@article{FischbachFrohmeGloekler2017, author = {Fischbach, Jens and Frohme, Marcus and Gl{\"o}kler, J{\"o}rn}, title = {Hinge-initiated Primer-dependent Amplification of Nucleic Acids (HIP) - A New Versatile Isothermal Amplification Method}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9824}, year = {2017}, abstract = {The growing demand for cost-effective nucleic acid detection assays leads to an increasing number of different isothermal amplification reaction methods. However, all of the most efficient methods suffer from highly complex assay conditions due to the use of complicated primer sets and/or auxiliary enzymes. The present study describes the application of a new linker moiety that can be incorporated between a primer and a secondary target binding site which can act both as a block to polymerase extension as well as a hinge for refolding. This novel "hinge-primer" approach results in an efficient regeneration of the primer binding site and thus improves the strand-displacement and amplification process under isothermal conditions. Our investigations revealed that the reaction with forward and reverse hinge-primer including an abasic site is very efficient. The assay complexity can be reduced by combining the hinge-primer with a corresponding linear primer. Furthermore, the reaction speed can be increased by reducing the length of the amplified target sequence. We tested the sensitivity down to 104 copies and found a linear correlation between reaction time and input copy number. Our approach overcomes the usually cumbersome primer-design and extends the range of isothermal amplification methods using a polymerase with strand-displacement activity.}, language = {en} } @article{KarakuşNasereddinOnayetal.2017, author = {Karaku{\c{s}}, Mehmet and Nasereddin, Abed and Onay, H{\"u}seyin and Karaca, Emin and {\"O}zkeklik{\c{c}}i, Ahmet and Jaffe, Charles L. and Kuhls, Katrin and {\"O}zbilgin, Ahmet and Ertabaklar, Hatice and Demir, Samiye and {\"O}zbel, Yusuf and T{\"o}z, Seray}, title = {Epidemiological analysis of Leishmania tropica strains and giemsa-stained smears from Syrian and Turkish leishmaniasis patients using multilocus microsatellite typing (MLMT)}, series = {PLoS Neglected Tropical Diseases}, volume = {11}, journal = {PLoS Neglected Tropical Diseases}, number = {4}, issn = {1935-2735}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9313}, pages = {12}, year = {2017}, abstract = {Turkey is located in an important geographical location, in terms of the epidemiology of vector-borne diseases, linking Asia and Europe. Cutaneous leishmaniasis (CL) is one of the endemic diseases in a Turkey and according to the Ministry Health of Turkey, 45\% of CL patients originate from Şanl{\i}urfa province located in southeastern Turkey. Herein, the epidemiological status of CL, caused by L. tropica, in Turkey was examined using multilocus microsatellite typing (MLMT) of strains obtained from Turkish and Syrian patients. A total of 38 cryopreserved strains and 20 Giemsa-stained smears were included in the present study. MLMT was performed using 12 highly specific microsatellite markers. Delta K (ΔK) calculation and Bayesian statistics were used to determine the population structure. Three main populations (POP A, B and C) were identified and further examination revealed the presence of three subpopulations for POP B and C. Combined analysis was performed using the data of previously typed L. tropica strains and Mediterranean and Şanl{\i}urfa populations were identified. This finding suggests that the epidemiological status of L. tropica is more complicated than expected when compared to previous studies. A new population, comprised of Syrian L. tropica samples, was reported for the first time in Turkey, and the data presented here will provide new epidemiological information for further studies.}, language = {en} } @article{GerhardStappenbeck2018, author = {Gerhard, Christoph and Stappenbeck, Marco}, title = {Impact of the Polishing Suspension Concentration on Laser Damage of Classically Manufactured and Plasma Post-Processed Zinc Crown Glass Surfaces}, series = {Applied Sciences}, volume = {8}, journal = {Applied Sciences}, number = {9}, publisher = {MDPI}, issn = {2076-3417}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10556}, pages = {1 -- 15}, year = {2018}, abstract = {The laser-induced damage threshold of optics is an issue of essential importance in high-power laser applications. However, the complex and partially interacting mechanisms as well as the underlying reasons for laser damage of glass surfaces are not yet fully understood. The aim of the present work is to contribute to a better understanding of such damage mechanisms by providing original results on the impact of classical glass surface machining on the laser-induced damage threshold. For this purpose, glass samples were prepared with well-defined process conditions in terms of the used lapping and polishing agents and suspensions. Further, the samples were post-processed by atmospheric pressure plasma for precision cleaning. The laser-induced damage threshold and surface contamination by residues from the manufacturing process were determined before and after plasma post-processing. It is shown that the polishing suspension concentration has a certain impact on the laser-induced damage threshold and surface contamination by residues from used working materials. The highest damage threshold of 15.2 J/cm² is found for the lowest surface contamination by carbon which occurs in the case of the highest polishing suspension concentration. After plasma treatment for merely 60 s, this value was increased to 20.3 J/cm² due to the removal of surface-adherent carbon. The results thus imply that the laser-induced damage threshold can notably be increased by first choosing appropriate process parameters during classical manufacturing and second plasma post-processing for surface finishing.}, language = {en} } @article{DimitrovHerzogNenkova2013, author = {Dimitrov, Kiril and Herzog, Michael and Nenkova, Sanchi}, title = {Fe3O4 Modification of Microcrystalline Cellulose for Composite Materials}, series = {American Journal of Chemistry}, volume = {3}, journal = {American Journal of Chemistry}, number = {5}, issn = {2165-8781}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9651}, pages = {140 -- 147}, year = {2013}, abstract = {A new synthesis method for producing cellulose ferrite micro- and nano- composites was developed and new material properties were studied. Microcrystalline cellulose was modified with a mixture of Fe+2/Fe+3 to produce surface bonded nanoparticles magnetite (Fe3O4). Optimal conditions were determined. Microsized hematite (Fe2O3) was mixed with microcrystalline cellulose and used as a reference. The magnetite modified microcrystalline cellulose and hematite filled microcrystalline cellulose were used together with polyurethane prepolymer. New composite crosslinked conductivity materials based on the magnetite modified microcrystalline or hematite filled microcrystalline cellulose and polyurethane were developed. Morphology, crystalline properties, water absorption and electro conductivity of these materials were characterized. The physical properties of these materials were characterized by different analytical methods: SEM, XRD, water absorption and electrical resistance.}, language = {en} } @article{MeierGrawBeyerleinetal.2017, author = {Meier, Richard and Graw, Stefan and Beyerlein, Peter and Koestler, Devin and Molina, Julian R. and Chien, Jeremy}, title = {digit—a tool for detection and identification of genomic interchromosomal translocations}, series = {Nucleic Acids Research}, volume = {45}, journal = {Nucleic Acids Research}, number = {9}, issn = {1362-4962}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9697}, pages = {e72}, year = {2017}, abstract = {Structural variations (SVs) in genomic DNA can have profound effects on the evolution of living organisms, on phenotypic variations and on disease processes. A critical step in discovering the full extent of structural variations is the development of tools to characterize these variations accurately in next generation sequencing data. Toward this goal, we developed a software pipeline named digit that implements a novel measure of mapping ambiguity to discover interchromosomal SVs from mate-pair and pair-end sequencing data. The workflow robustly handles the high numbers of artifacts present in mate-pair sequencing and reduces the false positive rate while maintaining sensitivity. In the simulated data set, our workflow recovered 96\% of simulated SVs. It generates a self-updating library of common translocations and allows for the investigation of patient- or group-specific events, making it suitable for discovering and cataloging chromosomal translocations associated with specific groups, traits, diseases or population structures.