@inproceedings{DuongJungFrotscheretal.2016, author = {Duong, Minh Tuan and Jung, Alexander and Frotscher, Ralf and Staat, Manfred}, title = {A 3D electromechanical FEM-based model for cardiac tissue}, series = {ECCOMAS Congress 2016, VII European Congress on Computational Methods in Applied Sciences and Engineering. Crete Island, Greece, 5-10 June 2016}, booktitle = {ECCOMAS Congress 2016, VII European Congress on Computational Methods in Applied Sciences and Engineering. Crete Island, Greece, 5-10 June 2016}, editor = {Papadrakakis, M.}, pages = {13 S.}, year = {2016}, language = {en} } @inproceedings{BhattaraiFrotscherSoraetal.2014, author = {Bhattarai, Aroj and Frotscher, Ralf and Sora, M.-C. and Staat, Manfred}, title = {A 3D finite element model of the female pelvic floor for the reconstruction of urinary incontinence}, series = {11th World Congress on Computational Mechanics (WCCM XI) ; 5th European Conference on Computational Mechanics (ECCM V) ; 6th European Conference on Computational Fluid Dynamics (ECFD VI) ; July 20-25, 2014, Barcelona}, booktitle = {11th World Congress on Computational Mechanics (WCCM XI) ; 5th European Conference on Computational Mechanics (ECCM V) ; 6th European Conference on Computational Fluid Dynamics (ECFD VI) ; July 20-25, 2014, Barcelona}, editor = {Onate, E.}, organization = {World Congress on Computational Mechanics <11, 2014, Barcelona>}, pages = {1 -- 12}, year = {2014}, language = {en} } @inproceedings{RabnerShacham2006, author = {Rabner, Arthur and Shacham, Yosi}, title = {A concept for a sensitive micro total analysis system for high throughput fluorescence imaging}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:a96-opus-1456}, year = {2006}, abstract = {This paper discusses possible methods for on-chip fluorescent imaging for integrated bio-sensors. The integration of optical and electro-optical accessories, according to suggested methods, can improve the performance of fluorescence imaging. It can boost the signal to background ratio by a few orders of magnitudes in comparison to conventional discrete setups. The methods that are present in this paper are oriented towards building reproducible arrays for high-throughput micro total analysis systems (µTAS). The first method relates to side illumination of the fluorescent material placed into microcompartments of the lab-on-chip. Its significance is in high utilization of excitation energy for low concentration of fluorescent material. The utilization of a transparent µLED chip, for the second method, allows the placement of the excitation light sources on the same optical axis with emission detector, such that the excitation and emission rays are directed controversly. The third method presents a spatial filtering of the excitation background.}, subject = {Biosensor}, language = {en} } @inproceedings{DigelDachwaldArtmannetal.2009, author = {Digel, Ilya and Dachwald, Bernd and Artmann, Gerhard and Linder, Peter and Funke, O.}, title = {A concept of a probe for particle analysis and life detection in icy environments}, year = {2009}, abstract = {A melting probe equipped with autofluorescence-based detection system combined with a light scattering unit, and, optionally, with a microarray chip would be ideally suited to probe icy environments like Europa's ice layer as well as the polar ice layers of Earth and Mars for recent and extinct live.}, subject = {Sonde}, language = {en} } @article{SildatkeKarwanniKraftetal.2023, author = {Sildatke, Michael and Karwanni, Hendrik and Kraft, Bodo and Z{\"u}ndorf, Albert}, title = {A distributed microservice architecture pattern for the automated generation of information extraction pipelines}, series = {SN Computer Science}, journal = {SN Computer Science}, number = {4, Article number: 833}, publisher = {Springer Singapore}, address = {Singapore}, issn = {2661-8907}, doi = {10.1007/s42979-023-02256-4}, pages = {19 Seiten}, year = {2023}, abstract = {Companies often build their businesses based on product information and therefore try to automate the process of information extraction (IE). Since the information source is usually heterogeneous and non-standardized, classic extract, transform, load techniques reach their limits. Hence, companies must implement the newest findings from research to tackle the challenges of process automation. They require a flexible and robust system that is extendable and ensures the optimal processing of the different document types. This paper provides a distributed microservice architecture pattern that enables the automated generation of IE pipelines. Since their optimal design is individual for each input document, the system ensures the ad-hoc generation of pipelines depending on specific document characteristics at runtime. Furthermore, it introduces the automated quality determination of each available pipeline and controls the integration of new microservices based on their impact on the business value. The introduced system enables fast prototyping of the newest approaches from research and supports companies in automating their IE processes. Based on the automated quality determination, it ensures that the generated pipelines always meet defined business requirements when they come into productive use.