@article{D'EliaTruuLahtietal.2023, author = {D'Elia, Domenica and Truu, Jaak and Lahti, Leo and Berland, Magali and Papoutsoglou, Georgios and Ceci, Michelangelo and Zomer, Aldert and Lopes, Marta B. and Ibrahimi, Eliana and Gruca, Aleksandra and Nechyporenko, Alina and Frohme, Marcus and Klammsteiner, Thomas and Carrillo de Santa Pau, Enrique and Marcos-Zambrano, Laura Judith and Hron, Karel and Pio, Gianvito and Simeon, Andrea and Suharoschi, Ramona and Moreno-Indias, Isabel and Temko, Andriy and Nedyalkova, Miroslava and Apostol, Elena-Simona and Truică, Ciprian-Octavian and Shigdel, Rajesh and Telalović, Jasminka Hasić and Bongcam-Rudloff, Erik and Przymus, Piotr and Jordamović, Naida Babić and Falquet, Laurent and Tarazona, Sonia and Sampri, Alexia and Isola, Gaetano and P{\´e}rez-Serrano, David and Trajkovik, Vladimir and Klucar, Lubos and Loncar-Turukalo, Tatjana and Havulinna, Aki S. and Jansen, Christian and Bertelsen, Randi J. and Claesson, Marcus Joakim}, title = {Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action}, series = {Frontiers in Microbiology}, volume = {14}, journal = {Frontiers in Microbiology}, publisher = {Frontiers}, issn = {1664-302X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18004}, year = {2023}, abstract = {The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory 'omics' features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices.}, language = {en} } @article{BeisserGrohmeKopkaetal.2012, author = {Beisser, Daniela and Grohme, Markus and Kopka, Joachim and Frohme, Marcus and Schill, Ralph O. and Hengherr, Steffen and Dandekar, Thomas and Klau, Gunnar W. and Dittrich, Marcus and M{\"u}ller, Tobias}, title = {Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum}, series = {BMC Systems Biology}, volume = {6}, journal = {BMC Systems Biology}, number = {72}, issn = {1752-0509}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6146}, pages = {13}, year = {2012}, abstract = {Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress.}, language = {en} } @article{MarcosZambranoLopezMolinaBakirGungoretal.2023, author = {Marcos-Zambrano, Laura Judith and L{\´o}pez-Molina, V{\´i}ctor Manuel and Bakir-Gungor, Burcu and Frohme, Marcus and Karaduzovic-Hadziabdic, Kanita and Klammsteiner, Thomas and Ibrahimi, Eliana and Lahti, Leo and Loncar-Turukalo, Tatjana and Dhamo, Xhilda and Simeon, Andrea and Nechyporenko, Alina and Pio, Gianvito and Przymus, Piotr and Sampri, Alexia and Trajkovik, Vladimir and Lacruz-Pleguezuelos, Blanca and Aasmets, Oliver and Araujo, Ricardo and Anagnostopoulos, Ioannis and Aydemir, {\"O}nder and Berland, Magali and Calle, M. Luz and Ceci, Michelangelo and Duman, Hatice and G{\"u}ndoğdu, Aycan and Havulinna, Aki S. and Kaka Bra, Kardokh Hama Najib and Kalluci, Eglantina and Karav, Sercan and Lode, Daniel and Lopes, Marta B. and May, Patrick and Nap, Bram and Nedyalkova, Miroslava and Paci{\^e}ncia, In{\^e}s and Pasic, Lejla and Pujolassos, Meritxell and Shigdel, Rajesh and Sus{\´i}n, Antonio and Thiele, Ines and Truică, Ciprian-Octavian and Wilmes, Paul and Yilmaz, Ercument and Yousef, Malik and Claesson, Marcus Joakim and Truu, Jaak and Carrillo de Santa Pau, Enrique}, title = {A toolbox of machine learning software to support microbiome analysis}, series = {Frontiers in Microbiology}, volume = {14}, journal = {Frontiers in Microbiology}, publisher = {Frontiers}, issn = {1664-302X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18271}, year = {2023}, abstract = {The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis.}, language = {en} } @article{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{KoberHollertFrohme2019, author = {Kober, Liane and Hollert, Henner and Frohme, Marcus}, title = {Quantification of nitroaromatic explosives in contaminated soil using MALDI-TOF mass spectrometry}, series = {Analytical and Bioanalytical Chemistry}, volume = {411}, journal = {Analytical and Bioanalytical Chemistry}, number = {23}, issn = {1618-2650}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12388}, pages = {5993 -- 6003}, year = {2019}, abstract = {Contamination from various sources is a global environmental and health threat, with mining and military activities in particular having spread nitroaromatic compounds, such as 2,4,6-trinitrotoluene and its degradation products and by-products, to the soil. The investigation and monitoring of large contaminated areas requires new detection methods since the established ones are expensive and time-consuming. Hence, we established a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI--TOF MS) method using 1,5-diaminonaphthalene as the matrix substance and an internal standard for quantification. Analyzing standard substances, we found specific signals for radical and fragment ions of different nitrotoluenes and nitrobenzenes with good reproducibility and detection limits down to 0.25 ng/μL. The analysis of soil sample extracts from a former production site showed clear signals for 2,4,6-trinitrotoluene and the primary degradation products aminodinitrotoluenes. Furthermore, quantification gave results comparable to those obtained by conventional liquid chromatography--tandem mass spectrometry analysis. The MALDI-TOF MS method has a comparatively lower reproducibility, with relative standard deviations of 6\% to 20\% for multiple measurements of standard solutions and soil sample extracts. Nevertheless, a comparison of both methods revealed the advantages of MALDI-TOF MS analysis of explosive-contaminated areas with regard to costs, time, and handling. Finally, our MALDI-TOF MS method fulfills all the needs for high sample throughput and can therefore be a valuable screening tool for explosive-contaminated areas.}, 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{HornemannSinningCortesetal.2017, author = {Hornemann, Andrea and Sinning, Denise and Cortes, Sofia and Campino, Lenea and Emmer, Peggy and Kuhls, Katrin and Ulm, Gerhard and Frohme, Marcus and Beckhoff, Burkhard}, title = {A pilot study on fingerprinting Leishmania species from the Old World using Fourier transform infrared spectroscopy}, series = {Analytical and Bioanalytical Chemistry}, journal = {Analytical and Bioanalytical Chemistry}, issn = {1432-1130}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10080}, year = {2017}, abstract = {Leishmania species are protozoan parasites and the causative agents of leishmaniasis, a vector borne disease that imposes a large health burden on individuals living mainly in tropical and subtropical regions. Different Leishmania species are responsible for the distinct clinical patterns, such as cutaneous, mucocutaneous, and visceral leishmaniasis, with the latter being potentially fatal if left untreated. For this reason, it is important to perform correct species identification and differentiation. Fourier transform infrared spectroscopy (FTIR) is an analytical spectroscopic technique increasingly being used as a potential tool for identification of microorganisms for diagnostic purposes. By employing mid-infrared (MIR) spectral data, it is not only possible to assess the chemical structures but also to achieve differentiation supported by multivariate statistic analysis. This work comprises a pilot study on differentiation of Leishmania species of the Old World (L. major, L. tropica, L. infantum, and L. donovani) as well as hybrids of distinct species by using vibrational spectroscopic fingerprints. Films of intact Leishmania parasites and their deoxyribonucleic acid (DNA) were characterized comparatively with respect to their biochemical nature and MIR spectral patterns. The strains' hyperspectral datasets were multivariately examined by means of variance-based principal components analysis (PCA) and distance-based hierarchical cluster analysis (HCA). With the implementation of MIR spectral datasets we show that a phenotypic differentiation of Leishmania at species and intra-species level is feasible. Thus, FTIR spectroscopy can be further exploited for building up spectral databases of Leishmania parasites in view of high-throughput analysis of clinical specimens.