}, language = {en} } @article{KinuthiaFrohmeBroedeletal.2017, author = {Kinuthia, Chuaga and Frohme, Marcus and Br{\"o}del, Oliver and Mugendi, Beatrice}, title = {LCMS Analysis of Biochemical Composition in Different Kenyan Coffee Classifications}, series = {Food Science and Quality Management}, volume = {69}, journal = {Food Science and Quality Management}, issn = {2225-0557}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10185}, pages = {44 -- 52}, year = {2017}, abstract = {Kenyan coffee is classified by defects after grading by the 'Devonshire method.' The method involves classification of the coffee beans into different classes based on the raw and roasted coffees and cup quality, with class one being the best and ten the poorest. In this study, the relationship between classification of the coffee and the content of sucrose, trigonelline, caffeine and chlorogenic acids was determined by simultaneous LC-MS analysis. By using the sensory variables the class 3 coffee portrayed the best quality, followed by class 4 and 5 which were placed further distinctively from the other classes (6, 7, 8 and 9). The class 3 coffee had a high percent of non-defective beans with 94.31\% and class 9 had a high defect count at 79.53\% hence the defective beans increased with decrease in coffee class. The caffeine concentration in green coffee for class 3 coffee was significantly different from the rest of the coffees at 1.23 ± 0.00g/100g. A higher content of trigonelline levels was observed as the quality of the green coffee decreased in classes 6, 7 and 8. The highest level of sucrose in green coffee beans was observed in class 3 coffee and the lowest in the class 9. Lower content of chlorogenic acids were observed among the high quality coffees i.e. class 3, 4 and 5 with class 3 having the lowest while a higher content was observed among the lower quality coffees i.e. classes 6, 7 and 9 with class 6 having a higher content was it significantly different in class 6 compared to 7 and 9?. Quantities of different chemical components among the classes are clear indicators that the classification method used on the Kenyan coffees brings out the differences in coffee quality based on the analysis of the green and the roasted coffees.}, language = {en} } @article{MaierClausiusRichteretal.2021, author = {Maier, Petra and Clausius, Benjamin and Richter, Asta and Bittner, Benjamin and Hort, Norbert and Menze, Roman}, title = {Crack Propagation in As-Extruded and Heat-Treated Mg-Dy-Nd-Zn-Zr Alloy Explained by the Effect of LPSO Structures and Their Micro- and Nanohardness}, series = {Materials}, volume = {14}, journal = {Materials}, number = {13}, publisher = {MDPI}, issn = {1996-1944}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14194}, year = {2021}, abstract = {The investigation of the crack propagation in as-extruded and heat-treated Mg-Dy-Nd-Zn-Zr alloy with a focus on the interaction of long-period stacking-ordered (LPSO) structures is the aim of this study. Solution heat treatment on a hot extruded Mg-Dy-Nd-Zn-Zr (RESOLOY®) was done to change the initial fine-grained microstructure, consisting of grain boundary blocky LPSO and lamellar LPSO structures within the matrix, into coarser grains of less lamellar and blocky LPSO phases. C-ring compression tests in Ringer solution were used to cause a fracture. Crack initiation and propagation is influenced by twin boundaries and LPSO lamellae. The blocky LPSO phases also clearly hinder crack growth, by increasing the energy to pass either through the phase or along its interface. The microstructural features were characterized by micro- and nanohardness as well as the amount and location of LPSO phases in dependence on the heat treatment condition. By applying nanoindentation, blocky LPSO phases show a higher hardness than the grains with or without lamellar LPSO phases and their hardness decreases with heat treatment time. On the other hand, the matrix increases in hardness by solid solution strengthening. The microstructure consisting of a good balance of grain size, matrix and blocky LPSO phases and twins shows the highest fracture energy.}, language = {en} } @article{GrebinykPrylutskaGrebinyketal.2021, author = {Grebinyk, Anna and Prylutska, Svitlana and Grebinyk, Sergii and Evstigneev, Maxim and Krysiuk, Iryna and Skaterna, Tetiana and Horak, Iryna and Sun, Yanfang and Drobot, Liudmyla and Matyshevska, Olga and Prylutskyy, Yuriy and Ritter, Uwe and Frohme, Marcus}, title = {Antitumor efficiency of the natural alkaloid berberine complexed with C60 fullerene in Lewis lung carcinoma in vitro and in vivo}, series = {Cancer Nanotechnology}, volume = {12}, journal = {Cancer Nanotechnology}, publisher = {BioMed Central}, issn = {1868-6966}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14749}, pages = {24}, year = {2021}, abstract = {Background Berberine (Ber) is a herbal alkaloid with pharmacological activity in general and a high anticancer potency in particular. However, due to its low bioavailability, the difficulty in reaching a target and choosing the right dose, there is a need to improve approaches of Ber use in anticancer therapy. In this study, Ber, noncovalently bound to a carbon nanostructure C60 fullerene (C60) at various molar ratios of the components, was explored against Lewis lung carcinoma (LLC). Methods C60-Ber noncovalent nanocomplexes were synthesized in 1:2, 1:1 and 2:1 molar ratios. Ber release from the nanocomplexes was studied after prolonged incubation at different pH with the liquid chromatography-mass spectrometry analysis of free Ber content. Biological effects of the free and C60-complaxated Ber were studied in vitro towards LLC cells with phase-contrast and fluorescence microscopy, flow cytometry, MTT reduction, caspase activity and wound closure assays. The treatment with C60-Ber nanocomplex was evaluated in vivo with the LLC-tumored C57Bl mice. The mice body weight, tumor size, tumor weight and tumor weight index were assessed for four groups, treated with saline, 15 mg C60/kg, 7.5 mg Ber/kg or 2:1 C60-Ber nanocomplex (15 mg C60/kg, 7.5 mg Ber/kg). Results Ber release from C60-Ber nanocomplexes was promoted with medium acidification. LLC cells treatment with C60-Ber nanocomplexes was followed by enhanced Ber intracellular uptake as compared to free Ber. The cytotoxicity of the studied agents followed the order: free Ber < 1:2 < 1:1 < 2:1 C60-Ber nanocomplex. The potency of cytotoxic effect of 2:1 C60-Ber nanocomplex was confirmed by 21.3-fold decrease of IC50 value (0.8 ± 0.3 µM) compared to IC50 for free Ber (17 ± 2 µM). C60-Ber nanocomplexes induced caspase 3/7 activation and suppressed the migration activity of LLC cells. The therapeutic potency of 2:1 C60-Ber nanocomplex was confirmed in a mouse model of LLC. The tumor growth in the group treated with 2:1 C60-Ber nanocomplex is suppressed by approximately 50\% at the end of experiment, while in the tumor-bearing group treated with free Ber no therapeutic effect was detected. Conclusions This study indicates that complexation of natural alkaloid Ber with C60 may be a novel therapeutic strategy against lung carcinoma.}, language = {en} } @article{GoldenbergKoehlerDreyer2021, author = {Goldenberg, Leonid and K{\"o}hler, Mathias and Dreyer, Christian}, title = {SiO2 Nanoparticles-Acrylate Formulations for Core and Cladding in Planar Optical Waveguides}, series = {Nanomaterials}, volume = {11}, journal = {Nanomaterials}, number = {5}, publisher = {MDPI}, issn = {2079-4991}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14057}, year = {2021}, abstract = {A combination of acrylate formulations and SiO2 nanoparticles is investigated with the aim to improve the optical properties of low-refractive index polymers that are used for the fabrication of planar optical waveguides. A decrease in refractive index and also in the thermo-optic coefficient of nanocomposite materials is clearly demonstrated, while some formulations exhibit an increase in the glass transition temperature. The possibility of using these nanocomposite materials to fabricate waveguiding layers with low optical propagation losses at telecommunication wavelengths around 1550 nm is also shown. The nanomaterials can be applied in optical microchips on polymer platforms.}, language = {en} } @article{GrytsenkoKsianzouKolomzarovetal.2021, author = {Grytsenko, Kostyantyn and Ksianzou, Viachaslau and Kolomzarov, Yurii and Lytvyn, Peter and Dietzel, Birgit and Schrader, Sigurd}, title = {Fluoropolymer Film Formation by Electron Activated Vacuum Deposition}, series = {Surfaces}, volume = {4}, journal = {Surfaces}, number = {1}, publisher = {MDPI}, issn = {2571-9637}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13786}, pages = {66 -- 80}, year = {2021}, abstract = {Polytetrafluoroethylene (PTFE), polyhexafluoropropylene (PHFP) and polychlorotrifluoroethylene (PCTFE) were heated to their decomposition temperature in a high vacuum. The emitted fragments passed an electron cloud, condensed on a substrate and formed fluoropolymer film. Growth rate of PTFE and PHFP films increased up to a factor five in the presence of the electron cloud. Mass spectrometry revealed changes in the mass spectra of fragments generated by thermal decomposition only and formed under electron activation. The observed changes were different for each fluoropolymer. Infrared spectroscopy (IRS) showed that the structure of the films was close to the structure of the bulk polymers. Atomic force microscopy (AFM) has revealed different morphologies of PTFE, PHFP and PCTFE films, suggesting a Volmer-Weber growth mechanism for PTFE and PHFP but a Frank-van der Merwe one for PCTFE. All films were smooth at nanoscale and transparent from ultraviolet to near-infrared region. Additional radio frequency (RF) plasma ignited in the emitted fragments at a low pressure increased mechanical characteristics of the films without losing their optical transparency and smoothness.