@article{GhafarianWielandLuettschwageretal.2022, author = {Ghafarian, Fatemeh and Wieland, Ralf and L{\"u}ttschwager, Dietmar and Nendel, Claas}, title = {Application of extreme gradient boosting and Shapley Additive explanations to predict temperature regimes inside forests from standard open-field meteorological data}, series = {Environmental modelling \& software with environment data news}, volume = {156}, journal = {Environmental modelling \& software with environment data news}, publisher = {Elsevier}, address = {Oxford}, issn = {1364-8152}, doi = {10.1016/j.envsoft.2022.105466}, pages = {11}, year = {2022}, abstract = {Forest microclimate can buffer biotic responses to summer heat waves, which are expected to become more extreme under climate warming. Prediction of forest microclimate is limited because meteorological observation standards seldom include situations inside forests. We use eXtreme Gradient Boosting - a Machine Learning technique - to predict the microclimate of forest sites in Brandenburg, Germany, using seasonal data comprising weather features. The analysis was amended by applying a SHapley Additive explanation to show the interaction effect of variables and individualised feature attributions. We evaluate model performance in comparison to artificial neural networks, random forest, support vector machine, and multi-linear regression. After implementing a feature selection, an ensemble approach was applied to combine individual models for each forest and improve robustness over a given single prediction model. The resulting model can be applied to translate climate change scenarios into temperatures inside forests to assess temperature-related ecosystem services provided by forests.}, language = {en} } @article{SobhkhizMiandehiYamazakiArrasetal.2022, author = {Sobhkhiz-Miandehi, Sahar and Yamazaki, Yosuke and Arras, Christina and Miyoshi, Yasunobu and Shinagawa, Hiroyuki}, title = {Comparison of the tidal signatures in sporadic E and vertical ion convergence rate, using FORMOSAT-3/COSMIC radio occultation observations and GAIA model}, series = {Earth, planets and space : EPS}, volume = {74}, journal = {Earth, planets and space : EPS}, number = {1}, publisher = {Springer}, address = {Heidelberg}, issn = {1880-5981}, doi = {10.1186/s40623-022-01637-y}, pages = {13}, year = {2022}, abstract = {Sporadic E or Es is a transient phenomenon where thin layers of enhanced electron density appear in the ionospheric E region (90-120 km altitude). The neutral wind shear caused by atmospheric tides can lead ions to converge vertically at E-region heights and form the Es layer. This research aims to determine the role of atmospheric solar and lunar tides in Es occurrence. For this purpose, radio occultation data of FORMOSAT-3/COSMIC have been used, which provide complete global coverage of Es events. Moreover, GAIA model simulations have been employed to evaluate the vertical ion convergence induced by solar tides. The results show both migrating and non-migrating solar tidal signatures and the semidiurnal migrating lunar tidal signature mainly in low and mid-latitude Es occurrence. The seasonal variation of the migrating solar tidal components of Es is in good agreement with those in the vertical ion convergence derived from GAIA at higher altitudes. Furthermore, some non-migrating components of solar tides, including semidiurnal westward wavenumbers 1 and 3 and diurnal eastward wavenumbers 2 and 3, also significantly affect the Es occurrence rate.}, language = {en} } @article{ArmstrongRadouskyAustinetal.2022, author = {Armstrong, Michael R. and Radousky, Harry B. and Austin, Ryan A. and Tschauner, Oliver and Brown, Shaughnessy and Gleason, Arianna E. and Goldman, Nir and Granados, Eduardo and Grivickas, Paulius and Holtgrewe, Nicholas and Kroonblawd, Matthew P. and Lee, Hae Ja and Lobanov, Sergey S. and Nagler, Bob and Nam, Inhyuk and Prakapenka, Vitali and Prescher, Clemens and Reed, Evan J. and Stavrou, Elissaios and Walter, Peter and Goncharov, Alexander F. and Belof, Jonathan L.