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AIM Consultants Team - Overview

Tobias Weigel, Caroline Arnold, Pavan Siligam, Sofiane Bendoukha
2020 Zenodo  
 Contact us at: consultant-helmholtz.ai@dkrz.de  Consultant Team (Tobias Weigel, DKRZ)  Counselling, training, technical support  Serves Helmholtz Centres on AI/ML in Earth & Environment AIM  ... 
doi:10.5281/zenodo.3741855 fatcat:njku7sws5bbqfopqqi4czhhaxi

Leveraging PIDs for object management in data infrastructures

Tobias Weigel
2019 Zenodo  
Weigel (DKRZ) RDA Recommendation on PID Kernel Information 7 Guiding Principles for PID Kernel Information • Independent of specific infrastructure or technologies • Geared towards minimizing  ...  TWITTER.COM/RESDATALL Data Fabric IG • Group has existed formally since P4 • Concerned with cross-group/discipline infrastructural challenges • Co-chairs: LI Jianhui (CNIC, CAS), Robert Quick (IU), Tobias  ... 
doi:10.5281/zenodo.3361619 fatcat:s3yqap4g3zclxpkgkbus75c32m

Persistent Identifiers for CMIP6: Implementation plan

Tobias Weigel, Michael Lautenschlager, Martin Juckes
2018 Zenodo  
Proposed co--chairs of the RDA working group: Bridget Almas, Frederik Baumgardt, Tobias Weigel, Tom Zastrow.  ... 
doi:10.5281/zenodo.4751913 fatcat:fohsetdi5nczdec2llb2smdfe4

AI Services for Earth and Environment

Tobias Weigel, Caroline Arnold, Pavan Siligam, Sofiane Bendoukha
2020 Zenodo  
Weigel (DKRZ) A glimpse on first use cases  Data uncertainty quantification and interaction with ML models  Observational data uncertainty, Bayesian NNs Helmholtz AI projects  Project calls  ...  support Training and knowledge exchange Counselling • Coding for data loading and transform • Scaling up your application • Use of Jupyter connected to computing and data sources • Vouchers Tobias  ... 
doi:10.5281/zenodo.3786290 fatcat:afaaxipssbesbpn6u6fhpyx2mi

Flexible tissue-like electrode as a seamless tissue-electronic interface

Tobias Weigel, Tobias Pfister, Tobias Schmitz, Maren Jannasch, Sebastian Schürlein, Reem Al Hijailan, Heike Walles, Jan Hansmann
2017 BioNanoMaterials  
AbstractCurrent implantable electrodes facilitate only a low cellular infiltration impairing the long-term integration into the host's tissue. To accomplish a seamless electronic-tissue interface, conductive three-dimensional (3D) scaffolds were generated by carbonization of electro-spun fiber meshes. When introducing NaCl particles as porogens, tailored tissue-like electrodes were generated. Characterization of the porous 3D fiber electrodes demonstrated improved material and electrical
more » ... eristics compared to standard carbon fiber meshes or flat gold surfaces. The feasibility of the porous 3D electrodes was assessed by cell culture experiments, confirming the migration of cells into the electrode and the formation of contracting cardiomyocyte clusters. Finally, a complex cardiac co-culture system proved the integration of the tissue into the 3D electrode in long-term culture of 7 weeks. These results strengthen the development of tissue-like 3D scaffolds as alternative to two-dimensional (2D) electrodes.
doi:10.1515/bnm-2017-0002 fatcat:nzzy4kzdgrce3k5zlgxiue4riq

Actionable Persistent Identifier Collections

Tobias Weigel, Stephan Kindermann, Michael Lautenschlager
2014 Data Science Journal  
It can also fulfill the requirements given in Weigel et al. (2013) from a technical perspective.  ...  PID and key-metadata together form a Persistent Entity (PE) (Weigel, Lautenschlager, Toussaint, & Kindermann, 2013) , which may be valuable enough to be preserved on its own terms even if the original  ... 
doi:10.2481/dsj.12-058 fatcat:xsnkzx7ldrgipferhc5qq6qtbm

Pid Usage At Dkrz, The Role Of Rda And Epic Policies

Tobias Weigel
2015 Zenodo  
Presented at: Persistent Identifiers: Enabling Services for Data Intensive Research DataCite and EPIC Monday, September 21, 2015 from 1:00 PM to 6:00 PM (CEST) Paris, France
doi:10.5281/zenodo.31790 fatcat:x4d2nsnujrhbpnx4twiagnoigq

Network-based approaches to climate knowledge discovery

Reinhard Budich, Per Nyberg, Tobias Weigel
2011 EOS  
.; E-mail: nyberg@cray.com; and ToBias Weigel, DKRZ, Hamburg, Germany Network-Based Approaches to Climate Knowledge Discovery Climate Knowledge Discovery Workshop; Hamburg, Germany, 30 March to 1 April  ... 
doi:10.1029/2011eo470007 fatcat:ht6a63nvjrcxlgvh7jgiy4vrpy