}, 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{PfeilFrohmeSchulze2018, author = {Pfeil, Juliane and Frohme, Marcus and Schulze, Katja}, title = {Mobile microscopy for the examination of blood samples}, series = {EMBnet.journal}, volume = {23}, journal = {EMBnet.journal}, issn = {2226-6089}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10509}, pages = {e904}, year = {2018}, abstract = {The analysis of blood is one of the best possibilities to diagnose and control diseases and deficiency symptoms. Common blood tests that are performed in medical laboratories are time-consuming and work-intensive. In under-developed areas, there is often also a lack of specialised staff and facilities. The development of a mobile microscopic system that contains an automated image analysis and that can be used via a smartphone, could represent a valuable help to improve the diagnostic care, especially in those areas. it aims to enable a very fast, cheap, location- and knowledge-independent application for many use cases.}, 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 = {C60 fullerene accumulation in human leukemic cells and perspectives of LED-mediated photodynamic therapy}, series = {Free Radical Biology and Medicine}, volume = {124}, journal = {Free Radical Biology and Medicine}, issn = {1873-4596}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10588}, pages = {319 -- 327}, year = {2018}, abstract = {Recent progress in nanobiotechnology has attracted interest to a biomedical application of the carbon nanostructure C60 fullerene since it possesses a unique structure and versatile biological activity. C60 fullerene potential application in the frame of cancer photodynamic therapy (PDT) relies on rapid development of new light sources as well as on better understanding of the fullerene interaction with cells. The aim of this study was to analyze C60 fullerene effects on human leukemic cells (CCRF-CEM) in combination with high power single chip light-emitting diodes (LEDs) light irradiation of different wavelengths: ultraviolet (UV, 365 nm), violet (405 nm), green (515 nm) and red (632 nm). The time-dependent accumulation of fullerene C60 in CCRF-CEM cells up to 250 ng/106 cells at 24 h with predominant localization within mitochondria was demonstrated with immunocytochemical staining and liquid chromatography mass spectrometry. In a cell viability assay we studied photoexcitation of the accumulated C60 nanostructures with ultraviolet or violet LEDs and could prove that significant phototoxic effects did arise. A less pronounced C60 fullerene phototoxic effect was observed after irradiation with green, and no effect was detected with red light. A C60 fullerene photoactivation with violet light induced substantial ROS generation and apoptotic cell death, confirmed by caspase3/7 activation and plasma membrane phosphatidylserine externalization. Our work proved C60 fullerene ability to induce apoptosis of leukemic cells after photoexcitation with high power single chip 405 nm LED as a light source. This underlined the potential for application of C60 nanostructure as a photosensitizer for anticancer therapy.}, 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{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{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} } @misc{SchulzeGloeklerKadolskyetal.2011, author = {Schulze, Katja and Gl{\"o}kler, J{\"o}rn and Kadolsky, Marianne and Frohme, Marcus}, title = {Detektion des Kartoffelspindelknollen Viroids mit Hilfe der Loop Mediated Isothermal Amplification}, series = {Wissenschaftliche Beitr{\"a}ge 2011}, volume = {15}, journal = {Wissenschaftliche Beitr{\"a}ge 2011}, issn = {0949-8214}, doi = {10.15771/0949-8214_2011_1_1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus-1025}, pages = {7 -- 12}, year = {2011}, abstract = {PSTV ist ein hoch infekti{\"o}ses Viroid, das in Kartoffeln verkleinerte und spindel{\"a}hnliche Knollen verursacht. Um Ernteverlusten vorzubeugen, ist eine Detektion in fr{\"u}hen Infektionsstadien von großer Bedeutung. Aufgrund ihrer hohen Sensitivit{\"a}t und Spezifit{\"a}t wird die PCR als Standardnachweisverfahren f{\"u}r PSTV verwendet. Nachteilig an dieser Methode sind der apparative Aufwand und die zeitaufw{\"a}ndige Durchf{\"u}hrung. Als viel versprechende Alternative konnte der Nachweis von PSTV mit Hilfe der Reverse Transcription Loop Mediated Isothermal Amplification (RT-LAMP) gezeigt werden. Hierbei handelt es sich um eine einfache und schnelle Methode, f{\"u}r die wenig aufw{\"a}ndige Laborausr{\"u}stung ben{\"o}tigt wird. Dabei erm{\"o}glichte eine an den Amplifikationsprozess gekoppelte Fluoreszenzreaktion die Detektion von Produkten direkt nach der Nachweisreaktion mit dem bloßen Auge (bzw. unter UV-Licht). Die Ergebnisse konnten mit Hilfe einer Real Time Detektion des auftretenden Fluoreszenzsignals best{\"a}tigt werden.}, language = {de} } @article{KoberMeyerAlertGrienitzetal.2015, author = {Kober, Liane and Meyer-Alert, Henriette and Grienitz, Desir{\´e}e and Hollert, Henner and Frohme, Marcus}, title = {Intact cell mass spectrometry as a rapid and specific tool for the differentiation of toxic effects in cell-based ecotoxicological test systems}, series = {Analytical and Bioanalytical Chemistry}, volume = {407}, journal = {Analytical and Bioanalytical Chemistry}, number = {25}, issn = {1618-2650}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5900}, pages = {7721 -- 7731}, year = {2015}, abstract = {In the last few decades, MALDI-TOF MS has become a useful technique not only in proteomics, but also as a fast and specific tool for whole cell analysis through intact cell mass spectrometry (IC-MS). The present study evaluated IC-MS as a novel tool for the detection of distinct patterns that can be observed after exposure to a certain toxin or concentration by utilizing the eukaryotic fish cell line RTL-W1. Two different viability assays were performed to define the range for IC-MS investigations, each of which employing copper sulfate, acridine, and β-naphthoflavone (BNF) as model compounds for several classes of environmental toxins. The IC-MS of RTL-W1 cells revealed not only specific spectral patterns for the various toxins, but also that the concentration used had an effect on RTL-W1 profiles. After the exposure with copper sulfate and acridine, the spectra of RTL-W1 showed a significant increase of certain peaks in the higher mass range (m/z >7000), which is probably attributed to the apoptosis of RTL-W1. On the contrary, exposure to BNF showed a distinct change of ion abundances only in the lower mass range (m/z <7000). Furthermore, a set of mass peaks could be identified as a specific biomarker for a single toxin treatment, so IC-MS demonstrates a new method for the distinction of toxic effects in fish cells. Due to fast sample preparation and high throughput, IC-MS offers great potential for ecotoxicological studies to investigate cellular effects of different substances and complex environmental samples.