}, title = {Highly ordered graphite (HOPG) to hexagonal diamond (lonsdaleite) phase transition observed on picosecond time scales using ultrafast x-ray diffraction}, series = {Journal of applied physics}, volume = {132}, journal = {Journal of applied physics}, number = {5}, publisher = {AIP Publishing}, address = {Melville}, issn = {0021-8979}, doi = {10.1063/5.0085297}, pages = {10}, year = {2022}, abstract = {The response of rapidly compressed highly oriented pyrolytic graphite (HOPG) normal to its basal plane was investigated at a pressure of \& SIM;80 GPa. Ultrafast x-ray diffraction using \& SIM;100 fs pulses at the Materials Under Extreme Conditions sector of the Linac Coherent Light Source was used to probe the changes in crystal structure resulting from picosecond timescale compression at laser drive energies ranging from 2.5 to 250 mJ. A phase transformation from HOPG to a highly textured hexagonal diamond structure is observed at the highest energy, followed by relaxation to a still highly oriented, but distorted graphite structure following release. We observe the formation of a highly oriented lonsdaleite within 20 ps, subsequent to compression. This suggests that a diffusionless martensitic mechanism may play a fundamental role in phase transition, as speculated in an early work on this system, and more recent static studies of diamonds formed in impact events. Published by AIP Publishing.}, language = {en} } @article{SchusterRybackiBonnelyeetal.2021, author = {Schuster, Valerian and Rybacki, Erik and Bonnelye, Audrey and Dresen, Georg}, title = {Authors' Reply to the Discussion by Crisci et al. (2021): Experimental deformation of Opalinus Clay at elevated temperature and pressure conditions}, series = {Rock mechanics and rock engineering}, volume = {55}, journal = {Rock mechanics and rock engineering}, publisher = {Springer}, address = {Wien}, issn = {0723-2632}, doi = {10.1007/s00603-021-02675-w}, pages = {467 -- 469}, year = {2021}, language = {en} } @article{KnoxBrownRindfleischGuentheretal.2020, author = {Knox-Brown, Patrick and Rindfleisch, Tobias and G{\"u}nther, Anne and Balow, Kim and Bremer, Anne and Walther, Dirk and Miettinen, Markus S. and Hincha, Dirk K. and Thalhammer, Anja}, title = {Similar Yet Different}, series = {International Journal of Molecular Sciences}, volume = {21}, journal = {International Journal of Molecular Sciences}, number = {8}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms21082794}, pages = {25}, year = {2020}, abstract = {The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.}, language = {en} } @article{RajuLiebigKlemkeetal.2020, author = {Raju, Rajarshi Roy and Liebig, Ferenc and Klemke, Bastian and Koetz, Joachim}, title = {Ultralight magnetic aerogels from Janus emulsions}, series = {RSC Advances}, volume = {10}, journal = {RSC Advances}, number = {13}, publisher = {RSC Publishing}, address = {London}, issn = {2046-2069}, doi = {10.1039/c9ra10247g}, pages = {7492 -- 7499}, year = {2020}, abstract = {Magnetite containing aerogels were synthesized by freeze-drying olive oil/silicone oil-based Janus emulsion gels containing gelatin and sodium carboxymethylcellulose (NaCMC). The magnetite nanoparticles dispersed in olive oil are processed into the gel and remain in the macroporous aerogel after removing the oil components. The coexistence of macropores from the Janus droplets and mesopores from freeze-drying of the hydrogels in combination with the magnetic properties offer a special hierarchical pore structure, which is of relevance for smart supercapacitors, biosensors, and spilled oil sorption and separation. The morphology of the final structure was investigated in dependence on initial compositions. More hydrophobic aerogels with magnetic responsiveness were synthesized by bisacrylamide-crosslinking of the hydrogel. The crosslinked aerogels can be successfully used in magnetically responsive clean up experiments of the cationic dye methylene blue.}, language = {en} } @article{ZiegeTheodorouJuenglingetal.2020, author = {Ziege, Madlen and Theodorou, Panagiotis and J{\"u}ngling, Hannah and Merker, Stefan and Plath, Martin and Streit, Bruno and Lerp, Hannes}, title = {Population genetics of the European rabbit along a rural-to-urban gradient}, series = {Scientific Reports}, volume = {10}, journal = {Scientific Reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-020-57962-3}, pages = {12}, year = {2020}, abstract = {The European rabbit (Oryctolagus cuniculus) is declining in large parts of Europe but populations in some German cities remained so far unaffected by this decline. The question arises of how urbanization affects patterns of population genetic variation and differentiation in German rabbit populations, as urban habitat fragmentation may result in altered meta-population dynamics. To address this question, we used microsatellite markers to genotype rabbit populations occurring along a rural-to-urban gradient in and around the city of Frankfurt, Germany. We found no effect of urbanization on allelic richness. However, the observed heterozygosity was significantly higher in urban than rural populations