TY - JOUR A1 - Pajčin, Ivana A1 - Vlajkov, Vanja A1 - Frohme, Marcus A1 - Grebinyk, Sergii A1 - Grahovac, Mila A1 - Mojićević, Marija A1 - Grahovac, Jovana T1 - Pepper Bacterial Spot Control by Bacillus velezensis: Bioprocess Solution JF - Microorganisms N2 - Pepper bacterial spot is one of the most severe plant diseases in terms of infection persistence and economic losses when it comes to fresh pepper fruits used in nutrition and industrial processing. In this study, Bacillus velezensis IP22 isolated from fresh cheese was used as a biocontrol agent of pepper bacterial spot, whose main causal agent is the cosmopolitan pathogen Xanthomonas euvesicatoria. After optimization of the cultivation medium composition aimed at maximizing of the antimicrobial activity against X. euvesicatoria and validation of the optimized medium at the scale of a laboratory bioreactor, in planta tests were performed. The results have showed significant suppression of bacterial spot symptoms in pepper plants by the produced biocontrol agent, as well as reduction of disease spreading on the healthy (uninoculated) pepper leaves. Furthermore, HPLC-MS (high pressure liquid chromatography–mass spectrometry) analysis was employed to examine antimicrobial metabolites produced by B. velezensis IP22, where lipopeptides were found with similar m/z values compared to lipopeptides from fengycin and locillomycin families. The bioprocess solution developed at the laboratory scale investigated in this study represents a promising strategy for production of pepper bacterial spot biocontrol agent based on B. velezensis IP22, a food isolate with a great perspective for application in plant protection. KW - Xanthomonas euvesicatoria KW - biological control KW - biocontrol agent KW - medium optimization KW - lipopeptide KW - fengycin KW - locillomycin KW - HPLC-MS KW - bioreactor KW - laboratory scale Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13510 SN - 2076-2607 VL - 8 IS - 10 PB - MDPI ER - TY - JOUR A1 - Goldenberg, Leonid A1 - Köhler, Mathias A1 - Kahle, Olaf A1 - Dreyer, Christian T1 - Impact of inorganic nanoparticles on optical properties of low refractive index waveguiding polymers JF - Optical Materials Express N2 - The objective of this work is to improve the optical properties of low refractive index polymers used for waveguide by introduction of inorganic nanoparticles. Copolymers of fluorinated monomers and glycidyl methacrylate are used. Introduction of SiO2 nanoparticles into polymer matrix is performed by direct mixing; copolymerization with SiO2 nanoparticles modified by monomer, and in situ sol-gel formation of SiO2 during photochemical cross-linking and annealing catalyzed by photoacid generator. It is demonstrated that nanoparticles are able to decrease thermo-optic coefficient. It is also possible to fabricate waveguiding layers by direct introduction of nanoparticles without compromising of optical propagation losses. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13521 SN - 2159-3930 VL - 10 IS - 11 SP - 2987 EP - 2997 ER - TY - JOUR A1 - Wolf, Bodo A1 - Richter, Asta T1 - The concept of differential hardness in depth sensing indentation JF - New Journal of Physics N2 - Since in-depth sensing indentation load–depth data of the entire loading–unloading cycle are available, more information than a single hardness value and an elastic modulus can be extracted from the experimental data. The conventional hardness H (h) = F (h)/Ac(h) and the differential hardness Hd(h)=dF/dAc are calculated as continuous functions of depth h and compared to each other in this paper (F: load, Ac: contact area). It turns out that Hd describes the momentary material resistance to deformation, whereas H integrates over deformation states from first tip–sample contact to current penetration h. This difference is particularly important for materials not homogeneous in depth (e.g. layer systems), and for situations where time-dependent external factors influence the momentary deformation resistance. Photoplasticity is considered as an example for the latter. Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5657 SN - 1367-2630 VL - 5 IS - 15 SP - 15.1 EP - 15.17 ER - TY - JOUR A1 - Khalid, Waqas A1 - Göbel, Gero A1 - Hühn, Dominik A1 - Montenegro, Jose-Maria A1 - Rivera-Gil, Pilar A1 - Lisdat, Fred A1 - Parak, Wolfgang J. T1 - Light triggered detection of aminophenyl phosphate with a quantum dot based enzyme electrode JF - Journal of Nanobiotechnology N2 - An electrochemical sensor for p-aminophenyl phosphate (p APP) is reported. It is based on the electrochemical conversion of 4-aminophenol (4AP) at a quantum dot (QD) modified electrode under illumination. Without illumination no electron transfer and thus no oxidation of 4AP can occur. p APP as substrate is converted by the enzyme alkaline phosphatase (ALP) to generate 4AP as a product. The QDs are coupled via 1,4-benzenedithiol (BDT) linkage to the surface of a gold electrode and thus allow potential-controlled photocurrent generation. The photocurrent is modified by the enzyme reaction providing access to the substrate detection. In order to develop a photobioelectrochemical sensor the enzyme is immobilized on top of the photo-switchable layer of the QDs. Immobilization of ALP is required for the potential possibility of spatially resolved measurements. Geometries with immobilized ALP are compared versus having the ALP in solution. Data indicate that functional immobilization with layer-by-layer assembly is possible. Enzymatic activity of ALP and thus the photocurrent can be described by Michaelis- Menten kinetics. p APP is detected as proof of principle investigation within the range of 25 μM - 1 mM. Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5808 SN - 1477-3155 VL - 9 IS - 46 ER - TY - JOUR A1 - Stern, Daniel A1 - Pauly, Diana A1 - Zydek, Martin A1 - Miller, Lilija A1 - Piesker, Janett A1 - Laue, Michael A1 - Lisdat, Fred A1 - Dorner, Martin B. A1 - Dorner, Brigitte G. A1 - Nitsche, Andreas T1 - Development of a Genus-Specific Antigen Capture ELISA for Orthopoxviruses – Target Selection and Optimized Screening JF - PLoS ONE N2 - Orthopoxvirus species like cowpox, vaccinia and monkeypox virus cause zoonotic infections in humans worldwide. Infections often occur in rural areas lacking proper diagnostic infrastructure as exemplified by monkeypox, which is endemic in Western and Central Africa. While PCR detection requires demanding equipment and is restricted to genome detection, the evidence of virus particles can complement or replace PCR. Therefore, an easily distributable and manageable antigen capture enzyme-linked immunosorbent assay (ELISA) for the detection of orthopoxviruses was developed to facilitate particle detection. By comparing the virus particle binding properties of polyclonal antibodies developed against surface-exposed attachment or fusion proteins, the surface protein A27 was found to be a well-bound, highly immunogenic and exposed target for antibodies aiming at virus particle detection. Subsequently, eight monoclonal anti-A27 antibodies were generated and characterized by peptide epitope mapping and surface plasmon resonance measurements. All antibodies were found to bind with high affinity to two epitopes at the heparin binding site of A27, toward either the N- or C-terminal of the crucial KKEP-segment of A27. Two antibodies recognizing different epitopes were implemented in an antigen capture ELISA. Validation showed robust detection of virus particles from 11 different orthopoxvirus isolates pathogenic to humans, with the exception of MVA, which is apathogenic to humans. Most orthopoxviruses could be detected reliably for viral loads above 1 × 103 PFU/mL. To our knowledge, this is the first solely monoclonal and therefore reproducible antibody-based antigen capture ELISA able to detect all human pathogenic orthopoxviruses including monkeypox virus, except variola virus which was not included. Therefore, the newly developed antibody-based assay represents important progress towards feasible particle detection of this important genus of viruses. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5830 SN - 1932-6203 VL - 11 IS - 3 ER - TY - JOUR A1 - Schulze, Katja A1 - Lang, Imke A1 - Enke, Heike A1 - Grohme, Diana A1 - Frohme, Marcus T1 - The use of fluorescence microscopy and image analysis for rapid detection of non-producing revertant cells of Synechocystis sp. PCC6803 and Synechococcus sp. PCC7002 JF - BMC Research Notes N2 - Ethanol production via genetically engineered cyanobacteria is a promising solution for the production of biofuels. Through the introduction of a pyruvate decarboxylase and alcohol dehydrogenase direct ethanol production becomes possible within the cells. However, during cultivation genetic instability can lead to mutations and thus loss of ethanol production. Cells then revert back to the wild type phenotype. A method for a rapid and simple detection of these non-producing revertant cells in an ethanol producing cell population is an important quality control measure in order to predict genetic stability and the longevity of a producing culture. Several comparable cultivation experiments revealed a difference in the pigmentation for non-producing and producing cells: the accessory pigment phycocyanin (PC) is reduced in case of the ethanol producer, resulting in a yellowish appearance of the culture. Microarray and western blot studies of Synechocystis sp. PCC6803 and Synechococcus sp. PCC7002 confirmed this PC reduction on the level of RNA and protein. KW - PCC6803 KW - PCC7002 KW - genetic instability KW - ethanol producer KW - 3D fluorescence scan KW - phycocyanin KW - absorption spectra KW - fluorescence microscopy KW - image analysis Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5911 SN - 1756-0500 VL - 8 IS - 160 ER - TY - JOUR A1 - Dimitriev, O. P. A1 - Grytsenko, Kostyantyn A1 - Tolmachev, O. I. A1 - Slominskii, Yu L. A1 - Kudinova, M. A. A1 - Schrader, Sigurd T1 - Effect of Concentration on Isomerization of Rhodanine Derivatives of Merocyanine Dyes in Polar Solvents JF - Advances in Physical Chemistry N2 - Rhodanine derivatives of merocyanine dyes with residues of 1,3,3-trimethyl-3H-indole and 3-ethylbenzothiazoline have been found to possess two molecular forms in diluted solutions of polar solvents such as dimethylformamide, dimethyl sulfoxide, and N-methylpyrrolidinone. The first molecular form was observed to prevail at low concentrations of the dyes, normally up to 10−5 M. The second one prevails at higher concentrations and is displayed through a new band in the electronic absorption spectrum, which is red-shifted with respect to the absorption band of the first form. No similar effect was found for these dyes by use of nonpolar solvents or upon alkyl-substitution of the molecules at nitrogen atom in the rhodanine moiety. We assign the above two forms to different molecular isomers and the analogous spectral changes were shown to take place by light or heat influence which correspond to a typical isomerization effect for the related merocyanine dyes. It is discussed that the isomer transformation is facilitated by the increased mobility of the proton bonded to the nitrogen atom of the rhodanine moiety in the polar environment and the increased amount of dye-dye collisions. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5931 SN - 1687-7993 VL - 2014 ER - TY - JOUR A1 - Bilous, Nataliya A1 - Malko, Vladyslav A1 - Frohme, Marcus A1 - Nechyporenko, Alina T1 - Comparison of CNN-Based Architectures for Detection of Different Object Classes JF - AI N2 - (1) Background: Detecting people and technical objects in various situations, such as natural disasters and warfare, is critical to search and rescue operations and the safety of civilians. A fast and accurate detection of people and equipment can significantly increase the effectiveness of search and rescue missions and provide timely assistance to people. Computer vision and deep learning technologies play a key role in detecting the required objects due to their ability to analyze big volumes of visual data in real-time. (2) Methods: The performance of the neural networks such as You Only Look Once (YOLO) v4-v8, Faster R-CNN, Single Shot MultiBox Detector (SSD), and EfficientDet has been analyzed using COCO2017, SARD, SeaDronesSee, and VisDrone2019 datasets. The main metrics for comparison were mAP, Precision, Recall, F1-Score, and the ability of the neural network to work in real-time. (3) Results: The most important metrics for evaluating the efficiency and performance of models for a given task are accuracy (mAP), F1-Score, and processing speed (FPS). These metrics allow us to evaluate both the accuracy of object recognition and the ability to use the models in real-world environments where high processing speed is important. (4) Conclusion: Although different neural networks perform better on certain types of metrics, YOLO outperforms them on all metrics, showing the best results of mAP-0.88, F1-0.88, and FPS-48, so the focus was on these models. KW - EfficientDet KW - SSD KW - YOLO KW - deep learning KW - neural network KW - object detection Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19634 VL - 5 IS - 4 SP - 2300 EP - 2320 PB - MDPI ER - TY - JOUR A1 - Przymus, Piotr A1 - Rykaczewski, Krzysztof A1 - Martín-Segura, Adrián A1 - Truu, Jaak A1 - De Santa Pau, Enrique Carrillo A1 - Kolev, Mikhail A1 - Naskinova, Irina A1 - Gruca, Aleksandra A1 - Sampri, Alexia A1 - Frohme, Marcus A1 - Nechyporenko, Alina T1 - Deep Learning in Microbiome Analysis: A Comprehensive Review of Neural Network Models JF - Frontiers in Microbiology N2 - Microbiome research, the study of microbial communities in diverse environments, has seen significant advances due to the integration of deep learning (DL) methods. These computational techniques have become essential for addressing the inherent complexity and high-dimensionality of microbiome data, which consist of different types of omics datasets. Deep learning algorithms have shown remarkable capabilities in pattern recognition, feature extraction, and predictive modeling, enabling researchers to uncover hidden relationships within microbial ecosystems. By automating the detection of functional genes, microbial interactions, and host-microbiome dynamics, DL methods offer unprecedented precision in understanding microbiome composition and its impact on health, disease, and the environment. However, despite their potential, deep learning approaches face significant challenges in microbiome research. Additionally, the biological variability in microbiome datasets requires tailored approaches to ensure robust and generalizable outcomes. As microbiome research continues to generate vast and complex datasets, addressing these challenges will be crucial for advancing microbiological insights and translating them into practical applications with DL. This review provides an overview of different deep learning models in microbiome research, discussing their strengths, practical uses, and implications for future studies. We examine how these models are being applied to solve key problems and highlight potential pathways to overcome current limitations, emphasizing the transformative impact DL could have on the field moving forward. KW - clasiffication KW - clustering KW - deep learning KW - natural language processing KW - microbiome Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19889 SN - 1664-302X VL - 15 PB - Frontiers ER - TY - JOUR A1 - Goldenberg, Leonid A1 - Köhler, Mathias A1 - Dreyer, Christian T1 - Fluorinated Polymers for Photonics—From Optical Waveguides to Polymer-Clad Glass Optical Fibers JF - Applied Sciences N2 - In this paper, our work in the field of fluorinated UV-curable polymers is reviewed. These polymers possessing tunable low refractive indices and low optical propagation losses for telecommunication wavelengths are intended to be used as core and cladding materials for the fabrication of passive channel waveguides in optical microchips on the polymer platform. This application requires low thermo-optic coefficients. With this goal, we used a combination of fluorinated polymers with low-refractive index inorganic nanoparticles of SiO2 and MgF2. Another application requiring extremely low refractive indices is polymer cladding for optical glass fibers. UV-curable fluorinated monomers/oligomers were used. KW - fluorinated acrylate KW - glass fiber KW - nanocomposite KW - nanoparticles KW - optical propagation losses KW - polymer cladding KW - thermo-optic coefficient Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19967 VL - 15 IS - 4 PB - MDPI ER - TY - JOUR A1 - Ichkitidze, Yuri A1 - Sarygulov, Askar A1 - Ungvári, László T1 - Potential for Enhancing Traffic Safety on Highways of Russia JF - Transportation Research Procedia N2 - The article investigates the correlation between the factors of enhancing traffic safety on highways and parameters of the economic growth in Russia and in countries with transition economy; such correlation does not always lead to traffic safety enhancement. As a rule, the population motorization (car density) level growth in such countries is not accompanied by efficient actions on accident rate decrease. Among the factors enhancing traffic safety on highways are the efficiency of traffic infrastructure planning (changing and removing traffic flows from cities’ centers, creation of a large amount of pedestrian and bicycle lanes separated from traffic flows) as well as harmonization of physical infrastructure and safety goals, ensuring conjugation of the developed transport infrastructure with the decrease of the share of private vehicle fleet and increase of the share of public transport. KW - car density KW - traffic infrastructure KW - safety goal Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-7229 SN - 2352-1465 VL - 20 SP - 242 EP - 246 ER - TY - JOUR A1 - Jänchen, Jochen A1 - Stach, Helmut T1 - Adsorption properties of porous materials for solar thermal energy storage and heat pump applications JF - Energy Procedia N2 - The water adsorption properties of modified porous sorbents for solar thermal energy storage and heat transformation have been investigated by thermogravimetry (TG) differential thermogravimetry (DTG), microcalorimetry, measurements of water adsorption isotherms, and storage tests. A chabazite type SAPO, a dealuminated faujasite type zeolite, and a mesostructured aluminosilicate, have been synthesized and compared with common zeolites X, Y and silica gel. It has been found that optimized lattice composition and pore architecture contribute to well adapt hydrophilic properties and a beneficial steep isotherm. KW - water adsorption KW - thermal adsorption storage KW - molecular sieve KW - SAPO-34 KW - MCM-41 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6160 SN - 1876-6102 VL - 30 IS - 2012 SP - 289 EP - 293 ER - TY - JOUR A1 - Tillich, Ulrich M. A1 - Lehmann, Sandra A1 - Schulze, Katja A1 - Dühring, Ulf A1 - Frohme, Marcus T1 - The Optimal Mutagen Dosage to Induce Point-Mutations in Synechocystis sp. PCC6803 and Its Application to Promote Temperature Tolerance JF - PLoS ONE N2 - Random mutagenesis is a useful tool to genetically modify organisms for various purposes, such as adaptation to cultivation conditions, the induction of tolerances, or increased yield of valuable substances. This is especially attractive for systems where it is not obvious which genes require modifications. Random mutagenesis has been extensively used to modify crop plants, but even with the renewed interest in microalgae and cyanobacteria for biofuel applications, there is relatively limited current research available on the application of random mutagenesis for these organisms, especially for cyanobacteria. In the presented work we characterized the lethality and rate of non-lethal point mutations for ultraviolet radiation and methyl methanesulphonate on the model cyanobacteria Synechocystis sp. PCC6803. Based on these results an optimal dosage of 10–50 J/m2 for UV and either 0.1 or 1 v% for MMS was determined. A Synechocystis wildtype culture was then mutagenized and selected for increased temperature tolerance in vivo. During the second round of mutagenesis the viability of the culture was monitored on a cell by cell level from the treatment of the cells up to the growth at an increased temperature. After four distinct rounds of treatment (two with each mutagen) the temperature tolerance of the strain was effectively raised by about 2°C. Coupled with an appropriate in vivo screening, the described methods should be applicable to induce a variety of desirable characteristics in various strains. Coupling random mutagenesis with high-throughput screening methods would additionally allow to select for important characteristics for biofuel production, which do not yield a higher fitness and can not be selected for in vivo, such as fatty acid concentration. In a combined approach with full genome sequencing random mutagenesis could be used to determine suitable target-genes for more focused methods. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6186 SN - 1932-6203 VL - 7 IS - 11 ER - TY - JOUR A1 - Schulze, Katja A1 - López, Diana A. A1 - Tillich, Ulrich M. A1 - Frohme, Marcus T1 - A simple viability analysis for unicellular cyanobacteria using a new autofluorescence assay, automated microscopy, and ImageJ JF - BMC Biotechnology N2 - Currently established methods to identify viable and non-viable cells of cyanobacteria are either time-consuming (eg. plating) or preparation-intensive (eg. fluorescent staining). In this paper we present a new and fast viability assay for unicellular cyanobacteria, which uses red chlorophyll fluorescence and an unspecific green autofluorescence for the differentiation of viable and non-viable cells without the need of sample preparation. Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6192 SN - 1472-6750 VL - 11 IS - 118 ER - TY - JOUR A1 - Andreas, Kristin A1 - Häupl, Thomas A1 - Lübke, Carsten A1 - Ringe, Jochen A1 - Morawietz, Lars A1 - Wachtel, Anja A1 - Sittinger, Michael A1 - Kaps, Christian T1 - Antirheumatic drug response signatures in human chondrocytes: potential molecular targets to stimulate cartilage regeneration JF - Arthritis Research & Therapy N2 - Rheumatoid arthritis (RA) leads to progressive destruction of articular cartilage. This study aimed to disclose major mechanisms of antirheumatic drug action on human chondrocytes and to reveal marker and pharmacological target genes that are involved in cartilage dysfunction and regeneration. Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6223 SN - 1465-9913 VL - 11 IS - R15 ER - TY - JOUR A1 - Schulze, Katja A1 - Tillich, Ulrich M. A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - PlanktoVision - an automated analysis system for the identification of phytoplankton JF - BMC Bioinformatics N2 - Phytoplankton communities are often used as a marker for the determination of fresh water quality. The routine analysis, however, is very time consuming and expensive as it is carried out manually by trained personnel. The goal of this work is to develop a system for an automated analysis. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6364 SN - 1471-2105 VL - 14 IS - 115 ER - TY - JOUR A1 - Grytsenko, Kostyantyn A1 - Lozovski, Valeri A1 - Strilchuk, Galyna A1 - Schrader, Sigurd T1 - Evaluation of the Mechanism of the Gold Cluster Growth during Heating of the Composite Gold-Polytetrafluoroethylene Thin Film JF - Nanomaterials N2 - Nanocomposite films consisting of gold inclusions in the polytetrafluoroethylene (PTFE) matrix were obtained by thermal vacuum deposition. Annealing of the obtained films with different temperatures was used to measure varying of film morphologies. The dependence of optical properties of the films on their morphology was studied. It was established that absorption and profile of the nanocomposite film obtained by thermal vacuum deposition can be changed with annealing owing to the fact that different annealing temperatures lead to different average particle sizes. A method to calculate the optical properties of nanocomposite thin films with inclusions of different sizes was proposed. Thus, comparison of experimental optical spectra with the spectra obtained during the simulation enables estimating average sizes of inclusions. The calculations give the possibility of understanding morphological changes in the structures. KW - nanocomposite KW - gold KW - polytetrafluoroethylene KW - optical spectroscopy KW - microscopy KW - thin film Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6387 SN - 2079-4991 VL - 2 IS - 4 SP - 366 EP - 378 ER - TY - JOUR A1 - Herzog, Thomas H. A1 - Jänchen, Jochen A1 - Kontogeorgopoulos, Eythymius M. A1 - Lutz, Wolfgang T1 - Steamed Zeolites for Heat Pump Applications and Solar Driven Thermal Adsorption Storage JF - Energy Procedia N2 - The influence of the dealumination degree of NaY with respect to the water adsorption properties was investigated by infrared spectroscopy, thermogravimetry and isotherm measurements. The modification of the samples is a result of a steaming process at different temperatures in dependence of time. It was found that dealumination controls the hydrophilic behavior of NaY and contributes to defined low desorption temperatures. Similar to microporous SAPO's steamed Y-zeolites can be used for low temperature applications of heat transformation and thermal adsorption storage. KW - dealumination KW - water adsorption KW - zeolite KW - adsorption heat pump KW - thermal adsorption storage Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5951 SN - 1876-6102 VL - 48 SP - 380 EP - 383 ER - TY - JOUR A1 - Tillich, Ulrich M. A1 - Wolter, Nick A1 - Schulze, Katja A1 - Kramer, Dan A1 - Brödel, Oliver A1 - Frohme, Marcus T1 - High-throughput cultivation and screening platform for unicellular phototrophs JF - BMC Microbiology N2 - In this work we describe and test high-throughput methods with the model organism Synechocystis sp. PCC6803. The required technical automation for these processes was achieved with a Tecan Freedom Evo 200 pipetting robot. The cultivation was performed in 2.2 ml deepwell microtiter plates within a cultivation chamber outfitted with programmable shaking conditions, variable illumination, variable temperature, and an adjustable CO2 atmosphere. Each microtiter-well within the chamber functions as a separate cultivation vessel with reproducible conditions. The automated measurement of various parameters such as growth, full absorption spectrum, chlorophyll concentration, MALDI-TOF-MS, as well as a novel vitality measurement protocol, have already been established and can be monitored during cultivation. Measurement of growth parameters can be used as inputs for the system to allow for periodic automatic dilutions and therefore a semi-continuous cultivation of hundreds of cultures in parallel. The system also allows the automatic generation of mid and long term backups of cultures to repeat experiments or to retrieve strains of interest. KW - cyanobacteria KW - synechocystis KW - HTS KW - high throughput KW - automated cultivation Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6007 SN - 1471-2180 VL - 14 IS - 239 ER - TY - JOUR A1 - Tillich, Ulrich M. A1 - Wolter, Nick A1 - Franke, Philipp A1 - Dühring, Ulf A1 - Frohme, Marcus T1 - Screening and genetic characterization of thermo-tolerant Synechocystis sp. PCC6803 strains created by adaptive evolution JF - BMC Biotechnology N2 - Temperature tolerance is an important aspect for commercial scale outdoor cultivation of microalgae and cyanobacteria. While various genes are known to be related to Synechocystis sp. PCC6803's heat shock response, there is very limited published data concerning the specific genes involved in long term thermal tolerance. We have previously used random mutagenesis and adaptive evolution to generate a mixture of strains of Synechocystis sp. PCC6803 with significantly increased thermal tolerance. The genetic modifications leading to the phenotypes of the newly generated strains are the focus of this work. KW - cyanobacteria KW - synechocystis KW - thermal tolerance KW - HTS KW - NGS KW - adaptive evolution Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6014 SN - 1472-6750 VL - 14 IS - 66 ER - TY - JOUR A1 - Herzog, Thomas H. A1 - Jänchen, Jochen T1 - Adsorption Properties of Modified Zeolites for Operating Range Enhancement of Adsorption Heat Pumps through the Use of Organic Adsorptive Agents JF - Energy Procedia N2 - Faujasite zeolites with the highest possible Al-content and different cations as well as a dealuminated zeolite Y have been chosen to study the impact on the adsorption behavior in view of differed adsorptive agents for heat pumps or thermochemical storages. Our results show advantages and disadvantages for water, methanol or ethanol adsorption due to the structure of the anion skeleton, kind of cations and size of the adsorbat molecule. KW - heat pump KW - water adsorption KW - zeolite KW - ethanol KW - methanol Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6614 SN - 1876-6102 VL - 91 SP - 155 EP - 160 ER - TY - JOUR A1 - Göbel, Gero A1 - Dietz, T. A1 - Lisdat, Fred T1 - Biosensor based on an oxygen reducing bilirubin oxidase electrode JF - Procedia Chemistry N2 - An oxygen reducing electrode made of bilirubin oxidase and multi-walled carbon nanotubes (BOD-MWCNT-Au electrode) is coupled to enzymes catalysing oxygen-consuming reactions such as glucose oxidase (GOD) to result in a membrane-free bienzyme electrode. The feasibility of such a molecularly assembled system stabilized by covalent linkage has been demonstrated. The electrochemical characterisation of the bienzyme electrode reveals sensitivity to the enzyme substrate. The results indicate that the BOD-electrode provides a suitable platform for sensing analytes for which oxidases of high activity are available. KW - bienzyme sensor KW - bilirubin oxidase KW - carbon nanotube KW - membran-free KW - mediator-less Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6237 SN - 1876-6196 VL - 1 IS - 1 SP - 273 EP - 276 ER - TY - JOUR A1 - Omar, Noorsharmimi A1 - Loh, Qiuting A1 - Tye, Gee Jun A1 - Choong, Yee Siew A1 - Noordin, Rahmah A1 - Glökler, Jörn A1 - Lim, Theam Soon T1 - Development of an Antigen-DNAzyme Based Probe for a Direct Antibody-Antigen Assay Using the Intrinsic DNAzyme Activity of a Daunomycin Aptamer JF - Sensors N2 - G-Quadruplex (G-4) structures are formed when G-rich DNA sequences fold into intra- or intermolecular four-stranded structures in the presence of metal ions. G-4-hemin complexes are often effective peroxidase-mimicking DNAzymes that are applied in many detection systems. This work reports the application of a G-rich daunomycin-specific aptamer for the development of an antibody-antigen detection assay. We investigated the ability of the daunomycin aptamer to efficiently catalyze the hemin-dependent peroxidase activity independent of daunomycin. A reporter probe consisting of biotinylated antigen and daunomycin aptamer coupled to streptavidin gold nanoparticles was successfully used to generate a colorimetric readout. In conclusion, the daunomycin aptamer can function as a robust alternative DNAzyme for the development of colorimetric assays. KW - G-quadruplex KW - DNAzyme KW - gold nanoparticle KW - antibody Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6267 SN - 1424-8220 VL - 14 IS - 1 SP - 346 EP - 355 ER - TY - JOUR A1 - Enders, Peter T1 - Historical Prospective: Boltzmann’s versus Planck’s State Counting—Why Boltzmann Did Not Arrive at Planck’s Distribution Law JF - Journal of Thermodynamics N2 - Why does Planck (1900), referring to Boltzmann’s 1877 probabilistic treatment, obtain his quantum distribution function while Boltzmann did not? To answer this question, both treatments are compared on the basis of Boltzmann’s 1868 three-level scheme (configuration—occupation—occupancy). Some calculations by Planck (1900, 1901, and 1913) and Einstein (1907) are also sketched. For obtaining a quantum distribution, it is crucial to stick with a discrete energy spectrum and to make the limit transitions to infinity at the right place. For correct state counting, the concept of interchangeability of particles is superior to that of indistinguishability. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6281 SN - 1687-9252 VL - 2016 ER - TY - JOUR A1 - Belinsky, Martin G. A1 - Rink, Lori A1 - Cai, Kathy Q. A1 - Capuzzi, Stephen J. A1 - Hoang, Yen A1 - Chien, Jeremy A1 - Godwin, Andrew K. A1 - von Mehren, Margaret T1 - Somatic loss of function mutations in neurofibromin 1 and MYC associated factor X genes identified by exome-wide sequencing in a wild-type GIST case JF - BMC Cancer N2 - Approximately 10–15 % of gastrointestinal stromal tumors (GISTs) lack gain of function mutations in the KIT and platelet-derived growth factor receptor alpha (PDGFRA) genes. An alternate mechanism of oncogenesis through loss of function of the succinate-dehydrogenase (SDH) enzyme complex has been identified for a subset of these “wild type” GISTs. KW - gastrointestinal stromal tumor (GIST) KW - wild type KW - KIT KW - PDGFRA KW - succinate dehydrogenase (SDH) KW - NF1 KW - MAX Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6292 SN - 1471-2407 VL - 15 IS - 887 ER - TY - JOUR A1 - Munchel, Sarah A1 - Hoang, Yen A1 - Yue, Zhao A1 - Cottrell, Joseph A1 - Klotzle, Brandy A1 - Godwin, Andrew K. A1 - Koestler, Devin A1 - Beyerlein, Peter A1 - Fan, Jian-Bing A1 - Bibikova, Marina A1 - Chien, Jeremy T1 - Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics JF - Oncotarget N2 - Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C·G > T·A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes. KW - cancer genomics KW - FFPE DNA KW - whole exome sequencing KW - whole genome sequencing KW - copy number alteration Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6307 SN - 1949-2553 VL - 6 IS - 28 SP - 25943 EP - 25961 ER - TY - JOUR A1 - Graw, Stefan A1 - Meier, Richard A1 - Minn, Kay A1 - Bloomer, Clark A1 - Godwin, Andrew K. A1 - Fridley, Brooke A1 - Vlad, Anda A1 - Beyerlein, Peter A1 - Chien, Jeremy T1 - Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples JF - Scientific Reports N2 - Current genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r > 0.89). In addition, sequence variations identified from FFPE RNA show 99.67% concordance with that from exome sequencing of matched frozen tumor samples. Because FFPE is a routine diagnostic sample preparation, the feasibility results reported here will facilitate the setup of large-scale research and clinical studies in medical genomics that are currently limited by the availability of fresh frozen samples. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6319 SN - 2045-2322 VL - 5 ER - TY - JOUR A1 - Kipkorir, R. A1 - Muhoho, S. A1 - Muliro, P. A1 - Mugendi, Beatrice A1 - Frohme, Marcus A1 - Brödel, Oliver T1 - Effects of Coffee Processing Technologies on Aroma Profiles and Sensory Quality of Ruiru 11 and SL 28 Kenyan Coffee Varieties JF - Asian Journal of Agriculture and Food Sciences N2 - The study aimed at comparing the effects of three coffee processing methods on aroma profiles and sensory quality of Ruiru 11 and SL 28 coffee varieties. The processing methods varied on stages of processing and method of mucilage removal. The green coffee beans obtained from the three processing methods were graded and roasted, ground and analyzed for the aroma profiles and sensory quality. Headspace Solid phase Microextraction fibre (SPME) technique were used for the extraction of aroma compounds from coffee samples and characterization of the compounds with use of gas chromatography mass spectrometry (GC-MS). Sensory quality were analyzed by an expert panelist. Various volatile aroma compounds were identified in roasted coffee and classified into their chemical classes involving furans, ketones, pyrazines ketones pyridines, pyrroles and acids. The intensity of aroma compounds were compared in terms of their peak areas and variations were noted between the processing methods with the ecopulper showing higher levels of pyrazines such as 2-methylpyrazine, 2-ethyl-6-methylpyrazine, and wet pulper showing higher levels of furans such as furfuryl formate and furfuryl alcohol, acetate. The hand pulper was high in the level of acids and esters such as acetic acid and propanoic acid, ethyl ester. Similar aroma compounds were identified in headspace of Ruiru 11 and SL 28 and there were variations in the intensities of aroma groups such as pyrroles and pyridines. It was concluded that the eco-pulper and hand pulper methods gives better aroma quality than the wet pulper while SL 28 variety gives higher sensory quality than Ruiru 11. KW - coffee KW - processing KW - aroma KW - sensory quality Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6482 UR - https://ajouronline.com/index.php/AJAFS/article/view/2551 SN - 2321-1571 VL - 3 IS - 2 SP - 178 EP - 188 ER - TY - JOUR A1 - Wegerich, F. A1 - Turano, Paola A1 - Allegrozzi, Marco A1 - Möhwald, H. A1 - Lisdat, Fred T1 - Superoxide Biosensing with Engineered Cytochrome c JF - Procedia Chemistry N2 - Several mutation positions have been chosen for introducing positively charged lysines in human cytochrome c (cyt c) with the aim of increasing the reaction rate with superoxide radicals (SO) and thus, the sensitivity of an electrochemical cyt c based SO biosensor. The impact of the mutations on structural and redox properties as well as on the reaction rate with SO are verified. Four mutants show a higher reaction rate with the radical compared to the wild type. These mutants are used for the construction of SO sensors based on thiol-modified gold electrodes and covalently fixed proteins. The E66K mutant electrode has a clearly higher sensitivity in comparison to the wildtype based sensor. KW - biosensor KW - cytochrome c KW - superoxide KW - protein engineering Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6523 SN - 1876-6196 VL - 1 IS - 1 SP - 1287 EP - 1290 ER - TY - JOUR A1 - Haider, Christian A1 - Aschauer, Gerald J. A1 - Schmidt, Conrad T1 - IT Based Attempt to Evaluate and Promote Intermodal Transport Solutions in Central and Southeast Europe JF - Transportation Research Procedia N2 - The transport sector is one of the main emitters of greenhouse gas emissions. The awareness about this is increasing because of heightened environmental sensitivity among customers, politicians and the media. Studies dealing with sustainability in logistics have been inducted to show that companies around the world are keen to promote “green solutions” through the management of logistics. From now, it is difficult to gauge how far these efforts reflect true desire to help the environment as opposed to enhance public relations. The paper addresses an IT based attempt to evaluate and promote intermodal transport procedures in the corridor of Central and Southeast Europe. Through the assessment of the relative importance of intermodal transport nodes the described tool is a useful instrument to demonstrate the most important advantages for environmental friendly transport solutions. In combination with accessibility as well as network scenario attempts stakeholders have full information available when preparing several transport plans due to transparent strengths of rail and inland waterway transports. KW - sustainability KW - web-based routing tool KW - intermodal transport KW - knowledge sharing Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6535 SN - 2352-1465 VL - 3 SP - 641 EP - 650 ER - TY - JOUR A1 - Kaltdorf, Kristin Verena A1 - Schulze, Katja A1 - Helmprobst, Frederik A1 - Kollmannsberger, Philip A1 - Dandekar, Thomas A1 - Stigloher, Christian T1 - FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms JF - PLoS Computational Biology N2 - Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial. Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9218 SN - 1553-7358 VL - 13 IS - 1 ER - TY - JOUR A1 - Schulze, Sven A1 - Wehrhold, Michel A1 - Hille, Carsten T1 - Femtosecond-Pulsed Laser Written and Etched Fiber Bragg Gratings for Fiber-Optical Biosensing JF - Sensors N2 - We present the development of a label-free, highly sensitive fiber-optical biosensor for online detection and quantification of biomolecules. Here, the advantages of etched fiber Bragg gratings (eFBG) were used, since they induce a narrowband Bragg wavelength peak in the reflection operation mode. The gratings were fabricated point-by-point via a nonlinear absorption process of a highly focused femtosecond-pulsed laser, without the need of prior coating removal or specific fiber doping. The sensitivity of the Bragg wavelength peak to the surrounding refractive index (SRI), as needed for biochemical sensing, was realized by fiber cladding removal using hydrofluoric acid etching. For evaluation of biosensing capabilities, eFBG fibers were biofunctionalized with a single-stranded DNA aptamer specific for binding the C-reactive protein (CRP). Thus, the CRP-sensitive eFBG fiber-optical biosensor showed a very low limit of detection of 0.82 pg/L, with a dynamic range of CRP detection from approximately 0.8 pg/L to 1.2 µg/L. The biosensor showed a high specificity to CRP even in the presence of interfering substances. These results suggest that the proposed biosensor is capable for quantification of CRP from trace amounts of clinical samples. In addition, the adaption of this eFBG fiber-optical biosensor for detection of other relevant analytes can be easily realized. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-10570 SN - 1424-8220 VL - 18 IS - 9 SP - 1 EP - 20 ER - TY - JOUR A1 - Bruun, Kristina A1 - Löhmannsröben, Hans-Gerd A1 - Hille, Carsten T1 - Benefits of Combined Fluorescence Lifetime Imaging Microscopy and Fluorescence Correlation Spectroscopy for Biomedical Studies Demonstrated by Using a Liposome Model System JF - Biophysica N2 - Drug delivery systems play a pivotal role in targeted pharmaceutical transport and controlled release at specific sites. Liposomes, commonly used as drug carriers, constitute a fundamental part of these systems. Moreover, the drug–liposome model serves as a robust platform for investigating interaction processes at both cellular and molecular levels. To advance our understanding of drug carrier uptake mechanisms, we employed fluorescence lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS), leveraging the unique benefits of two-photon (2P) excitation. Our approach utilized giant unilamellar vesicles (GUVs) as a simplified model system for cell membranes, labelled with the amphiphilic fluorescent dye 3,3′-dioctadecyloxa-carbocyanine (DiOC18(3)). Additionally, large unilamellar vesicles (LUVs) functioned as a drug carrier system, incorporating the spectrally distinct fluorescent sulforhodamine 101 (SRh101) as a surrogate drug. The investigation emphasized the diverse interactions between GUVs and LUVs based on the charged lipids employed. We examined the exchange kinetics and structural alterations of liposome carriers during the uptake process. Our study underscores the significance of employing 2P excitation in conjunction with FLIM and FCS. This powerful combination offers a valuable methodological approach for studying liposome interactions, positioning them as an exceptionally versatile model system with a distinct technical advantage. KW - drug delivery KW - fluorescence correlation spectroscopy KW - fluorescence lifetime imaging microscopy KW - liposome KW - membrane interaction Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19189 VL - 4 IS - 2 SP - 207 EP - 227 PB - MDPI ER - TY - JOUR A1 - Zhang, Youjun A1 - Sampathkumar, Arun A1 - Kerber, Sandra Mae-Lin A1 - Swart, Corné A1 - Hille, Carsten A1 - Seerangan, Kumar A1 - Graf, Alexander A1 - Sweetlove, Lee A1 - Fernie, Alisdair R. T1 - A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts JF - Nature Communications N2 - Glycolysis is one of the primordial pathways of metabolism, playing a pivotal role in energy metabolism and biosynthesis. Glycolytic enzymes are known to form transient multi-enzyme assemblies. Here we examine the wider protein-protein interactions of plant glycolytic enzymes and reveal a moonlighting role for specific glycolytic enzymes in mediating the co-localization of mitochondria and chloroplasts. Knockout mutation of phosphoglycerate mutase or enolase resulted in a significantly reduced association of the two organelles. We provide evidence that phosphoglycerate mutase and enolase form a substrate-channelling metabolon which is part of a larger complex of proteins including pyruvate kinase. These results alongside a range of genetic complementation experiments are discussed in the context of our current understanding of chloroplast-mitochondrial interactions within photosynthetic eukaryotes. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14812 SN - 2041-1723 VL - 11 SP - 4509 ER - TY - JOUR A1 - Bruun, Kristina A1 - Hille, Carsten T1 - Study on intracellular delivery of liposome encapsulated quantum dots using advanced fluorescence microscopy JF - Scientific Reports N2 - Quantum dots increasingly gain popularity for in vivo applications. However, their delivery and accumulation into cells can be challenging and there is still lack of detailed information. Thereby, the application of advanced fluorescence techniques can expand the portfolio of useful parameters for a more comprehensive evaluation. Here, we encapsulated hydrophilic quantum dots into liposomes for studying cellular uptake of these so-called lipodots into living cells. First, we investigated photophysical properties of free quantum dots and lipodots observing changes in the fluorescence decay time and translational diffusion behaviour. In comparison to empty liposomes, lipodots exhibited an altered zeta potential, whereas their hydrodynamic size did not change. Fluorescence lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS), both combined with two-photon excitation (2P), were used to investigate the interaction behaviour of lipodots with an insect epithelial tissue. In contrast to the application of free quantum dots, their successful delivery into the cytosol of salivary gland duct cells could be observed when applying lipodots. Lipodots with different lipid compositions and surface charges did not result in considerable differences in the intracellular labelling pattern, luminescence decay time and diffusion behaviour. However, quantum dot degradation after intracellular accumulation could be assumed from reduced luminescence decay times and blue-shifted luminescence signals. In addition to single diffusing quantum dots, possible intracellular clustering of quantum dots could be assumed from increased diffusion times. Thus, by using a simple and manageable liposome carrier system, 2P-FLIM and 2P-FCS recording protocols could be tested, which are promising for investigating the fate of quantum dots during cellular interaction. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-12476 SN - 2045-2322 VL - 9 SP - 10504 ER - TY - JOUR A1 - Günther, Erika A1 - Klauß, André A1 - Toro-Nahuelpan, Mauricio A1 - Schüler, Dirk A1 - Hille, Carsten A1 - Faivre, Damien T1 - The in vivo mechanics of the magnetotactic backbone as revealed by correlative FLIM-FRET and STED microscopy JF - Scientific Reports N2 - Protein interaction and protein imaging strongly benefit from the advancements in time-resolved and superresolution fluorescence microscopic techniques. However, the techniques were typically applied separately and ex vivo because of technical challenges and the absence of suitable fluorescent protein pairs. Here, we show correlative in vivo fluorescence lifetime imaging microscopy Förster resonance energy transfer (FLIM-FRET) and stimulated emission depletion (STED) microscopy to unravel protein mechanics and structure in living cells. We use magnetotactic bacteria as a model system where two proteins, MamJ and MamK, are used to assemble magnetic particles called magnetosomes. The filament polymerizes out of MamK and the magnetosomes are connected via the linker MamJ. Our system reveals that bacterial filamentous structures are more fragile than the connection of biomineralized particles to this filament. More importantly, we anticipate the technique to find wide applicability for the study and quantification of biological processes in living cells and at high resolution. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14802 SN - 2045-2322 VL - 9 ER - TY - JOUR A1 - Praia, Ana Beatriz A1 - Herkenhoff, Marcos Edgar A1 - Brödel, Oliver A1 - Frohme, Marcus A1 - Saad, Susana Marta Isay T1 - Sour Beer with Lacticaseibacillus paracasei subsp. paracasei F19: Feasibility and Influence of Supplementation with Spondias mombin L. Juice and/or By-Product JF - Foods N2 - This study aimed to evaluate the probiotic strain Lacticaseibacillus (L.) paracasei subsp. paracasei F19 (F19) with the yeast Saccharomyces cerevisiae US-05 (US-05), using Spondias mombin L. (‘taperebá’ or ‘cajá’) juice and by-product, in four sour-type beer formulations: control, with bagasse, juice, and juice and bagasse. The viability of F19 was evaluated by pour-plating and PMA-qPCR. Fermentability, in addition to physicochemical and sensory parameters, and aroma and flavor, were evaluated during brewery by using Headspace Solid-Phase Microextraction (HS-SPME) coupled with gas chromatography–mass spectrometry (GC–MS). F19 was successful in fermenting bagasse in a MRS medium (9.28 log CFU/mL in 24 h) but had a low viability in hopped wort, growing better in formulations without bagasse or juice. No difference between formulations was observed regarding sensory acceptability, and the HS-SPME/GC-MS revealed different flavors and aroma compounds. In conclusion, the production of a potential probiotic sour beer with F19 and US-05 is feasible regarding probiotic viability. However, S. mombin, as juice or bagasse, threatened probiotic survival. Different flavors and aroma compounds were detected, whereas no difference between formulations was found regarding sensory acceptability. The moderate alcohol content achieved is important for bacterial survival and for the development of a probiotic beer with health claims. KW - sour beer KW - probiotics KW - co-fermentation KW - fruit by-product Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16852 SN - 2304-8158 VL - 11 IS - 24 PB - MDPI ER - TY - JOUR A1 - Radivoievych, Aleksandar A1 - Kolp, Benjamin A1 - Grebinyk, Sergii A1 - Prylutska, Svitlana A1 - Ritter, Uwe A1 - Zolk, Oliver A1 - Glökler, Jörn A1 - Frohme, Marcus A1 - Grebinyk, Anna T1 - Silent Death by Sound: C60 Fullerene Sonodynamic Treatment of Cancer Cells JF - International Journal of Molecular Sciences N2 - The acoustic pressure waves of ultrasound (US) not only penetrate biological tissues deeper than light, but they also generate light emission, termed sonoluminescence. This promoted the idea of its use as an alternative energy source for photosensitizer excitation. Pristine C60 fullerene (C60), an excellent photosensitizer, was explored in the frame of cancer sonodynamic therapy (SDT). For that purpose, we analyzed C60 effects on human cervix carcinoma HeLa cells in combination with a low-intensity US treatment. The time-dependent accumulation of C60 in HeLa cells reached its maximum at 24 h (800 ± 66 ng/106 cells). Half of extranuclear C60 is localized within mitochondria. The efficiency of the C60 nanostructure’s sonoexcitation with 1 MHz US was tested with cell-based assays. A significant proapoptotic sonotoxic effect of C60 was found for HeLa cells. C60′s ability to induce apoptosis of carcinoma cells after sonoexcitation with US provides a promising novel approach for cancer treatment. KW - ultrasound KW - C60 fullerene KW - sonodynamic therapy KW - HeLa cells KW - apoptosis Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16877 SN - 1422-0067 VL - 24 IS - 2 PB - MDPI ER - TY - JOUR A1 - Rykova, Eugenia A1 - Stieben, Christine A1 - Dostovalova, Olga A1 - Wieker, Horst T1 - Connected Driving in German-Speaking Social Media JF - Social Sciences N2 - Intelligent transportation systems (ITS) have been steadily becoming part of our reality. For their successful integration, studying and understanding public opinions and acceptance is important. Social media platforms offer an extensive opportunity for opinion mining. While there have been studies on people’s attitudes towards automated driving, another important ITS concept—connected driving—has received little to no attention. In the current study, data on how connected driving is represented and perceived were collected from German(-speaking) Reddit and Twitter. In relevant Reddit entries, the necessity of communication between vehicles was discussed almost exclusively in the context of automated driving. On Twitter, mostly shared news and information on the topic are presented, while the number of personal opinions is low. The most concerning subtopic seems to be cybersecurity, which reflects a general trend of data protection issues discussed in society. KW - ITS KW - intelligent transportation system KW - connected driving KW - autonomous driving KW - social media KW - Twitter KW - Reddit Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16969 SN - 2076-0760 VL - 12 IS - 1 PB - MDPI ER - TY - JOUR A1 - Villringer, Claus A1 - Steglich, Patrick A1 - Pulwer, Silvio A1 - Schrader, Sigurd A1 - Laufer, Jan T1 - Electro-optical properties of doped polymers with high transparency in the visible wavelength range JF - Optical Materials Express N2 - The electro-optical (EO) properties of poly(methyl methacrylate) and the photopolymer poly(vinyl cinnamate) doped with varying concentrations of the EO chromophore 2-Methyl-4-nitroaniline were measured. The EO polymers were embedded in Fabry-Pérot etalons for the simultaneous determination of the Pockels and Kerr coefficients from measurements of the fringe shift induced by an external electric field. It was found that the host polymer has a significant impact on the EO performance and that the undoped host polymers exhibit a significant Pockels effect. Moreover, the Kerr effect provides a substantial contribution of 27% to the total change of the refractive index at relatively high electric field strengths of E = 91.2 MV m−1. KW - Bragg reflector KW - fiber optic coupler KW - refractive index KW - spatial light modulator KW - transparency KW - tunable filter Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15480 VL - 11 IS - 11 SP - 3801 EP - 3811 PB - Optica Publishing Group ER - TY - JOUR A1 - Roos, Andreas Hult A1 - Hoque, Ziaul A1 - Klimešová, Eva A1 - Ben Ltaief, Ltaief A1 - Medina, Cristian A1 - Jurkovič, Matej A1 - Albrecht, Martin A1 - Finke, Ondřej A1 - Hort, Ondřej A1 - Nejdl, Jaroslav A1 - Mudrich, Marcel A1 - Andreasson, Jakob A1 - Krikunova, Maria T1 - Electron correlation dynamics in atomic Kr excited by XUV pulses and controlled by NIR laser pulses of variable intensity JF - New Journal of Physics N2 - We have investigated the possibility to track and control correlation dynamics of valence electrons in krypton (Kr) initiated by the absorption of one extreme ultraviolet (XUV) photon. In this investigation, pump-probe experiments have been performed where monochromatized single high-harmonics at photon energies 29.6, 32.8, and 35.9 eV have been used as pump to populate different intermediate excited states. A temporally delayed near-infrared (NIR) pulse probes the population of various decay channels via the detection of Kr²⁺ ion yields and its transient profiles. We observe that by varying the NIR pulse intensity within a range from 0.3 x 10¹³ to 2.6 x 10¹³ W cm⁻², the shape of the Kr²+ transient profile changes significantly. We show that by varying the intensity of the NIR pulse, it is possible—(i) to control the ratio between sequential and