RDA Recommendation on PID Kernel Information (draft)

Tobias Weigel, Beth Plale, Mark Parsons, Gabriel Zhou, Yu Luo, Ulrich Schwardmann, Robert Quick
2018 Zenodo  
Global middleware infrastructure is insufficient for robust data identification, discovery, and use. While infrastructure is emerging within sub-ecosystems such as the DOI ecosystem of services purposed for data and literature objects (i.e., DataCite, CHORUS, CrossRef), in general the layers of abstraction that have made the Internet so easy to build on, is lacking for data especially for computer (machine) automated services. The goal of the PID Kernel Information recommendation is to advance
more » ... small change to middleware infrastructure by injecting a tiny amount of carefully selected metadata into a Persistent ID (PID) record. This carefully chosen and placed information has the potential to stimulate development of an entire ecosystem of third party services that can process the billions of expected PIDs and do so with more information at hand about an object (no need for costly link following) than just a unique ID. The key challenge of the PID Kernel Information working group was to determine which from amongst thousands of relevant metadata elements are suitable to embed in the PID record. This recommendation lays out principles to guide in the identification of information suitable for inclusion in the PID record. The information contained in a PID record is represented by a PID Kernel Information profile which must be publicly and globally available. For PID Kernel Information to be effective in stimulating an ecosystem of data services, the number of different profiles of PID Kernel Information must be small and their content stable. The recommendation includes a draft profile with illustrating examples and cases for adoption in practice.
doi:10.5281/zenodo.1462542 fatcat:y7ahmjb73rfyhl42puqpxj3xoe

Improvement of the Electronic—Neuronal Interface by Natural Deposition of ECM

Tobias Weigel, Julian Brennecke, Jan Hansmann
2021 Materials  
The foreign body reaction to neuronal electrode implants limits potential applications as well as the therapeutic period. Developments in the basic electrode design might improve the tissue compatibility and thereby reduce the foreign body reaction. In this work, the approach of embedding 3D carbon nanofiber electrodes in extracellular matrix (ECM) synthesized by human fibroblasts for a compatible connection to neuronal cells was investigated. Porous electrode material was manufactured by
more » ... on coelectrospinning of polyacrylonitrile and polyamide as a fibrous porogen. Moreover, NaCl represented an additional particulate porogen. To achieve the required conductivity for an electrical interface, meshes were carbonized. Through the application of two different porogens, the electrodes' flexibility and porosity was improved. Human dermal fibroblasts were cultured on the electrode surface for ECM generation and removed afterwards. Scanning electron microscopy imaging revealed a nano fibrous ECM network covering the carbon fibers. The collagen amount of the ECM coating was quantified by hydroxyproline-assays. The modification with the natural protein coating on the electrode functionality resulted in a minor increase of the electrical capacity, which slightly improved the already outstanding electrical interface properties. Increased cell numbers of SH-SY5Y cell line on ECM-modified electrodes demonstrated an improved cell adhesion. During cell differentiation, the natural ECM enhanced the formation of neurites regarding length and branching. The conducted experiments indicated the prevention of direct cell-electrode contacts by the modification, which might help to shield temporary the electrode from immunological cells to reduce the foreign body reaction and improve the electrodes' tissue integration.
doi:10.3390/ma14061378 pmid:33809094 fatcat:utwkxncxsvfphlnavudiwunrkm

Editorial: 20 Years of Persistent Identifiers – Applications and Future Directions

Jens Klump, Fiona Murphy, Tobias Weigel, Mark Parsons
2017 Data Science Journal  
roles in which PIDs have been recognized as enabling technology are regularly discussed within the Research Data Alliance and expressed for instance in the recommendations on PID Information Types (Weigel  ... 
doi:10.5334/dsj-2017-052 fatcat:wez5ysutujfsnjrfue4towu3m4

