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    <title language="eng">Machine learning and complex network analysis of drug effects on neuronal microelectrode biosensor data</title>
    <abstract language="eng">Biosensors, such as microelectrode arrays that record in vitro neuronal activity, provide powerful platforms for studying neuroactive substances. This study presents a machine learning workflow to analyze drug-induced changes in neuronal biosensor data using complex network measures from graph theory. Microelectrode array recordings of neuronal networks exposed to bicuculline, a GABA&#13;
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  receptor antagonist known to induce hypersynchrony, demonstrated the workflow’s ability to detect and characterize pharmacological effects. The workflow integrates network-based features with synchrony, optimizing preprocessing parameters, including spike train bin sizes, segmentation window sizes, and correlation methods. It achieved high classification accuracy (AUC up to 90%) and used Shapley Additive Explanations to interpret feature importance rankings. Significant reductions in network complexity and segregation, hallmarks of epileptiform activity induced by bicuculline, were revealed. While bicuculline’s effects are well established, this framework is designed to be broadly applicable for detecting both strong and subtle network alterations induced by neuroactive compounds. The results demonstrate the potential of this methodology for advancing biosensor applications in neuropharmacology and drug discovery.</abstract>
    <parentTitle language="eng">Scientific Reports</parentTitle>
    <identifier type="issn">2045-2322</identifier>
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    <author>Manuel Ciba</author>
    <author>Marc Petzold</author>
    <author>Caroline L. Alves</author>
    <author>Francisco A. Rodrigues</author>
    <author>Yasuhiko Jimbo</author>
    <author>Christiane Thielemann</author>
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      <value>Maschinelles Lernen</value>
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    <title language="eng">Revealing patterns in major depressive disorder with machine learning and networks</title>
    <abstract language="eng">Major depressive disorder (MDD) is a multifaceted condition that affects millions of people worldwide and is a leading cause of disability. There is an urgent need for an automated and objective method to detect MDD due to the limitations of traditional diagnostic approaches. In this paper, we propose a methodology based on machine and deep learning to classify patients with MDD and identify altered functional connectivity patterns from EEG data. We compare several connectivity metrics and machine learning algorithms. Complex network measures are used to identify structural brain abnormalities in MDD. Using Spearman correlation for network construction and the SVM classifier, we verify that it is possible to identify MDD patients with high accuracy, exceeding literature results. The SHAP (SHAPley Additive Explanations) summary plot highlights the importance of C4-F8 connections and also reveals dysfunction in certain brain areas and hyperconnectivity in others. Despite the lower performance of the complex network measures for the classification problem, assortativity was found to be a promising biomarker. Our findings suggest that understanding and diagnosing MDD may be aided by the use of machine learning methods and complex networks.</abstract>
    <parentTitle language="eng">Chaos, Solitons &amp; Fractals</parentTitle>
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    <author>Loriz Francisco Sallum</author>
    <author>Caroline L. Alves</author>
    <author>Thaise Graziele L de O Toutain</author>
    <author>Joel Augusto Moura Porto</author>
    <author>Christiane Thielemann</author>
    <author>Francisco A. Rodrigues</author>
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      <value>Depression</value>
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      <language>deu</language>
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      <value>Maschinelles Lernen</value>
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      <value>Elektroencephalographie</value>
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    <title language="eng">Radiation measurements in the stratosphere by the balloon experiment ASTRABAX</title>
    <abstract language="eng">Stratospheric balloons are a platform of choice for meteorology, climate and atmospheric research, offering some advantages over sounding rockets and satellites. The Aschaffenburg Stratospheric Balloon Experiment (ASTRABAX)&#13;
carries out experiments on material treatments and life sciences under the extreme radiation exposures at high altitude. The pioneer ASTRABAX flight took place mid of October 2024 in Germany. Measurements examined the UV spectral region by a miniature spectrometer and captured secondary cosmic rays employing a Geiger counter. Additional experiments assessed irradiation effects on polydopamine X-ray mirror coatings. The platform also carried samples of biological cells to evaluate effects of exposure to low-dose irradiation of high-energy particles, gamma rays and UV radiation simultaneously. Biological experiments under such realistic conditions are relevant for genetic research on Earth, for human space flights as well as for the understanding of astrobiological processes.</abstract>
    <parentTitle language="eng">EUV and X-ray Optics: Synergy between Laboratory and Space IX</parentTitle>
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    <title language="eng">Human cerebral organoids model tumor infiltration and migration supported by astrocytes in an autologous setting</title>
    <abstract language="eng">SummaryEfforts to achieve precise and efficient tumor targeting of highly malignant brain tumors are constrained by the dearth of appropriate models to study the effects and potential side effects of radiation, chemotherapy, and immunotherapy on the most complex human organ, the brain. We established a cerebral organoid model of brain tumorigenesis in an autologous setting by overexpressing c-MYC as one of the most common oncogenes in brain tumors. GFP+/c-MYChighcells were isolated from tumor organoids and used in two different culture approaches: assembloids comprising of a normal cerebral organoid with a GFP+/c-MYChightumor sphere and co-culture of cerebral organoid slices at air-liquid interface with GFP+/c-MYChighcells. GFP+/c-MYChighcells used in both approaches exhibited tumor-like properties, including overexpression of the c-MYC oncogene, high proliferative and invasive potential, and an immature phenotype as evidenced by increased expression of Ki-67, VIM, and CD133. Organoids and organoid slices served as suitable scaffolds for infiltrating tumor-like cells. Using our highly reproducible and powerful model system that allows long-term culture, we demonstrated that the migratory and infiltrative potential of tumor-like cells is shaped by the environment in which glia cells provide support to tumor-like cells.</abstract>
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    <abstract language="deu">Mit dem Aschaffenburger Stratosphären-Ballon-Experiment („ASTRABAX“) werden Experimente zu Material- und Biowissenschaften unter extremer Strahlungsexposition in großer Höhe durchgeführt. Der erste von drei geplanten Ballonflügen startete Mitte Oktober 2024 im norddeutschen Bad Pyrmont und erreichte eine Flughöhe von fast 35 km. Der Schwerpunkt der&#13;
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    <abstract language="mul">Poster</abstract>
    <parentTitle language="deu">DGaO-Proceedings</parentTitle>
    <identifier type="url">https://www.dgao-proceedings.de/abstract/abstract_only.php?id=3181</identifier>
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    <author>Thorsten Döhring</author>
    <author>Jan Pregler</author>
    <author>Lucia Krivanekova</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Stratosphärenballon</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>kosmische Strahlung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>ultraviolette Strahlung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Spektrometer</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Stratosphären-Ballon</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Kosmische Strahlung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Röntgenspiegel</value>
    </subject>
    <collection role="institutes" number="">Internationales Technisches Vertriebsmanagement (Bachelor)</collection>
    <collection role="institutes" number="">Angewandte Forschung in den Ingenieurwissenschaften (Master)</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/2572/DGaO_2025_Poster_ASTRABAX_4.pdf</file>
  </doc>
  <doc>
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    <pageFirst>1</pageFirst>
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    <edition/>
    <issue>126</issue>
    <volume>2025</volume>
    <type>conferenceobject</type>
    <publisherName>DGaO</publisherName>
    <publisherPlace/>
    <creatingCorporation>TH Aschaffenburg</creatingCorporation>
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    <completedDate>2025-10-04</completedDate>
    <publishedDate>2025-09-30</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Strahlungsmessungen beim Erstflug des Stratosphärenballon-Experiments ASTRABAX</title>
    <abstract language="deu">Der erste von drei geplanten Ballonflügen beim Aschaffenburger Stratosphären-&#13;
Ballon-Experiment („ASTRABAX“) startete im Oktober 2024 in Bad Pyrmont und&#13;
erreichte eine Flughöhe von fast 35 km. Der Schwerpunkt der physikalischen&#13;
Experimente lag auf der Vermessung des UV-C-Spektralbereichs mit einem&#13;
Miniatur-Spektrometer und der Strahlungsdosimetrie mit einem Geigerzähler.</abstract>
    <parentTitle language="deu">DGaO-Proceedings</parentTitle>
    <identifier type="issn">1614-8436</identifier>
    <identifier type="url">https://www.dgao-proceedings.de/download/126/126_p6.pdf</identifier>
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    <author>Thorsten Döhring</author>
    <author>Jan Pregler</author>
    <author>Lucia Krivanekova</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Stratosphärenballon</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>kosmische Strahlung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Ultraviolet</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Atmosphäre</value>
    </subject>
    <collection role="institutes" number="">Internationales Technisches Vertriebsmanagement (Bachelor)</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/2651/126_p6.pdf</file>
  </doc>
  <doc>
    <id>2679</id>
    <completedYear>2025</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>preprint</type>
    <publisherName>Springer Science and Business Media LLC</publisherName>
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    <belongsToBibliography>0</belongsToBibliography>
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    <title language="eng">Decoding Dystonia: unveiling neural patterns with interpretable EEG-Based Machine Learning</title>
    <abstract language="eng">Dystonia has a multifaceted and complex pathogenesis. Current diagnostic proce-dures, which focus primarily on clinical signs, may lack accuracy due to the variable presentationsof different dystonia types. There is a need for objective, interpretable, and non-invasive diagnostictools. This study aims to develop an interpretable electroencephalography (EEG)-basedmachine learning (ML) and deep learning (DL) approach to distinguish between focal upper limbdystonia (ULD), cervical dystonia (CD), and healthy controls (HC). EEG data were recorded during resting-state, writing-from-memory, and finger-tapping tasks. The EEG signals were segmented into windows to generate connectivity matricesusing various pairwise correlation metrics. Machine learning models were trained to classify thegroups, with performance evaluated using accuracy and area under the curve (AUC) metrics. Our approach achieved accuracy and AUC scores close to 100%. Transfer entropyemerged as the most effective connectivity metric, revealing altered brain connections in dystonia.Complex network measures outperformed traditional EEG features, highlighting the relevance offunctional connectivity. Resting-state EEG showed the highest classification performance for ULD,suggesting strong diagnostic potential. Conclusions: This study provides the first machine learning-based comparison between differenttypes of dystonia, introduces novel cervical dystonia EEG data, and yields medically interpretableinsights into altered brain connectivity. The findings enhance our understanding of dystonia and support using EEG as alow-cost, interpretable tool for diagnosing and developing brain-machine interfaces.</abstract>
    <identifier type="doi">https://doi.org/10.21203/rs.3.rs-7483388/v1</identifier>
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Current diagnostic proce-dures, which focus primarily on clinical signs, may lack accuracy due to the variable presentationsof different dystonia types. There is a need for objective, interpretable, and non-invasive diagnostictools. This study aims to develop an interpretable electroencephalography (EEG)-basedmachine learning (ML) and deep learning (DL) approach to distinguish between focal upper limbdystonia (ULD), cervical dystonia (CD), and healthy controls (HC). EEG data were recorded during resting-state, writing-from-memory, and finger-tapping tasks. The EEG signals were segmented into windows to generate connectivity matricesusing various pairwise correlation metrics. Machine learning models were trained to classify thegroups, with performance evaluated using accuracy and area under the curve (AUC) metrics.  Our approach achieved accuracy and AUC scores close to 100%. Transfer entropyemerged as the most effective connectivity metric, revealing altered brain connections in dystonia.Complex network measures outperformed traditional EEG features, highlighting the relevance offunctional connectivity. Resting-state EEG showed the highest classification performance for ULD,suggesting strong diagnostic potential. Conclusions: This study provides the first machine learning-based comparison between differenttypes of dystonia, introduces novel cervical dystonia EEG data, and yields medically interpretableinsights into altered brain connectivity. 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    <author>Caroline Alves</author>
    <author>Artur José Marques Paulo</author>
    <author>Danilo Donizete de Faria</author>
    <author>João Ricardo Sato</author>
    <author>Vanderci Borges</author>
    <author>Sonia de Azevedo Silva</author>
    <author>Henrique Ballalai Ferraz</author>
    <author>Francisco A. Rodrigues</author>
    <author>Christiane Thielemann</author>
    <author>Michael Moeckel</author>
    <author>Patricia de Carvalho Aguiar</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Dystonie</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Elektroencephalographie</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Maschinelles Lernen</value>
    </subject>
    <collection role="institutes" number="">BIOMEMS Lab</collection>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
  </doc>
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    <thesisYearAccepted/>
    <language>eng</language>
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    <pageNumber>1</pageNumber>
    <edition/>
    <issue/>
    <volume>2025</volume>
    <type>conferenceobject</type>
    <publisherName>Julius-Maximilians-Universität Würzburg</publisherName>
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    <creatingCorporation>TH Aschaffenburg</creatingCorporation>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2025-11-25</completedDate>
    <publishedDate>2025-11-24</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">ASTRABAX – Scientific results of two stratospheric balloon flights</title>
    <abstract language="eng">The ASTRABAX experiment ("Aschaffenburg Stratospheric Balloon Experiment") uses a multimodal platform to study radiation exposures in the upper atmosphere. We present a modular approach to accommodate the numerous setups under the weight restriction of light unmanned free stratospheric balloon. The compartmental setup allows flexibility to address current research questions with low expenditure in costs, manpower and technology expertise. Its easy implementation is suitable for educational purposes of students in the fields of astronomy, astrobiology, and material research. Recently, two stratospheric balloons were flown to test the feasibility and connectivity of different building blocks in a temperature-controlled gondola, and to characterize the stratospheric radiation environment.The focus of the physical experiments is the observation of the UV-C spectral region using miniature UV-VIS spectrometers, and cosmic ray dosimetry with a Geiger counter. A second set of experiments assesses the effects of irradiation on polydopamine coatings intended for the application in space-born X-ray telescopes. The platform also contains samples of biological cells that are simultaneously exposed to low-dose radiation of different compositions of particle, X-ray and UV radiation. Post-flight nanoscopic measurements aim to examine changes in the spatial chromatin organization playing a crucial role in DNA-repair mechanisms. Investigations in such natural environment are of importance for high altitude atmospheric as well as space flights, for comparable exposures on other objects of the solar system and for astrobiology.</abstract>
    <parentTitle language="eng">18th Pico- and Nanosatellite Workshop 2025, Abstracts Book</parentTitle>
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    <author>Thorsten Döhring</author>
    <author>Lucia Krivanekova</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>cosmic ray</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>radiation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>stratospheric balloon</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>atmosphere</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>UVC</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Stratosphären-Ballon</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Kosmische Strahlung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Röntgenspiegel</value>
    </subject>
    <collection role="institutes" number="">Internationales Technisches Vertriebsmanagement (Bachelor)</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/2670/ASTRABAX-Beitrag_1.pdf</file>
  </doc>
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    <language>eng</language>
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    <edition/>
    <issue/>
    <volume>31</volume>
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    <title language="eng">CellRex: Software platform for managing biological cell data</title>
    <abstract language="eng">This work introduces the software platform CellRex, a research data management system for laboratories capable of storing, searching, and enriching data with biological metadata. CellRex addresses data management challenges by storing data in an ontology-based directory structure within the filesystem, with metadata saved as JSON files and in a document-oriented SQLite database. The framework, deployed as container services in a software-as-a-service model, features a web-based GUI and API for user interaction and machine-readable access, providing functionalities such as duplicate detection, experiment grouping, and templating. CellRex improves research efficiency and facilitates data reuse, providing a targeted solution for laboratories focused on cell analysis research.</abstract>
    <parentTitle language="eng">SoftwareX</parentTitle>
    <identifier type="issn">2352-7110</identifier>
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    <abstract language="eng">High-precision deposition in material extrusion-based additive manufacturing (MEX-AM), especially in mid-air extrusion, is essential for creating microfluidic channels, integrated sensors, and tissue scaffolds with fine vascular features. However, despite advances in support-free slicing and multi-axis printing, no standardized method exists for fabricating enclosed air cavities with high shape fidelity, particularly in single-layer structures. Reliable deposition at sub-millimeter scales remains challenging, especially when printing low-stiffness polymers such as polypropylene (PP), due to delayed solidification and viscoelastic effects. This study introduces a flow-rate-dependent analytical model to predict extrusion behavior, interfacial bonding, and surface morphology in self-supporting single-layer PP structures. To validate the model, surface roughness, material distribution, and intralayer bonding were quantified using spectral analysis, cross-sectional thickness measurements, and Abbott–Firestone curve evaluation. Results show that reducing the flow rate (relative to 100% nominal flow through a 0.4 mm nozzle) to 40% improves surface roughness (Ra) to below 20 &#13;
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    <abstract language="eng">The ASTRABAX project ("Aschaffenburg Stratospheric Balloon Experiment"), being funded for the years 2024 to 2026, is designed as a multimodal platform for the investigation of radiation exposures at high altitude. The UV-C spectral region is of special interest. Spectral measurements observe this region of interest using miniature UV-VIS spectrometers. The platform also contains a radiation dosimetry, a power source for on-board electronics, and common shielding setups for multiple spectral combinations. Human cells are exposed simultaneously to radiation of different compositions as particle, X-ray and UV radiation. After the flight, possible changes in the spatial chromatin organization are examined. Material samples intended for the development of satellite components are irradiated also. Investigations under such conditions are realistic and crucial for high altitude flights in the atmosphere, for space flights as well as for comparable exposures on other objects of the solar system, and even for exoplanet habitats to some extent.</abstract>
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    <author>Manfred Stollenwerk</author>
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    <title language="deu">Forschung zu Strahlenschäden mit dem Stratosphärenballon-Experiment ASTRABAX</title>
    <abstract language="deu">Das für die Jahre 2024 bis 2026 geförderte Projekt ASTRABAX („Aschaffenburger Stratosphärenballon- Experiment“) ist als multimodale Plattform der Material- und Biowissenschaften für Untersuchungen bei extremen Strahlenbelastungen in großer Höhe konzipiert. Dabei ist der UV-C-Spektralbereich von besonderem Interesse und wird mit Miniatur-UV-Spektrometern untersucht. Die Plattform des Ballonexperimentes umfasst eine gemeinsame Strahlungsdosimetrie, eine Stromquelle für die Bordelektronik und Abschirmungen für mehrere Bestrahlungskombinationen. Biologische Zellen werden Kombinationen aus Partikel-, Röntgen- und UV-Strahlung ausgesetzt. Nach dem Flug werden mögliche Veränderungen in der räumlichen Chromatinorganisation mittels hochauflösender Mikroskopie untersucht. Auswirkungen von Kombinationen aus hoch- und niederenergetischer Strahlung sind bisher nicht ausreichend erforscht und beschrieben. Zusätzlich werden auch für Satelliten relevante Materialproben bestrahlt. Untersuchungen unter solchen Bedingungen sind realistisch und relevant für Flüge in der Stratosphäre, für Raumflüge sowie für vergleichbare Expositionen bei anderen Objekten des Sonnensystems oder Exoplaneten-Habitaten.</abstract>
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    <author>Jan Pregler</author>
    <author>Manfred Stollenwerk</author>
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    <title language="eng">Spectral measurements and life science experiments using extreme radiation exposures at high altitude</title>
    <abstract language="eng">The ASTRABAX project ("Aschaffenburg Stratospheric Balloon Experiment"), being funded for the years 2024 to 2026, is designed as a multimodal platform for the investigation of radiation exposures at high altitude. Miniature UV-VIS spectrometers observe the UV-C spectral region. The platform also contains a radiation dosimetry, a power source for on-board electronics, and common shielding setups for multiple spectral combinations. The effects of combinations of high- and low-energy rays on human cells haven´t been sufficiently investigated and described so far. Investigations under such conditions are realistic and crucial for high altitude flights in the atmosphere, for space flights as well as for comparable exposures on other objects of the solar system, and even for exoplanet habitats to some extent.</abstract>
    <abstract language="deu">Poster</abstract>
    <enrichment key="copyright">1</enrichment>
    <enrichment key="HAB_Review">nein</enrichment>
    <enrichment key="opus.source">publish</enrichment>
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    <enrichment key="opus.urn.autoCreate">false</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Eva Stanik</author>
    <author>Thorsten Döhring</author>
    <author>Jan Pregler</author>
    <author>Manfred Stollenwerk</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Balloons</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Diffusers</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Solar radiation</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Spectrometers</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Ultraviolet radiation</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Stahlenbelastung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Stratosphären-Ballon</value>
    </subject>
    <collection role="institutes" number="">Angewandte Forschung in den Ingenieurwissenschaften (Master)</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/2316/13024-25poster.pdf</file>
  </doc>
  <doc>
    <id>2439</id>
    <completedYear>2024</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>23</issue>
    <volume>25</volume>
    <type>article</type>
    <publisherName>MDPI AG</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Impact of Gold Nanoparticles and Ionizing Radiation on Whole Chromatin Organization as Detected by Single-Molecule Localization Microscopy</title>
    <abstract language="eng">In radiation tumor therapy, irradiation, on one hand, should cause cell death to the tumor. On the other hand, the surrounding non-tumor tissue should be maintained unaffected. Therefore, methods of local dose enhancements are highly interesting. Gold nanoparticles, which are preferentially uptaken by very-fast-proliferating tumor cells, may enhance damaging. However, the results in the literature obtained from cell culture and animal tissue experiments are very contradictory, i.e., only some experiments reveal increased cell killing but others do not. Thus, a better understanding of cellular mechanisms is required. Using the breast cancer cell model SkBr3, the effects of gold nanoparticles in combination with ionizing radiation on chromatin network organization were investigated by Single-Molecule Localization Microscopy (SMLM) and applications of mathematical topology calculations (e.g., Persistent Homology, Principal Component Analysis, etc.). The data reveal a dose and nanoparticle dependent re-organization of chromatin, although colony forming assays do not show a significant reduction of cell survival after the application of gold nanoparticles to the cells. In addition, the spatial organization of γH2AX clusters was elucidated, and characteristic changes were obtained depending on dose and gold nanoparticle application. The results indicate a complex response of ALU-related chromatin and heterochromatin organization correlating to ionizing radiation and gold nanoparticle incorporation. Such complex whole chromatin re-organization is usually associated with changes in genome function and supports the hypothesis that, with the application of gold nanoparticles, not only is DNA damage increasing but also the efficiency of DNA repair may be increased. The understanding of complex chromatin responses might help to improve the gold nanoparticle efficiency in radiation treatment.</abstract>
    <parentTitle language="eng">International Journal of Molecular Sciences</parentTitle>
    <identifier type="issn">1422-0067</identifier>
    <identifier type="doi">https://doi.org/10.3390/ijms252312843</identifier>
