@article{GrebinykPrylutskaChepurnaetal.2019, author = {Grebinyk, Anna and Prylutska, Svitlana and Chepurna, Oksana and Grebinyk, Sergii and Prylutskyy, Yuriy and Ritter, Uwe and Ohulchanskyy, Tymish Y. and Matyshevska, Olga and Dandekar, Thomas and Frohme, Marcus}, title = {Synergy of Chemo- and Photodynamic Therapies with C60 Fullerene-Doxorubicin Nanocomplex}, series = {Nanomaterials}, volume = {9}, journal = {Nanomaterials}, number = {11}, publisher = {MDPI}, issn = {2079-4991}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12940}, year = {2019}, abstract = {A nanosized drug complex was explored to improve the efficiency of cancer chemotherapy, complementing it with nanodelivery and photodynamic therapy. For this, nanomolar amounts of a non-covalent nanocomplex of Doxorubicin (Dox) with carbon nanoparticle C60 fullerene (C60) were applied in 1:1 and 2:1 molar ratio, exploiting C60 both as a drug-carrier and as a photosensitizer. The fluorescence microscopy analysis of human leukemic CCRF-CEM cells, in vitro cancer model, treated with nanocomplexes showed Dox's nuclear and C60's extranuclear localization. It gave an opportunity to realize a double hit strategy against cancer cells based on Dox's antiproliferative activity and C60's photoinduced pro-oxidant activity. When cells were treated with 2:1 C60-Dox and irradiated at 405 nm the high cytotoxicity of photo-irradiated C60-Dox enabled a nanomolar concentration of Dox and C60 to efficiently kill cancer cells in vitro. The high pro-oxidant and pro-apoptotic efficiency decreased IC50 16, 9 and 7 × 103-fold, if compared with the action of Dox, non-irradiated nanocomplex, and C60's photodynamic effect, correspondingly. Hereafter, a strong synergy of therapy arising from the combination of C60-mediated Dox delivery and C60 photoexcitation was revealed. Our data indicate that a combination of chemo- and photodynamic therapies with C60-Dox nanoformulation provides a promising synergetic approach for cancer treatment.}, language = {en} } @article{LuxEdlingLuccietal.2019, author = {Lux, Helge and Edling, Matthias and Lucci, Massimiliano and Kitzmann, Julia and Villringer, Claus and Siemroth, Peter and De Matteis, Fabio and Schrader, Sigurd}, title = {The Role of Substrate Temperature and Magnetic Filtering for DLC by Cathodic Arc Evaporation}, series = {Coatings}, volume = {9}, journal = {Coatings}, number = {5}, issn = {2079-6412}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12295}, pages = {345}, year = {2019}, abstract = {Diamond-like carbon (DLC) films were deposited using two different types of high current arc evaporation. The first process used a magnetic particle filter to remove droplets from the plasma. For the second process, the samples were put into a metallic cage which was placed directly above the plasma source. For both processes, we varied the substrate temperature from 21 to 350 °C in order to investigate the temperature effect. The samples were characterized using SEM, AFM, XPS, Raman Spectroscopy, Ellipsometry, Photometry, and Nano Indentation in order to compare both methods of deposition and provide a careful characterization of such DLC films. We found that the sp3 content and the hardness can be precisely adjusted by changing the substrate temperature. Furthermore, in the case of unfiltered deposition, the optical constants can be shifted in the direction of higher absorbance in order to produce black and hard carbon coatings.}, language = {en} } @article{SteglichVillringerDietzeletal.2019, author = {Steglich, Patrick and Villringer, Claus and Dietzel, Birgit and Mai, Christian and Schrader, Sigurd and Casalboni, Mauro and Mai, Andreas}, title = {On-Chip Dispersion Measurement of the Quadratic Electro-Optic Effect in Nonlinear Optical Polymers Using a Photonic Integrated Circuit Technology}, series = {IEEE Photonics Journal}, volume = {11}, journal = {IEEE Photonics Journal}, number = {3}, issn = {1943-0655}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12307}, year = {2019}, abstract = {A novel method to determine the dispersion of the quadratic electro-optic effect in nonlinear optical materials by using a silicon-on-insulator microring resonator is presented. The microring consists of a silicon slot waveguide enabling large dc electric field strength at low applied voltages. The dispersion of third-order hyperpolarizability of a linear conjugated dye is approximated by using a two-level model for the off-resonant spectral region. As an example, the dispersion of the resonance wavelength of the resonator filled with a dye doped polymer was measured in dependence of the applied dc voltage. The polymer was poly (methylmethacrylate) doped with 5 wt\% disperse red 1 (DR1), and the measurements have been carried out at the telecommunication wavelength band around 1550 nm (optical C-band). The described measurements represent a new technique to determine the dispersion of the third-order susceptibility and molecular hyperpolarizability of the material filled into the slot of the ring-resonator.}, language = {en} } @article{MikayelyanGroddKsianzouetal.2019, author = {Mikayelyan, Eduard and Grodd, Linda and Ksianzou, Viachaslau and Wesner, Daniel and Rodygin, Alexander I. and Sch{\"o}nherr, Holger and Luponosov, Yuriy N. and Ponomarenko, Sergei A. and Ivanov, Dimitri A. and Pietsch, Ullrich and Grigorian, Souren}, title = {Phase Transitions and Formation of a Monolayer-Type Structure in Thin Oligothiophene Films: Exploration with a Combined In Situ X-ray Diffraction and Electrical Measurements}, series = {Nanoscale Research Letters}, volume = {14}, journal = {Nanoscale Research Letters}, issn = {1556-276X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12314}, year = {2019}, abstract = {A combination of in situ electrical and grazing-incidence X-ray diffraction (GIXD) is a powerful tool for studies of correlations between the microstructure and charge transport in thin organic films. The information provided by such experimental approach can help optimizing the performance of the films as active layers of organic electronic devices. In this work, such combination of techniques was used to investigate the phase transitions in vacuum-deposited thin films of a common organic semiconductor dihexyl-quarterthiophene (DH4T). A transition from the initial highly crystalline phase to a mesophase was detected upon heating, while only a partial backward transition was observed upon cooling to room temperature. In situ electrical conductivity measurements revealed the impact of both transitions on charge transport. This is partly accounted for by the fact that the initial crystalline phase is characterized by inclination of molecules in the plane perpendicular to the π-π stacking direction, whereas the mesophase is built of molecules tilted in the direction of π-π stacking. Importantly, in addition to the two phases of DH4T characteristic of the bulk, a third interfacial substrate-stabilized monolayer-type phase was observed. The existence of such interfacial structure can have important implications for the charge mobility, being especially favorable for lateral two-dimensional charge transport in the organic field-effect transistors geometry.}, language = {en} } @article{BondarenkoVillringerSteglich2019, author = {Bondarenko, Siegfried and Villringer, Claus and Steglich, Patrick}, title = {Comparative Study of Nano-Slot Silicon Waveguides Covered by Dye Doped and Undoped Polymer Cladding}, series = {Applied Sciences}, volume = {9}, journal = {Applied Sciences}, number = {1}, publisher = {MDPI}, issn = {2076-3417}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10716}, year = {2019}, abstract = {Nonlinear optical dyes doped in optical polymer matrices are widely used for electro-optical devices. Linear optical properties change with dye concentration, which leads to a change in modal properties, especially in nano-structured integrated waveguides such as silicon slot-waveguides. Here, we investigate the influence of a nonlinear optical dye on the performance of a silicon-organic hybrid slot-waveguide. A simulation study of the modal and optical confinement properties is carried out and dependence of the structural parameters of the slot-waveguide and the organic cladding material is taken into account. As cladding material, a guest-host polymer system is employed comprising the nonlinear optical dye Disperse Red 1 (DR1) doped in a poly[methyl methacrylate] (PMMA) matrix. The refractive indices of doped and undoped PMMA were deduced from ellipsometric data. We present a guideline for an optimized slot-waveguide design for the fabrication in silicon-on-insulator technology giving rise to scalable, high-performance integrated electro-optical modulators.}, language = {en} } @article{SteglichHuelsemannDietzeletal.2019, author = {Steglich, Patrick and H{\"u}lsemann, Marcel and Dietzel, Birgit and Mai, Andreas}, title = {Optical Biosensors Based on Silicon-On-Insulator Ring Resonators: A Review}, series = {Molecules}, volume = {24}, journal = {Molecules}, number = {3}, issn = {1420-3049}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10822}, year = {2019}, abstract = {Recent developments in optical biosensors based on integrated photonic devices are reviewed with a special emphasis on silicon-on-insulator ring resonators. The review is mainly devoted to the following aspects: (1) Principles of sensing mechanism, (2) sensor design, (3) biofunctionalization procedures for specific molecule detection and (4) system integration and measurement set-ups. The inherent challenges of implementing photonics-based biosensors to meet specific requirements of applications in medicine, food analysis, and environmental monitoring are discussed.}, language = {en} } @article{GrebinykPrylutskaGrebinyketal.2019, author = {Grebinyk, Anna and Prylutska, Svitlana and Grebinyk, Sergii and Prylutskyy, Yuriy and Ritter, Uwe and Matyshevska, Olga and Dandekar, Thomas and Frohme, Marcus}, title = {Complexation with C60 Fullerene Increases Doxorubicin Efficiency against Leukemic Cells In Vitro}, series = {Nanoscale Research Letters}, volume = {14}, journal = {Nanoscale Research Letters}, issn = {1556-276X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10966}, year = {2019}, abstract = {Conventional anticancer chemotherapy is limited because of severe side effects as well as a quickly evolving multidrug resistance of the tumor cells. To address this problem, we have explored a C60 fullerene-based nanosized system as a carrier for anticancer drugs for an optimized drug delivery to leukemic cells. Here, we studied the physicochemical properties and anticancer activity of C60 fullerene noncovalent complexes with the commonly used anticancer drug doxorubicin. C60-Doxorubicin complexes in a ratio 1:1 and 2:1 were characterized with UV/Vis spectrometry, dynamic light scattering, and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The obtained analytical data indicated that the 140-nm complexes were stable and could be used for biological applications. In leukemic cell lines (CCRF-CEM, Jurkat, THP1 and Molt-16), the nanocomplexes revealed ≤ 3.5 higher cytotoxic potential in comparison with the free drug in a range of nanomolar concentrations. Also, the intracellular drug's level evidenced C60 fullerene considerable nanocarrier function. The results of this study indicated that C60 fullerene-based delivery nanocomplexes had a potential value for optimization of doxorubicin efficiency against leukemic cells.}, language = {en} } @article{GrebinykPrylutskaGrebinyketal.2019, author = {Grebinyk, Anna and Prylutska, Svitlana and Grebinyk, Sergii and Prylutskyy, Yuriy and Ritter, Uwe and Matyshevska, Olga and Dandekar, Thomas and Frohme, Marcus}, title = {Complexation with C60 Fullerene Increases Doxorubicin Efficiency against Leukemic Cells In Vitro}, series = {Nanoscale Research Letters}, volume = {14}, journal = {Nanoscale Research Letters}, issn = {1556-276X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-11415}, year = {2019}, abstract = {Conventional anticancer chemotherapy is limited because of severe side effects as well as a quickly evolving multidrug resistance of the tumor cells. To address this problem, we have explored a C60 fullerene-based nanosized system as a carrier for anticancer drugs for an optimized drug delivery to leukemic cells. Here, we studied the physicochemical properties and anticancer activity of C60 fullerene noncovalent complexes with the commonly used anticancer drug doxorubicin. C60-Doxorubicin complexes in a ratio 1:1 and 2:1 were characterized with UV/Vis spectrometry, dynamic light scattering, and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The obtained analytical data indicated that the 140-nm complexes were stable and could be used for biological applications. In leukemic cell lines (CCRF-CEM, Jurkat, THP1 and Molt-16), the nanocomplexes revealed ≤ 3.5 higher cytotoxic potential in comparison with the free drug in a range of nanomolar concentrations. Also, the intracellular drug's level evidenced C60 fullerene considerable nanocarrier function. The results of this study indicated that C60 fullerene-based delivery nanocomplexes had a potential value for optimization of doxorubicin efficiency against leukemic cells.}, language = {en} } @article{IdaChanGloekleretal.2019, author = {Ida, Jeunice and Chan, Soo Khim and Gl{\"o}kler, J{\"o}rn and Lim, Yee Ying and Choong, Yee Siew and Lim, Theam Soon}, title = {G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing}, series = {Molecules}, volume = {24}, journal = {Molecules}, number = {6}, issn = {1420-3049}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-11438}, year = {2019}, abstract = {G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.}, language = {en} } @article{LuxEdlingSiemrothetal.2018, author = {Lux, Helge and Edling, Matthias and Siemroth, Peter and Schrader, Sigurd}, title = {Fast and Cost-Effective Synthesis of High-Quality Graphene on Copper Foils Using High-Current Arc Evaporation}, series = {Materials}, volume = {11}, journal = {Materials}, number = {5}, issn = {1996-1944}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10359}, pages = {1 -- 10}, year = {2018}, abstract = {In this paper, we present an innovative and ultra-fast process for the deposition of high-quality graphene on different metal foils and thin metal films. The graphene layer can be homogeneously deposited in only 30 s process time. Due to the weak adhesion to the substrate material, the monolayer graphene is easy to transfer using the established processes. For the production, we use magnetic filtered high-current arc evaporation (Φ-HCA) with a solid, graphitic carbon source. This ultra-fast growth process can pave the way towards a cost-effective graphene synthesis for the mass production e.g., in a roll-to-roll process, avoiding time consuming established processes.}, language = {en} } @article{GrebinykGrebinykPrylutskaetal.2018, author = {Grebinyk, Anna and Grebinyk, Sergii and Prylutska, Svitlana and Ritter, Uwe and Matyshevska, Olga and Dandekar, Thomas and Frohme, Marcus}, title = {HPLC-ESI-MS method for C60 fullerene mitochondrial content quantification}, series = {Data in Brief}, volume = {19}, journal = {Data in Brief}, issn = {2352-3409}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10368}, pages = {2047 -- 2052}, year = {2018}, abstract = {The presented dataset describes the quantification of carbon nanoparticle C60 fullerene accumulated in mitochondria of human leukemic cells treated with nanostructure. Firstly, the high performance liquid chromatography-electro spray ionization-mass spectrometry (HPLC-ESI-MS) method was developed for quantitative analysis of pristine C60 fullerene. Then, human leukemic cells were incubated with C60 fullerene, homogenized and subjected to the differential centrifugation to retrieve mitochondrial fraction. The C60 fullerene content was quantified by HPLC-ESI-MS in extracts of cellular fractions. This data article refers to the research article "C60 Fullerene Accumulation in Human Leukemic Cells and Perspectives of LED-mediated Photodynamic Therapy" by Grebinyk et al.}, language = {en} } @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} } @article{FrickePsarianosSabbanetal.2022, author = {Fricke, Anna and Psarianos, Marios and Sabban, Jakob and Fitzner, Maria and Reipsch, Riccardo and Schl{\"u}ter, Oliver K. and Dreyer, Christian and Vogt, Julia H.-M. and Schreiner, Monika and Baldermann, Susanne}, title = {Composite materials for innovative urban farming of alternative food sources (macroalgae and crickets)}, series = {Frontiers in Sustainable Food Systems}, volume = {6}, journal = {Frontiers in Sustainable Food Systems}, publisher = {Frontiers}, issn = {2571-581X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16822}, year = {2022}, abstract = {Facing an inexorable growth of the human population along with substantial environmental changes, the assurance of food security is a major challenge of the present century. To ensure responsible food consumption and production (SDG 12), new approaches in the food system are required. Thus, environmentally controlled, sustainable production of alternative food sources are of key interest for both urban agriculture and food research. To face the current challenge of integrating food production systems within existing structures, multidisciplinary discourses are required. Here, we bring together novel technologies and indoor farming techniques with the aim of supporting the development of sustainable food production systems. For this purpose, we investigated the feasibility of 10 composite materials for their innovative use as structural support in macroalgal cultivation (settlement substrates) and cricket rearing (housing). Considering material resistance, rigidity, and direct material-organism interactions, the bio-based composite polylactic acid (PLA) was identified as a suitable material for joint farming. For macroalgae cultivation, PLA sustained the corrosive cultivation conditions and provided a suitable substrate without affecting the macroalgal physiology or nutritional composition (carotenoids and chlorophylls). For cricket rearing, PLA provided a suitable and recyclable shelter, which was quickly accepted by the animals without any observed harm. In contrast, other common composite components like phenolic resin or aramid were found to be unsuitable due to being harmful for the cultivated organisms or instable toward the applied sterilization procedure. This multidisciplinary study not only provides profound insights in the developing field of urban indoor food production from a new perspective, but also bridges material science and farming approaches to develop new sustainable and resilient food production systems.}, language = {en} } @article{MomanyiHerzogMuchiri2019, author = {Momanyi, Job and Herzog, Michael and Muchiri, Peter}, title = {Analysis of Thermomechanical Properties of Selected Class of Recycled Thermoplastic Materials Based on Their Applications}, series = {Recycling}, volume = {4}, journal = {Recycling}, issn = {2313-4321}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12509}, year = {2019}, abstract = {Polypropylene and polystyrene are petroleum-based thermoplastics which are commonly used and disposed of in the environment after their service life, leading to environmental degradation. There is a need to recycle polypropylene and polystyrene, but the effect of recycling on thermo-mechanical properties is not well understood. This study aims to determine thermo-mechanical properties of the recycled polypropylene and recycled polystyrene and compare them with corresponding virgin polypropylene and newly produced polystyrene (general purpose polystyrene 1540 and high impact polystyrene 7240). The study was carried out by preparing bar-shaped samples of recycled polypropylene, recycled polystyrene, general purpose polystyrene 1540, and high impact polystyrene 7240 by compression molding using a hot press and thermally characterizing them to determine glass transition temperature and melting temperature using differential scanning calorimetry. The changes in Young\’s modulus, tensile strength, hardness, and toughness due to recycling activities were determined at room temperature (24 °C), 40 °C, 60 °C, and 80 °C. The thermo-mechanical properties of recycled polystyrene (PS) were found to be comparable to those of high impact polystyrene (HIPS) 7240. The study revealed that the hardness and toughness for the recycled polymers were higher than those of corresponding virgin polymers. On the other hand, tensile strength and Young's modulus for the recycled polymers were lower than those of the virgin polymers. Understanding the thermo-mechanical properties of the recycled polymers will contribute to more industrial applications hence increase the rate of recycling, resulting in a reduction in environmental pollution.}, language = {en} } @article{NjugunaMuchiriMwemaetal.2021, author = {Njuguna, James K. and Muchiri, Peter and Mwema, Fredrick M. and Karuri, Nancy W. and Herzog, Michael and Dimitrov, Kiril}, title = {Determination of thermo-mechanical properties of recycled polyurethane from glycolysis polyol}, series = {Scientific African}, volume = {12}, journal = {Scientific African}, issn = {2468-2276}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14911}, year = {2021}, abstract = {Polyurethane foam is one of the most versatile polymers widely used in the automotive industry. However, due to the rising amount of polyurethane foam waste in the environment, there is growing research attention focusing on circular economy solutions to closing the material loop. This study aimed to determine the possible changes in thermo-mechanical properties between rigid polyurethane prepared using polyols derived from depolymerization of commercial polyurethane foam with benchmark rigid polyurethane (Ben PU). Polyurethane foams containing dispersion polyol were reacted with dipropylene glycol (DPG) and diethylene glycol (DEG) with a ratio of DPG: DEG of 1:1 in the presence of a consumable catalyst (Di-n-butyl amine). The recovered polyol was used as a raw material replacing 100\% benchmark rigid polyurethane petroleum-based polyester polyol to produce the recycled polyurethane (Rec PU). Thermal analysis was conducted to measure the recycled polyurethane's glass transition temperatures (Tg) using differential scanning calorimetry (DSC). Tensile strength, elastic modulus, toughness, and hardness test of the recycled polyurethane were conducted under three different temperatures; 24°C, 40°C, and 60°C. From the DSC results, the glass transition temperatures for the recycled and the benchmark rigid polyurethane occurred at 43°C and 50.4°C, respectively. Both polymers showed the brittle-ductile transition from 24°C to 40°C. Tensile strength for recycled polyurethane was lower than that of benchmark rigid polyurethane by 29-43\% and a corresponding 24-50\% decrease in elastic modulus. Recycled polyurethane recorded lower toughness than petroleum-based pure polyurethane by 13-16\%. However, the recycled polymer recorded high shored D values than the benchmark rigid polyurethane by 9-29\%. This study reveals that recycled polyol could be used as feedstock for polyurethane production with applications tailored to its mechanical properties.