}, language = {en} } @inproceedings{DuongStaat2014, author = {Duong, Minh Tuan and Staat, Manfred}, title = {A face-based smoothed finite element method for hyperelastic models and tissue growth}, series = {11th World Congress on Computational Mechanics (WCCM XI) ; 5th European Conference on Computational Mechanics (ECCM V) ; 6th European Conference on Computational Fluid Dynamics (ECFD VI) ; July 20-25, 2014, Barcelona}, booktitle = {11th World Congress on Computational Mechanics (WCCM XI) ; 5th European Conference on Computational Mechanics (ECCM V) ; 6th European Conference on Computational Fluid Dynamics (ECFD VI) ; July 20-25, 2014, Barcelona}, editor = {Onate, E.}, organization = {World Congress on Computational Mechanics <11, 2014, Barcelona>}, pages = {1 -- 12}, year = {2014}, language = {en} } @inproceedings{TranStaatStavroulakis2014, author = {Tran, Ngoc Trinh and Staat, Manfred and Stavroulakis, G. E.}, title = {A multicriteria method for truss optimization}, series = {11th World Congress on Computational Mechanics (WCCM XI) ; 5th European Conference on Computational Mechanics (ECCM V) ; 6th European Conference on Computational Fluid Dynamics (ECFD VI) ; July 20-25, 2014, Barcelona}, booktitle = {11th World Congress on Computational Mechanics (WCCM XI) ; 5th European Conference on Computational Mechanics (ECCM V) ; 6th European Conference on Computational Fluid Dynamics (ECFD VI) ; July 20-25, 2014, Barcelona}, editor = {Onate, E.}, organization = {World Congress on Computational Mechanics <11, 2014, Barcelona>}, pages = {1 -- 12}, year = {2014}, language = {en} } @article{KuehnHaugnerStaatetal.2004, author = {K{\"u}hn, Raoul-Roman and Haugner, Werner and Staat, Manfred and Sponagel, Stefan}, title = {A Two Phase Mixture Model based on Bone Observation}, year = {2004}, abstract = {An optimization method is developed to describe the mechanical behaviour of the human cancellous bone. The method is based on a mixture theory. A careful observation of the behaviour of the bone material leads to the hypothesis that the bone density is controlled by the principal stress trajectories (Wolff's law). The basic idea of the developed method is the coupling of a scalar value via an eigenvalue problem to the principal stress trajectories. On the one hand this theory will permit a prediction of the reaction of the biological bone structure after the implantation of a prosthesis, on the other hand it may be useful in engineering optimization problems. An analytical example shows its efficiency.}, subject = {Knochen}, language = {en} } @article{ZhubanovaAknazarovMansurovetal.2010, author = {Zhubanova, Azhar A. and Aknazarov, S. K. and Mansurov, Zulkhair and Digel, Ilya and Kozhalakova, A. A. and Akimbekov, Nuraly Shardarbekovich and O'Heras, Carlos and Tazhibayeva, S. and Artmann, Gerhard and Temiz Artmann, Ayseg{\"u}l}, title = {Adsorption of bacterial Lipopolysaccharides and blood plasma proteins on modified carbonized materials}, year = {2010}, abstract = {Bacterial lipopolysaccharides (endotoxins) show strong biological effects at very low concentrations in human beings and many animals when entering the blood stream. These include affecting structure and function of organs and cells, changing metabolic functions, raising body temperature, triggering the coagulation cascade, modifying hemodynamics and causing septic shock. Because of this toxicity, the removal of even minute amounts is essential for safe parenteral administration of drugs and also for septic shock patients' care. The absence of a general method for endotoxin removal from liquid interfaces urgently requires finding new methods and materials to overcome this gap. Nanostructured carbonized plant parts is a promising material that showed good adsorption properties due to its vast pore network and high surface area. The aim of this study was comparative measurement of endotoxin- and blood proteins-related adsorption rate and adsorption capacity for different carboneous materials produced at different temperatures and under different surface modifications. As a main surface modificator, positively cbarged polymer, polyethileneimine (PEl) was used. Activated carbon materials showed good adsorption properties for LPS and some proteins used in the experiments. During the batch experiments, several techniques (dust removal, autoclaving) were used and optimized for improving the material's adsorption behavior. Also, with the results obtained it was possible to differentiate the materials according to their adsorption capacity and kinetic characteristics. Modification of the surface apparently has not affected hemoglobin binding to the adsorbent's surface. Obtained adsorption isotherms can be used as a powerful tool for designing of future column-based setups for blood purification from LPS, which is especially important for septic shock treatment.