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Therefore, methods of local dose enhancements are highly interesting. Gold nanoparticles, which are preferentially uptaken by very-fast-proliferating tumor cells, may enhance damaging. However, the results in the literature obtained from cell culture and animal tissue experiments are very contradictory, i.e., only some experiments reveal increased cell killing but others do not. Thus, a better understanding of cellular mechanisms is required. Using the breast cancer cell model SkBr3, the effects of gold nanoparticles in combination with ionizing radiation on chromatin network organization were investigated by Single-Molecule Localization Microscopy (SMLM) and applications of mathematical topology calculations (e.g., Persistent Homology, Principal Component Analysis, etc.). The data reveal a dose and nanoparticle dependent re-organization of chromatin, although colony forming assays do not show a significant reduction of cell survival after the application of gold nanoparticles to the cells. In addition, the spatial organization of \u03b3H2AX clusters was elucidated, and characteristic changes were obtained depending on dose and gold nanoparticle application. The results indicate a complex response of ALU-related chromatin and heterochromatin organization correlating to ionizing radiation and gold nanoparticle incorporation. Such complex whole chromatin re-organization is usually associated with changes in genome function and supports the hypothesis that, with the application of gold nanoparticles, not only is DNA damage increasing but also the efficiency of DNA repair may be increased. 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    <title language="eng">Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment</title>
    <abstract language="eng">This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.</abstract>
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    <author>Alexey V. Verkhovtsev</author>
    <author>Nigel J. Mason</author>
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    <author>Brendan Dromey</author>
    <author>Martin Falk</author>
    <author>Juraj Fedor</author>
    <author>Luca Gerhards</author>
    <author>Michael Hausmann</author>
    <author>Georg Hildenbrand</author>
    <author>Miloš Hrabovský</author>
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    <author>Jaroslav Kočišek</author>
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    <title language="eng">Revealing patterns in major depressive disorder with machine learning and networks</title>
    <abstract language="eng">Major depressive disorder (MDD) is a multifaceted condition that affects millions of people worldwide and is a leading cause of disability. There is an urgent need for an automated and objective method to detect MDD due to the limitations of traditional diagnostic approaches. In this paper, we propose a methodology based on machine and deep learning to classify patients with MDD and identify altered functional connectivity patterns from EEG data. We compare several connectivity metrics and machine learning algorithms. Complex network measures are used to identify structural brain abnormalities in MDD. Using Spearman correlation for network construction and the SVM classifier, we verify that it is possible to identify MDD patients with high accuracy, exceeding literature results. The SHAP (SHAPley Additive Explanations) summary plot highlights the importance of C4-F8 connections and also reveals dysfunction in certain brain areas and hyperconnectivity in others. Despite the lower performance of the complex network measures for the classification problem, assortativity was found to be a promising biomarker. Our findings suggest that understanding and diagnosing MDD may be aided by the use of machine learning methods and complex networks.</abstract>
    <parentTitle language="eng">medrxiv</parentTitle>
    <identifier type="doi">doi.org/10.1101/2024.06.07.24308619</identifier>
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    <author>Loriz Francisco Sallum</author>
    <author>Caroline L. Alves</author>
    <author>Christiane Thielemann</author>
    <author>Francisco A. Rodrigues</author>
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      <language>deu</language>
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      <value>Depression</value>
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      <value>Elektroencephalographie</value>
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      <value>Maschinelles Lernen</value>
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    <title language="eng">How to obtain an integrated picture of the molecular networks involved in adaptation to microgravity in different biological systems?</title>
    <abstract language="eng">Periodically, the European Space Agency (ESA) updates scientific roadmaps in consultation with the scientific community. The ESA SciSpacE Science Community White Paper (SSCWP) 9, “Biology in Space and Analogue Environments”, focusses in 5 main topic areas, aiming to address key community-identified knowledge gaps in Space Biology. Here we present one of the identified topic areas, which is also an unanswered question of life science research in Space: “How to Obtain an Integrated Picture of the Molecular Networks Involved in Adaptation to Microgravity in Different Biological Systems?” The manuscript reports the main gaps of knowledge which have been identified by the community in the above topic area as well as the approach the community indicates to address the gaps not yet bridged. Moreover, the relevance that these research activities might have for the space exploration programs and also for application in industrial and technological fields on Earth is briefly discussed.</abstract>
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    <identifier type="doi">DOI: 10.1038/s41526-024-00395-3</identifier>
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    <author>Nathaniel J. Szewczyk</author>
    <author>Monica Monici</author>
    <author>Christiane Thielemann</author>
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    <title language="eng">How are cell and tissue structure and function influenced by gravity and what are the gravity perception mechanisms?</title>
    <abstract language="eng">Progress in mechanobiology allowed us to better understand the important role of mechanical forces in the regulation of biological processes. Space research in the field of life sciences clearly showed that gravity plays a crucial role in biological processes. The space environment offers the unique opportunity to carry out experiments without gravity, helping us not only to understand the effects of gravitational alterations on biological systems but also the mechanisms underlying mechanoperception and cell/tissue response to mechanical and gravitational stresses. Despite the progress made so far, for future space exploration programs it is necessary to increase our knowledge on the mechanotransduction processes as well as on the molecular mechanisms underlying microgravity-induced cell and tissue alterations. This white paper reports the suggestions and recommendations of the SciSpacE Science Community for the elaboration of the section of the European Space Agency roadmap “Biology in Space and Analogue Environments” focusing on “How are cells and tissues influenced by gravity and what are the gravity perception mechanisms?” The knowledge gaps that prevent the Science Community from fully answering this question and the activities proposed to fill them are discussed.</abstract>
    <parentTitle language="eng">npj Microgravity</parentTitle>
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    <identifier type="doi">10.1038/s41526-024-00357-9</identifier>
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    <author>Davis Trent</author>
    <author>Christiane Thielemann</author>
    <author>Monica Monici</author>
    <subject>
      <language>deu</language>
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      <value>Zellkultur</value>
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      <language>deu</language>
      <type>swd</type>
      <value>Schwere</value>
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    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Raumfahrtbiologie</value>
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  <doc>
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    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1</pageFirst>
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    <completedDate>2024-01-11</completedDate>
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    <title language="eng">On the advances in machine learning and complex network measures to an EEG dataset from DMT experiments</title>
    <abstract language="eng">There is a growing interest in the medical use of psychedelic substances, as preliminary studies using them for psychiatric disorders have shown positive results. In particular, one of these substances is N, N-dimethyltryptamine (DMT), an agonist serotonergic psychedelic that can induce profound alterations in the state of consciousness. In this work, we use an exploratory tool to reveal DMT-induced changes in brain activity using EEG data and provide new insights into the mechanisms of action of this psychedelic substance. We used a two-class classification based on (A) the connectivity matrix or (B) complex network measures derived from it as input to a support vector machine. We found that both approaches could detect changes in the brain's automatic activity, with case (B) showing the highest AUC (89%), indicating that complex network measurements best capture the brain changes that occur due to DMT use. In the second step, we ranked the features that contributed the most to this result. For case (A), we found that differences in the high alpha, low beta, and delta frequency bands were most important in distinguishing between the state before and after DMT inhalation, which is consistent with the results described in the literature. Further, the connection between the temporal (TP8) and central cortex (C3) and between the precentral gyrus (FC5) and the lateral occipital cortex (P8) contributed most to the classification result. The connection between regions TP8 and C3 has been found in the literature associated with finger movements that might have occurred during DMT consumption. However, the connection between cortical areas FC5 and P8 has not been found in the literature and is presumably related to the volunteers' emotional, visual, sensory, perceptual, and mystical experiences during DMT consumption. For case (B), closeness centrality was the most crucial complex network measure. Furthermore, we discovered larger communities and longer average path lengths when DMT was used and the converse when not, showing that the balance between functional segregation and integration had been disrupted. These findings support the idea that cortical brain activity becomes more entropic under psychedelics. Overall, a robust computational workflow has been developed here with interpretability of how DMT (or other psychedelics) modify brain networks and insights into their mechanism of action. Finally, the same methodology applied here may help interpret EEG time series from patients who consumed other psychedelic drugs.</abstract>
    <parentTitle language="eng">Journal of Physics: Complexity</parentTitle>
    <identifier type="doi">10.1088/2632-072X/ad1c68</identifier>
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    <author>Caroline L. Alves</author>
    <author>Manuel Ciba</author>
    <author>Thaise Graziele L de O Toutain</author>
    <author>Joel Augusto Moura Porto</author>
    <author>Eduardo Pondé de Sena</author>
    <author>Christiane Thielemann</author>
    <author>Francisco A. Rodrigues</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
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    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Halluzinogen</value>
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    <subject>
      <language>deu</language>
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      <value>Psychische Störung</value>
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    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>35</pageLast>
    <pageNumber/>
    <edition/>
    <issue>19(10)</issue>
    <volume>2024</volume>
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    <completedDate>2024-10-17</completedDate>
    <publishedDate>2024-10-17</publishedDate>
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    <title language="eng">Multiclass classification of Autism Spectrum Disorder, attention deficit hyperactivity disorder, and typically developed individuals using fMRI functional connectivity analysis</title>
    <abstract language="eng">Neurodevelopmental conditions, such as Autism Spectrum Disorder (ASD) and Attention Deficit Hyperactivity Disorder (ADHD), present unique challenges due to overlapping symptoms, making an accurate diagnosis and targeted intervention difficult. Our study employs advanced machine learning techniques to analyze functional magnetic resonance imaging (fMRI) data from individuals with ASD, ADHD, and typically developed (TD) controls, totaling 120 subjects in the study. Leveraging multiclass classification (ML) algorithms, we achieve superior accuracy in distinguishing between ASD, ADHD, and TD groups, surpassing existing benchmarks with an area under the ROC curve near 98%. Our analysis reveals distinct neural signatures associated with ASD and ADHD: individuals with ADHD exhibit altered connectivity patterns of regions involved in attention and impulse control, whereas those with ASD show disruptions in brain regions critical for social and cognitive functions. The observed connectivity patterns, on which the ML c</abstract>
    <parentTitle language="eng">plos one</parentTitle>
    <identifier type="url">https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0305630</identifier>
    <identifier type="doi">https://doi.org/10.1371/journal.pone.0305630</identifier>
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    <author>Caroline L. Alves</author>
    <author>Francisco A. Rodrigues</author>
    <author>Loriz Francisco Sallum</author>
    <author>Thaise Toutain</author>
    <author>Joel Porto</author>
    <author>Patricia Aguiar</author>
    <author>Christiane Thielemann</author>
    <author>Michael Möckel</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Aufmerksamkeitsdefizit-Syndrom</value>
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    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Autismus</value>
    </subject>
    <subject>
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      <type>swd</type>
      <value>Funktionelle Kernspintomografie</value>
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    <completedDate>2024-03-01</completedDate>
    <publishedDate>2024-03-01</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Enzymatic Self-Degradable PLA-Based Electrets</title>
    <abstract language="eng">In recent years, the demand for sustainable and degradable materials and electronic devices has increased significantly.&#13;
Among a range of biodegradable polymers, poly(lactic acid) (PLA) is a good alternative to conventional petrol-based polymers because of its attractive mechanical properties and its easy processability. Recently, PLA has also been described as a promising dielectric material with piezoelectric and electret properties. We expect that PLA—after further optimization— will play an important role as a material for environmentally friendly sensors in the future, where first applications such as air filters and pressure sensors have already been proposed. However, degradation under normal ambient conditions is very slow, and an accelerated and controllable degradation process is highly desirable for any type of PLA-based sensors.&#13;
Enzymatic hydrolysis with embedded enzymes has been proposed as an approach to accelerate and control degradation. In this work, we investigate the properties of PLA in terms of dielectric and mechanical properties with a focus on its ability to store charges after the enzyme proteinase K (Trit. album) has been incorporated. Results reveal that proteinase K has a positive effect on the charge stability of solvent-cast PLA electrets after complete evaporation of the solvent. Furthermore, we observed a concentration-dependent acceleration of mass loss in a Tris-HCl buffer. A fast degradation within only one day occurred at a concentration of 6 wt% proteinase K.</abstract>
    <parentTitle language="eng">Journal of Polymers and the Environment</parentTitle>
    <identifier type="doi">Journal of https://doi.org/10.1007/s10924-024-03240-6</identifier>
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    <author>Dennis Flachs</author>
    <author>Sergey Zhukov</author>
    <author>Isabella Zech</author>
    <author>Timo Schreck</author>
    <author>Stefan Belle</author>
    <author>Heinz von Seggern</author>
    <author>Mario Kupnik</author>
    <author>Alexander Anton Altmann</author>
    <author>Christiane Thielemann</author>
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      <language>deu</language>
      <type>swd</type>
      <value>Biologisch abbaubarer Kunststoff</value>
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    <title language="eng">Monolithic Wideband Air-Coupled Ultrasonic Transducer Based on Additively Manufactured Ferroelectrets</title>
    <abstract language="eng">Air-coupled ultrasonic transducers are widely used in non-destructive testing, acoustical sonar systems, and biomedical imaging. These applications require transducers that operate effectively across a broad acoustic frequency spectrum, offer adaptable geometric designs, and increasingly incorporate eco-friendly materials. In this work, we present a monolithic, 3D-printed air-coupled ultrasonic transducer based on ferroelectrets (FEs) and fabricated from biocompatible polylactic acid (PLA). We evaluated the transducer’s acoustical performance by measuring the surface velocity of its active area using laser Doppler vibrometry and assessed its robustness during continuous operation over a 19-day period. Additionally, we measured the sound pressure level (SPL) and wideband characteristics in an anechoic chamber across excitation frequencies from 1kHz to 100kHz. At a resonance frequency of 33kHz, our transducer achieved an SPL of 94.3dB and surface velocities up to 37mm/s. The measured bandwidth of 65.2kHz at the -6dB threshold corresponds to a fractional bandwidth of 189%. The observed exponential decay of the surface velocity, stabilizing at 15% of its initial amplitude, aligns with the isothermal surface potential decay typically observed in FE films made from PLA. These results demonstrate the effectiveness of the transducer, which features an adaptable backplate for tuning acoustic properties. The low-cost transducer, manufactured from biocompatible PLA, is particularly suited for imaging and biomedical applications furthering green electronics.</abstract>
    <parentTitle language="eng">2024 IEEE Ultrasonics, Ferroelectrics, and Frequency Control Joint Symposium (UFFC-JS)</parentTitle>
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    <author>Alexander Anton Altmann</author>
    <author>Sven Suppelt</author>
    <author>Max Ruhl</author>
    <author>Stephan Schaumann</author>
    <author>Bastian Latsch</author>
    <author>Omar Ben Dali</author>
    <author>Sergey Zhukov</author>
    <author>Dennis Flachs</author>
    <author>Xiaoqing Zhang</author>
    <author>Christiane Thielemann</author>
    <author>Heinz von Seggern</author>
    <author>Mario Kupnik</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Ultraschallwandler</value>
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    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Biomedizinische Technik</value>
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    <title language="eng">Fully 3D-Printed Rotational Energy Harvester Based On Bipolar Charged PLA Electrets</title>
    <abstract language="eng">Rotational energy harvesters have emerged as a promising solution for sustainable power generation in a variety of applications, ranging from small-scale devices to large-scale industrial systems. In this work, we present a fully 3D-printed electret rotational harvester based on the biodegradable and compostable polymer polylactic acid (PLA). The 3D-printed harvester consists of a rotor made from a bipolar-charged PLA electret, electrode pairs of conductive PLA that function as the stator, and a PLA bearing. An output power of 61μ W was achieved at a rotational speed of 400 rpm and a load resistance of 28.2MΩ. To assess the durability of the harvester, particularly the 3D-printed bearing, the extent of mechanical wear was examined after one million rotations at a rotational speed of 400 rpm. The findings indicate that the rollers undergo a 1.2% loss in mass, yet the functionality remains intact. The charge decay of PLA electrets is influenced by external factors such as elevated humidity and temperature. Future research will focus on improving the charge stability of PLA by addressing these factors, expanding the potential applications of this rotational energy harvester.</abstract>
    <parentTitle language="eng">Micro and Nanotechnology for Power Generation and Energy Conversion Applications (PowerMEMS)</parentTitle>
    <identifier type="isbn">979-8-3503-8020-0</identifier>
    <identifier type="url">https://ieeexplore.ieee.org/abstract/document/10814467</identifier>
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    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Dennis Flachs</author>
    <author>Levin Bernhard</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>rotational energy harvesting</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>PLA</value>
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    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>electret</value>
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    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>3D printing</value>
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    <title language="eng">Specific Patterns in Correlations of Super-Short Tandem Repeats (SSTRs) with G+C Content, Genic and Intergenic Regions, and Retrotransposons on All Human Chromosomes</title>
    <abstract language="eng">The specific characteristics of k-mer words (2 ≤ k ≤ 11) regarding genomic distribution and evolutionary conservation were recently found. Among them are, in high abundance, words with a tandem repeat structure (repeat unit length of 1 bp to 3 bp). Furthermore, there seems to be a class of extremely short tandem repeats (≤12 bp), so far overlooked, that are non-random-distributed and, therefore, may play a crucial role in the functioning of the genome. In the following article, the positional distributions of these motifs we call super-short tandem repeats (SSTRs) were compared to other functional elements, like genes and retrotransposons. We found length- and sequence-dependent correlations between the local SSTR density and G+C content, and also between the density of SSTRs and genes, as well as correlations with retrotransposon density. In addition to many general interesting relations, we found that SINE Alu has a strong influence on the local SSTR density. Moreover, the observed connection of SSTR patterns to pseudogenes and -exons might imply a special role of SSTRs in gene expression. In summary, our findings support the idea of a special role and the functional relevance of SSTRs in the genome.</abstract>
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    <title language="eng">Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes</title>
    <abstract language="eng">Dinucleotides are known as determinants for various structural and physiochemical properties of DNA and for binding affinities of proteins to DNA. These properties (e.g., stiffness) and bound proteins (e.g., transcription factors) are known to influence important biological functions, such as transcription regulation and 3D chromatin organization. Accordingly, the question arises of how the considerable variations in dinucleotide contents of eukaryotic chromosomes could still provide consistent DNA properties resulting in similar functions and 3D conformations. In this work, we investigate the hypothesis that coupled dinucleotide contents influence DNA properties in opposite directions to moderate each other’s influences. Analyzing all 2478 chromosomes of 155 eukaryotic species, considering bias from coding sequences and enhancers, we found sets of correlated and anti-correlated dinucleotide contents. Using computational models, we estimated changes of DNA properties resulting from this coupling. We found that especially pure A/T dinucleotides (AA, TT, AT, TA), known to influence histone positioning and AC/GT contents, are relevant moderators and that, e.g., the Roll property, which is known to influence histone affinity of DNA, is preferably moderated. We conclude that dinucleotide contents might indirectly influence transcription and chromatin 3D conformation, via regulation of histone occupancy and/or other mechanisms.</abstract>
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These properties (e.g., stiffness) and bound proteins (e.g., transcription factors) are known to influence important biological functions, such as transcription regulation and 3D chromatin organization. Accordingly, the question arises of how the considerable variations in dinucleotide contents of eukaryotic chromosomes could still provide consistent DNA properties resulting in similar functions and 3D conformations. In this work, we investigate the hypothesis that coupled dinucleotide contents influence DNA properties in opposite directions to moderate each other\u2019s influences. Analyzing all 2478 chromosomes of 155 eukaryotic species, considering bias from coding sequences and enhancers, we found sets of correlated and anti-correlated dinucleotide contents. Using computational models, we estimated changes of DNA properties resulting from this coupling. 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    <abstract language="eng">Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.</abstract>
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    <abstract language="eng">The present white paper concerns the indications and recommendations of the SciSpacE Science Community to make progress in filling the gaps of knowledge that prevent us from answering the question: “How Do Gravity Alterations Affect Animal and Human Systems at a Cellular/Tissue Level?” This is one of the five major scientific issues of the ESA roadmap “Biology in Space and Analogue Environments”. Despite the many studies conducted so far on spaceflight adaptation mechanisms and related pathophysiological alterations observed in astronauts, we are not yet able to elaborate a synthetic integrated model of the many changes occurring at different system and functional levels. Consequently, it is difficult to develop credible models for predicting long-term consequences of human adaptation to the space environment, as well as to implement medical support plans for long-term missions and a strategy for preventing the possible health risks due to prolonged exposure to spaceflight beyond the low Earth orbit (LEO). The research activities suggested by the scientific community have the aim to overcome these problems by striving to connect biological and physiological aspects in a more holistic view of space adaptation effects.</abstract>
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    <abstract language="eng">Autism is a multifaceted neurodevelopmental condition whose accurate diagnosis may be challenging because the associated symptoms and severity vary considerably. The wrong diagnosis can affect families and the educational system, raising the risk of depression, eating disorders, and self-harm. Recently, many works have proposed new methods for the diagnosis of autism based on machine learning and brain data. However, these works focus on only one pairwise statistical metric, ignoring the brain network organization. In this paper, we propose a method for the automatic diagnosis of autism based on functional brain imaging data recorded from 500 subjects, where 242 present autism spectrum disorder considering the regions of interest throughout Bootstrap Analysis of Stable Cluster map. Our method can distinguish the control group from autism spectrum disorder patients with high accuracy. Indeed the best performance provides an AUC near 1.0, which is higher than that found in the literature. We verify that the left ventral posterior cingulate cortex region is less connected to an area in the cerebellum of patients with this neurodevelopment disorder, which agrees with previous studies. The functional brain networks of autism spectrum disorder patients show more segregation, less distribution of information across the network, and less connectivity compared to the control cases. Our workflow provides medical interpretability and can be used on other fMRI and EEG data, including small data sets.</abstract>
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    <author>Nenad Krstić</author>
    <author>Jens Jüttner</author>
    <author>Lars Giegerich</author>
    <author>Margot Mayer</author>
    <author>Monika Knuth</author>
    <author>Achim Müller</author>