}, language = {en} } @article{ReinhardtMahdaviaslPrelletal.2024, author = {Reinhardt, Heiner and Mahdaviasl, Mahtab and Prell, Bastian and Mauersberger, Anton and Klimant, Philipp and Reiff-Stephan, J{\"o}rg and Ihlenfeldt, Steffen}, title = {Efficient data acquisition for traceability and analytics}, series = {Procedia CIRP}, volume = {122}, journal = {Procedia CIRP}, publisher = {Elsevier}, issn = {2212-8271}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19232}, pages = {73 -- 78}, year = {2024}, abstract = {Implementing processes for traceability is required in various industries to assure product quality during manufacturing, provide evidence on required processing conditions or facilitate product recalls. Commonly, radio-frequency identification (RFID) or code recognition techniques (e.g. Data Matrix) are applied to track the flow of workpieces through a manufacturing system and link processing data accordingly. Although the analysis of tracking data is well-examined, we still see a gap in the research on the trade-off between data acquisition, data analytics and data quality. Here, we present a framework to increase the value of existing data by enabling data analytics while addressing common pitfalls and reducing the costs of data management.}, language = {en} } @article{SchokraieHotzWagenblattWarnkenetal.2010, author = {Schokraie, Elham and Hotz-Wagenblatt, Agnes and Warnken, Uwe and Mali, Brahim and Frohme, Marcus and F{\"o}rster, Frank and Dandekar, Thomas and Hengherr, Steffen and Schill, Ralph O. and Schn{\"o}lzer, Martina}, title = {Proteomic Analysis of Tardigrades: Towards a Better Understanding of Molecular Mechanisms by Anhydrobiotic Organisms}, series = {PLoS ONE}, volume = {5}, journal = {PLoS ONE}, number = {3}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6214}, pages = {37}, year = {2010}, abstract = {Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered.}, language = {en} } @article{SchokraieWarnkenHotzWagenblattetal.2012, author = {Schokraie, Elham and Warnken, Uwe and Hotz-Wagenblatt, Agnes and Grohme, Markus and Hengherr, Steffen and F{\"o}rster, Frank and Schill, Ralph O. and Frohme, Marcus and Dandekar, Thomas and Schn{\"o}lzer, Martina}, title = {Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state}, series = {PLoS ONE}, volume = {7}, journal = {PLoS ONE}, number = {9}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6392}, pages = {25}, year = {2012}, abstract = {Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.}, language = {en} } @article{FoersterBeisserGrohmeetal.2012, author = {F{\"o}rster, Frank and Beisser, Daniela and Grohme, Markus and Liang, Chunguang and Mali, Brahim and Siegl, Alexander Matthias and Engelmann, Julia C. and Shkumatov, Alexander and Schokraie, Elham and M{\"u}ller, Tobias and Schn{\"o}lzer, Martina and Schill, Ralph O. and Frohme, Marcus and Dandekar, Thomas}, title = {Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations}, series = {Bioinformatics and Biology Insights}, volume = {2012}, journal = {Bioinformatics and Biology Insights}, number = {6}, issn = {1177-9322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6153}, pages = {69 -- 96}, year = {2012}, abstract = {Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.}, language = {en} } @article{FoersterLiangShkumatovetal.2009, author = {F{\"o}rster, Frank and Liang, Chunguang and Shkumatov, Alexander and Beisser, Daniela and Engelmann, Julia C. and Schn{\"o}lzer, Martina and Frohme, Marcus and M{\"u}ller, Tobias and Schill, Ralph O. and Dandekar, Thomas}, title = {Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades}, series = {BMC Genomics}, volume = {10}, journal = {BMC Genomics}, number = {469}, issn = {1471-2164}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6461}, pages = {10}, year = {2009}, abstract = {Background Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. Results To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3\% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data. Conclusion Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.}, language = {en} } @article{MaliGrohmeFoersteretal.2010, author = {Mali, Brahim and Grohme, Markus and F{\"o}rster, Frank and Dandekar, Thomas and Schn{\"o}lzer, Martina and Reuter, Dirk and Wełnicz, Weronika and Schill, Ralph O. and Frohme, Marcus}, title = {Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer}, series = {BMC Genomics}, volume = {11}, journal = {BMC Genomics}, number = {168}, issn = {1471-2164}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6207}, pages = {11}, year = {2010}, abstract = {The phenomenon of desiccation tolerance, also called anhydrobiosis, involves the ability of an organism to survive the loss of almost all cellular water without sustaining irreversible damage. Although there are several physiological, morphological and ecological studies on tardigrades, only limited DNA sequence information is available. Therefore, we explored the transcriptome in the active and anhydrobiotic state of the tardigrade Milnesium tardigradum which has extraordinary tolerance to desiccation and freezing. In this study, we present the first overview of the transcriptome of M. tardigradum and its response to desiccation and discuss potential parallels to stress responses in other organisms.}, language = {en} } @article{JanowskiGrossSauerGuerthetal.2016, author = {Janowski, Susann and Gross, Ina and Sauer-G{\"u}rth, Hedwig and Tietze, Dieter Thomas and Grohme, Markus and Frohme, Marcus and Becker, Peter and Wink, Michael}, title = {New Microsatellite Markers for the Common Tern (Sterna hirundo) Developed with 454 Shot-Gun Pyrosequencing}, series = {The Open Ornithology Journal}, volume = {9}, journal = {The Open Ornithology Journal}, issn = {1874-4532}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6789}, pages = {50 -- 59}, year = {2016}, abstract = {Long term studies, focusing on population- and socio-biology research, require the unequivocal identification of individuals. DNA studies with Short Tandem Repeats (STR loci) became a widespread tool in population genetics. We used the next-generation sequencing (NGS) approach with 454 shot-gun pyrosequencing to identify 13 new polymorphic STR loci for the Common Tern, Sterna hirundo. To enlarge the marker set we added two more loci originally developed for Black-legged Kittiwake (Rissa tridactyla) and Red-billed Gull (Chroicocephalus scopulinus) and arranged these 15 loci into three multiplex PCR panels for high throughput genotyping. Loci characterization demonstrated that our marker set is of high quality. A PIC value of about 0.67 and a power of exclusion value of 0.99 were reached. Deviation from Hardy-Weinberg expectations of some loci and low frequencies for null alleles are interpreted as a result of inbreeding and founder effect in the investigated tern colony. We used a test data set of this well-studied breeding colony of Common Tern at Banter Lake, Wilhelmshaven, Germany, to perform a parentage test. Parent-chick relationships, known from the social pedigree of that colony, were compared with genetically calculated ones. In order to test our markers and the used parentage program COLONY, we conducted six competing data sets with varying completeness of included parental genotypes. By including fully sampled parent pairs of known family assignment, results were correct for nest mates, single parents and parent pairs. Our marker set provides a powerful tool to investigate life-time reproductive success and other issues of population and socio-biology for Common Terns, e.g. in the aforementioned colony monitored for decades.}, language = {en} } @article{NitscheKurthDunkhorstetal.2007, author = {Nitsche, Andreas and Kurth, Andreas and Dunkhorst, Anna and P{\"a}nke, Oliver and Sielaff, Hendrik and Junge, Wolfgang and Muth, Doreen and Scheller, Frieder W. and St{\"o}cklein, Walter and Dahmen, Claudia and Pauli, Georg and Kage, Andreas}, title = {One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX}, series = {BMC Biotechnology}, volume = {7}, journal = {BMC Biotechnology}, number = {48}, issn = {1472-6750}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6246}, pages = {12}, year = {2007}, abstract = {As a new class of therapeutic and diagnostic reagents, more than fifteen years ago RNA and DNA aptamers were identified as binding molecules to numerous small compounds, proteins and rarely even to complete pathogen particles. Most aptamers were isolated from complex libraries of synthetic nucleic acids by a process termed SELEX based on several selection and amplification steps. Here we report the application of a new one-step selection method (MonoLEX) to acquire high-affinity DNA aptamers binding Vaccinia virus used as a model organism for complex target structures.}, language = {en} } @article{WangGrohmeMalietal.2014, author = {Wang, Chong and Grohme, Markus and Mali, Brahim and Schill, Ralph O. and Frohme, Marcus}, title = {Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome Sequencing}, series = {PLoS ONE}, volume = {9}, journal = {PLoS ONE}, number = {3}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6029}, pages = {15}, year = {2014}, abstract = {Many tardigrade species are capable of anhydrobiosis; however, mechanisms underlying their extreme desiccation resistance remain elusive. This study attempts to quantify the anhydrobiotic transcriptome of the limno-terrestrial tardigrade Milnesium tardigradum.}, language = {en} } @article{GrohmeMaliWełniczetal.2013, author = {Grohme, Markus and Mali, Brahim and Wełnicz, Weronika and Michel, Stephanie and Schill, Ralph O. and Frohme, Marcus}, title = {The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum}, series = {Bioinformatics and Biology Insights}, volume = {2013}, journal = {Bioinformatics and Biology Insights}, number = {7}, issn = {1177-9322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6092}, pages = {153 -- 165}, year = {2013}, abstract = {Limno-terrestrial tardigrades are small invertebrates that are subjected to periodic drought of their micro-environment. They have evolved to cope with these unfavorable conditions by anhydrobiosis, an ametabolic state of low cellular water. During drying and rehydration, tardigrades go through drastic changes in cellular water content. By our transcriptome sequencing effort of the limno-terrestrial tardigrade Milnesium tardigradum and by a combination of cloning and targeted sequence assembly, we identified transcripts encoding eleven putative aquaporins. Analysis of these sequences proposed 2 classical aquaporins, 8 aquaglyceroporins and a single potentially intracellular unorthodox aquaporin. Using quantitative real-time PCR we analyzed aquaporin transcript expression in the anhydrobiotic context. We have identified additional unorthodox aquaporins in various insect genomes and have identified a novel common conserved structural feature in these proteins. Analysis of the genomic organization of insect aquaporin genes revealed several conserved gene clusters.}, language = {en} } @article{BeisserGrohmeKopkaetal.2012, author = {Beisser, Daniela and Grohme, Markus and Kopka, Joachim and Frohme, Marcus and Schill, Ralph O. and Hengherr, Steffen and Dandekar, Thomas and Klau, Gunnar W. and Dittrich, Marcus and M{\"u}ller, Tobias}, title = {Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum}, series = {BMC Systems Biology}, volume = {6}, journal = {BMC Systems Biology}, number = {72}, issn = {1752-0509}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6146}, pages = {13}, year = {2012}, abstract = {Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress.}, language = {en} } @article{JanowskiGrohmeFrohmeetal.2014, author = {Janowski, Susann and Grohme, Markus and Frohme, Marcus and Wink, Michael}, title = {Development of New Microsatellite (STR) Markers for Montagu's Harrier (Circus pygargus) via 454 Shot-Gun Pyrosequencing}, series = {The Open Ornithology Journal}, volume = {7}, journal = {The Open Ornithology Journal}, issn = {1874-4532}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5966}, pages = {11 -- 18}, year = {2014}, abstract = {During the last decades the ground-breeding Montagu's harrier ( Circus pygargus , Linnaeus, 1758) has changed its breeding habitats in Europe to agricultural areas in which many local populations would be close to extinction without a special nest protection regime. Although Montagu's harrier is a well-studied species in terms of ecology and breeding biology, its genetic structure and population genetics are almost unknown. As there is a lack of good genetic markers we developed a set of 19 microsatellite markers comprising 16 new STR markers which were identified by next-generation sequencing (NGS) using 454 shot-gun pyrosequencing of genomic DNA. The STR markers were arranged into three multiplex PCR sets for high throughput genotyping and characterised. The marker set provides a powerful tool for kinship analysis. The combined non-exclusion probability for parent pairs was 1.13* 10-11. Only three loci showed PIC values < 0.50. In total, 121 known family relationships were compared with genetically calculated ones to test the markers suitability for parentage analysis. In 97.5\% of all cases full-sibships were accurately determined and 97.6\% of all mothers were assigned correctly to their chicks. The present multiplex PCR panels can be used to investigate several hypotheses concerning breeding behaviour, kinship, exchange rates between populations and phylogeography.}, language = {en} } @article{PetrilloFabbriKagklietal.2021, author = {Petrillo, Mauro and Fabbri, Marco and Kagkli, Dafni Maria and Querci, Maddalena and Van den Eede, Guy and Alm, Erik and Aytan-Aktug, Derya and Capella-Gutierrez, Salvador and Carrillo, Catherine and Cestaro, Alessandro and Chan, Kok-Gan and Coque, Teresa and Endrullat, Christoph and Gut, Ivo and Hammer, Paul and Kay, Gemma L. and Madec, Jean-Yves and Mather, Alison E. and McHardy, Alice Carolyn and Naas, Thierry and Paracchini, Valentina and Peter, Silke and Pightling, Arthur and Raffael, Barbara and Rossen, John and Rupp{\´e}, Etienne and Schlaberg, Robert and Vanneste, Kevin and Weber, Lukas M. and Westh, Henrik and Angers-Loustau, Alexandre}, title = {A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing [version 1; peer review: 2 approved with reservations]}, series = {F1000Research}, journal = {F1000Research}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15699}, year = {2021}, abstract = {Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain "live" (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines' implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.}, language = {en} } @article{EndrullatGloeklerFrankeetal.2016, author = {Endrullat, Christoph and Gl{\"o}kler, J{\"o}rn and Franke, Philipp and Frohme, Marcus}, title = {Standardization and quality management in next-generation sequencing}, series = {Applied \& Translational Genomics}, volume = {10}, journal = {Applied \& Translational Genomics}, issn = {2212-0661}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6637}, pages = {2 -- 9}, year = {2016}, abstract = {DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data.}, language = {en} } @article{MohrNowakowskiAltenburgetal.2020, author = {Mohr, Gunther and Nowakowski, Susanna and Altenburg, Simon J. and Maierhofer, Christiane and Hilgenberg, Kai}, title = {Experimental Determination of the Emissivity of Powder Layers and Bulk Material in Laser Powder Bed Fusion Using Infrared Thermography and Thermocouples}, series = {Metals}, volume = {10}, journal = {Metals}, number = {11}, publisher = {MDPI}, issn = {2075-4701}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13564}, year = {2020}, abstract = {Recording the temperature distribution of the layer under construction during laser powder bed fusion (L-PBF) is of utmost interest for a deep process understanding as well as for quality assurance and in situ monitoring means. While having a notable number of thermal monitoring approaches in additive manufacturing (AM), attempts at temperature calibration and emissivity determination are relatively rare. This study aims for the experimental temperature adjustment of an off-axis infrared (IR) thermography setup used for in situ thermal data acquisition in L-PBF processes. The temperature adjustment was conducted by means of the so-called contact method using thermocouples at two different surface conditions and two different materials: AISI 316L L-PBF bulk surface, AISI 316L powder surface, and IN718 powder surface. The apparent emissivity values for the particular setup were determined. For the first time, also corrected, closer to real emissivity values of the bulk or powder surface condition are published. In the temperature region from approximately 150 °C to 580 °C, the corrected emissivity was determined in a range from 0.2 to 0.25 for a 316L L-PBF bulk surface, in a range from 0.37 to 0.45 for 316L powder layer, and in a range from 0.37 to 0.4 for IN718 powder layer.}, language = {en} } @article{RistićFurboMoseretal.2016, author = {Ristić, Alenka and Furbo, Simon and Moser, Christoph and Schranzhofer, Hermann and Lazaro, Ana and Delgado, Monica and Pe{\~n}alosa, Conchita and Zalewski, Laurent and Diarce, Gonzalo and Alkan, Cemil and Gunasekara, Saman N. and Haussmann, Thomas and Gschwander, Stefan and Rathgeber, Christoph and Schmit, Henri and Barreneche, Camila and Cabeza, Luiza and Ferrer, Gerard and Konuklu, Yeliz and Paksoy, Halime and Rammelberg, Holger and Munz, Gunther and Herzog, Thomas H. and J{\"a}nchen, Jochen and del Barrio, Elena Palomo}, title = {IEA SHC Task 42 / ECES Annex 29 WG A1: Engineering and Processing of PCMs, TCMs and Sorption Materials}, series = {Energy Procedia}, volume = {91}, journal = {Energy Procedia}, issn = {1876-6102}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6629}, pages = {207 -- 217}, year = {2016}, abstract = {An overview on the recent results on the engineering and characterization of sorption materials, PCMs and TCMs investigated in the working group WG A1 "Engineering and processing of TES materials" of IEA SHC Task 42 / ECES Annex 29 (Task 4229) entitled "Compact Thermal Energy Storage" is presented.}, language = {en} } @article{GrebinykPrylutskaGrynyuketal.2018, author = {Grebinyk, Anna and Prylutska, Svitlana and Grynyuk, I. and Kolp, Benjamin and Hurmach, V. and Sliva, T. and Amirkhanov, Volodymyr and Trush, V. and Matyshevska, Olga and Slobodyanik, M. and Prylutskyy, Yuriy and Frohme, Marcus and Ritter, Uwe}, title = {C60 Fullerene Effects on Diphenyl-N-(trichloroacetyl)-amidophosphate Interaction with DNA In Silico and Its Cytotoxic Activity Against Human Leukemic Cell Line In Vitro}, series = {Nanoscale Research Letters}, volume = {2018}, journal = {Nanoscale Research Letters}, issn = {1556-276X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10515}, pages = {1 -- 9}, year = {2018}, abstract = {New representative of carbacylamidophosphates - diphenyl-N-(trichloroacetyl)-amidophosphate (HL), which contains two phenoxy substituents near the phosphoryl group, was synthesized, identified by elemental analysis and IR and NMR spectroscopy, and tested as a cytotoxic agent itself and in combination with C60 fullerene. According to molecular simulation results, C60 fullerene and HL could interact with DNA and form a rigid complex stabilized by stacking interactions of HL phenyl groups with C60 fullerene and DNA G nucleotide, as well as by interactions of HL CCl3 group by ion-π bonds with C60 molecule and by electrostatic bonds with DNA G nucleotide. With the use of MTT test, the cytotoxic activity of HL against human leukemic CCRF-CM cells with IC50 value detected at 10 μM concentration at 72 h of cells treatment was shown. Under combined action of 16 μM C60 fullerene and HL, the value of IC50 was detected at lower 5 μM HL concentration and at earlier 48 h period of incubation, besides the cytotoxic effect of HL was observed at a low 2.5 μM concentration at which HL by itself had no influence on cell viability. Binding of C60 fullerene and HL with minor DNA groove with formation of a stable complex is assumed to be one of the possible reasons of their synergistic inhibition of CCRF-CЕM cells proliferation. Application of C60 fullerene in combination with 2.5 μM HL was shown to have no harmful effect on structural stability of blood erythrocytes membrane. Thus, combined action of C60 fullerene and HL in a low concentration potentiated HL cytotoxic effect against human leukemic cells and was not followed by hemolytic effect.}, language = {en} } @article{HollmannFrohmeEndrullatetal.2020, author = {Hollmann, Susanne and Frohme, Marcus and Endrullat, Christoph and Kremer, Andreas and D'Elia, Domenica and Regierer, Babette and Nechyporenko, Alina}, title = {Ten simple rules on how to write a standard operating procedure}, series = {PLoS Computational Biology}, volume = {16}, journal = {PLoS Computational Biology}, number = {9}, issn = {1553-7358}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13598}, pages = {e1008095}, year = {2020}, abstract = {Research publications and data nowadays should be publicly available on the internet and, theoretically, usable for everyone to develop further research, products, or services. The long-term accessibility of research data is, therefore, fundamental in the economy of the research production process. However, the availability of data is not sufficient by itself, but also their quality must be verifiable. Measures to ensure reuse and reproducibility need to include the entire research life cycle, from the experimental design to the generation of data, quality control, statistical analysis, interpretation, and validation of the results. Hence, high-quality records, particularly for providing a string of documents for the verifiable origin of data, are essential elements that can act as a certificate for potential users (customers). These records also improve the traceability and transparency of data and processes, therefore, improving the reliability of results. Standards for data acquisition, analysis, and documentation have been fostered in the last decade driven by grassroot initiatives of researchers and organizations such as the Research Data Alliance (RDA). Nevertheless, what is still largely missing in the life science academic research are agreed procedures for complex routine research workflows. Here, well-crafted documentation like standard operating procedures (SOPs) offer clear direction and instructions specifically designed to avoid deviations as an absolute necessity for reproducibility. Therefore, this paper provides a standardized workflow that explains step by step how to write an SOP to be used as a starting point for appropriate research documentation.