non-sequential double ionization of Kr; (ii) to selectively probe quantum beating oscillations between Kr+* satellite states that are coherently excited within the bandwidth of the XUV pulse; and (iii) to specifically probe the relaxation dynamics of doubly excited (Kr**) decay channels. Our studies show that the contribution of different ionization and decay channels (i)–(iii) can be altered by the NIR pulse intensity, thus demonstrating an efficient way to control the ionization dynamics in rare gas atoms. KW - electron correlation KW - control ionization dynamics KW - krypton satellite states KW - XUV/NIR pump-probe KW - HHG KW - quantum beating oscillation KW - doubly excited states Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16987 VL - 25 PB - Institute of Physics Publishing (IOP) ER - TY - JOUR A1 - König, Hannes J. A1 - Kiffner, Christian A1 - Kuhls, Katrin A1 - Uthes, Sandra A1 - Harms, Verena A1 - Wieland, Ralf T1 - Planning for wolf-livestock coexistence: landscape context predicts livestock depredation risk in agricultural landscapes JF - animal N2 - Extensive pastoral livestock systems in Central Europe provide multiple ecosystem services and support biodiversity in agricultural landscapes but their viability is challenged by livestock depredation (LD) associated with the recovery of wolf populations. Variation in the spatial distribution of LD depends on a suite of factors, most of which are unavailable at the appropriate scales. To assess if LD patterns can be predicted sufficiently with land use data alone at the scale of one federal state in Germany, we employed a machine-learning-supported resource selection approach. The model used LD monitoring data, and publicly available land use data to describe the landscape configuration at LD and control sites (resolution 4 km * 4 km). We used SHapley Additive exPlanations to assess the importance and effects of landscape configuration and cross-validation to evaluate the model performance. Our model predicted the spatial distribution of LD events with a mean accuracy of 74%. The most influential land use features included grassland, farmland and forest. The risk of livestock depredation was high if these three landscape features co-occurred with a specific proportion. A high share of grassland, combined with a moderate proportion of forest and farmland, increased LD risk. We then used the model to predict the LD risk in five regions; the resulting risk maps showed high congruence with observed LD events. While of correlative nature and lacking specific information on wolf and livestock distribution and husbandry practices, our pragmatic modelling approach can guide spatial prioritisation of damage prevention or mitigation practices to improve livestock-wolf coexistence in agricultural landscapes. KW - decision support KW - grazing-based livestock KW - human-wildlife coexistence KW - machine learning KW - risk map Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17032 SN - 1751-7311 VL - 17 IS - 3 PB - Elsevier ER - TY - JOUR A1 - Falk, Constantin A1 - El Ghayed, Tarek A1 - van de Sand, Ron A1 - Reiff-Stephan, Jörg T1 - A Data-Driven Approach Towards the Application of Reinforcement Learning Based HVAC Control JF - Journal of the Nigerian Society of Physical Sciences N2 - Refrigeration applications consume a significant share of total electricity demand, with a high indirect impact on global warming through greenhouse gas emissions. Modern technology can help reduce the high power consumption and optimize the cooling control. This paper presents a case study of machine-learning for controlling a commercial refrigeration system. In particular, an approach to reinforcement learning is implemented, trained and validated utilizing a model of a real chiller plant. The reinforcement-learning controller learns to operate the plant based on its interactions with the modeled environment. The validation demonstrates the functionality of the approach, saving around 7% of the energy demand of the reference control. Limitations of the approach were identified in the discretization of the real environment and further model-based simplifications and should be addressed in future research. KW - refrigeration system KW - reinforcement learning KW - optimized control KW - Q-learning Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17066 SN - 2714-4704 VL - 5 IS - 1 PB - Department of Physics, Federal University Lafia Nasarawa State, Nigeria ; Nigerian Society of Physical Sciences ER - TY - JOUR A1 - Alekseeva, Victoriia A1 - Nechyporenko, Alina A1 - Frohme, Marcus A1 - Gargin, Vitaliy A1 - Meniailov, Ievgen A1 - Chumachenko, Dmytro T1 - Intelligent Decision Support System for Differential Diagnosis of Chronic Odontogenic Rhinosinusitis Based on U-Net Segmentation JF - Electronics N2 - The share of chronic odontogenic rhinosinusitis is 40% among all chronic rhinosinusitis. Using automated information systems for differential diagnosis will improve the efficiency of decision-making by doctors in diagnosing chronic odontogenic rhinosinusitis. Therefore, this study aimed to develop an intelligent decision support system for the differential diagnosis of chronic odontogenic rhinosinusitis based on computer vision methods. A dataset was collected and processed, including 162 MSCT images. A deep learning model for image segmentation was developed. A 23 convolutional layer U-Net network architecture has been used for the segmentation of multi-spiral computed tomography (MSCT) data with odontogenic maxillary sinusitis. The proposed model is implemented in such a way that each pair of repeated 3 × 3 convolutions layers is followed by an Exponential Linear Unit instead of a Rectified Linear Unit as an activation function. The model showed an accuracy of 90.09%. To develop a decision support system, an intelligent chatbot allows the user to conduct an automated patient survey and collect patient examination data from several doctors of various profiles. The intelligent information system proposed in this study made it possible to combine an image processing model with a patient interview and examination data, improving physician decision-making efficiency in the differential diagnosis of Chronic Odontogenic Rhinosinusitis. The proposed solution is the first comprehensive solution in this area. KW - CT data KW - deep learning KW - image segmentation KW - U-Net KW - decision support system KW - chronic odontogenic rhinosinusitis KW - machine learning KW - artificial intelligence Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17088 SN - 2079-9292 VL - 12 IS - 5 PB - MDPI ER - TY - JOUR A1 - Henning, Thorsten A1 - Wagner, Philipp A1 - Gedat, Egbert A1 - Kochlik, Bastian A1 - Kusch, Paula A1 - Sowoidnich, Kay A1 - Vastag, Marko A1 - Gleim, Jeannine A1 - Braune, Marcel A1 - Maiwald, Martin A1 - Sumpf, Bernd A1 - Grune, Tilman A1 - Weber, Daniela T1 - Evaluation of Modern Approaches for the Assessment of Dietary Carotenoids as Markers for Fruit and Vegetable Consumption JF - Nutrients N2 - The assessment of dietary carotenoids via blood measurements has been widely used as a marker for fruit and vegetable consumption. In the present study, modern, non-invasive approaches to assess dietary carotenoids, such as skin measurements and an app-based short dietary record (ASDR), were compared with conventional methods such as plasma status and handwritten 3-day dietary records. In an 8-week observational study, 21 healthy participants aged 50–65 years recorded their daily consumption of carotenoid-rich fruits and vegetables via a specially developed ASDR. Anthropometry, blood samplings and assessment of skin carotenoids via Raman and reflection spectroscopy were performed at baseline, after four weeks and at the end of the study. App-based intake data showed good correlations with plasma α-carotene (r = 0.74, p < 0.0001), β-carotene (r = 0.71, p < 0.0001), and total plasma carotenoids (r = 0.65, p < 0.0001); weak correlations with plasma lutein/zeaxanthin and β-cryptoxanthin (both r = 0.34, p < 0.05); and no correlation with plasma lycopene. Skin measurements via reflection and Raman spectroscopy correlated well with total plasma carotenoids (r = 0.81 and 0.72, respectively; both p < 0.0001), α-carotene (r = 0.75–0.62, p < 0.0001), and β-carotene (r = 0.79–0.71, p < 0.0001); moderately with plasma lutein/zeaxanthin (both r = 0.51, p < 0.0001); weakly with plasma β-cryptoxanthin (r = 0.40–0.31, p < 0.05); and showed no correlation with plasma lycopene. Skin measurements could provide a more convenient and noninvasive approach of estimating a person’s fruit and vegetable consumption compared to traditional methods, especially in studies that do not intend blood sampling. ASDR records might function as a suitable, convenient tool for dietary assessment in nutritional intervention studies. KW - carotenoid KW - vitamin KW - e-health KW - app KW - dietary record KW - blood KW - skin measurement KW - spectroscopy KW - Raman Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17280 SN - 2072-6643 VL - 15 IS - 7 PB - MDPI ER - TY - JOUR A1 - Langenberg, Anna A1 - Ma, Shih-Chi A1 - Ermakova, Tatiana A1 - Fabian, Benjamin T1 - Formal Group Fairness and Accuracy in Automated Decision Making JF - Mathematics N2 - Most research on fairness in Machine Learning assumes the relationship between fairness and accuracy to be a trade-off, with an increase in fairness leading to an unavoidable loss of accuracy. In this study, several approaches for fair Machine Learning are studied to experimentally analyze the relationship between accuracy and group fairness. The results indicated that group fairness and accuracy may even benefit each other, which emphasizes the importance of selecting appropriate measures for performance evaluation. This work provides a foundation for further studies on the adequate objectives of Machine Learning in the context of fair automated decision making. KW - AI KW - machine learning KW - automated decision making KW - algorithmic bias KW - metric KW - group fairness KW - artificial intelligence Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17323 SN - 2227-7390 VL - 11 IS - 8 PB - MDPI ER - TY - JOUR A1 - Chumachenko, Dmytro A1 - Butkevych, Mykola A1 - Lode, Daniel A1 - Frohme, Marcus A1 - Schmailzl, Kurt J. G. A1 - Nechyporenko, Alina T1 - Machine Learning Methods in Predicting Patients with Suspected Myocardial Infarction Based on Short-Time HRV Data JF - Sensors N2 - Diagnosis of cardiovascular diseases is an urgent task because they are the main cause of death for 32% of the world’s population. Particularly relevant are automated diagnostics using machine learning methods in the digitalization of healthcare and introduction of personalized medicine in healthcare institutions, including at the individual level when designing smart houses. Therefore, this study aims to analyze short 10-s electrocardiogram measurements taken from 12 leads. In addition, the task is to classify patients with suspected myocardial infarction using machine learning methods. We have developed four models based on the k-nearest neighbor classifier, radial basis function, decision tree, and random forest to do this. An analysis of time parameters showed that the most significant parameters for diagnosing myocardial infraction are SDNN, BPM, and IBI. An experimental investigation was conducted on the data of the open PTB-XL dataset for patients with suspected myocardial infarction. The results showed that, according to the parameters of the short ECG, it is possible to classify patients with a suspected myocardial infraction as sick and healthy with high accuracy. The optimized Random Forest model showed the best performance with an accuracy of 99.63%, and a root mean absolute error is less than 0.004. The proposed novel approach can be used for patients who do not have other indicators of heart attacks. KW - myocardial infraction KW - heart rate variability KW - 10-second heart rate variability KW - diagnostics KW - machine learning KW - k-nearest neighbor classifier KW - radial basis function KW - decision tree KW - random forest Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16521 SN - 1424-8220 VL - 22 IS - 18 PB - MDPI ER - TY - JOUR A1 - Mai, Andreas A1 - Mai, Christian A1 - Steglich, Patrick T1 - From Lab-on-chip to Lab-in-App: Challenges towards silicon photonic biosensors product developments JF - Results in Optics N2 - This work presents and evaluates different approaches of integrated optical sensors based on photonic integrated circuit (PIC) technologies for refractive index sensing. Bottlenecks in the fabrication flow towards an applicable system are discussed that hinder a cost-effective mass-production for disposable sensor chips. As sensor device, a waveguide coupled micro-ring based approach is chosen which is manufactured in an 8” wafer level process. We will show that the co-integration with a reproducible, scalable and low-cost microfluidic interface is the main challenge which needs to be overcome for future application of silicon technology based PIC sensor chips. KW - silicon photonic sensor KW - integrated optical sensor KW - photonic integrated circuit KW - optical ring resonator KW - photonic biosensor KW - refractive index sensing KW - interchangeable sensor chip Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16687 SN - 2666-9501 VL - 9 PB - Elsevier ER - TY - JOUR A1 - Grebinyk, Anna A1 - Prylutska, Svitlana A1 - Grebinyk, Sergii A1 - Ponomarenko, Stanislav A1 - Virych, Pavlo A1 - Chumachenko, Vasyl A1 - Kutsevol, Nataliya A1 - Prylutskyy, Yuriy A1 - Ritter, Uwe A1 - Frohme, Marcus T1 - Drug delivery with a pH-sensitive star-like dextran-graft polyacrylamide copolymer JF - Nanoscale Advances N2 - The development of precision cancer medicine relies on novel formulation strategies for targeted drug delivery to increase the therapeutic outcome. Biocompatible polymer nanoparticles, namely dextran-graft-polyacrylamide (D-g-PAA) copolymers, represent one of the innovative non-invasive approaches for drug delivery applications in cancer therapy. In this study, the star-like D-g-PAA copolymer in anionic form (D-g-PAAan) was developed for pH-triggered targeted drug delivery of the common chemotherapeutic drugs – doxorubicin (Dox) and cisplatin (Cis). The initial D-g-PAA copolymer was synthesized by the radical graft polymerization method, and then alkaline-hydrolyzed to get this polymer in anionic form for further use for drug encapsulation. The acidification of the buffer promoted the release of loaded drugs. D-g-PAAan nanoparticles increased the toxic potential of the drugs against human and mouse lung carcinoma cells (A549 and LLC), but not against normal human lung cells (HEL299). The drug-loaded D-g-PAAan-nanoparticles promoted further oxidative stress and apoptosis induction in LLC cells. D-g-PAAan-nanoparticles improved Dox accumulation and drugs’ toxicity in a 3D LLC multi-cellular spheroid model. The data obtained indicate that the strategy of chemotherapeutic drug encapsulation within the branched D-g-PAAan nanoparticle allows not only to realize pH-triggered drug release but also to potentiate its cytotoxic, prooxidant and proapoptotic effects against lung carcinoma cells. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16749 VL - 4 IS - 23 SP - 5077 EP - 5088 PB - Royal Society of Chemistry (RSC) ER - TY - JOUR A1 - Hagen, Dirk J. A1 - Yoon, Jiho A1 - Zhang, Haojie A1 - Kalkofen, Bodo A1 - Silinskas, Mindaugas A1 - Börrnert, Felix A1 - Han, Hyeon A1 - Parkin, Stuart S. P. T1 - Atomic Layer Deposition of the Conductive Delafossite PtCoO2 JF - Advanced Materials Interfaces N2 - The first atomic layer deposition process for a ternary oxide is reported, which contains a metal of the platinum group, the delafossite PtCoO2. The deposition with the precursors trimethyl-Pt-methylcyclopentadienyl, Co-bis(N-t-butyl-N′-ethylpropanimidamidate), and oxygen plasma results in a process with a nearly constant growth rate and stoichiometric composition over a wide temperature window from 100 to 320 °C. Annealing of the as-deposited amorphous films in an oxygen atmosphere in a temperature window from 700 to 800 °C leads to the formation of the delafossite phase. Very thin films show a pronounced preferred orientation with the Pt sheets being almost parallel to the substrate surface while arbitrary orientation is observed for thicker films. The conformal coating of narrow trenches highlights the potential of this atomic-layer-deposition process. Moreover, heterostructures with magnetic films are fabricated to demonstrate the potential of PtCoO2 for spintronic applications. KW - ALD KW - atomic layer deposition KW - conductive oxide KW - delafossite KW - PtCoO2 topological material Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16076 VL - 9 IS - 12 PB - Wiley ER - TY - JOUR A1 - Steglich, Patrick A1 - Schasfoort, Richard B. M. T1 - Surface Plasmon Resonance Imaging (SPRi) and Photonic Integrated Circuits (PIC) for COVID-19 Severity Monitoring JF - COVID N2 - Direct optical detection methods such as surface plasmon resonance imaging (SPRi) and photonic-integrated-circuits (PIC)-based biosensors provide a fast label-free detection of COVID-19 antibodies in real-time. Each technology, i.e., SPRi and PIC, has advantages and disadvantages in terms of throughput, miniaturization, multiplexing, system integration, and cost-effective mass production. However, both technologies share similarities in terms of sensing mechanism and both can be used as high-content diagnostics at or near to point of care, where the analyte is not just quantified but comprehensively characterized. This is significant because recent results suggest that not only the antibody concentration of the three isotypes IgM, IgG, and IgA but also the strength of binding (affinity) gives an indication of potential COVID-19 severity. COVID-19 patients with high titers of low affinity antibodies are associated with disease severity. In this perspective, we provide some insights into how SPR and PIC technologies can be effectively combined and complementarily used for a comprehensive COVID-19 severity monitoring. This opens a route toward an immediate therapy decision to provide patients a treatment in an early stage of the infection, which could drastically lowers the risk of a severe disease course. KW - COVID-19 KW - surface plasmon resonance KW - photonic integrated circuit KW - direct optical detection KW - COVID-19 antibody KW - COVID-19 severity KW - pandemic surveillance KW - immunity monitoring Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16004 SN - 2673-8112 VL - 2 IS - 3 SP - 389 EP - 397 PB - MDPI ER - TY - JOUR A1 - Steglich, Patrick A1 - Lecci, Giulia A1 - Mai, Andreas T1 - Surface Plasmon Resonance (SPR) Spectroscopy and Photonic Integrated Circuit (PIC) Biosensors: A Comparative Review JF - Sensors N2 - Label-free direct-optical biosensors such as surface-plasmon resonance (SPR) spectroscopy has become a gold standard in biochemical analytics in centralized laboratories. Biosensors based on photonic integrated circuits (PIC) are based on the same physical sensing mechanism: evanescent field sensing. PIC-based biosensors can play an important role in healthcare, especially for point-of-care diagnostics, if challenges for a transfer from research laboratory to industrial applications can be overcome. Research is at this threshold, which presents a great opportunity for innovative on-site analyses in the health and environmental sectors. A deeper understanding of the innovative PIC technology is possible by comparing it with the well-established SPR spectroscopy. In this work, we shortly introduce both technologies and reveal similarities and differences. Further, we review some latest advances and compare both technologies in terms of surface functionalization and sensor performance. KW - surface plasmon resonance KW - photonic integrated circuit KW - biosensor KW - surface functionalization KW - label-free detection Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16018 SN - 1424-8220 VL - 22 IS - 8 PB - MDPI ER - TY - JOUR A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Timetable merging for the Periodic Event Scheduling Problem JF - EURO Journal on Transportation and Logistics N2 - We propose a new mixed integer programming based heuristic for computing new benchmark primal solutions for instances of the PESPlib. The PESPlib is a collection of instances for the Periodic Event Scheduling Problem (PESP), comprising periodic timetabling problems inspired by real-world railway timetabling settings, and attracting several international research teams during the last years. We describe two strategies to merge a set of good periodic timetables. These make use of the instance structure and minimum weight cycle bases, finally leading to restricted mixed integer programming formulations with tighter variable bounds. Implementing this timetable merging approach in a concurrent solver, we improve the objective values of the best known solutions for the smallest and largest PESPlib instances by 1.7 and 4.3 percent, respectively. KW - periodic event scheduling problem KW - periodic timetabling KW - railway timetabling KW - PESPlib KW - benchmark solution KW - mixed-integer programming Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16054 SN - 2192-4376 VL - 11 PB - Elsevier ER - TY - JOUR A1 - De Rocchis, Vincenzo A1 - Roitsch, Thomas A1 - Franken, Philipp ED - Strobel, Gary A. T1 - Extracellular Glycolytic Activities in Root Endophytic Serendipitaceae and Their Regulation by Plant Sugars JF - Microorganisms N2 - Endophytic fungi that colonize the plant root live in an environment with relative high concentrations of different sugars. Analyses of genome sequences indicate that such endophytes can secrete carbohydrate-related enzymes to compete for these sugars with the surrounding plant cells. We hypothesized that typical plant sugars can be used as carbon source by root endophytes and that these sugars also serve as signals to induce the expression and secretion of glycolytic enzymes. The plant-growth-promoting endophytes Serendipita indica and Serendipita herbamans were selected to first determine which sugars promote their growth and biomass formation. Secondly, particular sugars were added to liquid cultures of the fungi to induce intracellular and extracellular enzymatic activities which were measured in mycelia and culture supernatants. The results showed that both fungi cannot feed on melibiose and lactose, but instead use glucose, fructose, sucrose, mannose, arabinose, galactose and xylose as carbohydrate sources. These sugars regulated the cytoplasmic activity of glycolytic enzymes and also their secretion. The levels of induction or repression depended on the type of sugars added to the cultures and differed between the two fungi. Since no conventional signal peptide could be detected in most of the genome sequences encoding the glycolytic enzymes, a non-conventional protein secretory pathway is assumed. The results of the study suggest that root endophytic fungi translocate glycolytic activities into the root, and this process is regulated by the availability of particular plant sugars. KW - endophytic fungi KW - sugar metabolism KW - glycolysis Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15774 SN - 2076-2607 VL - 10 IS - 2 PB - MDPI ER - TY - JOUR A1 - Pfeil, Juliane A1 - Nechyporenko, Alina A1 - Frohme, Marcus A1 - Hufert, Frank T. A1 - Schulze, Katja T1 - Examination of blood samples using deep learning and mobile microscopy JF - BMC Bioinformatics N2 - Microscopic examination of human blood samples is an excellent opportunity to assess general health status and diagnose diseases. Conventional blood tests are performed in medical laboratories by specialized professionals and are time and labor intensive. The development of a point-of-care system based on a mobile microscope and powerful algorithms would be beneficial for providing care directly at the patient's bedside. For this purpose human blood samples were visualized using a low-cost mobile microscope, an ocular camera and a smartphone. Training and optimisation of different deep learning methods for instance segmentation are used to detect and count the different blood cells. The accuracy of the results is assessed using quantitative and qualitative evaluation standards. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15802 SN - 1471-2105 VL - 23 PB - BioMed Central ER - TY - JOUR A1 - Bauer, Joachim A1 - Fursenko, Oksana A1 - Heinrich, Friedhelm A1 - Gutke, Marko A1 - Kornejew, Eckhart A1 - Brödel, Oliver A1 - Dietzel, Birgit A1 - Kaltenbach, Alexander A1 - Burkhardt, Martin A1 - Edling, Matthias A1 - Steglich, Patrick A1 - Herzog, Michael A1 - Schrader, Sigurd T1 - Determination of optical constants and scattering properties of transparent polymers for use in optoelectronics JF - Optical Materials Express N2 - Knowledge of optical constants, i.e. refractive index n and extinction coefficient k, and light scattering properties of optical polymers are required to optimize micro-optics for light-emitting diodes in terms of efficiency, color properties and light distribution. We present here a model-based diagnostic approach to determine the optical properties of polymers, which should be particularly useful in the development of plastics for optical applications. Optical constants and scattering coefficients were obtained from transmission and reflection measurements in a wavelength range from UV to NIR taking into account scattering effects due to rough surfaces and volume inhomogeneity. Based on the models for the dielectric function, the molecular optical transition energies Eg, critical point energies, Urbach energies and exciton transition energies were determined. Rayleigh and Mie scattering model and van de Hulst's anomalous diffraction theory were applied to characterize scattering due to volume inhomogeneities. Scalar diffraction theory was applied to account for surface roughness scattering. Atomic force microscopy with nanomechanical characterization was used to characterize domains in size and shape and to assign optical scattering to a suitable morphological model. The combined optical and mechanical characterization help to improve the qualification of new polymer materials for optical applications. KW - diffraction theory KW - light property KW - optical constant KW - optical material KW - optical property KW - scattering theory Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15666 VL - 12 IS - 1 SP - 204 EP - 224 PB - Optica Publishing Group ER - TY - JOUR A1 - Drost, Martin A1 - Marschmeyer, Steffen A1 - Fraschke, Mirko A1 - Fursenko, Oksana A1 - Bärwolf, Florian A1 - Costina, Ioan A1 - Kalishettyhalli Mahadevaiah, Mamathamba A1 - Lisker, Marco T1 - Etch mechanism of an Al₂O₃ hard mask in the Bosch process JF - Micro and Nano Engineering N2 - The etching of high aspect ratio structures in silicon via the Bosch process is essential in modern technologies such as microelectromechanical systems (MEMS) and through‑silicon vias (TSV) fabrication. The process can be very demanding on the mask selectivity due to long etching times, and it has been shown that an Al2O3 hard mask is very suitable in this regard, as it offers significantly higher selectivity compared to the conventional SiO2 or resist masks. In this work, we employ a combination of Scanning Electron Microscopy (SEM), Spectroscopic Ellipsometry (SE) and X-Ray Photoelectron Spectroscopy (XPS) depth profiling to scrutinize the Al2O3 mask etching mechanism and therefore the origin of the extraordinary high selectivity. We demonstrate that by increasing the passivation step time, a thicker fluorocarbon polymer layer is formed on the Al2O3, and Al2O3 is then removed with a minuscule average etch rate of 0.01 nm/min. XPS depth profiling reveals that during Deep Reactive Ion Etching (DRIE) using the Bosch process, an AlFx layer is formed between the polymer and Al2O3. As AlFx is non-volatile, it requires sputtering to be removed. If the polymer layer is thick enough to attenuate the incoming ions such that their energy is not sufficient to lead to desorption of AlFx, such as when using a longer passivation time, the mask is not eroded. By investigating the surface after different amounts of DRIE cycles, we also obtained information about the formation rate of AlFx and the changes in the Al2O3 and polymer thicknesses over the course of a DRIE process. These findings further expand the knowledge of DRIE and can help process engineers to tailor the processes accordingly. KW - Bosch process KW - deep reactive ion etching KW - aluminum oxide Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15678 SN - 2590-0072 VL - 14 PB - Elsevier ER - TY - JOUR A1 - Heinsohn, Natascha Katharina A1 - Niedl, Robert Raimund A1 - Anielski, Alexander A1 - Lisdat, Fred A1 - Beta, Carsten T1 - Electrophoretic µPAD for Purification and Analysis of DNA Samples JF - Biosensors N2 - In this work, the fabrication and characterization of a simple, inexpensive, and effective microfluidic paper analytic device (µPAD) for monitoring DNA samples is reported. The glass microfiber-based chip has been fabricated by a new wax-based transfer-printing technique and an electrode printing process. It is capable of moving DNA effectively in a time-dependent fashion. The nucleic acid sample is not damaged by this process and is accumulated in front of the anode, but not directly on the electrode. Thus, further DNA processing is feasible. The system allows the DNA to be purified by separating it from other components in sample mixtures such as proteins. Furthermore, it is demonstrated that DNA can be moved through several layers of the glass fiber material. This proof of concept will provide the basis for the development of rapid test systems, e.g., for the detection of pathogens in water samples. KW - microfluidic paper analytic device (µPAD) KW - patterning glass microfiber KW - fiber-electrophoresis chip KW - DNA KW - imprinted electrodes KW - cross layer chip KW - polymerase chain reaction (PCR) KW - purification Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-15763 SN - 2079-6374 VL - 12 IS - 2 PB - MDPI ER - TY - JOUR A1 - Kirchner, Thomas A1 - Villringer, Claus A1 - Laufer, Jan T1 - Evaluation of ultrasound sensors for transcranial photoacoustic sensing and imaging JF - Photoacoustics N2 - Photoacoustic imaging through skull bone causes strong attenuation and distortion of the acoustic wavefront, which diminishes image contrast and resolution. As a result, transcranial photoacoustic measurements in humans have been challenging to demonstrate. In this study, we investigated the acoustic transmission through the human skull to design an ultrasound sensor suitable for transcranial PA imaging and sensing. We measured the frequency dependent losses of human cranial bones ex vivo, compared the performance of a range of piezoelectric and optical ultrasound sensors, and imaged skull phantoms using a PA tomograph based on a planar Fabry–Perot sensor. All transcranial photoacoustic measurements show the typical effects of frequency and thickness dependent attenuation and aberration associated with acoustic propagation through bone. The performance of plano-concave optical resonator ultrasound sensors was found to be highly suitable for transcranial photoacoustic measurements. KW - transcranial KW - ultrasound sensor KW - photoacoustic KW - optoacoustic KW - Fabry-Perot Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17993 SN - 2213-5979 VL - 33 PB - Elsevier ER - TY - JOUR A1 - D'Elia, Domenica A1 - Truu, Jaak A1 - Lahti, Leo A1 - Berland, Magali A1 - Papoutsoglou, Georgios A1 - Ceci, Michelangelo A1 - Zomer, Aldert A1 - Lopes, Marta B. A1 - Ibrahimi, Eliana A1 - Gruca, Aleksandra A1 - Nechyporenko, Alina A1 - Frohme, Marcus A1 - Klammsteiner, Thomas A1 - Carrillo de Santa Pau, Enrique A1 - Marcos-Zambrano, Laura Judith A1 - Hron, Karel A1 - Pio, Gianvito A1 - Simeon, Andrea A1 - Suharoschi, Ramona A1 - Moreno-Indias, Isabel A1 - Temko, Andriy A1 - Nedyalkova, Miroslava A1 - Apostol, Elena-Simona A1 - Truică, Ciprian-Octavian A1 - Shigdel, Rajesh A1 - Telalović, Jasminka Hasić A1 - Bongcam-Rudloff, Erik A1 - Przymus, Piotr A1 - Jordamović, Naida Babić A1 - Falquet, Laurent A1 - Tarazona, Sonia A1 - Sampri, Alexia A1 - Isola, Gaetano A1 - Pérez-Serrano, David A1 - Trajkovik, Vladimir A1 - Klucar, Lubos A1 - Loncar-Turukalo, Tatjana A1 - Havulinna, Aki S. A1 - Jansen, Christian A1 - Bertelsen, Randi J. A1 - Claesson, Marcus Joakim T1 - Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action JF - Frontiers in Microbiology N2 - The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices. KW - microbiome KW - machine learning KW - artificial intelligence KW - standard KW - best practice Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18004 SN - 1664-302X VL - 14 PB - Frontiers ER - TY - CHAP A1 - Masing, Berenike A1 - Lindner, Niels A1 - Liebchen, Christian T1 - Integrating Line Planning for Construction Sites into Periodic Timetabling via Track Choice T2 - 23rd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2023) N2 - We consider maintenance sites for urban rail systems, where unavailable tracks typically require changes to the regular timetable, and often even to the line plan. In this paper, we present an integrated mixed-integer linear optimization model to compute an optimal line plan that makes best use of the available tracks, together with a periodic timetable, including its detailed routing on the tracks within the stations. The key component is a flexible, turn-sensitive event-activity network that allows to integrate line planning and train routing using a track choice extension of the Periodic Event Scheduling Problem (PESP). Major goals are to maintain as much of the regular service as possible, and to keep the necessary changes rather local. Moreover, we present computational results on real construction site scenarios on the S-Bahn Berlin network. We demonstrate that this integrated problem is indeed solvable on practically relevant instances. KW - periodic timetabling KW - line planning KW - track choice KW - mixed-integer programming KW - construction site KW - railway rescheduling Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17916 SN - 978-3-95977-302-7 SN - 2190-6807 VL - 115 SP - 5:1 EP - 5:15 ER - TY - JOUR A1 - Loos, Eugène A1 - Gröpler, Johanna A1 - Goudeau, Marie-Louise Sophie T1 - Using ChatGPT in Education: Human Reflection on ChatGPT’s Self-Reflection JF - Societies N2 - ChatGPT is a fascinating AI text generator tool. It is a language model developed by OpenAI, a research and deployment company with the mission, according to OpenAI’s website: “to ensure that artificial general intelligence benefits all of humanity”. ChatGPT is able to generate human-like texts. But how does it work? What about the quality of the texts it provides? And is it capable of being self-reflective? Information sources must be efficient, effective and reliable in education, in order to enhance students’ learning process. For this reason, we started a dialogue with ChatGPT-3 while using, among others, a SWOT analysis it generated about its own functioning in an educational setting. This enabled us, as human authors, to analyze the extent to which this AI system is able to practice self-reflection. Finally, the paper sketches implications for education and future research. KW - ChatGPT KW - AI KW - text generating KW - education KW - SWOT analysis KW - self-reflection KW - hallucination KW - artificial intelligence Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17966 SN - 2075-4698 VL - 13 IS - 8 PB - MDPI ER - TY - JOUR A1 - Walter, Andreas A1 - Kubica, Stefan A1 - Rocco, Vittorio T1 - Optimized fuel values for emission reduction JF - IOP Conference Series: Earth and Environmental Science N2 - Aviation is an integral and vital part of modern society. The growth over the last decades has consequences for greenhouse gas emissions and reducing this through efficiency within the same framework is difficult. Precision flight planning is crucial for reliably and optimized real environment aircraft operation. The presented study gives an overview of the status of the legal requirements for flight planning under the current fuel requirements of the European Union Aviation Safety Agency (EASA) and the emerging opportunities for fuel savings. As part of the larger study, planned and actual fuel figures of an international cargo airline were statistically analyzed. The overall analysis showed that there was no significant deviation between planned and consumed fuel. Based on the results, an adjustment of the planned alternative fuel quantity can be considered within the framework of an individual fuel plan. The possible savings potential using the example of Destination Alternate Airport fuel is presented. Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18148 SN - 1755-1315 N1 - 4th International Conference on Sustainable Futures: Environmental, Technological, Social and Economic Matters (ICSF-2023) 22/05/2023 - 26/05/2023 Kryvyi Rih, Ukraine VL - 1254 PB - Institute of Physics Publishing (IOP) ER - TY - JOUR A1 - Radivoievych, Aleksandar A1 - Prylutska, Svitlana A1 - Zolk, Oliver A1 - Ritter, Uwe A1 - Frohme, Marcus A1 - Grebinyk, Anna T1 - Comparison of Sonodynamic Treatment Set-Ups for Cancer Cells with Organic Sonosensitizers and Nanosonosensitizers JF - Pharmaceutics N2 - Cancer sonodynamic therapy (SDT) is the therapeutic strategy of a high-frequency ultrasound (US) combined with a special sonosensitizer that becomes cytotoxic upon US exposure. The growing number of newly discovered sonosensitizers and custom US in vitro treatment solutions push the SDT field into a need for systemic studies and reproducible in vitro experimental set-ups. In the current research, we aimed to compare two of the most used and suitable SDT in vitro set-ups—“sealed well” and “transducer in well”—in one systematic study. We assessed US pressure, intensity, and temperature distribution in wells under US irradiation. Treatment efficacy was evaluated for both set-ups towards cancer cell lines of different origins, treated with two promising sonosensitizer candidates—carbon nanoparticle C60 fullerene (C60) and herbal alkaloid berberine. C60 was found to exhibit higher sonotoxicity toward cancer cells than berberine. The higher efficacy of sonodynamic treatment with a “transducer in well” set-up than a “sealed well” set-up underlined its promising application for SDT in vitro studies. The “transducer in well” set-up is recommended for in vitro US treatment investigations based on its US-field homogeneity and pronounced cellular effects. Moreover, SDT with C60 and berberine could be exploited as a promising combinative approach for cancer treatment. KW - ultrasound KW - C60 fullerene KW - berberine KW - sonodynamic therapy KW - apoptosis Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18223 SN - 1999-4923 VL - 15 IS - 11 PB - MDPI ER - TY - JOUR A1 - Jurkovičová, Lucie A1 - Ben Ltaief, Ltaief A1 - Roos, Andreas Hult A1 - Hort, Ondřej A1 - Finke, Ondřej A1 - Albrecht, Martin A1 - Hoque, Ziaul A1 - Klimešová, Eva A1 - Sundaralingam, Akgash A1 - Antipenkov, Roman A1 - Grenfell, Annika A1 - Špaček, Alexandr A1 - Szuba, Wojciech A1 - Krikunova, Maria A1 - Mudrich, Marcel A1 - Nejdl, Jaroslav A1 - Andreasson, Jakob T1 - Bright continuously tunable vacuum ultraviolet source for ultrafast spectroscopy JF - Communications Physics N2 - Ultrafast electron dynamics drive phenomena such as photochemical reactions, catalysis, and light harvesting. To capture such dynamics in real-time, femtosecond to attosecond light sources are extensively used. However, an exact match between the excitation photon energy and a characteristic resonance is crucial. High-harmonic generation sources are advantageous in terms of pulse duration but limited in spectral tunability in the vacuum ultraviolet range. Here, we present a monochromatic femtosecond source continuously tunable around 21eV photon energy utilizing the second harmonic of an optical parametric chirped pulse amplification laser system to drive high-harmonic generation. The unique tunability of the source is verified in an experiment probing the interatomic Coulombic decay in doped He nanodroplets across the He absorption bands. Moreover, we achieved intensities sufficient for driving collective processes in multiply excited helium nanodroplets, which have been previously observed only at free electron lasers. Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18462 SN - 2399-3650 VL - 7 PB - Nature Publishing Group ER - TY - JOUR A1 - Medina, Cristian A1 - Lægdsmand, Asbjørn Ørnemark A1 - Ben Ltaief, Ltaief A1 - Hoque, Ziaul A1 - Roos, Andreas Hult A1 - Jurkovičová, Lucie A1 - Hort, Ondřej A1 - Finke, Ondřej A1 - Albrecht, Martin A1 - Nejdl, Jaroslav A1 - Stienkemeier, Frank A1 - Andreasson, Jakob A1 - Klimešová, Eva A1 - Krikunova, Maria A1 - Heidenreich, Andreas A1 - Mudrich, Marcel T1 - Long-lasting XUV activation of helium nanodroplets for avalanche ionization JF - New Journal of Physics N2 - We study the dynamics of avalanche ionization of pure helium nanodroplets activated by a weak extreme-ultraviolet (XUV) pulse and driven by an intense near-infrared (NIR) pulse. In addition to a transient enhancement of ignition of a nanoplasma at short delay times ${\sim}200$ fs, long-term activation of the nanodroplets lasting up to a few nanoseconds is observed. Molecular dynamics simulations suggest that the short-term activation is caused by the injection of seed electrons into the droplets by XUV photoemission. Long-term activation appears due to electrons remaining loosely bound to photoions which form stable 'snowball' structures in the droplets. Thus, we show that XUV irradiation can induce long-lasting changes of the strong-field optical properties of nanoparticles, potentially opening new routes to controlling avalanche-ionization phenomena in nanostructures and condensed-phase systems. KW - nanoplasma KW - helium nanodroplet KW - pump–probe spectroscopy KW - avalanche ionization KW - high-harmonic generation KW - extreme ultraviolet Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17701 VL - 25 PB - Institute of Physics (IOP) ER - TY - JOUR A1 - Schilling, Vincent A1 - Beyerlein, Peter A1 - Chien, Jeremy T1 - A Bioinformatics Analysis of Ovarian Cancer Data Using Machine Learning JF - Algorithms N2 - The identification of biomarkers is crucial for cancer diagnosis, understanding the underlying biological mechanisms, and developing targeted therapies. In this study, we propose a machine learning approach to predict ovarian cancer patients’ outcomes and platinum resistance status using publicly available gene expression data. Six classical machine-learning algorithms are compared on their predictive performance. Those with the highest score are analyzed by their feature importance using the SHAP algorithm. We were able to select multiple genes that correlated with the outcome and platinum resistance status of the patients and validated those using Kaplan–Meier plots. In comparison to similar approaches, the performance of the models was higher, and different genes using feature importance analysis were identified. The most promising identified genes that could be used as biomarkers are TMEFF2, ACSM3, SLC4A1, and ALDH4A1. KW - ovarian cancer KW - machine learning KW - SHAP KW - diagnostic biomarker KW - platinum resistance Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17751 VL - 16 IS - 7 PB - MDPI ER - TY - JOUR A1 - Prylutska, Svitlana A1 - Grebinyk, Anna A1 - Ponomarenko, Stanislav A1 - Gövem, Defne A1 - Chumachenko, Vasyl A1 - Kutsevol, Nataliya A1 - Petrovsky, Mykola A1 - Ritter, Uwe A1 - Frohme, Marcus A1 - Piosik, Jacek A1 - Prylutskyy, Yuriy T1 - Toxicity of Water-Soluble D-g-PNIPAM Polymers in a Complex with Chemotherapy Drugs and Mechanism of Their Action In Vitro JF - International Journal of Molecular Sciences N2 - The application of a biocompatible polymer nanocarrier can provide target delivery to tumor tissues, improved pharmacokinetics, controlled drug release, etc. Therefore, the proposed strategy was to use the water-soluble star-like copolymers with a Dextran core and Poly(N-isopropylacrylamide) grafts (D-g-PNIPAM) for conjugation with the widely used chemotherapy drugs in oncology–Cisplatin (Cis-Pt) and Doxorubicin (Dox). The molecular characteristics of the copolymer were received using size-exclusion chromatography. The physicochemical characterization of the D-g-PNIPAM-Cis-Pt (or Dox) nanosystem was conducted using dynamic light scattering and FTIR spectroscopy. Using traditional biochemical methods, a comparative analysis of the enhancement of the cytotoxic effect of free Cis-Pt and Dox in combination with D-g-PNIPAM copolymers was performed in cancer cells of the Lewis lung carcinoma line, which are both sensitive and resistant to Dox; in addition, the mechanism of their action in vitro was evaluated. KW - star-like copolymer KW - drug KW - Lewis lung carcinoma KW - cytotoxicity Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18790 SN - 1422-0067 VL - 25 IS - 5 PB - MDPI ER - TY - JOUR A1 - Fernholz, Yannick A1 - Ermakova, Tatiana A1 - Fabian, Benjamin A1 - Buxmann, Peter T1 - User-driven prioritization of ethical principles for artificial intelligence systems JF - Computers in Human Behavior: Artificial Humans N2 - Despite the progress of Artificial Intelligence (AI) and its contribution to the advancement of human society, the prioritization of ethical principles from the viewpoint of its users has not yet received much attention and empirical investigations. This is important to develop appropriate safeguards and increase the acceptance of AI-mediated technologies among all members of society. In this research, we collected, integrated, and prioritized ethical principles for AI systems with respect to their relevance in different real-life application scenarios. First, an overview of ethical principles for AI was systematically derived from various academic and non-academic sources. Our results clearly show that transparency, justice and fairness, non-maleficence, responsibility, and privacy are most frequently mentioned in this corpus of documents. Next, an empirical survey to systematically identify users’ priorities was designed and conducted in the context of selected scenarios: AI-mediated recruitment (human resources), predictive policing, autonomous vehicles, and hospital robots. We anticipate that the resulting ranking can serve as a valuable basis for formulating requirements for AI-mediated solutions and creating AI algorithms that prioritize user’s needs. Our target audience includes everyone who will be affected by AI systems, e.g., policy makers, algorithm developers, and system managers as our ranking clearly depicts user’s awareness regarding AI ethics. KW - artificial intelligence KW - ethics KW - ethical guidelines KW - trustworthy AI KW - requirements prioritization Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18509 SN - 2949-8821 VL - 2 IS - 1 PB - Elsevier ER - TY - JOUR A1 - Grytsenko, Kostyantyn A1 - Kolomzarov, Yurii A1 - Lytvyn, Peter A1 - Kondratenko, Olga A1 - Sopinskyy, Mykola A1 - Lebedyeva, Iryna A1 - Niemczyk, Agata A1 - Baranowska, Jolanta A1 - Moszyński, Dariusz A1 - Villringer, Claus A1 - Schrader, Sigurd T1 - Optical and Mechanical Properties of Thin PTFE Films, Deposited from a Gas Phase JF - Macromolecular Materials and Engineering N2 - Thin polytetrafluoroethylene (PTFE) films are produced by deposition from a gas phase by two methods: electron-enhanced vacuum deposition (EVD) and EVD + low-temperature plasma (LTP). Structure, morphology, and composition of the films are studied by IR spectroscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. They are close to the structure of bulk PTFE. The roughness of the films’ surface is changed with gas pressure and LTP power variations. Films are transparent from UV to near-infrared regions. Refractive and extinction indices and their anisotropy are measured by spectral ellipsometry. They are tuned by variations of deposition conditions. Hardness and Young modulus of the films are increased if EVD + low power LTP is used for film deposition. Use of EVD + LTP also increases thermal stability of the films. Contact angle of the films corresponds to the bulk PTFE. The PTFE molecules oriented are preferentially in perpendicular direction to the substrate surface. KW - deposition in vacuum KW - multiphase structure formation KW - optical property KW - plasma KW - polytetrafluoroethylene thin film Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17587 VL - 308 IS - 6 PB - Wiley ER - TY - JOUR A1 - Dhiman, Rachit A1 - Miteff, Sofia A1 - Wang, Yuancheng A1 - Ma, Shih-Chi A1 - Amirikas, Ramila A1 - Fabian, Benjamin T1 - Artificial Intelligence and Sustainability—A Review JF - Analytics N2 - In recent decades, artificial intelligence has undergone transformative advancements, reshaping diverse sectors such as healthcare, transport, agriculture, energy, and the media. Despite the enthusiasm surrounding AI’s potential, concerns persist about its potential negative impacts, including substantial energy consumption and ethical challenges. This paper critically reviews the evolving landscape of AI sustainability, addressing economic, social, and environmental dimensions. The literature is systematically categorized into “Sustainability of AI” and “AI for Sustainability”, revealing a balanced perspective between the two. The study also identifies a notable trend towards holistic approaches, with a surge in publications and empirical studies since 2019, signaling the field’s maturity. Future research directions emphasize delving into the relatively under-explored economic dimension, aligning with the United Nations’ Sustainable Development Goals (SDGs), and addressing stakeholders’ influence. KW - artificial intelligence KW - AI KW - sustainability KW - systematic mapping study Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18651 SN - 2813-2203 VL - 3 IS - 1 SP - 140 EP - 164 PB - MDPI ER - TY - JOUR A1 - Gavrylenko, Svitlana A1 - Poltoratskyi, Vadym A1 - Nechyporenko, Alina T1 - Intrusion Detection Model Based on Improved Transformer JF - Advanced Information Systems N2 - The object of the study is the process of identifying the state of a computer network. The subject of the study are the methods of identifying the state of computer networks. The purpose of the paper is to improve the efficacy of intrusion detection in computer networks by developing a method based on transformer models. The results obtained. The work analyzes traditional machine learning algorithms, deep learning methods and considers the advantages of using transformer models. A method for detecting intrusions in computer networks is proposed. This method differs from known approaches by utilizing the Vision Transformer for Small-size Datasets (ViTSD) deep learning algorithm. The method incorporates procedures to reduce the correlation of input data and transform data into a specific format required for model operations. The developed methods are implemented using Python and the GOOGLE COLAB cloud service with Jupyter Notebook. Conclusions. Experiments confirmed the efficiency of the proposed method. The use of the developed method based on the ViTSD algorithm and the data preprocessing procedure increases the model's accuracy to 98.7%. This makes it possible to recommend it for practical use, in order to improve the accuracy of identifying the state of a computer system. KW - data preprocessing KW - machine learning KW - neural network KW - RNN KW - SVM KW - KNN KW - transformer model KW - vision transformer Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-18750 SN - 2522-9052 VL - 8 IS - 1 SP - 94 EP - 99 PB - National Technical University Kharkiv Polytechnic Institute ER - TY - JOUR A1 - Radivoievych, Aleksandar A1 - Schnepel, Sophia A1 - Prylutska, Svitlana A1 - Ritter, Uwe A1 - Zolk, Oliver A1 - Frohme, Marcus A1 - Grebinyk, Anna T1 - From 2D to 3D In Vitro World: Sonodynamically-Induced Prooxidant Proapoptotic Effects of C60-Berberine Nanocomplex on Cancer Cells JF - Cancers N2 - Recently, sonodynamic therapy (SDT) has emerged as a promising non-invasive approach for treating cancer by activating sensitizers with ultrasound (US). In this context, we investigated C60 fullerene (C60) as a nanocarrier for the promising drug Berberine (Ber)—both potential aromatic sonosensitizers. The preferential mitochondrial accumulation of C60 and the proapoptotic effects of Ber also make the C60-Berberine nanocomplex (C60-Ber) a good candidate for direct induction of the intrinsic apoptotic cell death under US action. The in vitro research on C60-Ber can provide insights into novel, non-invasive cancer treatments. These findings lead to the development of targeted therapies with reduced side effects, inspire interdisciplinary collaboration, and open new avenues for drug delivery and cancer therapy research. KW - berberine KW - C60 fullerene KW - apoptosis KW - sonodynamic therapy KW - ultrasound Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19438 VL - 16 IS - 18 ER - TY - JOUR A1 - Nechyporenko, Alina A1 - Frohme, Marcus A1 - Strelchuk, Yaroslav A1 - Omelchenko, Vladyslav A1 - Gargin, Vitaliy A1 - Ishchenko, Liudmyla A1 - Alekseeva, Victoriia T1 - Galvanic Skin Response and Photoplethysmography for Stress Recognition Using Machine Learning and Wearable Sensors JF - Applied Sciences N2 - This study investigates stress recognition using galvanic skin response (GSR) and photoplethysmography (PPG) data and machine learning, with a new focus on air raid sirens as a stressor. It bridges laboratory and real-world conditions and highlights the reliability of wearable sensors in dynamic, high-stress environments such as war and conflict zones. The study involves 37 participants (20 men, 17 women), aged 20–30, who had not previously heard an air raid siren. A 70 dB “S-40 electric siren” (400–450 Hz) was delivered via headphones. The protocol included a 5 min resting period, followed by 3 min “no-stress” phase, followed by 3 min “stress” phase, and finally a 3 min recovery phase. GSR and PPG signals were recorded using Shimmer 3 GSR+ sensors on the fingers and earlobes. A single session was conducted to avoid sensitization. The workflow includes signal preprocessing to remove artifacts, feature extraction, feature selection, and application of different machine learning models to classify the “stress “and “no-stress” states. As a result, the best classification performance was shown by the k-Nearest Neighbors model, achieving 0.833 accuracy. This was achieved by using a particular combination of heart rate variability (HRV) and GSR features, which can be considered as new indicators of siren-induced stress. KW - galvanic skin response KW - machine learning KW - photoplethysmography KW - stress Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19803 VL - 14 IS - 24 PB - MDPI ER - TY - JOUR A1 - Klimesova, Eva A1 - Kulyk, Olena A1 - Martin, Lucas Janos A1 - Schütte, Bernd A1 - Frühling, Ulrike A1 - Drescher, Markus A1 - Pan, Rui A1 - Stojanovic, Nikola A1 - Bermudez Macias, Ivette J. A1 - Düsterer, Stefan A1 - Andreasson, Jakob A1 - Wieland, Marek A1 - Krikunova, Maria T1 - Electron thermalization and ion acceleration in XUV-produced plasma from nanoparticles in He gas environment JF - New Journal of Physics N2 - We use intense femtosecond extreme ultraviolet (XUV) pulses with a photon energy of 92 eV from the FLASH free electron laser to irradiate substrate-free CsCl nanoparticles surrounded by a He gas with a number density of around 1015 cm−3. By simultaneously detecting electrons and energetic ions from the laser-irradiated micron-size target we study the acceleration mechanism of light ions at the microplasma-vacuum boundary as