    <author>Christiane Thielemann</author>
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      <value>Biosensor</value>
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    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Zellkultur</value>
    </subject>
    <collection role="institutes" number="">BIOMEMS Lab</collection>
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    <title language="eng">3D printed biosensor for continuous glucose measurement in cell cultures</title>
    <abstract language="eng">A novel 3D-printed glucose sensor is presented for cell culture application. Glucose sensing was performed using a fluorescence resonance energy transfer (FRET)-based assay principle based on ConA and dextran. Both molecules are encapsulated in alginate microspheres and embedded in the UV-curable, stable hydrogel polyvinyl alcohol (PVA). The rheology of the formulation was adapted to obtain good properties for an extrusion-based printing process. The printed sensor structures were tested for their ability to detect glucose in vitro. A proportional increase in fluorescence intensity was observed in a concentration range of 0 - 2 g/L glucose. Tests with HEK cell cultures also showed good cell compatibility and excellent adhesion properties on plasma-treated Petri dishes. The printed sensors were able to detect the glucose decay associated with the metabolic activities of the fast-growing HEK cells in the cell culture medium over ten days. The proof-of-principle study shows that metabolic processes in cell cultures can be monitored with the new printed sensor using a standard fluorescence wide-field microscope.</abstract>
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    <author>Christiane Thielemann</author>
    <author>Nenad Krstić</author>
    <author>Jens Jüttner</author>
    <author>Lars Giegerich</author>
    <author>Margot Mayer</author>
    <author>Monika Knuth</author>
    <author>Achim Müller</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Bioprinting, FRET, Enzyme-free glucose sensor, PVA hydrogel</value>
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      <value>Biosensor</value>
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      <value>3D-Druck</value>
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    <subject>
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      <value>Zellkultur</value>
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    <title language="eng">Analysis of functional connectivity using machine learning and deep learning in different data modalities from individuals with schizophrenia</title>
    <abstract language="eng">Objective. Schizophrenia (SCZ) is a severe mental disorder associated with persistent or recurrent psychosis, hallucinations, delusions, and thought disorders that affect approximately 26 million people worldwide, according to the World Health Organization. Several studies encompass machine learning (ML) and deep learning algorithms to automate the diagnosis of this mental disorder. Others study SCZ brain networks to get new insights into the dynamics of information processing in individuals suffering from the condition. In this paper, we offer a rigorous approach with ML and deep learning techniques for evaluating connectivity matrices and measures of complex networks to establish an automated diagnosis and comprehend the topology and dynamics of brain networks in SCZ individuals. Approach. For this purpose, we employed an functional magnetic resonance imaging (fMRI) and electroencephalogram (EEG) dataset. In addition, we combined EEG measures, i.e. Hjorth mobility and complexity, with complex network measurements to be analyzed in our model for the first time in the literature. Main results. When comparing the SCZ group to the control group, we found a high positive correlation between the left superior parietal lobe and the left motor cortex and a positive correlation between the left dorsal posterior cingulate cortex and the left primary motor. Regarding complex network measures, the diameter, which corresponds to the longest shortest path length in a network, may be regarded as a biomarker because it is the most crucial measure in different data modalities. Furthermore, the SCZ brain networks exhibit less segregation and a lower distribution of information. As a result, EEG measures outperformed complex networks in capturing the brain alterations associated with SCZ. Significance. Our model achieved an area under receiver operating characteristic curve (AUC) of 100% and an accuracy of 98.5% for the fMRI, an AUC of 95%, and an accuracy of 95.4% for the EEG data set. These are excellent classification results. Furthermore, we investigated the impact of specific brain connections and network measures on these results, which helped us better describe changes in the diseased brain.</abstract>
    <parentTitle language="eng">Journal of Neural Engineering</parentTitle>
    <identifier type="doi">10.1088/1741-2552/acf734</identifier>
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    <author>Caroline L. Alves</author>
    <author>Thaise Toutain</author>
    <author>Joel Porto</author>
    <author>Patricia Aguiar</author>
    <author>Eduardo Pondé de Sena</author>
    <author>Francisco A. Rodrigues</author>
    <author>Aruane M. Pineda</author>
    <author>Christiane Thielemann</author>
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    <title language="eng">Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology</title>
    <abstract language="eng">The cell nucleus is a complex biological system in which simultaneous reactions and functions take place to keep the cell as an individualized, specialized system running well. The cell nucleus contains chromatin packed in various degrees of density and separated in volumes of chromosome territories and subchromosomal domains. Between the chromatin, however, there is enough “free” space for floating RNA, proteins, enzymes, ATPs, ions, water molecules, etc. which are trafficking by super- and supra-diffusion to the interaction points where they are required. It seems that this trafficking works somehow automatically and drives the system perfectly. After exposure to ionizing radiation causing DNA damage from single base damage up to chromatin double-strand breaks, the whole system “cell nucleus” responds, and repair processes are starting to recover the fully functional and intact system. In molecular biology, many individual epigenetic pathways of DNA damage response or repair of single and double-strand breaks are described. How these responses are embedded into the response of the system as a whole is often out of the focus of consideration. In this article, we want to follow the hypothesis of chromatin architecture’s impact on epigenetic pathways and vice versa. Based on the assumption that chromatin acts like an “aperiodic solid state within a limited volume,” functionally determined networks and local topologies (“islands”) can be defined that drive the appropriate repair process at a given damage site. Experimental results of investigations of the chromatin nano-architecture and DNA repair clusters obtained by means of single-molecule localization microscopy offer hints and perspectives that may contribute to verifying the hypothesis.</abstract>
    <parentTitle language="eng">Results and Problems in Cell Differentiation</parentTitle>
    <subTitle language="eng">(A Hypothesis and Experimental Verification Hints)</subTitle>
    <identifier type="isbn">9783031065729</identifier>
    <identifier type="issn">0080-1844</identifier>
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    <author>Michael Hausmann</author>
    <author>Georg Hildenbrand</author>
    <author>Götz Pilarczyk</author>
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    <language>eng</language>
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    <title language="eng">Assessing the Potential for Liquid Solvents from X-ray Sources: Considerations on Bodies Orbiting Active Galactic Nuclei</title>
    <abstract language="eng">We aim to establish a rough first prospect on the potential of certain biorelevant solvents (water, ammonia, and methane) being present in liquid form inside the uppermost few meters of several modeled rocky and icy surfaces of hypothetical bodies orbiting active galactic nuclei (AGNs) and investigate under which constraints this might occur. For this, we adjust and average X-ray spectra from a sample of 20 Type-1 Seyfert galaxies to calculate the mean snowline of the sample used. We then vary the hypothetical body’s orbit between 10% and 100% of the snowline radius and calculate a sub-surface attenuation within four different model surface compositions for each. We then use this as a continuous source term for a thermal model. Example bodies are systematically investigated with sizes between 1/30 and 20 earth radii, with further variations also considered (such as possible bound rotation), to end up with a perspective of solvent phases under a wide slew of different conditions. We find that liquid solvents are possible under a multitude of parameters, with temperature being the main constraint to liquid water whereas body size and pressure are the main constraint to liquid methane and ammonia.</abstract>
    <parentTitle language="eng">Galaxies</parentTitle>
    <identifier type="issn">2075-4434</identifier>
    <identifier type="doi">https://doi.org/10.3390/galaxies10050101</identifier>
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For this, we adjust and average X-ray spectra from a sample of 20 Type-1 Seyfert galaxies to calculate the mean snowline of the sample used. We then vary the hypothetical body\u2019s orbit between 10% and 100% of the snowline radius and calculate a sub-surface attenuation within four different model surface compositions for each. We then use this as a continuous source term for a thermal model. Example bodies are systematically investigated with sizes between 1\/30 and 20 earth radii, with further variations also considered (such as possible bound rotation), to end up with a perspective of solvent phases under a wide slew of different conditions. We find that liquid solvents are possible under a multitude of parameters, with temperature being the main constraint to liquid water whereas body size and pressure are the main constraint to liquid methane and ammonia.&lt;\/jats:p&gt;","DOI":"10.3390\/galaxies10050101","type":"journal-article","created":{"date-parts":[[2022,10,18]],"date-time":"2022-10-18T01:11:51Z","timestamp":1666055511000},"page":"101","source":"Crossref","is-referenced-by-count":0,"title":["Assessing the Potential for Liquid Solvents from X-ray Sources: Considerations on Bodies Orbiting Active Galactic Nuclei"],"prefix":"10.3390","volume":"10","author":[{"given":"Daniel","family":"Rodener","sequence":"first","affiliation":[{"name":"Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany"}]},{"given":"Myriam","family":"Sch\u00e4fer","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-9430-1987","authenticated-orcid":false,"given":"Michael","family":"Hausmann","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-1992-6025","authenticated-orcid":false,"given":"Georg","family":"Hildenbrand","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany"},{"name":"Faculty of Engineering, University of Applied Sciences Aschaffenburg, W\u00fcrzburger Stra\u00dfe 45, 63743 Aschaffenburg, Germany"}]}],"member":"1968","published-online":{"date-parts":[[2022,10,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e1400067","DOI":"10.1126\/sciadv.1400067","article-title":"Membrane alternatives in worlds without oxygen: Creation of an azotosome","volume":"1","author":"Stevenson","year":"2015","journal-title":"Sci. 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Astrophys."}],"container-title":["Galaxies"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2075-4434\/10\/5\/101\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T21:02:49Z","timestamp":1723064569000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2075-4434\/10\/5\/101"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,17]]},"references-count":46,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2022,10]]}},"alternative-id":["galaxies10050101"],"URL":"http:\/\/dx.doi.org\/10.3390\/galaxies10050101","relation":{},"ISSN":["2075-4434"],"issn-type":[{"type":"electronic","value":"2075-4434"}],"subject":[],"published":{"date-parts":[[2022,10,17]]}}}</enrichment>
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    <author>Daniel Rodener</author>
    <author>Myriam Schäfer</author>
    <author>Michael Hausmann</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Lösungsmittel</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Röntgenspektrum</value>
    </subject>
    <collection role="institutes" number="">Medical Engineering and Data Science (Bachelor)</collection>
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    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>26</pageLast>
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    <edition/>
    <issue>12</issue>
    <volume>2022</volume>
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    <title language="eng">Application of machine learning and complex network measures to an EEG dataset from ayahuasca experiments</title>
    <abstract language="eng">Ayahuasca is a blend of Amazonian plants that has been used for traditional medicine by&#13;
the inhabitants of this region for hundreds of years. Furthermore, this plant has been demon� strated to be a viable therapy for a variety of neurological and mental diseases. EEG experi� ments have found specific brain regions that changed significantly due to ayahuasca. Here,&#13;
we used an EEG dataset to investigate the ability to automatically detect changes in brain&#13;
activity using machine learning and complex networks. Machine learning was applied at&#13;
three different levels of data abstraction: (A) the raw EEG time series, (B) the correlation of&#13;
the EEG time series, and (C) the complex network measures calculated from (B). Further, at&#13;
the abstraction level of (C), we developed new measures of complex networks relating to&#13;
community detection. As a result, the machine learning method was able to automatically&#13;
detect changes in brain activity, with case (B) showing the highest accuracy (92%), followed&#13;
by (A) (88%) and (C) (83%), indicating that connectivity changes between brain regions are&#13;
more important for the detection of ayahuasca. The most activated areas were the frontal&#13;
and temporal lobe, which is consistent with the literature. F3 and PO4 were the most impor� tant brain connections, a significant new discovery for psychedelic literature. This connec� tion may point to a cognitive process akin to face recognition in individuals during&#13;
ayahuasca-mediated visual hallucinations. Furthermore, closeness centrality and assorta� tivity were the most important complex network measures. These two measures are also&#13;
associated with diseases such as Alzheimer’s disease, indicating a possible therapeutic&#13;
mechanism. Moreover, the new measures were crucial to the predictive model and sug� gested larger brain communities associated with the use of ayahuasca. This suggests that&#13;
the dissemination of information in functional brain networks is slower when this drug is&#13;
present. Overall, our methodology was able to automatically detect changes in brain activity&#13;
during ayahuasca consumption and interpret how these psychedelics alter brain networks,&#13;
as well as provide insights into their mechanisms of action</abstract>
    <parentTitle language="eng">PLOS ONE</parentTitle>
    <identifier type="doi">https://doi.org/10.1371/journal. pone.0277257</identifier>
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    <author>Caroline L. Alves</author>
    <author>Rubens G. Cury</author>
    <author>Kirstin Roster</author>
    <author>Aruane M. Pineda</author>
    <author>Francisco A. Rodrigues</author>
    <author>Christiane Thielemann</author>
    <author>Manuel Ciba</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Ayahuasca</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Elektroencephalographie</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Alzheimerkrankheit</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Gehirn</value>
    </subject>
    <collection role="institutes" number="">BIOMEMS Lab</collection>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/2072/journal.pone.0277257.pdf</file>
  </doc>
  <doc>
    <id>2062</id>
    <completedYear>2022</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst>e37</pageFirst>
    <pageLast>e47</pageLast>
    <pageNumber/>
    <edition/>
    <issue>137</issue>
    <volume>2022</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2022-11-17</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Functional connectivity and convolutional neural networks for automatic classification of EEG data</title>
    <parentTitle language="eng">Clinical Neurophysiology</parentTitle>
    <identifier type="doi">https://doi.org/10.1016/j.clinph.2022.01.086</identifier>
    <enrichment key="copyright">1</enrichment>
    <enrichment key="opus.source">publish</enrichment>
    <enrichment key="opus.doi.autoCreate">false</enrichment>
    <enrichment key="opus.urn.autoCreate">false</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Caroline L. Alves</author>
    <author>Lennart Wissel</author>
    <author>Philipp Capetian</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Elektroencephalographie</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
    </subject>
    <collection role="institutes" number="">BIOMEMS Lab</collection>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
  </doc>
  <doc>
    <id>2063</id>
    <completedYear>2022</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst>1</pageFirst>
    <pageLast>2</pageLast>
    <pageNumber/>
    <edition/>
    <issue>November</issue>
    <volume>2022</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2022-11-17</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Revisiting the involvement of tau in complex neural network remodeling: analysis of the extracellular neuronal activity in organotypic brain slice co-cultures</title>
    <abstract language="deu">Objective: Tau ablation has a protective effect in epilepsy due to inhibition of the hyperexcitability/hypersynchrony. Protection may also occur in transgenic models of Alzheimer's disease by reducing the epileptic activity and normalizing the excitation/inhibition imbalance. However, it is difficult to determine the exact functions of tau, because tau knockout (tauKO) brain networks exhibit elusive phenotypes. In this study, we aimed to further explore the physiological role of tau using brain network remodeling. Approach: The effect of tau ablation was investigated in hippocampal-entorhinal slice co-cultures during network remodeling. We recorded the spontaneous extracellular neuronal activity over two weeks in single-slice cultures and co-cultures from control and tauKO mice. We compared the burst parameters and applied concepts and analytical tools intended for the analysis of the network synchrony and connectivity. Main results: Comparison of the control and tauKO co-cultures revealed that tau ablation had an anti-synchrony effect on the hippocampal-entorhinal two-slice networks at late stages of culture, in line with the literature. Differences were also found between the single-slice and co-culture conditions, which indicated that tau ablation had differential effects at the sub-network scale. For instance, tau ablation was found to have an anti-synchrony effect on the co-cultured hippocampal slices throughout the culture, possibly due to a reduction in the excitation/inhibition ratio. Conversely, tau ablation led to increased synchrony in the entorhinal slices at early stages of the co-culture, possibly due to homogenization of the connectivity distribution. Significance: The new methodology presented here proved useful for investigating the role of tau in the remodeling of complex brain-derived neural networks. The results confirm previous findings and hypotheses concerning the effects of tau ablation on neural networks. Moreover, the results suggest, for the first time, that tau has multifaceted roles that vary in different brain sub-networks.</abstract>
    <parentTitle language="deu">Journal of Neural Engineering</parentTitle>
    <identifier type="doi">DOI 10.1088/1741-2552/aca261</identifier>
    <enrichment key="copyright">0</enrichment>
    <enrichment key="opus.source">publish</enrichment>
    <enrichment key="opus.doi.autoCreate">false</enrichment>
    <enrichment key="opus.urn.autoCreate">false</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Thomas Bouillet</author>
    <author>Manuel Ciba</author>
    <author>Caroline L. Alves</author>
    <author>Francisco A. Rodrigues</author>
    <author>Christiane Thielemann</author>
    <author>Morvane Colin</author>
    <author>Luc Buée</author>
    <author>Sophie Halliez</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Alzheimerkrankheit</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Gehirn</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Schnittpräparat</value>
    </subject>
    <collection role="institutes" number="">BIOMEMS Lab</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>2060</id>
    <completedYear>2022</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>13</pageLast>
    <pageNumber/>
    <edition/>
    <issue>3</issue>
    <volume>2022</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2022-11-17</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">EEG functional connectivity and deep learning for automatic diagnosis of brain disorders: Alzheimer’s disease and schizophrenia</title>
    <abstract language="eng">Mental disorders are among the leading causes of disability worldwide. The first step in treating&#13;
these conditions is to obtain an accurate diagnosis. Machine learning algorithms can provide a&#13;
possible solution to this problem, as we describe in this work. We present a method for the&#13;
automatic diagnosis of mental disorders based on the matrix of connections obtained from EEG&#13;
time series and deep learning. We show that our approach can classify patients with Alzheimer’s&#13;
disease and schizophrenia with a high level of accuracy. The comparison with the traditional cases,&#13;
that use raw EEG time series, shows that our method provides the highest precision. Therefore, the&#13;
application of deep neural networks on data from brain connections is a very promising method&#13;
for the diagnosis of neurological disorders.</abstract>
    <parentTitle language="eng">Journal of Physics: complexity</parentTitle>
    <identifier type="doi">DOI 10.1088/2632-072X/ac5f8d</identifier>
    <enrichment key="copyright">0</enrichment>
    <enrichment key="opus.source">publish</enrichment>
    <enrichment key="opus.doi.autoCreate">false</enrichment>
    <enrichment key="opus.urn.autoCreate">false</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Caroline L. Alves</author>
    <author>Aruane M. Pineda</author>
    <author>Kirstin Roster</author>
    <author>Christiane Thielemann</author>
    <author>Francisco A. Rodrigues</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>complex networks</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Machine learning</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Hirnfunktionsstörung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Alzheimerkrankheit</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Schizophrenie</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Elektroencephalographie</value>
    </subject>
    <collection role="institutes" number="">BIOMEMS Lab</collection>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
  </doc>
  <doc>
    <id>2396</id>
    <completedYear>2022</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>bookpart</type>
    <publisherName>IntechOpen</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Cryovolcanism in the Solar System and beyond: Considerations on Energy Sources, Geological Aspects, and Astrobiological Perspectives</title>
    <abstract language="eng">Volcanism based on melting rocks (silicate volcanism) is long known on Earth and has also been found on Jupiter’s moon Io. Remnants of this type of volcanism have been identified also on other bodies in the solar system. Energy sources powered by accretion and the decay of radioactive isotopes seem to be dominant mainly inside larger bodies, which have enough volume to accumulate and retain this energy in significant amounts. On the other hand, the impact of tidal forces allows even tiny bodies to melt up and pass into the stage of cryovolcanism. The dependence of tidal heating on the size of the object is minor, but the masses of and the distances to accompanying bodies as well as the inner compositions of the heated body are central factors. Even though Io as an example of a body supporting silicate volcanism is striking, the physics of tidal forces might suggest a relatively high probability for cryovolcanism. This chapter aims at considering the parameters known and objects found so far in our solar system to give insights into where in our system and other planetary systems cryovolcanism might be expected.</abstract>
    <parentTitle language="eng">Astronomy and Planetary Science - From Cryovolcanism to Black Holes and Galactic Evolution</parentTitle>
    <identifier type="isbn">9781803561196</identifier>
    <identifier type="doi">https://doi.org/10.5772/intechopen.105067</identifier>
    <enrichment key="opus_doi_flag">true</enrichment>
    <enrichment key="opus_import_data">x</enrichment>
    <enrichment key="local_crossrefDocumentType">book-chapter</enrichment>
    <enrichment key="local_crossrefLicence">https://creativecommons.org/licenses/by/3.0/legalcode</enrichment>
    <enrichment key="local_import_origin">crossref</enrichment>
    <enrichment key="local_doiImportPopulated">PersonAuthorFirstName_1,PersonAuthorLastName_1,PersonAuthorFirstName_2,PersonAuthorLastName_2,PersonAuthorFirstName_3,PersonAuthorLastName_3,PersonAuthorFirstName_4,PersonAuthorLastName_4,PublisherName,TitleMain_1,Language,TitleAbstract_1,TitleParent_1,CompletedYear,IdentifierIsbn,Enrichmentlocal_crossrefLicence</enrichment>
    <enrichment key="opus.source">doi-import</enrichment>
    <author>Georg Hildenbrand</author>
    <author>Klaus Paschek</author>
    <author>Myriam Schäfer</author>
    <author>Michael Hausmann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Sonnensystem</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Vulkanismus</value>
    </subject>
    <collection role="institutes" number="">Medical Engineering and Data Science (Bachelor)</collection>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
  </doc>
  <doc>
    <id>2397</id>
    <completedYear>2022</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>1</issue>
    <volume>14</volume>
    <type>article</type>
    <publisherName>MDPI AG</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Incorporation of Low Concentrations of Gold Nanoparticles: Complex Effects on Radiation Response and Fate of Cancer Cells</title>
    <abstract language="eng">(1) Background: In oncology research, a long-standing discussion exists about pros and cons of metal nanoparticle-enhanced radiotherapy and real mechanisms behind the tumor cell response to irradiation (IR) in presence of gold nanoparticles (GNPs). A better understanding of this response is, however, necessary to develop more efficient and safety nanoparticle (NP) types designed to disturb specific processes in tumor cells. (2) Aims and Methods: We combined 3D confocal microscopy and super-resolution single molecule localization microscopy (SMLM) to analyze, at the multiscale, the early and late effects of 10 nm-GNPs on DNA double strand break (DSB) induction and repair in tumor cells exposed to different doses of photonic low-LET (linear energy transfer) radiation. The results were correlated to different aspects of short and long-term cell viability. SkBr3 breast cancer cells (selected for the highest incidence of this cancer type among all cancers in women, and because most breast tumors are treated with IR) were incubated with low concentrations of GNPs and irradiated with 60Co γ-rays or 6 MV X-rays. In numerous post-irradiation (PI) times, ranging from 0.5 to 24 h PI, the cells were spatially (3D) fixed and labeled with specific antibodies against γH2AX, 53BP1 and H3K9me3. The extent of DSB induction, multi-parametric micro- and nano-morphology of γH2AX and 53BP1 repair foci, DSB repair kinetics, persistence of unrepaired DSBs, nanoscale clustering of γH2AX and nanoscale (hetero)chromatin re-organization were measured by means of the mentioned microscopy techniques in dependence of radiation dose and GNP concentration. (3) Results: The number of γH2AX/53BP1 signals increased after IR and an additional increase was observed in GNP-treated (GNP(+)) cells compared to untreated controls. However, this phenomenon reflected slight expansion of the G2-phase cell subpopulation in irradiated GNP(+) specimens instead of enhanced DNA damage induction by GNPs. This statement is further supported by some micro- and nano-morphological parameters of γH2AX/53BP1 foci, which slightly differed for cells irradiated in absence or presence of GNPs. At the nanoscale, Ripley’s distance frequency analysis of SMLM signal coordinate matrices also revealed relaxation of heterochromatin (H3K9me3) clusters upon IR. These changes were more prominent in presence of GNPs. The slight expansion of radiosensitive G2 cells correlated with mostly insignificant but systematic decrease in post-irradiation survival of GNP(+) cells. Interestingly, low GNP concentrations accelerated DSB repair kinetics; however, the numbers of persistent γH2AX/53BP1 repair foci were slightly increased in GNP(+) cells. (4) Conclusions: Low concentrations of 10-nm GNPs enhanced the G2/M cell cycle arrest and the proportion of radiosensitive G2 cells, but not the extent of DNA damage induction. GNPs also accelerated DSB repair kinetics and slightly increased presence of unrepaired γH2AX/53BP1 foci at 24 h PI. GNP-mediated cell effects correlated with slight radiosensitization of GNP(+) specimens, significant only for the highest radiation dose tested (4 Gy).</abstract>
