@article{HerkenhoffBroedelFrohme2024, author = {Herkenhoff, Marcos Edgar and Br{\"o}del, Oliver and Frohme, Marcus}, title = {Hops across Continents: Exploring How Terroir Transforms the Aromatic Profiles of Five Hop (Humulus lupulus) Varieties Grown in Their Countries of Origin and in Brazil}, series = {Plants}, volume = {13}, journal = {Plants}, number = {19}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19470}, year = {2024}, abstract = {Humulus lupulus, or hops, is a vital ingredient in brewing, contributing bitterness, flavor, and aroma. The female plants produce strobiles rich in essential oils and acids, along with bioactive compounds like polyphenols, humulene, and myrcene, which offer health benefits. This study examined the aromatic profiles of five hop varieties grown in Brazil versus their countries of origin. Fifty grams of pelletized hops from each strain were collected and analyzed using HS-SPME/GC-MS to identify volatile compounds, followed by statistical analysis with PLS-DA and ANOVA. The study identified 330 volatile compounds and found significant aromatic differences among hops from different regions. For instance, H. Mittelfr{\"u}her grown in Brazil has a fruity and herbaceous profile, while the German-grown variety is more herbal and spicy. Similar variations were noted in the Magnum, Nugget, Saaz, and Sorachi Ace varieties. The findings underscore the impact of terroir on hop aromatic profiles, with Brazilian-grown hops displaying distinct profiles compared to their counterparts from their countries of origin, including variations in aromatic notes and α-acid content.}, language = {en} } @article{HerkenhoffBroedelDilarrietal.2026, author = {Herkenhoff, Marcos Edgar and Br{\"o}del, Oliver and Dilarri, Guilherme and Bajay, Miklos Maximiliano and Frohme, Marcus and Costamilan, Carlos Andr{\´e} da Veiga Lima Rosa}, title = {Characterization of Volatile Compounds in Amarillo, Ariana, Cascade, Centennial, and El Dorado Hops Using HS-SPME/GC-MS}, series = {Compounds}, volume = {6}, journal = {Compounds}, number = {1}, publisher = {MDPI}, issn = {2673-6918}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21029}, year = {2026}, abstract = {Humulus lupulus L. (hops) is essential in brewing due to its contributions to bitterness, flavor, and aroma. This study compared the volatile profiles of five commercially important hop varieties—Amarillo, Ariana, Cascade, Centennial, and El Dorado—grown in their main regions of origin (United States for Amarillo, Cascade, and El Dorado; Germany for Ariana; and Brazil for Centennial). Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) enabled the identification of 312 volatile compounds, including monoterpenes (e.g., myrcene, linalool, geraniol), sesquiterpenes (e.g., humulene, caryophyllene), esters, alcohols, aldehydes, and ketones. Amarillo showed the highest myrcene content (22.61\% of the total volatile area), while Centennial was distinguished by elevated γ-muurolene (20.59\%), and El Dorado by the highest level of undecan-2-one (10.47\%), highlighting marked varietal differences in key aroma-active constituents. Multivariate, including principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), clearly discriminated the five varieties: PC1 (41.04\% of the variance) separated samples enriched in fruity/floral monoterpenes and esters from those dominated by woody/resinous sesquiterpenes, whereas PC2 (25.93\% of the variance) reflected variation in medium-chain esters, ketones, and waxy compounds. These chemometric patterns demonstrate that both genetic background and growing region terroir strongly shape hop volatile composition and, consequently, aroma potential, providing brewers with objective criteria for selecting hop varieties to achieve specific sensory profiles in beer.}, language = {en} } @article{KsianzouVillringerGrytsenkoetal.2025, author = {Ksianzou, Viachaslau and Villringer, Claus and Grytsenko, Kostyantyn and Pekur, Demyd and Lytvyn, Peter and Sopinskyy, Mykola and Lebedyeva, Iryna and Niemczyk, Agata and Baranowska, Jolanta}, title = {Structural and Optical Anomalies in Thin Films Grown in a Magnetic Field by Electron-Assisted Vacuum Deposition of PTFE}, series = {Macromolecular Materials and Engineering}, volume = {310}, journal = {Macromolecular Materials and Engineering}, number = {3}, publisher = {Wiley}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-19712}, year = {2025}, abstract = {Polytetrafluoroethylene (PTFE) films are deposited in parallel and perpendicular magnetic fields (MF) by electron-enhanced vacuum deposition (EVD) and EVD + low-temperature plasma (LTP) methods. The structure, morphology, and nanomechanical properties of the films are studied by infrared spectroscopy (IRS), atomic force microscopy (AFM), and spectroscopic ellipsometry. The structure of the thicker films is closer to that of bulk PTFE than that of thin films. The films' crystallinity and surface roughness are higher than those deposited without MF. The birefringence of the refractive index (n) of the films deposited in the MF is inverse to the anisotropy of the n of the films deposited without MF. The hardness of the films is close to that of bulk PTFE.}, language = {en} } @article{SishodiaBenLtaiefScheeletal.2026, author = {Sishodia, Keshav and Ben Ltaief, Ltaief and Scheel, Niklas and F{\"o}ldes, Istv{\´a}n B. and Roos, Andreas Hult and Albrecht, Martin and Staněk, Maty{\´a}š and Jurkovičov{\´a}, Lucie and Hort, Ondrej and Nejdl, Jaroslav and Garc{\´i}a-Alfonso, Ernesto and Halberstadt, Nadine and Andreasson, Jakob and Klimešov{\´a}, Eva and Krikunova, Maria and Krishnan, Sivarama and Heidenreich, Andreas and Mudrich, Marcel}, title = {XUV fluorescence as a probe of interatomic coulombic decay of resonantly excited He nanodroplets}, series = {Scientific Reports}, volume = {16}, journal = {Scientific Reports}, number = {1}, publisher = {Springer Nature}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21050}, year = {2026}, abstract = {Superfluid He nanodroplets resonantly excited by extreme ultraviolet (XUV) pulses can relax via interatomic coulombic decay (ICD), generally considered an ultrafast process. Here, we introduce a novel approach to probe the dynamics of ICD in He nanodroplets over timescales ranging from femtoseconds to nanoseconds. Our method relies on detecting XUV fluorescence emitted from the nanodroplets as they are driven into a nanoplasma by subsequent intense infrared pulses. Nanoplasma ignition is facilitated by tunnel ionization of XUV-excited He∗ atoms attached to the droplets; it thus serves as a sensitive probe of their relaxation dynamics. The observed nanosecond-scale decay is attributed to ICD between pairs of He∗ atoms undergoing roaming motion on the droplet surface, as supported by quantum-mechanical and classical model calculations.}, language = {en} } @inproceedings{GrossKuhlStephanetal.2023, author = {Gross, Matthias and Kuhl, Thorsten and Stephan, Frank and Li, Xiangkun and Philipp, Sebastian and Grebinyk, Anna and Khachatryan, Vitali and Qian, Houjun and Aboulbanine, Zakaria and Amirkhanyan, Zohrab and Riemer, Felix and Oppelt, Anne and Krasilnikov, Mikhail}, title = {A beam line setup for flash radiation therapy with focused electron beams at the Pitz facility at DESY in Zeuthen: basic concept and dosimetry simulations}, series = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, booktitle = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, editor = {Istituto Nazionale Di Fisca Nucleare,}, publisher = {JACoW Publishing}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21132}, pages = {5000 -- 5003}, year = {2023}, abstract = {The aim of this work is to demonstrate the principal possibility to enhance the electron beam dose deposition in the depth of the sample for radiation therapy purposes. Trains of electron bunches of 22 MeV generated at PITZ are focused inside the sample using a dedicated fast deflector and a solenoid magnet. To explore the capabilities of the proposed setup, dose distributions are calculated for multiple electron bunches focused in a single point inside a water phantom. Electron beam focusing produces dose peaks with a tunable maximal dose depth which is interesting for healthy tissue sparing at the surface and enhancing treatment quality. The duration of the full bunch train is 1 ms. During this time interval, the FLASH effect could be efficiently triggered inside the irradiated target volume. Monte Carlo simulations based on the FLUKA code were performed to evaluate the depth dose curves distributions in a water phantom. Using the PITZ electron beam parameters, simulations have shown the possibility to produce a peak dose in water seven times higher than compared to the dose at the surface. Moreover, the RMS size homogeneous area around the maximal dose is approximately 25 mm.}, language = {en} } @inproceedings{KrasilnikovAboulbanineAdhikarietal.2023, author = {Krasilnikov, Mikhail and Aboulbanine, Zakaria and Adhikari, Gowri and Aftab, Namra and Asoyan, Aida and Davtyan, Hakob and Georgiev, Georgi and Good, James and Grebinyk, Anna and Gross, Matthias and Hoffmann, Andreas and Kongmon, Ekkachai and Li, Xiangkun and Lueangaramwong, Anusorn and Melkumyan, David and Mohanty, Sandeep and Niemczyk, Raffael and Oppelt, Anne and Qian, Houjun and Richard, Christopher and Schneidmiller, Evgeny and Stephan, Frank and Vashchenko, Grygorii}, title = {THz SASE FEL at PITZ: lasing at a wavelength of 100μm}, series = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, booktitle = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, editor = {Istituto Nazionale Di Fisca Nucleare,}, publisher = {JACoW Publishing}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21113}, pages = {3948 -- 3951}, year = {2023}, abstract = {Development of an accelerator-based tunable THz source prototype for pump-probe experiments at the European XFEL is ongoing at the Photo Injector Test facility at DESY in Zeuthen (PITZ). The proof-of-principle experiments on the THz SASE FEL are performed utilizing the LCLS-I undulator installed in the PITZ beamline. The first lasing at a center wavelength of 100 µm was observed in the summer of 2022. The lasing of the narrowband THz source was achieved using an electron beam with an energy of ~17 MeV and a bunch charge up to several nC. Optimization of beam transport and matching resulted in the measurement of THz radiation with a pulse energy of tens of µJ, measured with pyroelectric detectors. The THz FEL gain curves were measured by means of specially designed short coils along the undulator. The results of the first characterization of the THz source at PITZ will be presented.}, language = {en} } @article{SpeckVeronaReiffStephanetal.2026, author = {Speck, Sandy and Verona, Claudio and Reiff-Stephan, J{\"o}rg and B{\"o}hme, Andrea and Foitzik, Andreas}, title = {Development of a Realistic Brain Phantom for Medical Education: An Ethical and Technical Alternative to Animal Testing}, series = {Key Engineering Materials}, volume = {1038}, journal = {Key Engineering Materials}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21070}, pages = {67 -- 72}, year = {2026}, abstract = {This study presents the development of a realistic brain phantom as a humane, practical alternative to animal use in medical training, in line with the 3R principles and Directive 2010/63/EU. The phantom is designed to support ultrasound-based education for diagnostic and interventional procedures while improving patient safety through controlled, repeatable practice. High‑resolution CT data were converted to CAD models and additively manufactured as moulds; a gelatin‑based soft‑tissue matrix with glycerin and potassium sorbate provides elasticity and durability. Functional features include fluid‑fillable ventricular structures enabling drainage and puncture simulations, and an integrated high‑density tumour insert to model advanced scenarios. Ultrasound evaluation demonstrated clear echogenic differentiation between tumour, ventricles, and surrounding tissue, confirming the model's imaging fidelity and suitability for hands‑on training. The phantom proved cost‑efficient and reusable, facilitating standardised teaching of complex procedures without ethical approval barriers. A limitation is the material's gradual mechanical instability under repeated probe contact, motivating investigations into synthetic or hybrid matrices to enhance longevity and reuse. Overall, the brain phantom constitutes an ethical, technically robust, and resource‑efficient training tool that addresses critical needs in healthcare quality and safety by reducing avoidable errors through simulation‑based competence development.