markus A1 - Leenen, Matthias A1 - Bald, Ilko T1 - Multivariate chemometrics as a key tool for prediction of K and Fe in a diverse German agricultural soil-set using EDXRF T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Within the framework of precision agriculture, the determination of various soil properties is moving into focus, especially the demand for sensors suitable for in-situ measurements. Energy-dispersive X-ray fluorescence (EDXRF) can be a powerful tool for this purpose. In this study a huge diverse soil set (n = 598) from 12 different study sites in Germany was analysed with EDXRF. First, a principal component analysis (PCA) was performed to identify possible similarities among the sample set. Clustering was observed within the four texture classes clay, loam, silt and sand, as clay samples contain high and sandy soils low iron mass fractions. Furthermore, the potential of uni- and multivariate data evaluation with partial least squares regression (PLSR) was assessed for accurate determination of nutrients in German agricultural samples using two calibration sample sets. Potassium and iron were chosen for testing the performance of both models. Prediction of these nutrients in 598 German soil samples with EDXRF was more accurate using PLSR which is confirmed by a better overall averaged deviation and PLSR should therefore be preferred. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 784 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439988 SN - 1866-8372 IS - 784 ER - TY - JOUR A1 - Büchele, Dominique A1 - Chao, Madlen A1 - Ostermann, Markus A1 - Leenen, Matthias A1 - Bald, Ilko T1 - Multivariate chemometrics as a key tool for prediction of K and Fe in a diverse German agricultural soil-set using EDXRF JF - Scientific Reports N2 - Within the framework of precision agriculture, the determination of various soil properties is moving into focus, especially the demand for sensors suitable for in-situ measurements. Energy-dispersive X-ray fluorescence (EDXRF) can be a powerful tool for this purpose. In this study a huge diverse soil set (n = 598) from 12 different study sites in Germany was analysed with EDXRF. First, a principal component analysis (PCA) was performed to identify possible similarities among the sample set. Clustering was observed within the four texture classes clay, loam, silt and sand, as clay samples contain high and sandy soils low iron mass fractions. Furthermore, the potential of uni- and multivariate data evaluation with partial least squares regression (PLSR) was assessed for accurate determination of nutrients in German agricultural samples using two calibration sample sets. Potassium and iron were chosen for testing the performance of both models. Prediction of these nutrients in 598 German soil samples with EDXRF was more accurate using PLSR which is confirmed by a better overall averaged deviation and PLSR should therefore be preferred. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-53426-5 SN - 2045-2322 VL - 9 PB - Macmillan Publishers Limited, part of Springer Nature CY - London ER - TY - JOUR A1 - Dunsing, Valentin A1 - Petrich, Annett A1 - Chiantia, Salvatore T1 - Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection JF - eLife N2 - Signaling pathways in biological systems rely on specific interactions between multiple biomolecules. Fluorescence fluctuation spectroscopy provides a powerful toolbox to quantify such interactions directly in living cells. Cross-correlation analysis of spectrally separated fluctuations provides information about intermolecular interactions but is usually limited to two fluorophore species. Here, we present scanning fluorescence spectral correlation spectroscopy (SFSCS), a versatile approach that can be implemented on commercial confocal microscopes, allowing the investigation of interactions between multiple protein species at the plasma membrane. We demonstrate that SFSCS enables cross-talk-free cross-correlation, diffusion, and oligomerization analysis of up to four protein species labeled with strongly overlapping fluorophores. As an example, we investigate the interactions of influenza A virus (IAV) matrix protein 2 with two cellular host factors simultaneously. We furthermore apply raster spectral image correlation spectroscopy for the simultaneous analysis of up to four species and determine the stoichiometry of ternary IAV polymerase complexes in the cell