and also the inbreeding coefficients were lower, most likely reflecting the small population sizes and possibly on-going loss of genetic diversity in structurally impoverished rural areas. Global FST and G'ST-values suggest moderate but significant differentiation between populations. Multiple matrix regression with randomization ascribed this differentiation to isolation-by-environment rather than isolation-by-distance. Analyses of migration rates revealed asymmetrical gene flow, which was higher from rural into urban populations than vice versa and may again reflect intensified agricultural land-use practices in rural areas. We discuss that populations inhabiting urban areas will likely play an important role in the future distribution of European rabbits.}, language = {en} } @article{ListekHoenowGossenetal.2020, author = {Listek, Martin and H{\"o}now, Anja and Gossen, Manfred and Hanack, Katja}, title = {A novel selection strategy for antibody producing hybridoma cells based on a new transgenic fusion cell line}, series = {Scientific Reports}, volume = {10}, journal = {Scientific Reports}, publisher = {Macmillan Publishers Limited, part of Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-020-58571-w}, pages = {12}, year = {2020}, abstract = {The use of monoclonal antibodies is ubiquitous in science and biomedicine but the generation and validation process of antibodies is nevertheless complicated and time-consuming. To address these issues we developed a novel selective technology based on an artificial cell surface construct by which secreted antibodies were connected to the corresponding hybridoma cell when they possess the desired antigen-specificity. Further the system enables the selection of desired isotypes and the screening for potential cross-reactivities in the same context. For the design of the construct we combined the transmembrane domain of the EGF-receptor with a hemagglutinin epitope and a biotin acceptor peptide and performed a transposon-mediated transfection of myeloma cell lines. The stably transfected myeloma cell line was used for the generation of hybridoma cells and an antigen- and isotype-specific screening method was established. The system has been validated for globular protein antigens as well as for haptens and enables a fast and early stage selection and validation of monoclonal antibodies in one step.}, language = {en} } @article{WippertDriessleinBecketal.2020, author = {Wippert, Pia-Maria and Drießlein, David and Beck, Heidrun and Schneider, Christian and Puschmann, Anne-Katrin and Banzer, Winfried and Schiltenwolf, Marcus}, title = {The Feasibility and Effectiveness of a New Practical Multidisciplinary Treatment for Low-Back Pain}, series = {Journal of Clinical Medicine}, volume = {9}, journal = {Journal of Clinical Medicine}, number = {115}, publisher = {MDPI}, address = {Basel}, issn = {2077-0383}, doi = {10.3390/jcm9010115}, pages = {15}, year = {2020}, abstract = {Low-back pain is a major health problem exacerbated by the fact that most treatments are not suitable for self-management in everyday life. Particularly, interdisciplinary programs consist of intensive therapy lasting several weeks. Additionally, therapy components are rarely coordinated regarding reinforcing effects, which would improve complaints in persons with higher pain. This study assesses the effectiveness of a self-management program, firstly for persons suffering from higher pain and secondly compared to regular routines. Study objectives were treated in a single-blind multicenter controlled trial. A total of n = 439 volunteers (age 18-65 years) were randomly assigned to a twelve-week multidisciplinary sensorimotor training (3-weeks-center- and 9-weeks-homebased) or control group. The primary outcome pain (Chronic-Pain-Grade) as well as mental health were assessed by questionnaires at baseline and follow-up (3/6/12/24 weeks, M2-M5). For statistical analysis, multiple linear regression models were used. N = 291 (age 39.7 ± 12.7 years, female = 61.1\%, 77\% CPG = 1) completed training (M1/M4/M5), showing a significantly stronger reduction of mental health complaints (anxiety, vital exhaustion) in people with higher than those with lower pain in multidisciplinary treatment. Compared to regular routines, the self-management-multidisciplinary treatment led to a clinically relevant reduction of pain-disability and significant mental health improvements. Low-cost exercise programs may provide enormous relief for therapeutic processes, rehabilitation aftercare, and thus, cost savings for the health system}, language = {en} } @article{MaierHartungdeWiljesetal.2020, author = {Maier, Corinna and Hartung, Niklas and de Wiljes, Jana and Kloft, Charlotte and Huisinga, Wilhelm}, title = {Bayesian Data Assimilation to Support Informed Decision Making in Individualized Chemotherapy}, series = {CPT: Pharmacometrics \& Systems Pharmacology}, volume = {XX}, journal = {CPT: Pharmacometrics \& Systems Pharmacology}, publisher = {Nature Publ. Group}, address = {London}, issn = {2163-8306}, doi = {10.1002/psp4.12492}, pages = {12}, year = {2020}, abstract = {An essential component of therapeutic drug/biomarker monitoring (TDM) is to combine patient data with prior knowledge for model-based predictions of therapy outcomes. Current Bayesian forecasting tools typically rely only on the most probable model parameters (maximum a posteriori (MAP) estimate). This MAP-based approach, however, does neither necessarily predict the most probable outcome nor does it quantify the risks of treatment inefficacy or toxicity. Bayesian data assimilation (DA) methods overcome these limitations by providing a comprehensive uncertainty quantification. We compare DA methods with MAP-based approaches and show how probabilistic statements about key markers related to chemotherapy-induced neutropenia can be leveraged for more informative decision support in individualized chemotherapy. Sequential Bayesian DA proved to be most computationally efficient for handling interoccasion variability and integrating TDM data. For new digital monitoring devices enabling more frequent data collection, these features will be of critical importance to improve patient care decisions in various therapeutic areas.}, language = {en} } @article{SchellChudobaLeboucheretal.2020, author = {Schell, Mareike and Chudoba, Chantal and Leboucher, Antoine and Alfine, Eugenia and Flore, Tanina and Ritter, Katrin and Weiper, Katharina and Wernitz, Andreas and Henkel, Janin and Kleinridders, Andr{\´e}}, title = {Interplay of Dietary Fatty Acids and Cholesterol Impacts Brain Mitochondria and Insulin Action}, series = {Nutrients}, volume = {12}, journal = {Nutrients}, number = {5}, publisher = {MDPI}, address = {Basel}, issn = {2072-6643}, doi = {10.3390/nu12051518}, pages = {22}, year = {2020}, abstract = {Overconsumption of high-fat and cholesterol-containing diets is detrimental for metabolism and mitochondrial function, causes inflammatory responses and impairs insulin action in peripheral tissues. Dietary fatty acids can enter the brain to mediate the nutritional status, but also to influence neuronal homeostasis. Yet, it is unclear whether cholesterol-containing high-fat diets (HFDs) with different combinations of fatty acids exert metabolic stress and impact mitochondrial function in the brain. To investigate whether cholesterol in combination with different fatty acids impacts neuronal metabolism and mitochondrial function, C57BL/6J mice received different cholesterol-containing diets with either high concentrations of long-chain saturated fatty acids or soybean oil-derived poly-unsaturated fatty acids. In addition, CLU183 neurons were stimulated with combinations of palmitate, linoleic acid and cholesterol to assess their effects on metabolic stress, mitochondrial function and insulin action. The dietary interventions resulted in a molecular signature of metabolic stress in the hypothalamus with decreased expression of occludin and subunits of mitochondrial electron chain complexes, elevated protein carbonylation, as well as c-Jun N-terminal kinase (JNK) activation. Palmitate caused mitochondrial dysfunction, oxidative stress, insulin and insulin-like growth factor-1 (IGF-1) resistance, while cholesterol and linoleic acid did not cause functional alterations. Finally, we defined insulin receptor as a novel negative regulator of metabolically stress-induced JNK activation.}, language = {en} } @article{LiebigSarhanBargheeretal.2020, author = {Liebig, Ferenc and Sarhan, Radwan Mohamed and Bargheer, Matias and Schmitt, Clemens Nikolaus Zeno and Poghosyan, Armen H. and Shahinyanf, Aram A. and Koetz, Joachim}, title = {Spiked gold nanotriangles}, series = {RSC Advances}, volume = {10}, journal = {RSC Advances}, number = {14}, publisher = {RSC Publishing}, address = {London}, issn = {2046-2069}, doi = {10.1039/d0ra00729c}, pages = {8152 -- 8160}, year = {2020}, abstract = {We show the formation of metallic spikes on the surface of gold nanotriangles (AuNTs) by using the same reduction process which has been used for the synthesis of gold nanostars. We confirm that silver nitrate operates as a shape-directing agent in combination