}, language = {en} } @article{PrylutskaGrynyukGrebinyketal.2017, author = {Prylutska, Svitlana and Grynyuk, I. and Grebinyk, Anna and Hurmach, V. and Shatrava, Iu. and Sliva, T. and Amirkhanov, Volodymyr and Prylutskyy, Yuriy and Matyshevska, Olga and Slobodyanik, M. and Frohme, Marcus and Ritter, Uwe}, title = {Cytotoxic Effects of Dimorfolido-N-Trichloroacetylphosphorylamide and Dimorfolido-N-Benzoylphosphorylamide in Combination with C60 Fullerene on Leukemic Cells and Docking Study of Their Interaction with DNA}, series = {Nanoscale Research Letters}, volume = {12}, journal = {Nanoscale Research Letters}, number = {124}, issn = {1556-276X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9273}, year = {2017}, abstract = {Dimorfolido-N-trichloroacetylphosphorylamide (HL1) and dimorfolido-N-benzoylphosphorylamide (HL2) as representatives of carbacylamidophosphates were synthesized and identified by the methods of IR, 1H, and 31P NMR spectroscopy. In vitro HL1 and HL2 at 1 mM concentration caused cell specific and time-dependent decrease of leukemic cell viability. Compounds caused the similar gradual decrease of Jurkat cells viability at 72 h (by 35\%). HL1 had earlier and more profound toxic effect as compared to HL2 regardless on leukemic cell line. Viability of Molt-16 and CCRF-CEM cells under the action of HL1 was decreased at 24 h (by 32 and 45\%, respectively) with no substantial further reducing up to 72 h. Toxic effect of HL2 was detected only at 72 h of incubation of Jurkat and Molt-16 cells (cell viability was decreased by 40 and 45\%, respectively). It was shown that C60 fullerene enhanced the toxic effect of HL2 on leukemic cells. Viability of Jurkat and CCRF-CEM cells at combined action of C60 fullerene and HL2 was decreased at 72 h (by 20 and 24\%, respectively) in comparison with the effect of HL2 taken separately. In silico study showed that HL1 and HL2 can interact with DNA and form complexes with DNA both separately and in combination with C60 fullerene. More stable complexes are formed when DNA interacts with HL1 or C60 + HL2 structure. Strong stacking interactions can be formed between HL2 and C60 fullerene. Differences in the types of identified bonds and ways of binding can determine distinction in cytotoxic effects of studied compounds.}, language = {en} } @article{AkhoundiKuhlsCannetetal.2016, author = {Akhoundi, Mohammad and Kuhls, Katrin and Cannet, Arnaud and Vot{\´y}pka, Jan and Marty, Pierre and Delaunay, Pascal and Sereno, Denis}, title = {A Historical Overview of the Classification, Evolution, and Dispersion of Leishmania Parasites and Sandflies}, series = {PLoS Neglected Tropical Diseases}, volume = {10}, journal = {PLoS Neglected Tropical Diseases}, number = {3}, issn = {1935-2735}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5853}, pages = {40}, year = {2016}, abstract = {The aim of this study is to describe the major evolutionary historical events among Leishmania, sandflies, and the associated animal reservoirs in detail, in accordance with the geographical evolution of the Earth, which has not been previously discussed on a large scale.}, language = {en} } @article{AmroAlDwibeGashoutetal.2017, author = {Amro, Ahmad and Al-Dwibe, Hamida and Gashout, Aisha and Moskalenko, Olga and Galafin, Marlena and Hamarsheh, Omar and Frohme, Marcus and Jaeschke, Anja and Sch{\"o}nian, Gabriele and Kuhls, Katrin}, title = {Spatiotemporal and molecular epidemiology of cutaneous leishmaniasis in Libya}, series = {PLoS Neglected Tropical Diseases}, volume = {11}, journal = {PLoS Neglected Tropical Diseases}, number = {9}, issn = {1935-2735}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10054}, year = {2017}, abstract = {Cutaneous leishmaniasis (CL) is a skin infection caused by a single-celled parasite that is transmitted by the bite of a phlebotomine sandfly. CL is the most common form of leishmaniasis characterized by localized lesions in the skin and mucous membranes. The disease is prevalent in all countries around the Mediterranean Basin. In this paper, we describe spatiotemporal and eco-epidemiological parameters of CL in Libya. Moreover, we explored current spatiotemporal distributions of CL cases and explored the future projection of the disease. Our study indicates the presence of higher risk of CL in the coastal regions of Libya. Future projection until 2060 showed a trend of increasing incidence of CL in the north-western part of Libya, a spread along the coastal region and a possible emergence of new endemics in the north-eastern districts of Libya. These scenarios should be considered by health authorities in order to develop appropriate intervention strategies and plan effective control programs.}, language = {en} } @article{KuhlsMoskalenkoSukiasyanetal.2021, author = {Kuhls, Katrin and Moskalenko, Olga and Sukiasyan, Anna and Manukyan, Dezdemonia and Melik-Andreasyan, Gayane and Atshemyan, Liana and Apresyan, Hripsime and Strelkova, Margarita V. and Jaeschke, Anja and Wieland, Ralf and Frohme, Marcus and Cortes, Sofia and Keshishyan, Ara}, title = {Microsatellite based molecular epidemiology of Leishmania infantum from re-emerging foci of visceral leishmaniasis in Armenia and pilot risk assessment by ecological niche modeling}, series = {PLoS Neglected Tropical Diseases}, volume = {15}, journal = {PLoS Neglected Tropical Diseases}, number = {4}, publisher = {Public Library of Science (PLoS)}, issn = {1935-2735}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14004}, pages = {e0009288}, year = {2021}, abstract = {Leishmaniasis is a vector-borne disease caused by protozoan parasites of the genus Leishmania. In Armenia visceral leishmaniasis (VL) is re-emerging since 1999 after a long break of 30 years, with 167 cases recorded until 2019. Molecular diagnosis of VL was implemented only in 2016, and the causative agent was identified as L. infantum. In the present study we expanded the investigation of the causative agent to a characterization at strain level and the identification of its phylogenetic position among the L. infantum genotypes circulating worldwide. This is the first study addressing genetic diversity and population structure of L. infantum in Armenia and in Transcaucasia. Armenia is an extremely interesting region due to its bio-geographic specificities e.g. the high number of different climates in this small mountainous country and the observed high diversity of sand fly species, part of which occurring in very high altitudes. Ecological niche modeling based on registered VL cases and sand fly vectors collected in active VL foci revealed that the risk of further spread of VL is very high due to climate change. Studies of this region should be expanded to enable targeted control measures.}, language = {en} } @article{AmroMoskalenkoHamarshehetal.2022, author = {Amro, Ahmad and Moskalenko, Olga and Hamarsheh, Omar and Frohme, Marcus}, title = {Spatiotemporal analysis of cutaneous leishmaniasis in Palestine and foresight study by projections modelling until 2060 based on climate change prediction}, series = {PLoS ONE}, volume = {17}, journal = {PLoS ONE}, number = {6}, publisher = {Public Library of Science (PLoS)}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16166}, year = {2022}, abstract = {Background Cutaneous leishmaniasis (CL) is a vector-borne parasitic diseases of public health importance that is prevalent in the West Bank but not in the Gaza Strip. The disease caused by parasitic protozoans from the genus Leishmania and it is transmitted by infected phlebotomine sand flies. The aim of our study is to investigate the eco-epidemiological parameters and spatiotemporal projections of CL in Palestine over a 30-years period from 1990 through 2020 and to explore future projections until 2060. Methodology/Principal findings This long-term descriptive epidemiological study includes investigation of demographic characteristics of reported patients by the Palestinian Ministry of Health (PMoH). Moreover, we explored spatiotemporal distribution of CL including future projection based on climate change scenarios. The number of CL patients reported during this period was 5855 cases, and the average annual incidence rate (AAIR) was 18.5 cases/105 population. The male to female ratio was 1.25:1. Patients-age ranged from 2 months to 89 years (mean = 22.5, std 18.67, and the median was 18 years). More than 65\% of the cases came from three governates in the West Bank; Jenin 29\% (1617 cases), Jericho 25\% (1403), and Tubas 12\% (658) with no cases reported in the Gaza Strip. Seasonal occurrence of CL starts to increase in December and peaked during March and April of the following year. Current distribution of CL indicate that Jericho, Tubas, Jenin and Nablus have the most suitable climatic settings for the sandfly vectors. Future projections until 2060 suggest an increasing incidence from northwest of Jenin down to the southwest of Ramallah, disappearance of the foci in Jericho and Tubas throughout the Jordan Vally, and possible emergence of new foci in Gaza Strip. Conclusions/Significance The future projection of CL in Palestine until 2060 show a tendency of increasing incidence in the north western parts of the West Bank, disappearance from Jericho and Tubas throughout the Jordan Vally, and emergence of new CL endemic foci in the Gaza Strip. These results should be considered to implement effective control and surveillance systems to counteract spatial expansion of CL vectors.}, language = {en} } @article{MarcosZambranoLopezMolinaBakirGungoretal.2023, author = {Marcos-Zambrano, Laura Judith and L{\´o}pez-Molina, V{\´i}ctor Manuel and Bakir-Gungor, Burcu and Frohme, Marcus and Karaduzovic-Hadziabdic, Kanita and Klammsteiner, Thomas and Ibrahimi, Eliana and Lahti, Leo and Loncar-Turukalo, Tatjana and Dhamo, Xhilda and Simeon, Andrea and Nechyporenko, Alina and Pio, Gianvito and Przymus, Piotr and Sampri, Alexia and Trajkovik, Vladimir and Lacruz-Pleguezuelos, Blanca and Aasmets, Oliver and Araujo, Ricardo and Anagnostopoulos, Ioannis and Aydemir, {\"O}nder and Berland, Magali and Calle, M. Luz and Ceci, Michelangelo and Duman, Hatice and G{\"u}ndoğdu, Aycan and Havulinna, Aki S. and Kaka Bra, Kardokh Hama Najib and Kalluci, Eglantina and Karav, Sercan and Lode, Daniel and Lopes, Marta B. and May, Patrick and Nap, Bram and Nedyalkova, Miroslava and Paci{\^e}ncia, In{\^e}s and Pasic, Lejla and Pujolassos, Meritxell and Shigdel, Rajesh and Sus{\´i}n, Antonio and Thiele, Ines and Truică, Ciprian-Octavian and Wilmes, Paul and Yilmaz, Ercument and Yousef, Malik and Claesson, Marcus Joakim and Truu, Jaak and Carrillo de Santa Pau, Enrique}, title = {A toolbox of machine learning software to support microbiome analysis}, 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-opus4-18271}, year = {2023}, abstract = {The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis.}, language = {en} } @article{HaklayFraislGreshakeTzovarasetal.2021, author = {Haklay, Muki and Fraisl, Dilek and Greshake Tzovaras, Bastian and Hecker, Susanne and Gold, Margaret and Hager, Gerid and Ceccaroni, Luigi and Kieslinger, Barbara and Wehn, Uta and Woods, Sasha and Nold, Christian and Bal{\´a}zs, B{\´a}lint and Mazzonetto, Marzia and R{\"u}fenacht, Simone and Shanley, Lea A. and Wagenknecht, Katherin and Motion, Alice and Sforzi, Andrea and Riemenschneider, Dorte and Dorler, Daniel and Heigl, Florian and Schaefer, Teresa and Lindner, Ariel and Weißpflug, Maike and Mačiulienė, Monika and Vohland, Katrin}, title = {Contours of citizen science: a vignette study}, series = {Royal Society Open Science}, volume = {8}, journal = {Royal Society Open Science}, number = {8}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14781}, year = {2021}, abstract = {Citizen science has expanded rapidly over the past decades. Yet, defining citizen science and its boundaries remained a challenge, and this is reflected in the literature—for example in the proliferation of typologies and definitions. There is a need for identifying areas of agreement and disagreement within the citizen science practitioners community on what should be considered as citizen science activity. This paper describes the development and results of a survey that examined this issue, through the use of vignettes—short case descriptions that describe an activity, while asking the respondents to rate the activity on a scale from 'not citizen science' (0\%) to 'citizen science' (100\%). The survey included 50 vignettes, of which five were developed as clear cases of not-citizen science activities, five as widely accepted citizen science activities and the others addressing 10 factors and 61 sub-factors that can lead to controversy about an activity. The survey has attracted 333 respondents, who provided over 5100 ratings. The analysis demonstrates the plurality of understanding of what citizen science is and calls for an open understanding of what activities are included in the field.}, language = {en} } @article{BoettcherHooglandDitsetal.2015, author = {B{\"o}ttcher, Ren{\´e} and Hoogland, A. Marije and Dits, Natasja and Verhoef, Esther and Kweldam, Charlotte and Waranecki, Piotr and Bangma, Chris H. and van Leenders, Geert J.L.H. and Jenster, Guido}, title = {Novel long non-coding RNAs are specific diagnostic and prognostic markers for prostate cancer}, series = {Oncotarget}, volume = {6}, journal = {Oncotarget}, number = {6}, issn = {1949-2553}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6329}, pages = {4036 -- 4050}, year = {2015}, abstract = {Current prostate cancer (PCa) biomarkers such as PSA are not optimal in distinguishing cancer from benign prostate diseases and predicting disease outcome. To discover additional biomarkers, we investigated PCa-specific expression of novel unannotated transcripts. Using the unique probe design of Affymetrix Human Exon Arrays, we identified 334 candidates (EPCATs), of which 15 were validated by RT-PCR. Combined into a diagnostic panel, 11 EPCATs classified 80\% of PCa samples correctly, while maintaining 100\% specificity. High specificity was confirmed by in situ hybridization for EPCAT4R966 and EPCAT2F176 (SChLAP1) on extensive tissue microarrays. Besides being diagnostic, EPCAT2F176 and EPCAT4R966 showed significant association with pT-stage and were present in PIN lesions. We also found EPCAT2F176 and EPCAT2R709 to be associated with development of metastases and PCa-related death, and EPCAT2F176 to be enriched in lymph node metastases. Functional significance of expression of 9 EPCATs was investigated by siRNA transfection, revealing that knockdown of 5 different EPCATs impaired growth of LNCaP and 22RV1 PCa cells. Only the minority of EPCATs appear to be controlled by androgen receptor or ERG. Although the underlying transcriptional regulation is not fully understood, the novel PCa-associated transcripts are new diagnostic and prognostic markers with functional relevance to prostate cancer growth.}, language = {en} } @article{SmekhovaSzyjkaLaTorreetal.2024, author = {Smekhova, Alevtina and Szyjka, Thomas and La Torre, Enrico and Ollefs, Katharina and Eggert, Benedikt and Coester, Birte and Wilhelm, Fabrice and Bali, Rantej and Lindner, J{\"u}rgen and Rogalev, Andrei and T{\"o}bbens, Daniel Maria and Weschke, Eugen and Luo, Chen and Chen, Kai and Radu, Florin and Schmitz-Antoniak, Carolin and Wende, Heiko}, title = {Irradiation-induced enhancement of Fe and Al magnetic polarizations in Fe60Al40 films}, series = {New Journal of Physics}, volume = {26}, journal = {New Journal of Physics}, publisher = {Institute of Physics Publishing (IOP)}, issn = {1367-2630}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18381}, year = {2024}, abstract = {The rise of Fe magnetic moment, changes in Al electronic structure and a variation of Al magnetic polarization in thin films of transition metal aluminide Fe60Al40 have been probed through the order-disorder phase transition by soft X-ray absorption spectroscopy and X-ray resonant magnetic reflectivity in the extreme ultraviolet regime. In a course of the transition induced by 20 keV Ne+ irradiation with low fluences (1014 ions·cm-2), X-ray magnetic circular dichroism spectra taken at the Fe L2,3 absorption edges at room and low temperatures revealed a pronounced increase of Fe 3d states spin-polarization. X-ray resonant magnetic reflectivity applied to the Al L2,3 and Fe M2,3 edges allowed to detect the magnetic polarization of Al atoms in the films. The changes in Al electronic structure have been seen by alteration of Al K edge X-ray absorption near edge structure. A difference in anisotropy fields for films before and after irradiation has been observed by element-specific hysteresis loops recorded at low temperatures in absorption and reflection geometries at the Fe L2,3 and M2,3 edges, respectively. An attempt to reduce the top oxide layer by an inductively coupled hydrogen plasma has shown a possibility to recover the chemically ordered phase.}, language = {en} } @article{KagelBierFrohmeetal.2019, author = {Kagel, Heike and Bier, Frank Fabian and Frohme, Marcus and Gl{\"o}kler, J{\"o}rn}, title = {A Novel Optical Method To Reversibly Control Enzymatic Activity Based On Photoacids}, series = {Scientific Reports}, volume = {9}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12685}, year = {2019}, abstract = {Most biochemical reactions depend on the pH value of the aqueous environment and some are strongly favoured to occur in an acidic environment. A non-invasive control of pH to tightly regulate such reactions with defined start and end points is a highly desirable feature in certain applications, but has proven difficult to achieve so far. We report a novel optical approach to reversibly control a typical biochemical reaction by changing the pH and using acid phosphatase as a model enzyme. The reversible photoacid G-acid functions as a proton donor, changing the pH rapidly and reversibly by using high power UV LEDs as an illumination source in our experimental setup. The reaction can be tightly controlled by simply switching the light on and off and should be applicable to a wide range of other enzymatic reactions, thus enabling miniaturization and parallelization through non-invasive optical means.}, language = {en} } @article{KagelJacobsBieretal.2019, author = {Kagel, Heike and Jacobs, Hannes and Bier, Frank Fabian and Gl{\"o}kler, J{\"o}rn and Frohme, Marcus}, title = {A Novel Microtiter Plate Format High Power Open Source LED Array}, series = {Photonics}, volume = {6}, journal = {Photonics}, number = {1}, issn = {2304-6732}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-11307}, year = {2019}, abstract = {Many photochemical or photobiological applications require the use of high power ultraviolet light sources, such as high-pressure mercury arc lamps. In addition, many photo-induced chemical, biochemical and biological applications require either a combinatorial setting or a parallel assay of multiple samples under the same environmental conditions to ensure reproducibility. To achieve this, alternative, controllable light sources, such as ultraviolet light emitting diodes (UV LEDs) with high power and spatial control are required. Preferably, LEDs are arranged in a suitable standardized 96-well microtiter plate format. We designed such an array and established the methods required for heat management and enabling stable, controllable illumination over time.}, language = {en} } @article{KnihaDvořakHaladaetal.2020, author = {Kniha, Edwin and Dvoř{\´a}k, V{\´i}t and Halada, Petr and Milchram, Markus and Obwaller, Adelheid G. and Kuhls, Katrin and Schlegel, Susanne and K{\"o}hsler, Martina and Poeppl, Wolfgang and Bakran-Lebl, Karin and Fuehrer, Hans-Peter and Volfov{\´a}, Věra and Mooseder, Gerhard and Ivovic, Vladimir and Volf, Petr and Walochnik, Julia}, title = {Integrative Approach to Phlebotomus mascittii Grassi, 1908: First Record in Vienna with New Morphological and Molecular Insights}, series = {Pathogens}, volume = {9}, journal = {Pathogens}, number = {12}, publisher = {MDPI}, issn = {2076-0817}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13600}, year = {2020}, abstract = {Sand flies (Diptera: Psychodidae: Phlebotominae) are blood-feeding insects that transmit the protozoan parasites Leishmania spp. and various arthropod-borne (arbo) viruses. While in Mediterranean parts of Europe the sand fly fauna is diverse, in Central European countries including Austria mainly Phlebotomus mascittii is found, an assumed but unproven vector of Leishmania infantum. To update the currently understudied sand fly distribution in Austria, a sand fly survey was performed and other entomological catches were screened for sand flies. Seven new trapping locations of Ph. mascittii are reported including the first record in Vienna, representing also one of the first findings of this species in a city. Morphological identification, supported by fluorescence microscopy, was confirmed by two molecular approaches, including sequencing and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) protein profiling. Sand fly occurrence and activity were evaluated based on surveyed locations, habitat requirements and climatic parameters. Moreover, a first comparison of European Ph. mascittii populations was made by two marker genes, cytochrome c oxidase subunit 1 (COI), and cytochrome b (cytb), as well as MALDI-TOF mass spectra. Our study provides new important records of Ph. mascittii in Austria and valuable data for prospective entomological surveys. MALDI-TOF MS protein profiling was shown to be a reliable tool for differentiation between sand fly species. Rising temperatures and globalization demand for regular entomological surveys to monitor changes in species distribution and composition. This is also important with respect to the possible vector competence of Ph. mascittii.}, language = {en} } @article{DemskiSeidlitzKukeetal.2025, author = {Demski, Nils Maximilian and Seidlitz, Holger and Kuke, Felix and Dorn, Oliver Niklas and Zoglauer, Janina and H{\"u}ckstaedt, Tobias and Kamm, Paul Hans and Garc{\´i}a-Moreno, Francisco and Kremp, Noah and Dreyer, Christian and Oberschmidt, Dirk}, title = {Flow-Line-Reducing Tetrahedral Metal Effect Pigments for Injection Molding: A Yield-Rate-Improved Particle Manufacturing Method Based on Soft UVImprint Lithography}, series = {Polymers}, volume = {17}, journal = {Polymers}, number = {19}, publisher = {MDPI}, issn = {2073-4360}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20850}, year = {2025}, abstract = {This publication presents an improved manufacturing method for tetrahedral metal effect pigment particles that demonstrates reduced flowlines in injection-molded polymer components compared with conventional platelet-shaped pigment particles. The previously published cold forming process for tetrahedral particles, made entirely from aluminum, faced manufacturing challenges, resulting in a high reject rate due to particle adhesion to the micro-structured mold roller. In contrast, this study introduces a new manufacturing method for tetrahedral particles, now consisting of metallized UV-cured thermoset polymer. These particles, dispersed in amorphous matrix thermoplastics, have shown to maintain their shape during the injection molding process. The manufacturing technique for these novel particles is based on UV imprint lithography, omitting the reject rates compared with the previously presented cold rolling process of tetrahedral full aluminum particles. Thus, the novel manufacturing technique for tetrahedral pigment particles shows increased potential for automation through roll-to-roll manufacturing in the future.}, language = {en} } @article{BaleelaLlewellynFitzpatricketal.2014, author = {Baleela, Rania and Llewellyn, Martin S. and Fitzpatrick, Sinead and Kuhls, Katrin and Sch{\"o}nian, Gabriele and Miles, Michael A. and Mauricio, Isabel L.