}, language = {en} } @article{OehlersFabian2021, author = {Oehlers, Milena and Fabian, Benjamin}, title = {Graph Metrics for Network Robustness—A Survey}, series = {Mathematics}, volume = {9}, journal = {Mathematics}, number = {8}, publisher = {MDPI}, issn = {2227-7390}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13954}, year = {2021}, abstract = {Research on the robustness of networks, and in particular the Internet, has gained critical importance in recent decades because more and more individuals, societies and firms rely on this global network infrastructure for communication, knowledge transfer, business processes and e-commerce. In particular, modeling the structure of the Internet has inspired several novel graph metrics for assessing important topological robustness features of large complex networks. This survey provides a comparative overview of these metrics, presents their strengths and limitations for analyzing the robustness of the Internet topology, and outlines a conceptual tool set in order to facilitate their future adoption by Internet research and practice but also other areas of network science.}, language = {en} } @article{KeNieLiebchenetal.2020, author = {Ke, Yu and Nie, Lei and Liebchen, Christian and Yuan, Wuyang and Wu, Xin}, title = {Improving Synchronization in an Air and High-Speed Rail Integration Service via Adjusting a Rail Timetable: A Real-World Case Study in China}, series = {Journal of Advanced Transportation}, volume = {2020}, journal = {Journal of Advanced Transportation}, publisher = {Hindawi}, issn = {2042-3195}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13105}, year = {2020}, abstract = {Air and high-speed rail (AH) integration services are gaining ground with the development of the high-speed railway and airline industries. A well-designed feeder train timetable with good synchronization is of great significance in an AH integration service, because it can improve the connectivity at transfer nodes and offer more opportunities for intermodal passengers to travel. In this study, we propose a multi-objective model of a feeder railway timetable problem in an AH integration service to improve synchronization. The aims of the optimization model are to maximize the number of synchronizations and the coverage of synchronized flights, as well as to minimize the transfer penalties of passengers. We focus on a scenario of a partial subnetwork in which one direction of a two-direction railroad line with one transfer station is considered. The model is applied to Shijiazhuang Zhengding International Airport, China. The results illustrate the effectiveness of the approach developed in the paper.}, language = {en} } @article{PajčinVlajkovFrohmeetal.2020, author = {Pajčin, Ivana and Vlajkov, Vanja and Frohme, Marcus and Grebinyk, Sergii and Grahovac, Mila and Mojićević, Marija and Grahovac, Jovana}, title = {Pepper Bacterial Spot Control by Bacillus velezensis: Bioprocess Solution}, series = {Microorganisms}, volume = {8}, journal = {Microorganisms}, number = {10}, publisher = {MDPI}, issn = {2076-2607}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13510}, year = {2020}, abstract = {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.}, language = {en} } @article{GoldenbergKoehlerKahleetal.2020, author = {Goldenberg, Leonid and K{\"o}hler, Mathias and Kahle, Olaf and Dreyer, Christian}, title = {Impact of inorganic nanoparticles on optical properties of low refractive index waveguiding polymers}, series = {Optical Materials Express}, volume = {10}, journal = {Optical Materials Express}, number = {11}, issn = {2159-3930}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13521}, pages = {2987 -- 2997}, year = {2020}, abstract = {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.}, language = {en} } @article{WolfRichter2003, author = {Wolf, Bodo and Richter, Asta}, title = {The concept of differential hardness in depth sensing indentation}, series = {New Journal of Physics}, volume = {5}, journal = {New Journal of Physics}, number = {15}, issn = {1367-2630}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5657}, pages = {15.1 -- 15.17}, year = {2003}, abstract = {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.}, language = {en} } @article{KhalidGoebelHuehnetal.2011, author = {Khalid, Waqas and G{\"o}bel, Gero and H{\"u}hn, Dominik and Montenegro, Jose-Maria and Rivera-Gil, Pilar and Lisdat, Fred and Parak, Wolfgang J.}, title = {Light triggered detection of aminophenyl phosphate with a quantum dot based enzyme electrode}, series = {Journal of Nanobiotechnology}, volume = {9}, journal = {Journal of Nanobiotechnology}, number = {46}, issn = {1477-3155}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5808}, pages = {10}, year = {2011}, abstract = {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.}, language = {en} } @article{SternPaulyZydeketal.2016, author = {Stern, Daniel and Pauly, Diana and Zydek, Martin and Miller, Lilija and Piesker, Janett and Laue, Michael and Lisdat, Fred and Dorner, Martin B. and Dorner, Brigitte G. and Nitsche, Andreas}, title = {Development of a Genus-Specific Antigen Capture ELISA for Orthopoxviruses - Target Selection and Optimized Screening}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {3}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5830}, pages = {22}, year = {2016}, abstract = {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.}, language = {en} } @article{SchulzeLangEnkeetal.2015, author = {Schulze, Katja and Lang, Imke and Enke, Heike and Grohme, Diana and Frohme, Marcus}, title = {The use of fluorescence microscopy and image analysis for rapid detection of non-producing revertant cells of Synechocystis sp. PCC6803 and Synechococcus sp. PCC7002}, series = {BMC Research Notes}, volume = {8}, journal = {BMC Research Notes}, number = {160}, issn = {1756-0500}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5911}, pages = {11}, year = {2015}, abstract = {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.}, language = {en} } @article{DimitrievGrytsenkoTolmachevetal.2014, author = {Dimitriev, O. P. and Grytsenko, Kostyantyn and Tolmachev, O. I. and Slominskii, Yu L. and Kudinova, M. A. and Schrader, Sigurd}, title = {Effect of Concentration on Isomerization of Rhodanine Derivatives of Merocyanine Dyes in Polar Solvents}, series = {Advances in Physical Chemistry}, volume = {2014}, journal = {Advances in Physical Chemistry}, issn = {1687-7993}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5931}, pages = {9}, year = {2014}, abstract = {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.}, language = {en} } @article{BilousMalkoFrohmeetal.2024, author = {Bilous, Nataliya and Malko, Vladyslav and Frohme, Marcus and Nechyporenko, Alina}, title = {Comparison of CNN-Based Architectures for Detection of Different Object Classes}, series = {AI}, volume = {5}, journal = {AI}, number = {4}, publisher = {MDPI}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19634}, pages = {2300 -- 2320}, year = {2024}, abstract = {(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.}, language = {en} } @article{PrzymusRykaczewskiMartinSeguraetal.2025, author = {Przymus, Piotr and Rykaczewski, Krzysztof and Mart{\´i}n-Segura, Adri{\´a}n and Truu, Jaak and De Santa Pau, Enrique Carrillo and Kolev, Mikhail and Naskinova, Irina and Gruca, Aleksandra and Sampri, Alexia and Frohme, Marcus and Nechyporenko, Alina}, title = {Deep Learning in Microbiome Analysis: A Comprehensive Review of Neural Network Models}, series = {Frontiers in Microbiology}, volume = {15}, journal = {Frontiers in Microbiology}, publisher = {Frontiers}, issn = {1664-302X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19889}, year = {2025}, abstract = {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.}, language = {en} } @article{GoldenbergKoehlerDreyer2025, author = {Goldenberg, Leonid and K{\"o}hler, Mathias and Dreyer, Christian}, title = {Fluorinated Polymers for Photonics—From Optical Waveguides to Polymer-Clad Glass Optical Fibers}, series = {Applied Sciences}, volume = {15}, journal = {Applied Sciences}, number = {4}, publisher = {MDPI}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19967}, year = {2025}, abstract = {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.}, language = {en} } @article{IchkitidzeSarygulovUngvari2017, author = {Ichkitidze, Yuri and Sarygulov, Askar and Ungv{\´a}ri, L{\´a}szl{\´o}}, title = {Potential for Enhancing Traffic Safety on Highways of Russia}, series = {Transportation Research Procedia}, volume = {20}, journal = {Transportation Research Procedia}, issn = {2352-1465}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-7229}, pages = {242 -- 246}, year = {2017}, abstract = {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.