nucleus. KW - fluorescence KW - optical microscopy KW - virus assembly KW - protein-protein KW - interactions KW - diffusion KW - Viruses Y1 - 2021 U6 - https://doi.org/10.7554/eLife.69687 SN - 2050-084X VL - 10 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Jentsch, Anna A1 - Düsing, Walter A1 - Jolie, Egbert A1 - Zimmer, Martin T1 - Monitoring the response of volcanic CO2 emissions to changes in the Los Humeros hydrothermal system JF - Scientific reports N2 - Carbon dioxide is the most abundant, non-condensable gas in volcanic systems, released into the atmosphere through either diffuse or advective fluid flow. The emission of substantial amounts of CO2 at Earth's surface is not only controlled by volcanic plumes during periods of eruptive activity or fumaroles, but also by soil degassing along permeable structures in the subsurface. Monitoring of these processes is of utmost importance for volcanic hazard analyses, and is also relevant for managing geothermal resources. Fluid-bearing faults are key elements of economic value for geothermal power generation. Here, we describe for the first time how sensitively and quickly natural gas emissions react to changes within a deep hydrothermal system due to geothermal fluid reinjection. For this purpose, we deployed an automated, multi-chamber CO2 flux monitoring system within the damage zone of a deep-rooted major normal fault in the Los Humeros Volcanic Complex (LHVC) in Mexico and recorded data over a period of five months. After removing the atmospheric effects on variations in CO2 flux, we calculated correlation coefficients between residual CO2 emissions and reinjection rates, identifying an inverse correlation of rho = - 0.51 to - 0.66. Our results indicate that gas emissions respond to changes in reinjection rates within 24 h, proving an active hydraulic communication between the hydrothermal system and Earth's surface. This finding is a promising indication not only for geothermal reservoir monitoring but also for advanced long-term volcanic risk analysis. Response times allow for estimation of fluid migration velocities, which is a key constraint for conceptual and numerical modelling of fluid flow in fracture-dominated systems. KW - Energy and society KW - Geochemistry KW - Geology KW - Geophysics KW - Volcanology Y1 - 2021 U6 - https://doi.org/10.1038/s41598-021-97023-x SN - 2045-2322 VL - 11 IS - 1 PB - Macmillan Publishers Limited, part of Springer Nature CY - [London] ER - TY - JOUR A1 - Chandra, Johan A1 - Krügel, André A1 - Engbert, Ralf T1 - Modulation of oculomotor control during reading of mirrored and inverted texts JF - Scientific Reports N2 - The interplay between cognitive and oculomotor processes during reading can be explored when the spatial layout of text deviates from the typical display. In this study, we investigate various eye-movement measures during reading of text with experimentally manipulated layout (word-wise and letter-wise mirrored-reversed text as well as inverted and scrambled text). While typical findings (e.g., longer mean fixation times, shorter mean saccades lengths) in reading manipulated texts compared to normal texts were reported in earlier work, little is known about changes of oculomotor targeting observed in within-word landing positions under the above text layouts. Here we carry out precise analyses of landing positions and find substantial changes in the so-called launch-site effect in addition to the expected overall slow-down of reading performance. Specifically, during reading of our manipulated text conditions with reversed letter order (against overall reading direction), we find a reduced launch-site effect, while in all other manipulated text conditions, we observe an increased launch-site effect. Our results clearly indicate that the oculomotor system is highly adaptive when confronted with unusual reading conditions. KW - human behaviour KW - psychology KW - eye-movement control KW - e-z reader KW - ideal-observer model KW - fixation locations KW - landing positions KW - saccade generation KW - cognitive-control KW - dynamical model KW - decision-theory KW - attention Y1 - 2019 U6 - https://doi.org/10.1038/s41598-020-60833-6 SN - 2045-2322 VL - 10 PB - Macmillan Publishers Limited, part of Springer Nature CY - London ER - TY - GEN A1 - Chandra, Johan A1 - Krügel, André A1 - Engbert, Ralf T1 - Modulation of oculomotor control during reading of mirrored and