}, title = {Leishmania donovani populations in Eastern Sudan: temporal structuring and a link between human and canine transmission}, series = {Parasites \& Vectors}, volume = {7}, journal = {Parasites \& Vectors}, number = {496}, issn = {1756-3305}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5921}, pages = {9}, year = {2014}, abstract = {Visceral leishmaniasis (VL), caused by the members of the Leishmania donovani complex, has been responsible for devastating VL epidemics in the Sudan. Multilocus microsatellite and sequence typing studies can provide valuable insights into the molecular epidemiology of leishmaniasis, when applied at local scales. Here we present population genetic data for a large panel of strains and clones collected in endemic Sudan between 1993 and 2001.}, language = {en} } @article{TanneKracherDietzeletal.2014, author = {Tanne, Johannes and Kracher, Daniel and Dietzel, Birgit and Schulz, Burkhard and Ludwig, Roland and Lisdat, Fred and Scheller, Frieder W. and Bier, Frank Fabian}, title = {Carboxylated or Aminated Polyaniline—Multiwalled Carbon Nanotubes Nanohybrids for Immobilization of Cellobiose Dehydrogenase on Gold Electrodes}, series = {Biosensors}, volume = {4}, journal = {Biosensors}, number = {4}, issn = {2079-6374}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5826}, pages = {370 -- 386}, year = {2014}, abstract = {Polymer-multiwalled carbon nanotube (MWCNT) nanohybrids, which differ in surface charge have been synthesized to study the bioelectrocatalysis of adsorbed cellobiose dehydrogenase (CDH) from Phanerochaete sordida on gold electrodes. To obtain negatively charged nanohybrids, poly(3-amino-4-methoxybenzoic acid-co-aniline) (P(AMB-A)) was covalently linked to the surface of MWCNTs while modification with p-phenylenediamine (PDA) converted the COOH-groups to positively charged amino groups. Fourier transform infrared spectroscopy (FTIR) measurements verified the p-phenylenediamine (PDA) modification of the polymer-CNT nanohybrids. The positively charged nanohybrid MWCNT-P(AMB-A)-PDA promoted direct electron transfer (DET) of CDH to the electrode and bioelectrocatalysis of lactose was observed. Amperometric measurements gave an electrochemical response with KMapp = 8.89 mM and a current density of 410 nA/cm2 (15 mM lactose). The catalytic response was tested at pH 3.5 and 4.5. Interference by ascorbic acid was not observed. The study proves that DET between the MWCNT-P(AMB-A)-PDA nanohybrids and CDH is efficient and allows the sensorial detection of lactose.}, language = {en} } @article{FischbachLohBieretal.2017, author = {Fischbach, Jens and Loh, Qiuting and Bier, Frank Fabian and Lim, Theam Soon and Frohme, Marcus and Gl{\"o}kler, J{\"o}rn}, title = {Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9248}, year = {2017}, abstract = {We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity. In addition, the newly identified properties may also be useful in other enzymatic assays which do not generate nucleic acids but are based on inorganic pyrophosphate. Finally, we propose that our screening method may provide a blueprint for rapid screening of compounds for detecting inorganic pyrophosphate.}, language = {en} } @article{RievajStopkaVrabeletal.2016, author = {Rievaj, Vladimir and Stopka, Ondrej and Vrabel, Jan and Mokrickova, Lenka and Schmidt, Conrad}, title = {The Impact of Air Resistance on the Fuel Consumption in Real Conditions within the Transport Operation}, series = {Communications - Scientific Letters of the University of Zilina}, volume = {18}, journal = {Communications - Scientific Letters of the University of Zilina}, number = {2}, publisher = {University of Žilina}, address = {Žilina}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21159}, pages = {57 -- 61}, year = {2016}, abstract = {This paper presents the impact of air resistance (air resistance) on fuel consumption of the particular vehicle under real traffic conditions. In the introductory and subsequent part of the paper, the individual resistances influencing the moving vehicle are characterized. In the following chapter, the specific factors such as air resistance, driving speed, air temperature and air resistance coefficient in the context of their impact on fuel consumption of the particular vehicle are identified and described; as well as the comparisons of fuel consumption when the vehicle is moving on the highway with closed and open windows under different conditions of road traffic are performed.}, language = {en} } @inproceedings{Neumann2025, author = {Neumann, Gaby}, title = {From human experts to AI agents: Agentic AI for knowledge-intense problem-solving in logistics?}, series = {Proceedings of the 26th European Conference on Knowledge Management : VOL 1}, booktitle = {Proceedings of the 26th European Conference on Knowledge Management : VOL 1}, publisher = {Academic Conferences and Publishing International}, address = {Reading}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21223}, pages = {719 -- 727}, year = {2025}, abstract = {Logistics planning is a complex and complicated problem solving process requiring a wide range of knowledge and competence. A planning person or team represents a particular set of knowledge, skills, experience and personal attitudes. His, her or their level of competence decides about success or failure of the planning and about the quality of its results. With this, logistics planning is knowledge-based and knowledge-creating. Because of this, Knowledge Management can provide tremendous support to the planning person. Even though, there is a wide variety of (software) tools applicable to solve specific sub-problems throughout the planning process, human expertise is the key to develop creative planning solutions so far. Latest developments with regard to Artificial Intelligence (AI) might change this picture. AI is one of the most promising technological advancements, but also one of the most ambivalently discussed topics these days. It has surpassed humans at a number of tasks already and continues in doing so at new tasks in an increasing rate. Because of this, AI is capable to assist humans in many different ways. The latest boost of development moved AI application from those sophisticated communicators or task-oriented AI to intelligent agents or agentic AI allowing for autonomous, goal-driven decision-making. Hybrid approaches combine those advanced AI capabilities with human oversight, offering context-aware adaptability without full autonomy. In this way, artificial intelligence and human intelligence join forces in teams, for example, to solve complex problems creatively. Against this background, the paper analyses agentic AI with regard to its potential to support creative problem solving in a knowledge-intense field like logistics planning. Will AI agents become co-workers in logistics planning teams or can agentic AI design logistics solutions autonomously? With this, the paper focusses on chances and challenges coming with the highly dynamic evolution of AI within a complex, knowledge-intense application area where human experience, problem-solving capability and creativity is decisive. It contributes to discussions about necessary adjustments in how organizations manage their knowledge considering artificial and human intelligence.}, language = {en} } @article{PopaSchmidt2013, author = {Popa, Mihaela and Schmidt, Conrad}, title = {On the Rail-Based Freight Corridor Between CE and SEE Regions and the Main Obstacles on Romanian Territory}, series = {Transport Problems}, volume = {8}, journal = {Transport Problems}, number = {1}, publisher = {Silesian University of Technology}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21193}, pages = {47 -- 56}, year = {2013}, abstract = {The project "Freight and Logistics Advancement in Central/South-East Europe - Validation of trade and transport processes, Implementation of improvement actions, Application of co-coordinated structures" (in short - FLAVIA) is carried out under the Central Europe - Cooperation for Success Programme, cofunded by the European Regional Development Fund. One of the main objectives of FLAVIA project is to consolidate a logistic corridor from Central Europe (CE) to the South-East Europe (SEE) and the Black Sea Region, based on rail and inland waterways intermodal transport. In this paper we discuss the partial outputs of FLAVIA project, mainly related to the identified actual status of rail-based intermodal transport and trade obstacles of the freight flows on the Romanian territory and the used methodology. Several operational and long-term measures to improve the trade and intermodal transport are listed, considering the advantages of the geo-strategic potential of Romania location, connected with the several improvement directions already considered into the new released intermodal strategy.}, language = {en} } @article{VrabelStopkaRievajetal.2016, author = {Vrabel, Jan and Stopka, Ondrej and Rievaj, Vladimir and Sarkan, Branislav and Pruskova, Kristyna and Michalk, Philip}, title = {Measuring the Resistance of Tires for Passenger Vehicle against the Rolling and Sliding on Loading Area of the Flatbed Truck when Providing the Transport Services}, series = {Communications - Scientific Letters of the University of Zilina}, volume = {18}, journal = {Communications - Scientific Letters of the University of Zilina}, number = {2}, publisher = {University of Žilina}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21168}, pages = {124 -- 128}, year = {2016}, abstract = {This paper deals with the size of the forces affecting the vehicle during the transportation on a flatbed truck, railway wagon or container. It is necessary to secure the vehicle against these forces properly in order to prevent vehicles replacement. The laboratory measurements were performed in order to find out the size of coefficient of friction between the tire and the vehicles loading area. During the measurements, vehicle had different gears in order to determine to what extent the size of mechanical resistances affects the fixing and securing the vehicle against its replacement on the loading area. However, this paper does not propose the solution for securing the passenger vehicle on the loading area of a truck, railway wagon or container.}, language = {en} } @article{KubanovaSchmidt2016, author = {Kubanova, Jaroslava and Schmidt, Conrad}, title = {Multimodal and Intermodal Transportation Systems}, series = {Communications - Scientific Letters of the University of Zilina}, volume = {18}, journal = {Communications - Scientific Letters of the University of Zilina}, number = {2}, publisher = {University of Žilina}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21177}, pages = {104 -- 108}, year = {2016}, abstract = {The aim of this paper is to provide information on the general characterization of multimodal transport, intermodal and combined transport. There is also mentioned the distribution of basic transport processes and types of transhipment. Finally, this paper describes the practical examples of multimodal transport.}, language = {en} } @article{LizbetinVejsCahaetal.2016, author = {Lizbetin, Jan and Vejs, Petr and Caha, Zdenek and Lizbetinova, Lenka and Michalk, Philip}, title = {The Possibilities of Dynamic Shipment Weighing in Rail Freight Transport}, series = {Communications - Scientific Letters of the University of Zilina}, volume = {18}, journal = {Communications - Scientific Letters of the University of Zilina}, number = {2}, publisher = {University of Žilina}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21186}, pages = {113 -- 117}, year = {2016}, abstract = {This article deals with an analysis of the methods of the dynamic weighing of rail vehicles. The measurement of axle load (both static and dynamic) is one of the current standard processes within the technical specifications for interoperability (TSI).}, language = {en} } @article{LehnertLiebchenSchiefelbuschetal.2026, author = {Lehnert, Martin and Liebchen, Christian and Schiefelbusch, Martin and Bruder, Peter and Harmann, Dennis}, title = {Insights into Ridepooling efficiency: A case study analysis using a novel operational performance measure framework}, series = {Journal of Urban Mobility}, volume = {9}, journal = {Journal of Urban Mobility}, publisher = {Elsevier}, issn = {2667-0917}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20971}, year = {2026}, abstract = {The efficiency of demand responsive transport (DRT) services, such as ridepooling, has garnered significant attention across various (simulation) studies. However, a deeper look into the metrics employed to assess system performance exposes notable discrepancies in their utilization. Notably, certain indicators, such as the pooling rate, demonstrate a susceptibility to manipulation based on input parameters, potentially skewing results to give a more favorable impression of service performance. In this paper, we show that, under such circumstances, achieving a fair comparison between study outcomes and with traditional (public) transport modes becomes challenging. In light of these challenges, this study introduces a novel operational performance indicator: Operational System Efficiency (OSE). OSE is tailored to evaluate the operational efficiency of ridepooling systems in a holistic way. In particular, it combines important operational indicators such as detour factor and empty kilometers share, which are considered in numerous analyses. Hereby, OSE is fostering a more equitable assessment of service performance. We applied this methodology and calculated the indicators provided in other studies to two real-world trip datasets from ridepooling services in Berlin and M{\"u}nster, Germany, and compared the results. Distinct disparities emerge in comparison with conventional efficiency indicators. Consequently, the proposed OSE holds promise for stakeholders, including service providers, public transport companies, and regulatory authorities, as a valuable tool for determining the suitability of a ridepooling service for a given locale relative to other transport modalities, while also providing a transparent assessment of its efficiency.}, language = {en} } @article{HerkenhoffBroedelFrohme2024, author = {Herkenhoff, Marcos Edgar and Br{\"o}del, Oliver and Frohme, Marcus}, title = {Hops across Continents: Exploring How Terroir Transforms the Aromatic Profiles of Five Hop (Humulus lupulus) Varieties Grown in Their Countries of Origin and in Brazil}, series = {Plants}, volume = {13}, journal = {Plants}, number = {19}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19470}, year = {2024}, abstract = {Humulus lupulus, or hops, is a vital ingredient in brewing, contributing bitterness, flavor, and aroma. The female plants produce strobiles rich in essential oils and acids, along with bioactive compounds like polyphenols, humulene, and myrcene, which offer health benefits. This study examined the aromatic profiles of five hop varieties grown in Brazil versus their countries of origin. Fifty grams of pelletized hops from each strain were collected and analyzed using HS-SPME/GC-MS to identify volatile compounds, followed by statistical analysis with PLS-DA and ANOVA. The study identified 330 volatile compounds and found significant aromatic differences among hops from different regions. For instance, H. Mittelfr{\"u}her grown in Brazil has a fruity and herbaceous profile, while the German-grown variety is more herbal and spicy. Similar variations were noted in the Magnum, Nugget, Saaz, and Sorachi Ace varieties. The findings underscore the impact of terroir on hop aromatic profiles, with Brazilian-grown hops displaying distinct profiles compared to their counterparts from their countries of origin, including variations in aromatic notes and α-acid content.}, language = {en} } @article{HerkenhoffBroedelDilarrietal.2026, author = {Herkenhoff, Marcos Edgar and Br{\"o}del, Oliver and Dilarri, Guilherme and Bajay, Miklos Maximiliano and Frohme, Marcus and Costamilan, Carlos Andr{\´e} da Veiga Lima Rosa}, title = {Characterization of Volatile Compounds in Amarillo, Ariana, Cascade, Centennial, and El Dorado Hops Using HS-SPME/GC-MS}, series = {Compounds}, volume = {6}, journal = {Compounds}, number = {1}, publisher = {MDPI}, issn = {2673-6918}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21029}, year = {2026}, abstract = {Humulus lupulus L. (hops) is essential in brewing due to its contributions to bitterness, flavor, and aroma. This study compared the volatile profiles of five commercially important hop varieties—Amarillo, Ariana, Cascade, Centennial, and El Dorado—grown in their main regions of origin (United States for Amarillo, Cascade, and El Dorado; Germany for Ariana; and Brazil for Centennial). Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) enabled the identification of 312 volatile compounds, including monoterpenes (e.g., myrcene, linalool, geraniol), sesquiterpenes (e.g., humulene, caryophyllene), esters, alcohols, aldehydes, and ketones. Amarillo showed the highest myrcene content (22.61\% of the total volatile area), while Centennial was distinguished by elevated γ-muurolene (20.59\%), and El Dorado by the highest level of undecan-2-one (10.47\%), highlighting marked varietal differences in key aroma-active constituents. Multivariate, including principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), clearly discriminated the five varieties: PC1 (41.04\% of the variance) separated samples enriched in fruity/floral monoterpenes and esters from those dominated by woody/resinous sesquiterpenes, whereas PC2 (25.93\% of the variance) reflected variation in medium-chain esters, ketones, and waxy compounds. These chemometric patterns demonstrate that both genetic background and growing region terroir strongly shape hop volatile composition and, consequently, aroma potential, providing brewers with objective criteria for selecting hop varieties to achieve specific sensory profiles in beer.}, language = {en} } @article{KsianzouVillringerGrytsenkoetal.2025, author = {Ksianzou, Viachaslau and Villringer, Claus and Grytsenko, Kostyantyn and Pekur, Demyd and Lytvyn, Peter and Sopinskyy, Mykola and Lebedyeva, Iryna and Niemczyk, Agata and Baranowska, Jolanta}, title = {Structural and Optical Anomalies in Thin Films Grown in a Magnetic Field by Electron-Assisted Vacuum Deposition of PTFE}, series = {Macromolecular Materials and Engineering}, volume = {310}, journal = {Macromolecular Materials and Engineering}, number = {3}, publisher = {Wiley}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19712}, year = {2025}, abstract = {Polytetrafluoroethylene (PTFE) films are deposited in parallel and perpendicular magnetic fields (MF) by electron-enhanced vacuum deposition (EVD) and EVD + low-temperature plasma (LTP) methods. The structure, morphology, and nanomechanical properties of the films are studied by infrared spectroscopy (IRS), atomic force microscopy (AFM), and spectroscopic ellipsometry. The structure of the thicker films is closer to that of bulk PTFE than that of thin films. The films' crystallinity and surface roughness are higher than those deposited without MF. The birefringence of the refractive index (n) of the films deposited in the MF is inverse to the anisotropy of the n of the films deposited without MF. The hardness of the films is close to that of bulk PTFE.}, language = {en} } @article{SishodiaBenLtaiefScheeletal.2026, author = {Sishodia, Keshav and Ben Ltaief, Ltaief and Scheel, Niklas and F{\"o}ldes, Istv{\´a}n B. and Roos, Andreas Hult and Albrecht, Martin and Staněk, Maty{\´a}š and Jurkovičov{\´a}, Lucie and Hort, Ondrej and Nejdl, Jaroslav and Garc{\´i}a-Alfonso, Ernesto and Halberstadt, Nadine and Andreasson, Jakob and Klimešov{\´a}, Eva and Krikunova, Maria and Krishnan, Sivarama and Heidenreich, Andreas and Mudrich, Marcel}, title = {XUV fluorescence as a probe of interatomic coulombic decay of resonantly excited He nanodroplets}, series = {Scientific Reports}, volume = {16}, journal = {Scientific Reports}, number = {1}, publisher = {Springer Nature}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21050}, year = {2026}, abstract = {Superfluid He nanodroplets resonantly excited by extreme ultraviolet (XUV) pulses can relax via interatomic coulombic decay (ICD), generally considered an ultrafast process. Here, we introduce a novel approach to probe the dynamics of ICD in He nanodroplets over timescales ranging from femtoseconds to nanoseconds. Our method relies on detecting XUV fluorescence emitted from the nanodroplets as they are driven into a nanoplasma by subsequent intense infrared pulses. Nanoplasma ignition is facilitated by tunnel ionization of XUV-excited He∗ atoms attached to the droplets; it thus serves as a sensitive probe of their relaxation dynamics. The observed nanosecond-scale decay is attributed to ICD between pairs of He∗ atoms undergoing roaming motion on the droplet surface, as supported by quantum-mechanical and classical model calculations.}, language = {en} } @inproceedings{GrossKuhlStephanetal.2023, author = {Gross, Matthias and Kuhl, Thorsten and Stephan, Frank and Li, Xiangkun and Philipp, Sebastian and Grebinyk, Anna and Khachatryan, Vitali and Qian, Houjun and Aboulbanine, Zakaria and Amirkhanyan, Zohrab and Riemer, Felix and Oppelt, Anne and Krasilnikov, Mikhail}, title = {A beam line setup for flash radiation therapy with focused electron beams at the Pitz facility at DESY in Zeuthen: basic concept and dosimetry simulations}, series = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, booktitle = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, editor = {Istituto Nazionale Di Fisca Nucleare,}, publisher = {JACoW Publishing}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21132}, pages = {5000 -- 5003}, year = {2023}, abstract = {The aim of this work is to demonstrate the principal possibility to enhance the electron beam dose deposition in the depth of the sample for radiation therapy purposes. Trains of electron bunches of 22 MeV generated at PITZ are focused inside the sample using a dedicated fast deflector and a solenoid magnet. To explore the capabilities of the proposed setup, dose distributions are calculated for multiple electron bunches focused in a single point inside a water phantom. Electron beam focusing produces dose peaks with a tunable maximal dose depth which is interesting for healthy tissue sparing at the surface and enhancing treatment quality. The duration of the full bunch train is 1 ms. During this time interval, the FLASH effect could be efficiently triggered inside the irradiated target volume. Monte Carlo simulations based on the FLUKA code were performed to evaluate the depth dose curves distributions in a water phantom. Using the PITZ electron beam parameters, simulations have shown the possibility to produce a peak dose in water seven times higher than compared to the dose at the surface. Moreover, the RMS size homogeneous area around the maximal dose is approximately 25 mm.