}, language = {en} } @inproceedings{GrossHoffmannGeorgievetal.2023, author = {Gross, Matthias and Hoffmann, Andreas and Georgiev, Georgi and Kuhl, Thorsten and Li, Xiangkun and Oppelt, Anne and Boonpornprasert, Prach and Philipp, Sebastian and Grebinyk, Anna and Vashchenko, Grygorii and Aftab, Namra and Adhikari, Gowri and Richard, Christopher and Stephan, Frank and Khachatryan, Vitali and Riemer, Felix and Krasilnikov, Mikhail and Amirkhanyan, Zohrab}, title = {Comparison of measurements and simulation results of dose for the FLASH radiation therapy beamline at PITZ}, series = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, booktitle = {IPAC'23 : 14th International Particle Accelerator Conference, 7-12 May 2023, Venice, Italy : proceedings}, editor = {Istituto Nazionale Di Fisca Nucleare,}, publisher = {JACoW Publishing}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21126}, pages = {4996 -- 4999}, year = {2023}, abstract = {The high-brightness electron beam at the Photo Injector Test facility at DESY in Zeuthen (PITZ) is now also used for FLASHlab@PITZ: an R\&D platform for studying radiation biology and the FLASH effect in radiation therapy. The available parameter space of the electron beam with a momentum of 22 MeV/c allows bunch charges from 10 pC up to 5nC, bunch durations of 0.1-60ps, and bunch train lengths up to 1 ms. The number of bunches in the single train can currently be varied between 1 and 1000 bunches, with an upgrade to 4500 foreseen in 2023. Radiation biology studies require accurate dose prediction, therefore Monte Carlo simulations based on the FLUKA code were performed. According to estimations, dose delivery of 0.002 Gy (low charge case 0.1pC) and 10Gy (high charge case 5nC) is possible, if the beam is confined to a circular area with a radius of 5 mm with a lead collimator. For the Monte Carlo simulations, the experimental setup was accurately modeled, including the exit window, lead collimator, etc. Dose measurements were used to compare simulations with experiments. Dose profiles were experimentally measured with Gafchromic films and then compared with Monte Carlo simulations. The first experiments at FLASHlab@PITZ in 2023 have demonstrated flexible dose options for studying the FLASH effect and radiation biology studies.}, language = {en} } @article{RoggeZinnProspositoetal.2017, author = {Rogge, Christian and Zinn, Steffen and Prosposito, Paolo and Francini, Roberto and Foitzik, Andreas}, title = {Transmitted light pH optode for small sample volumes}, series = {Journal of Sensors and Sensor Systems}, volume = {6}, journal = {Journal of Sensors and Sensor Systems}, number = {2}, issn = {2194-878X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10093}, pages = {351 -- 359}, year = {2017}, abstract = {An innovative concept of a low-cost pH optode with working volumes of less than 150 µL is presented. The pH monitoring is based on the color changing effect of pH indicators. The optode includes an RGB color sensor patch TCS34725 from Adafruit, a controllable LED and reactor slides and is addressed by a self-written LabVIEW© software. Utilizing the hue value of the HSV color model, it is possible to analyze the color change of the indicator and estimate the pH value of the analyzed samples by exploiting sigmoidal fit models. Measurements carried out with phenol red and DMEM (Dulbecco's Modified Eagle's Medium) reported a standard error of calibration in the physiologic pH range (6.5-7.5) of ±0.04 pH units.}, language = {en} } @article{KrausBoehmeRinati2026, author = {Kraus, Mirjam and B{\"o}hme, Andrea and Rinati, Gianluca Verona}, title = {Verification of a Novel Mathematical Model for Determination of the Biomass Specific Growth Rate in Bioprocesses Using Relative Change in Biomass Measurements}, series = {Defect and Diffusion Forum}, volume = {446}, journal = {Defect and Diffusion Forum}, publisher = {Trans Tech Publications}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21081}, pages = {57 -- 62}, year = {2026}, abstract = {This study presents a new mathematical model for determining the specific growth rate of biomass in biotechnological production processes, which aims to optimize the production of biotechnological products such as the advanced material polyhydroxyalkanoates. The specific growth rate is classified by the FDA as a critical process parameter that affects product quality and quantity, but is difficult for laboratory personnel to determine. Therefore, a simple and robust method for real-time monitoring and control is crucial. According to the current state of the art, the established Luedeking-Piret model for determining the specific growth rate requires the determination of the biomass as an absolute value to initialize the model and to determine two further model parameters. However, determining the biomass is time-consuming and error-prone. The new relative model replaces this value with the relative change in biomass, which can be easily recorded using standard laboratory methods such as optical density measurement. This eliminates the need for time-consuming and resource-intensive preliminary work. Despite this simplification, simulation tests have shown that the new model delivers identical results to the established model. It represents an independent, precise alternative and offers advantages in terms of handling. The results underline the model's potential to make bioprocesses more sustainable and efficient. Especially in research, material consumption, laboratory time and costs can be reduced compared to the established model. Future experiments will further investigate the performance of the new approach compared to the established model.}, language = {en} } @article{RoedenbeckHerold2026, author = {Roedenbeck, Marc and Herold, Marcel}, title = {Personality Profiles in Online Job Advertisements: Applying a Weighted Closed Vocabulary Approach to Identify Generic Profiles and Clusters}, series = {SAGE Open}, volume = {16}, journal = {SAGE Open}, number = {1}, publisher = {Sage}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21282}, year = {2026}, abstract = {On the background of the supplementary applicant-job fit theory, this study tests the application of a weighted closed vocabulary approach as introduced by Ostendorf on a large corpus of online job advertisements (OJA). Therefore, a large dataset of online job advertisements (OJAs) was scraped from a German job portal (N = 151k), and a sample (n = 3,239) was selected based upon Porter's Value Chain and corresponding job functions. The dataset was pre-processed with techniques of natural language processing, and the predefined words extracted from the OJAs were weighted with the average subject matter expert rating, as offered in the vocabulary of Ostendorf. The results reveal that, first, 0 to 12 words describing personality are used across OJAs, second, that HR, sales, and finance positions show values higher than sample mean (3.22), third, that HR positions show loadings across all dimensions of personality above the sample means (extroversion: 2.32, agreeableness: 3.98, conscientiousness: 4.28, emotional stability: 3.54, openness: 2.0) followed by sales. The job profiles being significantly parallel on equal levels are HR clerk and referee, as well as IT, R\&D, and procurement. While conscientiousness is reported to be an important predictor of performance, our study showed only low to average importance in OJAs.}, language = {en} } @article{ShamsSchmitzSmekhovaetal.2021, author = {Shams, S. Fatemeh and Schmitz, Detlef and Smekhova, Alevtina and Ghazanfari, Mohammad Reza and Giesen, Margret and Weschke, Eugen and Chen, Kai and Luo, Chen and Radu, Florin and Schmitz-Antoniak, Carolin}, title = {Element-specific contributions to improved magnetic heating of theranostic CoFe2O4 nanoparticles decorated with Pd}, series = {Scientific Reports}, volume = {11}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14756}, year = {2021}, abstract = {Decoration with Pd clusters increases the magnetic heating ability of cobalt ferrite (CFO) nanoparticles by a factor of two. The origin of this previous finding is unraveled by element-specific X-ray absorption spectroscopy (XAS) and magnetic circular dichroism (XMCD) combined with atomic multiplet simulations and density functional theory (DFT) calculations. While the comparison of XAS spectra with atomic multiplet simulations show that the inversion degree is not affected by Pd decoration and, thus, can be excluded as a reason for the improved heating performance, XMCD reveals two interrelated responsible sources: significantly larger Fe and Co magnetic moments verify an increased total magnetization which enhances the magnetic heating ability. This is accompanied by a remarkable change in the field-dependent magnetization particularly for Co ions which exhibit an increased low-field susceptibility and a reduced spin canting behavior in higher magnetic fields. Using DFT calculations, these findings are explained by reduced superexchange between ions on octahedral lattice sites via oxygen in close vicinity of Pd, which reinforces the dominating antiparallel superexchange interaction between ions on octahedral and tetrahedral lattice sites and thus reduces spin canting. The influence of the delocalized nature of Pd 4d electrons on the neighboring ions is discussed and the conclusions are illustrated with spin density isosurfaces of the involved ions. The presented results pave the way to design nanohybrids with tailored electronic structure and magnetic properties.}, language = {en} } @article{KalishettyhalliMahadevaiahPerezLiskeretal.2022, author = {Kalishettyhalli Mahadevaiah, Mamathamba and P{\´e}rez, Eduardo and Lisker, Marco and Schubert, Markus Andreas and Perez-Bosch Quesada, Emilio and Wenger, Christian and Mai, Andreas}, title = {Modulating the Filamentary-Based Resistive Switching Properties of HfO₂ Memristive Devices by Adding Al₂O₃ Layers}, series = {Electronics}, volume = {11}, journal = {Electronics}, number = {10}, address = {MDPI}, issn = {2079-9292}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16172}, year = {2022}, abstract = {The resistive switching properties of HfO₂ based 1T-1R memristive devices are electrically modified by adding ultra-thin layers of Al₂O₃ into the memristive device. Three different types of memristive stacks are fabricated in the 130 nm CMOS technology of IHP. The switching properties of the memristive devices are discussed with respect to forming voltages, low resistance state and high resistance state characteristics and their variabilities. The experimental I-V characteristics of set and reset operations are evaluated by using the quantum point contact model. The properties of the conduction filament in the on and off states of the memristive devices are discussed with respect to the model parameters obtained from the QPC fit.