@article{BernauKnoedlerEmontsetal.2022, author = {Bernau, C. R. and Kn{\"o}dler, Matthias and Emonts, Jessica and J{\"a}pel, Ronald Colin and Buyel, Johannes Felix}, title = {The use of predictive models to develop chromatography-based purification processes}, series = {Frontiers in Bioengineering and Biotechnology}, journal = {Frontiers in Bioengineering and Biotechnology}, number = {10}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-4185 (online-ressource)}, doi = {10.3389/fbioe.2022.1009102}, pages = {25 Seiten}, year = {2022}, abstract = {Chromatography is the workhorse of biopharmaceutical downstream processing because it can selectively enrich a target product while removing impurities from complex feed streams. This is achieved by exploiting differences in molecular properties, such as size, charge and hydrophobicity (alone or in different combinations). Accordingly, many parameters must be tested during process development in order to maximize product purity and recovery, including resin and ligand types, conductivity, pH, gradient profiles, and the sequence of separation operations. The number of possible experimental conditions quickly becomes unmanageable. Although the range of suitable conditions can be narrowed based on experience, the time and cost of the work remain high even when using high-throughput laboratory automation. In contrast, chromatography modeling using inexpensive, parallelized computer hardware can provide expert knowledge, predicting conditions that achieve high purity and efficient recovery. The prediction of suitable conditions in silico reduces the number of empirical tests required and provides in-depth process understanding, which is recommended by regulatory authorities. In this article, we discuss the benefits and specific challenges of chromatography modeling. We describe the experimental characterization of chromatography devices and settings prior to modeling, such as the determination of column porosity. We also consider the challenges that must be overcome when models are set up and calibrated, including the cross-validation and verification of data-driven and hybrid (combined data-driven and mechanistic) models. This review will therefore support researchers intending to establish a chromatography modeling workflow in their laboratory.}, language = {en} } @article{EmontsBuyel2023, author = {Emonts, Jessica and Buyel, Johannes Felix}, title = {An overview of descriptors to capture protein properties - Tools and perspectives in the context of QSAR modeling}, series = {Computational and Structural Biotechnology Journal}, journal = {Computational and Structural Biotechnology Journal}, number = {21}, publisher = {Research Network of Computational and Structural Biotechnology}, address = {Gotenburg}, issn = {2001-0370 (online-ressource)}, doi = {10.1016/j.csbj.2023.05.022}, pages = {3234 -- 3247}, year = {2023}, abstract = {Proteins are important ingredients in food and feed, they are the active components of many pharmaceutical products, and they are necessary, in the form of enzymes, for the success of many technical processes. However, production can be challenging, especially when using heterologous host cells such as bacteria to express and assemble recombinant mammalian proteins. The manufacturability of proteins can be hindered by low solubility, a tendency to aggregate, or inefficient purification. Tools such as in silico protein engineering and models that predict separation criteria can overcome these issues but usually require the complex shape and surface properties of proteins to be represented by a small number of quantitative numeric values known as descriptors, as similarly used to capture the features of small molecules. Here, we review the current status of protein descriptors, especially for application in quantitative structure activity relationship (QSAR) models. First, we describe the complexity of proteins and the properties that descriptors must accommodate. Then we introduce descriptors of shape and surface properties that quantify the global and local features of proteins. Finally, we highlight the current limitations of protein descriptors and propose strategies for the derivation of novel protein descriptors that are more informative.}, language = {en} } @article{RieplPettrakFaulstichetal.2010, author = {Riepl, Herbert Matthias and Pettrak, J{\"u}rgen and Faulstich, Martin and Herrmann, Wolfgang Anton}, title = {Self metathesis of fatty alcohols and amines to provide monomers for polyester and polyamide products}, series = {Macromolecular Symposia}, volume = {293}, journal = {Macromolecular Symposia}, number = {1}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1521-3900 (eISSN)}, doi = {10.1002/masy.200900041}, pages = {39 -- 42}, year = {2010}, abstract = {Self metathesis of oleochemicals offers a variety of bifunctional compounds, that can be used as monomer for polymer production. Many precursors are in huge scales available, like oleic acid ester (biodiesel), oleyl alcohol (tensides), oleyl amines (tensides, lubricants). We show several ways to produce and separate and purify C18-α,ω-bifunctional compounds, using Grubbs 2nd Generation catalysts, starting from technical grade educts.