}, language = {en} } @inproceedings{KrasilnikovAboulbanineAdhikarietal.2023, author = {Krasilnikov, Mikhail and Aboulbanine, Zakaria and Adhikari, Gowri and Aftab, Namra and Asoyan, Aida and Davtyan, Hakob and Georgiev, Georgi and Good, James and Grebinyk, Anna and Gross, Matthias and Hoffmann, Andreas and Kongmon, Ekkachai and Li, Xiangkun and Lueangaramwong, Anusorn and Melkumyan, David and Mohanty, Sandeep and Niemczyk, Raffael and Oppelt, Anne and Qian, Houjun and Richard, Christopher and Schneidmiller, Evgeny and Stephan, Frank and Vashchenko, Grygorii}, title = {THz SASE FEL at PITZ: lasing at a wavelength of 100μm}, series = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, booktitle = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, editor = {Istituto Nazionale Di Fisca Nucleare,}, publisher = {JACoW Publishing}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21113}, pages = {3948 -- 3951}, year = {2023}, abstract = {Development of an accelerator-based tunable THz source prototype for pump-probe experiments at the European XFEL is ongoing at the Photo Injector Test facility at DESY in Zeuthen (PITZ). The proof-of-principle experiments on the THz SASE FEL are performed utilizing the LCLS-I undulator installed in the PITZ beamline. The first lasing at a center wavelength of 100 µm was observed in the summer of 2022. The lasing of the narrowband THz source was achieved using an electron beam with an energy of ~17 MeV and a bunch charge up to several nC. Optimization of beam transport and matching resulted in the measurement of THz radiation with a pulse energy of tens of µJ, measured with pyroelectric detectors. The THz FEL gain curves were measured by means of specially designed short coils along the undulator. The results of the first characterization of the THz source at PITZ will be presented.}, language = {en} } @article{SpeckVeronaReiffStephanetal.2026, author = {Speck, Sandy and Verona, Claudio and Reiff-Stephan, J{\"o}rg and B{\"o}hme, Andrea and Foitzik, Andreas}, title = {Development of a Realistic Brain Phantom for Medical Education: An Ethical and Technical Alternative to Animal Testing}, series = {Key Engineering Materials}, volume = {1038}, journal = {Key Engineering Materials}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21070}, pages = {67 -- 72}, year = {2026}, abstract = {This study presents the development of a realistic brain phantom as a humane, practical alternative to animal use in medical training, in line with the 3R principles and Directive 2010/63/EU. The phantom is designed to support ultrasound-based education for diagnostic and interventional procedures while improving patient safety through controlled, repeatable practice. High‑resolution CT data were converted to CAD models and additively manufactured as moulds; a gelatin‑based soft‑tissue matrix with glycerin and potassium sorbate provides elasticity and durability. Functional features include fluid‑fillable ventricular structures enabling drainage and puncture simulations, and an integrated high‑density tumour insert to model advanced scenarios. Ultrasound evaluation demonstrated clear echogenic differentiation between tumour, ventricles, and surrounding tissue, confirming the model's imaging fidelity and suitability for hands‑on training. The phantom proved cost‑efficient and reusable, facilitating standardised teaching of complex procedures without ethical approval barriers. A limitation is the material's gradual mechanical instability under repeated probe contact, motivating investigations into synthetic or hybrid matrices to enhance longevity and reuse. Overall, the brain phantom constitutes an ethical, technically robust, and resource‑efficient training tool that addresses critical needs in healthcare quality and safety by reducing avoidable errors through simulation‑based competence development.}, language = {en} } @inproceedings{GrossHoffmannGeorgievetal.2023, author = {Gross, Matthias and Hoffmann, Andreas and Georgiev, Georgi and Kuhl, Thorsten and Li, Xiangkun and Oppelt, Anne and Boonpornprasert, Prach and Philipp, Sebastian and Grebinyk, Anna and Vashchenko, Grygorii and Aftab, Namra and Adhikari, Gowri and Richard, Christopher and Stephan, Frank and Khachatryan, Vitali and Riemer, Felix and Krasilnikov, Mikhail and Amirkhanyan, Zohrab}, title = {Comparison of measurements and simulation results of dose for the FLASH radiation therapy beamline at PITZ}, series = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, booktitle = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, editor = {Istituto Nazionale Di Fisca Nucleare,}, publisher = {JACoW Publishing}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21126}, pages = {4996 -- 4999}, year = {2023}, abstract = {The high-brightness electron beam at the Photo Injector Test facility at DESY in Zeuthen (PITZ) is now also used for FLASHlab@PITZ: an R\&D platform for studying radiation biology and the FLASH effect in radiation therapy. The available parameter space of the electron beam with a momentum of 22 MeV/c allows bunch charges from 10 pC up to 5nC, bunch durations of 0.1-60ps, and bunch train lengths up to 1 ms. The number of bunches in the single train can currently be varied between 1 and 1000 bunches, with an upgrade to 4500 foreseen in 2023. Radiation biology studies require accurate dose prediction, therefore Monte Carlo simulations based on the FLUKA code were performed. According to estimations, dose delivery of 0.002 Gy (low charge case 0.1pC) and 10Gy (high charge case 5nC) is possible, if the beam is confined to a circular area with a radius of 5 mm with a lead collimator. For the Monte Carlo simulations, the experimental setup was accurately modeled, including the exit window, lead collimator, etc. Dose measurements were used to compare simulations with experiments. Dose profiles were experimentally measured with Gafchromic films and then compared with Monte Carlo simulations. The first experiments at FLASHlab@PITZ in 2023 have demonstrated flexible dose options for studying the FLASH effect and radiation biology studies.}, language = {en} } @article{RoggeZinnProspositoetal.2017, author = {Rogge, Christian and Zinn, Steffen and Prosposito, Paolo and Francini, Roberto and Foitzik, Andreas}, title = {Transmitted light pH optode for small sample volumes}, series = {Journal of Sensors and Sensor Systems}, volume = {6}, journal = {Journal of Sensors and Sensor Systems}, number = {2}, issn = {2194-878X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10093}, pages = {351 -- 359}, year = {2017}, abstract = {An innovative concept of a low-cost pH optode with working volumes of less than 150 µL is presented. The pH monitoring is based on the color changing effect of pH indicators. The optode includes an RGB color sensor patch TCS34725 from Adafruit, a controllable LED and reactor slides and is addressed by a self-written LabVIEW© software. Utilizing the hue value of the HSV color model, it is possible to analyze the color change of the indicator and estimate the pH value of the analyzed samples by exploiting sigmoidal fit models. Measurements carried out with phenol red and DMEM (Dulbecco's Modified Eagle's Medium) reported a standard error of calibration in the physiologic pH range (6.5-7.5) of ±0.04 pH units.}, language = {en} } @article{KrausBoehmeRinati2026, author = {Kraus, Mirjam and B{\"o}hme, Andrea and Rinati, Gianluca Verona}, title = {Verification of a Novel Mathematical Model for Determination of the Biomass Specific Growth Rate in Bioprocesses Using Relative Change in Biomass Measurements}, series = {Defect and Diffusion Forum}, volume = {446}, journal = {Defect and Diffusion Forum}, publisher = {Trans Tech Publications}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21081}, pages = {57 -- 62}, year = {2026}, abstract = {This study presents a new mathematical model for determining the specific growth rate of biomass in biotechnological production processes, which aims to optimize the production of biotechnological products such as the advanced material polyhydroxyalkanoates. The specific growth rate is classified by the FDA as a critical process parameter that affects product quality and quantity, but is difficult for laboratory personnel to determine. Therefore, a simple and robust method for real-time monitoring and control is crucial. According to the current state of the art, the established Luedeking-Piret model for determining the specific growth rate requires the determination of the biomass as an absolute value to initialize the model and to determine two further model parameters. However, determining the biomass is time-consuming and error-prone. The new relative model replaces this value with the relative change in biomass, which can be easily recorded using standard laboratory methods such as optical density measurement. This eliminates the need for time-consuming and resource-intensive preliminary work. Despite this simplification, simulation tests have shown that the new model delivers identical results to the established model. It represents an independent, precise alternative and offers advantages in terms of handling. The results underline the model's potential to make bioprocesses more sustainable and efficient. Especially in research, material consumption, laboratory time and costs can be reduced compared to the established model. Future experiments will further investigate the performance of the new approach compared to the established model.}, language = {en} } @article{RoedenbeckHerold2026, author = {Roedenbeck, Marc and Herold, Marcel}, title = {Personality Profiles in Online Job Advertisements: Applying a Weighted Closed Vocabulary Approach to Identify Generic Profiles and Clusters}, series = {SAGE Open}, volume = {16}, journal = {SAGE Open}, number = {1}, publisher = {Sage}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21282}, year = {2026}, abstract = {On the background of the supplementary applicant-job fit theory, this study tests the application of a weighted closed vocabulary approach as introduced by Ostendorf on a large corpus of online job advertisements (OJA). Therefore, a large dataset of online job advertisements (OJAs) was scraped from a German job portal (N = 151k), and a sample (n = 3,239) was selected based upon Porter's Value Chain and corresponding job functions. The dataset was pre-processed with techniques of natural language processing, and the predefined words extracted from the OJAs were weighted with the average subject matter expert rating, as offered in the vocabulary of Ostendorf. The results reveal that, first, 0 to 12 words describing personality are used across OJAs, second, that HR, sales, and finance positions show values higher than sample mean (3.22), third, that HR positions show loadings across all dimensions of personality above the sample means (extroversion: 2.32, agreeableness: 3.98, conscientiousness: 4.28, emotional stability: 3.54, openness: 2.0) followed by sales. The job profiles being significantly parallel on equal levels are HR clerk and referee, as well as IT, R\&D, and procurement. While conscientiousness is reported to be an important predictor of performance, our study showed only low to average importance in OJAs.}, language = {en} } @article{ShamsSchmitzSmekhovaetal.2021, author = {Shams, S. Fatemeh and Schmitz, Detlef and Smekhova, Alevtina and Ghazanfari, Mohammad Reza and Giesen, Margret and Weschke, Eugen and Chen, Kai and Luo, Chen and Radu, Florin and Schmitz-Antoniak, Carolin}, title = {Element-specific contributions to improved magnetic heating of theranostic CoFe2O4 nanoparticles decorated with Pd}, series = {Scientific Reports}, volume = {11}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14756}, year = {2021}, abstract = {Decoration with Pd clusters increases the magnetic heating ability of cobalt ferrite (CFO) nanoparticles by a factor of two. The origin of this previous finding is unraveled by element-specific X-ray absorption spectroscopy (XAS) and magnetic circular dichroism (XMCD) combined with atomic multiplet simulations and density functional theory (DFT) calculations. While the comparison of XAS spectra with atomic multiplet simulations show that the inversion degree is not affected by Pd decoration and, thus, can be excluded as a reason for the improved heating performance, XMCD reveals two interrelated responsible sources: significantly larger Fe and Co magnetic moments verify an increased total magnetization which enhances the magnetic heating ability. This is accompanied by a remarkable change in the field-dependent magnetization particularly for Co ions which exhibit an increased low-field susceptibility and a reduced spin canting behavior in higher magnetic fields. Using DFT calculations, these findings are explained by reduced superexchange between ions on octahedral lattice sites via oxygen in close vicinity of Pd, which reinforces the dominating antiparallel superexchange interaction between ions on octahedral and tetrahedral lattice sites and thus reduces spin canting. The influence of the delocalized nature of Pd 4d electrons on the neighboring ions is discussed and the conclusions are illustrated with spin density isosurfaces of the involved ions. The presented results pave the way to design nanohybrids with tailored electronic structure and magnetic properties.}, language = {en} } @article{KalishettyhalliMahadevaiahPerezLiskeretal.2022, author = {Kalishettyhalli Mahadevaiah, Mamathamba and P{\´e}rez, Eduardo and Lisker, Marco and Schubert, Markus Andreas and Perez-Bosch Quesada, Emilio and Wenger, Christian and Mai, Andreas}, title = {Modulating the Filamentary-Based Resistive Switching Properties of HfO₂ Memristive Devices by Adding Al₂O₃ Layers}, series = {Electronics}, volume = {11}, journal = {Electronics}, number = {10}, address = {MDPI}, issn = {2079-9292}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16172}, year = {2022}, abstract = {The resistive switching properties of HfO₂ based 1T-1R memristive devices are electrically modified by adding ultra-thin layers of Al₂O₃ into the memristive device. Three different types of memristive stacks are fabricated in the 130 nm CMOS technology of IHP. The switching properties of the memristive devices are discussed with respect to forming voltages, low resistance state and high resistance state characteristics and their variabilities. The experimental I-V characteristics of set and reset operations are evaluated by using the quantum point contact model. The properties of the conduction filament in the on and off states of the memristive devices are discussed with respect to the model parameters obtained from the QPC fit.}, language = {en} } @article{HooglandBoettcherVerhoefetal.2016, author = {Hoogland, A. Marije and B{\"o}ttcher, Ren{\´e} and Verhoef, Esther and Jenster, Guido and van Leenders, Geert J.L.H.}, title = {Gene-expression analysis of gleason grade 3 tumor glands embedded in low- and high-risk prostate cancer}, series = {Oncotarget}, volume = {7}, journal = {Oncotarget}, number = {25}, issn = {1949-2553}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6573}, pages = {37846 -- 37856}, year = {2016}, abstract = {The Gleason score (GS) of prostate cancer on diagnostic biopsies is an important parameter for therapeutic decision-making. Biopsy GS under-estimates the actual GS at radical prostatectomy in a significant number of patients due to samplingartifact. The aim of this study was to identify markers that are differentially expressed in Gleason grade 3 (GG3) tumor glands embedded in GS 4 + 3 = 7 and GS 3 + 3 = 6 prostate cancer using laser capture microdissection and RNA sequencing. GG3 tumor glands embedded in nine GS 3 + 3 = 6 and nine GS 4 + 3 = 7 prostate cancers were isolated by laser capture microdissection of frozen radical prostatectomy specimens. After RNA amplification and RNA sequencing, differentially expressed genes in both GG3 components were identified by a 2log fold change > 1.0 and p-value < 0.05. We applied immunohistochemistry on a tissue micro-array representing 481 radical prostatectomy samples for further validation on protein level. A total of 501 genes were up-regulated and 421 down-regulated in GG3 glands embedded in GS 4 + 3 = 7 as compared to GS 3 + 3 = 6 prostate cancer. We selected HELLS, ZIC2 and ZIC5 genes for further validation. ZIC5 mRNA was up-regulated 17 fold (p = 8.4E-07), ZIC2 8 fold (p = 1.3E-05) and HELLS 2 fold (p = 0.006) in GG3 glands derived from GS 4 + 3 = 7. HELLS expression of ≥ 1\% occurred in 10\% GS < 7, 17\% GS 7 and 43\% GS >7 prostate cancer (p < 0.001). Using a cut-off of ≥ 1\%, protein expression of ZIC5 was present in 28\% GS < 7, 43\% GS 7 and 57\% GS > 7 cancer (p < 0.001). ZIC2 was neither associated with GS nor outcome in our validation set. HELLS was independently predictive for biochemical-recurrence after radical prostatectomy (HR 2.3; CI 1.5-3.6; p < 0.01). In conclusion, HELLS and ZIC5 might be promising candidate markers for selection of biopsy GS 6 prostate cancer being at risk for up-grading at prostatectomy.}, language = {en} } @article{GrebinykPrylutskaBuchelnikovetal.2019, author = {Grebinyk, Anna and Prylutska, Svitlana and Buchelnikov, Anatoliy and Tverdokhleb, Nina and Grebinyk, Sergii and Evstigneev, Maxim and Matyshevska, Olga and Cherepanov, Vsevolod and Prylutskyy, Yuriy and Yashchuk, Valeriy and Naumovets, Anton and Ritter, Uwe and Dandekar, Thomas and Frohme, Marcus}, title = {C60 Fullerene as an Effective Nanoplatform of Alkaloid Berberine Delivery into Leukemic Cells}, series = {Pharmaceutics}, volume = {11}, journal = {Pharmaceutics}, number = {11}, publisher = {MDPI}, issn = {1999-4923}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12932}, year = {2019}, abstract = {A herbal alkaloid Berberine (Ber), used for centuries in Ayurvedic, Chinese, Middle-Eastern, and native American folk medicines, is nowadays proved to function as a safe anticancer agent. Yet, its poor water solubility, stability, and bioavailability hinder clinical application. In this study, we have explored a nanosized carbon nanoparticle—C60 fullerene (C60)—for optimized Ber delivery into leukemic cells. Water dispersions of noncovalent C60-Ber nanocomplexes in the 1:2, 1:1, and 2:1 molar ratios were prepared. UV-Vis spectroscopy, dynamic light scattering (DLS), and atomic force microscopy (AFM) evidenced a complexation of the Ber cation with the negatively charged C60 molecule. The computer simulation showed that π-stacking dominates in Ber and C60 binding in an aqueous solution. Complexation with C60 was found to promote Ber intracellular uptake. By increasing C60 concentration, the C60-Ber nanocomplexes exhibited higher antiproliferative potential towards CCRF-CEM cells, in accordance with the following order: free Ber < 1:2 < 1:1 < 2:1 (the most toxic). The activation of caspase 3/7 and accumulation in the sub-G1 phase of CCRF-CEM cells treated with C60-Ber nanocomplexes evidenced apoptosis induction. Thus, this study indicates that the fast and easy noncovalent complexation of alkaloid Ber with C60 improved its in vitro efficiency against cancer cells.}, language = {en} } @article{KoeberleinBankRothetal.2022, author = {K{\"o}berlein, Jana and Bank, Lukas and Roth, Stefan and K{\"o}se, Ekrem and Kuhlmann, Timm and Prell, Bastian and Stange, Maximilian and M{\"u}nnich, Marc and Flum, Dominik and Moog, Daniel and Ihlenfeldt, Steffen and Sauer, Alexander and Weigold, Matthias and Schilp, Johannes}, title = {Simulation Modeling for Energy-Flexible Manufacturing: Pitfalls and How to Avoid Them}, series = {Energies}, volume = {15}, journal = {Energies}, number = {10}, publisher = {MDPI}, issn = {1996-1073}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16152}, year = {2022}, abstract = {Due to the high share of industry in total electricity consumption, industrial demand-side management can make a relevant contribution to the stability of power systems. At the same time, companies get the opportunity to reduce their electricity procurement costs by taking advantage of increasingly fluctuating prices on short-term electricity markets, the provision of system services on balancing power markets, or by increasing the share of their own consumption from on-site generated renewable energy. Demand-side management requires the ability to react flexibly to the power supply situation without negatively affecting production targets. It also means that the management and operation of production must consider not only production-related parameters but also parameters of energy availability, which further increase the complexity of decision-making. Although simulation studies are a recognized tool for supporting decision-making processes in production and logistics, the simultaneous simulation of material and energy flows has so far been limited mainly to issues of energy efficiency as opposed to energy flexibility, where application-oriented experience is still limited. We assume that the consideration of energy flexibility in the simulation of manufacturing systems will amplify already known pitfalls in conducting simulation studies. Based on five representative industrial use cases, this article provides practitioners with application-oriented experiences of the coupling of energy and material flows in simulation modeling of energy-flexible manufacturing, identifies challenges in the simulation of energy-flexible production systems, and proposes approaches to face these challenges. Seven pitfalls that pose a particular challenge in simulating energy-flexible manufacturing have been identified, and possible solutions and measures for avoiding them are shown. It has been found that, among other things, consistent management of all parties involved, early clarification of energy-related, logistical, and resulting technical requirements for models and software, as well as the application of suitable methods for validation and verification are central to avoiding these pitfalls. The identification and characterization of challenges and the derivation of recommendations for coping with them can raise awareness of typical pitfalls. This paper thus helps to ensure that simulation studies of energy-flexible production systems can be carried out more efficiently in the future.}, language = {en} } @article{KoelschRadonGolubetal.2020, author = {K{\"o}lsch, Adrian and Radon, C. and Golub, M. and Baumert, A. and B{\"u}rger, J{\"o}rg and Mielke, Thorsten and Lisdat, Fred and Feoktystov, Artem and Pieper, J{\"o}rg and Zouni, Athina and Wendler, Petra}, title = {Current limits of structural biology: The transient interaction between cytochrome c6 and photosystem I}, series = {Current Research in Structural Biology}, volume = {2}, journal = {Current Research in Structural Biology}, issn = {2665-928X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13628}, pages = {171 -- 179}, year = {2020}, abstract = {Trimeric photosystem I from the cyanobacterium Thermosynechococcus elongatus (TePSI) is an intrinsic membrane protein, which converts solar energy into electrical energy by oxidizing the soluble redox mediator cytochrome c6 (Cyt c6) and reducing ferredoxin. Here, we use cryo-electron microscopy and small angle neutron scattering (SANS) to characterize the transient binding of Cyt c6 to TePSI. The structure of TePSI cross-linked to Cyt c6 was solved at a resolution of 2.9 {\AA} and shows additional cofactors as well as side chain density for 84\% of the peptide chain of subunit PsaK, revealing a hydrophobic, membrane intrinsic loop that enables binding of associated proteins. Due to the poor binding specificity, Cyt c6 could not be localized with certainty in our cryo-EM analysis. SANS measurements confirm that Cyt c6 does not bind to TePSI at protein concentrations comparable to those for cross-linking. However, SANS data indicate a complex formation between TePSI and the non-native mitochondrial cytochrome from horse heart (Cyt cHH). Our study pinpoints the difficulty of identifying very small binding partners (less than 5\% of the overall size) in EM structures when binding affinities are poor. We relate our results to well resolved co-structures with known binding affinities and recommend confirmatory methods for complexes with KM values higher than 20 μM.