with ascorbic acid as the reducing agent and investigate the mechanism by dissecting the contribution of each component, i.e., anionic surfactant dioctyl sodium sulfosuccinate (AOT), ascorbic acid (AA), and AgNO3. Molecular dynamics (MD) simulations show that AA attaches to the AOT bilayer of nanotriangles, and covers the surface of gold clusters, which is of special relevance for the spike formation process at the AuNT surface. The surface modification goes hand in hand with a change of the optical properties. The increased thickness of the triangles and a sizeable fraction of silver atoms covering the spikes lead to a blue-shift of the intense near infrared absorption of the AuNTs. The sponge-like spiky surface increases both the surface enhanced Raman scattering (SERS) cross section of the particles and the photo-catalytic activity in comparison with the unmodified triangles, which is exemplified by the plasmon-driven dimerization of 4-nitrothiophenol (4-NTP) to 4,4'-dimercaptoazobenzene (DMAB).}, language = {en} } @article{ReppertMatternPudelletal.2020, author = {Reppert, Alexander von and Mattern, Maximilian and Pudell, Jan-Etienne and Zeuschner, Steffen Peer and Dumesnil, Karine and Bargheer, Matias}, title = {Unconventional picosecond strain pulses resulting from the saturation of magnetic stress within a photoexcited rare earth layer}, series = {Structural Dynamics}, volume = {7}, journal = {Structural Dynamics}, number = {024303}, publisher = {AIP Publishing LLC}, address = {Melville, NY}, issn = {2329-7778}, doi = {10.1063/1.5145315}, pages = {13}, year = {2020}, abstract = {Optical excitation of spin-ordered rare earth metals triggers a complex response of the crystal lattice since expansive stresses from electron and phonon excitations compete with a contractive stress induced by spin disorder. Using ultrafast x-ray diffraction experiments, we study the layer specific strain response of a dysprosium film within a metallic heterostructure upon femtosecond laser-excitation. The elastic and diffusive transport of energy to an adjacent, non-excited detection layer clearly separates the contributions of strain pulses and thermal excitations in the time domain. We find that energy transfer processes to magnetic excitations significantly modify the observed conventional bipolar strain wave into a unipolar pulse. By modeling the spin system as a saturable energy reservoir that generates substantial contractive stress on ultrafast timescales, we can reproduce the observed strain response and estimate the time- and space dependent magnetic stress. The saturation of the magnetic stress contribution yields a non-monotonous total stress within the nanolayer, which leads to unconventional picosecond strain pulses.}, language = {en} } @article{OmidbakhshfardNeerakkalGuptaetal.2020, author = {Omidbakhshfard, Mohammad Amin and Neerakkal, Sujeeth and Gupta, Saurabh and Omranian, Nooshin and Guinan, Kieran J. and Brotman, Yariv and Nikoloski, Zoran and Fernie, Alisdair and Mueller-Roeber, Bernd and Gechev, Tsanko S.}, title = {A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress}, series = {International Journal of Molecular Sciences}, volume = {21}, journal = {International Journal of Molecular Sciences}, number = {2}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms21020474}, pages = {26}, year = {2020}, abstract = {Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were unaffected by PQ. Transcriptome analysis revealed induction of reactive oxygen species (ROS) marker genes, genes involved in ROS-induced programmed cell death, and autophagy-related genes after PQ treatment. These changes did not occur in PQ-stressed plants primed with SF. In contrast, upregulation of several carbohydrate metabolism genes, growth, and hormone signaling as well as antioxidant-related genes were specific to SF-primed plants. Metabolomic analyses revealed accumulation of the stress-protective metabolite maltose and the tricarboxylic acid cycle intermediates fumarate and malate in SF-primed plants. Lipidome analysis indicated that those lipids associated with oxidative stress-induced cell death and chloroplast degradation, such as triacylglycerols (TAGs), declined upon SF priming. Our study demonstrated that SF confers tolerance to PQ-induced oxidative stress in A. thaliana, an effect achieved by modulating a range of processes at the transcriptomic, metabolic, and lipid levels.