inverted texts T2 - Postprints der Universität Potsdam : Humanwissenschaftliche Reihe N2 - The interplay between cognitive and oculomotor processes during reading can be explored when the spatial layout of text deviates from the typical display. In this study, we investigate various eye-movement measures during reading of text with experimentally manipulated layout (word-wise and letter-wise mirrored-reversed text as well as inverted and scrambled text). While typical findings (e.g., longer mean fixation times, shorter mean saccades lengths) in reading manipulated texts compared to normal texts were reported in earlier work, little is known about changes of oculomotor targeting observed in within-word landing positions under the above text layouts. Here we carry out precise analyses of landing positions and find substantial changes in the so-called launch-site effect in addition to the expected overall slow-down of reading performance. Specifically, during reading of our manipulated text conditions with reversed letter order (against overall reading direction), we find a reduced launch-site effect, while in all other manipulated text conditions, we observe an increased launch-site effect. Our results clearly indicate that the oculomotor system is highly adaptive when confronted with unusual reading conditions. T3 - Zweitveröffentlichungen der Universität Potsdam : Humanwissenschaftliche Reihe - 659 KW - human behaviour KW - psychology KW - eye-movement control KW - e-z reader KW - ideal-observer model KW - fixation locations KW - landing positions KW - saccade generation KW - cognitive-control KW - dynamical model KW - decision-theory KW - attention Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-494879 SN - 1866-8364 IS - 659 ER - TY - JOUR A1 - Li, Yuanqing A1 - Chen, Li A1 - Nofal, Issam A1 - Chen, Mo A1 - Wang, Haibin A1 - Liu, Rui A1 - Chen, Qingyu A1 - Krstić, Miloš A1 - Shi, Shuting A1 - Guo, Gang A1 - Baeg, Sang H. A1 - Wen, Shi-Jie A1 - Wong, Richard T1 - Modeling and analysis of single-event transient sensitivity of a 65 nm clock tree JF - Microelectronics reliability N2 - The soft error rate (SER) due to heavy-ion irradiation of a clock tree is investigated in this paper. A method for clock tree SER prediction is developed, which employs a dedicated soft error analysis tool to characterize the single-event transient (SET) sensitivities of clock inverters and other commercial tools to calculate the SER through fault-injection simulations. A test circuit including a flip-flop chain and clock tree in a 65 nm CMOS technology is developed through the automatic ASIC design flow. This circuit is analyzed with the developed method to calculate its clock tree SER. In addition, this circuit is implemented in a 65 nm test chip and irradiated by heavy ions to measure its SER resulting from the SETs in the clock tree. The experimental and calculation results of this case study present good correlation, which verifies the effectiveness of the developed method. KW - Clock tree KW - Modeling KW - Single-event transient (SET) Y1 - 2018 U6 - https://doi.org/10.1016/j.microrel.2018.05.016 SN - 0026-2714 VL - 87 SP - 24 EP - 32 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Straube, Nicolas A1 - Preick, Michaela A1 - Naylor, Gavin J. P. A1 - Hofreiter, Michael T1 - Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae) JF - Royal Society Open Science N2 - After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy. KW - museum specimens KW - archival DNA KW - deep-sea sharks KW - Etmopterus pusillus KW - Etmopterus joungi KW - taxonomy Y1 - 2021 U6 - https://doi.org/10.1098/rsos.210474 SN - 2054-5703 VL - 8 IS - 9 PB - Royal Society CY - London ER - TY - JOUR A1 - Schaefer, Laura A1 - Löffler, Nils A1 - Klein, Julia A1 - Bittmann, Frank T1 - Mechanomyography and acceleration show interlimb asymmetries in Parkinson patients without tremor compared to controls during a unilateral motor task JF - Scientific reports N2 - The mechanical muscular oscillations are rarely the objective of investigations regarding the identification of a biomarker for Parkinson's disease (PD). Therefore, the aim of this study was to investigate whether or not this specific motor output differs between PD patients and controls. The novelty is that patients without tremor are investigated performing a unilateral isometric motor task. The force of armflexors and the forearm acceleration (ACC) were recorded as well as the mechanomyography of the biceps brachii (MMGbi), brachioradialis (MMGbra) and pectoralis major (MMGpect) muscles using a piezoelectric-sensor-based system during a unilateral motor task at 70% of the MVIC. The frequency, a power-frequency-ratio, the amplitude variation, the slope of amplitudes and their interlimb asymmetries were analysed. The results indicate that the oscillatory behavior of muscular output in PD without tremor deviates from controls in some parameters: Significant differences appeared for the power-frequency-ratio (p=0.001, r=0.43) and for the amplitude variation (p=0.003, r=0.34) of MMGpect. The interlimb asymmetries differed significantly concerning the power-frequency-ratio of MMGbi (p=0.013, r=0.42) and MMGbra (p=0.048, r=0.39) as well as regarding the mean frequency (p=0.004, r=0.48) and amplitude variation of MMGpect (p=0.033, r=0.37). The mean (M) and variation coefficient (CV) of slope of ACC differed significantly (M: p=0.022, r=0.33; CV: p=0.004, r=0.43). All other parameters showed no significant differences between PD and controls. It remains open, if this altered mechanical muscular output is reproducible and specific for PD. KW - Diseases KW - Neurology KW - Neuroscience Y1 - 2021 U6 - https://doi.org/10.1038/s41598-021-81672-z SN - 2045-2322 VL - 11 IS - 1 PB - Macmillan CY - London ER - TY - GEN A1 - Nagel, Rebecca A1 - Kirschbaum, Frank A1 - Engelmann, Jacob A1 - Hofmann, Volker A1 - Pawelzik, Felix A1 - Tiedemann, Ralph T1 - Male-mediated species recognition among African weakly electric fishes T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Effective communication among sympatric species is often instrumental for behavioural isolation, where the failure to successfully discriminate between potential mates could lead to less fit hybrid offspring. Discrimination between con- and heterospecifics tends to occur more often in the sex that invests more in offspring production, i.e. females, but males may also mediate reproductive isolation. In this study, we show that among two Campylomormyrus Africanweakly electric fish species, males preferentially associate with conspecific females during choice tests using live fish as stimuli, i.e. when all sensory modalities potentially used for communication were present. We then conducted playback experiments to determine whether the species-specific electric organ discharge (EOD) used for electrocommunication serves as the cue for this conspecific association preference. Interestingly, only C. compressirostris males associated significantly more with the conspecific EOD waveform when playback stimuli were provided, while no such association preference was observed in C. tamandua males. Given our results, the EOD appears to serve, in part, as a male-mediated pre-zygotic isolation mechanism among sympatric species. However, the failure of C. tamandua males to discriminate between con- and heterospecific playback discharges suggests that multiple modalities may be necessary for species recognition in some African weakly electric fish species. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 645 KW - Campylomormyrus KW - communication KW - electric fishes KW - pre-zygotic isolation KW - species recognition Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-425016 SN - 1866-8372 IS - 645 ER - TY - JOUR A1 - Nagel, Rebecca A1 - Kirschbaum, Frank A1 - Engelmann, Jacob A1 - Hofmann, Volker A1 - Pawelzik, Felix A1 - Tiedemann, Ralph T1 - Male-mediated species recognition among African weakly electric fishes JF - Royal Society Open Science N2 - Effective communication among sympatric species is often instrumental for behavioural isolation, where the failure to successfully discriminate between potential mates could lead to less fit hybrid offspring. Discrimination between con- and heterospecifics tends to occur more often in the sex that invests more in offspring production, i.e. females, but males may also mediate reproductive isolation. In this study, we show that among two Campylomormyrus Africanweakly electric fish species, males preferentially associate with conspecific females during choice tests using live fish as stimuli, i.e. when all sensory modalities potentially used for communication were present. We then conducted playback experiments to determine whether the species-specific electric organ discharge (EOD) used for electrocommunication serves as