}, language = {en} } @article{DevulapallyBuergerMielkeetal.2018, author = {Devulapally, Praneeth Reddy and B{\"u}rger, J{\"o}rg and Mielke, Thorsten and Konthur, Zolt{\´a}n and Lehrach, Hans and Yaspo, Marie-Laure and Gl{\"o}kler, J{\"o}rn and Warnatz, Hans-J{\"o}rg}, title = {Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes}, series = {Genome Medicine}, volume = {10}, journal = {Genome Medicine}, issn = {1756-994X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10538}, pages = {1 -- 12}, year = {2018}, abstract = {Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple and cost-effective emulsion-based single-cell paired antibody repertoire sequencing method that employs only basic laboratory equipment. We performed a proof-of-concept using mixed mouse hybridoma cells and we also showed that our method can be used for discovery of novel antigen-specific monoclonal antibodies by sequencing human CD19+ B cell IgM and IgG repertoires isolated from peripheral whole blood before and seven days after Td (Tetanus toxoid/Diphtheria toxoid) booster immunization. We anticipate broad applicability of our method for providing insights into adaptive immune responses associated with various diseases, vaccinations, and cancer immunotherapies.}, language = {en} } @article{BaumannPohleZhangetal.2021, author = {Baumann, Elisabeth and Pohle, Ulrike and Zhang, Edward and Allen, Thomas and Villringer, Claus and Pulwer, Silvio and Gerhardt, Holger and Laufer, Jan}, title = {A backward-mode optical-resolution photoacoustic microscope for 3D imaging using a planar Fabry-P{\´e}rot sensor}, series = {Photoacoustics}, volume = {24}, journal = {Photoacoustics}, publisher = {Elsevier}, issn = {2213-5979}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14701}, pages = {100293}, year = {2021}, abstract = {Optical-resolution photoacoustic microscopy (OR-PAM) combines high spatial resolution and strong absorption-based contrast in tissue, which has enabled structural and spectroscopic imaging of endogenous chromophores, primarily hemoglobin. Conventional piezoelectric ultrasound transducers are typically placed far away from the photoacoustic source due to their opacity, which reduces acoustic sensitivity. Optical ultrasound sensors are an alternative as their transparency allows them to be positioned close to the sample with minimal source-detector distances. In this work, a backward-mode OR-PAM system based on a planar Fabry-P{\´e}rot ultrasound sensor and coaxially aligned excitation and interrogation beams was developed. Two 3D imaging modes, using raster-scanning for enhanced image quality and continuous-scanning for fast imaging, were implemented and tested on a leaf skeleton phantom. In fast imaging mode, a scan-rate of 100,000 A-lines/s was achieved. 3D images of a zebrafish embryo were acquired in vivo in raster-scanning mode. The transparency of the FP sensor in the visible and near-infrared wavelength region makes it suitable for combined functional and molecular imaging applications using OR-PAM and multi-photon fluorescence microscopy.}, language = {en} } @article{StumperBergerKlotscheetal.2025, author = {Stumper, Nele and Berger, J{\"o}rn and Klotsche, Jens and Gedat, Egbert and Hoff, Paula and Schmittat, Gabriela and Burmester, Gerd-R{\"u}diger and Kr{\"o}nke, Gerhard and Backhaus, Marina and Haugen, Ida Kristin and Ohrndorf, Sarah}, title = {To optimise the diagnostic process of rheumatic diseases affecting the hands using fluorescence optical imaging (FOI)}, series = {RMD Open}, volume = {11}, journal = {RMD Open}, number = {3}, publisher = {EULAR}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20698}, year = {2025}, abstract = {Background Accurate and rapid diagnosis of rheumatic diseases is essential for further treatment decision. Different rheumatic diseases present characteristic patterns (image features) in fluorescence optical imaging (FOI). We developed an atlas of FOI image features and tested its ability to differentiate various rheumatic diseases. Methods FOI images from patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA), connective tissue diseases (CTD) and osteoarthritis (OA) were analysed by two readers blinded for diagnosis and calibrated against each other, using the prima vista mode (PVM) and an automated 5-phase model. Twenty-six different reoccurring typical signal enhancement patterns (features) indicating inflamed joints, nail or skin were defined and all FOI images were scored accordingly. The feature frequency in each patient cohort and phase (PVM, 5-phase) was counted. Contingency tables were created with categorical variable counts and diagnosis using common formulae. Findings Four hundred thirty-eight patients with RA (n=117), PsA (n=110), CTD (n=121) and OA (n=90) were included. Once the data had been categorised, a two-step diagnostic pathway was developed: in the first step, OA was best distinguished from the other diseases with high specificity by five patterns (specificity >0.9, diagnostic OR between 2.34 and 8.24). In a second step, the remaining autoimmune diseases were differentiated from each other by a certain number of features (five for RA, 12 for PsA and four for CTD). Interpretation This was the first study to show that feature analysis in FOI helps to differentiate typical rheumatic diseases from each other, potentially simplifying and speeding up the diagnostic process. Therefore, FOI could be considered an additional component of a wider range of imaging techniques used in rheumatology.}, language = {en} } @article{GedatBergerKieseletal.2022, author = {Gedat, Egbert and Berger, J{\"o}rn and Kiesel, Denise and Failli, Vieri and Briel, Andreas and Welker, Pia}, title = {Features Found in Indocyanine Green-Based Fluorescence Optical Imaging of Inflammatory Diseases of the Hands}, series = {Diagnostics}, volume = {12}, journal = {Diagnostics}, number = {8}, publisher = {MDPI}, issn = {2075-4418}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16359}, year = {2022}, abstract = {Rheumatologists in Europe and the USA increasingly rely on fluorescence optical imaging (FOI, Xiralite) for the diagnosis of inflammatory diseases. Those include rheumatoid arthritis, psoriatic arthritis, and osteoarthritis, among others. Indocyanine green (ICG)-based FOI allows visualization of impaired microcirculation caused by inflammation in both hands in one examination. Thousands of patients are now documented and most literature focuses on inflammatory arthritides, which affect synovial joints and their related structures, making it a powerful tool in the diagnostic process of early undifferentiated arthritis and rheumatoid arthritis. However, it has become gradually clear that this technique has the potential to go even further than that. FOI allows visualization of other types of tissues. This means that FOI can also support the diagnostic process of vasculopathies, myositis, collagenoses, and other connective tissue diseases. This work summarizes the most prominent imaging features found in FOI examinations of inflammatory diseases, outlines the underlying anatomical structures, and introduces a nomenclature for the features and, thus, supports the idea that this tool is a useful part of the imaging repertoire in rheumatology clinical practice, particularly where other imaging methods are not easily available.}, language = {en} } @article{BayBuschLisdatetal.2017, author = {Bay, Daniyah H. and Busch, Annika and Lisdat, Fred and Iida, Keisuke and Ikebukuro, Kazunori and Nagasawa, Kazuo and Karube, Isao and Yoshida, Wataru}, title = {Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands}, series = {BMC Molecular Biology}, volume = {18}, journal = {BMC Molecular Biology}, number = {17}, issn = {1471-2199}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9811}, year = {2017}, abstract = {G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. In this study, the biological function of the 10 G-quadruplex-forming sequences in the transcriptional regulation has been analyzed using a reporter assay.}, language = {en} } @article{BelchevaErmakovaFabian2023, author = {Belcheva, Veronika and Ermakova, Tatiana and Fabian, Benjamin}, title = {Understanding Website Privacy Policies—A Longitudinal Analysis Using Natural Language Processing}, series = {Information}, volume = {14}, journal = {Information}, number = {11}, publisher = {MDPI}, issn = {2078-2489}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18268}, year = {2023}, abstract = {Privacy policies are the main method for informing Internet users of how their data are collected and shared. This study aims to analyze the deficiencies of privacy policies in terms of readability, vague statements, and the use of pacifying phrases concerning privacy. This represents the undertaking of a step forward in the literature on this topic through a comprehensive analysis encompassing both time and website coverage. It characterizes trends across website categories, top-level domains, and popularity ranks. Furthermore, studying the development in the context of the General Data Protection Regulation (GDPR) offers insights into the impact of regulations on policy comprehensibility. The findings reveal a concerning trend: privacy policies have grown longer and more ambiguous, making it challenging for users to comprehend them. Notably, there is an increased proportion of vague statements, while clear statements have seen a decrease. Despite this, the study highlights a steady rise in the inclusion of reassuring statements aimed at alleviating readers' privacy concerns.}, language = {en} } @article{RotheBergerWelkeretal.2023, author = {Rothe, Felix and Berger, J{\"o}rn and Welker, Pia and Fiebelkorn, Richard and Kupper, Stefan and Kiesel, Denise and Gedat, Egbert and Ohrndorf, Sarah}, title = {Fluorescence optical imaging feature selection with machine learning for differential diagnosis of selected rheumatic diseases}, series = {Frontiers in Medicine}, volume = {10}, journal = {Frontiers in Medicine}, publisher = {Frontiers}, issn = {2296-858X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17922}, year = {2023}, abstract = {Background and objective: Accurate and fast diagnosis of rheumatic diseases affecting the hands is essential for further treatment decisions. Fluorescence optical imaging (FOI) visualizes inflammation-induced impaired microcirculation by increasing signal intensity, resulting in different image features. This analysis aimed to find specific image features in FOI that might be important for accurately diagnosing different rheumatic diseases. Patients and methods: FOI images of the hands of patients with different types of rheumatic diseases, such as rheumatoid arthritis (RA), osteoarthritis (OA), and connective tissue diseases (CTD), were assessed in a reading of 20 different image features in three phases of the contrast agent dynamics, yielding 60 different features for each patient. The readings were analyzed for mutual differential diagnosis of the three diseases (One-vs-One) and each disease in all data (One-vs-Rest). In the first step, statistical tools and machine-learning-based methods were applied to reveal the importance rankings of the features, that is, to find features that contribute most to the model-based classification. In the second step machine learning with a stepwise increasing number of features was applied, sequentially adding at each step the most crucial remaining feature to extract a minimized subset that yields the highest diagnostic accuracy. Results: In total, n = 605 FOI of both hands were analyzed (n = 235 with RA, n = 229 with OA, and n = 141 with CTD). All classification problems showed maximum accuracy with a reduced set of image features. For RA-vs.-OA, five features were needed for high accuracy. For RA-vs.-CTD ten, OA-vs.-CTD sixteen, RA-vs.-Rest five, OA-vs.-Rest eleven, and CTD-vs-Rest fifteen, features were needed, respectively. For all problems, the final importance ranking of the features with respect to the contrast agent dynamics was determined. Conclusions: With the presented investigations, the set of features in FOI examinations relevant to the differential diagnosis of the selected rheumatic diseases could be remarkably reduced, providing helpful information for the physician.}, language = {en} } @article{GossingFrohmeRadke2020, author = {Gossing, Wilhelm and Frohme, Marcus and Radke, Lars}, title = {Biomarkers for Liquid Biopsies of Pituitary Neuroendocrine Tumors}, series = {Biomedicines}, volume = {8}, journal = {Biomedicines}, number = {6}, issn = {2227-9059}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13307}, year = {2020}, abstract = {Pituitary neuroendocrine tumors (PitNET) do not only belong to the most common intracranial neoplasms but seem to be generally more common than has been thought. Minimally invasive liquid biopsies have the potential to improve their early screening efficiency as well as monitor prognosis by facilitating the diagnostic procedures. This review aims to assess the potential of using liquid biopsies of different kinds of biomarker species that have only been obtained from solid pituitary tissues so far. Numerous molecules have been associated with the development of a PitNET, suggesting that it often develops from the cumulative effects of many smaller genetic or epigenetic changes. These minor changes eventually pile up to switch critical molecules into tumor-promoting states, which may be the key regulatory nodes representing the most potent marker substances for a diagnostic test. Drugs targeting these nodes may be superior for the therapeutic outcome and therefore the identification of such pituitary-specific cellular key nodes will help to accelerate their application in medicine. The ongoing genetic degeneration in pituitary adenomas suggests that repeated tumor profiling via liquid biopsies will be necessary for personalized and effective treatment solutions.}, language = {en} } @article{GossingRadkeBieringetal.2021, author = {Gossing, Wilhelm and Radke, Lars and Biering, Henrik and Diederich, Sven and Mai, Knut and Frohme, Marcus}, title = {The ElonginB/C-Cullin5-SOCS-Box-Complex Is a Potential Biomarker for Growth Hormone Disorders}, series = {Biomedicines}, volume = {9}, journal = {Biomedicines}, number = {2}, publisher = {MDPI}, issn = {2227-9059}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13802}, year = {2021}, abstract = {Insulin-like growth factor 1 (IGF-1) is the standard biochemical marker for the diagnosis and treatment control of acromegaly and growth hormone deficiency (GHD). However, its limitations necessitate the screening for new specific and sensitive biomarkers. The elonginB/C-cullin5-SOCS-box-complex (ECS-complex) (an intracellular five-protein complex) is stimulated by circulating growth hormone (GH) and regulates GH receptor levels through a negative feedback loop. It mediates the cells' sensitivity for GH and therefore, represents a potent new biomarker for those diseases. In this study, individual ECS-complex proteins were measured in whole blood samples of patients with acromegaly (n = 32) or GHD (n = 12) via ELISA and compared to controls. Hierarchical clustering of the results revealed that by combining the three ECS-complex proteins suppressor of cytokine signaling 2 (SOCS2), cullin-5 and ring-box protein 2 (Rbx-2), 93\% of patient samples could be separated from controls, despite many patients having a normal IGF-1 or not receiving medical treatment. SOCS2 showed the best individual diagnostic performance with an overall accuracy of 0.93, while the combination of the three proteins correctly identified all patients and controls. This resulted in perfect sensitivity and specificity for all patient groups, which demonstrates potential benefits of the ECS-complex proteins as clinical biomarkers for the diagnostics of GH-related diseases and substantiates their important role in GH metabolism.}, language = {en} } @article{MarehnWilhelmPospisiletal.2019, author = {Marehn, David Thomas and Wilhelm, Detlef and Pospisil, Heike and Pizzoferrato, Roberto}, title = {Double entry method for the verification of data a chromatography data system receives}, series = {Journal of Sensors and Sensor Systems}, volume = {8}, journal = {Journal of Sensors and Sensor Systems}, issn = {2194-878X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12349}, pages = {207 -- 214}, year = {2019}, abstract = {The importance of software validation increases since the need for high usability and suitability of software applications grows. In order to reduce costs and manage risk factors, more and more recommendations and rules have been established. In the field of pharmacy the vendors of so-called chromatography data systems (CDSs) had to implement the guidelines of the Code of Federal Regulations Title 21 (CFR 21) during the last few years in order to fulfill the increasing requirements. The CFR 21 part 11 deals with electronic records and signatures. This part is binding for each company in the regulated environment that wishes to create, edit and sign electronic information instead of printing them on paper. Subsection CFR 21 part 11.10(h) explains how to perform an input check for manual user entries as well as for data that will be collected from an external device. In this article we present an approach performing the double entry method on data provided by the hardware instrument in order to investigate possible influences on the raw data by the handling CDS. A software tool has been written which allows us to communicate with a high-performance liquid chromatography (HPLC) detector and acquire data from it. The communication is completely independent of a CDS which is started separately and connected to the same system. Using this configuration we made a parallel data acquisition of two instances at the same time possible. Two CDSs have been tested and for at least one of them it has been shown that a comparison of the acquired data can be done as with the double entry method for the data verification. For the second CDS we checked whether it would be applicable after a few modifications. The given approach could be either used for a live data verification of produced raw data or as a single test during a software operational qualification to verify the data acquisition functionality of the software.}, language = {en} } @article{TannenbergTscheuschnerRaabetal.2026, author = {Tannenberg, Robert and Tscheuschner, Georg and Raab, Christopher and Flemig, Sabine and D{\"o}ring, Sarah and Ponader, Marco and Thurmann, Melinda and Paul, Martin and Weller, Michael G.}, title = {Simplified Sample Preparation and Lateral Flow Immunoassay for the Detection of Plant Viruses}, series = {Biosensors}, volume = {16}, journal = {Biosensors}, number = {2}, publisher = {MDPI}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21294}, year = {2026}, abstract = {Lateral flow immunoassays (LFAs) are widely used for on-site testing; however, their use for the rapid detection of plant viruses in the field is often limited by inconvenient sample preparation. Here, we present a new sampling method and a simplified dipstick LFA format for the detection and monitoring of cowpea chlorotic mottle virus (CCMV) as a model plant pathogen. The assay employs a monoclonal mouse antibody for capture and a poly-clonal rabbit antibody conjugated to 80 nm gold nanoparticles for detection. Conventional sample and conjugate pads are omitted, allowing the test strips to be dipped directly into wells containing plant extract and antibody-gold conjugate. No plastic casing was required, which could lead to a reduction in waste. It was shown that CCMV concentrations as low as 3.5 μg/L or 350 pg per sample could be reliably detected in 15 min. Specificity tests confirmed that other plant viruses, cowpea mosaic virus (CPMV) and tobacco mosaic virus (TMV), did not produce false-positive results. In addition, we describe a new method for on-site sampling using a manual punch and a syringe equipped with a frit. This step combines grinding the sample, extraction, filtration, and reconstitution and mixing of the antibody-gold conjugate, enabling the analysis of punched leaf disks without laboratory equipment. When applied to CCMV-infected cowpea plants, the assay revealed systemic infection before visual symptoms became apparent. This work demonstrates that simplified LFAs combined with innovative sampling techniques can provide sensitive, specific, and rapid diagnostics for crop monitoring and support early intervention strategies in agriculture.}, language = {en} } @article{ZeschFinkelsteinRegehlyetal.2026, author = {Zesch, Christoph and Finkelstein, Daniel and Regehly, Martin and Reif, J{\"u}rgen and Schrader, Sigurd}, title = {Efficient nanosecond barium nitrate Raman laser for the visible spectral range}, series = {Optics Express}, volume = {34}, journal = {Optics Express}, number = {4}, publisher = {Optica}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21320}, pages = {6355 -- 6363}, year = {2026}, abstract = {We report on the design and performance of two solid-state Raman lasers, pumped by a frequency-doubled Nd:YAG laser at 532 nm (8 ns FWHM, 10 Hz, up to 10 mJ), that generate either the first or second Stokes radiation with wavelengths of 563 nm and 598 nm. Barium nitrate crystals with a 1 cm² face area and lengths of 3 cm and 5 cm were used as the Raman-active medium in stable semi-spherical resonators. The Raman lasers produced first Stokes and second Stokes pulses, achieving pulse energies up to 2.3 mJ and conversion efficiencies up to 35\% (first Stokes, 5 cm crystal) and 21\% (second Stokes, 5 cm crystal). The output beams exhibit nearly Gaussian profiles with beam quality factors of M² = 1.67 and M² = 1.83, respectively. The proposed design and characterization demonstrated a Raman laser with high efficiency and superior beam quality. After subsequent frequency doubling, the output appears well dedicated for future differential absorption LiDAR (DIAL) applications.}, language = {en} } @article{SteglichMaiVillringeretal.2021, author = {Steglich, Patrick and Mai, Christian and Villringer, Claus and Dietzel, Birgit and Bondarenko, Siegfried and Ksianzou, Viachaslau and Villasmunta, Francesco and Zesch, Christoph and Pulwer, Silvio and Burger, Martin and Bauer, Joachim and Heinrich, Friedhelm and Schrader, Sigurd and Vitale, Francesco and De Matteis, Fabio and Prosposito, Paolo and Casalboni, Mauro and Mai, Andreas}, title = {Silicon-organic hybrid photonics: an overview of recent advances, electro-optical effects and CMOS integration concepts}, series = {Journal of Physics: Photonics}, volume = {3}, journal = {Journal of Physics: Photonics}, number = {2}, issn = {2515-7647}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13882}, year = {2021}, abstract = {In recent decades, much research effort has been invested in the development of photonic integrated circuits, and silicon-on-insulator technology has been established as a reliable platform for highly scalable silicon-based electro-optical modulators. However, the performance of such devices is restricted by the inherent material properties of silicon. An approach to overcoming these deficiencies is to integrate organic materials with exceptionally high optical nonlinearities into a silicon-on-insulator photonic platform. Silicon-organic hybrid photonics has been shown to overcome the drawbacks of silicon-based modulators in terms of operating speed, bandwidth, and energy consumption. This work reviews recent advances in silicon-organic hybrid photonics and covers the latest improvements to single components and device concepts. Special emphasis is given to the in-device performance of novel electro-optical polymers and the use of different electro-optical effects, such as the linear and quadratic electro-optical effect, as well as the electric-field-induced linear electro-optical effect. Finally, the inherent challenges of implementing non-linear optical polymers on a silicon photonic platform are discussed and a perspective for future directions is given.