TY - JOUR A1 - Bertz, Morten A1 - Molinnus, Denise A1 - Schöning, Michael Josef A1 - Homma, Takayuki T1 - Real-time monitoring of H₂O₂ sterilization on individual bacillus atrophaeus spores by optical sensing with trapping Raman spectroscopy JF - Chemosensors N2 - Hydrogen peroxide (H₂O₂), a strong oxidizer, is a commonly used sterilization agent employed during aseptic food processing and medical applications. To assess the sterilization efficiency with H₂O₂, bacterial spores are common microbial systems due to their remarkable robustness against a wide variety of decontamination strategies. Despite their widespread use, there is, however, only little information about the detailed time-resolved mechanism underlying the oxidative spore death by H₂O₂. In this work, we investigate chemical and morphological changes of individual Bacillus atrophaeus spores undergoing oxidative damage using optical sensing with trapping Raman microscopy in real-time. The time-resolved experiments reveal that spore death involves two distinct phases: (i) an initial phase dominated by the fast release of dipicolinic acid (DPA), a major spore biomarker, which indicates the rupture of the spore’s core; and (ii) the oxidation of the remaining spore material resulting in the subsequent fragmentation of the spores’ coat. Simultaneous observation of the spore morphology by optical microscopy corroborates these mechanisms. The dependence of the onset of DPA release and the time constant of spore fragmentation on H₂O₂ shows that the formation of reactive oxygen species from H₂O₂ is the rate-limiting factor of oxidative spore death. KW - DPA (dipicolinic acid) KW - sterilization KW - Bacillus atrophaeus spores KW - optical trapping KW - Raman spectroscopy KW - optical sensor setup Y1 - 2023 U6 - https://doi.org/10.3390/chemosensors11080445 SN - 2227-9040 N1 - This article belongs to the Special Issue "Biosensors and Chemical Sensors for Food and Healthcare Monitoring—Celebrating the 10th Anniversary" VL - 8 IS - 11 PB - MDPI CY - Basel ER - TY - JOUR A1 - Mikucki, Jill Ann A1 - Schuler, C. G. A1 - Digel, Ilya A1 - Kowalski, Julia A1 - Tuttle, M. J. A1 - Chua, Michelle A1 - Davis, R. A1 - Purcell, Alicia A1 - Ghosh, D. A1 - Francke, G. A1 - Feldmann, M. A1 - Espe, C. A1 - Heinen, Dirk A1 - Dachwald, Bernd A1 - Clemens, Joachim A1 - Lyons, W. B. A1 - Tulaczyk, S. T1 - Field-Based planetary protection operations for melt probes: validation of clean access into the blood falls, antarctica, englacial ecosystem JF - Astrobiology N2 - Subglacial environments on Earth offer important analogs to Ocean World targets in our solar system. These unique microbial ecosystems remain understudied due to the challenges of access through thick glacial ice (tens to hundreds of meters). Additionally, sub-ice collections must be conducted in a clean manner to ensure sample integrity for downstream microbiological and geochemical analyses. We describe the field-based cleaning of a melt probe that was used to collect brine samples from within a glacier conduit at Blood Falls, Antarctica, for geomicrobiological studies. We used a thermoelectric melting probe called the IceMole that was designed to be minimally invasive in that the logistical requirements in support of drilling operations were small and the probe could be cleaned, even in a remote field setting, so as to minimize potential contamination. In our study, the exterior bioburden on the IceMole was reduced to levels measured in most clean rooms, and below that of the ice surrounding our sampling target. Potential microbial contaminants were identified during the cleaning process; however, very few were detected in the final englacial sample collected with the IceMole and were present in extremely low abundances (∼0.063% of 16S rRNA gene amplicon sequences). This cleaning protocol can help minimize contamination when working in remote field locations, support microbiological sampling of terrestrial subglacial environments using melting probes, and help inform planetary protection challenges for Ocean World analog mission concepts. Y1 - 2023 U6 - https://doi.org/10.1089/ast.2021.0102 SN - 1557-8070 (online) SN - 153-1074 (print) VL - 23 IS - 11 SP - 1165 EP - 1178 PB - Liebert CY - New York, NY ER - TY - JOUR A1 - Grajewski, Matthias A1 - Kleefeld, Andreas T1 - Detecting and approximating decision boundaries in low-dimensional spaces JF - Numerical Algorithms N2 - A method for detecting and approximating fault lines or surfaces, respectively, or decision curves in two and three dimensions with guaranteed accuracy is presented. Reformulated as a classification problem, our method starts from a set of scattered points along with the corresponding classification algorithm to construct a representation of a decision curve