@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} }