}, language = {en} } @article{HooglandBoettcherVerhoefetal.2016, author = {Hoogland, A. Marije and B{\"o}ttcher, Ren{\´e} and Verhoef, Esther and Jenster, Guido and van Leenders, Geert J.L.H.}, title = {Gene-expression analysis of gleason grade 3 tumor glands embedded in low- and high-risk prostate cancer}, series = {Oncotarget}, volume = {7}, journal = {Oncotarget}, number = {25}, issn = {1949-2553}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6573}, pages = {37846 -- 37856}, year = {2016}, abstract = {The Gleason score (GS) of prostate cancer on diagnostic biopsies is an important parameter for therapeutic decision-making. Biopsy GS under-estimates the actual GS at radical prostatectomy in a significant number of patients due to samplingartifact. The aim of this study was to identify markers that are differentially expressed in Gleason grade 3 (GG3) tumor glands embedded in GS 4 + 3 = 7 and GS 3 + 3 = 6 prostate cancer using laser capture microdissection and RNA sequencing. GG3 tumor glands embedded in nine GS 3 + 3 = 6 and nine GS 4 + 3 = 7 prostate cancers were isolated by laser capture microdissection of frozen radical prostatectomy specimens. After RNA amplification and RNA sequencing, differentially expressed genes in both GG3 components were identified by a 2log fold change > 1.0 and p-value < 0.05. We applied immunohistochemistry on a tissue micro-array representing 481 radical prostatectomy samples for further validation on protein level. A total of 501 genes were up-regulated and 421 down-regulated in GG3 glands embedded in GS 4 + 3 = 7 as compared to GS 3 + 3 = 6 prostate cancer. We selected HELLS, ZIC2 and ZIC5 genes for further validation. ZIC5 mRNA was up-regulated 17 fold (p = 8.4E-07), ZIC2 8 fold (p = 1.3E-05) and HELLS 2 fold (p = 0.006) in GG3 glands derived from GS 4 + 3 = 7. HELLS expression of ≥ 1\% occurred in 10\% GS < 7, 17\% GS 7 and 43\% GS >7 prostate cancer (p < 0.001). Using a cut-off of ≥ 1\%, protein expression of ZIC5 was present in 28\% GS < 7, 43\% GS 7 and 57\% GS > 7 cancer (p < 0.001). ZIC2 was neither associated with GS nor outcome in our validation set. HELLS was independently predictive for biochemical-recurrence after radical prostatectomy (HR 2.3; CI 1.5-3.6; p < 0.01). In conclusion, HELLS and ZIC5 might be promising candidate markers for selection of biopsy GS 6 prostate cancer being at risk for up-grading at prostatectomy.}, language = {en} } @article{GrebinykPrylutskaBuchelnikovetal.2019, author = {Grebinyk, Anna and Prylutska, Svitlana and Buchelnikov, Anatoliy and Tverdokhleb, Nina and Grebinyk, Sergii and Evstigneev, Maxim and Matyshevska, Olga and Cherepanov, Vsevolod and Prylutskyy, Yuriy and Yashchuk, Valeriy and Naumovets, Anton and Ritter, Uwe and Dandekar, Thomas and Frohme, Marcus}, title = {C60 Fullerene as an Effective Nanoplatform of Alkaloid Berberine Delivery into Leukemic Cells}, series = {Pharmaceutics}, volume = {11}, journal = {Pharmaceutics}, number = {11}, publisher = {MDPI}, issn = {1999-4923}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12932}, year = {2019}, abstract = {A herbal alkaloid Berberine (Ber), used for centuries in Ayurvedic, Chinese, Middle-Eastern, and native American folk medicines, is nowadays proved to function as a safe anticancer agent. Yet, its poor water solubility, stability, and bioavailability hinder clinical application. In this study, we have explored a nanosized carbon nanoparticle—C60 fullerene (C60)—for optimized Ber delivery into leukemic cells. Water dispersions of noncovalent C60-Ber nanocomplexes in the 1:2, 1:1, and 2:1 molar ratios were prepared. UV-Vis spectroscopy, dynamic light scattering (DLS), and atomic force microscopy (AFM) evidenced a complexation of the Ber cation with the negatively charged C60 molecule. The computer simulation showed that π-stacking dominates in Ber and C60 binding in an aqueous solution. Complexation with C60 was found to promote Ber intracellular uptake. By increasing C60 concentration, the C60-Ber nanocomplexes exhibited higher antiproliferative potential towards CCRF-CEM cells, in accordance with the following order: free Ber < 1:2 < 1:1 < 2:1 (the most toxic). The activation of caspase 3/7 and accumulation in the sub-G1 phase of CCRF-CEM cells treated with C60-Ber nanocomplexes evidenced apoptosis induction. Thus, this study indicates that the fast and easy noncovalent complexation of alkaloid Ber with C60 improved its in vitro efficiency against cancer cells.}, language = {en} } @article{KoeberleinBankRothetal.2022, author = {K{\"o}berlein, Jana and Bank, Lukas and Roth, Stefan and K{\"o}se, Ekrem and Kuhlmann, Timm and Prell, Bastian and Stange, Maximilian and M{\"u}nnich, Marc and Flum, Dominik and Moog, Daniel and Ihlenfeldt, Steffen and Sauer, Alexander and Weigold, Matthias and Schilp, Johannes}, title = {Simulation Modeling for Energy-Flexible Manufacturing: Pitfalls and How to Avoid Them}, series = {Energies}, volume = {15}, journal = {Energies}, number = {10}, publisher = {MDPI}, issn = {1996-1073}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16152}, year = {2022}, abstract = {Due to the high share of industry in total electricity consumption, industrial demand-side management can make a relevant contribution to the stability of power systems. At the same time, companies get the opportunity to reduce their electricity procurement costs by taking advantage of increasingly fluctuating prices on short-term electricity markets, the provision of system services on balancing power markets, or by increasing the share of their own consumption from on-site generated renewable energy. Demand-side management requires the ability to react flexibly to the power supply situation without negatively affecting production targets. It also means that the management and operation of production must consider not only production-related parameters but also parameters of energy availability, which further increase the complexity of decision-making. Although simulation studies are a recognized tool for supporting decision-making processes in production and logistics, the simultaneous simulation of material and energy flows has so far been limited mainly to issues of energy efficiency as opposed to energy flexibility, where application-oriented experience is still limited. We assume that the consideration of energy flexibility in the simulation of manufacturing systems will amplify already known pitfalls in conducting simulation studies. Based on five representative industrial use cases, this article provides practitioners with application-oriented experiences of the coupling of energy and material flows in simulation modeling of energy-flexible manufacturing, identifies challenges in the simulation of energy-flexible production systems, and proposes approaches to face these challenges. Seven pitfalls that pose a particular challenge in simulating energy-flexible manufacturing have been identified, and possible solutions and measures for avoiding them are shown. It has been found that, among other things, consistent management of all parties involved, early clarification of energy-related, logistical, and resulting technical requirements for models and software, as well as the application of suitable methods for validation and verification are central to avoiding these pitfalls. The identification and characterization of challenges and the derivation of recommendations for coping with them can raise awareness of typical pitfalls. This paper thus helps to ensure that simulation studies of energy-flexible production systems can be carried out more efficiently in the future.}, language = {en} } @article{KoelschRadonGolubetal.2020, author = {K{\"o}lsch, Adrian and Radon, C. and Golub, M. and Baumert, A. and B{\"u}rger, J{\"o}rg and Mielke, Thorsten and Lisdat, Fred and Feoktystov, Artem and Pieper, J{\"o}rg and Zouni, Athina and Wendler, Petra}, title = {Current limits of structural biology: The transient interaction between cytochrome c6 and photosystem I}, series = {Current Research in Structural Biology}, volume = {2}, journal = {Current Research in Structural Biology}, issn = {2665-928X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13628}, pages = {171 -- 179}, year = {2020}, abstract = {Trimeric photosystem I from the cyanobacterium Thermosynechococcus elongatus (TePSI) is an intrinsic membrane protein, which converts solar energy into electrical energy by oxidizing the soluble redox mediator cytochrome c6 (Cyt c6) and reducing ferredoxin. Here, we use cryo-electron microscopy and small angle neutron scattering (SANS) to characterize the transient binding of Cyt c6 to TePSI. The structure of TePSI cross-linked to Cyt c6 was solved at a resolution of 2.9 {\AA} and shows additional cofactors as well as side chain density for 84\% of the peptide chain of subunit PsaK, revealing a hydrophobic, membrane intrinsic loop that enables binding of associated proteins. Due to the poor binding specificity, Cyt c6 could not be localized with certainty in our cryo-EM analysis. SANS measurements confirm that Cyt c6 does not bind to TePSI at protein concentrations comparable to those for cross-linking. However, SANS data indicate a complex formation between TePSI and the non-native mitochondrial cytochrome from horse heart (Cyt cHH). Our study pinpoints the difficulty of identifying very small binding partners (less than 5\% of the overall size) in EM structures when binding affinities are poor. We relate our results to well resolved co-structures with known binding affinities and recommend confirmatory methods for complexes with KM values higher than 20 μM.}, language = {en} } @article{DevulapallyBuergerMielkeetal.2018, author = {Devulapally, Praneeth Reddy and B{\"u}rger, J{\"o}rg and Mielke, Thorsten and Konthur, Zolt{\´a}n and Lehrach, Hans and Yaspo, Marie-Laure and Gl{\"o}kler, J{\"o}rn and Warnatz, Hans-J{\"o}rg}, title = {Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes}, series = {Genome Medicine}, volume = {10}, journal = {Genome Medicine}, issn = {1756-994X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10538}, pages = {1 -- 12}, year = {2018}, abstract = {Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple and cost-effective emulsion-based single-cell paired antibody repertoire sequencing method that employs only basic laboratory equipment. We performed a proof-of-concept using mixed mouse hybridoma cells and we also showed that our method can be used for discovery of novel antigen-specific monoclonal antibodies by sequencing human CD19+ B cell IgM and IgG repertoires isolated from peripheral whole blood before and seven days after Td (Tetanus toxoid/Diphtheria toxoid) booster immunization. We anticipate broad applicability of our method for providing insights into adaptive immune responses associated with various diseases, vaccinations, and cancer immunotherapies.