}, 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{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{NarvekarBerrielDiazKronesHerzigetal.2009, author = {Narvekar, Prachiti and Berriel Diaz, Mauricio and Krones-Herzig, Anja and Hardeland, Ulrike and Strzoda, Daniela and St{\"o}hr, Sigrid and Frohme, Marcus and Herzig, Stephan}, title = {Liver-specific loss of lipolysis-stimulated lipoprotein receptor triggers systemic hyperlipidemia in mice}, series = {Diabetes}, volume = {58}, journal = {Diabetes}, number = {5}, publisher = {American Diabetes Association}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19954}, pages = {1040 -- 1049}, year = {2009}, abstract = {In mammals, proper storage and distribution of lipids in and between tissues is essential for the maintenance of energy homeostasis. In contrast, aberrantly high levels of triglycerides in the blood ("hypertriglyceridemia") represent a hallmark of the metabolic syndrome and type 2 diabetes. As hypertriglyceridemia has been identified as an important risk factor for cardiovascular complications, in this study we aimed to identify molecular mechanisms in aberrant triglyceride elevation under these conditions. To determine the importance of hepatic lipid handling for systemic dyslipidemia, we profiled the expression patterns of various hepatic lipid transporters and receptors under healthy and type 2 diabetic conditions. A differentially expressed lipoprotein receptor was functionally characterized by generating acute, liver-specific loss- and gain-of-function animal models. We show that the hepatic expression of lipid transporter lipolysis-stimulated lipoprotein receptor (LSR) is specifically impaired in mouse models of obesity and type 2 diabetes and can be restored by leptin replacement. Experimental imitation of this pathophysiological situation by liver-specific knockdown of LSR promotes hypertriglyceridemia and elevated apolipoprotein (Apo)B and E serum levels in lean wild-type and ApoE knockout mice. In contrast, genetic restoration of LSR expression in obese animals to wild-type levels improves serum triglyceride levels and serum profiles in these mice. The dysregulation of hepatic LSR under obese and diabetic conditions may provide a molecular rationale for systemic dyslipidemia in type 2 diabetes and the metabolic syndrome and represent a novel target for alternative treatment strategies in these patients.}, language = {en} } @article{ReunerHengherrMalietal.2010, author = {Reuner, Andy and Hengherr, Steffen and Mali, Brahim and F{\"o}rster, Frank and Arndt, Detlev and Reinhardt, Richard and Dandekar, Thomas and Frohme, Marcus and Br{\"u}mmer, Franz and Schill, Ralph O.}, title = {Stress response in tardigrades: differential gene expression of molecular chaperones}, series = {Cell Stress and Chaperones}, volume = {15}, journal = {Cell Stress and Chaperones}, number = {4}, publisher = {Springer}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19994}, pages = {423 -- 430}, year = {2010}, abstract = {Semi-terrestrial tardigrades exhibit a remarkable tolerance to desiccation by entering a state called anhydrobiosis. In this state, they show a strong resistance against several kinds of physical extremes. Because of the probable importance of stress proteins during the phases of dehydration and rehydration, the relative abundance of transcripts coding for two α-crystallin heat-shock proteins (Mt-sHsp17.2 and Mt-sHsp19.5), as well for the heat-shock proteins Mt-sHsp10, Mt-Hsp60, Mt-Hsp70 and Mt-Hsp90, were analysed in active and anhydrobiotic tardigrades of the species Milnesium tardigradum. They were also analysed in the transitional stage (I) of dehydration, the transitional stage (II) of rehydration and in heat-shocked specimens. A variable pattern of expression was detected, with most candidates being downregulated. Gene transcripts of one Mt-hsp70 isoform in the transitional stage I and Mt-hsp90 in the anhydrobiotic stage were significantly upregulated. A high gene expression (778.6-fold) was found for the small α-crystallin heat-shock protein gene Mt-sHsp17.2 after heat shock. We discuss the limited role of the stress-gene expression in the transitional stages between the active and anhydrobiotic tardigrades and other mechanisms which allow tardigrades to survive desiccation.}, 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{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{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{KipkorirMuhohoMuliroetal.2015, author = {Kipkorir, R. and Muhoho, S. and Muliro, P. and Mugendi, Beatrice and Frohme, Marcus and Br{\"o}del, Oliver}, title = {Effects of Coffee Processing Technologies on Aroma Profiles and Sensory Quality of Ruiru 11 and SL 28 Kenyan Coffee Varieties}, series = {Asian Journal of Agriculture and Food Sciences}, volume = {3}, journal = {Asian Journal of Agriculture and Food Sciences}, number = {2}, issn = {2321-1571}, doi = {10.15771/2321-1571_2015_1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6482}, pages = {178 -- 188}, year = {2015}, abstract = {The study aimed at comparing the effects of three coffee processing methods on aroma profiles and sensory quality of Ruiru 11 and SL 28 coffee varieties. The processing methods varied on stages of processing and method of mucilage removal. The green coffee beans obtained from the three processing methods were graded and roasted, ground and analyzed for the aroma profiles and sensory quality. Headspace Solid phase Microextraction fibre (SPME) technique were used for the extraction of aroma compounds from coffee samples and characterization of the compounds with use of gas chromatography mass spectrometry (GC-MS). Sensory quality were analyzed by an expert panelist. Various volatile aroma compounds were identified in roasted coffee and classified into their chemical classes involving furans, ketones, pyrazines ketones pyridines, pyrroles and acids. The intensity of aroma compounds were compared in terms of their peak areas and variations were noted between the processing methods with the ecopulper showing higher levels of pyrazines such as 2-methylpyrazine, 2-ethyl-6-methylpyrazine, and wet pulper showing higher levels of furans such as furfuryl formate and furfuryl alcohol, acetate. The hand pulper was high in the level of acids and esters such as acetic acid and propanoic acid, ethyl ester. Similar aroma compounds were identified in headspace of Ruiru 11 and SL 28 and there were variations in the intensities of aroma groups such as pyrroles and pyridines. It was concluded that the eco-pulper and hand pulper methods gives better aroma quality than the wet pulper while SL 28 variety gives higher sensory quality than Ruiru 11.}, language = {en} } @article{PraiaHerkenhoffBroedeletal.2022, author = {Praia, Ana Beatriz and Herkenhoff, Marcos Edgar and Br{\"o}del, Oliver and Frohme, Marcus and Saad, Susana Marta Isay}, title = {Sour Beer with Lacticaseibacillus paracasei subsp. paracasei F19: Feasibility and Influence of Supplementation with Spondias mombin L. Juice and/or By-Product}, series = {Foods}, volume = {11}, journal = {Foods}, number = {24}, publisher = {MDPI}, issn = {2304-8158}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16852}, year = {2022}, abstract = {This study aimed to evaluate the probiotic strain Lacticaseibacillus (L.) paracasei subsp. paracasei F19 (F19) with the yeast Saccharomyces cerevisiae US-05 (US-05), using Spondias mombin L. ('tapereb{\´a}' or 'caj{\´a}') juice and by-product, in four sour-type beer formulations: control, with bagasse, juice, and juice and bagasse. The viability of F19 was evaluated by pour-plating and PMA-qPCR. Fermentability, in addition to physicochemical and sensory parameters, and aroma and flavor, were evaluated during brewery by using Headspace Solid-Phase Microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS). F19 was successful in fermenting bagasse in a MRS medium (9.28 log CFU/mL in 24 h) but had a low viability in hopped wort, growing better in formulations without bagasse or juice. No difference between formulations was observed regarding sensory acceptability, and the HS-SPME/GC-MS revealed different flavors and aroma compounds. In conclusion, the production of a potential probiotic sour beer with F19 and US-05 is feasible regarding probiotic viability. However, S. mombin, as juice or bagasse, threatened probiotic survival. Different flavors and aroma compounds were detected, whereas no difference between formulations was found regarding sensory acceptability. The moderate alcohol content achieved is important for bacterial survival and for the development of a probiotic beer with health claims.