@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} }