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    Application of Matched-Filter Concepts to Unbiased Selection of Data in Pump-Probe Experiments with Free Electron Lasers
    (Basel : MDPI, 2017-06-16) Callegari, Carlo; Takanashi, Tsukasa; Fukuzawa, Hironobu; Motomura, Koji; Iablonskyi, Denys; Kumagai, Yoshiaki; Mondal, Subhendu; Tachibana, Tetsuya; Nagaya, Kiyonobu; Nishiyama, Toshiyuki; Matsunami, Kenji; Johnsson, Per; Piseri, Paolo; Sansone, Giuseppe; Dubrouil, Antoine; Reduzzi, Maurizio; Carpeggiani, Paolo; Vozzi, Caterina; Devetta, Michele; Faccialà, Davide; Calegari, Francesca; Castrovilli, Mattea; Coreno, Marcello; Alagia, Michele; Schütte, Bernd; Berrah, Nora; Plekan, Oksana; Finetti, Paola; Ferrari, Eugenio; Prince, Kevin; Ueda, Kiyoshi
    Pump-probe experiments are commonly used at Free Electron Lasers (FEL) to elucidate the femtosecond dynamics of atoms, molecules, clusters, liquids and solids. Maximizing the signal-to-noise ratio of the measurements is often a primary need of the experiment, and the aggregation of repeated, rapid, scans of the pump-probe delay is preferable to a single long-lasting scan. The limited availability of beamtime makes it impractical to repeat measurements indiscriminately, and the large, rapid flow of single-shot data that need to be processed and aggregated into a dataset, makes it difficult to assess the quality of a measurement in real time. In post-analysis it is then necessary to devise unbiased criteria to select or reject datasets, and to assign the weight with which they enter the analysis. One such case was the measurement of the lifetime of Intermolecular Coulombic Decay in the weakly-bound neon dimer. We report on the method we used to accomplish this goal for the pump-probe delay scans that constitute the core of the measurement; namely we report on the use of simple auto- and cross-correlation techniques based on the general concept of “matched filter”. We are able to unambiguously assess the signal-to-noise ratio (SNR) of each scan, which then becomes the weight with which a scan enters the average of multiple scans. We also observe a clear gap in the values of SNR, and we discard all the scans below a SNR of 0.45. We are able to generate an average delay scan profile, suitable for further analysis: in our previous work we used it for comparison with theory. Here we argue that the method is sufficiently simple and devoid of human action to be applicable not only in post-analysis, but also for the real-time assessment of the quality of a dataset.
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    New Source of 3D Chitin Scaffolds: The Red Sea Demosponge Pseudoceratina arabica (Pseudoceratinidae, Verongiida)
    (Basel : MDPI, 2019) Shaala, Lamiaa A.; Asfour, Hani Z.; Youssef, Diaa T.A.; Żółtowska-Aksamitowska, Sonia; Wysokowski, Marcin; Tsurkan, Mikhail; Galli, Roberta; Meissner, Heike; Petrenko, Iaroslav; Tabachnick, Konstantin; Ivanenko, Viatcheslav N.; Bechmann, Nicole; Muzychka, Lyubov V.; Smolii, Oleg B.; Martinović, Rajko; Joseph, Yvonne; Jesionowski, Teofil; Ehrlich, Hermann
    The bioactive bromotyrosine-derived alkaloids and unique morphologically-defined fibrous skeleton of chitin origin have been found recently in marine demosponges of the order Verongiida. The sophisticated three-dimensional (3D) structure of skeletal chitinous scaffolds supported their use in biomedicine, tissue engineering as well as in diverse modern technologies. The goal of this study was the screening of new species of the order Verongiida to find another renewable source of naturally prefabricated 3D chitinous scaffolds. Special attention was paid to demosponge species, which could be farmed on large scale using marine aquaculture methods. In this study, the demosponge Pseudoceratina arabica collected in the coastal waters of the Egyptian Red Sea was examined as a potential source of chitin for the first time. Various bioanalytical tools including scanning electron microscopy (SEM), fluorescence microscopy, FTIR analysis, Calcofluor white staining, electrospray ionization mass spectrometry (ESI-MS), as well as a chitinase digestion assay were successfully used to confirm the discovery of a-chitin within the skeleton of P. arabica. The current finding should make an important contribution to the field of application of this verongiid sponge as a novel renewable source of biologically-active metabolites and chitin, which are important for development of the blue biotechnology especially in marine oriented biomedicine. © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (
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    Diffusive Motion of Linear Microgel Assemblies in Solution
    (Basel : MDPI, 2016) Schürings, Marco-Philipp; Nevskyi, Oleksii; Eliasch, Kamill; Michel, Ann-Katrin; Liu, Bing; Pich, Andrij; Böker, Alexander; Von Plessen, Gero; Wöll, Dominik