}, language = {en} } @article{GrafeBatsiosMeyeretal.2019, author = {Grafe, Marianne and Batsios, Petros and Meyer, Irene and Lisin, Daria and Baumann, Otto and Goldberg, Martin W. and Gr{\"a}f, Ralph}, title = {Supramolecular Structures of the Dictyostelium Lamin NE81}, series = {Cells}, volume = {8}, journal = {Cells}, number = {2}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {2073-4409}, doi = {10.3390/cells8020162}, pages = {17}, year = {2019}, abstract = {Nuclear lamins are nucleus-specific intermediate filaments (IF) found at the inner nuclear membrane (INM) of the nuclear envelope (NE). Together with nuclear envelope transmembrane proteins, they form the nuclear lamina and are crucial for gene regulation and mechanical robustness of the nucleus and the whole cell. Recently, we characterized Dictyostelium NE81 as an evolutionarily conserved lamin-like protein, both on the sequence and functional level. Here, we show on the structural level that the Dictyostelium NE81 is also capable of assembling into filaments, just as metazoan lamin filament assemblies. Using field-emission scanning electron microscopy, we show that NE81 expressed in Xenopous oocytes forms filamentous structures with an overall appearance highly reminiscent of Xenopus lamin B2. The in vitro assembly properties of recombinant His-tagged NE81 purified from Dictyostelium extracts are very similar to those of metazoan lamins. Super-resolution stimulated emission depletion (STED) and expansion microscopy (ExM), as well as transmission electron microscopy of negatively stained purified NE81, demonstrated its capability of forming filamentous structures under low-ionic-strength conditions. These results recommend Dictyostelium as a non-mammalian model organism with a well-characterized nuclear envelope involving all relevant protein components known in animal cells.}, language = {en} } @article{ChoiSchmidtTinnefeldetal.2019, author = {Choi, Youngeun and Schmidt, Carsten and Tinnefeld, Philip and Bald, Ilko and R{\"o}diger, Stefan}, title = {A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads}, series = {Scientific Reports}, journal = {Scientific Reports}, number = {9}, publisher = {Macmillan Publishers Limited}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-41136-x}, pages = {8}, year = {2019}, abstract = {The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters.}, language = {en} } @article{ŚlęzakMetzlerMagdziarz2019, author = {Ślęzak, Jakub and Metzler, Ralf and Magdziarz, Marcin}, title = {Codifference can detect ergodicity breaking and non-Gaussianity}, series = {New Journal of Physics}, volume = {21}, journal = {New Journal of Physics}, publisher = {Deutsche Physikalische Gesellschaft}, address = {Bad Honnef}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab13f3}, pages = {25}, year = {2019}, abstract = {We show that the codifference is a useful tool in studying the ergodicity breaking and non-Gaussianity properties of stochastic time series. While the codifference is a measure of dependence that was previously studied mainly in the context of stable processes, we here extend its range of applicability to random-parameter and diffusing-diffusivity models which are important in contemporary physics, biology and financial engineering. We prove that the codifference detects forms of dependence and ergodicity breaking which are not visible from analysing the covariance and correlation functions. We also discuss a related measure of dispersion, which is a nonlinear analogue of the mean squared displacement.}, language = {en} } @article{RawelHuschekSaguTchewonpietal.2019, author = {Rawel, Harshadrai Manilal and Huschek, Gerd and Sagu Tchewonpi, Sorel and Homann, Thomas}, title = {Cocoa Bean Proteins}, series = {Nutrients}, volume = {11}, journal = {Nutrients}, number = {2}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {2072-6643}, doi = {10.3390/nu11020428}, pages = {20}, year = {2019}, abstract = {The protein fractions of cocoa have been implicated influencing both the bioactive potential and sensory properties of cocoa and cocoa products. The objective of the present review is to show the impact of different stages of cultivation and processing with regard to the changes induced in the protein fractions. Special focus has been laid on the major seed storage proteins throughout the different stages of processing. The study starts with classical introduction of the extraction and the characterization methods used, while addressing classification approaches of cocoa proteins evolved during the timeline. The changes in protein composition during ripening and maturation of cocoa seeds, together with the possible modifications during the post-harvest processing (fermentation, drying, and roasting), have been documented. Finally, the bioactive potential arising directly or indirectly from cocoa proteins has been elucidated. The "state of the art" suggests that exploration of other potentially bioactive components in cocoa needs to be undertaken, while considering the complexity of reaction products occurring during the roasting phase of the post-harvest processing. Finally, the utilization of partially processed cocoa beans (e.g., fermented, conciliatory thermal treatment) can be recommended, providing a large reservoir of bioactive potentials arising from the protein components that could be instrumented in functionalizing foods.