    <parentTitle language="eng">Pharmaceutics</parentTitle>
    <identifier type="issn">1999-4923</identifier>
    <identifier type="doi">https://doi.org/10.3390/pharmaceutics14010166</identifier>
    <enrichment key="opus_doi_flag">true</enrichment>
    <enrichment key="opus_import_data">x</enrichment>
    <enrichment key="local_crossrefDocumentType">journal-article</enrichment>
    <enrichment key="local_crossrefLicence">https://creativecommons.org/licenses/by/4.0/</enrichment>
    <enrichment key="local_import_origin">crossref</enrichment>
    <enrichment key="local_doiImportPopulated">PersonAuthorFirstName_1,PersonAuthorLastName_1,PersonAuthorFirstName_2,PersonAuthorLastName_2,PersonAuthorFirstName_3,PersonAuthorLastName_3,PersonAuthorFirstName_4,PersonAuthorLastName_4,PersonAuthorFirstName_5,PersonAuthorLastName_5,PersonAuthorIdentifierOrcid_5,PersonAuthorFirstName_6,PersonAuthorLastName_6,PersonAuthorFirstName_7,PersonAuthorLastName_7,PersonAuthorFirstName_8,PersonAuthorLastName_8,PersonAuthorFirstName_9,PersonAuthorLastName_9,PersonAuthorIdentifierOrcid_9,PersonAuthorFirstName_10,PersonAuthorLastName_10,PersonAuthorFirstName_11,PersonAuthorLastName_11,PersonAuthorIdentifierOrcid_11,PersonAuthorFirstName_12,PersonAuthorLastName_12,PersonAuthorFirstName_13,PersonAuthorLastName_13,PersonAuthorIdentifierOrcid_13,PersonAuthorFirstName_14,PersonAuthorLastName_14,PersonAuthorIdentifierOrcid_14,PublisherName,TitleMain_1,Language,TitleAbstract_1,TitleParent_1,ArticleNumber,Issue,Volume,CompletedYear,IdentifierIssn,Enrichmentlocal_crossrefLicence</enrichment>
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    <author>Lucie Dobešová</author>
    <author>Theresa Gier</author>
    <author>Olga Kopecna</author>
    <author>Eva Pagáčová</author>
    <author>Tomáš Vičar</author>
    <author>Felix Bestvater</author>
    <author>Jiří Toufar</author>
    <author>Alena Bačíková</author>
    <author>Pavel Kopel</author>
    <author>Radek Fedr</author>
    <author>Georg Hildenbrand</author>
    <author>Iva Falková</author>
    <author>Martin Falk</author>
    <author>Michael Hausmann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Strahlentherapie</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Krebs, Medizin</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Tumorzelle</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Gold</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Nanopartikel</value>
    </subject>
    <collection role="institutes" number="">Medical Engineering and Data Science (Bachelor)</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>2068</id>
    <completedYear>2022</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>0</pageFirst>
    <pageLast>0</pageLast>
    <pageNumber/>
    <edition/>
    <issue>November</issue>
    <volume>2022</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2022-12-12</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Fabrication process for FEP piezoelectrets based on photolithographically structured thermoforming templates</title>
    <abstract language="eng">Piezoelectrets fabricated from fluoroethylenepropylene (FEP)-foils have shown drastic increase of their piezoelectric&#13;
properties during the last decade. This led to the development of FEP-based energy harvesters, which are about to evolve&#13;
into a technology with a power-generation-capacity of milliwatt per square-centimeter at their resonance frequency. Recent&#13;
studies focus on piezoelectrets with solely negative charges, as they have a better charge stability and a better suitability for&#13;
implementation in rising technologies, like the internet of things (IOT) or portable electronics. With these developments&#13;
heading towards applications of piezoelectrets in the near future, there is an urgent need to also address the fabrication&#13;
process in terms of scalability, reproducibility and miniaturization. In this study, we firstly present a comprehensive review&#13;
of the literature for a deep insight into the research that has been done in the field of FEP-based piezoelectrets. For the first&#13;
time, we propose the employment of microsystem-technology and present a process for the fabrication of thermoformed&#13;
FEP piezoelectrets based on thermoforming SU-8 templates. Following this process, unipolar piezoelectrets were fabri� cated with air void dimensions in the range of 300–1000 lm in width and approx. 90 lm in height. For samples with a void&#13;
size of 1000 lm, a d33-coefficient up to 26,508 pC/N has been achieved, depending on the applied seismic mass. Finally,&#13;
the properties as energy harvester were characterized. At the best, an electrical power output of 0.51 mW was achieved for&#13;
an acceleration of 1 �  g with a seismic mass of 101 g. Such piezoelectrets with highly defined dimensions show good&#13;
energy output in relation to volume, with high potential for widespread applications.</abstract>
    <parentTitle language="eng">Microsystem Technologies</parentTitle>
    <identifier type="url">Microsystem Technologies https://doi.org/10.1007/s00542-022-05405-6</identifier>
    <identifier type="doi">doi.org/10.1007/s00542-022-05405-6</identifier>
    <enrichment key="copyright">1</enrichment>
    <enrichment key="opus.source">publish</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Dennis Flachs</author>
    <author>Florian Emmerich</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Mikrosystemtechnik</value>
    </subject>
    <collection role="institutes" number="">BIOMEMS Lab</collection>
    <collection role="forschungsschwerpunkte" number="">Innovative Material Processing</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/2068/f2675faa-60f0-4d35-8e9d-0d5db94997e6.pdf</file>
  </doc>
  <doc>
    <id>2061</id>
    <completedYear>2022</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>2</pageLast>
    <pageNumber/>
    <edition/>
    <issue>4</issue>
    <volume>2022</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2022-11-17</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Characterization of electrically conductive, printable ink based on alginate hydrogel and graphene nanoplatelets</title>
    <abstract language="eng">In recent years, there has been an increasing interest in electrically conductive hydrogels for a wide range of biomedical applications, like tissue engineering or biosensors. In this study, we present a cost-effective conductive hydrogel based on alginate and graphene nanoplatelets for extrusion-based bioprinters. The hydrogel is prepared under ambient conditions avoiding high temperatures detrimental for cell culture environments. Investigation of the hydrogel revealed a conductivity of up to 7.5 S/cm, depending on the ratio of platelets. Furthermore, in vitro tests with human embyronic kidney cells - as an example cell type - showed good adhesion of the cells to the surface of the conductive hydrogel. Electrochemical measurements revealed a low electrode impedance which is desirable for the extracellular recording, but also low electrode capacitance, which is unfavorable for electrical stimulation purposes. Therefore, future experiments with the graphene nanoplatelets-based hydrogels will focus on electrodes for biosensors and extracellular recordings of neurons or cardiac myocytes.</abstract>
    <parentTitle language="eng">Biomedical Engineering Advances</parentTitle>
    <identifier type="doi">https://doi.org/10.1016/j.bea.2022.100045</identifier>
    <enrichment key="copyright">0</enrichment>
    <enrichment key="opus.source">publish</enrichment>
    <enrichment key="opus.doi.autoCreate">false</enrichment>
    <enrichment key="opus.urn.autoCreate">false</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Dennis Flachs</author>
    <author>Johannes Etzel</author>
    <author>Margot Mayer</author>
    <author>Frederic Harbecke</author>
    <author>Stefan Belle</author>
    <author>Tim Rickmeyer</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Hydrogel</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Biosensor</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Alginate</value>
    </subject>
    <collection role="institutes" number="">BIOMEMS Lab</collection>
    <collection role="forschungsschwerpunkte" number="">Innovative Material Processing</collection>
  </doc>
  <doc>
    <id>2402</id>
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    <title language="eng">Eukaryotic Genomes Show Strong Evolutionary Conservation of k-mer Composition and Correlation Contributions between Introns and Intergenic Regions</title>
    <abstract language="eng">Several strongly conserved DNA sequence patterns in and between introns and intergenic regions (IIRs) consisting of short tandem repeats (STRs) with repeat lengths &amp;lt;3 bp have already been described in the kingdom of Animalia. In this work, we expanded the search and analysis of conserved DNA sequence patterns to a wider range of eukaryotic genomes. Our aims were to confirm the conservation of these patterns, to support the hypothesis on their functional constraints and/or the identification of unknown patterns. We pairwise compared genomic DNA sequences of genes, exons, CDS, introns and intergenic regions of 34 Embryophyta (land plants), 30 Protista and 29 Fungi using established k-mer-based (alignment-free) comparison methods. Additionally, the results were compared with values derived for Animalia in former studies. We confirmed strong correlations between the sequence structures of IIRs spanning over the entire domain of Eukaryotes. We found that the high correlations within introns, intergenic regions and between the two are a result of conserved abundancies of STRs with repeat units ≤2 bp (e.g., (AT)n). For some sequence patterns and their inverse complementary sequences, we found a violation of equal distribution on complementary DNA strands in a subset of genomes. Looking at mismatches within the identified STR patterns, we found specific preferences for certain nucleotides stable over all four phylogenetic kingdoms. We conclude that all of these conserved patterns between IIRs indicate a shared function of these sequence structures related to STRs.</abstract>
    <parentTitle language="eng">Genes</parentTitle>
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    <identifier type="doi">https://doi.org/10.3390/genes12101571</identifier>
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Our aims were to confirm the conservation of these patterns, to support the hypothesis on their functional constraints and\/or the identification of unknown patterns. We pairwise compared genomic DNA sequences of genes, exons, CDS, introns and intergenic regions of 34 Embryophyta (land plants), 30 Protista and 29 Fungi using established k-mer-based (alignment-free) comparison methods. Additionally, the results were compared with values derived for Animalia in former studies. We confirmed strong correlations between the sequence structures of IIRs spanning over the entire domain of Eukaryotes. We found that the high correlations within introns, intergenic regions and between the two are a result of conserved abundancies of STRs with repeat units \u22642 bp (e.g., (AT)n). For some sequence patterns and their inverse complementary sequences, we found a violation of equal distribution on complementary DNA strands in a subset of genomes. 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    <author>Aaron Sievers</author>
    <author>Liane Sauer</author>
    <author>Michael Hausmann</author>
    <author>Georg Hildenbrand</author>
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    <title language="eng">Analysis of Tidal Accelerations in the Solar System and in Extrasolar Planetary Systems</title>
    <abstract language="eng">Volcanism powered by tidal forces inside celestial bodies can provide enough energy to keep important solvents for living systems in the liquid phase. A prerequisite to calculate such tidal interactions and consequences is depending on simulations for tidal accelerations in a multi-body system. Unfortunately, from measurements in many extrasolar planetary systems, only few physical and orbital parameters are well-known enough for investigated celestial bodies. For calculating tidal acceleration vectors under missing most orbital parameter exactly, a simulation method is developed that is only based on a few basic parameters, easily measurable even in extrasolar planetary systems. Such a method as the one presented here allows finding a relation between the tidal acceleration vectors and potential heating inside celestial objects. Using the values and results of our model approach to our solar system as a “gold standard” for feasibility allowed us to classify this heating in relation to different forms of volcanism. This “gold standard” approach gave us a classification measure for the relevance of tidal heating in other extrasolar systems with a reduced availability of exact physical parameters. We help to estimate conditions for the identification of potential candidates for further sophisticated investigations by more complex established methods such as viscoelastic multi-body theories. As a first example, we applied the procedures developed here to the extrasolar planetary system TRAPPIST-1 as an example to check our working hypothesis.</abstract>
    <parentTitle language="eng">Applied Sciences</parentTitle>
    <identifier type="issn">2076-3417</identifier>
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    <author>Klaus Paschek</author>
    <author>Arthur Roßmann</author>
    <author>Michael Hausmann</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Sonnensystem</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Vulkanismus</value>
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    <collection role="institutes" number="">Medical Engineering and Data Science (Bachelor)</collection>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
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    <title language="eng">Analysis of Tidal Accelerations in the Solar System and in Extrasolar Planetary Systems</title>
    <abstract language="eng">Volcanism powered by tidal forces inside celestial bodies can provide enough energy to keep important solvents for living systems in the liquid phase. Moreover, tidal forces and their environmental consequences may strongly influence habitability of planets and other celestial bodies and may result in special forms of live and living conditions. A prerequisite to calculate such tidal interactions and consequences is depending on simulations for tidal accelerations in a multi-body system. Unfortunately, from measurements in many extrasolar planetary systems only few physical and orbital parameters are well enough known for investigated celestial bodies. For calculating tidal acceleration vectors under missing most orbital parameter exactly, a simulation method is developed that is only based on a few basic parameters, easily measurable even in extrasolar planetary systems. Such a method as being presented here, allows finding a relation between the tidal acceleration vectors and potential heating inside celestial objects. Using values and results of our model approach to our solar system as a “gold standard” for feasibility allowed us to classify this heating in relation to different forms of volcanism. This “gold standard” approach gave us a classification measure for the relevance of tidal heating in other extrasolar systems with a reduced availability of exact physical parameters. We would help to estimate conditions for the identification of potential candidates for further sophisticated investigations by more complex established methods like viscoelastic multi-body theories. As a first example, we applied the procedures developed here to the extrasolar planetary system TRAPPIST-1 as an example to check our working hypothesis.</abstract>
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    <title language="eng">Space and Time in the Universe of the Cell Nucleus after Ionizing Radiation Attacks: A Comparison of Cancer and Non-Cancer Cell Response</title>
    <parentTitle language="eng">The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response</parentTitle>
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    <title language="eng">An Experimental Workflow for Studying Barrier Integrity, Permeability, and Tight Junction Composition and Localization in a Single Endothelial Cell Monolayer: Proof of Concept</title>
    <abstract language="eng">Endothelial and epithelial barrier function is crucial for the maintenance of physiological processes. The barrier paracellular permeability depends on the composition and spatial distribution of the cell-to-cell tight junctions (TJ). Here, we provide an experimental workflow that yields several layers of physiological data in the setting of a single endothelial cell monolayer. Human umbilical vein endothelial cells were grown on Transwell filters. Transendothelial electrical resistance (TER) and 10 kDa FITC dextran flux were measured using Alanyl-Glutamine (AlaGln) as a paracellular barrier modulator. Single monolayers were immunolabelled for Zonula Occludens-1 (ZO-1) and Claudin-5 (CLDN5) and used for automated immunofluorescence imaging. Finally, the same monolayers were used for single molecule localization microscopy (SMLM) of ZO-1 and CLDN5 at the nanoscale for spatial clustering analysis. The TER increased and the paracellular dextran flux decreased after the application of AlaGln and these functional changes of the monolayer were mediated by an increase in the ZO-1 and CLDN5 abundance in the cell–cell interface. At the nanoscale level, the functional and protein abundance data were accompanied by non-random increased clustering of CLDN5. Our experimental workflow provides multiple data from a single monolayer and has wide applicability in the setting of paracellular studies in endothelia and epithelia.</abstract>
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The barrier paracellular permeability depends on the composition and spatial distribution of the cell-to-cell tight junctions (TJ). Here, we provide an experimental workflow that yields several layers of physiological data in the setting of a single endothelial cell monolayer. Human umbilical vein endothelial cells were grown on Transwell filters. Transendothelial electrical resistance (TER) and 10 kDa FITC dextran flux were measured using Alanyl-Glutamine (AlaGln) as a paracellular barrier modulator. Single monolayers were immunolabelled for Zonula Occludens-1 (ZO-1) and Claudin-5 (CLDN5) and used for automated immunofluorescence imaging. Finally, the same monolayers were used for single molecule localization microscopy (SMLM) of ZO-1 and CLDN5 at the nanoscale for spatial clustering analysis. The TER increased and the paracellular dextran flux decreased after the application of AlaGln and these functional changes of the monolayer were mediated by an increase in the ZO-1 and CLDN5 abundance in the cell\u2013cell interface. At the nanoscale level, the functional and protein abundance data were accompanied by non-random increased clustering of CLDN5. Our experimental workflow provides multiple data from a single monolayer and has wide applicability in the setting of paracellular studies in endothelia and epithelia.&lt;\/jats:p&gt;","DOI":"10.3390\/ijms22158178","type":"journal-article","created":{"date-parts":[[2021,7,30]],"date-time":"2021-07-30T07:46:42Z","timestamp":1627631202000},"page":"8178","source":"Crossref","is-referenced-by-count":9,"title":["An Experimental Workflow for Studying Barrier Integrity, Permeability, and Tight Junction Composition and Localization in a Single Endothelial Cell Monolayer: Proof of Concept"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"http:\/\/orcid.org\/0000-0003-1127-3453","authenticated-orcid":false,"given":"Maria","family":"Bartosova","sequence":"first","affiliation":[{"name":"Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-0189-3168","authenticated-orcid":false,"given":"David","family":"Ridinger","sequence":"additional","affiliation":[{"name":"Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-0418-2561","authenticated-orcid":false,"given":"Iva","family":"Marinovic","sequence":"additional","affiliation":[{"name":"Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-1706-4591","authenticated-orcid":false,"given":"Jana","family":"Heigwer","sequence":"additional","affiliation":[{"name":"Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-4296-4054","authenticated-orcid":false,"given":"Conghui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-6149-3254","authenticated-orcid":false,"given":"Eszter","family":"Levai","sequence":"additional","affiliation":[{"name":"Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany"},{"name":"1st Department of Pediatrics, Semmelweis University, 1083 Budapest, Hungary"},{"name":"ELKH-SE Pediatrics and Nephrology Research Group, 1083 Budapest, Hungary"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-9837-9383","authenticated-orcid":false,"given":"Jens H.","family":"Westhoff","sequence":"additional","affiliation":[{"name":"Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-7564-9937","authenticated-orcid":false,"given":"Franz","family":"Schaefer","sequence":"additional","affiliation":[{"name":"Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany"}]},{"given":"Stefan","family":"Terjung","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, Advanced Light Microscopy Facility, 69117 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-1992-6025","authenticated-orcid":false,"given":"Georg","family":"Hildenbrand","sequence":"additional","affiliation":[{"name":"Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany"}]},{"given":"Damir","family":"Krunic","sequence":"additional","affiliation":[{"name":"German Cancer Research Center, 69120 Heidelberg, Germany"}]},{"given":"Felix","family":"Bestvater","sequence":"additional","affiliation":[{"name":"German Cancer Research Center, 69120 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-9430-1987","authenticated-orcid":false,"given":"Michael","family":"Hausmann","sequence":"additional","affiliation":[{"name":"Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany"}]},{"given":"Claus Peter","family":"Schmitt","sequence":"additional","affiliation":[{"name":"Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany"}]},{"given":"Sotirios G.","family":"Zarogiannis","sequence":"additional","affiliation":[{"name":"Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany"},{"name":"Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500 Larissa, Greece"}]}],"member":"1968","published-online":{"date-parts":[[2021,7,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1242\/jcs.193482","article-title":"The mucosal barrier at a glance","volume":"130","author":"France","year":"2017","journal-title":"J. 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    <author>Maria Bartosova</author>
    <author>David Ridinger</author>
    <author>Iva Marinovic</author>
    <author>Jana Heigwer</author>
    <author>Conghui Zhang</author>
    <author>Eszter Levai</author>
    <author>Jens H. Westhoff</author>
    <author>Franz Schaefer</author>
    <author>Stefan Terjung</author>
    <author>Georg Hildenbrand</author>
    <author>Damir Krunic</author>
    <author>Felix Bestvater</author>
    <author>Michael Hausmann</author>
    <author>Claus Peter Schmitt</author>
    <author>Sotirios G. Zarogiannis</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Endothelzelle</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Nabelvene</value>
    </subject>
    <collection role="institutes" number="">Medical Engineering and Data Science (Bachelor)</collection>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
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    <issue>5</issue>
    <volume>129</volume>
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    <title language="eng">Glucose Derivative Induced Vasculopathy in Children on Chronic Peritoneal Dialysis</title>
    <abstract language="eng">Rationale:&#13;
 Patients with chronic kidney disease (CKD) have an exceedingly high cardiovascular risk; which further increases in patients on peritoneal dialysis (PD). The pathophysiological role of reactive metabolites accumulating in CKD such as glucose degradation products (GDP) is uncertain.&#13;
 &#13;
 &#13;
 Objective:&#13;
 Delineating the impact of GDP present in PD fluids in accelerated vasculopathy development in patients with CKD.&#13;
 &#13;
 &#13;
 Methods and Results:&#13;
 Omental and parietal peritoneal tissues were obtained from 107 children with CKD before dialysis and 90 children on chronic PD with PD fluids containing very low or high concentrations of GDP. Omental arterioles, protected from local PD fluid exposure by surrounding fat, were microdissected for multiomics analyses. High-GDP exposed omental arterioles exhibited 3-fold higher advanced glycation endproduct concentrations and upregulated genes involved in cell death/apoptosis and suppressed genes related to cell viability/survival, cytoskeleton organization, and immune response biofunctions. Vasculopathy-associated canonical pathways concordantly regulated on gene and protein level with high-GDP exposure included cell death/proliferation, apoptosis, cytoskeleton organization, metabolism and detoxification, cell junction signaling, and immune response. Parietal peritoneal arterioles of patients exposed to high-GDP fluids exhibited lumen narrowing compared to patients with CKD stage 5 (end-stage kidney disease) and patients on low-GDP PD, intima thickness was increased. Protein quantification verified increased proapoptotic activity and cytoskeleton disintegration, single-molecule-localization microscopy demonstrated arteriolar endothelial ZO-1 (zonula occludens-1) disruption. Absolute and per endoluminal surface length, arteriolar endothelial cell counts inversely correlated with GDP exposure, caspase-3, TGF (transforming growth factor)-β–induced pSMAD2/3 (phosphorylated SMAD2/3), interleukin-6, ZO-1 abundance, and lumen narrowing. In vitro, 3,4-dideoxyglucosone-3-ene reduced lamin-A/C and membrane ZO-1 assembly, increased pSMAD2/3, and ionic and 4 and 10 kDa permeability of arterial endothelial cells.&#13;
 &#13;
 &#13;
 Conclusions:&#13;
 Our findings indicate a fundamental role of GDP in PD-associated vasculopathy, exerted by endothelial cell junction and cytoskeleton disruption, and induction of apoptosis. They should redirect the focus of research and intervention on targeting reactive metabolite overload in CKD and PD.&#13;
 &#13;
 &#13;
 Registration:&#13;
  URL: https://www.clinicaltrials.gov ; Unique identifier: NCT01893710.</abstract>
    <parentTitle language="eng">Circulation Research</parentTitle>
    <identifier type="issn">0009-7330</identifier>