}, language = {en} } @article{JaenchenStach2012, author = {J{\"a}nchen, Jochen and Stach, Helmut}, title = {Adsorption properties of porous materials for solar thermal energy storage and heat pump applications}, series = {Energy Procedia}, volume = {30}, journal = {Energy Procedia}, number = {2012}, issn = {1876-6102}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6160}, pages = {289 -- 293}, year = {2012}, abstract = {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.}, language = {en} } @article{TillichLehmannSchulzeetal.2012, author = {Tillich, Ulrich M. and Lehmann, Sandra and Schulze, Katja and D{\"u}hring, Ulf and Frohme, Marcus}, title = {The Optimal Mutagen Dosage to Induce Point-Mutations in Synechocystis sp. PCC6803 and Its Application to Promote Temperature Tolerance}, series = {PLoS ONE}, volume = {7}, journal = {PLoS ONE}, number = {11}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6186}, pages = {8}, year = {2012}, abstract = {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.}, language = {en} } @article{SchulzeLopezTillichetal.2011, author = {Schulze, Katja and L{\´o}pez, Diana A. and Tillich, Ulrich M. and Frohme, Marcus}, title = {A simple viability analysis for unicellular cyanobacteria using a new autofluorescence assay, automated microscopy, and ImageJ}, series = {BMC Biotechnology}, volume = {11}, journal = {BMC Biotechnology}, number = {118}, issn = {1472-6750}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6192}, pages = {8}, year = {2011}, abstract = {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.}, language = {en} } @article{AndreasHaeuplLuebkeetal.2009, author = {Andreas, Kristin and H{\"a}upl, Thomas and L{\"u}bke, Carsten and Ringe, Jochen and Morawietz, Lars and Wachtel, Anja and Sittinger, Michael and Kaps, Christian}, title = {Antirheumatic drug response signatures in human chondrocytes: potential molecular targets to stimulate cartilage regeneration}, series = {Arthritis Research \& Therapy}, volume = {11}, journal = {Arthritis Research \& Therapy}, number = {R15}, issn = {1465-9913}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6223}, pages = {14}, year = {2009}, abstract = {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.}, language = {en} } @article{SchulzeTillichDandekaretal.2013, author = {Schulze, Katja and Tillich, Ulrich M. and Dandekar, Thomas and Frohme, Marcus}, title = {PlanktoVision - an automated analysis system for the identification of phytoplankton}, series = {BMC Bioinformatics}, volume = {14}, journal = {BMC Bioinformatics}, number = {115}, issn = {1471-2105}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6364}, pages = {10}, year = {2013}, abstract = {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.}, language = {en} } @article{GrytsenkoLozovskiStrilchuketal.2012, author = {Grytsenko, Kostyantyn and Lozovski, Valeri and Strilchuk, Galyna and Schrader, Sigurd}, title = {Evaluation of the Mechanism of the Gold Cluster Growth during Heating of the Composite Gold-Polytetrafluoroethylene Thin Film}, series = {Nanomaterials}, volume = {2}, journal = {Nanomaterials}, number = {4}, issn = {2079-4991}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6387}, pages = {366 -- 378}, year = {2012}, abstract = {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.}, language = {en} } @article{HerzogJaenchenKontogeorgopoulosetal.2014, author = {Herzog, Thomas H. and J{\"a}nchen, Jochen and Kontogeorgopoulos, Eythymius M. and Lutz, Wolfgang}, title = {Steamed Zeolites for Heat Pump Applications and Solar Driven Thermal Adsorption Storage}, series = {Energy Procedia}, volume = {48}, journal = {Energy Procedia}, issn = {1876-6102}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5951}, pages = {380 -- 383}, year = {2014}, abstract = {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.}, language = {en} } @article{TillichWolterSchulzeetal.2014, author = {Tillich, Ulrich M. and Wolter, Nick and Schulze, Katja and Kramer, Dan and Br{\"o}del, Oliver and Frohme, Marcus}, title = {High-throughput cultivation and screening platform for unicellular phototrophs}, series = {BMC Microbiology}, volume = {14}, journal = {BMC Microbiology}, number = {239}, issn = {1471-2180}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6007}, pages = {13}, year = {2014}, abstract = {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.}, language = {en} } @article{TillichWolterFrankeetal.2014, author = {Tillich, Ulrich M. and Wolter, Nick and Franke, Philipp and D{\"u}hring, Ulf and Frohme, Marcus}, title = {Screening and genetic characterization of thermo-tolerant Synechocystis sp. PCC6803 strains created by adaptive evolution}, series = {BMC Biotechnology}, volume = {14}, journal = {BMC Biotechnology}, number = {66}, issn = {1472-6750}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6014}, pages = {15}, year = {2014}, abstract = {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.}, language = {en} } @article{HerzogJaenchen2016, author = {Herzog, Thomas H. and J{\"a}nchen, Jochen}, title = {Adsorption Properties of Modified Zeolites for Operating Range Enhancement of Adsorption Heat Pumps through the Use of Organic Adsorptive Agents}, series = {Energy Procedia}, volume = {91}, journal = {Energy Procedia}, issn = {1876-6102}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6614}, pages = {155 -- 160}, year = {2016}, abstract = {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.}, language = {en} } @article{GoebelDietzLisdat2009, author = {G{\"o}bel, Gero and Dietz, T. and Lisdat, Fred}, title = {Biosensor based on an oxygen reducing bilirubin oxidase electrode}, series = {Procedia Chemistry}, volume = {1}, journal = {Procedia Chemistry}, number = {1}, issn = {1876-6196}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6237}, pages = {273 -- 276}, year = {2009}, abstract = {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.}, language = {en} } @article{OmarLohTyeetal.2013, author = {Omar, Noorsharmimi and Loh, Qiuting and Tye, Gee Jun and Choong, Yee Siew and Noordin, Rahmah and Gl{\"o}kler, J{\"o}rn and Lim, Theam Soon}, title = {Development of an Antigen-DNAzyme Based Probe for a Direct Antibody-Antigen Assay Using the Intrinsic DNAzyme Activity of a Daunomycin Aptamer}, series = {Sensors}, volume = {14}, journal = {Sensors}, number = {1}, issn = {1424-8220}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6267}, pages = {346 -- 355}, year = {2013}, abstract = {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.}, language = {en} } @article{Enders2016, author = {Enders, Peter}, title = {Historical Prospective: Boltzmann's versus Planck's State Counting—Why Boltzmann Did Not Arrive at Planck's Distribution Law}, series = {Journal of Thermodynamics}, volume = {2016}, journal = {Journal of Thermodynamics}, issn = {1687-9252}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6281}, pages = {13}, year = {2016}, abstract = {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.}, language = {en} } @article{BelinskyRinkCaietal.2015, author = {Belinsky, Martin G. and Rink, Lori and Cai, Kathy Q. and Capuzzi, Stephen J. and Hoang, Yen and Chien, Jeremy and Godwin, Andrew K. and von Mehren, Margaret}, title = {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}, series = {BMC Cancer}, volume = {15}, journal = {BMC Cancer}, number = {887}, issn = {1471-2407}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6292}, year = {2015}, abstract = {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.}, language = {en} } @article{MunchelHoangYueetal.2015, author = {Munchel, Sarah and Hoang, Yen and Yue, Zhao and Cottrell, Joseph and Klotzle, Brandy and Godwin, Andrew K. and Koestler, Devin and Beyerlein, Peter and Fan, Jian-Bing and Bibikova, Marina and Chien, Jeremy}, title = {Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics}, series = {Oncotarget}, volume = {6}, journal = {Oncotarget}, number = {28}, issn = {1949-2553}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6307}, pages = {25943 -- 25961}, year = {2015}, abstract = {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.}, language = {en} } @article{GrawMeierMinnetal.2015, author = {Graw, Stefan and Meier, Richard and Minn, Kay and Bloomer, Clark and Godwin, Andrew K. and Fridley, Brooke and Vlad, Anda and Beyerlein, Peter and Chien, Jeremy}, title = {Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples}, series = {Scientific Reports}, volume = {5}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6319}, pages = {11}, year = {2015}, abstract = {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.}, language = {en} } @article{KipkorirMuhohoMuliroetal.2015, author = {Kipkorir, R. and Muhoho, S. and Muliro, P. and Mugendi, Beatrice and Frohme, Marcus and Br{\"o}del, Oliver}, title = {Effects of Coffee Processing Technologies on Aroma Profiles and Sensory Quality of Ruiru 11 and SL 28 Kenyan Coffee Varieties}, series = {Asian Journal of Agriculture and Food Sciences}, volume = {3}, journal = {Asian Journal of Agriculture and Food Sciences}, number = {2}, issn = {2321-1571}, doi = {10.15771/2321-1571_2015_1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6482}, pages = {178 -- 188}, year = {2015}, abstract = {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.