Radar-Based Heart Sound Detection

Christoph Will, Kilin Shi, Sven Schellenberger, Tobias Steigleder, Fabian Michler, Jonas Fuchs, Robert Weigel, Christoph Ostgathe, Alexander Koelpin
2018 Scientific Reports  
This paper introduces heart sound detection by radar systems, which enables touch-free and continuous monitoring of heart sounds. The proposed measurement principle entails two enhancements in modern vital sign monitoring. First, common touch-based auscultation with a phonocardiograph can be simplified by using biomedical radar systems. Second, detecting heart sounds offers a further feasibility in radar-based heartbeat monitoring. To analyse the performance of the proposed measurement
more » ... , 9930 seconds of eleven persons-under-tests' vital signs were acquired and stored in a database using multiple, synchronised sensors: a continuous wave radar system, a phonocardiograph (PCG), an electrocardiograph (ECG), and a temperature-based respiration sensor. A hidden semi-Markov model is utilised to detect the heart sounds in the phonocardiograph and radar data and additionally, an advanced template matching (ATM) algorithm is used for state-of-the-art radar-based heartbeat detection. The feasibility of the proposed measurement principle is shown by a morphology analysis between the data acquired by radar and PCG for the dominant heart sounds S1 and S2: The correlation is 82.97 ± 11.15% for 5274 used occurrences of S1 and 80.72 ± 12.16% for 5277 used occurrences of S2. The performance of the proposed detection method is evaluated by comparing the F-scores for radar and PCG-based heart sound detection with ECG as reference: Achieving an F1 value of 92.22 ± 2.07%, the radar system approximates the score of 94.15 ± 1.61% for the PCG. The accuracy regarding the detection timing of heartbeat occurrences is analysed by means of the root-mean-square error: In comparison to the ATM algorithm (144.9 ms) and the PCG-based variant (59.4 ms), the proposed method has the lowest error value (44.2 ms). Based on these results, utilising the detected heart sounds considerably improves radar-based heartbeat monitoring, while the achieved performance is also competitive to phonocardiography.
doi:10.1038/s41598-018-29984-5 pmid:30068983 pmcid:PMC6070547 fatcat:x75hy4wjnzc27guy3kinlalekq

Nanotopographical Coatings Induce an Early Phenotype-Specific Response of Primary Material-Resident M1 and M2 Macrophages

Tobias Schmitz, Maren Jannasch, Tobias Weigel, Claus Moseke, Uwe Gbureck, Jürgen Groll, Heike Walles, Jan Hansmann
2020 Materials  
Implants elicit an immunological response after implantation that results in the worst case in a complete implant rejection. This biomaterial-induced inflammation is modulated by macrophages and can be influenced by nanotopographical surface structures such as titania nanotubes or fractal titanium nitride (TiN) surfaces. However, their specific impact on a distinct macrophage phenotype has not been identified. By using two different levels of nanostructures and smooth samples as controls, the
more » ... fluence of tubular TiO2 and fractal TiN nanostructures on primary human macrophages with M1 or M2-phenotype was investigated. Therefore, nanotopographical coatings were either, directly generated by physical vapor deposition (PVD) or by electrochemical anodization of titanium PVD coatings. The cellular response of macrophages was quantitatively assessed to demonstrate a difference in biocompatibility of nanotubes in respect to human M1 and M2-macrophages. Depending on the tube diameter of the nanotubular surfaces, low cell numbers and impaired cellular activity, was detected for M2-macrophages, whereas the impact of nanotubes on M1-polarized macrophages was negligible. Importantly, we could confirm this phenotypic response on the fractal TiN surfaces. The results indicate that the investigated topographies specifically impact the macrophage M2-subtype that modulates the formation of the fibrotic capsule and the long-term response to an implant.
doi:10.3390/ma13051142 pmid:32143448 pmcid:PMC7084960 fatcat:lbi7qig7wnhdhbhmgff7p4byky

A Framework for Extended Persistent Identification of Scientific Assets

Tobias Weigel, Michael Lautenschlager, Frank Toussaint, Stephan Kindermann
2013 Data Science Journal  
Several scientific communities relying on e-science infrastructures are in need of persistent identifiers for data and contextual information. In this article, we present a framework for persistent identification that fundamentally supports context information. It is installed as a number of low-level requirements and abstract data type descriptions, flexible enough to envelope context information while remaining compatible with existing definitions and infrastructures. The abstract data type
more » ... finitions we draw from the requirements and exemplary use cases can act as an evaluation tool for existing implementations or as a blueprint for future persistent identification infrastructures. A prototypic implementation based on the Handle System is briefly introduced. We also lay the groundwork for establishing a graph of persistent entities that can act as a base layer for more sophisticated information schemas to preserve context information.
doi:10.2481/dsj.12-036 fatcat:u77wtxtnorhdbettwbg7pgw7di

Initial Persistent Identifier (PID) policy for the European Open Science Cloud (EOSC) [article]

Maggie Hellström, André Heughebaert, Rachael Kotarski, Paolo Manghi, Brian Matthews, Raphael Ritz, Anders Sparre Conrad, Tobias Weigel, Peter Wittenburg
2019 Zenodo  
This policy was authored by representatives of the EOSC FAIR Working Group and EOSC Architecture Working group. See Appendix 3 for details. This initial policy was released in December 2019 for community feedback and comment. We welcome responses to and comments on this first version. Please share them with the wider community on https://pidforum.org or email them to us pid-policy@eoscsecretariat.eu. We understand that some areas may require discussion and encourage you to have that discussion
more » ... n https://pidforum.org. That is where we will also provide details of opportunities for face-to-face feedback and discussion. We will develop a second version for March 2020 and a final policy will be delivered to the EOSC Governance Board in October 2020.
doi:10.5281/zenodo.3574203 fatcat:t4zqzpakwbbvljgq6hnppiikfe
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