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The pathophysiological role of reactive metabolites accumulating in CKD such as glucose degradation products (GDP) is uncertain.&lt;\/jats:p&gt;\n          &lt;\/jats:sec&gt;\n          &lt;jats:sec&gt;\n            &lt;jats:title&gt;Objective:&lt;\/jats:title&gt;\n            &lt;jats:p&gt;Delineating the impact of GDP present in PD fluids in accelerated vasculopathy development in patients with CKD.&lt;\/jats:p&gt;\n          &lt;\/jats:sec&gt;\n          &lt;jats:sec&gt;\n            &lt;jats:title&gt;Methods and Results:&lt;\/jats:title&gt;\n            &lt;jats:p&gt;Omental and parietal peritoneal tissues were obtained from 107 children with CKD before dialysis and 90 children on chronic PD with PD fluids containing very low or high concentrations of GDP. Omental arterioles, protected from local PD fluid exposure by surrounding fat, were microdissected for multiomics analyses. High-GDP exposed omental arterioles exhibited 3-fold higher advanced glycation endproduct concentrations and upregulated genes involved in cell death\/apoptosis and suppressed genes related to cell viability\/survival, cytoskeleton organization, and immune response biofunctions. Vasculopathy-associated canonical pathways concordantly regulated on gene and protein level with high-GDP exposure included cell death\/proliferation, apoptosis, cytoskeleton organization, metabolism and detoxification, cell junction signaling, and immune response. Parietal peritoneal arterioles of patients exposed to high-GDP fluids exhibited lumen narrowing compared to patients with CKD stage 5 (end-stage kidney disease) and patients on low-GDP PD, intima thickness was increased. Protein quantification verified increased proapoptotic activity and cytoskeleton disintegration, single-molecule-localization microscopy demonstrated arteriolar endothelial ZO-1 (zonula occludens-1) disruption. Absolute and per endoluminal surface length, arteriolar endothelial cell counts inversely correlated with GDP exposure, caspase-3, TGF (transforming growth factor)-\u03b2\u2013induced pSMAD2\/3 (phosphorylated SMAD2\/3), interleukin-6, ZO-1 abundance, and lumen narrowing. In vitro, 3,4-dideoxyglucosone-3-ene reduced lamin-A\/C and membrane ZO-1 assembly, increased pSMAD2\/3, and ionic and 4 and 10 kDa permeability of arterial endothelial cells.&lt;\/jats:p&gt;\n          &lt;\/jats:sec&gt;\n          &lt;jats:sec&gt;\n            &lt;jats:title&gt;Conclusions:&lt;\/jats:title&gt;\n            &lt;jats:p&gt;Our findings indicate a fundamental role of GDP in PD-associated vasculopathy, exerted by endothelial cell junction and cytoskeleton disruption, and induction of apoptosis. 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    <author>Maria Bartosova</author>
    <author>Conghui Zhang</author>
    <author>Betti Schaefer</author>
    <author>Rebecca Herzog</author>
    <author>David Ridinger</author>
    <author>Ivan Damgov</author>
    <author>Eszter Levai</author>
    <author>Iva Marinovic</author>
    <author>Christoph Eckert</author>
    <author>Philipp Romero</author>
    <author>Peter Sallay</author>
    <author>Akos Ujszaszi</author>
    <author>Markus Unterwurzacher</author>
    <author>Anja Wagner</author>
    <author>Georg Hildenbrand</author>
    <author>Bradley A. Warady</author>
    <author>Franz Schaefer</author>
    <author>Sotirios G. Zarogiannis</author>
    <author>Klaus Kratochwill</author>
    <author>Claus Peter Schmitt</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Peritonealdialyse</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Gefäßkrankheit</value>
    </subject>
    <subject>
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      <value>Kind</value>
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    <collection role="institutes" number="">Medical Engineering and Data Science (Bachelor)</collection>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
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    <volume>36</volume>
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    <publisherName>Oxford University Press (OUP)</publisherName>
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    <title language="eng">Glucose Derivative Induced Vasculopathy in Children on Chronic Peritoneal Dialysis</title>
    <abstract language="eng">Abstract&#13;
 &#13;
 Background and Aims&#13;
 Patients with chronic kidney disease patients (CKD) have an exceedingly high cardiovascular risk. While vasculopathy is further accelerated during peritoneal dialysis (PD), the pathophysiological role of reactive metabolites such as glucose degradation products (GDP) is uncertain.&#13;
 &#13;
 &#13;
 Method&#13;
 Omental and parietal peritoneal tissues from 100 non-CKD individuals, 107 children with CKD5, 60 children treated with neutral pH, low GDP, and 30 children treated with acidic pH, high GDP PD fluids underwent standardized digital histomorphometry. Omental arterioles localized within the fat tissue, protected from direct PD fluid exposure were microdissected for multi-omics analysis. Key regulated pathways were validated by quantitative immunostaining, with localization microscopy in peritoneal tissues of matched cohorts and in vitro in human umbilical vein endothelial cells.&#13;
 &#13;
 &#13;
 Results&#13;
 Arterioles from children with CKD5 exhibited reduced lumen to vessel ratio (L/V) and reduced endothelial telomere length compared to non-CKD individuals; gene ontology analysis identified enrichment of arteriolar genes associated with nuclear telomere cap complex and focal adhesion. Pathway analysis of arteriolar cross-omics identified top canonical pathways including telomere extension by telomerase, actin cytoskeleton, integrin and tight junction signalling.&#13;
 Peritoneal vasculopathy progressed with PD vintage and was more pronounced with high versus low GDP exposure (p&amp;amp;lt;0.001). Compared to CKD5, low GDP-PD upregulated 145/110 and downregulated 38/34 arteriolar genes/proteins, high GDP-PD upregulated 684/137 and supressed 1560/55 genes/proteins (p&amp;amp;lt;0.01). High GDP milieu induced upregulation of arteriolar genes involved in cell death/apoptosis and suppressed genes related to cell viability/survival, cytoskeleton organization and immune response biofunctions. Vasculopathy associated canonical pathways concordantly regulated on arteriolar gene and protein level with high GDP exposure included cell death/proliferation, apoptosis, cytoskeleton organization, metabolism and detoxification, cell junction signalling, and immune response.&#13;
 Quantitative validation in PD cohorts with similar PD vintage, dialytic glucose exposure and age (n=15 / group) verified increased proapoptotic activity and cytoskeleton disintegration with high-GDP exposure; single-molecule-localization microscopy demonstrated arteriolar endothelial zonula occludens-1 (ZO-1) disruption. Absolute and relative to endoluminal surface length, arteriolar endothelial cell counts were inversely correlated with GDP exposure, with apoptosis marker caspase-3, TGF-ß induced pSMAD2/3, interleukin-6, ZO-1 protein abundance and the degree of vasculopathy. In vitro, exposure to GDP 3,4-dideoxyglucosone-3-ene dose-dependently reduced nuclear endothelial lamin-A/C and membrane ZO-1 assembly. Transendothelial electrical resistance was decreased. ZO-1 and sealing tight junction claudin-5 protein abundance were decreased in cells after incubation with high GDP compared to low GDP PD fluid and culture media. On nanoscale level GDP reduced junction cluster formation in the membrane area.&#13;
 &#13;
 &#13;
 Conclusion&#13;
 Multi-omics analysis of omental arterioles from children without pre-existing vasculopathy and life-style related confounders identified key mechanisms of vascular aging in CKD5 and the major contribution of GDP to accelerated vasculopathy during PD, i.e. disruption of endothelial cell junctions and cytoskeleton and induction of apoptosis.</abstract>
    <parentTitle language="eng">Nephrology Dialysis Transplantation</parentTitle>
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    <identifier type="doi">https://doi.org/10.1093/ndt/gfab126.004</identifier>
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While vasculopathy is further accelerated during peritoneal dialysis (PD), the pathophysiological role of reactive metabolites such as glucose degradation products (GDP) is uncertain.&lt;\/jats:p&gt;\n               &lt;\/jats:sec&gt;\n               &lt;jats:sec&gt;\n                  &lt;jats:title&gt;Method&lt;\/jats:title&gt;\n                  &lt;jats:p&gt;Omental and parietal peritoneal tissues from 100 non-CKD individuals, 107 children with CKD5, 60 children treated with neutral pH, low GDP, and 30 children treated with acidic pH, high GDP PD fluids underwent standardized digital histomorphometry. Omental arterioles localized within the fat tissue, protected from direct PD fluid exposure were microdissected for multi-omics analysis. Key regulated pathways were validated by quantitative immunostaining, with localization microscopy in peritoneal tissues of matched cohorts and in vitro in human umbilical vein endothelial cells.&lt;\/jats:p&gt;\n               &lt;\/jats:sec&gt;\n               &lt;jats:sec&gt;\n                  &lt;jats:title&gt;Results&lt;\/jats:title&gt;\n                  &lt;jats:p&gt;Arterioles from children with CKD5 exhibited reduced lumen to vessel ratio (L\/V) and reduced endothelial telomere length compared to non-CKD individuals; gene ontology analysis identified enrichment of arteriolar genes associated with nuclear telomere cap complex and focal adhesion. Pathway analysis of arteriolar cross-omics identified top canonical pathways including telomere extension by telomerase, actin cytoskeleton, integrin and tight junction signalling.&lt;\/jats:p&gt;\n                  &lt;jats:p&gt;Peritoneal vasculopathy progressed with PD vintage and was more pronounced with high versus low GDP exposure (p&amp;amp;lt;0.001). Compared to CKD5, low GDP-PD upregulated 145\/110 and downregulated 38\/34 arteriolar genes\/proteins, high GDP-PD upregulated 684\/137 and supressed 1560\/55 genes\/proteins (p&amp;amp;lt;0.01). High GDP milieu induced upregulation of arteriolar genes involved in cell death\/apoptosis and suppressed genes related to cell viability\/survival, cytoskeleton organization and immune response biofunctions. 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    <title language="eng">Elucidation of the Clustered Nano-Architecture of Radiation-Induced DNA Damage Sites and Surrounding Chromatin in Cancer Cells: A Single Molecule Localization Microscopy Approach</title>
    <abstract language="eng">In cancer therapy, the application of (fractionated) harsh radiation treatment is state of the art for many types of tumors. However, ionizing radiation is a “double-edged sword”—it can kill the tumor but can also promote the selection of radioresistant tumor cell clones or even initiate carcinogenesis in the normal irradiated tissue. Individualized radiotherapy would reduce these risks and boost the treatment, but its development requires a deep understanding of DNA damage and repair processes and the corresponding control mechanisms. DNA double strand breaks (DSBs) and their repair play a critical role in the cellular response to radiation. In previous years, it has become apparent that, beyond genetic and epigenetic determinants, the structural aspects of damaged chromatin (i.e., not only of DSBs themselves but also of the whole damage-surrounding chromatin domains) form another layer of complex DSB regulation. In the present article, we summarize the application of super-resolution single molecule localization microscopy (SMLM) for investigations of these structural aspects with emphasis on the relationship between the nano-architecture of radiation-induced repair foci (IRIFs), represented here by γH2AX foci, and their chromatin environment. Using irradiated HeLa cell cultures as an example, we show repair-dependent rearrangements of damaged chromatin and analyze the architecture of γH2AX repair clusters according to topological similarities. Although HeLa cells are known to have highly aberrant genomes, the topological similarity of γH2AX was high, indicating a functional, presumptively genome type-independent relevance of structural aspects in DSB repair. Remarkably, nano-scaled chromatin rearrangements during repair depended both on the chromatin domain type and the treatment. Based on these results, we demonstrate how the nano-architecture and topology of IRIFs and chromatin can be determined, point to the methodological relevance of SMLM, and discuss the consequences of the observed phenomena for the DSB repair network regulation or, for instance, radiation treatment outcomes.</abstract>
    <parentTitle language="eng">International Journal of Molecular Sciences</parentTitle>
    <identifier type="issn">1422-0067</identifier>
    <identifier type="doi">https://doi.org/10.3390/ijms22073636</identifier>
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    <author>Michael Hausmann</author>
    <author>Martin Falk</author>
    <author>Charlotte Neitzel</author>
    <author>Andreas Hofmann</author>
    <author>Abin Biswas</author>
    <author>Theresa Gier</author>
    <author>Iva Falkova</author>
    <author>Dieter W. Heermann</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Krebszelle</value>
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      <value>Strahlentherapie</value>
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    <completedDate>2020-03-18</completedDate>
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    <title language="eng">Comparison of Different Spike Train Synchrony Measures Regarding Their Robustness to Erroneous Data from Bicuculline-Induced Epileptiform Activity</title>
    <abstract language="eng">As synchronized activity is associated with basic brain functions and pathological states, spike train synchrony has become an important measure to analyze experimental neuronal data. Many measures of spike train synchrony have been proposed, but there is no gold standard allowing for comparison of results from different experiments. This work aims to provide guidance on which synchrony measure is best suited to quantify the effect of epileptiform-inducing substances (e.g., bicuculline, BIC) in in vitro neuronal spike train data. Spike train data from recordings are likely to suffer from erroneous spike detection, such as missed spikes (false negative) or noise (false positive). Therefore, different timescale-dependent (cross-correlation, mutual information, spike time tiling coefficient) and timescale-independent (Spike-contrast, phase synchronization (PS), A-SPIKE-synchronization, A-ISI-distance, ARI-SPIKE-distance) synchrony measures were compared in terms of their robustness to erroneous spike trains. For this purpose, erroneous spike trains were generated by randomly adding (false positive) or deleting (false negative) spikes (in silico manipulated data) from experimental data. In addition, experimental data were analyzed using different spike detection threshold factors in order to confirm the robustness of the synchrony measures. All experimental data were recorded from cortical neuronal networks on microelectrode array chips, which show epileptiform activity induced by the substance BIC. As a result of the in silico manipulated data, Spike-contrast was the only measure that was robust to false-negative as well as false-positive spikes. Analyzing the experimental data set revealed that all measures were able to capture the effect of BIC in a statistically significant way, with Spike-contrast showing the highest statistical significance even at low spike detection thresholds. In summary, we suggest using Spike contrast to complement established synchrony measures because it is timescale independent and robust to erroneous spike trains.</abstract>
    <parentTitle language="eng">Neural Computation</parentTitle>
    <identifier type="doi">10.1162/neco_a_01277</identifier>
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    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Manuel Ciba</author>
    <author>Robert Bestel</author>
    <author>Christoph Nick</author>
    <author>Guilherme Ferraz de Arruda</author>
    <author>Thomas Peron</author>
    <author>Comin César Henrique</author>
    <author>Luciano da Fontoura Costa</author>
    <author>Francisco Aparecido Rodrigues</author>
    <author>Christiane Thielemann</author>
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      <value>Neuronales Netz</value>
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    <title language="eng">Single Molecule Localization Microscopy Analyses of DNA-Repair Foci and Clusters Detected Along Particle Damage Tracks</title>
    <parentTitle language="eng">Frontiers in Physics</parentTitle>
    <identifier type="issn">2296-424X</identifier>
    <identifier type="doi">https://doi.org/10.3389/fphy.2020.578662</identifier>
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    <title language="eng">Super-resolution microscopy of nanogold-labelling</title>
    <parentTitle language="eng">Nanoparticle Enhanced Radiation Therapy</parentTitle>
    <identifier type="isbn">9780750323963</identifier>
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      <type>swd</type>
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    <title language="eng">3D DNA FISH for analyses of chromatin-nuclear architecture</title>
    <parentTitle language="eng">Epigenetics Methods</parentTitle>
    <identifier type="isbn">9780128194140</identifier>
    <identifier type="doi">https://doi.org/10.1016/B978-0-12-819414-0.00020-3</identifier>
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    <author>Michael Hausmann</author>
    <author>Jin-Ho Lee</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Genom</value>
    </subject>
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  </doc>
  <doc>
    <id>1521</id>
    <completedYear>2019</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>427</pageFirst>
    <pageLast>435</pageLast>
    <pageNumber/>
    <edition/>
    <issue>5:4</issue>
    <volume>2019</volume>
    <type>article</type>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2019-01-02</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Electrochemical Characterization of Graphene Microelectrodes for Biological Applications</title>
    <abstract language="eng">Graphene is a promising material both as a coating for existing neural electrodes as well as for transparent electrodes made exclusively from graphene. We studied graphene‐based microelectrodes by investigating their recording and stimulation properties in order to evaluate their suitability for neuronal implants. In this work, we compare three different electrode material compositions. Microelectrode arrays (MEA) with an electrode size of about 700 μm2 were prepared of gold, graphene on gold, and plain graphene on glass substrate. In order to reduce polymer contamination during graphene transfer, we employed a polymer‐free transfer and lift‐off process. Impedance studies revealed a value of 2.3 MΩ at 1 kHz for plain, and 0.88 MΩ for graphene on gold. Neuronal recording experiments showed a sufficient SNR for both graphene‐based materials and a stable impedance, unaffected by surface degradation metal electrodes are known for. Stimulation measurements yielded a charge injection capacity of 0.15 mC/cm2 using biphasic pulses of 1 ms and 1 μA transparent graphene electrodes. Cyclic voltammetry revealed a large voltage range of −1.4 V to +1.6 V before water electrolysis occurs. Graphene‐coated gold microelectrodes show enhanced recording properties, whereas plain graphene electrodes might be better suited for stimulation applications.</abstract>
    <parentTitle language="eng">ChemNanoMat</parentTitle>
    <identifier type="doi">10.1002/cnma.201800652</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Berit Silke Körbitzer</author>
    <author>Peter Krauß</author>
    <author>Stefan Belle</author>
    <author>Jörg Schneider</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Graphene</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Microelectrodes</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Stimulation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Neural Recording</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Neural Interface</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Mikroelektrode</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Array</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
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  </doc>
  <doc>
    <id>1512</id>
    <completedYear>2019</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>169</pageFirst>
    <pageLast>181</pageLast>
    <pageNumber/>
    <edition/>
    <issue>312</issue>
    <volume>312</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2019-01-15</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Total spiking probability edges: A cross-correlation based method for effective connectivity estimation of cortical spiking neurons</title>
    <abstract language="eng">Background: Connectivity is a relevant parameter for the information flow within neuronal networks. Network connectivity can be reconstructed from recorded spike train data. Various methods have been developed to estimate connectivity from spike trains. New method: In this work, a novel effective connectivity estimation algorithm called Total Spiking Probability Edges (TSPE) is proposed and evaluated. First, a cross-correlation between pairs of spike trains is calculated. Second, to distinguish between excitatory and inhibitory connections, edge filters are applied on the resulting cross-correlogram. Results: TSPE was evaluated with large scale in silico networks and enables almost perfect reconstructions (true positive rate of approx. 99% at a false positive rate of 1% for low density random networks) depending on the network topology and the spike train duration. A distinction between excitatory and inhibitory connections was possible. TSPE is computational effective and takes less than 3 min on a high-performance computer to estimate the connectivity of an 1 h dataset of 1000 spike trains. Comparison of existing methods: TSPE was compared with connectivity estimation algorithms like Transfer Entropy based methods, Filtered and Normalized Cross-Correlation Histogram and Normalized Cross-Correlation. In all test cases, TSPE outperformed the compared methods in the connectivity reconstruction accuracy. Conclusions: The results show that the accuracy of functional connectivity estimation of large scale neuronal networks has been enhanced by TSPE compared to state of the art methods. Furthermore, TSPE enables the classification of excitatory and inhibitory synaptic effects.</abstract>
    <parentTitle language="eng">Journal of Neuroscience Methods</parentTitle>
    <identifier type="doi">10.1016/j.jneumeth.2018.11.013</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Stefano De Blasi</author>
    <author>Manuel Ciba</author>
    <author>Andreas Bahmer</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Connectivity Estimation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Neuronal Networks</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Parallel Spike Trains</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Inhibitory and Excitatory</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
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  </doc>
  <doc>
    <id>1518</id>
    <completedYear>2019</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2020-03-13</completedDate>
    <publishedDate>--</publishedDate>
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    <title language="eng">Experimental setup to investigate the effect of psychedelics on in vitro neuronal networks</title>
    <abstract language="eng">Experimental setup to investigate the effect of psychedelics on in vitro neuronal networks: A demonstration of the application of in vitro neuronal networks on high-density-microelectrode arrays (HDMEA) to study electrophysiological properties of neuronal networks in response to psychedelics.</abstract>
    <abstract language="deu">Poster</abstract>
    <identifier type="doi">10.6084/m9.figshare.11980434.v1</identifier>
    <identifier type="url">https://doi.org/10.6084/m9.figshare.11980434.v1</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Manuel Ciba</author>
    <author>Margot Mayer</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
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    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>2412</id>
    <completedYear>2019</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>3</issue>
    <volume>20</volume>
    <type>article</type>
    <publisherName>MDPI AG</publisherName>
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    <creatingCorporation/>
    <contributingCorporation/>
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    <title language="eng">Challenges and Contradictions of Metal Nano-Particle Applications for Radio-Sensitivity Enhancement in Cancer Therapy</title>
    <abstract language="eng">From the very beginnings of radiotherapy, a crucial question persists with how to target the radiation effectiveness into the tumor while preserving surrounding tissues as undamaged as possible. One promising approach is to selectively pre-sensitize tumor cells by metallic nanoparticles. However, though the “physics” behind nanoparticle-mediated radio-interaction has been well elaborated, practical applications in medicine remain challenging and often disappointing because of limited knowledge on biological mechanisms leading to cell damage enhancement and eventually cell death. In the present study, we analyzed the influence of different nanoparticle materials (platinum (Pt), and gold (Au)), cancer cell types (HeLa, U87, and SKBr3), and doses (up to 4 Gy) of low-Linear Energy Transfer (LET) ionizing radiation (γ- and X-rays) on the extent, complexity and reparability of radiation-induced γH2AX + 53BP1 foci, the markers of double stand breaks (DSBs). Firstly, we sensitively compared the focus presence in nuclei during a long period of time post-irradiation (24 h) in spatially (three-dimensionally, 3D) fixed cells incubated and non-incubated with Pt nanoparticles by means of high-resolution immunofluorescence confocal microscopy. The data were compared with our preliminary results obtained for Au nanoparticles and recently published results for gadolinium (Gd) nanoparticles of approximately the same size (2–3 nm). Next, we introduced a novel super-resolution approach—single molecule localization microscopy (SMLM)—to study the internal structure of the repair foci. In these experiments, 10 nm Au nanoparticles were used that could be also visualized by SMLM. Altogether, the data show that different nanoparticles may or may not enhance radiation damage to DNA, so multi-parameter effects have to be considered to better interpret the radiosensitization. Based on these findings, we discussed on conclusions and contradictions related to the effectiveness and presumptive mechanisms of the cell radiosensitization by nanoparticles. We also demonstrate that SMLM offers new perspectives to study internal structures of repair foci with the goal to better evaluate potential differences in DNA damage patterns.</abstract>
    <parentTitle language="eng">International Journal of Molecular Sciences</parentTitle>
    <identifier type="issn">1422-0067</identifier>
    <identifier type="doi">https://doi.org/10.3390/ijms20030588</identifier>
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    <author>Eva Pagáčová</author>
    <author>Lenka Štefančíková</author>
    <author>Franz Schmidt-Kaler</author>
    <author>Georg Hildenbrand</author>
    <author>Tomáš Vičar</author>
    <author>Daniel Depeš</author>
    <author>Jin-Ho Lee</author>
    <author>Felix Bestvater</author>
    <author>Sandrine Lacombe</author>
    <author>Erika Porcel</author>
    <author>Stéphane Roux</author>
    <author>Frederik Wenz</author>
    <author>Olga Kopecna</author>
    <author>Iva Falková</author>
    <author>Michael Hausmann</author>
    <author>Martin Falk</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Krebs, Medizin</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Strahlentherapie</value>
    </subject>
    <collection role="institutes" number="">Medical Engineering and Data Science (Bachelor)</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>2425</id>
    <completedYear>2019</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
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    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Mechanisms and Challenges for Understanding Radiation Induced Changes in Chromatin Nanoarchitecture</title>
    <abstract language="eng">The three-dimensional architecture of genomes acts as an additional level of mode for fundamental biological processes such as DNA damage response. In this context, nanoprobing and super-resolution microscopy are powerful methods for structural analyses of genomic targets in native chromatin of single cells at resolutions of single antibodies, proteins, histones, short DNA stretches, etc. We used multi-color chromatin nanoprobing and single molecule localization microscopy of established DNA damage and chromatin markers in 3D-conserved nuclei of different cell types exposed to various types and doses of ionizing radiation. Similarly, effect of gold nanoparticles on extent and direction of cellular radiation response was assessed. Our studies revealed the nanoarchitecture of damage foci with respect to γH2AX, Mre11 or 53BP1 and their molecular rearrangements during repair processes. Nanoscopy of genomic Alu resulted in linear-quadratic dose-effects for low to higher dose ranges and in changes of H3K9me3 distribution around Alu clusters upon radiation exposure. Preliminary results show post-irradiation time dependent changes in Alu chromatin. Moreover, gold nanoparticles incorporated into cells seem to act by an interplay of radiation enhancement and chromatin remodeling leading to altered radiosensitivity. Our results contribute to the understanding of cellular radiation responses, thereby laying the basis for improved biological dosimetry and radiotherapies in future.</abstract>