}, language = {en} } @article{BaumannPohleZhangetal.2021, author = {Baumann, Elisabeth and Pohle, Ulrike and Zhang, Edward and Allen, Thomas and Villringer, Claus and Pulwer, Silvio and Gerhardt, Holger and Laufer, Jan}, title = {A backward-mode optical-resolution photoacoustic microscope for 3D imaging using a planar Fabry-P{\´e}rot sensor}, series = {Photoacoustics}, volume = {24}, journal = {Photoacoustics}, publisher = {Elsevier}, issn = {2213-5979}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-14701}, pages = {100293}, year = {2021}, abstract = {Optical-resolution photoacoustic microscopy (OR-PAM) combines high spatial resolution and strong absorption-based contrast in tissue, which has enabled structural and spectroscopic imaging of endogenous chromophores, primarily hemoglobin. Conventional piezoelectric ultrasound transducers are typically placed far away from the photoacoustic source due to their opacity, which reduces acoustic sensitivity. Optical ultrasound sensors are an alternative as their transparency allows them to be positioned close to the sample with minimal source-detector distances. In this work, a backward-mode OR-PAM system based on a planar Fabry-P{\´e}rot ultrasound sensor and coaxially aligned excitation and interrogation beams was developed. Two 3D imaging modes, using raster-scanning for enhanced image quality and continuous-scanning for fast imaging, were implemented and tested on a leaf skeleton phantom. In fast imaging mode, a scan-rate of 100,000 A-lines/s was achieved. 3D images of a zebrafish embryo were acquired in vivo in raster-scanning mode. The transparency of the FP sensor in the visible and near-infrared wavelength region makes it suitable for combined functional and molecular imaging applications using OR-PAM and multi-photon fluorescence microscopy.}, language = {en} } @article{StumperBergerKlotscheetal.2025, author = {Stumper, Nele and Berger, J{\"o}rn and Klotsche, Jens and Gedat, Egbert and Hoff, Paula and Schmittat, Gabriela and Burmester, Gerd-R{\"u}diger and Kr{\"o}nke, Gerhard and Backhaus, Marina and Haugen, Ida Kristin and Ohrndorf, Sarah}, title = {To optimise the diagnostic process of rheumatic diseases affecting the hands using fluorescence optical imaging (FOI)}, series = {RMD Open}, volume = {11}, journal = {RMD Open}, number = {3}, publisher = {EULAR}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20698}, year = {2025}, abstract = {Background Accurate and rapid diagnosis of rheumatic diseases is essential for further treatment decision. Different rheumatic diseases present characteristic patterns (image features) in fluorescence optical imaging (FOI). We developed an atlas of FOI image features and tested its ability to differentiate various rheumatic diseases. Methods FOI images from patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA), connective tissue diseases (CTD) and osteoarthritis (OA) were analysed by two readers blinded for diagnosis and calibrated against each other, using the prima vista mode (PVM) and an automated 5-phase model. Twenty-six different reoccurring typical signal enhancement patterns (features) indicating inflamed joints, nail or skin were defined and all FOI images were scored accordingly. The feature frequency in each patient cohort and phase (PVM, 5-phase) was counted. Contingency tables were created with categorical variable counts and diagnosis using common formulae. Findings Four hundred thirty-eight patients with RA (n=117), PsA (n=110), CTD (n=121) and OA (n=90) were included. Once the data had been categorised, a two-step diagnostic pathway was developed: in the first step, OA was best distinguished from the other diseases with high specificity by five patterns (specificity >0.9, diagnostic OR between 2.34 and 8.24). In a second step, the remaining autoimmune diseases were differentiated from each other by a certain number of features (five for RA, 12 for PsA and four for CTD). Interpretation This was the first study to show that feature analysis in FOI helps to differentiate typical rheumatic diseases from each other, potentially simplifying and speeding up the diagnostic process. Therefore, FOI could be considered an additional component of a wider range of imaging techniques used in rheumatology.}, language = {en} } @article{GedatBergerKieseletal.2022, author = {Gedat, Egbert and Berger, J{\"o}rn and Kiesel, Denise and Failli, Vieri and Briel, Andreas and Welker, Pia}, title = {Features Found in Indocyanine Green-Based Fluorescence Optical Imaging of Inflammatory Diseases of the Hands}, series = {Diagnostics}, volume = {12}, journal = {Diagnostics}, number = {8}, publisher = {MDPI}, issn = {2075-4418}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16359}, year = {2022}, abstract = {Rheumatologists in Europe and the USA increasingly rely on fluorescence optical imaging (FOI, Xiralite) for the diagnosis of inflammatory diseases. Those include rheumatoid arthritis, psoriatic arthritis, and osteoarthritis, among others. Indocyanine green (ICG)-based FOI allows visualization of impaired microcirculation caused by inflammation in both hands in one examination. Thousands of patients are now documented and most literature focuses on inflammatory arthritides, which affect synovial joints and their related structures, making it a powerful tool in the diagnostic process of early undifferentiated arthritis and rheumatoid arthritis. However, it has become gradually clear that this technique has the potential to go even further than that. FOI allows visualization of other types of tissues. This means that FOI can also support the diagnostic process of vasculopathies, myositis, collagenoses, and other connective tissue diseases. This work summarizes the most prominent imaging features found in FOI examinations of inflammatory diseases, outlines the underlying anatomical structures, and introduces a nomenclature for the features and, thus, supports the idea that this tool is a useful part of the imaging repertoire in rheumatology clinical practice, particularly where other imaging methods are not easily available.}, language = {en} } @article{BayBuschLisdatetal.2017, author = {Bay, Daniyah H. and Busch, Annika and Lisdat, Fred and Iida, Keisuke and Ikebukuro, Kazunori and Nagasawa, Kazuo and Karube, Isao and Yoshida, Wataru}, title = {Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands}, series = {BMC Molecular Biology}, volume = {18}, journal = {BMC Molecular Biology}, number = {17}, issn = {1471-2199}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9811}, year = {2017}, abstract = {G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. In this study, the biological function of the 10 G-quadruplex-forming sequences in the transcriptional regulation has been analyzed using a reporter assay.}, language = {en} } @article{BelchevaErmakovaFabian2023, author = {Belcheva, Veronika and Ermakova, Tatiana and Fabian, Benjamin}, title = {Understanding Website Privacy Policies—A Longitudinal Analysis Using Natural Language Processing}, series = {Information}, volume = {14}, journal = {Information}, number = {11}, publisher = {MDPI}, issn = {2078-2489}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-18268}, year = {2023}, abstract = {Privacy policies are the main method for informing Internet users of how their data are collected and shared. This study aims to analyze the deficiencies of privacy policies in terms of readability, vague statements, and the use of pacifying phrases concerning privacy. This represents the undertaking of a step forward in the literature on this topic through a comprehensive analysis encompassing both time and website coverage. It characterizes trends across website categories, top-level domains, and popularity ranks. Furthermore, studying the development in the context of the General Data Protection Regulation (GDPR) offers insights into the impact of regulations on policy comprehensibility. The findings reveal a concerning trend: privacy policies have grown longer and more ambiguous, making it challenging for users to comprehend them. Notably, there is an increased proportion of vague statements, while clear statements have seen a decrease. Despite this, the study highlights a steady rise in the inclusion of reassuring statements aimed at alleviating readers' privacy concerns.}, language = {en} } @article{RotheBergerWelkeretal.2023, author = {Rothe, Felix and Berger, J{\"o}rn and Welker, Pia and Fiebelkorn, Richard and Kupper, Stefan and Kiesel, Denise and Gedat, Egbert and Ohrndorf, Sarah}, title = {Fluorescence optical imaging feature selection with machine learning for differential diagnosis of selected rheumatic diseases}, series = {Frontiers in Medicine}, volume = {10}, journal = {Frontiers in Medicine}, publisher = {Frontiers}, issn = {2296-858X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17922}, year = {2023}, abstract = {Background and objective: Accurate and fast diagnosis of rheumatic diseases affecting the hands is essential for further treatment decisions. Fluorescence optical imaging (FOI) visualizes inflammation-induced impaired microcirculation by increasing signal intensity, resulting in different image features. This analysis aimed to find specific image features in FOI that might be important for accurately diagnosing different rheumatic diseases. Patients and methods: FOI images of the hands of patients with different types of rheumatic diseases, such as rheumatoid arthritis (RA), osteoarthritis (OA), and connective tissue diseases (CTD), were assessed in a reading of 20 different image features in three phases of the contrast agent dynamics, yielding 60 different features for each patient. The readings were analyzed for mutual differential diagnosis of the three diseases (One-vs-One) and each disease in all data (One-vs-Rest). In the first step, statistical tools and machine-learning-based methods were applied to reveal the importance rankings of the features, that is, to find features that contribute most to the model-based classification. In the second step machine learning with a stepwise increasing number of features was applied, sequentially adding at each step the most crucial remaining feature to extract a minimized subset that yields the highest diagnostic accuracy. Results: In total, n = 605 FOI of both hands were analyzed (n = 235 with RA, n = 229 with OA, and n = 141 with CTD). All classification problems showed maximum accuracy with a reduced set of image features. For RA-vs.-OA, five features were needed for high accuracy. For RA-vs.-CTD ten, OA-vs.-CTD sixteen, RA-vs.-Rest five, OA-vs.-Rest eleven, and CTD-vs-Rest fifteen, features were needed, respectively. For all problems, the final importance ranking of the features with respect to the contrast agent dynamics was determined. Conclusions: With the presented investigations, the set of features in FOI examinations relevant to the differential diagnosis of the selected rheumatic diseases could be remarkably reduced, providing helpful information for the physician.}, language = {en} } @article{GossingFrohmeRadke2020, author = {Gossing, Wilhelm and Frohme, Marcus and Radke, Lars}, title = {Biomarkers for Liquid Biopsies of Pituitary Neuroendocrine Tumors}, series = {Biomedicines}, volume = {8}, journal = {Biomedicines}, number = {6}, issn = {2227-9059}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13307}, year = {2020}, abstract = {Pituitary neuroendocrine tumors (PitNET) do not only belong to the most common intracranial neoplasms but seem to be generally more common than has been thought. Minimally invasive liquid biopsies have the potential to improve their early screening efficiency as well as monitor prognosis by facilitating the diagnostic procedures. This review aims to assess the potential of using liquid biopsies of different kinds of biomarker species that have only been obtained from solid pituitary tissues so far. Numerous molecules have been associated with the development of a PitNET, suggesting that it often develops from the cumulative effects of many smaller genetic or epigenetic changes. These minor changes eventually pile up to switch critical molecules into tumor-promoting states, which may be the key regulatory nodes representing the most potent marker substances for a diagnostic test. Drugs targeting these nodes may be superior for the therapeutic outcome and therefore the identification of such pituitary-specific cellular key nodes will help to accelerate their application in medicine. The ongoing genetic degeneration in pituitary adenomas suggests that repeated tumor profiling via liquid biopsies will be necessary for personalized and effective treatment solutions.