}, language = {en} } @article{RegehlyHecht2025, author = {Regehly, Martin and Hecht, Stefan}, title = {Split-Aperture Xolography - Linear Volumetric Photoactivation with Short Axial Dimension and Low out of Focus Excitation}, series = {Advanced Science}, volume = {12}, journal = {Advanced Science}, number = {31}, publisher = {Wiley}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20749}, year = {2025}, abstract = {Spatially confined photo-excitation with the lowest possible activation of the remaining volume is of central importance for high-resolution high-density optical data storage, fluorescence microscopy, 3D-lithography, and 3D-printing. Two-photon absorption (2PA) enables such applications yet leads to slow processing speed due to the underlying non-linear absorption process. Here, Split-Aperture Xolography (SAX), is introduced which uses stepwise excitation of dual-color responsive molecules to initiate a linear volumetric photo-reaction process that is up to several orders of magnitude more efficient than 2PA. The capabilities of SAX are investigated in a scenario study for focusing systems with high numerical aperture (NA) using a Python implementation of vectorial diffraction theory. The intersecting half-cones generated by the split illuminated entrance aperture of the objective reduce the axial focal spot size of the activation distribution by up to a factor of two compared to 2PA targeting the same electronic transition. A steep average decline of the activation probability with the fifth power away from focus is found for a wide range of directions. This is significantly better in comparison to 2PA and prevents that undesired out-of-focus excitation events sum-up with subsequent irradiations. This approach is expected to be advantageous for volumetric methods at the nanoscale.}, language = {en} } @article{BauerHeinrichVillasmuntaetal.2025, author = {Bauer, Joachim and Heinrich, Friedhelm and Villasmunta, Francesco and Villringer, Claus and Reck, Johanna and Peters, Sven and Treffer, Alexander and Kuhnt, Christian and Marschmeyer, Steffen and Fursenko, Oksana and Stolarek, David and Mai, Andreas and Regehly, Martin}, title = {Reflectometric method for measuring residual oxides in through-silicon vias for 3D chip integration}, series = {Optics Express}, volume = {33}, journal = {Optics Express}, number = {15}, publisher = {Optica}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20633}, pages = {32175 -- 32189}, year = {2025}, abstract = {A significant aspect of fabricating 3D chip architectures is ensuring proper contact between the different layers of the chip, which often requires removing the underside of isolation layers before filling vias with conductive material. Currently, scanning electron microscopy is the established method for investigating such structures. In this paper, we propose a rapid, non-destructive optical analysis technique for the simultaneous measurement of through-silicon vias (TSV) depths, silicon wafer thickness, and residual oxide thickness. The proposed method utilizes Fourier peak shift analysis (FPSA) of reflectance measurements in the near-infrared (1200 nm—2200 nm) spectral regions. The application of FPSA to representative samples taken from a commercial TSV integration process for MEMS and CMOS fabrication demonstrated good agreement with reference scanning electron microscopy measurements, confirming the feasibility of the method for in-line and in-situ metrology. The results indicate that FPSA has great potential for real-time process monitoring and control during 3D chip manufacturing.}, language = {en} } @article{HollandMoritzVandenhouten2013, author = {Holland-Moritz, Ralph and Vandenhouten, Ralf}, title = {Detection of Movement Profiles in Facility Management Using Complex Event Processing}, series = {International Journal of Information Science}, volume = {3}, journal = {International Journal of Information Science}, number = {1}, issn = {2163-193X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9495}, pages = {7 -- 12}, year = {2013}, abstract = {This paper presents a solution for detecting movement and spreading profiles by analyzing sensor data in the facility management. First of all, a scenario is defined and described. On the basis of this scenario an approach is made using integration of events over time and location. For making the integration possible the required information, which the data objects have to provide, is identified. At the end a solution is presented using Complex Event Processing to implement the integration of events.}, language = {en} } @article{BalabanovWilhelmVenzetal.2013, author = {Balabanov, Stefan and Wilhelm, Thomas and Venz, Simone and Keller, Gunhild and Scharf, Christian and Pospisil, Heike and Braig, Melanie and Barett, Christine and Bokemeyer, Carsten and Walther, Reinhard and Br{\"u}mmendorf, Tim H. and Schuppert, Andreas}, title = {Combination of a Proteomics Approach and Reengineering of Meso Scale Network Models for Prediction of Mode-of-Action for Tyrosine Kinase Inhibitors}, series = {PLoS ONE}, volume = {8}, journal = {PLoS ONE}, number = {1}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6370}, pages = {14}, year = {2013}, abstract = {In drug discovery, the characterisation of the precise modes of action (MoA) and of unwanted off-target effects of novel molecularly targeted compounds is of highest relevance. Recent approaches for identification of MoA have employed various techniques for modeling of well defined signaling pathways including structural information, changes in phenotypic behavior of cells and gene expression patterns after drug treatment. However, efficient approaches focusing on proteome wide data for the identification of MoA including interference with mutations are underrepresented. As mutations are key drivers of drug resistance in molecularly targeted tumor therapies, efficient analysis and modeling of downstream effects of mutations on drug MoA is a key to efficient development of improved targeted anti-cancer drugs. Here we present a combination of a global proteome analysis, reengineering of network models and integration of apoptosis data used to infer the mode-of-action of various tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML) cell lines expressing wild type as well as TKI resistance conferring mutants of BCR-ABL. The inferred network models provide a tool to predict the main MoA of drugs as well as to grouping of drugs with known similar kinase inhibitory activity patterns in comparison to drugs with an additional MoA. We believe that our direct network reconstruction approach, demonstrated on proteomics data, can provide a complementary method to the established network reconstruction approaches for the preclinical modeling of the MoA of various types of targeted drugs in cancer treatment. Hence it may contribute to the more precise prediction of clinically relevant on- and off-target effects of TKIs.}, language = {en} } @article{ThiemannFuSeifertetal.2014, author = {Thiemann, Alexander and Fu, Junjie and Seifert, Felix and Grant-Downton, Robert T and Schrag, Tobias A and Pospisil, Heike and Frisch, Matthias and Melchinger, Albrecht E and Scholten, Stefan}, title = {Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci}, series = {BMC Plant Biology}, volume = {14}, journal = {BMC Plant Biology}, number = {88}, issn = {1471-2229}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5999}, pages = {14}, year = {2014}, abstract = {The identification of QTL involved in heterosis formation is one approach to unravel the not yet fully understood genetic basis of heterosis - the improved agronomic performance of hybrid F1 plants compared to their inbred parents. The identification of candidate genes underlying a QTL is important both for developing markers and determining the molecular genetic basis of a trait, but remains difficult owing to the large number of genes often contained within individual QTL. To address this problem in heterosis analysis, we applied a meta-analysis strategy for grain yield (GY) of Zea mays L. as example, incorporating QTL-, hybrid field-, and parental gene expression data.}, language = {en} } @article{UmmanniMundtPospisiletal.2011, author = {Ummanni, Ramesh and Mundt, Frederike and Pospisil, Heike and Venz, Simone and Scharf, Christian and Barett, Christine and F{\"a}lth, Maria and K{\"o}llermann, Jens and Walther, Reinhard and Schlomm, Thorsten and Sauter, Guido and Bokemeyer, Carsten and S{\"u}ltmann, Holger and Schuppert, Andreas and Br{\"u}mmendorf, Tim H. and Balabanov, Stefan}, title = {Identification of Clinically Relevant Protein Targets in Prostate Cancer with 2D-DIGE Coupled Mass Spectrometry and Systems Biology Network Platform}, series = {PLoS ONE}, volume = {6}, journal = {PLoS ONE}, number = {2}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6432}, pages = {14}, year = {2011}, abstract = {Prostate cancer (PCa) is the most common type of cancer found in men and among the leading causes of cancer death in the western world. In the present study, we compared the individual protein expression patterns from histologically characterized PCa and the surrounding benign tissue obtained by manual micro dissection using highly sensitive two-dimensional differential gel electrophoresis (2D-DIGE) coupled with mass spectrometry. Proteomic data revealed 118 protein spots to be differentially expressed in cancer (n = 24) compared to benign (n = 21) prostate tissue. These spots were analysed by MALDI-TOF-MS/MS and 79 different proteins were identified. Using principal component analysis we could clearly separate tumor and normal tissue and two distinct tumor groups based on the protein expression pattern. By using a systems biology approach, we could map many of these proteins both into major pathways involved in PCa progression as well as into a group of potential diagnostic and/or prognostic markers. Due to complexity of the highly interconnected shortest pathway network, the functional sub networks revealed some of the potential candidate biomarker proteins for further validation. By using a systems biology approach, our study revealed novel proteins and molecular networks with altered expression in PCa. Further functional validation of individual proteins is ongoing and might provide new insights in PCa progression potentially leading to the design of novel diagnostic and therapeutic strategies.}, language = {en} } @article{StandfussPospisilKlein2012, author = {Standfuß, Christoph and Pospisil, Heike and Klein, Andreas}, title = {SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT/t driven mice breast cancer}, series = {BMC Cancer}, volume = {12}, journal = {BMC Cancer}, number = {380}, issn = {1471-2407}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6414}, pages = {15}, year = {2012}, abstract = {Tumor development is known to be a stepwise process involving dynamic changes that affect cellular integrity and cellular behavior. This complex interaction between genomic organization and gene, as well as protein expression is not yet fully understood. Tumor characterization by gene expression analyses is not sufficient, since expression levels are only available as a snapshot of the cell status. So far, research has mainly focused on gene expression profiling or alterations in oncogenes, even though DNA microarray platforms would allow for high-throughput analyses of copy number alterations (CNAs).}, language = {en} } @article{KleinPospisil2014, author = {Klein, Andreas and Pospisil, Heike}, title = {Gene Expression Profiling of Pancreatic Cancer Reveals a Significant Deregulation of the TGF-β Pathway and the Discovery of Genes for Prognosis}, series = {Global Journal of Human Genetics \& Gene Therapy}, volume = {2}, journal = {Global Journal of Human Genetics \& Gene Therapy}, number = {1}, issn = {2311-0309}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6519}, pages = {30 -- 39}, year = {2014}, abstract = {We have re-analyzed previously published gene expression data from ninety-four pancreatic ductal adenocarcinomas (PDAC) samples. We determined the gene expression profile of genes differentially expressed in PDAC compared to non-malignant pancreatic tissue. Using the 100 top-ranked genes, we were able to discriminate between PDAC and non-malignant pancreatic tissue. A hierarchical cluster analysis revealed only a 6 \% false discovery rate. The prognostic strength of these discriminative genes was underscored by a SVM classification and 3-fold cross validation with an 89 \% correct class assignment. The annotation of the 100 top-ranked genes revealed that most of the genes were involved in the processes of signal transduction, cell adhesion, extracellular matrix organization and cell migration. The most greatly affected signal cascade was the transforming growth factor β receptor signaling pathway, which was significantly enriched in the top-ranked genes. Furthermore, we identified eleven genes that were associated with good prognosis.}, language = {en} } @article{HannemannMeyerStaecklingKemmingetal.2011, author = {Hannemann, Juliane and Meyer-Staeckling, S{\"o}nke and Kemming, Dirk and Alpers, Iris and Joosse, Simon A. and Pospisil, Heike and Kurtz, Stefan and G{\"o}rndt, Jennifer and P{\"u}schel, Klaus and Riethdorf, Sabine and Pantel, Klaus and Brandt, Burkhard}, title = {Quantitative High-Resolution Genomic Analysis of Single Cancer Cells}, series = {PLoS ONE}, volume = {6}, journal = {PLoS ONE}, number = {11}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6426}, pages = {6}, year = {2011}, abstract = {During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.}, language = {en} } @article{SilbermannWernickePospisiletal.2013, author = {Silbermann, Jascha and Wernicke, Catrin and Pospisil, Heike and Frohme, Marcus}, title = {RefPrimeCouch—a reference gene primer CouchApp}, series = {Database: The Journal of Biological Databases and Curation}, volume = {2013}, journal = {Database: The Journal of Biological Databases and Curation}, issn = {1758-0463}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6330}, pages = {8}, year = {2013}, abstract = {To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License.}, language = {en} } @article{DuscharlaBhumireddyLakshettietal.2016, author = {Duscharla, Divya and Bhumireddy, Sudarshana Reddy and Lakshetti, Sridhar and Pospisil, Heike and Murthy, P. V. L. N. and Walther, Reinhard and Sripadi, Prabhakar and Ummanni, Ramesh}, title = {Prostate Cancer Associated Lipid Signatures in Serum Studied by ESI-Tandem Mass Spectrometryas Potential New Biomarkers}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {3}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5863}, pages = {21}, year = {2016}, abstract = {Prostate cancer (PCa) is one amongst the most common cancersin western men. Incidence rate ofPCa is on the rise worldwide. The present study deals with theserum lipidome profiling of patients diagnosed with PCa to identify potential new biomarkers. We employed ESI-MS/MS and GC-MS for identification of significantly altered lipids in cancer patient's serum compared to controls. Lipidomic data revealed 24 lipids are significantly altered in cancer patinet's serum (n = 18) compared to normal (n = 18) with no history of PCa. By using hierarchical clustering and principal component analysis (PCA) we could clearly separate cancer patients from control group. Correlation and partition analysis along with Formal Concept Analysis (FCA) have identified that PC (39:6) and FA (22:3) could classify samples with higher certainty. Both the lipids, PC (39:6) and FA (22:3) could influence the cataloging of patients with 100\% sensitivity (all 18 control samples are classified correctly) and 77.7\% specificity (of 18 tumor samples 4 samples are misclassified) with p-value of 1.612×10-6 in Fischer's exact test. Further, we performed GC-MS to denote fatty acids altered in PCa patients and found that alpha-linolenic acid (ALA) levels are altered in PCa. We also performed an in vitro proliferation assay to determine the effect of ALA in survival of classical human PCa cell lines LNCaP and PC3. We hereby report that the altered lipids PC (39:6) and FA (22:3) offer a new set of biomarkers in addition to the existing diagnostic tests that could significantly improve sensitivity and specificity in PCa diagnosis.}, language = {en} } @article{GladischSarauliSchaeferetal.2016, author = {Gladisch, Johannes and Sarauli, David and Sch{\"a}fer, Daniel and Dietzel, Birgit and Schulz, Burkhard and Lisdat, Fred}, title = {Towards a novel bioelectrocatalytic platform based on "wiring" of pyrroloquinoline quinone-dependent glucose dehydrogenase with an electrospun conductive polymeric fiber architecture}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5846}, pages = {10}, year = {2016}, abstract = {Electrospinning is known as a fabrication technique for electrode architectures that serve as immobilization matrices for biomolecules. The current work demonstrates a novel approach to construct a conductive polymeric platform, capable not only of immobilization, but also of electrical connection of the biomolecule with the electrode. It is produced upon electrospinning from mixtures of three different highly conductive sulfonated polyanilines and polyacrylonitrile on ITO electrodes. The resulting fiber mats are with a well-retained conductivity. After coupling the enzyme pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH) to polymeric structures and addition of the substrate glucose an efficient bioelectrocatalysis is demonstrated. Depending on the choice of the sulfonated polyanilline mediatorless bioelectrocatalysis starts at low potentials; no large overpotential is needed to drive the reaction. Thus, the electrospun conductive immobilization matrix acts here as a transducing element, representing a promising strategy to use 3D polymeric scaffolds as wiring agents for active enzymes. In addition, the mild and well reproducible fabrication process and the active role of the polymer film in withdrawing electrons from the reduced PQQ-GDH lead to a system with high stability. This could provide access to a larger group of enzymes for bioelectrochemical applications including biosensors and biofuel cells.}, language = {en} } @article{SeifertThiemannPospisiletal.2012, author = {Seifert, Felix and Thiemann, Alexander and Pospisil, Heike and Scholten, Stefan}, title = {Re-annotation of the maize oligonucleotide array}, series = {Maydica}, volume = {57}, journal = {Maydica}, number = {1}, issn = {0025-6153}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6178}, pages = {49 -- 55}, year = {2012}, abstract = {The microarray technology has become an established approach for large-scale gene expression analysis with mature protocols for sample, microarray, and data processing. The maize oligonucleotide array (maizearray) is one of the few microarray platforms designed for genome-wide gene expression analysis in Zea mays L. Many datas-ets addressing various genetic, physiological and developmental topics generated with this platform are available. The original 57,452 microarray probes were compiled based on expressed sequence tags (ESTs). Meanwhile the maize genome sequence became available providing the possibility for an improved annotation of the microar-ray probe set. In this study we determined the genome positions of all maizearray probes to obtain current gene annotations and generated current Gene Ontology (GO) annotations. These new data allow tracing redundancy of the probe set and interfering cross-hybridizations, and doubled the number of genes with functional GO data. Our re-annotation will largely improve the functional analysis of available and future datasets generated on this microarray platform.}, language = {en} } @article{MarczokBortzWangetal.2016, author = {Marczok, Stefanie and Bortz, Birgit and Wang, Chong and Pospisil, Heike}, title = {Comprehensive Analysis of Genome Rearrangements in Eight Human Malignant Tumor Tissues}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {7}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6607}, pages = {18}, year = {2016}, abstract = {Carcinogenesis is a complex multifactorial, multistage process, but the precise mechanisms are not well understood. In this study, we performed a genome-wide analysis of the copy number variation (CNV), breakpoint region (BPR) and fragile sites in 2,737 tumor samples from eight tumor entities and in 432 normal samples. CNV detection and BPR identification revealed that BPRs tended to accumulate in specific genomic regions in tumor samples whereas being dispersed genome-wide in the normal samples. Hotspots were observed, at which segments with similar alteration in copy number were overlapped along with BPRs adjacently clustered. Evaluation of BPR occurrence frequency showed that at least one was detected in about and more than 15\% of samples for each tumor entity while BPRs were maximal in 12\% of the normal samples. 127 of 2,716 tumor-relevant BPRs (termed 'common BPRs') exhibited also a noticeable occurrence frequency in the normal samples. Colocalization assessment identified 20,077 CNV-affecting genes and 169 of these being known tumor-related genes. The most noteworthy genes are KIAA0513 important for immunologic, synaptic and apoptotic signal pathways, intergenic non-coding RNA RP11-115C21.2 possibly acting as oncogene or tumor suppressor by changing the structure of chromatin, and ADAM32 likely importance in cancer cell proliferation and progression by ectodomain-shedding of diverse growth factors, and the well-known tumor suppressor gene p53. The BPR distributions indicate that CNV mutations are likely non-random in tumor genomes. The marked recurrence of BPRs at specific regions supports common progression mechanisms in tumors. The presence of hotspots together with common BPRs, despite its small group size, imply a relation between fragile sites and cancer-gene alteration. Our data further suggest that both protein-coding and non-coding genes possessing a range of biological functions might play a causative or functional role in tumor biology. This research enhances our understanding of the mechanisms for tumorigenesis and progression.