    Due to the ability of microgels to rapidly contract and expand in response to external stimuli, assemblies of interconnected microgels are promising for actuation applications, e.g., as contracting fibers for artificial muscles. Among the properties determining the suitability of microgel assemblies for actuation are mechanical parameters such as bending stiffness and mobility. Here, we study the properties of linear, one-dimensional chains of poly(N-vinylcaprolactam) microgels dispersed in water. They were fabricated by utilizing wrinkled surfaces as templates and UV-cross-linking the microgels. We image the shapes of the chains on surfaces and in solution using atomic force microscopy (AFM) and fluorescence microscopy, respectively. In solution, the chains are observed to execute translational and rotational diffusive motions. Evaluation of the motions yields translational and rotational diffusion coefficients and, from the translational diffusion coefficient, the chain mobility. The microgel chains show no perceptible bending, which yields a lower limit on their bending stiffness
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    Study of Water Productivity of Industrial Hemp under Hot and Dry Conditions in Brandenburg (Germany) in the Year 2018
    (Basel : MDPI, 2020) Drastig, Katrin; Flemming, Inken; Gusovius, Hans-Jörg; Herppich, Werner B.
    Hemp (Cannabis sativa L.) is a high-yielding multi-purpose crop, but its hydrological functioning is poorly understood. Studies on the interception processes in hemp have been lacking so far. This study contributes to the understanding of the influences of evaporation of intercepted water and other hydrological fluxes within plants of two cultivars, “Santhica 27” and “Ivory”, on the water productivity. To determine water productivity and evaporation from interception, field measurements were conducted on plants of both cultivars at different stages of development. Precipitation (P), throughfall (TF), transpiration (T), and volumetric water content (VWC) were measured along with leaf area index (LAI) and yield of selected plant components. For the entire vegetation period, the cumulative P of 44 mm was converted into 13 mm TF (30%). The inferred evaporation of intercepted water (I) was high at 31 mm (71%). For the assessment water fluxes, the evaporation of intercepted water must be considered in the decision-making process. Besides the LAI, the plant architecture and the meteorological conditions during the cropping cycle seem to be the main factors determining I in the case of plants of both cultivars. Water productivity (WPDM) of the whole plant varied between 3.07 kg m−3 for Ivory and 3.49 for Santhica 27. In the case of bast yield, WPDM was 0.39 kg m-3 for Santhica 27 and 0.45 kg m−3 for Ivory. After the propagation of the uncertainties, the bandwidth of the WPDM of the whole plant was between 0.42 kg m−3 and 2.57 kg m−3. For bast fiber a bandwidth of the WP between 0.06 kg m−3 and 0.33 kg m−3 was calculated. The results show furthermore that even with a precise examination of water productivity, a high bandwidth of local values is revealed on different cultivars. However, generic WP values for fiber crops are not attainable.
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    Decoding Galactic Merger Histories
    (Basel : MDPI, 2017) Bell, Eric; Monachesi, Antonela; D’Souza, Richard; Harmsen, Benjamin; de Jong, Roelof; Radburn-Smith, David; Bailin, Jeremy; Holwerda, Benne
    Galaxy mergers are expected to influence galaxy properties, yet measurements of individual merger histories are lacking. Models predict that merger histories can be measured using stellar halos and that these halos can be quantified using observations of resolved stars along their minor axis. Such observations reveal that Milky Way-mass galaxies have a wide range of stellar halo properties and show a correlation between their stellar halo masses and metallicities. This correlation agrees with merger-driven models where stellar halos are formed by satellite galaxy disruption. In these models, the largest accreted satellite dominates the stellar halo properties. Consequently, the observed diversity in the stellar halos of MilkyWay-mass galaxies implies a large range in the masses of their largest merger partners. In particular, the Milky Way's low mass halo implies an unusually quiet merger history. We used these measurements to seek predicted correlations between the bulge and central black hole (BH) mass and the mass of the largest merger partner. We found no significant correlations: while some galaxies with large bulges and BHs have large stellar halos and thus experienced a major or minor merger, half have small stellar halos and never experienced a significant merger event. These results indicate that bulge and BH growth is not solely driven by merger-related processes.