}, language = {en} } @article{GossingRadkeBieringetal.2021, author = {Gossing, Wilhelm and Radke, Lars and Biering, Henrik and Diederich, Sven and Mai, Knut and Frohme, Marcus}, title = {The ElonginB/C-Cullin5-SOCS-Box-Complex Is a Potential Biomarker for Growth Hormone Disorders}, series = {Biomedicines}, volume = {9}, journal = {Biomedicines}, number = {2}, publisher = {MDPI}, issn = {2227-9059}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13802}, year = {2021}, abstract = {Insulin-like growth factor 1 (IGF-1) is the standard biochemical marker for the diagnosis and treatment control of acromegaly and growth hormone deficiency (GHD). However, its limitations necessitate the screening for new specific and sensitive biomarkers. The elonginB/C-cullin5-SOCS-box-complex (ECS-complex) (an intracellular five-protein complex) is stimulated by circulating growth hormone (GH) and regulates GH receptor levels through a negative feedback loop. It mediates the cells' sensitivity for GH and therefore, represents a potent new biomarker for those diseases. In this study, individual ECS-complex proteins were measured in whole blood samples of patients with acromegaly (n = 32) or GHD (n = 12) via ELISA and compared to controls. Hierarchical clustering of the results revealed that by combining the three ECS-complex proteins suppressor of cytokine signaling 2 (SOCS2), cullin-5 and ring-box protein 2 (Rbx-2), 93\% of patient samples could be separated from controls, despite many patients having a normal IGF-1 or not receiving medical treatment. SOCS2 showed the best individual diagnostic performance with an overall accuracy of 0.93, while the combination of the three proteins correctly identified all patients and controls. This resulted in perfect sensitivity and specificity for all patient groups, which demonstrates potential benefits of the ECS-complex proteins as clinical biomarkers for the diagnostics of GH-related diseases and substantiates their important role in GH metabolism.}, language = {en} } @article{MarehnWilhelmPospisiletal.2019, author = {Marehn, David Thomas and Wilhelm, Detlef and Pospisil, Heike and Pizzoferrato, Roberto}, title = {Double entry method for the verification of data a chromatography data system receives}, series = {Journal of Sensors and Sensor Systems}, volume = {8}, journal = {Journal of Sensors and Sensor Systems}, issn = {2194-878X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12349}, pages = {207 -- 214}, year = {2019}, abstract = {The importance of software validation increases since the need for high usability and suitability of software applications grows. In order to reduce costs and manage risk factors, more and more recommendations and rules have been established. In the field of pharmacy the vendors of so-called chromatography data systems (CDSs) had to implement the guidelines of the Code of Federal Regulations Title 21 (CFR 21) during the last few years in order to fulfill the increasing requirements. The CFR 21 part 11 deals with electronic records and signatures. This part is binding for each company in the regulated environment that wishes to create, edit and sign electronic information instead of printing them on paper. Subsection CFR 21 part 11.10(h) explains how to perform an input check for manual user entries as well as for data that will be collected from an external device. In this article we present an approach performing the double entry method on data provided by the hardware instrument in order to investigate possible influences on the raw data by the handling CDS. A software tool has been written which allows us to communicate with a high-performance liquid chromatography (HPLC) detector and acquire data from it. The communication is completely independent of a CDS which is started separately and connected to the same system. Using this configuration we made a parallel data acquisition of two instances at the same time possible. Two CDSs have been tested and for at least one of them it has been shown that a comparison of the acquired data can be done as with the double entry method for the data verification. For the second CDS we checked whether it would be applicable after a few modifications. The given approach could be either used for a live data verification of produced raw data or as a single test during a software operational qualification to verify the data acquisition functionality of the software.}, language = {en} } @article{TannenbergTscheuschnerRaabetal.2026, author = {Tannenberg, Robert and Tscheuschner, Georg and Raab, Christopher and Flemig, Sabine and D{\"o}ring, Sarah and Ponader, Marco and Thurmann, Melinda and Paul, Martin and Weller, Michael G.}, title = {Simplified Sample Preparation and Lateral Flow Immunoassay for the Detection of Plant Viruses}, series = {Biosensors}, volume = {16}, journal = {Biosensors}, number = {2}, publisher = {MDPI}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21294}, year = {2026}, abstract = {Lateral flow immunoassays (LFAs) are widely used for on-site testing; however, their use for the rapid detection of plant viruses in the field is often limited by inconvenient sample preparation. Here, we present a new sampling method and a simplified dipstick LFA format for the detection and monitoring of cowpea chlorotic mottle virus (CCMV) as a model plant pathogen. The assay employs a monoclonal mouse antibody for capture and a poly-clonal rabbit antibody conjugated to 80 nm gold nanoparticles for detection. Conventional sample and conjugate pads are omitted, allowing the test strips to be dipped directly into wells containing plant extract and antibody-gold conjugate. No plastic casing was required, which could lead to a reduction in waste. It was shown that CCMV concentrations as low as 3.5 μg/L or 350 pg per sample could be reliably detected in 15 min. Specificity tests confirmed that other plant viruses, cowpea mosaic virus (CPMV) and tobacco mosaic virus (TMV), did not produce false-positive results. In addition, we describe a new method for on-site sampling using a manual punch and a syringe equipped with a frit. This step combines grinding the sample, extraction, filtration, and reconstitution and mixing of the antibody-gold conjugate, enabling the analysis of punched leaf disks without laboratory equipment. When applied to CCMV-infected cowpea plants, the assay revealed systemic infection before visual symptoms became apparent. This work demonstrates that simplified LFAs combined with innovative sampling techniques can provide sensitive, specific, and rapid diagnostics for crop monitoring and support early intervention strategies in agriculture.}, language = {en} } @article{ZeschFinkelsteinRegehlyetal.2026, author = {Zesch, Christoph and Finkelstein, Daniel and Regehly, Martin and Reif, J{\"u}rgen and Schrader, Sigurd}, title = {Efficient nanosecond barium nitrate Raman laser for the visible spectral range}, series = {Optics Express}, volume = {34}, journal = {Optics Express}, number = {4}, publisher = {Optica}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-21320}, pages = {6355 -- 6363}, year = {2026}, abstract = {We report on the design and performance of two solid-state Raman lasers, pumped by a frequency-doubled Nd:YAG laser at 532 nm (8 ns FWHM, 10 Hz, up to 10 mJ), that generate either the first or second Stokes radiation with wavelengths of 563 nm and 598 nm. Barium nitrate crystals with a 1 cm² face area and lengths of 3 cm and 5 cm were used as the Raman-active medium in stable semi-spherical resonators. The Raman lasers produced first Stokes and second Stokes pulses, achieving pulse energies up to 2.3 mJ and conversion efficiencies up to 35\% (first Stokes, 5 cm crystal) and 21\% (second Stokes, 5 cm crystal). The output beams exhibit nearly Gaussian profiles with beam quality factors of M² = 1.67 and M² = 1.83, respectively. The proposed design and characterization demonstrated a Raman laser with high efficiency and superior beam quality. After subsequent frequency doubling, the output appears well dedicated for future differential absorption LiDAR (DIAL) applications.}, language = {en} } @article{SteglichMaiVillringeretal.2021, author = {Steglich, Patrick and Mai, Christian and Villringer, Claus and Dietzel, Birgit and Bondarenko, Siegfried and Ksianzou, Viachaslau and Villasmunta, Francesco and Zesch, Christoph and Pulwer, Silvio and Burger, Martin and Bauer, Joachim and Heinrich, Friedhelm and Schrader, Sigurd and Vitale, Francesco and De Matteis, Fabio and Prosposito, Paolo and Casalboni, Mauro and Mai, Andreas}, title = {Silicon-organic hybrid photonics: an overview of recent advances, electro-optical effects and CMOS integration concepts}, series = {Journal of Physics: Photonics}, volume = {3}, journal = {Journal of Physics: Photonics}, number = {2}, issn = {2515-7647}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-13882}, year = {2021}, abstract = {In recent decades, much research effort has been invested in the development of photonic integrated circuits, and silicon-on-insulator technology has been established as a reliable platform for highly scalable silicon-based electro-optical modulators. However, the performance of such devices is restricted by the inherent material properties of silicon. An approach to overcoming these deficiencies is to integrate organic materials with exceptionally high optical nonlinearities into a silicon-on-insulator photonic platform. Silicon-organic hybrid photonics has been shown to overcome the drawbacks of silicon-based modulators in terms of operating speed, bandwidth, and energy consumption. This work reviews recent advances in silicon-organic hybrid photonics and covers the latest improvements to single components and device concepts. Special emphasis is given to the in-device performance of novel electro-optical polymers and the use of different electro-optical effects, such as the linear and quadratic electro-optical effect, as well as the electric-field-induced linear electro-optical effect. Finally, the inherent challenges of implementing non-linear optical polymers on a silicon photonic platform are discussed and a perspective for future directions is given.}, language = {en} } @article{RegehlyHecht2025, author = {Regehly, Martin and Hecht, Stefan}, title = {Split-Aperture Xolography - Linear Volumetric Photoactivation with Short Axial Dimension and Low out of Focus Excitation}, series = {Advanced Science}, volume = {12}, journal = {Advanced Science}, number = {31}, publisher = {Wiley}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20749}, year = {2025}, abstract = {Spatially confined photo-excitation with the lowest possible activation of the remaining volume is of central importance for high-resolution high-density optical data storage, fluorescence microscopy, 3D-lithography, and 3D-printing. Two-photon absorption (2PA) enables such applications yet leads to slow processing speed due to the underlying non-linear absorption process. Here, Split-Aperture Xolography (SAX), is introduced which uses stepwise excitation of dual-color responsive molecules to initiate a linear volumetric photo-reaction process that is up to several orders of magnitude more efficient than 2PA. The capabilities of SAX are investigated in a scenario study for focusing systems with high numerical aperture (NA) using a Python implementation of vectorial diffraction theory. The intersecting half-cones generated by the split illuminated entrance aperture of the objective reduce the axial focal spot size of the activation distribution by up to a factor of two compared to 2PA targeting the same electronic transition. A steep average decline of the activation probability with the fifth power away from focus is found for a wide range of directions. This is significantly better in comparison to 2PA and prevents that undesired out-of-focus excitation events sum-up with subsequent irradiations. This approach is expected to be advantageous for volumetric methods at the nanoscale.