}, subject = {Kohlenstofffaser}, language = {en} } @article{KaulenSchwabedalSchneideretal.2022, author = {Kaulen, Lars and Schwabedal, Justus T. C. and Schneider, Jules and Ritter, Philipp and Bialonski, Stephan}, title = {Advanced sleep spindle identification with neural networks}, series = {Scientific Reports}, volume = {12}, journal = {Scientific Reports}, number = {Article number: 7686}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-022-11210-y}, pages = {1 -- 10}, year = {2022}, abstract = {Sleep spindles are neurophysiological phenomena that appear to be linked to memory formation and other functions of the central nervous system, and that can be observed in electroencephalographic recordings (EEG) during sleep. Manually identified spindle annotations in EEG recordings suffer from substantial intra- and inter-rater variability, even if raters have been highly trained, which reduces the reliability of spindle measures as a research and diagnostic tool. The Massive Online Data Annotation (MODA) project has recently addressed this problem by forming a consensus from multiple such rating experts, thus providing a corpus of spindle annotations of enhanced quality. Based on this dataset, we present a U-Net-type deep neural network model to automatically detect sleep spindles. Our model's performance exceeds that of the state-of-the-art detector and of most experts in the MODA dataset. We observed improved detection accuracy in subjects of all ages, including older individuals whose spindles are particularly challenging to detect reliably. Our results underline the potential of automated methods to do repetitive cumbersome tasks with super-human performance.}, language = {en} } @inproceedings{SchoeningAbdelghani2009, author = {Sch{\"o}ning, Michael Josef and Abdelghani, Adnane}, title = {Advancements in Nanotechnology and Microelectronics (ANM '09) <2009, Tunisia>: Proceedings book ; Tunisia, November, 13 \& 14, 2009 / Humboldt Kolleg. Ed. by Michael J. Sch{\"o}ning ; Adnane Abdelghani}, organization = {Humboldt-Kolleg Advancements in Nanotechnology and Microelectronics (ANM '09) <2009, Tunisia>}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:a96-opus-3113}, year = {2009}, abstract = {The ANM'09 multi-disciplinary scientific program includes topics in the fields of "Nanotechnology and Microelectronics" ranging from "Bio/Micro/Nano Materials and Interfacing" aspects, "Chemical and Bio-Sensors", "Magnetic and Superconducting Devices", "MEMS and Microfluidics" over "Theoretical Aspects, Methods and Modelling" up to the important bridging "Academics meet Industry".}, subject = {Nanopartikel}, language = {en} } @article{BassamArtmannHescheleretal.2011, author = {Bassam, Rasha and Artmann, Gerhard and Hescheler, J{\"u}rgen and Graef, T. and Temiz Artmann, Ayseg{\"u}l and Porst, Dariusz and Linder, Peter and Kayser, Peter and Arinkin, Vladimir and Gossmann, Matthias and Digel, Ilya}, title = {Alterations in human hemoglobin structure related to red blood cell storage}, year = {2011}, abstract = {The importance of the availability of stored blood or blood cells, respectively, for urgent transfusion cannot be overestimated. Nowadays, blood storage becomes even more important since blood products are used for epidemiological studies, bio-technical research or banked for transfusion purposes. Thus blood samples must not only be processed, stored, and shipped to preserve their efficacy and safety, but also all parameters of storage must be recorded and reported for Quality Assurance. Therefore, blood banks and clinical research facilities are seeking more accurate, automated means for blood storage and blood processing.}, subject = {H{\"a}moglobin}, language = {en} } @article{VuStaat2004, author = {Vu, Duc-Khoi and Staat, Manfred}, title = {An algorithm for shakedown analysis of structure with temperature dependent yield stress}, year = {2004}, abstract = {This work is an attempt to answer the question: How to use convex programming in shakedown analysis of structures made of materials with temperature-dependent properties. Based on recently established shakedown theorems and formulations, a dual relationship between upper and lower bounds of the shakedown limit load is found, an algorithmfor shakedown analysis is proposed. While the original problem is neither convex nor concave, the algorithm presented here has the advantage of employing convex programming tools.