}, language = {en} } @article{RakeEnningKurthetal.1994, author = {Rake, Heinrich and Enning, Manfred and Kurth, Johannes and Schr{\"o}der, Walter}, title = {Automatic uncoupler completes automation at the hump}, series = {RGI - Railway Gazette International}, volume = {150}, journal = {RGI - Railway Gazette International}, number = {6}, publisher = {Reed Business}, address = {Sutton}, issn = {0373-5346}, pages = {371 -- 374}, year = {1994}, language = {en} } @article{AsarStapenhorst2020, author = {Asar, Hande and Stapenhorst, Carolin}, title = {Zvi Hecker: Drawing on drawing}, series = {Archives of Design Research}, volume = {33}, journal = {Archives of Design Research}, number = {3}, publisher = {Korean Society of Design Science}, address = {Seongnam}, issn = {1226-8046}, doi = {10.15187/adr.2020.08.33.3.45}, pages = {45 -- 53}, year = {2020}, abstract = {Background: Architectural representation, nurtured by the interaction between design thinking and design action, is inherently multi-layered. However, the representation object cannot always reflect these layers. Therefore, it is claimed that these reflections and layerings can gain visibility through 'performativity in personal knowledge', which basically has a performative character. The specific layers of representation produced during the performativity in personal knowledge permit insights about the 'personal way of designing' [1]. Therefore, the question, 'how can these layered drawings be decomposed to understand the personal way of designing', can be defined as the beginning of the study. On the other hand, performativity in personal knowledge in architectural design is handled through the relationship between explicit and tacit knowledge and representational and non-representational theory. To discuss the practical dimension of these theoretical relations, Zvi Hecker's drawing of the Heinz-Galinski-School is examined as an example. The study aims to understand the relationships between the layers by decomposing a layered drawing analytically in order to exemplify personal ways of designing. Methods: The study is based on qualitative research methodologies. First, a model has been formed through theoretical readings to discuss the performativity in personal knowledge. This model is used to understand the layered representations and to research the personal way of designing. Thus, one drawing of Hecker's Heinz-Galinski-School project is chosen. Second, its layers are decomposed to detect and analyze diverse objects, which hint to different types of design tools and their application. Third, Zvi Hecker's statements of the design process are explained through the interview data [2] and other sources. The obtained data are compared with each other. Results: By decomposing the drawing, eleven layers are defined. These layers are used to understand the relation between the design idea and its representation. They can also be thought of as a reading system. In other words, a method to discuss Hecker's performativity in personal knowledge is developed. Furthermore, the layers and their interconnections are described in relation to Zvi Hecker's personal way of designing. Conclusions: It can be said that layered representations, which are associated with the multilayered structure of performativity in personal knowledge, form the personal way of designing.}, language = {en} } @article{StapenhorstZabekHildebrand2018, author = {Stapenhorst, Carolin and Zabek, Magdalena and Hildebrand, Linda}, title = {Communication process and information flow in the architectural planning context}, series = {Creativity game : theory and practice of spatial planning}, journal = {Creativity game : theory and practice of spatial planning}, number = {6}, publisher = {University of Ljubljana}, address = {Ljubljana}, doi = {10.15292/IU-CG.2018.06.066-073}, pages = {66 -- 73}, year = {2018}, abstract = {Against the background of growing data in everyday life, data processing tools become more powerful to deal with the increasing complexity in building design. The architectural planning process is offered a variety of new instruments to design, plan and communicate planning decisions. Ideally the access to information serves to secure and document the quality of the building and in the worst case, the increased data absorbs time by collection and processing without any benefit for the building and its user. Process models can illustrate the impact of information on the design- and planning process so that architect and planner can steer the process. This paper provides historic and contemporary models to visualize the architectural planning process and introduces means to describe today's situation consisting of stakeholders, events and instruments. It explains conceptions during Renaissance in contrast to models used in the second half of the 20th century. Contemporary models are discussed regarding their value against the background of increasing computation in the building process.