}, language = {en} } @article{WegerichTuranoAllegrozzietal.2009, author = {Wegerich, F. and Turano, Paola and Allegrozzi, Marco and M{\"o}hwald, H. and Lisdat, Fred}, title = {Superoxide Biosensing with Engineered Cytochrome c}, series = {Procedia Chemistry}, volume = {1}, journal = {Procedia Chemistry}, number = {1}, issn = {1876-6196}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6523}, pages = {1287 -- 1290}, year = {2009}, abstract = {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.}, language = {en} } @article{HaiderAschauerSchmidt2014, author = {Haider, Christian and Aschauer, Gerald J. and Schmidt, Conrad}, title = {IT Based Attempt to Evaluate and Promote Intermodal Transport Solutions in Central and Southeast Europe}, series = {Transportation Research Procedia}, volume = {3}, journal = {Transportation Research Procedia}, issn = {2352-1465}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6535}, pages = {641 -- 650}, year = {2014}, abstract = {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.}, language = {en} } @article{KaltdorfSchulzeHelmprobstetal.2017, author = {Kaltdorf, Kristin Verena and Schulze, Katja and Helmprobst, Frederik and Kollmannsberger, Philip and Dandekar, Thomas and Stigloher, Christian}, title = {FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms}, series = {PLoS Computational Biology}, volume = {13}, journal = {PLoS Computational Biology}, number = {1}, issn = {1553-7358}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9218}, year = {2017}, abstract = {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.}, language = {en} } @article{SchulzeWehrholdHille2018, author = {Schulze, Sven and Wehrhold, Michel and Hille, Carsten}, title = {Femtosecond-Pulsed Laser Written and Etched Fiber Bragg Gratings for Fiber-Optical Biosensing}, series = {Sensors}, volume = {18}, journal = {Sensors}, number = {9}, issn = {1424-8220}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10570}, pages = {1 -- 20}, year = {2018}, abstract = {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.}, language = {en} } @article{BruunLoehmannsroebenHille2024, author = {Bruun, Kristina and L{\"o}hmannsr{\"o}ben, Hans-Gerd and Hille, Carsten}, title = {Benefits of Combined Fluorescence Lifetime Imaging Microscopy and Fluorescence Correlation Spectroscopy for Biomedical Studies Demonstrated by Using a Liposome Model System}, series = {Biophysica}, volume = {4}, journal = {Biophysica}, number = {2}, publisher = {MDPI}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19189}, pages = {207 -- 227}, year = {2024}, abstract = {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.}, language = {en} } @article{ZhangSampathkumarKerberetal.2020, author = {Zhang, Youjun and Sampathkumar, Arun and Kerber, Sandra Mae-Lin and Swart, Corn{\´e} and Hille, Carsten and Seerangan, Kumar and Graf, Alexander and Sweetlove, Lee and Fernie, Alisdair R.}, title = {A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts}, series = {Nature Communications}, volume = {11}, journal = {Nature Communications}, issn = {2041-1723}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14812}, pages = {4509}, year = {2020}, abstract = {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.}, language = {en} } @article{BruunHille2019, author = {Bruun, Kristina and Hille, Carsten}, title = {Study on intracellular delivery of liposome encapsulated quantum dots using advanced fluorescence microscopy}, series = {Scientific Reports}, volume = {9}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12476}, pages = {10504}, year = {2019}, abstract = {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.}, language = {en} } @article{GuentherKlaussToroNahuelpanetal.2019, author = {G{\"u}nther, Erika and Klauß, Andr{\´e} and Toro-Nahuelpan, Mauricio and Sch{\"u}ler, Dirk and Hille, Carsten and Faivre, Damien}, title = {The in vivo mechanics of the magnetotactic backbone as revealed by correlative FLIM-FRET and STED microscopy}, series = {Scientific Reports}, volume = {9}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14802}, year = {2019}, abstract = {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 F{\"o}rster 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.}, language = {en} } @article{PraiaHerkenhoffBroedeletal.2022, author = {Praia, Ana Beatriz and Herkenhoff, Marcos Edgar and Br{\"o}del, Oliver and Frohme, Marcus and Saad, Susana Marta Isay}, title = {Sour Beer with Lacticaseibacillus paracasei subsp. paracasei F19: Feasibility and Influence of Supplementation with Spondias mombin L. Juice and/or By-Product}, series = {Foods}, volume = {11}, journal = {Foods}, number = {24}, publisher = {MDPI}, issn = {2304-8158}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16852}, year = {2022}, abstract = {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. ('tapereb{\´a}' or 'caj{\´a}') 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.}, language = {en} } @article{RadivoievychKolpGrebinyketal.2023, author = {Radivoievych, Aleksandar and Kolp, Benjamin and Grebinyk, Sergii and Prylutska, Svitlana and Ritter, Uwe and Zolk, Oliver and Gl{\"o}kler, J{\"o}rn and Frohme, Marcus and Grebinyk, Anna}, title = {Silent Death by Sound: C60 Fullerene Sonodynamic Treatment of Cancer Cells}, series = {International Journal of Molecular Sciences}, volume = {24}, journal = {International Journal of Molecular Sciences}, number = {2}, publisher = {MDPI}, issn = {1422-0067}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16877}, year = {2023}, abstract = {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.}, language = {en} } @article{RykovaStiebenDostovalovaetal.2023, author = {Rykova, Eugenia and Stieben, Christine and Dostovalova, Olga and Wieker, Horst}, title = {Connected Driving in German-Speaking Social Media}, series = {Social Sciences}, volume = {12}, journal = {Social Sciences}, number = {1}, publisher = {MDPI}, issn = {2076-0760}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16969}, year = {2023}, abstract = {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.}, language = {en} } @article{VillringerSteglichPulweretal.2021, author = {Villringer, Claus and Steglich, Patrick and Pulwer, Silvio and Schrader, Sigurd and Laufer, Jan}, title = {Electro-optical properties of doped polymers with high transparency in the visible wavelength range}, series = {Optical Materials Express}, volume = {11}, journal = {Optical Materials Express}, number = {11}, publisher = {Optica Publishing Group}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15480}, pages = {3801 -- 3811}, year = {2021}, abstract = {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-P{\´e}rot 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.}, language = {en} } @article{RoosHoqueKlimešovaetal.2023, author = {Roos, Andreas Hult and Hoque, Ziaul and Klimešov{\´a}, Eva and Ben Ltaief, Ltaief and Medina, Cristian and Jurkovič, Matej and Albrecht, Martin and Finke, Ondřej and Hort, Ondřej and Nejdl, Jaroslav and Mudrich, Marcel and Andreasson, Jakob and Krikunova, Maria}, title = {Electron correlation dynamics in atomic Kr excited by XUV pulses and controlled by NIR laser pulses of variable intensity}, series = {New Journal of Physics}, volume = {25}, journal = {New Journal of Physics}, publisher = {Institute of Physics Publishing (IOP)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16987}, year = {2023}, abstract = {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.}, language = {en} } @article{KoenigKiffnerKuhlsetal.2023, author = {K{\"o}nig, Hannes J. and Kiffner, Christian and Kuhls, Katrin and Uthes, Sandra and Harms, Verena and Wieland, Ralf}, title = {Planning for wolf-livestock coexistence: landscape context predicts livestock depredation risk in agricultural landscapes}, series = {animal}, volume = {17}, journal = {animal}, number = {3}, publisher = {Elsevier}, issn = {1751-7311}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17032}, year = {2023}, abstract = {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.}, language = {en} } @article{FalkElGhayedvandeSandetal.2023, author = {Falk, Constantin and El Ghayed, Tarek and van de Sand, Ron and Reiff-Stephan, J{\"o}rg}, title = {A Data-Driven Approach Towards the Application of Reinforcement Learning Based HVAC Control}, series = {Journal of the Nigerian Society of Physical Sciences}, volume = {5}, journal = {Journal of the Nigerian Society of Physical Sciences}, number = {1}, publisher = {Department of Physics, Federal University Lafia Nasarawa State, Nigeria ; Nigerian Society of Physical Sciences}, issn = {2714-4704}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17066}, year = {2023}, abstract = {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.}, language = {en} } @article{AlekseevaNechyporenkoFrohmeetal.2023, author = {Alekseeva, Victoriia and Nechyporenko, Alina and Frohme, Marcus and Gargin, Vitaliy and Meniailov, Ievgen and Chumachenko, Dmytro}, title = {Intelligent Decision Support System for Differential Diagnosis of Chronic Odontogenic Rhinosinusitis Based on U-Net Segmentation}, series = {Electronics}, volume = {12}, journal = {Electronics}, number = {5}, publisher = {MDPI}, issn = {2079-9292}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17088}, year = {2023}, abstract = {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.