    <abstract language="deu">Poster</abstract>
    <parentTitle language="deu">DRO 2018</parentTitle>
    <identifier type="doi">https://doi.org/10.13140/RG.2.2.31391.20647</identifier>
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    <enrichment key="conference_title">DRO 2018</enrichment>
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    <author>Jin-Ho Lee</author>
    <author>Elizaveta Bobkova</author>
    <author>Theresa Gier</author>
    <author>Martin Gote</author>
    <author>Fanz Schmidt-kaler</author>
    <author>Emily Brieger</author>
    <author>Emanuel Maus</author>
    <author>Matthias Krufczik</author>
    <author>Robert Chojowski</author>
    <author>Friederike Korn</author>
    <author>Schumann Sarah</author>
    <author>Harry Scherthan</author>
    <author>Iva Falkova</author>
    <author>Martin Falk</author>
    <author>Michael Hausmann</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Genom</value>
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  <doc>
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    <issue>012107</issue>
    <volume>1407</volume>
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    <completedDate>2019-12-05</completedDate>
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    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Laser-bonding of FEP/FEP interfaces for a flexiblemanufacturing process of ferroelectrets</title>
    <abstract language="eng">This paper presents an optimized laser-bonding process for piezoelectric energy-harvesters based on thin fluorinated-ethylene-propylene (FEP) foils, using an ultra-short-pulse(USP) laser. Due to the minimized thermal stress in the material during bonding, achieved bypulse durations of few picoseconds, we created seams down to 40μm width without generatingholes in the 12.5μm thick FEP-foils. Using a galvanometer scanning system allowed for fastbonding-speed up to several centimeters per second, making the process also suitable for largestructures and areas.  The achieved bond strength of the seams under influence of shearingstress was examined using tensile testing, which showed a sufficient strength of about 25 % of the maximum strength of an unbonded, single layer of FEP.</abstract>
    <parentTitle language="eng">Journal of Physics: Conference Series</parentTitle>
    <identifier type="doi">10.1088/1742-6596/1407/1/012107</identifier>
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    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Dennis Flachs</author>
    <author>Florian Emmerich</author>
    <author>Gian-Luca Roth</author>
    <author>Ralf Hellmann</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Ultrakurzzeitlaser</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Piezoelektrizität</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Innovative Material Processing</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>2414</id>
    <completedYear>2018</completedYear>
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    <language>eng</language>
    <pageFirst/>
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    <pageNumber/>
    <edition/>
    <issue>10</issue>
    <volume>9</volume>
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    <title language="eng">Conservation of k-mer Composition and Correlation Contribution between Introns and Intergenic Regions of Animalia Genomes</title>
    <abstract language="eng">In this study, we pairwise-compared multiple genome regions, including genes, exons, coding DNA sequences (CDS), introns, and intergenic regions of 39 Animalia genomes, including Deuterostomia (27 species) and Protostomia (12 species), by applying established k-mer-based (alignment-free) comparison methods. We found strong correlations between the sequence structure of introns and intergenic regions, individual organisms, and within wider phylogenetical ranges, indicating the conservation of certain structures over the full range of analyzed organisms. We analyzed these sequence structures by quantifying the contribution of different sets of DNA words to the average correlation value by decomposing the correlation coefficients with respect to these word sets. We found that the conserved structures within introns, intergenic regions, and between the two were mainly a result of conserved tandem repeats with repeat units ≤ 2 bp (e.g., (AT)n), while other conserved sequence structures, such as those found between exons and CDS, were dominated by tandem repeats with repeat unit sizes of 3 bp in length and more complex DNA word patterns. We conclude that the conservation between intron and intergenic regions indicates a shared function of these sequence structures. Also, the similar differences in conserved structures with known origin, especially to the conservation between exons and CDS resulting from DNA codons, indicate that k-mer composition-based functional properties of introns and intergenic regions may differ from those of exons and CDS.</abstract>
    <parentTitle language="eng">Genes</parentTitle>
    <identifier type="issn">2073-4425</identifier>
    <identifier type="doi">https://doi.org/10.3390/genes9100482</identifier>
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We found strong correlations between the sequence structure of introns and intergenic regions, individual organisms, and within wider phylogenetical ranges, indicating the conservation of certain structures over the full range of analyzed organisms. We analyzed these sequence structures by quantifying the contribution of different sets of DNA words to the average correlation value by decomposing the correlation coefficients with respect to these word sets. We found that the conserved structures within introns, intergenic regions, and between the two were mainly a result of conserved tandem repeats with repeat units \u2264 2 bp (e.g., (AT)n), while other conserved sequence structures, such as those found between exons and CDS, were dominated by tandem repeats with repeat unit sizes of 3 bp in length and more complex DNA word patterns. We conclude that the conservation between intron and intergenic regions indicates a shared function of these sequence structures. Also, the similar differences in conserved structures with known origin, especially to the conservation between exons and CDS resulting from DNA codons, indicate that k-mer composition-based functional properties of introns and intergenic regions may differ from those of exons and CDS.&lt;\/jats:p&gt;","DOI":"10.3390\/genes9100482","type":"journal-article","created":{"date-parts":[[2018,10,4]],"date-time":"2018-10-04T16:29:57Z","timestamp":1538670597000},"page":"482","source":"Crossref","is-referenced-by-count":13,"title":["Conservation of k-mer Composition and Correlation Contribution between Introns and Intergenic Regions of Animalia Genomes"],"prefix":"10.3390","volume":"9","author":[{"given":"Aaron","family":"Sievers","sequence":"first","affiliation":[{"name":"Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany"}]},{"given":"Frederik","family":"Wenz","sequence":"additional","affiliation":[{"name":"Department of Radiation Oncology, Medical Faculty Mannheim, Universit\u00e4tsmedizin Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-9430-1987","authenticated-orcid":false,"given":"Michael","family":"Hausmann","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany"}]},{"given":"Georg","family":"Hildenbrand","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany"},{"name":"Department of Radiation Oncology, Medical Faculty Mannheim, Universit\u00e4tsmedizin Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany"}]}],"member":"1968","published-online":{"date-parts":[[2018,10,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1588","DOI":"10.1073\/pnas.47.10.1588","article-title":"The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides","volume":"47","author":"Nirenberg","year":"1961","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_2","first-page":"3","article-title":"Origin, development, and maturation of organelles and organelle systems of the cell surface in Paramecium","volume":"9","author":"Ehret","year":"1963","journal-title":"Sci. Direct."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Palazzo, A.F., and Gregory, T.R. (2014). The Case of Junk DNA. PLoS Genet., 10.","DOI":"10.1371\/journal.pgen.1004351"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1093\/molbev\/msg111","article-title":"High intron sequence conservation across three mammalian orders suggests functional constraints","volume":"20","author":"Hare","year":"2003","journal-title":"Mol. Biol. Evol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Zhou, F., Olman, V., and Xu, Y. (2008). Barcodes for genomes and applications. 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Evol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1745-6150-8-3","article-title":"Next-generation phylogenetics","volume":"8","author":"Chan","year":"2013","journal-title":"Biol. Direct"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S0378-1119(02)01206-4","article-title":"Pentamer vocabularies characterizing introns and intron-like intergenic tracts from Caenorhabditis elegans and Drosophila melanogaster","volume":"304","author":"Bultrini","year":"2003","journal-title":"Gene"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Sievers, A., Boesik, K., Bisch, M., Dreessen, C., Riedel, J., Fro\u00df, P., Hausmann, M., and Hildenbrand, G. (2017). K-mer content, correlation, and position analysis of genome DNA sequences for the identification of function and evolutionary features. Genes, 8.","DOI":"10.3390\/genes8040122"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1098\/rspl.1895.0041","article-title":"Note on regression and inheritance in the case of two parents","volume":"58","author":"Pearson","year":"1895","journal-title":"Proc. R. Soc. Lond."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"D34","DOI":"10.1093\/nar\/gki063","article-title":"GenBank","volume":"33","author":"Benson","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1080\/07391102.1986.10507643","article-title":"Linguistics of nucleotide sequences: Morphology and comparison of vocabularies","volume":"4","author":"Brendel","year":"1986","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2677","DOI":"10.1073\/pnas.0813249106","article-title":"Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions","volume":"106","author":"Sims","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"72","DOI":"10.2307\/1412159","article-title":"The proof and measurement of association between two things","volume":"15","author":"Spearman","year":"1904","journal-title":"Am. J. Psychol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/s41588-018-0062-7","article-title":"The human noncoding genome defined by genetic diversity","volume":"50","author":"Bartha","year":"2018","journal-title":"Nat. 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Eng."},{"key":"ref_23","first-page":"11","article-title":"Deciphering the transcriptional cis-regulatory code","volume":"1","author":"Kvon","year":"2013","journal-title":"Trends Genet."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1770","DOI":"10.1101\/gad.17268411","article-title":"Ending the message: Poly(A) signals then and now","volume":"25","author":"Proudfoot","year":"2011","journal-title":"Genes Dev."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1093\/bib\/bbt003","article-title":"Understanding and identifying amino acid repeats","volume":"15","author":"Luo","year":"2014","journal-title":"Brief. Bioinform."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.1016\/j.cub.2009.07.049","article-title":"Emergence of a new gene from an intergenic region","volume":"19","author":"Heinen","year":"2009","journal-title":"Curr. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1146\/annurev.genet.37.040103.103949","article-title":"Pseudogenes: Are They \u201cJunk\u201d or Functional DNA?","volume":"37","author":"Balakirev","year":"2003","journal-title":"Annu. Rev. Genet."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Ohno, S. (1970). Evolution by Gene Duplication, Springer-Verlag.","DOI":"10.1007\/978-3-642-86659-3"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/S1672-0229(07)60009-6","article-title":"A brief review of short tandem repeat mutation","volume":"5","author":"Fan","year":"2007","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1111\/nyas.12637","article-title":"A LINE-1-encoded reverse transcriptase-dependent regulatory mechanism is active in embryogenesis and tumorigenesis","volume":"1341","author":"Spadafora","year":"2015","journal-title":"Ann. N. Y. Acad Sci."},{"key":"ref_31","unstructured":"Smit, A.F.A., Hubley, R., and Green, P. (2018, July 02). Repeat Master Open 4.0. 2013\u20132015. Available online: http:\/\/www.repeatmasker.org."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase Update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"Bao","year":"2015","journal-title":"Mob. DNA"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nrg3682","article-title":"Transcriptional enhancers: From properties to genome-wide predictions","volume":"15","author":"Shlyueva","year":"2014","journal-title":"Nat. Rev. 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Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2511","DOI":"10.1002\/elps.201300227","article-title":"Evaluation of DNA bending models in their capacity to predict electrophoretic migration anomalies of satellite DNA sequences","volume":"34","year":"2013","journal-title":"Electrophoresis"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Johnson, S., Chen, Y., and Phillips, R. (2013). Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0075799"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/9\/10\/482\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T23:27:38Z","timestamp":1718234858000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/9\/10\/482"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,4]]},"references-count":38,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2018,10]]}},"alternative-id":["genes9100482"],"URL":"http:\/\/dx.doi.org\/10.3390\/genes9100482","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,10,4]]}}}</enrichment>
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    <author>Aaron Sievers</author>
    <author>Frederik Wenz</author>
    <author>Michael Hausmann</author>
    <author>Georg Hildenbrand</author>
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      <language>deu</language>
      <type>swd</type>
      <value>Genom</value>
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    <language>eng</language>
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    <title language="eng">Localization Microscopy Analyses of MRE11 Clusters in 3D-Conserved Cell Nuclei of Different Cell Lines</title>
    <abstract language="eng">In radiation biophysics, it is a subject of nowadays research to investigate DNA strand break repair in detail after damage induction by ionizing radiation. It is a subject of debate as to what makes up the cell’s decision to use a certain repair pathway and how the repair machinery recruited in repair foci is spatially and temporarily organized. Single-molecule localization microscopy (SMLM) allows super-resolution analysis by precise localization of single fluorescent molecule tags, resulting in nuclear structure analysis with a spatial resolution in the 10 nm regime. Here, we used SMLM to study MRE11 foci. MRE11 is one of three proteins involved in the MRN-complex (MRE11-RAD50-NBS1 complex), a prominent DNA strand resection and broken end bridging component involved in homologous recombination repair (HRR) and alternative non-homologous end joining (a-NHEJ). We analyzed the spatial arrangements of antibody-labelled MRE11 proteins in the nuclei of a breast cancer and a skin fibroblast cell line along a time-course of repair (up to 48 h) after irradiation with a dose of 2 Gy. Different kinetics for cluster formation and relaxation were determined. Changes in the internal nano-scaled structure of the clusters were quantified and compared between the two cell types. The results indicate a cell type-dependent DNA damage response concerning MRE11 recruitment and cluster formation. The MRE11 data were compared to H2AX phosphorylation detected by γH2AX molecule distribution. These data suggested modulations of MRE11 signal frequencies that were not directly correlated to DNA damage induction. The application of SMLM in radiation biophysics offers new possibilities to investigate spatial foci organization after DNA damaging and during subsequent repair.</abstract>
    <parentTitle language="eng">Cancers</parentTitle>
    <identifier type="issn">2072-6694</identifier>
    <identifier type="doi">https://doi.org/10.3390/cancers10010025</identifier>
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Single-molecule localization microscopy (SMLM) allows super-resolution analysis by precise localization of single fluorescent molecule tags, resulting in nuclear structure analysis with a spatial resolution in the 10 nm regime. Here, we used SMLM to study MRE11 foci. MRE11 is one of three proteins involved in the MRN-complex (MRE11-RAD50-NBS1 complex), a prominent DNA strand resection and broken end bridging component involved in homologous recombination repair (HRR) and alternative non-homologous end joining (a-NHEJ). We analyzed the spatial arrangements of antibody-labelled MRE11 proteins in the nuclei of a breast cancer and a skin fibroblast cell line along a time-course of repair (up to 48 h) after irradiation with a dose of 2 Gy. Different kinetics for cluster formation and relaxation were determined. Changes in the internal nano-scaled structure of the clusters were quantified and compared between the two cell types. The results indicate a cell type-dependent DNA damage response concerning MRE11 recruitment and cluster formation. The MRE11 data were compared to H2AX phosphorylation detected by \u03b3H2AX molecule distribution. These data suggested modulations of MRE11 signal frequencies that were not directly correlated to DNA damage induction. The application of SMLM in radiation biophysics offers new possibilities to investigate spatial foci organization after DNA damaging and during subsequent repair.&lt;\/jats:p&gt;","DOI":"10.3390\/cancers10010025","type":"journal-article","created":{"date-parts":[[2018,1,22]],"date-time":"2018-01-22T18:40:39Z","timestamp":1516646439000},"page":"25","source":"Crossref","is-referenced-by-count":27,"title":["Localization Microscopy Analyses of MRE11 Clusters in 3D-Conserved Cell Nuclei of Different Cell Lines"],"prefix":"10.3390","volume":"10","author":[{"given":"Marion","family":"Eryilmaz","sequence":"first","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Eberhard","family":"Schmitt","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Matthias","family":"Krufczik","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Franziska","family":"Theda","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Jin-Ho","family":"Lee","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Christoph","family":"Cremer","sequence":"additional","affiliation":[{"name":"Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany"}]},{"given":"Felix","family":"Bestvater","sequence":"additional","affiliation":[{"name":"German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany"}]},{"given":"Wladimir","family":"Schaufler","sequence":"additional","affiliation":[{"name":"German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-9430-1987","authenticated-orcid":false,"given":"Michael","family":"Hausmann","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-1992-6025","authenticated-orcid":false,"given":"Georg","family":"Hildenbrand","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"},{"name":"Department Radiation Oncology, Universit\u00e4tsmedizin Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 3-5, 68159 Mannheim, Germany"}]}],"member":"1968","published-online":{"date-parts":[[2018,1,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1007\/BF01342199","article-title":"Das Elektronenmikroskop","volume":"78","author":"Knoll","year":"1932","journal-title":"Zeitschrift f\u00fcr Physik"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1080\/14786440808564615","article-title":"A suggested method for extending the microscopic resolution into the ultramicroscopic region","volume":"6","author":"Synge","year":"1928","journal-title":"Philos. 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    <author>Marion Eryilmaz</author>
    <author>Eberhard Schmitt</author>
    <author>Matthias Krufczik</author>
    <author>Franziska Theda</author>
    <author>Jin-Ho Lee</author>
    <author>Christoph Cremer</author>
    <author>Felix Bestvater</author>
    <author>Wladimir Schaufler</author>
    <author>Michael Hausmann</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Krebs, Medizin</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Strahlentherapie</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Brustkrebs</value>
    </subject>
    <collection role="institutes" number="">Medical Engineering and Data Science (Bachelor)</collection>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>1517</id>
    <completedYear>2018</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>462</pageFirst>
    <pageLast>468</pageLast>
    <pageNumber/>
    <edition/>
    <issue>100</issue>
    <volume>2018</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2017-09-19</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Electrophysiological investigation of human embryonic stem cell derived neurospheres using a novel spike detection algorithm</title>
    <abstract language="eng">Microelectrode array (MEA) technology in combination with three-dimensional (3D) neuronal cell models derived from human embryonic stem cells (hESC) provide an excellent tool for neurotoxicity screening. Yet, there are significant challenges in terms of data processing and analysis, since neuronal signals have very small amplitudes and the 3D structure enhances the level of background noise. Thus, neuronal signal analysis requires the application of highly sophisticated algorithms. In this study, we present a new approach optimized for the detection of spikes recorded from 3D neurospheres (NS) with a very low signal-to-noise ratio. This was achieved by extending simple threshold-based spike detection utilizing a highly sensitive algorithm named SWTTEO. This analysis procedure was applied to data obtained from hESC-derived NS grown on MEA chips. Specifically, we examined changes in the activity pattern occurring within the first ten days of electrical activity. We further analyzed the response of NS to the GABA receptor antagonist bicuculline. With this new algorithm method we obtained more reliable results compared to the simple threshold-based spike detection.</abstract>
    <parentTitle language="eng">Biosensors and Bioelectronics</parentTitle>
    <identifier type="doi">10.1016/j.bios.2017.09.034</identifier>
    <enrichment key="copyright">1</enrichment>
    <licence>Creative Commons - CC BY-NC-ND - Namensnennung - Nicht kommerziell - Keine Bearbeitungen 4.0 International</licence>
    <author>Margot Mayer</author>
    <author>Onetsine Arrizabalaga</author>
    <author>Florian Lieb</author>
    <author>Manuel Ciba</author>
    <author>Sylvia Ritter</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Microelectrode array</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Neurosphere</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Spike detection algorithm</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Human embryonic stem cell-derived neurons</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>SWTTEO</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Embryonale Stammzelle</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/1517/ElectrophysiologicalInvestigationOfHuman.pdf</file>
  </doc>
  <doc>
    <id>1516</id>
    <completedYear>2018</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>7</pageLast>
    <pageNumber/>
    <edition/>
    <issue>162</issue>
    <volume>2018</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2017-12-19</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Terrestrial Trunked Radio (TETRA) exposure of neuronal in vitro networks</title>
    <abstract language="eng">Terrestrial Trunked Radio (TETRA) is a worldwide common mobile communication standard, used by authorities and organizations with security tasks. Previous studies reported on health effects of TETRA, with focus on the specific pulse frequency of 17.64 Hz, which affects calcium efflux in neuronal cells. Likewise among others, it was reported that TETRA affects heart rate variability, neurophysiology and leads to headaches. In contrast, other studies conclude that TETRA does not affect calcium efflux of cells and has no effect on people's health.&#13;
&#13;
In the present study we examine whether TETRA short- and long-term exposure could affect the electrophysiology of neuronal in vitro networks. Experiments were performed with a carrier frequency of 395 MHz, a pulse frequency of 17.64 Hz and a differential quaternary phase-shift keying (π/4 DQPSK) modulation. Specific absorption rates (SAR) of 1.17 W/kg and 2.21 W/kg were applied.&#13;
&#13;
In conclusion, the present results do not indicate any effect of TETRA exposure on electrophysiology of neuronal in vitro networks, neither for short-term nor long-term exposure. This applies to the examined parameters spike rate, burst rate, burst duration and network synchrony.</abstract>
    <parentTitle language="eng">Environmental Research</parentTitle>
    <identifier type="doi">10.1016/j.envres.2017.12.007</identifier>
    <enrichment key="copyright">1</enrichment>
    <licence>Creative Commons - CC BY-NC-ND - Namensnennung - Nicht kommerziell - Keine Bearbeitungen 4.0 International</licence>
    <author>Tim Köhler</author>
    <author>Maximilian Wölfel</author>
    <author>Manuel Ciba</author>
    <author>Ulrich Bochtler</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Electronics and Electric Drives</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/1516/TerrestrialTrunkedRadio.pdf</file>
  </doc>
  <doc>
    <id>1513</id>
    <completedYear>2018</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>46</pageFirst>
    <pageLast>51</pageLast>
    <pageNumber/>
    <edition/>
    <issue>2</issue>
    <volume>48</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-01-01</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Workflow for bioprinting of cell-laden bioink</title>
    <abstract language="eng">Applying technologies of additive manufacturing to the field of tissue engineering created a pioneering new approach to model complex cell systems artificially. Regarding its huge potential, bioprinting is still in its infancies and many questions are still unanswered. To address this issue, an extrusion-based bioprinting (EBB) process was used to deposit human embryonic kidney (HEK) cells in a defined pattern. It was shown that the bioprinted construct featured a high degree in viability reaching up to 77% 10 days after printing (DAP). This work displays a proof of principle for a controlled cell formation which shall later be applied to in vitro drug screening tests using various types of cells.</abstract>
    <parentTitle language="eng">Lekar a technika – Clinician and Technology</parentTitle>
    <enrichment key="copyright">1</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Sebastian Allig</author>
    <author>Margot Mayer</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Extrusion-based bioprinting</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>bioink</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>tissue engineering</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>in vitro cell systems</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Biomaterial</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Biomedizinische Technik</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/1513/WorkflowForBioprintingOfCellladenBioink.pdf</file>
  </doc>
  <doc>
    <id>1520</id>
    <completedYear>2018</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2019-01-17</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Human Embryonic Stem Cell Derived Neurospheres – 2D and 3D Cell Culture in one sample</title>
    <abstract language="eng">Various studies have shown that two dimensional (2D) neuronal cell cultures does not recapitulate structure and physiology of three-dimensional (3D) in vivo tissues. These findings are of paramount importance for drug screening, since the response to neurotoxicological substances may differ for 2D und 3D cell culture models. To address this topic, we present human embryonic stem cell (hESC) derived neurospheres (NS) coupled onto microelectrode array (MEA) chips as a model system that includes a 3D NS as well as an outgrowing 2D monolayer allowing direct comparison of functionality within one culture. Preliminary results revealed an enhanced functional reactions of 3D NS to GABA receptor antagonist bicuculline compared to the 2D domain. Thus we have the first evidence that hESC derived NS are a promising model system for neurotoxicity testing enabling a direct comparison between functionality of neurons grown in 2D or 3D.</abstract>