}, language = {en} } @article{PfeilSiptrothPospisiletal.2023, author = {Pfeil, Juliane and Siptroth, Julienne and Pospisil, Heike and Frohme, Marcus and Hufert, Frank T. and Moskalenko, Olga and Yateem, Murad and Nechyporenko, Alina}, title = {Classification of Microbiome Data from Type 2 Diabetes Mellitus Individuals with Deep Learning Image Recognition}, series = {Big Data and Cognitive Computing}, volume = {7}, journal = {Big Data and Cognitive Computing}, number = {1}, publisher = {MDPI}, issn = {2504-2289}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17184}, year = {2023}, abstract = {Microbiomic analysis of human gut samples is a beneficial tool to examine the general well-being and various health conditions. The balance of the intestinal flora is important to prevent chronic gut infections and adiposity, as well as pathological alterations connected to various diseases. The evaluation of microbiome data based on next-generation sequencing (NGS) is complex and their interpretation is often challenging and can be ambiguous. Therefore, we developed an innovative approach for the examination and classification of microbiomic data into healthy and diseased by visualizing the data as a radial heatmap in order to apply deep learning (DL) image classification. The differentiation between 674 healthy and 272 type 2 diabetes mellitus (T2D) samples was chosen as a proof of concept. The residual network with 50 layers (ResNet-50) image classification model was trained and optimized, providing discrimination with 96\% accuracy. Samples from healthy persons were detected with a specificity of 97\% and those from T2D individuals with a sensitivity of 92\%. Image classification using DL of NGS microbiome data enables precise discrimination between healthy and diabetic individuals. In the future, this tool could enable classification of different diseases and imbalances of the gut microbiome and their causative genera.}, language = {en} } @article{SiptrothMoskalenkoKrumbiegeletal.2023, author = {Siptroth, Julienne and Moskalenko, Olga and Krumbiegel, Carsten and Ackermann, J{\"o}rg and Koch, Ina and Pospisil, Heike}, title = {Variation of butyrate production in the gut microbiome in type 2 diabetes patients}, series = {International Microbiology}, volume = {26}, journal = {International Microbiology}, publisher = {Springer Nature}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17802}, pages = {601 -- 610}, year = {2023}, abstract = {Background Diabetes mellitus type 2 is a common disease that poses a challenge to the healthcare system. The disease is very often diagnosed late. A better understanding of the relationship between the gut microbiome and type 2 diabetes can support early detection and form an approach for therapies. Microbiome analysis offers a potential opportunity to find markers for this disease. Next-generation sequencing methods can be used to identify the bacteria present in the stool sample and to generate a microbiome profile through an analysis pipeline. Statistical analysis, e.g., using Student's t-test, allows the identification of significant differences. The investigations are not only focused on single bacteria, but on the determination of a comprehensive profile. Also, the consideration of the functional microbiome is included in the analyses. The dataset is not from a clinical survey, but very extensive. Results By examining 946 microbiome profiles of diabetes mellitus type 2 sufferers (272) and healthy control persons (674), a large number of significant genera (25) are revealed. It is possible to identify a large profile for type 2 diabetes disease. Furthermore, it is shown that the diversity of bacteria per taxonomic level in the group of persons with diabetes mellitus type 2 is significantly reduced compared to a healthy control group. In addition, six pathways are determined to be significant for type 2 diabetes describing the fermentation to butyrate. These parameters tend to have high potential for disease detection. Conclusions With this investigation of the gut microbiome of persons with diabetes type 2 disease, we present significant bacteria and pathways characteristic of this disease.}, language = {en} } @article{SiptrothMoskalenkoKrumbiegeletal.2023, author = {Siptroth, Julienne and Moskalenko, Olga and Krumbiegel, Carsten and Ackermann, J{\"o}rg and Koch, Ina and Pospisil, Heike}, title = {Investigation of metabolic pathways from gut microbiome analyses regarding type 2 diabetes mellitus using artificial neural networks}, series = {Discover Artificial Intelligence}, volume = {3}, journal = {Discover Artificial Intelligence}, number = {1}, publisher = {Springer Nature}, issn = {2731-0809}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17497}, year = {2023}, abstract = {Background Type 2 diabetes mellitus is a prevalent disease that contributes to the development of various health issues, including kidney failure and strokes. As a result, it poses a significant challenge to the worldwide healthcare system. Research into the gut microbiome has enabled the identification and description of various diseases, with bacterial pathways playing a critical role in this context. These pathways link individual bacteria based on their biological functions. This study deals with the classification of microbiome pathway profiles of type 2 diabetes mellitus patients. Methods Pathway profiles were determined by next-generation sequencing of 16S rDNA from stool samples, which were subsequently assigned to bacteria. Then, the involved pathways were assigned by the identified gene families. The classification of type 2 diabetes mellitus is enabled by a constructed neural network. Furthermore, a feature importance analysis was performed via a game theoretic approach (SHapley Additive exPlanations). The study not only focuses on the classification using neural networks, but also on identifying crucial bacterial pathways. Results It could be shown that a neural network classification of type 2 diabetes mellitus and a healthy comparison group is possible with an excellent prediction accuracy. It was possible to create a ranking to identify the pathways that have a high impact on the model prediction accuracy. In this way, new associations between the alteration of, e.g. a biosynthetic pathway and the presence of diabetes mellitus type 2 disease can also be discovered. The basis is formed by 946 microbiome pathway profiles from diabetes mellitus type 2 patients (272) and healthy comparison persons (674). Conclusion With this study of the gut microbiome, we present an approach using a neural network to obtain a classification of healthy and type 2 diabetes mellitus and to identify the critical features. Intestinal bacteria pathway profiles form the basis.}, language = {en} } @book{OPUS4-1931, title = {Radlogistik: Grundlagen zu Logistik und Wirtschaftsverkehr mit Lasten- und Transportr{\"a}dern}, editor = {Assmann, Tom and B{\"u}rklen, Anna and Gruber, Johannes and Knese, Dennis and Mayregger, Patrick and Rudolph, Christian}, isbn = {978-3-658-44449-5}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19318}, publisher = {Technische Hochschule Wildau}, year = {2024}, abstract = {Aus den Straßen europ{\"a}ischer St{\"a}dte sind sie kaum noch wegzudenken: Lasten- und Transportr{\"a}der. Im Personenverkehr sind sie f{\"u}r Eink{\"a}ufe und Kindertransporte bereits Standard, ebenso im Kuriersegment sowie der Paketzustellung. Besonders in der Logistik und im Wirtschaftsverkehr liegt noch ein sehr breit gef{\"a}chertes und ausdifferenziertes Einsatzpotenzial. Die Renaissance des Lastenrads als Transportmittel nimmt auch im gewerblichen Sektor an Bedeutung zu. Das Open Access-Buch bietet in dieser Form erstmals systematisch aufbereitetes Wissen f{\"u}r Praktiker in Wirtschaft, Politik und Verwaltung sowie f{\"u}r Studierende in den Bereichen Logistik und Verkehrsplanung. Zu den einzelnen Aspekten der Radlogistik (u. a. Fahrzeuge und Technik, gewerblicher Einsatz, logistischer Einsatz, Planung, Infrastrukturen, intermodale Einbindung, Best-Practice-Beispiele, Entwicklungstrends) haben national renommierte Wissenschaftler:innen Beitr{\"a}ge verfasst. Dieses Buch b{\"u}ndelt den aktuellen Wissensstand auf Basis von Forschungsergebnissen und stellt ihn kompakt und {\"u}bersichtlich dar.}, language = {de} } @article{HeroldRoedenbeck2025, author = {Herold, Marcel and Roedenbeck, Marc}, title = {AI-Driven Research in the Recruitment and Selection Process: Application of an AI Taxonomy With a Systematic Literature Review}, series = {SAGE Open}, volume = {15}, journal = {SAGE Open}, number = {3}, publisher = {Sage}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20736}, year = {2025}, abstract = {A review of the literature on the application of artificial intelligence (AI) in the recruitment and selection process (RSP) was conducted, but no relevant studies were identified. While several reviews have focussed on AI in human resource management in general, none of these have examined the RSP in detail or employed an AI taxonomy for clustering. Consequently, we applied an AI taxonomy identified in the literature with the aim to identify the stages of the RSP in the focus of research and the algorithms mostly used. We conducted a systematic literature review underpinned by a concept matrix, complemented by a computational literature review (CLR), that employed natural language processing (NLP). The initial 4,579 studies were sourced from three databases and narrowed down to a total of 502. Our major findings indicate that the majority of studies were categorised under the stages "assessment \& selection" and "processing incoming applications" in the RSP. The predominant algorithms in use pertain to the field of NLP and machine learning. The CLR emphasised the significance of ethics in AI research. While our study has expanded the general AI taxonomy by incorporating an ethical perspective and is one of the studies with the most articles used to reflect this topic, it is solely focussing on describing the past. Nevertheless, this article helps to align research on exploring and testing alternative approaches with those most frequently used.}, language = {en} } @article{FeifelStiegerKappetal.2016, author = {Feifel, Sven Christian and Stieger, Kai Ralf and Kapp, Andreas and Weber, Dennis and Allegrozzi, Marco and Piccioli, Mario and Turano, Paola and Lisdat, Fred}, title = {Insights into Interprotein Electron Transfer of Human Cytochrome c Variants Arranged in Multilayer Architectures by Means of an Artificial Silica Nanoparticle Matrix}, series = {ACS Omega}, volume = {1}, journal = {ACS Omega}, number = {6}, issn = {2470-1343}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6753}, pages = {1058 -- 1066}, year = {2016}, abstract = {The redox behavior of proteins plays a crucial part in the design of bioelectronic systems. We have demonstrated several functional systems exploiting the electron exchange properties of the redox protein cytochrome c (cyt c) in combination with enzymes and photoactive proteins. The operation is based on an effective reaction at modified electrodes but also to a large extent on the capability of self-exchange between cyt c molecules in a surface-fixed state. In this context, different variants of human cyt c have been examined here with respect to an altered heterogeneous electron transfer (ET) rate in a monolayer on electrodes as well as an enhanced self-exchange rate while being incorporated in multilayer architectures. For this purpose, mutants of the wild-type (WT) protein have been prepared to change the chemical nature of the surface contact area near the heme edge. The structural integrity of the variants has been verified by NMR and UV-vis measurements. It is shown that the single-point mutations can significantly influence the heterogeneous ET rate at thiol-modified gold electrodes and that electroactive protein/silica nanoparticle multilayers can be constructed with all forms of human cyt c prepared. The kinetic behavior of electron exchange for the mutant proteins in comparison with that of the WT has been found altered in some multilayer arrangements. Higher self-exchange rates have been found for K79A. The results demonstrate that the position of the introduced change in the charge situation of cyt c has a profound influence on the exchange behavior. In addition, the behavior of the cyt c variants in assembled multilayers is found to be rather similar to the situation of cyt c self-exchange in solution verified by NMR.}, language = {en} } @article{FeifelLisdat2011, author = {Feifel, Sven Christian and Lisdat, Fred}, title = {Silica nanoparticles for the layer-by-layer assembly of fully electro-active cytochrome c multilayers}, series = {Journal of Nanobiotechnology}, volume = {9}, journal = {Journal of Nanobiotechnology}, number = {59}, issn = {1477-3155}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5819}, pages = {12}, year = {2011}, abstract = {For bioanalytical systems sensitivity and biomolecule activity are critical issues. The immobilization of proteins into multilayer systems by the layer-by-layer deposition has become one of the favorite methods with this respect. Moreover, the combination of nanoparticles with biomolecules on electrodes is a matter of particular interest since several examples with high activities and direct electron transfer have been found. Our study describes the investigation on silica nanoparticles and the redox protein cytochrome c for the construction of electro-active multilayer architectures, and the electron transfer within such systems. The novelty of this work is the construction of such artificial architectures with a non-conducting building block. Furthermore a detailed study of the size influence of silica nanoparticles is performed with regard to formation and electrochemical behavior of these systems.}, language = {en} } @incollection{GruberPlenerRudolphetal.2024, author = {Gruber, Johannes and Plener, Martin and Rudolph, Christian and Seiffert, Robert}, title = {Gewerblicher Einsatz von Lastenr{\"a}dern - Vielfalt der Nutzungsm{\"o}glichkeiten}, series = {Radlogistik: Grundlagen zu Logistik und Wirtschaftsverkehr mit Lasten- und Transportr{\"a}dern}, booktitle = {Radlogistik: Grundlagen zu Logistik und Wirtschaftsverkehr mit Lasten- und Transportr{\"a}dern}, editor = {Assmann, Tom and B{\"u}rklen, Anna and Gruber, Johannes and Knese, Dennis and Mayregger, Patrick and Rudolph, Christian}, publisher = {Springer Fachmedien Wiesbaden}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19737}, publisher = {Technische Hochschule Wildau}, pages = {67 -- 88}, year = {2024}, abstract = {Dieser Beitrag beleuchtet die Vielfalt der Nutzungsm{\"o}glichkeiten von Lastenr{\"a}dern im gewerblichen Einsatz, welche sich am stetig wachsenden Interesse von privatwirtschaftlichen und {\"o}ffentlichen Organisationen an der Lastenradnutzung zeigt. Am Beispiel der rund 750 Teilnehmenden an einem deutschlandweiten Lastenrad-Testprogramm werden gewerbliche Nutzer charakterisiert. Des Weiteren bietet der Beitrag einen Vorschlag zur Segmentierung der {\"a}ußerst heterogenen Anwendungsfelder, die sich nicht nur auf Logistik- und Dienstleistungsbranchen beschr{\"a}nken.}, language = {de} } @article{AdomavičiũtėGrabusovėHinkelUsenovetal.2022, author = {Adomavičiũtė-Grabusovė, Sonata and Hinkel, Jonas and Usenov, Iskander and Novikov, Alexander S. and Sakharova, Tatiana and D{\"o}hler, Torsten and Geißler, Ute and Feliksberger, Elena and Artyushenko, Viacheslav}, title = {Microstructuring of the end-surface for silver halide polycrystalline fibers to suppress Fresnel reflection}, 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-opus4-15549}, pages = {34 -- 48}, year = {2022}, abstract = {Silver halide polycrystalline infrared fibers (PIR) have unique properties such as excellent transmittance in the spectral range from 3 to 17 µm, while also being highly flexible, non-toxic, and non-hygroscopic. They are used in industry and medicine for CO2-laser power delivery, flexible infrared imaging, and remote process spectroscopy. While PIR fibers possess a quite low attenuation (0.1-0.5 dB/m) in the 8-12 µm range, their total transmittance is limited by significant Fresnel reflections at the fiber end faces due to the high refractive index of silver halide (>2.1). Functionalization of these surfaces with specially designed Anti-Reflective Microstructures (ARMs) enables a striking enhancement of fiber transmittance. In this work, direct imprinting (or embossing) of microstructures to fiber ends and their profiling with a microstructured knife was applied to fabricate such ARMs. The resulting two-dimensional Moth-eye microstructures and one-dimensional microgrooves at the PIR-fiber ends enable to an increase of fiber transmittance in a broadband range of (5-17 µm) as well as to reach up to 20\% improvement for PIR-fiber laser cables used for power delivery of CO2-lasers at 10.6 µm.}, language = {en} } @article{TarabrinBushunovTeslenkoetal.2021, author = {Tarabrin, Mikhail K. and Bushunov, Andrey A. and Teslenko, Andrei A. and Sakharova, Tatiana and Hinkel, Jonas and Usenov, Iskander and D{\"o}hler, Torsten and Geißler, Ute and Artyushenko, Viacheslav and Lazarev, Vladimir A.}, title = {Fabrication of an antireflection microstructure on AgClBr polycrystalline fiber by single pulse femtosecond laser ablation}, series = {Optical Materials Express}, volume = {11}, journal = {Optical Materials Express}, number = {2}, publisher = {Optical Society of America}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15384}, pages = {487 -- 496}, year = {2021}, abstract = {Polycrystalline infrared (PIR) fibers are used for numerous applications, one of those being power delivery for CO2 lasers. However, the fiber tip surface's transmittance cannot be increased with conventional antireflection coatings due to the surface unevenness. Antireflection microstructures (ARMs) offer an alternative way of increasing transmittance. In this work, ARMs were fabricated on the fiber tip surface of an AgClBr fiber by single-pulse femtosecond laser ablation. A single-surface transmittance of 92.8\% at 10.6 μm, a CO2 laser operation wavelength, was achieved. The proposed method can help significantly improve the systems' efficiency, where power delivery for CO2 lasers or sources operating in the wide wavelength range is required.}, language = {en} } @article{HauschultzFriedoGeissleretal.2026, author = {Hauschultz, Mike Thomas and Friedo, Maria Helene and Geißler, Ute and B{\"o}hme, Andrea and Krenz-Baath, Ren{\´e}}, title = {Influence of Process Parameters Variation on Microstructure and Mechanical Properties of SLM-Printed 316L Stainless Steel}, series = {Solid State Phenomena}, volume = {383}, journal = {Solid State Phenomena}, publisher = {Trans Tech Publications}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21048}, pages = {75 -- 80}, year = {2026}, abstract = {This study presents the characterization of 316L stainless steels fabricated by selective laser melting (SLM), focusing on the influence of printing parameters on microstructure and mechanical properties. The choice of process parameters is crucial for achieving desired material properties, as it directly affects the microstructure and mechanical behavior, which is important when optimizing for potential applications in several fields, such as aerospace and automotive. In this study, different scanning speeds were tested to identify optimal settings, followed by the evaluation of the effects of orientation relative to the build plate and hatching strategies to enhance performance. To assess the impact of these factors, tensile tests, microhardness measurements, and X-ray diffraction (XRD) analyses were conducted. Tensile tests revealed that higher laser scanning speed generally reduces ultimate tensile strength and elongation, likely due to an increase in porosity and a less homogeneous fusion of layers. The analysis of samples printed with different orientation relative to the build plate highlighted a strong mechanical anisotropy, with the samples printed vertically exhibiting lower tensile strength and ductility compared to horizontally printed samples. Microhardness testing further confirmed an anisotropy in material properties. XRD analysis reveals a preferential orientation of austenitic grains depending on building direction. This, in turn, influences the anisotropic behavior. These findings highlight the critical role of process parameters in tailoring the microstructure and mechanical performance of SLM-produced parts, thereby providing insights into the optimization of additive manufacturing for specific applications.}, language = {en} } @article{EngelsSpeckSchlegeletal.2026, author = {Engels, Andreas and Speck, Sandy and Schlegel, Volker and Jacobs, Hannes and Krenz-Baath, Ren{\´e} and B{\"o}hme, Andrea}, title = {Substrate Tubing Heater Suitable for Large Volume 3D Printing with Extrusion of Thermo-Reversible Hydrogels}, series = {Key Engineering Materials}, volume = {1038}, journal = {Key Engineering Materials}, publisher = {Trans Tech Publications}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21092}, pages = {25 -- 30}, year = {2026}, abstract = {The advancement of 3-dimensional printing technology over the past ten years has raised interest in and accessibility to these devices. Due to its consistent growth and demand, 3D printing is becoming a consumer-friendly, reasonably priced craft. Due to technological advancements, it is becoming increasingly integrated into broader fields of science and research, as well as the manufacturing sector. The need for customized solutions is constantly growing across several industries. The 3D extrusion of hydrogels is advancing in the field of biomaterials with a broad spectrum of biomedical applications. Hydrogel extrusion prints heads often use stepper motors or pneumatic pressure systems to push the substrate onto a surface. These techniques are well-suited for materials with high viscosity. While these systems are usually bound to the syringe volume, a refillable reservoir enables them to print above the syringe's limitations. We developed a low-cost standalone heating system for flexible tubes to control the temperature, hence avoiding jellification and clogging of the tubing system leading to the nozzle of the print head. The system connects to an in-house made peristaltic pump, which forces the e.g. gelatin through the nozzle with low pulsation, enabling us to extrude multiple layers of precise tempered gelatin. The heating system is based on easily available materials and electronic components and does not require expensive tools.}, language = {en} } @article{WernerProspositoBoehmeetal.2026, author = {Werner, Ronald and Prosposito, Paolo and B{\"o}hme, Andrea and Krenz-Baath, Ren{\´e}}, title = {Optimization of Hydrogen Alarm Sensor on Semiconductor Basis}, series = {Key Engineering Materials}, volume = {1039}, journal = {Key Engineering Materials}, publisher = {Trans Tech Publications}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21104}, pages = {9 -- 14}, year = {2026}, abstract = {A semiconductor based hydrogen sensor system was optimized by various modifications, which allow an improved detection of very low concentrations of hydrogen in air. The foundation for new investigations on the sensor structure are modifications of substrate and gate structures. Establishment of reference structures is a major aim. A possible drift compensation could be the use of aluminum or alloys for sensor system in order to stabilize signal in Metal Oxide Semiconductor (MOS) respectively Metal Electrolyte Insulator Semiconductor (MEIS) structures. Gold is more likely not capable to function for drift compensation as a pure metal. Nafion™ treatment for cover up the palladium gate seems not to be suitable as a reference, besides could be an option to stabilize sensor signal responses and protect sensors from environmental influences.}, language = {en} }