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- Westfälisches Institut für Gesundheit (141) (entfernen)
The algorithm for automated functional groups detection and extraction of organic molecules developed by Peter Ertl is implemented on the basis of the Chemistry Development Kit (CDK).
Folder Basic contains the basic ErtlFunctionalGroupsFinder code and test code for integration in Java projects.
Folder CDK contains CDK library jar file cdk-2.2.jar that ErtlFunctionalGroupsFinder works with.
Folder Evaluation contains sample code for evaluation of functional groups with ErtlFunctionalGroupsFinder.
Folder JUnit 4 contains library jar files for unit testing.
Folder Performance contains a jar library for performance tests.
ErtlFunctionalGroupsFinder is described in the scientific literature
Streptavidin is a 58 kDa tetrameric protein with the highest known affinity to biotin with a wide range of applications in bionanotechnology and molecular biology. Dissolved streptavidin is stable at a broad range of temperature, pH, proteolytic enzymes and exhibits low non‐specific binding. In this study, a streptavidin monolayer was assembled directly on a biotinylated TiO2‐surface to investigate its stability against proteolytic digestion and its suppression of initial bacterial adsorption of Escherichia coli, Bacillus subtilis, and Streptococcus intermedius. In contrast to nonmodified TiO2 surfaces, streptavidin‐coated substrates showed only a negligible non‐specific protein adsorption at physiological protein concentrations as well as a significantly reduced bacterial adhesion. The antiadhesive properties were demonstrated to be the main reason for the suppression of bacterial adhesion, which makes this approach a promising option for future surface biofunctionalization applications.
Steps Towards an Open All-in-one Rich-Client Environment for Particle-Based Mesoscopic Simulation
(2018)
SPICES (Simplified Particle Input ConnEction Specification) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like Dissipative Particle Dynamics by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box. An open Java library for SPICES structure handling and mesoscopic simulation support in combination with an open Java Graphical User Interface viewer application for visual topological inspection of SPICES definitions are provided.
Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The new kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated “all-in-one” simulation systems.
CIP is an open-source high-level function library for (non-linear) curve fitting and data smoothing (with cubic splines), clustering (k-medoids, ART-2a) and machine learning (multiple linear/polynomial regression, feed-forward perceptron-type shallow and deep neural networks and support vector machines). In addition it provides several heuristics for the selection of training and test data or methods to estimate the relevance of data input components. CIP is built on top of the computing platform Mathematica to exploit its algorithmic and graphical capabilities.
CIP is an open-source high-level function library for (non-linear) curve fitting and data smoothing (with cubic splines), clustering (k-medoids, ART-2a) and machine learning (multiple linear/polynomial regression, feed-forward perceptron-type shallow and deep neural networks and support vector machines). In addition it provides several heuristics for the selection of training and test data or methods to estimate the relevance of data input components. CIP is built on top of the computing platform Mathematica to exploit its algorithmic and graphical capabilities.
A Robust Interface for Head Motion based Control of a Robot Arm using MARG and Visual Sensors
(2018)
Head-controlled human machine interfaces have gained popularity over the past years, especially in the restoration of the autonomy of severely disabled people, like tetraplegics. These interfaces need to be reliable and robust regarding the environmental conditions to guarantee safety of the user and enable a direct interaction between a human and a machine. This paper presents a hybrid MARG and visual sensor system for head orientation estimation which is in this case used to teleoperate a robotic arm. The system contains a Magnetic Angular Rate Gravity (MARG)-sensor and a Tobii eye tracker 4C. A MARG sensor consists of tri-axis accelerometer, gyroscope as well as a magnetometer which enable a complete measurement of orientation relative to the direction of gravity and magnetic field of the earth. The tri-axis magnetometer is sensitive to external magnetic fields which result in incorrect orientation estimation from the sensor fusion process. In this work the Tobii eye tracker 4C is used to increase head orientation estimation because it also features head tracking even though it is commonly used for eye tracking. This type of visual sensor does not suffer magnetic drift. However, it computes orientation data only, if a user is detectable. Within this work a state machine is presented which enables data fusion of the MARG and visual sensor to improve orientation estimation. The fusion of the orientation data of MARG and visual sensors enables a robust interface, which is immune against external magnetic fields. Therefore, it increases the safety of the human machine interaction.
Improved Plasma Membrane Models as Test Systems for the Membrane
Disrupting Activity of Kalata B1
(2017)
The wireless data logger system “Cor/log® BAN BT” (CL) allows seamless 24/7 monitoring of relevant vital sign parameters. CL covers the entire period of acute point of care inside the hospital and the recovery period, when first mobility is achieved and when the patient is released into an ambulatory or homecare environment. The CL records the relevant vital signs such as ECG, respiration, pulse oximetry with plethysmogram and movement. The vital data collected with the CL data logger is saved on a memory card for further analysis and is simultaneously transmitted in real-time to a telemedicine server via a smartphone or tablet. The smartphone also provides GPS location information. In addition Cor/log View, an Android Application for viewing recorded vital sign data originating from the CL, was developed. CL has also a connector to the generic MedM health cloud. MedM is a generic patient data management system (PDMS) consisting of a cloud portal and a mobile health app. The app runs on Android, iOS and Windows. The app can connects wirelessly to the CL physiologic monitor and stores the vital signs in the cloud.