the cue for this conspecific association preference. Interestingly, only C. compressirostris males associated significantly more with the conspecific EOD waveform when playback stimuli were provided, while no such association preference was observed in C. tamandua males. Given our results, the EOD appears to serve, in part, as a male-mediated pre-zygotic isolation mechanism among sympatric species. However, the failure of C. tamandua males to discriminate between con- and heterospecific playback discharges suggests that multiple modalities may be necessary for species recognition in some African weakly electric fish species. KW - Campylomormyrus KW - communication KW - electric fishes KW - pre-zygotic isolation KW - species recognition Y1 - 2018 U6 - https://doi.org/10.1098/rsos.170443 SN - 2054-5703 VL - 5 IS - 2 PB - Royal Society CY - London ER - TY - CHAP A1 - Klippert, Monika A1 - Stolpmann, Robert A1 - Grum, Marcus A1 - Thim, Christof A1 - Gronau, Norbert A1 - Albers, Albert T1 - Knowledge transfer quality improvement BT - the quality enhancement of knowledge transfers in product engineering T2 - Procedia CIRP N2 - Developing a new product generation requires the transfer of knowledge among various knowledge carriers. Several factors influence knowledge transfer, e.g., the complexity of engineering tasks or the competence of employees, which can decrease the efficiency and effectiveness of knowledge transfers in product engineering. Hence, improving those knowledge transfers obtains great potential, especially against the backdrop of experienced employees leaving the company due to retirement, so far, research results show, that the knowledge transfer velocity can be raised by following the Knowledge Transfer Velocity Model and implementing so-called interventions in a product engineering context. In most cases, the implemented interventions have a positive effect on knowledge transfer speed improvement. In addition to that, initial theoretical findings describe factors influencing the quality of knowledge transfers and outline a setting to empirically investigate how the quality can be improved by introducing a general description of knowledge transfer reference situations and principles to measure the quality of knowledge artifacts. To assess the quality of knowledge transfers in a product engineering context, the Knowledge Transfer Quality Model (KTQM) is created, which serves as a basis to develop and implement quality-dependent interventions for different knowledge transfer situations. As a result, this paper introduces the specifications of eight situation-adequate interventions to improve the quality of knowledge transfers in product engineering following an intervention template. Those interventions are intended to be implemented in an industrial setting to measure the quality of knowledge transfers and validate their effect. KW - knowledge transfer KW - product generation engineering KW - improvement KW - quality KW - intervention Y1 - 2023 U6 - https://doi.org/10.1016/j.procir.2023.02.171 SN - 2212-8271 VL - 119 SP - 919 EP - 925 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Wojnarowska, Zaneta A1 - Lange, Alyna A1 - Taubert, Andreas A1 - Paluch, Marian T1 - Ion and proton transport in aqueous/nonaqueous acidic tonic liquids for fuel-cell applications-insight from high-pressure dielectric studies JF - ACS applied materials & interfaces / American Chemical Society N2 - The use of acidic ionic liquids and solids as electrolytes in fuel cells is an emerging field due to their efficient proton conductivity and good thermal stability. Despite multiple reports describing conducting properties of acidic ILs, little is known on the charge-transport mechanism in the vicinity of liquid-glass transition and the structural factors governing the proton hopping. To address these issues, we studied two acidic imidazolium-based ILs with the same cation, however, different anions-bulk tosylate vs small methanesulfonate. High-pressure dielectric studies of anhydrous and water-saturated materials performed in the close vicinity of T-g have revealed significant differences in the charge-transport mechanism in these two systems being undetectable at ambient conditions. Thereby, we demonstrated the effect of molecular architecture on proton hopping, being crucial in the potential electrochemical applications of acidic ILs. KW - proton hopping KW - dielectric