}, language = {en} } @article{StapenhorstDutto2016, author = {Stapenhorst, Carolin and Dutto, Andrea Alberto}, title = {Notes on conceptual learning in architecture}, series = {Cartha - The Form of Form}, journal = {Cartha - The Form of Form}, address = {Basel}, year = {2016}, language = {en} } @article{KohlKraemerFohryetal.2024, author = {Kohl, Philipp and Kr{\"a}mer, Yoka and Fohry, Claudia and Kraft, Bodo}, title = {Scoping review of active learning strategies and their evaluation environments for entity recognition tasks}, series = {Deep learning theory and applications}, journal = {Deep learning theory and applications}, editor = {Fred, Ana and Hadjali, Allel and Gusikhin, Oleg and Sansone, Carlo}, publisher = {Springer}, address = {Cham}, isbn = {978-3-031-66694-0 (online ISBN)}, doi = {10.1007/978-3-031-66694-0_6}, pages = {84 -- 106}, year = {2024}, abstract = {We conducted a scoping review for active learning in the domain of natural language processing (NLP), which we summarize in accordance with the PRISMA-ScR guidelines as follows: Objective: Identify active learning strategies that were proposed for entity recognition and their evaluation environments (datasets, metrics, hardware, execution time). Design: We used Scopus and ACM as our search engines. We compared the results with two literature surveys to assess the search quality. We included peer-reviewed English publications introducing or comparing active learning strategies for entity recognition. Results: We analyzed 62 relevant papers and identified 106 active learning strategies. We grouped them into three categories: exploitation-based (60x), exploration-based (14x), and hybrid strategies (32x). We found that all studies used the F1-score as an evaluation metric. Information about hardware (6x) and execution time (13x) was only occasionally included. The 62 papers used 57 different datasets to evaluate their respective strategies. Most datasets contained newspaper articles or biomedical/medical data. Our analysis revealed that 26 out of 57 datasets are publicly accessible. Conclusion: Numerous active learning strategies have been identified, along with significant open questions that still need to be addressed. Researchers and practitioners face difficulties when making data-driven decisions about which active learning strategy to adopt. Conducting comprehensive empirical comparisons using the evaluation environment proposed in this study could help establish best practices in the domain.}, language = {en} } @article{MikuckiSchulerDigeletal.2023, author = {Mikucki, Jill Ann and Schuler, C. G. and Digel, Ilya and Kowalski, Julia and Tuttle, M. J. and Chua, Michelle and Davis, R. and Purcell, Alicia and Ghosh, D. and Francke, G. and Feldmann, M. and Espe, C. and Heinen, Dirk and Dachwald, Bernd and Clemens, Joachim and Lyons, W. B. and Tulaczyk, S.}, title = {Field-Based planetary protection operations for melt probes: validation of clean access into the blood falls, antarctica, englacial ecosystem}, series = {Astrobiology}, volume = {23}, journal = {Astrobiology}, number = {11}, publisher = {Liebert}, address = {New York, NY}, issn = {1557-8070 (online)}, doi = {10.1089/ast.2021.0102}, pages = {1165 -- 1178}, year = {2023}, abstract = {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.}, language = {en} } @article{AkimbekovDigelTastambeketal.2024, author = {Akimbekov, Nuraly S. and Digel, Ilya and Tastambek, Kuanysh T. and Kozhahmetova, Marzhan and Sherelkhan, Dinara K. and Tauanov, Zhandos}, title = {Hydrogenotrophic methanogenesis in coal-bearing environments: Methane production, carbon sequestration, and hydrogen availability}, series = {International Journal of Hydrogen Energy}, volume = {52}, journal = {International Journal of Hydrogen Energy}, number = {Part D}, publisher = {Elsevier}, address = {New York}, issn = {1879-3487 (online)}, doi = {10.1016/j.ijhydene.2023.09.223}, pages = {1264 -- 1277}, year = {2024}, abstract = {Methane is a valuable energy source helping to mitigate the growing energy demand worldwide. However, as a potent greenhouse gas, it has also gained additional attention due to its environmental impacts. The biological production of methane is performed primarily hydrogenotrophically from H2 and CO2 by methanogenic archaea. Hydrogenotrophic methanogenesis also represents a great interest with respect to carbon re-cycling and H2 storage. The most significant carbon source, extremely rich in complex organic matter for microbial degradation and biogenic methane production, is coal. Although interest in enhanced microbial coalbed methane production is continuously increasing globally, limited knowledge exists regarding the exact origins of the coalbed methane and the associated microbial communities, including hydrogenotrophic methanogens. Here, we give an overview of hydrogenotrophic methanogens in coal beds and related environments in terms of their energy production mechanisms, unique metabolic pathways, and associated ecological functions.}, language = {en} }