well as at the layer close to the nanoparticle surface. When the XUV pulse interacts with the gas alone, helium ions are accelerated to energies exceeding 100 eV. In the presence of the nanoparticle, light ions gain additional energy in the electric field around the ionized nanoparticle and their energy spectrum changes considerably. We present an electrostatic model to explain the ion acceleration mechanisms both with and without the nanoparticle and discuss the role of the gas environment in experiments. KW - light–matter interaction KW - free electron laser KW - nanoparticle injection KW - electron and ion spectroscopy Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19818 VL - 27 PB - Institute of Physics Publishing (IOP); Deutsche Physikalische Gesellschaft ER - TY - JOUR A1 - Nechyporenko, Alina A1 - Nazaryan, Rosana A1 - Semko, Galyna A1 - Lupyr, Andrii A1 - Yurevych, Nadiia A1 - Fomenko, Yuliia A1 - Kostiukov, Eduard A1 - Alekseeva, Victoriia T1 - Application of spiral computed tomography for determination of the minimal bone density variability of the maxillary sinus walls in chronic odontogenic and rhinogenic sinusitis JF - Ukrainian Journal of Radiology and Oncology N2 - Background. There are many questions regarding the peculiarities of the course of odontogenic maxillary sinusitis, the likelihood of complications and the correct dosage of load during dental implantation. Purpose – to identify changes in minimal bone density in chronic odontogenic maxillary sinusitis and to compare it with chronic rhinogenic catarrhal maxillary sinusitis and physiological state of maxillary sinus. Materials and Methods. Our study involved 10 patients with chronic odontogenic maxillary sinusitis, 10 patients with chronic maxillary non-polyposis sinusitis of rhinogenic etiology, combined with hyperplasia of the sinus mucosa up to 1 cm. The control group comprised 10 patients with physiological condition of maxillary sinuses. In all subjects minimal bone density of superior, medial and inferior walls of maxillary sinus was analyzed. Results. The study showed that the maximum in physiological conditions is the minimal density of the upper wall of the maxillary sinus, the minimum is the lower wall. The minimal density of the lower wall was shown to undergo a statistically significant reduction in chronic catarrhal maxillary sinusitis only by 2%, the upper by 5%, the medial by 4% compared with the intact sinus, but with the odontogenic nature of maxillary sinusitis, this figure was 31% in the lower wall, 27% in the medial region. Only the density of the upper wall of the maxillary sinus remained quite stable, it decreased relative to the physiological one only by 6%. Conclusions. Minimal physiological densitometric parameters of lower, medial and upper walls were calculated. The reduction of minimal density of bone tissue in the cases of rhinogenic chronic catarrhal maxillary sinusitis. In the cases of chronic odontogenic maxillary sinusitis, maximum significant decrease of minimal density of both lower and medial walls is determined. KW - bone density KW - computed tomography KW - maxillary sinus KW - odontogenic maxillary sinusitis Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19121 SN - 2708-7166 VL - 29 IS - 4 SP - 65 EP - 75 ER - TY - JOUR A1 - Dreyer, Christian A1 - Motoc, Dana Luca A1 - Koehler, Mathias A1 - Goldenberg, Leonid T1 - UV LED Curable Perfluoropolyether (PFPE)-Urethane Methacrylate Transparent Coatings for Photonic Applications: Synthesis and Characterization JF - Polymers N2 - The contribution aims to bring forth a novel synthesis route in developing transparent UV LED-curable coatings accounting for various exposure options. A selection of perfluoropolyether (PFPE)-urethane methacrylate and acrylate resins, free-radical photo-initiator Omnirad 2100, and two distinct silane-based crosslinking agents were blended under a weight ratio of 75:20:5 (without crosslinker) and 70:15:5:10, respectively. The coatings were cured under a UV LED 4 × 3 matrix light emitting source, in a chamber under a controlled atmosphere, by means of an in-house developed conveyor belt type platform, at different conveyor belt speeds (5, 50, 150, 250, and 500 mm/s). The morphologies of fabricated coatings were characterized by FTIR revealing high conversion rates (e.g., from 98 to 100%) for increased exposure time as a result of the 5 or 50 mm/s values, on all combinations. Dynamic–mechanical and optical properties of UV LED-cured transparent coatings were also investigated. A negative shift of the glass transition temperature values with a decrease in exposure time, in all combinations, from about 60 °C to 30 °C, along with storage moduli lowering in the glassy plateau further favors higher exposure times for curing. The refractive indices of poly-mers were from 1.38 to 1.40, whereas the thermo-optic coefficients are showing minor changes around the value of 2.55∙10−4 K−1. KW - perfluoropolyether (PFPE) KW - fluoroacrylate KW - UV LED curable coating KW - viscoelastic property KW - refractive index KW - thermo-optic coefficient KW - optical loss KW - dielectric property Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19139 VL - 15 IS - 14 PB - MDPI ER - TY - JOUR A1 - Fünning, Tabea A1 - Paul, Martin A1 - Manganelli, Costanza Lucia A1 - Wenger, Christian A1 - Mai, Andreas A1 - Steglich, Patrick T1 - Comparative simulation analysis of photonic ultrasound sensors based on silicon waveguides JF - Scientific Reports N2 - Pressure sensors based on photonic integrated circuits (PIC) offer the prospect of outstanding sensitivities, extreme miniaturization and have the potential for highly scalable production using CMOS compatible processing. PIC-based pressure sensors detect the change in optical properties, i.e. the intensity or phase of the optical carrier wave inside miniaturized waveguide structures. The detection of ultrasound is achieved by engineering the waveguide architecture such that a pressure causes a high change in the effective refractive index of the waveguide. A range of PIC-based pressure sensors have been reported, but a comparison of the sensitivity of the different approaches is not straightforward, since different pressure sensitive waveguide architectures as well as photonic layouts and measurement setups impact the performance. Additionally, the used sensitivity unit is not uniform throughout the different studies, further complicating a comparison. In this work, a detailed simulation study is carried out by finite element modeling of different pressure sensitive waveguide architectures for a consistent comparison. We analyze three different sensor architectures: (A) a free standing membrane located within a tiny air gap above the waveguide, (B) a waveguide located on top of a deflectable membrane as well as (C) a waveguide embedded inside a pressure-sensitive polymer cladding. The mechanical response of the structures and the resulting changes in mode propagation, i.e. the change of the effective refractive index, are analyzed. The waveguide sensitivities in RIU/MPa for different waveguide types (strip, slot) and polarization states (TE, TM) are compared. The results reveal inherent limitations of the different waveguide designs and create a basis for the selection of suitable designs for further ultrasound sensor development. Possibilities for enhancing waveguide sensitivity are identified and discussed. Additionally, we have shown that the studied approaches are extensible to SiN waveguides. Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-20560 VL - 15 PB - Springer Nature ER - TY - JOUR A1 - Seeliger, Frank T1 - Betriebliche Einstiegsqualifizierung als zweite Chance JF - BuB : Forum für Bibliothek und Information N2 - Die Ausbildung zum Fachangestellten für Medien und Informationsdienste (FaMI) in der Fachrichtung Bibliothek ist sehr anspruchsvoll und verlangt einiges von den Jugendlichen ab. Daher gilt in der Wildauer Hochschulbibliothek für Lehrlinge der gleiche Grundsatz wie für Studierende: Scheitern ist erlaubt – was sich in der bislang zehnjährigen Erfahrung als Ausbildungsbetrieb allerdings nur einmal bewahrheitet hat. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9608 UR - http://www.b-u-b.de/pdfarchiv/Heft-BuB_03_2013.pdf SN - 0340-0301 VL - 65 IS - 3 SP - 182 EP - 183 ER - TY - JOUR A1 - Grytsenko, Kostyantyn A1 - Schrader, Sigurd A1 - Detert, Heiner T1 - Ultra-stable dye-filled polytetrafluoroethylene thin films JF - Nanoscience & Technology: Open Access N2 - Polytetrafluoroethylene (PTFE) and polyparaphenylene sulphide (PPS) thin films filled with molecules of different dyes were obtained by co-deposition in vacuum. The PTFE matrix prevented aggregation of dye molecules more strongly, than PPS matrix. During heating PTFE matrix kept the dye molecules in not aggregated state up to dye decomposition temperature. Dyes of all types, buried in the PTFE matrix, exhibited high stability toward actions of external factors: light, temperature, acids. KW - dye KW - PTF KW - PPS KW - nanocomposite KW - thin film KW - optical spectra KW - stability Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5947 SN - 2374-8141 VL - 1 IS - 2 ER - TY - JOUR A1 - Radke, Lars A1 - Sandig, Grit A1 - Lubitz, Annika A1 - Schließer, Ulrike A1 - von Horsten, Hans Henning A1 - Blanchard, Véronique A1 - Keil, Karolin A1 - Sandig, Volker A1 - Giese, Christoph A1 - Hummel, Michael A1 - Hinderlich, Stephan A1 - Frohme, Marcus T1 - In Vitro Evaluation of Glycoengineered RSV-F in the Human Artificial Lymph Node Reactor JF - Bioengineering N2 - Subunit vaccines often require adjuvants to elicit sustained immune activity. Here, a method is described to evaluate the efficacy of single vaccine candidates in the preclinical stage based on cytokine and gene expression analysis. As a model, the recombinant human respiratory syncytial virus (RSV) fusion protein (RSV-F) was produced in CHO cells. For comparison, wild-type and glycoengineered, afucosylated RSV-F were established. Both glycoprotein vaccines were tested in a commercial Human Artificial Lymph Node in vitro model (HuALN®). The analysis of six key cytokines in cell culture supernatants showed well-balanced immune responses for the afucosylated RSV-F, while immune response of wild-type RSV-F was more Th1 accentuated. In particular, stronger and specific secretion of interleukin-4 after each round of re-stimulation underlined higher potency and efficacy of the afucosylated vaccine candidate. Comprehensive gene expression analysis by nCounter gene expression assay confirmed the stronger onset of the immunologic reaction in stimulation experiments with the afucosylated vaccine in comparison to wild-type RSV-F and particularly revealed prominent activation of Th17 related genes, innate immunity, and comprehensive activation of humoral immunity. We, therefore, show that our method is suited to distinguish the potency of two vaccine candidates with minor structural differences. KW - glycoengineering KW - fucosylation KW - RSV KW - F-protein KW - NanoString Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9831 SN - 2306-5354 VL - 4 IS - 3 ER - TY - JOUR A1 - Sandig, Grit A1 - von Horsten, Hans Henning A1 - Radke, Lars A1 - Blanchard, Véronique A1 - Frohme, Marcus A1 - Giese, Christoph A1 - Sandig, Volker A1 - Hinderlich, Stephan T1 - Engineering of CHO Cells for the Production of Recombinant Glycoprotein Vaccines with Xylosylated N-glycans JF - Bioengineering N2 - Xylose is a general component of O-glycans in mammals. Core-xylosylation of N-glycans is only found in plants and helminth. Consequently, xylosylated N-glycans cause immunological response in humans. We have used the F-protein of the human respiratory syncytial virus (RSV), one of the main causes of respiratory tract infection in infants and elderly, as a model protein for vaccination. The RSV-F protein was expressed in CHO-DG44 cells, which were further modified by co-expression of β1,2-xylosyltransferase from Nicotiana tabacum. Xylosylation of RSV-F N-glycans was shown by monosaccharide analysis and MALDI-TOF mass spectrometry. In immunogenic studies with a human artificial lymph node model, the engineered RSV-F protein revealed improved vaccination efficacy. KW - CHO KW - glycoengineering KW - respiratory syncytial virus KW - vaccine KW - xylose Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9620 SN - 2306-5354 VL - 4 IS - 2 ER - TY - JOUR A1 - Lukose, Rasuole A1 - Lisker, Marco A1 - Akhtar, Fatima A1 - Fraschke, Mirko A1 - Grabolla, T. A1 - Mai, Andreas A1 - Lukosius, Mindaugas T1 - Influence of plasma treatment on SiO2/Si and Si3N4/Si substrates for large-scale transfer of graphene JF - Scientific Reports N2 - One of the limiting factors of graphene integration into electronic, photonic, or sensing devices is the unavailability of large-scale graphene directly grown on the isolators. Therefore, it is necessary to transfer graphene from the donor growth wafers onto the isolating target wafers. In the present research, graphene was transferred from the chemical vapor deposited 200 mm Germanium/Silicon (Ge/Si) wafers onto isolating (SiO2/Si and Si3N4/Si) wafers by electrochemical delamination procedure, employing poly(methylmethacrylate) as an intermediate support layer. In order to influence the adhesion properties of graphene, the wettability properties of the target substrates were investigated in this study. To increase the adhesion of the graphene on the isolating surfaces, they were pre-treated with oxygen plasma prior the transfer process of graphene. The wetting contact angle measurements revealed the increase of the hydrophilicity after surface interaction with oxygen plasma, leading to improved adhesion of the graphene on 200 mm target wafers and possible proof-of-concept development of graphene-based devices in standard Si technologies. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14179 SN - 2045-2322 VL - 11 ER - TY - JOUR A1 - Elviretti, M. A1 - Lisker, Marco A1 - Lukose, Rasuole A1 - Lukosius, Mindaugas A1 - Akhtar, Fatima A1 - Mai, Andreas T1 - Reliable metal–graphene contact formation process flows in a CMOS-compatible environment JF - Nanoscale Advances N2 - The possibility of exploiting the enormous potential of graphene for microelectronics and photonics must go through the optimization of the graphene–metal contact. Achieving low contact resistance is essential for the consideration of graphene as a candidate material for electronic and photonic devices. This work has been carried out in an 8′′ wafer pilot-line for the integration of graphene into a CMOS environment. The main focus is to study the impact of the patterning of graphene and passivation on metal–graphene contact resistance. The latter is measured by means of transmission line measurement (TLM) with several contact designs. The presented approaches enable reproducible formation of contact resistivity as low as 660 Ω μm with a sheet resistance of 1.8 kΩ/□ by proper graphene patterning, passivation of the channel and a post-processing treatment such as annealing. Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16581 VL - 4 SP - 4373 EP - 4380 PB - Royal Society of Chemistry (RSC) ER - TY - JOUR A1 - Bauer, Joachim A1 - Gutke, Marko A1 - Heinrich, Friedhelm A1 - Edling, Matthias A1 - Stoycheva, Vesela A1 - Kaltenbach, Alexander A1 - Burkhardt, Martin A1 - Gruenefeld, Martin A1 - Gamp, Matthias A1 - Gerhard, Christoph A1 - Steglich, Patrick A1 - Steffen, Sebastian A1 - Herzog, Michael A1 - Dreyer, Christian A1 - Schrader, Sigurd T1 - Novel UV-transparent 2-component polyurethane resin for chip-on-board LED micro lenses JF - Optical Materials Express N2 - In this work we present a novel optical polymer system based on polyurethane elastomer components, which combines excellent UV transparency with high thermal stability, good hardness, high surface tension and long pot life. The material looks very promising for encapsulation and microlensing applications for chip-on-board (CoB) light-emitting diodes (LED). The extinction coefficient k, refractive index n, and bandgap parameters were derived from transmission and reflection measurements in a wavelength range of 200-890 nm. Thermogravimetry and differential scanning calorimetry were used to provide glass transition and degradation temperatures. The surface tension was determined by means of contact angle measurements. As proof of concept, a commercial InGaN-CoB-LED is used to demonstrate the suitability of the new material for the production of microlenses. Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13472 SN - 2159-3930 VL - 10 IS - 9 SP - 2085 EP - 2099 ER - TY - JOUR A1 - Krause, Antje A1 - Stoye, Jens A1 - Vingron, Martin T1 - Large scale hierarchical clustering of protein sequences JF - BMC Bioinformatics N2 - Background: Searching a biological sequence database with a query sequence looking for homologues has become a routine operation in computational biology. In spite of the high degree of sophistication of currently available search routines it is still virtually impossible to identify quickly and clearly a group of sequences that a given query sequence belongs to. Results: We report on our developments in grouping all known protein sequences hierarchically into superfamily and family clusters. Our graph-based algorithms take into account the topology of the sequence space induced by the data itself to construct a biologically meaningful partitioning. We have applied our clustering procedures to a non-redundant set of about 1,000,000 sequences resulting in a hierarchical clustering which is being made available for querying and browsing at http://systers.molgen.mpg.de/. Conclusions: Comparisons with other widely used clustering methods on various data sets show the abilities and strengths of our clustering methods in producing a biologically meaningful grouping of protein sequences. KW - Protein KW - Sequenz KW - Clusteralgorithmus KW - Hierarchisches Clustern KW - Proteinfamilie KW - protein KW - sequence KW - cluster algorithm KW - hierarchical clustering KW - protein family Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-153 SN - 1471-2105 PB - BioMed Central ER - TY - BOOK A1 - Karp, Markus T1 - Homo remotus - Kritik zur Führung auf Distanz N2 - Wie sich die Welt um uns herum verändert, nehmen wir wohl so wahr, als würde darunter eine Beschleunigungskraft wirken. Die Entwicklung gesellschaftlicher Interaktionen wird von uns Menschen selbst angetrieben. Je mehr sich die eine oder andere Gruppe in eine bestimmte Richtung verhält, umso mehr wirkt das Gruppenverhalten als Entwicklungstendenz. Die technisch vernetzte Welt drängt seit über 20 Jahren in unseren Lebens- und Arbeitsalltag vor. Die fast drei Jahre andauernde Corona- Pandemie hat unter Druck von Kontaktbeschränkungen die Nutzung der technischen Möglichkeiten beschleunigt und damit Arbeitsflexibilität und -mobilität in einer Weise realisiert, wie dies zuvor noch nie der Fall war. Arbeitswelt ist Lebenswelt; und deshalb wirkt sich ein zunehmendes Potenzial an Distanzinteraktionen auf wirtschaftliche, soziale, psychische, rechtliche und/oder kulturelle Bedingungen aus. Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-17368 UR - https://www.kompakt.media/product/homo-remotus-kritik-zur-fuehrung-auf-distanz-markus-karp/ PB - KOMPAKT MEDIA CY - Magdeburg ER - TY - INPR A1 - Hollmann, Susanne A1 - Kremer, Andreas A1 - Baebler, Špela A1 - Trefois, Christophe A1 - Gruden, Kristina A1 - Rudnicki, Witold R. A1 - Tong, Weida A1 - Gruca, Aleksandra A1 - Bongcam-Rudloff, Erik A1 - Evelo, Chris T. A1 - Nechyporenko, Alina A1 - Frohme, Marcus A1 - Šafránek, David A1 - Regierer, Babette A1 - D'Elia, Domenica T1 - The need for standardisation in life science research - an approach to excellence and trust. [version 1; peer review: 3 approved] T2 - F1000Research N2 - Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly and transparently. Digitalisation plays a major role here because it permeates all areas of business, science and society and is one of the key drivers for innovation and international cooperation. To address the resulting opportunities, the EU promotes the development and use of collaborative ways to produce and share knowledge and data as early as possible in the research process, but also to appropriately secure results with the European strategy for Open Science (OS). It is now widely recognised that making research results more accessible to all societal actors contributes to more effective and efficient science; it also serves as a boost for innovation in the public and private sectors. However for research data to be findable, accessible, interoperable and reusable the use of standards is essential. At the metadata level, considerable efforts in standardisation have already been made (e.g. Data Management Plan and FAIR Principle etc.), whereas in context with the raw data these fundamental efforts are still fragmented and in some cases completely missing. The CHARME consortium, funded by the European Cooperation in Science and Technology (COST) Agency, has identified needs and gaps in the field of standardisation in the life sciences and also discussed potential hurdles for implementation of standards in current practice. Here, the authors suggest four measures in response to current challenges to ensure a high quality of life science research data and their re-usability for research and innovation. KW - Open Data KW - Open Access KW - Open Science KW - FAIR Principles KW - standardisation KW - education KW - quality management Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13891 SN - 2046-1402 VL - 9 ER - TY - JOUR A1 - Fricke, Anna A1 - Psarianos, Marios A1 - Sabban, Jakob A1 - Fitzner, Maria A1 - Reipsch, Riccardo A1 - Schlüter, Oliver K. A1 - Dreyer, Christian A1 - Vogt, Julia H.-M. A1 - Schreiner, Monika A1 - Baldermann, Susanne T1 - Composite materials for innovative urban farming of alternative food sources (macroalgae and crickets) JF - Frontiers in Sustainable Food Systems N2 - Facing an inexorable growth of the human population along with substantial environmental changes, the assurance of food security is a major challenge of the present century. To ensure responsible food consumption and production (SDG 12), new approaches in the food system are required. Thus, environmentally controlled, sustainable production of alternative food sources are of key interest for both urban agriculture and food research. To face the current challenge of integrating food production systems within existing structures, multidisciplinary discourses are required. Here, we bring together novel technologies and indoor farming techniques with the aim of supporting the development of sustainable food production systems. For this purpose, we investigated the feasibility of 10 composite materials for their innovative use as structural support in macroalgal cultivation (settlement substrates) and cricket rearing (housing). Considering material resistance, rigidity, and direct material-organism interactions, the bio-based composite polylactic acid (PLA) was identified as a suitable material for joint farming. For macroalgae cultivation, PLA sustained the corrosive cultivation conditions and provided a suitable substrate without affecting the macroalgal physiology or nutritional composition (carotenoids and chlorophylls). For cricket rearing, PLA provided a suitable and recyclable shelter, which was quickly accepted by the animals without any observed harm. In contrast, other common composite components like phenolic resin or aramid were found to be unsuitable due to being harmful for the cultivated organisms or instable toward the applied sterilization procedure. This multidisciplinary study not only provides profound insights in the developing field of urban indoor food production from a new perspective, but also bridges material science and farming approaches to develop new sustainable and resilient food production systems. KW - polylactic acid (PLA) KW - Ulva fenestrata KW - Acheta domesticus (house cricket) KW - composite light-weight materials KW - urban aquaculture KW - controlled environment agriculture (CEA) Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-16822 SN - 2571-581X VL - 6 PB - Frontiers ER - TY - JOUR A1 - Momanyi, Job A1 - Herzog, Michael A1 - Muchiri, Peter T1 - Analysis of Thermomechanical Properties of Selected Class of Recycled Thermoplastic Materials Based on Their Applications JF - Recycling N2 - Polypropylene and polystyrene are petroleum-based thermoplastics which are commonly used and disposed of in the environment after their service life, leading to environmental degradation. There is a need to recycle polypropylene and polystyrene, but the effect of recycling on thermo-mechanical properties is not well understood. This study aims to determine thermo-mechanical properties of the recycled polypropylene and recycled polystyrene and compare them with corresponding virgin polypropylene and newly produced polystyrene (general purpose polystyrene 1540 and high impact polystyrene 7240). The study was carried out by preparing bar-shaped samples of recycled polypropylene, recycled polystyrene, general purpose polystyrene 1540, and high impact polystyrene 7240 by compression molding using a hot press and thermally characterizing them to determine glass transition temperature and melting temperature using differential scanning calorimetry. The changes in Young’s modulus, tensile strength, hardness, and toughness due to recycling activities were determined at room temperature (24 °C), 40 °C, 60 °C, and 80 °C. The thermo-mechanical properties of recycled polystyrene (PS) were found to be comparable to those of high impact polystyrene (HIPS) 7240. The study revealed that the hardness and toughness for the recycled polymers were higher than those of corresponding virgin polymers. On the other hand, tensile strength and Young's modulus for the recycled polymers were lower than those of the virgin polymers. Understanding the thermo-mechanical properties of the recycled polymers will contribute to more industrial applications hence increase the rate of recycling, resulting in a reduction in environmental pollution. KW - polymer KW - thermoplastic KW - thermo-mechanical property KW - recycled polypropylene KW - recycled polystyrene Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-12509 SN - 2313-4321 VL - 4 ER - TY - JOUR A1 - Njuguna, James K. A1 - Muchiri, Peter A1 - Mwema, Fredrick M. A1 - Karuri, Nancy W. A1 - Herzog, Michael A1 - Dimitrov, Kiril T1 - Determination of thermo-mechanical properties of recycled polyurethane from glycolysis polyol JF - Scientific African N2 - Polyurethane foam is one of the most versatile polymers widely used in the automotive industry. However, due to the rising amount of polyurethane foam waste in the environment, there is growing research attention focusing on circular economy solutions to closing the material loop. This study aimed to determine the possible changes in thermo-mechanical properties between rigid polyurethane prepared using polyols derived from depolymerization of commercial polyurethane foam with benchmark rigid polyurethane (Ben PU). Polyurethane foams containing dispersion polyol were reacted with dipropylene glycol (DPG) and diethylene glycol (DEG) with a ratio of DPG: DEG of 1:1 in the presence of a consumable catalyst (Di-n-butyl amine). The recovered polyol was used as a raw material replacing 100% benchmark rigid polyurethane petroleum-based polyester polyol to produce the recycled polyurethane (Rec PU). Thermal analysis was conducted to measure the recycled polyurethane's glass transition temperatures (Tg) using differential scanning calorimetry (DSC). Tensile strength, elastic modulus, toughness, and hardness test of the recycled polyurethane were conducted under three different temperatures; 24°C, 40°C, and 60°C. From the DSC results, the glass transition temperatures for the recycled and the benchmark rigid polyurethane occurred at 43°C and 50.4°C, respectively. Both polymers showed the brittle-ductile transition from 24°C to 40°C. Tensile strength for recycled polyurethane was lower than that of benchmark rigid polyurethane by 29-43% and a corresponding 24-50% decrease in elastic modulus. Recycled polyurethane recorded lower toughness than petroleum-based pure polyurethane by 13-16%. However, the recycled polymer recorded high shored D values than the benchmark rigid polyurethane by 9-29%. This study reveals that recycled polyol could be used as feedstock for polyurethane production with applications tailored to its mechanical properties. KW - polyurethane foam KW - recycling KW - glycolysis KW - rigid polyurethane KW - thermo-mechanical property KW - circular economy Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-14911 SN - 2468-2276 VL - 12 ER - TY - JOUR A1 - Reinhardt, Heiner A1 - Mahdaviasl, Mahtab A1 - Prell, Bastian A1 - Mauersberger, Anton A1 - Klimant, Philipp A1 - Reiff-Stephan, Jörg A1 - Ihlenfeldt, Steffen T1 - Efficient data acquisition for traceability and analytics JF - Procedia CIRP N2 - Implementing processes for traceability is required in various industries to assure product quality during manufacturing, provide evidence on required processing conditions or facilitate product recalls. Commonly, radio-frequency identification (RFID) or code recognition techniques (e.g. Data Matrix) are applied to track the flow of workpieces through a manufacturing system and link processing data accordingly. Although the analysis of tracking data is well-examined, we still see a gap in the research on the trade-off between data acquisition, data analytics and data quality. Here, we present a framework to increase the value of existing data by enabling data analytics while addressing common pitfalls and reducing the costs of data management. KW - identification KW - knowledge management KW - manufacturing system KW - process control KW - quality assurance KW - sustainable development KW - decision making KW - complexity KW - analysis KW - design Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-19232 SN - 2212-8271 VL - 122 SP - 73 EP - 78 PB - Elsevier ER - TY - JOUR A1 - Schokraie, Elham A1 - Hotz-Wagenblatt, Agnes A1 - Warnken, Uwe A1 - Mali, Brahim A1 - Frohme, Marcus A1 - Förster, Frank A1 - Dandekar, Thomas A1 - Hengherr, Steffen A1 - Schill, Ralph O. A1 - Schnölzer, Martina T1 - Proteomic Analysis of Tardigrades: Towards a Better Understanding of Molecular Mechanisms by Anhydrobiotic Organisms JF - PLoS ONE N2 - Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6214 SN - 1932-6203 VL - 5 IS - 3 ER - TY - JOUR A1 - Schokraie, Elham A1 - Warnken, Uwe A1 - Hotz-Wagenblatt, Agnes A1 - Grohme, Markus A1 - Hengherr, Steffen A1 - Förster, Frank A1 - Schill, Ralph O. A1 - Frohme, Marcus A1 - Dandekar, Thomas A1 - Schnölzer, Martina T1 - Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state JF - PLoS ONE N2 - Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6392 SN - 1932-6203 VL - 7 IS - 9 ER - TY - JOUR A1 - Förster, Frank A1 - Beisser, Daniela A1 - Grohme, Markus A1 - Liang, Chunguang A1 - Mali, Brahim A1 - Siegl, Alexander Matthias A1 - Engelmann, Julia C. A1 - Shkumatov, Alexander A1 - Schokraie, Elham A1 - Müller, Tobias A1 - Schnölzer, Martina A1 - Schill, Ralph O. A1 - Frohme, Marcus A1 - Dandekar, Thomas T1 - Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations JF - Bioinformatics and Biology Insights N2 - Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant. KW - RNA KW - expressed sequence tag KW - cluster KW - protein family KW - adaptation KW - tardigrada KW - transcriptome Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6153 SN - 1177-9322 VL - 2012 IS - 6 SP - 69 EP - 96 ER - TY - JOUR A1 - Förster, Frank A1 - Liang, Chunguang A1 - Shkumatov, Alexander A1 - Beisser, Daniela A1 - Engelmann, Julia C. A1 - Schnölzer, Martina A1 - Frohme, Marcus A1 - Müller, Tobias A1 - Schill, Ralph O. A1 - Dandekar, Thomas T1 - Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades JF - BMC Genomics N2 - Background Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. Results To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data. Conclusion Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences. Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6461 SN - 1471-2164 VL - 10 IS - 469 ER - TY - JOUR A1 - Mali, Brahim A1 - Grohme, Markus A1 - Förster, Frank A1 - Dandekar, Thomas A1 - Schnölzer, Martina A1 - Reuter, Dirk A1 - Wełnicz, Weronika A1 - Schill, Ralph O. A1 - Frohme, Marcus T1 - Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer JF - BMC Genomics N2 - The phenomenon of desiccation tolerance, also called anhydrobiosis, involves the ability of an organism to survive the loss of almost all cellular water without sustaining irreversible damage. Although there are several physiological, morphological and ecological studies on tardigrades, only limited DNA sequence information is available. Therefore, we explored the transcriptome in the active and anhydrobiotic state of the tardigrade Milnesium tardigradum which has extraordinary tolerance to desiccation and freezing. In this study, we present the first overview of the transcriptome of M. tardigradum and its response to desiccation and discuss potential parallels to stress responses in other organisms. Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6207 SN - 1471-2164 VL - 11 IS - 168 ER - TY - JOUR A1 - Janowski, Susann A1 - Gross, Ina A1 - Sauer-Gürth, Hedwig A1 - Tietze, Dieter Thomas A1 - Grohme, Markus A1 - Frohme, Marcus A1 - Becker, Peter A1 - Wink, Michael T1 - New Microsatellite Markers for the Common Tern (Sterna hirundo) Developed with 454 Shot-Gun Pyrosequencing JF - The Open Ornithology Journal N2 - Long term studies, focusing on population- and socio-biology research, require the unequivocal identification of individuals. DNA studies with Short Tandem Repeats (STR loci) became a widespread tool in population genetics. We used the next-generation sequencing (NGS) approach with 454 shot-gun pyrosequencing to identify 13 new polymorphic STR loci for the Common Tern, Sterna hirundo. To enlarge the marker set we added two more loci originally developed for Black-legged Kittiwake (Rissa tridactyla) and Red-billed Gull (Chroicocephalus scopulinus) and arranged these 15 loci into three multiplex PCR panels for high throughput genotyping. Loci characterization demonstrated that our marker set is of high quality. A PIC value of about 0.67 and a power of exclusion value of 0.99 were reached. Deviation from Hardy-Weinberg expectations of some loci and low frequencies for null alleles are interpreted as a result of inbreeding and founder effect in the investigated tern colony. We used a test data set of this well-studied breeding colony of Common Tern at Banter Lake, Wilhelmshaven, Germany, to perform a parentage test. Parent-chick relationships, known from the social pedigree of that colony, were compared with genetically calculated ones. In order to test our markers and the used parentage program COLONY, we conducted six competing data sets with varying completeness of included parental genotypes. By including fully sampled parent pairs of known family assignment, results were correct for nest mates, single parents and parent pairs. Our marker set provides a powerful tool to investigate life-time reproductive success and other issues of population and socio-biology for Common Terns, e.g. in the aforementioned colony monitored for decades. KW - common tern KW - COLONY software KW - genotyping KW - microsatellite KW - multiplex PCR KW - next-generation sequencing KW - parentage analysis KW - Sterna hirundo Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6789 SN - 1874-4532 VL - 9 SP - 50 EP - 59 ER - TY - JOUR A1 - Nitsche, Andreas A1 - Kurth, Andreas A1 - Dunkhorst, Anna A1 - Pänke, Oliver A1 - Sielaff, Hendrik A1 - Junge, Wolfgang A1 - Muth, Doreen A1 - Scheller, Frieder W. A1 - Stöcklein, Walter A1 - Dahmen, Claudia A1 - Pauli, Georg A1 - Kage, Andreas T1 - One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX JF - BMC Biotechnology N2 - As a new class of therapeutic and diagnostic reagents, more than fifteen years ago RNA and DNA aptamers were identified as binding molecules to numerous small compounds, proteins and rarely even to complete pathogen particles. Most aptamers were isolated from complex libraries of synthetic nucleic acids by a process termed SELEX based on several selection and amplification steps. Here we report the application of a new one-step selection method (MonoLEX) to acquire high-affinity DNA aptamers binding Vaccinia virus used as a model organism for complex target structures. Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6246 SN - 1472-6750 VL - 7 IS - 48 ER - TY - JOUR A1 - Wang, Chong A1 - Grohme, Markus A1 - Mali, Brahim A1 - Schill, Ralph O. A1 - Frohme, Marcus T1 - Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome Sequencing JF - PLoS ONE N2 - Many tardigrade species are capable of anhydrobiosis; however, mechanisms underlying their extreme desiccation resistance remain elusive. This study attempts to quantify the anhydrobiotic transcriptome of the limno-terrestrial tardigrade Milnesium tardigradum. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6029 SN - 1932-6203 VL - 9 IS - 3 ER -