spectroscopy KW - high pressure KW - ion transport KW - acidic ionic liquids Y1 - 2021 U6 - https://doi.org/10.1021/acsami.1c06260 SN - 1944-8244 SN - 1944-8252 VL - 13 IS - 26 SP - 30614 EP - 30624 PB - American Chemical Society CY - Washington ER - TY - GEN A1 - Schnitzler, Joseph G. A1 - Pinzone, Marianna A1 - Autenrieth, Marijke A1 - van Neer, Abbo A1 - IJsseldijk, Lonneke L. A1 - Barber, Jonathan L. A1 - Deaville, Rob A1 - Jepson, Paul A1 - Brownlow, Andrew A1 - Schaffeld, Tobias A1 - Thomé, Jean-Pierre A1 - Tiedemann, Ralph A1 - Das, Krishna A1 - Siebert, Ursula T1 - Inter-individual differences in contamination profiles as tracer of social group association in stranded sperm whales T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Ecological and physiological factors lead to different contamination patterns in individual marine mammals. The objective of the present study was to assess whether variations in contamination profiles are indicative of social structures of young male sperm whales as they might reflect a variation in feeding preferences and/or in utilized feeding grounds. We used a total of 61 variables associated with organic compounds and trace element concentrations measured in muscle, liver, kidney and blubber gained from 24 sperm whales that stranded in the North Sea in January and February 2016. Combining contaminant and genetic data, there is evidence for at least two cohorts with different origin among these stranded sperm whales; one from the Canary Island region and one from the northern part of the Atlantic. While genetic data unravel relatedness and kinship, contamination data integrate over areas, where animals occured during their lifetime. Especially in long-lived animals with a large migratory potential, as sperm whales, contamination data may carry highly relevant information about aggregation through time and space. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 692 KW - porpoises phococena-phococena KW - North-sea KW - physeter-macrocephalus KW - Galapagos-Islands KW - harbor porpoises KW - cetacean strandings KW - aggregations KW - pollutants KW - behavior KW - mammals Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-426525 SN - 1866-8372 IS - 692 ER - TY - JOUR A1 - Schnitzler, Joseph G. A1 - Pinzone, Marianna A1 - Autenrieth, Marijke A1 - van Neer, Abbo A1 - IJsseldijk, Lonneke L. A1 - Barber, Jonathan L. A1 - Deaville, Rob A1 - Jepson, Paul A1 - Brownlow, Andrew A1 - Schaffeld, Tobias A1 - Thome, Jean-Pierre A1 - Tiedemann, Ralph A1 - Das, Krishna A1 - Siebert, Ursula T1 - Inter-individual differences in contamination profiles as tracer of social group association in stranded sperm whales JF - Scientific reports N2 - Ecological and physiological factors lead to different contamination patterns in individual marine mammals. The objective of the present study was to assess whether variations in contamination profiles are indicative of social structures of young male sperm whales as they might reflect a variation in feeding preferences and/or in utilized feeding grounds. We used a total of 61 variables associated with organic compounds and trace element concentrations measured in muscle, liver, kidney and blubber gained from 24 sperm whales that stranded in the North Sea in January and February 2016. Combining contaminant and genetic data, there is evidence for at least two cohorts with different origin among these stranded sperm whales; one from the Canary Island region and one from the northern part of the Atlantic. While genetic data unravel relatedness and kinship, contamination data integrate over areas, where animals occured during their lifetime. Especially in long-lived animals with a large migratory potential, as sperm whales, contamination data may carry highly relevant information about aggregation through time and space. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-29186-z SN - 2045-2322 VL - 8 PB - Nature Publ. Group CY - London ER - TY - THES A1 - Perscheid, Cindy T1 - Integrative biomarker detection using prior knowledge on gene expression data sets T1 - Integrative Biomarker-Erkennung auf Genexpressions-Daten mithilfe von biologischem Vorwissen N2 - Gene expression data is analyzed to identify biomarkers, e.g. relevant genes, which serve for diagnostic, predictive, or prognostic use. Traditional approaches for biomarker detection select distinctive features from the data based exclusively on the signals therein, facing multiple shortcomings in regards to overfitting, biomarker robustness, and actual biological relevance. Prior knowledge approaches are expected to address these issues by incorporating prior biological knowledge, e.g. on gene-disease associations, into the actual analysis. However, prior knowledge approaches are currently not widely applied in practice because they are often use-case specific and seldom applicable in a different scope. This leads to a lack of comparability of prior knowledge approaches, which in turn makes it currently impossible to assess their effectiveness in a broader context. Our work addresses the aforementioned issues with three contributions. Our first contribution provides formal definitions for both prior knowledge and the flexible integration thereof into the feature selection process. Central to these concepts is the automatic retrieval of prior knowledge from online knowledge bases, which allows for streamlining the retrieval process and agreeing on a uniform definition for prior knowledge. We subsequently describe novel and generalized prior knowledge approaches that are flexible regarding the used prior knowledge and applicable to varying use case domains. Our second contribution is the benchmarking platform Comprior. Comprior applies the aforementioned concepts in practice and allows for flexibly setting up comprehensive benchmarking studies for examining the performance of existing and novel prior knowledge approaches. It streamlines the retrieval of prior knowledge and allows for combining it with prior knowledge approaches. Comprior demonstrates the practical applicability of our concepts and further fosters the overall development and comparability of prior knowledge approaches. Our third contribution is a comprehensive case study on the effectiveness of prior knowledge approaches. For that, we used Comprior and tested a broad range of both traditional and prior knowledge approaches in combination with multiple knowledge bases on data sets from multiple disease domains. Ultimately, our case study constitutes a thorough assessment of a) the suitability of selected knowledge bases for integration, b) the impact of prior knowledge being applied at different integration levels, and c) the improvements in terms of classification performance, biological relevance, and overall robustness. In summary, our contributions demonstrate that generalized concepts for prior knowledge and a streamlined retrieval process improve the applicability of prior knowledge approaches. Results from our case study show that the integration of prior knowledge positively affects biomarker results, particularly regarding their robustness. Our findings provide the first in-depth insights on the effectiveness of prior knowledge approaches and build a valuable foundation for future research. N2 - Biomarker sind charakteristische biologische Merkmale mit diagnostischer oder prognostischer Aussagekraft. Auf der molekularen Ebene sind dies Gene mit einem krankheitsspezifischen Expressionsmuster, welche mittels der Analyse von Genexpressionsdaten identifiziert werden. Traditionelle Ansätze für diese Art von Biomarker Detection wählen Gene als Biomarker ausschließlich anhand der vorhandenen Signale im Datensatz aus. Diese Vorgehensweise zeigt jedoch Schwächen insbesondere in Bezug auf die Robustheit und tatsächliche biologische Relevanz der identifizierten Biomarker. Verschiedene Forschungsarbeiten legen nahe, dass die Berücksichtigung des biologischen Kontexts während des Selektionsprozesses diese Schwächen ausgleichen kann. Sogenannte wissensbasierte Ansätze für Biomarker Detection beziehen vorhandenes biologisches Wissen, beispielsweise über Zusammenhänge zwischen bestimmten Genen und Krankheiten, direkt in die Analyse mit ein. Die Anwendung solcher Verfahren ist in der Praxis jedoch derzeit nicht weit verbreitet, da existierende Methoden oft spezifisch für einen bestimmten Anwendungsfall entwickelt wurden und sich nur mit großem Aufwand auf andere Anwendungsgebiete übertragen lassen. Dadurch sind Vergleiche untereinander kaum möglich, was es wiederum nicht erlaubt die Effektivität von wissensbasierten Methoden in einem breiteren Kontext zu untersuchen. Die vorliegende Arbeit befasst sich mit den vorgenannten Herausforderungen für wissensbasierte Ansätze. In einem ersten Schritt legen wir formale und einheitliche Definitionen für vorhandenes