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    Applications of Electronic Nose, Electronic Eye and Electronic Tongue in Quality, Safety and Shelf Life of Meat and Meat Products: A Review
    (Basel : MDPI, 2023) Munekata, Paulo E. S.; Finardi, Sarah; de Souza, Carolina Krebs; Meinert, Caroline; Pateiro, Mirian; Hoffmann, Tuany Gabriela; Domínguez, Rubén; Bertoli, Sávio Leandro; Kumar, Manoj; Lorenzo, José M.
    The quality and shelf life of meat and meat products are key factors that are usually evaluated by complex and laborious protocols and intricate sensory methods. Devices with attractive characteristics (fast reading, portability, and relatively low operational costs) that facilitate the measurement of meat and meat products characteristics are of great value. This review aims to provide an overview of the fundamentals of electronic nose (E-nose), eye (E-eye), and tongue (E-tongue), data preprocessing, chemometrics, the application in the evaluation of quality and shelf life of meat and meat products, and advantages and disadvantages related to these electronic systems. E-nose is the most versatile technology among all three electronic systems and comprises applications to distinguish the application of different preservation methods (chilling vs. frozen, for instance), processing conditions (especially temperature and time), detect adulteration (meat from different species), and the monitoring of shelf life. Emerging applications include the detection of pathogenic microorganisms using E-nose. E-tongue is another relevant technology to determine adulteration, processing conditions, and to monitor shelf life. Finally, E-eye has been providing accurate measuring of color evaluation and grade marbling levels in fresh meat. However, advances are necessary to obtain information that are more related to industrial conditions. Advances to include industrial scenarios (cut sorting in continuous processing, for instance) are of great value.
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    Separation, characterization, and handling of microalgae by dielectrophoresis
    (Basel : MDPI, 2020) Abt, Vinzenz; Gringel, Fabian; Han, Arum; Neubauer, Peter; Birkholz, Mario
    Microalgae biotechnology has a high potential for sustainable bioproduction of diverse highvalue biomolecules. Some of the main bottlenecks in cell-based bioproduction, and more specifically in microalgae-based bioproduction, are due to insufficient methods for rapid and efficient cell characterization, which contributes to having only a few industrially established microalgal species in commercial use. Dielectrophoresis-based microfluidic devices have been long established as promising tools for label-free handling, characterization, and separation of broad ranges of cells. The technique is based on differences in dielectric properties and sizes, which results in different degrees of cell movement under an applied inhomogeneous electrical field. The method has also earned interest for separating microalgae based on their intrinsic properties, since their dielectric properties may significantly change during bioproduction, in particular for lipid-producing species. Here, we provide a comprehensive review of dielectrophoresis-based microfluidic devices that are used for handling, characterization, and separation of microalgae. Additionally, we provide a perspective on related areas of research in cell-based bioproduction that can benefit from dielectrophoresis-based microdevices. This work provides key information that will be useful for microalgae researchers to decide whether dielectrophoresis and which method is most suitable for their particular application. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
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    Degradation Kinetics of Lignocellulolytic Enzymes in a Biogas Reactor Using Quantitative Mass Spectrometry
    (Basel : MDPI, 2023) Küchler, Jan; Willenbücher, Katharina; Reiß, Elisabeth; Nuß, Lea; Conrady, Marius; Ramm, Patrice; Schimpf, Ulrike; Reichl, Udo; Szewzyk, Ulrich; Benndorf, Dirk
    The supplementation of lignocellulose-degrading enzymes can be used to enhance the performance of biogas production in industrial biogas plants. Since the structural stability of these enzyme preparations is essential for efficient application, reliable methods for the assessment of enzyme stability are crucial. Here, a mass-spectrometric-based assay was established to monitor the structural stability of enzymes, i.e., the structural integrity of these proteins, in anaerobic digestion (AD). The analysis of extracts of Lentinula edodes revealed the rapid degradation of lignocellulose-degrading enzymes, with an approximate half-life of 1.5 h. The observed low structural stability of lignocellulose-degrading enzymes in AD corresponded with previous results obtained for biogas content. The established workflow can be easily adapted for the monitoring of other enzyme formulations and provides a platform for evaluating the effects of enzyme additions in AD, together with a characterization of the biochemical methane potential used in order to determine the biodegradability of organic substrates.