}, language = {en} } @article{WeithoffBeisner2019, author = {Weithoff, Guntram and Beisner, Beatrix E.}, title = {Measures and Approaches in Trait-Based Phytoplankton Community Ecology}, series = {Frontiers in Marine Science}, volume = {6}, journal = {Frontiers in Marine Science}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-7745}, doi = {10.3389/fmars.2019.00040}, pages = {11}, year = {2019}, abstract = {Trait-based approaches to investigate (short- and long-term) phytoplankton dynamics and community assembly have become increasingly popular in freshwater and marine science. Although the nature of the pelagic habitat and the main phytoplankton taxa and ecology are relatively similar in both marine and freshwater systems, the lines of research have evolved, at least in part, separately. We compare and contrast the approaches adopted in marine and freshwater ecosystems with respect to phytoplankton functional traits. We note differences in study goals relating to functional trait use that assess community assembly and those that relate to ecosystem processes and biogeochemical cycling that affect the type of characteristics assigned as traits to phytoplankton taxa. Specific phytoplankton traits relevant for ecological function are examined in relation to herbivory, amplitude of environmental change and spatial and temporal scales of study. Major differences are identified, including the shorter time scale for regular environmental change in freshwater ecosystems compared to that in the open oceans as well as the type of sampling done by researchers based on site-accessibility. Overall, we encourage researchers to better motivate why they apply trait-based analyses to their studies and to make use of process-driven approaches, which are more common in marine studies. We further propose fully comparative trait studies conducted along the habitat gradient spanning freshwater to brackish to marine systems, or along geographic gradients. Such studies will benefit from the combined strength of both fields.}, language = {en} } @article{KriegerowskiCescaOhrnbergeretal.2019, author = {Kriegerowski, Marius and Cesca, Simone and Ohrnberger, Matthias and Dahm, Torsten and Kr{\"u}ger, Frank}, title = {Event couple spectral ratio Q method for earthquake clusters}, series = {Solid Earth}, journal = {Solid Earth}, number = {10}, publisher = {Copernicus Publications}, address = {G{\"o}ttingen}, issn = {1869-9529}, doi = {10.5194/se-10-317-2019}, pages = {317 -- 328}, year = {2019}, abstract = {We develop an amplitude spectral ratio method for event couples from clustered earthquakes to estimate seismic wave attenuation (Q-1) in the source volume. The method allows to study attenuation within the source region of earthquake swarms or aftershocks at depth, independent of wave path and attenuation between source region and surface station. We exploit the high-frequency slope of phase spectra using multitaper spectral estimates. The method is tested using simulated full wave-field seismograms affected by recorded noise and finite source rupture. The synthetic tests verify the approach and show that solutions are independent of focal mechanisms but also show that seismic noise may broaden the scatter of results. We apply the event couple spectral ratio method to northwest Bohemia, Czech Republic, a region characterized by the persistent occurrence of earthquake swarms in a confined source region at mid-crustal depth. Our method indicates a strong anomaly of high attenuation in the source region of the swarm with an averaged attenuation factor of Qp < 100. The application to S phases fails due to scattered P-phase energy interfering with S phases. The Qp anomaly supports the common hypothesis of highly fractured and fluid saturated rocks in the source region of the swarms in northwest Bohemia. However, high temperatures in a small volume around the swarms cannot be excluded to explain our observations.}, language = {en} }