}, language = {en} } @article{RadivoievychKolpGrebinyketal.2023, author = {Radivoievych, Aleksandar and Kolp, Benjamin and Grebinyk, Sergii and Prylutska, Svitlana and Ritter, Uwe and Zolk, Oliver and Gl{\"o}kler, J{\"o}rn and Frohme, Marcus and Grebinyk, Anna}, title = {Silent Death by Sound: C60 Fullerene Sonodynamic Treatment of Cancer Cells}, series = {International Journal of Molecular Sciences}, volume = {24}, journal = {International Journal of Molecular Sciences}, number = {2}, publisher = {MDPI}, issn = {1422-0067}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16877}, year = {2023}, abstract = {The acoustic pressure waves of ultrasound (US) not only penetrate biological tissues deeper than light, but they also generate light emission, termed sonoluminescence. This promoted the idea of its use as an alternative energy source for photosensitizer excitation. Pristine C60 fullerene (C60), an excellent photosensitizer, was explored in the frame of cancer sonodynamic therapy (SDT). For that purpose, we analyzed C60 effects on human cervix carcinoma HeLa cells in combination with a low-intensity US treatment. The time-dependent accumulation of C60 in HeLa cells reached its maximum at 24 h (800 ± 66 ng/106 cells). Half of extranuclear C60 is localized within mitochondria. The efficiency of the C60 nanostructure's sonoexcitation with 1 MHz US was tested with cell-based assays. A significant proapoptotic sonotoxic effect of C60 was found for HeLa cells. C60′s ability to induce apoptosis of carcinoma cells after sonoexcitation with US provides a promising novel approach for cancer treatment.}, language = {en} } @article{AlekseevaNechyporenkoFrohmeetal.2023, author = {Alekseeva, Victoriia and Nechyporenko, Alina and Frohme, Marcus and Gargin, Vitaliy and Meniailov, Ievgen and Chumachenko, Dmytro}, title = {Intelligent Decision Support System for Differential Diagnosis of Chronic Odontogenic Rhinosinusitis Based on U-Net Segmentation}, series = {Electronics}, volume = {12}, journal = {Electronics}, number = {5}, publisher = {MDPI}, issn = {2079-9292}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17088}, year = {2023}, abstract = {The share of chronic odontogenic rhinosinusitis is 40\% among all chronic rhinosinusitis. Using automated information systems for differential diagnosis will improve the efficiency of decision-making by doctors in diagnosing chronic odontogenic rhinosinusitis. Therefore, this study aimed to develop an intelligent decision support system for the differential diagnosis of chronic odontogenic rhinosinusitis based on computer vision methods. A dataset was collected and processed, including 162 MSCT images. A deep learning model for image segmentation was developed. A 23 convolutional layer U-Net network architecture has been used for the segmentation of multi-spiral computed tomography (MSCT) data with odontogenic maxillary sinusitis. The proposed model is implemented in such a way that each pair of repeated 3 × 3 convolutions layers is followed by an Exponential Linear Unit instead of a Rectified Linear Unit as an activation function. The model showed an accuracy of 90.09\%. To develop a decision support system, an intelligent chatbot allows the user to conduct an automated patient survey and collect patient examination data from several doctors of various profiles. The intelligent information system proposed in this study made it possible to combine an image processing model with a patient interview and examination data, improving physician decision-making efficiency in the differential diagnosis of Chronic Odontogenic Rhinosinusitis. The proposed solution is the first comprehensive solution in this area.}, language = {en} } @article{ChumachenkoButkevychLodeetal.2022, author = {Chumachenko, Dmytro and Butkevych, Mykola and Lode, Daniel and Frohme, Marcus and Schmailzl, Kurt J. G. and Nechyporenko, Alina}, title = {Machine Learning Methods in Predicting Patients with Suspected Myocardial Infarction Based on Short-Time HRV Data}, series = {Sensors}, volume = {22}, journal = {Sensors}, number = {18}, publisher = {MDPI}, issn = {1424-8220}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16521}, year = {2022}, abstract = {Diagnosis of cardiovascular diseases is an urgent task because they are the main cause of death for 32\% of the world's population. Particularly relevant are automated diagnostics using machine learning methods in the digitalization of healthcare and introduction of personalized medicine in healthcare institutions, including at the individual level when designing smart houses. Therefore, this study aims to analyze short 10-s electrocardiogram measurements taken from 12 leads. In addition, the task is to classify patients with suspected myocardial infarction using machine learning methods. We have developed four models based on the k-nearest neighbor classifier, radial basis function, decision tree, and random forest to do this. An analysis of time parameters showed that the most significant parameters for diagnosing myocardial infraction are SDNN, BPM, and IBI. An experimental investigation was conducted on the data of the open PTB-XL dataset for patients with suspected myocardial infarction. The results showed that, according to the parameters of the short ECG, it is possible to classify patients with a suspected myocardial infraction as sick and healthy with high accuracy. The optimized Random Forest model showed the best performance with an accuracy of 99.63\%, and a root mean absolute error is less than 0.004. The proposed novel approach can be used for patients who do not have other indicators of heart attacks.}, language = {en} } @article{GrebinykPrylutskaGrebinyketal.2022, author = {Grebinyk, Anna and Prylutska, Svitlana and Grebinyk, Sergii and Ponomarenko, Stanislav and Virych, Pavlo and Chumachenko, Vasyl and Kutsevol, Nataliya and Prylutskyy, Yuriy and Ritter, Uwe and Frohme, Marcus}, title = {Drug delivery with a pH-sensitive star-like dextran-graft polyacrylamide copolymer}, series = {Nanoscale Advances}, volume = {4}, journal = {Nanoscale Advances}, number = {23}, publisher = {Royal Society of Chemistry (RSC)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16749}, pages = {5077 -- 5088}, year = {2022}, abstract = {The development of precision cancer medicine relies on novel formulation strategies for targeted drug delivery to increase the therapeutic outcome. Biocompatible polymer nanoparticles, namely dextran-graft-polyacrylamide (D-g-PAA) copolymers, represent one of the innovative non-invasive approaches for drug delivery applications in cancer therapy. In this study, the star-like D-g-PAA copolymer in anionic form (D-g-PAAan) was developed for pH-triggered targeted drug delivery of the common chemotherapeutic drugs - doxorubicin (Dox) and cisplatin (Cis). The initial D-g-PAA copolymer was synthesized by the radical graft polymerization method, and then alkaline-hydrolyzed to get this polymer in anionic form for further use for drug encapsulation. The acidification of the buffer promoted the release of loaded drugs. D-g-PAAan nanoparticles increased the toxic potential of the drugs against human and mouse lung carcinoma cells (A549 and LLC), but not against normal human lung cells (HEL299). The drug-loaded D-g-PAAan-nanoparticles promoted further oxidative stress and apoptosis induction in LLC cells. D-g-PAAan-nanoparticles improved Dox accumulation and drugs' toxicity in a 3D LLC multi-cellular spheroid model. The data obtained indicate that the strategy of chemotherapeutic drug encapsulation within the branched D-g-PAAan nanoparticle allows not only to realize pH-triggered drug release but also to potentiate its cytotoxic, prooxidant and proapoptotic effects against lung carcinoma cells.