biologisches Wissen sowie ihre flexible Integration in den Biomarker-Auswahlprozess fest. Der Kerngedanke unseres Ansatzes ist die automatisierte Beschaffung von biologischem Wissen aus im Internet frei verfügbaren Wissens-Datenbanken. Dies erlaubt eine Vereinfachung der Kuratierung sowie die Festlegung einer einheitlichen Definition für biologisches Wissen. Darauf aufbauend beschreiben wir generalisierte wissensbasierte Verfahren, welche flexibel auf verschiedene Anwendungsfalle anwendbar sind. In einem zweiten Schritt haben wir die Benchmarking-Plattform Comprior entwickelt, welche unsere theoretischen Konzepte in einer praktischen Anwendung realisiert. Comprior ermöglicht die schnelle Umsetzung von umfangreichen Experimenten für den Vergleich von wissensbasierten Ansätzen. Comprior übernimmt die Beschaffung von biologischem Wissen und ermöglicht dessen beliebige Kombination mit wissensbasierten Ansätzen. Comprior demonstriert damit die praktische Umsetzbarkeit unserer theoretischen Konzepte und unterstützt zudem die technische Realisierung und Vergleichbarkeit wissensbasierter Ansätze. In einem dritten Schritt untersuchen wir die Effektivität wissensbasierter Ansätze im Rahmen einer umfangreichen Fallstudie. Mithilfe von Comprior vergleichen wir die Ergebnisse traditioneller und wissensbasierter Ansätze im Kontext verschiedener Krankheiten, wobei wir für wissensbasierte Ansätze auch verschiedene Wissens-Datenbanken verwenden. Unsere Fallstudie untersucht damit a) die Eignung von ausgewählten Wissens-Datenbanken für deren Einsatz bei wissensbasierten Ansätzen, b) den Einfluss verschiedener Integrationskonzepte für biologisches Wissen auf den Biomarker-Auswahlprozess, und c) den Grad der Verbesserung in Bezug auf die Klassifikationsleistung, biologische Relevanz und allgemeine Robustheit der selektierten Biomarker. Zusammenfassend demonstriert unsere Arbeit, dass generalisierte Konzepte für biologisches Wissen und dessen vereinfachte Kuration die praktische Anwendbarkeit von wissensbasierten Ansätzen erleichtern. Die Ergebnisse unserer Fallstudie zeigen, dass die Integration von vorhandenem biologischen Wissen einen positiven Einfluss auf die selektierten Biomarker hat, insbesondere in Bezug auf ihre biologische Relevanz. Diese erstmals umfassenderen Erkenntnisse zur Effektivität von wissensbasierten Ansätzen bilden eine wertvolle Grundlage für zukünftige Forschungsarbeiten. KW - gene expression KW - biomarker detection KW - prior knowledge KW - feature selection KW - Biomarker-Erkennung KW - Merkmalsauswahl KW - Gen-Expression KW - biologisches Vorwissen Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-582418 ER - TY - JOUR A1 - Pries, Christopher A1 - Razaghi-Moghadam, Zahra A1 - Kopka, Joachim A1 - Nikoloski, Zoran T1 - Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism JF - Scientific reports N2 - Ribosome biogenesis is tightly associated to plant metabolism due to the usage of ribosomes in the synthesis of proteins necessary to drive metabolic pathways. Given the central role of ribosome biogenesis in cell physiology, it is important to characterize the impact of different components involved in this process on plant metabolism. Double mutants of the Arabidopsis thaliana cytosolic 60S maturation factors REIL1 and REIL2 do not resume growth after shift to moderate 10 degrees C chilling conditions. To gain mechanistic insights into the metabolic effects of this ribosome biogenesis defect on metabolism, we developed TC-iReMet2, a constraint-based modelling approach that integrates relative metabolomics and transcriptomics time-course data to predict differential fluxes on a genome-scale level. We employed TC-iReMet2 with metabolomics and transcriptomics data from the Arabidopsis Columbia 0 wild type and the reil1-1 reil2-1 double mutant before and after cold shift. We identified reactions and pathways that are highly altered in a mutant relative to the wild type. These pathways include the Calvin-Benson cycle, photorespiration, gluconeogenesis, and glycolysis. Our findings also indicated differential NAD(P)/NAD(P)H ratios after cold shift. TC-iReMet2 allows for mechanistic hypothesis generation and interpretation of system biology experiments related to metabolic fluxes on a genome-scale level. Y1 - 2021 U6 - https://doi.org/10.1038/s41598-021-84114-y SN - 2045-2322 VL - 11 IS - 1 PB - Macmillan Publishers Limited, part of Springer Nature CY - London ER -