}, subject = {Einspielen }, language = {en} } @article{BogoyavlenskiyDigelBerezin1997, author = {Bogoyavlenskiy, A. P. and Digel, Ilya and Berezin, V. E.}, title = {Assessment of dot-blot ELISA sensitivity on membrane sorbent using various peroxidase substrates}, year = {1997}, abstract = {The sensitivity of the peroxidase reaction in dot-blot ELISA significantly depends on the substrate. The highest sensitivity is observed using benzidine and diamine- phenol combinations as the substrates due to the reaction of the coupled oxidation (NADI)}, subject = {Enzyme-linked immunosorbent assay}, language = {en} } @article{GriegerSchwabedalWendeletal.2021, author = {Grieger, Niklas and Schwabedal, Justus T. C. and Wendel, Stefanie and Ritze, Yvonne and Bialonski, Stephan}, title = {Automated scoring of pre-REM sleep in mice with deep learning}, series = {Scientific Reports}, volume = {11}, journal = {Scientific Reports}, number = {Art. 12245}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-021-91286-0}, year = {2021}, abstract = {Reliable automation of the labor-intensive manual task of scoring animal sleep can facilitate the analysis of long-term sleep studies. In recent years, deep-learning-based systems, which learn optimal features from the data, increased scoring accuracies for the classical sleep stages of Wake, REM, and Non-REM. Meanwhile, it has been recognized that the statistics of transitional stages such as pre-REM, found between Non-REM and REM, may hold additional insight into the physiology of sleep and are now under vivid investigation. We propose a classification system based on a simple neural network architecture that scores the classical stages as well as pre-REM sleep in mice. When restricted to the classical stages, the optimized network showed state-of-the-art classification performance with an out-of-sample F1 score of 0.95 in male C57BL/6J mice. When unrestricted, the network showed lower F1 scores on pre-REM (0.5) compared to the classical stages. The result is comparable to previous attempts to score transitional stages in other species such as transition sleep in rats or N1 sleep in humans. Nevertheless, we observed that the sequence of predictions including pre-REM typically transitioned from Non-REM to REM reflecting sleep dynamics observed by human scorers. Our findings provide further evidence for the difficulty of scoring transitional sleep stages, likely because such stages of sleep are under-represented in typical data sets or show large inter-scorer variability. We further provide our source code and an online platform to run predictions with our trained network.}, language = {en} } @article{DigelAkimbekovRogachevetal.2023, author = {Digel, Ilya and Akimbekov, Nuraly and Rogachev, Evgeniy and Pogorelova, Natalia}, title = {Bacterial cellulose produced by Medusomyces gisevii on glucose and sucrose: biosynthesis and structural properties}, series = {Cellulose}, journal = {Cellulose}, publisher = {Springer Science + Business Media}, address = {Dordrecht}, issn = {1572-882X (Online)}, doi = {10.1007/s10570-023-05592-z}, pages = {15 Seiten}, year = {2023}, abstract = {In this work, the effects of carbon sources and culture media on the production and structural properties of bacterial cellulose (BC) synthesized by Medusomyces gisevii have been studied. The culture medium was composed of different initial concentrations of glucose or sucrose dissolved in 0.4\% extract of plain green tea. Parameters of the culture media (titratable acidity, substrate conversion degree etc.) were monitored daily for 20 days of cultivation. The BC pellicles produced on different carbon sources were characterized in terms of biomass yield, crystallinity and morphology by field emission scanning electron microscopy (FE-SEM), atomic force microscopy and X-ray diffraction. Our results showed that Medusomyces gisevii had higher BC yields in media with sugar concentrations close to 10 g L-1 after a 18-20 days incubation period. Glucose in general lead to a higher BC yield (173 g L-1) compared to sucrose (163.5 g L-1). The BC crystallinity degree and surface roughness were higher in the samples synthetized from sucrose. Obtained FE-SEM micrographs show that the BC pellicles synthesized in the sucrose media contained densely packed tangles of cellulose fibrils whereas the BC produced in the glucose media displayed rather linear geometry of the BC fibrils without noticeable aggregates.