}, language = {en} } @article{KoberSchaeferHollertetal.2023, author = {Kober, Liane and Schaefer, Paul and Hollert, Henner and Frohme, Marcus}, title = {A novel strategy for high-throughput sample collection, analysis and visualization of explosives' concentrations for contaminated areas}, series = {International Journal of Environmental Science and Technology}, volume = {20}, journal = {International Journal of Environmental Science and Technology}, number = {2}, publisher = {Springer Nature}, issn = {1735-2630}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15981}, pages = {1399 -- 1410}, year = {2023}, abstract = {The use of explosives has led to a widespread distribution of 2,4,6-trinitrotoluene (TNT) and its by- and degradation products in the soil on former production and testing sites. The investigation of those large contaminated sites is so far based on a few selected soil samples, due to high costs of conventional HPLC and GC analysis, although huge differences in concentrations can already be found in small areas and different collection depths. We introduce a novel high-throughput screening system for those areas, which combines a smartphone-based collection of GPS data and soil characteristics with a fast MALDI-TOF MS quantification of explosives in soil sample extracts and finally a heatmap visualization of the explosives' spread in soil and an analysis of correlation between concentrations and soil characteristics. The analysis of a 400 m2 area presented an extensive contamination with TNT and lower concentrations of the degradation and by-products aminodinitrotoluenes (ADNT) and dinitrotoluenes (DNT) next to a former production facility for TNT. The contamination decreased in deeper soil levels and depended on the soil type. Pure humus samples showed significantly lower contaminations compared to sand and humus/sand mixtures, which is likely to be caused by an increased binding potential of the humic material. No correlation was found between the vegetation and the concentration of explosives. Since the results were obtained and visualized within several hours, the MALDI-TOF MS based comprehensive screening and heatmap analysis might be valuable for a fast and high-throughput characterization of contaminated areas.}, language = {en} } @article{PfeilNechyporenkoFrohmeetal.2022, author = {Pfeil, Juliane and Nechyporenko, Alina and Frohme, Marcus and Hufert, Frank T. and Schulze, Katja}, title = {Examination of blood samples using deep learning and mobile microscopy}, series = {BMC Bioinformatics}, volume = {23}, journal = {BMC Bioinformatics}, publisher = {BioMed Central}, issn = {1471-2105}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15802}, year = {2022}, abstract = {Microscopic examination of human blood samples is an excellent opportunity to assess general health status and diagnose diseases. Conventional blood tests are performed in medical laboratories by specialized professionals and are time and labor intensive. The development of a point-of-care system based on a mobile microscope and powerful algorithms would be beneficial for providing care directly at the patient's bedside. For this purpose human blood samples were visualized using a low-cost mobile microscope, an ocular camera and a smartphone. Training and optimisation of different deep learning methods for instance segmentation are used to detect and count the different blood cells. The accuracy of the results is assessed using quantitative and qualitative evaluation standards.}, language = {en} } @article{HerkenhoffBovolentaBroedeletal.2021, author = {Herkenhoff, Marcos Edgar and Bovolenta, Luiz A. and Br{\"o}del, Oliver and dos Santos, Lucilene Delazari and de Oliveira, Arthur C. and Chuffa, Luiz G.A. and Ribeiro, Amanda O. and Lupi, Luiz A. and Dias, Marco A.D. and Hilsdorf, Alexandre W.S. and Frohme, Marcus and Pinhal, Danillo}, title = {Variant expression signatures of microRNAs and protein related to growth in a crossbreed between two strains of Nile tilapia (Oreochromis niloticus)}, series = {Genomics}, volume = {113}, journal = {Genomics}, number = {6}, publisher = {Elsevier}, issn = {0888-7543}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15571}, pages = {4303 -- 4312}, year = {2021}, abstract = {Nile tilapia (Oreochromis niloticus) is a species of worldwide importance for aquaculture. A crossbred lineage was developed through introgressive backcross breeding techniques and combines the high growth performance of the Chitralada (CHIT) lwith attractive reddish color of the Red Stirling (REDS) strains. Since the crossbreed has an unknown genetically improved background, the objective of this work was to characterize expression signatures that portray the advantageous phenotype of the crossbreeds. We characterized the microRNA transcriptome by high throughput sequencing (RNA-seq) and the proteome through mass spectrometry (ESI-Q-TOF-MS) and applied bioinformatics for the comparative analysis of such molecular data on the three strains. Crossbreed expressed a distinct set of miRNAs and proteins compared to the parents. They comprised several microRNAs regulate traits of economic interest. Proteomic profiles revealed differences between parental and crossbreed in expression of proteins associated with glycolisis. Distinctive miRNA and protein signatures contribute to the phenotype of crossbreed.}, language = {en} } @article{GloeklerLimIdaetal.2021, author = {Gl{\"o}kler, J{\"o}rn and Lim, Theam Soon and Ida, Jeunice and Frohme, Marcus}, title = {Isothermal amplifications - a comprehensive review on current methods}, series = {Critical Reviews in Biochemistry and Molecular Biology}, journal = {Critical Reviews in Biochemistry and Molecular Biology}, publisher = {Taylor \& Francis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15154}, pages = {1 -- 44}, year = {2021}, abstract = {AbstractThe introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.}, language = {en} } @article{RadivoievychPrylutskaZolketal.2023, author = {Radivoievych, Aleksandar and Prylutska, Svitlana and Zolk, Oliver and Ritter, Uwe and Frohme, Marcus and Grebinyk, Anna}, title = {Comparison of Sonodynamic Treatment Set-Ups for Cancer Cells with Organic Sonosensitizers and Nanosonosensitizers}, series = {Pharmaceutics}, volume = {15}, journal = {Pharmaceutics}, number = {11}, publisher = {MDPI}, issn = {1999-4923}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18223}, year = {2023}, abstract = {Cancer sonodynamic therapy (SDT) is the therapeutic strategy of a high-frequency ultrasound (US) combined with a special sonosensitizer that becomes cytotoxic upon US exposure. The growing number of newly discovered sonosensitizers and custom US in vitro treatment solutions push the SDT field into a need for systemic studies and reproducible in vitro experimental set-ups. In the current research, we aimed to compare two of the most used and suitable SDT in vitro set-ups—"sealed well" and "transducer in well"—in one systematic study. We assessed US pressure, intensity, and temperature distribution in wells under US irradiation. Treatment efficacy was evaluated for both set-ups towards cancer cell lines of different origins, treated with two promising sonosensitizer candidates—carbon nanoparticle C60 fullerene (C60) and herbal alkaloid berberine. C60 was found to exhibit higher sonotoxicity toward cancer cells than berberine. The higher efficacy of sonodynamic treatment with a "transducer in well" set-up than a "sealed well" set-up underlined its promising application for SDT in vitro studies. The "transducer in well" set-up is recommended for in vitro US treatment investigations based on its US-field homogeneity and pronounced cellular effects. Moreover, SDT with C60 and berberine could be exploited as a promising combinative approach for cancer treatment.