    <identifier type="url">https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00078/event_abstract</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Margot Mayer</author>
    <author>Onetsine Arrizabalaga</author>
    <author>Insa Schröder</author>
    <author>Sylvia Ritter</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>MEA Chips</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>neurospheres</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>human embryonic stem cells</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>3D</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Bicuculline</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Embryonale Stammzelle</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>1519</id>
    <completedYear>2018</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2019-01-17</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Synchrony changes on different time-scales during in vitro neuronal network development</title>
    <identifier type="url">https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00081/event_abstract</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Manuel Ciba</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Synchrony</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Time-scales</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>spike-contrast</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>developing neuronal networks</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>spike train analysis</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>1515</id>
    <completedYear>2018</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>93</pageFirst>
    <pageLast>100</pageLast>
    <pageNumber/>
    <edition/>
    <issue>16</issue>
    <volume>2018</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-02-01</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">High LET radiation shows no major cellular and functional effects on primary cardiomyocytes in vitro</title>
    <abstract language="eng">It is well known that ionizing radiation causes adverse effects on various mammalian tissues. However, there is little information on the biological effects of heavy ion radiation on the heart. In order to fill this gap, we systematically examined DNA-damage induction and repair, as well as proliferation and apoptosis in avian cardiomyocyte cultures irradiated with heavy ions such as titanium and iron, relevant for manned space-flight, and carbon ions, as used for radiotherapy. Further, and to our knowledge for the first time, we analyzed the effect of heavy ion radiation on the electrophysiology of primary cardiomyocytes derived from chicken embryos using the non-invasive microelectrode array (MEA) technology. As electrophysiological endpoints beat rate and field action potential duration were analyzed.&#13;
&#13;
The cultures clearly exhibited the capacity to repair induced DNA damage almost completely within 24 h, even at doses of 7 Gy, and almost completely recovered from radiation-induced changes in proliferative behavior. Interestingly, no significant effects on apoptosis could be detected. Especially the functionality of primary cardiac cells exhibited a surprisingly high robustness against heavy ion radiation, even at doses of up to 7 Gy. In contrast to our previous study with X-rays the beat rate remained more or less unaffected after heavy ion radiation, independently of beam quality. The only change we could observe was an increase of the field action potential duration of up to 30% after titanium irradiation, diminishing within the following three days. This potentially pathological observation may be an indication that heavy ion irradiation at high doses could bear a long-term risk for cardiovascular disease induction.</abstract>
    <parentTitle language="eng">Life Sciences in Space Research</parentTitle>
    <identifier type="doi">10.1016/j.lssr.2018.01.001</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Anja Heselich</author>
    <author>Johannes Frieß</author>
    <author>Sylvia Ritter</author>
    <author>Naja Benz</author>
    <author>Paul Layer</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Cardiomyocytes</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Heavy ion irradiation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Space radiation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Electrophysiology</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>MEA-technology</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Zellkultur</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Herzmuskelzelle</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>2413</id>
    <completedYear>2018</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>12</issue>
    <volume>19</volume>
    <type>article</type>
    <publisherName>MDPI AG</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Recruitment of 53BP1 Proteins for DNA Repair and Persistence of Repair Clusters Differ for Cell Types as Detected by Single Molecule Localization Microscopy</title>
    <abstract language="eng">DNA double stranded breaks (DSBs) are the most serious type of lesions introduced into chromatin by ionizing radiation. During DSB repair, cells recruit different proteins to the damaged sites in a manner dependent on local chromatin structure, DSB location in the nucleus, and the repair pathway entered. 53BP1 is one of the important players participating in repair pathway decision of the cell. Although many molecular biology details have been investigated, the architecture of 53BP1 repair foci and its development during the post-irradiation time, especially the period of protein recruitment, remains to be elucidated. Super-resolution light microscopy is a powerful new tool to approach such studies in 3D-conserved cell nuclei. Recently, we demonstrated the applicability of single molecule localization microscopy (SMLM) as one of these highly resolving methods for analyses of dynamic repair protein distribution and repair focus internal nano-architecture in intact cell nuclei. In the present study, we focused our investigation on 53BP1 foci in differently radio-resistant cell types, moderately radio-resistant neonatal human dermal fibroblasts (NHDF) and highly radio-resistant U87 glioblastoma cells, exposed to high-LET 15N-ion radiation. At given time points up to 24 h post irradiation with doses of 1.3 Gy and 4.0 Gy, the coordinates and spatial distribution of fluorescently tagged 53BP1 molecules was quantitatively evaluated at the resolution of 10–20 nm. Clusters of these tags were determined as sub-units of repair foci according to SMLM parameters. The formation and relaxation of such clusters was studied. The higher dose generated sufficient numbers of DNA breaks to compare the post-irradiation dynamics of 53BP1 during DSB processing for the cell types studied. A perpendicular (90°) irradiation scheme was used with the 4.0 Gy dose to achieve better separation of a relatively high number of particle tracks typically crossing each nucleus. For analyses along ion-tracks, the dose was reduced to 1.3 Gy and applied in combination with a sharp angle irradiation (10° relative to the cell plane). The results reveal a higher ratio of 53BP1 proteins recruited into SMLM defined clusters in fibroblasts as compared to U87 cells. Moreover, the speed of foci and thus cluster formation and relaxation also differed for the cell types. In both NHDF and U87 cells, a certain number of the detected and functionally relevant clusters remained persistent even 24 h post irradiation; however, the number of these clusters again varied for the cell types. Altogether, our findings indicate that repair cluster formation as determined by SMLM and the relaxation (i.e., the remaining 53BP1 tags no longer fulfill the cluster definition) is cell type dependent and may be functionally explained and correlated to cell specific radio-sensitivity. The present study demonstrates that SMLM is a highly appropriate method for investigations of spatiotemporal protein organization in cell nuclei and how it influences the cell decision for a particular repair pathway at a given DSB site.</abstract>
    <parentTitle language="eng">International Journal of Molecular Sciences</parentTitle>
    <identifier type="issn">1422-0067</identifier>
    <identifier type="doi">https://doi.org/10.3390/ijms19123713</identifier>
    <enrichment key="opus_doi_flag">true</enrichment>
    <enrichment key="opus_import_data">{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,27]],"date-time":"2024-08-27T05:45:45Z","timestamp":1724737545582},"reference-count":64,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2018,11,22]],"date-time":"2018-11-22T00:00:00Z","timestamp":1542844800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003243","name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["16-29835A"],"id":[{"id":"10.13039\/501100003243","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001824","name":"Czech Science Foundation","doi-asserted-by":"publisher","award":["16-12454S"],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"&lt;jats:p&gt;DNA double stranded breaks (DSBs) are the most serious type of lesions introduced into chromatin by ionizing radiation. During DSB repair, cells recruit different proteins to the damaged sites in a manner dependent on local chromatin structure, DSB location in the nucleus, and the repair pathway entered. 53BP1 is one of the important players participating in repair pathway decision of the cell. Although many molecular biology details have been investigated, the architecture of 53BP1 repair foci and its development during the post-irradiation time, especially the period of protein recruitment, remains to be elucidated. Super-resolution light microscopy is a powerful new tool to approach such studies in 3D-conserved cell nuclei. Recently, we demonstrated the applicability of single molecule localization microscopy (SMLM) as one of these highly resolving methods for analyses of dynamic repair protein distribution and repair focus internal nano-architecture in intact cell nuclei. In the present study, we focused our investigation on 53BP1 foci in differently radio-resistant cell types, moderately radio-resistant neonatal human dermal fibroblasts (NHDF) and highly radio-resistant U87 glioblastoma cells, exposed to high-LET 15N-ion radiation. At given time points up to 24 h post irradiation with doses of 1.3 Gy and 4.0 Gy, the coordinates and spatial distribution of fluorescently tagged 53BP1 molecules was quantitatively evaluated at the resolution of 10\u201320 nm. Clusters of these tags were determined as sub-units of repair foci according to SMLM parameters. The formation and relaxation of such clusters was studied. The higher dose generated sufficient numbers of DNA breaks to compare the post-irradiation dynamics of 53BP1 during DSB processing for the cell types studied. A perpendicular (90\u00b0) irradiation scheme was used with the 4.0 Gy dose to achieve better separation of a relatively high number of particle tracks typically crossing each nucleus. For analyses along ion-tracks, the dose was reduced to 1.3 Gy and applied in combination with a sharp angle irradiation (10\u00b0 relative to the cell plane). The results reveal a higher ratio of 53BP1 proteins recruited into SMLM defined clusters in fibroblasts as compared to U87 cells. Moreover, the speed of foci and thus cluster formation and relaxation also differed for the cell types. In both NHDF and U87 cells, a certain number of the detected and functionally relevant clusters remained persistent even 24 h post irradiation; however, the number of these clusters again varied for the cell types. Altogether, our findings indicate that repair cluster formation as determined by SMLM and the relaxation (i.e., the remaining 53BP1 tags no longer fulfill the cluster definition) is cell type dependent and may be functionally explained and correlated to cell specific radio-sensitivity. The present study demonstrates that SMLM is a highly appropriate method for investigations of spatiotemporal protein organization in cell nuclei and how it influences the cell decision for a particular repair pathway at a given DSB site.&lt;\/jats:p&gt;","DOI":"10.3390\/ijms19123713","type":"journal-article","created":{"date-parts":[[2018,11,22]],"date-time":"2018-11-22T14:18:25Z","timestamp":1542896305000},"page":"3713","source":"Crossref","is-referenced-by-count":35,"title":["Recruitment of 53BP1 Proteins for DNA Repair and Persistence of Repair Clusters Differ for Cell Types as Detected by Single Molecule Localization Microscopy"],"prefix":"10.3390","volume":"19","author":[{"given":"Elizaveta","family":"Bobkova","sequence":"first","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Daniel","family":"Depes","sequence":"additional","affiliation":[{"name":"Czech Academy of Sciences, 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    <title language="eng">Dose enhancement effects of gold nanoparticles specifically targeting RNA in breast cancer cells</title>
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    <author>Georg Hildenbrand</author>
    <editor>Pedro V. Baptista</editor>
    <author>Philipp Metzler</author>
    <author>Götz Pilarczyk</author>
    <author>Vladimir Bobu</author>
    <author>Wilhelm Kriz</author>
    <author>Hiltraud Hosser</author>
    <author>Jens Fleckenstein</author>
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    <author>Felix Bestvater</author>
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      <value>Krebs, Medizin</value>
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      <value>Brustkrebs</value>
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      <value>Strahlentherapie</value>
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    <title language="eng">Transparent poly(3,4-ethylenedioxythiophene)-based microelectrodes for extracellular recording</title>
    <abstract language="eng">It is well known that at the interface between neuronal tissue and recording electrode low electrical impedance is required. However, if simultaneous optical detection or stimulation is an issue, good optical transmittance of the electrode material is desirable as well. State-of-the-art titanium nitride electrodes provide superior low impedance compared to gold or iridium, but are nontransparent. Transparent electrode materials like the transparent conducting oxide, indium tin oxide (ITO), or graphene offer high light transmittance (&gt;80%) but reveal relatively high impedance. In this paper, the authors propose the conducting polymer poly(3,4-ethylenedioxythiophene) with the counter ion NO−3 as the electrode material for low impedance and good optical transmittance properties. The polymer is electrochemically deposited onto ITO improving the relatively high impedance of ITO. This multilayer electrode allows not only for electrophysiological recordings of cardiomyocytes but also for monitoring of cell contraction under the microscope. Electrochemical impedance spectroscopy and action potential recordings reveal that the new transparent electrodes are a good compromise in terms of low impedance and transparency if deposition parameters are optimized.</abstract>
    <parentTitle language="eng">Biointerphases</parentTitle>
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    <author>Tim Köhler</author>
    <author>Christiane Thielemann</author>
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      <value>Impedanzspektroskopie</value>
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      <type>swd</type>
      <value>Mikroelektrode</value>
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    <title language="eng">Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research</title>
    <abstract language="eng">Understanding molecular interactions and regulatory mechanisms in tumor initiation, progression, and treatment response are key requirements towards advanced cancer diagnosis and novel treatment procedures in personalized medicine. Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP) tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2) in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine.</abstract>
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Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP) tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2) in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine.&lt;\/jats:p&gt;","DOI":"10.3390\/ijms18102066","type":"journal-article","created":{"date-parts":[[2017,9,28]],"date-time":"2017-09-28T15:22:44Z","timestamp":1506612164000},"page":"2066","source":"Crossref","is-referenced-by-count":33,"title":["Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"http:\/\/orcid.org\/0000-0001-9430-1987","authenticated-orcid":false,"given":"Michael","family":"Hausmann","sequence":"first","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Nata\u0161a","family":"Ili\u0107","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold ST, Safed 1311502, Israel"}]},{"given":"G\u00f6tz","family":"Pilarczyk","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Jin-Ho","family":"Lee","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Abiramy","family":"Logeswaran","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Aurora","family":"Borroni","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold ST, Safed 1311502, Israel"}]},{"given":"Matthias","family":"Krufczik","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Franziska","family":"Theda","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Nadine","family":"Waltrich","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"}]},{"given":"Felix","family":"Bestvater","sequence":"additional","affiliation":[{"name":"German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany"}]},{"given":"Georg","family":"Hildenbrand","sequence":"additional","affiliation":[{"name":"Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany"},{"name":"Department of Radiation Oncology, Universit\u00e4tsmedizin Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 3-5, 68159 Mannheim, Germany"}]},{"given":"Christoph","family":"Cremer","sequence":"additional","affiliation":[{"name":"Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany"}]},{"given":"Michael","family":"Blank","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold ST, Safed 1311502, Israel"}]}],"member":"1968","published-online":{"date-parts":[[2017,9,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1667\/RR13515.1","article-title":"DNA damage response genes and the development of cancer metastasis","volume":"181","author":"Broustas","year":"2014","journal-title":"Radiat. 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    <author>Michael Hausmann</author>
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    <title language="eng">Combining Low Temperature Fluorescence DNA-Hybridization, Immunostaining, and Super-Resolution Localization Microscopy for Nano-Structure Analysis of ALU Elements and Their Influence on Chromatin Structure</title>
    <abstract language="eng">Immunostaining and fluorescence in situ hybridization (FISH) are well established methods for specific labelling of chromatin in the cell nucleus. COMBO-FISH (combinatorial oligonucleotide fluorescence in situ hybridization) is a FISH method using computer designed oligonucleotide probes specifically co-localizing at given target sites. In combination with super resolution microscopy which achieves spatial resolution far beyond the Abbe Limit, it allows new insights into the nano-scaled structure and organization of the chromatin of the nucleus. To avoid nano-structural changes of the chromatin, the COMBO-FISH labelling protocol was optimized omitting heat treatment for denaturation of the target. As an example, this protocol was applied to ALU elements—dispersed short stretches of DNA which appear in different kinds in large numbers in primate genomes. These ALU elements seem to be involved in gene regulation, genomic diversity, disease induction, DNA repair, etc. By computer search, we developed a unique COMBO-FISH probe which specifically binds to ALU consensus elements and combined this DNA–DNA labelling procedure with heterochromatin immunostainings in formaldehyde-fixed cell specimens. By localization microscopy, the chromatin network-like arrangements of ALU oligonucleotide repeats and heterochromatin antibody labelling sites were simultaneously visualized and quantified. This novel approach which simultaneously combines COMBO-FISH and immunostaining was applied to chromatin analysis on the nanoscale after low-linear-energy-transfer (LET) radiation exposure at different doses. Dose-correlated curves were obtained from the amount of ALU representing signals, and the chromatin re-arrangements during DNA repair after irradiation were quantitatively studied on the nano-scale. Beyond applications in radiation research, the labelling strategy of immunostaining and COMBO-FISH with localization microscopy will also offer new potentials for analyses of subcellular elements in combination with other specific chromatin targets.</abstract>
    <parentTitle language="eng">International Journal of Molecular Sciences</parentTitle>
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In combination with super resolution microscopy which achieves spatial resolution far beyond the Abbe Limit, it allows new insights into the nano-scaled structure and organization of the chromatin of the nucleus. To avoid nano-structural changes of the chromatin, the COMBO-FISH labelling protocol was optimized omitting heat treatment for denaturation of the target. As an example, this protocol was applied to ALU elements\u2014dispersed short stretches of DNA which appear in different kinds in large numbers in primate genomes. These ALU elements seem to be involved in gene regulation, genomic diversity, disease induction, DNA repair, etc. By computer search, we developed a unique COMBO-FISH probe which specifically binds to ALU consensus elements and combined this DNA\u2013DNA labelling procedure with heterochromatin immunostainings in formaldehyde-fixed cell specimens. 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    <title language="eng">K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features</title>
    <abstract language="eng">In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of standard k-mer analysis.</abstract>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2017-03-30</completedDate>
    <publishedDate>2017-03-30</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A stationary wavelet transform and a time-frequency based spike detection algorithm for extracellular recorded data</title>
    <abstract language="eng">Objective. Spike detection from extracellular recordings is a crucial preprocessing step when analyzing neuronal activity. The decision whether a specific part of the signal is a spike or not is important for any kind of other subsequent preprocessing steps, like spike sorting or burst detection in order to reduce the classification of erroneously identified spikes. Many spike detection algorithms have already been suggested, all working reasonably well whenever the signal-to-noise ratio is large enough. When the noise level is high, however, these algorithms have a poor performance. Approach. In this paper we present two new spike detection algorithms. The first is based on a stationary wavelet energy operator and the second is based on the time-frequency representation of spikes. Both algorithms are more reliable than all of the most commonly used methods. Main results. The performance of the algorithms is confirmed by using simulated data, resembling original data recorded from cortical neurons with multielectrode arrays. In order to demonstrate that the performance of the algorithms is not restricted to only one specific set of data, we also verify the performance using a simulated publicly available data set. We show that both proposed algorithms have the best performance under all tested methods, regardless of the signal-to-noise ratio in both data sets. Significance. This contribution will redound to the benefit of electrophysiological investigations of human cells. Especially the spatial and temporal analysis of neural network communications is improved by using the proposed spike detection algorithms.</abstract>
    <parentTitle language="eng">Journal of Neural Engineering</parentTitle>
    <identifier type="doi">10.1088/1741-2552/aa654b</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Florian Lieb</author>
    <author>Hans-Georg Stark</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>spike detection</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>wavelet TEO</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>extracellular recording</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>1530</id>
    <completedYear>2017</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>501</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>2</issue>
    <volume>10</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2017-03-01</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">In vitro platform for acoustic and electrophysiological investigations of ultrasound stimulation</title>
    <abstract language="eng">Since the first time discovered that ultrasound can influence neuronal activity - more than half a century ago - a lot of progress has been made in this field. The possibilities of ultrasound for neuromodulation have been demonstrated in many experiments such as in vivo stimulation of rodent brain or of human cochlear, Further, in vitro experiments with hippocampal slices and other cell types have been performed as well.</abstract>
    <parentTitle language="eng">Brain Stimulation</parentTitle>
    <identifier type="doi">10.1016/j.brs.2017.01.465</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Mario Kupnik</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Ultraschall</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>1525</id>
    <completedYear>2017</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>4</pageLast>
    <pageNumber/>
    <edition/>
    <issue>1052</issue>
    <volume>2018</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-07-26</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Optimizing dimensions of unipolar Teflon-FEP piezoelectrets with micro-system-technology</title>
    <abstract language="eng">In this work we present a new micro-system-technology based production process for&#13;
unipolar ferroelectrets. Theoretical analysis of the influence of the air-gap size on the electric&#13;
field distribution as well as on the induced charge on the electrodes shows superior performance&#13;
of unipolar piezoelectrets with small air-gaps. For the production of these small air-gaps we&#13;
developed a new design using a photoresist thermoforming master, an integrated micro-heater&#13;
and shadow masks for metallization. Unipolar piezoelectrets produced with this technology&#13;
exhibit increased d33-coefficients compared to designs in previous publications. These&#13;
piezoelectrets are highly preferable for energy-harvesting applications, as they promise high&#13;
electric power output.</abstract>
    <parentTitle language="eng">Journal of Physics: Conference Series</parentTitle>
    <enrichment key="copyright">1</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Florian Emmerich</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Mikrosystemtechnik</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/1525/OptimizingTeflonFEP.pdf</file>
  </doc>
  <doc>
    <id>1526</id>
    <completedYear>2017</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>136</pageFirst>
    <pageLast>143</pageLast>
    <pageNumber/>
    <edition/>
    <issue>293</issue>
    <volume>2018</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-01-01</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Spike-contrast: A novel time scale independent and multivariate measure of spike train synchrony</title>
    <abstract language="eng">Background: Synchrony within neuronal networks is thought to be a fundamental feature of neuronal networks. In order to quantify synchrony between spike trains, various synchrony measures were developed. Most of them are time scale dependent and thus require the setting of an appropriate time scale. Recently, alternative methods have been developed, such as the time scale independent SPIKE-distance by Kreuz et al. New method: In this study, a novel time-scale independent spike train synchrony measure called Spike-contrast is proposed. The algorithm is based on the temporal “contrast” (activity vs. non-activity in certain temporal bins) and not only provides a single synchrony value, but also a synchrony curve as a function of the bin size. Results: For most test data sets synchrony values obtained with Spike-contrast are highly correlated with those of the SPIKE-distance (Spearman correlation value of 0.99). Correlation was lower for data containing multiple time scales (Spearman correlation value of 0.89). When analyzing large sets of data, Spike-contrast performed faster. Comparison of existing method: &#13;