The Unfitted Discontinuous Galerkin Method for Solving the EEG Forward Problem: A Second Order Study
(2016)
Biofunktionalisierung von Titanimplantaten mit einem Multilayersystem aus BMP-2 und Fibronektin
(2016)
Patient specific simulation of brain stimulation using the unfitted discontinuous galerkin method
(2015)
To achieve high temperature stable insulation materials for the electrical insulation of fine copper wires two different bis(alkoxysilylalkyl)pyromellitamide acids 1 and 2 were prepared. These organic–inorganic sol–gel hybrid precursors were obtained via reactions of pyromellitic dianhydride and alkoxysilylalkylamines. The molecular single-source precursors 1 and 2 were comprehensively studied using FT-IR, 1H, 13C and 29Si NMR spectroscopy as well as elemental analyses. Besides, the hydrolysis and condensation processes of the different precursors were examined with solution 29Si NMR spectroscopy. The imidization process was investigated using 13C NMR spectroscopy, FT-IR spectroscopy as well as thermal analysis methods. The different precursors were applied to coat fine copper wires using an industrial coating device. The obtained coatings were cured at temperatures between 380 and 425 °C, and tested regarding thicknesses, number of pinholes, electrical breakdown voltage and elongation. FT-IR spectroscopy was used to determine the chemical structure and scanning electron microscopy to investigate the morphology of the coating materials. The obtained coatings showed very promising mechanical, thermal and electrical properties, i.e. highest breakdown voltage values well above 200 V/µm. They possess high flexibility without cracking and no pinholes or other defects were detected.
The biomodification of surfaces, especially titanium, is an important issue in current biomedical research. Regarding titanium, it is also important to ensure a specific protein modification of its surface because here protein binding that is too random can be observed. Specific nanoscale architectures can be applied to overcome this problem. As recently shown, streptavidin can be used as a coupling agent to immobilize biotinylated fibronectin (bFn) on a TiOX surface. Because of the conformation of adsorbed biotinylated fibronectin on a streptavidin monolayer, it is possible to adsorb more streptavidin and biotinylated fibronectin layers. On this basis, an alternating protein multilayer can be built up. In contrast to common layer-by-layer technology, in this procedure the mechanism of layer adsorption is very specific because of the interaction of biotin and streptavidin. In addition, we showed that the assembly of this multilayer system and its stability are dependent on the degree of labeling of biotinylated fibronectin. Hence we conclude that it is possible to build up well-defined nanoscale protein architectures by varying the degree of labeling of biotinylated fibronectin.
Streptavidin-coated TiO2 surfaces are biologically inert: Protein adsorption and osteoblast adhesion
(2012)
Non‐fouling TiO2 surfaces are attractive for a wide range of applications such as biosensors and medical devices, where biologically inert surfaces are needed. Typically, this is achieved by controlled surface modifications which prevent protein adsorption. For example, polyethylene glycol (PEG) or PEG‐derived polymers have been widely applied to render TiO2 surfaces biologically inert. These surfaces have been further modified in order to achieve specific bio‐activation. Therefore, there have been efforts to specifically functionalize TiO2 surfaces with polymers with embedded biotin motives, which can be used to couple streptavidin for further functionalization. As an alternative, here a streptavidin layer was immobilized by self‐assembly directly on a biotinylated TiO2 surface, thus forming an anti‐adhesive matrix, which can be selectively bio‐activated. The anti‐adhesive properties of these substrates were analyzed by studying the interaction of the surface coating with fibronectin, lysozym, and osteoblast cells using surface plasmon resonance spectroscopy, atomic force microscopy, and light microscopy. In contrast to non‐modified TiO2 surfaces, streptavidin‐coated TiO2 surfaces led to a very biologically inert substrate, making this type of surface coating a promising alternative to polymer coatings of TiO2 surfaces.
It is well-known that protein-modified implant surfaces such as TiO2 show a higher bioconductivity. Fibronectin is a glycoprotein from the extracellular matrix (ECM) with a major role in cell adhesion. It can be applied on titanium oxide surfaces to accelerate implant integration. Not only the surface concentration but also the presentation of the protein plays an important role for the cellular response. We were able to show that TiOX surfaces modified with biotinylated fibronectin adsorbed on a streptavidin-silane self-assembly multilayer system are more effective regarding osteoblast adhesion than surfaces modified with nonspecifically bound fibronectin. The adsorption and conformation behavior of biotinylated and nonbiotinylated (native) fibronectin was studied by surface plasmon resonance (SPR) spectroscopy and atomic force microscopy (AFM). Imaging of the protein modification revealed that fibronectin adopts different conformations on nonmodified compared to streptavidin-modified TiOX surfaces. This conformational change of biotinylated fibronectin on the streptavidin monolayer delivers a fibronectin structure similar to the conformation inside the ECM and therefore explains the higher cell affinity for these surfaces.
Open-Source-Workflows
(2010)