}, language = {en} } @article{ShchotkinaPalamarchukSkorokhodetal.2023, author = {Shchotkina, Nataliia and Palamarchuk, Y. and Skorokhod, Iryna and Dolinchuk, Liudmyla and Sokol, Anatoliy and Motronenko, Valentina and Besarab, A. and Gorchakova, N. and Frohme, Marcus and Herzog, Michael}, title = {Features of technological regulation for cardiac bioimplants}, series = {Cell and Organ Transplantology}, volume = {11}, journal = {Cell and Organ Transplantology}, number = {1}, publisher = {Institute of Cell Therapy}, address = {Kiev}, issn = {2311-021X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18248}, pages = {26 -- 33}, year = {2023}, abstract = {Patients with congenital heart defects and cardiovascular diseases are required new approaches to surgical intervention. The use of biological cardiac implants, which are made from the extracellular matrix, is a promising trend in modern regenerative medicine. These bioimplants can completely replace defective tissue or organs, and when manufactured with strict protocols and quality control measures, can be safe and effective for therapeutic applications. The process of manufacturing bioimplants involves various risks that need to be assessed and mitigated with ongoing monitoring and evaluation necessary to ensure the highest standards of quality. Overall, this study was successfully evaluated the requirements for introducing a new medical device into practice and created a technical file that meets all necessary documentation for certification.}, language = {en} } @article{PrylutskaGrebinykPonomarenkoetal.2024, author = {Prylutska, Svitlana and Grebinyk, Anna and Ponomarenko, Stanislav and G{\"o}vem, Defne and Chumachenko, Vasyl and Kutsevol, Nataliya and Petrovsky, Mykola and Ritter, Uwe and Frohme, Marcus and Piosik, Jacek and Prylutskyy, Yuriy}, title = {Toxicity of Water-Soluble D-g-PNIPAM Polymers in a Complex with Chemotherapy Drugs and Mechanism of Their Action In Vitro}, series = {International Journal of Molecular Sciences}, volume = {25}, journal = {International Journal of Molecular Sciences}, number = {5}, publisher = {MDPI}, issn = {1422-0067}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18790}, year = {2024}, abstract = {The application of a biocompatible polymer nanocarrier can provide target delivery to tumor tissues, improved pharmacokinetics, controlled drug release, etc. Therefore, the proposed strategy was to use the water-soluble star-like copolymers with a Dextran core and Poly(N-isopropylacrylamide) grafts (D-g-PNIPAM) for conjugation with the widely used chemotherapy drugs in oncology-Cisplatin (Cis-Pt) and Doxorubicin (Dox). The molecular characteristics of the copolymer were received using size-exclusion chromatography. The physicochemical characterization of the D-g-PNIPAM-Cis-Pt (or Dox) nanosystem was conducted using dynamic light scattering and FTIR spectroscopy. Using traditional biochemical methods, a comparative analysis of the enhancement of the cytotoxic effect of free Cis-Pt and Dox in combination with D-g-PNIPAM copolymers was performed in cancer cells of the Lewis lung carcinoma line, which are both sensitive and resistant to Dox; in addition, the mechanism of their action in vitro was evaluated.}, language = {en} } @inproceedings{AlekseevaReshetnikFrohmeetal.2023, author = {Alekseeva, Victoriia and Reshetnik, Viktor and Frohme, Marcus and Kachailo, Irina and Murizyna, Irina and Nechyporenko, Alina}, title = {Investigation of the Impact of Insulin Resistance on the Bone Density of the Upper Wall of the Maxillary Sinus}, series = {Proceedings of the 3rd International Workshop of IT-professionals on Artificial Intelligence, ProfIT AI 2023, Waterloo, Canada, November 20-22, 2023}, volume = {3641}, booktitle = {Proceedings of the 3rd International Workshop of IT-professionals on Artificial Intelligence, ProfIT AI 2023, Waterloo, Canada, November 20-22, 2023}, editor = {Chumachenko, Dmytro and Kaur, Jasleen and Yakovlev, Sergiy and Morita, Plinio P.}, publisher = {CEUR-WS.org}, url = {http://nbn-resolving.de/urn:nbn:de:0074-3641-3}, pages = {216 -- 223}, year = {2023}, abstract = {The aim of our study was to investigate the impact of insulin resistance on the bone density of the upper wall of the maxillary sinus. Materials and Methods: The study included 100 female participants aged 18 to 44 years, divided into two groups. The first group consisted of individuals with insulin resistance, while the control group comprised individuals without signs of insulin resistance. In each group, we conducted an investigation of the radiological density of the upper wall of the maxillary sinus using uncertainty calculations. Results of the study suggest a potential influence of insulin resistance on the density of bone tissue around the nasal sinuses, specifically the upper wall of the maxillary sinus in our case. This parameter was found to be minimal in the group of individuals with insulin resistance. It is particularly noteworthy that both minimum and maximum bone density decreased in this group. Conclusions. The research focused on how insulin resistance affects the density of the upper wall of the maxillary sinus. By employing uncertainty calculations, the study revealed that insulin resistance is associated with a decrease in the minimum density of the upper wall of the maxillary sinus. This tendency may act as a catalyst for the emergence of significant inflammatory alterations in the nasal sinuses, serving as a foundation for the initiation of complications.}, language = {en} } @article{RadivoievychSchnepelPrylutskaetal.2024, author = {Radivoievych, Aleksandar and Schnepel, Sophia and Prylutska, Svitlana and Ritter, Uwe and Zolk, Oliver and Frohme, Marcus and Grebinyk, Anna}, title = {From 2D to 3D In Vitro World: Sonodynamically-Induced Prooxidant Proapoptotic Effects of C60-Berberine Nanocomplex on Cancer Cells}, series = {Cancers}, volume = {16}, journal = {Cancers}, number = {18}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19438}, year = {2024}, abstract = {Recently, sonodynamic therapy (SDT) has emerged as a promising non-invasive approach for treating cancer by activating sensitizers with ultrasound (US). In this context, we investigated C60 fullerene (C60) as a nanocarrier for the promising drug Berberine (Ber)—both potential aromatic sonosensitizers. The preferential mitochondrial accumulation of C60 and the proapoptotic effects of Ber also make the C60-Berberine nanocomplex (C60-Ber) a good candidate for direct induction of the intrinsic apoptotic cell death under US action. The in vitro research on C60-Ber can provide insights into novel, non-invasive cancer treatments. These findings lead to the development of targeted therapies with reduced side effects, inspire interdisciplinary collaboration, and open new avenues for drug delivery and cancer therapy research.}, language = {en} } @article{NechyporenkoFrohmeStrelchuketal.2024, author = {Nechyporenko, Alina and Frohme, Marcus and Strelchuk, Yaroslav and Omelchenko, Vladyslav and Gargin, Vitaliy and Ishchenko, Liudmyla and Alekseeva, Victoriia}, title = {Galvanic Skin Response and Photoplethysmography for Stress Recognition Using Machine Learning and Wearable Sensors}, series = {Applied Sciences}, volume = {14}, journal = {Applied Sciences}, number = {24}, publisher = {MDPI}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19803}, year = {2024}, abstract = {This study investigates stress recognition using galvanic skin response (GSR) and photoplethysmography (PPG) data and machine learning, with a new focus on air raid sirens as a stressor. It bridges laboratory and real-world conditions and highlights the reliability of wearable sensors in dynamic, high-stress environments such as war and conflict zones. The study involves 37 participants (20 men, 17 women), aged 20-30, who had not previously heard an air raid siren. A 70 dB "S-40 electric siren" (400-450 Hz) was delivered via headphones. The protocol included a 5 min resting period, followed by 3 min "no-stress" phase, followed by 3 min "stress" phase, and finally a 3 min recovery phase. GSR and PPG signals were recorded using Shimmer 3 GSR+ sensors on the fingers and earlobes. A single session was conducted to avoid sensitization. The workflow includes signal preprocessing to remove artifacts, feature extraction, feature selection, and application of different machine learning models to classify the "stress "and "no-stress" states. As a result, the best classification performance was shown by the k-Nearest Neighbors model, achieving 0.833 accuracy. This was achieved by using a particular combination of heart rate variability (HRV) and GSR features, which can be considered as new indicators of siren-induced stress.