Spike-contrast is compared to the SPIKE-distance algorithm. The test data consisted of artificial spike trains with various levels of synchrony, including Poisson spike trains and bursts, spike trains from simulated neuronal Izhikevich networks, and bursts made of smaller bursts (sub-bursts). Conclusions: The high correlation of Spike-contrast with the established SPIKE-distance for most test data, suggests the suitability of the proposed measure. Both measures are complementary as SPIKE-distance provides a synchrony profile over time, whereas Spike-contrast provides a synchrony curve over bin size.</abstract>
    <parentTitle language="eng">Journal of Neuroscience Methods</parentTitle>
    <identifier type="doi">10.1016/j.jneumeth.2017.09.008</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Manuel Ciba</author>
    <author>Takuya Isomura</author>
    <author>Yasuhiko Jimbo</author>
    <author>Andreas Bahmer</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Synchrony</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Neuronal Networks</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Point processes</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Time series analysis</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Parallel spike trains</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>1527</id>
    <completedYear>2017</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>2955</pageFirst>
    <pageLast>2978</pageLast>
    <pageNumber/>
    <edition/>
    <issue>29</issue>
    <volume>2017</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2017-10-17</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Effect of Morphologic Features of Neurons on the Extracellular Electric Potential: A Simulation Study Using Cable Theory and Electro-Quasi-Static Equations</title>
    <abstract language="eng">Microelectrode arrays serve as an indispensable tool in electro-physiological research to study the electrical activity of neural cells, enabling measurements of single cell as well as network communication analysis. Recent experimental studies have reported that the neuronal geometry has an influence on electrical signaling and extracellular recordings. However, the corresponding mechanisms are not yet fully understood and require further investigation. Allowing systematic parameter studies, computational modeling provides the opportunity to examine the underlying effects that influence extracellular potentials. In this letter, we present an in silico single cell model to analyze the effect of geometrical variability on the extracellular electric potentials. We describe finite element models of a single neuron with varying geometric complexity in three-dimensional space. The electric potential generation of the neuron is modeled using Hodgkin-Huxley equations. The signal propagation is described with electro-quasi-static equations, and results are compared with corresponding cable equation descriptions. Our results show that both the geometric dimensions and the distribution of ion channels of a neuron are critical factors that significantly influence both the amplitude and shape of extracellular potentials.</abstract>
    <parentTitle language="eng">Neural Computation</parentTitle>
    <identifier type="doi">10.1162/neco_a_01019</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Robert Bestel</author>
    <author>Revathi Appali</author>
    <author>Ursula van Rienen</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Mikroelektrode</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Array</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>1528</id>
    <completedYear>2017</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber>269</pageNumber>
    <edition/>
    <issue>18</issue>
    <volume>2017</volume>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2017-08-17</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Application of spike train synchrony measure Spike‑contrast to quantify the effect of bicuculline on cortical networks grown on microelectrode arrays</title>
    <parentTitle language="eng">BMC Neuroscience</parentTitle>
    <identifier type="doi">10.1186/s12868-017-0372-1</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Manuel Ciba</author>
    <author>Andreas Bahmer</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Mikroelektrode</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Array</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>2424</id>
    <completedYear>2017</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>624</pageFirst>
    <pageLast>637</pageLast>
    <pageNumber>14</pageNumber>
    <edition/>
    <issue>3</issue>
    <volume>97</volume>
    <type>article</type>
    <publisherName>Elsevier BV</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Smart Radiation Therapy Biomaterials</title>
    <parentTitle language="eng">International Journal of Radiation Oncology*Biology*Physics</parentTitle>
    <identifier type="issn">0360-3016</identifier>
    <identifier type="doi">https://doi.org/10.1016/j.ijrobp.2016.10.034</identifier>
    <enrichment key="opus_doi_flag">true</enrichment>
    <enrichment key="opus_import_data">x</enrichment>
    <enrichment key="local_crossrefDocumentType">journal-article</enrichment>
    <enrichment key="local_crossrefLicence">https://www.elsevier.com/tdm/userlicense/1.0/</enrichment>
    <enrichment key="local_import_origin">crossref</enrichment>
    <enrichment key="local_doiImportPopulated">PersonAuthorFirstName_1,PersonAuthorLastName_1,PersonAuthorFirstName_2,PersonAuthorLastName_2,PersonAuthorFirstName_3,PersonAuthorLastName_3,PersonAuthorFirstName_4,PersonAuthorLastName_4,PersonAuthorFirstName_5,PersonAuthorLastName_5,PersonAuthorFirstName_6,PersonAuthorLastName_6,PersonAuthorFirstName_7,PersonAuthorLastName_7,PersonAuthorFirstName_8,PersonAuthorLastName_8,PersonAuthorFirstName_9,PersonAuthorLastName_9,PersonAuthorFirstName_10,PersonAuthorLastName_10,PersonAuthorFirstName_11,PersonAuthorLastName_11,PersonAuthorFirstName_12,PersonAuthorLastName_12,PublisherName,TitleMain_1,Language,TitleParent_1,PageNumber,PageFirst,PageLast,Issue,Volume,CompletedYear,IdentifierIssn,Enrichmentlocal_crossrefLicence</enrichment>
    <enrichment key="opus.source">doi-import</enrichment>
    <author>Wilfred Ngwa</author>
    <author>Francis Boateng</author>
    <author>Rajiv Kumar</author>
    <author>Darrell J. Irvine</author>
    <author>Silvia Formenti</author>
    <author>Twalib Ngoma</author>
    <author>Carsten Herskind</author>
    <author>Marlon R. Veldwijk</author>
    <author>Georg Hildenbrand</author>
    <author>Michael Hausmann</author>
    <author>Frederik Wenz</author>
    <author>Jürgen Hesser</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Krebs, Medizin</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Strahlentherapie</value>
    </subject>
    <collection role="institutes" number="">Medical Engineering and Data Science (Bachelor)</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>755</id>
    <completedYear>2016</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>10</pageLast>
    <pageNumber/>
    <edition/>
    <issue>27</issue>
    <volume>2016</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2016-04-13</completedDate>
    <publishedDate>2016-04-07</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Real-space measurement of potential distribution in PECVD ONO electrets by Kelvin probe force microscopy</title>
    <abstract language="eng">Multilayers of silicon oxide/silicon nitride/silicon oxide (ONO) are known for their good&#13;
electret properties due to deep energy traps near the material interfaces, facilitating charge&#13;
storage. However, measurement of the space charge distribution in such multilayers is a&#13;
challenge for conventional methods if layer thickness dimensions shrink below 1 μm. In this&#13;
paper, we propose an atomic force microscope based method to determine charge distributions in&#13;
ONO layers with spatial resolution below 100 nm. By applying Kelvin probe force microscopy&#13;
(KPFM) on freshly cleaved, corona-charged multilayers, the surface potential is measured&#13;
directly along the z-axis and across the interfaces. This new method gives insights into charge&#13;
distribution and charge movement in inorganic electrets with a high spatial resolution.</abstract>
    <parentTitle language="eng">Nanotechnology</parentTitle>
    <enrichment key="copyright">1</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Florian Emmerich</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>electret, multilayer, charge distribution, Kelvin probe force microscopy</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Kelvin-Sonde</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Rasterkraftmikroskopie</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
    <file>https://opus4.kobv.de/opus4-h-ab/files/755/ONO.pdf</file>
  </doc>
  <doc>
    <id>1536</id>
    <completedYear>2016</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>194</pageFirst>
    <pageLast>203</pageLast>
    <pageNumber/>
    <edition/>
    <issue>257</issue>
    <volume>2016</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2016-01-15</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Growing neuronal islands on multi-electrode arrays using an accurate positioning-μCP device</title>
    <abstract language="eng">Background: Multi-electrode arrays (MEAs) allow non-invasive multi-unit recording in-vitro from cultured neuronal networks. For sufficient neuronal growth and adhesion on such MEAs, substrate preparation is required. Plating of dissociated neurons on a uniformly prepared MEA's surface results in the formation of spatially extended random networks with substantial inter-sample variability. Such cultures are not optimally suited to study the relationship between defined structure and dynamics in neuronal networks. To overcome these shortcomings, neurons can be cultured with pre-defined topology by spatially structured surface modification. Spatially structuring a MEA surface accurately and reproducibly with the equipment of a typical cell-culture laboratory is challenging. New method: In this paper, we present a novel approach utilizing micro-contact printing (μCP) combined with a custom-made device to accurately position patterns on MEAs with high precision. We call this technique AP-μCP (accurate positioning micro-contact printing). Comparison with existing methods: Other approaches presented in the literature using μCP for patterning either relied on facilities or techniques not readily available in a standard cell culture laboratory, or they did not specify means of precise pattern positioning. Conclusion: Here we present a relatively simple device for reproducible and precise patterning in a standard cell-culture laboratory setting. The patterned neuronal islands on MEAs provide a basis for high throughput electrophysiology to study the dynamics of single neurons and neuronal networks.</abstract>
    <parentTitle language="eng">Journal of Neuroscience Methods</parentTitle>
    <identifier type="doi">10.1016/j.jneumeth.2015.09.022</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Robert Samhaber</author>
    <author>Manuel Schottdorf</author>
    <author>Ahmed El Hady</author>
    <author>Kai Bröking</author>
    <author>Andreas Daus</author>
    <author>Christiane Thielemann</author>
    <author>Walter Stühmer</author>
    <author>Fred Wolf</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>MEA</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Patterning</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>μCP</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Mehrfachelektrode</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>1533</id>
    <completedYear>2016</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>MEA Meeting 2016</issue>
    <volume>2016</volume>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2016-06-24</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Human Embryonic Stem Cell Derived Neurospheres - A Novel Three Dimensional Model For Neurotoxicological Studies</title>
    <abstract language="eng">At present, most neurotoxicological studies in the field of microelectrode array (MEA) technology are based on in vivo or in vitro animal models, particularly in mice or rats. These models contributed much to our knowledge about molecular and cellular mechanisms of neurotoxins affecting the central nervous system. Yet, animal models are not necessarily capable to forecasting the effectiveness of treatment in clinical trials. Therefore the development and characterization of suitable neuronal cell models derived from human cells is emerging in the field of toxicity testing. In this study, we present neurospheres (NS) as a new three dimensional (3D) neuronal cell model based on human embryonic stem cells (hESC), coupled onto microelectrode arrays (MEA). This cell-based assay serves as platform to investigate effects of neuroactive substances on network communication. In order to characterize the neurospheres’ reaction, the well-known GABA receptor antagonist bicuculline and the sodium channel blocker carbamazepine are applied. Preliminary results reveal anticipated and physiologically reasonable alterations in network activity. Thus, we have the first evidence that hESC derived NS are a promising 3D cell model for neurotoxicity testing. In further studies, this model will be used to investigate effects of ionizing radiation on network signaling.</abstract>
    <parentTitle language="eng">Frontiers</parentTitle>
    <identifier type="doi">10.3389/conf.fnins.2016.93.00081</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 4.0 International</licence>
    <author>Margot Mayer</author>
    <author>Onetsine Arrizabalaga</author>
    <author>Sylvia Ritter</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>human embryonic stem cells</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>neurospheres</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>MEA chips</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>3D</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Mikroelektrode</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Array</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Embryonale Stammzelle</value>
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  <doc>
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    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>264</pageFirst>
    <pageLast>278</pageLast>
    <pageNumber/>
    <edition/>
    <issue>37</issue>
    <volume>2016</volume>
    <type>article</type>
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    <completedDate>2016-04-12</completedDate>
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    <title language="eng">Long‐term electromagnetic exposure of developing neuronal networks: A flexible experimental setup</title>
    <abstract language="eng">Neuronal networks in vitro are considered one of the most promising targets of research to assess potential electromagnetic field induced effects on neuronal functionality. A few exposure studies revealed there is currently no evidence of any adverse health effects caused by weak electromagnetic fields. Nevertheless, some published results are inconsistent. Particularly, doubts have been raised regarding possible athermal biological effects in the young brain during neuronal development. Therefore, we developed and characterized a flexible experimental setup based on a transverse electromagnetic waveguide, allowing controlled, reproducible exposure of developing neuronal networks in vitro. Measurement of S‐parameters confirmed very good performance of the Stripline in the band of 800–1000 MHz. Simulations suggested a flexible positioning of cell culture dishes throughout a large exposure area, as specific absorption rate values were quite independent of their position (361.7 ± 11.4 mW/kg) at 1 W, 900 MHz. During exposure, thermal drift inside cellular medium did not exceed 0.1 K. Embryonic rat cortical neurons were cultivated on microelectrode array chips to non‐invasively assess electrophysiological properties of electrogenic networks. Measurements were taken for several weeks, which attest to the experimental setup being a reliable system for long‐term studies on developing neuronal tissue.</abstract>
    <parentTitle language="eng">Bioelectromagnetics</parentTitle>
    <identifier type="doi">10.1002/bem.21974</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Stefan Oster</author>
    <author>Andreas Daus</author>
    <author>Christian Erbes</author>
    <author>Michael Goldhammer</author>
    <author>Ulrich Bochtler</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>RF exposure setup</value>
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    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>mobile communication frequencies</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>SAR dosimetry</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>microelectrode array</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>electrophysiology</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
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    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Mikroelektrode</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Array</value>
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  </doc>
  <doc>
    <id>1531</id>
    <completedYear>2016</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>MEA Meeting 2016</issue>
    <volume>2016</volume>
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    <creatingCorporation/>
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    <completedDate>2016-06-24</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Characterization Of Graphene-Coated Microelectrode Arrays For Recording And Stimulation Of Neuronal Cells</title>
    <parentTitle language="eng">Frontiers</parentTitle>
    <identifier type="doi">10.3389/conf.fnins.2016.93.00013</identifier>
    <enrichment key="copyright">0</enrichment>
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    <author>Berit Silke Körbitzer</author>
    <author>Peter Krauß</author>
    <author>Jörg Schneider</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Mikroelektrode</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Array</value>
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    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Nervenstimulation</value>
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    <id>1532</id>
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    <publishedYear/>
    <thesisYearAccepted/>
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    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
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    <completedDate>2016-06-05</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">TETRA specific long-term exposure of neuronal in vitro networks</title>
    <parentTitle language="eng">BioEM2016</parentTitle>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Tim Köhler</author>
    <author>Maximilian Wölfel</author>
    <author>Ulrich Bochtler</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Neuronales Netz</value>
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    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
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    <title language="eng">Cellular Uptake of Gold Nanoparticles and Their Behavior as Labels for Localization Microscopy</title>
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    <author>Georg Hildenbrand</author>
    <author>Patrick Müller</author>
    <author>Alexander Al Saroori</author>
    <author>Abin Biswas</author>
    <author>Margund Bach</author>
    <author>Frederik Wenz</author>
    <author>Christoph Cremer</author>
    <author>Nina Burger</author>
    <author>Marlon R. Veldwijk</author>
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    <title language="eng">Perspectives on Comets, Comet-like Asteroids, and Their Predisposition to Provide an Environment That Is Friendly to Life</title>
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    <author>Katharina Bosiek</author>
    <author>Michael Hausmann</author>
    <author>Georg Hildenbrand</author>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Komet</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Planetoid</value>
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  </doc>
  <doc>
    <id>1540</id>
    <completedYear>2015</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>1</pageLast>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2015-07-06</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A three-dimensional microelectrode array composed of vertically aligned ultra-dense carbon nanotube networks</title>
    <abstract language="eng">Electrodes based on carbon nanotubes are a promising approach to manufacture highly sensitive sensors with a low limit of signal detection and a high signal-to-noise ratio. This is achieved by dramatically increasing the electrochemical active surface area without increasing the overall geometrical dimensions. Typically, carbon nanotube electrodes are nearly planar and composed of randomly distributed carbon nanotube networks having a limited surface gain for a specific geometrical surface area. To overcome this limitation, we have introduced vertically aligned carbon nanotube (VACNT) networks as electrodes, which are arranged in a microelectrode pattern of 60 single electrodes. Each microelectrode features a very high aspect ratio of more than 300 and thus a dramatically increased surface area. These microelectrodes composed of VACNT networks display dramatically decreased impedance over the entire frequency range compared to planar microelectrodes caused by the enormous capacity increase. This is experimentally verified by electrochemical impedance spectroscopy and cyclic voltammetry.</abstract>
    <parentTitle language="eng">Applied Physics Letters</parentTitle>
    <identifier type="doi">10.1063/1.4926330</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Christoph Nick</author>
    <author>Sandeep Yadav</author>
    <author>Ravi Joshi</author>
    <author>Jörg Schneider</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Microelectrode arrays</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Electrochemical impedance spectroscopy</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Chemical compounds and components</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Electrolytes</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Signal processing</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Mikroelektrode</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Array</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Kohlenstoff-Nanoröhre</value>
    </subject>
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    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
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  </doc>
  <doc>
    <id>1538</id>
    <completedYear>2015</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2016-03-07</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Ultrathin gold as sensor platform for biomolecules</title>
    <abstract language="eng">Due to the increasing number of diabetes patients worldwide there is an enormous need for accurate, fast and someday also continuous or even closed loop monitoring of blood glucose level. More than 50 years after Clark and Lyons proposed the first glucose enzyme electrodes this concept is still widely in use today. Most concepts use the enzyme glucose oxidase (GOx) that reacts with glucose. These reactions cause a current that is proportional to the amount of glucose present at the sensor. Thus, if the sample volume is known, the blood sugar level can be measured. Although these electrodes have been in use for so long they have the disadvantage of a limited shelf time. In this work we present an enzyme free approach for glucose detection applying ultrathin gold films. According to the basic Fuchs-Sondheimer-theory and other more sophisticated models the resistivity of ultrathin metal films is dominated by scattering effects at their surface. Chemical reactions at the metallic surface are expected to change the conductivity properties and thus these changes can be used to detect molecules. This can be done by creating a self-assembled monolayer at the gold surface. When molecules such as glucose bind to the end groups of this layer the electron scattering and thus the conductivity of the film is expected to change. Ultrathin gold films with a thickness of 6 nm show the largest relative change in resistivity and are thus the preferred film thickness for this application. These gold films show a significant change in resistance when model molecules sodium sulfide and dextran are present, whereas the resistance of a platinum reference electrode does not change significantly.</abstract>
    <parentTitle language="eng">2015 International Conference on Manipulation, Manufacturing and Measurement on the Nanoscale (3M-NANO), Changchun, China</parentTitle>
    <identifier type="doi">10.1109/3M-NANO.2015.7425462</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Christoph Nick</author>
    <author>Christina Hock</author>
    <author>Florian Emmerich</author>
    <author>Stefan Belle</author>
    <author>Christiane Thielemann</author>
    <author>Tim Asmus</author>
    <author>Thomas Loose</author>
    <author>Karlheinz Wienand</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>ultrathin gold</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>biosensor</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>glucose</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>enzyme free glucose sensor</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Biosensor</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Dünne Schicht</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Gold</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
  <doc>
    <id>1537</id>
    <completedYear>2015</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2016-03-07</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Patterning of PMMA by gold-nanoparticle initiated localized decomposition</title>
    <abstract language="eng">The need for manipulating matter at its smallest scale has been a hot topic in research for the last decades. As the final goal of arranging single atoms has been achieved, research focuses on two targets: firstly, improving the capabilities of existing technologies towards nanometer resolution and secondly, finding new methods for producing nanostructures in a fast and easy way. Here, we present a new maskless method for sub-micro-patterning of poly(methyl methacrylate) (PMMA) thin films. By applying atomic-force-microscope (AFM) assisted nano-xerography, electric charges were locally injected with an AFM-tip into PMMA. The resulting electrostatic patterns attracted charged gold-nanoparticles, which were selectively deposited onto the PMMA layers with lateral dimensions below 200 nm. In a second step, heat treatment at 275 °C initiated a selective decomposition of the PMMA layer, only observed in PMMA-areas covered with nanoparticles, whereas uncovered areas were not modified by the heat treatment. Analyzing the grooves with the AFM, we found that lines with a width in the sub-micrometer range to several micrometers have successfully been realized. We propose this new and promising method to manufacture nano-grooves used as masking for lift-off processes, for functionalization of underlying areas, or for micro-contact-printing.</abstract>
    <parentTitle language="eng">2015 International Conference on Manipulation, Manufacturing and Measurement on the Nanoscale (3M-NANO), Changchun, China</parentTitle>
    <identifier type="doi">10.1109/3M-NANO.2015.7425480</identifier>
    <enrichment key="copyright">0</enrichment>
    <licence>Keine Lizenz - es gilt das deutsche Urheberrecht</licence>
    <author>Florian Emmerich</author>
    <author>Christiane Thielemann</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Nanoparticles</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Gold</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Thermal stability</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Heating</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Electrostatics</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Polymethylmethacrylate</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>swd</type>
      <value>Dünnschichttechnik</value>
    </subject>
    <collection role="forschungsschwerpunkte" number="">Artifical Intelligence and Data Science</collection>
    <collection role="forschungsschwerpunkte" number="">Clean Tech</collection>
    <collection role="forschungsschwerpunkte" number="">Intelligent Sensors and Signals</collection>
    <collection role="forschungsschwerpunkte" number="">Material Testing &amp; Sensor Technology</collection>
  </doc>
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