}, language = {en} } @article{BauerHeinrichVillasmuntaetal.2025, author = {Bauer, Joachim and Heinrich, Friedhelm and Villasmunta, Francesco and Villringer, Claus and Reck, Johanna and Peters, Sven and Treffer, Alexander and Kuhnt, Christian and Marschmeyer, Steffen and Fursenko, Oksana and Stolarek, David and Mai, Andreas and Regehly, Martin}, title = {Reflectometric method for measuring residual oxides in through-silicon vias for 3D chip integration}, series = {Optics Express}, volume = {33}, journal = {Optics Express}, number = {15}, publisher = {Optica}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20633}, pages = {32175 -- 32189}, year = {2025}, abstract = {A significant aspect of fabricating 3D chip architectures is ensuring proper contact between the different layers of the chip, which often requires removing the underside of isolation layers before filling vias with conductive material. Currently, scanning electron microscopy is the established method for investigating such structures. In this paper, we propose a rapid, non-destructive optical analysis technique for the simultaneous measurement of through-silicon vias (TSV) depths, silicon wafer thickness, and residual oxide thickness. The proposed method utilizes Fourier peak shift analysis (FPSA) of reflectance measurements in the near-infrared (1200 nm—2200 nm) spectral regions. The application of FPSA to representative samples taken from a commercial TSV integration process for MEMS and CMOS fabrication demonstrated good agreement with reference scanning electron microscopy measurements, confirming the feasibility of the method for in-line and in-situ metrology. The results indicate that FPSA has great potential for real-time process monitoring and control during 3D chip manufacturing.}, language = {en} } @article{HollandMoritzVandenhouten2013, author = {Holland-Moritz, Ralph and Vandenhouten, Ralf}, title = {Detection of Movement Profiles in Facility Management Using Complex Event Processing}, series = {International Journal of Information Science}, volume = {3}, journal = {International Journal of Information Science}, number = {1}, issn = {2163-193X}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9495}, pages = {7 -- 12}, year = {2013}, abstract = {This paper presents a solution for detecting movement and spreading profiles by analyzing sensor data in the facility management. First of all, a scenario is defined and described. On the basis of this scenario an approach is made using integration of events over time and location. For making the integration possible the required information, which the data objects have to provide, is identified. At the end a solution is presented using Complex Event Processing to implement the integration of events.}, language = {en} } @article{BalabanovWilhelmVenzetal.2013, author = {Balabanov, Stefan and Wilhelm, Thomas and Venz, Simone and Keller, Gunhild and Scharf, Christian and Pospisil, Heike and Braig, Melanie and Barett, Christine and Bokemeyer, Carsten and Walther, Reinhard and Br{\"u}mmendorf, Tim H. and Schuppert, Andreas}, title = {Combination of a Proteomics Approach and Reengineering of Meso Scale Network Models for Prediction of Mode-of-Action for Tyrosine Kinase Inhibitors}, series = {PLoS ONE}, volume = {8}, journal = {PLoS ONE}, number = {1}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6370}, pages = {14}, year = {2013}, abstract = {In drug discovery, the characterisation of the precise modes of action (MoA) and of unwanted off-target effects of novel molecularly targeted compounds is of highest relevance. Recent approaches for identification of MoA have employed various techniques for modeling of well defined signaling pathways including structural information, changes in phenotypic behavior of cells and gene expression patterns after drug treatment. However, efficient approaches focusing on proteome wide data for the identification of MoA including interference with mutations are underrepresented. As mutations are key drivers of drug resistance in molecularly targeted tumor therapies, efficient analysis and modeling of downstream effects of mutations on drug MoA is a key to efficient development of improved targeted anti-cancer drugs. Here we present a combination of a global proteome analysis, reengineering of network models and integration of apoptosis data used to infer the mode-of-action of various tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML) cell lines expressing wild type as well as TKI resistance conferring mutants of BCR-ABL. The inferred network models provide a tool to predict the main MoA of drugs as well as to grouping of drugs with known similar kinase inhibitory activity patterns in comparison to drugs with an additional MoA. We believe that our direct network reconstruction approach, demonstrated on proteomics data, can provide a complementary method to the established network reconstruction approaches for the preclinical modeling of the MoA of various types of targeted drugs in cancer treatment. Hence it may contribute to the more precise prediction of clinically relevant on- and off-target effects of TKIs.}, language = {en} } @article{ThiemannFuSeifertetal.2014, author = {Thiemann, Alexander and Fu, Junjie and Seifert, Felix and Grant-Downton, Robert T and Schrag, Tobias A and Pospisil, Heike and Frisch, Matthias and Melchinger, Albrecht E and Scholten, Stefan}, title = {Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci}, series = {BMC Plant Biology}, volume = {14}, journal = {BMC Plant Biology}, number = {88}, issn = {1471-2229}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5999}, pages = {14}, year = {2014}, abstract = {The identification of QTL involved in heterosis formation is one approach to unravel the not yet fully understood genetic basis of heterosis - the improved agronomic performance of hybrid F1 plants compared to their inbred parents. The identification of candidate genes underlying a QTL is important both for developing markers and determining the molecular genetic basis of a trait, but remains difficult owing to the large number of genes often contained within individual QTL. To address this problem in heterosis analysis, we applied a meta-analysis strategy for grain yield (GY) of Zea mays L. as example, incorporating QTL-, hybrid field-, and parental gene expression data.}, language = {en} } @article{UmmanniMundtPospisiletal.2011, author = {Ummanni, Ramesh and Mundt, Frederike and Pospisil, Heike and Venz, Simone and Scharf, Christian and Barett, Christine and F{\"a}lth, Maria and K{\"o}llermann, Jens and Walther, Reinhard and Schlomm, Thorsten and Sauter, Guido and Bokemeyer, Carsten and S{\"u}ltmann, Holger and Schuppert, Andreas and Br{\"u}mmendorf, Tim H. and Balabanov, Stefan}, title = {Identification of Clinically Relevant Protein Targets in Prostate Cancer with 2D-DIGE Coupled Mass Spectrometry and Systems Biology Network Platform}, series = {PLoS ONE}, volume = {6}, journal = {PLoS ONE}, number = {2}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6432}, pages = {14}, year = {2011}, abstract = {Prostate cancer (PCa) is the most common type of cancer found in men and among the leading causes of cancer death in the western world. In the present study, we compared the individual protein expression patterns from histologically characterized PCa and the surrounding benign tissue obtained by manual micro dissection using highly sensitive two-dimensional differential gel electrophoresis (2D-DIGE) coupled with mass spectrometry. Proteomic data revealed 118 protein spots to be differentially expressed in cancer (n = 24) compared to benign (n = 21) prostate tissue. These spots were analysed by MALDI-TOF-MS/MS and 79 different proteins were identified. Using principal component analysis we could clearly separate tumor and normal tissue and two distinct tumor groups based on the protein expression pattern. By using a systems biology approach, we could map many of these proteins both into major pathways involved in PCa progression as well as into a group of potential diagnostic and/or prognostic markers. Due to complexity of the highly interconnected shortest pathway network, the functional sub networks revealed some of the potential candidate biomarker proteins for further validation. By using a systems biology approach, our study revealed novel proteins and molecular networks with altered expression in PCa. Further functional validation of individual proteins is ongoing and might provide new insights in PCa progression potentially leading to the design of novel diagnostic and therapeutic strategies.}, language = {en} } @article{StandfussPospisilKlein2012, author = {Standfuß, Christoph and Pospisil, Heike and Klein, Andreas}, title = {SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT/t driven mice breast cancer}, series = {BMC Cancer}, volume = {12}, journal = {BMC Cancer}, number = {380}, issn = {1471-2407}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6414}, pages = {15}, year = {2012}, abstract = {Tumor development is known to be a stepwise process involving dynamic changes that affect cellular integrity and cellular behavior. This complex interaction between genomic organization and gene, as well as protein expression is not yet fully understood. Tumor characterization by gene expression analyses is not sufficient, since expression levels are only available as a snapshot of the cell status. So far, research has mainly focused on gene expression profiling or alterations in oncogenes, even though DNA microarray platforms would allow for high-throughput analyses of copy number alterations (CNAs).}, language = {en} } @article{KleinPospisil2014, author = {Klein, Andreas and Pospisil, Heike}, title = {Gene Expression Profiling of Pancreatic Cancer Reveals a Significant Deregulation of the TGF-β Pathway and the Discovery of Genes for Prognosis}, series = {Global Journal of Human Genetics \& Gene Therapy}, volume = {2}, journal = {Global Journal of Human Genetics \& Gene Therapy}, number = {1}, issn = {2311-0309}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6519}, pages = {30 -- 39}, year = {2014}, abstract = {We have re-analyzed previously published gene expression data from ninety-four pancreatic ductal adenocarcinomas (PDAC) samples. We determined the gene expression profile of genes differentially expressed in PDAC compared to non-malignant pancreatic tissue. Using the 100 top-ranked genes, we were able to discriminate between PDAC and non-malignant pancreatic tissue. A hierarchical cluster analysis revealed only a 6 \% false discovery rate. The prognostic strength of these discriminative genes was underscored by a SVM classification and 3-fold cross validation with an 89 \% correct class assignment. The annotation of the 100 top-ranked genes revealed that most of the genes were involved in the processes of signal transduction, cell adhesion, extracellular matrix organization and cell migration. The most greatly affected signal cascade was the transforming growth factor β receptor signaling pathway, which was significantly enriched in the top-ranked genes. Furthermore, we identified eleven genes that were associated with good prognosis.