}, language = {en} } @article{HerkenhoffBroedelFrohme2024, author = {Herkenhoff, Marcos Edgar and Br{\"o}del, Oliver and Frohme, Marcus}, title = {Aroma component analysis by HS-SPME/GC-MS to characterize Lager, Ale, and sour beer styles}, series = {Food Research International}, volume = {194}, journal = {Food Research International}, publisher = {Elsevier}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19830}, year = {2024}, abstract = {The world of beer is a rich tapestry woven with diverse styles, each with its unique character. Lager, known for its crispness, ferments at lower temperatures, while ale, at warmer ones, boasts a wide spectrum of aromas. Belgian beers dazzle with their complexity, from fruity Trappist ales to sour lambics. German wheat beers, like hefeweizens, charm with their effervescence and fruity undertones. India Pale Ales (IPAs) showcase a hoppy burst, while sour ales tantalize with their tanginess. Craftsmanship, history, and regional ingredients intertwine in this world of brewing, offering aficionados an array of delightful experiences. Research on craft beer aromas is limited, and molecular fingerprint could be crucial. To date, there have been no studies focused on characterizing compound profiles to differentiate beer styles. The Headspace Solid Phase Microextraction (HS-SPME) method provides a rapid and solvent-free approach to volatile compound. The present study aims to characterize the aroma profile of a wide range of beers by using HS-SPME/GC-MS technique combined with multivariate data processing. A total of 120 beer samples were collected and divided into five categories: Pilsen (n = 28); Lager (n = 23); Ale (n = 32); Sour (n = 24); and Belgian Ales (n = 13). Among the Pilsen beers, 18 unique compounds were found for beers with hop extract and hops, and 2 for beers with hop extract (Octyl acetate; and alpha-Terpineol). When comparing the remaining groups to each other, Belgian beers exhibited 5 unique compounds, and Lagers had one (nonanal). Sours and Ales did not have unique compounds but shared 2 distinct compounds with the Belgian group each. We concluded that Belgian beers are the most complex in terms of various aroma-related compounds, and that it is possible to distinguish beers that use pure hops from hop extract.}, language = {en} } @article{SuzukiHerkenhoffBroedeletal.2024, author = {Suzuki, Juliana Yumi and Herkenhoff, Marcos Edgar and Br{\"o}del, Oliver and Cucick, Ana Clara Candelaria and Frohme, Marcus and Saad, Susana Marta Isay}, title = {Exploring the potential of red pitaya pulp (Hylocererus sp.) as a plant-based matrix for probiotic delivery and effects on betacyanin content and flavoromics}, series = {Food Research International}, volume = {192}, journal = {Food Research International}, publisher = {Elsevier}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19843}, year = {2024}, abstract = {This study evaluated the potential of red pitaya pulp fermented with Lacticaseibacillus paracasei subsp. paracasei F-19 (F-19) as a base for probiotic products. Physicochemical parameters, sugar, betacyanin, and phenolic contents, and antioxidant activity were analyzed over 28 days at 4 °C and compared to a non-fermented pulp, and to a pulp fermented with Bifidobacterium animalis subsp. lactis BB-12 (BB-12). Volatile compounds were identified using HS-SPME/GC-MS. Probiotic viability during storage and survival through in vitro-simulated gastrointestinal tract (GIT) stress were assessed. Red pitaya pulp, rich in moisture (85.83 g/100 g), carbohydrates (11.65 g/100 g), and fibers (2.49 g/100 g), supported fermentation by both strains. F-19 and BB-12 lowered pH, with F-19 showing stronger acidification, and maintained high viability (8.85-8.90 log CFU/mL). Fermentation altered sugar profiles and produced unique volatile compounds, enhancing aroma and sensory attributes. F-19 generated 2-phenylethanol, a unique flavor compound, absent in BB-12. Phenolic content initially increased but antioxidant activity decreased during storage. Betacyanin remained stable for up to 14 days. Red pitaya improved F-19 viability through the simulated GIT, while BB-12 populations significantly decreased (p < 0.05). These results suggest red pitaya pulp is a promising plant-based matrix for F-19, offering protection during digestion and highlighting its potential as a functional food with enhanced bioactive compound bioavailability and sensory attributes.}, language = {en} } @article{HerkenhoffBattistiniPraiaetal.2023, author = {Herkenhoff, Marcos Edgar and Battistini, Carolina and Praia, Ana Beatriz and Rossini, Bruno Cesar and dos Santos, Lucilene Delazari and Br{\"o}del, Oliver and Frohme, Marcus and Saad, Susana Marta Isay}, title = {The combination of omics strategies to evaluate starter and probiotic strains in the Catharina sour Brazilian-style beer}, series = {Food Research International}, volume = {167}, journal = {Food Research International}, publisher = {Elsevier}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19858}, year = {2023}, abstract = {Catharina sour, the first internationally recognized Brazilian beer, is characterized by fermentation with lactic acid bacteria (LAB), which may have probiotic potential, and the addition of fruit juice. This study aimed to evaluate the use of the starter Streptococcus thermophilus TH-4 (TH-4) and the probiotics Lacticaseibacillus paracasei F19 and 431, associated with Saccharomyces cerevisiae US-05, in the absence (control)/presence of passion fruit or peach juices. Evaluation proceeded during fermentation and storage by enumeration using pour-plate and qPCR; gene expressions of hop resistance; proteome by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS); and odor, flavor, and metabolome by Headspace Solid-Phase Microextraction (HS-SPME), coupled with the gas chromatography-mass spectrometry (GC-MS) analysis. We concluded that the strains studied are recommended for applications in sour beers, due to the presence of defense mechanisms like membrane adhesion and H+ pump. Furthermore, HS-SPME/GC-MS indicated that the strains may contribute to the beer flavor and odor.}, language = {en} } @article{FalckenhaynBoerjanRaddatzetal.2013, author = {Falckenhayn, Cassandra and Boerjan, Bart and Raddatz, G{\"u}nter and Frohme, Marcus and Schoofs, Liliane and Lyko, Frank}, title = {Characterization of genome methylation patterns in the desert locust Schistocerca gregaria}, series = {The Journal of Experimental Biology}, volume = {216}, journal = {The Journal of Experimental Biology}, issn = {0022-0949}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6350}, pages = {1423 -- 1429}, year = {2013}, abstract = {DNA methylation is a widely conserved epigenetic modification. The analysis of genome-scale DNA methylation patterns in various organisms suggests that major features of animal methylomes are widely conserved. However, based on the variation of DNA methyltransferase genes in invertebrates, it has also been proposed that DNA methylation could provide a molecular mechanism for ecological adaptation. We have now analyzed the methylome of the desert locust, Schistocerca gregaria, which represents an organism with a high degree of phenotypic plasticity. Using genome-scale bisulfite sequencing, we show here that the S. gregaria methylome is characterized by CpG- and exon-specific methylation and thus shares two major features with other animal methylomes. In contrast to other invertebrates, however, overall methylation levels were substantially higher and a significant fraction of transposons was methylated. Additionally, genic sequences were densely methylated in a pronounced bimodal pattern, suggesting a role for DNA methylation in the regulation of locust gene expression. Our results thus uncover a unique pattern of genome methylation in locusts and provide an important foundation for investigating the role of DNA methylation in locust phase polyphenism.