by points with prescribed maximal distance to the true decision curve. Hereby, our algorithm ensures that the representing point set covers the decision curve in its entire extent and features local refinement based on the geometric properties of the decision curve. We demonstrate applications of our method to problems related to the detection of faults, to multi-criteria decision aid and, in combination with Kirsch’s factorization method, to solving an inverse acoustic scattering problem. In all applications we considered in this work, our method requires significantly less pointwise classifications than previously employed algorithms. KW - MCDA KW - Inverse scattering problem KW - Fault approximation KW - Fault detection Y1 - 2023 SN - 1572-9265 N1 - Corresponding author: Matthias Grajewski VL - 93 IS - 4 PB - Springer Science+Business Media CY - Dordrecht ER - TY - INPR A1 - Bornheim, Tobias A1 - Grieger, Niklas A1 - Blaneck, Patrick Gustav A1 - Bialonski, Stephan T1 - Preprint: Speaker attribution in German parliamentary debates with QLoRA-adapted large language models T2 - Journal for Language Technology and Computational Linguistics N2 - The growing body of political texts opens up new opportunities for rich insights into political dynamics and ideologies but also increases the workload for manual analysis. Automated speaker attribution, which detects who said what to whom in a speech event and is closely related to semantic role labeling, is an important processing step for computational text analysis. We study the potential of the large language model family Llama 2 to automate speaker attribution in German parliamentary debates from 2017-2021. We fine-tune Llama 2 with QLoRA, an efficient training strategy, and observe our approach to achieve competitive performance in the GermEval 2023 Shared Task On Speaker Attribution in German News Articles and Parliamentary Debates. Our results shed light on the capabilities of large language models in automating speaker attribution, revealing a promising avenue for computational analysis of political discourse and the development of semantic role labeling systems. Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2309.09902 N1 - Veröffentlichte Version verfügbar unter: https://doi.org/10.21248/jlcl.37.2024.244 ER - TY - CHAP A1 - Maurer, Florian A1 - Miskiw, Kim K. A1 - Acosta, Rebeca Ramirez A1 - Harder, Nick A1 - Sander, Volker A1 - Lehnhoff, Sebastian ED - Jorgensen, Bo Norregaard ED - Pereira da Silva, Luiz Carlos ED - Ma, Zheng T1 - Market abstraction of energy markets and policies - application in an agent-based modeling toolbox T2 - EI.A 2023: Energy Informatics N2 - In light of emerging challenges in energy systems, markets are prone to changing dynamics and market design. Simulation models are commonly used to understand the changing dynamics of future electricity markets. However, existing market models were often created with specific use cases in mind, which limits their flexibility and usability. This can impose challenges for using a single model to compare different market designs. This paper introduces a new method of defining market designs for energy market simulations. The proposed concept makes it easy to incorporate different market designs into electricity market models by using relevant parameters derived from analyzing existing simulation tools, morphological categorization and ontologies. These parameters are then used to derive a market abstraction and integrate it into an agent-based simulation framework, allowing for a unified analysis of diverse market designs. Furthermore, we showcase the usability of integrating new types of long-term contracts and over-the-counter trading. To validate this approach, two case studies are demonstrated: a pay-as-clear market and a pay-as-bid long-term market. These examples demonstrate the capabilities of the proposed framework. KW - Energy market design KW - Agent-based simulation KW - Market modeling Y1 - 2023 SN - 978-3-031-48651-7 (Print) SN - 978-3-031-48652-4 (eBook) U6 - https://doi.org/10.1007/978-3-031-48652-4_10 N1 - Third Energy Informatics Academy Conference, EI.A 2023, Campinas, Brazil, December 6–8, 2023 N1 - Part of the Lecture Notes in Computer Science book series (LNCS,volume 14468). SP - 139 EP - 157 PB - Springer CY - Cham ER - TY - JOUR A1 - Bertz, Morten A1 - Schöning, Michael Josef A1 - Molinnus, Denise A1 - Homma, Takayuki T1 - Influence of temperature, light, and H₂O₂ concentration on microbial spore inactivation: in-situ Raman spectroscopy combined with optical trapping JF - Physica status solidi (a) applications and materials science N2 - To gain insight on chemical sterilization processes, the influence of temperature (up to 70 °C), intense green light, and hydrogen peroxide (H₂O₂) concentration (up to 30% in aqueous solution) on microbial spore inactivation is evaluated by in-situ Raman spectroscopy with an optical trap. Bacillus atrophaeus is utilized as a model organism. Individual spores are isolated and their chemical makeup is monitored under dynamically changing conditions (temperature, light, and H₂O₂ concentration) to mimic industrially relevant process parameters for sterilization in the field of aseptic food processing. While isolated spores in water are highly stable, even at elevated temperatures of 70 °C, exposure to H₂O₂ leads to a loss of spore integrity characterized by the release of the key spore biomarker dipicolinic acid (DPA) in a concentration-dependent manner, which indicates damage to the inner membrane of the spore. Intensive light or heat, both of which accelerate the decomposition of H₂O₂ into reactive oxygen species (ROS), drastically shorten the spore lifetime, suggesting the formation of ROS as a rate-limiting step during sterilization. It is concluded that Raman spectroscopy can deliver mechanistic insight into the mode of action of H₂O₂-based sterilization and reveal the individual contributions of different sterilization methods acting in tandem. KW - hydrogen peroxide KW - optical spore trapping KW - Raman spectroscopy KW - sterilization conditions KW - temperature Y1 - 2024 U6 - https://doi.org/10.1002/pssa.202300866 SN - 1862-6319 (Online) SN - 1862-6300 (Print) N1 - Corresponding author: Michael J. Schöning IS - Early View PB - Wiley-VCH CY - Berlin ER - TY - JOUR A1 - Schoenrock, Britt A1 - Muckelt, Paul E. A1 - Hastermann, Maria A1 - Albracht, Kirsten A1 - MacGregor, Robert A1 - Martin, David A1 - Gunga, Hans-Christian A1 - Salanova, Michele A1 - Stokes, Maria J. A1 - Warner, Martin B. A1 - Blottner, Dieter T1 - Muscle stiffness indicating mission crew health in space JF - Scientific Reports N2 - Muscle function is compromised by gravitational unloading in space affecting overall musculoskeletal health. Astronauts perform daily exercise programmes to mitigate these effects but knowing which muscles to target would optimise effectiveness. Accurate inflight assessment to inform exercise programmes is critical due to lack of technologies suitable for spaceflight. Changes in mechanical properties indicate muscle health status and can be measured rapidly and non-invasively using novel technology. A hand-held MyotonPRO device enabled monitoring of muscle health for the first time in spaceflight (> 180 days). Greater/maintained stiffness indicated countermeasures were effective. Tissue stiffness was preserved in the majority of muscles (neck, shoulder, back, thigh) but Tibialis Anterior (foot lever muscle) stiffness decreased inflight vs. preflight (p < 0.0001; mean difference 149 N/m) in all 12 crewmembers. The calf muscles showed opposing effects, Gastrocnemius increasing in stiffness Soleus decreasing. Selective stiffness decrements indicate lack of preservation despite daily inflight countermeasures. This calls for more targeted exercises for lower leg muscles with vital roles as ankle joint stabilizers and in gait. Muscle stiffness is a digital biomarker for risk monitoring during future planetary explorations (Moon, Mars), for healthcare management in challenging environments or clinical disorders in people on Earth, to enable effective tailored exercise programmes. KW - Ageing KW - Anatomy KW - Muscle KW - Musculoskeletal system KW - Physiology Y1 - 2024 U6 - https://doi.org/10.1038/s41598-024-54759-6 SN - 2045-2322 N1 - Corresponding author: Dieter Blottner VL - 14 IS - Article number: 4196 PB - Springer Nature CY - London ER - TY - JOUR A1 - Bornheim, Tobias A1 - Grieger, Niklas A1 - Blaneck, Patrick Gustav A1 - Bialonski, Stephan T1 - Speaker Attribution in German Parliamentary Debates with QLoRA-adapted Large Language Models JF - Journal for language technology and computational linguistics : JLCL N2 - The growing body of political texts opens up new opportunities for rich insights into political dynamics and ideologies but also increases the workload for manual analysis. Automated speaker attribution, which detects who said what to whom in a speech event and is closely related to semantic role labeling, is an important processing step for computational text analysis. We study the potential of the large language model family Llama 2 to automate speaker attribution in German parliamentary debates from 2017-2021. We fine-tune Llama 2 with QLoRA, an efficient training strategy, and observe our approach to achieve competitive performance in the GermEval 2023 Shared Task On Speaker Attribution in German News Articles and Parliamentary Debates. Our results shed light on the capabilities of large language models in automating speaker attribution, revealing