}, language = {en} } @article{HenningWagnerGedatetal.2023, author = {Henning, Thorsten and Wagner, Philipp and Gedat, Egbert and Kochlik, Bastian and Kusch, Paula and Sowoidnich, Kay and Vastag, Marko and Gleim, Jeannine and Braune, Marcel and Maiwald, Martin and Sumpf, Bernd and Grune, Tilman and Weber, Daniela}, title = {Evaluation of Modern Approaches for the Assessment of Dietary Carotenoids as Markers for Fruit and Vegetable Consumption}, series = {Nutrients}, volume = {15}, journal = {Nutrients}, number = {7}, publisher = {MDPI}, issn = {2072-6643}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17280}, year = {2023}, abstract = {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.}, language = {en} } @article{LangenbergMaErmakovaetal.2023, author = {Langenberg, Anna and Ma, Shih-Chi and Ermakova, Tatiana and Fabian, Benjamin}, title = {Formal Group Fairness and Accuracy in Automated Decision Making}, series = {Mathematics}, volume = {11}, journal = {Mathematics}, number = {8}, publisher = {MDPI}, issn = {2227-7390}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17323}, year = {2023}, abstract = {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.}, language = {en} } @article{ChumachenkoButkevychLodeetal.2022, author = {Chumachenko, Dmytro and Butkevych, Mykola and Lode, Daniel and Frohme, Marcus and Schmailzl, Kurt J. G. and Nechyporenko, Alina}, title = {Machine Learning Methods in Predicting Patients with Suspected Myocardial Infarction Based on Short-Time HRV Data}, series = {Sensors}, volume = {22}, journal = {Sensors}, number = {18}, publisher = {MDPI}, issn = {1424-8220}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16521}, year = {2022}, abstract = {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.}, language = {en} } @article{MaiMaiSteglich2022, author = {Mai, Andreas and Mai, Christian and Steglich, Patrick}, title = {From Lab-on-chip to Lab-in-App: Challenges towards silicon photonic biosensors product developments}, series = {Results in Optics}, volume = {9}, journal = {Results in Optics}, publisher = {Elsevier}, issn = {2666-9501}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16687}, year = {2022}, abstract = {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.}, language = {en} } @article{GrebinykPrylutskaGrebinyketal.2022, author = {Grebinyk, Anna and Prylutska, Svitlana and Grebinyk, Sergii and Ponomarenko, Stanislav and Virych, Pavlo and Chumachenko, Vasyl and Kutsevol, Nataliya and Prylutskyy, Yuriy and Ritter, Uwe and Frohme, Marcus}, title = {Drug delivery with a pH-sensitive star-like dextran-graft polyacrylamide copolymer}, series = {Nanoscale Advances}, volume = {4}, journal = {Nanoscale Advances}, number = {23}, publisher = {Royal Society of Chemistry (RSC)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16749}, pages = {5077 -- 5088}, year = {2022}, abstract = {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.}, language = {en} } @article{HagenYoonZhangetal.2022, author = {Hagen, Dirk J. and Yoon, Jiho and Zhang, Haojie and Kalkofen, Bodo and Silinskas, Mindaugas and B{\"o}rrnert, Felix and Han, Hyeon and Parkin, Stuart S. P.}, title = {Atomic Layer Deposition of the Conductive Delafossite PtCoO2}, series = {Advanced Materials Interfaces}, volume = {9}, journal = {Advanced Materials Interfaces}, number = {12}, publisher = {Wiley}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16076}, year = {2022}, abstract = {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.}, language = {en} } @article{SteglichSchasfoort2022, author = {Steglich, Patrick and Schasfoort, Richard B. M.}, title = {Surface Plasmon Resonance Imaging (SPRi) and Photonic Integrated Circuits (PIC) for COVID-19 Severity Monitoring}, series = {COVID}, volume = {2}, journal = {COVID}, number = {3}, publisher = {MDPI}, issn = {2673-8112}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16004}, pages = {389 -- 397}, year = {2022}, abstract = {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.}, language = {en} } @article{SteglichLecciMai2022, author = {Steglich, Patrick and Lecci, Giulia and Mai, Andreas}, title = {Surface Plasmon Resonance (SPR) Spectroscopy and Photonic Integrated Circuit (PIC) Biosensors: A Comparative Review}, series = {Sensors}, volume = {22}, journal = {Sensors}, number = {8}, publisher = {MDPI}, issn = {1424-8220}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16018}, year = {2022}, abstract = {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.}, language = {en} } @article{LindnerLiebchen2022, author = {Lindner, Niels and Liebchen, Christian}, title = {Timetable merging for the Periodic Event Scheduling Problem}, series = {EURO Journal on Transportation and Logistics}, volume = {11}, journal = {EURO Journal on Transportation and Logistics}, publisher = {Elsevier}, issn = {2192-4376}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16054}, year = {2022}, abstract = {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.}, language = {en} } @article{DeRocchisRoitschFranken2022, author = {De Rocchis, Vincenzo and Roitsch, Thomas and Franken, Philipp}, title = {Extracellular Glycolytic Activities in Root Endophytic Serendipitaceae and Their Regulation by Plant Sugars}, series = {Microorganisms}, volume = {10}, journal = {Microorganisms}, number = {2}, editor = {Strobel, Gary A.}, publisher = {MDPI}, issn = {2076-2607}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15774}, year = {2022}, abstract = {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.}, language = {en} } @article{PfeilNechyporenkoFrohmeetal.2022, author = {Pfeil, Juliane and Nechyporenko, Alina and Frohme, Marcus and Hufert, Frank T. and Schulze, Katja}, title = {Examination of blood samples using deep learning and mobile microscopy}, series = {BMC Bioinformatics}, volume = {23}, journal = {BMC Bioinformatics}, publisher = {BioMed Central}, issn = {1471-2105}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15802}, year = {2022}, abstract = {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.}, language = {en} } @article{BauerFursenkoHeinrichetal.2022, author = {Bauer, Joachim and Fursenko, Oksana and Heinrich, Friedhelm and Gutke, Marko and Kornejew, Eckhart and Br{\"o}del, Oliver and Dietzel, Birgit and Kaltenbach, Alexander and Burkhardt, Martin and Edling, Matthias and Steglich, Patrick and Herzog, Michael and Schrader, Sigurd}, title = {Determination of optical constants and scattering properties of transparent polymers for use in optoelectronics}, series = {Optical Materials Express}, volume = {12}, journal = {Optical Materials Express}, number = {1}, publisher = {Optica Publishing Group}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15666}, pages = {204 -- 224}, year = {2022}, abstract = {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\&\#x0027;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.}, language = {en} } @article{DrostMarschmeyerFraschkeetal.2022, author = {Drost, Martin and Marschmeyer, Steffen and Fraschke, Mirko and Fursenko, Oksana and B{\"a}rwolf, Florian and Costina, Ioan and Kalishettyhalli Mahadevaiah, Mamathamba and Lisker, Marco}, title = {Etch mechanism of an Al₂O₃ hard mask in the Bosch process}, series = {Micro and Nano Engineering}, volume = {14}, journal = {Micro and Nano Engineering}, publisher = {Elsevier}, issn = {2590-0072}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15678}, year = {2022}, abstract = {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.}, language = {en} } @article{HeinsohnNiedlAnielskietal.2022, author = {Heinsohn, Natascha Katharina and Niedl, Robert Raimund and Anielski, Alexander and Lisdat, Fred and Beta, Carsten}, title = {Electrophoretic µPAD for Purification and Analysis of DNA Samples}, series = {Biosensors}, volume = {12}, journal = {Biosensors}, number = {2}, publisher = {MDPI}, issn = {2079-6374}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15763}, year = {2022}, abstract = {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.}, language = {en} } @article{KirchnerVillringerLaufer2023, author = {Kirchner, Thomas and Villringer, Claus and Laufer, Jan}, title = {Evaluation of ultrasound sensors for transcranial photoacoustic sensing and imaging}, series = {Photoacoustics}, volume = {33}, journal = {Photoacoustics}, publisher = {Elsevier}, issn = {2213-5979}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17993}, year = {2023}, abstract = {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.}, language = {en} } @article{D'EliaTruuLahtietal.2023, author = {D'Elia, Domenica and Truu, Jaak and Lahti, Leo and Berland, Magali and Papoutsoglou, Georgios and Ceci, Michelangelo and Zomer, Aldert and Lopes, Marta B. and Ibrahimi, Eliana and Gruca, Aleksandra and Nechyporenko, Alina and Frohme, Marcus and Klammsteiner, Thomas and Carrillo de Santa Pau, Enrique and Marcos-Zambrano, Laura Judith and Hron, Karel and Pio, Gianvito and Simeon, Andrea and Suharoschi, Ramona and Moreno-Indias, Isabel and Temko, Andriy and Nedyalkova, Miroslava and Apostol, Elena-Simona and Truică, Ciprian-Octavian and Shigdel, Rajesh and Telalović, Jasminka Hasić and Bongcam-Rudloff, Erik and Przymus, Piotr and Jordamović, Naida Babić and Falquet, Laurent and Tarazona, Sonia and Sampri, Alexia and Isola, Gaetano and P{\´e}rez-Serrano, David and Trajkovik, Vladimir and Klucar, Lubos and Loncar-Turukalo, Tatjana and Havulinna, Aki S. and Jansen, Christian and Bertelsen, Randi J. and Claesson, Marcus Joakim}, title = {Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action}, series = {Frontiers in Microbiology}, volume = {14}, journal = {Frontiers in Microbiology}, publisher = {Frontiers}, issn = {1664-302X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18004}, year = {2023}, abstract = {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.