Biomechanical Soft Tissue Modeling - Techniques, Implementation and Application

The reaction of soft tissue to applied forces can be calculated with biomechanical simulation algorithms. Several modeling approaches exist. A scheme is suggested which allows the classification of arbitrary modeling approaches with respect to the degree of physical realism contained in the model (physical and descriptive models). Besides well known approaches like mass-spring, finite element, particle models and others the ChainMail algorithm is investigated. Where ChainMail in its original formulation lacked the capability to model inhomogeneous material, it is exceptionally stable and converges in one step to a valid configuration. In this thesis ChainMail is generalized to the Enhanced ChainMail algorithm which is capable to model inhomogeneous, volumetric objects and is fast enough for real time simulations. While now in principle being able to simulate and visualize an object in real time, a software architecture is required to team up simulation and visualization. As visualization and simulation have so far evolved independently, they work with different data structures. Multiplicity of data representations leads to the problems of data consistency and high memory consumption. A software architecture is developed which provides a universal data structure for several simulation and visualization approaches. The versatility of the developed architecture is demonstrated by two medical simulations. The first is the simulation of an intra-ocular surgery, which makes heavy use of Virtual Reality techniques. Designed as a training and educational tool the simulator EyeSi relies on descriptive real time ti me tissue simulation and visualization. The second deals with the simulation of decompressive craniotomy. The medical problem requires a physical model as the project's goal is to provide exact predictions on tissue behavior to support surgeons in surgery planning

Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer

<p>Abstract</p> <p>Background</p> <p>The phenomenon of desiccation tolerance, also called anhydrobiosis, involves the ability of an organism to survive the loss of almost all cellular water without sustaining irreversible damage. Although there are several physiological, morphological and ecological studies on tardigrades, only limited DNA sequence information is available. Therefore, we explored the transcriptome in the active and anhydrobiotic state of the tardigrade <it>Milnesium tardigradum </it>which has extraordinary tolerance to desiccation and freezing. In this study, we present the first overview of the transcriptome of <it>M. tardigradum </it>and its response to desiccation and discuss potential parallels to stress responses in other organisms.</p> <p>Results</p> <p>We sequenced a total of 9984 expressed sequence tags (ESTs) from two cDNA libraries from the eutardigrade <it>M. tardigradum </it>in its active and inactive, anhydrobiotic (tun) stage. Assembly of these ESTs resulted in 3283 putative unique transcripts, whereof ~50% showed significant sequence similarity to known genes. The resulting unigenes were functionally annotated using the Gene Ontology (GO) vocabulary. A GO term enrichment analysis revealed several GOs that were significantly underrepresented in the inactive stage. Furthermore we compared the putative unigenes of <it>M. tardigradum </it>with ESTs from two other eutardigrade species that are available from public sequence databases, namely <it>Richtersius coronifer </it>and <it>Hypsibius dujardini</it>. The processed sequences of the three tardigrade species revealed similar functional content and the <it>M. tardigradum </it>dataset contained additional sequences from tardigrades not present in the other two.</p> <p>Conclusions</p> <p>This study describes novel sequence data from the tardigrade <it>M. tardigradum</it>, which significantly contributes to the available tardigrade sequence data and will help to establish this extraordinary tardigrade as a model for studying anhydrobiosis. Functional comparison of active and anhydrobiotic tardigrades revealed a differential distribution of Gene Ontology terms associated with chromatin structure and the translation machinery, which are underrepresented in the inactive animals. These findings imply a widespread metabolic response of the animals on dehydration. The collective tardigrade transcriptome data will serve as a reference for further studies and support the identification and characterization of genes involved in the anhydrobiotic response.</p

Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant

Collins and Sivers asymmetries in muonproduction of pions and kaons off transversely polarised protons

Measurements of the Collins and Sivers asymmetries for charged pions and charged and neutral kaons produced in semi-inclusive deep-inelastic scattering of high energy muons off transversely polarised protons are presented. The results were obtained using all the available COMPASS proton data, which were taken in the years 2007 and 2010. The Collins asymmetries exhibit in the valence region a non-zero signal for pions and there are hints of non-zero signal also for kaons. The Sivers asymmetries are found to be positive for positive pions and kaons and compatible with zero otherwise. © 2015

Collision Detection and Tissue Modeling in a VR-Simulator for Eye Surgery

This paper gives a survey of techniques for tissue interaction and discusses their application in the context of the intra-ocular training system EyeSi. As key interaction techniques collision detection and soft tissue modeling are identified. For collision detection in EyeSi, an enhanced image-based approach for collisions between deformable surfaces and rigid objects is presented. By exploiting the computing power of graphics processing units, it achieves higher performance than existing geometry-based approaches. Deformation vectors are computed and used for the biomechanical model. A mass-spring approach is shown to be powerful enough to bridge the gap between low computational demands and a convincing tissue behavior

Robust Real-time Tracking of Surgical Instruments in the Eye Surgery Simulator (EyeSi)

In this paper we propose a real-time solution to localize the surgical instruments in an eye surgery simulator, Eye Si. The hardware consists of three synchronized cameras that capture the movements of the instruments, and an FPGA card for grabbing and preprocessing the images. The surgical instruments are localized using the method of Hough transform combined with the technique of stereo vision. The proposed method is robust to noise and low quality camera images. A fast algorithm of voting in Hough transform is also proposed

Biomechanical Simulation of the Falx cerebri Using the Finite Element Method

Keywords: Intracranial Pressure (ICP), Intercranial Pressure Monitoring, Falx cerebri, Biomechanical Simulation, Finite Element Analysis. A method is introduced which uses a biomechanical model of the Falx cerebri (F.c.) to determine the pressure difference in the scull that is necessary for a shunting of the F.c.. It therefore allows a correction of ICP measured in one hemisphere to the ICP in the other one. Introduction Intracranial Pressure (ICP) monitoring is a common tool in dealing with traumatic brain injury or other cerebral disorders. In intensive care medicine it is of great importance to know the exact level of the ICP. In general ICP is considered as a global value which has no space dependence. This assumption is based on a model of incompressible fluids and the herewith connected hydrostatic pressure. All ICP monitoring techniques currently being used, rely upon the validity of this assumption since they are based on sensors which are introduced into the skull via a cath..