a promising avenue for computational analysis of political discourse and the development of semantic role labeling systems. KW - large language models KW - German KW - speaker attribution KW - semantic role labeling Y1 - 2024 U6 - https://doi.org/10.21248/jlcl.37.2024.244 SN - 2190-6858 VL - 37 IS - 1 PB - Gesellschaft für Sprachtechnologie und Computerlinguistik CY - Regensburg ER - TY - JOUR A1 - Özsoylu, Dua A1 - Aliazizi, Fereshteh A1 - Wagner, Patrick A1 - Schöning, Michael Josef T1 - Template bacteria-free fabrication of surface imprinted polymer-based biosensor for E. coli detection using photolithographic mimics: Hacking bacterial adhesion JF - Biosensors and Bioelectronics N2 - As one class of molecular imprinted polymers (MIPs), surface imprinted polymer (SIP)-based biosensors show great potential in direct whole-bacteria detection. Micro-contact imprinting, that involves stamping the template bacteria immobilized on a substrate into a pre-polymerized polymer matrix, is the most straightforward and prominent method to obtain SIP-based biosensors. However, the major drawbacks of the method arise from the requirement for fresh template bacteria and often non-reproducible bacteria distribution on the stamp substrate. Herein, we developed a positive master stamp containing photolithographic mimics of the template bacteria (E. coli) enabling reproducible fabrication of biomimetic SIP-based biosensors without the need for the “real” bacteria cells. By using atomic force and scanning electron microscopy imaging techniques, respectively, the E. coli-capturing ability of the SIP samples was tested, and compared with non-imprinted polymer (NIP)-based samples and control SIP samples, in which the cavity geometry does not match with E. coli cells. It was revealed that the presence of the biomimetic E. coli imprints with a specifically designed geometry increases the sensor E. coli-capturing ability by an “imprinting factor” of about 3. These findings show the importance of geometry-guided physical recognition in bacterial detection using SIP-based biosensors. In addition, this imprinting strategy was employed to interdigitated electrodes and QCM (quartz crystal microbalance) chips. E. coli detection performance of the sensors was demonstrated with electrochemical impedance spectroscopy (EIS) and QCM measurements with dissipation monitoring technique (QCM-D). KW - Surface imprinted polymer KW - E. coli detection KW - Photolithographic mimics KW - Master stamp KW - Quartz crystal microbalance Y1 - 2024 U6 - https://doi.org/10.1016/j.bios.2024.116491 SN - 1873-4235 (eISSN) SN - 0956-5663 N1 - Corresponding author: Michael J. Schöning VL - 261 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Pogorelova, Natalia A1 - Rogachev, Evgeniy A1 - Akimbekov, Nuraly S. A1 - Digel, Ilya T1 - Effect of dehydration method on the micro- and nanomorphological properties of bacterial cellulose produced by Medusomyces gisevii on different substrates JF - Journal of materials science N2 - Many important properties of bacterial cellulose (BC), such as moisture absorption capacity, elasticity and tensile strength, largely depend on its structure. This paper presents a study on the effect of the drying method on BC films produced by Medusomyces gisevii using two different procedures: room temperature drying (RT, (24 ± 2 °C, humidity 65 ± 1%, dried until a constant weight was reached) and freeze-drying (FD, treated at − 75 °C for 48 h). BC was synthesized using one of two different carbon sources—either glucose or sucrose. Structural differences in the obtained BC films were evaluated using atomic force microscopy (AFM), scanning electron microscopy (SEM), and X-ray diffraction. Macroscopically, the RT samples appeared semi-transparent and smooth, whereas the FD group exhibited an opaque white color and sponge-like structure. SEM examination showed denser packing of fibrils in FD samples while RT-samples displayed smaller average fiber diameter, lower surface roughness and less porosity. AFM confirmed the SEM observations and showed that the FD material exhibited a more branched structure and a higher surface roughness. The samples cultivated in a glucose-containing nutrient medium, generally displayed a straight and ordered shape of fibrils compared to the sucrose-derived BC, characterized by a rougher and wavier structure. The BC films dried under different conditions showed distinctly different crystallinity degrees, whereas the carbon source in the culture medium was found to have a relatively small effect on the BC crystallinity. Y1 - 2024 U6 - https://doi.org/10.1007/s10853-024-09596-3 SN - 1573-4803 (Online) SN - 0022-2461 (Print) N1 - Corresponding author: Ilya Digel VL - 2024 PB - Springer Science + Business Media CY - Dordrecht ER -