}, language = {en} } @inproceedings{MasingLindnerLiebchen2023, author = {Masing, Berenike and Lindner, Niels and Liebchen, Christian}, title = {Integrating Line Planning for Construction Sites into Periodic Timetabling via Track Choice}, series = {23rd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2023)}, volume = {115}, booktitle = {23rd Symposium on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2023)}, isbn = {978-3-95977-302-7}, issn = {2190-6807}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17916}, pages = {5:1 -- 5:15}, year = {2023}, abstract = {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.}, language = {en} } @article{LoosGroeplerGoudeau2023, author = {Loos, Eug{\`e}ne and Gr{\"o}pler, Johanna and Goudeau, Marie-Louise Sophie}, title = {Using ChatGPT in Education: Human Reflection on ChatGPT's Self-Reflection}, series = {Societies}, volume = {13}, journal = {Societies}, number = {8}, publisher = {MDPI}, issn = {2075-4698}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17966}, year = {2023}, abstract = {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.}, language = {en} } @article{WalterKubicaRocco2023, author = {Walter, Andreas and Kubica, Stefan and Rocco, Vittorio}, title = {Optimized fuel values for emission reduction}, series = {IOP Conference Series: Earth and Environmental Science}, volume = {1254}, journal = {IOP Conference Series: Earth and Environmental Science}, publisher = {Institute of Physics Publishing (IOP)}, issn = {1755-1315}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18148}, year = {2023}, abstract = {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.}, language = {en} } @article{RadivoievychPrylutskaZolketal.2023, author = {Radivoievych, Aleksandar and Prylutska, Svitlana and Zolk, Oliver and Ritter, Uwe and Frohme, Marcus and Grebinyk, Anna}, title = {Comparison of Sonodynamic Treatment Set-Ups for Cancer Cells with Organic Sonosensitizers and Nanosonosensitizers}, series = {Pharmaceutics}, volume = {15}, journal = {Pharmaceutics}, number = {11}, publisher = {MDPI}, issn = {1999-4923}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18223}, year = {2023}, abstract = {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.}, language = {en} } @article{JurkovičovaBenLtaiefRoosetal.2024, author = {Jurkovičov{\´a}, Lucie and Ben Ltaief, Ltaief and Roos, Andreas Hult and Hort, Ondřej and Finke, Ondřej and Albrecht, Martin and Hoque, Ziaul and Klimešov{\´a}, Eva and Sundaralingam, Akgash and Antipenkov, Roman and Grenfell, Annika and Špaček, Alexandr and Szuba, Wojciech and Krikunova, Maria and Mudrich, Marcel and Nejdl, Jaroslav and Andreasson, Jakob}, title = {Bright continuously tunable vacuum ultraviolet source for ultrafast spectroscopy}, series = {Communications Physics}, volume = {7}, journal = {Communications Physics}, publisher = {Nature Publishing Group}, issn = {2399-3650}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18462}, year = {2024}, abstract = {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.}, language = {en} } @article{MedinaLagdsmandBenLtaiefetal.2023, author = {Medina, Cristian and L{\ae}gdsmand, Asbj{\o}rn {\O}rnemark and Ben Ltaief, Ltaief and Hoque, Ziaul and Roos, Andreas Hult and Jurkovičov{\´a}, Lucie and Hort, Ondřej and Finke, Ondřej and Albrecht, Martin and Nejdl, Jaroslav and Stienkemeier, Frank and Andreasson, Jakob and Klimešov{\´a}, Eva and Krikunova, Maria and Heidenreich, Andreas and Mudrich, Marcel}, title = {Long-lasting XUV activation of helium nanodroplets for avalanche ionization}, series = {New Journal of Physics}, volume = {25}, journal = {New Journal of Physics}, publisher = {Institute of Physics (IOP)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17701}, year = {2023}, abstract = {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.}, language = {en} } @article{SchillingBeyerleinChien2023, author = {Schilling, Vincent and Beyerlein, Peter and Chien, Jeremy}, title = {A Bioinformatics Analysis of Ovarian Cancer Data Using Machine Learning}, series = {Algorithms}, volume = {16}, journal = {Algorithms}, number = {7}, publisher = {MDPI}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17751}, year = {2023}, abstract = {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.}, language = {en} } @article{PrylutskaGrebinykPonomarenkoetal.2024, author = {Prylutska, Svitlana and Grebinyk, Anna and Ponomarenko, Stanislav and G{\"o}vem, Defne and Chumachenko, Vasyl and Kutsevol, Nataliya and Petrovsky, Mykola and Ritter, Uwe and Frohme, Marcus and Piosik, Jacek and Prylutskyy, Yuriy}, title = {Toxicity of Water-Soluble D-g-PNIPAM Polymers in a Complex with Chemotherapy Drugs and Mechanism of Their Action In Vitro}, series = {International Journal of Molecular Sciences}, volume = {25}, journal = {International Journal of Molecular Sciences}, number = {5}, publisher = {MDPI}, issn = {1422-0067}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18790}, year = {2024}, abstract = {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.}, language = {en} } @article{FernholzErmakovaFabianetal.2024, author = {Fernholz, Yannick and Ermakova, Tatiana and Fabian, Benjamin and Buxmann, Peter}, title = {User-driven prioritization of ethical principles for artificial intelligence systems}, series = {Computers in Human Behavior: Artificial Humans}, volume = {2}, journal = {Computers in Human Behavior: Artificial Humans}, number = {1}, publisher = {Elsevier}, issn = {2949-8821}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18509}, year = {2024}, abstract = {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.}, language = {en} } @article{GrytsenkoKolomzarovLytvynetal.2023, author = {Grytsenko, Kostyantyn and Kolomzarov, Yurii and Lytvyn, Peter and Kondratenko, Olga and Sopinskyy, Mykola and Lebedyeva, Iryna and Niemczyk, Agata and Baranowska, Jolanta and Moszyński, Dariusz and Villringer, Claus and Schrader, Sigurd}, title = {Optical and Mechanical Properties of Thin PTFE Films, Deposited from a Gas Phase}, series = {Macromolecular Materials and Engineering}, volume = {308}, journal = {Macromolecular Materials and Engineering}, number = {6}, publisher = {Wiley}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17587}, year = {2023}, abstract = {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.}, language = {en} } @article{DhimanMiteffWangetal.2024, author = {Dhiman, Rachit and Miteff, Sofia and Wang, Yuancheng and Ma, Shih-Chi and Amirikas, Ramila and Fabian, Benjamin}, title = {Artificial Intelligence and Sustainability—A Review}, series = {Analytics}, volume = {3}, journal = {Analytics}, number = {1}, publisher = {MDPI}, issn = {2813-2203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18651}, pages = {140 -- 164}, year = {2024}, abstract = {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.}, language = {en} } @article{GavrylenkoPoltoratskyiNechyporenko2024, author = {Gavrylenko, Svitlana and Poltoratskyi, Vadym and Nechyporenko, Alina}, title = {Intrusion Detection Model Based on Improved Transformer}, series = {Advanced Information Systems}, volume = {8}, journal = {Advanced Information Systems}, number = {1}, publisher = {National Technical University Kharkiv Polytechnic Institute}, issn = {2522-9052}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18750}, pages = {94 -- 99}, year = {2024}, abstract = {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.}, language = {en} } @article{RadivoievychSchnepelPrylutskaetal.2024, author = {Radivoievych, Aleksandar and Schnepel, Sophia and Prylutska, Svitlana and Ritter, Uwe and Zolk, Oliver and Frohme, Marcus and Grebinyk, Anna}, title = {From 2D to 3D In Vitro World: Sonodynamically-Induced Prooxidant Proapoptotic Effects of C60-Berberine Nanocomplex on Cancer Cells}, series = {Cancers}, volume = {16}, journal = {Cancers}, number = {18}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19438}, year = {2024}, abstract = {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.}, language = {en} } @article{NechyporenkoFrohmeStrelchuketal.2024, author = {Nechyporenko, Alina and Frohme, Marcus and Strelchuk, Yaroslav and Omelchenko, Vladyslav and Gargin, Vitaliy and Ishchenko, Liudmyla and Alekseeva, Victoriia}, title = {Galvanic Skin Response and Photoplethysmography for Stress Recognition Using Machine Learning and Wearable Sensors}, series = {Applied Sciences}, volume = {14}, journal = {Applied Sciences}, number = {24}, publisher = {MDPI}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19803}, year = {2024}, abstract = {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.