}, language = {en} } @article{HannemannMeyerStaecklingKemmingetal.2011, author = {Hannemann, Juliane and Meyer-Staeckling, S{\"o}nke and Kemming, Dirk and Alpers, Iris and Joosse, Simon A. and Pospisil, Heike and Kurtz, Stefan and G{\"o}rndt, Jennifer and P{\"u}schel, Klaus and Riethdorf, Sabine and Pantel, Klaus and Brandt, Burkhard}, title = {Quantitative High-Resolution Genomic Analysis of Single Cancer Cells}, series = {PLoS ONE}, volume = {6}, journal = {PLoS ONE}, number = {11}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6426}, pages = {6}, year = {2011}, abstract = {During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.}, language = {en} } @article{SilbermannWernickePospisiletal.2013, author = {Silbermann, Jascha and Wernicke, Catrin and Pospisil, Heike and Frohme, Marcus}, title = {RefPrimeCouch—a reference gene primer CouchApp}, series = {Database: The Journal of Biological Databases and Curation}, volume = {2013}, journal = {Database: The Journal of Biological Databases and Curation}, issn = {1758-0463}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6330}, pages = {8}, year = {2013}, abstract = {To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License.}, language = {en} } @article{DuscharlaBhumireddyLakshettietal.2016, author = {Duscharla, Divya and Bhumireddy, Sudarshana Reddy and Lakshetti, Sridhar and Pospisil, Heike and Murthy, P. V. L. N. and Walther, Reinhard and Sripadi, Prabhakar and Ummanni, Ramesh}, title = {Prostate Cancer Associated Lipid Signatures in Serum Studied by ESI-Tandem Mass Spectrometryas Potential New Biomarkers}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {3}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5863}, pages = {21}, year = {2016}, abstract = {Prostate cancer (PCa) is one amongst the most common cancersin western men. Incidence rate ofPCa is on the rise worldwide. The present study deals with theserum lipidome profiling of patients diagnosed with PCa to identify potential new biomarkers. We employed ESI-MS/MS and GC-MS for identification of significantly altered lipids in cancer patient's serum compared to controls. Lipidomic data revealed 24 lipids are significantly altered in cancer patinet's serum (n = 18) compared to normal (n = 18) with no history of PCa. By using hierarchical clustering and principal component analysis (PCA) we could clearly separate cancer patients from control group. Correlation and partition analysis along with Formal Concept Analysis (FCA) have identified that PC (39:6) and FA (22:3) could classify samples with higher certainty. Both the lipids, PC (39:6) and FA (22:3) could influence the cataloging of patients with 100\% sensitivity (all 18 control samples are classified correctly) and 77.7\% specificity (of 18 tumor samples 4 samples are misclassified) with p-value of 1.612×10-6 in Fischer's exact test. Further, we performed GC-MS to denote fatty acids altered in PCa patients and found that alpha-linolenic acid (ALA) levels are altered in PCa. We also performed an in vitro proliferation assay to determine the effect of ALA in survival of classical human PCa cell lines LNCaP and PC3. We hereby report that the altered lipids PC (39:6) and FA (22:3) offer a new set of biomarkers in addition to the existing diagnostic tests that could significantly improve sensitivity and specificity in PCa diagnosis.}, language = {en} } @article{GladischSarauliSchaeferetal.2016, author = {Gladisch, Johannes and Sarauli, David and Sch{\"a}fer, Daniel and Dietzel, Birgit and Schulz, Burkhard and Lisdat, Fred}, title = {Towards a novel bioelectrocatalytic platform based on "wiring" of pyrroloquinoline quinone-dependent glucose dehydrogenase with an electrospun conductive polymeric fiber architecture}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, issn = {2045-2322}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5846}, pages = {10}, year = {2016}, abstract = {Electrospinning is known as a fabrication technique for electrode architectures that serve as immobilization matrices for biomolecules. The current work demonstrates a novel approach to construct a conductive polymeric platform, capable not only of immobilization, but also of electrical connection of the biomolecule with the electrode. It is produced upon electrospinning from mixtures of three different highly conductive sulfonated polyanilines and polyacrylonitrile on ITO electrodes. The resulting fiber mats are with a well-retained conductivity. After coupling the enzyme pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH) to polymeric structures and addition of the substrate glucose an efficient bioelectrocatalysis is demonstrated. Depending on the choice of the sulfonated polyanilline mediatorless bioelectrocatalysis starts at low potentials; no large overpotential is needed to drive the reaction. Thus, the electrospun conductive immobilization matrix acts here as a transducing element, representing a promising strategy to use 3D polymeric scaffolds as wiring agents for active enzymes. In addition, the mild and well reproducible fabrication process and the active role of the polymer film in withdrawing electrons from the reduced PQQ-GDH lead to a system with high stability. This could provide access to a larger group of enzymes for bioelectrochemical applications including biosensors and biofuel cells.}, language = {en} } @article{SeifertThiemannPospisiletal.2012, author = {Seifert, Felix and Thiemann, Alexander and Pospisil, Heike and Scholten, Stefan}, title = {Re-annotation of the maize oligonucleotide array}, series = {Maydica}, volume = {57}, journal = {Maydica}, number = {1}, issn = {0025-6153}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6178}, pages = {49 -- 55}, year = {2012}, abstract = {The microarray technology has become an established approach for large-scale gene expression analysis with mature protocols for sample, microarray, and data processing. The maize oligonucleotide array (maizearray) is one of the few microarray platforms designed for genome-wide gene expression analysis in Zea mays L. Many datas-ets addressing various genetic, physiological and developmental topics generated with this platform are available. The original 57,452 microarray probes were compiled based on expressed sequence tags (ESTs). Meanwhile the maize genome sequence became available providing the possibility for an improved annotation of the microar-ray probe set. In this study we determined the genome positions of all maizearray probes to obtain current gene annotations and generated current Gene Ontology (GO) annotations. These new data allow tracing redundancy of the probe set and interfering cross-hybridizations, and doubled the number of genes with functional GO data. Our re-annotation will largely improve the functional analysis of available and future datasets generated on this microarray platform.}, language = {en} } @article{MarczokBortzWangetal.2016, author = {Marczok, Stefanie and Bortz, Birgit and Wang, Chong and Pospisil, Heike}, title = {Comprehensive Analysis of Genome Rearrangements in Eight Human Malignant Tumor Tissues}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {7}, issn = {1932-6203}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6607}, pages = {18}, year = {2016}, abstract = {Carcinogenesis is a complex multifactorial, multistage process, but the precise mechanisms are not well understood. In this study, we performed a genome-wide analysis of the copy number variation (CNV), breakpoint region (BPR) and fragile sites in 2,737 tumor samples from eight tumor entities and in 432 normal samples. CNV detection and BPR identification revealed that BPRs tended to accumulate in specific genomic regions in tumor samples whereas being dispersed genome-wide in the normal samples. Hotspots were observed, at which segments with similar alteration in copy number were overlapped along with BPRs adjacently clustered. Evaluation of BPR occurrence frequency showed that at least one was detected in about and more than 15\% of samples for each tumor entity while BPRs were maximal in 12\% of the normal samples. 127 of 2,716 tumor-relevant BPRs (termed 'common BPRs') exhibited also a noticeable occurrence frequency in the normal samples. Colocalization assessment identified 20,077 CNV-affecting genes and 169 of these being known tumor-related genes. The most noteworthy genes are KIAA0513 important for immunologic, synaptic and apoptotic signal pathways, intergenic non-coding RNA RP11-115C21.2 possibly acting as oncogene or tumor suppressor by changing the structure of chromatin, and ADAM32 likely importance in cancer cell proliferation and progression by ectodomain-shedding of diverse growth factors, and the well-known tumor suppressor gene p53. The BPR distributions indicate that CNV mutations are likely non-random in tumor genomes. The marked recurrence of BPRs at specific regions supports common progression mechanisms in tumors. The presence of hotspots together with common BPRs, despite its small group size, imply a relation between fragile sites and cancer-gene alteration. Our data further suggest that both protein-coding and non-coding genes possessing a range of biological functions might play a causative or functional role in tumor biology. This research enhances our understanding of the mechanisms for tumorigenesis and progression.}, language = {en} } @article{PfeilSiptrothPospisiletal.2023, author = {Pfeil, Juliane and Siptroth, Julienne and Pospisil, Heike and Frohme, Marcus and Hufert, Frank T. and Moskalenko, Olga and Yateem, Murad and Nechyporenko, Alina}, title = {Classification of Microbiome Data from Type 2 Diabetes Mellitus Individuals with Deep Learning Image Recognition}, series = {Big Data and Cognitive Computing}, volume = {7}, journal = {Big Data and Cognitive Computing}, number = {1}, publisher = {MDPI}, issn = {2504-2289}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17184}, year = {2023}, abstract = {Microbiomic analysis of human gut samples is a beneficial tool to examine the general well-being and various health conditions. The balance of the intestinal flora is important to prevent chronic gut infections and adiposity, as well as pathological alterations connected to various diseases. The evaluation of microbiome data based on next-generation sequencing (NGS) is complex and their interpretation is often challenging and can be ambiguous. Therefore, we developed an innovative approach for the examination and classification of microbiomic data into healthy and diseased by visualizing the data as a radial heatmap in order to apply deep learning (DL) image classification. The differentiation between 674 healthy and 272 type 2 diabetes mellitus (T2D) samples was chosen as a proof of concept. The residual network with 50 layers (ResNet-50) image classification model was trained and optimized, providing discrimination with 96\% accuracy. Samples from healthy persons were detected with a specificity of 97\% and those from T2D individuals with a sensitivity of 92\%. Image classification using DL of NGS microbiome data enables precise discrimination between healthy and diabetic individuals. In the future, this tool could enable classification of different diseases and imbalances of the gut microbiome and their causative genera.