}, language = {en} } @article{Staat2000, author = {Staat, Manfred}, title = {Basis Reduction for the Shakedown Problem for Bounded Kinematic Hardening Material}, year = {2000}, abstract = {Limit and shakedown analysis are effective methods for assessing the load carrying capacity of a given structure. The elasto-plastic behavior of the structure subjected to loads varying in a given load domain is characterized by the shakedown load factor, defined as the maximum factor which satisfies the sufficient conditions stated in the corresponding static shakedown theorem. The finite element dicretization of the problem may lead to very large convex optimization. For the effective solution a basis reduction method has been developed that makes use of the special problem structure for perfectly plastic material. The paper proposes a modified basis reduction method for direct application to the two-surface plasticity model of bounded kinematic hardening material. The considered numerical examples show an enlargement of the load carrying capacity due to bounded hardening.}, subject = {Finite-Elemente-Methode}, language = {en} } @inproceedings{ArtmannDigelLinderetal.2011, author = {Artmann, Gerhard and Digel, Ilya and Linder, Peter and Temiz Artmann, Ayseg{\"u}l}, title = {Biophysical and Engineering Contributions to Plant Research}, year = {2011}, abstract = {Tests with palm tree leaves have just started yet and scan data are in the process to be analyzed. The final goal of future project for palm tree gender and species recognition will be to develop optical scanning technology to be applied to date palm tree leaves for in-situ screening purposes. Depending on the software used and the particular requirements of the users the technology potentially shall be able to identify palm tree diseases, palm tree gender, and species of young date palm trees by scanning leaves.}, subject = {Pflanzenphysiologie}, language = {en} } @article{OliveiraMolinnusBegingetal.2021, author = {Oliveira, Danilo A. and Molinnus, Denise and Beging, Stefan and Siqueira Jr, Jos{\´e} R. and Sch{\"o}ning, Michael Josef}, title = {Biosensor Based on Self-Assembled Films of Graphene Oxide and Polyaniline Using a Field-Effect Device Platform}, series = {physica status solidi (a) applications and materials science}, volume = {218}, journal = {physica status solidi (a) applications and materials science}, number = {13}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1862-6319}, doi = {10.1002/pssa.202000747}, pages = {1 -- 9}, year = {2021}, abstract = {A new functionalization method to modify capacitive electrolyte-insulator-semiconductor (EIS) structures with nanofilms is presented. Layers of polyallylamine hydrochloride (PAH) and graphene oxide (GO) with the compound polyaniline:poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PANI:PAAMPSA) are deposited onto a p-Si/SiO2 chip using the layer-by-layer technique (LbL). Two different enzymes (urease and penicillinase) are separately immobilized on top of a five-bilayer stack of the PAH:GO/PANI:PAAMPSA-modified EIS chip, forming a biosensor for detection of urea and penicillin, respectively. Electrochemical characterization is performed by constant capacitance (ConCap) measurements, and the film morphology is characterized by atomic force microscopy (AFM) and scanning electron microscopy (SEM). An increase in the average sensitivity of the modified biosensors (EIS-nanofilm-enzyme) of around 15\% is found in relation to sensors, only carrying the enzyme but without the nanofilm (EIS-enzyme). In this sense, the nanofilm acts as a stable bioreceptor onto the EIS chip improving the output signal in terms of sensitivity and stability.}, language = {en} } @inproceedings{LeiMulchandaniChenetal.2006, author = {Lei, Yu and Mulchandani, Priti and Chen, Wilfred and Mulchandani, Ashok}, title = {Biosensor for direct determination of fenitrothion and EPN using recombinant Pseudomonas putida JS444 with surface expressed organophosphorus hydrolase. 1. modified clark oxygen electrode}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:a96-opus-1573}, year = {2006}, abstract = {This paper reports a first microbial biosensor for rapid and cost-effective determination of organophosphorus pesticides fenitrothion and EPN. The biosensor consisted of recombinant PNP-degrading/oxidizing bacteria Pseudomonas putida JS444 anchoring and displaying organophosphorus hydrolase (OPH) on its cell surface as biological sensing element and a dissolved oxygen electrode as the transducer. Surfaceexpressed OPH catalyzed the hydrolysis of fenitrothion and EPN to release 3-methyl-4-nitrophenol and p-nitrophenol, respectively, which were oxidized by the enzymatic machinery of Pseudomonas putida JS444 to carbon dioxide while consuming oxygen, which was measured and correlated to the concentration of organophosphates. Under the optimum operating conditions, the biosensor was able to measure as low as 277 ppb of fenitrothion and 1.6 ppm of EPN without interference from phenolic compounds and other commonly used pesticides such as carbamate pesticides, triazine herbicides and organophosphate pesticides without nitrophenyl substituent. The applicability of the biosensor to lake water was also demonstrated.}, subject = {Biosensor}, language = {en} }