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    Influence of redox stress on crosstalk between fibroblasts and keratinocytes
    (Basel : MDPI, 2021) Bhartiya, Pradeep; Masur, Kai; Shome, Debarati; Kaushik, Neha; Nguyen, Linh N.; Kaushik, Nagendra Kumar; Choi, Eun Ha
    Although the skin is constantly subjected to endogenous and exogenous stress, it maintains a homeostatic state through wound repair and regeneration pathways. Treatment for skin diseases and injury requires a significant understanding of the various mechanisms and interactions that occur within skin cells. Keratinocytes and fibroblasts interact with each other and act as key players in the repair process. Although fibroblasts and keratinocytes are widely studied in wound healing and skin remodeling under different conditions, the influence of redox stress on keratinocyte-fibroblast crosstalk has not been thoroughly investigated. In this study, we used cold atmospheric plasma (CAP) to generate and deliver oxidative stress to keratinocytes and fibroblasts and to assess its impact on their interactions. To this end, we used a well-established in vitro 3D co-culture model imitating a realistic scenario. Our study shows that low CAP exposure is biocompatible and does not affect the viability or energetics of fibroblasts and keratinocytes. Exposure to low doses of CAP enhanced the proliferation rate of cells and stimulated the expression of key genes (KGF, MMP2, GMCSF, IL-6, and IL-8) in fibroblasts, indicating the activation and initiation of the skin repair process. Additionally, enhanced migration was observed under co-culture conditions under the given redox stress conditions, and expression of the upstream regulator and the effectors of the Hippo pathway (YAP and CYR61, respectively), which are associated with enhanced migration, were elevated. Overall, this study reinforces the application of CAP and redox stress in skin repair physiology.
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    First Report on Chitin in a Non-Verongiid Marine Demosponge: The Mycale euplectellioides Case
    (Basel : MDPI, 2018) Żółtowska-Aksamitowska, Sonia; Shaala, Lamiaa A.; Youssef, Diaa T.A.; Elhady, Sameh S.; Tsurkan, Mikhail V.; Petrenko, Iaroslav; Wysokowski, Marcin; Tabachnick, Konstantin; Meissner, Heike; Ivanenko, Viatcheslav N.; Bechmann, Nicole; Joseph, Yvonne; Jesionowski, Teofil; Ehrlich, Hermann
    Sponges (Porifera) are recognized as aquatic multicellular organisms which developed an effective biochemical pathway over millions of years of evolution to produce both biologically active secondary metabolites and biopolymer-based skeletal structures. Among marine demosponges, only representatives of the Verongiida order are known to synthetize biologically active substances as well as skeletons made of structural polysaccharide chitin. The unique three-dimensional (3D) architecture of such chitinous skeletons opens the widow for their recent applications as adsorbents, as well as scaffolds for tissue engineering and biomimetics. This study has the ambitious goal of monitoring other orders beyond Verongiida demosponges and finding alternative sources of naturally prestructured chitinous scaffolds; especially in those demosponge species which can be cultivated at large scales using marine farming conditions. Special attention has been paid to the demosponge Mycale euplectellioides (Heteroscleromorpha: Poecilosclerida: Mycalidae) collected in the Red Sea. For the first time, we present here a detailed study of the isolation of chitin from the skeleton of this sponge, as well as its identification using diverse bioanalytical tools. Calcofluor white staining, Fourier-transform Infrared Spcetcroscopy (FTIR), electrospray ionization mass spectrometry (ESI-MS), scanning electron microscopy (SEM), and fluorescence microscopy, as well as a chitinase digestion assay were applied in order to confirm with strong evidence the finding of a-chitin in the skeleton of M. euplectellioides. We suggest that the discovery of chitin within representatives of the Mycale genus is a promising step in their evaluation of these globally distributed sponges as new renewable sources for both biologically active metabolites and chitin, which are of prospective use for pharmacology and biomaterials oriented biomedicine, respectively.