}, language = {en} } @article{KlimesovaKulykMartinetal.2025, author = {Klimesova, Eva and Kulyk, Olena and Martin, Lucas Janos and Sch{\"u}tte, Bernd and Fr{\"u}hling, Ulrike and Drescher, Markus and Pan, Rui and Stojanovic, Nikola and Bermudez Macias, Ivette J. and D{\"u}sterer, Stefan and Andreasson, Jakob and Wieland, Marek and Krikunova, Maria}, title = {Electron thermalization and ion acceleration in XUV-produced plasma from nanoparticles in He gas environment}, series = {New Journal of Physics}, volume = {27}, journal = {New Journal of Physics}, publisher = {Institute of Physics Publishing (IOP); Deutsche Physikalische Gesellschaft}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19818}, year = {2025}, abstract = {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.}, language = {en} } @article{NechyporenkoNazaryanSemkoetal.2021, author = {Nechyporenko, Alina and Nazaryan, Rosana and Semko, Galyna and Lupyr, Andrii and Yurevych, Nadiia and Fomenko, Yuliia and Kostiukov, Eduard and Alekseeva, Victoriia}, title = {Application of spiral computed tomography for determination of the minimal bone density variability of the maxillary sinus walls in chronic odontogenic and rhinogenic sinusitis}, series = {Ukrainian Journal of Radiology and Oncology}, volume = {29}, journal = {Ukrainian Journal of Radiology and Oncology}, number = {4}, issn = {2708-7166}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19121}, pages = {65 -- 75}, year = {2021}, abstract = {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.}, language = {en} } @article{DreyerMotocKoehleretal.2023, author = {Dreyer, Christian and Motoc, Dana Luca and Koehler, Mathias and Goldenberg, Leonid}, title = {UV LED Curable Perfluoropolyether (PFPE)-Urethane Methacrylate Transparent Coatings for Photonic Applications: Synthesis and Characterization}, series = {Polymers}, volume = {15}, journal = {Polymers}, number = {14}, publisher = {MDPI}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19139}, pages = {1}, year = {2023}, abstract = {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.}, language = {en} } @article{FuenningPaulManganellietal.2025, author = {F{\"u}nning, Tabea and Paul, Martin and Manganelli, Costanza Lucia and Wenger, Christian and Mai, Andreas and Steglich, Patrick}, title = {Comparative simulation analysis of photonic ultrasound sensors based on silicon waveguides}, series = {Scientific Reports}, volume = {15}, journal = {Scientific Reports}, publisher = {Springer Nature}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20560}, year = {2025}, abstract = {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.}, language = {en} } @article{Seeliger2013, author = {Seeliger, Frank}, title = {Betriebliche Einstiegsqualifizierung als zweite Chance}, series = {BuB : Forum f{\"u}r Bibliothek und Information}, volume = {65}, journal = {BuB : Forum f{\"u}r Bibliothek und Information}, number = {3}, issn = {0340-0301}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9608}, pages = {182 -- 183}, year = {2013}, abstract = {Die Ausbildung zum Fachangestellten f{\"u}r Medien und Informationsdienste (FaMI) in der Fachrichtung Bibliothek ist sehr anspruchsvoll und verlangt einiges von den Jugendlichen ab. Daher gilt in der Wildauer Hochschulbibliothek f{\"u}r Lehrlinge der gleiche Grundsatz wie f{\"u}r Studierende: Scheitern ist erlaubt - was sich in der bislang zehnj{\"a}hrigen Erfahrung als Ausbildungsbetrieb allerdings nur einmal bewahrheitet hat.}, language = {de} } @article{GrytsenkoSchraderDetert2014, author = {Grytsenko, Kostyantyn and Schrader, Sigurd and Detert, Heiner}, title = {Ultra-stable dye-filled polytetrafluoroethylene thin films}, series = {Nanoscience \& Technology: Open Access}, volume = {1}, journal = {Nanoscience \& Technology: Open Access}, number = {2}, issn = {2374-8141}, doi = {10.15771/2374-8141_2014_1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5947}, pages = {5}, year = {2014}, abstract = {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.}, language = {en} } @article{RadkeSandigLubitzetal.2017, author = {Radke, Lars and Sandig, Grit and Lubitz, Annika and Schließer, Ulrike and von Horsten, Hans Henning and Blanchard, V{\´e}ronique and Keil, Karolin and Sandig, Volker and Giese, Christoph and Hummel, Michael and Hinderlich, Stephan and Frohme, Marcus}, title = {In Vitro Evaluation of Glycoengineered RSV-F in the Human Artificial Lymph Node Reactor}, series = {Bioengineering}, volume = {4}, journal = {Bioengineering}, number = {3}, issn = {2306-5354}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9831}, year = {2017}, abstract = {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.}, language = {en} } @article{SandigvonHorstenRadkeetal.2017, author = {Sandig, Grit and von Horsten, Hans Henning and Radke, Lars and Blanchard, V{\´e}ronique and Frohme, Marcus and Giese, Christoph and Sandig, Volker and Hinderlich, Stephan}, title = {Engineering of CHO Cells for the Production of Recombinant Glycoprotein Vaccines with Xylosylated N-glycans}, series = {Bioengineering}, volume = {4}, journal = {Bioengineering}, number = {2}, issn = {2306-5354}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9620}, year = {2017}, abstract = {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.}, language = {en} } @article{LukoseLiskerAkhtaretal.2021, author = {Lukose, Rasuole and Lisker, Marco and Akhtar, Fatima and Fraschke, Mirko and Grabolla, T. and Mai, Andreas and Lukosius, Mindaugas}, title = {Influence of plasma treatment on SiO2/Si and Si3N4/Si substrates for large-scale transfer of graphene}, series = {Scientific Reports}, volume = {11}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14179}, year = {2021}, abstract = {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.}, language = {en} } @article{ElvirettiLiskerLukoseetal.2022, author = {Elviretti, M. and Lisker, Marco and Lukose, Rasuole and Lukosius, Mindaugas and Akhtar, Fatima and Mai, Andreas}, title = {Reliable metal-graphene contact formation process flows in a CMOS-compatible environment}, series = {Nanoscale Advances}, volume = {4}, journal = {Nanoscale Advances}, publisher = {Royal Society of Chemistry (RSC)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16581}, pages = {4373 -- 4380}, year = {2022}, abstract = {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.}, language = {en} } @article{BauerGutkeHeinrichetal.2020, author = {Bauer, Joachim and Gutke, Marko and Heinrich, Friedhelm and Edling, Matthias and Stoycheva, Vesela and Kaltenbach, Alexander and Burkhardt, Martin and Gruenefeld, Martin and Gamp, Matthias and Gerhard, Christoph and Steglich, Patrick and Steffen, Sebastian and Herzog, Michael and Dreyer, Christian and Schrader, Sigurd}, title = {Novel UV-transparent 2-component polyurethane resin for chip-on-board LED micro lenses}, series = {Optical Materials Express}, volume = {10}, journal = {Optical Materials Express}, number = {9}, issn = {2159-3930}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13472}, pages = {2085 -- 2099}, year = {2020}, abstract = {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.}, language = {en} } @article{KrauseStoyeVingron2005, author = {Krause, Antje and Stoye, Jens and Vingron, Martin}, title = {Large scale hierarchical clustering of protein sequences}, series = {BMC Bioinformatics}, journal = {BMC Bioinformatics}, publisher = {BioMed Central}, issn = {1471-2105}, doi = {10.15771/1471-2105_2005_6_15}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus-153}, year = {2005}, abstract = {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.}, language = {en} } @book{Karp2023, author = {Karp, Markus}, title = {Homo remotus - Kritik zur F{\"u}hrung auf Distanz}, publisher = {KOMPAKT MEDIA}, address = {Magdeburg}, doi = {10.15771/1736}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17368}, publisher = {Technische Hochschule Wildau}, pages = {100}, year = {2023}, abstract = {Wie sich die Welt um uns herum ver{\"a}ndert, nehmen wir wohl so wahr, als w{\"u}rde 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 verh{\"a}lt, umso mehr wirkt das Gruppenverhalten als Entwicklungstendenz. Die technisch vernetzte Welt dr{\"a}ngt seit {\"u}ber 20 Jahren in unseren Lebens- und Arbeitsalltag vor. Die fast drei Jahre andauernde Corona- Pandemie hat unter Druck von Kontaktbeschr{\"a}nkungen die Nutzung der technischen M{\"o}glichkeiten beschleunigt und damit Arbeitsflexibilit{\"a}t und -mobilit{\"a}t 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.}, language = {de} } @unpublished{HollmannKremerBaebleretal.2020, author = {Hollmann, Susanne and Kremer, Andreas and Baebler, Špela and Trefois, Christophe and Gruden, Kristina and Rudnicki, Witold R. and Tong, Weida and Gruca, Aleksandra and Bongcam-Rudloff, Erik and Evelo, Chris T. and Nechyporenko, Alina and Frohme, Marcus and Šafr{\´a}nek, David and Regierer, Babette and D'Elia, Domenica}, title = {The need for standardisation in life science research - an approach to excellence and trust. [version 1; peer review: 3 approved]}, series = {F1000Research}, volume = {9}, journal = {F1000Research}, issn = {2046-1402}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13891}, year = {2020}, abstract = {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.}, language = {en} }