}, language = {en} } @inproceedings{NechyporenkoReshetnikFrohmeetal.2024, author = {Nechyporenko, Alina and Reshetnik, Viktor and Frohme, Marcus and Alekseeva, Victoriia and Lupyr, Andrii and Gargin, Vitaliy}, title = {Evaluation of Bone Radiodensity in Smokers}, series = {Proceedings of the 4th International Workshop of IT-professionals on Artificial Intelligence (ProfIT AI 2024) 2024, Cambridge, MA, USA, September 25-27, 2024}, booktitle = {Proceedings of the 4th International Workshop of IT-professionals on Artificial Intelligence (ProfIT AI 2024) 2024, Cambridge, MA, USA, September 25-27, 2024}, number = {3777}, editor = {Chumachenko, Dmytro and Golland, Polina and Yakovlev, Sergiy}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19616}, pages = {238 -- 244}, year = {2024}, abstract = {One of the most prevalent harmful habits that affect people daily is smoking. The aim of our study was to investigate changes in the bone density of the human paranasal sinuses under the influence of smoking using uncertainty calculation. Material and Methods. The study involved 150 male and female individuals aged 20-40 years, which helps to exclude other factors that could influence the reduction in bone radiodensity (e.g., menopause in women, age-related changes, etc.). The participants were divided into three groups based on the duration of their smoking habits. Results. Smoking has almost no effect on the maximum bone density. All groups show nearly identical values. In the first group, consisting of individuals who smoked for up to 5 years, the maximum density is 75.22 ± 37.61 Hu. In the second group, those who smoked for up to 10 years have a density of 84.22 ± 42.11 Hu, while in the third control group, the density is 74.29 ± 37.15 Hu. On the other hand, smoking has a greater impact on the minimum radiological bone density of the upper wall of the maxillary sinus. The lowest values are found in the group of individuals who smoked for 10 or more years, with a minimum density of 23.86 ± 11.93 Hu. For those who smoked for up to 5 years, the radiological bone density was 52.65 ± 26.32 Hu. In the control group, the density values were slightly higher than those of individuals who smoked for up to 5 years, with the highest values being 58.12 ± 29.06 Hu. Conclusion. The study investigated changes in the bone density of the human paranasal sinuses under the influence of smoking, utilizing uncertainty calculation. It was found that the most sensitive indicator to nicotine exposure is the minimum radiological density, which can significantly increase the risk of developing complications. Specifically, the lowest radiological density was observed in the group of individuals who smoked for 10 years or more, with a value of 23.86 ± 11.93 Hu.}, language = {en} } @inproceedings{ReshetnikMuryzinaFrohmeetal.2024, author = {Reshetnik, Viktor and Muryzina, Irina and Frohme, Marcus and Alekseeva, Victoriia and Dzyza, Alla and Nechyporenko, Alina}, title = {Uncertainty Estimation Method for Determining Bone Density in Patients with Infiltrating Intraductal Carcinoma Undergoing Anti-Cancer Therapy}, series = {Proceedings of the 4th International Workshop of IT-professionals on Artificial Intelligence (ProfIT AI 2024) 2024, Cambridge, MA, USA, September 25-27, 2024}, booktitle = {Proceedings of the 4th International Workshop of IT-professionals on Artificial Intelligence (ProfIT AI 2024) 2024, Cambridge, MA, USA, September 25-27, 2024}, number = {3777}, editor = {Chumachenko, Dmytro and Golland, Polina and Yakovlev, Sergiy}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19628}, pages = {222 -- 228}, year = {2024}, abstract = {Identification of a bone density is crucial in all branches of medicine. Assessing bone density is a labor-intensive process. Bone density is quite unstable and depends on many factors, both physiological (aging, hormonal balance) and pathological (medication use, various underlying conditions). The aim of our study is to determine bone density in patients with malignant breast tumors undergoing anti-cancer therapy. Material and Methods. The study included 50 women aged 60-70 years who were diagnosed with infiltrating intraductal carcinoma. According to established protocols, MSCT is recommended for this category of women at intervals of once every six months. The first MSCT scan was performed immediately after the diagnosis was made, before the start of treatment, and the second scan was conducted six months later. Results. The maximum radiological density was 75.8954±37.9477 Hu in the group of women who had been receiving treatment for six months, compared to 93.9388±46.9694 Hu in the group of patients who did not take the drug. Meanwhile, the minimum density showed a slight increase from 29.7295±14.8647 Hu to 38.6919±19.3460 Hu, which can be attributed to the compensatory mechanisms of the body. Conclusions. In the course of this study, bone density in patients with infiltrating intraductal carcinoma undergoing anti-cancer therapy was determined using uncertainty estimation. It was found that after six months, the first to respond to changes in density was the maximum bone density.}, language = {en} } @article{RadkeSandigLubitzetal.2017, author = {Radke, Lars and Sandig, Grit and Lubitz, Annika and Schließer, Ulrike and von Horsten, Hans Henning and Blanchard, V{\´e}ronique and Keil, Karolin and Sandig, Volker and Giese, Christoph and Hummel, Michael and Hinderlich, Stephan and Frohme, Marcus}, title = {In Vitro Evaluation of Glycoengineered RSV-F in the Human Artificial Lymph Node Reactor}, series = {Bioengineering}, volume = {4}, journal = {Bioengineering}, number = {3}, issn = {2306-5354}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9831}, year = {2017}, abstract = {Subunit vaccines often require adjuvants to elicit sustained immune activity. Here, a method is described to evaluate the efficacy of single vaccine candidates in the preclinical stage based on cytokine and gene expression analysis. As a model, the recombinant human respiratory syncytial virus (RSV) fusion protein (RSV-F) was produced in CHO cells. For comparison, wild-type and glycoengineered, afucosylated RSV-F were established. Both glycoprotein vaccines were tested in a commercial Human Artificial Lymph Node in vitro model (HuALN®). The analysis of six key cytokines in cell culture supernatants showed well-balanced immune responses for the afucosylated RSV-F, while immune response of wild-type RSV-F was more Th1 accentuated. In particular, stronger and specific secretion of interleukin-4 after each round of re-stimulation underlined higher potency and efficacy of the afucosylated vaccine candidate. Comprehensive gene expression analysis by nCounter gene expression assay confirmed the stronger onset of the immunologic reaction in stimulation experiments with the afucosylated vaccine in comparison to wild-type RSV-F and particularly revealed prominent activation of Th17 related genes, innate immunity, and comprehensive activation of humoral immunity. We, therefore, show that our method is suited to distinguish the potency of two vaccine candidates with minor structural differences.}, language = {en} }