}, language = {en} } @article{SiptrothMoskalenkoKrumbiegeletal.2023, author = {Siptroth, Julienne and Moskalenko, Olga and Krumbiegel, Carsten and Ackermann, J{\"o}rg and Koch, Ina and Pospisil, Heike}, title = {Variation of butyrate production in the gut microbiome in type 2 diabetes patients}, series = {International Microbiology}, volume = {26}, journal = {International Microbiology}, publisher = {Springer Nature}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17802}, pages = {601 -- 610}, year = {2023}, abstract = {Background Diabetes mellitus type 2 is a common disease that poses a challenge to the healthcare system. The disease is very often diagnosed late. A better understanding of the relationship between the gut microbiome and type 2 diabetes can support early detection and form an approach for therapies. Microbiome analysis offers a potential opportunity to find markers for this disease. Next-generation sequencing methods can be used to identify the bacteria present in the stool sample and to generate a microbiome profile through an analysis pipeline. Statistical analysis, e.g., using Student's t-test, allows the identification of significant differences. The investigations are not only focused on single bacteria, but on the determination of a comprehensive profile. Also, the consideration of the functional microbiome is included in the analyses. The dataset is not from a clinical survey, but very extensive. Results By examining 946 microbiome profiles of diabetes mellitus type 2 sufferers (272) and healthy control persons (674), a large number of significant genera (25) are revealed. It is possible to identify a large profile for type 2 diabetes disease. Furthermore, it is shown that the diversity of bacteria per taxonomic level in the group of persons with diabetes mellitus type 2 is significantly reduced compared to a healthy control group. In addition, six pathways are determined to be significant for type 2 diabetes describing the fermentation to butyrate. These parameters tend to have high potential for disease detection. Conclusions With this investigation of the gut microbiome of persons with diabetes type 2 disease, we present significant bacteria and pathways characteristic of this disease.}, language = {en} } @article{SiptrothMoskalenkoKrumbiegeletal.2023, author = {Siptroth, Julienne and Moskalenko, Olga and Krumbiegel, Carsten and Ackermann, J{\"o}rg and Koch, Ina and Pospisil, Heike}, title = {Investigation of metabolic pathways from gut microbiome analyses regarding type 2 diabetes mellitus using artificial neural networks}, series = {Discover Artificial Intelligence}, volume = {3}, journal = {Discover Artificial Intelligence}, number = {1}, publisher = {Springer Nature}, issn = {2731-0809}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17497}, year = {2023}, abstract = {Background Type 2 diabetes mellitus is a prevalent disease that contributes to the development of various health issues, including kidney failure and strokes. As a result, it poses a significant challenge to the worldwide healthcare system. Research into the gut microbiome has enabled the identification and description of various diseases, with bacterial pathways playing a critical role in this context. These pathways link individual bacteria based on their biological functions. This study deals with the classification of microbiome pathway profiles of type 2 diabetes mellitus patients. Methods Pathway profiles were determined by next-generation sequencing of 16S rDNA from stool samples, which were subsequently assigned to bacteria. Then, the involved pathways were assigned by the identified gene families. The classification of type 2 diabetes mellitus is enabled by a constructed neural network. Furthermore, a feature importance analysis was performed via a game theoretic approach (SHapley Additive exPlanations). The study not only focuses on the classification using neural networks, but also on identifying crucial bacterial pathways. Results It could be shown that a neural network classification of type 2 diabetes mellitus and a healthy comparison group is possible with an excellent prediction accuracy. It was possible to create a ranking to identify the pathways that have a high impact on the model prediction accuracy. In this way, new associations between the alteration of, e.g. a biosynthetic pathway and the presence of diabetes mellitus type 2 disease can also be discovered. The basis is formed by 946 microbiome pathway profiles from diabetes mellitus type 2 patients (272) and healthy comparison persons (674). Conclusion With this study of the gut microbiome, we present an approach using a neural network to obtain a classification of healthy and type 2 diabetes mellitus and to identify the critical features. Intestinal bacteria pathway profiles form the basis.}, language = {en} } @article{HeroldRoedenbeck2025, author = {Herold, Marcel and Roedenbeck, Marc}, title = {AI-Driven Research in the Recruitment and Selection Process: Application of an AI Taxonomy With a Systematic Literature Review}, series = {SAGE Open}, volume = {15}, journal = {SAGE Open}, number = {3}, publisher = {Sage}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-20736}, year = {2025}, abstract = {A review of the literature on the application of artificial intelligence (AI) in the recruitment and selection process (RSP) was conducted, but no relevant studies were identified. While several reviews have focussed on AI in human resource management in general, none of these have examined the RSP in detail or employed an AI taxonomy for clustering. Consequently, we applied an AI taxonomy identified in the literature with the aim to identify the stages of the RSP in the focus of research and the algorithms mostly used. We conducted a systematic literature review underpinned by a concept matrix, complemented by a computational literature review (CLR), that employed natural language processing (NLP). The initial 4,579 studies were sourced from three databases and narrowed down to a total of 502. Our major findings indicate that the majority of studies were categorised under the stages "assessment \& selection" and "processing incoming applications" in the RSP. The predominant algorithms in use pertain to the field of NLP and machine learning. The CLR emphasised the significance of ethics in AI research. While our study has expanded the general AI taxonomy by incorporating an ethical perspective and is one of the studies with the most articles used to reflect this topic, it is solely focussing on describing the past. Nevertheless, this article helps to align research on exploring and testing alternative approaches with those most frequently used.}, language = {en} } @article{FeifelStiegerKappetal.2016, author = {Feifel, Sven Christian and Stieger, Kai Ralf and Kapp, Andreas and Weber, Dennis and Allegrozzi, Marco and Piccioli, Mario and Turano, Paola and Lisdat, Fred}, title = {Insights into Interprotein Electron Transfer of Human Cytochrome c Variants Arranged in Multilayer Architectures by Means of an Artificial Silica Nanoparticle Matrix}, series = {ACS Omega}, volume = {1}, journal = {ACS Omega}, number = {6}, issn = {2470-1343}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-6753}, pages = {1058 -- 1066}, year = {2016}, abstract = {The redox behavior of proteins plays a crucial part in the design of bioelectronic systems. We have demonstrated several functional systems exploiting the electron exchange properties of the redox protein cytochrome c (cyt c) in combination with enzymes and photoactive proteins. The operation is based on an effective reaction at modified electrodes but also to a large extent on the capability of self-exchange between cyt c molecules in a surface-fixed state. In this context, different variants of human cyt c have been examined here with respect to an altered heterogeneous electron transfer (ET) rate in a monolayer on electrodes as well as an enhanced self-exchange rate while being incorporated in multilayer architectures. For this purpose, mutants of the wild-type (WT) protein have been prepared to change the chemical nature of the surface contact area near the heme edge. The structural integrity of the variants has been verified by NMR and UV-vis measurements. It is shown that the single-point mutations can significantly influence the heterogeneous ET rate at thiol-modified gold electrodes and that electroactive protein/silica nanoparticle multilayers can be constructed with all forms of human cyt c prepared. The kinetic behavior of electron exchange for the mutant proteins in comparison with that of the WT has been found altered in some multilayer arrangements. Higher self-exchange rates have been found for K79A. The results demonstrate that the position of the introduced change in the charge situation of cyt c has a profound influence on the exchange behavior. In addition, the behavior of the cyt c variants in assembled multilayers is found to be rather similar to the situation of cyt c self-exchange in solution verified by NMR.}, language = {en} } @article{FeifelLisdat2011, author = {Feifel, Sven Christian and Lisdat, Fred}, title = {Silica nanoparticles for the layer-by-layer assembly of fully electro-active cytochrome c multilayers}, series = {Journal of Nanobiotechnology}, volume = {9}, journal = {Journal of Nanobiotechnology}, number = {59}, issn = {1477-3155}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-5819}, pages = {12}, year = {2011}, abstract = {For bioanalytical systems sensitivity and biomolecule activity are critical issues. The immobilization of proteins into multilayer systems by the layer-by-layer deposition has become one of the favorite methods with this respect. Moreover, the combination of nanoparticles with biomolecules on electrodes is a matter of particular interest since several examples with high activities and direct electron transfer have been found. Our study describes the investigation on silica nanoparticles and the redox protein cytochrome c for the construction of electro-active multilayer architectures, and the electron transfer within such systems. The novelty of this work is the construction of such artificial architectures with a non-conducting building block. Furthermore a detailed study of the size influence of silica nanoparticles is performed with regard to formation and electrochemical behavior of these systems.}, language = {en} } @article{AdomavičiũtėGrabusovėHinkelUsenovetal.2022, author = {Adomavičiũtė-Grabusovė, Sonata and Hinkel, Jonas and Usenov, Iskander and Novikov, Alexander S. and Sakharova, Tatiana and D{\"o}hler, Torsten and Geißler, Ute and Feliksberger, Elena and Artyushenko, Viacheslav}, title = {Microstructuring of the end-surface for silver halide polycrystalline fibers to suppress Fresnel reflection}, series = {Optical Materials Express}, volume = {12}, journal = {Optical Materials Express}, number = {1}, publisher = {Optica Publishing Group}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15549}, pages = {34 -- 48}, year = {2022}, abstract = {Silver halide polycrystalline infrared fibers (PIR) have unique properties such as excellent transmittance in the spectral range from 3 to 17 µm, while also being highly flexible, non-toxic, and non-hygroscopic. They are used in industry and medicine for CO2-laser power delivery, flexible infrared imaging, and remote process spectroscopy. While PIR fibers possess a quite low attenuation (0.1-0.5 dB/m) in the 8-12 µm range, their total transmittance is limited by significant Fresnel reflections at the fiber end faces due to the high refractive index of silver halide (>2.1). Functionalization of these surfaces with specially designed Anti-Reflective Microstructures (ARMs) enables a striking enhancement of fiber transmittance. In this work, direct imprinting (or embossing) of microstructures to fiber ends and their profiling with a microstructured knife was applied to fabricate such ARMs. The resulting two-dimensional Moth-eye microstructures and one-dimensional microgrooves at the PIR-fiber ends enable to an increase of fiber transmittance in a broadband range of (5-17 µm) as well as to reach up to 20\% improvement for PIR-fiber laser cables used for power delivery of CO2-lasers at 10.6 µm.}, language = {en} }